From e58453a6936579ce15320541e69cd783c6a95a10 Mon Sep 17 00:00:00 2001 From: Filip Leonarski Date: Sun, 25 Oct 2026 00:03:05 +0200 Subject: [PATCH] Refinement restraints: the CCP4 Monomer Library subset embedded in rugnux, read through gemmi's MonLib A restraint dictionary carried in the binary, so refinement reads nothing from disk and needs no CLIBD_MON: the 20 amino acids and MSE, the DNA/RNA nucleotides, ATP/ADP/AMP/GTP/GDP/GMP, DMSO, PEG fragments (PEG, PGE, PG4, 1PE), GOL, EDO, SO4, PO4, ACT, MPD, water and common ions - copied verbatim from the CCP4 Monomer Library (LGPL-3.0) - plus links_and_mods.cif cut down to the links and modifications those compounds can take (peptide, cis-peptide, proline, N-methyl, disulfide, nucleic-acid backbone, termini, metal-Cys/His) and ener_lib.cif cut to its atom-type table. monomers/update_monomers.py holds the compound list and regenerates the subset; CMake embeds every .cif of the directory as string pieces under MSVC's literal limit; EmbeddedMonomerLibrary() parses them from memory into a gemmi::MonLib once per process. About 0.7 MB of text in the binary. gemmi v0.7.5's monlib.cpp, topo.cpp and riding_h.cpp vendored verbatim (prepare_topology). Licence text in licenses/, rows and a note in THIRD_PARTY_NOTICES.md. Co-Authored-By: Claude Opus 5.5 Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 38034718052c4a300691393b5b817f476c83dfc2) --- .gitignore | 2 + THIRD_PARTY_NOTICES.md | 7 + gemmi_gph/CMakeLists.txt | 4 + gemmi_gph/monlib.cpp | 633 +++ gemmi_gph/riding_h.cpp | 480 ++ gemmi_gph/topo.cpp | 1084 ++++ .../structure_refinement/CMakeLists.txt | 39 +- .../structure_refinement/MonomerLibrary.cpp | 41 + .../structure_refinement/MonomerLibrary.h | 25 + .../structure_refinement/monomers/1PE.cif | 228 + .../structure_refinement/monomers/A.cif | 271 + .../structure_refinement/monomers/ACT.cif | 104 + .../structure_refinement/monomers/ADP.cif | 283 + .../structure_refinement/monomers/ALA.cif | 182 + .../structure_refinement/monomers/AMP.cif | 279 + .../structure_refinement/monomers/ARG.cif | 284 + .../structure_refinement/monomers/ASN.cif | 214 + .../structure_refinement/monomers/ASP.cif | 198 + .../structure_refinement/monomers/ATP.cif | 301 ++ .../structure_refinement/monomers/BR.cif | 30 + .../structure_refinement/monomers/C.cif | 255 + .../structure_refinement/monomers/CA.cif | 30 + .../structure_refinement/monomers/CD.cif | 30 + .../structure_refinement/monomers/CL.cif | 30 + .../structure_refinement/monomers/CO.cif | 30 + .../structure_refinement/monomers/COPYING | 166 + .../structure_refinement/monomers/CU.cif | 30 + .../structure_refinement/monomers/CYS.cif | 188 + .../structure_refinement/monomers/DA.cif | 266 + .../structure_refinement/monomers/DC.cif | 250 + .../structure_refinement/monomers/DG.cif | 271 + .../structure_refinement/monomers/DMS.cif | 117 + .../structure_refinement/monomers/DT.cif | 256 + .../structure_refinement/monomers/EDO.cif | 108 + .../structure_refinement/monomers/FE.cif | 30 + .../structure_refinement/monomers/FE2.cif | 30 + .../structure_refinement/monomers/G.cif | 276 + .../structure_refinement/monomers/GDP.cif | 299 ++ .../structure_refinement/monomers/GLN.cif | 233 + .../structure_refinement/monomers/GLU.cif | 217 + .../structure_refinement/monomers/GLY.cif | 153 + .../structure_refinement/monomers/GMP.cif | 256 + .../structure_refinement/monomers/GOL.cif | 134 + .../structure_refinement/monomers/GTP.cif | 312 ++ .../structure_refinement/monomers/HIS.cif | 247 + .../structure_refinement/monomers/HOH.cif | 79 + .../structure_refinement/monomers/ILE.cif | 240 + .../structure_refinement/monomers/IOD.cif | 30 + .../structure_refinement/monomers/K.cif | 30 + .../structure_refinement/monomers/LEU.cif | 240 + .../structure_refinement/monomers/LYS.cif | 258 + .../structure_refinement/monomers/MET.cif | 226 + .../structure_refinement/monomers/MG.cif | 30 + .../structure_refinement/monomers/MN.cif | 30 + .../structure_refinement/monomers/MPD.cif | 170 + .../structure_refinement/monomers/MSE.cif | 201 + .../structure_refinement/monomers/NA.cif | 30 + .../structure_refinement/monomers/NI.cif | 30 + .../structure_refinement/monomers/PEG.cif | 138 + .../structure_refinement/monomers/PG4.cif | 198 + .../structure_refinement/monomers/PGE.cif | 168 + .../structure_refinement/monomers/PHE.cif | 261 + .../structure_refinement/monomers/PO4.cif | 86 + .../structure_refinement/monomers/PRO.cif | 216 + .../structure_refinement/monomers/SER.cif | 188 + .../structure_refinement/monomers/SO4.cif | 86 + .../structure_refinement/monomers/THR.cif | 208 + .../structure_refinement/monomers/TRP.cif | 301 ++ .../structure_refinement/monomers/TYR.cif | 268 + .../structure_refinement/monomers/U.cif | 248 + .../structure_refinement/monomers/VAL.cif | 221 + .../structure_refinement/monomers/ZN.cif | 30 + .../monomers/ener_lib.cif | 219 + .../monomers/links_and_mods.cif | 4698 +++++++++++++++++ .../monomers/update_monomers.py | 96 + licenses/COLLECT.sh | 1 + licenses/ccp4-monomer-library.txt | 166 + 77 files changed, 18293 insertions(+), 1 deletion(-) create mode 100644 gemmi_gph/monlib.cpp create mode 100644 gemmi_gph/riding_h.cpp create mode 100644 gemmi_gph/topo.cpp create mode 100644 image_analysis/structure_refinement/MonomerLibrary.cpp create mode 100644 image_analysis/structure_refinement/MonomerLibrary.h create mode 100644 image_analysis/structure_refinement/monomers/1PE.cif create mode 100644 image_analysis/structure_refinement/monomers/A.cif create mode 100644 image_analysis/structure_refinement/monomers/ACT.cif create mode 100644 image_analysis/structure_refinement/monomers/ADP.cif create mode 100644 image_analysis/structure_refinement/monomers/ALA.cif create mode 100644 image_analysis/structure_refinement/monomers/AMP.cif create mode 100644 image_analysis/structure_refinement/monomers/ARG.cif create mode 100644 image_analysis/structure_refinement/monomers/ASN.cif create mode 100644 image_analysis/structure_refinement/monomers/ASP.cif create mode 100644 image_analysis/structure_refinement/monomers/ATP.cif create mode 100644 image_analysis/structure_refinement/monomers/BR.cif create mode 100644 image_analysis/structure_refinement/monomers/C.cif create mode 100644 image_analysis/structure_refinement/monomers/CA.cif create mode 100644 image_analysis/structure_refinement/monomers/CD.cif create mode 100644 image_analysis/structure_refinement/monomers/CL.cif create mode 100644 image_analysis/structure_refinement/monomers/CO.cif create mode 100644 image_analysis/structure_refinement/monomers/COPYING create mode 100644 image_analysis/structure_refinement/monomers/CU.cif create mode 100644 image_analysis/structure_refinement/monomers/CYS.cif create mode 100644 image_analysis/structure_refinement/monomers/DA.cif create mode 100644 image_analysis/structure_refinement/monomers/DC.cif create mode 100644 image_analysis/structure_refinement/monomers/DG.cif create mode 100644 image_analysis/structure_refinement/monomers/DMS.cif create mode 100644 image_analysis/structure_refinement/monomers/DT.cif create mode 100644 image_analysis/structure_refinement/monomers/EDO.cif create mode 100644 image_analysis/structure_refinement/monomers/FE.cif create mode 100644 image_analysis/structure_refinement/monomers/FE2.cif create mode 100644 image_analysis/structure_refinement/monomers/G.cif create mode 100644 image_analysis/structure_refinement/monomers/GDP.cif create mode 100644 image_analysis/structure_refinement/monomers/GLN.cif create mode 100644 image_analysis/structure_refinement/monomers/GLU.cif create mode 100644 image_analysis/structure_refinement/monomers/GLY.cif create mode 100644 image_analysis/structure_refinement/monomers/GMP.cif create mode 100644 image_analysis/structure_refinement/monomers/GOL.cif create mode 100644 image_analysis/structure_refinement/monomers/GTP.cif create mode 100644 image_analysis/structure_refinement/monomers/HIS.cif create mode 100644 image_analysis/structure_refinement/monomers/HOH.cif create mode 100644 image_analysis/structure_refinement/monomers/ILE.cif create mode 100644 image_analysis/structure_refinement/monomers/IOD.cif create mode 100644 image_analysis/structure_refinement/monomers/K.cif create mode 100644 image_analysis/structure_refinement/monomers/LEU.cif create mode 100644 image_analysis/structure_refinement/monomers/LYS.cif create mode 100644 image_analysis/structure_refinement/monomers/MET.cif create mode 100644 image_analysis/structure_refinement/monomers/MG.cif create mode 100644 image_analysis/structure_refinement/monomers/MN.cif create mode 100644 image_analysis/structure_refinement/monomers/MPD.cif create mode 100644 image_analysis/structure_refinement/monomers/MSE.cif create mode 100644 image_analysis/structure_refinement/monomers/NA.cif create mode 100644 image_analysis/structure_refinement/monomers/NI.cif create mode 100644 image_analysis/structure_refinement/monomers/PEG.cif create mode 100644 image_analysis/structure_refinement/monomers/PG4.cif create mode 100644 image_analysis/structure_refinement/monomers/PGE.cif create mode 100644 image_analysis/structure_refinement/monomers/PHE.cif create mode 100644 image_analysis/structure_refinement/monomers/PO4.cif create mode 100644 image_analysis/structure_refinement/monomers/PRO.cif create mode 100644 image_analysis/structure_refinement/monomers/SER.cif create mode 100644 image_analysis/structure_refinement/monomers/SO4.cif create mode 100644 image_analysis/structure_refinement/monomers/THR.cif create mode 100644 image_analysis/structure_refinement/monomers/TRP.cif create mode 100644 image_analysis/structure_refinement/monomers/TYR.cif create mode 100644 image_analysis/structure_refinement/monomers/U.cif create mode 100644 image_analysis/structure_refinement/monomers/VAL.cif create mode 100644 image_analysis/structure_refinement/monomers/ZN.cif create mode 100644 image_analysis/structure_refinement/monomers/ener_lib.cif create mode 100644 image_analysis/structure_refinement/monomers/links_and_mods.cif create mode 100644 image_analysis/structure_refinement/monomers/update_monomers.py create mode 100644 licenses/ccp4-monomer-library.txt diff --git a/.gitignore b/.gitignore index 69b687423..3ce9253bb 100644 --- a/.gitignore +++ b/.gitignore @@ -48,3 +48,5 @@ __pycache__/ # tools/battery: the local site config (paths of this machine, private manifest); site.example.json is the template tools/battery/site.json +# the restraint dictionary rugnux embeds (image_analysis/structure_refinement/monomers/update_monomers.py) +!image_analysis/structure_refinement/monomers/*.cif diff --git a/THIRD_PARTY_NOTICES.md b/THIRD_PARTY_NOTICES.md index 3093e081e..95d52f504 100644 --- a/THIRD_PARTY_NOTICES.md +++ b/THIRD_PARTY_NOTICES.md @@ -61,6 +61,7 @@ These live in the source tree (see the path) rather than being fetched; traccc a | [LZ4](https://github.com/lz4/lz4) | `compression/lz4/` | Yann Collet | BSD-2-Clause | [lz4.txt](licenses/lz4.txt) | | [HLS arbitrary-precision types](https://github.com/Xilinx/HLS_arbitrary_Precision_Types) | `fpga/include/` | Xilinx, Inc. | Apache-2.0 | [xilinx-hls-headers.txt](licenses/xilinx-hls-headers.txt) | | [GEMMI](https://github.com/project-gemmi/gemmi) | `gemmi_gph/` | Global Phasing Ltd. | MPL-2.0 | [gemmi.txt](licenses/gemmi.txt) | +| [CCP4 Monomer Library](https://github.com/MonomerLibrary/monomers) (subset: restraint dictionary data) | `image_analysis/structure_refinement/monomers/` | CCP4 / the Monomer Library authors (Vagin et al.) | LGPL-3.0-only | [ccp4-monomer-library.txt](licenses/ccp4-monomer-library.txt) | | [PEGTL](https://github.com/taocpp/PEGTL) | `gemmi_gph/gemmi/third_party/tao/` | Dr. Colin Hirsch and Daniel Frey | MIT | [pegtl.txt](licenses/pegtl.txt) | | [sajson](https://github.com/chadaustin/sajson) | `gemmi_gph/gemmi/third_party/sajson.h` | Chad Austin | MIT | [sajson.txt](licenses/sajson.txt) | | [fast_float](https://github.com/fastfloat/fast_float) | `gemmi_gph/gemmi/third_party/fast_float.h` | The fast_float authors (Daniel Lemire et al.) | Apache-2.0 OR MIT OR BSL-1.0 | [fast-float.txt](licenses/fast-float.txt) | @@ -131,6 +132,12 @@ served frontend, so the shipped web UI carries its own attribution. * **FFTW** is GPL-2.0-or-later — compatible with, and absorbed by, this project's GPL-3.0 license. * **Apache-2.0** components: where upstream ships a `NOTICE` file, it is reproduced in the corresponding `licenses/` text. +* **CCP4 Monomer Library (LGPL-3.0)** is data, not code: the restraint dictionaries of the compounds + rugnux's refinement restrains, copied unmodified per compound into + `image_analysis/structure_refinement/monomers/` (`links_and_mods.cif` and `ener_lib.cif` cut down to + the entries those compounds use), with the library's own `COPYING`. The build embeds them in the binary + as text, and `monomers/update_monomers.py` regenerates the subset from the upstream library, so the + copy can be replaced by a user with a version of their own. * **Qt (LGPL-3.0)** and **NVIDIA CUDA (EULA)** carry redistribution conditions beyond a copyright notice; see their dedicated notice files. The verbatim LGPL-3.0 and CUDA EULA texts are bundled (`licenses/Qt6-LGPL-3.0.txt`, `licenses/NVIDIA-CUDA-EULA.txt`); the CUDA EULA is the one shipped diff --git a/gemmi_gph/CMakeLists.txt b/gemmi_gph/CMakeLists.txt index c9c129ecf..c2e2b01ed 100644 --- a/gemmi_gph/CMakeLists.txt +++ b/gemmi_gph/CMakeLists.txt @@ -11,11 +11,15 @@ # against the data on disk. to_mmcif.cpp calls use_hetatm() out of to_pdb.cpp, so the two come together. # # assembly.cpp expands a deposited model's strict-NCS operators into the full asymmetric unit. +# +# monlib/topo/riding_h are the restraint side: a monomer library read from memory (MonLib) and the +# topology of a model built from it (prepare_topology), for rugnux's restrained refinement. ADD_LIBRARY(gemmi STATIC symmetry.cpp gz.cpp mtz.cpp sprintf.cpp xds_ascii.cpp pdb.cpp resinfo.cpp polyheur.cpp calculate.cpp eig3.cpp ccp4.cpp read_cif.cpp mmcif.cpp json.cpp mmread_gz.cpp to_mmcif.cpp to_pdb.cpp assembly.cpp + monlib.cpp topo.cpp riding_h.cpp gemmi/cellred.hpp gemmi/symmetry.hpp gemmi/fail.hpp diff --git a/gemmi_gph/monlib.cpp b/gemmi_gph/monlib.cpp new file mode 100644 index 000000000..887529b7f --- /dev/null +++ b/gemmi_gph/monlib.cpp @@ -0,0 +1,633 @@ +// Copyright 2018-2023 Global Phasing Ltd. + +#include +#include // for calculate_chiral_volume +#include // for rename_atom_names +#include // for read_cif_gz +#include // for as_number + +namespace gemmi { + +int ChemLink::calculate_score(const Residue& res1, const Residue* res2, + char alt, char alt2, + const ChemComp::Aliasing* aliasing1, + const ChemComp::Aliasing* aliasing2) const { + int link_score = side1.specificity() + side2.specificity(); + + auto get_from = [&](const Restraints::AtomId& atomid) { + const auto* aliasing = (atomid.comp != 2 || res2 == nullptr) ? aliasing1 : aliasing2; + if (aliasing) + if (const std::string* real_id = aliasing->name_from_alias(atomid.atom)) + return Restraints::AtomId{atomid.comp, *real_id}.get_from(res1, res2, alt, alt2); + return atomid.get_from(res1, res2, alt, alt2); + }; + + // check chirality + for (const Restraints::Chirality& chirality : rt.chirs) + if (chirality.sign != ChiralityType::Both) { + const Atom* a1 = get_from(chirality.id_ctr); + const Atom* a2 = get_from(chirality.id1); + const Atom* a3 = get_from(chirality.id2); + const Atom* a4 = get_from(chirality.id3); + if (a1 && a2 && a3 && a4) { + double vol = calculate_chiral_volume(a1->pos, a2->pos, + a3->pos, a4->pos); + if (chirality.is_wrong(vol)) + link_score -= 10; + } + } + // check fixed torsion angle (_chem_link_tor.period == 0) + for (const Restraints::Torsion& tor : rt.torsions) + if (tor.period == 0) { + const Atom* a1 = get_from(tor.id1); + const Atom* a2 = get_from(tor.id2); + const Atom* a3 = get_from(tor.id3); + const Atom* a4 = get_from(tor.id4); + double z = 10.; + if (a1 && a2 && a3 && a4) + z = angle_z(calculate_dihedral(a1->pos, a2->pos, a3->pos, a4->pos), + tor); + link_score -= (int) z; + } + return link_score; +} + +namespace { + +Restraints read_link_restraints(const cif::Block& block_) { + auto read_aid = [](cif::Table::Row& row, int n) { + return Restraints::AtomId{cif::as_int(row[n]), row.str(n+1)}; + }; + Restraints rt; + cif::Block& block = const_cast(block_); + for (auto row : block.find("_chem_link_bond.", + {"atom_1_comp_id", "atom_id_1", + "atom_2_comp_id", "atom_id_2", + "type", + "value_dist", "value_dist_esd"})) + rt.bonds.push_back({read_aid(row, 0), read_aid(row, 2), + bond_type_from_string(row[4]), false, + cif::as_number(row[5]), cif::as_number(row[6]), + NAN, NAN}); + for (auto row : block.find("_chem_link_angle.", + {"atom_1_comp_id", "atom_id_1", + "atom_2_comp_id", "atom_id_2", + "atom_3_comp_id", "atom_id_3", + "value_angle", "value_angle_esd"})) + rt.angles.push_back({read_aid(row, 0), read_aid(row, 2), read_aid(row, 4), + cif::as_number(row[6]), cif::as_number(row[7])}); + for (auto row : block.find("_chem_link_tor.", + {"id", + "atom_1_comp_id", "atom_id_1", + "atom_2_comp_id", "atom_id_2", + "atom_3_comp_id", "atom_id_3", + "atom_4_comp_id", "atom_id_4", + "value_angle", "value_angle_esd", + "period"})) + rt.torsions.push_back({row.str(0), + read_aid(row, 1), read_aid(row, 3), + read_aid(row, 5), read_aid(row, 7), + cif::as_number(row[9]), cif::as_number(row[10]), + cif::as_int(row[11])}); + for (auto row : block.find("_chem_link_chir.", + {"atom_centre_comp_id", "atom_id_centre", + "atom_1_comp_id", "atom_id_1", + "atom_2_comp_id", "atom_id_2", + "atom_3_comp_id", "atom_id_3", + "volume_sign"})) + if (row[4][0] != 'c') // ignore crossN + rt.chirs.push_back({read_aid(row, 0), read_aid(row, 2), + read_aid(row, 4), read_aid(row, 6), + chirality_from_string(row[8])}); + for (auto row : block.find("_chem_link_plane.", + {"plane_id", "atom_comp_id", "atom_id", + "dist_esd"})) { + Restraints::Plane& plane = rt.get_or_add_plane(row.str(0)); + if (plane.esd == 0.0) + plane.esd = cif::as_number(row[3]); + plane.ids.push_back(read_aid(row, 1)); + } + return rt; +} + +void insert_chemlinks_into(const cif::Document& doc, std::map& links) { + const cif::Block* list_block = doc.find_block("link_list"); + auto use_chem_link = [](const cif::Block& block, ChemLink& link) { + for (auto row : const_cast(block).find("_chem_link.", + {"id", "?name", + "?comp_id_1", "?mod_id_1", "?group_comp_1", + "?comp_id_2", "?mod_id_2", "?group_comp_2"})) { + if (row.str(0) == link.id) { + if (row.has2(1)) + link.name = row.str(1); + if (row.has2(2)) + link.side1.comp = row.str(2); + if (row.has2(3)) + link.side1.mod = row.str(3); + if (row.has2(4)) + link.side1.group = ChemComp::read_group(row[4]); + if (row.has2(5)) + link.side2.comp = row.str(5); + if (row.has2(6)) + link.side2.mod = row.str(6); + link.side2.group = ChemComp::read_group(row[7]); + break; + } + } + }; + for (const cif::Block& block : doc.blocks) + if (starts_with(block.name, "link_") && block.name != "link_list") { + ChemLink link; + link.id = block.name.substr(5); + if (list_block) + use_chem_link(*list_block, link); + use_chem_link(block, link); + link.rt = read_link_restraints(block); + link.block = block; + links.emplace(link.id, link); + } +} + +// Helper function. str is one of "add", "delete", "change". +int chem_mod_type(const std::string& str) { + char c = str[0] | 0x20; + if (c != 'a' && c != 'd' && c != 'c') + fail("Unexpected value of _chem_mod_*.function: " + str); + return c; +} + +Restraints read_restraint_modifications(const cif::Block& block_) { + Restraints rt; + cif::Block& block = const_cast(block_); + for (auto row : block.find("_chem_mod_bond.", + {"function", "atom_id_1", "atom_id_2", + "new_type", + "new_value_dist", "new_value_dist_esd", + "?new_value_dist_nucleus", "?new_value_dist_nucleus_esd"})) + rt.bonds.push_back({Restraints::AtomId{chem_mod_type(row[0]), row.str(1)}, + Restraints::AtomId{1, row.str(2)}, + bond_type_from_string(row[3]), false, + cif::as_number(row[4]), cif::as_number(row[5]), + row.has(6) ? cif::as_number(row[6]) : NAN, + row.has(7) ? cif::as_number(row[7]) : NAN}); + for (auto row : block.find("_chem_mod_angle.", + {"function", "atom_id_1", + "atom_id_2", "atom_id_3", + "new_value_angle", "new_value_angle_esd"})) + rt.angles.push_back({{chem_mod_type(row[0]), row.str(1)}, + {1, row.str(2)}, {1, row.str(3)}, + cif::as_number(row[4]), cif::as_number(row[5])}); + for (auto row : block.find("_chem_mod_tor.", + {"function", "?id", "atom_id_1", + "atom_id_2", "atom_id_3", "atom_id_4", + "new_value_angle", "new_value_angle_esd", + "?new_period"})) + rt.torsions.push_back({row.has(1) ? row.str(1) : "", + {chem_mod_type(row[0]), row.str(2)}, + {1, row.str(3)}, {1, row.str(4)}, {1, row.str(5)}, + cif::as_number(row[6]), cif::as_number(row[7]), + row.has(8) ? cif::as_int(row[8], 0) : -1}); + for (auto row : block.find("_chem_mod_chir.", + {"function", "atom_id_centre", "atom_id_1", + "atom_id_2", "atom_id_3", + "new_volume_sign"})) + rt.chirs.push_back({{1, row.str(1)}, {chem_mod_type(row[0]), row.str(2)}, + {1, row.str(3)}, {1, row.str(4)}, + chirality_from_string(row[5])}); + for (auto row : block.find("_chem_mod_plane_atom.", + {"function", "plane_id", "atom_id" , + "new_dist_esd"})) { + Restraints::Plane& plane = rt.get_or_add_plane(row.str(1)); + if (plane.esd == 0.0) + plane.esd = cif::as_number(row[3]); + plane.ids.push_back({chem_mod_type(row[0]), row.str(2)}); + } + return rt; +} + +void insert_chemmods_into(const cif::Document& doc, std::map& mods) { + const cif::Block* list_block = doc.find_block("mod_list"); + auto use_chem_mod = [](const cif::Block& block, ChemMod& mod) { + for (auto row : const_cast(block).find("_chem_mod.", + {"id", "?name", "?comp_id", "?group_id"})) + if (row.str(0) == mod.id) { + if (row.has2(1)) + mod.name = row.str(1); + if (row.has2(2)) + mod.comp_id = row.str(2); + if (row.has2(3)) + mod.group_id = row.str(3); + break; + } + }; + for (const cif::Block& block : doc.blocks) + if (starts_with(block.name, "mod_") && block.name != "mod_list") { + ChemMod mod; + mod.id = block.name.substr(4); + if (list_block) + use_chem_mod(*list_block, mod); + use_chem_mod(block, mod); + for (auto ra : const_cast(block).find("_chem_mod_atom.", + {"function", "atom_id", "new_atom_id", + "new_type_symbol", "new_type_energy", + "?new_charge", "?new_partial_charge"})) + mod.atom_mods.push_back({chem_mod_type(ra[0]), ra.str(1), ra.str(2), + Element(ra.str(3)), + (float) cif::as_number(ra.one_of(5, 6)), + ra.str(4)}); + mod.rt = read_restraint_modifications(block); + mod.block = block; + mods.emplace(mod.id, mod); + } +} + +} // anonymous namespace + +void ChemMod::apply_to(ChemComp& chemcomp, ChemComp::Group alias_group) const { + auto real = [&chemcomp, alias_group](const std::string& atom_id) -> const std::string& { + if (alias_group != ChemComp::Group::Null) { + const ChemComp::Aliasing& aliasing = chemcomp.get_aliasing(alias_group); + if (const std::string* real_id = aliasing.name_from_alias(atom_id)) + return *real_id; + } + return atom_id; // NOLINT(bugprone-return-const-ref-from-parameter) + }; + cat_to(chemcomp.name, '+', id); + // _chem_mod_atom + for (const AtomMod& mod : atom_mods) { + if (mod.func == 'a') { + if (mod.new_id.empty()) + fail("New atom id is not given"); + if (!chemcomp.has_atom(real(mod.new_id))) + chemcomp.atoms.push_back({mod.new_id, "", mod.el, + std::isnan(mod.charge) ? mod.charge : 0, + mod.chem_type, "", Position()}); + continue; + } + const std::string& old = real(mod.old_id); + auto it = chemcomp.find_atom(old); + switch (mod.func) { + case 'd': + if (it != chemcomp.atoms.end()) { + chemcomp.atoms.erase(it); + // delete restraints containing mod.old_id + vector_remove_if(chemcomp.rt.bonds, [&](const Restraints::Bond& b) { + return b.id1 == old || b.id2 == old; + }); + vector_remove_if(chemcomp.rt.angles, [&](const Restraints::Angle& a) { + return a.id1 == old || a.id2 == old || a.id3 == old; + }); + vector_remove_if(chemcomp.rt.torsions, + [&](const Restraints::Torsion& t) { + return t.id1 == old || t.id2 == old || t.id3 == old || + t.id4 == old; + }); + vector_remove_if(chemcomp.rt.chirs, + [&](const Restraints::Chirality& c) { + return c.id_ctr == old || c.id1 == old || c.id2 == old || + c.id3 == old; + }); + for (Restraints::Plane& plane : chemcomp.rt.planes) + vector_remove_if(plane.ids, [&](const Restraints::AtomId& a) { + return a.atom == old; + }); + } + break; + case 'c': + if (it != chemcomp.atoms.end()) { + // the modification shouldn't change the atom name, so we don't do: + // if (!mod.new_id.empty()) + // it->id = mod.new_id; + if (mod.el != El::X) + it->el = mod.el; + if (!std::isnan(mod.charge)) + it->charge = mod.charge; + if (!mod.chem_type.empty()) + it->chem_type = mod.chem_type; + } + break; + } + } + + // _chem_mod_bond + for (const Restraints::Bond& mod : rt.bonds) { + auto it = chemcomp.rt.find_bond(real(mod.id1.atom), real(mod.id2.atom)); + switch (mod.id1.comp) { + case 'a': + if (it == chemcomp.rt.bonds.end()) { + chemcomp.rt.bonds.push_back(mod); + // id1.comp was temporarily set to 'a', set it back to 1 + chemcomp.rt.bonds.back().id1.comp = 1; + } + break; + case 'd': + if (it != chemcomp.rt.bonds.end()) + chemcomp.rt.bonds.erase(it); + break; + case 'c': + if (it != chemcomp.rt.bonds.end()) { + if (mod.type != BondType::Unspec) + it->type = mod.type; + if (!std::isnan(mod.value)) + it->value = mod.value; + if (!std::isnan(mod.esd)) + it->esd = mod.esd; + if (!std::isnan(mod.value_nucleus)) + it->value_nucleus = mod.value_nucleus; + if (!std::isnan(mod.esd_nucleus)) + it->esd_nucleus = mod.esd_nucleus; + } + break; + } + } + + // _chem_mod_angle + for (const Restraints::Angle& mod : rt.angles) { + auto it = chemcomp.rt.find_angle(real(mod.id1.atom), + real(mod.id2.atom), + real(mod.id3.atom)); + switch (mod.id1.comp) { + case 'a': + if (it == chemcomp.rt.angles.end()) { + chemcomp.rt.angles.push_back(mod); + chemcomp.rt.angles.back().id1.comp = 1; + } + break; + case 'd': + if (it != chemcomp.rt.angles.end()) + chemcomp.rt.angles.erase(it); + break; + case 'c': + if (it != chemcomp.rt.angles.end()) { + if (!std::isnan(mod.value)) + it->value = mod.value; + if (!std::isnan(mod.esd)) + it->esd = mod.esd; + } + break; + } + } + + // _chem_mod_tor + for (const Restraints::Torsion& mod : rt.torsions) { + auto it = chemcomp.rt.find_torsion(real(mod.id1.atom), real(mod.id2.atom), + real(mod.id3.atom), real(mod.id4.atom)); + switch (mod.id1.comp) { + case 'a': + if (it == chemcomp.rt.torsions.end()) { + chemcomp.rt.torsions.push_back(mod); + chemcomp.rt.torsions.back().id1.comp = 1; + } + break; + case 'd': + if (it != chemcomp.rt.torsions.end()) + chemcomp.rt.torsions.erase(it); + break; + case 'c': + if (it != chemcomp.rt.torsions.end()) { + if (!mod.label.empty()) + it->label = mod.label; + if (!std::isnan(mod.value)) + it->value = mod.value; + if (!std::isnan(mod.esd)) + it->esd = mod.esd; + if (mod.period != -1) + it->period = mod.period; + } + break; + } + } + + // _chem_mod_chir + for (const Restraints::Chirality& mod : rt.chirs) { + auto it = chemcomp.rt.find_chir(real(mod.id_ctr.atom), real(mod.id1.atom), + real(mod.id2.atom), real(mod.id3.atom)); + switch (mod.id1.comp) { + case 'a': + if (it == chemcomp.rt.chirs.end()) { + chemcomp.rt.chirs.push_back(mod); + chemcomp.rt.chirs.back().id1.comp = 1; + } + break; + case 'd': + if (it != chemcomp.rt.chirs.end()) + chemcomp.rt.chirs.erase(it); + break; + case 'c': + if (it != chemcomp.rt.chirs.end()) + it->sign = mod.sign; + break; + } + } + + // _chem_mod_plane_atom + for (const Restraints::Plane& mod : rt.planes) + for (const Restraints::AtomId& atom_id : mod.ids) { + const std::string& real_id = real(atom_id.atom); + if (atom_id.comp == 'a') { + Restraints::Plane& plane = chemcomp.rt.get_or_add_plane(mod.label); + if (plane.esd == 0.0 && !std::isnan(mod.esd)) + plane.esd = mod.esd; + auto it = std::find(plane.ids.begin(), plane.ids.end(), real_id); + if (it == plane.ids.end()) + plane.ids.push_back({1, real_id}); + } else if (atom_id.comp == 'd') { + auto it = chemcomp.rt.get_plane(mod.label); + if (it != chemcomp.rt.planes.end()) { + auto item = std::find(it->ids.begin(), it->ids.end(), real_id); + if (item != it->ids.end()) + it->ids.erase(item); + } + } + } +} + +void EnerLib::read(const cif::Document& doc) { + cif::Block& block = const_cast(doc.blocks[0]); + for (const auto& row : block.find("_lib_atom.", + {"type", "hb_type", "vdw_radius", "vdwh_radius", + "ion_radius", "element", "valency", "sp"})) + atoms.emplace(row[0], Atom{Element(row[5]), row[1][0], cif::as_number(row[2]), + cif::as_number(row[3]), cif::as_number(row[4]), + cif::as_int(row[6], -1), cif::as_int(row[7], -1)}); + for (const auto& row : block.find("_lib_bond.", + {"atom_type_1", "atom_type_2", "type", "length", "value_esd"})) + bonds.emplace(row.str(0), Bond{row.str(1), bond_type_from_string(row[2]), + cif::as_number(row[3]), cif::as_number(row[4])}); +} + +std::string MonLib::relative_monomer_path(const std::string& code) { + std::string path; + if (!code.empty()) { + path += lower(code[0]); + path += '/'; // works also on Windows + path += code; + // On Windows several names are reserved (CON, PRN, AUX, ...), see + // https://docs.microsoft.com/en-us/windows/win32/fileio/naming-a-file + // The workaround in CCP4 monomer library is to use CON_CON.cif, etc. + if (code.size() == 3) + switch (ialpha3_id(code.c_str())) { + case ialpha3_id("AUX"): + case ialpha3_id("COM"): + case ialpha3_id("CON"): + case ialpha3_id("LPT"): + case ialpha3_id("PRN"): + path += '_'; + path += code; + } + path += ".cif"; + } + return path; +} + +void MonLib::read_monomer_doc(const cif::Document& doc) { + // ChemComp + if (const cif::Block* block = doc.find_block("comp_list")) + for (auto row : const_cast(block)->find("_chem_comp.", {"id", "group"})) + cc_groups.emplace(row.str(0), ChemComp::read_group(row.str(1))); + for (const cif::Block& block : doc.blocks) + add_monomer_if_present(block); + // ChemLink + insert_chemlinks_into(doc, links); + // ChemMod + insert_chemmods_into(doc, modifications); +} + +namespace { + +const std::string* find_chemtype(const std::map& monomers, + const const_CRA& cra) { + auto cc = monomers.find(cra.residue->name); + if (cc != monomers.end()) { + auto cc_atom = cc->second.find_atom(cra.atom->name); + if (cc_atom != cc->second.atoms.end()) + return &cc_atom->chem_type; + } + return nullptr; +} + +// Searches data from _lib_atom in ener_lib.cif. +double find_radius(const EnerLib& ener_lib, const std::string& chemtype, + EnerLib::RadiusType type) { + double r = 0; + auto it = ener_lib.atoms.find(chemtype); + if (it != ener_lib.atoms.end()) { + if (type == EnerLib::RadiusType::Ion) + r = it->second.ion_radius; + else if (type == EnerLib::RadiusType::Vdw) + r = it->second.vdw_radius; + else if (type == EnerLib::RadiusType::Vdwh) + r = it->second.vdwh_radius; + } + return std::isnan(r) ? 0 : r; +} + +} // anonymous namespace + +void MonLib::read_monomer_cif(const std::string& path_) { + read_monomer_doc(read_cif_gz(path_)); +} + +bool MonLib::read_monomer_lib(const std::string& monomer_dir_, + const std::vector& resnames, + const Logger& logger) { + if (monomer_dir_.empty()) + fail("read_monomer_lib: monomer_dir not specified."); + set_monomer_dir(monomer_dir_); + + // Only recent versions of CCP4 Monomer Library have links_and_mods.cif + try { + read_monomer_cif(monomer_dir + "links_and_mods.cif"); + } catch (std::system_error&) { + read_monomer_cif(monomer_dir + "list/mon_lib_list.cif"); + } + ener_lib.read(read_cif_gz(monomer_dir + "ener_lib.cif")); + + bool ok = true; + for (const std::string& name : resnames) { + if (monomers.find(name) != monomers.end()) + continue; + try { + const cif::Document& doc = read_cif_gz(path(name)); + read_monomer_doc(doc); + } catch (std::system_error& err) { + if (err.code().value() == ENOENT) + logger.mesg("Monomer not in the library: ", name, '.'); + else + logger.mesg("Failed to read ", name, ": ", err.what(), '.'); + ok = false; + } catch (std::runtime_error& err) { + logger.mesg("Failed to read ", name, ": ", err.what(), '.'); + ok = false; + } + } + return ok; +} + + +double MonLib::find_ideal_distance(const const_CRA& cra1, const const_CRA& cra2) const { + std::string types[2] = {cra1.atom->element.uname(), + cra2.atom->element.uname()}; + if (const std::string* tmp = find_chemtype(monomers, cra1)) + types[0] = *tmp; + if (const std::string* tmp = find_chemtype(monomers, cra2)) + types[1] = *tmp; + // if either one is metal, use ion radius + ion radius + if (cra1.atom->element.is_metal() != cra2.atom->element.is_metal()) { + // return if ion radius is found for both of them + double r1 = find_radius(ener_lib, types[0], EnerLib::RadiusType::Ion); + double r2 = find_radius(ener_lib, types[1], EnerLib::RadiusType::Ion); + if (r1 > 0 && r2 > 0) + return r1 + r2; + } + // otherwise, look for defined distance or use average of distances + double r[2] = {0, 0}; + for (int j = 0; j < 2; ++j) { + auto range = ener_lib.bonds.equal_range(types[j]); + for (auto i = range.first; i != range.second; ++i) + if (i->second.atom_type_2 == types[1-j] && !std::isnan(i->second.length)) + return i->second.length; + else if (i->second.atom_type_2.empty() && i->second.type == BondType::Single) + r[j] = i->second.length / 2; + if ((r[j] == 0 || std::isnan(r[j])) && range.first != range.second) + r[j] = range.first->second.length / 2; + if (r[j] == 0 || std::isnan(r[j])) + r[j] = (j==0 ? cra1 : cra2).atom->element.covalent_r(); + } + return r[0] + r[1]; +} + +void MonLib::update_old_atom_names(Structure& st, const Logger& logger) const { + for (const auto& it : monomers) + // monomers should have only monomers needed for this structure. + // Few of them (usually none or one) have old names defined. + if (it.second.has_old_names()) { + const std::string& resname = it.first; + const ChemComp& cc = it.second; + int old_vs_new = 0; + for (const Model& model : st.models) + for (const Chain& chain : model.chains) + for (const Residue& res : chain.residues) + if (res.name == resname) { + for (const Atom& atom : res.atoms) { + if (cc.find_atom(atom.name) == cc.atoms.end()) + ++old_vs_new; + if (cc.find_atom_by_old_name(atom.name) == cc.atoms.end()) + --old_vs_new; + } + } + if (old_vs_new > 0) { + std::string msg = cat("Updating atom names in ", resname, ':'); + std::map mapping; + for (const ChemComp::Atom& a : cc.atoms) + if (!a.old_id.empty() && a.old_id != a.id) { + mapping.emplace(a.old_id, a.id); + cat_to(msg, ' ', a.old_id, "->", a.id); + } + logger.mesg(msg); + rename_atom_names(st, resname, mapping); + } + } +} + +} // namespace gemmi diff --git a/gemmi_gph/riding_h.cpp b/gemmi_gph/riding_h.cpp new file mode 100644 index 000000000..2b2dee439 --- /dev/null +++ b/gemmi_gph/riding_h.cpp @@ -0,0 +1,480 @@ +// Copyright 2018-2022 Global Phasing Ltd. + +#include + +namespace gemmi { + +namespace { + +struct BondedAtom { + Atom* ptr; + Position& pos; // == ptr->pos; + double dist; +}; + +// Calculate position using one angle (theta) and one dihedral angle (tau). +// Returns position of x4 in x1-x2-x3-x4, where dist=|x3-x4| and +// theta is angle(x2, x3, x4). +// Based on section 3.3 of Paciorek et al, Acta Cryst. A52, 349 (1996). +Position position_from_angle_and_torsion(const Position& x1, + const Position& x2, + const Position& x3, + double dist, // |x3-x4| + double theta, // angle x2-x3-x4 + double tau) { // dihedral angle + Vec3 u = x2 - x1; + Vec3 v = x3 - x2; + Vec3 e1 = v.normalized(); + Vec3 e2 = -(u - u.dot(e1) * e1).normalized(); + Vec3 e3 = e1.cross(e2); + Vec3 e23 = std::cos(tau) * e2 + std::sin(tau) * e3; + return x3 + Position(dist * (-std::cos(theta) * e1 + std::sin(theta) * e23)); +} + +// Similar to position_from_angle_and_torsion(), but x1 and tau are not given. +Position arbitrary_position_from_angle(const Position& x2, + const Position& x3, + double dist, // |x3-x4| + double theta) { // angle x2-x3-x4 + Vec3 u(1, 0, 0); + Vec3 v = x3 - x2; + Vec3 e1 = v.normalized(); + Vec3 e2_ = -(u - u.dot(e1) * e1); + if (e2_.length_sq() < 1e-6) { + // u || v, let's take any non-parallel u + u = Vec3(0, 1, 0); + e2_ = -(u - u.dot(e1) * e1); + } + Vec3 e2 = e2_.normalized(); + return x3 + Position(dist * (-std::cos(theta) * e1 + std::sin(theta) * e2)); +} + + +Vec3 get_vector_to_line(const Position& point, + const Position& point_on_the_line, + const Vec3& unit_vector) { + // en.wikipedia.org/wiki/Distance_from_a_point_to_a_line#Vector_formulation + // the component of a - p perpendicular to the line is: (a-p) - ((a-p).n)n + Vec3 ap = point_on_the_line - point; + return ap - ap.dot(unit_vector) * unit_vector; +} + +// If no points satisfy the distances returns a pair of NaNs +std::pair trilaterate(const Position& p1, double r1sq, + const Position& p2, double r2sq, + const Position& p3, double r3sq) { + // It was based on https://en.wikipedia.org/wiki/Trilateration + // but apparently that page has changed in the meantime. + Vec3 ex = (p2 - p1).normalized(); + double i = ex.dot(p3-p1); + Vec3 ey = (Vec3(p3) - p1 - i*ex).normalized(); + Vec3 ez = ex.cross(ey); + double d = (p2-p1).length(); + double j = ey.dot(p3-p1); + double x = (r1sq - r2sq + d*d) / (2*d); + double y = (r1sq - r3sq + i*i + j*j) / (2*j) - x*i/j; + double z2 = r1sq - x*x - y*y; + double z = std::sqrt(z2); // may result in NaN + return std::make_pair(p1 + Position(x*ex + y*ey + z*ez), + p1 + Position(x*ex + y*ey - z*ez)); +} + +// Calculate position using two angles. +// Returns p4. Topology: p1 is bonded to p2, p3 and p4. +std::pair +position_from_two_angles(const Position& p1, + const Position& p2, + const Position& p3, + double dist14, // |p4-p1| + double theta214, // angle p2-p1-p4 + double theta314) { // angle p3-p1-p4 + double d12sq = p1.dist_sq(p2); + double d13sq = p1.dist_sq(p3); + double d14sq = dist14 * dist14; + // the law of cosines + double d24sq = d14sq + d12sq - 2 * std::sqrt(d14sq * d12sq) * cos(theta214); + double d34sq = d14sq + d13sq - 2 * std::sqrt(d14sq * d13sq) * cos(theta314); + return trilaterate(p1, d14sq, p2, d24sq, p3, d34sq); +} + +// Returns angle between hydrogen and the plane of heavy atoms +// in 2H tetrahedral configuration. theta0 is the angle between heavy atoms. +double calculate_tetrahedral_delta(double theta0, double theta1, double theta2) { + // simplified trilateration: + // auto r = trilaterate(Position(0, 0, 0), 1, + // Position(1, 0, 0), 2 - 2 * std::cos(theta1), + // Position(std::cos(theta0), std::sin(theta0), 0), + // 2 - 2 * std::cos(theta2)); + // return std::asin(std::fabs(r.first.z)); + double x = std::cos(theta1); + double y = (std::cos(theta2) - x * std::cos(theta0)) / std::sin(theta0); + double z2 = 1 - x*x - y*y; + double z = std::sqrt(z2); // may result in NaN + return std::asin(z); +} + +double angle_in_triangle(double a, double b, double c) { + return std::acos((a * a + c * c - b * b) / (2 * a * c)); +} + +// Used in rare cases when one angle is missing in 2H-tetrahedral configuration. +// Currently it can happen only with metal sites. +// b c(metal) +// \ / +// atom -- h (possibly two H atoms, symmetric wrt plane abc) +// Angle c-atom-h is missing, b-atom-h is equal alpha, b-atom-c is theta. +// For two H atoms we also need angle h-atom-h. +double missing_angle_2H_tetrahedral(const Topo& topo, const Atom& atom, + const std::vector& hs, + double alpha, double theta) { + if (hs.size() == 1) + return 2 * pi() - alpha - theta; // make it coplanar + if (hs.size() == 2) { + if (const Restraints::Angle* hh = topo.take_angle(hs[0].ptr, &atom, hs[1].ptr)) { + double xh = std::cos(alpha); + double zh = std::sin(0.5 * hh->radians()); + double yh = std::sqrt(1 - xh*xh - zh*zh); + double st = std::sin(theta); + double ct = std::cos(theta); + Vec3 ah = Vec3(xh, -yh * st, zh * st); + double angle = std::acos((ct * ah.x + st * ah.y) / ah.length()); + //printf("missing_angle: %s %g\n", atom.name.c_str(), deg(angle)); + return angle; + } + } + return 0; +} + +[[noreturn]] +void giveup(const std::string& message, const std::vector& hs) { + for (const BondedAtom& bonded_h : hs) { + bonded_h.ptr->occ = 0; + bonded_h.ptr->calc_flag = CalcFlag::Dummy; + } + fail(message); +} + +// known and hs are lists of heavy atoms and hydrogens bonded to atom. +// hs is const, but nevertheless atoms it points to are modified. +void place_hydrogens(const Topo& topo, const Atom& atom, + const std::vector& known, + const std::vector& hs) { + using Angle = Restraints::Angle; + assert(!hs.empty()); + + for (const BondedAtom& bonded_h : hs) + bonded_h.ptr->calc_flag = CalcFlag::Calculated; + + // ==== only hydrogens ==== + if (known.size() == 0) { + // we can only arbitrarily pick directions of atoms + for (const BondedAtom& bonded_h : hs) + bonded_h.ptr->occ = 0; + hs[0].pos = atom.pos + Position(hs[0].dist, 0, 0); + if (hs.size() > 1) { + double theta = pi(); + if (const Angle* ang = topo.take_angle(hs[1].ptr, &atom, hs[0].ptr)) + theta = ang->radians(); + hs[1].pos = atom.pos + Position(hs[1].dist * cos(theta), + hs[1].dist * sin(theta), 0); + } + if (hs.size() > 2) { + const Angle* ang0 = topo.take_angle(hs[2].ptr, &atom, hs[0].ptr); + const Angle* ang1 = topo.take_angle(hs[2].ptr, &atom, hs[1].ptr); + double theta0 = rad(ang0 ? ang0->value : 109.47122); + double theta1 = rad(ang1 ? ang1->value : 109.47122); + auto pos = position_from_two_angles(atom.pos, hs[0].pos, hs[1].pos, + hs[2].dist, theta0, theta1); + hs[2].pos = pos.first; + // 3 hydrogens: for now happens only NH3 (NH2.cif and NH3.cif) + // 4 hydrogens: CH4 (CH2.cif) and NH4 (NH4.cif) + if (hs.size() == 4) + hs[3].pos = pos.second; + } + + // ==== one heavy atom and hydrogens ==== + } else if (known.size() == 1) { + const BondedAtom& h = hs[0]; + const BondedAtom& heavy = known[0]; + const Restraints::Angle* angle = topo.take_angle(h.ptr, &atom, heavy.ptr); + if (!angle) + giveup("No angle restraint for " + h.ptr->name + ".\n", hs); + if (std::abs(angle->value - 180.0) < 0.5) { + Vec3 u = atom.pos - h.pos; + h.pos = atom.pos + Position(u * (h.dist / u.length())); + if (hs.size() > 1) + giveup("Unusual: one of two H atoms has angle restraint 180 deg.", hs); + return; + } + double theta = angle->radians(); + double tau = 0.0; + int period = 0; + const Atom* tau_end = nullptr; + auto plane_range = topo.plane_index.equal_range(&atom); + for (auto i = plane_range.first; i != plane_range.second; ++i) { + const Topo::Plane& plane = *i->second; + // only Topo::Plane with atoms.size() >= 4 is put into planes + if (plane.has(h.ptr) && plane.has(heavy.ptr)) { + for (const Atom* a : plane.atoms) { + if (!a->is_hydrogen() && a != &atom && a != heavy.ptr) { + tau_end = a; + break; + } + } + break; + } + } + Atom* torsion_h = nullptr; + if (!tau_end) { + // Using one dihedral angle. + // We don't check here for which hydrogen the torsion angle is defined. + // If an atom has 2 or 3 hydrogens, the torsion angle may not be given + // for the first one, but only for the 2nd or 3rd (e.g. HD22 in ASN). + auto tor_range = topo.torsion_index.equal_range(&atom); + for (auto i = tor_range.first; i != tor_range.second; ++i) { + const Topo::Torsion& tor = *i->second; + if (tor.atoms[1] == &atom && tor.atoms[2] == heavy.ptr && + tor.atoms[0]->is_hydrogen() && !tor.atoms[3]->is_hydrogen()) { + tau = rad(tor.restr->value); + torsion_h = tor.atoms[0]; + tau_end = tor.atoms[3]; + period = tor.restr->period; + break; + } + if (tor.atoms[2] == &atom && tor.atoms[1] == heavy.ptr && + tor.atoms[3]->is_hydrogen() && !tor.atoms[0]->is_hydrogen()) { + tau = rad(tor.restr->value); + torsion_h = tor.atoms[3]; + tau_end = tor.atoms[0]; + period = tor.restr->period; + break; + } + } + } + + if (tau_end) + h.pos = position_from_angle_and_torsion(tau_end->pos, heavy.pos, atom.pos, + h.dist, theta, tau); + else + h.pos = arbitrary_position_from_angle(heavy.pos, atom.pos, h.dist, theta); + if (std::isnan(h.pos.x)) { + h.pos = Position(0, 0, 0); + giveup("bonded atoms are exactly overlapping (case 1).", hs); + } + if (hs.size() == 2) { + // I think we can assume the two hydrogens are symmetric. + Vec3 axis = (heavy.pos - atom.pos).normalized(); + Vec3 perpendicular = get_vector_to_line(hs[0].pos, atom.pos, axis); + hs[1].pos = hs[0].pos + Position(2 * perpendicular); + } else if (hs.size() == 3) { + // Here we assume the three hydrogens are in the same distance from + // the parent atom and that they make an equilateral triangle. + // First check for which hydrogen was the torsion restraint (if any). + int idx = 0; + for (int i : {1, 2}) + if (torsion_h == hs[i].ptr) { + idx = i; + hs[i].pos = h.pos; + } + // Now get the other positions by rotation + Vec3 axis = (heavy.pos - atom.pos).normalized(); + Vec3 v1 = h.pos - atom.pos; + Vec3 v2 = rotate_about_axis(v1, axis, rad(120)); + Vec3 v3 = rotate_about_axis(v1, axis, rad(-120)); + hs[(idx+1) % 3].pos = atom.pos + Position(v2); + hs[(idx+2) % 3].pos = atom.pos + Position(v3); + } else if (hs.size() >= 4) { + giveup("Unusual: atom bonded to one heavy atoms and 4+ hydrogens.", hs); + } + if (!tau_end || period > (int)hs.size()) + for (const BondedAtom& bonded_h : hs) + bonded_h.ptr->occ = 0; + // ==== two heavy atoms and hydrogens ==== + } else if (known.size() == 2) { + if (hs.size() >= 3) + giveup("Unusual: atom bonded to 2+ heavy atoms and 3+ hydrogens.", hs); + const Angle* ang1 = topo.take_angle(hs[0].ptr, &atom, known[0].ptr); + const Angle* ang2 = topo.take_angle(hs[0].ptr, &atom, known[1].ptr); + const Angle* ang3 = topo.take_angle(known[0].ptr, &atom, known[1].ptr); + + double theta1 = ang1 ? ang1->radians() : 0; + double theta2 = ang2 ? ang2->radians() : 0; + double theta3 = ang3 ? ang3->radians() : 0; + if (!ang3) { + // If ang3 atoms form a bonded triangle (e.g. C11-C12-PT in DVW), + // we can calculate theta3 from the bond lengths. + const Restraints::Bond* aptr = topo.take_bond(&atom, known[1].ptr); + const Restraints::Bond* bptr = topo.take_bond(known[0].ptr, known[1].ptr); + const Restraints::Bond* cptr = topo.take_bond(known[0].ptr, &atom); + if (!aptr || !bptr || !cptr) + giveup(cat("Missing angle restraint ", known[0].ptr->name, '-', atom.name, + '-', known[1].ptr->name, ".\n"), hs); + theta3 = angle_in_triangle(aptr->value, bptr->value, cptr->value); + } + // Some configurations with metals have only distance restraints. + // In such cases, we assume that hydrogens are as far as possible from the metal. + if (!ang1 && ang2 && known[0].ptr->element.is_metal()) + theta1 = missing_angle_2H_tetrahedral(topo, atom, hs, theta2, theta3); + if (!ang2 && ang1 && known[1].ptr->element.is_metal()) + theta2 = missing_angle_2H_tetrahedral(topo, atom, hs, theta1, theta3); + if (theta1 == 0 || theta2 == 0) + giveup(cat("Missing angle restraint ", hs[0].ptr->name, '-', atom.name, + '-', known[theta1 == 0 ? 0 : 1].ptr->name, ".\n"), hs); + + // Co-planar case. The sum of angles should be 360 degrees, + // but in some cif files it differs slightly. + if (theta1 + theta2 + theta3 > rad(360 - 3)) { + Vec3 v12 = known[0].pos - atom.pos; + Vec3 v13 = known[1].pos - atom.pos; + // theta3 is the ideal restraint value, cur_theta3 is the current value + double cur_theta3 = v12.angle(v13); + double ratio = (2 * pi() - cur_theta3) / (theta1 + theta2); + Vec3 axis = v13.cross(v12).normalized(); + Vec3 v14 = rotate_about_axis(v12, axis, theta1 * ratio); + hs[0].pos = atom.pos + Position(hs[0].dist / v14.length() * v14); + if (hs.size() > 1) { + topo.logger.err("Unhandled topology of ", hs.size(), " hydrogens bonded to ", atom.name); + for (size_t i = 1; i < hs.size(); ++i) { + hs[i].ptr->occ = 0; + hs[i].ptr->calc_flag = CalcFlag::Dummy; + } + } + return; + } + + // Tetrahedral or similar configuration. + double hh_half = 0; + if (hs.size() == 2) + if (const Angle* hh = topo.take_angle(hs[0].ptr, &atom, hs[1].ptr)) + hh_half = 0.5 * hh->radians(); + if (hh_half == 0) + hh_half = calculate_tetrahedral_delta(theta3, theta1, theta2); + + // Based on Liebschner et al (2020) doi:10.1016/bs.mie.2020.01.007 + // sec. 2.3. 2H-tetrahedral configuration + double c0 = std::cos(theta3); + double c1 = std::cos(theta1); + double c2 = std::cos(theta2); + double den = 1 / (1 - c0*c0); + double a = den * (c1 - c0 * c2); + double b = den * (c2 - c0 * c1); + // I think the paper defines u10 and u20 in the opposite direction, + // but I had to reverse it somewhere to make it work. + Vec3 u10 = (known[0].pos - atom.pos).normalized(); + Vec3 u20 = (known[1].pos - atom.pos).normalized(); + Vec3 v = u10.cross(u20); + if (std::isnan(v.x)) + giveup("bonded atoms are exactly overlapping (case 2).", hs); + Vec3 d = a * u10 + b * u20; + double dist_sin = hs[0].dist * std::sin(hh_half); + double dist_cos = hs[0].dist * std::cos(hh_half); + Vec3 v0s = v.changed_magnitude(dist_sin); + Vec3 d0c = d.changed_magnitude(dist_cos); + hs[0].pos = atom.pos + Position(d0c + v0s); + Position other_pos = atom.pos + Position(d0c - v0s); + + if (hs.size() == 1) { + const Topo::Chirality* chir = topo.get_chirality(&atom); + if (chir && chir->restr->sign != ChiralityType::Both) { + if (!chir->check()) + hs[0].pos = other_pos; + } else { + hs[0].ptr->occ = 0; + } + } else { // hs.size() == 2 + hs[1].pos = other_pos; + } + + } else { // known.size() >= 3 + if (hs.size() > 1) + giveup("Unusual: atom bonded to 3+ heavy atoms and 2+ hydrogens.", hs); + // Based on Liebschner et al (2020) doi:10.1016/bs.mie.2020.01.007 + // sec. 2.4. 1H-tetrahedral configuration + Vec3 u10 = (known[0].pos - atom.pos).normalized(); + Vec3 u20 = (known[1].pos - atom.pos).normalized(); + Vec3 u30 = (known[2].pos - atom.pos).normalized(); + auto cos_tetrahedral = [&](size_t n) { + const Angle* angle = topo.take_angle(known[n].ptr, &atom, hs[0].ptr); + return angle ? std::cos(angle->radians()) : -1./3.; + }; + SMat33 m{1., 1., 1., u10.dot(u20), u10.dot(u30), u20.dot(u30)}; + Vec3 rhs(cos_tetrahedral(0), cos_tetrahedral(1), cos_tetrahedral(2)); + double det = m.determinant(); + if (std::fabs(det) < 1e-12) + giveup("tetrahedral configuration with four co-planar atoms.", hs); + Vec3 abc = m.inverse_(det).multiply(rhs); + Vec3 h_dir = abc.x * u10 + abc.y * u20 + abc.z * u30; + hs[0].pos = atom.pos + Position(h_dir.changed_magnitude(hs[0].dist)); + } +} + +} // anonymous namespace + +void place_hydrogens_on_all_atoms(Topo& topo) { + std::vector known; + std::vector hs; + auto filter = [](char alt, const std::vector& v) { + std::vector out; + out.reserve(v.size()); + for (const BondedAtom& ba : v) + if (ba.ptr->altloc_matches(alt)) + out.push_back(ba); + return out; + }; + for (Topo::ChainInfo& chain_info : topo.chain_infos) + for (Topo::ResInfo& ri : chain_info.res_infos) { + // If we don't have monomer description from a cif file, + // only ad-hoc restraints, don't try to place hydrogens. + if (ri.orig_chemcomp == nullptr) + continue; + for (Atom& atom : ri.res->atoms) { + if (atom.is_hydrogen()) + continue; + try { + // gather bonded atoms + known.clear(); + hs.clear(); + auto range = topo.bond_index.equal_range(&atom); + for (auto i = range.first; i != range.second; ++i) { + const Topo::Bond* t = i->second; + Atom* other = t->atoms[t->atoms[0] == &atom ? 1 : 0]; + if (other->altloc && atom.altloc) { + // We support links between different altlocs in Topo (e.g. link A-B), + // although these are rare, special cases. + // But if we had bonds between atom 1 (A/B) and atom 2 (A/B/C), + // and we had bonds B-B and B-C, we'd want to use only one of them (B-B). + // Checking atom's name is not robust, but should suffice here. + if (atom.altloc != other->altloc && + in_vector_f([&](const BondedAtom& a) { return a.ptr->name == other->name; }, + known)) + continue; + } + auto& atom_list = other->is_hydrogen() ? hs : known; + atom_list.push_back({other, other->pos, t->restr->value}); + } + if (hs.size() == 0) + continue; + std::string altlocs; + // In a special case: Hs with altlocs on a parent without altloc, + // we need to process conformations one by one. + if (atom.altloc == '\0') + for (const auto& h : hs) { + char alt = h.ptr->altloc; + if (alt && altlocs.find(alt) == std::string::npos) { + altlocs += alt; + place_hydrogens(topo, atom, filter(alt, known), filter(alt, hs)); + } + } + // In all other cases, all bonded atoms are from the same conformation. + if (altlocs.empty()) + place_hydrogens(topo, atom, known, hs); + } catch (const std::runtime_error& e) { + topo.logger.err("Placing of hydrogen bonded to ", + atom_str(chain_info.chain_ref, *ri.res, atom), + " failed:\n ", e.what()); + } + } + } +} + +} // namespace gemmi diff --git a/gemmi_gph/topo.cpp b/gemmi_gph/topo.cpp new file mode 100644 index 000000000..673a487da --- /dev/null +++ b/gemmi_gph/topo.cpp @@ -0,0 +1,1084 @@ +// Copyright 2018-2022 Global Phasing Ltd. + +#include +#include // for sqrt, round +#include // for multimap +#include // for unordered_multimap +#include // for get_or_check_polymer_type, ... +#include // for place_hydrogens_on_all_atoms, ... +#include // for remove_hydrogens + +namespace gemmi { + +std::unique_ptr make_chemcomp_with_restraints(const Residue& res) { + std::unique_ptr cc(new ChemComp()); + cc->name = res.name; + cc->group = ChemComp::Group::Null; + cc->has_coordinates = true; + // add atoms + cc->atoms.reserve(res.atoms.size()); + for (const Atom& a : res.atoms) { + if (a.altloc != '\0' && cc->has_atom(a.name)) + continue; + Element el = a.element; + if (el == El::X) + el = El::N; + if (el == El::D) + el = El::H; + const std::string& chem_type = el.uname(); + cc->atoms.push_back(ChemComp::Atom{a.name, "", el, float(a.charge), chem_type, "", a.pos}); + } + // prepare pairs of atoms + struct Pair { + size_t n1, n2; + double dist; + }; + std::vector pairs; + // first heavy atoms only + for (size_t i = 0; i != res.atoms.size(); ++i) { + const Atom& at1 = res.atoms[i]; + if (at1.is_hydrogen()) + continue; + float r1 = at1.element.covalent_r(); + for (size_t j = i+1; j != res.atoms.size(); ++j) { + const Atom& at2 = res.atoms[j]; + if (at2.is_hydrogen() || !at2.same_conformer(at1)) + continue; + double d2 = at1.pos.dist_sq(at2.pos); + float r2 = at2.element.covalent_r(); + double dmax = std::max(2.0, 1.3 * std::max(r1, r2)); + if (d2 < sq(dmax)) + pairs.push_back(Pair{i, j, std::sqrt(d2)}); + } + } + // now each hydrogen with the nearest heavy atom + for (size_t i = 0; i != res.atoms.size(); ++i) { + const Atom& at1 = res.atoms[i]; + if (at1.is_hydrogen()) { + size_t nearest = (size_t)-1; + double min_d2 = sq(2.5); + for (size_t j = 0; j != res.atoms.size(); ++j) { + const Atom& at2 = res.atoms[j]; + if (!at2.is_hydrogen() && at2.same_conformer(at1)) { + double d2 = at1.pos.dist_sq(at2.pos); + if (d2 < min_d2) { + min_d2 = d2; + nearest = j; + } + } + } + if (nearest != (size_t)-1) { + pairs.push_back(Pair{nearest, i, std::sqrt(min_d2)}); + } + } + } + + // add bonds + // note: duplicated bonds (from different conformations) are not a problem + for (const Pair& p : pairs) { + Restraints::Bond bond; + bond.id1 = Restraints::AtomId{1, res.atoms[p.n1].name}; + bond.id2 = Restraints::AtomId{1, res.atoms[p.n2].name}; + bond.type = BondType::Unspec; + bond.aromatic = false; + double rounded_dist = 0.001 * std::round(1000 * p.dist); + bond.value = bond.value_nucleus = rounded_dist; + bond.esd = bond.esd_nucleus = 0.02; + cc->rt.bonds.push_back(bond); + } + // add angles + struct Triple { + size_t n1, n2, n3; + }; + std::vector triples; + for (size_t i = 0; i != pairs.size(); ++i) + for (size_t j = i+1; j != pairs.size(); ++j) { + if (pairs[i].n1 == pairs[j].n1) + triples.push_back(Triple{pairs[i].n2, pairs[i].n1, pairs[j].n2}); + else if (pairs[i].n1 == pairs[j].n2) + triples.push_back(Triple{pairs[i].n2, pairs[i].n1, pairs[j].n1}); + else if (pairs[i].n2 == pairs[j].n1) + triples.push_back(Triple{pairs[i].n1, pairs[i].n2, pairs[j].n2}); + else if (pairs[i].n2 == pairs[j].n2) + triples.push_back(Triple{pairs[i].n1, pairs[i].n2, pairs[j].n1}); + } + for (const Triple& triple : triples) { + Restraints::Angle angle; + angle.id1 = Restraints::AtomId{1, res.atoms[triple.n1].name}; + angle.id2 = Restraints::AtomId{1, res.atoms[triple.n2].name}; + angle.id3 = Restraints::AtomId{1, res.atoms[triple.n3].name}; + double angle_rad = calculate_angle(res.atoms[triple.n1].pos, + res.atoms[triple.n2].pos, + res.atoms[triple.n3].pos); + angle.value = 0.01 * std::round(100 * deg(angle_rad)); + angle.esd = 3.0; + cc->rt.angles.push_back(angle); + } + return cc; +} + +Topo::ChainInfo::ChainInfo(ResidueSpan& subchain, const Chain& chain, const Entity* ent) + : chain_ref(chain) { + subchain_name = subchain.at(0).subchain; + res_infos.reserve(subchain.size()); + if (ent) { + entity_id = ent->name; + polymer = ent->entity_type == EntityType::Polymer; + polymer_type = get_or_check_polymer_type(ent, subchain); + } else { + polymer = false; + polymer_type = PolymerType::Unknown; + } + for (Residue& res : subchain) + res_infos.emplace_back(&res); +} + +// Add a ChemLink that restraints only bond length. +static +const std::string& add_auto_chemlink(MonLib& monlib, + const std::string& resname1, const std::string& aname1, + const std::string& resname2, const std::string& aname2, + double ideal_dist, double esd) { + ChemLink cl; + cl.side1.comp = resname1; + cl.side2.comp = resname2; + cl.id = resname1 + resname2; + cl.name = "auto-" + cl.id; + cl.rt.bonds.push_back({Restraints::AtomId{1, aname1}, + Restraints::AtomId{2, aname2}, + BondType::Unspec, false, + ideal_dist, esd, + ideal_dist, esd}); + // ensure unique link id + size_t orig_len = cl.id.size(); + for (int n = 0; monlib.get_link(cl.id) != nullptr; ++n) + cl.id.replace(orig_len, cl.id.size(), std::to_string(n)); + + auto it = monlib.links.emplace(cl.id, cl); + return it.first->first; +} + +static const ChemLink* setup_link_if_matches(Topo::Link& link, const MonLib& monlib, + const std::string& atom1, + const std::string& atom2) { + bool invert; + const ChemLink* match = nullptr; + std::tie(match, invert, link.aliasing1, link.aliasing2) = + monlib.match_link(*link.res1, atom1, link.alt1, *link.res2, atom2, link.alt2); + if (match) { + link.link_id = match->id; + if (invert) { + std::swap(link.res1, link.res2); + std::swap(link.alt1, link.alt2); + std::swap(link.atom1_name_id, link.atom2_name_id); + std::swap(link.aliasing1, link.aliasing2); + } + } + return match; +} + +static int atom_name_id(const std::string& s) { + int id = 0; + if (s.size() > 0) // there is '\0' at the end + id = (s[0] << 24 | s[1] << 16); + if (s.size() > 2) + id |= (s[2] << 8 | s[3]); + return id | 0x20202020; +} + +static void add_polymer_links(PolymerType polymer_type, + const Topo::ResInfo& ri1, + Topo::ResInfo& ri2, + MonLib* monlib) { + Topo::Link link; + link.res1 = ri1.res; + link.res2 = ri2.res; + assert(&ri1 - &ri2 == link.res_distance()); + bool groups_ok = (ri1.orig_chemcomp != nullptr && ri2.orig_chemcomp != nullptr); + + if (is_polypeptide(polymer_type)) { + std::string c = "C"; + std::string ca1 = "CA"; + std::string n = "N"; + std::string ca2 = "CA"; + if (ri1.orig_chemcomp && !ChemComp::is_peptide_group(ri1.orig_chemcomp->group)) { + for (const ChemComp::Aliasing& aliasing : ri1.orig_chemcomp->aliases) + if (ChemComp::is_peptide_group(aliasing.group)) { + link.aliasing1 = &aliasing; + if (const std::string* ptr = aliasing.name_from_alias(c)) + c = *ptr; + if (const std::string* ptr = aliasing.name_from_alias(ca1)) + ca1 = *ptr; + break; + } + if (!link.aliasing1) + groups_ok = false; + } + ChemComp::Group n_terminus_group = ri2.orig_chemcomp ? ri2.orig_chemcomp->group + : ChemComp::Group::Null; + if (ri2.orig_chemcomp && !ChemComp::is_peptide_group(ri2.orig_chemcomp->group)) { + for (const ChemComp::Aliasing& aliasing : ri2.orig_chemcomp->aliases) + if (ChemComp::is_peptide_group(aliasing.group)) { + link.aliasing2 = &aliasing; + n_terminus_group = aliasing.group; + if (const std::string* ptr = aliasing.name_from_alias(n)) + n = *ptr; + if (const std::string* ptr = aliasing.name_from_alias(ca2)) + ca2 = *ptr; + break; + } + if (!link.aliasing2) + groups_ok = false; + } + for (const Atom& a1 : ri1.res->atoms) + if (a1.name == c && a1.element == El::C) { + for (const Atom& a2 : ri2.res->atoms) + if (a2.name == n && a2.element == El::N && + (a2.altloc == a1.altloc || a2.altloc == '\0' || a1.altloc == '\0') && + in_peptide_bond_distance(&a1, &a2)) { + // One C-N pair of atoms can create here only one link. + // Ignoring artificial configuration of no-altloc C and N atoms, + // and CA atoms in 2+ conformations making both CIS and TRANS links. + link.alt1 = a1.altloc; + link.alt2 = a2.altloc; + link.atom1_name_id = atom_name_id(a1.name); + link.atom2_name_id = atom_name_id(a2.name); + if (groups_ok) { + // Deciding CIS/TRANS based on omega angle. + char alt = a1.altloc_or(a2.altloc_or('*')); + const Atom* ca1_atom = ri1.res->find_atom(ca1, alt, El::C); + const Atom* ca2_atom = ri2.res->find_atom(ca2, alt, El::C); + link.is_cis = is_peptide_bond_cis(ca1_atom, &a1, &a2, ca2_atom, 60.); + if (n_terminus_group == ChemComp::Group::PPeptide) + link.link_id = link.is_cis ? "PCIS" : "PTRANS"; + else if (n_terminus_group == ChemComp::Group::MPeptide) + link.link_id = link.is_cis ? "NMCIS" : "NMTRANS"; + else + link.link_id = link.is_cis ? "CIS" : "TRANS"; + } else if (monlib) { + if (!setup_link_if_matches(link, *monlib, c, n)) + link.link_id = add_auto_chemlink(*monlib, + ri1.res->name, c, + ri2.res->name, n, + 1.34, 0.04); + } + ri2.prev.push_back(link); + } + } + + } else if (is_polynucleotide(polymer_type)) { + std::string o3p = "O3'"; + std::string p = "P"; + if (ri1.orig_chemcomp && !ChemComp::is_nucleotide_group(ri1.orig_chemcomp->group)) { + for (const ChemComp::Aliasing& aliasing : ri1.orig_chemcomp->aliases) + if (ChemComp::is_nucleotide_group(aliasing.group)) { + link.aliasing1 = &aliasing; + if (const std::string* o3p_ptr = aliasing.name_from_alias(o3p)) + o3p = *o3p_ptr; + break; + } + if (!link.aliasing1) + groups_ok = false; + } + if (ri2.orig_chemcomp && !ChemComp::is_nucleotide_group(ri2.orig_chemcomp->group)) { + for (const ChemComp::Aliasing& aliasing : ri2.orig_chemcomp->aliases) + if (ChemComp::is_nucleotide_group(aliasing.group)) { + link.aliasing2 = &aliasing; + if (const std::string* p_ptr = aliasing.name_from_alias(p)) + p = *p_ptr; + break; + } + if (!link.aliasing2) + groups_ok = false; + } + for (const Atom& a1 : ri1.res->atoms) + if (a1.name == o3p && a1.element == El::O) { + for (const Atom& a2 : ri2.res->atoms) + if (a2.name == p && a2.element == El::P && + (a2.altloc == a1.altloc || a2.altloc == '\0' || a1.altloc == '\0') && + in_nucleotide_bond_distance(&a1, &a2)) { + link.alt1 = a1.altloc; + link.alt2 = a2.altloc; + link.atom1_name_id = atom_name_id(a1.name); + link.atom2_name_id = atom_name_id(a2.name); + if (groups_ok) { + link.link_id = "p"; + } else if (monlib) { + if (!setup_link_if_matches(link, *monlib, o3p, p)) + link.link_id = add_auto_chemlink(*monlib, + ri1.res->name, o3p, + ri2.res->name, p, + 1.606, 0.02); + } + ri2.prev.push_back(link); + } + } + } + + if (ri2.prev.empty()) { + link.link_id = "gap"; + ri2.prev.push_back(link); + } +} + +double Topo::ideal_chiral_abs_volume(const Chirality &ch) const { + const Restraints::Bond* bond_c1 = take_bond(ch.atoms[0], ch.atoms[1]); + const Restraints::Bond* bond_c2 = take_bond(ch.atoms[0], ch.atoms[2]); + const Restraints::Bond* bond_c3 = take_bond(ch.atoms[0], ch.atoms[3]); + const Restraints::Angle* angle_1c2 = take_angle(ch.atoms[1], ch.atoms[0], ch.atoms[2]); + const Restraints::Angle* angle_2c3 = take_angle(ch.atoms[2], ch.atoms[0], ch.atoms[3]); + const Restraints::Angle* angle_3c1 = take_angle(ch.atoms[3], ch.atoms[0], ch.atoms[1]); + if (bond_c1 && bond_c2 && bond_c3 && angle_1c2 && angle_2c3 && angle_3c1) + return chiral_abs_volume(bond_c1->value, bond_c2->value, bond_c3->value, + angle_1c2->value, angle_2c3->value, angle_3c1->value); + return std::numeric_limits::quiet_NaN(); +} + +std::vector Topo::apply_restraints(const Restraints& rt, + Residue& res, Residue* res2, Asu asu, + char altloc1, char altloc2, bool require_alt) { + std::string altlocs; + if (altloc1 == '\0' && altloc2 == '\0') { + add_distinct_altlocs(res, altlocs); + if (res2) + add_distinct_altlocs(*res2, altlocs); + } + if (altlocs.empty()) + altlocs += altloc1 != 0 ? altloc1 : altloc2; + + std::vector rules; + for (const Restraints::Bond& bond : rt.bonds) + for (char alt : altlocs) + if (Atom* at1 = bond.id1.get_from(res, res2, alt, altloc2)) + if (Atom* at2 = bond.id2.get_from(res, res2, alt, altloc2)) { + bool with_alt = at1->altloc || at2->altloc; + if (with_alt || !require_alt) { + rules.push_back({RKind::Bond, bonds.size()}); + bonds.push_back({&bond, {{at1, at2}}, asu}); + } + if (!with_alt) + break; + } + + if (only_bonds) + return rules; + + for (const Restraints::Angle& angle : rt.angles) + for (char alt : altlocs) + if (Atom* at1 = angle.id1.get_from(res, res2, alt, altloc2)) + if (Atom* at2 = angle.id2.get_from(res, res2, alt, altloc2)) + if (Atom* at3 = angle.id3.get_from(res, res2, alt, altloc2)) { + bool with_alt = at1->altloc || at2->altloc || at3->altloc; + if (with_alt || !require_alt) { + rules.push_back({RKind::Angle, angles.size()}); + angles.push_back({&angle, {{at1, at2, at3}}}); + } + if (!with_alt) + break; + } + for (const Restraints::Torsion& tor : rt.torsions) + for (char alt : altlocs) + if (Atom* at1 = tor.id1.get_from(res, res2, alt, altloc2)) + if (Atom* at2 = tor.id2.get_from(res, res2, alt, altloc2)) + if (Atom* at3 = tor.id3.get_from(res, res2, alt, altloc2)) + if (Atom* at4 = tor.id4.get_from(res, res2, alt, altloc2)) { + bool with_alt = at1->altloc || at2->altloc || at3->altloc || at4->altloc; + if (with_alt || !require_alt) { + rules.push_back({RKind::Torsion, torsions.size()}); + torsions.push_back({&tor, {{at1, at2, at3, at4}}}); + } + if (!with_alt) + break; + } + for (const Restraints::Chirality& chir : rt.chirs) + for (char alt : altlocs) + if (Atom* at1 = chir.id_ctr.get_from(res, res2, alt, altloc2)) + if (Atom* at2 = chir.id1.get_from(res, res2, alt, altloc2)) + if (Atom* at3 = chir.id2.get_from(res, res2, alt, altloc2)) + if (Atom* at4 = chir.id3.get_from(res, res2, alt, altloc2)) { + bool with_alt = at1->altloc || at2->altloc || at3->altloc || at4->altloc; + if (with_alt || !require_alt) { + rules.push_back({RKind::Chirality, chirs.size()}); + chirs.push_back({&chir, {{at1, at2, at3, at4}}}); + } + if (!with_alt) + break; + } + for (const Restraints::Plane& plane : rt.planes) + for (char alt : altlocs) { + std::vector atoms; + bool with_alt = false; + for (const Restraints::AtomId& id : plane.ids) + if (Atom* atom = id.get_from(res, res2, alt, altloc2)) { + with_alt = with_alt || atom->altloc; + atoms.push_back(atom); + } + if (atoms.size() >= 4 && (with_alt || !require_alt)) { + rules.push_back({RKind::Plane, planes.size()}); + planes.push_back({&plane, atoms}); + } + if (!with_alt) + break; + } + return rules; +} + +void Topo::apply_restraints_from_link(Link& link, const MonLib& monlib) { + if (link.link_id.empty() || link.link_id == "gap") + return; + const ChemLink* chem_link = monlib.get_link(link.link_id); + if (!chem_link) { + logger.err("ignoring link '", link.link_id, "' as it is not in the monomer library"); + return; + } + const Restraints* rt = &chem_link->rt; + if (link.alt1 && link.alt2 && link.alt1 != link.alt2) + logger.err("LINK between different conformers: ", link.alt1, " (in ", + link.res1->name, ") and ", link.alt2, " (in ", link.res2->name, ")."); + // aliases are a new feature - introduced in 2022 + if (link.aliasing1 || link.aliasing2) { + std::unique_ptr rt_copy(new Restraints(*rt)); + if (link.aliasing1) + for (const auto& p : link.aliasing1->related) + rt_copy->rename_atom(Restraints::AtomId{1, p.second}, p.first); + if (link.aliasing2) + for (const auto& p : link.aliasing2->related) + rt_copy->rename_atom(Restraints::AtomId{2, p.second}, p.first); + rt = rt_copy.get(); + rt_storage.push_back(std::move(rt_copy)); + } + link.link_rules = apply_restraints(*rt, *link.res1, link.res2, link.asu, + link.alt1, link.alt2, false); +} + +// see comments above the declaration +void Topo::initialize_refmac_topology(Structure& st, Model& model0, + MonLib& monlib, bool ignore_unknown_links) { + // initialize chain_infos + for (Chain& chain : model0.chains) + for (ResidueSpan& sub : chain.subchains()) { + // set Residue::group_idx which is used in Restraints::AtomId::get_from() + for (size_t i = 0; i != sub.size(); ++i) { + sub[i].group_idx = 0; + if (i != 0 && sub[i-1].seqid == sub[i].seqid) + sub[i].group_idx = sub[i-1].group_idx + 1; + } + const Entity* ent = st.get_entity_of(sub); + chain_infos.emplace_back(sub, chain, ent); + } + + // add modifications from MODRES records (Refmac's extension) + for (const ModRes& modres : st.mod_residues) + if (!modres.mod_id.empty()) { + for (Topo::ChainInfo& chain_info : chain_infos) + if (chain_info.chain_ref.name == modres.chain_name) { + for (Topo::ResInfo& res_info : chain_info.res_infos) + if (*res_info.res == modres.res_id) + res_info.add_mod(modres.mod_id, nullptr, '\0'); + } + } + + // setup pointers to monomers and links in the polymer + for (ChainInfo& ci : chain_infos) { + for (ResInfo& ri : ci.res_infos) { + auto it = monlib.monomers.find(ri.res->name); + if (it != monlib.monomers.end()) + ri.orig_chemcomp = &it->second; + // orig_chemcomp is left null for missing monomers + } + // setup polymer links + if (ci.polymer && !ci.res_infos.empty()) { + // handling of microheterogeneities makes it more complicated + // and it should be even more complex to handle partial bonding + auto prev_begin = ci.res_infos.begin(); + auto prev_end = ci.group_end(prev_begin); + while (prev_end != ci.res_infos.end()) { + auto group_begin = prev_end; + auto group_end = ci.group_end(group_begin); + for (auto ri = group_begin; ri != group_end; ++ri) + for (auto prev_ri = prev_begin; prev_ri != prev_end; ++prev_ri) { + MonLib* monlib_ptr = ignore_unknown_links ? nullptr : &monlib; + add_polymer_links(ci.polymer_type, *prev_ri, *ri, monlib_ptr); + } + prev_begin = group_begin; + prev_end = group_end; + } + } + } + + // add extra links + for (Connection& conn : st.connections) + if (conn.type != Connection::Hydrog) // ignoring hydrogen bonds + setup_connection(conn, model0, monlib, ignore_unknown_links); + + // Add modifications from standard links. We do it here b/c polymer links + // could be disabled (link_id.clear()) in setup_connection(). + for (ChainInfo& ci : chain_infos) + for (ResInfo& ri : ci.res_infos) + for (Link& prev : ri.prev) + if (const ChemLink* chem_link = monlib.get_link(prev.link_id)) { + ResInfo* ri_prev = &ri + prev.res_distance(); + ri_prev->add_mod(chem_link->side1.mod, prev.aliasing1, prev.alt1); + ri.add_mod(chem_link->side2.mod, prev.aliasing2, prev.alt2); + } + + // Apply modifications to monomer restraints + for (ChainInfo& chain_info : chain_infos) + for (ResInfo& ri : chain_info.res_infos) { + if (ri.orig_chemcomp) { + // The final ChemComp restraints that we'll use are made from + // original (_chem_comp) restraints with modifications (_chem_mod) + // applied. There is a corner case in which different conformations + // of the residue have different modifications applied. + bool has_mod_altlocs = false; + for (const Mod& mod : ri.mods) + if (mod.altloc != '\0') + has_mod_altlocs = true; + std::string altlocs; + if (has_mod_altlocs) + add_distinct_altlocs(*ri.res, altlocs); // cf. apply_restraints + if (altlocs.empty()) + altlocs += '\0'; + for (char altloc : altlocs) { + // key for caching in Topo::cc_cache: ChemComp::name + modifications + std::string key = ri.orig_chemcomp->name; + for (const Mod& mod : ri.mods) + if (!mod.altloc || altloc == mod.altloc) { + key += char(1 + static_cast(mod.alias)); + key += mod.id; + } + auto it = cc_cache.find(key); + if (it != cc_cache.end()) { + ri.chemcomps.push_back({altloc, it->second.get()}); + } else { // it's not in cache yet - we need to add it + std::unique_ptr cc_copy(new ChemComp(*ri.orig_chemcomp)); + // apply modifications + for (const Mod& mod : ri.mods) { + if (!mod.altloc || altloc == mod.altloc) { + if (const ChemMod* chem_mod = monlib.get_mod(mod.id)) { + try { + chem_mod->apply_to(*cc_copy, mod.alias); + } catch(std::runtime_error& e) { + logger.err("failed to apply modification ", chem_mod->id, + " to ", ri.res->name, ": ", e.what()); + } + } else { + logger.err("modification not found: ", mod.id); + } + } + } + ri.chemcomps.push_back({altloc, cc_copy.get()}); + cc_cache.emplace(key, std::move(cc_copy)); + } + } + // Usually the same modifications are applied to all conformers. + // In such case reduce chemcomps to a single value. + if (ri.chemcomps.size() > 0 && + std::all_of(ri.chemcomps.begin() + 1, ri.chemcomps.end(), + [&](const FinalChemComp& f) { return f.cc == ri.chemcomps[0].cc; })) { + ri.chemcomps.resize(1); + ri.chemcomps[0].altloc = '\0'; + } + } else { // orig_chemcomp not set - make ChemComp with ad-hoc restraints + // no cache - ad-hoc restraints are separate for each residue + cc_storage.emplace_back(make_chemcomp_with_restraints(*ri.res)); + ri.chemcomps.push_back({'\0', cc_storage.back().get()}); + } + } +} + +void Topo::apply_all_restraints(const MonLib& monlib) { + bonds.clear(); + angles.clear(); + torsions.clear(); + chirs.clear(); + planes.clear(); + rt_storage.clear(); + for (ChainInfo& chain_info : chain_infos) + for (ResInfo& ri : chain_info.res_infos) { + // link restraints + for (Link& link : ri.prev) + apply_restraints_from_link(link, monlib); + // monomer restraints + auto it = ri.chemcomps.cbegin(); + ri.monomer_rules = apply_restraints(it->cc->rt, *ri.res, nullptr, Asu::Same, + it->altloc, '\0', /*require_alt=*/false); + while (++it != ri.chemcomps.end()) { + auto rules = apply_restraints(it->cc->rt, *ri.res, nullptr, Asu::Same, + it->altloc, '\0', /*require_alt=*/true); + // calling reserve avoids bogus GCC warning -Wstringop-overflow + ri.monomer_rules.reserve(ri.monomer_rules.size() + rules.size()); + vector_move_extend(ri.monomer_rules, std::move(rules)); + } + } + for (Link& link : extras) + apply_restraints_from_link(link, monlib); +} + +void Topo::create_indices() { + bond_index.clear(); + for (Bond& bond : bonds) { + bond_index.emplace(bond.atoms[0], &bond); + if (bond.atoms[1] != bond.atoms[0]) + bond_index.emplace(bond.atoms[1], &bond); + } + angle_index.clear(); + for (Angle& ang : angles) + angle_index.emplace(ang.atoms[1], &ang); + torsion_index.clear(); + for (Torsion& tor : torsions) { + torsion_index.emplace(tor.atoms[1], &tor); + if (tor.atoms[1] != tor.atoms[2]) + torsion_index.emplace(tor.atoms[2], &tor); + } + plane_index.clear(); + for (Plane& plane : planes) + for (Atom* atom : plane.atoms) + plane_index.emplace(atom, &plane); +} + +Topo::Link* Topo::find_polymer_link(const AtomAddress& aa1, const AtomAddress& aa2) { + auto are_bonded = [&](const Link& link, const AtomAddress& a1, const AtomAddress& a2) { + return a1.res_id.matches_noseg(*link.res1) && + a2.res_id.matches_noseg(*link.res2) && + a1.altloc == link.alt1 && + a2.altloc == link.alt2 && + (a1.atom_name.empty() || atom_name_id(a1.atom_name) == link.atom1_name_id) && + (a2.atom_name.empty() || atom_name_id(a2.atom_name) == link.atom2_name_id); + }; + if (aa1.chain_name != aa2.chain_name) + return nullptr; + for (ChainInfo& ci : chain_infos) + if (aa1.chain_name == ci.chain_ref.name) { + for (ResInfo& ri : ci.res_infos) + for (Link& link : ri.prev) { + assert(link.res1 && link.res2); + if (are_bonded(link, aa1, aa2) || are_bonded(link, aa2, aa1)) + return &link; + } + } + return nullptr; +} + +// Tries to construct Topo::Link and append it to extras. +// Side-effects: it may modify conn.link_id and add ChemLink to monlib.links. +void Topo::setup_connection(Connection& conn, Model& model0, MonLib& monlib, + bool ignore_unknown_links) { + if (conn.link_id == "gap") { + if (Link* polymer_link = find_polymer_link(conn.partner1, conn.partner2)) + polymer_link->link_id.clear(); // disable polymer link + return; + } + + Link extra; + CRA cra1 = model0.find_cra(conn.partner1, true); + CRA cra2 = model0.find_cra(conn.partner2, true); + if (!cra1.atom || !cra2.atom) + return; + extra.res1 = cra1.residue; + extra.res2 = cra2.residue; + extra.alt1 = conn.partner1.altloc; + extra.alt2 = conn.partner2.altloc; + extra.asu = conn.asu; + + const ChemLink* match = nullptr; + + // If we have link_id find ChemLink by name (and check if it matches). + if (!conn.link_id.empty()) { + match = monlib.get_link(conn.link_id); + if (!match) { + logger.err("link not found in monomer library: ", conn.link_id); + return; + } + if (match->rt.bonds.empty() || + !monlib.link_side_matches_residue(match->side1, extra.res1->name, &extra.aliasing1) || + !monlib.link_side_matches_residue(match->side2, extra.res2->name, &extra.aliasing2) || + !atom_match_with_alias(match->rt.bonds[0].id1.atom, + conn.partner1.atom_name, extra.aliasing1) || + !atom_match_with_alias(match->rt.bonds[0].id2.atom, + conn.partner2.atom_name, extra.aliasing2)) { + logger.err("link from the monomer library does not match: ", conn.link_id); + return; + } + } else { + // we don't have link_id - use the best matching link (if any) + match = setup_link_if_matches(extra, monlib, + conn.partner1.atom_name, conn.partner2.atom_name); + if (match) + conn.link_id = match->id; + } + + // If a polymer link is also given in LINK/struct_conn, + // use only one of them. If LINK has explicit name (ccp4_link_id), + // or if it matches residue-specific link from monomer library, use it; + // otherwise, LINK is repetition of TRANS/CIS, so ignore LINK. + if (Link* polymer_link = find_polymer_link(conn.partner1, conn.partner2)) { + if (!conn.link_id.empty() || // conn has explicit link name + // polymer link was not really identified + cif::is_null(polymer_link->link_id) || polymer_link->link_id == "gap" || + // conn is residue-specific + (match && !(match->side1.comp.empty() && match->side2.comp.empty()))) + polymer_link->link_id.clear(); // disable polymer link, use conn + else + return; + } + + if (match) { + extra.link_id = match->id; + // add modifications from the link + find_resinfo(extra.res1)->add_mod(match->side1.mod, extra.aliasing1, extra.alt1); + find_resinfo(extra.res2)->add_mod(match->side2.mod, extra.aliasing2, extra.alt2); + } else { + if (ignore_unknown_links) + return; + // create a new ChemLink and add it to the monomer library + double ideal_dist = monlib.find_ideal_distance(cra1, cra2); + extra.link_id = add_auto_chemlink(monlib, + extra.res1->name, conn.partner1.atom_name, + extra.res2->name, conn.partner2.atom_name, + ideal_dist, 0.02); + } + extras.push_back(extra); +} + +void Topo::set_cispeps_in_structure(Structure& st) { + st.cispeps.clear(); + if (chain_infos.empty()) + return; + // model is not stored in Topo, let's determine it from chain_infos[0] + int model_num = 0; + for (const Model& model : st.models) + if (!model.chains.empty() && + &model.chains[0] == &chain_infos[0].chain_ref) + model_num = model.num; + for (ChainInfo& chain_info : chain_infos) + for (ResInfo& res_info : chain_info.res_infos) + for (Link& link : res_info.prev) + if (link.is_cis) { + CisPep cp; + cp.model_num = model_num; + cp.partner_c = AtomAddress(chain_info.chain_ref.name, *link.res1, "", link.alt1); + cp.partner_n = AtomAddress(chain_info.chain_ref.name, *link.res2, "", link.alt2); + cp.only_altloc = link.alt1 ? link.alt1 : link.alt2; + for (const Rule& rule : link.link_rules) + if (rule.rkind == RKind::Torsion) { + const Torsion& tor = torsions[rule.index]; + if (tor.restr->label == "omega") { + cp.reported_angle = tor.calculate(); + break; + } + } + st.cispeps.push_back(cp); + } +} + +namespace { + +void remove_hydrogens_from_atom(Topo::ResInfo* ri, + const std::string& atom_name, char alt) { + if (!ri) + return; + std::vector& atoms = ri->res->atoms; + const Restraints& rt = ri->get_final_chemcomp(alt).rt; + for (auto it = atoms.end(); it-- != atoms.begin(); ) { + if (it->is_hydrogen() && is_same_conformer(it->altloc, alt)) { + const Restraints::AtomId* heavy = rt.first_bonded_atom(it->name); + if (heavy && heavy->atom == atom_name) + atoms.erase(it); + } + } +} + +void set_cis_in_link(Topo::Link& link, bool is_cis) { + if (is_cis) { + if (ends_with(link.link_id, "TRANS")) + link.link_id.replace(link.link_id.size() - 5, 5, "CIS"); + } else { + if (ends_with(link.link_id, "CIS")) + link.link_id.replace(link.link_id.size() - 3, 3, "TRANS"); + } + link.is_cis = is_cis; +} + +void force_cispeps(Topo& topo, bool single_model, const Model& model, + const std::vector& cispeps) { + std::multimap cispep_index; + for (const CisPep& cp : cispeps) { + if (single_model || model.num == cp.model_num) + if (const Residue* res_n = model.find_cra(cp.partner_n).residue) + cispep_index.emplace(res_n, &cp); + } + for (Topo::ChainInfo& chain_info : topo.chain_infos) + for (Topo::ResInfo& res_info : chain_info.res_infos) { + auto range = cispep_index.equal_range(res_info.res); + for (Topo::Link& link : res_info.prev) { + bool is_cis = false; + for (auto i = range.first; i != range.second; ++i) { + const CisPep& cp = *i->second; + if (cp.partner_c.res_id.matches_noseg(*link.res1) && + (cp.only_altloc == '\0' || cp.only_altloc == link.alt1 + || cp.only_altloc == link.alt2)) + is_cis = true; + } + if (is_cis != link.is_cis) { + set_cis_in_link(link, is_cis); + const std::string& ch_name = chain_info.chain_ref.name; + topo.logger.note("link between ", atom_str(ch_name, *link.res1, "", link.alt1), + " and ", atom_str(ch_name, *link.res2, "", link.alt2), + " forced to ", link.link_id); + } + } + } +} + +struct Neigh { + char alt; + float occ; +}; +using NeighMap = std::unordered_multimap; + +// Assumes no hydrogens in the residue. +// Position and serial number are not assigned for new atoms. +void add_hydrogens_without_positions(Topo::ResInfo& ri, const NeighMap& neighbor_altlocs) { + std::vector& atoms = ri.res->atoms; + // Add H atom for each conformation (altloc) of the parent atom and its + // first neighbors. + for (size_t i = 0, size = atoms.size(); i != size; ++i) { + if (atoms[i].calc_flag == CalcFlag::NoHydrogen) + continue; + char parent_alt = atoms[i].altloc; + float parent_occ = atoms[i].occ; + std::map altlocs; // altloc + occupancy + if (parent_alt == '\0') { + // We could have neighbor 1 with altlocs A,B and neighbor 2 with C,D. + // Or A,B and A,B,C. Or, neighbor 1 could have different occupancy + // of altloc A than neighbor 2. We don't want to check for all possible + // weird cases. Only ensure that the added H has total occupancy <= 1. + float occ_sum = 0; + auto range = neighbor_altlocs.equal_range(atoms[i].serial); + for (auto it = range.first; it != range.second; ++it) { + const Neigh& neigh = it->second; + if (altlocs.count(neigh.alt) == 0 && neigh.occ < 1.0f && occ_sum + neigh.occ <= 1.001f) { + occ_sum += neigh.occ; + altlocs.emplace(neigh.alt, neigh.occ); + } + } + if (occ_sum - parent_occ > 0.001f) + for (auto& it : altlocs) + it.second *= parent_occ; + } + if (altlocs.empty()) + altlocs.emplace(parent_alt, parent_occ); + const ChemComp& cc = ri.get_final_chemcomp(parent_alt); + for (const Restraints::Bond& bond : cc.rt.bonds) { + // atoms may get re-allocated, so we can't set parent earlier + const Atom& parent = atoms[i]; + assert(!parent.is_hydrogen()); + const Restraints::AtomId* atom_id = bond.other(parent.name); + if (!atom_id) + continue; + auto it = cc.find_atom(atom_id->atom); + if (it == cc.atoms.end()) + fail("inconsistent _chem_comp " + cc.name); + if (it->is_hydrogen()) { + gemmi::Atom atom; + atom.name = it->id; + atom.element = it->el; + // calc_flag will be changed to Calculated when the position is set + atom.calc_flag = CalcFlag::Dummy; + atom.b_iso = parent.b_iso; + for (auto alt_occ : altlocs) { + atom.altloc = alt_occ.first; + atom.occ = alt_occ.second; + atoms.push_back(atom); + } + } + } + } +} + +NeighMap prepare_neighbor_altlocs(Topo& topo, const MonLib& monlib) { + // disable warnings here, so they are not printed twice + topo.logger.suspend(); + // Prepare bonds. Fills topo.bonds, monomer_rules/link_rules and rt_storage, + // but they are all reset when apply_all_restraints() is called again. + topo.only_bonds = true; + topo.apply_all_restraints(monlib); + topo.only_bonds = false; + topo.logger.resume(); // re-enable warnings + NeighMap neighbors; + for (const Topo::Bond& bond : topo.bonds) { + const Atom* a1 = bond.atoms[0]; + const Atom* a2 = bond.atoms[1]; + if (a2->altloc) + neighbors.emplace(a1->serial, Neigh{a2->altloc, a2->occ}); + if (a1->altloc && a1 != a2) + neighbors.emplace(a2->serial, Neigh{a1->altloc, a1->occ}); + } + return neighbors; +} + +} // anonymous namespace + +std::unique_ptr +prepare_topology(Structure& st, MonLib& monlib, size_t model_index, + HydrogenChange h_change, bool reorder, + const Logger& logger, bool ignore_unknown_links, bool use_cispeps) { + std::unique_ptr topo(new Topo); + topo->logger = logger; + if (model_index >= st.models.size()) + fail("no such model index: " + std::to_string(model_index)); + Model& model = st.models[model_index]; + topo->initialize_refmac_topology(st, model, monlib, ignore_unknown_links); + + if (use_cispeps) + force_cispeps(*topo, st.models.size() == 1, model, st.cispeps); + + // remove hydrogens, or change deuterium to fraction, or nothing + // and then check atom names + for (Topo::ChainInfo& chain_info : topo->chain_infos) + for (Topo::ResInfo& ri : chain_info.res_infos) { + Residue& res = *ri.res; + if (h_change != HydrogenChange::NoChange && h_change != HydrogenChange::Shift + // don't re-add H's if we don't have chemical component description + && (ri.orig_chemcomp != nullptr || h_change == HydrogenChange::Remove)) { + // remove/add hydrogens + remove_hydrogens(res); + } else { + // Special handling of Deuterium - mostly for Refmac. + // Note: if the model has deuterium, it gets modified. + if (replace_deuterium_with_fraction(res)) { + // deuterium names usually differ from the names in dictionary + for (Atom& atom : res.atoms) + if (atom.name[0] == 'D' && atom.fraction != 0) { + const ChemComp& cc = ri.get_final_chemcomp(atom.altloc); + if (cc.find_atom(atom.name) == cc.atoms.end()) + atom.name[0] = 'H'; + } + st.has_d_fraction = true; + } + } + // check atom names + for (Atom& atom : res.atoms) { + const ChemComp& cc = ri.get_final_chemcomp(atom.altloc); + if (!cc.has_atom(atom.name)) { + std::string msg = "definition not found for " + + atom_str(chain_info.chain_ref, *ri.res, atom); + if (ri.orig_chemcomp && ri.orig_chemcomp->has_atom(atom.name)) { + msg += " (linkage should remove this atom)"; + } else { + auto it = cc.find_atom_by_old_name(atom.name); + if (it != cc.atoms.end()) + cat_to(msg, " (replace ", atom.name, " with ", it->id, ')'); + } + topo->logger.err(msg); + } + } + } + + // add hydrogens + if (h_change == HydrogenChange::ReAdd || + h_change == HydrogenChange::ReAddButWater || + h_change == HydrogenChange::ReAddKnown) { + NeighMap neighbor_altlocs = prepare_neighbor_altlocs(*topo, monlib); + for (Topo::ChainInfo& chain_info : topo->chain_infos) + for (Topo::ResInfo& ri : chain_info.res_infos) { + Residue& res = *ri.res; + if (ri.orig_chemcomp != nullptr && + (h_change == HydrogenChange::ReAdd || !res.is_water())) { + add_hydrogens_without_positions(ri, neighbor_altlocs); + + // a special handling of HIS for compatibility with Refmac + if (res.name == "HIS") { + for (gemmi::Atom& atom : ri.res->atoms) + if (atom.name == "HD1" || atom.name == "HE2") + atom.occ = 0; + } + } + } + } + + // sort atoms in residues + for (Topo::ChainInfo& chain_info : topo->chain_infos) + for (Topo::ResInfo& ri : chain_info.res_infos) + if (reorder && ri.orig_chemcomp) { + Residue& res = *ri.res; + const ChemComp& cc = *ri.orig_chemcomp; + for (Atom& atom : res.atoms) { + auto it = cc.find_atom(atom.name); + // If atom.name is not found (b/c it was added in a modification), + // the atom will be put after original atoms. + atom.serial = int(it - cc.atoms.begin()); // temporary, for sorting only + } + std::sort(res.atoms.begin(), res.atoms.end(), [](const Atom& a, const Atom& b) { + return a.serial != b.serial ? a.serial < b.serial + : a.altloc < b.altloc; + }); + // check for missing altloc + for (auto atom = res.atoms.begin(); atom + 1 < res.atoms.end(); ++atom) + if (atom->name == (atom + 1)->name && atom->altloc == '\0') + topo->logger.err("missing altloc in ", atom_str(chain_info.chain_ref, *ri.res, *atom)); + } + + // for atoms with ad-hoc links, for now we don't want hydrogens + if (!ignore_unknown_links && h_change != HydrogenChange::NoChange) { + auto remove_h_from_auto_links = [&](const Topo::Link& link) { + const ChemLink* cl = monlib.get_link(link.link_id); + if (cl && starts_with(cl->name, "auto-")) { + const Restraints::Bond& bond = cl->rt.bonds.at(0); + remove_hydrogens_from_atom(topo->find_resinfo(link.res1), bond.id1.atom, link.alt1); + remove_hydrogens_from_atom(topo->find_resinfo(link.res2), bond.id2.atom, link.alt2); + } + }; + for (const Topo::ChainInfo& chain_info : topo->chain_infos) + for (const Topo::ResInfo& res_info : chain_info.res_infos) + for (const Topo::Link& link : res_info.prev) + remove_h_from_auto_links(link); + for (const Topo::Link& link : topo->extras) + remove_h_from_auto_links(link); + } + + // fill Topo::bonds, angles, ... and ResInfo::monomer_rules, Links::link_rules + topo->apply_all_restraints(monlib); + // fill bond_index, angle_index, etc + topo->create_indices(); + + // the hydrogens added previously have positions not set + if (h_change != HydrogenChange::NoChange) + place_hydrogens_on_all_atoms(*topo); + + if (h_change == HydrogenChange::ReAddKnown) { + // To leave only known hydrogens, we remove Hs with zero occupancy. + // As a side-effect, it removes any H atoms on zero-occupancy parents. + for (Chain& chain : model.chains) + for (Residue& res : chain.residues) + vector_remove_if(res.atoms, [](Atom& a) { return a.is_hydrogen() && a.occ == 0; }); + + // disable warnings here, so they are not printed twice + topo->logger.suspend(); + // re-set restraints and indices + topo->apply_all_restraints(monlib); + topo->create_indices(); + topo->logger.resume(); + } + + assign_serial_numbers(model); + return topo; +} + +std::vector find_missing_atoms(const Topo& topo, bool including_hydrogen) { + std::vector ret; + for (const Topo::ChainInfo& chain_info : topo.chain_infos) + for (const Topo::ResInfo& ri : chain_info.res_infos) { + // check only the first conformation + const Topo::FinalChemComp& fcc = ri.chemcomps.at(0); + char altloc = fcc.altloc != '\0' ? fcc.altloc : '*'; + for (const ChemComp::Atom& at : fcc.cc->atoms) + if ((including_hydrogen || !at.is_hydrogen()) && + ri.res->find_atom(at.id, altloc) == nullptr) + ret.emplace_back(chain_info.chain_ref.name, *ri.res, at.id, fcc.altloc); + } + return ret; +} + +} diff --git a/image_analysis/structure_refinement/CMakeLists.txt b/image_analysis/structure_refinement/CMakeLists.txt index 62ac58f77..1f98395e0 100644 --- a/image_analysis/structure_refinement/CMakeLists.txt +++ b/image_analysis/structure_refinement/CMakeLists.txt @@ -16,7 +16,44 @@ ADD_LIBRARY(JFJochStructureRefinement STATIC $<$:ModelStructureFactorsGPU.cu> ModelStructureFactorsGPU.h ModelStructureFactorsGPUEngine.h $<$:ModelScaleGPU.cu> ModelScaleGPU.h - SigmaA.cpp SigmaA.h) + SigmaA.cpp SigmaA.h + MonomerLibrary.cpp MonomerLibrary.h + ${CMAKE_CURRENT_BINARY_DIR}/MonomerLibraryData.cpp) + +# The subset of the CCP4 Monomer Library that refinement restrains with (monomers/, chosen by +# monomers/update_monomers.py), carried in the binary so that nothing is read from disk: every .cif of the +# directory as a string, cut into pieces of at most 12000 characters - under the 16380 a single literal may +# hold with MSVC - which MonomerLibrary.cpp joins again. A .cif added or edited re-runs the configure. +FILE(GLOB MONOMER_CIFS ${CMAKE_CURRENT_SOURCE_DIR}/monomers/*.cif) +SET_PROPERTY(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS ${MONOMER_CIFS} ${CMAKE_CURRENT_SOURCE_DIR}/monomers) +SET(monomer_source "// Generated from image_analysis/structure_refinement/monomers by its CMakeLists.txt - do not edit.\n") +STRING(APPEND monomer_source "#include \"MonomerLibrary.h\"\n\n") +SET(monomer_table "") +SET(monomer_count 0) +FOREACH(cif ${MONOMER_CIFS}) + GET_FILENAME_COMPONENT(cif_name ${cif} NAME) + FILE(READ ${cif} text) + STRING(LENGTH "${text}" text_length) + SET(pieces "") + SET(n_pieces 0) + SET(offset 0) + WHILE(offset LESS text_length) + STRING(SUBSTRING "${text}" ${offset} 12000 piece) + STRING(APPEND pieces "R\"MONLIB(${piece})MONLIB\",\n") + MATH(EXPR offset "${offset} + 12000") + MATH(EXPR n_pieces "${n_pieces} + 1") + ENDWHILE() + STRING(APPEND monomer_source "static const char *const file_${monomer_count}[] = {\n${pieces}};\n") + STRING(APPEND monomer_table " {\"${cif_name}\", file_${monomer_count}, ${n_pieces}},\n") + MATH(EXPR monomer_count "${monomer_count} + 1") +ENDFOREACH() +STRING(APPEND monomer_source "\nextern const EmbeddedMonomerFile embedded_monomer_files[] = {\n${monomer_table}};\n") +STRING(APPEND monomer_source "extern const size_t embedded_monomer_file_count = ${monomer_count};\n") +# Written only when it changed, so a configure does not rebuild the library. +FILE(WRITE ${CMAKE_CURRENT_BINARY_DIR}/MonomerLibraryData.cpp.tmp "${monomer_source}") +CONFIGURE_FILE(${CMAKE_CURRENT_BINARY_DIR}/MonomerLibraryData.cpp.tmp + ${CMAKE_CURRENT_BINARY_DIR}/MonomerLibraryData.cpp COPYONLY) +TARGET_INCLUDE_DIRECTORIES(JFJochStructureRefinement PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}) # JFJochIndexing for CUDAMemHelpers.h and, under CUDA, to put cuFFT (RigidBodyGPU.cu) after these # objects on the link line. diff --git a/image_analysis/structure_refinement/MonomerLibrary.cpp b/image_analysis/structure_refinement/MonomerLibrary.cpp new file mode 100644 index 000000000..df908fdd0 --- /dev/null +++ b/image_analysis/structure_refinement/MonomerLibrary.cpp @@ -0,0 +1,41 @@ +// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute +// SPDX-License-Identifier: GPL-3.0-only + +#include "MonomerLibrary.h" + +#include + +#include "gemmi/read_cif.hpp" // read_cif_from_memory + +// Generated by CMakeLists.txt from monomers/*.cif (MonomerLibraryData.cpp in the build tree). +extern const EmbeddedMonomerFile embedded_monomer_files[]; +extern const size_t embedded_monomer_file_count; + +namespace { + +gemmi::MonLib ReadEmbeddedMonomerLibrary() { + gemmi::MonLib monlib; + for (size_t i = 0; i < embedded_monomer_file_count; i++) { + const EmbeddedMonomerFile &f = embedded_monomer_files[i]; + std::string text; + for (size_t k = 0; k < f.n_pieces; k++) + text += f.pieces[k]; + const gemmi::cif::Document doc = gemmi::read_cif_from_memory(text.data(), text.size(), f.name); + if (std::strcmp(f.name, "ener_lib.cif") == 0) + monlib.ener_lib.read(doc); + else + monlib.read_monomer_doc(doc); + } + return monlib; +} + +} // namespace + +const gemmi::MonLib &EmbeddedMonomerLibrary() { + static const gemmi::MonLib monlib = ReadEmbeddedMonomerLibrary(); + return monlib; +} + +bool InEmbeddedMonomerLibrary(const std::string &code) { + return EmbeddedMonomerLibrary().monomers.count(code) > 0; +} diff --git a/image_analysis/structure_refinement/MonomerLibrary.h b/image_analysis/structure_refinement/MonomerLibrary.h new file mode 100644 index 000000000..1a21fe274 --- /dev/null +++ b/image_analysis/structure_refinement/MonomerLibrary.h @@ -0,0 +1,25 @@ +// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute +// SPDX-License-Identifier: GPL-3.0-only + +#pragma once + +#include +#include + +#include "gemmi/monlib.hpp" + +// The restraint dictionary refinement uses: the subset of the CCP4 Monomer Library (Vagin et al. 2004, +// LGPL-3.0) carried in the binary - the standard amino acids and nucleotides, their links and +// modifications, a few common ligands and additives, water and ions; monomers/update_monomers.py holds +// the list. Parsed from memory once per process; no file is read. +const gemmi::MonLib &EmbeddedMonomerLibrary(); + +// Whether `code` (a residue name) has a description in it. +bool InEmbeddedMonomerLibrary(const std::string &code); + +// One .cif of monomers/, as CMakeLists.txt embeds it: its name and its text in pieces. +struct EmbeddedMonomerFile { + const char *name; + const char *const *pieces; + size_t n_pieces; +}; diff --git a/image_analysis/structure_refinement/monomers/1PE.cif b/image_analysis/structure_refinement/monomers/1PE.cif new file mode 100644 index 000000000..426368f17 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/1PE.cif @@ -0,0 +1,228 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +1PE 1PE "PENTAETHYLENE GLYCOL" NON-POLYMER 38 16 . +# +data_comp_1PE +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +1PE OH2 O OH1 0 21.840 38.426 32.717 +1PE C12 C CH2 0 21.457 39.572 31.984 +1PE C22 C CH2 0 22.615 40.477 31.702 +1PE OH3 O O2 0 22.207 41.540 30.844 +1PE C13 C CH2 0 21.271 43.721 30.536 +1PE C23 C CH2 0 21.666 42.667 31.529 +1PE OH4 O O2 0 22.390 44.073 29.724 +1PE C14 C CH2 0 24.698 44.588 30.044 +1PE C24 C CH2 0 23.288 45.017 30.307 +1PE OH5 O O2 0 24.933 43.322 30.652 +1PE C15 C CH2 0 26.417 41.501 31.086 +1PE C25 C CH2 0 26.288 42.896 30.557 +1PE OH6 O O2 0 26.057 41.474 32.464 +1PE C16 C CH2 0 25.748 40.226 34.478 +1PE C26 C CH2 0 26.168 40.178 33.042 +1PE OH7 O OH1 0 26.621 41.011 35.266 +1PE HO2 H H 0 21.179 37.901 32.781 +1PE H121 H H 0 20.778 40.064 32.492 +1PE H122 H H 0 21.055 39.289 31.136 +1PE H221 H H 0 23.332 39.966 31.269 +1PE H222 H H 0 22.967 40.837 32.546 +1PE H131 H H 0 20.932 44.514 31.009 +1PE H132 H H 0 20.549 43.378 29.966 +1PE H231 H H 0 22.333 43.031 32.150 +1PE H232 H H 0 20.880 42.393 32.049 +1PE H141 H H 0 25.320 45.254 30.410 +1PE H142 H H 0 24.850 44.524 29.076 +1PE H241 H H 0 23.142 45.083 31.276 +1PE H242 H H 0 23.134 45.903 29.913 +1PE H151 H H 0 27.342 41.191 30.979 +1PE H152 H H 0 25.829 40.900 30.579 +1PE H251 H H 0 26.862 43.501 31.075 +1PE H252 H H 0 26.581 42.922 29.619 +1PE H161 H H 0 25.725 39.315 34.837 +1PE H162 H H 0 24.843 40.599 34.536 +1PE H261 H H 0 27.097 39.867 32.979 +1PE H262 H H 0 25.598 39.547 32.551 +1PE HO7 H H 0 26.588 41.816 35.006 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +1PE OH2 C12 SINGLE n 1.414 0.0200 1.414 0.0200 +1PE C12 C22 SINGLE n 1.496 0.0200 1.496 0.0200 +1PE C22 OH3 SINGLE n 1.423 0.0106 1.423 0.0106 +1PE OH3 C23 SINGLE n 1.423 0.0106 1.423 0.0106 +1PE C13 C23 SINGLE n 1.496 0.0200 1.496 0.0200 +1PE C13 OH4 SINGLE n 1.423 0.0106 1.423 0.0106 +1PE OH4 C24 SINGLE n 1.423 0.0106 1.423 0.0106 +1PE C14 C24 SINGLE n 1.496 0.0200 1.496 0.0200 +1PE C14 OH5 SINGLE n 1.423 0.0106 1.423 0.0106 +1PE OH5 C25 SINGLE n 1.423 0.0106 1.423 0.0106 +1PE C15 C25 SINGLE n 1.496 0.0200 1.496 0.0200 +1PE C15 OH6 SINGLE n 1.423 0.0106 1.423 0.0106 +1PE OH6 C26 SINGLE n 1.423 0.0106 1.423 0.0106 +1PE C16 C26 SINGLE n 1.496 0.0200 1.496 0.0200 +1PE C16 OH7 SINGLE n 1.414 0.0200 1.414 0.0200 +1PE OH2 HO2 SINGLE n 0.970 0.0120 0.846 0.0200 +1PE C12 H121 SINGLE n 1.089 0.0100 0.980 0.0144 +1PE C12 H122 SINGLE n 1.089 0.0100 0.980 0.0144 +1PE C22 H221 SINGLE n 1.089 0.0100 0.982 0.0175 +1PE C22 H222 SINGLE n 1.089 0.0100 0.982 0.0175 +1PE C13 H131 SINGLE n 1.089 0.0100 0.982 0.0175 +1PE C13 H132 SINGLE n 1.089 0.0100 0.982 0.0175 +1PE C23 H231 SINGLE n 1.089 0.0100 0.982 0.0175 +1PE C23 H232 SINGLE n 1.089 0.0100 0.982 0.0175 +1PE C14 H141 SINGLE n 1.089 0.0100 0.982 0.0175 +1PE C14 H142 SINGLE n 1.089 0.0100 0.982 0.0175 +1PE C24 H241 SINGLE n 1.089 0.0100 0.982 0.0175 +1PE C24 H242 SINGLE n 1.089 0.0100 0.982 0.0175 +1PE C15 H151 SINGLE n 1.089 0.0100 0.982 0.0175 +1PE C15 H152 SINGLE n 1.089 0.0100 0.982 0.0175 +1PE C25 H251 SINGLE n 1.089 0.0100 0.982 0.0175 +1PE C25 H252 SINGLE n 1.089 0.0100 0.982 0.0175 +1PE C16 H161 SINGLE n 1.089 0.0100 0.980 0.0144 +1PE C16 H162 SINGLE n 1.089 0.0100 0.980 0.0144 +1PE C26 H261 SINGLE n 1.089 0.0100 0.982 0.0175 +1PE C26 H262 SINGLE n 1.089 0.0100 0.982 0.0175 +1PE OH7 HO7 SINGLE n 0.970 0.0120 0.846 0.0200 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +1PE C12 OH2 HO2 109.347 1.86 +1PE OH2 C12 C22 112.284 1.56 +1PE OH2 C12 H121 109.012 1.50 +1PE OH2 C12 H122 109.012 1.50 +1PE C22 C12 H121 109.198 1.50 +1PE C22 C12 H122 109.198 1.50 +1PE H121 C12 H122 108.093 1.50 +1PE C12 C22 OH3 109.904 1.68 +1PE C12 C22 H221 109.795 1.50 +1PE C12 C22 H222 109.795 1.50 +1PE OH3 C22 H221 109.691 1.50 +1PE OH3 C22 H222 109.691 1.50 +1PE H221 C22 H222 108.274 1.50 +1PE C22 OH3 C23 112.795 1.50 +1PE C23 C13 OH4 109.613 1.74 +1PE C23 C13 H131 109.729 1.50 +1PE C23 C13 H132 109.729 1.50 +1PE OH4 C13 H131 109.691 1.50 +1PE OH4 C13 H132 109.691 1.50 +1PE H131 C13 H132 108.274 1.50 +1PE OH3 C23 C13 109.613 1.74 +1PE OH3 C23 H231 109.691 1.50 +1PE OH3 C23 H232 109.691 1.50 +1PE C13 C23 H231 109.729 1.50 +1PE C13 C23 H232 109.729 1.50 +1PE H231 C23 H232 108.274 1.50 +1PE C13 OH4 C24 112.795 1.50 +1PE C24 C14 OH5 109.613 1.74 +1PE C24 C14 H141 109.729 1.50 +1PE C24 C14 H142 109.729 1.50 +1PE OH5 C14 H141 109.691 1.50 +1PE OH5 C14 H142 109.691 1.50 +1PE H141 C14 H142 108.274 1.50 +1PE OH4 C24 C14 109.613 1.74 +1PE OH4 C24 H241 109.691 1.50 +1PE OH4 C24 H242 109.691 1.50 +1PE C14 C24 H241 109.729 1.50 +1PE C14 C24 H242 109.729 1.50 +1PE H241 C24 H242 108.274 1.50 +1PE C14 OH5 C25 112.795 1.50 +1PE C25 C15 OH6 109.613 1.74 +1PE C25 C15 H151 109.729 1.50 +1PE C25 C15 H152 109.729 1.50 +1PE OH6 C15 H151 109.691 1.50 +1PE OH6 C15 H152 109.691 1.50 +1PE H151 C15 H152 108.274 1.50 +1PE OH5 C25 C15 109.613 1.74 +1PE OH5 C25 H251 109.691 1.50 +1PE OH5 C25 H252 109.691 1.50 +1PE C15 C25 H251 109.729 1.50 +1PE C15 C25 H252 109.729 1.50 +1PE H251 C25 H252 108.274 1.50 +1PE C15 OH6 C26 112.795 1.50 +1PE C26 C16 OH7 112.284 1.56 +1PE C26 C16 H161 109.198 1.50 +1PE C26 C16 H162 109.198 1.50 +1PE OH7 C16 H161 109.012 1.50 +1PE OH7 C16 H162 109.012 1.50 +1PE H161 C16 H162 108.093 1.50 +1PE OH6 C26 C16 109.904 1.68 +1PE OH6 C26 H261 109.691 1.50 +1PE OH6 C26 H262 109.691 1.50 +1PE C16 C26 H261 109.795 1.50 +1PE C16 C26 H262 109.795 1.50 +1PE H261 C26 H262 108.274 1.50 +1PE C16 OH7 HO7 109.347 1.86 +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +1PE sp3_sp3_1 C22 C12 OH2 HO2 180.000 10.0 3 +1PE sp3_sp3_49 OH6 C15 C25 OH5 180.000 10.0 3 +1PE sp3_sp3_58 C25 C15 OH6 C26 180.000 10.0 3 +1PE sp3_sp3_61 C16 C26 OH6 C15 180.000 10.0 3 +1PE sp3_sp3_64 OH7 C16 C26 OH6 180.000 10.0 3 +1PE sp3_sp3_73 C26 C16 OH7 HO7 180.000 10.0 3 +1PE sp3_sp3_4 OH2 C12 C22 OH3 180.000 10.0 3 +1PE sp3_sp3_13 C12 C22 OH3 C23 180.000 10.0 3 +1PE sp3_sp3_16 C13 C23 OH3 C22 180.000 10.0 3 +1PE sp3_sp3_19 OH4 C13 C23 OH3 180.000 10.0 3 +1PE sp3_sp3_28 C23 C13 OH4 C24 180.000 10.0 3 +1PE sp3_sp3_31 C14 C24 OH4 C13 180.000 10.0 3 +1PE sp3_sp3_34 OH5 C14 C24 OH4 180.000 10.0 3 +1PE sp3_sp3_43 C24 C14 OH5 C25 180.000 10.0 3 +1PE sp3_sp3_46 C15 C25 OH5 C14 180.000 10.0 3 +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +1PE SMILES ACDLabs 10.04 O(CCO)CCOCCOCCOCCO +1PE SMILES_CANONICAL CACTVS 3.341 OCCOCCOCCOCCOCCO +1PE SMILES CACTVS 3.341 OCCOCCOCCOCCOCCO +1PE SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(COCCOCCOCCOCCO)O +1PE SMILES "OpenEye OEToolkits" 1.5.0 C(COCCOCCOCCOCCO)O +1PE InChI InChI 1.03 InChI=1S/C10H22O6/c11-1-3-13-5-7-15-9-10-16-8-6-14-4-2-12/h11-12H,1-10H2 +1PE InChIKey InChI 1.03 JLFNLZLINWHATN-UHFFFAOYSA-N +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +1PE acedrg 243 "dictionary generator" +1PE acedrg_database 11 "data source" +1PE rdkit 2017.03.2 "Chemoinformatics tool" +1PE refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/A.cif b/image_analysis/structure_refinement/monomers/A.cif new file mode 100644 index 000000000..613cc0cea --- /dev/null +++ b/image_analysis/structure_refinement/monomers/A.cif @@ -0,0 +1,271 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +A A "ADENOSINE-5'-MONOPHOSPHATE" RNA 35 23 . +# +data_comp_A +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +A OP3 O OP -1 22.184 9.416 -6.467 +A P P P 0 23.061 10.073 -7.517 +A OP1 O O 0 22.426 10.079 -8.894 +A OP2 O OP -1 24.478 9.532 -7.523 +A "O5'" O O2 0 23.184 11.622 -7.081 +A "C5'" C CH2 0 23.997 12.510 -7.889 +A "C4'" C CH1 0 23.959 13.900 -7.302 +A "O4'" O O2 0 24.489 13.865 -5.952 +A "C3'" C CH1 0 24.795 14.957 -8.033 +A "O3'" O OH1 0 24.040 15.590 -9.060 +A "C2'" C CH1 0 25.162 15.917 -6.899 +A "O2'" O OH1 0 24.142 16.849 -6.609 +A "C1'" C CH1 0 25.367 14.950 -5.735 +A N9 N NR5 0 26.737 14.457 -5.612 +A C8 C CR15 0 27.206 13.184 -5.839 +A N7 N NRD5 0 28.493 13.056 -5.636 +A C5 C CR56 0 28.908 14.321 -5.248 +A C6 C CR6 0 30.172 14.840 -4.890 +A N6 N NH2 0 31.287 14.114 -4.866 +A N1 N NRD6 0 30.240 16.155 -4.553 +A C2 C CR16 0 29.111 16.881 -4.579 +A N3 N NRD6 0 27.874 16.499 -4.898 +A C4 C CR56 0 27.833 15.193 -5.227 +A "H5'" H H 0 23.653 12.531 -8.815 +A "H5''" H H 0 24.931 12.185 -7.909 +A "H4'" H H 0 23.023 14.194 -7.269 +A "H3'" H H 0 25.613 14.544 -8.414 +A "HO3'" H H 0 24.512 16.204 -9.407 +A "H2'" H H 0 26.008 16.394 -7.110 +A "HO2'" H H 0 24.469 17.486 -6.152 +A "H1'" H H 0 25.116 15.407 -4.901 +A H8 H H 0 26.656 12.471 -6.115 +A H61 H H 0 31.972 14.381 -4.386 +A H62 H H 0 31.333 13.371 -5.331 +A H2 H H 0 29.207 17.789 -4.337 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +A OP3 P SINGLE n 1.517 0.0192 1.517 0.0192 +A P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192 +A P OP2 SINGLE n 1.517 0.0192 1.517 0.0192 +A P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 +A "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +A "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +A "C4'" "O4'" SINGLE n 1.451 0.0100 1.451 0.0100 +A "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 +A "O4'" "C1'" SINGLE n 1.409 0.0100 1.409 0.0100 +A "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +A "C3'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100 +A "C2'" "O2'" SINGLE n 1.411 0.0100 1.411 0.0100 +A "C2'" "C1'" SINGLE n 1.525 0.0100 1.525 0.0100 +A "C1'" N9 SINGLE n 1.458 0.0100 1.458 0.0100 +A N9 C8 SINGLE y 1.372 0.0100 1.372 0.0100 +A N9 C4 SINGLE y 1.374 0.0101 1.374 0.0101 +A C8 N7 DOUBLE y 1.310 0.0100 1.310 0.0100 +A N7 C5 SINGLE y 1.388 0.0100 1.388 0.0100 +A C5 C6 SINGLE y 1.408 0.0100 1.408 0.0100 +A C5 C4 DOUBLE y 1.381 0.0100 1.381 0.0100 +A C6 N6 SINGLE n 1.330 0.0100 1.330 0.0100 +A C6 N1 DOUBLE y 1.354 0.0100 1.354 0.0100 +A N1 C2 SINGLE y 1.339 0.0100 1.339 0.0100 +A C2 N3 DOUBLE y 1.330 0.0100 1.330 0.0100 +A N3 C4 SINGLE y 1.343 0.0100 1.343 0.0100 +A "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +A "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 +A "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 +A "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +A "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +A "C2'" "H2'" SINGLE n 1.089 0.0100 0.994 0.0200 +A "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 +A "C1'" "H1'" SINGLE n 1.089 0.0100 0.984 0.0200 +A C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170 +A N6 H61 SINGLE n 1.016 0.0100 0.877 0.0200 +A N6 H62 SINGLE n 1.016 0.0100 0.877 0.0200 +A C2 H2 SINGLE n 1.082 0.0130 0.945 0.0200 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +A OP3 P OP1 112.864 1.69 +A OP3 P OP2 112.864 1.69 +A OP3 P "O5'" 105.808 2.07 +A OP1 P OP2 112.864 1.69 +A OP1 P "O5'" 105.808 2.07 +A OP2 P "O5'" 105.808 2.07 +A P "O5'" "C5'" 118.783 1.50 +A "O5'" "C5'" "C4'" 109.342 1.50 +A "O5'" "C5'" "H5'" 109.845 1.50 +A "O5'" "C5'" "H5''" 109.845 1.50 +A "C4'" "C5'" "H5'" 109.624 1.50 +A "C4'" "C5'" "H5''" 109.624 1.50 +A "H5'" "C5'" "H5''" 108.472 1.50 +A "C5'" "C4'" "O4'" 109.123 1.50 +A "C5'" "C4'" "C3'" 116.008 1.52 +A "C5'" "C4'" "H4'" 108.268 1.50 +A "O4'" "C4'" "C3'" 105.388 1.50 +A "O4'" "C4'" "H4'" 108.947 1.50 +A "C3'" "C4'" "H4'" 109.363 1.86 +A "C4'" "O4'" "C1'" 109.903 1.50 +A "C4'" "C3'" "O3'" 111.281 2.46 +A "C4'" "C3'" "C2'" 102.602 1.50 +A "C4'" "C3'" "H3'" 110.452 2.54 +A "O3'" "C3'" "C2'" 111.581 2.83 +A "O3'" "C3'" "H3'" 110.380 1.67 +A "C2'" "C3'" "H3'" 110.504 1.75 +A "C3'" "O3'" "HO3'" 108.744 3.00 +A "C3'" "C2'" "O2'" 112.782 2.45 +A "C3'" "C2'" "C1'" 101.239 1.50 +A "C3'" "C2'" "H2'" 110.596 1.51 +A "O2'" "C2'" "C1'" 111.715 2.69 +A "O2'" "C2'" "H2'" 110.448 1.97 +A "C1'" "C2'" "H2'" 110.636 1.70 +A "C2'" "O2'" "HO2'" 109.103 2.13 +A "O4'" "C1'" "C2'" 106.047 1.50 +A "O4'" "C1'" N9 108.477 1.50 +A "O4'" "C1'" "H1'" 109.807 1.50 +A "C2'" "C1'" N9 113.824 1.50 +A "C2'" "C1'" "H1'" 109.015 1.50 +A N9 "C1'" "H1'" 109.561 1.50 +A "C1'" N9 C8 126.848 1.91 +A "C1'" N9 C4 127.459 1.80 +A C8 N9 C4 105.693 1.50 +A N9 C8 N7 113.469 1.50 +A N9 C8 H8 123.206 1.50 +A N7 C8 H8 123.326 1.50 +A C8 N7 C5 104.739 1.50 +A N7 C5 C6 132.250 1.50 +A N7 C5 C4 110.483 1.50 +A C6 C5 C4 117.267 1.50 +A C5 C6 N6 123.792 1.50 +A C5 C6 N1 117.409 1.50 +A N6 C6 N1 118.799 1.50 +A C6 N6 H61 119.723 1.50 +A C6 N6 H62 119.723 1.50 +A H61 N6 H62 120.554 1.88 +A C6 N1 C2 118.521 1.50 +A N1 C2 N3 129.332 1.50 +A N1 C2 H2 115.313 1.50 +A N3 C2 H2 115.355 1.50 +A C2 N3 C4 110.982 1.50 +A N9 C4 C5 105.616 1.50 +A N9 C4 N3 127.895 1.50 +A C5 C4 N3 126.489 1.50 +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +A C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +A C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +A C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +A C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +A C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +A C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +A C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +A C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +A C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +A C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +A C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +A C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +A alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +A beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +A epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +A gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +A sp3_sp3_52 "C3'" "C2'" "O2'" "HO2'" 180.000 10.00 3 +A const_14 N7 C8 N9 "C1'" 180.000 10.0 2 +A const_26 C5 C4 N9 "C1'" 180.000 10.0 2 +A const_17 N9 C8 N7 C5 0.000 10.0 2 +A const_20 C6 C5 N7 C8 180.000 10.0 2 +A const_sp2_sp2_4 N7 C5 C6 N6 0.000 5.0 2 +A const_21 N9 C4 C5 N7 0.000 10.0 2 +A sp2_sp2_1 C5 C6 N6 H61 180.000 5.0 2 +A const_sp2_sp2_6 N6 C6 N1 C2 180.000 5.0 2 +A const_sp2_sp2_7 N3 C2 N1 C6 0.000 5.0 2 +A const_sp2_sp2_9 N1 C2 N3 C4 0.000 5.0 2 +A const_12 N9 C4 N3 C2 180.000 10.0 2 +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +A chir_1 P "O5'" OP3 OP2 both +A chir_2 "C4'" "O4'" "C3'" "C5'" negative +A chir_3 "C3'" "O3'" "C4'" "C2'" positive +A chir_4 "C2'" "O2'" "C1'" "C3'" negative +A chir_5 "C1'" "O4'" N9 "C2'" negative +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +A plan-1 "C1'" 0.020 +A plan-1 C2 0.020 +A plan-1 C4 0.020 +A plan-1 C5 0.020 +A plan-1 C6 0.020 +A plan-1 C8 0.020 +A plan-1 H2 0.020 +A plan-1 H8 0.020 +A plan-1 N1 0.020 +A plan-1 N3 0.020 +A plan-1 N6 0.020 +A plan-1 N7 0.020 +A plan-1 N9 0.020 +A plan-2 C6 0.020 +A plan-2 H61 0.020 +A plan-2 H62 0.020 +A plan-2 N6 0.020 +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +A SMILES ACDLabs 10.04 O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O +A SMILES_CANONICAL CACTVS 3.341 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O +A SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O +A SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N +A SMILES "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N +A InChI InChI 1.03 InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1 +A InChIKey InChI 1.03 UDMBCSSLTHHNCD-KQYNXXCUSA-N +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +A acedrg 243 "dictionary generator" +A acedrg_database 11 "data source" +A rdkit 2017.03.2 "Chemoinformatics tool" +A refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/ACT.cif b/image_analysis/structure_refinement/monomers/ACT.cif new file mode 100644 index 000000000..c46c46947 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/ACT.cif @@ -0,0 +1,104 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +ACT ACT "ACETATE ION" NON-POLYMER 7 4 . +# +data_comp_ACT +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +ACT C C C 0 50.652 -7.080 41.537 +ACT O O O 0 50.915 -7.323 42.732 +ACT OXT O OC -1 51.516 -6.945 40.648 +ACT CH3 C CH3 0 49.181 -6.939 41.139 +ACT H1 H H 0 49.117 -6.760 40.187 +ACT H2 H H 0 48.780 -6.205 41.632 +ACT H3 H H 0 48.708 -7.761 41.345 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +ACT C O DOUBLE n 1.247 0.0187 1.247 0.0187 +ACT C OXT SINGLE n 1.247 0.0187 1.247 0.0187 +ACT C CH3 SINGLE n 1.530 0.0200 1.530 0.0200 +ACT CH3 H1 SINGLE n 1.089 0.0100 0.971 0.0140 +ACT CH3 H2 SINGLE n 1.089 0.0100 0.971 0.0140 +ACT CH3 H3 SINGLE n 1.089 0.0100 0.971 0.0140 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +ACT O C OXT 123.884 1.50 +ACT O C CH3 118.052 1.94 +ACT OXT C CH3 118.052 1.94 +ACT C CH3 H1 109.670 1.50 +ACT C CH3 H2 109.670 1.50 +ACT C CH3 H3 109.670 1.50 +ACT H1 CH3 H2 109.424 1.50 +ACT H1 CH3 H3 109.424 1.50 +ACT H2 CH3 H3 109.424 1.50 +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +ACT sp2_sp3_1 O C CH3 H1 0.000 10.0 6 +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +ACT plan-1 C 0.020 +ACT plan-1 CH3 0.020 +ACT plan-1 O 0.020 +ACT plan-1 OXT 0.020 +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +ACT SMILES ACDLabs 10.04 "[O-]C(=O)C" +ACT SMILES_CANONICAL CACTVS 3.341 CC([O-])=O +ACT SMILES CACTVS 3.341 CC([O-])=O +ACT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC(=O)[O-] +ACT SMILES "OpenEye OEToolkits" 1.5.0 CC(=O)[O-] +ACT InChI InChI 1.03 InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1 +ACT InChIKey InChI 1.03 QTBSBXVTEAMEQO-UHFFFAOYSA-M +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +ACT acedrg 243 "dictionary generator" +ACT acedrg_database 11 "data source" +ACT rdkit 2017.03.2 "Chemoinformatics tool" +ACT refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/ADP.cif b/image_analysis/structure_refinement/monomers/ADP.cif new file mode 100644 index 000000000..8dd58c16f --- /dev/null +++ b/image_analysis/structure_refinement/monomers/ADP.cif @@ -0,0 +1,283 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +ADP ADP "ADENOSINE-5'-DIPHOSPHATE" NON-POLYMER 39 27 . +# +data_comp_ADP +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +ADP PB P P 0 46.212 2.934 41.132 +ADP O1B O O 0 47.352 3.648 41.816 +ADP O2B O OP -1 46.188 3.167 39.642 +ADP O3B O OP -1 46.138 1.471 41.495 +ADP PA P P 0 43.308 3.312 41.426 +ADP O1A O O 0 42.947 3.885 40.095 +ADP O2A O OP -1 43.043 1.862 41.663 +ADP O3A O O2 0 44.860 3.603 41.708 +ADP "O5'" O O2 0 42.611 4.176 42.585 +ADP "C5'" C CH2 0 42.803 5.614 42.612 +ADP "C4'" C CH1 0 41.916 6.217 43.675 +ADP "O4'" O O2 0 42.237 5.618 44.957 +ADP "C3'" C CH1 0 42.060 7.727 43.896 +ADP "O3'" O OH1 0 40.836 8.295 44.347 +ADP "C2'" C CH1 0 43.161 7.787 44.958 +ADP "O2'" O OH1 0 43.139 8.979 45.714 +ADP "C1'" C CH1 0 42.808 6.577 45.819 +ADP N9 N NR5 0 43.956 5.966 46.481 +ADP C8 C CR15 0 45.032 5.373 45.867 +ADP N7 N NRD5 0 45.919 4.902 46.707 +ADP C5 C CR56 0 45.398 5.197 47.958 +ADP C6 C CR6 0 45.872 4.953 49.266 +ADP N6 N NH2 0 47.020 4.334 49.530 +ADP N1 N NRD6 0 45.104 5.379 50.303 +ADP C2 C CR16 0 43.948 6.003 50.029 +ADP N3 N NRD6 0 43.405 6.285 48.844 +ADP C4 C CR56 0 44.184 5.853 47.833 +ADP "H5'1" H H 0 42.575 6.001 41.731 +ADP "H5'2" H H 0 43.749 5.824 42.811 +ADP "H4'" H H 0 40.984 6.008 43.451 +ADP "H3'" H H 0 42.359 8.172 43.061 +ADP "HO3'" H H 0 40.903 9.141 44.325 +ADP "H2'" H H 0 44.053 7.669 44.537 +ADP "HO2'" H H 0 43.755 8.950 46.297 +ADP "H1'" H H 0 42.146 6.850 46.493 +ADP H8 H H 0 45.124 5.315 44.932 +ADP HN61 H H 0 47.233 4.142 50.360 +ADP HN62 H H 0 47.561 4.119 48.873 +ADP H2 H H 0 43.448 6.281 50.782 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +ADP PB O1B DOUBLE n 1.509 0.0200 1.509 0.0200 +ADP PB O2B SINGLE n 1.509 0.0200 1.509 0.0200 +ADP PB O3B SINGLE n 1.509 0.0200 1.509 0.0200 +ADP PB O3A SINGLE n 1.614 0.0178 1.614 0.0178 +ADP PA O1A DOUBLE n 1.493 0.0122 1.493 0.0122 +ADP PA O2A SINGLE n 1.493 0.0122 1.493 0.0122 +ADP PA O3A SINGLE n 1.604 0.0133 1.604 0.0133 +ADP PA "O5'" SINGLE n 1.604 0.0133 1.604 0.0133 +ADP "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +ADP "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +ADP "C4'" "O4'" SINGLE n 1.451 0.0100 1.451 0.0100 +ADP "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 +ADP "O4'" "C1'" SINGLE n 1.409 0.0100 1.409 0.0100 +ADP "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +ADP "C3'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100 +ADP "C2'" "O2'" SINGLE n 1.411 0.0100 1.411 0.0100 +ADP "C2'" "C1'" SINGLE n 1.525 0.0100 1.525 0.0100 +ADP "C1'" N9 SINGLE n 1.458 0.0100 1.458 0.0100 +ADP N9 C8 SINGLE y 1.372 0.0100 1.372 0.0100 +ADP N9 C4 SINGLE y 1.374 0.0101 1.374 0.0101 +ADP C8 N7 DOUBLE y 1.310 0.0100 1.310 0.0100 +ADP N7 C5 SINGLE y 1.388 0.0100 1.388 0.0100 +ADP C5 C6 SINGLE y 1.408 0.0100 1.408 0.0100 +ADP C5 C4 DOUBLE y 1.381 0.0100 1.381 0.0100 +ADP C6 N6 SINGLE n 1.330 0.0100 1.330 0.0100 +ADP C6 N1 DOUBLE y 1.354 0.0100 1.354 0.0100 +ADP N1 C2 SINGLE y 1.339 0.0100 1.339 0.0100 +ADP C2 N3 DOUBLE y 1.330 0.0100 1.330 0.0100 +ADP N3 C4 SINGLE y 1.343 0.0100 1.343 0.0100 +ADP "C5'" "H5'1" SINGLE n 1.089 0.0100 0.989 0.0200 +ADP "C5'" "H5'2" SINGLE n 1.089 0.0100 0.989 0.0200 +ADP "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 +ADP "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +ADP "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +ADP "C2'" "H2'" SINGLE n 1.089 0.0100 0.994 0.0200 +ADP "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 +ADP "C1'" "H1'" SINGLE n 1.089 0.0100 0.984 0.0200 +ADP C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170 +ADP N6 HN61 SINGLE n 1.016 0.0100 0.877 0.0200 +ADP N6 HN62 SINGLE n 1.016 0.0100 0.877 0.0200 +ADP C2 H2 SINGLE n 1.082 0.0130 0.945 0.0200 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +ADP O1B PB O2B 112.716 1.50 +ADP O1B PB O3B 112.716 1.50 +ADP O1B PB O3A 105.965 2.38 +ADP O2B PB O3B 112.716 1.50 +ADP O2B PB O3A 105.965 2.38 +ADP O3B PB O3A 105.965 2.38 +ADP O1A PA O2A 118.411 2.35 +ADP O1A PA O3A 108.816 2.14 +ADP O1A PA "O5'" 109.410 1.50 +ADP O2A PA O3A 108.816 2.14 +ADP O2A PA "O5'" 109.410 1.50 +ADP O3A PA "O5'" 101.065 1.97 +ADP PB O3A PA 132.584 3.00 +ADP PA "O5'" "C5'" 118.553 2.41 +ADP "O5'" "C5'" "C4'" 109.342 1.50 +ADP "O5'" "C5'" "H5'1" 109.845 1.50 +ADP "O5'" "C5'" "H5'2" 109.845 1.50 +ADP "C4'" "C5'" "H5'1" 109.624 1.50 +ADP "C4'" "C5'" "H5'2" 109.624 1.50 +ADP "H5'1" "C5'" "H5'2" 108.472 1.50 +ADP "C5'" "C4'" "O4'" 109.123 1.50 +ADP "C5'" "C4'" "C3'" 116.008 1.52 +ADP "C5'" "C4'" "H4'" 108.268 1.50 +ADP "O4'" "C4'" "C3'" 105.388 1.50 +ADP "O4'" "C4'" "H4'" 108.947 1.50 +ADP "C3'" "C4'" "H4'" 109.363 1.86 +ADP "C4'" "O4'" "C1'" 109.903 1.50 +ADP "C4'" "C3'" "O3'" 111.281 2.46 +ADP "C4'" "C3'" "C2'" 102.602 1.50 +ADP "C4'" "C3'" "H3'" 110.452 2.54 +ADP "O3'" "C3'" "C2'" 111.581 2.83 +ADP "O3'" "C3'" "H3'" 110.380 1.67 +ADP "C2'" "C3'" "H3'" 110.504 1.75 +ADP "C3'" "O3'" "HO3'" 108.744 3.00 +ADP "C3'" "C2'" "O2'" 112.782 2.45 +ADP "C3'" "C2'" "C1'" 101.239 1.50 +ADP "C3'" "C2'" "H2'" 110.596 1.51 +ADP "O2'" "C2'" "C1'" 111.715 2.69 +ADP "O2'" "C2'" "H2'" 110.448 1.97 +ADP "C1'" "C2'" "H2'" 110.636 1.70 +ADP "C2'" "O2'" "HO2'" 109.103 2.13 +ADP "O4'" "C1'" "C2'" 106.047 1.50 +ADP "O4'" "C1'" N9 108.477 1.50 +ADP "O4'" "C1'" "H1'" 109.807 1.50 +ADP "C2'" "C1'" N9 113.824 1.50 +ADP "C2'" "C1'" "H1'" 109.015 1.50 +ADP N9 "C1'" "H1'" 109.561 1.50 +ADP "C1'" N9 C8 126.848 1.91 +ADP "C1'" N9 C4 127.459 1.80 +ADP C8 N9 C4 105.693 1.50 +ADP N9 C8 N7 113.469 1.50 +ADP N9 C8 H8 123.206 1.50 +ADP N7 C8 H8 123.326 1.50 +ADP C8 N7 C5 104.739 1.50 +ADP N7 C5 C6 132.250 1.50 +ADP N7 C5 C4 110.483 1.50 +ADP C6 C5 C4 117.267 1.50 +ADP C5 C6 N6 123.792 1.50 +ADP C5 C6 N1 117.409 1.50 +ADP N6 C6 N1 118.799 1.50 +ADP C6 N6 HN61 119.723 1.50 +ADP C6 N6 HN62 119.723 1.50 +ADP HN61 N6 HN62 120.554 1.88 +ADP C6 N1 C2 118.521 1.50 +ADP N1 C2 N3 129.332 1.50 +ADP N1 C2 H2 115.313 1.50 +ADP N3 C2 H2 115.355 1.50 +ADP C2 N3 C4 110.982 1.50 +ADP N9 C4 C5 105.616 1.50 +ADP N9 C4 N3 127.895 1.50 +ADP C5 C4 N3 126.489 1.50 +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +ADP sp3_sp3_27 PA O3A PB O1B 60.000 10.0 3 +ADP sp3_sp3_2 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3 +ADP sp3_sp3_50 "O3'" "C3'" "C4'" "C5'" 180.000 10.0 3 +ADP sp3_sp3_4 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3 +ADP sp3_sp3_55 "C4'" "C3'" "O3'" "HO3'" 180.000 10.0 3 +ADP sp3_sp3_20 "O2'" "C2'" "C3'" "O3'" -60.000 10.0 3 +ADP sp3_sp3_58 "C3'" "C2'" "O2'" "HO2'" 180.000 10.0 3 +ADP sp3_sp3_8 "O4'" "C1'" "C2'" "O2'" 180.000 10.0 3 +ADP sp2_sp3_1 C8 N9 "C1'" "O4'" 150.000 10.0 6 +ADP const_14 N7 C8 N9 "C1'" 180.000 10.0 2 +ADP const_26 C5 C4 N9 "C1'" 180.000 10.0 2 +ADP const_17 N9 C8 N7 C5 0.000 10.0 2 +ADP const_20 C6 C5 N7 C8 180.000 10.0 2 +ADP const_sp2_sp2_4 N7 C5 C6 N6 0.000 5.0 2 +ADP const_21 N9 C4 C5 N7 0.000 10.0 2 +ADP sp2_sp2_1 C5 C6 N6 HN61 180.000 5.0 2 +ADP const_sp2_sp2_6 N6 C6 N1 C2 180.000 5.0 2 +ADP const_sp2_sp2_7 N3 C2 N1 C6 0.000 5.0 2 +ADP const_sp2_sp2_9 N1 C2 N3 C4 0.000 5.0 2 +ADP const_12 N9 C4 N3 C2 180.000 10.0 2 +ADP sp3_sp3_30 PB O3A PA O1A 60.000 10.0 3 +ADP sp3_sp3_33 "C5'" "O5'" PA O1A 60.000 10.0 3 +ADP sp3_sp3_34 "C4'" "C5'" "O5'" PA 180.000 10.0 3 +ADP sp3_sp3_37 "O4'" "C4'" "C5'" "O5'" 180.000 10.0 3 +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +ADP chir_1 PB O3A O2B O3B both +ADP chir_2 PA O3A "O5'" O2A both +ADP chir_3 "C4'" "O4'" "C3'" "C5'" negative +ADP chir_4 "C3'" "O3'" "C4'" "C2'" positive +ADP chir_5 "C2'" "O2'" "C1'" "C3'" negative +ADP chir_6 "C1'" "O4'" N9 "C2'" negative +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +ADP plan-1 "C1'" 0.020 +ADP plan-1 C2 0.020 +ADP plan-1 C4 0.020 +ADP plan-1 C5 0.020 +ADP plan-1 C6 0.020 +ADP plan-1 C8 0.020 +ADP plan-1 H2 0.020 +ADP plan-1 H8 0.020 +ADP plan-1 N1 0.020 +ADP plan-1 N3 0.020 +ADP plan-1 N6 0.020 +ADP plan-1 N7 0.020 +ADP plan-1 N9 0.020 +ADP plan-2 C6 0.020 +ADP plan-2 HN61 0.020 +ADP plan-2 HN62 0.020 +ADP plan-2 N6 0.020 +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +ADP SMILES ACDLabs 10.04 O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O +ADP SMILES_CANONICAL CACTVS 3.341 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O +ADP SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O +ADP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N +ADP SMILES "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N +ADP InChI InChI 1.03 InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1 +ADP InChIKey InChI 1.03 XTWYTFMLZFPYCI-KQYNXXCUSA-N +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +ADP acedrg 243 "dictionary generator" +ADP acedrg_database 11 "data source" +ADP rdkit 2017.03.2 "Chemoinformatics tool" +ADP refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/ALA.cif b/image_analysis/structure_refinement/monomers/ALA.cif new file mode 100644 index 000000000..be45c4253 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/ALA.cif @@ -0,0 +1,182 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +ALA ALA ALANINE peptide 13 6 . + +data_comp_ALA +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +ALA N N NT3 1 2.474 26.375 12.879 +ALA CA C CH1 0 1.190 26.935 13.368 +ALA C C C 0 1.429 28.314 13.990 +ALA O O O 0 2.253 28.383 14.929 +ALA CB C CH3 0 0.557 25.983 14.359 +ALA OXT O OC -1 0.782 29.274 13.516 +ALA H H H 0 3.050 26.285 13.567 +ALA H2 H H 0 2.832 26.925 12.260 +ALA H3 H H 0 2.330 25.565 12.507 +ALA HA H H 0 0.581 27.046 12.587 +ALA HB3 H H 0 -0.324 26.308 14.608 +ALA HB2 H H 0 1.113 25.921 15.155 +ALA HB1 H H 0 0.472 25.102 13.958 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +ALA N n/a CA START +ALA H N . . +ALA H2 N . . +ALA H3 N . . +ALA CA N C . +ALA HA CA . . +ALA CB CA HB3 . +ALA HB1 CB . . +ALA HB2 CB . . +ALA HB3 CB . . +ALA C CA . END +ALA O C . . +ALA OXT C . . + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +ALA N N(CCCH)(H)3 +ALA CA C(CH3)(NH3)(COO)(H) +ALA C C(CCHN)(O)2 +ALA O O(CCO) +ALA CB C(CCHN)(H)3 +ALA OXT O(CCO) +ALA H H(NCHH) +ALA H2 H(NCHH) +ALA H3 H(NCHH) +ALA HA H(CCCN) +ALA HB3 H(CCHH) +ALA HB2 H(CCHH) +ALA HB1 H(CCHH) + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +ALA N CA SINGLE n 1.483 0.0100 1.483 0.0100 +ALA CA C SINGLE n 1.531 0.0100 1.531 0.0100 +ALA CA CB SINGLE n 1.513 0.0158 1.513 0.0158 +ALA C O DOUBLE n 1.251 0.0183 1.251 0.0183 +ALA C OXT SINGLE n 1.251 0.0183 1.251 0.0183 +ALA N H SINGLE n 1.018 0.0520 0.902 0.0102 +ALA N H2 SINGLE n 1.018 0.0520 0.902 0.0102 +ALA N H3 SINGLE n 1.018 0.0520 0.902 0.0102 +ALA CA HA SINGLE n 1.092 0.0100 0.997 0.0200 +ALA CB HB3 SINGLE n 1.092 0.0100 0.972 0.0148 +ALA CB HB2 SINGLE n 1.092 0.0100 0.972 0.0148 +ALA CB HB1 SINGLE n 1.092 0.0100 0.972 0.0148 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +ALA CA N H 109.611 2.03 +ALA CA N H2 109.611 2.03 +ALA CA N H3 109.611 2.03 +ALA H N H2 109.032 3.00 +ALA H N H3 109.032 3.00 +ALA H2 N H3 109.032 3.00 +ALA N CA C 109.720 1.50 +ALA N CA CB 109.927 1.50 +ALA N CA HA 108.247 1.50 +ALA C CA CB 111.515 1.50 +ALA C CA HA 108.267 1.50 +ALA CB CA HA 109.172 1.57 +ALA CA C O 117.191 2.33 +ALA CA C OXT 117.191 2.33 +ALA O C OXT 125.618 1.50 +ALA CA CB HB3 109.742 1.50 +ALA CA CB HB2 109.742 1.50 +ALA CA CB HB1 109.742 1.50 +ALA HB3 CB HB2 109.365 1.60 +ALA HB3 CB HB1 109.365 1.60 +ALA HB2 CB HB1 109.365 1.60 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +ALA hh1 N CA CB HB3 180.000 10.0 3 +ALA sp3_sp3_1 C CA N H 180.000 10.0 3 +ALA sp2_sp3_1 O C CA N 0.000 10.0 6 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +ALA chir_1 CA N C CB positive + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +ALA plan-1 C 0.020 +ALA plan-1 CA 0.020 +ALA plan-1 O 0.020 +ALA plan-1 OXT 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +ALA SMILES ACDLabs 10.04 O=C(O)C(N)C +ALA SMILES_CANONICAL CACTVS 3.341 C[C@H](N)C(O)=O +ALA SMILES CACTVS 3.341 C[CH](N)C(O)=O +ALA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[C@@H](C(=O)O)N +ALA SMILES "OpenEye OEToolkits" 1.5.0 CC(C(=O)O)N +ALA InChI InChI 1.03 InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1 +ALA InChIKey InChI 1.03 QNAYBMKLOCPYGJ-REOHCLBHSA-N + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +ALA acedrg 278 "dictionary generator" +ALA acedrg_database 12 "data source" +ALA rdkit 2019.09.1 "Chemoinformatics tool" +ALA refmac5 5.8.0419 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/AMP.cif b/image_analysis/structure_refinement/monomers/AMP.cif new file mode 100644 index 000000000..af979b28b --- /dev/null +++ b/image_analysis/structure_refinement/monomers/AMP.cif @@ -0,0 +1,279 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +AMP AMP "ADENOSINE MONOPHOSPHATE" NON-POLYMER 35 23 . + +data_comp_AMP +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +AMP P P P 0 7.785 40.217 19.087 +AMP O1P O O 0 7.126 41.546 19.404 +AMP O2P O OP -1 6.783 39.104 18.848 +AMP O3P O OP -1 8.858 39.838 20.091 +AMP "O5'" O O2 0 8.550 40.429 17.682 +AMP "C5'" C CH2 0 9.613 41.413 17.608 +AMP "C4'" C CH1 0 10.179 41.441 16.209 +AMP "O4'" O O2 0 10.693 40.125 15.878 +AMP "C3'" C CH1 0 9.188 41.799 15.089 +AMP "O3'" O OH1 0 9.786 42.675 14.141 +AMP "C2'" C CH1 0 8.844 40.434 14.483 +AMP "O2'" O OH1 0 8.453 40.504 13.128 +AMP "C1'" C CH1 0 10.173 39.703 14.640 +AMP N9 N NR5 0 10.056 38.248 14.658 +AMP C8 C CR15 0 9.355 37.497 15.568 +AMP N7 N NRD5 0 9.424 36.209 15.347 +AMP C5 C CR56 0 10.226 36.096 14.221 +AMP C6 C CR6 0 10.678 34.979 13.484 +AMP N6 N NH2 0 10.371 33.721 13.791 +AMP N1 N NRD6 0 11.469 35.215 12.406 +AMP C2 C CR16 0 11.775 36.486 12.102 +AMP N3 N NRD6 0 11.408 37.609 12.720 +AMP C4 C CR56 0 10.625 37.349 13.785 +AMP "H5'1" H H 0 10.329 41.183 18.250 +AMP "H5'2" H H 0 9.260 42.307 17.841 +AMP "H4'" H H 0 10.923 42.081 16.196 +AMP "H3'" H H 0 8.376 42.217 15.476 +AMP "HO3'" H H 0 9.174 43.023 13.667 +AMP "H2'" H H 0 8.135 39.989 15.017 +AMP "HO2'" H H 0 8.294 39.721 12.844 +AMP "H1'" H H 0 10.777 39.979 13.915 +AMP H8 H H 0 8.867 37.874 16.281 +AMP HN61 H H 0 10.832 33.060 13.441 +AMP HN62 H H 0 9.709 33.556 14.343 +AMP H2 H H 0 12.327 36.601 11.344 + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +AMP P O1P DOUBLE n 1.517 0.0192 1.517 0.0192 +AMP P O2P SINGLE n 1.517 0.0192 1.517 0.0192 +AMP P O3P SINGLE n 1.517 0.0192 1.517 0.0192 +AMP P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 +AMP "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +AMP "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +AMP "C4'" "O4'" SINGLE n 1.451 0.0100 1.451 0.0100 +AMP "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 +AMP "O4'" "C1'" SINGLE n 1.409 0.0100 1.409 0.0100 +AMP "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +AMP "C3'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100 +AMP "C2'" "O2'" SINGLE n 1.411 0.0100 1.411 0.0100 +AMP "C2'" "C1'" SINGLE n 1.525 0.0100 1.525 0.0100 +AMP "C1'" N9 SINGLE n 1.458 0.0100 1.458 0.0100 +AMP N9 C8 SINGLE y 1.372 0.0100 1.372 0.0100 +AMP N9 C4 SINGLE y 1.374 0.0101 1.374 0.0101 +AMP C8 N7 DOUBLE y 1.310 0.0100 1.310 0.0100 +AMP N7 C5 SINGLE y 1.388 0.0100 1.388 0.0100 +AMP C5 C6 SINGLE y 1.408 0.0100 1.408 0.0100 +AMP C5 C4 DOUBLE y 1.381 0.0100 1.381 0.0100 +AMP C6 N6 SINGLE n 1.330 0.0100 1.330 0.0100 +AMP C6 N1 DOUBLE y 1.354 0.0100 1.354 0.0100 +AMP N1 C2 SINGLE y 1.339 0.0100 1.339 0.0100 +AMP C2 N3 DOUBLE y 1.330 0.0100 1.330 0.0100 +AMP N3 C4 SINGLE y 1.343 0.0100 1.343 0.0100 +AMP "C5'" "H5'1" SINGLE n 1.089 0.0100 0.989 0.0200 +AMP "C5'" "H5'2" SINGLE n 1.089 0.0100 0.989 0.0200 +AMP "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 +AMP "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +AMP "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +AMP "C2'" "H2'" SINGLE n 1.089 0.0100 0.994 0.0200 +AMP "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 +AMP "C1'" "H1'" SINGLE n 1.089 0.0100 0.984 0.0200 +AMP C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170 +AMP N6 HN61 SINGLE n 1.016 0.0100 0.877 0.0200 +AMP N6 HN62 SINGLE n 1.016 0.0100 0.877 0.0200 +AMP C2 H2 SINGLE n 1.082 0.0130 0.945 0.0200 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +AMP O1P P O2P 112.864 1.69 +AMP O1P P O3P 112.864 1.69 +AMP O1P P "O5'" 105.808 2.07 +AMP O2P P O3P 112.864 1.69 +AMP O2P P "O5'" 105.808 2.07 +AMP O3P P "O5'" 105.808 2.07 +AMP P "O5'" "C5'" 118.783 1.50 +AMP "O5'" "C5'" "C4'" 109.342 1.50 +AMP "O5'" "C5'" "H5'1" 109.845 1.50 +AMP "O5'" "C5'" "H5'2" 109.845 1.50 +AMP "C4'" "C5'" "H5'1" 109.624 1.50 +AMP "C4'" "C5'" "H5'2" 109.624 1.50 +AMP "H5'1" "C5'" "H5'2" 108.472 1.50 +AMP "C5'" "C4'" "O4'" 109.123 1.50 +AMP "C5'" "C4'" "C3'" 116.008 1.52 +AMP "C5'" "C4'" "H4'" 108.268 1.50 +AMP "O4'" "C4'" "C3'" 105.388 1.50 +AMP "O4'" "C4'" "H4'" 108.947 1.50 +AMP "C3'" "C4'" "H4'" 109.363 1.86 +AMP "C4'" "O4'" "C1'" 109.903 1.50 +AMP "C4'" "C3'" "O3'" 111.281 2.46 +AMP "C4'" "C3'" "C2'" 102.602 1.50 +AMP "C4'" "C3'" "H3'" 110.452 2.54 +AMP "O3'" "C3'" "C2'" 111.581 2.83 +AMP "O3'" "C3'" "H3'" 110.380 1.67 +AMP "C2'" "C3'" "H3'" 110.504 1.75 +AMP "C3'" "O3'" "HO3'" 108.744 3.00 +AMP "C3'" "C2'" "O2'" 112.782 2.45 +AMP "C3'" "C2'" "C1'" 101.239 1.50 +AMP "C3'" "C2'" "H2'" 110.596 1.51 +AMP "O2'" "C2'" "C1'" 111.715 2.69 +AMP "O2'" "C2'" "H2'" 110.448 1.97 +AMP "C1'" "C2'" "H2'" 110.636 1.70 +AMP "C2'" "O2'" "HO2'" 109.103 2.13 +AMP "O4'" "C1'" "C2'" 106.047 1.50 +AMP "O4'" "C1'" N9 108.477 1.50 +AMP "O4'" "C1'" "H1'" 109.807 1.50 +AMP "C2'" "C1'" N9 113.824 1.50 +AMP "C2'" "C1'" "H1'" 109.015 1.50 +AMP N9 "C1'" "H1'" 109.561 1.50 +AMP "C1'" N9 C8 126.848 1.91 +AMP "C1'" N9 C4 127.459 1.80 +AMP C8 N9 C4 105.693 1.50 +AMP N9 C8 N7 113.469 1.50 +AMP N9 C8 H8 123.206 1.50 +AMP N7 C8 H8 123.326 1.50 +AMP C8 N7 C5 104.739 1.50 +AMP N7 C5 C6 132.250 1.50 +AMP N7 C5 C4 110.483 1.50 +AMP C6 C5 C4 117.267 1.50 +AMP C5 C6 N6 123.792 1.50 +AMP C5 C6 N1 117.409 1.50 +AMP N6 C6 N1 118.799 1.50 +AMP C6 N6 HN61 119.723 1.50 +AMP C6 N6 HN62 119.723 1.50 +AMP HN61 N6 HN62 120.554 1.88 +AMP C6 N1 C2 118.521 1.50 +AMP N1 C2 N3 129.332 1.50 +AMP N1 C2 H2 115.313 1.50 +AMP N3 C2 H2 115.355 1.50 +AMP C2 N3 C4 110.982 1.50 +AMP N9 C4 C5 105.616 1.50 +AMP N9 C4 N3 127.895 1.50 +AMP C5 C4 N3 126.489 1.50 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +AMP sp3_sp3_27 "C5'" "O5'" P O1P 60.000 10.0 3 +AMP sp3_sp3_52 "C3'" "C2'" "O2'" "HO2'" 180.000 10.0 3 +AMP sp3_sp3_8 "O4'" "C1'" "C2'" "O2'" 180.000 10.0 3 +AMP sp2_sp3_1 C8 N9 "C1'" "O4'" 150.000 10.0 6 +AMP const_14 N7 C8 N9 "C1'" 180.000 10.0 2 +AMP const_26 C5 C4 N9 "C1'" 180.000 10.0 2 +AMP const_17 N9 C8 N7 C5 0.000 10.0 2 +AMP const_20 C6 C5 N7 C8 180.000 10.0 2 +AMP const_sp2_sp2_4 N7 C5 C6 N6 0.000 5.0 2 +AMP const_21 N9 C4 C5 N7 0.000 10.0 2 +AMP sp2_sp2_1 C5 C6 N6 HN61 180.000 5.0 2 +AMP const_sp2_sp2_6 N6 C6 N1 C2 180.000 5.0 2 +AMP const_sp2_sp2_7 N3 C2 N1 C6 0.000 5.0 2 +AMP const_sp2_sp2_9 N1 C2 N3 C4 0.000 5.0 2 +AMP const_12 N9 C4 N3 C2 180.000 10.0 2 +AMP sp3_sp3_28 "C4'" "C5'" "O5'" P 180.000 10.0 3 +AMP sp3_sp3_31 "O4'" "C4'" "C5'" "O5'" 180.000 10.0 3 +AMP sp3_sp3_2 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3 +AMP sp3_sp3_44 "O3'" "C3'" "C4'" "C5'" 180.000 10.0 3 +AMP sp3_sp3_4 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3 +AMP sp3_sp3_20 "O2'" "C2'" "C3'" "O3'" -60.000 10.0 3 +AMP sp3_sp3_49 "C4'" "C3'" "O3'" "HO3'" 180.000 10.0 3 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +AMP chir_1 P "O5'" O2P O3P both +AMP chir_2 "C4'" "O4'" "C3'" "C5'" negative +AMP chir_3 "C3'" "O3'" "C4'" "C2'" positive +AMP chir_4 "C2'" "O2'" "C1'" "C3'" negative +AMP chir_5 "C1'" "O4'" N9 "C2'" negative + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +AMP plan-1 "C1'" 0.020 +AMP plan-1 C2 0.020 +AMP plan-1 C4 0.020 +AMP plan-1 C5 0.020 +AMP plan-1 C6 0.020 +AMP plan-1 C8 0.020 +AMP plan-1 H2 0.020 +AMP plan-1 H8 0.020 +AMP plan-1 N1 0.020 +AMP plan-1 N3 0.020 +AMP plan-1 N6 0.020 +AMP plan-1 N7 0.020 +AMP plan-1 N9 0.020 +AMP plan-2 C6 0.020 +AMP plan-2 HN61 0.020 +AMP plan-2 HN62 0.020 +AMP plan-2 N6 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +AMP SMILES ACDLabs 12.01 O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O +AMP InChI InChI 1.03 InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1 +AMP InChIKey InChI 1.03 UDMBCSSLTHHNCD-KQYNXXCUSA-N +AMP SMILES_CANONICAL CACTVS 3.370 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O +AMP SMILES CACTVS 3.370 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O +AMP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N +AMP SMILES "OpenEye OEToolkits" 1.7.6 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +AMP acedrg 243 "dictionary generator" +AMP acedrg_database 11 "data source" +AMP rdkit 2017.03.2 "Chemoinformatics tool" +AMP refmac5 5.8.0238 "optimization tool" + +loop_ +_chem_comp_alias.comp_id +_chem_comp_alias.group +_chem_comp_alias.atom_id +_chem_comp_alias.atom_id_standard +AMP DNA/RNA O2P OP2 +AMP DNA/RNA O1P OP1 +AMP DNA/RNA O3P OP3 diff --git a/image_analysis/structure_refinement/monomers/ARG.cif b/image_analysis/structure_refinement/monomers/ARG.cif new file mode 100644 index 000000000..f92a52e96 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/ARG.cif @@ -0,0 +1,284 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +ARG ARG ARGININE peptide 27 12 . + +data_comp_ARG +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +ARG N N NT3 1 70.130 14.992 90.045 +ARG CA C CH1 0 70.443 14.368 91.360 +ARG C C C 0 71.906 13.892 91.367 +ARG O O O 0 72.245 13.075 90.483 +ARG CB C CH2 0 69.504 13.191 91.652 +ARG CG C CH2 0 68.033 13.562 91.785 +ARG CD C CH2 0 67.166 12.373 92.178 +ARG NE N NC1 0 67.123 11.321 91.154 +ARG CZ C C 0 66.488 10.157 91.270 +ARG NH1 N NC2 0 65.818 9.861 92.371 +ARG NH2 N NC2 1 66.525 9.285 90.278 +ARG OXT O OC -1 72.653 14.357 92.256 +ARG H H H 0 70.064 14.355 89.409 +ARG H2 H H 0 70.776 15.575 89.808 +ARG H3 H H 0 69.349 15.441 90.092 +ARG HA H H 0 70.328 15.054 92.065 +ARG HB3 H H 0 69.794 12.761 92.485 +ARG HB2 H H 0 69.597 12.533 90.931 +ARG HG3 H H 0 67.712 13.922 90.930 +ARG HG2 H H 0 67.938 14.265 92.464 +ARG HD3 H H 0 66.255 12.690 92.348 +ARG HD2 H H 0 67.510 11.993 93.012 +ARG HE H H 0 67.542 11.468 90.404 +ARG HH11 H H 0 66.247 9.797 93.142 +ARG HH12 H H 0 64.945 9.729 92.332 +ARG HH21 H H 0 66.438 9.566 89.444 +ARG HH22 H H 0 66.637 8.426 90.452 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +ARG N n/a CA START +ARG H N . . +ARG H2 N . . +ARG H3 N . . +ARG CA N C . +ARG HA CA . . +ARG CB CA CG . +ARG HB3 CB . . +ARG HB2 CB . . +ARG CG CB CD . +ARG HG3 CG . . +ARG HG2 CG . . +ARG CD CG NE . +ARG HD3 CD . . +ARG HD2 CD . . +ARG NE CD CZ . +ARG HE NE . . +ARG CZ NE NH2 . +ARG NH1 CZ HH12 . +ARG HH11 NH1 . . +ARG HH12 NH1 . . +ARG NH2 CZ HH22 . +ARG HH21 NH2 . . +ARG HH22 NH2 . . +ARG C CA . END +ARG O C . . +ARG OXT C . . + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +ARG N N(CCCH)(H)3 +ARG CA C(CCHH)(NH3)(COO)(H) +ARG C C(CCHN)(O)2 +ARG O O(CCO) +ARG CB C(CCHH)(CCHN)(H)2 +ARG CG C(CCHH)(CHHN)(H)2 +ARG CD C(CCHH)(NCH)(H)2 +ARG NE N(CCHH)(CNN)(H) +ARG CZ C(NCH)(NHH)2 +ARG NH1 N(CNN)(H)2 +ARG NH2 N(CNN)(H)2 +ARG OXT O(CCO) +ARG H H(NCHH) +ARG H2 H(NCHH) +ARG H3 H(NCHH) +ARG HA H(CCCN) +ARG HB3 H(CCCH) +ARG HB2 H(CCCH) +ARG HG3 H(CCCH) +ARG HG2 H(CCCH) +ARG HD3 H(CCHN) +ARG HD2 H(CCHN) +ARG HE H(NCC) +ARG HH11 H(NCH) +ARG HH12 H(NCH) +ARG HH21 H(NCH) +ARG HH22 H(NCH) + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +ARG N CA SINGLE n 1.487 0.0100 1.487 0.0100 +ARG CA C SINGLE n 1.538 0.0113 1.538 0.0113 +ARG CA CB SINGLE n 1.533 0.0100 1.533 0.0100 +ARG C O DOUBLE n 1.251 0.0183 1.251 0.0183 +ARG C OXT SINGLE n 1.251 0.0183 1.251 0.0183 +ARG CB CG SINGLE n 1.522 0.0100 1.522 0.0100 +ARG CG CD SINGLE n 1.521 0.0200 1.521 0.0200 +ARG CD NE SINGLE n 1.467 0.0100 1.467 0.0100 +ARG NE CZ SINGLE n 1.327 0.0153 1.327 0.0153 +ARG CZ NH1 SINGLE n 1.321 0.0134 1.321 0.0134 +ARG CZ NH2 DOUBLE n 1.321 0.0134 1.321 0.0134 +ARG N H SINGLE n 1.018 0.0520 0.902 0.0102 +ARG N H2 SINGLE n 1.018 0.0520 0.902 0.0102 +ARG N H3 SINGLE n 1.018 0.0520 0.902 0.0102 +ARG CA HA SINGLE n 1.092 0.0100 0.991 0.0200 +ARG CB HB3 SINGLE n 1.092 0.0100 0.981 0.0141 +ARG CB HB2 SINGLE n 1.092 0.0100 0.981 0.0141 +ARG CG HG3 SINGLE n 1.092 0.0100 0.982 0.0161 +ARG CG HG2 SINGLE n 1.092 0.0100 0.982 0.0161 +ARG CD HD3 SINGLE n 1.092 0.0100 0.979 0.0175 +ARG CD HD2 SINGLE n 1.092 0.0100 0.979 0.0175 +ARG NE HE SINGLE n 1.013 0.0120 0.871 0.0200 +ARG NH1 HH11 SINGLE n 1.013 0.0120 0.884 0.0200 +ARG NH1 HH12 SINGLE n 1.013 0.0120 0.884 0.0200 +ARG NH2 HH21 SINGLE n 1.013 0.0120 0.884 0.0200 +ARG NH2 HH22 SINGLE n 1.013 0.0120 0.884 0.0200 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +ARG CA N H 109.990 3.00 +ARG CA N H2 109.990 3.00 +ARG CA N H3 109.990 3.00 +ARG H N H2 109.032 3.00 +ARG H N H3 109.032 3.00 +ARG H2 N H3 109.032 3.00 +ARG N CA C 109.258 1.50 +ARG N CA CB 110.440 2.46 +ARG N CA HA 108.387 1.58 +ARG C CA CB 111.059 3.00 +ARG C CA HA 108.774 1.79 +ARG CB CA HA 109.080 2.33 +ARG CA C O 117.148 1.60 +ARG CA C OXT 117.148 1.60 +ARG O C OXT 125.704 1.50 +ARG CA CB CG 114.160 3.00 +ARG CA CB HB3 108.677 1.74 +ARG CA CB HB2 108.677 1.74 +ARG CG CB HB3 108.721 1.50 +ARG CG CB HB2 108.721 1.50 +ARG HB3 CB HB2 107.655 1.50 +ARG CB CG CD 112.025 3.00 +ARG CB CG HG3 109.216 1.64 +ARG CB CG HG2 109.216 1.64 +ARG CD CG HG3 108.991 1.50 +ARG CD CG HG2 108.991 1.50 +ARG HG3 CG HG2 107.958 2.23 +ARG CG CD NE 112.275 3.00 +ARG CG CD HD3 109.172 2.35 +ARG CG CD HD2 109.172 2.35 +ARG NE CD HD3 109.193 1.50 +ARG NE CD HD2 109.193 1.50 +ARG HD3 CD HD2 107.932 1.94 +ARG CD NE CZ 124.614 2.32 +ARG CD NE HE 117.935 2.37 +ARG CZ NE HE 117.451 2.77 +ARG NE CZ NH1 120.032 1.90 +ARG NE CZ NH2 120.032 1.90 +ARG NH1 CZ NH2 119.937 1.95 +ARG CZ NH1 HH11 119.775 3.00 +ARG CZ NH1 HH12 119.775 3.00 +ARG HH11 NH1 HH12 120.450 3.00 +ARG CZ NH2 HH21 119.775 3.00 +ARG CZ NH2 HH22 119.775 3.00 +ARG HH21 NH2 HH22 120.450 3.00 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +ARG chi1 N CA CB CG -60.000 10.0 3 +ARG chi2 CA CB CG CD 180.000 10.0 3 +ARG chi3 CB CG CD NE 60.000 10.0 3 +ARG chi4 CG CD NE CZ 180.000 10.0 6 +ARG chi5 CD NE CZ NH2 0.000 5.0 2 +ARG hh1 NE CZ NH1 HH12 0.000 5.0 2 +ARG hh2 NE CZ NH2 HH22 0.000 5.0 2 +ARG sp3_sp3_1 C CA N H 180.000 10.0 3 +ARG sp2_sp3_1 O C CA N 0.000 10.0 6 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +ARG chir_1 CA N C CB positive + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +ARG plan-1 C 0.020 +ARG plan-1 CA 0.020 +ARG plan-1 O 0.020 +ARG plan-1 OXT 0.020 +ARG plan-2 CD 0.020 +ARG plan-2 CZ 0.020 +ARG plan-2 HE 0.020 +ARG plan-2 NE 0.020 +ARG plan-3 CZ 0.020 +ARG plan-3 NE 0.020 +ARG plan-3 NH1 0.020 +ARG plan-3 NH2 0.020 +ARG plan-4 CZ 0.020 +ARG plan-4 HH11 0.020 +ARG plan-4 HH12 0.020 +ARG plan-4 NH1 0.020 +ARG plan-5 CZ 0.020 +ARG plan-5 HH21 0.020 +ARG plan-5 HH22 0.020 +ARG plan-5 NH2 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +ARG SMILES ACDLabs 10.04 O=C(O)C(N)CCCN\C(=[NH2+])N +ARG SMILES_CANONICAL CACTVS 3.341 N[C@@H](CCCNC(N)=[NH2+])C(O)=O +ARG SMILES CACTVS 3.341 N[CH](CCCNC(N)=[NH2+])C(O)=O +ARG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(C[C@@H](C(=O)O)N)CNC(=[NH2+])N +ARG SMILES "OpenEye OEToolkits" 1.5.0 C(CC(C(=O)O)N)CNC(=[NH2+])N +ARG InChI InChI 1.03 InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p+1/t4-/m0/s1 +ARG InChIKey InChI 1.03 ODKSFYDXXFIFQN-BYPYZUCNSA-O + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +ARG acedrg 278 "dictionary generator" +ARG acedrg_database 12 "data source" +ARG rdkit 2019.09.1 "Chemoinformatics tool" +ARG refmac5 5.8.0419 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/ASN.cif b/image_analysis/structure_refinement/monomers/ASN.cif new file mode 100644 index 000000000..50e7df06f --- /dev/null +++ b/image_analysis/structure_refinement/monomers/ASN.cif @@ -0,0 +1,214 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +ASN ASN ASPARAGINE peptide 17 9 . + +data_comp_ASN +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +ASN N N NT3 1 14.911 16.808 19.868 +ASN CA C CH1 0 15.816 17.894 20.345 +ASN C C C 0 15.155 18.638 21.512 +ASN O O O 0 15.771 18.659 22.602 +ASN CB C CH2 0 16.178 18.868 19.226 +ASN CG C C 0 16.898 18.214 18.068 +ASN OD1 O O 0 17.108 16.995 18.059 +ASN ND2 N NH2 0 17.282 19.004 17.075 +ASN OXT O OC -1 14.046 19.172 21.292 +ASN H H H 0 14.283 17.146 19.316 +ASN H2 H H 0 14.499 16.402 20.561 +ASN H3 H H 0 15.385 16.183 19.422 +ASN HA H H 0 16.651 17.482 20.665 +ASN HB3 H H 0 16.746 19.574 19.593 +ASN HB2 H H 0 15.359 19.286 18.893 +ASN HD21 H H 0 16.894 19.794 16.957 +ASN HD22 H H 0 17.928 18.741 16.527 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +ASN N n/a CA START +ASN H N . . +ASN H2 N . . +ASN H3 N . . +ASN CA N C . +ASN HA CA . . +ASN CB CA CG . +ASN HB3 CB . . +ASN HB2 CB . . +ASN CG CB ND2 . +ASN OD1 CG . . +ASN ND2 CG HD22 . +ASN HD21 ND2 . . +ASN HD22 ND2 . . +ASN C CA . END +ASN O C . . +ASN OXT C . . + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +ASN N N(CCCH)(H)3 +ASN CA C(CCHH)(NH3)(COO)(H) +ASN C C(CCHN)(O)2 +ASN O O(CCO) +ASN CB C(CCHN)(CNO)(H)2 +ASN CG C(CCHH)(NHH)(O) +ASN OD1 O(CCN) +ASN ND2 N(CCO)(H)2 +ASN OXT O(CCO) +ASN H H(NCHH) +ASN H2 H(NCHH) +ASN H3 H(NCHH) +ASN HA H(CCCN) +ASN HB3 H(CCCH) +ASN HB2 H(CCCH) +ASN HD21 H(NCH) +ASN HD22 H(NCH) + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +ASN N CA SINGLE n 1.490 0.0100 1.490 0.0100 +ASN CA C SINGLE n 1.533 0.0100 1.533 0.0100 +ASN CA CB SINGLE n 1.525 0.0100 1.525 0.0100 +ASN C O DOUBLE n 1.251 0.0183 1.251 0.0183 +ASN C OXT SINGLE n 1.251 0.0183 1.251 0.0183 +ASN CB CG SINGLE n 1.510 0.0100 1.510 0.0100 +ASN CG OD1 DOUBLE n 1.236 0.0100 1.236 0.0100 +ASN CG ND2 SINGLE n 1.325 0.0100 1.325 0.0100 +ASN N H SINGLE n 1.018 0.0520 0.902 0.0102 +ASN N H2 SINGLE n 1.018 0.0520 0.902 0.0102 +ASN N H3 SINGLE n 1.018 0.0520 0.902 0.0102 +ASN CA HA SINGLE n 1.092 0.0100 0.984 0.0200 +ASN CB HB3 SINGLE n 1.092 0.0100 0.978 0.0143 +ASN CB HB2 SINGLE n 1.092 0.0100 0.978 0.0143 +ASN ND2 HD21 SINGLE n 1.013 0.0120 0.887 0.0200 +ASN ND2 HD22 SINGLE n 1.013 0.0120 0.887 0.0200 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +ASN CA N H 109.990 3.00 +ASN CA N H2 109.990 3.00 +ASN CA N H3 109.990 3.00 +ASN H N H2 109.032 3.00 +ASN H N H3 109.032 3.00 +ASN H2 N H3 109.032 3.00 +ASN N CA C 109.258 1.50 +ASN N CA CB 111.558 1.50 +ASN N CA HA 108.387 1.58 +ASN C CA CB 111.904 3.00 +ASN C CA HA 108.774 1.79 +ASN CB CA HA 107.748 1.50 +ASN CA C O 117.148 1.60 +ASN CA C OXT 117.148 1.60 +ASN O C OXT 125.704 1.50 +ASN CA CB CG 112.193 1.50 +ASN CA CB HB3 109.177 1.50 +ASN CA CB HB2 109.177 1.50 +ASN CG CB HB3 109.132 1.50 +ASN CG CB HB2 109.132 1.50 +ASN HB3 CB HB2 108.039 1.50 +ASN CB CG OD1 120.239 1.50 +ASN CB CG ND2 117.180 1.62 +ASN OD1 CG ND2 122.581 1.50 +ASN CG ND2 HD21 119.917 2.87 +ASN CG ND2 HD22 119.917 2.87 +ASN HD21 ND2 HD22 120.165 3.00 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +ASN chi1 N CA CB CG -60.000 10.0 3 +ASN chi2 CA CB CG ND2 180.000 10.0 6 +ASN hh1 CB CG ND2 HD22 180.000 5.0 2 +ASN sp3_sp3_1 C CA N H 180.000 10.0 3 +ASN sp2_sp3_1 O C CA N 0.000 10.0 6 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +ASN chir_1 CA N C CB positive + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +ASN plan-1 C 0.020 +ASN plan-1 CA 0.020 +ASN plan-1 O 0.020 +ASN plan-1 OXT 0.020 +ASN plan-2 CB 0.020 +ASN plan-2 CG 0.020 +ASN plan-2 ND2 0.020 +ASN plan-2 OD1 0.020 +ASN plan-3 CG 0.020 +ASN plan-3 HD21 0.020 +ASN plan-3 HD22 0.020 +ASN plan-3 ND2 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +ASN SMILES ACDLabs 12.01 O=C(N)CC(N)C(=O)O +ASN InChI InChI 1.03 InChI=1S/C4H8N2O3/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H2,6,7)(H,8,9)/t2-/m0/s1 +ASN InChIKey InChI 1.03 DCXYFEDJOCDNAF-REOHCLBHSA-N +ASN SMILES_CANONICAL CACTVS 3.370 N[C@@H](CC(N)=O)C(O)=O +ASN SMILES CACTVS 3.370 N[CH](CC(N)=O)C(O)=O +ASN SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 C([C@@H](C(=O)O)N)C(=O)N +ASN SMILES "OpenEye OEToolkits" 1.7.2 C(C(C(=O)O)N)C(=O)N + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +ASN acedrg 278 "dictionary generator" +ASN acedrg_database 12 "data source" +ASN rdkit 2019.09.1 "Chemoinformatics tool" +ASN refmac5 5.8.0419 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/ASP.cif b/image_analysis/structure_refinement/monomers/ASP.cif new file mode 100644 index 000000000..08958a6f6 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/ASP.cif @@ -0,0 +1,198 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +ASP ASP "ASPARTIC ACID" peptide 15 9 . + +data_comp_ASP +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +ASP N N NT3 1 33.542 17.835 39.145 +ASP CA C CH1 0 34.991 17.614 38.867 +ASP C C C 0 35.178 17.161 37.413 +ASP O O O 0 36.268 17.442 36.867 +ASP CB C CH2 0 35.617 16.650 39.866 +ASP CG C C 0 34.932 15.299 40.037 +ASP OD1 O O 0 35.515 14.435 40.725 +ASP OD2 O OC -1 33.817 15.122 39.501 +ASP OXT O OC -1 34.232 16.542 36.875 +ASP H H H 0 33.408 17.940 40.031 +ASP H2 H H 0 33.045 17.139 38.857 +ASP H3 H H 0 33.263 18.581 38.722 +ASP HA H H 0 35.453 18.476 38.978 +ASP HB3 H H 0 35.641 17.087 40.742 +ASP HB2 H H 0 36.543 16.483 39.592 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +ASP N n/a CA START +ASP H N . . +ASP H2 N . . +ASP H3 N . . +ASP CA N C . +ASP HA CA . . +ASP CB CA CG . +ASP HB3 CB . . +ASP HB2 CB . . +ASP CG CB OD2 . +ASP OD1 CG . . +ASP OD2 CG . . +ASP C CA . END +ASP O C . . +ASP OXT C . . + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +ASP N N(CCCH)(H)3 +ASP CA C(CCHH)(NH3)(COO)(H) +ASP C C(CCHN)(O)2 +ASP O O(CCO) +ASP CB C(CCHN)(COO)(H)2 +ASP CG C(CCHH)(O)2 +ASP OD1 O(CCO) +ASP OD2 O(CCO) +ASP OXT O(CCO) +ASP H H(NCHH) +ASP H2 H(NCHH) +ASP H3 H(NCHH) +ASP HA H(CCCN) +ASP HB3 H(CCCH) +ASP HB2 H(CCCH) + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +ASP N CA SINGLE n 1.490 0.0100 1.490 0.0100 +ASP CA C SINGLE n 1.533 0.0100 1.533 0.0100 +ASP CA CB SINGLE n 1.521 0.0100 1.521 0.0100 +ASP C O DOUBLE n 1.251 0.0183 1.251 0.0183 +ASP C OXT SINGLE n 1.251 0.0183 1.251 0.0183 +ASP CB CG SINGLE n 1.522 0.0100 1.522 0.0100 +ASP CG OD1 DOUBLE n 1.249 0.0161 1.249 0.0161 +ASP CG OD2 SINGLE n 1.249 0.0161 1.249 0.0161 +ASP N H SINGLE n 1.018 0.0520 0.902 0.0102 +ASP N H2 SINGLE n 1.018 0.0520 0.902 0.0102 +ASP N H3 SINGLE n 1.018 0.0520 0.902 0.0102 +ASP CA HA SINGLE n 1.092 0.0100 0.984 0.0200 +ASP CB HB3 SINGLE n 1.092 0.0100 0.980 0.0165 +ASP CB HB2 SINGLE n 1.092 0.0100 0.980 0.0165 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +ASP CA N H 109.990 3.00 +ASP CA N H2 109.990 3.00 +ASP CA N H3 109.990 3.00 +ASP H N H2 109.032 3.00 +ASP H N H3 109.032 3.00 +ASP H2 N H3 109.032 3.00 +ASP N CA C 109.258 1.50 +ASP N CA CB 111.400 1.50 +ASP N CA HA 108.387 1.58 +ASP C CA CB 112.421 3.00 +ASP C CA HA 108.774 1.79 +ASP CB CA HA 108.472 2.65 +ASP CA C O 117.148 1.60 +ASP CA C OXT 117.148 1.60 +ASP O C OXT 125.704 1.50 +ASP CA CB CG 115.436 1.50 +ASP CA CB HB3 108.799 3.00 +ASP CA CB HB2 108.799 3.00 +ASP CG CB HB3 108.242 2.79 +ASP CG CB HB2 108.242 2.79 +ASP HB3 CB HB2 107.976 2.66 +ASP CB CG OD1 117.985 1.50 +ASP CB CG OD2 117.985 1.50 +ASP OD1 CG OD2 124.031 1.82 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +ASP chi1 N CA CB CG -60.000 10.0 3 +ASP chi2 CA CB CG OD1 180.000 10.0 6 +ASP sp3_sp3_1 C CA N H 180.000 10.0 3 +ASP sp2_sp3_1 O C CA N 0.000 10.0 6 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +ASP chir_1 CA N C CB positive + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +ASP plan-1 C 0.020 +ASP plan-1 CA 0.020 +ASP plan-1 O 0.020 +ASP plan-1 OXT 0.020 +ASP plan-2 CB 0.020 +ASP plan-2 CG 0.020 +ASP plan-2 OD1 0.020 +ASP plan-2 OD2 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +ASP SMILES ACDLabs 12.01 O=C(O)CC(N)C(=O)O +ASP SMILES_CANONICAL CACTVS 3.370 N[C@@H](CC(O)=O)C(O)=O +ASP SMILES CACTVS 3.370 N[CH](CC(O)=O)C(O)=O +ASP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 C([C@@H](C(=O)O)N)C(=O)O +ASP SMILES "OpenEye OEToolkits" 1.7.0 C(C(C(=O)O)N)C(=O)O +ASP InChI InChI 1.03 InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)/t2-/m0/s1 +ASP InChIKey InChI 1.03 CKLJMWTZIZZHCS-REOHCLBHSA-N + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +ASP acedrg 278 "dictionary generator" +ASP acedrg_database 12 "data source" +ASP rdkit 2019.09.1 "Chemoinformatics tool" +ASP refmac5 5.8.0419 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/ATP.cif b/image_analysis/structure_refinement/monomers/ATP.cif new file mode 100644 index 000000000..d59d901cc --- /dev/null +++ b/image_analysis/structure_refinement/monomers/ATP.cif @@ -0,0 +1,301 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +ATP ATP "ADENOSINE-5'-TRIPHOSPHATE" NON-POLYMER 43 31 . +# +data_comp_ATP +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +ATP PG P P 0 44.662 45.077 58.117 +ATP O1G O O 0 43.261 45.625 58.004 +ATP O2G O OP -1 45.679 45.923 57.392 +ATP O3G O OP -1 45.059 44.781 59.542 +ATP PB P P 0 44.268 43.226 55.860 +ATP O1B O O 0 44.078 41.746 55.818 +ATP O2B O OP -1 43.182 44.124 55.365 +ATP O3B O O2 0 44.645 43.653 57.356 +ATP PA P P 0 46.020 43.596 53.536 +ATP O1A O O 0 47.423 44.087 53.400 +ATP O2A O OP -1 44.948 44.301 52.771 +ATP O3A O O2 0 45.624 43.591 55.090 +ATP "O5'" O O2 0 45.968 42.029 53.199 +ATP "C5'" C CH2 0 46.946 41.148 53.808 +ATP "C4'" C CH1 0 46.681 39.728 53.369 +ATP "O4'" O O2 0 46.924 39.620 51.943 +ATP "C3'" C CH1 0 47.567 38.650 54.004 +ATP "O3'" O OH1 0 46.881 37.406 54.075 +ATP "C2'" C CH1 0 48.756 38.611 53.041 +ATP "O2'" O OH1 0 49.451 37.383 53.067 +ATP "C1'" C CH1 0 48.066 38.829 51.697 +ATP N9 N NT 0 48.916 39.514 50.718 +ATP C8 C CR15 0 48.960 40.860 50.413 +ATP N7 N NRD5 0 49.847 41.139 49.485 +ATP C5 C CR56 0 50.421 39.915 49.166 +ATP C6 C CR6 0 51.429 39.540 48.250 +ATP N6 N NH2 0 52.063 40.400 47.457 +ATP N1 N NRD6 0 51.760 38.223 48.186 +ATP C2 C CR16 0 51.117 37.359 48.990 +ATP N3 N NRD6 0 50.158 37.599 49.885 +ATP C4 C CR56 0 49.852 38.909 49.924 +ATP "H5'1" H H 0 46.885 41.207 54.794 +ATP "H5'2" H H 0 47.858 41.415 53.533 +ATP "H4'" H H 0 45.738 39.523 53.548 +ATP "H3'" H H 0 47.862 38.933 54.908 +ATP "HO3'" H H 0 47.400 36.827 54.416 +ATP "H2'" H H 0 49.382 39.360 53.233 +ATP "HO2'" H H 0 50.094 37.416 52.513 +ATP "H1'" H H 0 47.793 37.957 51.333 +ATP H8 H H 0 48.417 41.517 50.815 +ATP HN61 H H 0 52.825 40.173 47.086 +ATP HN62 H H 0 51.716 41.193 47.308 +ATP H2 H H 0 51.382 36.456 48.909 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +ATP PG O1G DOUBLE n 1.509 0.0200 1.509 0.0200 +ATP PG O2G SINGLE n 1.509 0.0200 1.509 0.0200 +ATP PG O3G SINGLE n 1.509 0.0200 1.509 0.0200 +ATP PG O3B SINGLE n 1.614 0.0178 1.614 0.0178 +ATP PB O1B DOUBLE n 1.493 0.0157 1.493 0.0157 +ATP PB O2B SINGLE n 1.493 0.0157 1.493 0.0157 +ATP PB O3B SINGLE n 1.601 0.0114 1.601 0.0114 +ATP PB O3A SINGLE n 1.601 0.0114 1.601 0.0114 +ATP PA O1A DOUBLE n 1.493 0.0122 1.493 0.0122 +ATP PA O2A SINGLE n 1.493 0.0122 1.493 0.0122 +ATP PA O3A SINGLE n 1.604 0.0133 1.604 0.0133 +ATP PA "O5'" SINGLE n 1.604 0.0133 1.604 0.0133 +ATP "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +ATP "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +ATP "C4'" "O4'" SINGLE n 1.451 0.0100 1.451 0.0100 +ATP "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 +ATP "O4'" "C1'" SINGLE n 1.409 0.0100 1.409 0.0100 +ATP "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +ATP "C3'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100 +ATP "C2'" "O2'" SINGLE n 1.411 0.0100 1.411 0.0100 +ATP "C2'" "C1'" SINGLE n 1.525 0.0100 1.525 0.0100 +ATP "C1'" N9 SINGLE n 1.458 0.0200 1.458 0.0200 +ATP N9 C8 SINGLE y 1.372 0.0200 1.372 0.0200 +ATP N9 C4 SINGLE y 1.372 0.0100 1.372 0.0100 +ATP C8 N7 DOUBLE y 1.310 0.0100 1.310 0.0100 +ATP N7 C5 SINGLE y 1.388 0.0100 1.388 0.0100 +ATP C5 C6 SINGLE y 1.408 0.0100 1.408 0.0100 +ATP C5 C4 DOUBLE y 1.381 0.0100 1.381 0.0100 +ATP C6 N6 SINGLE n 1.330 0.0100 1.330 0.0100 +ATP C6 N1 DOUBLE y 1.354 0.0100 1.354 0.0100 +ATP N1 C2 SINGLE y 1.339 0.0100 1.339 0.0100 +ATP C2 N3 DOUBLE y 1.330 0.0100 1.330 0.0100 +ATP N3 C4 SINGLE y 1.343 0.0100 1.343 0.0100 +ATP "C5'" "H5'1" SINGLE n 1.089 0.0100 0.989 0.0200 +ATP "C5'" "H5'2" SINGLE n 1.089 0.0100 0.989 0.0200 +ATP "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 +ATP "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +ATP "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +ATP "C2'" "H2'" SINGLE n 1.089 0.0100 0.994 0.0200 +ATP "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 +ATP "C1'" "H1'" SINGLE n 1.089 0.0100 0.984 0.0200 +ATP C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170 +ATP N6 HN61 SINGLE n 1.016 0.0100 0.877 0.0200 +ATP N6 HN62 SINGLE n 1.016 0.0100 0.877 0.0200 +ATP C2 H2 SINGLE n 1.082 0.0130 0.945 0.0200 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +ATP O1G PG O2G 112.716 1.50 +ATP O1G PG O3G 112.716 1.50 +ATP O1G PG O3B 105.965 2.38 +ATP O2G PG O3G 112.716 1.50 +ATP O2G PG O3B 105.965 2.38 +ATP O3G PG O3B 105.965 2.38 +ATP O1B PB O2B 119.630 1.50 +ATP O1B PB O3B 108.678 2.29 +ATP O1B PB O3A 108.678 2.29 +ATP O2B PB O3B 108.678 2.29 +ATP O2B PB O3A 108.678 2.29 +ATP O3B PB O3A 100.890 2.10 +ATP PG O3B PB 132.584 3.00 +ATP O1A PA O2A 118.411 2.35 +ATP O1A PA O3A 108.816 2.14 +ATP O1A PA "O5'" 109.410 1.50 +ATP O2A PA O3A 108.816 2.14 +ATP O2A PA "O5'" 109.410 1.50 +ATP O3A PA "O5'" 101.065 1.97 +ATP PB O3A PA 132.542 3.00 +ATP PA "O5'" "C5'" 118.553 2.41 +ATP "O5'" "C5'" "C4'" 109.342 1.50 +ATP "O5'" "C5'" "H5'1" 109.845 1.50 +ATP "O5'" "C5'" "H5'2" 109.845 1.50 +ATP "C4'" "C5'" "H5'1" 109.624 1.50 +ATP "C4'" "C5'" "H5'2" 109.624 1.50 +ATP "H5'1" "C5'" "H5'2" 108.472 1.50 +ATP "C5'" "C4'" "O4'" 109.123 1.50 +ATP "C5'" "C4'" "C3'" 116.008 1.52 +ATP "C5'" "C4'" "H4'" 108.268 1.50 +ATP "O4'" "C4'" "C3'" 105.388 1.50 +ATP "O4'" "C4'" "H4'" 108.947 1.50 +ATP "C3'" "C4'" "H4'" 109.363 1.86 +ATP "C4'" "O4'" "C1'" 109.903 1.50 +ATP "C4'" "C3'" "O3'" 111.281 2.46 +ATP "C4'" "C3'" "C2'" 102.602 1.50 +ATP "C4'" "C3'" "H3'" 110.452 2.54 +ATP "O3'" "C3'" "C2'" 111.581 2.83 +ATP "O3'" "C3'" "H3'" 110.380 1.67 +ATP "C2'" "C3'" "H3'" 110.504 1.75 +ATP "C3'" "O3'" "HO3'" 108.744 3.00 +ATP "C3'" "C2'" "O2'" 112.782 2.45 +ATP "C3'" "C2'" "C1'" 101.239 1.50 +ATP "C3'" "C2'" "H2'" 110.596 1.51 +ATP "O2'" "C2'" "C1'" 111.715 2.69 +ATP "O2'" "C2'" "H2'" 110.448 1.97 +ATP "C1'" "C2'" "H2'" 110.636 1.70 +ATP "C2'" "O2'" "HO2'" 109.103 2.13 +ATP "O4'" "C1'" "C2'" 106.047 1.50 +ATP "O4'" "C1'" N9 108.167 1.51 +ATP "O4'" "C1'" "H1'" 109.807 1.50 +ATP "C2'" "C1'" N9 113.752 2.20 +ATP "C2'" "C1'" "H1'" 109.015 1.50 +ATP N9 "C1'" "H1'" 109.246 1.50 +ATP "C1'" N9 C8 126.078 2.46 +ATP "C1'" N9 C4 125.158 1.54 +ATP C8 N9 C4 107.594 1.50 +ATP N9 C8 N7 112.130 1.94 +ATP N9 C8 H8 124.701 2.19 +ATP N7 C8 H8 123.170 1.50 +ATP C8 N7 C5 103.927 1.50 +ATP N7 C5 C6 132.145 1.50 +ATP N7 C5 C4 110.588 1.50 +ATP C6 C5 C4 117.267 1.50 +ATP C5 C6 N6 123.792 1.50 +ATP C5 C6 N1 117.409 1.50 +ATP N6 C6 N1 118.799 1.50 +ATP C6 N6 HN61 119.723 1.50 +ATP C6 N6 HN62 119.723 1.50 +ATP HN61 N6 HN62 120.554 1.88 +ATP C6 N1 C2 118.521 1.50 +ATP N1 C2 N3 129.332 1.50 +ATP N1 C2 H2 115.313 1.50 +ATP N3 C2 H2 115.355 1.50 +ATP C2 N3 C4 110.982 1.50 +ATP N9 C4 C5 107.666 1.69 +ATP N9 C4 N3 125.845 1.50 +ATP C5 C4 N3 126.489 1.50 +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +ATP sp3_sp3_27 PB O3B PG O1G 60.000 10.0 3 +ATP sp3_sp3_40 "C4'" "C5'" "O5'" PA 180.000 10.0 3 +ATP sp3_sp3_43 "O4'" "C4'" "C5'" "O5'" 180.000 10.0 3 +ATP sp3_sp3_2 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3 +ATP sp3_sp3_56 "O3'" "C3'" "C4'" "C5'" 180.000 10.0 3 +ATP sp3_sp3_4 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3 +ATP sp3_sp3_61 "C4'" "C3'" "O3'" "HO3'" 180.000 10.0 3 +ATP sp3_sp3_20 "O2'" "C2'" "C3'" "O3'" -60.000 10.0 3 +ATP sp3_sp3_64 "C3'" "C2'" "O2'" "HO2'" 180.000 10.0 3 +ATP sp3_sp3_8 "O4'" "C1'" "C2'" "O2'" 180.000 10.0 3 +ATP sp2_sp3_1 C8 N9 "C1'" "O4'" 150.000 10.0 6 +ATP const_14 N7 C8 N9 "C1'" 180.000 10.0 2 +ATP const_26 C5 C4 N9 "C1'" 180.000 10.0 2 +ATP const_17 N9 C8 N7 C5 0.000 10.0 2 +ATP const_20 C6 C5 N7 C8 180.000 10.0 2 +ATP const_sp2_sp2_4 N7 C5 C6 N6 0.000 5.0 2 +ATP const_21 N9 C4 C5 N7 0.000 10.0 2 +ATP sp2_sp2_1 C5 C6 N6 HN61 180.000 5.0 2 +ATP const_sp2_sp2_6 N6 C6 N1 C2 180.000 5.0 2 +ATP const_sp2_sp2_7 N3 C2 N1 C6 0.000 5.0 2 +ATP const_sp2_sp2_9 N1 C2 N3 C4 0.000 5.0 2 +ATP const_12 N9 C4 N3 C2 180.000 10.0 2 +ATP sp3_sp3_33 PA O3A PB O1B 60.000 10.0 3 +ATP sp3_sp3_30 PG O3B PB O1B 60.000 10.0 3 +ATP sp3_sp3_36 PB O3A PA O1A 60.000 10.0 3 +ATP sp3_sp3_39 "C5'" "O5'" PA O1A 60.000 10.0 3 +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +ATP chir_1 PG O3B O2G O3G both +ATP chir_2 PB O3A O3B O2B both +ATP chir_3 PA O3A "O5'" O2A both +ATP chir_4 "C4'" "O4'" "C3'" "C5'" negative +ATP chir_5 "C3'" "O3'" "C4'" "C2'" positive +ATP chir_6 "C2'" "O2'" "C1'" "C3'" negative +ATP chir_7 "C1'" "O4'" N9 "C2'" negative +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +ATP plan-1 "C1'" 0.020 +ATP plan-1 C2 0.020 +ATP plan-1 C4 0.020 +ATP plan-1 C5 0.020 +ATP plan-1 C6 0.020 +ATP plan-1 C8 0.020 +ATP plan-1 H2 0.020 +ATP plan-1 H8 0.020 +ATP plan-1 N1 0.020 +ATP plan-1 N3 0.020 +ATP plan-1 N6 0.020 +ATP plan-1 N7 0.020 +ATP plan-1 N9 0.020 +ATP plan-2 C6 0.020 +ATP plan-2 HN61 0.020 +ATP plan-2 HN62 0.020 +ATP plan-2 N6 0.020 +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +ATP SMILES ACDLabs 10.04 O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O +ATP SMILES_CANONICAL CACTVS 3.341 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O +ATP SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O +ATP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N +ATP SMILES "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N +ATP InChI InChI 1.03 InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1 +ATP InChIKey InChI 1.03 ZKHQWZAMYRWXGA-KQYNXXCUSA-N +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +ATP acedrg 243 "dictionary generator" +ATP acedrg_database 11 "data source" +ATP rdkit 2017.03.2 "Chemoinformatics tool" +ATP refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/BR.cif b/image_analysis/structure_refinement/monomers/BR.cif new file mode 100644 index 000000000..64698cd70 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/BR.cif @@ -0,0 +1,30 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +BR BR 'BROMIDE ION ' NON-POLYMER 1 1 . + +data_comp_BR +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.partial_charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +BR BR BR BR -1.000 0.000 0.000 0.000 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +BR BR n/a . END diff --git a/image_analysis/structure_refinement/monomers/C.cif b/image_analysis/structure_refinement/monomers/C.cif new file mode 100644 index 000000000..0d0c89011 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/C.cif @@ -0,0 +1,255 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +C C "CYTIDINE-5'-MONOPHOSPHATE" RNA 33 21 . +# +data_comp_C +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +C OP3 O OP -1 26.264 21.286 -11.211 +C P P P 0 27.065 20.768 -12.391 +C OP1 O O 0 26.731 21.481 -13.688 +C OP2 O OP -1 27.015 19.258 -12.520 +C "O5'" O O2 0 28.604 21.132 -12.071 +C "C5'" C CH2 0 28.962 22.520 -11.845 +C "C4'" C CH1 0 30.463 22.648 -11.735 +C "O4'" O O2 0 30.967 21.749 -10.719 +C "C3'" C CH1 0 31.273 22.268 -12.980 +C "O3'" O OH1 0 31.285 23.333 -13.923 +C "C2'" C CH1 0 32.660 21.973 -12.387 +C "O2'" O OH1 0 33.494 23.113 -12.311 +C "C1'" C CH1 0 32.329 21.476 -10.970 +C N1 N NR6 0 32.565 20.011 -10.805 +C C2 C CR6 0 33.589 19.539 -9.963 +C O2 O O 0 34.302 20.347 -9.344 +C N3 N NRD6 0 33.778 18.197 -9.840 +C C4 C CR6 0 33.005 17.329 -10.512 +C N4 N NH2 0 33.237 16.032 -10.352 +C C5 C CR16 0 31.965 17.787 -11.373 +C C6 C CR16 0 31.786 19.115 -11.490 +C "H5'" H H 0 28.541 22.842 -11.010 +C "H5''" H H 0 28.636 23.077 -12.594 +C "H4'" H H 0 30.676 23.570 -11.475 +C "H3'" H H 0 30.904 21.447 -13.396 +C "HO3'" H H 0 31.819 23.134 -14.553 +C "H2'" H H 0 33.101 21.267 -12.901 +C "HO2'" H H 0 33.087 23.744 -11.913 +C "H1'" H H 0 32.871 21.976 -10.317 +C H41 H H 0 33.920 15.764 -9.869 +C H42 H H 0 32.707 15.443 -10.731 +C H5 H H 0 31.420 17.183 -11.847 +C H6 H H 0 31.112 19.446 -12.046 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +C OP3 P SINGLE n 1.517 0.0192 1.517 0.0192 +C P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192 +C P OP2 SINGLE n 1.517 0.0192 1.517 0.0192 +C P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 +C "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +C "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +C "C4'" "O4'" SINGLE n 1.451 0.0111 1.451 0.0111 +C "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 +C "O4'" "C1'" SINGLE n 1.411 0.0100 1.411 0.0100 +C "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +C "C3'" "C2'" SINGLE n 1.533 0.0109 1.533 0.0109 +C "C2'" "O2'" SINGLE n 1.412 0.0100 1.412 0.0100 +C "C2'" "C1'" SINGLE n 1.532 0.0100 1.532 0.0100 +C "C1'" N1 SINGLE n 1.487 0.0100 1.487 0.0100 +C N1 C2 SINGLE y 1.397 0.0100 1.397 0.0100 +C N1 C6 SINGLE y 1.364 0.0108 1.364 0.0108 +C C2 O2 DOUBLE n 1.241 0.0100 1.241 0.0100 +C C2 N3 SINGLE y 1.355 0.0119 1.355 0.0119 +C N3 C4 DOUBLE y 1.339 0.0110 1.339 0.0110 +C C4 N4 SINGLE n 1.325 0.0109 1.325 0.0109 +C C4 C5 SINGLE y 1.422 0.0123 1.422 0.0123 +C C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 +C "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +C "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 +C "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 +C "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +C "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +C "C2'" "H2'" SINGLE n 1.089 0.0100 0.978 0.0200 +C "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 +C "C1'" "H1'" SINGLE n 1.089 0.0100 0.985 0.0100 +C N4 H41 SINGLE n 1.016 0.0100 0.877 0.0200 +C N4 H42 SINGLE n 1.016 0.0100 0.877 0.0200 +C C5 H5 SINGLE n 1.082 0.0130 0.941 0.0174 +C C6 H6 SINGLE n 1.082 0.0130 0.935 0.0143 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +C OP3 P OP1 112.864 1.69 +C OP3 P OP2 112.864 1.69 +C OP3 P "O5'" 105.808 2.07 +C OP1 P OP2 112.864 1.69 +C OP1 P "O5'" 105.808 2.07 +C OP2 P "O5'" 105.808 2.07 +C P "O5'" "C5'" 118.783 1.50 +C "O5'" "C5'" "C4'" 109.342 1.50 +C "O5'" "C5'" "H5'" 109.845 1.50 +C "O5'" "C5'" "H5''" 109.845 1.50 +C "C4'" "C5'" "H5'" 109.624 1.50 +C "C4'" "C5'" "H5''" 109.624 1.50 +C "H5'" "C5'" "H5''" 108.472 1.50 +C "C5'" "C4'" "O4'" 109.615 1.50 +C "C5'" "C4'" "C3'" 116.008 1.52 +C "C5'" "C4'" "H4'" 108.268 1.50 +C "O4'" "C4'" "C3'" 104.439 1.50 +C "O4'" "C4'" "H4'" 108.698 1.50 +C "C3'" "C4'" "H4'" 109.363 1.86 +C "C4'" "O4'" "C1'" 109.578 1.50 +C "C4'" "C3'" "O3'" 111.281 2.46 +C "C4'" "C3'" "C2'" 102.071 1.50 +C "C4'" "C3'" "H3'" 110.452 2.54 +C "O3'" "C3'" "C2'" 111.993 3.00 +C "O3'" "C3'" "H3'" 110.380 1.67 +C "C2'" "C3'" "H3'" 110.108 1.66 +C "C3'" "O3'" "HO3'" 108.744 3.00 +C "C3'" "C2'" "O2'" 112.861 2.52 +C "C3'" "C2'" "C1'" 101.269 1.50 +C "C3'" "C2'" "H2'" 110.799 1.82 +C "O2'" "C2'" "C1'" 109.476 3.00 +C "O2'" "C2'" "H2'" 111.022 1.77 +C "C1'" "C2'" "H2'" 110.760 1.63 +C "C2'" "O2'" "HO2'" 109.449 1.85 +C "O4'" "C1'" "C2'" 106.825 1.50 +C "O4'" "C1'" N1 108.667 1.50 +C "O4'" "C1'" "H1'" 109.327 1.50 +C "C2'" "C1'" N1 112.859 1.50 +C "C2'" "C1'" "H1'" 109.776 1.83 +C N1 "C1'" "H1'" 109.166 1.50 +C "C1'" N1 C2 118.189 2.26 +C "C1'" N1 C6 121.301 1.52 +C C2 N1 C6 120.510 1.50 +C N1 C2 O2 118.710 1.50 +C N1 C2 N3 118.927 1.50 +C O2 C2 N3 122.370 1.50 +C C2 N3 C4 120.266 1.50 +C N3 C4 N4 117.855 1.50 +C N3 C4 C5 121.269 1.50 +C N4 C4 C5 120.876 1.50 +C C4 N4 H41 119.818 1.59 +C C4 N4 H42 119.818 1.59 +C H41 N4 H42 120.363 1.85 +C C4 C5 C6 117.808 1.50 +C C4 C5 H5 121.350 1.50 +C C6 C5 H5 120.848 1.50 +C N1 C6 C5 121.215 1.50 +C N1 C6 H6 118.510 1.50 +C C5 C6 H6 120.275 1.75 +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +C C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +C C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +C C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +C C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +C C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +C C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +C C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +C C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +C C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +C C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +C C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +C C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +C alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +C beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +C epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +C gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +C sp3_sp3_52 "C3'" "C2'" "O2'" "HO2'" 180.000 10.00 3 +C const_sp2_sp2_4 O2 C2 N1 "C1'" 0.000 5.0 2 +C const_18 C5 C6 N1 "C1'" 180.000 10.0 2 +C const_sp2_sp2_6 O2 C2 N3 C4 180.000 5.0 2 +C const_sp2_sp2_8 N4 C4 N3 C2 180.000 5.0 2 +C sp2_sp2_3 N3 C4 N4 H41 0.000 5.0 2 +C const_11 N4 C4 C5 C6 180.000 10.0 2 +C const_13 C4 C5 C6 N1 0.000 10.0 2 +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +C chir_1 P "O5'" OP3 OP2 both +C chir_2 "C4'" "O4'" "C3'" "C5'" negative +C chir_3 "C3'" "O3'" "C4'" "C2'" positive +C chir_4 "C2'" "O2'" "C1'" "C3'" negative +C chir_5 "C1'" "O4'" N1 "C2'" negative +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +C plan-1 "C1'" 0.020 +C plan-1 C2 0.020 +C plan-1 C4 0.020 +C plan-1 C5 0.020 +C plan-1 C6 0.020 +C plan-1 H5 0.020 +C plan-1 H6 0.020 +C plan-1 N1 0.020 +C plan-1 N3 0.020 +C plan-1 N4 0.020 +C plan-1 O2 0.020 +C plan-2 C4 0.020 +C plan-2 H41 0.020 +C plan-2 H42 0.020 +C plan-2 N4 0.020 +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +C SMILES ACDLabs 10.04 O=C1N=C(N)C=CN1C2OC(C(O)C2O)COP(=O)(O)O +C SMILES_CANONICAL CACTVS 3.341 NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O +C SMILES CACTVS 3.341 NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O +C SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O +C SMILES "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O +C InChI InChI 1.03 InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1 +C InChIKey InChI 1.03 IERHLVCPSMICTF-XVFCMESISA-N +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +C acedrg 243 "dictionary generator" +C acedrg_database 11 "data source" +C rdkit 2017.03.2 "Chemoinformatics tool" +C refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/CA.cif b/image_analysis/structure_refinement/monomers/CA.cif new file mode 100644 index 000000000..d1cacc170 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/CA.cif @@ -0,0 +1,30 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +CA CA 'CALCIUM ION ' NON-POLYMER 1 1 . + +data_comp_CA +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.partial_charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +CA CA CA CA 2.000 0.000 0.000 0.000 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +CA CA n/a . END diff --git a/image_analysis/structure_refinement/monomers/CD.cif b/image_analysis/structure_refinement/monomers/CD.cif new file mode 100644 index 000000000..fbdd3d2de --- /dev/null +++ b/image_analysis/structure_refinement/monomers/CD.cif @@ -0,0 +1,30 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +CD CD 'CADMIUM ION ' NON-POLYMER 1 1 . + +data_comp_CD +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.partial_charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +CD CD CD CD 2.000 0.000 0.000 0.000 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +CD CD n/a . END diff --git a/image_analysis/structure_refinement/monomers/CL.cif b/image_analysis/structure_refinement/monomers/CL.cif new file mode 100644 index 000000000..0d614ea71 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/CL.cif @@ -0,0 +1,30 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +CL CL 'CHLORIDE ION ' NON-POLYMER 1 1 . + +data_comp_CL +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.partial_charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +CL CL CL CL -1.000 0.000 0.000 0.000 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +CL CL n/a . END diff --git a/image_analysis/structure_refinement/monomers/CO.cif b/image_analysis/structure_refinement/monomers/CO.cif new file mode 100644 index 000000000..6942e5689 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/CO.cif @@ -0,0 +1,30 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +CO CO 'COBALT (II) ION ' NON-POLYMER 1 1 . + +data_comp_CO +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.partial_charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +CO CO CO CO 2.000 0.000 0.000 0.000 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +CO CO n/a . END diff --git a/image_analysis/structure_refinement/monomers/COPYING b/image_analysis/structure_refinement/monomers/COPYING new file mode 100644 index 000000000..3f7b8b1e5 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/COPYING @@ -0,0 +1,166 @@ + GNU LESSER GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + + This version of the GNU Lesser General Public License incorporates +the terms and conditions of version 3 of the GNU General Public +License, supplemented by the additional permissions listed below. + + 0. Additional Definitions. + + As used herein, "this License" refers to version 3 of the GNU Lesser +General Public License, and the "GNU GPL" refers to version 3 of the GNU +General Public License. + + "The Library" refers to a covered work governed by this License, +other than an Application or a Combined Work as defined below. + + An "Application" is any work that makes use of an interface provided +by the Library, but which is not otherwise based on the Library. +Defining a subclass of a class defined by the Library is deemed a mode +of using an interface provided by the Library. + + A "Combined Work" is a work produced by combining or linking an +Application with the Library. The particular version of the Library +with which the Combined Work was made is also called the "Linked +Version". + + The "Minimal Corresponding Source" for a Combined Work means the +Corresponding Source for the Combined Work, excluding any source code +for portions of the Combined Work that, considered in isolation, are +based on the Application, and not on the Linked Version. + + The "Corresponding Application Code" for a Combined Work means the +object code and/or source code for the Application, including any data +and utility programs needed for reproducing the Combined Work from the +Application, but excluding the System Libraries of the Combined Work. + + 1. Exception to Section 3 of the GNU GPL. + + You may convey a covered work under sections 3 and 4 of this License +without being bound by section 3 of the GNU GPL. + + 2. Conveying Modified Versions. + + If you modify a copy of the Library, and, in your modifications, a +facility refers to a function or data to be supplied by an Application +that uses the facility (other than as an argument passed when the +facility is invoked), then you may convey a copy of the modified +version: + + a) under this License, provided that you make a good faith effort to + ensure that, in the event an Application does not supply the + function or data, the facility still operates, and performs + whatever part of its purpose remains meaningful, or + + b) under the GNU GPL, with none of the additional permissions of + this License applicable to that copy. + + 3. Object Code Incorporating Material from Library Header Files. + + The object code form of an Application may incorporate material from +a header file that is part of the Library. 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Combined Works. + + You may convey a Combined Work under terms of your choice that, +taken together, effectively do not restrict modification of the +portions of the Library contained in the Combined Work and reverse +engineering for debugging such modifications, if you also do each of +the following: + + a) Give prominent notice with each copy of the Combined Work that + the Library is used in it and that the Library and its use are + covered by this License. + + b) Accompany the Combined Work with a copy of the GNU GPL and this license + document. + + c) For a Combined Work that displays copyright notices during + execution, include the copyright notice for the Library among + these notices, as well as a reference directing the user to the + copies of the GNU GPL and this license document. + + d) Do one of the following: + + 0) Convey the Minimal Corresponding Source under the terms of this + License, and the Corresponding Application Code in a form + suitable for, and under terms that permit, the user to + recombine or relink the Application with a modified version of + the Linked Version to produce a modified Combined Work, in the + manner specified by section 6 of the GNU GPL for conveying + Corresponding Source. + + 1) Use a suitable shared library mechanism for linking with the + Library. A suitable mechanism is one that (a) uses at run time + a copy of the Library already present on the user's computer + system, and (b) will operate properly with a modified version + of the Library that is interface-compatible with the Linked + Version. + + e) Provide Installation Information, but only if you would otherwise + be required to provide such information under section 6 of the + GNU GPL, and only to the extent that such information is + necessary to install and execute a modified version of the + Combined Work produced by recombining or relinking the + Application with a modified version of the Linked Version. (If + you use option 4d0, the Installation Information must accompany + the Minimal Corresponding Source and Corresponding Application + Code. If you use option 4d1, you must provide the Installation + Information in the manner specified by section 6 of the GNU GPL + for conveying Corresponding Source.) + + 5. Combined Libraries. + + You may place library facilities that are a work based on the +Library side by side in a single library together with other library +facilities that are not Applications and are not covered by this +License, and convey such a combined library under terms of your +choice, if you do both of the following: + + a) Accompany the combined library with a copy of the same work based + on the Library, uncombined with any other library facilities, + conveyed under the terms of this License. + + b) Give prominent notice with the combined library that part of it + is a work based on the Library, and explaining where to find the + accompanying uncombined form of the same work. + + 6. Revised Versions of the GNU Lesser General Public License. + + The Free Software Foundation may publish revised and/or new versions +of the GNU Lesser General Public License from time to time. Such new +versions will be similar in spirit to the present version, but may +differ in detail to address new problems or concerns. + + Each version is given a distinguishing version number. If the +Library as you received it specifies that a certain numbered version +of the GNU Lesser General Public License "or any later version" +applies to it, you have the option of following the terms and +conditions either of that published version or of any later version +published by the Free Software Foundation. If the Library as you +received it does not specify a version number of the GNU Lesser +General Public License, you may choose any version of the GNU Lesser +General Public License ever published by the Free Software Foundation. + + If the Library as you received it specifies that a proxy can decide +whether future versions of the GNU Lesser General Public License shall +apply, that proxy's public statement of acceptance of any version is +permanent authorization for you to choose that version for the +Library. + diff --git a/image_analysis/structure_refinement/monomers/CU.cif b/image_analysis/structure_refinement/monomers/CU.cif new file mode 100644 index 000000000..138b89fac --- /dev/null +++ b/image_analysis/structure_refinement/monomers/CU.cif @@ -0,0 +1,30 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +CU CU 'COPPER (II) ION ' NON-POLYMER 1 1 . + +data_comp_CU +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.partial_charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +CU CU CU CU 2.000 0.000 0.000 0.000 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +CU CU n/a . END diff --git a/image_analysis/structure_refinement/monomers/CYS.cif b/image_analysis/structure_refinement/monomers/CYS.cif new file mode 100644 index 000000000..190d34acf --- /dev/null +++ b/image_analysis/structure_refinement/monomers/CYS.cif @@ -0,0 +1,188 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +CYS CYS CYSTEINE peptide 14 7 . + +data_comp_CYS +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +CYS N N NT3 1 22.713 13.517 37.695 +CYS CA C CH1 0 22.373 13.685 39.137 +CYS C C C 0 22.022 15.153 39.440 +CYS O O O 0 22.838 16.024 39.065 +CYS CB C CH2 0 23.514 13.225 40.038 +CYS SG S SH1 0 25.070 14.106 39.742 +CYS OXT O OC -1 20.945 15.370 40.038 +CYS H H H 0 23.605 13.433 37.588 +CYS H2 H H 0 22.430 14.227 37.214 +CYS H3 H H 0 22.308 12.777 37.375 +CYS HA H H 0 21.577 13.127 39.328 +CYS HB3 H H 0 23.668 12.265 39.898 +CYS HB2 H H 0 23.255 13.357 40.977 +CYS HG H HSH1 0 25.737 13.537 40.579 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +CYS N n/a CA START +CYS H N . . +CYS H2 N . . +CYS H3 N . . +CYS CA N C . +CYS HA CA . . +CYS CB CA SG . +CYS HB3 CB . . +CYS HB2 CB . . +CYS SG CB . . +CYS HG SG . . +CYS C CA . END +CYS O C . . +CYS OXT C . . + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +CYS N N(CCCH)(H)3 +CYS CA C(CHHS)(NH3)(COO)(H) +CYS C C(CCHN)(O)2 +CYS O O(CCO) +CYS CB C(CCHN)(SH)(H)2 +CYS SG S(CCHH)(H) +CYS OXT O(CCO) +CYS H H(NCHH) +CYS H2 H(NCHH) +CYS H3 H(NCHH) +CYS HA H(CCCN) +CYS HB3 H(CCHS) +CYS HB2 H(CCHS) +CYS HG H(SC) + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +CYS N CA SINGLE n 1.487 0.0100 1.487 0.0100 +CYS CA C SINGLE n 1.538 0.0113 1.538 0.0113 +CYS CA CB SINGLE n 1.524 0.0100 1.524 0.0100 +CYS C O DOUBLE n 1.251 0.0183 1.251 0.0183 +CYS C OXT SINGLE n 1.251 0.0183 1.251 0.0183 +CYS CB SG SINGLE n 1.812 0.0101 1.812 0.0101 +CYS N H SINGLE n 1.018 0.0520 0.902 0.0102 +CYS N H2 SINGLE n 1.018 0.0520 0.902 0.0102 +CYS N H3 SINGLE n 1.018 0.0520 0.902 0.0102 +CYS CA HA SINGLE n 1.092 0.0100 0.991 0.0200 +CYS CB HB3 SINGLE n 1.092 0.0100 0.983 0.0131 +CYS CB HB2 SINGLE n 1.092 0.0100 0.983 0.0131 +CYS SG HG SINGLE n 1.338 0.0100 1.212 0.0200 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +CYS CA N H 109.684 2.12 +CYS CA N H2 109.684 2.12 +CYS CA N H3 109.684 2.12 +CYS H N H2 109.032 3.00 +CYS H N H3 109.032 3.00 +CYS H2 N H3 109.032 3.00 +CYS N CA C 109.504 1.50 +CYS N CA CB 110.927 1.50 +CYS N CA HA 107.886 1.50 +CYS C CA CB 110.126 3.00 +CYS C CA HA 108.362 1.50 +CYS CB CA HA 108.525 2.42 +CYS CA C O 117.126 1.50 +CYS CA C OXT 117.126 1.50 +CYS O C OXT 125.747 1.50 +CYS CA CB SG 113.492 1.50 +CYS CA CB HB3 109.109 1.50 +CYS CA CB HB2 109.109 1.50 +CYS SG CB HB3 108.513 1.50 +CYS SG CB HB2 108.513 1.50 +CYS HB3 CB HB2 107.963 1.50 +CYS CB SG HG 97.543 3.00 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +CYS chi1 N CA CB SG -60.000 10.0 3 +CYS chi2 CA CB SG HG 180.000 10.0 3 +CYS sp3_sp3_1 C CA N H 180.000 10.0 3 +CYS sp2_sp3_1 O C CA N 0.000 10.0 6 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +CYS chir_1 CA N CB C negative + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +CYS plan-1 C 0.020 +CYS plan-1 CA 0.020 +CYS plan-1 O 0.020 +CYS plan-1 OXT 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +CYS SMILES ACDLabs 10.04 O=C(O)C(N)CS +CYS SMILES_CANONICAL CACTVS 3.341 N[C@@H](CS)C(O)=O +CYS SMILES CACTVS 3.341 N[CH](CS)C(O)=O +CYS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@@H](C(=O)O)N)S +CYS SMILES "OpenEye OEToolkits" 1.5.0 C(C(C(=O)O)N)S +CYS InChI InChI 1.03 InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1 +CYS InChIKey InChI 1.03 XUJNEKJLAYXESH-REOHCLBHSA-N + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +CYS acedrg 278 "dictionary generator" +CYS acedrg_database 12 "data source" +CYS rdkit 2019.09.1 "Chemoinformatics tool" +CYS refmac5 5.8.0419 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/DA.cif b/image_analysis/structure_refinement/monomers/DA.cif new file mode 100644 index 000000000..268788579 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/DA.cif @@ -0,0 +1,266 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +DA DA "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" DNA 34 22 . +# +data_comp_DA +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +DA OP3 O OP -1 -6.497 8.522 9.951 +DA P P P 0 -5.346 9.062 9.122 +DA OP1 O O 0 -4.898 10.441 9.565 +DA OP2 O OP -1 -5.605 8.977 7.630 +DA "O5'" O O2 0 -4.097 8.080 9.408 +DA "C5'" C CH2 0 -3.640 7.912 10.774 +DA "C4'" C CH1 0 -2.470 6.958 10.801 +DA "O4'" O O2 0 -2.888 5.686 10.260 +DA "C3'" C CH1 0 -1.251 7.408 9.993 +DA "O3'" O OH1 0 -0.049 7.159 10.716 +DA "C2'" C CH2 0 -1.324 6.542 8.739 +DA "C1'" C CH1 0 -1.962 5.267 9.263 +DA N9 N NR5 0 -2.687 4.489 8.258 +DA C8 C CR15 0 -3.753 4.911 7.501 +DA N7 N NRD5 0 -4.206 3.997 6.680 +DA C5 C CR56 0 -3.393 2.896 6.907 +DA C6 C CR6 0 -3.368 1.602 6.342 +DA N6 N NH2 0 -4.214 1.192 5.400 +DA N1 N NRD6 0 -2.423 0.736 6.793 +DA C2 C CR16 0 -1.573 1.156 7.744 +DA N3 N NRD6 0 -1.504 2.345 8.344 +DA C4 C CR56 0 -2.450 3.184 7.880 +DA "H5'" H H 0 -4.373 7.554 11.332 +DA "H5''" H H 0 -3.363 8.786 11.145 +DA "H4'" H H 0 -2.203 6.829 11.743 +DA "H3'" H H 0 -1.322 8.365 9.759 +DA "HO3'" H H 0 0.583 7.601 10.361 +DA "H2'" H H 0 -0.433 6.369 8.376 +DA "H2''" H H 0 -1.875 6.962 8.051 +DA "H1'" H H 0 -1.264 4.700 9.685 +DA H8 H H 0 -4.120 5.776 7.565 +DA H61 H H 0 -4.304 0.334 5.236 +DA H62 H H 0 -4.679 1.782 4.946 +DA H2 H H 0 -0.933 0.520 8.026 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +DA OP3 P SINGLE n 1.517 0.0192 1.517 0.0192 +DA P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192 +DA P OP2 SINGLE n 1.517 0.0192 1.517 0.0192 +DA P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 +DA "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +DA "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +DA "C4'" "O4'" SINGLE n 1.442 0.0100 1.442 0.0100 +DA "C4'" "C3'" SINGLE n 1.526 0.0115 1.526 0.0115 +DA "O4'" "C1'" SINGLE n 1.425 0.0100 1.425 0.0100 +DA "C3'" "O3'" SINGLE n 1.424 0.0100 1.424 0.0100 +DA "C3'" "C2'" SINGLE n 1.526 0.0101 1.526 0.0101 +DA "C2'" "C1'" SINGLE n 1.521 0.0118 1.521 0.0118 +DA "C1'" N9 SINGLE n 1.462 0.0111 1.462 0.0111 +DA N9 C8 SINGLE y 1.373 0.0100 1.373 0.0100 +DA N9 C4 SINGLE y 1.377 0.0100 1.377 0.0100 +DA C8 N7 DOUBLE y 1.310 0.0100 1.310 0.0100 +DA N7 C5 SINGLE y 1.388 0.0100 1.388 0.0100 +DA C5 C6 SINGLE y 1.408 0.0100 1.408 0.0100 +DA C5 C4 DOUBLE y 1.381 0.0100 1.381 0.0100 +DA C6 N6 SINGLE n 1.330 0.0100 1.330 0.0100 +DA C6 N1 DOUBLE y 1.354 0.0100 1.354 0.0100 +DA N1 C2 SINGLE y 1.339 0.0100 1.339 0.0100 +DA C2 N3 DOUBLE y 1.330 0.0100 1.330 0.0100 +DA N3 C4 SINGLE y 1.343 0.0100 1.343 0.0100 +DA "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +DA "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 +DA "C4'" "H4'" SINGLE n 1.089 0.0100 0.987 0.0170 +DA "C3'" "H3'" SINGLE n 1.089 0.0100 0.988 0.0189 +DA "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +DA "C2'" "H2'" SINGLE n 1.089 0.0100 0.977 0.0113 +DA "C2'" "H2''" SINGLE n 1.089 0.0100 0.977 0.0113 +DA "C1'" "H1'" SINGLE n 1.089 0.0100 0.993 0.0101 +DA C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170 +DA N6 H61 SINGLE n 1.016 0.0100 0.877 0.0200 +DA N6 H62 SINGLE n 1.016 0.0100 0.877 0.0200 +DA C2 H2 SINGLE n 1.082 0.0130 0.945 0.0200 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +DA OP3 P OP1 112.864 1.69 +DA OP3 P OP2 112.864 1.69 +DA OP3 P "O5'" 105.808 2.07 +DA OP1 P OP2 112.864 1.69 +DA OP1 P "O5'" 105.808 2.07 +DA OP2 P "O5'" 105.808 2.07 +DA P "O5'" "C5'" 118.783 1.50 +DA "O5'" "C5'" "C4'" 109.342 1.50 +DA "O5'" "C5'" "H5'" 109.845 1.50 +DA "O5'" "C5'" "H5''" 109.845 1.50 +DA "C4'" "C5'" "H5'" 109.624 1.50 +DA "C4'" "C5'" "H5''" 109.624 1.50 +DA "H5'" "C5'" "H5''" 108.472 1.50 +DA "C5'" "C4'" "O4'" 109.123 1.50 +DA "C5'" "C4'" "C3'" 114.866 1.63 +DA "C5'" "C4'" "H4'" 108.268 1.50 +DA "O4'" "C4'" "C3'" 105.506 1.50 +DA "O4'" "C4'" "H4'" 108.947 1.50 +DA "C3'" "C4'" "H4'" 109.069 1.50 +DA "C4'" "O4'" "C1'" 108.795 1.50 +DA "C4'" "C3'" "O3'" 110.527 2.37 +DA "C4'" "C3'" "C2'" 102.433 1.50 +DA "C4'" "C3'" "H3'" 110.775 1.50 +DA "O3'" "C3'" "C2'" 111.424 1.96 +DA "O3'" "C3'" "H3'" 110.713 1.50 +DA "C2'" "C3'" "H3'" 110.846 1.50 +DA "C3'" "O3'" "HO3'" 109.026 2.38 +DA "C3'" "C2'" "C1'" 102.663 1.50 +DA "C3'" "C2'" "H2'" 111.194 1.50 +DA "C3'" "C2'" "H2''" 111.194 1.50 +DA "C1'" "C2'" "H2'" 111.213 1.50 +DA "C1'" "C2'" "H2''" 111.213 1.50 +DA "H2'" "C2'" "H2''" 109.148 1.50 +DA "O4'" "C1'" "C2'" 106.035 1.50 +DA "O4'" "C1'" N9 108.236 1.50 +DA "O4'" "C1'" "H1'" 109.059 1.50 +DA "C2'" "C1'" N9 114.190 1.67 +DA "C2'" "C1'" "H1'" 109.272 1.50 +DA N9 "C1'" "H1'" 109.282 1.50 +DA "C1'" N9 C8 127.636 2.81 +DA "C1'" N9 C4 126.671 2.93 +DA C8 N9 C4 105.693 1.50 +DA N9 C8 N7 113.469 1.50 +DA N9 C8 H8 123.206 1.50 +DA N7 C8 H8 123.326 1.50 +DA C8 N7 C5 104.739 1.50 +DA N7 C5 C6 132.250 1.50 +DA N7 C5 C4 110.483 1.50 +DA C6 C5 C4 117.267 1.50 +DA C5 C6 N6 123.792 1.50 +DA C5 C6 N1 117.409 1.50 +DA N6 C6 N1 118.799 1.50 +DA C6 N6 H61 119.723 1.50 +DA C6 N6 H62 119.723 1.50 +DA H61 N6 H62 120.554 1.88 +DA C6 N1 C2 118.521 1.50 +DA N1 C2 N3 129.332 1.50 +DA N1 C2 H2 115.313 1.50 +DA N3 C2 H2 115.355 1.50 +DA C2 N3 C4 110.982 1.50 +DA N9 C4 C5 105.616 1.50 +DA N9 C4 N3 127.895 1.50 +DA C5 C4 N3 126.489 1.50 +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +DA C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +DA C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +DA C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +DA C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +DA C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +DA C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +DA C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +DA C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +DA C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +DA C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +DA C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +DA C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +DA alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +DA beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +DA epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +DA gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +DA const_14 N7 C8 N9 "C1'" 180.000 10.0 2 +DA const_26 C5 C4 N9 "C1'" 180.000 10.0 2 +DA const_17 N9 C8 N7 C5 0.000 10.0 2 +DA const_20 C6 C5 N7 C8 180.000 10.0 2 +DA const_sp2_sp2_4 N7 C5 C6 N6 0.000 5.0 2 +DA const_21 N9 C4 C5 N7 0.000 10.0 2 +DA sp2_sp2_1 C5 C6 N6 H61 180.000 5.0 2 +DA const_sp2_sp2_6 N6 C6 N1 C2 180.000 5.0 2 +DA const_sp2_sp2_7 N3 C2 N1 C6 0.000 5.0 2 +DA const_sp2_sp2_9 N1 C2 N3 C4 0.000 5.0 2 +DA const_12 N9 C4 N3 C2 180.000 10.0 2 +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +DA chir_1 P "O5'" OP3 OP2 both +DA chir_2 "C4'" "O4'" "C3'" "C5'" negative +DA chir_3 "C3'" "O3'" "C4'" "C2'" positive +DA chir_4 "C1'" "O4'" N9 "C2'" negative +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +DA plan-1 "C1'" 0.020 +DA plan-1 C2 0.020 +DA plan-1 C4 0.020 +DA plan-1 C5 0.020 +DA plan-1 C6 0.020 +DA plan-1 C8 0.020 +DA plan-1 H2 0.020 +DA plan-1 H8 0.020 +DA plan-1 N1 0.020 +DA plan-1 N3 0.020 +DA plan-1 N6 0.020 +DA plan-1 N7 0.020 +DA plan-1 N9 0.020 +DA plan-2 C6 0.020 +DA plan-2 H61 0.020 +DA plan-2 H62 0.020 +DA plan-2 N6 0.020 +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +DA SMILES ACDLabs 10.04 O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O +DA SMILES_CANONICAL CACTVS 3.341 Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3 +DA SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3 +DA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N +DA SMILES "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)O)O)N +DA InChI InChI 1.03 InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1 +DA InChIKey InChI 1.03 KHWCHTKSEGGWEX-RRKCRQDMSA-N +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +DA acedrg 243 "dictionary generator" +DA acedrg_database 11 "data source" +DA rdkit 2017.03.2 "Chemoinformatics tool" +DA refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/DC.cif b/image_analysis/structure_refinement/monomers/DC.cif new file mode 100644 index 000000000..f0373996c --- /dev/null +++ b/image_analysis/structure_refinement/monomers/DC.cif @@ -0,0 +1,250 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +DC DC "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" DNA 32 20 . +# +data_comp_DC +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +DC OP3 O OP -1 4.759 -6.216 1.740 +DC P P P 0 5.427 -6.783 0.501 +DC OP1 O O 0 5.450 -8.300 0.487 +DC OP2 O OP -1 6.788 -6.171 0.232 +DC "O5'" O O2 0 4.494 -6.346 -0.742 +DC "C5'" C CH2 0 3.097 -6.734 -0.736 +DC "C4'" C CH1 0 2.438 -6.261 -2.009 +DC "O4'" O O2 0 2.537 -4.821 -2.097 +DC "C3'" C CH1 0 3.044 -6.825 -3.297 +DC "O3'" O OH1 0 2.035 -7.363 -4.147 +DC "C2'" C CH2 0 3.705 -5.618 -3.951 +DC "C1'" C CH1 0 2.890 -4.454 -3.414 +DC N1 N NR6 0 3.622 -3.158 -3.358 +DC C2 C CR6 0 3.233 -2.087 -4.185 +DC O2 O O 0 2.273 -2.221 -4.961 +DC N3 N NRD6 0 3.923 -0.917 -4.114 +DC C4 C CR6 0 4.961 -0.779 -3.274 +DC N4 N NH2 0 5.596 0.387 -3.250 +DC C5 C CR16 0 5.371 -1.854 -2.432 +DC C6 C CR16 0 4.683 -3.007 -2.507 +DC "H5'" H H 0 2.640 -6.331 0.044 +DC "H5''" H H 0 3.022 -7.718 -0.669 +DC "H4'" H H 0 1.482 -6.507 -1.967 +DC "H3'" H H 0 3.719 -7.516 -3.087 +DC "HO3'" H H 0 1.460 -6.765 -4.330 +DC "H2'" H H 0 3.647 -5.668 -4.930 +DC "H2''" H H 0 4.648 -5.546 -3.691 +DC "H1'" H H 0 2.063 -4.358 -3.951 +DC H41 H H 0 5.385 1.014 -3.827 +DC H42 H H 0 6.226 0.528 -2.656 +DC H5 H H 0 6.097 -1.763 -1.841 +DC H6 H H 0 4.929 -3.731 -1.969 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +DC OP3 P SINGLE n 1.517 0.0192 1.517 0.0192 +DC P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192 +DC P OP2 SINGLE n 1.517 0.0192 1.517 0.0192 +DC P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 +DC "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +DC "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +DC "C4'" "O4'" SINGLE n 1.445 0.0100 1.445 0.0100 +DC "C4'" "C3'" SINGLE n 1.526 0.0115 1.526 0.0115 +DC "O4'" "C1'" SINGLE n 1.413 0.0100 1.413 0.0100 +DC "C3'" "O3'" SINGLE n 1.424 0.0100 1.424 0.0100 +DC "C3'" "C2'" SINGLE n 1.522 0.0100 1.522 0.0100 +DC "C2'" "C1'" SINGLE n 1.520 0.0100 1.520 0.0100 +DC "C1'" N1 SINGLE n 1.480 0.0115 1.480 0.0115 +DC N1 C2 SINGLE y 1.397 0.0100 1.397 0.0100 +DC N1 C6 SINGLE y 1.360 0.0118 1.360 0.0118 +DC C2 O2 DOUBLE n 1.241 0.0100 1.241 0.0100 +DC C2 N3 SINGLE y 1.355 0.0119 1.355 0.0119 +DC N3 C4 DOUBLE y 1.339 0.0110 1.339 0.0110 +DC C4 N4 SINGLE n 1.325 0.0109 1.325 0.0109 +DC C4 C5 SINGLE y 1.422 0.0123 1.422 0.0123 +DC C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 +DC "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +DC "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 +DC "C4'" "H4'" SINGLE n 1.089 0.0100 0.987 0.0170 +DC "C3'" "H3'" SINGLE n 1.089 0.0100 0.988 0.0189 +DC "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +DC "C2'" "H2'" SINGLE n 1.089 0.0100 0.982 0.0200 +DC "C2'" "H2''" SINGLE n 1.089 0.0100 0.982 0.0200 +DC "C1'" "H1'" SINGLE n 1.089 0.0100 0.991 0.0103 +DC N4 H41 SINGLE n 1.016 0.0100 0.877 0.0200 +DC N4 H42 SINGLE n 1.016 0.0100 0.877 0.0200 +DC C5 H5 SINGLE n 1.082 0.0130 0.941 0.0174 +DC C6 H6 SINGLE n 1.082 0.0130 0.935 0.0143 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +DC OP3 P OP1 112.864 1.69 +DC OP3 P OP2 112.864 1.69 +DC OP3 P "O5'" 105.808 2.07 +DC OP1 P OP2 112.864 1.69 +DC OP1 P "O5'" 105.808 2.07 +DC OP2 P "O5'" 105.808 2.07 +DC P "O5'" "C5'" 118.783 1.50 +DC "O5'" "C5'" "C4'" 109.342 1.50 +DC "O5'" "C5'" "H5'" 109.845 1.50 +DC "O5'" "C5'" "H5''" 109.845 1.50 +DC "C4'" "C5'" "H5'" 109.624 1.50 +DC "C4'" "C5'" "H5''" 109.624 1.50 +DC "H5'" "C5'" "H5''" 108.472 1.50 +DC "C5'" "C4'" "O4'" 109.615 1.50 +DC "C5'" "C4'" "C3'" 114.866 1.63 +DC "C5'" "C4'" "H4'" 108.268 1.50 +DC "O4'" "C4'" "C3'" 105.770 1.50 +DC "O4'" "C4'" "H4'" 108.698 1.50 +DC "C3'" "C4'" "H4'" 109.069 1.50 +DC "C4'" "O4'" "C1'" 109.692 1.50 +DC "C4'" "C3'" "O3'" 110.527 2.37 +DC "C4'" "C3'" "C2'" 102.800 1.50 +DC "C4'" "C3'" "H3'" 110.775 1.50 +DC "O3'" "C3'" "C2'" 110.636 2.59 +DC "O3'" "C3'" "H3'" 110.713 1.50 +DC "C2'" "C3'" "H3'" 110.862 1.50 +DC "C3'" "O3'" "HO3'" 109.026 2.38 +DC "C3'" "C2'" "C1'" 102.834 1.50 +DC "C3'" "C2'" "H2'" 111.310 1.50 +DC "C3'" "C2'" "H2''" 111.310 1.50 +DC "C1'" "C2'" "H2'" 111.187 1.50 +DC "C1'" "C2'" "H2''" 111.187 1.50 +DC "H2'" "C2'" "H2''" 108.952 1.50 +DC "O4'" "C1'" "C2'" 106.308 1.50 +DC "O4'" "C1'" N1 107.584 1.50 +DC "O4'" "C1'" "H1'" 109.550 1.50 +DC "C2'" "C1'" N1 114.268 1.50 +DC "C2'" "C1'" "H1'" 109.741 1.50 +DC N1 "C1'" "H1'" 109.342 1.50 +DC "C1'" N1 C2 118.777 1.50 +DC "C1'" N1 C6 120.713 1.50 +DC C2 N1 C6 120.510 1.50 +DC N1 C2 O2 118.710 1.50 +DC N1 C2 N3 118.927 1.50 +DC O2 C2 N3 122.370 1.50 +DC C2 N3 C4 120.266 1.50 +DC N3 C4 N4 117.855 1.50 +DC N3 C4 C5 121.269 1.50 +DC N4 C4 C5 120.876 1.50 +DC C4 N4 H41 119.818 1.59 +DC C4 N4 H42 119.818 1.59 +DC H41 N4 H42 120.363 1.85 +DC C4 C5 C6 117.808 1.50 +DC C4 C5 H5 121.350 1.50 +DC C6 C5 H5 120.848 1.50 +DC N1 C6 C5 121.215 1.50 +DC N1 C6 H6 118.510 1.50 +DC C5 C6 H6 120.275 1.75 +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +DC C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +DC C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +DC C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +DC C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +DC C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +DC C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +DC C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +DC C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +DC C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +DC C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +DC C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +DC C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +DC alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +DC beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +DC epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +DC gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +DC const_sp2_sp2_4 O2 C2 N1 "C1'" 0.000 5.0 2 +DC const_18 C5 C6 N1 "C1'" 180.000 10.0 2 +DC const_sp2_sp2_6 O2 C2 N3 C4 180.000 5.0 2 +DC const_sp2_sp2_8 N4 C4 N3 C2 180.000 5.0 2 +DC sp2_sp2_3 N3 C4 N4 H41 0.000 5.0 2 +DC const_11 N4 C4 C5 C6 180.000 10.0 2 +DC const_13 C4 C5 C6 N1 0.000 10.0 2 +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +DC chir_1 P "O5'" OP3 OP2 both +DC chir_2 "C4'" "O4'" "C3'" "C5'" negative +DC chir_3 "C3'" "O3'" "C4'" "C2'" positive +DC chir_4 "C1'" "O4'" N1 "C2'" negative +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +DC plan-1 "C1'" 0.020 +DC plan-1 C2 0.020 +DC plan-1 C4 0.020 +DC plan-1 C5 0.020 +DC plan-1 C6 0.020 +DC plan-1 H5 0.020 +DC plan-1 H6 0.020 +DC plan-1 N1 0.020 +DC plan-1 N3 0.020 +DC plan-1 N4 0.020 +DC plan-1 O2 0.020 +DC plan-2 C4 0.020 +DC plan-2 H41 0.020 +DC plan-2 H42 0.020 +DC plan-2 N4 0.020 +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +DC SMILES ACDLabs 10.04 O=C1N=C(N)C=CN1C2OC(C(O)C2)COP(=O)(O)O +DC SMILES_CANONICAL CACTVS 3.341 NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2 +DC SMILES CACTVS 3.341 NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2 +DC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)O)O +DC SMILES "OpenEye OEToolkits" 1.5.0 C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)O)O +DC InChI InChI 1.03 InChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1 +DC InChIKey InChI 1.03 NCMVOABPESMRCP-SHYZEUOFSA-N +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +DC acedrg 243 "dictionary generator" +DC acedrg_database 11 "data source" +DC rdkit 2017.03.2 "Chemoinformatics tool" +DC refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/DG.cif b/image_analysis/structure_refinement/monomers/DG.cif new file mode 100644 index 000000000..1073727b3 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/DG.cif @@ -0,0 +1,271 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +DG DG "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" DNA 35 23 . +# +data_comp_DG +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +DG OP3 O OP -1 0.424 -8.734 -9.816 +DG P P P 0 0.296 -8.811 -11.326 +DG OP1 O O 0 -0.898 -9.631 -11.775 +DG OP2 O OP -1 1.587 -9.229 -12.005 +DG "O5'" O O2 0 0.007 -7.303 -11.822 +DG "C5'" C CH2 0 -1.170 -6.617 -11.324 +DG "C4'" C CH1 0 -1.206 -5.213 -11.876 +DG "O4'" O O2 0 -0.018 -4.512 -11.450 +DG "C3'" C CH1 0 -1.259 -5.123 -13.404 +DG "O3'" O OH1 0 -2.248 -4.188 -13.827 +DG "C2'" C CH2 0 0.144 -4.654 -13.783 +DG "C1'" C CH1 0 0.565 -3.849 -12.566 +DG N9 N NR5 0 2.012 -3.775 -12.354 +DG C8 C CR15 0 2.857 -4.830 -12.111 +DG N7 N NRD5 0 4.108 -4.471 -11.958 +DG C5 C CR56 0 4.088 -3.091 -12.106 +DG C6 C CR6 0 5.150 -2.149 -12.042 +DG O6 O O 0 6.352 -2.369 -11.834 +DG N1 N NR16 0 4.698 -0.841 -12.249 +DG C2 C CR6 0 3.388 -0.485 -12.487 +DG N2 N NH2 0 3.138 0.820 -12.662 +DG N3 N NRD6 0 2.387 -1.368 -12.548 +DG C4 C CR56 0 2.803 -2.647 -12.350 +DG "H5'" H H 0 -1.147 -6.585 -10.336 +DG "H5''" H H 0 -1.985 -7.104 -11.602 +DG "H4'" H H 0 -1.996 -4.756 -11.498 +DG "H3'" H H 0 -1.441 -6.012 -13.795 +DG "HO3'" H H 0 -2.096 -3.427 -13.481 +DG "H2'" H H 0 0.125 -4.097 -14.586 +DG "H2''" H H 0 0.741 -5.412 -13.932 +DG "H1'" H H 0 0.190 -2.932 -12.632 +DG H8 H H 0 2.565 -5.725 -12.063 +DG H1 H H 0 5.314 -0.188 -12.222 +DG H21 H H 0 2.584 1.078 -13.291 +DG H22 H H 0 3.528 1.412 -12.146 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +DG OP3 P SINGLE n 1.517 0.0192 1.517 0.0192 +DG P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192 +DG P OP2 SINGLE n 1.517 0.0192 1.517 0.0192 +DG P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 +DG "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +DG "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +DG "C4'" "O4'" SINGLE n 1.442 0.0100 1.442 0.0100 +DG "C4'" "C3'" SINGLE n 1.526 0.0115 1.526 0.0115 +DG "O4'" "C1'" SINGLE n 1.425 0.0100 1.425 0.0100 +DG "C3'" "O3'" SINGLE n 1.424 0.0100 1.424 0.0100 +DG "C3'" "C2'" SINGLE n 1.526 0.0101 1.526 0.0101 +DG "C2'" "C1'" SINGLE n 1.521 0.0118 1.521 0.0118 +DG "C1'" N9 SINGLE n 1.462 0.0111 1.462 0.0111 +DG N9 C8 SINGLE y 1.373 0.0100 1.373 0.0100 +DG N9 C4 SINGLE y 1.375 0.0100 1.375 0.0100 +DG C8 N7 DOUBLE y 1.312 0.0100 1.312 0.0100 +DG N7 C5 SINGLE y 1.390 0.0100 1.390 0.0100 +DG C5 C6 SINGLE y 1.417 0.0103 1.417 0.0103 +DG C5 C4 DOUBLE y 1.377 0.0100 1.377 0.0100 +DG C6 O6 DOUBLE n 1.239 0.0100 1.239 0.0100 +DG C6 N1 SINGLE y 1.396 0.0107 1.396 0.0107 +DG N1 C2 SINGLE y 1.374 0.0100 1.374 0.0100 +DG C2 N2 SINGLE n 1.340 0.0101 1.340 0.0101 +DG C2 N3 DOUBLE y 1.333 0.0104 1.333 0.0104 +DG N3 C4 SINGLE y 1.355 0.0100 1.355 0.0100 +DG "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +DG "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 +DG "C4'" "H4'" SINGLE n 1.089 0.0100 0.987 0.0170 +DG "C3'" "H3'" SINGLE n 1.089 0.0100 0.988 0.0189 +DG "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +DG "C2'" "H2'" SINGLE n 1.089 0.0100 0.977 0.0113 +DG "C2'" "H2''" SINGLE n 1.089 0.0100 0.977 0.0113 +DG "C1'" "H1'" SINGLE n 1.089 0.0100 0.993 0.0101 +DG C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170 +DG N1 H1 SINGLE n 1.016 0.0100 0.897 0.0200 +DG N2 H21 SINGLE n 1.016 0.0100 0.877 0.0200 +DG N2 H22 SINGLE n 1.016 0.0100 0.877 0.0200 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +DG OP3 P OP1 112.864 1.69 +DG OP3 P OP2 112.864 1.69 +DG OP3 P "O5'" 105.808 2.07 +DG OP1 P OP2 112.864 1.69 +DG OP1 P "O5'" 105.808 2.07 +DG OP2 P "O5'" 105.808 2.07 +DG P "O5'" "C5'" 118.783 1.50 +DG "O5'" "C5'" "C4'" 109.342 1.50 +DG "O5'" "C5'" "H5'" 109.845 1.50 +DG "O5'" "C5'" "H5''" 109.845 1.50 +DG "C4'" "C5'" "H5'" 109.624 1.50 +DG "C4'" "C5'" "H5''" 109.624 1.50 +DG "H5'" "C5'" "H5''" 108.472 1.50 +DG "C5'" "C4'" "O4'" 109.123 1.50 +DG "C5'" "C4'" "C3'" 114.866 1.63 +DG "C5'" "C4'" "H4'" 108.268 1.50 +DG "O4'" "C4'" "C3'" 105.506 1.50 +DG "O4'" "C4'" "H4'" 108.947 1.50 +DG "C3'" "C4'" "H4'" 109.069 1.50 +DG "C4'" "O4'" "C1'" 108.795 1.50 +DG "C4'" "C3'" "O3'" 110.527 2.37 +DG "C4'" "C3'" "C2'" 102.433 1.50 +DG "C4'" "C3'" "H3'" 110.775 1.50 +DG "O3'" "C3'" "C2'" 111.424 1.96 +DG "O3'" "C3'" "H3'" 110.713 1.50 +DG "C2'" "C3'" "H3'" 110.846 1.50 +DG "C3'" "O3'" "HO3'" 109.026 2.38 +DG "C3'" "C2'" "C1'" 102.663 1.50 +DG "C3'" "C2'" "H2'" 111.194 1.50 +DG "C3'" "C2'" "H2''" 111.194 1.50 +DG "C1'" "C2'" "H2'" 111.213 1.50 +DG "C1'" "C2'" "H2''" 111.213 1.50 +DG "H2'" "C2'" "H2''" 109.148 1.50 +DG "O4'" "C1'" "C2'" 106.035 1.50 +DG "O4'" "C1'" N9 108.236 1.50 +DG "O4'" "C1'" "H1'" 109.059 1.50 +DG "C2'" "C1'" N9 114.190 1.67 +DG "C2'" "C1'" "H1'" 109.272 1.50 +DG N9 "C1'" "H1'" 109.282 1.50 +DG "C1'" N9 C8 127.617 2.81 +DG "C1'" N9 C4 126.652 2.93 +DG C8 N9 C4 105.731 1.50 +DG N9 C8 N7 113.507 1.50 +DG N9 C8 H8 123.187 1.50 +DG N7 C8 H8 123.307 1.50 +DG C8 N7 C5 104.778 1.50 +DG N7 C5 C6 130.030 1.50 +DG N7 C5 C4 110.574 1.50 +DG C6 C5 C4 119.397 1.50 +DG C5 C6 O6 128.244 1.50 +DG C5 C6 N1 111.367 1.50 +DG O6 C6 N1 120.389 1.50 +DG C6 N1 C2 125.351 1.50 +DG C6 N1 H1 116.978 2.44 +DG C2 N1 H1 117.677 2.71 +DG N1 C2 N2 116.576 1.50 +DG N1 C2 N3 123.602 1.50 +DG N2 C2 N3 119.821 1.50 +DG C2 N2 H21 119.868 1.50 +DG C2 N2 H22 119.868 1.50 +DG H21 N2 H22 120.263 1.96 +DG C2 N3 C4 112.066 1.50 +DG N9 C4 C5 105.411 1.50 +DG N9 C4 N3 126.378 1.50 +DG C5 C4 N3 128.211 1.50 +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +DG C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +DG C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +DG C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +DG C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +DG C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +DG C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +DG C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +DG C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +DG C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +DG C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +DG C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +DG C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +DG alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +DG beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +DG epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +DG gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +DG const_18 N7 C8 N9 "C1'" 180.000 10.0 2 +DG const_30 C5 C4 N9 "C1'" 180.000 10.0 2 +DG const_21 N9 C8 N7 C5 0.000 10.0 2 +DG const_24 C6 C5 N7 C8 180.000 10.0 2 +DG const_sp2_sp2_4 N7 C5 C6 O6 0.000 5.0 2 +DG const_25 N9 C4 C5 N7 0.000 10.0 2 +DG const_sp2_sp2_7 O6 C6 N1 C2 180.000 5.0 2 +DG const_11 N2 C2 N1 C6 180.000 10.0 2 +DG sp2_sp2_1 N1 C2 N2 H21 180.000 5.0 2 +DG const_14 N2 C2 N3 C4 180.000 10.0 2 +DG const_16 N9 C4 N3 C2 180.000 10.0 2 +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +DG chir_1 P "O5'" OP3 OP2 both +DG chir_2 "C4'" "O4'" "C3'" "C5'" negative +DG chir_3 "C3'" "O3'" "C4'" "C2'" positive +DG chir_4 "C1'" "O4'" N9 "C2'" negative +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +DG plan-1 "C1'" 0.020 +DG plan-1 C2 0.020 +DG plan-1 C4 0.020 +DG plan-1 C5 0.020 +DG plan-1 C6 0.020 +DG plan-1 C8 0.020 +DG plan-1 H1 0.020 +DG plan-1 H8 0.020 +DG plan-1 N1 0.020 +DG plan-1 N2 0.020 +DG plan-1 N3 0.020 +DG plan-1 N7 0.020 +DG plan-1 N9 0.020 +DG plan-1 O6 0.020 +DG plan-2 C2 0.020 +DG plan-2 H21 0.020 +DG plan-2 H22 0.020 +DG plan-2 N2 0.020 +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +DG SMILES ACDLabs 10.04 O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3)COP(=O)(O)O +DG SMILES_CANONICAL CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3 +DG SMILES CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3 +DG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N=C(NC2=O)N +DG SMILES "OpenEye OEToolkits" 1.5.0 c1nc2c(n1C3CC(C(O3)COP(=O)(O)O)O)N=C(NC2=O)N +DG InChI InChI 1.03 InChI=1S/C10H14N5O7P/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(22-6)2-21-23(18,19)20/h3-6,16H,1-2H2,(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1 +DG InChIKey InChI 1.03 LTFMZDNNPPEQNG-KVQBGUIXSA-N +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +DG acedrg 243 "dictionary generator" +DG acedrg_database 11 "data source" +DG rdkit 2017.03.2 "Chemoinformatics tool" +DG refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/DMS.cif b/image_analysis/structure_refinement/monomers/DMS.cif new file mode 100644 index 000000000..209672234 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/DMS.cif @@ -0,0 +1,117 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +DMS DMS "DIMETHYL SULFOXIDE" NON-POLYMER 10 4 . +# +data_comp_DMS +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +DMS S S S3 0 63.218 46.394 -11.587 +DMS O O O 0 63.732 46.133 -12.975 +DMS C1 C CH3 0 64.619 46.928 -10.638 +DMS C2 C CH3 0 63.010 44.801 -10.834 +DMS H11 H H 0 64.347 47.082 -9.723 +DMS H12 H H 0 64.967 47.748 -11.014 +DMS H13 H H 0 65.302 46.245 -10.662 +DMS H21 H H 0 63.858 44.337 -10.825 +DMS H22 H H 0 62.366 44.288 -11.340 +DMS H23 H H 0 62.693 44.913 -9.927 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +DMS S O DOUBLE n 1.503 0.0200 1.503 0.0200 +DMS S C1 SINGLE n 1.774 0.0176 1.774 0.0176 +DMS S C2 SINGLE n 1.774 0.0176 1.774 0.0176 +DMS C1 H11 SINGLE n 1.089 0.0100 0.967 0.0136 +DMS C1 H12 SINGLE n 1.089 0.0100 0.967 0.0136 +DMS C1 H13 SINGLE n 1.089 0.0100 0.967 0.0136 +DMS C2 H21 SINGLE n 1.089 0.0100 0.967 0.0136 +DMS C2 H22 SINGLE n 1.089 0.0100 0.967 0.0136 +DMS C2 H23 SINGLE n 1.089 0.0100 0.967 0.0136 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +DMS O S C1 106.047 1.50 +DMS O S C2 106.047 1.50 +DMS C1 S C2 97.789 1.50 +DMS S C1 H11 109.408 1.50 +DMS S C1 H12 109.408 1.50 +DMS S C1 H13 109.408 1.50 +DMS H11 C1 H12 109.545 1.50 +DMS H11 C1 H13 109.545 1.50 +DMS H12 C1 H13 109.545 1.50 +DMS S C2 H21 109.408 1.50 +DMS S C2 H22 109.408 1.50 +DMS S C2 H23 109.408 1.50 +DMS H21 C2 H22 109.545 1.50 +DMS H21 C2 H23 109.545 1.50 +DMS H22 C2 H23 109.545 1.50 +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +DMS sp3_sp3_1 H11 C1 S O 180.000 10.0 3 +DMS sp3_sp3_8 H21 C2 S O -60.000 10.0 3 +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +DMS chir_1 S O C1 C2 both +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +DMS SMILES ACDLabs 10.04 sulfinyldimethane +DMS SMILES_CANONICAL CACTVS 3.341 C[S](C)=O +DMS SMILES CACTVS 3.341 C[S](C)=O +DMS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CS(=O)C +DMS SMILES "OpenEye OEToolkits" 1.5.0 CS(=O)C +DMS InChI InChI 1.03 InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 +DMS InChIKey InChI 1.03 IAZDPXIOMUYVGZ-UHFFFAOYSA-N +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +DMS acedrg 243 "dictionary generator" +DMS acedrg_database 11 "data source" +DMS rdkit 2017.03.2 "Chemoinformatics tool" +DMS refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/DT.cif b/image_analysis/structure_refinement/monomers/DT.cif new file mode 100644 index 000000000..affc26c5a --- /dev/null +++ b/image_analysis/structure_refinement/monomers/DT.cif @@ -0,0 +1,256 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +DT DT "THYMIDINE-5'-MONOPHOSPHATE" DNA 34 21 . +# +data_comp_DT +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +DT OP3 O OP -1 -9.033 1.811 3.710 +DT P P P 0 -8.813 3.246 4.151 +DT OP1 O O 0 -9.790 3.689 5.223 +DT OP2 O OP -1 -8.738 4.214 2.986 +DT "O5'" O O2 0 -7.356 3.277 4.843 +DT "C5'" C CH2 0 -7.098 2.397 5.967 +DT "C4'" C CH1 0 -5.688 2.610 6.462 +DT "O4'" O O2 0 -4.754 2.345 5.391 +DT "C3'" C CH1 0 -5.391 4.024 6.970 +DT "O3'" O OH1 0 -4.766 3.989 8.251 +DT "C2'" C CH2 0 -4.437 4.599 5.930 +DT "C1'" C CH1 0 -3.760 3.359 5.367 +DT N1 N NR6 0 -3.270 3.502 3.966 +DT C2 C CR6 0 -1.905 3.474 3.713 +DT O2 O O 0 -1.053 3.332 4.583 +DT N3 N NR16 0 -1.559 3.618 2.388 +DT C4 C CR6 0 -2.414 3.786 1.310 +DT O4 O O 0 -1.948 3.903 0.172 +DT C5 C CR6 0 -3.824 3.809 1.640 +DT C7 C CH3 0 -4.824 3.988 0.535 +DT C6 C CR16 0 -4.178 3.669 2.932 +DT "H5'" H H 0 -7.213 1.455 5.689 +DT "H5''" H H 0 -7.738 2.588 6.696 +DT "H4'" H H 0 -5.520 1.964 7.190 +DT "H3'" H H 0 -6.221 4.559 7.010 +DT "HO3'" H H 0 -4.051 3.531 8.213 +DT "H2'" H H 0 -3.782 5.203 6.342 +DT "H2''" H H 0 -4.926 5.088 5.233 +DT "H1'" H H 0 -3.014 3.092 5.967 +DT H3 H H 0 -0.682 3.600 2.215 +DT H71 H H 0 -5.705 3.724 0.845 +DT H72 H H 0 -4.574 3.437 -0.224 +DT H73 H H 0 -4.846 4.920 0.263 +DT H6 H H 0 -5.103 3.686 3.152 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +DT OP3 P SINGLE n 1.517 0.0192 1.517 0.0192 +DT P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192 +DT P OP2 SINGLE n 1.517 0.0192 1.517 0.0192 +DT P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 +DT "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +DT "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +DT "C4'" "O4'" SINGLE n 1.445 0.0100 1.445 0.0100 +DT "C4'" "C3'" SINGLE n 1.526 0.0115 1.526 0.0115 +DT "O4'" "C1'" SINGLE n 1.422 0.0100 1.422 0.0100 +DT "C3'" "O3'" SINGLE n 1.424 0.0100 1.424 0.0100 +DT "C3'" "C2'" SINGLE n 1.522 0.0100 1.522 0.0100 +DT "C2'" "C1'" SINGLE n 1.523 0.0130 1.523 0.0130 +DT "C1'" N1 SINGLE n 1.477 0.0139 1.477 0.0139 +DT N1 C2 SINGLE y 1.379 0.0100 1.379 0.0100 +DT N1 C6 SINGLE y 1.380 0.0107 1.380 0.0107 +DT C2 O2 DOUBLE n 1.224 0.0111 1.224 0.0111 +DT C2 N3 SINGLE y 1.373 0.0100 1.373 0.0100 +DT N3 C4 SINGLE y 1.383 0.0100 1.383 0.0100 +DT C4 O4 DOUBLE n 1.234 0.0141 1.234 0.0141 +DT C4 C5 SINGLE y 1.446 0.0100 1.446 0.0100 +DT C5 C7 SINGLE n 1.500 0.0100 1.500 0.0100 +DT C5 C6 DOUBLE y 1.343 0.0112 1.343 0.0112 +DT "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +DT "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 +DT "C4'" "H4'" SINGLE n 1.089 0.0100 0.987 0.0170 +DT "C3'" "H3'" SINGLE n 1.089 0.0100 0.988 0.0189 +DT "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +DT "C2'" "H2'" SINGLE n 1.089 0.0100 0.982 0.0200 +DT "C2'" "H2''" SINGLE n 1.089 0.0100 0.982 0.0200 +DT "C1'" "H1'" SINGLE n 1.089 0.0100 0.996 0.0200 +DT N3 H3 SINGLE n 1.016 0.0100 0.893 0.0200 +DT C7 H71 SINGLE n 1.089 0.0100 0.971 0.0135 +DT C7 H72 SINGLE n 1.089 0.0100 0.971 0.0135 +DT C7 H73 SINGLE n 1.089 0.0100 0.971 0.0135 +DT C6 H6 SINGLE n 1.082 0.0130 0.951 0.0200 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +DT OP3 P OP1 112.864 1.69 +DT OP3 P OP2 112.864 1.69 +DT OP3 P "O5'" 105.808 2.07 +DT OP1 P OP2 112.864 1.69 +DT OP1 P "O5'" 105.808 2.07 +DT OP2 P "O5'" 105.808 2.07 +DT P "O5'" "C5'" 118.783 1.50 +DT "O5'" "C5'" "C4'" 109.342 1.50 +DT "O5'" "C5'" "H5'" 109.845 1.50 +DT "O5'" "C5'" "H5''" 109.845 1.50 +DT "C4'" "C5'" "H5'" 109.624 1.50 +DT "C4'" "C5'" "H5''" 109.624 1.50 +DT "H5'" "C5'" "H5''" 108.472 1.50 +DT "C5'" "C4'" "O4'" 109.615 1.50 +DT "C5'" "C4'" "C3'" 114.866 1.63 +DT "C5'" "C4'" "H4'" 108.268 1.50 +DT "O4'" "C4'" "C3'" 105.770 1.50 +DT "O4'" "C4'" "H4'" 108.698 1.50 +DT "C3'" "C4'" "H4'" 109.069 1.50 +DT "C4'" "O4'" "C1'" 109.692 1.50 +DT "C4'" "C3'" "O3'" 110.527 2.37 +DT "C4'" "C3'" "C2'" 102.800 1.50 +DT "C4'" "C3'" "H3'" 110.775 1.50 +DT "O3'" "C3'" "C2'" 110.636 2.59 +DT "O3'" "C3'" "H3'" 110.713 1.50 +DT "C2'" "C3'" "H3'" 110.862 1.50 +DT "C3'" "O3'" "HO3'" 109.026 2.38 +DT "C3'" "C2'" "C1'" 102.834 1.50 +DT "C3'" "C2'" "H2'" 111.310 1.50 +DT "C3'" "C2'" "H2''" 111.310 1.50 +DT "C1'" "C2'" "H2'" 111.187 1.50 +DT "C1'" "C2'" "H2''" 111.187 1.50 +DT "H2'" "C2'" "H2''" 108.952 1.50 +DT "O4'" "C1'" "C2'" 106.308 1.50 +DT "O4'" "C1'" N1 107.584 1.50 +DT "O4'" "C1'" "H1'" 109.550 1.50 +DT "C2'" "C1'" N1 114.268 1.50 +DT "C2'" "C1'" "H1'" 109.741 1.50 +DT N1 "C1'" "H1'" 109.342 1.50 +DT "C1'" N1 C2 118.265 1.50 +DT "C1'" N1 C6 120.492 1.50 +DT C2 N1 C6 121.243 1.50 +DT N1 C2 O2 122.872 1.50 +DT N1 C2 N3 114.786 1.50 +DT O2 C2 N3 122.342 1.50 +DT C2 N3 C4 127.106 1.50 +DT C2 N3 H3 115.584 1.79 +DT C4 N3 H3 117.311 1.81 +DT N3 C4 O4 119.787 1.50 +DT N3 C4 C5 115.265 1.50 +DT O4 C4 C5 124.948 1.50 +DT C4 C5 C7 118.650 1.50 +DT C4 C5 C6 118.305 1.50 +DT C7 C5 C6 123.045 1.50 +DT C5 C7 H71 109.652 1.50 +DT C5 C7 H72 109.652 1.50 +DT C5 C7 H73 109.652 1.50 +DT H71 C7 H72 109.348 1.50 +DT H71 C7 H73 109.348 1.50 +DT H72 C7 H73 109.348 1.50 +DT N1 C6 C5 123.296 1.50 +DT N1 C6 H6 117.926 1.56 +DT C5 C6 H6 118.779 1.68 +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +DT C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +DT C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +DT C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +DT C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +DT C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +DT C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +DT C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +DT C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +DT C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +DT C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +DT C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +DT C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +DT alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +DT beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +DT epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +DT gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +DT const_sp2_sp2_4 O2 C2 N1 "C1'" 0.000 5.0 2 +DT const_22 C5 C6 N1 "C1'" 180.000 10.0 2 +DT const_sp2_sp2_7 O2 C2 N3 C4 180.000 5.0 2 +DT const_11 O4 C4 N3 C2 180.000 10.0 2 +DT const_16 O4 C4 C5 C7 0.000 10.0 2 +DT sp2_sp3_7 C4 C5 C7 H71 150.000 10.0 6 +DT const_19 C7 C5 C6 N1 180.000 10.0 2 +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +DT chir_1 P "O5'" OP3 OP2 both +DT chir_2 "C4'" "O4'" "C3'" "C5'" negative +DT chir_3 "C3'" "O3'" "C4'" "C2'" positive +DT chir_4 "C1'" "O4'" N1 "C2'" negative +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +DT plan-1 "C1'" 0.020 +DT plan-1 C2 0.020 +DT plan-1 C4 0.020 +DT plan-1 C5 0.020 +DT plan-1 C6 0.020 +DT plan-1 C7 0.020 +DT plan-1 H3 0.020 +DT plan-1 H6 0.020 +DT plan-1 N1 0.020 +DT plan-1 N3 0.020 +DT plan-1 O2 0.020 +DT plan-1 O4 0.020 +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +DT SMILES ACDLabs 10.04 O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)COP(=O)(O)O +DT SMILES_CANONICAL CACTVS 3.341 CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O +DT SMILES CACTVS 3.341 CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O +DT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O +DT SMILES "OpenEye OEToolkits" 1.5.0 CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O +DT InChI InChI 1.03 InChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1 +DT InChIKey InChI 1.03 GYOZYWVXFNDGLU-XLPZGREQSA-N +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +DT acedrg 243 "dictionary generator" +DT acedrg_database 11 "data source" +DT rdkit 2017.03.2 "Chemoinformatics tool" +DT refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/EDO.cif b/image_analysis/structure_refinement/monomers/EDO.cif new file mode 100644 index 000000000..9d74e7fbe --- /dev/null +++ b/image_analysis/structure_refinement/monomers/EDO.cif @@ -0,0 +1,108 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +EDO EDO 1,2-ETHANEDIOL NON-POLYMER 10 4 . +# +data_comp_EDO +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +EDO C1 C CH2 0 5.160 28.149 5.379 +EDO O1 O OH1 0 6.106 28.471 4.378 +EDO C2 C CH2 0 3.762 28.430 4.968 +EDO O2 O OH1 0 3.416 27.839 3.730 +EDO H11 H H 0 5.362 28.666 6.186 +EDO H12 H H 0 5.240 27.198 5.599 +EDO HO1 H H 0 6.871 28.201 4.619 +EDO H21 H H 0 3.642 29.401 4.901 +EDO H22 H H 0 3.156 28.097 5.661 +EDO HO2 H H 0 3.485 26.998 3.790 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +EDO C1 O1 SINGLE n 1.414 0.0200 1.414 0.0200 +EDO C1 C2 SINGLE n 1.483 0.0200 1.483 0.0200 +EDO C2 O2 SINGLE n 1.414 0.0200 1.414 0.0200 +EDO C1 H11 SINGLE n 1.089 0.0100 0.980 0.0144 +EDO C1 H12 SINGLE n 1.089 0.0100 0.980 0.0144 +EDO O1 HO1 SINGLE n 0.970 0.0120 0.846 0.0200 +EDO C2 H21 SINGLE n 1.089 0.0100 0.980 0.0144 +EDO C2 H22 SINGLE n 1.089 0.0100 0.980 0.0144 +EDO O2 HO2 SINGLE n 0.970 0.0120 0.846 0.0200 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +EDO O1 C1 C2 113.236 3.00 +EDO O1 C1 H11 109.012 1.50 +EDO O1 C1 H12 109.012 1.50 +EDO C2 C1 H11 108.881 1.50 +EDO C2 C1 H12 108.881 1.50 +EDO H11 C1 H12 108.093 1.50 +EDO C1 O1 HO1 109.347 1.86 +EDO C1 C2 O2 113.236 3.00 +EDO C1 C2 H21 108.881 1.50 +EDO C1 C2 H22 108.881 1.50 +EDO O2 C2 H21 109.012 1.50 +EDO O2 C2 H22 109.012 1.50 +EDO H21 C2 H22 108.093 1.50 +EDO C2 O2 HO2 109.347 1.86 +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +EDO sp3_sp3_1 C2 C1 O1 HO1 180.000 10.0 3 +EDO sp3_sp3_4 O1 C1 C2 O2 180.000 10.0 3 +EDO sp3_sp3_13 C1 C2 O2 HO2 180.000 10.0 3 +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +EDO SMILES ACDLabs 10.04 OCCO +EDO SMILES_CANONICAL CACTVS 3.341 OCCO +EDO SMILES CACTVS 3.341 OCCO +EDO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(CO)O +EDO SMILES "OpenEye OEToolkits" 1.5.0 C(CO)O +EDO InChI InChI 1.03 InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2 +EDO InChIKey InChI 1.03 LYCAIKOWRPUZTN-UHFFFAOYSA-N +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +EDO acedrg 243 "dictionary generator" +EDO acedrg_database 11 "data source" +EDO rdkit 2017.03.2 "Chemoinformatics tool" +EDO refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/FE.cif b/image_analysis/structure_refinement/monomers/FE.cif new file mode 100644 index 000000000..eabe098cd --- /dev/null +++ b/image_analysis/structure_refinement/monomers/FE.cif @@ -0,0 +1,30 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +FE FE 'FE (III) ION ' NON-POLYMER 1 1 . + +data_comp_FE +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.partial_charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +FE FE FE FE 3.000 0.000 0.000 0.000 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +FE FE n/a . END diff --git a/image_analysis/structure_refinement/monomers/FE2.cif b/image_analysis/structure_refinement/monomers/FE2.cif new file mode 100644 index 000000000..fb5535321 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/FE2.cif @@ -0,0 +1,30 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +FE2 FE2 'FE (II) ION ' NON-POLYMER 1 1 . + +data_comp_FE2 +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.partial_charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +FE2 FE FE FE 2.000 0.000 0.000 0.000 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +FE2 FE n/a . END diff --git a/image_analysis/structure_refinement/monomers/G.cif b/image_analysis/structure_refinement/monomers/G.cif new file mode 100644 index 000000000..a948bdc2c --- /dev/null +++ b/image_analysis/structure_refinement/monomers/G.cif @@ -0,0 +1,276 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +G G "GUANOSINE-5'-MONOPHOSPHATE" RNA 36 24 . +# +data_comp_G +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +G OP3 O OP -1 34.040 3.415 -1.077 +G P P P 0 34.210 4.003 0.312 +G OP1 O O 0 34.487 5.494 0.290 +G OP2 O OP -1 35.203 3.231 1.161 +G "O5'" O O2 0 32.781 3.831 1.041 +G "C5'" C CH2 0 32.260 2.493 1.252 +G "C4'" C CH1 0 30.851 2.571 1.788 +G "O4'" O O2 0 30.831 3.382 2.990 +G "C3'" C CH1 0 29.808 3.223 0.875 +G "O3'" O OH1 0 29.289 2.285 -0.060 +G "C2'" C CH1 0 28.754 3.698 1.881 +G "O2'" O OH1 0 27.799 2.707 2.202 +G "C1'" C CH1 0 29.604 4.073 3.097 +G N9 N NR5 0 29.861 5.508 3.212 +G C8 C CR15 0 31.057 6.172 3.071 +G N7 N NRD5 0 30.958 7.468 3.239 +G C5 C CR56 0 29.612 7.676 3.509 +G C6 C CR6 0 28.906 8.880 3.777 +G O6 O O 0 29.357 10.033 3.827 +G N1 N NR16 0 27.544 8.645 3.999 +G C2 C CR6 0 26.939 7.407 3.968 +G N2 N NH2 0 25.620 7.371 4.205 +G N3 N NRD6 0 27.601 6.273 3.716 +G C4 C CR56 0 28.926 6.478 3.499 +G "H5'" H H 0 32.833 2.008 1.895 +G "H5''" H H 0 32.261 1.995 0.397 +G "H4'" H H 0 30.559 1.662 2.015 +G "H3'" H H 0 30.200 3.999 0.398 +G "HO3'" H H 0 28.659 2.653 -0.495 +G "H2'" H H 0 28.286 4.500 1.527 +G "HO2'" H H 0 28.188 2.026 2.527 +G "H1'" H H 0 29.136 3.771 3.909 +G H8 H H 0 31.870 5.740 2.872 +G H1 H H 0 27.031 9.361 4.176 +G H21 H H 0 25.105 6.850 3.723 +G H22 H H 0 25.277 7.868 4.840 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +G OP3 P SINGLE n 1.517 0.0192 1.517 0.0192 +G P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192 +G P OP2 SINGLE n 1.517 0.0192 1.517 0.0192 +G P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 +G "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +G "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +G "C4'" "O4'" SINGLE n 1.451 0.0100 1.451 0.0100 +G "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 +G "O4'" "C1'" SINGLE n 1.409 0.0100 1.409 0.0100 +G "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +G "C3'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100 +G "C2'" "O2'" SINGLE n 1.411 0.0100 1.411 0.0100 +G "C2'" "C1'" SINGLE n 1.525 0.0100 1.525 0.0100 +G "C1'" N9 SINGLE n 1.458 0.0100 1.458 0.0100 +G N9 C8 SINGLE y 1.372 0.0100 1.372 0.0100 +G N9 C4 SINGLE y 1.375 0.0100 1.375 0.0100 +G C8 N7 DOUBLE y 1.312 0.0100 1.312 0.0100 +G N7 C5 SINGLE y 1.390 0.0100 1.390 0.0100 +G C5 C6 SINGLE y 1.417 0.0103 1.417 0.0103 +G C5 C4 DOUBLE y 1.377 0.0100 1.377 0.0100 +G C6 O6 DOUBLE n 1.239 0.0100 1.239 0.0100 +G C6 N1 SINGLE y 1.396 0.0107 1.396 0.0107 +G N1 C2 SINGLE y 1.374 0.0100 1.374 0.0100 +G C2 N2 SINGLE n 1.340 0.0101 1.340 0.0101 +G C2 N3 DOUBLE y 1.333 0.0104 1.333 0.0104 +G N3 C4 SINGLE y 1.355 0.0100 1.355 0.0100 +G "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +G "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 +G "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 +G "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +G "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +G "C2'" "H2'" SINGLE n 1.089 0.0100 0.994 0.0200 +G "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 +G "C1'" "H1'" SINGLE n 1.089 0.0100 0.984 0.0200 +G C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170 +G N1 H1 SINGLE n 1.016 0.0100 0.897 0.0200 +G N2 H21 SINGLE n 1.016 0.0100 0.877 0.0200 +G N2 H22 SINGLE n 1.016 0.0100 0.877 0.0200 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +G OP3 P OP1 112.864 1.69 +G OP3 P OP2 112.864 1.69 +G OP3 P "O5'" 105.808 2.07 +G OP1 P OP2 112.864 1.69 +G OP1 P "O5'" 105.808 2.07 +G OP2 P "O5'" 105.808 2.07 +G P "O5'" "C5'" 118.783 1.50 +G "O5'" "C5'" "C4'" 109.342 1.50 +G "O5'" "C5'" "H5'" 109.845 1.50 +G "O5'" "C5'" "H5''" 109.845 1.50 +G "C4'" "C5'" "H5'" 109.624 1.50 +G "C4'" "C5'" "H5''" 109.624 1.50 +G "H5'" "C5'" "H5''" 108.472 1.50 +G "C5'" "C4'" "O4'" 109.123 1.50 +G "C5'" "C4'" "C3'" 116.008 1.52 +G "C5'" "C4'" "H4'" 108.268 1.50 +G "O4'" "C4'" "C3'" 105.388 1.50 +G "O4'" "C4'" "H4'" 108.947 1.50 +G "C3'" "C4'" "H4'" 109.363 1.86 +G "C4'" "O4'" "C1'" 109.903 1.50 +G "C4'" "C3'" "O3'" 111.281 2.46 +G "C4'" "C3'" "C2'" 102.602 1.50 +G "C4'" "C3'" "H3'" 110.452 2.54 +G "O3'" "C3'" "C2'" 111.581 2.83 +G "O3'" "C3'" "H3'" 110.380 1.67 +G "C2'" "C3'" "H3'" 110.504 1.75 +G "C3'" "O3'" "HO3'" 108.744 3.00 +G "C3'" "C2'" "O2'" 112.782 2.45 +G "C3'" "C2'" "C1'" 101.239 1.50 +G "C3'" "C2'" "H2'" 110.596 1.51 +G "O2'" "C2'" "C1'" 111.715 2.69 +G "O2'" "C2'" "H2'" 110.448 1.97 +G "C1'" "C2'" "H2'" 110.636 1.70 +G "C2'" "O2'" "HO2'" 109.103 2.13 +G "O4'" "C1'" "C2'" 106.047 1.50 +G "O4'" "C1'" N9 108.477 1.50 +G "O4'" "C1'" "H1'" 109.807 1.50 +G "C2'" "C1'" N9 113.824 1.50 +G "C2'" "C1'" "H1'" 109.015 1.50 +G N9 "C1'" "H1'" 109.561 1.50 +G "C1'" N9 C8 126.829 1.91 +G "C1'" N9 C4 127.440 1.80 +G C8 N9 C4 105.731 1.50 +G N9 C8 N7 113.507 1.50 +G N9 C8 H8 123.187 1.50 +G N7 C8 H8 123.307 1.50 +G C8 N7 C5 104.778 1.50 +G N7 C5 C6 130.030 1.50 +G N7 C5 C4 110.574 1.50 +G C6 C5 C4 119.397 1.50 +G C5 C6 O6 128.244 1.50 +G C5 C6 N1 111.367 1.50 +G O6 C6 N1 120.389 1.50 +G C6 N1 C2 125.351 1.50 +G C6 N1 H1 116.978 2.44 +G C2 N1 H1 117.677 2.71 +G N1 C2 N2 116.576 1.50 +G N1 C2 N3 123.602 1.50 +G N2 C2 N3 119.821 1.50 +G C2 N2 H21 119.868 1.50 +G C2 N2 H22 119.868 1.50 +G H21 N2 H22 120.263 1.96 +G C2 N3 C4 112.066 1.50 +G N9 C4 C5 105.411 1.50 +G N9 C4 N3 126.378 1.50 +G C5 C4 N3 128.211 1.50 +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +G C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +G C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +G C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +G C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +G C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +G C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +G C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +G C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +G C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +G C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +G C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +G C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +G alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +G beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +G epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +G gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +G sp3_sp3_52 "C3'" "C2'" "O2'" "HO2'" 180.000 10.00 3 +G const_18 N7 C8 N9 "C1'" 180.000 10.0 2 +G const_30 C5 C4 N9 "C1'" 180.000 10.0 2 +G const_21 N9 C8 N7 C5 0.000 10.0 2 +G const_24 C6 C5 N7 C8 180.000 10.0 2 +G const_sp2_sp2_4 N7 C5 C6 O6 0.000 5.0 2 +G const_25 N9 C4 C5 N7 0.000 10.0 2 +G const_sp2_sp2_7 O6 C6 N1 C2 180.000 5.0 2 +G const_11 N2 C2 N1 C6 180.000 10.0 2 +G sp2_sp2_1 N1 C2 N2 H21 180.000 5.0 2 +G const_14 N2 C2 N3 C4 180.000 10.0 2 +G const_16 N9 C4 N3 C2 180.000 10.0 2 +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +G chir_1 P "O5'" OP3 OP2 both +G chir_2 "C4'" "O4'" "C3'" "C5'" negative +G chir_3 "C3'" "O3'" "C4'" "C2'" positive +G chir_4 "C2'" "O2'" "C1'" "C3'" negative +G chir_5 "C1'" "O4'" N9 "C2'" negative +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +G plan-1 "C1'" 0.020 +G plan-1 C2 0.020 +G plan-1 C4 0.020 +G plan-1 C5 0.020 +G plan-1 C6 0.020 +G plan-1 C8 0.020 +G plan-1 H1 0.020 +G plan-1 H8 0.020 +G plan-1 N1 0.020 +G plan-1 N2 0.020 +G plan-1 N3 0.020 +G plan-1 N7 0.020 +G plan-1 N9 0.020 +G plan-1 O6 0.020 +G plan-2 C2 0.020 +G plan-2 H21 0.020 +G plan-2 H22 0.020 +G plan-2 N2 0.020 +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +G SMILES ACDLabs 10.04 O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3O)COP(=O)(O)O +G SMILES_CANONICAL CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O +G SMILES CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O +G SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N +G SMILES "OpenEye OEToolkits" 1.5.0 c1nc2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)N +G InChI InChI 1.03 InChI=1S/C10H14N5O8P/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(23-9)1-22-24(19,20)21/h2-3,5-6,9,16-17H,1H2,(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1 +G InChIKey InChI 1.03 RQFCJASXJCIDSX-UUOKFMHZSA-N +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +G acedrg 243 "dictionary generator" +G acedrg_database 11 "data source" +G rdkit 2017.03.2 "Chemoinformatics tool" +G refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/GDP.cif b/image_analysis/structure_refinement/monomers/GDP.cif new file mode 100644 index 000000000..833d710c0 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/GDP.cif @@ -0,0 +1,299 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +GDP GDP "GUANOSINE-5'-DIPHOSPHATE" NON-POLYMER 40 28 . + +data_comp_GDP +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +GDP PB P P 0 13.504 16.639 28.649 +GDP O1B O O 0 13.923 17.830 29.476 +GDP O2B O OP -1 14.420 15.453 28.828 +GDP O3B O OP -1 12.049 16.284 28.833 +GDP O3A O O2 0 13.659 17.092 27.107 +GDP PA P P 0 12.620 17.691 26.043 +GDP O1A O O 0 11.548 16.681 25.800 +GDP O2A O OP -1 12.214 19.058 26.485 +GDP "O5'" O O2 0 13.547 17.806 24.737 +GDP "C5'" C CH2 0 14.774 18.580 24.803 +GDP "C4'" C CH1 0 15.248 18.905 23.407 +GDP "O4'" O O2 0 15.427 17.678 22.656 +GDP "C3'" C CH1 0 14.302 19.747 22.544 +GDP "O3'" O OH1 0 14.480 21.136 22.797 +GDP "C2'" C CH1 0 14.722 19.349 21.125 +GDP "O2'" O OH1 0 15.810 20.102 20.630 +GDP "C1'" C CH1 0 15.090 17.873 21.298 +GDP N9 N NR5 0 14.017 16.952 20.924 +GDP C8 C CR15 0 13.290 16.120 21.742 +GDP N7 N NRD5 0 12.395 15.408 21.100 +GDP C5 C CR56 0 12.541 15.792 19.774 +GDP C6 C CR6 0 11.843 15.360 18.614 +GDP O6 O O 0 10.930 14.526 18.539 +GDP N1 N NR6 0 12.305 16.006 17.460 +GDP C2 C CR6 0 13.311 16.946 17.429 +GDP N2 N NH2 0 13.623 17.460 16.231 +GDP N3 N NRD6 0 13.969 17.354 18.519 +GDP C4 C CR56 0 13.538 16.739 19.651 +GDP "H5'" H H 0 15.470 18.062 25.277 +GDP "H5''" H H 0 14.616 19.420 25.301 +GDP "H4'" H H 0 16.113 19.362 23.477 +GDP "H3'" H H 0 13.359 19.490 22.706 +GDP "HO3'" H H 0 14.000 21.576 22.253 +GDP "H2'" H H 0 13.951 19.442 20.505 +GDP "HO2'" H H 0 16.487 19.998 21.132 +GDP "H1'" H H 0 15.878 17.683 20.741 +GDP H8 H H 0 13.418 16.065 22.673 +GDP HN1 H H 0 11.910 15.784 16.684 +GDP HN21 H H 0 13.778 18.320 16.152 +GDP HN22 H H 0 13.671 16.936 15.530 + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +GDP PB O1B DOUBLE n 1.509 0.0200 1.509 0.0200 +GDP PB O2B SINGLE n 1.509 0.0200 1.509 0.0200 +GDP PB O3B SINGLE n 1.509 0.0200 1.509 0.0200 +GDP PB O3A SINGLE n 1.614 0.0178 1.614 0.0178 +GDP O3A PA SINGLE n 1.604 0.0133 1.604 0.0133 +GDP PA O1A DOUBLE n 1.493 0.0122 1.493 0.0122 +GDP PA O2A SINGLE n 1.493 0.0122 1.493 0.0122 +GDP PA "O5'" SINGLE n 1.604 0.0133 1.604 0.0133 +GDP "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +GDP "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +GDP "C4'" "O4'" SINGLE n 1.451 0.0100 1.451 0.0100 +GDP "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 +GDP "O4'" "C1'" SINGLE n 1.409 0.0100 1.409 0.0100 +GDP "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +GDP "C3'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100 +GDP "C2'" "O2'" SINGLE n 1.411 0.0100 1.411 0.0100 +GDP "C2'" "C1'" SINGLE n 1.525 0.0100 1.525 0.0100 +GDP "C1'" N9 SINGLE n 1.458 0.0100 1.458 0.0100 +GDP N9 C8 SINGLE y 1.372 0.0100 1.372 0.0100 +GDP N9 C4 SINGLE y 1.375 0.0100 1.375 0.0100 +GDP C8 N7 DOUBLE y 1.312 0.0100 1.312 0.0100 +GDP N7 C5 SINGLE y 1.390 0.0100 1.390 0.0100 +GDP C5 C6 SINGLE y 1.417 0.0103 1.417 0.0103 +GDP C5 C4 DOUBLE y 1.377 0.0100 1.377 0.0100 +GDP C6 O6 DOUBLE n 1.239 0.0100 1.239 0.0100 +GDP C6 N1 SINGLE y 1.396 0.0107 1.396 0.0107 +GDP N1 C2 SINGLE y 1.374 0.0100 1.374 0.0100 +GDP C2 N2 SINGLE n 1.340 0.0101 1.340 0.0101 +GDP C2 N3 DOUBLE y 1.333 0.0104 1.333 0.0104 +GDP N3 C4 SINGLE y 1.355 0.0100 1.355 0.0100 +GDP "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +GDP "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 +GDP "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 +GDP "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +GDP "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +GDP "C2'" "H2'" SINGLE n 1.089 0.0100 0.994 0.0200 +GDP "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 +GDP "C1'" "H1'" SINGLE n 1.089 0.0100 0.984 0.0200 +GDP C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170 +GDP N1 HN1 SINGLE n 1.016 0.0100 0.897 0.0200 +GDP N2 HN21 SINGLE n 1.016 0.0100 0.877 0.0200 +GDP N2 HN22 SINGLE n 1.016 0.0100 0.877 0.0200 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +GDP O1B PB O2B 112.716 1.50 +GDP O1B PB O3B 112.716 1.50 +GDP O1B PB O3A 105.965 2.38 +GDP O2B PB O3B 112.716 1.50 +GDP O2B PB O3A 105.965 2.38 +GDP O3B PB O3A 105.965 2.38 +GDP PB O3A PA 132.584 3.00 +GDP O3A PA O1A 108.816 2.14 +GDP O3A PA O2A 108.816 2.14 +GDP O3A PA "O5'" 101.065 1.97 +GDP O1A PA O2A 118.411 2.35 +GDP O1A PA "O5'" 109.410 1.50 +GDP O2A PA "O5'" 109.410 1.50 +GDP PA "O5'" "C5'" 118.553 2.41 +GDP "O5'" "C5'" "C4'" 109.342 1.50 +GDP "O5'" "C5'" "H5'" 109.845 1.50 +GDP "O5'" "C5'" "H5''" 109.845 1.50 +GDP "C4'" "C5'" "H5'" 109.624 1.50 +GDP "C4'" "C5'" "H5''" 109.624 1.50 +GDP "H5'" "C5'" "H5''" 108.472 1.50 +GDP "C5'" "C4'" "O4'" 109.123 1.50 +GDP "C5'" "C4'" "C3'" 116.008 1.52 +GDP "C5'" "C4'" "H4'" 108.268 1.50 +GDP "O4'" "C4'" "C3'" 105.388 1.50 +GDP "O4'" "C4'" "H4'" 108.947 1.50 +GDP "C3'" "C4'" "H4'" 109.363 1.86 +GDP "C4'" "O4'" "C1'" 109.903 1.50 +GDP "C4'" "C3'" "O3'" 111.281 2.46 +GDP "C4'" "C3'" "C2'" 102.602 1.50 +GDP "C4'" "C3'" "H3'" 110.452 2.54 +GDP "O3'" "C3'" "C2'" 111.581 2.83 +GDP "O3'" "C3'" "H3'" 110.380 1.67 +GDP "C2'" "C3'" "H3'" 110.504 1.75 +GDP "C3'" "O3'" "HO3'" 108.744 3.00 +GDP "C3'" "C2'" "O2'" 112.782 2.45 +GDP "C3'" "C2'" "C1'" 101.239 1.50 +GDP "C3'" "C2'" "H2'" 110.596 1.51 +GDP "O2'" "C2'" "C1'" 111.715 2.69 +GDP "O2'" "C2'" "H2'" 110.448 1.97 +GDP "C1'" "C2'" "H2'" 110.636 1.70 +GDP "C2'" "O2'" "HO2'" 109.103 2.13 +GDP "O4'" "C1'" "C2'" 106.047 1.50 +GDP "O4'" "C1'" N9 108.477 1.50 +GDP "O4'" "C1'" "H1'" 109.807 1.50 +GDP "C2'" "C1'" N9 113.824 1.50 +GDP "C2'" "C1'" "H1'" 109.015 1.50 +GDP N9 "C1'" "H1'" 109.561 1.50 +GDP "C1'" N9 C8 126.829 1.91 +GDP "C1'" N9 C4 127.440 1.80 +GDP C8 N9 C4 105.731 1.50 +GDP N9 C8 N7 113.507 1.50 +GDP N9 C8 H8 123.187 1.50 +GDP N7 C8 H8 123.307 1.50 +GDP C8 N7 C5 104.778 1.50 +GDP N7 C5 C6 130.030 1.50 +GDP N7 C5 C4 110.574 1.50 +GDP C6 C5 C4 119.397 1.50 +GDP C5 C6 O6 128.244 1.50 +GDP C5 C6 N1 111.367 1.50 +GDP O6 C6 N1 120.389 1.50 +GDP C6 N1 C2 125.351 1.50 +GDP C6 N1 HN1 116.978 2.44 +GDP C2 N1 HN1 117.677 2.71 +GDP N1 C2 N2 116.576 1.50 +GDP N1 C2 N3 123.602 1.50 +GDP N2 C2 N3 119.821 1.50 +GDP C2 N2 HN21 119.868 1.50 +GDP C2 N2 HN22 119.868 1.50 +GDP HN21 N2 HN22 120.263 1.96 +GDP C2 N3 C4 112.066 1.50 +GDP N9 C4 C5 105.411 1.50 +GDP N9 C4 N3 126.378 1.50 +GDP C5 C4 N3 128.211 1.50 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +GDP C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +GDP C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +GDP C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +GDP C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +GDP C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +GDP C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +GDP C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +GDP C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +GDP C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +GDP C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +GDP C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +GDP C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +GDP epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +GDP gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +GDP sp3_sp3_52 "C3'" "C2'" "O2'" "HO2'" 180.000 10.00 3 +GDP sp3_sp3_27 PA O3A PB O1B 60.000 10.0 3 +GDP const_18 N7 C8 N9 "C1'" 180.000 10.0 2 +GDP const_30 C5 C4 N9 "C1'" 180.000 10.0 2 +GDP const_21 N9 C8 N7 C5 0.000 10.0 2 +GDP const_24 C6 C5 N7 C8 180.000 10.0 2 +GDP const_sp2_sp2_4 N7 C5 C6 O6 0.000 5.0 2 +GDP const_25 N9 C4 C5 N7 0.000 10.0 2 +GDP const_sp2_sp2_7 O6 C6 N1 C2 180.000 5.0 2 +GDP const_11 N2 C2 N1 C6 180.000 10.0 2 +GDP sp2_sp2_1 N1 C2 N2 HN21 180.000 5.0 2 +GDP const_14 N2 C2 N3 C4 180.000 10.0 2 +GDP const_16 N9 C4 N3 C2 180.000 10.0 2 +GDP sp3_sp3_30 PB O3A PA O1A 60.000 10.0 3 +GDP sp3_sp3_31 "C5'" "O5'" PA O3A 180.000 10.0 3 +GDP sp3_sp3_34 "C4'" "C5'" "O5'" PA 180.000 10.0 3 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +GDP chir_1 PB O3A O2B O3B both +GDP chir_2 PA O3A "O5'" O2A both +GDP chir_3 "C4'" "O4'" "C3'" "C5'" negative +GDP chir_4 "C3'" "O3'" "C4'" "C2'" positive +GDP chir_5 "C2'" "O2'" "C1'" "C3'" negative +GDP chir_6 "C1'" "O4'" N9 "C2'" negative + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +GDP plan-1 "C1'" 0.020 +GDP plan-1 C2 0.020 +GDP plan-1 C4 0.020 +GDP plan-1 C5 0.020 +GDP plan-1 C6 0.020 +GDP plan-1 C8 0.020 +GDP plan-1 H8 0.020 +GDP plan-1 HN1 0.020 +GDP plan-1 N1 0.020 +GDP plan-1 N2 0.020 +GDP plan-1 N3 0.020 +GDP plan-1 N7 0.020 +GDP plan-1 N9 0.020 +GDP plan-1 O6 0.020 +GDP plan-2 C2 0.020 +GDP plan-2 HN21 0.020 +GDP plan-2 HN22 0.020 +GDP plan-2 N2 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +GDP SMILES ACDLabs 12.01 O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O +GDP InChI InChI 1.03 InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1 +GDP InChIKey InChI 1.03 QGWNDRXFNXRZMB-UUOKFMHZSA-N +GDP SMILES_CANONICAL CACTVS 3.385 NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O +GDP SMILES CACTVS 3.385 NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O +GDP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N +GDP SMILES "OpenEye OEToolkits" 1.7.6 c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +GDP acedrg 243 "dictionary generator" +GDP acedrg_database 11 "data source" +GDP rdkit 2017.03.2 "Chemoinformatics tool" +GDP refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/GLN.cif b/image_analysis/structure_refinement/monomers/GLN.cif new file mode 100644 index 000000000..ab85e9d2d --- /dev/null +++ b/image_analysis/structure_refinement/monomers/GLN.cif @@ -0,0 +1,233 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +GLN GLN GLUTAMINE peptide 20 10 . + +data_comp_GLN +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +GLN N N NT3 1 -13.189 34.859 120.921 +GLN CA C CH1 0 -12.155 35.335 119.962 +GLN C C C 0 -10.823 35.547 120.705 +GLN O O O 0 -9.774 35.259 120.087 +GLN CB C CH2 0 -12.610 36.599 119.226 +GLN CG C CH2 0 -12.991 37.771 120.127 +GLN CD C C 0 -13.453 38.985 119.351 +GLN OE1 O O 0 -14.437 38.935 118.605 +GLN NE2 N NH2 0 -12.747 40.094 119.519 +GLN OXT O OC -1 -10.882 35.991 121.873 +GLN H H H 0 -14.005 34.886 120.536 +GLN H2 H H 0 -13.202 35.368 121.666 +GLN H3 H H 0 -13.012 34.007 121.158 +GLN HA H H 0 -12.019 34.624 119.285 +GLN HB3 H H 0 -13.381 36.370 118.666 +GLN HB2 H H 0 -11.887 36.885 118.629 +GLN HG3 H H 0 -12.221 38.023 120.680 +GLN HG2 H H 0 -13.713 37.495 120.731 +GLN HE21 H H 0 -11.862 40.066 119.472 +GLN HE22 H H 0 -13.160 40.862 119.679 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +GLN N n/a CA START +GLN H N . . +GLN H2 N . . +GLN H3 N . . +GLN CA N C . +GLN HA CA . . +GLN CB CA CG . +GLN HB3 CB . . +GLN HB2 CB . . +GLN CG CB CD . +GLN HG3 CG . . +GLN HG2 CG . . +GLN CD CG NE2 . +GLN OE1 CD . . +GLN NE2 CD HE22 . +GLN HE21 NE2 . . +GLN HE22 NE2 . . +GLN C CA . END +GLN O C . . +GLN OXT C . . + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +GLN N N(CCCH)(H)3 +GLN CA C(CCHH)(NH3)(COO)(H) +GLN C C(CCHN)(O)2 +GLN O O(CCO) +GLN CB C(CCHH)(CCHN)(H)2 +GLN CG C(CCHH)(CNO)(H)2 +GLN CD C(CCHH)(NHH)(O) +GLN OE1 O(CCN) +GLN NE2 N(CCO)(H)2 +GLN OXT O(CCO) +GLN H H(NCHH) +GLN H2 H(NCHH) +GLN H3 H(NCHH) +GLN HA H(CCCN) +GLN HB3 H(CCCH) +GLN HB2 H(CCCH) +GLN HG3 H(CCCH) +GLN HG2 H(CCCH) +GLN HE21 H(NCH) +GLN HE22 H(NCH) + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +GLN N CA SINGLE n 1.487 0.0100 1.487 0.0100 +GLN CA C SINGLE n 1.538 0.0113 1.538 0.0113 +GLN CA CB SINGLE n 1.529 0.0100 1.529 0.0100 +GLN C O DOUBLE n 1.251 0.0183 1.251 0.0183 +GLN C OXT SINGLE n 1.251 0.0183 1.251 0.0183 +GLN CB CG SINGLE n 1.525 0.0100 1.525 0.0100 +GLN CG CD SINGLE n 1.513 0.0100 1.513 0.0100 +GLN CD OE1 DOUBLE n 1.236 0.0100 1.236 0.0100 +GLN CD NE2 SINGLE n 1.325 0.0100 1.325 0.0100 +GLN N H SINGLE n 1.018 0.0520 0.902 0.0102 +GLN N H2 SINGLE n 1.018 0.0520 0.902 0.0102 +GLN N H3 SINGLE n 1.018 0.0520 0.902 0.0102 +GLN CA HA SINGLE n 1.092 0.0100 0.991 0.0200 +GLN CB HB3 SINGLE n 1.092 0.0100 0.980 0.0168 +GLN CB HB2 SINGLE n 1.092 0.0100 0.980 0.0168 +GLN CG HG3 SINGLE n 1.092 0.0100 0.981 0.0172 +GLN CG HG2 SINGLE n 1.092 0.0100 0.981 0.0172 +GLN NE2 HE21 SINGLE n 1.013 0.0120 0.887 0.0200 +GLN NE2 HE22 SINGLE n 1.013 0.0120 0.887 0.0200 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +GLN CA N H 109.990 3.00 +GLN CA N H2 109.990 3.00 +GLN CA N H3 109.990 3.00 +GLN H N H2 109.032 3.00 +GLN H N H3 109.032 3.00 +GLN H2 N H3 109.032 3.00 +GLN N CA C 109.258 1.50 +GLN N CA CB 110.440 2.46 +GLN N CA HA 108.387 1.58 +GLN C CA CB 111.059 3.00 +GLN C CA HA 108.774 1.79 +GLN CB CA HA 109.080 2.33 +GLN CA C O 117.148 1.60 +GLN CA C OXT 117.148 1.60 +GLN O C OXT 125.704 1.50 +GLN CA CB CG 113.998 1.50 +GLN CA CB HB3 108.677 1.74 +GLN CA CB HB2 108.677 1.74 +GLN CG CB HB3 108.907 1.50 +GLN CG CB HB2 108.907 1.50 +GLN HB3 CB HB2 107.655 1.50 +GLN CB CG CD 113.265 1.50 +GLN CB CG HG3 109.355 1.50 +GLN CB CG HG2 109.355 1.50 +GLN CD CG HG3 108.958 1.89 +GLN CD CG HG2 108.958 1.89 +GLN HG3 CG HG2 107.827 1.56 +GLN CG CD OE1 121.487 1.50 +GLN CG CD NE2 116.074 1.76 +GLN OE1 CD NE2 122.439 1.50 +GLN CD NE2 HE21 119.917 2.87 +GLN CD NE2 HE22 119.917 2.87 +GLN HE21 NE2 HE22 120.165 3.00 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +GLN chi1 N CA CB CG -60.000 10.0 3 +GLN chi2 CA CB CG CD 180.000 10.0 3 +GLN chi3 CB CG CD NE2 180.000 10.0 6 +GLN hh1 CG CD NE2 HE22 180.000 5.0 2 +GLN sp3_sp3_1 C CA N H 180.000 10.0 3 +GLN sp2_sp3_1 O C CA N 0.000 10.0 6 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +GLN chir_1 CA N C CB positive + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +GLN plan-1 C 0.020 +GLN plan-1 CA 0.020 +GLN plan-1 O 0.020 +GLN plan-1 OXT 0.020 +GLN plan-2 CD 0.020 +GLN plan-2 CG 0.020 +GLN plan-2 NE2 0.020 +GLN plan-2 OE1 0.020 +GLN plan-3 CD 0.020 +GLN plan-3 HE21 0.020 +GLN plan-3 HE22 0.020 +GLN plan-3 NE2 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +GLN SMILES ACDLabs 10.04 O=C(N)CCC(N)C(=O)O +GLN SMILES_CANONICAL CACTVS 3.341 N[C@@H](CCC(N)=O)C(O)=O +GLN SMILES CACTVS 3.341 N[CH](CCC(N)=O)C(O)=O +GLN SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(CC(=O)N)[C@@H](C(=O)O)N +GLN SMILES "OpenEye OEToolkits" 1.5.0 C(CC(=O)N)C(C(=O)O)N +GLN InChI InChI 1.03 InChI=1S/C5H10N2O3/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H2,7,8)(H,9,10)/t3-/m0/s1 +GLN InChIKey InChI 1.03 ZDXPYRJPNDTMRX-VKHMYHEASA-N + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +GLN acedrg 278 "dictionary generator" +GLN acedrg_database 12 "data source" +GLN rdkit 2019.09.1 "Chemoinformatics tool" +GLN refmac5 5.8.0419 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/GLU.cif b/image_analysis/structure_refinement/monomers/GLU.cif new file mode 100644 index 000000000..1eefa693b --- /dev/null +++ b/image_analysis/structure_refinement/monomers/GLU.cif @@ -0,0 +1,217 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +GLU GLU "GLUTAMIC ACID" peptide 18 10 . + +data_comp_GLU +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +GLU N N NT3 1 88.319 -7.751 -10.089 +GLU CA C CH1 0 87.677 -7.162 -11.296 +GLU C C C 0 88.359 -5.826 -11.640 +GLU O O O 0 88.389 -4.954 -10.744 +GLU CB C CH2 0 86.177 -6.950 -11.080 +GLU CG C CH2 0 85.390 -8.247 -10.908 +GLU CD C C 0 83.891 -8.048 -10.773 +GLU OE1 O O 0 83.281 -7.495 -11.711 +GLU OE2 O OC -1 83.334 -8.447 -9.728 +GLU OXT O OC -1 88.836 -5.708 -12.790 +GLU H H H 0 88.066 -7.298 -9.352 +GLU H2 H H 0 89.218 -7.717 -10.158 +GLU H3 H H 0 88.077 -8.615 -9.999 +GLU HA H H 0 87.806 -7.788 -12.054 +GLU HB3 H H 0 85.814 -6.460 -11.847 +GLU HB2 H H 0 86.049 -6.394 -10.284 +GLU HG3 H H 0 85.714 -8.714 -10.110 +GLU HG2 H H 0 85.559 -8.827 -11.681 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +GLU N n/a CA START +GLU H N . . +GLU H2 N . . +GLU H3 N . . +GLU CA N C . +GLU HA CA . . +GLU CB CA CG . +GLU HB3 CB . . +GLU HB2 CB . . +GLU CG CB CD . +GLU HG3 CG . . +GLU HG2 CG . . +GLU CD CG OE2 . +GLU OE1 CD . . +GLU OE2 CD . . +GLU C CA . END +GLU O C . . +GLU OXT C . . + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +GLU N N(CCCH)(H)3 +GLU CA C(CCHH)(NH3)(COO)(H) +GLU C C(CCHN)(O)2 +GLU O O(CCO) +GLU CB C(CCHH)(CCHN)(H)2 +GLU CG C(CCHH)(COO)(H)2 +GLU CD C(CCHH)(O)2 +GLU OE1 O(CCO) +GLU OE2 O(CCO) +GLU OXT O(CCO) +GLU H H(NCHH) +GLU H2 H(NCHH) +GLU H3 H(NCHH) +GLU HA H(CCCN) +GLU HB3 H(CCCH) +GLU HB2 H(CCCH) +GLU HG3 H(CCCH) +GLU HG2 H(CCCH) + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +GLU N CA SINGLE n 1.487 0.0100 1.487 0.0100 +GLU CA C SINGLE n 1.538 0.0113 1.538 0.0113 +GLU CA CB SINGLE n 1.529 0.0100 1.529 0.0100 +GLU C O DOUBLE n 1.251 0.0183 1.251 0.0183 +GLU C OXT SINGLE n 1.251 0.0183 1.251 0.0183 +GLU CB CG SINGLE n 1.526 0.0100 1.526 0.0100 +GLU CG CD SINGLE n 1.518 0.0135 1.518 0.0135 +GLU CD OE1 DOUBLE n 1.249 0.0161 1.249 0.0161 +GLU CD OE2 SINGLE n 1.249 0.0161 1.249 0.0161 +GLU N H SINGLE n 1.018 0.0520 0.902 0.0102 +GLU N H2 SINGLE n 1.018 0.0520 0.902 0.0102 +GLU N H3 SINGLE n 1.018 0.0520 0.902 0.0102 +GLU CA HA SINGLE n 1.092 0.0100 0.991 0.0200 +GLU CB HB3 SINGLE n 1.092 0.0100 0.980 0.0168 +GLU CB HB2 SINGLE n 1.092 0.0100 0.980 0.0168 +GLU CG HG3 SINGLE n 1.092 0.0100 0.981 0.0172 +GLU CG HG2 SINGLE n 1.092 0.0100 0.981 0.0172 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +GLU CA N H 109.990 3.00 +GLU CA N H2 109.990 3.00 +GLU CA N H3 109.990 3.00 +GLU H N H2 109.032 3.00 +GLU H N H3 109.032 3.00 +GLU H2 N H3 109.032 3.00 +GLU N CA C 109.258 1.50 +GLU N CA CB 110.440 2.46 +GLU N CA HA 108.387 1.58 +GLU C CA CB 111.059 3.00 +GLU C CA HA 108.774 1.79 +GLU CB CA HA 109.080 2.33 +GLU CA C O 117.148 1.60 +GLU CA C OXT 117.148 1.60 +GLU O C OXT 125.704 1.50 +GLU CA CB CG 113.294 1.61 +GLU CA CB HB3 108.677 1.74 +GLU CA CB HB2 108.677 1.74 +GLU CG CB HB3 108.696 2.80 +GLU CG CB HB2 108.696 2.80 +GLU HB3 CB HB2 107.655 1.50 +GLU CB CG CD 114.140 3.00 +GLU CB CG HG3 108.968 1.50 +GLU CB CG HG2 108.968 1.50 +GLU CD CG HG3 108.472 1.50 +GLU CD CG HG2 108.472 1.50 +GLU HG3 CG HG2 107.541 1.92 +GLU CG CD OE1 118.251 3.00 +GLU CG CD OE2 118.251 3.00 +GLU OE1 CD OE2 123.498 1.82 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +GLU chi1 N CA CB CG -60.000 10.0 3 +GLU chi2 CA CB CG CD 180.000 10.0 3 +GLU chi3 CB CG CD OE1 180.000 10.0 6 +GLU sp3_sp3_1 C CA N H 180.000 10.0 3 +GLU sp2_sp3_1 O C CA N 0.000 10.0 6 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +GLU chir_1 CA N C CB positive + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +GLU plan-1 C 0.020 +GLU plan-1 CA 0.020 +GLU plan-1 O 0.020 +GLU plan-1 OXT 0.020 +GLU plan-2 CD 0.020 +GLU plan-2 CG 0.020 +GLU plan-2 OE1 0.020 +GLU plan-2 OE2 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +GLU SMILES ACDLabs 12.01 O=C(O)C(N)CCC(=O)O +GLU SMILES_CANONICAL CACTVS 3.370 N[C@@H](CCC(O)=O)C(O)=O +GLU SMILES CACTVS 3.370 N[CH](CCC(O)=O)C(O)=O +GLU SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 C(CC(=O)O)[C@@H](C(=O)O)N +GLU SMILES "OpenEye OEToolkits" 1.7.0 C(CC(=O)O)C(C(=O)O)N +GLU InChI InChI 1.03 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/t3-/m0/s1 +GLU InChIKey InChI 1.03 WHUUTDBJXJRKMK-VKHMYHEASA-N + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +GLU acedrg 278 "dictionary generator" +GLU acedrg_database 12 "data source" +GLU rdkit 2019.09.1 "Chemoinformatics tool" +GLU refmac5 5.8.0419 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/GLY.cif b/image_analysis/structure_refinement/monomers/GLY.cif new file mode 100644 index 000000000..1eab291b6 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/GLY.cif @@ -0,0 +1,153 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +GLY GLY GLYCINE peptide 10 5 . + +data_comp_GLY +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +GLY N N NT3 1 25.320 35.545 47.014 +GLY CA C CH2 0 25.532 37.001 46.897 +GLY C C C 0 26.039 37.376 45.517 +GLY O O O 0 27.114 36.860 45.146 +GLY OXT O OC -1 25.343 38.172 44.853 +GLY H H H 0 26.098 35.105 46.869 +GLY H2 H H 0 24.710 35.270 46.405 +GLY H3 H H 0 25.019 35.342 47.843 +GLY HA3 H H 0 26.185 37.288 47.578 +GLY HA2 H H 0 24.682 37.467 47.075 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +GLY N n/a CA START +GLY H N . . +GLY H2 N . . +GLY H3 N . . +GLY CA N C . +GLY HA3 CA . . +GLY HA2 CA . . +GLY C CA . END +GLY O C . . +GLY OXT C . . + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +GLY N N(CCHH)(H)3 +GLY CA C(NH3)(COO)(H)2 +GLY C C(CHHN)(O)2 +GLY O O(CCO) +GLY OXT O(CCO) +GLY H H(NCHH) +GLY H2 H(NCHH) +GLY H3 H(NCHH) +GLY HA3 H(CCHN) +GLY HA2 H(CCHN) + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +GLY N CA SINGLE n 1.476 0.0106 1.476 0.0106 +GLY CA C SINGLE n 1.517 0.0121 1.517 0.0121 +GLY C O DOUBLE n 1.249 0.0161 1.249 0.0161 +GLY C OXT SINGLE n 1.249 0.0161 1.249 0.0161 +GLY N H SINGLE n 1.018 0.0520 0.905 0.0200 +GLY N H2 SINGLE n 1.018 0.0520 0.905 0.0200 +GLY N H3 SINGLE n 1.018 0.0520 0.905 0.0200 +GLY CA HA3 SINGLE n 1.092 0.0100 0.986 0.0200 +GLY CA HA2 SINGLE n 1.092 0.0100 0.986 0.0200 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +GLY CA N H 110.151 2.94 +GLY CA N H2 110.151 2.94 +GLY CA N H3 110.151 2.94 +GLY H N H2 109.089 3.00 +GLY H N H3 109.089 3.00 +GLY H2 N H3 109.089 3.00 +GLY N CA C 111.292 1.50 +GLY N CA HA3 109.172 1.50 +GLY N CA HA2 109.172 1.50 +GLY C CA HA3 109.620 1.50 +GLY C CA HA2 109.620 1.50 +GLY HA3 CA HA2 108.054 1.50 +GLY CA C O 117.080 1.50 +GLY CA C OXT 117.080 1.50 +GLY O C OXT 125.839 1.50 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +GLY sp3_sp3_1 C CA N H 180.000 10.0 3 +GLY sp2_sp3_1 O C CA HA3 0.000 10.0 6 + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +GLY plan-1 C 0.020 +GLY plan-1 CA 0.020 +GLY plan-1 O 0.020 +GLY plan-1 OXT 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +GLY SMILES ACDLabs 10.04 O=C(O)CN +GLY SMILES_CANONICAL CACTVS 3.341 NCC(O)=O +GLY SMILES CACTVS 3.341 NCC(O)=O +GLY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(C(=O)O)N +GLY SMILES "OpenEye OEToolkits" 1.5.0 C(C(=O)O)N +GLY InChI InChI 1.03 InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) +GLY InChIKey InChI 1.03 DHMQDGOQFOQNFH-UHFFFAOYSA-N + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +GLY acedrg 278 "dictionary generator" +GLY acedrg_database 12 "data source" +GLY rdkit 2019.09.1 "Chemoinformatics tool" +GLY refmac5 5.8.0419 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/GMP.cif b/image_analysis/structure_refinement/monomers/GMP.cif new file mode 100644 index 000000000..8c4b2aa55 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/GMP.cif @@ -0,0 +1,256 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +GMP GMP GUANOSINE NON-POLYMER 33 20 . +# +data_comp_GMP +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +GMP "O5'" O OH1 0 31.023 62.348 13.095 +GMP "C5'" C CH2 0 30.880 60.990 13.491 +GMP "C4'" C CH1 0 32.039 60.141 13.016 +GMP "O4'" O O2 0 32.223 60.322 11.591 +GMP "C3'" C CH1 0 33.402 60.499 13.617 +GMP "O3'" O OH1 0 33.583 59.871 14.880 +GMP "C2'" C CH1 0 34.373 59.978 12.551 +GMP "O2'" O OH1 0 34.741 58.628 12.744 +GMP "C1'" C CH1 0 33.583 60.160 11.252 +GMP N9 N NR5 0 33.999 61.321 10.471 +GMP C8 C CR15 0 33.932 62.634 10.866 +GMP N7 N NRD5 0 34.376 63.473 9.962 +GMP C5 C CR56 0 34.763 62.661 8.903 +GMP C6 C CR6 0 35.321 63.006 7.643 +GMP O6 O O 0 35.589 64.136 7.210 +GMP N1 N NR6 0 35.569 61.874 6.857 +GMP C2 C CR6 0 35.310 60.575 7.237 +GMP N2 N NH2 0 35.612 59.614 6.354 +GMP N3 N NRD6 0 34.785 60.248 8.422 +GMP C4 C CR56 0 34.537 61.332 9.203 +GMP "HO5'" H H 0 30.412 62.808 13.461 +GMP "H5'1" H H 0 30.045 60.632 13.121 +GMP "H5'2" H H 0 30.824 60.943 14.469 +GMP "H4'" H H 0 31.840 59.197 13.196 +GMP "H3'" H H 0 33.489 61.482 13.709 +GMP "HO3'" H H 0 34.374 60.022 15.150 +GMP "H2'" H H 0 35.192 60.542 12.533 +GMP "HO2'" H H 0 34.046 58.141 12.763 +GMP "H1'" H H 0 33.686 59.348 10.707 +GMP H8 H H 0 33.598 62.904 11.704 +GMP HN1 H H 0 35.923 62.012 6.043 +GMP HN21 H H 0 35.993 58.873 6.627 +GMP HN22 H H 0 35.427 59.728 5.504 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +GMP "O5'" "C5'" SINGLE n 1.421 0.0131 1.421 0.0131 +GMP "C5'" "C4'" SINGLE n 1.511 0.0177 1.511 0.0177 +GMP "C4'" "O4'" SINGLE n 1.451 0.0100 1.451 0.0100 +GMP "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 +GMP "O4'" "C1'" SINGLE n 1.409 0.0100 1.409 0.0100 +GMP "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +GMP "C3'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100 +GMP "C2'" "O2'" SINGLE n 1.411 0.0100 1.411 0.0100 +GMP "C2'" "C1'" SINGLE n 1.525 0.0100 1.525 0.0100 +GMP "C1'" N9 SINGLE n 1.458 0.0100 1.458 0.0100 +GMP N9 C8 SINGLE y 1.372 0.0100 1.372 0.0100 +GMP N9 C4 SINGLE y 1.375 0.0100 1.375 0.0100 +GMP C8 N7 DOUBLE y 1.312 0.0100 1.312 0.0100 +GMP N7 C5 SINGLE y 1.390 0.0100 1.390 0.0100 +GMP C5 C6 SINGLE y 1.417 0.0103 1.417 0.0103 +GMP C5 C4 DOUBLE y 1.377 0.0100 1.377 0.0100 +GMP C6 O6 DOUBLE n 1.239 0.0100 1.239 0.0100 +GMP C6 N1 SINGLE y 1.396 0.0107 1.396 0.0107 +GMP N1 C2 SINGLE y 1.374 0.0100 1.374 0.0100 +GMP C2 N2 SINGLE n 1.340 0.0101 1.340 0.0101 +GMP C2 N3 DOUBLE y 1.333 0.0104 1.333 0.0104 +GMP N3 C4 SINGLE y 1.355 0.0100 1.355 0.0100 +GMP "O5'" "HO5'" SINGLE n 0.970 0.0120 0.848 0.0200 +GMP "C5'" "H5'1" SINGLE n 1.089 0.0100 0.981 0.0200 +GMP "C5'" "H5'2" SINGLE n 1.089 0.0100 0.981 0.0200 +GMP "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 +GMP "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +GMP "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +GMP "C2'" "H2'" SINGLE n 1.089 0.0100 0.994 0.0200 +GMP "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 +GMP "C1'" "H1'" SINGLE n 1.089 0.0100 0.984 0.0200 +GMP C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170 +GMP N1 HN1 SINGLE n 1.016 0.0100 0.897 0.0200 +GMP N2 HN21 SINGLE n 1.016 0.0100 0.877 0.0200 +GMP N2 HN22 SINGLE n 1.016 0.0100 0.877 0.0200 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +GMP "C5'" "O5'" "HO5'" 109.007 3.00 +GMP "O5'" "C5'" "C4'" 111.279 1.98 +GMP "O5'" "C5'" "H5'1" 109.280 1.50 +GMP "O5'" "C5'" "H5'2" 109.280 1.50 +GMP "C4'" "C5'" "H5'1" 109.326 2.00 +GMP "C4'" "C5'" "H5'2" 109.326 2.00 +GMP "H5'1" "C5'" "H5'2" 108.248 2.26 +GMP "C5'" "C4'" "O4'" 109.170 1.50 +GMP "C5'" "C4'" "C3'" 114.598 1.97 +GMP "C5'" "C4'" "H4'" 109.037 1.87 +GMP "O4'" "C4'" "C3'" 105.388 1.50 +GMP "O4'" "C4'" "H4'" 108.947 1.50 +GMP "C3'" "C4'" "H4'" 109.363 1.86 +GMP "C4'" "O4'" "C1'" 109.903 1.50 +GMP "C4'" "C3'" "O3'" 111.281 2.46 +GMP "C4'" "C3'" "C2'" 102.602 1.50 +GMP "C4'" "C3'" "H3'" 110.452 2.54 +GMP "O3'" "C3'" "C2'" 111.581 2.83 +GMP "O3'" "C3'" "H3'" 110.380 1.67 +GMP "C2'" "C3'" "H3'" 110.504 1.75 +GMP "C3'" "O3'" "HO3'" 108.744 3.00 +GMP "C3'" "C2'" "O2'" 112.782 2.45 +GMP "C3'" "C2'" "C1'" 101.239 1.50 +GMP "C3'" "C2'" "H2'" 110.596 1.51 +GMP "O2'" "C2'" "C1'" 111.715 2.69 +GMP "O2'" "C2'" "H2'" 110.448 1.97 +GMP "C1'" "C2'" "H2'" 110.636 1.70 +GMP "C2'" "O2'" "HO2'" 109.103 2.13 +GMP "O4'" "C1'" "C2'" 106.047 1.50 +GMP "O4'" "C1'" N9 108.477 1.50 +GMP "O4'" "C1'" "H1'" 109.807 1.50 +GMP "C2'" "C1'" N9 113.824 1.50 +GMP "C2'" "C1'" "H1'" 109.015 1.50 +GMP N9 "C1'" "H1'" 109.561 1.50 +GMP "C1'" N9 C8 126.829 1.91 +GMP "C1'" N9 C4 127.440 1.80 +GMP C8 N9 C4 105.731 1.50 +GMP N9 C8 N7 113.507 1.50 +GMP N9 C8 H8 123.187 1.50 +GMP N7 C8 H8 123.307 1.50 +GMP C8 N7 C5 104.778 1.50 +GMP N7 C5 C6 130.030 1.50 +GMP N7 C5 C4 110.574 1.50 +GMP C6 C5 C4 119.397 1.50 +GMP C5 C6 O6 128.244 1.50 +GMP C5 C6 N1 111.367 1.50 +GMP O6 C6 N1 120.389 1.50 +GMP C6 N1 C2 125.351 1.50 +GMP C6 N1 HN1 116.978 2.44 +GMP C2 N1 HN1 117.677 2.71 +GMP N1 C2 N2 116.576 1.50 +GMP N1 C2 N3 123.602 1.50 +GMP N2 C2 N3 119.821 1.50 +GMP C2 N2 HN21 119.868 1.50 +GMP C2 N2 HN22 119.868 1.50 +GMP HN21 N2 HN22 120.263 1.96 +GMP C2 N3 C4 112.066 1.50 +GMP N9 C4 C5 105.411 1.50 +GMP N9 C4 N3 126.378 1.50 +GMP C5 C4 N3 128.211 1.50 +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +GMP sp3_sp3_25 "C4'" "C5'" "O5'" "HO5'" 180.000 10.0 3 +GMP const_21 N9 C8 N7 C5 0.000 10.0 2 +GMP const_24 C6 C5 N7 C8 180.000 10.0 2 +GMP const_sp2_sp2_4 N7 C5 C6 O6 0.000 5.0 2 +GMP const_25 N9 C4 C5 N7 0.000 10.0 2 +GMP const_sp2_sp2_7 O6 C6 N1 C2 180.000 5.0 2 +GMP const_11 N2 C2 N1 C6 180.000 10.0 2 +GMP sp2_sp2_1 N1 C2 N2 HN21 180.000 5.0 2 +GMP const_14 N2 C2 N3 C4 180.000 10.0 2 +GMP const_16 N9 C4 N3 C2 180.000 10.0 2 +GMP sp3_sp3_28 "O4'" "C4'" "C5'" "O5'" 180.000 10.0 3 +GMP sp3_sp3_2 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3 +GMP sp3_sp3_41 "O3'" "C3'" "C4'" "C5'" 180.000 10.0 3 +GMP sp3_sp3_4 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3 +GMP sp3_sp3_46 "C4'" "C3'" "O3'" "HO3'" 180.000 10.0 3 +GMP sp3_sp3_20 "O2'" "C2'" "C3'" "O3'" -60.000 10.0 3 +GMP sp3_sp3_49 "C3'" "C2'" "O2'" "HO2'" 180.000 10.0 3 +GMP sp3_sp3_8 "O4'" "C1'" "C2'" "O2'" 180.000 10.0 3 +GMP sp2_sp3_1 C8 N9 "C1'" "O4'" 150.000 10.0 6 +GMP const_18 N7 C8 N9 "C1'" 180.000 10.0 2 +GMP const_30 C5 C4 N9 "C1'" 180.000 10.0 2 +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +GMP chir_1 "C4'" "O4'" "C3'" "C5'" negative +GMP chir_2 "C3'" "O3'" "C4'" "C2'" positive +GMP chir_3 "C2'" "O2'" "C1'" "C3'" negative +GMP chir_4 "C1'" "O4'" N9 "C2'" negative +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +GMP plan-1 "C1'" 0.020 +GMP plan-1 C2 0.020 +GMP plan-1 C4 0.020 +GMP plan-1 C5 0.020 +GMP plan-1 C6 0.020 +GMP plan-1 C8 0.020 +GMP plan-1 H8 0.020 +GMP plan-1 HN1 0.020 +GMP plan-1 N1 0.020 +GMP plan-1 N2 0.020 +GMP plan-1 N3 0.020 +GMP plan-1 N7 0.020 +GMP plan-1 N9 0.020 +GMP plan-1 O6 0.020 +GMP plan-2 C2 0.020 +GMP plan-2 HN21 0.020 +GMP plan-2 HN22 0.020 +GMP plan-2 N2 0.020 +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +GMP SMILES ACDLabs 10.04 O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3O)CO +GMP InChI InChI 1.03 InChI=1S/C10H13N5O5/c11-10-13-7-4(8(19)14-10)12-2-15(7)9-6(18)5(17)3(1-16)20-9/h2-3,5-6,9,16-18H,1H2,(H3,11,13,14,19)/t3-,5-,6-,9-/m1/s1 +GMP InChIKey InChI 1.03 NYHBQMYGNKIUIF-UUOKFMHZSA-N +GMP SMILES_CANONICAL CACTVS 3.385 NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O +GMP SMILES CACTVS 3.385 NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO)[CH](O)[CH]3O +GMP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5 c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N=C(NC2=O)N +GMP SMILES "OpenEye OEToolkits" 1.7.5 c1nc2c(n1C3C(C(C(O3)CO)O)O)N=C(NC2=O)N +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +GMP acedrg 243 "dictionary generator" +GMP acedrg_database 11 "data source" +GMP rdkit 2017.03.2 "Chemoinformatics tool" +GMP refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/GOL.cif b/image_analysis/structure_refinement/monomers/GOL.cif new file mode 100644 index 000000000..f4a3e10af --- /dev/null +++ b/image_analysis/structure_refinement/monomers/GOL.cif @@ -0,0 +1,134 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +GOL GOL GLYCEROL NON-POLYMER 14 6 . +# +data_comp_GOL +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +GOL C1 C CH2 0 29.630 3.832 30.945 +GOL O1 O OH1 0 28.425 3.137 31.257 +GOL C2 C CH1 0 30.401 3.142 29.840 +GOL O2 O OH1 0 31.484 3.970 29.416 +GOL C3 C CH2 0 30.919 1.777 30.241 +GOL O3 O OH1 0 31.679 1.174 29.197 +GOL H11 H H 0 30.196 3.882 31.753 +GOL H12 H H 0 29.411 4.753 30.662 +GOL HO1 H H 0 28.030 3.557 31.876 +GOL H2 H H 0 29.790 3.020 29.074 +GOL HO2 H H 0 32.019 4.078 30.068 +GOL H31 H H 0 30.155 1.193 30.467 +GOL H32 H H 0 31.486 1.869 31.045 +GOL HO3 H H 0 31.160 1.020 28.546 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +GOL C1 O1 SINGLE n 1.425 0.0100 1.425 0.0100 +GOL C1 C2 SINGLE n 1.514 0.0105 1.514 0.0105 +GOL C2 O2 SINGLE n 1.427 0.0100 1.427 0.0100 +GOL C2 C3 SINGLE n 1.514 0.0105 1.514 0.0105 +GOL C3 O3 SINGLE n 1.425 0.0100 1.425 0.0100 +GOL C1 H11 SINGLE n 1.089 0.0100 0.988 0.0200 +GOL C1 H12 SINGLE n 1.089 0.0100 0.988 0.0200 +GOL O1 HO1 SINGLE n 0.970 0.0120 0.846 0.0200 +GOL C2 H2 SINGLE n 1.089 0.0100 0.987 0.0186 +GOL O2 HO2 SINGLE n 0.970 0.0120 0.848 0.0200 +GOL C3 H31 SINGLE n 1.089 0.0100 0.988 0.0200 +GOL C3 H32 SINGLE n 1.089 0.0100 0.988 0.0200 +GOL O3 HO3 SINGLE n 0.970 0.0120 0.846 0.0200 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +GOL O1 C1 C2 111.586 1.51 +GOL O1 C1 H11 109.268 1.50 +GOL O1 C1 H12 109.268 1.50 +GOL C2 C1 H11 109.193 1.50 +GOL C2 C1 H12 109.193 1.50 +GOL H11 C1 H12 108.313 1.50 +GOL C1 O1 HO1 108.280 3.00 +GOL C1 C2 O2 110.247 1.72 +GOL C1 C2 C3 113.504 1.50 +GOL C1 C2 H2 108.441 1.50 +GOL O2 C2 C3 110.247 1.72 +GOL O2 C2 H2 108.721 1.50 +GOL C3 C2 H2 108.441 1.50 +GOL C2 O2 HO2 107.936 3.00 +GOL C2 C3 O3 111.586 1.51 +GOL C2 C3 H31 109.193 1.50 +GOL C2 C3 H32 109.193 1.50 +GOL O3 C3 H31 109.268 1.50 +GOL O3 C3 H32 109.268 1.50 +GOL H31 C3 H32 108.313 1.50 +GOL C3 O3 HO3 108.280 3.00 +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +GOL sp3_sp3_1 C2 C1 O1 HO1 180.000 10.0 3 +GOL sp3_sp3_4 O1 C1 C2 O2 180.000 10.0 3 +GOL sp3_sp3_14 C1 C2 O2 HO2 60.000 10.0 3 +GOL sp3_sp3_16 C1 C2 C3 O3 180.000 10.0 3 +GOL sp3_sp3_25 C2 C3 O3 HO3 180.000 10.0 3 +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +GOL chir_1 C2 O2 C1 C3 both +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +GOL SMILES ACDLabs 12.01 OCC(O)CO +GOL SMILES_CANONICAL CACTVS 3.370 OCC(O)CO +GOL SMILES CACTVS 3.370 OCC(O)CO +GOL SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 C(C(CO)O)O +GOL SMILES "OpenEye OEToolkits" 1.7.0 C(C(CO)O)O +GOL InChI InChI 1.03 InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2 +GOL InChIKey InChI 1.03 PEDCQBHIVMGVHV-UHFFFAOYSA-N +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +GOL acedrg 243 "dictionary generator" +GOL acedrg_database 11 "data source" +GOL rdkit 2017.03.2 "Chemoinformatics tool" +GOL refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/GTP.cif b/image_analysis/structure_refinement/monomers/GTP.cif new file mode 100644 index 000000000..53fdeff81 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/GTP.cif @@ -0,0 +1,312 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +GTP GTP "GUANOSINE-5'-TRIPHOSPHATE" NON-POLYMER 44 32 . +# +data_comp_GTP +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +GTP PG P P 0 4.560 31.688 21.477 +GTP O1G O O 0 4.404 32.256 22.874 +GTP O2G O OP -1 4.031 32.621 20.405 +GTP O3G O OP -1 4.007 30.282 21.352 +GTP O3B O O2 0 6.154 31.567 21.217 +GTP PB P P 0 7.014 30.840 20.078 +GTP O1B O O 0 7.367 29.484 20.548 +GTP O2B O OP -1 6.320 31.011 18.784 +GTP O3A O O2 0 8.339 31.740 20.070 +GTP PA P P 0 8.640 33.246 19.616 +GTP O1A O O 0 8.465 33.336 18.144 +GTP O2A O OP -1 7.853 34.171 20.471 +GTP "O5'" O O2 0 10.195 33.377 19.964 +GTP "C5'" C CH2 0 10.583 33.182 21.348 +GTP "C4'" C CH1 0 12.036 33.553 21.524 +GTP "O4'" O O2 0 12.846 32.727 20.657 +GTP "C3'" C CH1 0 12.389 35.007 21.180 +GTP "O3'" O OH1 0 13.296 35.538 22.138 +GTP "C2'" C CH1 0 13.016 34.892 19.786 +GTP "O2'" O OH1 0 13.937 35.921 19.490 +GTP "C1'" C CH1 0 13.732 33.549 19.908 +GTP N9 N NR5 0 14.014 32.895 18.629 +GTP C8 C CR15 0 13.089 32.464 17.714 +GTP N7 N NRD5 0 13.617 31.910 16.650 +GTP C5 C CR56 0 14.986 31.978 16.880 +GTP C6 C CR6 0 16.070 31.533 16.074 +GTP O6 O O 0 16.021 30.976 14.968 +GTP N1 N NR16 0 17.307 31.793 16.676 +GTP C2 C CR6 0 17.480 32.406 17.902 +GTP N2 N NH2 0 18.744 32.578 18.332 +GTP N3 N NRD6 0 16.461 32.825 18.660 +GTP C4 C CR56 0 15.250 32.581 18.093 +GTP "H5'" H H 0 10.452 32.234 21.605 +GTP "H5''" H H 0 10.026 33.747 21.941 +GTP "H4'" H H 0 12.287 33.371 22.464 +GTP "H3'" H H 0 11.567 35.560 21.142 +GTP "HO3'" H H 0 14.015 35.710 21.778 +GTP "H2'" H H 0 12.311 34.844 19.092 +GTP "HO2'" H H 0 14.731 35.591 19.468 +GTP "H1'" H H 0 14.596 33.678 20.425 +GTP H8 H H 0 12.160 32.561 17.840 +GTP HN1 H H 0 18.034 31.538 16.221 +GTP HN21 H H 0 18.891 32.964 19.107 +GTP HN22 H H 0 19.424 32.310 17.847 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +GTP PG O1G DOUBLE n 1.516 0.0200 1.516 0.0200 +GTP PG O2G SINGLE n 1.516 0.0200 1.516 0.0200 +GTP PG O3G SINGLE n 1.516 0.0200 1.516 0.0200 +GTP PG O3B SINGLE n 1.620 0.0143 1.620 0.0143 +GTP O3B PB SINGLE n 1.601 0.0108 1.601 0.0108 +GTP PB O1B DOUBLE n 1.478 0.0100 1.478 0.0100 +GTP PB O2B SINGLE n 1.478 0.0100 1.478 0.0100 +GTP PB O3A SINGLE n 1.602 0.0126 1.602 0.0126 +GTP O3A PA SINGLE n 1.600 0.0185 1.600 0.0185 +GTP PA O1A DOUBLE n 1.485 0.0100 1.485 0.0100 +GTP PA O2A SINGLE n 1.485 0.0100 1.485 0.0100 +GTP PA "O5'" SINGLE n 1.598 0.0100 1.598 0.0100 +GTP "O5'" "C5'" SINGLE n 1.445 0.0200 1.445 0.0200 +GTP "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +GTP "C4'" "O4'" SINGLE n 1.444 0.0100 1.444 0.0100 +GTP "C4'" "C3'" SINGLE n 1.532 0.0100 1.532 0.0100 +GTP "O4'" "C1'" SINGLE n 1.423 0.0100 1.423 0.0100 +GTP "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +GTP "C3'" "C2'" SINGLE n 1.532 0.0103 1.532 0.0103 +GTP "C2'" "O2'" SINGLE n 1.412 0.0100 1.412 0.0100 +GTP "C2'" "C1'" SINGLE n 1.528 0.0100 1.528 0.0100 +GTP "C1'" N9 SINGLE n 1.462 0.0102 1.462 0.0102 +GTP N9 C8 SINGLE y 1.371 0.0100 1.371 0.0100 +GTP N9 C4 SINGLE y 1.383 0.0114 1.383 0.0114 +GTP C8 N7 DOUBLE y 1.311 0.0104 1.311 0.0104 +GTP N7 C5 SINGLE y 1.390 0.0100 1.390 0.0100 +GTP C5 C6 SINGLE y 1.418 0.0111 1.418 0.0111 +GTP C5 C4 DOUBLE y 1.377 0.0100 1.377 0.0100 +GTP C6 O6 DOUBLE n 1.240 0.0104 1.240 0.0104 +GTP C6 N1 SINGLE y 1.394 0.0120 1.394 0.0120 +GTP N1 C2 SINGLE y 1.374 0.0124 1.374 0.0124 +GTP C2 N2 SINGLE n 1.341 0.0143 1.341 0.0143 +GTP C2 N3 DOUBLE y 1.331 0.0119 1.331 0.0119 +GTP N3 C4 SINGLE y 1.355 0.0100 1.355 0.0100 +GTP "C5'" "H5'" SINGLE n 1.089 0.0100 0.991 0.0200 +GTP "C5'" "H5''" SINGLE n 1.089 0.0100 0.991 0.0200 +GTP "C4'" "H4'" SINGLE n 1.089 0.0100 0.990 0.0200 +GTP "C3'" "H3'" SINGLE n 1.089 0.0100 0.991 0.0200 +GTP "O3'" "HO3'" SINGLE n 0.970 0.0120 0.839 0.0200 +GTP "C2'" "H2'" SINGLE n 1.089 0.0100 0.991 0.0200 +GTP "O2'" "HO2'" SINGLE n 0.970 0.0120 0.839 0.0200 +GTP "C1'" "H1'" SINGLE n 1.089 0.0100 1.016 0.0200 +GTP C8 H8 SINGLE n 1.082 0.0130 0.942 0.0168 +GTP N1 HN1 SINGLE n 1.016 0.0100 0.894 0.0200 +GTP N2 HN21 SINGLE n 1.016 0.0100 0.877 0.0200 +GTP N2 HN22 SINGLE n 1.016 0.0100 0.877 0.0200 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +GTP O1G PG O2G 112.609 3.00 +GTP O1G PG O3G 112.609 3.00 +GTP O1G PG O3B 106.004 3.00 +GTP O2G PG O3G 112.609 3.00 +GTP O2G PG O3B 106.004 3.00 +GTP O3G PG O3B 106.004 3.00 +GTP PG O3B PB 132.613 3.00 +GTP O3B PB O1B 108.634 3.00 +GTP O3B PB O2B 108.634 3.00 +GTP O3B PB O3A 100.990 3.00 +GTP O1B PB O2B 119.776 1.50 +GTP O1B PB O3A 108.634 3.00 +GTP O2B PB O3A 108.634 3.00 +GTP PB O3A PA 133.108 3.00 +GTP O3A PA O1A 109.053 3.00 +GTP O3A PA O2A 109.053 3.00 +GTP O3A PA "O5'" 100.137 3.00 +GTP O1A PA O2A 118.805 3.00 +GTP O1A PA "O5'" 109.340 2.31 +GTP O2A PA "O5'" 109.340 2.31 +GTP PA "O5'" "C5'" 116.362 1.50 +GTP "O5'" "C5'" "C4'" 109.454 1.61 +GTP "O5'" "C5'" "H5'" 109.882 1.50 +GTP "O5'" "C5'" "H5''" 109.882 1.50 +GTP "C4'" "C5'" "H5'" 109.589 1.50 +GTP "C4'" "C5'" "H5''" 109.589 1.50 +GTP "H5'" "C5'" "H5''" 108.471 1.50 +GTP "C5'" "C4'" "O4'" 109.154 1.50 +GTP "C5'" "C4'" "C3'" 115.288 1.50 +GTP "C5'" "C4'" "H4'" 108.351 1.59 +GTP "O4'" "C4'" "C3'" 105.318 1.50 +GTP "O4'" "C4'" "H4'" 109.120 1.50 +GTP "C3'" "C4'" "H4'" 109.322 2.54 +GTP "C4'" "O4'" "C1'" 109.502 2.85 +GTP "C4'" "C3'" "O3'" 110.713 3.00 +GTP "C4'" "C3'" "C2'" 102.593 1.50 +GTP "C4'" "C3'" "H3'" 110.577 3.00 +GTP "O3'" "C3'" "C2'" 111.671 3.00 +GTP "O3'" "C3'" "H3'" 110.541 2.08 +GTP "C2'" "C3'" "H3'" 110.454 1.85 +GTP "C3'" "O3'" "HO3'" 109.389 3.00 +GTP "C3'" "C2'" "O2'" 112.677 3.00 +GTP "C3'" "C2'" "C1'" 101.406 1.50 +GTP "C3'" "C2'" "H2'" 110.788 1.91 +GTP "O2'" "C2'" "C1'" 110.814 3.00 +GTP "O2'" "C2'" "H2'" 110.904 1.50 +GTP "C1'" "C2'" "H2'" 110.342 1.91 +GTP "C2'" "O2'" "HO2'" 109.217 3.00 +GTP "O4'" "C1'" "C2'" 106.114 1.65 +GTP "O4'" "C1'" N9 108.577 1.50 +GTP "O4'" "C1'" "H1'" 109.833 2.53 +GTP "C2'" "C1'" N9 113.380 2.77 +GTP "C2'" "C1'" "H1'" 109.222 1.50 +GTP N9 "C1'" "H1'" 109.411 1.50 +GTP "C1'" N9 C8 127.058 3.00 +GTP "C1'" N9 C4 126.955 2.94 +GTP C8 N9 C4 105.987 1.50 +GTP N9 C8 N7 113.721 1.50 +GTP N9 C8 H8 122.935 1.50 +GTP N7 C8 H8 123.345 1.50 +GTP C8 N7 C5 103.926 1.50 +GTP N7 C5 C6 129.926 1.50 +GTP N7 C5 C4 110.770 1.50 +GTP C6 C5 C4 119.304 1.50 +GTP C5 C6 O6 128.237 1.50 +GTP C5 C6 N1 111.514 1.50 +GTP O6 C6 N1 120.248 1.50 +GTP C6 N1 C2 125.452 1.50 +GTP C6 N1 HN1 117.160 2.45 +GTP C2 N1 HN1 117.387 2.97 +GTP N1 C2 N2 116.657 1.50 +GTP N1 C2 N3 123.538 1.50 +GTP N2 C2 N3 119.805 1.50 +GTP C2 N2 HN21 119.712 3.00 +GTP C2 N2 HN22 119.712 3.00 +GTP HN21 N2 HN22 120.576 3.00 +GTP C2 N3 C4 111.926 1.50 +GTP N9 C4 C5 105.596 1.50 +GTP N9 C4 N3 126.138 1.50 +GTP C5 C4 N3 128.265 1.50 +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +GTP sp3_sp3_27 PB O3B PG O1G 60.000 10.0 3 +GTP sp3_sp3_40 "C4'" "C5'" "O5'" PA 180.000 10.0 3 +GTP sp3_sp3_43 "O4'" "C4'" "C5'" "O5'" 180.000 10.0 3 +GTP sp3_sp3_2 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3 +GTP sp3_sp3_56 "O3'" "C3'" "C4'" "C5'" 180.000 10.0 3 +GTP sp3_sp3_4 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3 +GTP sp3_sp3_61 "C4'" "C3'" "O3'" "HO3'" 180.000 10.0 3 +GTP sp3_sp3_20 "O2'" "C2'" "C3'" "O3'" -60.000 10.0 3 +GTP sp3_sp3_64 "C3'" "C2'" "O2'" "HO2'" 180.000 10.0 3 +GTP sp3_sp3_8 "O4'" "C1'" "C2'" "O2'" 180.000 10.0 3 +GTP sp2_sp3_1 C8 N9 "C1'" "O4'" 150.000 10.0 6 +GTP const_18 N7 C8 N9 "C1'" 180.000 0.0 2 +GTP const_30 C5 C4 N9 "C1'" 180.000 0.0 2 +GTP const_21 N9 C8 N7 C5 0.000 0.0 2 +GTP const_24 C6 C5 N7 C8 180.000 0.0 2 +GTP const_sp2_sp2_4 N7 C5 C6 O6 0.000 0.0 2 +GTP const_25 N9 C4 C5 N7 0.000 0.0 2 +GTP const_sp2_sp2_7 O6 C6 N1 C2 180.000 0.0 2 +GTP const_11 N2 C2 N1 C6 180.000 0.0 2 +GTP sp2_sp2_33 N1 C2 N2 HN21 180.000 5.0 2 +GTP const_14 N2 C2 N3 C4 180.000 0.0 2 +GTP const_16 N9 C4 N3 C2 180.000 0.0 2 +GTP sp3_sp3_30 PG O3B PB O1B 60.000 10.0 3 +GTP sp3_sp3_32 PA O3A PB O3B -60.000 10.0 3 +GTP sp3_sp3_36 PB O3A PA O1A 60.000 10.0 3 +GTP sp3_sp3_37 "C5'" "O5'" PA O3A 180.000 10.0 3 +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +GTP chir_1 PB O3A O3B O2B both +GTP chir_2 PA O3A "O5'" O2A both +GTP chir_3 "C4'" "O4'" "C3'" "C5'" negative +GTP chir_4 "C3'" "O3'" "C4'" "C2'" positive +GTP chir_5 "C2'" "O2'" "C1'" "C3'" negative +GTP chir_6 "C1'" "O4'" N9 "C2'" negative +GTP chir_7 PG O3B O2G O3G both +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +GTP plan-1 "C1'" 0.020 +GTP plan-1 C4 0.020 +GTP plan-1 C5 0.020 +GTP plan-1 C6 0.020 +GTP plan-1 C8 0.020 +GTP plan-1 H8 0.020 +GTP plan-1 N3 0.020 +GTP plan-1 N7 0.020 +GTP plan-1 N9 0.020 +GTP plan-2 C2 0.020 +GTP plan-2 C4 0.020 +GTP plan-2 C5 0.020 +GTP plan-2 C6 0.020 +GTP plan-2 HN1 0.020 +GTP plan-2 N1 0.020 +GTP plan-2 N2 0.020 +GTP plan-2 N3 0.020 +GTP plan-2 N7 0.020 +GTP plan-2 N9 0.020 +GTP plan-2 O6 0.020 +GTP plan-3 C2 0.020 +GTP plan-3 HN21 0.020 +GTP plan-3 HN22 0.020 +GTP plan-3 N2 0.020 +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +GTP SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O" +GTP InChI InChI 1.03 "InChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1" +GTP InChIKey InChI 1.03 XKMLYUALXHKNFT-UUOKFMHZSA-N +GTP SMILES_CANONICAL CACTVS 3.370 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O" +GTP SMILES CACTVS 3.370 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O" +GTP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N" +GTP SMILES "OpenEye OEToolkits" 1.7.6 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N" +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +GTP acedrg 271 "dictionary generator" +GTP acedrg_database 12 "data source" +GTP rdkit 2019.09.1 "Chemoinformatics tool" +GTP refmac5 5.8.0405 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/HIS.cif b/image_analysis/structure_refinement/monomers/HIS.cif new file mode 100644 index 000000000..9aa774d8a --- /dev/null +++ b/image_analysis/structure_refinement/monomers/HIS.cif @@ -0,0 +1,247 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +HIS HIS HISTIDINE peptide 21 11 . + +data_comp_HIS +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +HIS N N NT3 1 33.660 42.779 -4.734 +HIS CA C CH1 0 33.418 41.805 -5.835 +HIS C C C 0 33.362 42.558 -7.170 +HIS O O O 0 32.473 43.428 -7.296 +HIS CB C CH2 0 32.141 40.999 -5.566 +HIS CG C CR5 0 31.907 39.881 -6.528 +HIS ND1 N NR15 1 32.388 38.605 -6.324 +HIS CD2 C CR15 0 31.249 39.846 -7.694 +HIS CE1 C CR15 0 32.025 37.834 -7.339 +HIS NE2 N NR15 0 31.332 38.567 -8.183 +HIS OXT O OC -1 34.210 42.245 -8.036 +HIS H H H 0 32.989 43.381 -4.702 +HIS H2 H H 0 34.439 43.213 -4.870 +HIS H3 H H 0 33.701 42.345 -3.944 +HIS HA H H 0 34.186 41.182 -5.863 +HIS HB3 H H 0 31.373 41.610 -5.597 +HIS HB2 H H 0 32.189 40.630 -4.657 +HIS HD1 H H 0 32.878 38.369 -5.655 +HIS HD2 H H 0 30.808 40.561 -8.109 +HIS HE1 H H 0 32.229 36.920 -7.437 +HIS HE2 H H 0 30.960 38.279 -8.940 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +HIS N n/a CA START +HIS H N . . +HIS H2 N . . +HIS H3 N . . +HIS CA N C . +HIS HA CA . . +HIS CB CA CG . +HIS HB3 CB . . +HIS HB2 CB . . +HIS CG CB ND1 . +HIS ND1 CG CE1 . +HIS HD1 ND1 . . +HIS CE1 ND1 NE2 . +HIS HE1 CE1 . . +HIS NE2 CE1 CD2 . +HIS HE2 NE2 . . +HIS CD2 NE2 HD2 . +HIS HD2 CD2 . . +HIS C CA . END +HIS O C . . +HIS OXT C . . +HIS CD2 CG . ADD + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +HIS N N(CCCH)(H)3 +HIS CA C(CC[5]HH)(NH3)(COO)(H) +HIS C C(CCHN)(O)2 +HIS O O(CCO) +HIS CB C(C[5]C[5]N[5])(CCHN)(H)2 +HIS CG C[5](C[5]N[5]H)(N[5]C[5]H)(CCHH){2|H<1>} +HIS ND1 N[5](C[5]C[5]C)(C[5]N[5]H)(H){2|H<1>} +HIS CD2 C[5](C[5]N[5]C)(N[5]C[5]H)(H){2|H<1>} +HIS CE1 C[5](N[5]C[5]H)2(H){1|C<4>,1|H<1>} +HIS NE2 N[5](C[5]C[5]H)(C[5]N[5]H)(H){1|C<4>,1|H<1>} +HIS OXT O(CCO) +HIS H H(NCHH) +HIS H2 H(NCHH) +HIS H3 H(NCHH) +HIS HA H(CCCN) +HIS HB3 H(CC[5]CH) +HIS HB2 H(CC[5]CH) +HIS HD1 H(N[5]C[5]2) +HIS HD2 H(C[5]C[5]N[5]) +HIS HE1 H(C[5]N[5]2) +HIS HE2 H(N[5]C[5]2) + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +HIS N CA SINGLE n 1.489 0.0100 1.489 0.0100 +HIS CA C SINGLE n 1.533 0.0100 1.533 0.0100 +HIS CA CB SINGLE n 1.533 0.0104 1.533 0.0104 +HIS C O DOUBLE n 1.251 0.0183 1.251 0.0183 +HIS C OXT SINGLE n 1.251 0.0183 1.251 0.0183 +HIS CB CG SINGLE n 1.493 0.0146 1.493 0.0146 +HIS CG ND1 SINGLE y 1.378 0.0100 1.378 0.0100 +HIS CG CD2 DOUBLE y 1.338 0.0174 1.338 0.0174 +HIS ND1 CE1 DOUBLE y 1.326 0.0133 1.326 0.0133 +HIS CD2 NE2 SINGLE y 1.371 0.0154 1.371 0.0154 +HIS CE1 NE2 SINGLE y 1.316 0.0157 1.316 0.0157 +HIS N H SINGLE n 1.018 0.0520 0.902 0.0102 +HIS N H2 SINGLE n 1.018 0.0520 0.902 0.0102 +HIS N H3 SINGLE n 1.018 0.0520 0.902 0.0102 +HIS CA HA SINGLE n 1.092 0.0100 0.989 0.0200 +HIS CB HB3 SINGLE n 1.092 0.0100 0.982 0.0176 +HIS CB HB2 SINGLE n 1.092 0.0100 0.982 0.0176 +HIS ND1 HD1 SINGLE n 1.013 0.0120 0.881 0.0200 +HIS CD2 HD2 SINGLE n 1.085 0.0150 0.937 0.0104 +HIS CE1 HE1 SINGLE n 1.085 0.0150 0.942 0.0200 +HIS NE2 HE2 SINGLE n 1.013 0.0120 0.877 0.0200 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +HIS CA N H 109.992 2.14 +HIS CA N H2 109.992 2.14 +HIS CA N H3 109.992 2.14 +HIS H N H2 109.032 3.00 +HIS H N H3 109.032 3.00 +HIS H2 N H3 109.032 3.00 +HIS N CA C 109.292 1.55 +HIS N CA CB 110.573 1.50 +HIS N CA HA 108.019 2.27 +HIS C CA CB 111.874 3.00 +HIS C CA HA 108.290 1.50 +HIS CB CA HA 108.890 2.34 +HIS CA C O 117.058 3.00 +HIS CA C OXT 117.058 3.00 +HIS O C OXT 125.883 1.50 +HIS CA CB CG 113.931 1.83 +HIS CA CB HB3 108.697 1.50 +HIS CA CB HB2 108.697 1.50 +HIS CG CB HB3 108.948 1.50 +HIS CG CB HB2 108.948 1.50 +HIS HB3 CB HB2 107.846 2.68 +HIS CB CG ND1 122.940 3.00 +HIS CB CG CD2 131.173 3.00 +HIS ND1 CG CD2 105.887 1.50 +HIS CG ND1 CE1 109.313 1.50 +HIS CG ND1 HD1 125.337 2.60 +HIS CE1 ND1 HD1 125.350 3.00 +HIS CG CD2 NE2 107.589 1.50 +HIS CG CD2 HD2 126.688 3.00 +HIS NE2 CD2 HD2 125.723 3.00 +HIS ND1 CE1 NE2 108.287 1.50 +HIS ND1 CE1 HE1 125.729 2.42 +HIS NE2 CE1 HE1 125.984 1.51 +HIS CD2 NE2 CE1 108.930 1.50 +HIS CD2 NE2 HE2 125.575 3.00 +HIS CE1 NE2 HE2 125.489 3.00 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +HIS chi1 N CA CB CG -60.000 10.0 3 +HIS chi2 CA CB CG CD2 90.000 10.0 6 +HIS sp3_sp3_1 C CA N H 180.000 10.0 3 +HIS const_17 NE2 CD2 CG ND1 0.000 0.0 1 +HIS const_13 CG CD2 NE2 CE1 0.000 0.0 1 +HIS const_sp2_sp2_5 NE2 CE1 ND1 CG 0.000 0.0 1 +HIS const_sp2_sp2_9 ND1 CE1 NE2 CD2 0.000 0.0 1 +HIS const_sp2_sp2_1 CD2 CG ND1 CE1 0.000 0.0 1 +HIS sp2_sp3_1 O C CA N 0.000 10.0 6 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +HIS chir_1 CA N C CB positive + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +HIS plan-1 CB 0.020 +HIS plan-1 CD2 0.020 +HIS plan-1 CE1 0.020 +HIS plan-1 CG 0.020 +HIS plan-1 HD1 0.020 +HIS plan-1 HD2 0.020 +HIS plan-1 HE1 0.020 +HIS plan-1 HE2 0.020 +HIS plan-1 ND1 0.020 +HIS plan-1 NE2 0.020 +HIS plan-2 C 0.020 +HIS plan-2 CA 0.020 +HIS plan-2 O 0.020 +HIS plan-2 OXT 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +HIS SMILES ACDLabs 10.04 "O=C(O)C(N)Cc1cnc[nH+]1" +HIS SMILES_CANONICAL CACTVS 3.341 "N[C@@H](Cc1c[nH]c[nH+]1)C(O)=O" +HIS SMILES CACTVS 3.341 "N[CH](Cc1c[nH]c[nH+]1)C(O)=O" +HIS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1c([nH+]c[nH]1)C[C@@H](C(=O)O)N" +HIS SMILES "OpenEye OEToolkits" 1.5.0 "c1c([nH+]c[nH]1)CC(C(=O)O)N" +HIS InChI InChI 1.03 "InChI=1S/C6H9N3O2/c7-5(6(10)11)1-4-2-8-3-9-4/h2-3,5H,1,7H2,(H,8,9)(H,10,11)/p+1/t5-/m0/s1" +HIS InChIKey InChI 1.03 HNDVDQJCIGZPNO-YFKPBYRVSA-O + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +HIS acedrg 278 "dictionary generator" +HIS acedrg_database 12 "data source" +HIS rdkit 2019.09.1 "Chemoinformatics tool" +HIS refmac5 5.8.0419 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/HOH.cif b/image_analysis/structure_refinement/monomers/HOH.cif new file mode 100644 index 000000000..9b16b4d26 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/HOH.cif @@ -0,0 +1,79 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +HOH HOH WATER NON-POLYMER 3 1 . + +data_comp_HOH +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.alt_atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +HOH O O O OH2 0 -23.107 18.382 -21.639 +HOH H1 H1 H H 0 -22.244 18.382 -21.639 +HOH H2 H2 H H 0 -23.365 19.206 -21.639 + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +HOH O O(H)2 +HOH H1 H(OH) +HOH H2 H(OH) + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.value_order +_chem_comp_bond.pdbx_aromatic_flag +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +HOH O H1 SINGLE n 0.972 0.0180 0.863 0.0200 +HOH O H2 SINGLE n 0.972 0.0180 0.863 0.0200 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +HOH H1 O H2 107.391 3.00 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +HOH SMILES ACDLabs 10.04 O +HOH SMILES_CANONICAL CACTVS 3.341 O +HOH SMILES CACTVS 3.341 O +HOH SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 O +HOH SMILES "OpenEye OEToolkits" 1.5.0 O +HOH InChI InChI 1.03 InChI=1S/H2O/h1H2 +HOH InChIKey InChI 1.03 XLYOFNOQVPJJNP-UHFFFAOYSA-N + +loop_ +_acedrg_chem_comp_descriptor.comp_id +_acedrg_chem_comp_descriptor.program_name +_acedrg_chem_comp_descriptor.program_version +_acedrg_chem_comp_descriptor.type +HOH acedrg 285 "dictionary generator" +HOH acedrg_database 12 "data source" +HOH rdkit 2019.09.1 "Chemoinformatics tool" +HOH servalcat 0.4.57 'optimization tool' diff --git a/image_analysis/structure_refinement/monomers/ILE.cif b/image_analysis/structure_refinement/monomers/ILE.cif new file mode 100644 index 000000000..5a1718d9b --- /dev/null +++ b/image_analysis/structure_refinement/monomers/ILE.cif @@ -0,0 +1,240 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +ILE ILE ISOLEUCINE peptide 22 9 . + +data_comp_ILE +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +ILE N N NT3 1 52.911 76.465 68.493 +ILE CA C CH1 0 53.201 77.811 67.902 +ILE C C C 0 51.886 78.441 67.404 +ILE O O O 0 51.005 77.667 66.962 +ILE CB C CH1 0 54.273 77.728 66.792 +ILE CG1 C CH2 0 54.806 79.117 66.415 +ILE CG2 C CH3 0 53.775 76.967 65.560 +ILE CD1 C CH3 0 55.991 79.094 65.464 +ILE OXT O OC -1 51.789 79.686 67.476 +ILE H H H 0 53.671 75.992 68.596 +ILE H2 H H 0 52.344 75.994 67.973 +ILE H3 H H 0 52.530 76.571 69.304 +ILE HA H H 0 53.554 78.378 68.615 +ILE HB H H 0 55.027 77.224 67.158 +ILE HG12 H H 0 55.071 79.584 67.234 +ILE HG13 H H 0 54.084 79.629 65.999 +ILE HG21 H H 0 53.180 76.249 65.830 +ILE HG22 H H 0 54.534 76.591 65.082 +ILE HG23 H H 0 53.296 77.576 64.972 +ILE HD11 H H 0 56.404 78.209 65.466 +ILE HD12 H H 0 56.648 79.757 65.749 +ILE HD13 H H 0 55.687 79.307 64.562 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +ILE N n/a CA START +ILE H N . . +ILE H2 N . . +ILE H3 N . . +ILE CA N C . +ILE HA CA . . +ILE CB CA CG2 . +ILE HB CB . . +ILE CG1 CB CD1 . +ILE HG13 CG1 . . +ILE HG12 CG1 . . +ILE CD1 CG1 HD13 . +ILE HD11 CD1 . . +ILE HD12 CD1 . . +ILE HD13 CD1 . . +ILE CG2 CB HG23 . +ILE HG21 CG2 . . +ILE HG22 CG2 . . +ILE HG23 CG2 . . +ILE C CA . END +ILE O C . . +ILE OXT C . . + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +ILE N N(CCCH)(H)3 +ILE CA C(CCCH)(NH3)(COO)(H) +ILE C C(CCHN)(O)2 +ILE O O(CCO) +ILE CB C(CCHH)(CCHN)(CH3)(H) +ILE CG1 C(CCCH)(CH3)(H)2 +ILE CG2 C(CCCH)(H)3 +ILE CD1 C(CCHH)(H)3 +ILE OXT O(CCO) +ILE H H(NCHH) +ILE H2 H(NCHH) +ILE H3 H(NCHH) +ILE HA H(CCCN) +ILE HB H(CC3) +ILE HG12 H(CCCH) +ILE HG13 H(CCCH) +ILE HG21 H(CCHH) +ILE HG22 H(CCHH) +ILE HG23 H(CCHH) +ILE HD11 H(CCHH) +ILE HD12 H(CCHH) +ILE HD13 H(CCHH) + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +ILE N CA SINGLE n 1.495 0.0100 1.495 0.0100 +ILE CA C SINGLE n 1.538 0.0100 1.538 0.0100 +ILE CA CB SINGLE n 1.540 0.0102 1.540 0.0102 +ILE C O DOUBLE n 1.251 0.0183 1.251 0.0183 +ILE C OXT SINGLE n 1.251 0.0183 1.251 0.0183 +ILE CB CG1 SINGLE n 1.529 0.0200 1.529 0.0200 +ILE CB CG2 SINGLE n 1.529 0.0119 1.529 0.0119 +ILE CG1 CD1 SINGLE n 1.518 0.0129 1.518 0.0129 +ILE N H SINGLE n 1.018 0.0520 0.902 0.0102 +ILE N H2 SINGLE n 1.018 0.0520 0.902 0.0102 +ILE N H3 SINGLE n 1.018 0.0520 0.902 0.0102 +ILE CA HA SINGLE n 1.092 0.0100 0.977 0.0200 +ILE CB HB SINGLE n 1.092 0.0100 0.978 0.0189 +ILE CG1 HG12 SINGLE n 1.092 0.0100 0.979 0.0127 +ILE CG1 HG13 SINGLE n 1.092 0.0100 0.979 0.0127 +ILE CG2 HG21 SINGLE n 1.092 0.0100 0.972 0.0156 +ILE CG2 HG22 SINGLE n 1.092 0.0100 0.972 0.0156 +ILE CG2 HG23 SINGLE n 1.092 0.0100 0.972 0.0156 +ILE CD1 HD11 SINGLE n 1.092 0.0100 0.976 0.0140 +ILE CD1 HD12 SINGLE n 1.092 0.0100 0.976 0.0140 +ILE CD1 HD13 SINGLE n 1.092 0.0100 0.976 0.0140 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +ILE CA N H 109.990 2.80 +ILE CA N H2 109.990 2.80 +ILE CA N H3 109.990 2.80 +ILE H N H2 109.032 3.00 +ILE H N H3 109.032 3.00 +ILE H2 N H3 109.032 3.00 +ILE N CA C 108.738 1.50 +ILE N CA CB 110.837 1.50 +ILE N CA HA 108.328 1.50 +ILE C CA CB 111.703 1.50 +ILE C CA HA 108.550 1.50 +ILE CB CA HA 108.373 1.50 +ILE CA C O 117.155 1.50 +ILE CA C OXT 117.155 1.50 +ILE O C OXT 125.690 1.50 +ILE CA CB CG1 111.638 1.50 +ILE CA CB CG2 110.951 1.50 +ILE CA CB HB 107.422 1.50 +ILE CG1 CB CG2 111.728 1.50 +ILE CG1 CB HB 107.389 1.50 +ILE CG2 CB HB 107.597 1.50 +ILE CB CG1 CD1 114.066 1.50 +ILE CB CG1 HG12 108.686 1.50 +ILE CB CG1 HG13 108.686 1.50 +ILE CD1 CG1 HG12 108.722 1.50 +ILE CD1 CG1 HG13 108.722 1.50 +ILE HG12 CG1 HG13 107.774 1.50 +ILE CB CG2 HG21 109.633 1.50 +ILE CB CG2 HG22 109.633 1.50 +ILE CB CG2 HG23 109.633 1.50 +ILE HG21 CG2 HG22 109.390 1.50 +ILE HG21 CG2 HG23 109.390 1.50 +ILE HG22 CG2 HG23 109.390 1.50 +ILE CG1 CD1 HD11 109.644 2.81 +ILE CG1 CD1 HD12 109.644 2.81 +ILE CG1 CD1 HD13 109.644 2.81 +ILE HD11 CD1 HD12 109.381 1.50 +ILE HD11 CD1 HD13 109.381 1.50 +ILE HD12 CD1 HD13 109.381 1.50 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +ILE chi1 N CA CB CG2 -60.000 10.0 3 +ILE chi2 CA CB CG1 CD1 180.000 10.0 3 +ILE hh1 CA CB CG2 HG23 -60.000 10.0 3 +ILE hh2 CB CG1 CD1 HD13 60.000 10.0 3 +ILE sp3_sp3_1 C CA N H 180.000 10.0 3 +ILE sp2_sp3_1 O C CA N 0.000 10.0 6 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +ILE chir_1 CA N C CB positive +ILE chir_2 CB CA CG1 CG2 positive + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +ILE plan-1 C 0.020 +ILE plan-1 CA 0.020 +ILE plan-1 O 0.020 +ILE plan-1 OXT 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +ILE SMILES ACDLabs 10.04 O=C(O)C(N)C(C)CC +ILE SMILES_CANONICAL CACTVS 3.341 CC[C@H](C)[C@H](N)C(O)=O +ILE SMILES CACTVS 3.341 CC[CH](C)[CH](N)C(O)=O +ILE SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC[C@H](C)[C@@H](C(=O)O)N +ILE SMILES "OpenEye OEToolkits" 1.5.0 CCC(C)C(C(=O)O)N +ILE InChI InChI 1.03 InChI=1S/C6H13NO2/c1-3-4(2)5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t4-,5-/m0/s1 +ILE InChIKey InChI 1.03 AGPKZVBTJJNPAG-WHFBIAKZSA-N + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +ILE acedrg 278 "dictionary generator" +ILE acedrg_database 12 "data source" +ILE rdkit 2019.09.1 "Chemoinformatics tool" +ILE refmac5 5.8.0419 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/IOD.cif b/image_analysis/structure_refinement/monomers/IOD.cif new file mode 100644 index 000000000..fe8d1dcfc --- /dev/null +++ b/image_analysis/structure_refinement/monomers/IOD.cif @@ -0,0 +1,30 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +IOD IOD 'IODIDE ION ' NON-POLYMER 1 1 . + +data_comp_IOD +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.partial_charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +IOD I I I -1.000 0.000 0.000 0.000 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +IOD I n/a . END diff --git a/image_analysis/structure_refinement/monomers/K.cif b/image_analysis/structure_refinement/monomers/K.cif new file mode 100644 index 000000000..656dfa7f1 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/K.cif @@ -0,0 +1,30 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +K K 'POTASSIUM ION ' NON-POLYMER 1 1 . + +data_comp_K +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.partial_charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +K K K K 1.000 0.000 0.000 0.000 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +K K n/a . END diff --git a/image_analysis/structure_refinement/monomers/LEU.cif b/image_analysis/structure_refinement/monomers/LEU.cif new file mode 100644 index 000000000..d7a7bc7e4 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/LEU.cif @@ -0,0 +1,240 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +LEU LEU LEUCINE peptide 22 9 . + +data_comp_LEU +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +LEU N N NT3 1 16.397 16.089 52.368 +LEU CA C CH1 0 15.211 16.954 52.118 +LEU C C C 0 13.931 16.126 52.332 +LEU O O O 0 13.023 16.642 53.022 +LEU CB C CH2 0 15.230 17.562 50.712 +LEU CG C CH1 0 16.388 18.503 50.342 +LEU CD1 C CH3 0 16.596 19.599 51.384 +LEU CD2 C CH3 0 17.703 17.774 50.057 +LEU OXT O OC -1 13.888 14.994 51.800 +LEU H H H 0 16.605 15.616 51.628 +LEU H2 H H 0 16.242 15.512 53.045 +LEU H3 H H 0 17.102 16.600 52.600 +LEU HA H H 0 15.218 17.683 52.788 +LEU HB3 H H 0 14.387 18.055 50.587 +LEU HB2 H H 0 15.214 16.822 50.062 +LEU HG H H 0 16.133 18.961 49.500 +LEU HD11 H H 0 15.741 20.011 51.596 +LEU HD12 H H 0 17.200 20.273 51.030 +LEU HD13 H H 0 16.978 19.215 52.192 +LEU HD21 H H 0 17.517 16.879 49.726 +LEU HD22 H H 0 18.230 17.713 50.871 +LEU HD23 H H 0 18.205 18.266 49.386 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +LEU N n/a CA START +LEU H N . . +LEU H2 N . . +LEU H3 N . . +LEU CA N C . +LEU HA CA . . +LEU CB CA CG . +LEU HB3 CB . . +LEU HB2 CB . . +LEU CG CB CD2 . +LEU HG CG . . +LEU CD1 CG HD13 . +LEU HD11 CD1 . . +LEU HD12 CD1 . . +LEU HD13 CD1 . . +LEU CD2 CG HD23 . +LEU HD21 CD2 . . +LEU HD22 CD2 . . +LEU HD23 CD2 . . +LEU C CA . END +LEU O C . . +LEU OXT C . . + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +LEU N N(CCCH)(H)3 +LEU CA C(CCHH)(NH3)(COO)(H) +LEU C C(CCHN)(O)2 +LEU O O(CCO) +LEU CB C(CCCH)(CCHN)(H)2 +LEU CG C(CCHH)(CH3)2(H) +LEU CD1 C(CCCH)(H)3 +LEU CD2 C(CCCH)(H)3 +LEU OXT O(CCO) +LEU H H(NCHH) +LEU H2 H(NCHH) +LEU H3 H(NCHH) +LEU HA H(CCCN) +LEU HB3 H(CCCH) +LEU HB2 H(CCCH) +LEU HG H(CC3) +LEU HD11 H(CCHH) +LEU HD12 H(CCHH) +LEU HD13 H(CCHH) +LEU HD21 H(CCHH) +LEU HD22 H(CCHH) +LEU HD23 H(CCHH) + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +LEU N CA SINGLE n 1.487 0.0100 1.487 0.0100 +LEU CA C SINGLE n 1.538 0.0113 1.538 0.0113 +LEU CA CB SINGLE n 1.528 0.0100 1.528 0.0100 +LEU C O DOUBLE n 1.251 0.0183 1.251 0.0183 +LEU C OXT SINGLE n 1.251 0.0183 1.251 0.0183 +LEU CB CG SINGLE n 1.532 0.0100 1.532 0.0100 +LEU CG CD1 SINGLE n 1.519 0.0200 1.519 0.0200 +LEU CG CD2 SINGLE n 1.519 0.0200 1.519 0.0200 +LEU N H SINGLE n 1.018 0.0520 0.902 0.0102 +LEU N H2 SINGLE n 1.018 0.0520 0.902 0.0102 +LEU N H3 SINGLE n 1.018 0.0520 0.902 0.0102 +LEU CA HA SINGLE n 1.092 0.0100 0.991 0.0200 +LEU CB HB3 SINGLE n 1.092 0.0100 0.985 0.0129 +LEU CB HB2 SINGLE n 1.092 0.0100 0.985 0.0129 +LEU CG HG SINGLE n 1.092 0.0100 0.992 0.0164 +LEU CD1 HD11 SINGLE n 1.092 0.0100 0.972 0.0156 +LEU CD1 HD12 SINGLE n 1.092 0.0100 0.972 0.0156 +LEU CD1 HD13 SINGLE n 1.092 0.0100 0.972 0.0156 +LEU CD2 HD21 SINGLE n 1.092 0.0100 0.972 0.0156 +LEU CD2 HD22 SINGLE n 1.092 0.0100 0.972 0.0156 +LEU CD2 HD23 SINGLE n 1.092 0.0100 0.972 0.0156 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +LEU CA N H 109.990 3.00 +LEU CA N H2 109.990 3.00 +LEU CA N H3 109.990 3.00 +LEU H N H2 109.032 3.00 +LEU H N H3 109.032 3.00 +LEU H2 N H3 109.032 3.00 +LEU N CA C 109.258 1.50 +LEU N CA CB 109.859 2.63 +LEU N CA HA 108.387 1.58 +LEU C CA CB 111.627 1.50 +LEU C CA HA 108.774 1.79 +LEU CB CA HA 109.261 1.50 +LEU CA C O 117.148 1.60 +LEU CA C OXT 117.148 1.60 +LEU O C OXT 125.704 1.50 +LEU CA CB CG 115.973 1.50 +LEU CA CB HB3 108.172 1.50 +LEU CA CB HB2 108.172 1.50 +LEU CG CB HB3 108.390 1.50 +LEU CG CB HB2 108.390 1.50 +LEU HB3 CB HB2 107.673 3.00 +LEU CB CG CD1 110.898 3.00 +LEU CB CG CD2 110.898 3.00 +LEU CB CG HG 108.090 1.50 +LEU CD1 CG CD2 110.647 1.82 +LEU CD1 CG HG 107.962 1.81 +LEU CD2 CG HG 107.962 1.81 +LEU CG CD1 HD11 109.527 1.50 +LEU CG CD1 HD12 109.527 1.50 +LEU CG CD1 HD13 109.527 1.50 +LEU HD11 CD1 HD12 109.390 1.50 +LEU HD11 CD1 HD13 109.390 1.50 +LEU HD12 CD1 HD13 109.390 1.50 +LEU CG CD2 HD21 109.527 1.50 +LEU CG CD2 HD22 109.527 1.50 +LEU CG CD2 HD23 109.527 1.50 +LEU HD21 CD2 HD22 109.390 1.50 +LEU HD21 CD2 HD23 109.390 1.50 +LEU HD22 CD2 HD23 109.390 1.50 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +LEU chi1 N CA CB CG -60.000 10.0 3 +LEU chi2 CA CB CG CD1 180.000 10.0 3 +LEU hh1 CB CG CD1 HD13 60.000 10.0 3 +LEU hh2 CB CG CD2 HD23 180.000 10.0 3 +LEU sp3_sp3_1 C CA N H 180.000 10.0 3 +LEU sp2_sp3_1 O C CA N 0.000 10.0 6 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +LEU chir_1 CA N C CB positive +LEU chir_2 CG CB CD1 CD2 both + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +LEU plan-1 C 0.020 +LEU plan-1 CA 0.020 +LEU plan-1 O 0.020 +LEU plan-1 OXT 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +LEU SMILES ACDLabs 10.04 O=C(O)C(N)CC(C)C +LEU SMILES_CANONICAL CACTVS 3.341 CC(C)C[C@H](N)C(O)=O +LEU SMILES CACTVS 3.341 CC(C)C[CH](N)C(O)=O +LEU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC(C)C[C@@H](C(=O)O)N +LEU SMILES "OpenEye OEToolkits" 1.5.0 CC(C)CC(C(=O)O)N +LEU InChI InChI 1.03 InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t5-/m0/s1 +LEU InChIKey InChI 1.03 ROHFNLRQFUQHCH-YFKPBYRVSA-N + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +LEU acedrg 278 "dictionary generator" +LEU acedrg_database 12 "data source" +LEU rdkit 2019.09.1 "Chemoinformatics tool" +LEU refmac5 5.8.0419 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/LYS.cif b/image_analysis/structure_refinement/monomers/LYS.cif new file mode 100644 index 000000000..edcceab06 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/LYS.cif @@ -0,0 +1,258 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +LYS LYS LYSINE peptide 25 10 . + +data_comp_LYS +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +LYS N N NT3 1 38.447 40.683 -3.403 +LYS CA C CH1 0 39.289 39.686 -4.119 +LYS C C C 0 38.638 39.335 -5.470 +LYS O O O 0 37.393 39.207 -5.493 +LYS CB C CH2 0 39.527 38.438 -3.257 +LYS CG C CH2 0 38.287 37.697 -2.761 +LYS CD C CH2 0 38.607 36.502 -1.871 +LYS CE C CH2 0 37.387 35.753 -1.425 +LYS NZ N NT3 1 36.499 36.554 -0.576 +LYS OXT O OC -1 39.402 39.203 -6.452 +LYS H H H 0 38.746 40.791 -2.559 +LYS H2 H H 0 37.585 40.417 -3.374 +LYS H3 H H 0 38.489 41.477 -3.829 +LYS HA H H 0 40.169 40.104 -4.300 +LYS HB3 H H 0 40.055 38.704 -2.474 +LYS HB2 H H 0 40.071 37.807 -3.775 +LYS HG3 H H 0 37.773 37.386 -3.537 +LYS HG2 H H 0 37.724 38.326 -2.260 +LYS HD3 H H 0 39.096 36.816 -1.080 +LYS HD2 H H 0 39.195 35.888 -2.363 +LYS HE3 H H 0 37.662 34.961 -0.931 +LYS HE2 H H 0 36.889 35.459 -2.208 +LYS HZ1 H H 0 36.983 37.027 0.027 +LYS HZ2 H H 0 35.931 36.006 -0.132 +LYS HZ3 H H 0 36.017 37.126 -1.086 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +LYS N n/a CA START +LYS H N . . +LYS H2 N . . +LYS H3 N . . +LYS CA N C . +LYS HA CA . . +LYS CB CA CG . +LYS HB3 CB . . +LYS HB2 CB . . +LYS CG CB CD . +LYS HG3 CG . . +LYS HG2 CG . . +LYS CD CG CE . +LYS HD3 CD . . +LYS HD2 CD . . +LYS CE CD NZ . +LYS HE3 CE . . +LYS HE2 CE . . +LYS NZ CE HZ3 . +LYS HZ1 NZ . . +LYS HZ2 NZ . . +LYS HZ3 NZ . . +LYS C CA . END +LYS O C . . +LYS OXT C . . + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +LYS N N(CCCH)(H)3 +LYS CA C(CCHH)(NH3)(COO)(H) +LYS C C(CCHN)(O)2 +LYS O O(CCO) +LYS CB C(CCHH)(CCHN)(H)2 +LYS CG C(CCHH)2(H)2 +LYS CD C(CCHH)(CHHN)(H)2 +LYS CE C(CCHH)(NH3)(H)2 +LYS NZ N(CCHH)(H)3 +LYS OXT O(CCO) +LYS H H(NCHH) +LYS H2 H(NCHH) +LYS H3 H(NCHH) +LYS HA H(CCCN) +LYS HB3 H(CCCH) +LYS HB2 H(CCCH) +LYS HG3 H(CCCH) +LYS HG2 H(CCCH) +LYS HD3 H(CCCH) +LYS HD2 H(CCCH) +LYS HE3 H(CCHN) +LYS HE2 H(CCHN) +LYS HZ1 H(NCHH) +LYS HZ2 H(NCHH) +LYS HZ3 H(NCHH) + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +LYS N CA SINGLE n 1.487 0.0100 1.487 0.0100 +LYS CA C SINGLE n 1.538 0.0113 1.538 0.0113 +LYS CA CB SINGLE n 1.533 0.0100 1.533 0.0100 +LYS C O DOUBLE n 1.251 0.0183 1.251 0.0183 +LYS C OXT SINGLE n 1.251 0.0183 1.251 0.0183 +LYS CB CG SINGLE n 1.523 0.0189 1.523 0.0189 +LYS CG CD SINGLE n 1.524 0.0122 1.524 0.0122 +LYS CD CE SINGLE n 1.496 0.0200 1.496 0.0200 +LYS CE NZ SINGLE n 1.465 0.0130 1.465 0.0130 +LYS N H SINGLE n 1.018 0.0520 0.902 0.0102 +LYS N H2 SINGLE n 1.018 0.0520 0.902 0.0102 +LYS N H3 SINGLE n 1.018 0.0520 0.902 0.0102 +LYS CA HA SINGLE n 1.092 0.0100 0.991 0.0200 +LYS CB HB3 SINGLE n 1.092 0.0100 0.981 0.0141 +LYS CB HB2 SINGLE n 1.092 0.0100 0.981 0.0141 +LYS CG HG3 SINGLE n 1.092 0.0100 0.982 0.0163 +LYS CG HG2 SINGLE n 1.092 0.0100 0.982 0.0163 +LYS CD HD3 SINGLE n 1.092 0.0100 0.982 0.0163 +LYS CD HD2 SINGLE n 1.092 0.0100 0.982 0.0163 +LYS CE HE3 SINGLE n 1.092 0.0100 0.974 0.0147 +LYS CE HE2 SINGLE n 1.092 0.0100 0.974 0.0147 +LYS NZ HZ1 SINGLE n 1.018 0.0520 0.906 0.0200 +LYS NZ HZ2 SINGLE n 1.018 0.0520 0.906 0.0200 +LYS NZ HZ3 SINGLE n 1.018 0.0520 0.906 0.0200 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +LYS CA N H 109.990 3.00 +LYS CA N H2 109.990 3.00 +LYS CA N H3 109.990 3.00 +LYS H N H2 109.032 3.00 +LYS H N H3 109.032 3.00 +LYS H2 N H3 109.032 3.00 +LYS N CA C 109.258 1.50 +LYS N CA CB 110.440 2.46 +LYS N CA HA 108.387 1.58 +LYS C CA CB 111.059 3.00 +LYS C CA HA 108.774 1.79 +LYS CB CA HA 109.080 2.33 +LYS CA C O 117.148 1.60 +LYS CA C OXT 117.148 1.60 +LYS O C OXT 125.704 1.50 +LYS CA CB CG 115.148 2.35 +LYS CA CB HB3 108.677 1.74 +LYS CA CB HB2 108.677 1.74 +LYS CG CB HB3 108.413 1.50 +LYS CG CB HB2 108.413 1.50 +LYS HB3 CB HB2 107.655 1.50 +LYS CB CG CD 113.403 3.00 +LYS CB CG HG3 108.381 1.50 +LYS CB CG HG2 108.381 1.50 +LYS CD CG HG3 108.819 1.50 +LYS CD CG HG2 108.819 1.50 +LYS HG3 CG HG2 107.566 1.82 +LYS CG CD CE 112.541 3.00 +LYS CG CD HD3 108.993 1.92 +LYS CG CD HD2 108.993 1.92 +LYS CE CD HD3 109.016 1.50 +LYS CE CD HD2 109.016 1.50 +LYS HD3 CD HD2 107.958 2.23 +LYS CD CE NZ 111.716 3.00 +LYS CD CE HE3 109.468 2.65 +LYS CD CE HE2 109.468 2.65 +LYS NZ CE HE3 108.972 2.23 +LYS NZ CE HE2 108.972 2.23 +LYS HE3 CE HE2 108.144 2.57 +LYS CE NZ HZ1 109.659 3.00 +LYS CE NZ HZ2 109.659 3.00 +LYS CE NZ HZ3 109.659 3.00 +LYS HZ1 NZ HZ2 109.089 3.00 +LYS HZ1 NZ HZ3 109.089 3.00 +LYS HZ2 NZ HZ3 109.089 3.00 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +LYS chi1 N CA CB CG -60.000 10.0 3 +LYS chi2 CA CB CG CD 180.000 10.0 3 +LYS chi3 CB CG CD CE 180.000 10.0 3 +LYS chi4 CG CD CE NZ 180.000 10.0 3 +LYS hh1 CD CE NZ HZ3 180.000 10.0 3 +LYS sp3_sp3_1 C CA N H 180.000 10.0 3 +LYS sp2_sp3_1 O C CA N 0.000 10.0 6 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +LYS chir_1 CA N C CB positive + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +LYS plan-1 C 0.020 +LYS plan-1 CA 0.020 +LYS plan-1 O 0.020 +LYS plan-1 OXT 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +LYS SMILES ACDLabs 10.04 O=C(O)C(N)CCCC[NH3+] +LYS SMILES_CANONICAL CACTVS 3.341 N[C@@H](CCCC[NH3+])C(O)=O +LYS SMILES CACTVS 3.341 N[CH](CCCC[NH3+])C(O)=O +LYS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(CC[NH3+])C[C@@H](C(=O)O)N +LYS SMILES "OpenEye OEToolkits" 1.5.0 C(CC[NH3+])CC(C(=O)O)N +LYS InChI InChI 1.03 InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/p+1/t5-/m0/s1 +LYS InChIKey InChI 1.03 KDXKERNSBIXSRK-YFKPBYRVSA-O + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +LYS acedrg 278 "dictionary generator" +LYS acedrg_database 12 "data source" +LYS rdkit 2019.09.1 "Chemoinformatics tool" +LYS refmac5 5.8.0419 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/MET.cif b/image_analysis/structure_refinement/monomers/MET.cif new file mode 100644 index 000000000..28a95f5e7 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/MET.cif @@ -0,0 +1,226 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +MET MET METHIONINE peptide 20 9 . + +data_comp_MET +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +MET N N NT3 1 16.235 16.083 52.229 +MET CA C CH1 0 15.074 16.893 51.770 +MET C C C 0 13.874 15.966 51.506 +MET O O O 0 12.749 16.368 51.879 +MET CB C CH2 0 15.401 17.671 50.489 +MET CG C CH2 0 16.529 18.680 50.635 +MET SD S S2 0 18.171 17.933 50.684 +MET CE C CH3 0 18.367 17.396 48.979 +MET OXT O OC -1 14.108 14.877 50.937 +MET H H H 0 16.577 15.615 51.537 +MET H2 H H 0 15.985 15.507 52.876 +MET H3 H H 0 16.877 16.622 52.563 +MET HA H H 0 14.833 17.529 52.491 +MET HB3 H H 0 14.592 18.143 50.197 +MET HB2 H H 0 15.638 17.028 49.787 +MET HG3 H H 0 16.395 19.191 51.458 +MET HG2 H H 0 16.495 19.307 49.886 +MET HE3 H H 0 18.130 18.128 48.379 +MET HE2 H H 0 17.783 16.634 48.809 +MET HE1 H H 0 19.294 17.136 48.825 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +MET N n/a CA START +MET H N . . +MET H2 N . . +MET H3 N . . +MET CA N C . +MET HA CA . . +MET CB CA CG . +MET HB3 CB . . +MET HB2 CB . . +MET CG CB SD . +MET HG3 CG . . +MET HG2 CG . . +MET SD CG CE . +MET CE SD HE3 . +MET HE1 CE . . +MET HE2 CE . . +MET HE3 CE . . +MET C CA . END +MET O C . . +MET OXT C . . + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +MET N N(CCCH)(H)3 +MET CA C(CCHH)(NH3)(COO)(H) +MET C C(CCHN)(O)2 +MET O O(CCO) +MET CB C(CCHN)(CHHS)(H)2 +MET CG C(CCHH)(SC)(H)2 +MET SD S(CCHH)(CH3) +MET CE C(SC)(H)3 +MET OXT O(CCO) +MET H H(NCHH) +MET H2 H(NCHH) +MET H3 H(NCHH) +MET HA H(CCCN) +MET HB3 H(CCCH) +MET HB2 H(CCCH) +MET HG3 H(CCHS) +MET HG2 H(CCHS) +MET HE3 H(CHHS) +MET HE2 H(CHHS) +MET HE1 H(CHHS) + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +MET N CA SINGLE n 1.487 0.0100 1.487 0.0100 +MET CA C SINGLE n 1.538 0.0113 1.538 0.0113 +MET CA CB SINGLE n 1.533 0.0100 1.533 0.0100 +MET C O DOUBLE n 1.251 0.0183 1.251 0.0183 +MET C OXT SINGLE n 1.251 0.0183 1.251 0.0183 +MET CB CG SINGLE n 1.517 0.0186 1.517 0.0186 +MET CG SD SINGLE n 1.804 0.0100 1.804 0.0100 +MET SD CE SINGLE n 1.798 0.0100 1.798 0.0100 +MET N H SINGLE n 1.018 0.0520 0.902 0.0102 +MET N H2 SINGLE n 1.018 0.0520 0.902 0.0102 +MET N H3 SINGLE n 1.018 0.0520 0.902 0.0102 +MET CA HA SINGLE n 1.092 0.0100 0.991 0.0200 +MET CB HB3 SINGLE n 1.092 0.0100 0.981 0.0141 +MET CB HB2 SINGLE n 1.092 0.0100 0.981 0.0141 +MET CG HG3 SINGLE n 1.092 0.0100 0.978 0.0200 +MET CG HG2 SINGLE n 1.092 0.0100 0.978 0.0200 +MET CE HE3 SINGLE n 1.092 0.0100 0.975 0.0110 +MET CE HE2 SINGLE n 1.092 0.0100 0.975 0.0110 +MET CE HE1 SINGLE n 1.092 0.0100 0.975 0.0110 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +MET CA N H 109.990 3.00 +MET CA N H2 109.990 3.00 +MET CA N H3 109.990 3.00 +MET H N H2 109.032 3.00 +MET H N H3 109.032 3.00 +MET H2 N H3 109.032 3.00 +MET N CA C 109.258 1.50 +MET N CA CB 110.970 1.50 +MET N CA HA 108.387 1.58 +MET C CA CB 109.608 2.17 +MET C CA HA 108.774 1.79 +MET CB CA HA 109.550 1.56 +MET CA C O 117.148 1.60 +MET CA C OXT 117.148 1.60 +MET O C OXT 125.704 1.50 +MET CA CB CG 113.978 1.60 +MET CA CB HB3 108.606 1.50 +MET CA CB HB2 108.606 1.50 +MET CG CB HB3 108.930 1.50 +MET CG CB HB2 108.930 1.50 +MET HB3 CB HB2 107.726 1.50 +MET CB CG SD 112.846 3.00 +MET CB CG HG3 109.287 1.50 +MET CB CG HG2 109.287 1.50 +MET SD CG HG3 108.733 1.50 +MET SD CG HG2 108.733 1.50 +MET HG3 CG HG2 107.881 1.50 +MET CG SD CE 100.693 3.00 +MET SD CE HE3 109.472 1.50 +MET SD CE HE2 109.472 1.50 +MET SD CE HE1 109.472 1.50 +MET HE3 CE HE2 109.569 2.44 +MET HE3 CE HE1 109.569 2.44 +MET HE2 CE HE1 109.569 2.44 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +MET chi1 N CA CB CG -60.000 10.0 3 +MET chi2 CA CB CG SD 180.000 10.0 3 +MET chi3 CB CG SD CE 180.000 10.0 3 +MET hh1 CG SD CE HE3 60.000 10.0 3 +MET sp3_sp3_1 C CA N H 180.000 10.0 3 +MET sp2_sp3_1 O C CA N 0.000 10.0 6 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +MET chir_1 CA N C CB positive + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +MET plan-1 C 0.020 +MET plan-1 CA 0.020 +MET plan-1 O 0.020 +MET plan-1 OXT 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +MET SMILES ACDLabs 10.04 O=C(O)C(N)CCSC +MET SMILES_CANONICAL CACTVS 3.341 CSCC[C@H](N)C(O)=O +MET SMILES CACTVS 3.341 CSCC[CH](N)C(O)=O +MET SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CSCC[C@@H](C(=O)O)N +MET SMILES "OpenEye OEToolkits" 1.5.0 CSCCC(C(=O)O)N +MET InChI InChI 1.03 InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m0/s1 +MET InChIKey InChI 1.03 FFEARJCKVFRZRR-BYPYZUCNSA-N + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +MET acedrg 278 "dictionary generator" +MET acedrg_database 12 "data source" +MET rdkit 2019.09.1 "Chemoinformatics tool" +MET refmac5 5.8.0419 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/MG.cif b/image_analysis/structure_refinement/monomers/MG.cif new file mode 100644 index 000000000..1b723799b --- /dev/null +++ b/image_analysis/structure_refinement/monomers/MG.cif @@ -0,0 +1,30 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +MG MG 'MAGNESIUM ION ' NON-POLYMER 1 1 . + +data_comp_MG +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.partial_charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +MG MG MG MG 2.000 0.000 0.000 0.000 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +MG MG n/a . END diff --git a/image_analysis/structure_refinement/monomers/MN.cif b/image_analysis/structure_refinement/monomers/MN.cif new file mode 100644 index 000000000..ee5537884 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/MN.cif @@ -0,0 +1,30 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +MN MN 'MANGANESE (II) ION ' NON-POLYMER 1 1 . + +data_comp_MN +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.partial_charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +MN MN MN MN 2.000 0.000 0.000 0.000 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +MN MN n/a . END diff --git a/image_analysis/structure_refinement/monomers/MPD.cif b/image_analysis/structure_refinement/monomers/MPD.cif new file mode 100644 index 000000000..bc29cd330 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/MPD.cif @@ -0,0 +1,170 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +MPD MPD (4S)-2-METHYL-2,4-PENTANEDIOL NON-POLYMER 22 8 . +# +data_comp_MPD +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +MPD C1 C CH3 0 -2.742 -3.513 8.489 +MPD C2 C CT 0 -3.104 -4.028 9.879 +MPD O2 O OH1 0 -3.051 -5.468 9.845 +MPD CM C CH3 0 -4.531 -3.659 10.262 +MPD C3 C CH2 0 -2.100 -3.522 10.924 +MPD C4 C CH1 0 -2.174 -4.161 12.300 +MPD O4 O OH1 0 -1.753 -5.524 12.217 +MPD C5 C CH3 0 -1.373 -3.434 13.348 +MPD H11 H H 0 -2.205 -2.707 8.574 +MPD H12 H H 0 -3.550 -3.311 7.989 +MPD H13 H H 0 -2.231 -4.191 8.014 +MPD HO2 H H 0 -2.246 -5.731 9.774 +MPD HM1 H H 0 -4.554 -2.734 10.562 +MPD HM2 H H 0 -4.831 -4.241 10.980 +MPD HM3 H H 0 -5.116 -3.767 9.494 +MPD H31 H H 0 -2.230 -2.555 11.026 +MPD H32 H H 0 -1.197 -3.662 10.569 +MPD H4 H H 0 -3.118 -4.168 12.600 +MPD HO4 H H 0 -0.938 -5.565 11.984 +MPD H51 H H 0 -0.836 -4.069 13.855 +MPD H52 H H 0 -1.976 -2.969 13.955 +MPD H53 H H 0 -0.783 -2.784 12.924 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +MPD C1 C2 SINGLE n 1.520 0.0101 1.520 0.0101 +MPD C2 O2 SINGLE n 1.437 0.0141 1.437 0.0141 +MPD C2 CM SINGLE n 1.520 0.0101 1.520 0.0101 +MPD C2 C3 SINGLE n 1.531 0.0100 1.531 0.0100 +MPD C3 C4 SINGLE n 1.506 0.0200 1.506 0.0200 +MPD C4 O4 SINGLE n 1.424 0.0199 1.424 0.0199 +MPD C4 C5 SINGLE n 1.501 0.0160 1.501 0.0160 +MPD C1 H11 SINGLE n 1.089 0.0100 0.972 0.0148 +MPD C1 H12 SINGLE n 1.089 0.0100 0.972 0.0148 +MPD C1 H13 SINGLE n 1.089 0.0100 0.972 0.0148 +MPD O2 HO2 SINGLE n 0.970 0.0120 0.848 0.0200 +MPD CM HM1 SINGLE n 1.089 0.0100 0.972 0.0148 +MPD CM HM2 SINGLE n 1.089 0.0100 0.972 0.0148 +MPD CM HM3 SINGLE n 1.089 0.0100 0.972 0.0148 +MPD C3 H31 SINGLE n 1.089 0.0100 0.981 0.0160 +MPD C3 H32 SINGLE n 1.089 0.0100 0.981 0.0160 +MPD C4 H4 SINGLE n 1.089 0.0100 0.992 0.0184 +MPD O4 HO4 SINGLE n 0.970 0.0120 0.848 0.0200 +MPD C5 H51 SINGLE n 1.089 0.0100 0.974 0.0145 +MPD C5 H52 SINGLE n 1.089 0.0100 0.974 0.0145 +MPD C5 H53 SINGLE n 1.089 0.0100 0.974 0.0145 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +MPD C2 C1 H11 109.123 1.50 +MPD C2 C1 H12 109.123 1.50 +MPD C2 C1 H13 109.123 1.50 +MPD H11 C1 H12 109.441 1.50 +MPD H11 C1 H13 109.441 1.50 +MPD H12 C1 H13 109.441 1.50 +MPD C1 C2 O2 107.291 2.44 +MPD C1 C2 CM 110.915 1.50 +MPD C1 C2 C3 111.119 1.58 +MPD O2 C2 CM 107.291 2.44 +MPD O2 C2 C3 107.760 2.12 +MPD CM C2 C3 111.119 1.58 +MPD C2 O2 HO2 109.561 1.92 +MPD C2 CM HM1 109.123 1.50 +MPD C2 CM HM2 109.123 1.50 +MPD C2 CM HM3 109.123 1.50 +MPD HM1 CM HM2 109.441 1.50 +MPD HM1 CM HM3 109.441 1.50 +MPD HM2 CM HM3 109.441 1.50 +MPD C2 C3 C4 111.094 2.85 +MPD C2 C3 H31 108.201 1.50 +MPD C2 C3 H32 108.201 1.50 +MPD C4 C3 H31 108.468 1.50 +MPD C4 C3 H32 108.468 1.50 +MPD H31 C3 H32 107.715 1.50 +MPD C3 C4 O4 109.024 2.32 +MPD C3 C4 C5 113.468 3.00 +MPD C3 C4 H4 108.603 1.50 +MPD O4 C4 C5 109.534 2.02 +MPD O4 C4 H4 107.545 2.92 +MPD C5 C4 H4 108.620 2.54 +MPD C4 O4 HO4 109.880 2.07 +MPD C4 C5 H51 109.852 1.50 +MPD C4 C5 H52 109.852 1.50 +MPD C4 C5 H53 109.852 1.50 +MPD H51 C5 H52 109.425 1.50 +MPD H51 C5 H53 109.425 1.50 +MPD H52 C5 H53 109.425 1.50 +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +MPD sp3_sp3_2 H11 C1 C2 O2 -60.000 10.0 3 +MPD sp3_sp3_10 C1 C2 O2 HO2 180.000 10.0 3 +MPD sp3_sp3_19 C1 C2 CM HM1 -60.000 10.0 3 +MPD sp3_sp3_25 C1 C2 C3 C4 60.000 10.0 3 +MPD sp3_sp3_31 C2 C3 C4 O4 180.000 10.0 3 +MPD sp3_sp3_40 C3 C4 O4 HO4 180.000 10.0 3 +MPD sp3_sp3_43 C3 C4 C5 H51 180.000 10.0 3 +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +MPD chir_1 C2 O2 C3 C1 both +MPD chir_2 C4 O4 C3 C5 positive +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +MPD SMILES ACDLabs 11.02 OC(C)CC(O)(C)C +MPD SMILES_CANONICAL CACTVS 3.352 C[C@H](O)CC(C)(C)O +MPD SMILES CACTVS 3.352 C[CH](O)CC(C)(C)O +MPD SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 C[C@@H](CC(C)(C)O)O +MPD SMILES "OpenEye OEToolkits" 1.7.0 CC(CC(C)(C)O)O +MPD InChI InChI 1.03 InChI=1S/C6H14O2/c1-5(7)4-6(2,3)8/h5,7-8H,4H2,1-3H3/t5-/m0/s1 +MPD InChIKey InChI 1.03 SVTBMSDMJJWYQN-YFKPBYRVSA-N +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +MPD acedrg 243 "dictionary generator" +MPD acedrg_database 11 "data source" +MPD rdkit 2017.03.2 "Chemoinformatics tool" +MPD refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/MSE.cif b/image_analysis/structure_refinement/monomers/MSE.cif new file mode 100644 index 000000000..d73f9f68b --- /dev/null +++ b/image_analysis/structure_refinement/monomers/MSE.cif @@ -0,0 +1,201 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +MSE MSE SELENOMETHIONINE peptide 20 9 . + +data_comp_MSE +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +MSE N N NT3 1 10.980 -7.344 20.020 +MSE CA C CH1 0 10.215 -8.538 19.563 +MSE C C C 0 8.775 -8.458 20.089 +MSE O O O 0 8.605 -7.967 21.223 +MSE OXT O OC -1 7.876 -8.895 19.344 +MSE CB C CH2 0 10.896 -9.824 20.043 +MSE CG C CH2 0 12.189 -10.151 19.325 +MSE SE SE SE 0 12.850 -11.935 19.808 +MSE CE C CH3 0 13.628 -11.498 21.557 +MSE H H H 0 11.808 -7.339 19.642 +MSE H2 H H 0 11.069 -7.358 20.927 +MSE H3 H H 0 10.544 -6.581 19.779 +MSE HA H H 0 10.192 -8.533 18.579 +MSE HB2 H H 0 10.295 -10.556 19.923 +MSE HB3 H H 0 11.082 -9.746 20.975 +MSE HG2 H H 0 12.870 -9.483 19.555 +MSE HG3 H H 0 12.044 -10.114 18.355 +MSE HE1 H H 0 14.013 -12.298 21.947 +MSE HE2 H H 0 12.935 -11.153 22.141 +MSE HE3 H H 0 14.320 -10.828 21.443 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +MSE N n/a CA START +MSE H N . . +MSE H2 N . . +MSE H3 N . . +MSE CA N C . +MSE HA CA . . +MSE CB CA CG . +MSE HB2 CB . . +MSE HB3 CB . . +MSE CG CB SE . +MSE HG2 CG . . +MSE HG3 CG . . +MSE SE CG CE . +MSE CE SE HE1 . +MSE HE3 CE . . +MSE HE2 CE . . +MSE HE1 CE . . +MSE C CA . END +MSE O C . . +MSE OXT C . . + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +MSE N CA SINGLE n 1.488 0.0100 1.488 0.0100 +MSE CA C SINGLE n 1.533 0.0100 1.533 0.0100 +MSE CA CB SINGLE n 1.532 0.0100 1.532 0.0100 +MSE C O DOUBLE n 1.247 0.0187 1.247 0.0187 +MSE C OXT SINGLE n 1.247 0.0187 1.247 0.0187 +MSE CB CG SINGLE n 1.514 0.0200 1.514 0.0200 +MSE CG SE SINGLE n 1.963 0.0200 1.963 0.0200 +MSE SE CE SINGLE n 1.963 0.0200 1.963 0.0200 +MSE N H SINGLE n 1.036 0.0160 0.911 0.0200 +MSE N H2 SINGLE n 1.036 0.0160 0.911 0.0200 +MSE N H3 SINGLE n 1.036 0.0160 0.911 0.0200 +MSE CA HA SINGLE n 1.089 0.0100 0.985 0.0200 +MSE CB HB2 SINGLE n 1.089 0.0100 0.954 0.0200 +MSE CB HB3 SINGLE n 1.089 0.0100 0.954 0.0200 +MSE CG HG2 SINGLE n 1.089 0.0100 0.981 0.0167 +MSE CG HG3 SINGLE n 1.089 0.0100 0.981 0.0167 +MSE CE HE1 SINGLE n 1.089 0.0100 0.970 0.0162 +MSE CE HE2 SINGLE n 1.089 0.0100 0.970 0.0162 +MSE CE HE3 SINGLE n 1.089 0.0100 0.970 0.0162 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +MSE CA N H 110.062 1.93 +MSE CA N H2 110.062 1.93 +MSE CA N H3 110.062 1.93 +MSE H N H2 109.028 2.41 +MSE H N H3 109.028 2.41 +MSE H2 N H3 109.028 2.41 +MSE N CA C 109.241 1.50 +MSE N CA CB 110.245 1.51 +MSE N CA HA 108.487 1.50 +MSE C CA CB 110.728 2.07 +MSE C CA HA 108.824 1.50 +MSE CB CA HA 109.207 1.50 +MSE CA C O 117.124 1.50 +MSE CA C OXT 117.124 1.50 +MSE O C OXT 125.752 1.50 +MSE CA CB CG 113.897 1.50 +MSE CA CB HB2 108.567 1.50 +MSE CA CB HB3 108.567 1.50 +MSE CG CB HB2 108.056 1.50 +MSE CG CB HB3 108.056 1.50 +MSE HB2 CB HB3 107.715 1.50 +MSE CB CG SE 111.593 3.00 +MSE CB CG HG2 109.535 1.63 +MSE CB CG HG3 109.535 1.63 +MSE SE CG HG2 109.134 1.50 +MSE SE CG HG3 109.134 1.50 +MSE HG2 CG HG3 108.011 1.50 +MSE CG SE CE 98.689 1.50 +MSE SE CE HE1 109.134 1.50 +MSE SE CE HE2 109.134 1.50 +MSE SE CE HE3 109.134 1.50 +MSE HE1 CE HE2 109.290 1.50 +MSE HE1 CE HE3 109.290 1.50 +MSE HE2 CE HE3 109.290 1.50 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +MSE sp3_sp3_1 C CA N H 180.000 10.0 3 +MSE sp2_sp3_1 O C CA N 0.000 10.0 6 +MSE sp3_sp3_10 N CA CB CG 180.000 10.0 3 +MSE sp3_sp3_19 CA CB CG SE 180.000 10.0 3 +MSE sp3_sp3_28 CB CG SE CE 180.000 10.0 3 +MSE sp3_sp3_31 HE1 CE SE CG 180.000 10.0 3 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +MSE chir_1 CA N C CB positive + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +MSE plan-1 C 0.020 +MSE plan-1 CA 0.020 +MSE plan-1 O 0.020 +MSE plan-1 OXT 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +MSE SMILES ACDLabs 10.04 O=C(O)C(N)CC[Se]C +MSE SMILES_CANONICAL CACTVS 3.341 C[Se]CC[C@H](N)C(O)=O +MSE SMILES CACTVS 3.341 C[Se]CC[CH](N)C(O)=O +MSE SMILES_CANONICAL ""OpenEye OEToolkits" 1.5.0 C[Se]CC[C@@H](C(=O)O)N +MSE SMILES ""OpenEye OEToolkits" 1.5.0 C[Se]CCC(C(=O)O)N +MSE InChI InChI 1.03 InChI=1S/C5H11NO2Se/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m0/s1 +MSE InChIKey InChI 1.03 RJFAYQIBOAGBLC-BYPYZUCNSA-N + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +MSE acedrg 243 ""dictionary generator" +MSE acedrg_database 11 ""data source" +MSE rdkit 2017.03.2 ""Chemoinformatics tool" +MSE refmac5 5.8.0238 ""optimization tool" diff --git a/image_analysis/structure_refinement/monomers/NA.cif b/image_analysis/structure_refinement/monomers/NA.cif new file mode 100644 index 000000000..e9d8ecd98 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/NA.cif @@ -0,0 +1,30 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +NA NA 'SODIUM ION ' NON-POLYMER 1 1 . + +data_comp_NA +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.partial_charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +NA NA NA NA 1.000 0.000 0.000 0.000 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +NA NA n/a . END diff --git a/image_analysis/structure_refinement/monomers/NI.cif b/image_analysis/structure_refinement/monomers/NI.cif new file mode 100644 index 000000000..fb5249865 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/NI.cif @@ -0,0 +1,30 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +NI NI 'NICKEL (II) ION ' NON-POLYMER 1 1 . + +data_comp_NI +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.partial_charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +NI NI NI NI 2.000 0.000 0.000 0.000 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +NI NI n/a . END diff --git a/image_analysis/structure_refinement/monomers/PEG.cif b/image_analysis/structure_refinement/monomers/PEG.cif new file mode 100644 index 000000000..08009cba8 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/PEG.cif @@ -0,0 +1,138 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +PEG PEG DI(HYDROXYETHYL)ETHER NON-POLYMER 17 7 . +# +data_comp_PEG +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +PEG C1 C CH2 0 41.561 37.152 47.063 +PEG O1 O OH1 0 41.065 36.188 46.155 +PEG C2 C CH2 0 42.802 36.690 47.759 +PEG O2 O O2 0 42.505 35.564 48.578 +PEG C3 C CH2 0 43.645 35.062 49.268 +PEG C4 C CH2 0 43.253 33.888 50.109 +PEG O4 O OH1 0 44.370 33.256 50.702 +PEG H11 H H 0 40.870 37.346 47.731 +PEG H12 H H 0 41.754 37.980 46.576 +PEG HO1 H H 0 40.396 36.506 45.747 +PEG H21 H H 0 43.160 37.417 48.314 +PEG H22 H H 0 43.482 36.446 47.095 +PEG H31 H H 0 44.023 35.766 49.839 +PEG H32 H H 0 44.330 34.791 48.620 +PEG H41 H H 0 42.777 33.237 49.552 +PEG H42 H H 0 42.643 34.187 50.815 +PEG HO4 H H 0 44.736 33.789 51.248 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +PEG C1 O1 SINGLE n 1.414 0.0200 1.414 0.0200 +PEG C1 C2 SINGLE n 1.496 0.0200 1.496 0.0200 +PEG C2 O2 SINGLE n 1.423 0.0106 1.423 0.0106 +PEG O2 C3 SINGLE n 1.423 0.0106 1.423 0.0106 +PEG C3 C4 SINGLE n 1.496 0.0200 1.496 0.0200 +PEG C4 O4 SINGLE n 1.414 0.0200 1.414 0.0200 +PEG C1 H11 SINGLE n 1.089 0.0100 0.980 0.0144 +PEG C1 H12 SINGLE n 1.089 0.0100 0.980 0.0144 +PEG O1 HO1 SINGLE n 0.970 0.0120 0.846 0.0200 +PEG C2 H21 SINGLE n 1.089 0.0100 0.982 0.0175 +PEG C2 H22 SINGLE n 1.089 0.0100 0.982 0.0175 +PEG C3 H31 SINGLE n 1.089 0.0100 0.982 0.0175 +PEG C3 H32 SINGLE n 1.089 0.0100 0.982 0.0175 +PEG C4 H41 SINGLE n 1.089 0.0100 0.980 0.0144 +PEG C4 H42 SINGLE n 1.089 0.0100 0.980 0.0144 +PEG O4 HO4 SINGLE n 0.970 0.0120 0.846 0.0200 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +PEG O1 C1 C2 112.284 1.56 +PEG O1 C1 H11 109.012 1.50 +PEG O1 C1 H12 109.012 1.50 +PEG C2 C1 H11 109.198 1.50 +PEG C2 C1 H12 109.198 1.50 +PEG H11 C1 H12 108.093 1.50 +PEG C1 O1 HO1 109.347 1.86 +PEG C1 C2 O2 109.904 1.68 +PEG C1 C2 H21 109.795 1.50 +PEG C1 C2 H22 109.795 1.50 +PEG O2 C2 H21 109.691 1.50 +PEG O2 C2 H22 109.691 1.50 +PEG H21 C2 H22 108.274 1.50 +PEG C2 O2 C3 112.795 1.50 +PEG O2 C3 C4 109.904 1.68 +PEG O2 C3 H31 109.691 1.50 +PEG O2 C3 H32 109.691 1.50 +PEG C4 C3 H31 109.795 1.50 +PEG C4 C3 H32 109.795 1.50 +PEG H31 C3 H32 108.274 1.50 +PEG C3 C4 O4 112.284 1.56 +PEG C3 C4 H41 109.198 1.50 +PEG C3 C4 H42 109.198 1.50 +PEG O4 C4 H41 109.012 1.50 +PEG O4 C4 H42 109.012 1.50 +PEG H41 C4 H42 108.093 1.50 +PEG C4 O4 HO4 109.347 1.86 +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +PEG sp3_sp3_1 C2 C1 O1 HO1 180.000 10.0 3 +PEG sp3_sp3_4 O1 C1 C2 O2 180.000 10.0 3 +PEG sp3_sp3_13 C1 C2 O2 C3 180.000 10.0 3 +PEG sp3_sp3_16 C4 C3 O2 C2 180.000 10.0 3 +PEG sp3_sp3_19 O2 C3 C4 O4 180.000 10.0 3 +PEG sp3_sp3_28 C3 C4 O4 HO4 180.000 10.0 3 +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +PEG SMILES ACDLabs 12.01 OCCOCCO +PEG InChI InChI 1.03 InChI=1S/C4H10O3/c5-1-3-7-4-2-6/h5-6H,1-4H2 +PEG InChIKey InChI 1.03 MTHSVFCYNBDYFN-UHFFFAOYSA-N +PEG SMILES_CANONICAL CACTVS 3.370 OCCOCCO +PEG SMILES CACTVS 3.370 OCCOCCO +PEG SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C(COCCO)O +PEG SMILES "OpenEye OEToolkits" 1.7.6 C(COCCO)O +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +PEG acedrg 243 "dictionary generator" +PEG acedrg_database 11 "data source" +PEG rdkit 2017.03.2 "Chemoinformatics tool" +PEG refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/PG4.cif b/image_analysis/structure_refinement/monomers/PG4.cif new file mode 100644 index 000000000..77efd2c07 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/PG4.cif @@ -0,0 +1,198 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +PG4 PG4 "TETRAETHYLENE GLYCOL" NON-POLYMER 31 13 . +# +data_comp_PG4 +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +PG4 O1 O OH1 0 -3.161 60.725 73.637 +PG4 C1 C CH2 0 -2.073 60.164 74.345 +PG4 C2 C CH2 0 -1.379 59.093 73.563 +PG4 O2 O O2 0 -0.854 59.637 72.355 +PG4 C3 C CH2 0 0.478 60.128 72.474 +PG4 C4 C CH2 0 0.861 60.848 71.220 +PG4 O3 O O2 0 2.240 61.204 71.277 +PG4 C5 C CH2 0 2.663 62.051 70.212 +PG4 C6 C CH2 0 2.490 63.484 70.609 +PG4 O4 O O2 0 2.911 64.332 69.543 +PG4 C7 C CH2 0 4.287 64.696 69.603 +PG4 C8 C CH2 0 4.670 65.446 68.364 +PG4 O5 O OH1 0 3.831 66.560 68.126 +PG4 HO1 H H 0 -3.573 61.267 74.139 +PG4 H11 H H 0 -2.401 59.786 75.187 +PG4 H12 H H 0 -1.432 60.874 74.560 +PG4 H21 H H 0 -2.017 58.377 73.349 +PG4 H22 H H 0 -0.655 58.704 74.102 +PG4 H31 H H 0 1.095 59.379 72.627 +PG4 H32 H H 0 0.541 60.741 73.239 +PG4 H41 H H 0 0.311 61.656 71.122 +PG4 H42 H H 0 0.699 60.270 70.443 +PG4 H51 H H 0 2.138 61.866 69.401 +PG4 H52 H H 0 3.608 61.877 70.010 +PG4 H61 H H 0 3.016 63.670 71.419 +PG4 H62 H H 0 1.546 63.659 70.813 +PG4 H71 H H 0 4.841 63.889 69.685 +PG4 H72 H H 0 4.447 65.258 70.392 +PG4 H81 H H 0 4.623 64.841 67.594 +PG4 H82 H H 0 5.596 65.757 68.450 +PG4 HO5 H H 0 3.919 67.118 68.756 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +PG4 O1 C1 SINGLE n 1.414 0.0200 1.414 0.0200 +PG4 C1 C2 SINGLE n 1.496 0.0200 1.496 0.0200 +PG4 C2 O2 SINGLE n 1.423 0.0106 1.423 0.0106 +PG4 O2 C3 SINGLE n 1.423 0.0106 1.423 0.0106 +PG4 C3 C4 SINGLE n 1.496 0.0200 1.496 0.0200 +PG4 C4 O3 SINGLE n 1.423 0.0106 1.423 0.0106 +PG4 O3 C5 SINGLE n 1.423 0.0106 1.423 0.0106 +PG4 C5 C6 SINGLE n 1.496 0.0200 1.496 0.0200 +PG4 C6 O4 SINGLE n 1.423 0.0106 1.423 0.0106 +PG4 O4 C7 SINGLE n 1.423 0.0106 1.423 0.0106 +PG4 C7 C8 SINGLE n 1.496 0.0200 1.496 0.0200 +PG4 C8 O5 SINGLE n 1.414 0.0200 1.414 0.0200 +PG4 O1 HO1 SINGLE n 0.970 0.0120 0.846 0.0200 +PG4 C1 H11 SINGLE n 1.089 0.0100 0.980 0.0144 +PG4 C1 H12 SINGLE n 1.089 0.0100 0.980 0.0144 +PG4 C2 H21 SINGLE n 1.089 0.0100 0.982 0.0175 +PG4 C2 H22 SINGLE n 1.089 0.0100 0.982 0.0175 +PG4 C3 H31 SINGLE n 1.089 0.0100 0.982 0.0175 +PG4 C3 H32 SINGLE n 1.089 0.0100 0.982 0.0175 +PG4 C4 H41 SINGLE n 1.089 0.0100 0.982 0.0175 +PG4 C4 H42 SINGLE n 1.089 0.0100 0.982 0.0175 +PG4 C5 H51 SINGLE n 1.089 0.0100 0.982 0.0175 +PG4 C5 H52 SINGLE n 1.089 0.0100 0.982 0.0175 +PG4 C6 H61 SINGLE n 1.089 0.0100 0.982 0.0175 +PG4 C6 H62 SINGLE n 1.089 0.0100 0.982 0.0175 +PG4 C7 H71 SINGLE n 1.089 0.0100 0.982 0.0175 +PG4 C7 H72 SINGLE n 1.089 0.0100 0.982 0.0175 +PG4 C8 H81 SINGLE n 1.089 0.0100 0.980 0.0144 +PG4 C8 H82 SINGLE n 1.089 0.0100 0.980 0.0144 +PG4 O5 HO5 SINGLE n 0.970 0.0120 0.846 0.0200 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +PG4 C1 O1 HO1 109.347 1.86 +PG4 O1 C1 C2 112.284 1.56 +PG4 O1 C1 H11 109.012 1.50 +PG4 O1 C1 H12 109.012 1.50 +PG4 C2 C1 H11 109.198 1.50 +PG4 C2 C1 H12 109.198 1.50 +PG4 H11 C1 H12 108.093 1.50 +PG4 C1 C2 O2 109.904 1.68 +PG4 C1 C2 H21 109.795 1.50 +PG4 C1 C2 H22 109.795 1.50 +PG4 O2 C2 H21 109.691 1.50 +PG4 O2 C2 H22 109.691 1.50 +PG4 H21 C2 H22 108.274 1.50 +PG4 C2 O2 C3 112.795 1.50 +PG4 O2 C3 C4 109.613 1.74 +PG4 O2 C3 H31 109.691 1.50 +PG4 O2 C3 H32 109.691 1.50 +PG4 C4 C3 H31 109.729 1.50 +PG4 C4 C3 H32 109.729 1.50 +PG4 H31 C3 H32 108.274 1.50 +PG4 C3 C4 O3 109.613 1.74 +PG4 C3 C4 H41 109.729 1.50 +PG4 C3 C4 H42 109.729 1.50 +PG4 O3 C4 H41 109.691 1.50 +PG4 O3 C4 H42 109.691 1.50 +PG4 H41 C4 H42 108.274 1.50 +PG4 C4 O3 C5 112.795 1.50 +PG4 O3 C5 C6 109.613 1.74 +PG4 O3 C5 H51 109.691 1.50 +PG4 O3 C5 H52 109.691 1.50 +PG4 C6 C5 H51 109.729 1.50 +PG4 C6 C5 H52 109.729 1.50 +PG4 H51 C5 H52 108.274 1.50 +PG4 C5 C6 O4 109.613 1.74 +PG4 C5 C6 H61 109.729 1.50 +PG4 C5 C6 H62 109.729 1.50 +PG4 O4 C6 H61 109.691 1.50 +PG4 O4 C6 H62 109.691 1.50 +PG4 H61 C6 H62 108.274 1.50 +PG4 C6 O4 C7 112.795 1.50 +PG4 O4 C7 C8 109.904 1.68 +PG4 O4 C7 H71 109.691 1.50 +PG4 O4 C7 H72 109.691 1.50 +PG4 C8 C7 H71 109.795 1.50 +PG4 C8 C7 H72 109.795 1.50 +PG4 H71 C7 H72 108.274 1.50 +PG4 C7 C8 O5 112.284 1.56 +PG4 C7 C8 H81 109.198 1.50 +PG4 C7 C8 H82 109.198 1.50 +PG4 O5 C8 H81 109.012 1.50 +PG4 O5 C8 H82 109.012 1.50 +PG4 H81 C8 H82 108.093 1.50 +PG4 C8 O5 HO5 109.347 1.86 +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +PG4 sp3_sp3_1 C2 C1 O1 HO1 180.000 10.0 3 +PG4 sp3_sp3_49 O4 C7 C8 O5 180.000 10.0 3 +PG4 sp3_sp3_58 C7 C8 O5 HO5 180.000 10.0 3 +PG4 sp3_sp3_4 O1 C1 C2 O2 180.000 10.0 3 +PG4 sp3_sp3_13 C1 C2 O2 C3 180.000 10.0 3 +PG4 sp3_sp3_16 C4 C3 O2 C2 180.000 10.0 3 +PG4 sp3_sp3_19 O2 C3 C4 O3 180.000 10.0 3 +PG4 sp3_sp3_28 C3 C4 O3 C5 180.000 10.0 3 +PG4 sp3_sp3_31 C6 C5 O3 C4 180.000 10.0 3 +PG4 sp3_sp3_34 O3 C5 C6 O4 180.000 10.0 3 +PG4 sp3_sp3_43 C5 C6 O4 C7 180.000 10.0 3 +PG4 sp3_sp3_46 C8 C7 O4 C6 180.000 10.0 3 +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +PG4 SMILES ACDLabs 10.04 OCCOCCOCCOCCO +PG4 SMILES_CANONICAL CACTVS 3.341 OCCOCCOCCOCCO +PG4 SMILES CACTVS 3.341 OCCOCCOCCOCCO +PG4 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(COCCOCCOCCO)O +PG4 SMILES "OpenEye OEToolkits" 1.5.0 C(COCCOCCOCCO)O +PG4 InChI InChI 1.03 InChI=1S/C8H18O5/c9-1-3-11-5-7-13-8-6-12-4-2-10/h9-10H,1-8H2 +PG4 InChIKey InChI 1.03 UWHCKJMYHZGTIT-UHFFFAOYSA-N +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +PG4 acedrg 243 "dictionary generator" +PG4 acedrg_database 11 "data source" +PG4 rdkit 2017.03.2 "Chemoinformatics tool" +PG4 refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/PGE.cif b/image_analysis/structure_refinement/monomers/PGE.cif new file mode 100644 index 000000000..63666644b --- /dev/null +++ b/image_analysis/structure_refinement/monomers/PGE.cif @@ -0,0 +1,168 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +PGE PGE "TRIETHYLENE GLYCOL" NON-POLYMER 24 10 . +# +data_comp_PGE +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +PGE C1 C CH2 0 18.715 -18.946 34.930 +PGE O1 O OH1 0 18.098 -20.073 34.339 +PGE C2 C CH2 0 19.228 -19.237 36.305 +PGE O2 O O2 0 18.136 -19.500 37.182 +PGE C3 C CH2 0 18.527 -19.893 38.496 +PGE C4 C CH2 0 18.196 -21.337 38.706 +PGE O4 O OH1 0 19.209 -25.686 36.980 +PGE C6 C CH2 0 19.520 -24.306 36.972 +PGE C5 C CH2 0 18.689 -23.532 37.946 +PGE O3 O O2 0 18.956 -22.140 37.808 +PGE H1 H H 0 18.064 -18.215 34.977 +PGE H12 H H 0 19.459 -18.656 34.363 +PGE HO1 H H 0 17.842 -19.875 33.558 +PGE H2 H H 0 19.741 -18.468 36.636 +PGE H22 H H 0 19.826 -20.016 36.277 +PGE H3 H H 0 18.049 -19.347 39.157 +PGE H32 H H 0 19.492 -19.753 38.624 +PGE H4 H H 0 17.237 -21.483 38.551 +PGE H42 H H 0 18.400 -21.592 39.632 +PGE HO4 H H 0 19.421 -26.016 37.730 +PGE H6 H H 0 19.375 -23.952 36.071 +PGE H62 H H 0 20.468 -24.192 37.195 +PGE H5 H H 0 18.897 -23.819 38.861 +PGE H52 H H 0 17.737 -23.704 37.778 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +PGE C1 O1 SINGLE n 1.414 0.0200 1.414 0.0200 +PGE C1 C2 SINGLE n 1.496 0.0200 1.496 0.0200 +PGE C2 O2 SINGLE n 1.423 0.0106 1.423 0.0106 +PGE O2 C3 SINGLE n 1.423 0.0106 1.423 0.0106 +PGE C3 C4 SINGLE n 1.496 0.0200 1.496 0.0200 +PGE C4 O3 SINGLE n 1.423 0.0106 1.423 0.0106 +PGE O4 C6 SINGLE n 1.414 0.0200 1.414 0.0200 +PGE C6 C5 SINGLE n 1.496 0.0200 1.496 0.0200 +PGE C5 O3 SINGLE n 1.423 0.0106 1.423 0.0106 +PGE C1 H1 SINGLE n 1.089 0.0100 0.980 0.0144 +PGE C1 H12 SINGLE n 1.089 0.0100 0.980 0.0144 +PGE O1 HO1 SINGLE n 0.970 0.0120 0.846 0.0200 +PGE C2 H2 SINGLE n 1.089 0.0100 0.982 0.0175 +PGE C2 H22 SINGLE n 1.089 0.0100 0.982 0.0175 +PGE C3 H3 SINGLE n 1.089 0.0100 0.982 0.0175 +PGE C3 H32 SINGLE n 1.089 0.0100 0.982 0.0175 +PGE C4 H4 SINGLE n 1.089 0.0100 0.982 0.0175 +PGE C4 H42 SINGLE n 1.089 0.0100 0.982 0.0175 +PGE O4 HO4 SINGLE n 0.970 0.0120 0.846 0.0200 +PGE C6 H6 SINGLE n 1.089 0.0100 0.980 0.0144 +PGE C6 H62 SINGLE n 1.089 0.0100 0.980 0.0144 +PGE C5 H5 SINGLE n 1.089 0.0100 0.982 0.0175 +PGE C5 H52 SINGLE n 1.089 0.0100 0.982 0.0175 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +PGE O1 C1 C2 112.284 1.56 +PGE O1 C1 H1 109.012 1.50 +PGE O1 C1 H12 109.012 1.50 +PGE C2 C1 H1 109.198 1.50 +PGE C2 C1 H12 109.198 1.50 +PGE H1 C1 H12 108.093 1.50 +PGE C1 O1 HO1 109.347 1.86 +PGE C1 C2 O2 109.904 1.68 +PGE C1 C2 H2 109.795 1.50 +PGE C1 C2 H22 109.795 1.50 +PGE O2 C2 H2 109.691 1.50 +PGE O2 C2 H22 109.691 1.50 +PGE H2 C2 H22 108.274 1.50 +PGE C2 O2 C3 112.795 1.50 +PGE O2 C3 C4 109.613 1.74 +PGE O2 C3 H3 109.691 1.50 +PGE O2 C3 H32 109.691 1.50 +PGE C4 C3 H3 109.729 1.50 +PGE C4 C3 H32 109.729 1.50 +PGE H3 C3 H32 108.274 1.50 +PGE C3 C4 O3 109.613 1.74 +PGE C3 C4 H4 109.729 1.50 +PGE C3 C4 H42 109.729 1.50 +PGE O3 C4 H4 109.691 1.50 +PGE O3 C4 H42 109.691 1.50 +PGE H4 C4 H42 108.274 1.50 +PGE C6 O4 HO4 109.347 1.86 +PGE O4 C6 C5 112.284 1.56 +PGE O4 C6 H6 109.012 1.50 +PGE O4 C6 H62 109.012 1.50 +PGE C5 C6 H6 109.198 1.50 +PGE C5 C6 H62 109.198 1.50 +PGE H6 C6 H62 108.093 1.50 +PGE C6 C5 O3 109.904 1.68 +PGE C6 C5 H5 109.795 1.50 +PGE C6 C5 H52 109.795 1.50 +PGE O3 C5 H5 109.691 1.50 +PGE O3 C5 H52 109.691 1.50 +PGE H5 C5 H52 108.274 1.50 +PGE C4 O3 C5 112.795 1.50 +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +PGE sp3_sp3_1 C2 C1 O1 HO1 180.000 10.0 3 +PGE sp3_sp3_4 O1 C1 C2 O2 180.000 10.0 3 +PGE sp3_sp3_13 C1 C2 O2 C3 180.000 10.0 3 +PGE sp3_sp3_16 C4 C3 O2 C2 180.000 10.0 3 +PGE sp3_sp3_19 O2 C3 C4 O3 180.000 10.0 3 +PGE sp3_sp3_28 C3 C4 O3 C5 180.000 10.0 3 +PGE sp3_sp3_31 C5 C6 O4 HO4 180.000 10.0 3 +PGE sp3_sp3_34 O3 C5 C6 O4 180.000 10.0 3 +PGE sp3_sp3_43 C6 C5 O3 C4 180.000 10.0 3 +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +PGE SMILES ACDLabs 10.04 OCCOCCOCCO +PGE SMILES_CANONICAL CACTVS 3.341 OCCOCCOCCO +PGE SMILES CACTVS 3.341 OCCOCCOCCO +PGE SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(COCCOCCO)O +PGE SMILES "OpenEye OEToolkits" 1.5.0 C(COCCOCCO)O +PGE InChI InChI 1.03 InChI=1S/C6H14O4/c7-1-3-9-5-6-10-4-2-8/h7-8H,1-6H2 +PGE InChIKey InChI 1.03 ZIBGPFATKBEMQZ-UHFFFAOYSA-N +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +PGE acedrg 243 "dictionary generator" +PGE acedrg_database 11 "data source" +PGE rdkit 2017.03.2 "Chemoinformatics tool" +PGE refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/PHE.cif b/image_analysis/structure_refinement/monomers/PHE.cif new file mode 100644 index 000000000..57e42ec86 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/PHE.cif @@ -0,0 +1,261 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +PHE PHE PHENYLALANINE peptide 23 12 . + +data_comp_PHE +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +PHE N N NT3 1 3.215 22.308 6.140 +PHE CA C CH1 0 4.240 21.287 5.785 +PHE C C C 0 5.492 21.998 5.258 +PHE O O O 0 5.348 22.751 4.269 +PHE CB C CH2 0 3.652 20.304 4.767 +PHE CG C CR6 0 4.548 19.121 4.423 +PHE CD1 C CR16 0 4.526 17.959 5.195 +PHE CD2 C CR16 0 5.408 19.169 3.325 +PHE CE1 C CR16 0 5.344 16.878 4.879 +PHE CE2 C CR16 0 6.225 18.087 3.012 +PHE CZ C CR16 0 6.192 16.943 3.789 +PHE OXT O OC -1 6.569 21.775 5.853 +PHE H H H 0 2.984 22.781 5.407 +PHE H2 H H 0 3.541 22.872 6.764 +PHE H3 H H 0 2.480 21.902 6.470 +PHE HA H H 0 4.482 20.785 6.608 +PHE HB3 H H 0 3.450 20.797 3.941 +PHE HB2 H H 0 2.802 19.961 5.122 +PHE HD1 H H 0 3.950 17.907 5.941 +PHE HD2 H H 0 5.437 19.946 2.791 +PHE HE1 H H 0 5.320 16.099 5.411 +PHE HE2 H H 0 6.803 18.134 2.267 +PHE HZ H H 0 6.746 16.210 3.575 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +PHE N n/a CA START +PHE H N . . +PHE H2 N . . +PHE H3 N . . +PHE CA N C . +PHE HA CA . . +PHE CB CA CG . +PHE HB3 CB . . +PHE HB2 CB . . +PHE CG CB CD1 . +PHE CD1 CG CE1 . +PHE HD1 CD1 . . +PHE CE1 CD1 CZ . +PHE HE1 CE1 . . +PHE CZ CE1 CE2 . +PHE HZ CZ . . +PHE CE2 CZ CD2 . +PHE HE2 CE2 . . +PHE CD2 CE2 HD2 . +PHE HD2 CD2 . . +PHE C CA . END +PHE O C . . +PHE OXT C . . +PHE CD2 CG . ADD + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +PHE N N(CCCH)(H)3 +PHE CA C(CC[6a]HH)(NH3)(COO)(H) +PHE C C(CCHN)(O)2 +PHE O O(CCO) +PHE CB C(C[6a]C[6a]2)(CCHN)(H)2 +PHE CG C[6a](C[6a]C[6a]H)2(CCHH){1|C<3>,2|H<1>} +PHE CD1 C[6a](C[6a]C[6a]C)(C[6a]C[6a]H)(H){1|C<3>,2|H<1>} +PHE CD2 C[6a](C[6a]C[6a]C)(C[6a]C[6a]H)(H){1|C<3>,2|H<1>} +PHE CE1 C[6a](C[6a]C[6a]H)2(H){1|C<3>,1|C<4>,1|H<1>} +PHE CE2 C[6a](C[6a]C[6a]H)2(H){1|C<3>,1|C<4>,1|H<1>} +PHE CZ C[6a](C[6a]C[6a]H)2(H){1|C<3>,2|H<1>} +PHE OXT O(CCO) +PHE H H(NCHH) +PHE H2 H(NCHH) +PHE H3 H(NCHH) +PHE HA H(CCCN) +PHE HB3 H(CC[6a]CH) +PHE HB2 H(CC[6a]CH) +PHE HD1 H(C[6a]C[6a]2) +PHE HD2 H(C[6a]C[6a]2) +PHE HE1 H(C[6a]C[6a]2) +PHE HE2 H(C[6a]C[6a]2) +PHE HZ H(C[6a]C[6a]2) + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +PHE N CA SINGLE n 1.489 0.0100 1.489 0.0100 +PHE CA C SINGLE n 1.531 0.0171 1.531 0.0171 +PHE CA CB SINGLE n 1.532 0.0100 1.532 0.0100 +PHE C O DOUBLE n 1.251 0.0183 1.251 0.0183 +PHE C OXT SINGLE n 1.251 0.0183 1.251 0.0183 +PHE CB CG SINGLE n 1.523 0.0100 1.523 0.0100 +PHE CG CD1 DOUBLE y 1.390 0.0116 1.390 0.0116 +PHE CG CD2 SINGLE y 1.390 0.0116 1.390 0.0116 +PHE CD1 CE1 SINGLE y 1.386 0.0131 1.386 0.0131 +PHE CD2 CE2 DOUBLE y 1.386 0.0131 1.386 0.0131 +PHE CE1 CZ DOUBLE y 1.376 0.0151 1.376 0.0151 +PHE CE2 CZ SINGLE y 1.376 0.0151 1.376 0.0151 +PHE N H SINGLE n 1.018 0.0520 0.902 0.0102 +PHE N H2 SINGLE n 1.018 0.0520 0.902 0.0102 +PHE N H3 SINGLE n 1.018 0.0520 0.902 0.0102 +PHE CA HA SINGLE n 1.092 0.0100 0.994 0.0200 +PHE CB HB3 SINGLE n 1.092 0.0100 0.983 0.0163 +PHE CB HB2 SINGLE n 1.092 0.0100 0.983 0.0163 +PHE CD1 HD1 SINGLE n 1.085 0.0150 0.944 0.0143 +PHE CD2 HD2 SINGLE n 1.085 0.0150 0.944 0.0143 +PHE CE1 HE1 SINGLE n 1.085 0.0150 0.944 0.0180 +PHE CE2 HE2 SINGLE n 1.085 0.0150 0.944 0.0180 +PHE CZ HZ SINGLE n 1.085 0.0150 0.944 0.0170 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +PHE CA N H 109.791 3.00 +PHE CA N H2 109.791 3.00 +PHE CA N H3 109.791 3.00 +PHE H N H2 109.032 3.00 +PHE H N H3 109.032 3.00 +PHE H2 N H3 109.032 3.00 +PHE N CA C 109.085 1.50 +PHE N CA CB 109.965 3.00 +PHE N CA HA 108.547 1.50 +PHE C CA CB 111.980 3.00 +PHE C CA HA 108.746 1.50 +PHE CB CA HA 108.686 1.50 +PHE CA C O 117.219 3.00 +PHE CA C OXT 117.219 3.00 +PHE O C OXT 125.562 1.50 +PHE CA CB CG 114.693 2.05 +PHE CA CB HB3 108.494 1.50 +PHE CA CB HB2 108.494 1.50 +PHE CG CB HB3 108.859 1.50 +PHE CG CB HB2 108.859 1.50 +PHE HB3 CB HB2 107.843 2.16 +PHE CB CG CD1 120.965 1.50 +PHE CB CG CD2 120.965 1.50 +PHE CD1 CG CD2 118.071 1.50 +PHE CG CD1 CE1 120.673 1.50 +PHE CG CD1 HD1 119.564 1.50 +PHE CE1 CD1 HD1 119.763 1.50 +PHE CG CD2 CE2 120.673 1.50 +PHE CG CD2 HD2 119.564 1.50 +PHE CE2 CD2 HD2 119.763 1.50 +PHE CD1 CE1 CZ 120.297 1.50 +PHE CD1 CE1 HE1 119.796 1.50 +PHE CZ CE1 HE1 119.907 1.50 +PHE CD2 CE2 CZ 120.297 1.50 +PHE CD2 CE2 HE2 119.796 1.50 +PHE CZ CE2 HE2 119.907 1.50 +PHE CE1 CZ CE2 119.995 1.50 +PHE CE1 CZ HZ 120.000 1.50 +PHE CE2 CZ HZ 120.000 1.50 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +PHE chi1 N CA CB CG -60.000 10.0 3 +PHE chi2 CA CB CG CD1 90.000 10.0 6 +PHE CONST_1 CB CG CD1 CE1 0.000 0.0 1 +PHE CONST_2 CG CD1 CE1 CZ 0.000 0.0 1 +PHE CONST_3 CZ CE2 CD2 CG 0.000 0.0 1 +PHE CONST_4 CD1 CE1 CZ CE2 0.000 0.0 1 +PHE CONST_5 CE1 CZ CE2 CD2 0.000 0.0 1 +PHE sp3_sp3_1 C CA N H 180.000 10.0 3 +PHE const_21 CE2 CD2 CG CD1 0.000 0.0 1 +PHE sp2_sp3_1 O C CA N 0.000 10.0 6 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +PHE chir_1 CA N C CB positive + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +PHE plan-1 CB 0.020 +PHE plan-1 CD1 0.020 +PHE plan-1 CD2 0.020 +PHE plan-1 CE1 0.020 +PHE plan-1 CE2 0.020 +PHE plan-1 CG 0.020 +PHE plan-1 CZ 0.020 +PHE plan-1 HD1 0.020 +PHE plan-1 HD2 0.020 +PHE plan-1 HE1 0.020 +PHE plan-1 HE2 0.020 +PHE plan-1 HZ 0.020 +PHE plan-2 C 0.020 +PHE plan-2 CA 0.020 +PHE plan-2 O 0.020 +PHE plan-2 OXT 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +PHE SMILES ACDLabs 10.04 O=C(O)C(N)Cc1ccccc1 +PHE SMILES_CANONICAL CACTVS 3.341 N[C@@H](Cc1ccccc1)C(O)=O +PHE SMILES CACTVS 3.341 N[CH](Cc1ccccc1)C(O)=O +PHE SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1ccc(cc1)C[C@@H](C(=O)O)N +PHE SMILES "OpenEye OEToolkits" 1.5.0 c1ccc(cc1)CC(C(=O)O)N +PHE InChI InChI 1.03 InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)/t8-/m0/s1 +PHE InChIKey InChI 1.03 COLNVLDHVKWLRT-QMMMGPOBSA-N + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +PHE acedrg 278 "dictionary generator" +PHE acedrg_database 12 "data source" +PHE rdkit 2019.09.1 "Chemoinformatics tool" +PHE refmac5 5.8.0419 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/PO4.cif b/image_analysis/structure_refinement/monomers/PO4.cif new file mode 100644 index 000000000..6c80df723 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/PO4.cif @@ -0,0 +1,86 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +PO4 PO4 "PHOSPHATE ION" NON-POLYMER 5 5 . +# +data_comp_PO4 +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +PO4 P P P 0 29.978 23.532 13.276 +PO4 O1 O O 0 31.126 22.989 14.118 +PO4 O2 O OP -1 30.372 24.882 12.690 +PO4 O3 O OP -1 29.672 22.557 12.145 +PO4 O4 O OP -1 28.741 23.699 14.151 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +PO4 P O1 DOUBLE n 1.524 0.0200 1.524 0.0200 +PO4 P O2 SINGLE n 1.524 0.0200 1.524 0.0200 +PO4 P O3 SINGLE n 1.524 0.0200 1.524 0.0200 +PO4 P O4 SINGLE n 1.524 0.0200 1.524 0.0200 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +PO4 O1 P O2 109.461 1.50 +PO4 O1 P O3 109.461 1.50 +PO4 O1 P O4 109.461 1.50 +PO4 O2 P O3 109.461 1.50 +PO4 O2 P O4 109.461 1.50 +PO4 O3 P O4 109.461 1.50 +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +PO4 chir_1 P O2 O3 O4 both +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +PO4 SMILES ACDLabs 10.04 "[O-]P([O-])([O-])=O" +PO4 SMILES_CANONICAL CACTVS 3.341 "[O-][P]([O-])([O-])=O" +PO4 SMILES CACTVS 3.341 "[O-][P]([O-])([O-])=O" +PO4 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "[O-]P(=O)([O-])[O-]" +PO4 SMILES "OpenEye OEToolkits" 1.5.0 "[O-]P(=O)([O-])[O-]" +PO4 InChI InChI 1.03 InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3 +PO4 InChIKey InChI 1.03 NBIIXXVUZAFLBC-UHFFFAOYSA-K +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +PO4 acedrg 243 "dictionary generator" +PO4 acedrg_database 11 "data source" +PO4 rdkit 2017.03.2 "Chemoinformatics tool" +PO4 refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/PRO.cif b/image_analysis/structure_refinement/monomers/PRO.cif new file mode 100644 index 000000000..2330d47a9 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/PRO.cif @@ -0,0 +1,216 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +PRO PRO PROLINE P-peptide 17 8 . + +data_comp_PRO +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.alt_atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +PRO N N N NT2 1 39.160 37.649 83.026 +PRO CA CA C CH1 0 38.550 38.680 82.125 +PRO C C C C 0 37.155 39.077 82.602 +PRO O O O O 0 36.450 38.196 83.146 +PRO CB CB C CH2 0 38.553 38.007 80.756 +PRO CG CG C CH2 0 38.265 36.558 81.098 +PRO CD CD C CH2 0 38.934 36.298 82.416 +PRO OXT OXT O OC -1 36.821 40.268 82.409 +PRO H H H H 0 40.054 37.806 83.097 +PRO H2 H2 H H 0 38.800 37.681 83.862 +PRO HA HA H H 0 39.125 39.473 82.102 +PRO HB3 HB3 H H 0 39.422 38.100 80.320 +PRO HB2 HB2 H H 0 37.858 38.378 80.178 +PRO HG3 HG3 H H 0 38.625 35.964 80.410 +PRO HG2 HG2 H H 0 37.302 36.406 81.169 +PRO HD3 HD3 H H 0 38.363 35.755 82.994 +PRO HD2 HD2 H H 0 39.785 35.835 82.289 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +PRO N n/a CA START +PRO CA N C . +PRO HA CA . . +PRO CB CA CG . +PRO HB3 CB . . +PRO HB2 CB . . +PRO CG CB CD . +PRO HG3 CG . . +PRO HG2 CG . . +PRO CD CG HD2 . +PRO HD3 CD . . +PRO HD2 CD . . +PRO C CA . END +PRO O C . . +PRO OXT C . . +PRO H N . . +PRO H2 N . . +PRO CD N . ADD + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +PRO N N[5](C[5]C[5]CH)(C[5]C[5]HH)(H)2{4|H<1>} +PRO CA C[5](C[5]C[5]HH)(N[5]C[5]HH)(COO)(H){4|H<1>} +PRO C C(C[5]C[5]N[5]H)(O)2 +PRO O O(CC[5]O) +PRO CB C[5](C[5]C[5]HH)(C[5]N[5]CH)(H)2{4|H<1>} +PRO CG C[5](C[5]C[5]HH)(C[5]N[5]HH)(H)2{1|C<3>,3|H<1>} +PRO CD C[5](C[5]C[5]HH)(N[5]C[5]HH)(H)2{1|C<3>,3|H<1>} +PRO OXT O(CC[5]O) +PRO H H(N[5]C[5]2H) +PRO H2 H(N[5]C[5]2H) +PRO HA H(C[5]C[5]N[5]C) +PRO HB3 H(C[5]C[5]2H) +PRO HB2 H(C[5]C[5]2H) +PRO HG3 H(C[5]C[5]2H) +PRO HG2 H(C[5]C[5]2H) +PRO HD3 H(C[5]C[5]N[5]H) +PRO HD2 H(C[5]C[5]N[5]H) + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.value_order +_chem_comp_bond.pdbx_aromatic_flag +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +PRO N CA SINGLE n 1.496 0.0142 1.496 0.0142 +PRO N CD SINGLE n 1.499 0.0135 1.499 0.0135 +PRO CA C SINGLE n 1.525 0.0103 1.525 0.0103 +PRO CA CB SINGLE n 1.526 0.0157 1.526 0.0157 +PRO C O DOUBLE n 1.252 0.0117 1.252 0.0117 +PRO C OXT SINGLE n 1.252 0.0117 1.252 0.0117 +PRO CB CG SINGLE n 1.516 0.0179 1.516 0.0179 +PRO CG CD SINGLE n 1.497 0.0200 1.497 0.0200 +PRO N H SINGLE n 1.018 0.0520 0.910 0.0200 +PRO N H2 SINGLE n 1.018 0.0520 0.910 0.0200 +PRO CA HA SINGLE n 1.092 0.0100 0.980 0.0200 +PRO CB HB3 SINGLE n 1.092 0.0100 0.977 0.0145 +PRO CB HB2 SINGLE n 1.092 0.0100 0.977 0.0145 +PRO CG HG3 SINGLE n 1.092 0.0100 0.978 0.0181 +PRO CG HG2 SINGLE n 1.092 0.0100 0.978 0.0181 +PRO CD HD3 SINGLE n 1.092 0.0100 0.977 0.0199 +PRO CD HD2 SINGLE n 1.092 0.0100 0.977 0.0199 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +PRO CA N CD 107.978 1.50 +PRO CA N H 109.889 3.00 +PRO CA N H2 109.889 3.00 +PRO CD N H 110.257 3.00 +PRO CD N H2 110.257 3.00 +PRO H N H2 108.772 3.00 +PRO N CA C 110.397 1.50 +PRO N CA CB 103.994 1.50 +PRO N CA HA 109.579 1.50 +PRO C CA CB 113.159 3.00 +PRO C CA HA 109.687 1.50 +PRO CB CA HA 109.910 1.89 +PRO CA C O 116.979 3.00 +PRO CA C OXT 116.979 3.00 +PRO O C OXT 126.043 1.52 +PRO CA CB CG 101.701 3.00 +PRO CA CB HB3 110.865 1.50 +PRO CA CB HB2 110.865 1.50 +PRO CG CB HB3 110.891 1.59 +PRO CG CB HB2 110.891 1.59 +PRO HB3 CB HB2 108.880 2.25 +PRO CB CG CD 105.541 3.00 +PRO CB CG HG3 110.897 1.50 +PRO CB CG HG2 110.897 1.50 +PRO CD CG HG3 110.621 1.50 +PRO CD CG HG2 110.621 1.50 +PRO HG3 CG HG2 108.871 1.50 +PRO N CD CG 104.386 2.30 +PRO N CD HD3 110.569 1.50 +PRO N CD HD2 110.569 1.50 +PRO CG CD HD3 111.131 1.62 +PRO CG CD HD2 111.131 1.62 +PRO HD3 CD HD2 109.116 1.50 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +PRO chi1 N CA CB CG -60.000 10.0 3 +PRO chi2 CA CB CG CD 180.000 10.0 3 +PRO sp3_sp3_1 CB CA N CD 60.000 10.0 3 +PRO sp3_sp3_28 N CD CG CB -60.000 10.0 3 +PRO sp3_sp3_37 CG CD N CA 180.000 10.0 3 +PRO sp2_sp3_1 O C CA N 0.000 10.0 6 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +PRO chir_1 CA N C CB positive + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +PRO plan-1 C 0.020 +PRO plan-1 CA 0.020 +PRO plan-1 O 0.020 +PRO plan-1 OXT 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +PRO SMILES ACDLabs 10.04 "O=C(O)C1NCCC1" +PRO SMILES_CANONICAL CACTVS 3.341 "OC(=O)[C@@H]1CCCN1" +PRO SMILES CACTVS 3.341 "OC(=O)[CH]1CCCN1" +PRO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1C[C@H](NC1)C(=O)O" +PRO SMILES "OpenEye OEToolkits" 1.5.0 "C1CC(NC1)C(=O)O" +PRO InChI InChI 1.03 "InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1" +PRO InChIKey InChI 1.03 ONIBWKKTOPOVIA-BYPYZUCNSA-N + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +PRO acedrg 281 "dictionary generator" +PRO acedrg_database 12 "data source" +PRO rdkit 2019.09.1 "Chemoinformatics tool" +PRO refmac5 5.8.0419 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/SER.cif b/image_analysis/structure_refinement/monomers/SER.cif new file mode 100644 index 000000000..f16baafc7 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/SER.cif @@ -0,0 +1,188 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +SER SER SERINE peptide 14 7 . + +data_comp_SER +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +SER N N NT3 1 88.105 -7.500 -9.831 +SER CA C CH1 0 87.822 -7.221 -11.265 +SER C C C 0 88.475 -5.896 -11.689 +SER O O O 0 88.336 -4.918 -10.921 +SER CB C CH2 0 86.337 -7.203 -11.533 +SER OG O OH1 0 85.742 -8.447 -11.190 +SER OXT O OC -1 89.099 -5.887 -12.773 +SER H H H 0 87.553 -7.016 -9.304 +SER H2 H H 0 88.960 -7.295 -9.626 +SER H3 H H 0 87.971 -8.377 -9.665 +SER HA H H 0 88.226 -7.948 -11.803 +SER HB3 H H 0 86.182 -7.019 -12.479 +SER HB2 H H 0 85.923 -6.490 -11.011 +SER HG H H 0 84.904 -8.380 -11.287 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +SER N n/a CA START +SER H N . . +SER H2 N . . +SER H3 N . . +SER CA N C . +SER HA CA . . +SER CB CA OG . +SER HB3 CB . . +SER HB2 CB . . +SER OG CB HG . +SER HG OG . . +SER C CA . END +SER O C . . +SER OXT C . . + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +SER N N(CCCH)(H)3 +SER CA C(CHHO)(NH3)(COO)(H) +SER C C(CCHN)(O)2 +SER O O(CCO) +SER CB C(CCHN)(OH)(H)2 +SER OG O(CCHH)(H) +SER OXT O(CCO) +SER H H(NCHH) +SER H2 H(NCHH) +SER H3 H(NCHH) +SER HA H(CCCN) +SER HB3 H(CCHO) +SER HB2 H(CCHO) +SER HG H(OC) + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +SER N CA SINGLE n 1.487 0.0100 1.487 0.0100 +SER CA C SINGLE n 1.536 0.0100 1.536 0.0100 +SER CA CB SINGLE n 1.508 0.0190 1.508 0.0190 +SER C O DOUBLE n 1.251 0.0183 1.251 0.0183 +SER C OXT SINGLE n 1.251 0.0183 1.251 0.0183 +SER CB OG SINGLE n 1.421 0.0108 1.421 0.0108 +SER N H SINGLE n 1.018 0.0520 0.902 0.0102 +SER N H2 SINGLE n 1.018 0.0520 0.902 0.0102 +SER N H3 SINGLE n 1.018 0.0520 0.902 0.0102 +SER CA HA SINGLE n 1.092 0.0100 0.991 0.0200 +SER CB HB3 SINGLE n 1.092 0.0100 0.976 0.0180 +SER CB HB2 SINGLE n 1.092 0.0100 0.976 0.0180 +SER OG HG SINGLE n 0.972 0.0180 0.846 0.0200 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +SER CA N H 109.696 3.00 +SER CA N H2 109.696 3.00 +SER CA N H3 109.696 3.00 +SER H N H2 109.032 3.00 +SER H N H3 109.032 3.00 +SER H2 N H3 109.032 3.00 +SER N CA C 109.839 1.50 +SER N CA CB 111.152 1.50 +SER N CA HA 108.129 1.50 +SER C CA CB 111.300 1.50 +SER C CA HA 108.235 1.50 +SER CB CA HA 108.445 1.50 +SER CA C O 117.199 1.50 +SER CA C OXT 117.189 1.50 +SER O C OXT 125.593 1.50 +SER CA CB OG 110.934 1.86 +SER CA CB HB3 109.238 1.50 +SER CA CB HB2 109.238 1.50 +SER OG CB HB3 109.353 1.50 +SER OG CB HB2 109.353 1.50 +SER HB3 CB HB2 108.095 1.88 +SER CB OG HG 108.539 3.00 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +SER chi1 N CA CB OG -60.000 10.0 3 +SER hh1 CA CB OG HG 180.000 10.0 3 +SER sp3_sp3_1 C CA N H 180.000 10.0 3 +SER sp2_sp3_1 O C CA N 0.000 10.0 6 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +SER chir_1 CA N C CB positive + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +SER plan-1 C 0.020 +SER plan-1 CA 0.020 +SER plan-1 O 0.020 +SER plan-1 OXT 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +SER SMILES ACDLabs 10.04 O=C(O)C(N)CO +SER SMILES_CANONICAL CACTVS 3.341 N[C@@H](CO)C(O)=O +SER SMILES CACTVS 3.341 N[CH](CO)C(O)=O +SER SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@@H](C(=O)O)N)O +SER SMILES "OpenEye OEToolkits" 1.5.0 C(C(C(=O)O)N)O +SER InChI InChI 1.03 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m0/s1 +SER InChIKey InChI 1.03 MTCFGRXMJLQNBG-REOHCLBHSA-N + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +SER acedrg 278 "dictionary generator" +SER acedrg_database 12 "data source" +SER rdkit 2019.09.1 "Chemoinformatics tool" +SER refmac5 5.8.0419 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/SO4.cif b/image_analysis/structure_refinement/monomers/SO4.cif new file mode 100644 index 000000000..1f560acff --- /dev/null +++ b/image_analysis/structure_refinement/monomers/SO4.cif @@ -0,0 +1,86 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +SO4 SO4 "SULFATE ION" NON-POLYMER 5 5 . +# +data_comp_SO4 +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +SO4 S S S3 0 16.537 34.975 5.493 +SO4 O1 O O 0 17.831 34.952 4.866 +SO4 O2 O O 0 16.570 35.855 6.629 +SO4 O3 O OS -1 15.557 35.444 4.551 +SO4 O4 O OS -1 16.190 33.647 5.924 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +SO4 S O1 DOUBLE n 1.438 0.0156 1.438 0.0156 +SO4 S O2 DOUBLE n 1.438 0.0156 1.438 0.0156 +SO4 S O3 SINGLE n 1.438 0.0156 1.438 0.0156 +SO4 S O4 SINGLE n 1.438 0.0156 1.438 0.0156 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +SO4 O1 S O2 109.467 1.50 +SO4 O1 S O3 109.467 1.50 +SO4 O1 S O4 109.467 1.50 +SO4 O2 S O3 109.467 1.50 +SO4 O2 S O4 109.467 1.50 +SO4 O3 S O4 109.467 1.50 +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +SO4 chir_1 S O1 O2 O3 both +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +SO4 SMILES ACDLabs 10.04 "[O-]S([O-])(=O)=O" +SO4 SMILES_CANONICAL CACTVS 3.341 "[O-][S]([O-])(=O)=O" +SO4 SMILES CACTVS 3.341 "[O-][S]([O-])(=O)=O" +SO4 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "[O-]S(=O)(=O)[O-]" +SO4 SMILES "OpenEye OEToolkits" 1.5.0 "[O-]S(=O)(=O)[O-]" +SO4 InChI InChI 1.03 InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2 +SO4 InChIKey InChI 1.03 QAOWNCQODCNURD-UHFFFAOYSA-L +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +SO4 acedrg 243 "dictionary generator" +SO4 acedrg_database 11 "data source" +SO4 rdkit 2017.03.2 "Chemoinformatics tool" +SO4 refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/THR.cif b/image_analysis/structure_refinement/monomers/THR.cif new file mode 100644 index 000000000..ecef5ae40 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/THR.cif @@ -0,0 +1,208 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +THR THR THREONINE peptide 17 8 . + +data_comp_THR +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +THR N N NT3 1 36.284 31.964 31.738 +THR CA C CH1 0 35.016 31.199 31.745 +THR C C C 0 34.952 30.333 30.501 +THR O O O 0 35.086 30.909 29.398 +THR CB C CH1 0 33.833 32.166 31.829 +THR OG1 O OH1 0 34.044 32.962 32.993 +THR CG2 C CH3 0 32.493 31.457 31.927 +THR OXT O OC -1 34.770 29.107 30.668 +THR H H H 0 36.319 32.492 31.007 +THR H2 H H 0 36.984 31.395 31.731 +THR H3 H H 0 36.331 32.480 32.477 +THR HA H H 0 35.006 30.619 32.537 +THR HB H H 0 33.830 32.749 31.033 +THR HG1 H H 0 34.002 32.475 33.707 +THR HG21 H H 0 32.588 30.657 32.470 +THR HG22 H H 0 32.191 31.210 31.037 +THR HG23 H H 0 31.841 32.050 32.336 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +THR N n/a CA START +THR H N . . +THR H2 N . . +THR H3 N . . +THR CA N C . +THR HA CA . . +THR CB CA CG2 . +THR HB CB . . +THR OG1 CB HG1 . +THR HG1 OG1 . . +THR CG2 CB HG23 . +THR HG21 CG2 . . +THR HG22 CG2 . . +THR HG23 CG2 . . +THR C CA . END +THR O C . . +THR OXT C . . + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +THR N N(CCCH)(H)3 +THR CA C(CCHO)(NH3)(COO)(H) +THR C C(CCHN)(O)2 +THR O O(CCO) +THR CB C(CCHN)(CH3)(OH)(H) +THR OG1 O(CCCH)(H) +THR CG2 C(CCHO)(H)3 +THR OXT O(CCO) +THR H H(NCHH) +THR H2 H(NCHH) +THR H3 H(NCHH) +THR HA H(CCCN) +THR HB H(CCCO) +THR HG1 H(OC) +THR HG21 H(CCHH) +THR HG22 H(CCHH) +THR HG23 H(CCHH) + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +THR N CA SINGLE n 1.480 0.0122 1.480 0.0122 +THR CA C SINGLE n 1.515 0.0129 1.515 0.0129 +THR CA CB SINGLE n 1.528 0.0100 1.528 0.0100 +THR C O DOUBLE n 1.251 0.0183 1.251 0.0183 +THR C OXT SINGLE n 1.251 0.0183 1.251 0.0183 +THR CB OG1 SINGLE n 1.424 0.0100 1.424 0.0100 +THR CB CG2 SINGLE n 1.518 0.0100 1.518 0.0100 +THR N H SINGLE n 1.018 0.0520 0.902 0.0102 +THR N H2 SINGLE n 1.018 0.0520 0.902 0.0102 +THR N H3 SINGLE n 1.018 0.0520 0.902 0.0102 +THR CA HA SINGLE n 1.092 0.0100 0.982 0.0200 +THR CB HB SINGLE n 1.092 0.0100 0.987 0.0100 +THR OG1 HG1 SINGLE n 0.972 0.0180 0.864 0.0200 +THR CG2 HG21 SINGLE n 1.092 0.0100 0.972 0.0156 +THR CG2 HG22 SINGLE n 1.092 0.0100 0.972 0.0156 +THR CG2 HG23 SINGLE n 1.092 0.0100 0.972 0.0156 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +THR CA N H 109.577 1.50 +THR CA N H2 109.577 1.50 +THR CA N H3 109.577 1.50 +THR H N H2 109.032 3.00 +THR H N H3 109.032 3.00 +THR H2 N H3 109.032 3.00 +THR N CA C 109.121 1.50 +THR N CA CB 109.645 1.84 +THR N CA HA 108.639 1.50 +THR C CA CB 111.778 1.58 +THR C CA HA 109.055 1.50 +THR CB CA HA 108.870 1.50 +THR CA C O 117.098 1.50 +THR CA C OXT 117.098 1.50 +THR O C OXT 125.804 1.50 +THR CA CB OG1 105.245 3.00 +THR CA CB CG2 112.544 1.50 +THR CA CB HB 109.595 2.39 +THR OG1 CB CG2 109.974 3.00 +THR OG1 CB HB 109.323 1.86 +THR CG2 CB HB 109.170 2.61 +THR CB OG1 HG1 109.544 3.00 +THR CB CG2 HG21 109.532 1.50 +THR CB CG2 HG22 109.532 1.50 +THR CB CG2 HG23 109.532 1.50 +THR HG21 CG2 HG22 109.425 1.50 +THR HG21 CG2 HG23 109.425 1.50 +THR HG22 CG2 HG23 109.425 1.50 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +THR chi1 N CA CB CG2 -60.000 10.0 3 +THR hh1 CA CB OG1 HG1 -60.000 10.0 3 +THR hh2 CA CB CG2 HG23 -60.000 10.0 3 +THR sp3_sp3_1 C CA N H 180.000 10.0 3 +THR sp2_sp3_1 O C CA N 0.000 10.0 6 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +THR chir_1 CA N C CB positive +THR chir_2 CB OG1 CA CG2 negative + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +THR plan-1 C 0.020 +THR plan-1 CA 0.020 +THR plan-1 O 0.020 +THR plan-1 OXT 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +THR SMILES ACDLabs 10.04 O=C(O)C(N)C(O)C +THR SMILES_CANONICAL CACTVS 3.341 C[C@@H](O)[C@H](N)C(O)=O +THR SMILES CACTVS 3.341 C[CH](O)[CH](N)C(O)=O +THR SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[C@H]([C@@H](C(=O)O)N)O +THR SMILES "OpenEye OEToolkits" 1.5.0 CC(C(C(=O)O)N)O +THR InChI InChI 1.03 InChI=1S/C4H9NO3/c1-2(6)3(5)4(7)8/h2-3,6H,5H2,1H3,(H,7,8)/t2-,3+/m1/s1 +THR InChIKey InChI 1.03 AYFVYJQAPQTCCC-GBXIJSLDSA-N + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +THR acedrg 278 "dictionary generator" +THR acedrg_database 12 "data source" +THR rdkit 2019.09.1 "Chemoinformatics tool" +THR refmac5 5.8.0419 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/TRP.cif b/image_analysis/structure_refinement/monomers/TRP.cif new file mode 100644 index 000000000..8c24a618c --- /dev/null +++ b/image_analysis/structure_refinement/monomers/TRP.cif @@ -0,0 +1,301 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +TRP TRP TRYPTOPHAN peptide 27 15 . + +data_comp_TRP +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +TRP N N NT3 1 75.046 60.221 32.550 +TRP CA C CH1 0 74.659 61.570 32.056 +TRP C C C 0 73.758 61.438 30.822 +TRP O O O 0 72.787 62.222 30.736 +TRP CB C CH2 0 75.903 62.411 31.737 +TRP CG C CR5 0 76.760 62.727 32.935 +TRP CD1 C CR15 0 77.836 62.019 33.383 +TRP CD2 C CR56 0 76.605 63.839 33.843 +TRP NE1 N NR15 0 78.364 62.608 34.501 +TRP CE2 C CR56 0 77.632 63.725 34.809 +TRP CE3 C CR16 0 75.707 64.913 33.936 +TRP CZ2 C CR16 0 77.780 64.645 35.849 +TRP CZ3 C CR16 0 75.854 65.821 34.965 +TRP CH2 C CR16 0 76.878 65.687 35.909 +TRP OXT O OC -1 74.059 60.555 29.988 +TRP H H H 0 75.680 59.865 32.016 +TRP H2 H H 0 74.332 59.671 32.560 +TRP H3 H H 0 75.369 60.277 33.391 +TRP HA H H 0 74.147 62.030 32.775 +TRP HB3 H H 0 75.613 63.253 31.325 +TRP HB2 H H 0 76.446 61.928 31.078 +TRP HD1 H H 0 78.177 61.234 32.984 +TRP HE1 H H 0 79.056 62.317 34.946 +TRP HE3 H H 0 75.014 65.011 33.305 +TRP HZ2 H H 0 78.468 64.556 36.485 +TRP HZ3 H H 0 75.254 66.545 35.034 +TRP HH2 H H 0 76.954 66.321 36.599 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +TRP N n/a CA START +TRP H N . . +TRP H2 N . . +TRP H3 N . . +TRP CA N C . +TRP HA CA . . +TRP CB CA CG . +TRP HB3 CB . . +TRP HB2 CB . . +TRP CG CB CD1 . +TRP CD1 CG NE1 . +TRP HD1 CD1 . . +TRP NE1 CD1 CE2 . +TRP HE1 NE1 . . +TRP CE2 NE1 CD2 . +TRP CD2 CE2 CE3 . +TRP CE3 CD2 CZ3 . +TRP HE3 CE3 . . +TRP CZ3 CE3 CH2 . +TRP HZ3 CZ3 . . +TRP CH2 CZ3 CZ2 . +TRP HH2 CH2 . . +TRP CZ2 CH2 HZ2 . +TRP HZ2 CZ2 . . +TRP C CA . END +TRP O C . . +TRP OXT C . . +TRP CD2 CG . ADD + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +TRP N N(CCCH)(H)3 +TRP CA C(CC[5a]HH)(NH3)(COO)(H) +TRP C C(CCHN)(O)2 +TRP O O(CCO) +TRP CB C(C[5a]C[5a,6a]C[5a])(CCHN)(H)2 +TRP CG C[5a](C[5a,6a]C[5a,6a]C[6a])(C[5a]N[5a]H)(CCHH){2|C<3>,2|H<1>} +TRP CD1 C[5a](C[5a]C[5a,6a]C)(N[5a]C[5a,6a]H)(H){2|C<3>} +TRP CD2 C[5a,6a](C[5a,6a]C[6a]N[5a])(C[5a]C[5a]C)(C[6a]C[6a]H){1|C<3>,4|H<1>} +TRP NE1 N[5a](C[5a,6a]C[5a,6a]C[6a])(C[5a]C[5a]H)(H){1|C<4>,1|H<1>,2|C<3>} +TRP CE2 C[5a,6a](C[5a,6a]C[5a]C[6a])(C[6a]C[6a]H)(N[5a]C[5a]H){1|C<3>,1|C<4>,3|H<1>} +TRP CE3 C[6a](C[5a,6a]C[5a,6a]C[5a])(C[6a]C[6a]H)(H){1|C<4>,1|H<1>,1|N<3>,2|C<3>} +TRP CZ2 C[6a](C[5a,6a]C[5a,6a]N[5a])(C[6a]C[6a]H)(H){2|H<1>,3|C<3>} +TRP CZ3 C[6a](C[6a]C[5a,6a]H)(C[6a]C[6a]H)(H){1|H<1>,2|C<3>} +TRP CH2 C[6a](C[6a]C[5a,6a]H)(C[6a]C[6a]H)(H){1|C<3>,1|H<1>,1|N<3>} +TRP OXT O(CCO) +TRP H H(NCHH) +TRP H2 H(NCHH) +TRP H3 H(NCHH) +TRP HA H(CCCN) +TRP HB3 H(CC[5a]CH) +TRP HB2 H(CC[5a]CH) +TRP HD1 H(C[5a]C[5a]N[5a]) +TRP HE1 H(N[5a]C[5a,6a]C[5a]) +TRP HE3 H(C[6a]C[5a,6a]C[6a]) +TRP HZ2 H(C[6a]C[5a,6a]C[6a]) +TRP HZ3 H(C[6a]C[6a]2) +TRP HH2 H(C[6a]C[6a]2) + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +TRP N CA SINGLE n 1.486 0.0100 1.486 0.0100 +TRP CA C SINGLE n 1.532 0.0129 1.532 0.0129 +TRP CA CB SINGLE n 1.535 0.0100 1.535 0.0100 +TRP C O DOUBLE n 1.251 0.0183 1.251 0.0183 +TRP C OXT SINGLE n 1.251 0.0183 1.251 0.0183 +TRP CB CG SINGLE n 1.506 0.0100 1.506 0.0100 +TRP CG CD1 DOUBLE y 1.364 0.0100 1.364 0.0100 +TRP CG CD2 SINGLE y 1.445 0.0100 1.445 0.0100 +TRP CD1 NE1 SINGLE y 1.369 0.0100 1.369 0.0100 +TRP CD2 CE2 DOUBLE y 1.412 0.0100 1.412 0.0100 +TRP CD2 CE3 SINGLE y 1.399 0.0100 1.399 0.0100 +TRP NE1 CE2 SINGLE y 1.370 0.0100 1.370 0.0100 +TRP CE2 CZ2 SINGLE y 1.393 0.0100 1.393 0.0100 +TRP CE3 CZ3 DOUBLE y 1.377 0.0100 1.377 0.0100 +TRP CZ2 CH2 DOUBLE y 1.376 0.0101 1.376 0.0101 +TRP CZ3 CH2 SINGLE y 1.394 0.0120 1.394 0.0120 +TRP N H SINGLE n 1.018 0.0520 0.902 0.0102 +TRP N H2 SINGLE n 1.018 0.0520 0.902 0.0102 +TRP N H3 SINGLE n 1.018 0.0520 0.902 0.0102 +TRP CA HA SINGLE n 1.092 0.0100 0.995 0.0200 +TRP CB HB3 SINGLE n 1.092 0.0100 0.981 0.0100 +TRP CB HB2 SINGLE n 1.092 0.0100 0.981 0.0100 +TRP CD1 HD1 SINGLE n 1.085 0.0150 0.944 0.0195 +TRP NE1 HE1 SINGLE n 1.013 0.0120 0.873 0.0200 +TRP CE3 HE3 SINGLE n 1.085 0.0150 0.942 0.0199 +TRP CZ2 HZ2 SINGLE n 1.085 0.0150 0.942 0.0181 +TRP CZ3 HZ3 SINGLE n 1.085 0.0150 0.943 0.0167 +TRP CH2 HH2 SINGLE n 1.085 0.0150 0.941 0.0176 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +TRP CA N H 109.786 3.00 +TRP CA N H2 109.786 3.00 +TRP CA N H3 109.786 3.00 +TRP H N H2 109.032 3.00 +TRP H N H3 109.032 3.00 +TRP H2 N H3 109.032 3.00 +TRP N CA C 109.790 1.50 +TRP N CA CB 110.346 1.50 +TRP N CA HA 108.404 1.50 +TRP C CA CB 111.156 1.50 +TRP C CA HA 108.682 1.50 +TRP CB CA HA 108.429 1.50 +TRP CA C O 117.155 2.01 +TRP CA C OXT 117.155 2.01 +TRP O C OXT 125.691 1.50 +TRP CA CB CG 113.870 1.50 +TRP CA CB HB3 108.522 1.50 +TRP CA CB HB2 108.522 1.50 +TRP CG CB HB3 108.877 1.50 +TRP CG CB HB2 108.877 1.50 +TRP HB3 CB HB2 107.959 3.00 +TRP CB CG CD1 126.940 2.13 +TRP CB CG CD2 126.837 1.66 +TRP CD1 CG CD2 106.223 1.50 +TRP CG CD1 NE1 110.303 1.50 +TRP CG CD1 HD1 125.325 2.99 +TRP NE1 CD1 HD1 124.372 1.81 +TRP CG CD2 CE2 106.978 1.50 +TRP CG CD2 CE3 134.327 1.50 +TRP CE2 CD2 CE3 118.695 1.50 +TRP CD1 NE1 CE2 109.057 1.50 +TRP CD1 NE1 HE1 125.366 3.00 +TRP CE2 NE1 HE1 125.577 3.00 +TRP CD2 CE2 NE1 107.438 1.50 +TRP CD2 CE2 CZ2 122.273 1.50 +TRP NE1 CE2 CZ2 130.289 1.50 +TRP CD2 CE3 CZ3 118.811 1.50 +TRP CD2 CE3 HE3 120.479 1.50 +TRP CZ3 CE3 HE3 120.709 1.50 +TRP CE2 CZ2 CH2 117.418 1.50 +TRP CE2 CZ2 HZ2 121.196 1.50 +TRP CH2 CZ2 HZ2 121.386 1.50 +TRP CE3 CZ3 CH2 121.228 1.50 +TRP CE3 CZ3 HZ3 119.424 1.50 +TRP CH2 CZ3 HZ3 119.348 1.50 +TRP CZ2 CH2 CZ3 121.574 1.50 +TRP CZ2 CH2 HH2 119.154 1.50 +TRP CZ3 CH2 HH2 119.272 1.50 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +TRP chi1 N CA CB CG -60.000 10.0 3 +TRP chi2 CA CB CG CD1 90.000 10.0 6 +TRP CONST_1 CB CG CD1 NE1 0.000 0.0 1 +TRP CONST_2 CG CD1 NE1 CE2 0.000 0.0 1 +TRP CONST_3 NE1 CE2 CD2 CE3 0.000 0.0 1 +TRP CONST_4 CE2 CD2 CE3 CZ3 0.000 0.0 1 +TRP CONST_5 CD1 NE1 CE2 CD2 0.000 0.0 1 +TRP CONST_6 CD2 CE3 CZ3 CH2 0.000 0.0 1 +TRP CONST_7 CZ3 CH2 CZ2 CE2 0.000 0.0 1 +TRP CONST_8 CE3 CZ3 CH2 CZ2 0.000 0.0 1 +TRP sp3_sp3_1 C CA N H 180.000 10.0 3 +TRP const_33 CE2 CD2 CG CD1 0.000 0.0 1 +TRP const_17 CD2 CE2 CZ2 CH2 0.000 0.0 1 +TRP sp2_sp3_1 O C CA N 0.000 10.0 6 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +TRP chir_1 CA N C CB positive + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +TRP plan-1 CD2 0.020 +TRP plan-1 CE2 0.020 +TRP plan-1 CE3 0.020 +TRP plan-1 CG 0.020 +TRP plan-1 CH2 0.020 +TRP plan-1 CZ2 0.020 +TRP plan-1 CZ3 0.020 +TRP plan-1 HE3 0.020 +TRP plan-1 HH2 0.020 +TRP plan-1 HZ2 0.020 +TRP plan-1 HZ3 0.020 +TRP plan-1 NE1 0.020 +TRP plan-2 CB 0.020 +TRP plan-2 CD1 0.020 +TRP plan-2 CD2 0.020 +TRP plan-2 CE2 0.020 +TRP plan-2 CE3 0.020 +TRP plan-2 CG 0.020 +TRP plan-2 CZ2 0.020 +TRP plan-2 HD1 0.020 +TRP plan-2 HE1 0.020 +TRP plan-2 NE1 0.020 +TRP plan-3 C 0.020 +TRP plan-3 CA 0.020 +TRP plan-3 O 0.020 +TRP plan-3 OXT 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +TRP SMILES ACDLabs 10.04 "O=C(O)C(N)Cc2c1ccccc1nc2" +TRP SMILES_CANONICAL CACTVS 3.341 "N[C@@H](Cc1c[nH]c2ccccc12)C(O)=O" +TRP SMILES CACTVS 3.341 "N[CH](Cc1c[nH]c2ccccc12)C(O)=O" +TRP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)O)N" +TRP SMILES "OpenEye OEToolkits" 1.5.0 "c1ccc2c(c1)c(c[nH]2)CC(C(=O)O)N" +TRP InChI InChI 1.03 "InChI=1S/C11H12N2O2/c12-9(11(14)15)5-7-6-13-10-4-2-1-3-8(7)10/h1-4,6,9,13H,5,12H2,(H,14,15)/t9-/m0/s1" +TRP InChIKey InChI 1.03 QIVBCDIJIAJPQS-VIFPVBQESA-N + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +TRP acedrg 278 "dictionary generator" +TRP acedrg_database 12 "data source" +TRP rdkit 2019.09.1 "Chemoinformatics tool" +TRP refmac5 5.8.0419 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/TYR.cif b/image_analysis/structure_refinement/monomers/TYR.cif new file mode 100644 index 000000000..f1a4e5bee --- /dev/null +++ b/image_analysis/structure_refinement/monomers/TYR.cif @@ -0,0 +1,268 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +TYR TYR TYROSINE peptide 24 13 . + +data_comp_TYR +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +TYR N N NT3 1 5.311 5.160 15.589 +TYR CA C CH1 0 5.358 6.374 16.456 +TYR C C C 0 4.823 7.578 15.662 +TYR O O O 0 3.988 8.305 16.245 +TYR CB C CH2 0 6.763 6.679 16.994 +TYR CG C CR6 0 7.348 5.630 17.938 +TYR CD1 C CR16 0 7.096 5.672 19.314 +TYR CD2 C CR16 0 8.161 4.597 17.458 +TYR CE1 C CR16 0 7.628 4.720 20.176 +TYR CE2 C CR16 0 8.697 3.641 18.313 +TYR CZ C CR6 0 8.431 3.702 19.674 +TYR OH O OH1 0 8.982 2.738 20.476 +TYR OXT O OC -1 5.248 7.759 14.496 +TYR H H H 0 5.552 4.421 16.046 +TYR H2 H H 0 5.856 5.257 14.876 +TYR H3 H H 0 4.470 5.038 15.288 +TYR HA H H 0 4.756 6.220 17.232 +TYR HB3 H H 0 6.733 7.543 17.464 +TYR HB2 H H 0 7.369 6.788 16.227 +TYR HD1 H H 0 6.552 6.358 19.667 +TYR HD2 H H 0 8.350 4.543 16.534 +TYR HE1 H H 0 7.444 4.765 21.099 +TYR HE2 H H 0 9.240 2.953 17.971 +TYR HH H H 0 8.782 2.828 21.308 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +TYR N n/a CA START +TYR H N . . +TYR H2 N . . +TYR H3 N . . +TYR CA N C . +TYR HA CA . . +TYR CB CA CG . +TYR HB3 CB . . +TYR HB2 CB . . +TYR CG CB CD1 . +TYR CD1 CG CE1 . +TYR HD1 CD1 . . +TYR CE1 CD1 CZ . +TYR HE1 CE1 . . +TYR CZ CE1 CE2 . +TYR OH CZ HH . +TYR HH OH . . +TYR CE2 CZ CD2 . +TYR HE2 CE2 . . +TYR CD2 CE2 HD2 . +TYR HD2 CD2 . . +TYR C CA . END +TYR O C . . +TYR OXT C . . +TYR CD2 CG . ADD + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +TYR N N(CCCH)(H)3 +TYR CA C(CC[6a]HH)(NH3)(COO)(H) +TYR C C(CCHN)(O)2 +TYR O O(CCO) +TYR CB C(C[6a]C[6a]2)(CCHN)(H)2 +TYR CG C[6a](C[6a]C[6a]H)2(CCHH){1|C<3>,2|H<1>} +TYR CD1 C[6a](C[6a]C[6a]C)(C[6a]C[6a]H)(H){1|C<3>,1|H<1>,1|O<2>} +TYR CD2 C[6a](C[6a]C[6a]C)(C[6a]C[6a]H)(H){1|C<3>,1|H<1>,1|O<2>} +TYR CE1 C[6a](C[6a]C[6a]H)(C[6a]C[6a]O)(H){1|C<3>,1|C<4>,1|H<1>} +TYR CE2 C[6a](C[6a]C[6a]H)(C[6a]C[6a]O)(H){1|C<3>,1|C<4>,1|H<1>} +TYR CZ C[6a](C[6a]C[6a]H)2(OH){1|C<3>,2|H<1>} +TYR OH O(C[6a]C[6a]2)(H) +TYR OXT O(CCO) +TYR H H(NCHH) +TYR H2 H(NCHH) +TYR H3 H(NCHH) +TYR HA H(CCCN) +TYR HB3 H(CC[6a]CH) +TYR HB2 H(CC[6a]CH) +TYR HD1 H(C[6a]C[6a]2) +TYR HD2 H(C[6a]C[6a]2) +TYR HE1 H(C[6a]C[6a]2) +TYR HE2 H(C[6a]C[6a]2) +TYR HH H(OC[6a]) + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +TYR N CA SINGLE n 1.489 0.0100 1.489 0.0100 +TYR CA C SINGLE n 1.531 0.0171 1.531 0.0171 +TYR CA CB SINGLE n 1.532 0.0100 1.532 0.0100 +TYR C O DOUBLE n 1.251 0.0183 1.251 0.0183 +TYR C OXT SINGLE n 1.251 0.0183 1.251 0.0183 +TYR CB CG SINGLE n 1.523 0.0100 1.523 0.0100 +TYR CG CD1 DOUBLE y 1.390 0.0116 1.390 0.0116 +TYR CG CD2 SINGLE y 1.390 0.0116 1.390 0.0116 +TYR CD1 CE1 SINGLE y 1.385 0.0100 1.385 0.0100 +TYR CD2 CE2 DOUBLE y 1.385 0.0100 1.385 0.0100 +TYR CE1 CZ DOUBLE y 1.383 0.0100 1.383 0.0100 +TYR CE2 CZ SINGLE y 1.383 0.0100 1.383 0.0100 +TYR CZ OH SINGLE n 1.365 0.0137 1.365 0.0137 +TYR N H SINGLE n 1.018 0.0520 0.902 0.0102 +TYR N H2 SINGLE n 1.018 0.0520 0.902 0.0102 +TYR N H3 SINGLE n 1.018 0.0520 0.902 0.0102 +TYR CA HA SINGLE n 1.092 0.0100 0.994 0.0200 +TYR CB HB3 SINGLE n 1.092 0.0100 0.983 0.0163 +TYR CB HB2 SINGLE n 1.092 0.0100 0.983 0.0163 +TYR CD1 HD1 SINGLE n 1.085 0.0150 0.944 0.0143 +TYR CD2 HD2 SINGLE n 1.085 0.0150 0.944 0.0143 +TYR CE1 HE1 SINGLE n 1.085 0.0150 0.942 0.0174 +TYR CE2 HE2 SINGLE n 1.085 0.0150 0.942 0.0174 +TYR OH HH SINGLE n 0.966 0.0059 0.858 0.0200 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +TYR CA N H 109.791 3.00 +TYR CA N H2 109.791 3.00 +TYR CA N H3 109.791 3.00 +TYR H N H2 109.032 3.00 +TYR H N H3 109.032 3.00 +TYR H2 N H3 109.032 3.00 +TYR N CA C 109.085 1.50 +TYR N CA CB 109.965 3.00 +TYR N CA HA 108.547 1.50 +TYR C CA CB 111.980 3.00 +TYR C CA HA 108.746 1.50 +TYR CB CA HA 108.686 1.50 +TYR CA C O 117.219 3.00 +TYR CA C OXT 117.219 3.00 +TYR O C OXT 125.562 1.50 +TYR CA CB CG 114.693 2.05 +TYR CA CB HB3 108.494 1.50 +TYR CA CB HB2 108.494 1.50 +TYR CG CB HB3 108.859 1.50 +TYR CG CB HB2 108.859 1.50 +TYR HB3 CB HB2 107.843 2.16 +TYR CB CG CD1 121.060 1.50 +TYR CB CG CD2 121.060 1.50 +TYR CD1 CG CD2 117.879 1.50 +TYR CG CD1 CE1 121.468 1.50 +TYR CG CD1 HD1 119.327 1.50 +TYR CE1 CD1 HD1 119.205 1.50 +TYR CG CD2 CE2 121.468 1.50 +TYR CG CD2 HD2 119.327 1.50 +TYR CE2 CD2 HD2 119.205 1.50 +TYR CD1 CE1 CZ 119.794 1.50 +TYR CD1 CE1 HE1 120.177 1.50 +TYR CZ CE1 HE1 120.029 1.50 +TYR CD2 CE2 CZ 119.794 1.50 +TYR CD2 CE2 HE2 120.177 1.50 +TYR CZ CE2 HE2 120.029 1.50 +TYR CE1 CZ CE2 119.597 1.50 +TYR CE1 CZ OH 120.202 3.00 +TYR CE2 CZ OH 120.202 3.00 +TYR CZ OH HH 109.970 3.00 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +TYR chi1 N CA CB CG -60.000 10.0 3 +TYR chi2 CA CB CG CD1 90.000 10.0 6 +TYR CONST_1 CB CG CD1 CE1 0.000 0.0 1 +TYR CONST_2 CG CD1 CE1 CZ 0.000 0.0 1 +TYR CONST_3 CZ CE2 CD2 CG 0.000 0.0 1 +TYR CONST_4 CD1 CE1 CZ CE2 0.000 0.0 1 +TYR CONST_5 CE1 CZ CE2 CD2 0.000 0.0 1 +TYR hh1 CE1 CZ OH HH 0.000 5.0 2 +TYR sp3_sp3_1 C CA N H 180.000 10.0 3 +TYR const_21 CE2 CD2 CG CD1 0.000 0.0 1 +TYR sp2_sp3_1 O C CA N 0.000 10.0 6 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +TYR chir_1 CA N C CB positive + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +TYR plan-1 CB 0.020 +TYR plan-1 CD1 0.020 +TYR plan-1 CD2 0.020 +TYR plan-1 CE1 0.020 +TYR plan-1 CE2 0.020 +TYR plan-1 CG 0.020 +TYR plan-1 CZ 0.020 +TYR plan-1 HD1 0.020 +TYR plan-1 HD2 0.020 +TYR plan-1 HE1 0.020 +TYR plan-1 HE2 0.020 +TYR plan-1 OH 0.020 +TYR plan-2 C 0.020 +TYR plan-2 CA 0.020 +TYR plan-2 O 0.020 +TYR plan-2 OXT 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +TYR SMILES ACDLabs 10.04 "O=C(O)C(N)Cc1ccc(O)cc1" +TYR SMILES_CANONICAL CACTVS 3.341 "N[C@@H](Cc1ccc(O)cc1)C(O)=O" +TYR SMILES CACTVS 3.341 "N[CH](Cc1ccc(O)cc1)C(O)=O" +TYR SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1cc(ccc1C[C@@H](C(=O)O)N)O" +TYR SMILES "OpenEye OEToolkits" 1.5.0 "c1cc(ccc1CC(C(=O)O)N)O" +TYR InChI InChI 1.03 "InChI=1S/C9H11NO3/c10-8(9(12)13)5-6-1-3-7(11)4-2-6/h1-4,8,11H,5,10H2,(H,12,13)/t8-/m0/s1" +TYR InChIKey InChI 1.03 OUYCCCASQSFEME-QMMMGPOBSA-N + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +TYR acedrg 278 "dictionary generator" +TYR acedrg_database 12 "data source" +TYR rdkit 2019.09.1 "Chemoinformatics tool" +TYR refmac5 5.8.0419 "optimization tool" +TYR servalcat 0.4.57 'optimization tool' diff --git a/image_analysis/structure_refinement/monomers/U.cif b/image_analysis/structure_refinement/monomers/U.cif new file mode 100644 index 000000000..608cab6db --- /dev/null +++ b/image_analysis/structure_refinement/monomers/U.cif @@ -0,0 +1,248 @@ +# +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +U U "URIDINE-5'-MONOPHOSPHATE" RNA 32 21 . +# +data_comp_U +# +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +U OP3 O OP -1 28.643 1.174 0.256 +U P P P 0 28.819 1.986 -1.013 +U OP1 O O 0 28.329 1.258 -2.251 +U OP2 O OP -1 30.224 2.536 -1.171 +U "O5'" O O2 0 27.859 3.273 -0.849 +U "C5'" C CH2 0 26.439 3.063 -0.635 +U "C4'" C CH1 0 25.718 4.389 -0.671 +U "O4'" O O2 0 26.311 5.305 0.281 +U "C3'" C CH1 0 25.778 5.166 -1.991 +U "O3'" O OH1 0 24.835 4.654 -2.925 +U "C2'" C CH1 0 25.458 6.596 -1.533 +U "O2'" O OH1 0 24.071 6.867 -1.498 +U "C1'" C CH1 0 26.019 6.633 -0.106 +U N1 N NR6 0 27.258 7.450 0.002 +U C2 C CR6 0 27.205 8.658 0.693 +U O2 O O 0 26.192 9.093 1.231 +U N3 N NR16 0 28.393 9.351 0.740 +U C4 C CR6 0 29.603 8.978 0.180 +U O4 O O 0 30.583 9.712 0.310 +U C5 C CR16 0 29.578 7.725 -0.520 +U C6 C CR16 0 28.433 7.023 -0.585 +U "H5'" H H 0 26.293 2.630 0.242 +U "H5''" H H 0 26.078 2.471 -1.340 +U "H4'" H H 0 24.781 4.238 -0.422 +U "H3'" H H 0 26.692 5.130 -2.374 +U "HO3'" H H 0 24.819 5.164 -3.604 +U "H2'" H H 0 25.919 7.246 -2.101 +U "HO2'" H H 0 23.948 7.707 -1.488 +U "H1'" H H 0 25.334 6.986 0.500 +U H3 H H 0 28.372 10.124 1.182 +U H5 H H 0 30.354 7.400 -0.928 +U H6 H H 0 28.431 6.206 -1.045 +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +U OP3 P SINGLE n 1.517 0.0192 1.517 0.0192 +U P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192 +U P OP2 SINGLE n 1.517 0.0192 1.517 0.0192 +U P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 +U "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +U "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +U "C4'" "O4'" SINGLE n 1.451 0.0111 1.451 0.0111 +U "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 +U "O4'" "C1'" SINGLE n 1.412 0.0100 1.412 0.0100 +U "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +U "C3'" "C2'" SINGLE n 1.533 0.0109 1.533 0.0109 +U "C2'" "O2'" SINGLE n 1.412 0.0100 1.412 0.0100 +U "C2'" "C1'" SINGLE n 1.529 0.0100 1.529 0.0100 +U "C1'" N1 SINGLE n 1.476 0.0133 1.476 0.0133 +U N1 C2 SINGLE y 1.383 0.0100 1.383 0.0100 +U N1 C6 SINGLE y 1.375 0.0106 1.375 0.0106 +U C2 O2 DOUBLE n 1.224 0.0111 1.224 0.0111 +U C2 N3 SINGLE y 1.372 0.0112 1.372 0.0112 +U N3 C4 SINGLE y 1.381 0.0100 1.381 0.0100 +U C4 O4 DOUBLE n 1.231 0.0100 1.231 0.0100 +U C4 C5 SINGLE y 1.434 0.0100 1.434 0.0100 +U C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 +U "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +U "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 +U "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 +U "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +U "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +U "C2'" "H2'" SINGLE n 1.089 0.0100 0.978 0.0200 +U "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 +U "C1'" "H1'" SINGLE n 1.089 0.0100 0.981 0.0118 +U N3 H3 SINGLE n 1.016 0.0100 0.889 0.0200 +U C5 H5 SINGLE n 1.082 0.0130 0.935 0.0100 +U C6 H6 SINGLE n 1.082 0.0130 0.938 0.0107 +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +U OP3 P OP1 112.864 1.69 +U OP3 P OP2 112.864 1.69 +U OP3 P "O5'" 105.808 2.07 +U OP1 P OP2 112.864 1.69 +U OP1 P "O5'" 105.808 2.07 +U OP2 P "O5'" 105.808 2.07 +U P "O5'" "C5'" 118.783 1.50 +U "O5'" "C5'" "C4'" 109.342 1.50 +U "O5'" "C5'" "H5'" 109.845 1.50 +U "O5'" "C5'" "H5''" 109.845 1.50 +U "C4'" "C5'" "H5'" 109.624 1.50 +U "C4'" "C5'" "H5''" 109.624 1.50 +U "H5'" "C5'" "H5''" 108.472 1.50 +U "C5'" "C4'" "O4'" 109.615 1.50 +U "C5'" "C4'" "C3'" 116.008 1.52 +U "C5'" "C4'" "H4'" 108.268 1.50 +U "O4'" "C4'" "C3'" 104.439 1.50 +U "O4'" "C4'" "H4'" 108.698 1.50 +U "C3'" "C4'" "H4'" 109.363 1.86 +U "C4'" "O4'" "C1'" 109.578 1.50 +U "C4'" "C3'" "O3'" 111.281 2.46 +U "C4'" "C3'" "C2'" 102.071 1.50 +U "C4'" "C3'" "H3'" 110.452 2.54 +U "O3'" "C3'" "C2'" 111.993 3.00 +U "O3'" "C3'" "H3'" 110.380 1.67 +U "C2'" "C3'" "H3'" 110.108 1.66 +U "C3'" "O3'" "HO3'" 108.744 3.00 +U "C3'" "C2'" "O2'" 112.861 2.52 +U "C3'" "C2'" "C1'" 101.269 1.50 +U "C3'" "C2'" "H2'" 110.799 1.82 +U "O2'" "C2'" "C1'" 109.476 3.00 +U "O2'" "C2'" "H2'" 111.022 1.77 +U "C1'" "C2'" "H2'" 110.760 1.63 +U "C2'" "O2'" "HO2'" 109.449 1.85 +U "O4'" "C1'" "C2'" 106.825 1.50 +U "O4'" "C1'" N1 108.667 1.50 +U "O4'" "C1'" "H1'" 109.327 1.50 +U "C2'" "C1'" N1 112.859 1.50 +U "C2'" "C1'" "H1'" 109.776 1.83 +U N1 "C1'" "H1'" 109.166 1.50 +U "C1'" N1 C2 117.109 1.50 +U "C1'" N1 C6 121.471 1.52 +U C2 N1 C6 121.419 1.50 +U N1 C2 O2 122.841 1.50 +U N1 C2 N3 114.848 1.50 +U O2 C2 N3 122.311 1.50 +U C2 N3 C4 126.992 1.50 +U C2 N3 H3 115.772 1.79 +U C4 N3 H3 117.236 1.73 +U N3 C4 O4 119.401 1.50 +U N3 C4 C5 114.659 1.50 +U O4 C4 C5 125.940 1.50 +U C4 C5 C6 119.525 1.50 +U C4 C5 H5 120.151 1.50 +U C6 C5 H5 120.325 1.50 +U N1 C6 C5 122.557 1.50 +U N1 C6 H6 118.477 1.50 +U C5 C6 H6 118.966 1.50 +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +U C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +U C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +U C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +U C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +U C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +U C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +U C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +U C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +U C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +U C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +U C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +U C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +U alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +U beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +U epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +U gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +U sp3_sp3_52 "C3'" "C2'" "O2'" "HO2'" 180.000 10.00 3 +U const_sp2_sp2_4 O2 C2 N1 "C1'" 0.000 5.0 2 +U const_22 C5 C6 N1 "C1'" 180.000 10.0 2 +U const_sp2_sp2_7 O2 C2 N3 C4 180.000 5.0 2 +U const_11 O4 C4 N3 C2 180.000 10.0 2 +U const_15 O4 C4 C5 C6 180.000 10.0 2 +U const_17 C4 C5 C6 N1 0.000 10.0 2 +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +U chir_1 P "O5'" OP3 OP2 both +U chir_2 "C4'" "O4'" "C3'" "C5'" negative +U chir_3 "C3'" "O3'" "C4'" "C2'" positive +U chir_4 "C2'" "O2'" "C1'" "C3'" negative +U chir_5 "C1'" "O4'" N1 "C2'" negative +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +U plan-1 "C1'" 0.020 +U plan-1 C2 0.020 +U plan-1 C4 0.020 +U plan-1 C5 0.020 +U plan-1 C6 0.020 +U plan-1 H3 0.020 +U plan-1 H5 0.020 +U plan-1 H6 0.020 +U plan-1 N1 0.020 +U plan-1 N3 0.020 +U plan-1 O2 0.020 +U plan-1 O4 0.020 +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +U SMILES ACDLabs 10.04 O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=O)(O)O +U SMILES_CANONICAL CACTVS 3.341 O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O +U SMILES CACTVS 3.341 O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O +U SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O +U SMILES "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O +U InChI InChI 1.03 InChI=1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1 +U InChIKey InChI 1.03 DJJCXFVJDGTHFX-XVFCMESISA-N +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +U acedrg 243 "dictionary generator" +U acedrg_database 11 "data source" +U rdkit 2017.03.2 "Chemoinformatics tool" +U refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/VAL.cif b/image_analysis/structure_refinement/monomers/VAL.cif new file mode 100644 index 000000000..af42ed1b8 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/VAL.cif @@ -0,0 +1,221 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +VAL VAL VALINE peptide 19 8 . + +data_comp_VAL +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +VAL N N NT3 1 11.307 2.990 48.522 +VAL CA C CH1 0 10.346 4.137 48.590 +VAL C C C 0 9.715 4.163 49.994 +VAL O O O 0 9.179 3.107 50.398 +VAL CB C CH1 0 9.259 4.073 47.494 +VAL CG1 C CH3 0 8.396 5.334 47.475 +VAL CG2 C CH3 0 9.849 3.802 46.112 +VAL OXT O OC -1 9.782 5.237 50.630 +VAL H H H 0 11.930 3.145 47.888 +VAL H2 H H 0 10.867 2.229 48.319 +VAL H3 H H 0 11.735 2.877 49.308 +VAL HA H H 0 10.853 4.963 48.468 +VAL HB H H 0 8.670 3.315 47.717 +VAL HG11 H H 0 8.964 6.117 47.567 +VAL HG12 H H 0 7.763 5.306 48.212 +VAL HG13 H H 0 7.907 5.387 46.637 +VAL HG21 H H 0 10.555 4.444 45.928 +VAL HG22 H H 0 9.155 3.884 45.436 +VAL HG23 H H 0 10.217 2.902 46.084 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +VAL N n/a CA START +VAL H N . . +VAL H2 N . . +VAL H3 N . . +VAL CA N C . +VAL HA CA . . +VAL CB CA CG2 . +VAL HB CB . . +VAL CG1 CB HG13 . +VAL HG11 CG1 . . +VAL HG12 CG1 . . +VAL HG13 CG1 . . +VAL CG2 CB HG23 . +VAL HG21 CG2 . . +VAL HG22 CG2 . . +VAL HG23 CG2 . . +VAL C CA . END +VAL O C . . +VAL OXT C . . + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +VAL N N(CCCH)(H)3 +VAL CA C(CCCH)(NH3)(COO)(H) +VAL C C(CCHN)(O)2 +VAL O O(CCO) +VAL CB C(CCHN)(CH3)2(H) +VAL CG1 C(CCCH)(H)3 +VAL CG2 C(CCCH)(H)3 +VAL OXT O(CCO) +VAL H H(NCHH) +VAL H2 H(NCHH) +VAL H3 H(NCHH) +VAL HA H(CCCN) +VAL HB H(CC3) +VAL HG11 H(CCHH) +VAL HG12 H(CCHH) +VAL HG13 H(CCHH) +VAL HG21 H(CCHH) +VAL HG22 H(CCHH) +VAL HG23 H(CCHH) + +loop_ +_chem_comp_bond.comp_id +_chem_comp_bond.atom_id_1 +_chem_comp_bond.atom_id_2 +_chem_comp_bond.type +_chem_comp_bond.aromatic +_chem_comp_bond.value_dist_nucleus +_chem_comp_bond.value_dist_nucleus_esd +_chem_comp_bond.value_dist +_chem_comp_bond.value_dist_esd +VAL N CA SINGLE n 1.495 0.0100 1.495 0.0100 +VAL CA C SINGLE n 1.538 0.0100 1.538 0.0100 +VAL CA CB SINGLE n 1.541 0.0101 1.541 0.0101 +VAL C O DOUBLE n 1.251 0.0183 1.251 0.0183 +VAL C OXT SINGLE n 1.251 0.0183 1.251 0.0183 +VAL CB CG1 SINGLE n 1.524 0.0131 1.524 0.0131 +VAL CB CG2 SINGLE n 1.524 0.0131 1.524 0.0131 +VAL N H SINGLE n 1.018 0.0520 0.902 0.0102 +VAL N H2 SINGLE n 1.018 0.0520 0.902 0.0102 +VAL N H3 SINGLE n 1.018 0.0520 0.902 0.0102 +VAL CA HA SINGLE n 1.092 0.0100 0.977 0.0200 +VAL CB HB SINGLE n 1.092 0.0100 0.986 0.0184 +VAL CG1 HG11 SINGLE n 1.092 0.0100 0.972 0.0156 +VAL CG1 HG12 SINGLE n 1.092 0.0100 0.972 0.0156 +VAL CG1 HG13 SINGLE n 1.092 0.0100 0.972 0.0156 +VAL CG2 HG21 SINGLE n 1.092 0.0100 0.972 0.0156 +VAL CG2 HG22 SINGLE n 1.092 0.0100 0.972 0.0156 +VAL CG2 HG23 SINGLE n 1.092 0.0100 0.972 0.0156 + +loop_ +_chem_comp_angle.comp_id +_chem_comp_angle.atom_id_1 +_chem_comp_angle.atom_id_2 +_chem_comp_angle.atom_id_3 +_chem_comp_angle.value_angle +_chem_comp_angle.value_angle_esd +VAL CA N H 109.990 2.80 +VAL CA N H2 109.990 2.80 +VAL CA N H3 109.990 2.80 +VAL H N H2 109.032 3.00 +VAL H N H3 109.032 3.00 +VAL H2 N H3 109.032 3.00 +VAL N CA C 108.738 1.50 +VAL N CA CB 111.627 2.88 +VAL N CA HA 108.328 1.50 +VAL C CA CB 111.231 1.50 +VAL C CA HA 108.550 1.50 +VAL CB CA HA 108.536 1.50 +VAL CA C O 117.155 1.50 +VAL CA C OXT 117.155 1.50 +VAL O C OXT 125.690 1.50 +VAL CA CB CG1 111.834 1.50 +VAL CA CB CG2 111.834 1.50 +VAL CA CB HB 107.069 1.50 +VAL CG1 CB CG2 110.700 1.76 +VAL CG1 CB HB 107.681 2.06 +VAL CG2 CB HB 107.681 2.06 +VAL CB CG1 HG11 109.510 1.50 +VAL CB CG1 HG12 109.510 1.50 +VAL CB CG1 HG13 109.510 1.50 +VAL HG11 CG1 HG12 109.390 1.50 +VAL HG11 CG1 HG13 109.390 1.50 +VAL HG12 CG1 HG13 109.390 1.50 +VAL CB CG2 HG21 109.510 1.50 +VAL CB CG2 HG22 109.510 1.50 +VAL CB CG2 HG23 109.510 1.50 +VAL HG21 CG2 HG22 109.390 1.50 +VAL HG21 CG2 HG23 109.390 1.50 +VAL HG22 CG2 HG23 109.390 1.50 + +loop_ +_chem_comp_tor.comp_id +_chem_comp_tor.id +_chem_comp_tor.atom_id_1 +_chem_comp_tor.atom_id_2 +_chem_comp_tor.atom_id_3 +_chem_comp_tor.atom_id_4 +_chem_comp_tor.value_angle +_chem_comp_tor.value_angle_esd +_chem_comp_tor.period +VAL chi1 N CA CB CG2 -60.000 10.0 3 +VAL hh1 CA CB CG1 HG13 180.000 10.0 3 +VAL hh2 CA CB CG2 HG23 -60.000 10.0 3 +VAL sp3_sp3_1 C CA N H 180.000 10.0 3 +VAL sp2_sp3_1 O C CA N 0.000 10.0 6 + +loop_ +_chem_comp_chir.comp_id +_chem_comp_chir.id +_chem_comp_chir.atom_id_centre +_chem_comp_chir.atom_id_1 +_chem_comp_chir.atom_id_2 +_chem_comp_chir.atom_id_3 +_chem_comp_chir.volume_sign +VAL chir_1 CA N C CB positive +VAL chir_2 CB CA CG1 CG2 both + +loop_ +_chem_comp_plane_atom.comp_id +_chem_comp_plane_atom.plane_id +_chem_comp_plane_atom.atom_id +_chem_comp_plane_atom.dist_esd +VAL plan-1 C 0.020 +VAL plan-1 CA 0.020 +VAL plan-1 O 0.020 +VAL plan-1 OXT 0.020 + +loop_ +_pdbx_chem_comp_descriptor.comp_id +_pdbx_chem_comp_descriptor.type +_pdbx_chem_comp_descriptor.program +_pdbx_chem_comp_descriptor.program_version +_pdbx_chem_comp_descriptor.descriptor +VAL SMILES ACDLabs 10.04 O=C(O)C(N)C(C)C +VAL SMILES_CANONICAL CACTVS 3.341 CC(C)[C@H](N)C(O)=O +VAL SMILES CACTVS 3.341 CC(C)[CH](N)C(O)=O +VAL SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC(C)[C@@H](C(=O)O)N +VAL SMILES "OpenEye OEToolkits" 1.5.0 CC(C)C(C(=O)O)N +VAL InChI InChI 1.03 InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1 +VAL InChIKey InChI 1.03 KZSNJWFQEVHDMF-BYPYZUCNSA-N + +loop_ +_pdbx_chem_comp_description_generator.comp_id +_pdbx_chem_comp_description_generator.program_name +_pdbx_chem_comp_description_generator.program_version +_pdbx_chem_comp_description_generator.descriptor +VAL acedrg 278 "dictionary generator" +VAL acedrg_database 12 "data source" +VAL rdkit 2019.09.1 "Chemoinformatics tool" +VAL refmac5 5.8.0419 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/ZN.cif b/image_analysis/structure_refinement/monomers/ZN.cif new file mode 100644 index 000000000..aada536e8 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/ZN.cif @@ -0,0 +1,30 @@ +data_comp_list +loop_ +_chem_comp.id +_chem_comp.three_letter_code +_chem_comp.name +_chem_comp.group +_chem_comp.number_atoms_all +_chem_comp.number_atoms_nh +_chem_comp.desc_level +ZN ZN 'ZINC ION ' NON-POLYMER 1 1 . + +data_comp_ZN +loop_ +_chem_comp_atom.comp_id +_chem_comp_atom.atom_id +_chem_comp_atom.type_symbol +_chem_comp_atom.type_energy +_chem_comp_atom.partial_charge +_chem_comp_atom.x +_chem_comp_atom.y +_chem_comp_atom.z +ZN ZN ZN ZN 2.000 0.000 0.000 0.000 + +loop_ +_chem_comp_tree.comp_id +_chem_comp_tree.atom_id +_chem_comp_tree.atom_back +_chem_comp_tree.atom_forward +_chem_comp_tree.connect_type +ZN ZN n/a . END diff --git a/image_analysis/structure_refinement/monomers/ener_lib.cif b/image_analysis/structure_refinement/monomers/ener_lib.cif new file mode 100644 index 000000000..717864eb2 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/ener_lib.cif @@ -0,0 +1,219 @@ +data_energy +loop_ +_lib_atom.type +_lib_atom.weight +_lib_atom.hb_type +_lib_atom.vdw_radius +_lib_atom.vdwh_radius +_lib_atom.ion_radius +_lib_atom.element +_lib_atom.valency +_lib_atom.sp +CSP 12.01150 N 1.700 1.700 . C 4 1 +CSP1 12.01150 N 1.700 1.700 . C 4 1 +C 12.01150 N 1.700 1.750 . C 4 2 +C1 12.01150 N 1.700 1.820 . C 4 2 +C2 12.01150 N 1.700 1.800 . C 4 2 +CR1 12.01150 N 1.700 1.800 . C 4 2 +CR2 12.01150 N 1.700 1.800 . C 4 2 +CR1H 12.01150 N 1.700 1.800 . C 4 2 +CR15 12.01150 N 1.700 1.740 . C 4 2 +CR5 12.01150 N 1.700 1.740 . C 4 2 +CR56 12.01150 N 1.700 1.740 . C 4 2 +CR55 12.01150 N 1.700 1.740 . C 4 2 +CR16 12.01150 N 1.700 1.820 . C 4 2 +CR6 12.01150 N 1.700 1.740 . C 4 2 +CR66 12.01150 N 1.700 1.740 . C 4 2 +CH1 12.01150 N 1.700 1.950 . C 4 3 +CH2 12.01150 N 1.700 1.920 . C 4 3 +CH3 12.01150 N 1.700 1.940 . C 4 3 +CT 12.01150 N 1.700 1.850 . C 4 3 +NS 14.00670 A 1.550 1.600 1.32 N 3 1 +NSP 14.00670 A 1.550 1.600 1.32 N 3 1 +NS1 14.00670 D 1.550 1.600 1.32 N 3 1 +NSP1 14.00670 D 1.550 1.600 1.32 N 3 1 +N 14.00670 N 1.550 1.600 1.32 N 3 2 +NC1 14.00670 D 1.550 1.600 1.32 N 3 2 +NH0 14.00670 N 1.550 1.600 1.32 N 3 2 +NH1 14.00670 D 1.550 1.600 1.32 N 3 2 +NC2 14.00670 D 1.550 1.600 1.32 N 3 2 +NH2 14.00670 D 1.550 1.600 1.32 N 3 2 +NC3 14.00670 D 1.550 1.600 1.32 N 3 2 +N20 14.00670 A 1.550 1.600 1.32 N 3 2 +N21 14.00670 B 1.550 1.600 1.32 N 3 2 +NT 14.00670 N 1.550 1.600 1.32 N 3 3 +NT1 14.00670 D 1.550 1.600 1.32 N 3 3 +NT2 14.00670 D 1.550 1.600 1.32 N 3 3 +NT3 14.00670 D 1.550 1.600 1.32 N 3 3 +NT4 14.00670 D 1.550 1.600 1.32 N 3 3 +N30 14.00670 A 1.550 1.600 1.32 N 3 3 +N31 14.00670 B 1.550 1.600 1.32 N 3 3 +N32 14.00670 B 1.550 1.600 1.32 N 3 3 +N33 14.00670 B 1.550 1.600 1.32 N 3 3 +NPA 14.00670 A 1.550 1.600 1.32 N 3 2 +NPB 14.00670 A 1.550 1.600 1.32 N 3 2 +NR5 14.00670 A 1.550 1.600 1.32 N 3 2 +NR15 14.00670 D 1.550 1.600 1.32 N 3 2 +NRD5 14.00670 A 1.550 1.600 1.32 N 3 2 +NR56 14.00670 N 1.550 1.600 1.32 N 3 2 +NR55 14.00670 N 1.550 1.600 1.32 N 3 2 +NR6 14.00670 A 1.550 1.600 1.32 N 3 2 +NR66 14.00670 N 1.550 1.600 1.32 N 3 2 +NR16 14.00670 D 1.550 1.600 1.32 N 3 2 +NRD6 14.00670 A 1.550 1.600 1.32 N 3 2 +OS 15.99940 A 1.520 1.520 1.28 O 2 2 +O 15.99940 A 1.520 1.520 1.28 O 2 2 +AF 15.99940 A 1.520 1.520 1.28 AF 2 2 +O2 15.99940 A 1.520 1.520 1.28 O 2 3 +OH1 15.99940 B 1.520 1.520 1.28 O 2 3 +OH2 15.99940 B 1.520 1.520 1.28 O 2 3 +OHA 15.99940 B 1.520 1.680 1.28 O 2 3 +OHB 15.99940 B 1.520 1.680 1.28 O 2 3 +OHC 15.99940 B 1.520 1.680 1.28 O 2 3 +OC2 15.99940 A 1.520 1.520 1.28 O 2 2 +OC 15.99940 A 1.520 1.520 1.28 O 2 2 +OP 15.99940 A 1.520 1.520 1.28 O 2 2 +OB 15.99940 A 1.520 1.520 1.28 O 2 2 +P 30.97380 N 1.800 1.88 1.79 P 5 . +P1 30.97380 N 1.800 1.88 1.79 P 5 . +PS 30.97380 N 1.800 1.90 1.79 P 5 . +S 32.06400 A 1.800 1.88 1.7 S 2 . +S3 32.06400 A 1.800 1.88 1.7 S 4 . +S2 32.06400 A 1.800 1.88 1.7 S 2 . +S1 32.06400 A 1.800 1.88 1.7 S 2 . +ST 32.06400 A 1.800 1.88 1.7 S 6 3 +SH1 32.06400 B 1.800 1.950 1.7 S 2 . +H 1.00800 N 1.200 . . H 1 . +HCH 1.00800 N 1.200 . . H 1 . +HCH1 1.00800 N 1.200 . . H 1 . +HCH2 1.00800 N 1.200 . . H 1 . +HCH3 1.00800 N 1.200 . . H 1 . +HCR1 1.00800 N 1.200 . . H 1 . +HC2 1.00800 N 1.200 . . H 1 . +HC1 1.00800 N 1.200 . . H 1 . +HC2 1.00800 N 1.200 . . H 1 . +HCR5 1.00800 N 1.200 . . H 1 . +HCR6 1.00800 N 1.200 . . H 1 . +HNC1 1.00800 H 1.200 . . H 1 . +HNC2 1.00800 H 1.200 . . H 1 . +HNH1 1.00800 H 1.200 . . H 1 . +HNH2 1.00800 H 1.200 . . H 1 . +HNR5 1.00800 H 1.200 . . H 1 . +HNR6 1.00800 H 1.200 . . H 1 . +HNT1 1.00800 H 1.200 . . H 1 . +HNT2 1.00800 H 1.200 . . H 1 . +HNT3 1.00800 H 1.200 . . H 1 . +HOH1 1.00800 H 1.200 . . H 1 . +HOH2 1.00800 H 1.200 . . H 1 . +HOHA 1.00800 H 1.200 . . H 1 . +HOHB 1.00800 H 1.200 . . H 1 . +HOHC 1.00800 H 1.200 . . H 1 . +HSH1 1.00800 H 1.200 . . H 1 . +SI 28.0855 N 2.10 . 0.40 SI 4 3 +SI1 28.0855 N 2.10 . 0.40 SI 4 . +GE 72.59 N 2.10 . 0.40 GE 1 . +GE1 72.59 N 2.10 . 0.40 GE 1 . +SN 118.69 N 2.17 . 0.69 SN 1 . +PB 207.2 N 2.02 . 0.79 PB 1 . +LI 6.941 N 1.82 . 0.73 LI 1 . +NA 22.990 N 2.27 . 1.13 NA 1 . +K 30.0983 N 2.75 . 1.51 K 1 . +RB 85.468 N 2.00 . 1.48 RB 1 . +CS 132.905 N 2.98 . 1.81 CS 1 . +FR 223.0 N . . 1.94 FR 1 . +BE 9.0123 N 1.12 . 0.41 BE 1 . +MG 24.30500 N 1.73 . 0.71 MG 1 . +CA 40.08000 N 1.94 . 1.14 CA 1 . +SR 87.62 N 2.19 . 1.32 SR 1 . +BA 137.33 N 2.53 . 1.49 BA 1 . +RA 226.025 N 2.15 . 1.62 RA 1 . +SC 44.9559 N 1.60 . 0.885 SC 1 . +Y 88.9059 N 1.80 . 1.04 Y 1 . +LA 138.9055 N 1.95 . 1.172 LA 1 . +CE 140.12 N 1.85 . 1.01 CE 1 . +PR 140.9077 N 1.85 . 0.99 PR 1 . +ND 144.24 N 1.85 . 1.123 ND 1 . +PM . N . . 1.11 PM 1 . +SM 150.36 N 1.85 . 1.098 SM 1 . +EU 151.96 N 1.85 . 1.087 EU 1 . +GD 157.25 N 1.80 . 1.078 GD 1 . +TB 158.9254 N 1.75 . 0.90 TB 1 . +DY 162.50 N 1.75 . 1.052 DY 1 . +HO 164.9304 N 1.75 . 1.041 HO 1 . +ER 167.26 N 1.75 . 1.03 ER 1 . +TM 168.9342 N 1.75 . 1.02 TM 1 . +YB 173.04 N 1.75 . 1.008 YB 1 . +LU 174.967 N 1.75 . 1.001 LU 1 . +AC 227.028 N 1.95 . 1.26 AC 1 . +TH 232.0 N 1.80 . 1.08 TH 1 . +PA 231.0 N 1.80 . 0.92 PA 1 . +U 238.0 N 1.86 . 0.66 U 1 . +NP 237.0 N 1.75 . 0.85 NP 1 . +PU 239.0 N 1.75 . 0.85 PU 1 . +AM 241.0 N 1.75 . 0.99 AM 1 . +CM 244.0 N . . 0.99 CM 1 . +BK 249.0 N . . 0.97 BK 1 . +CF 252.0 N . . 0.961 CF 1 . +ES 253.0 N . . . ES 1 . +FM 257.0 N . . . FM 1 . +MD 256.0 N . . . MD 1 . +NO 255.0 N . . . NO 1 . +LR 256.0 N . . . LR 1 . +TI 47.88 N 1.40 . 0.56 TI 1 . +ZR 91.22 N 1.55 . 0.73 ZR 1 . +HF 178.49 N 1.55 . 0.72 HF 1 . +RF . N . . . RF 1 . +V 50.9415 N 1.35 . 0.68 V 1 . +NB 92.9064 N 1.45 . 0.62 NB 1 . +TA 180.9479 N 1.45 . 0.78 TA 1 . +DB . N . . . DB 1 . +CR 51.996 N 1.40 . 0.53 CR 1 . +MO 95.94 N 1.45 . 0.55 MO 1 . +W 183.85 N 1.35 . 0.56 W 1 . +SG . N . . . SG 1 . +MN 54.938 N 1.40 . 0.46 MN 1 . +TC 98.906 N 1.35 . 0.51 TC 1 . +RE 186.207 N 1.35 . 0.52 RE 1 . +BH . N . . . BH 1 . +FE 55.847 N 1.40 . 0.68 FE 1 . +RU 101.07 N 1.30 . 0.52 RU 1 . +OSE 190.2 N 1.30 . 0.53 OS 1 . +HS . N . . . HS 1 . +CO 58.9332 N 1.35 . 0.54 CO 1 . +RH 102.9055 N 1.35 . 0.69 RH 1 . +IR 192.22 N 1.35 . 0.71 IR 1 . +MT . N . . . MT 1 . +NI 58.69 N 1.63 . 0.63 NI 1 . +PD 106.42 N 1.63 . 0.78 PD 1 . +PT 195.08 N 1.75 . 0.71 PT 1 . +CU 63.546 N 1.40 . 0.71 CU 1 . +AG 107.868 N 1.72 . 0.81 AG 1 . +AU 196.9665 N 1.66 . 0.71 AU 1 . +ZN 65.38 N 1.39 . 0.74 ZN 1 . +CD 112.41 N 1.58 . 0.92 CD 1 . +HG 200.59 N 1.55 . 1.10 HG 1 . +B 10.81 N 0.85 . 0.25 B 1 . +AL 26.98154 N 1.25 . 0.53 AL 1 . +GA 69.72 N 1.87 . 0.61 GA 1 . +IN 114.82 N 1.93 . 0.76 IN 1 . +TL 204.383 N 1.96 . 0.89 TL 1 . +AS 74.9216 N 1.85 . 0.475 AS 1 . +AS1 74.9216 N 1.85 . 0.475 AS 1 . +SB 121.75 N 1.8 . 0.90 SB 1 . +BI 208.9804 N 1.8 . 0.90 BI 1 . +SE 78.96 N 1.90 . 0.42 SE 1 . +TE 127.60 N 2.06 . 0.57 TE 1 . +PO 210.0 N 2.0 . 0.81 PO 1 . +F 18.998 B 1.47 . 1.19 F 1 . +CL 35.453 A 1.75 . 1.67 CL 1 . +BR 79.904 N 1.85 . 0.73 BR 1 . +I 126.9045 N 1.98 . 0.56 I 1 . +AT 210.0 N 1.80 . 0.76 AT 1 . +HE 4.0026 N 1.40 . . HE 1 . +NE 20.179 N 1.54 . 1.12 NE 1 . +AR 39.948 N 1.88 . 1.54 AR 1 . +KR 83.80 N 2.02 . 1.69 KR 1 . +XE 131.29 N 2.16 . 1.90 XE 1 . +RN 222.0 N 2.20 . 2.0 RN 1 . +DUM 16.0 N 0.6 0.6 0.6 O . . +. . B 1.7 1.5 1.7 C 4 3 diff --git a/image_analysis/structure_refinement/monomers/links_and_mods.cif b/image_analysis/structure_refinement/monomers/links_and_mods.cif new file mode 100644 index 000000000..6747c388d --- /dev/null +++ b/image_analysis/structure_refinement/monomers/links_and_mods.cif @@ -0,0 +1,4698 @@ +data_link_list +loop_ +_chem_link.id +_chem_link.comp_id_1 +_chem_link.mod_id_1 +_chem_link.group_comp_1 +_chem_link.comp_id_2 +_chem_link.mod_id_2 +_chem_link.group_comp_2 +_chem_link.name +DNA-SER . DEL_OP3 DNA/RNA SER SERm1 peptide DNA-SER +DNA-TYR . DEL_OP3 DNA/RNA TYR TYRmod5 peptide DNA-TYR +SS . CYS-SS peptide . CYS-SS peptide SS-bridge +disulf CYS CYS-SS peptide CYS CYS-SS peptide SS-bridge +TRANS . DEL-OXT peptide . DEL-HN1 peptide TRANS +CIS . DEL-OXT peptide . DEL-HN1 peptide CIS +PTRANS . DEL-OXT peptide . DEL-HNP P-peptide PTRANS +PCIS . DEL-OXT peptide . DEL-HNP P-peptide PCIS +NMTRANS . DEL-OXT1 peptide . DEL-NMH M-peptide NMTRANS +NMCIS . DEL-OXT1 peptide . DEL-NMH M-peptide NMCIS +gap . . . . . . gap-link +p . DEL_HO3p DNA/RNA . DEL_OP3 DNA/RNA default-DNA/RNA-link +AA-RNA . DEL-OXT peptide . DEL_HO3p DNA/RNA aminoacyl-RNA +ZN-CYS ZN . NON-POLYMER CYS CYSmod1 peptide bond_ZN_=_CYS-SG +ZN-HISND ZN . NON-POLYMER HIS DEL-HD1 peptide bond_ZN_=_HIS-ND1 +ZN-HISNE ZN . NON-POLYMER HIS DEL-HE2 peptide bond_ZN_=_HIS-NE2 +FE-CYS FE . NON-POLYMER CYS CYSmod1 peptide bond_FE_=_CYS-SG +FE-HISND FE . NON-POLYMER HIS DEL-HD1 peptide bond_FE_=_HIS-ND1 +FE-HISNE FE . NON-POLYMER HIS DEL-HE2 peptide bond_FE_=_HIS-NE2 +symmetry . . . . . . dummy_link +GTP-p GTP GTPmod1 NON-POLYMER . DEL_OP3 DNA/RNA GTP-p +HIS_TYR1 HIS HISmod1 peptide TYR TYRmod1 peptide HIS_TYR1 +HIS_TYR2 HIS HISmod3 peptide TYR TYRmod2 peptide HIS_TYR2 +LYS-CYS LYS LYSmod1 peptide CYS CYSmod1 peptide LYS-CYS +LYS-ASN LYS LYSmod3 peptide ASN ASNmod1 peptide LYS-ASN +MET-TYR MET METmod1 peptide TYR TYRmod3 peptide MET-TYR +TRP-TYR TRP TRPmod1 peptide TYR TYRmod4 peptide TRP-TYR + +data_mod_list +loop_ +_chem_mod.id +_chem_mod.name +_chem_mod.comp_id +_chem_mod.group_id +SERm1 SERINE SER peptide +CYS-SS HG-deletete CYS peptide +CYSmod1 CYS-HG-delete_with_atom_type CYS peptide +NH3 NH3-terminus . peptide +NH1 NH1-terminus . peptide +NH2 NH2-terminus_for_proline . peptide +NH2N NH2-terminus_proline_type_with_CN . peptide +COO COO-terminus . peptide +AA-STAND AA_to_residue_modification . peptide +AA-STPRO AA_to_residue_modification_for_proline . peptide +NA-STAND DNA/RNA_to_residue_modification . DNA/RNA +5*END DNA/RNA-5*-terminus . DNA/RNA +3*END DNA/RNA-3*-terminus . DNA/RNA +p5*END DNA/RNA-p5*-terminus . DNA/RNA +p3*END DNA/RNA-p3*-terminus . DNA/RNA +DEL_OP3 DN/RNA-OP3-delete . DNA/RNA +DEL_HO3p DNA/RNA-OP3-delete . DNA/RNA +FOR-N N-terminus_of_formyl . . +FOR-C C-terminus_of_formyl . . +G-N2 delete_N2_from_guanosine . DNA/RNA +DEL-HD1 delete_HD1_from_HIS HIS peptide +DEL-HE2 delete_HE2_from_HIS HIS peptide +DEL-OXT delete_OXT_from_peptide . peptide +DEL-OXT1 delete_OXT_from_peptide . peptide +DEL-HN1 delete_Hs_from_peptide . peptide +DEL-NMH delete_Hs_from_NMpeptide . peptide +DEL-HNP delete_Hs_from_peptide . peptide +PEPT-D change_peptide_to_D . peptide +1MA N1-metyl_of_adenosine . DNA/RNA +1MG N1-metyl_of_guanosine . DNA/RNA +2MG N2-metyl_of_guanosine . DNA/RNA +M2G N2-dimetyl_of_guanosine . DNA/RNA +O2*MET O2*_metyl . DNA/RNA +C5MET C5_metyl . DNA/RNA +N7MET N7_metyl . DNA/RNA +RNA-O2* delete_O2*_from_RNA . DNA/RNA +XYS-O1 delete_O1_from_XYS . . +B2C replace_B_to_C . peptide +B2C_D replace_B_to_C_for_D-peptide . peptide +RENAME change_monomer"s_name . . +TERMINUS chain_terminus_without_modification . . +DEL-HD22 delete_HD22_from_ASN ASN peptide +DEL-HG delete_HG_from_SER SER peptide +DEL-HG1 delete_HG1_from_THR THR peptide +HISmod1 HISTIDINE HIS peptide +HISmod2 HISTIDINE HIS peptide +GTPmod1 "GUANOSINE-5'-TRIPHOSPHATE" GTP NON-POLYMER +TYRmod1 TYROSINE TYR peptide +HISmod3 HISTIDINE HIS peptide +TYRmod2 TYROSINE TYR peptide +LYSmod1 LYSINE LYS peptide +CYSmod2 CYSTEINE CYS peptide +LYSmod2 LYSINE LYS peptide +LYSmod3 LYSINE LYS peptide +ASNmod1 ASPARAGINE ASN peptide +METmod1 METHIONINE MET peptide +TYRmod3 TYROSINE TYR peptide +LEUmod1 LEUCINE LEU peptide +LYSmod4 LYSINE LYS peptide +TRPmod1 TRYPTOPHAN TRP peptide +TYRmod4 TYROSINE TYR peptide +TYRmod5 TYROSINE TYR peptide +LYSmod5 LYSINE LYS peptide +MS6mod2 DEL-HN1_equiv_for_MS6-pept . peptide +ASPprot "Protonation of ASP" ASP peptide +GLUprot "Protonation of GLU" GLU peptide +HISprot1 HISTIDINE HIS peptide +HISprot2 HISTIDINE HIS peptide + +data_link_DNA-SER +loop_ +_chem_link_bond.link_id +_chem_link_bond.atom_1_comp_id +_chem_link_bond.atom_id_1 +_chem_link_bond.atom_2_comp_id +_chem_link_bond.atom_id_2 +_chem_link_bond.type +_chem_link_bond.value_dist +_chem_link_bond.value_dist_esd +DNA-SER 1 P 2 OG SINGLE 1.607 0.0108 + +loop_ +_chem_link_angle.link_id +_chem_link_angle.atom_1_comp_id +_chem_link_angle.atom_id_1 +_chem_link_angle.atom_2_comp_id +_chem_link_angle.atom_id_2 +_chem_link_angle.atom_3_comp_id +_chem_link_angle.atom_id_3 +_chem_link_angle.value_angle +_chem_link_angle.value_angle_esd +DNA-SER 1 OP1 1 P 2 OG 107.777 3.00 +DNA-SER 1 OP2 1 P 2 OG 107.777 3.00 +DNA-SER 1 "O5'" 1 P 2 OG 103.482 3.00 +DNA-SER 2 CB 2 OG 1 P 119.008 2.40 + +loop_ +_chem_link_tor.link_id +_chem_link_tor.id +_chem_link_tor.atom_1_comp_id +_chem_link_tor.atom_id_1 +_chem_link_tor.atom_2_comp_id +_chem_link_tor.atom_id_2 +_chem_link_tor.atom_3_comp_id +_chem_link_tor.atom_id_3 +_chem_link_tor.atom_4_comp_id +_chem_link_tor.atom_id_4 +_chem_link_tor.value_angle +_chem_link_tor.value_angle_esd +_chem_link_tor.period +DNA-SER sp3_sp3_1 2 CB 2 OG 1 P 1 OP1 60.000 10.0 3 +DNA-SER sp3_sp3_2 2 CA 2 CB 2 OG 1 P 180.000 10.0 3 + +loop_ +_chem_link_chir.link_id +_chem_link_chir.atom_centre_comp_id +_chem_link_chir.atom_id_centre +_chem_link_chir.atom_1_comp_id +_chem_link_chir.atom_id_1 +_chem_link_chir.atom_2_comp_id +_chem_link_chir.atom_id_2 +_chem_link_chir.atom_3_comp_id +_chem_link_chir.atom_id_3 +_chem_link_chir.volume_sign +DNA-SER 1 P 1 "O5'" 2 OG 1 OP2 both + +data_link_DNA-TYR +loop_ +_chem_link_bond.link_id +_chem_link_bond.atom_1_comp_id +_chem_link_bond.atom_id_1 +_chem_link_bond.atom_2_comp_id +_chem_link_bond.atom_id_2 +_chem_link_bond.type +_chem_link_bond.value_dist +_chem_link_bond.value_dist_esd +DNA-TYR 1 P 2 OH SINGLE 1.618 0.0100 + +loop_ +_chem_link_angle.link_id +_chem_link_angle.atom_1_comp_id +_chem_link_angle.atom_id_1 +_chem_link_angle.atom_2_comp_id +_chem_link_angle.atom_id_2 +_chem_link_angle.atom_3_comp_id +_chem_link_angle.atom_id_3 +_chem_link_angle.value_angle +_chem_link_angle.value_angle_esd +DNA-TYR 1 OP1 1 P 2 OH 108.075 3.00 +DNA-TYR 1 OP2 1 P 2 OH 108.075 3.00 +DNA-TYR 1 "O5'" 1 P 2 OH 101.281 3.00 +DNA-TYR 2 CZ 2 OH 1 P 121.950 3.00 + +loop_ +_chem_link_tor.link_id +_chem_link_tor.id +_chem_link_tor.atom_1_comp_id +_chem_link_tor.atom_id_1 +_chem_link_tor.atom_2_comp_id +_chem_link_tor.atom_id_2 +_chem_link_tor.atom_3_comp_id +_chem_link_tor.atom_id_3 +_chem_link_tor.atom_4_comp_id +_chem_link_tor.atom_id_4 +_chem_link_tor.value_angle +_chem_link_tor.value_angle_esd +_chem_link_tor.period +DNA-TYR sp3_sp3_1 1 OP1 1 P 2 OH 2 CZ 180.000 10.0 3 +DNA-TYR sp2_sp2_1 2 CE1 2 CZ 2 OH 1 P 180.000 5.0 2 + +loop_ +_chem_link_chir.link_id +_chem_link_chir.atom_centre_comp_id +_chem_link_chir.atom_id_centre +_chem_link_chir.atom_1_comp_id +_chem_link_chir.atom_id_1 +_chem_link_chir.atom_2_comp_id +_chem_link_chir.atom_id_2 +_chem_link_chir.atom_3_comp_id +_chem_link_chir.atom_id_3 +_chem_link_chir.volume_sign +DNA-TYR 1 P 1 "O5'" 2 OH 1 OP2 both + +data_link_SS +loop_ +_chem_link_bond.link_id +_chem_link_bond.atom_1_comp_id +_chem_link_bond.atom_id_1 +_chem_link_bond.atom_2_comp_id +_chem_link_bond.atom_id_2 +_chem_link_bond.type +_chem_link_bond.value_dist +_chem_link_bond.value_dist_esd +SS 1 SG 2 SG single 2.031 .020 + +loop_ +_chem_link_angle.link_id +_chem_link_angle.atom_1_comp_id +_chem_link_angle.atom_id_1 +_chem_link_angle.atom_2_comp_id +_chem_link_angle.atom_id_2 +_chem_link_angle.atom_3_comp_id +_chem_link_angle.atom_id_3 +_chem_link_angle.value_angle +_chem_link_angle.value_angle_esd +SS 1 CB 1 SG 2 SG 103.800 1.800 +SS 1 SG 2 SG 2 CB 103.800 1.800 + +loop_ +_chem_link_tor.link_id +_chem_link_tor.id +_chem_link_tor.atom_1_comp_id +_chem_link_tor.atom_id_1 +_chem_link_tor.atom_2_comp_id +_chem_link_tor.atom_id_2 +_chem_link_tor.atom_3_comp_id +_chem_link_tor.atom_id_3 +_chem_link_tor.atom_4_comp_id +_chem_link_tor.atom_id_4 +_chem_link_tor.value_angle +_chem_link_tor.value_angle_esd +_chem_link_tor.period +SS ss 1 CB 1 SG 2 SG 2 CB 90.00 10.0 2 + +data_link_disulf +loop_ +_chem_link_bond.link_id +_chem_link_bond.atom_1_comp_id +_chem_link_bond.atom_id_1 +_chem_link_bond.atom_2_comp_id +_chem_link_bond.atom_id_2 +_chem_link_bond.type +_chem_link_bond.value_dist +_chem_link_bond.value_dist_esd +disulf 1 SG 2 SG single 2.031 .020 + +loop_ +_chem_link_angle.link_id +_chem_link_angle.atom_1_comp_id +_chem_link_angle.atom_id_1 +_chem_link_angle.atom_2_comp_id +_chem_link_angle.atom_id_2 +_chem_link_angle.atom_3_comp_id +_chem_link_angle.atom_id_3 +_chem_link_angle.value_angle +_chem_link_angle.value_angle_esd +disulf 1 CB 1 SG 2 SG 103.800 1.800 +disulf 1 SG 2 SG 2 CB 103.800 1.800 + +loop_ +_chem_link_tor.link_id +_chem_link_tor.id +_chem_link_tor.atom_1_comp_id +_chem_link_tor.atom_id_1 +_chem_link_tor.atom_2_comp_id +_chem_link_tor.atom_id_2 +_chem_link_tor.atom_3_comp_id +_chem_link_tor.atom_id_3 +_chem_link_tor.atom_4_comp_id +_chem_link_tor.atom_id_4 +_chem_link_tor.value_angle +_chem_link_tor.value_angle_esd +_chem_link_tor.period +disulf ss 1 CB 1 SG 2 SG 2 CB 90.00 10.0 2 + +data_link_TRANS +loop_ +_chem_link_bond.link_id +_chem_link_bond.atom_1_comp_id +_chem_link_bond.atom_id_1 +_chem_link_bond.atom_2_comp_id +_chem_link_bond.atom_id_2 +_chem_link_bond.type +_chem_link_bond.value_dist +_chem_link_bond.value_dist_esd +TRANS 1 C 2 N SINGLE 1.337 0.011 + +loop_ +_chem_link_angle.link_id +_chem_link_angle.atom_1_comp_id +_chem_link_angle.atom_id_1 +_chem_link_angle.atom_2_comp_id +_chem_link_angle.atom_id_2 +_chem_link_angle.atom_3_comp_id +_chem_link_angle.atom_id_3 +_chem_link_angle.value_angle +_chem_link_angle.value_angle_esd +TRANS 1 CA 1 C 2 N 115.917 1.50 +TRANS 1 O 1 C 2 N 123.469 1.50 +TRANS 1 C 2 N 2 CA 122.095 1.76 +TRANS 1 C 2 N 2 H 119.176 1.83 + +loop_ +_chem_link_tor.link_id +_chem_link_tor.id +_chem_link_tor.atom_1_comp_id +_chem_link_tor.atom_id_1 +_chem_link_tor.atom_2_comp_id +_chem_link_tor.atom_id_2 +_chem_link_tor.atom_3_comp_id +_chem_link_tor.atom_id_3 +_chem_link_tor.atom_4_comp_id +_chem_link_tor.atom_id_4 +_chem_link_tor.value_angle +_chem_link_tor.value_angle_esd +_chem_link_tor.period +TRANS psi 1 N 1 CA 1 C 2 N 160.00 30.0 2 +TRANS omega 1 CA 1 C 2 N 2 CA 180.00 5.0 0 +TRANS phi 1 C 2 N 2 CA 2 C 60.00 20.0 3 + +loop_ +_chem_link_plane.link_id +_chem_link_plane.plane_id +_chem_link_plane.atom_comp_id +_chem_link_plane.atom_id +_chem_link_plane.dist_esd +TRANS plan-1 1 CA 0.020 +TRANS plan-1 1 C 0.020 +TRANS plan-1 2 N 0.020 +TRANS plan-1 1 O 0.020 +TRANS plan-2 2 CA 0.020 +TRANS plan-2 1 C 0.020 +TRANS plan-2 2 H 0.020 +TRANS plan-2 2 N 0.020 + +data_link_CIS +loop_ +_chem_link_bond.link_id +_chem_link_bond.atom_1_comp_id +_chem_link_bond.atom_id_1 +_chem_link_bond.atom_2_comp_id +_chem_link_bond.atom_id_2 +_chem_link_bond.type +_chem_link_bond.value_dist +_chem_link_bond.value_dist_esd +CIS 1 C 2 N SINGLE 1.337 0.011 + +loop_ +_chem_link_angle.link_id +_chem_link_angle.atom_1_comp_id +_chem_link_angle.atom_id_1 +_chem_link_angle.atom_2_comp_id +_chem_link_angle.atom_id_2 +_chem_link_angle.atom_3_comp_id +_chem_link_angle.atom_id_3 +_chem_link_angle.value_angle +_chem_link_angle.value_angle_esd +CIS 1 CA 1 C 2 N 115.917 1.50 +CIS 1 O 1 C 2 N 123.469 1.50 +CIS 1 C 2 N 2 CA 122.095 1.76 +CIS 1 C 2 N 2 H 119.176 1.83 + +loop_ +_chem_link_tor.link_id +_chem_link_tor.id +_chem_link_tor.atom_1_comp_id +_chem_link_tor.atom_id_1 +_chem_link_tor.atom_2_comp_id +_chem_link_tor.atom_id_2 +_chem_link_tor.atom_3_comp_id +_chem_link_tor.atom_id_3 +_chem_link_tor.atom_4_comp_id +_chem_link_tor.atom_id_4 +_chem_link_tor.value_angle +_chem_link_tor.value_angle_esd +_chem_link_tor.period +CIS psi 1 N 1 CA 1 C 2 N 160.00 30.0 2 +CIS omega 1 CA 1 C 2 N 2 CA 0.00 5.0 0 +CIS phi 1 C 2 N 2 CA 2 C 60.00 20.0 3 + +loop_ +_chem_link_plane.link_id +_chem_link_plane.plane_id +_chem_link_plane.atom_comp_id +_chem_link_plane.atom_id +_chem_link_plane.dist_esd +CIS plan-1 1 CA 0.020 +CIS plan-1 1 C 0.020 +CIS plan-1 2 N 0.020 +CIS plan-1 1 O 0.020 +CIS plan-2 2 CA 0.020 +CIS plan-2 1 C 0.020 +CIS plan-2 2 H 0.020 +CIS plan-2 2 N 0.020 + +data_link_PTRANS +loop_ +_chem_link_bond.link_id +_chem_link_bond.atom_1_comp_id +_chem_link_bond.atom_id_1 +_chem_link_bond.atom_2_comp_id +_chem_link_bond.atom_id_2 +_chem_link_bond.type +_chem_link_bond.value_dist +_chem_link_bond.value_dist_esd +PTRANS 1 C 2 N SINGLE 1.352 0.010 + +loop_ +_chem_link_angle.link_id +_chem_link_angle.atom_1_comp_id +_chem_link_angle.atom_id_1 +_chem_link_angle.atom_2_comp_id +_chem_link_angle.atom_id_2 +_chem_link_angle.atom_3_comp_id +_chem_link_angle.atom_id_3 +_chem_link_angle.value_angle +_chem_link_angle.value_angle_esd +PTRANS 1 CA 1 C 2 N 118.415 1.50 +PTRANS 1 O 1 C 2 N 121.016 1.53 +PTRANS 2 CA 2 N 1 C 120.469 1.50 +PTRANS 2 CD 2 N 1 C 124.005 1.50 + +loop_ +_chem_link_tor.link_id +_chem_link_tor.id +_chem_link_tor.atom_1_comp_id +_chem_link_tor.atom_id_1 +_chem_link_tor.atom_2_comp_id +_chem_link_tor.atom_id_2 +_chem_link_tor.atom_3_comp_id +_chem_link_tor.atom_id_3 +_chem_link_tor.atom_4_comp_id +_chem_link_tor.atom_id_4 +_chem_link_tor.value_angle +_chem_link_tor.value_angle_esd +_chem_link_tor.period +PTRANS psi 1 N 1 CA 1 C 2 N 160.00 30.0 2 +PTRANS omega 1 CA 1 C 2 N 2 CA 180.00 5.0 0 +PTRANS phi 1 C 2 N 2 CA 2 C 60.00 20.0 3 + +loop_ +_chem_link_plane.link_id +_chem_link_plane.plane_id +_chem_link_plane.atom_comp_id +_chem_link_plane.atom_id +_chem_link_plane.dist_esd +PTRANS plan-1 1 CA 0.020 +PTRANS plan-1 1 C 0.020 +PTRANS plan-1 2 N 0.020 +PTRANS plan-1 1 O 0.020 +PTRANS plan-2 1 C .020 +PTRANS plan-2 2 N .020 +PTRANS plan-2 2 CA .020 +PTRANS plan-2 2 CD .020 + +data_link_PCIS +loop_ +_chem_link_bond.link_id +_chem_link_bond.atom_1_comp_id +_chem_link_bond.atom_id_1 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CD2 2 CE2 1 CH2 120.621 2.79 +TRP-TYR 2 CZ 2 CE2 1 CH2 121.366 3.00 + +loop_ +_chem_link_tor.link_id +_chem_link_tor.id +_chem_link_tor.atom_1_comp_id +_chem_link_tor.atom_id_1 +_chem_link_tor.atom_2_comp_id +_chem_link_tor.atom_id_2 +_chem_link_tor.atom_3_comp_id +_chem_link_tor.atom_id_3 +_chem_link_tor.atom_4_comp_id +_chem_link_tor.atom_id_4 +_chem_link_tor.value_angle +_chem_link_tor.value_angle_esd +_chem_link_tor.period +TRP-TYR sp2_sp2_1 1 CZ2 1 CH2 2 CE2 2 CD2 180.000 5.0 2 + +loop_ +_chem_link_plane.link_id +_chem_link_plane.plane_id +_chem_link_plane.atom_comp_id +_chem_link_plane.atom_id +_chem_link_plane.dist_esd +TRP-TYR plan-1 1 CE2 0.020 +TRP-TYR plan-1 1 CE3 0.020 +TRP-TYR plan-1 1 CZ2 0.020 +TRP-TYR plan-1 1 CZ3 0.020 +TRP-TYR plan-1 1 CH2 0.020 +TRP-TYR plan-1 2 CE2 0.020 +TRP-TYR plan-1 1 CG 0.020 +TRP-TYR plan-1 1 CD2 0.020 +TRP-TYR plan-1 1 HE3 0.020 +TRP-TYR plan-1 1 HZ2 0.020 +TRP-TYR plan-1 1 HZ3 0.020 +TRP-TYR plan-1 1 NE1 0.020 +TRP-TYR plan-2 1 CH2 0.020 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H H 0 +SERm1 change OG . O O2 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +SERm1 delete OG HG single . . . . +SERm1 change CA CB single 1.516 0.0100 1.516 0.0100 +SERm1 change CB OG single 1.438 0.0200 1.438 0.0200 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +SERm1 delete CB OG HG . . +SERm1 change CA CB OG 108.381 1.50 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.id +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +_chem_mod_tor.new_period +SERm1 delete CA CB OG HG . . . 3 +SERm1 change OG CB CA N sp3_sp3_199 180.000 10.0 3 + +data_mod_CYS-SS +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +CYS-SS delete HG . . . .000 + +data_mod_CYSmod1 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +CYSmod1 delete HG . H HSH1 0 +CYSmod1 change SG . S S2 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +CYSmod1 delete SG HG single . . . . +CYSmod1 change CB HB3 single 0.980 0.0104 1.089 0.0100 +CYSmod1 change CB HB2 single 0.980 0.0104 1.089 0.0100 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +CYSmod1 delete CB SG HG . . +CYSmod1 change N CA CB 109.354 2.20 +CYSmod1 change C CA CB 110.419 3.00 +CYSmod1 change CA CB SG 114.974 2.42 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.id +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +_chem_mod_tor.new_period +CYSmod1 delete CA CB SG HG . . . 0 +CYSmod1 change N CA CB SG sp3_sp3_19 180.000 10.0 3 + +data_mod_NH3 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +NH3 change N N . NT3 -1.000 +NH3 add H H H HNT3 .000 +NH3 add . H2 H HNT3 .000 +NH3 add . H3 H HNT3 .000 +NH3 delete HN1 . . . .000 +NH3 delete HN2 . . . .000 +NH3 delete HN3 . . . .000 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +NH3 change N n/a . CA START +NH3 add H N . . . +NH3 add H2 N . . . +NH3 add H3 N . . . + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +NH3 add N H2 single 0.914 0.010 1.036 0.016 +NH3 add N H3 single 0.914 0.010 1.036 0.016 +NH3 change N CA single 1.491 .021 1.491 .021 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +NH3 add H2 N H3 109.470 3.000 +NH3 add H3 N CA 109.470 3.000 +NH3 add H2 N CA 109.470 3.000 +NH3 add H N H2 109.470 3.000 +NH3 add H N H3 109.470 3.000 +NH3 change H N CA 109.470 3.000 + +data_mod_NH1 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +NH1 change N N . NH1 .000 +NH1 add . H H HNH1 .000 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +NH1 change N n/a . CA START +NH1 add H N . . . + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +NH1 add N H single 0.914 0.010 1.036 0.016 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +NH1 add H N CA 109.307 3.000 +NH1 add H N CD 106.136 2.250 + +data_mod_NH2 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +NH2 change N N . NH1 .000 +NH2 add . H H HNH1 .000 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +NH2 change N n/a . CA START +NH2 add H N . . . + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +NH2 add N H single 0.914 0.010 1.036 0.016 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +NH2 add H N CA 109.307 3.000 +NH2 add H N CD 106.136 2.250 + +data_mod_NH2N +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +NH2N change N N . NH2 .000 + +data_mod_COO +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +COO change C C . C .000 +COO change O O . OC -.500 +COO add . OXT O OC -.500 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +COO add OXT C . . END +COO change C n/a . OXT . + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +COO change C O deloc 1.231 .020 1.231 .020 +COO add C OXT deloc 1.231 .020 1.231 .020 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +COO change CA C O 121.000 3.000 +COO add CA C OXT 121.000 3.000 +COO add O C OXT 118.000 3.000 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.id +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +_chem_mod_tor.new_period +COO add psi N CA C OXT 160.00 30.0 2 + +loop_ +_chem_mod_plane_atom.mod_id +_chem_mod_plane_atom.function +_chem_mod_plane_atom.plane_id +_chem_mod_plane_atom.atom_id +_chem_mod_plane_atom.new_dist_esd +COO add oxt C .020 +COO add oxt CA .020 +COO add oxt O .020 +COO add oxt OXT .020 + +data_mod_AA-STAND + +data_mod_AA-STPRO +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +AA-STPRO delete HN . . . .000 + +data_mod_NA-STAND + +data_mod_5*END +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +5*END delete P . . . .000 +5*END delete OP1 . . . .000 +5*END delete OP2 . . . .000 +5*END delete OP3 . . . .000 +5*END change 'O5'' 'O5'' . OH1 0.000 +5*END add . 'HO5'' H HOH1 0.000 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +5*END delete P n/a . . . +5*END delete O1P n/a . . . +5*END delete O2P n/a . . . +5*END change 'O5'' n/a . 'C5'' START +5*END add 'HO5'' 'O5'' . . . + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +5*END add 'O5'' 'HO5'' single 0.839 0.010 0.970 0.012 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +5*END add 'C5'' 'O5'' 'HO5'' 120.000 3.000 + +data_mod_3*END +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +3*END change 'O3'' 'O3'' . OH1 0.000 +3*END add . 'HO3'' H HOH1 0.000 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +3*END change 'O3'' 'C3'' . . END +3*END add 'HO3'' 'O3'' . . . + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +3*END add 'O3'' 'HO3'' single 0.839 0.010 0.970 0.012 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +3*END add 'C3'' 'O3'' 'HO3'' 120.000 3.000 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.id +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +_chem_mod_tor.new_period +3*END add hh 'C4'' 'C3'' 'O3'' 'HO3'' .00 30.0 3 + +data_mod_p5*END +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +p5*END change OP3 OP3 O OP -.330 + +data_mod_p3*END +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +p3*END change 'O3'' 'O3'' . OH1 0.000 +p3*END add . 'HO3'' H HOH1 0.000 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +p3*END change 'O3'' 'C3'' . . END +p3*END add 'HO3'' 'O3'' . . . + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +p3*END add 'O3'' 'HO3'' single 0.839 0.010 0.970 0.012 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +p3*END add 'C3'' 'O3'' 'HO3'' 120.000 3.000 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.id +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +_chem_mod_tor.new_period +p3*END add hh 'C4'' 'C3'' 'O3'' 'HO3'' .00 30.0 3 + +data_mod_DEL_OP3 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +DEL_OP3 delete OP3 . O OP -1 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +DEL_OP3 delete OP3 P single . . . . +DEL_OP3 change P OP1 double 1.491 0.0100 1.491 0.0100 +DEL_OP3 change P OP2 single 1.491 0.0100 1.491 0.0100 +DEL_OP3 change P "O5'" single 1.599 0.0103 1.599 0.0103 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +DEL_OP3 delete OP3 P OP1 . . +DEL_OP3 delete OP3 P OP2 . . +DEL_OP3 delete OP3 P "O5'" . . +DEL_OP3 change OP1 P OP2 118.304 1.50 +DEL_OP3 change OP1 P "O5'" 108.008 3.00 +DEL_OP3 change OP2 P "O5'" 108.008 3.00 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +DEL_OP3 delete "C5'" "O5'" P OP3 . . + +data_mod_DEL_HO3p +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +DEL_HO3p delete "HO3'" . H H 0 +DEL_HO3p change "O3'" . O O2 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +DEL_HO3p delete "O3'" "HO3'" single . . . . +DEL_HO3p change "C3'" "O3'" single 1.421 0.0119 1.421 0.0119 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +DEL_HO3p delete "C3'" "O3'" "HO3'" . . + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +DEL_HO3p delete "C4'" "C3'" "O3'" "HO3'" . . + +data_mod_FOR-N +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +FOR-N add . H H HC1 .000 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +FOR-N add H C . . . + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +FOR-N add C H single 0.988 0.010 1.089 0.010 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +FOR-N add H C O 121.000 3.000 + +data_mod_FOR-C +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +FOR-C change O O . OC -0.500 +FOR-C add . OXT O OC -0.500 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +FOR-C add OXT C . . . + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +FOR-C change C O deloc 1.231 .020 1.231 .020 +FOR-C add C OXT deloc 1.231 .020 1.231 .020 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +FOR-C add O C OXT 120.000 3.000 + +data_mod_G-N2 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +G-N2 delete N2 . . . .000 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +G-N2 delete N2 n/a . . . + +data_mod_DEL-HD1 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +DEL-HD1 delete HD1 . . . .000 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +DEL-HD1 change ND1 n/a . . END + +data_mod_DEL-HE2 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +DEL-HE2 delete HE2 . . . .000 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +DEL-HE2 change NE2 n/a . . END + +data_mod_DEL-OXT +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +DEL-OXT delete OXT . O OC -1 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +DEL-OXT delete C OXT single . . . . +DEL-OXT change CA C single 1.526 0.010 1.526 0.010 +DEL-OXT change C O double 1.229 0.012 1.229 0.012 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +DEL-OXT delete CA C OXT . . +DEL-OXT delete O C OXT . . +DEL-OXT change CA C O 120.614 1.50 + +loop_ +_chem_mod_plane_atom.mod_id +_chem_mod_plane_atom.function +_chem_mod_plane_atom.plane_id +_chem_mod_plane_atom.atom_id +_chem_mod_plane_atom.new_dist_esd +DEL-OXT delete plan-1 C 0.020 +DEL-OXT delete plan-1 CA 0.020 +DEL-OXT delete plan-1 O 0.020 +DEL-OXT delete plan-1 OXT 0.020 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +DEL-OXT delete O C CA N 0.000 10.0 + +data_mod_DEL-OXT1 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +DEL-OXT1 delete OXT . O OC -1 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +DEL-OXT1 delete C OXT single . . . . +DEL-OXT1 change CA C single 1.526 0.010 1.526 0.010 +DEL-OXT1 change C O double 1.232 0.010 1.232 0.010 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +DEL-OXT1 delete CA C OXT . . +DEL-OXT1 delete O C OXT . . +DEL-OXT1 change CA C O 120.082 1.50 + +loop_ +_chem_mod_plane_atom.mod_id +_chem_mod_plane_atom.function +_chem_mod_plane_atom.plane_id +_chem_mod_plane_atom.atom_id +_chem_mod_plane_atom.new_dist_esd +DEL-OXT1 delete plan-1 C 0.020 +DEL-OXT1 delete plan-1 CA 0.020 +DEL-OXT1 delete plan-1 O 0.020 +DEL-OXT1 delete plan-1 OXT 0.020 + +data_mod_DEL-HN1 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +DEL-HN1 delete H2 . H H 0 +DEL-HN1 delete H3 . H H 0 +DEL-HN1 change N . N NH1 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +DEL-HN1 delete N H2 single . . . . +DEL-HN1 delete N H3 single . . . . +DEL-HN1 change CA N single 1.453 0.010 1.453 0.010 +DEL-HN1 change N H single 0.914 0.010 1.036 0.016 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +DEL-HN1 delete CA N H2 . . +DEL-HN1 delete CA N H3 . . +DEL-HN1 delete H N H2 . . +DEL-HN1 delete H N H3 . . +DEL-HN1 delete H2 N H3 . . +DEL-HN1 change CA N H 118.729 1.50 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +DEL-HN1 delete C CA N H 180 10 + +data_mod_DEL-NMH +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +DEL-NMH delete H . H H 0 +DEL-NMH change N . N N 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +DEL-NMH delete N H single . . . . +DEL-NMH change N CN single 1.450 0.0200 1.450 0.0200 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +DEL-NMH delete CN N H . . +DEL-NMH delete CA N H . . +DEL-NMH change CN N CA 118.119 2.78 +DEL-NMH change N CA C 111.097 3.00 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.id +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +_chem_mod_tor.new_period +DEL-NMH change CN N CA C sp2_sp3_13 0.000 10.0 6 +DEL-NMH change CA N CN HN1 sp2_sp3_7 0.000 10.0 6 + +loop_ +_chem_mod_chir.mod_id +_chem_mod_chir.function +_chem_mod_chir.atom_id_centre +_chem_mod_chir.atom_id_1 +_chem_mod_chir.atom_id_2 +_chem_mod_chir.atom_id_3 +_chem_mod_chir.new_volume_sign +DEL-NMH delete N CA CN H . + +data_mod_DEL-HNP +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +DEL-HNP delete H . H H 0 +DEL-HNP delete H2 . H H 0 +DEL-HNP change N . N NH0 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +DEL-HNP delete N H single . . . . +DEL-HNP delete N H2 single . . . . +DEL-HNP change N CA single 1.459 0.0100 1.459 0.0100 +DEL-HNP change N CD single 1.472 0.0100 1.472 0.0100 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +DEL-HNP delete CA N H . . +DEL-HNP delete CA N H2 . . +DEL-HNP delete CD N H . . +DEL-HNP delete CD N H2 . . +DEL-HNP delete H N H2 . . +DEL-HNP change CA N CD 112.597 1.50 +DEL-HNP change N CA C 113.251 1.50 +DEL-HNP change N CD CG 102.887 1.50 + +data_mod_PEPT-D +loop_ +_chem_mod_chir.mod_id +_chem_mod_chir.function +_chem_mod_chir.atom_id_centre +_chem_mod_chir.atom_id_1 +_chem_mod_chir.atom_id_2 +_chem_mod_chir.atom_id_3 +_chem_mod_chir.new_volume_sign +PEPT-D change CA N CB C positiv + +data_mod_1MA +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +1MA change N1 . . NR6 .000 +1MA add . C1 C CH3 .000 +1MA add . H11 H HCH .000 +1MA add . H12 H HGH .000 +1MA add . H13 H HCH .000 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +1MA add C1 N1 . H13 . +1MA add H11 C1 . . . +1MA add H12 C1 . . . +1MA add H13 C1 . . . + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +1MA add C1 N1 single 1.465 .020 1.465 .020 +1MA add C1 H11 single 0.988 0.010 1.089 0.010 +1MA add C1 H12 single 0.988 0.010 1.089 0.010 +1MA add C1 H13 single 0.988 0.010 1.089 0.010 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +1MA add N1 C1 H11 109.470 3.000 +1MA add N1 C1 H12 109.470 3.000 +1MA add N1 C1 H13 109.470 3.000 +1MA add H12 C1 H11 109.470 3.000 +1MA add H13 C1 H11 109.470 3.000 +1MA add H13 C1 H12 109.470 3.000 + +data_mod_1MG +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +1MG change N1 . . NR6 .000 +1MG add . C1A C CH3 .000 +1MG add . H1A1 H HCH .000 +1MG add . H1A2 H HGH .000 +1MG add . H1A3 H HCH .000 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +1MG add C1A N1 . H1A3 . +1MG add H1A1 C1A . . . +1MG add H1A2 C1A . . . +1MG add H1A3 C1A . . . + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +1MG add C1A N1 single 1.465 .020 1.465 .020 +1MG add C1A H1A1 single 0.988 0.010 1.089 0.010 +1MG add C1A H1A2 single 0.988 0.010 1.089 0.010 +1MG add C1A H1A3 single 0.988 0.010 1.089 0.010 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +1MG add N1 C1A H1A1 109.470 3.000 +1MG add N1 C1A H1A2 109.470 3.000 +1MG add N1 C1A H1A3 109.470 3.000 +1MG add H1A2 C1A H1A1 109.470 3.000 +1MG add H1A3 C1A H1A1 109.470 3.000 +1MG add H1A3 C1A H1A2 109.470 3.000 + +data_mod_2MG +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +2MG change N2 . . NH1 .000 +2MG add . C2A C CH3 .000 +2MG add . H2A1 H HCH .000 +2MG add . H2A2 H HGH .000 +2MG add . H2A3 H HCH .000 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +2MG change N2 C2 . C2A . +2MG add C2A N2 . H2A3 . +2MG add H2A1 C2A . . . +2MG add H2A2 C2A . . . +2MG add H2A3 C2A . . . + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +2MG add C2A N2 single 1.465 .020 1.465 .020 +2MG add C2A H2A1 single 0.988 0.010 1.089 0.010 +2MG add C2A H2A2 single 0.988 0.010 1.089 0.010 +2MG add C2A H2A3 single 0.988 0.010 1.089 0.010 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +2MG add C2 N2 C2A 115.000 3.000 +2MG add N2 C2A H2A1 109.470 3.000 +2MG add N2 C2A H2A2 109.470 3.000 +2MG add N2 C2A H2A3 109.470 3.000 +2MG add H2A2 C2A H2A1 109.470 3.000 +2MG add H2A3 C2A H2A1 109.470 3.000 +2MG add H2A3 C2A H2A2 109.470 3.000 + +data_mod_M2G +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +M2G change N2 . . N .000 +M2G add . C2A C CH3 .000 +M2G add . H2A1 H HCH .000 +M2G add . H2A2 H HGH .000 +M2G add . H2A3 H HCH .000 +M2G add . C2B C CH3 .000 +M2G add . H2B1 H HCH .000 +M2G add . H2B2 H HGH .000 +M2G add . H2B3 H HCH .000 +M2G delete H21 . . . .000 +M2G delete H22 . . . .000 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +M2G change N2 C2 . C2A . +M2G add C2A N2 . H2A3 . +M2G add H2A1 C2A . . . +M2G add H2A2 C2A . . . +M2G add H2A3 C2A . . . +M2G add C2B N2 . H2B3 . +M2G add H2B1 C2B . . . +M2G add H2B2 C2B . . . +M2G add H2B3 C2B . . . + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +M2G add C2A N2 single 1.465 .020 1.465 .020 +M2G add C2A H2A1 single 0.988 0.010 1.089 0.010 +M2G add C2A H2A2 single 0.988 0.010 1.089 0.010 +M2G add C2A H2A3 single 0.988 0.010 1.089 0.010 +M2G add C2B N2 single 1.465 .020 1.465 .020 +M2G add C2B H2B1 single 0.988 0.010 1.089 0.010 +M2G add C2B H2B2 single 0.988 0.010 1.089 0.010 +M2G add C2B H2B3 single 0.988 0.010 1.089 0.010 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +M2G add C2 N2 C2A 118.000 3.000 +M2G add C2 N2 C2B 118.000 3.000 +M2G add C2A N2 C2B 124.000 3.000 +M2G add N2 C2A H2A1 109.470 3.000 +M2G add N2 C2A H2A2 109.470 3.000 +M2G add N2 C2A H2A3 109.470 3.000 +M2G add H2A2 C2A H2A1 109.470 3.000 +M2G add H2A3 C2A H2A1 109.470 3.000 +M2G add H2A3 C2A H2A2 109.470 3.000 +M2G add N2 C2B H2B1 109.470 3.000 +M2G add N2 C2B H2B2 109.470 3.000 +M2G add N2 C2B H2B3 109.470 3.000 +M2G add H2B2 C2B H2B1 109.470 3.000 +M2G add H2B3 C2B H2B1 109.470 3.000 +M2G add H2B3 C2B H2B2 109.470 3.000 + +data_mod_O2*MET +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +O2*MET change 'O2'' . . OC2 .000 +O2*MET delete 'HO2'' . . . .000 +O2*MET add . C2A C CH3 .000 +O2*MET add . H2A1 H HCH .000 +O2*MET add . H2A2 H HGH .000 +O2*MET add . H2A3 H HCH .000 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +O2*MET change 'O2'' 'C2'' . C2A . +O2*MET add C2A 'O2'' . H2A3 . +O2*MET add H2A1 C2A . . . +O2*MET add H2A2 C2A . . . +O2*MET add H2A3 C2A . . . + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +O2*MET add 'O2'' C2A single 1.420 .020 1.420 .020 +O2*MET add C2A H2A1 single 0.988 0.010 1.089 0.010 +O2*MET add C2A H2A2 single 0.988 0.010 1.089 0.010 +O2*MET add C2A H2A3 single 0.988 0.010 1.089 0.010 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +O2*MET add 'C2'' 'O2'' C2A 120.000 3.000 +O2*MET add 'O2'' C2A H2A1 109.470 3.000 +O2*MET add 'O2'' C2A H2A2 109.470 3.000 +O2*MET add 'O2'' C2A H2A3 109.470 3.000 +O2*MET add H2A2 C2A H2A1 109.470 3.000 +O2*MET add H2A3 C2A H2A1 109.470 3.000 +O2*MET add H2A3 C2A H2A2 109.470 3.000 + +data_mod_C5MET +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +C5MET change C5 . . CR6 .000 +C5MET add . C5A C CH3 .000 +C5MET add . H5A1 H HCH .000 +C5MET add . H5A2 H HGH .000 +C5MET add . H5A3 H HCH .000 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +C5MET add C5A C5 . H5A3 . +C5MET add H5A1 C5A . . . +C5MET add H5A2 C5A . . . +C5MET add H5A3 C5A . . . + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +C5MET add C5A C5 single 1.500 .020 1.500 .020 +C5MET add C5A H5A1 single 0.988 0.010 1.089 0.010 +C5MET add C5A H5A2 single 0.988 0.010 1.089 0.010 +C5MET add C5A H5A3 single 0.988 0.010 1.089 0.010 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +C5MET add C4 C5 C5A 122.000 3.000 +C5MET add C6 C5 C5A 118.000 3.000 +C5MET add C5 C5A H5A2 109.470 3.000 +C5MET add C5 C5A H5A3 109.470 3.000 +C5MET add H5A2 C5A H5A1 109.470 3.000 +C5MET add H5A3 C5A H5A1 109.470 3.000 +C5MET add H5A3 C5A H5A2 109.470 3.000 + +data_mod_N7MET +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +N7MET change N7 . . NR5 .000 +N7MET add . C7 C CH3 .000 +N7MET add . H71 H HCH .000 +N7MET add . H72 H HGH .000 +N7MET add . H73 H HCH .000 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +N7MET add C7 N7 . H73 . +N7MET add H71 C7 . . . +N7MET add H72 C7 . . . +N7MET add H73 C7 . . . + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +N7MET add C7 N7 single 1.465 .020 1.465 .020 +N7MET add C7 H71 single 0.988 0.010 1.089 0.010 +N7MET add C7 H72 single 0.988 0.010 1.089 0.010 +N7MET add C7 H73 single 0.988 0.010 1.089 0.010 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +N7MET add C5 N7 C7 126.000 3.000 +N7MET add C8 N7 C7 126.000 3.000 +N7MET add N7 C7 H71 109.470 3.000 +N7MET add N7 C7 H72 109.470 3.000 +N7MET add N7 C7 H73 109.470 3.000 +N7MET add H72 C7 H71 109.470 3.000 +N7MET add H73 C7 H71 109.470 3.000 +N7MET add H73 C7 H72 109.470 3.000 + +data_mod_RNA-O2* +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +RNA-O2* delete 'O2'' . . . .000 +RNA-O2* delete 'HO2'' . . . .000 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +RNA-O2* delete 'O2'' n/a . . . +RNA-O2* delete 'HO2'' n/a . . . + +data_mod_XYS-O1 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +XYS-O1 delete O1 . . . .000 +XYS-O1 delete HO1 . . . .000 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +XYS-O1 delete O1 n/a . . . +XYS-O1 delete HO1 n/a . . . + +data_mod_B2C +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +B2C change N N . NT3 -1.000 +B2C add . H1 H HNT3 0.000 +B2C add . H2 H HNT3 0.000 +B2C add . H3 H HNT3 0.000 +B2C delete H . . . .000 +B2C change C B B B .000 +B2C change O O1 O O .000 +B2C add . O2 O O .000 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +B2C change N n/a . CA START +B2C add H1 N . . . +B2C add H2 N . . . +B2C add H3 N . . . +B2C change B CA . . END +B2C change CA N . B . +B2C change O1 B . . . +B2C add O2 B . . . + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +B2C add N H1 single 0.914 0.010 1.036 0.016 +B2C add N H2 single 0.914 0.010 1.036 0.016 +B2C add N H3 single 0.914 0.010 1.036 0.016 +B2C change N CA single 1.491 .021 1.491 .021 +B2C change B CA single 1.560 .020 1.560 .020 +B2C change B O1 deloc 1.480 .020 1.480 .020 +B2C add B O2 deloc 1.480 .020 1.480 .020 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +B2C add H2 N H3 109.470 3.000 +B2C add H3 N CA 109.470 3.000 +B2C add H2 N CA 109.470 3.000 +B2C add H1 N H2 109.470 3.000 +B2C add H1 N H3 109.470 3.000 +B2C add H1 N CA 109.470 3.000 +B2C add O1 B O2 112.000 3.000 +B2C change CA B O1 126.000 3.000 +B2C add CA B O2 126.000 3.000 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.id +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +_chem_mod_tor.new_period +B2C add hhb N CA B O2 .00 30.0 3 + +loop_ +_chem_mod_chir.mod_id +_chem_mod_chir.function +_chem_mod_chir.atom_id_centre +_chem_mod_chir.atom_id_1 +_chem_mod_chir.atom_id_2 +_chem_mod_chir.atom_id_3 +_chem_mod_chir.new_volume_sign +B2C change CA N CB B negativ + +data_mod_B2C_D +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_partial_charge +B2C_D change N N . NT3 -1.000 +B2C_D add . H1 H HNT3 0.000 +B2C_D add . H2 H HNT3 0.00 +B2C_D add . H3 H HNT3 0.00 +B2C_D delete H . . . .000 +B2C_D change C B B B .000 +B2C_D change O O1 O O .000 +B2C_D add . O2 O O .000 + +loop_ +_chem_mod_tree.mod_id +_chem_mod_tree.function +_chem_mod_tree.atom_id +_chem_mod_tree.atom_back +_chem_mod_tree.back_type +_chem_mod_tree.atom_forward +_chem_mod_tree.connect_type +B2C_D change N n/a . CA START +B2C_D add H1 N . . . +B2C_D add H2 N . . . +B2C_D add H3 N . . . +B2C_D change B CA . . END +B2C_D change CA N . B . +B2C_D change O1 B . . . +B2C_D add O2 B . . . + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +B2C_D add N H1 single 0.914 0.010 1.036 0.016 +B2C_D add N H2 single 0.914 0.010 1.036 0.016 +B2C_D add N H3 single 0.914 0.010 1.036 0.016 +B2C_D change N CA single 1.491 .021 1.491 .021 +B2C_D change B CA single 1.560 .020 1.560 .020 +B2C_D change B O1 deloc 1.480 .020 1.480 .020 +B2C_D add B O2 deloc 1.480 .020 1.480 .020 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +B2C_D add H2 N H3 109.470 3.000 +B2C_D add H3 N CA 109.470 3.000 +B2C_D add H2 N CA 109.470 3.000 +B2C_D add H1 N H2 109.470 3.000 +B2C_D add H1 N H3 109.470 3.000 +B2C_D add H1 N CA 109.470 3.000 +B2C_D add O1 B O2 112.000 3.000 +B2C_D change CA B O1 126.000 3.000 +B2C_D add CA B O2 126.000 3.000 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.id +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +_chem_mod_tor.new_period +B2C_D add hhb N CA B O2 .00 30.0 3 + +loop_ +_chem_mod_chir.mod_id +_chem_mod_chir.function +_chem_mod_chir.atom_id_centre +_chem_mod_chir.atom_id_1 +_chem_mod_chir.atom_id_2 +_chem_mod_chir.atom_id_3 +_chem_mod_chir.new_volume_sign +B2C_D change CA N CB B positiv + +data_mod_RENAME + +data_mod_TERMINUS + +data_mod_DEL-HD22 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +DEL-HD22 delete HD22 . H H 0 +DEL-HD22 change ND2 . N NH1 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +DEL-HD22 delete ND2 HD22 single . . . . +DEL-HD22 change CB CG single 1.520 0.0174 1.520 0.0174 +DEL-HD22 change CG OD1 double 1.227 0.0138 1.227 0.0138 +DEL-HD22 change ND2 HD21 single 0.863 0.0200 1.013 0.0120 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +DEL-HD22 delete CG ND2 HD22 . . +DEL-HD22 delete HD21 ND2 HD22 . . +DEL-HD22 change CA CB CG 112.357 3.00 +DEL-HD22 change OD1 CG ND2 123.445 2.69 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.id +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +_chem_mod_tor.new_period +DEL-HD22 delete CB CG ND2 HD22 . . . 2 + +loop_ +_chem_mod_plane_atom.mod_id +_chem_mod_plane_atom.function +_chem_mod_plane_atom.plane_id +_chem_mod_plane_atom.atom_id +_chem_mod_plane_atom.new_dist_esd +DEL-HD22 delete plan-3 CG 0.020 +DEL-HD22 delete plan-3 HD21 0.020 +DEL-HD22 delete plan-3 HD22 0.020 +DEL-HD22 delete plan-3 ND2 0.020 + +data_mod_DEL-HG +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +DEL-HG delete HG . H H 0 +DEL-HG change OG . O O2 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +DEL-HG delete OG HG single . . . . +DEL-HG change CA CB single 1.518 0.0126 1.518 0.0126 +DEL-HG change CB OG single 1.426 0.0176 1.426 0.0176 +DEL-HG change CB HB3 single 0.982 0.0125 1.092 0.0100 +DEL-HG change CB HB2 single 0.982 0.0125 1.092 0.0100 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +DEL-HG delete CB OG HG . . +DEL-HG change N CA CB 113.399 3.00 +DEL-HG change C CA CB 111.339 3.00 +DEL-HG change CA CB OG 109.581 3.00 +DEL-HG change OG CB HB3 109.634 2.46 +DEL-HG change OG CB HB2 109.634 2.46 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.id +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +_chem_mod_tor.new_period +DEL-HG delete CA CB OG HG . . . 3 + +data_mod_DEL-HG1 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +DEL-HG1 delete HG1 . H H 0 +DEL-HG1 change OG1 . O O2 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +DEL-HG1 delete OG1 HG1 single . . . . +DEL-HG1 change CA CB single 1.538 0.0100 1.538 0.0100 +DEL-HG1 change CB OG1 single 1.440 0.0100 1.440 0.0100 +DEL-HG1 change CB CG2 single 1.508 0.0200 1.508 0.0200 +DEL-HG1 change CB HB single 0.993 0.0134 1.092 0.0100 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +DEL-HG1 delete CB OG1 HG1 . . +DEL-HG1 change N CA CB 113.399 3.00 +DEL-HG1 change C CA CB 111.339 3.00 +DEL-HG1 change CA CB OG1 111.145 1.50 +DEL-HG1 change CA CB CG2 110.837 3.00 +DEL-HG1 change CG2 CB HB 109.492 1.50 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.id +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +_chem_mod_tor.new_period +DEL-HG1 delete CA CB OG1 HG1 . . . 3 + +data_mod_HISmod1 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +HISmod1 delete HD1 . H H 0 +HISmod1 change ND1 . N NR5 1 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +HISmod1 delete ND1 HD1 single . . . . +HISmod1 change CB CG single 1.491 0.0100 1.491 0.0100 +HISmod1 change CG ND1 single 1.352 0.0200 1.352 0.0200 +HISmod1 change CG CD2 double 1.357 0.0100 1.357 0.0100 +HISmod1 change ND1 CE1 double 1.351 0.0200 1.351 0.0200 +HISmod1 change CE1 HE1 single 0.939 0.0134 1.082 0.0130 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +HISmod1 delete CG ND1 HD1 . . +HISmod1 delete CE1 ND1 HD1 . . +HISmod1 change CB CG ND1 123.044 1.50 +HISmod1 change CG CD2 HD2 126.231 1.50 +HISmod1 change ND1 CE1 HE1 125.433 1.50 + +loop_ +_chem_mod_plane_atom.mod_id +_chem_mod_plane_atom.function +_chem_mod_plane_atom.plane_id +_chem_mod_plane_atom.atom_id +_chem_mod_plane_atom.new_dist_esd +HISmod1 delete plan-1 CB 0.020 +HISmod1 delete plan-1 CD2 0.020 +HISmod1 delete plan-1 CE1 0.020 +HISmod1 delete plan-1 CG 0.020 +HISmod1 delete plan-1 HD1 0.020 +HISmod1 delete plan-1 HD2 0.020 +HISmod1 delete plan-1 HE1 0.020 +HISmod1 delete plan-1 HE2 0.020 +HISmod1 delete plan-1 ND1 0.020 +HISmod1 delete plan-1 NE2 0.020 + +data_mod_HISmod2 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +HISmod2 delete HE2 . H H 0 +HISmod2 change NE2 . N NR5 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +HISmod2 delete NE2 HE2 single . . . . +HISmod2 change CG CD2 double 1.366 0.0178 1.366 0.0178 +HISmod2 change ND1 CE1 double 1.344 0.0200 1.344 0.0200 +HISmod2 change CE1 NE2 single 1.322 0.0100 1.322 0.0100 +HISmod2 change CD2 HD2 single 0.949 0.0120 1.082 0.0130 +HISmod2 change CE1 HE1 single 0.939 0.0134 1.082 0.0130 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +HISmod2 delete CD2 NE2 HE2 . . +HISmod2 delete CE1 NE2 HE2 . . +HISmod2 change NE2 CD2 HD2 125.717 1.62 + +loop_ +_chem_mod_plane_atom.mod_id +_chem_mod_plane_atom.function +_chem_mod_plane_atom.plane_id +_chem_mod_plane_atom.atom_id +_chem_mod_plane_atom.new_dist_esd +HISmod2 delete plan-1 CB 0.020 +HISmod2 delete plan-1 CD2 0.020 +HISmod2 delete plan-1 CE1 0.020 +HISmod2 delete plan-1 CG 0.020 +HISmod2 delete plan-1 HD1 0.020 +HISmod2 delete plan-1 HD2 0.020 +HISmod2 delete plan-1 HE1 0.020 +HISmod2 delete plan-1 HE2 0.020 +HISmod2 delete plan-1 ND1 0.020 +HISmod2 delete plan-1 NE2 0.020 + +data_mod_GTPmod1 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +GTPmod1 delete "HO3'" . H H 0 +GTPmod1 change "O3'" . O O2 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +GTPmod1 delete "O3'" "HO3'" single . . . . + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +GTPmod1 delete "C3'" "O3'" "HO3'" . . +GTPmod1 change "C5'" "C4'" "C3'" 114.817 2.32 +GTPmod1 change "C3'" "C4'" "H4'" 109.150 1.50 +GTPmod1 change "C2'" "C3'" "H3'" 110.368 2.92 +GTPmod1 change "C3'" "C2'" "H2'" 110.368 2.92 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.id +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +_chem_mod_tor.new_period +GTPmod1 delete "C4'" "C3'" "O3'" "HO3'" . . . 0 + +data_mod_TYRmod1 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +TYRmod1 delete HB3 . H H 0 +TYRmod1 change CB . C CH1 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +TYRmod1 delete CB HB3 single . . . . +TYRmod1 change CA C single 1.533 0.0111 1.533 0.0111 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +TYRmod1 delete CA CB HB3 . . +TYRmod1 delete CG CB HB3 . . +TYRmod1 delete HB3 CB HB2 . . +TYRmod1 change N CA CB 113.399 3.00 +TYRmod1 change CA C O 117.156 1.94 +TYRmod1 change CA C OXT 117.156 1.94 +TYRmod1 change CA CB CG 113.308 3.00 +TYRmod1 change CA CB HB2 106.713 1.50 +TYRmod1 change CG CB HB2 107.067 3.00 +TYRmod1 change CB CG CD1 120.731 3.00 +TYRmod1 change CB CG CD2 120.731 3.00 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.id +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +_chem_mod_tor.new_period +TYRmod1 change N CA CB CG sp3_sp3_28 180.000 10.0 3 +TYRmod1 change CD1 CG CB CA sp2_sp3_19 150.000 10.0 6 + +data_mod_HISmod3 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +HISmod3 delete HE2 . H H 0 +HISmod3 change NE2 . N NR5 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +HISmod3 delete NE2 HE2 single . . . . +HISmod3 change CG CD2 double 1.364 0.0129 1.364 0.0129 +HISmod3 change ND1 CE1 double 1.351 0.0200 1.351 0.0200 +HISmod3 change CD2 NE2 single 1.376 0.0100 1.376 0.0100 +HISmod3 change CE1 NE2 single 1.338 0.0162 1.338 0.0162 +HISmod3 change CD2 HD2 single 0.947 0.0141 1.082 0.0130 +HISmod3 change CE1 HE1 single 0.928 0.0133 1.082 0.0130 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +HISmod3 delete CD2 NE2 HE2 . . +HISmod3 delete CE1 NE2 HE2 . . +HISmod3 change CG ND1 CE1 108.905 3.00 +HISmod3 change CG CD2 NE2 108.374 2.83 +HISmod3 change CG CD2 HD2 126.805 1.50 + +loop_ +_chem_mod_plane_atom.mod_id +_chem_mod_plane_atom.function +_chem_mod_plane_atom.plane_id +_chem_mod_plane_atom.atom_id +_chem_mod_plane_atom.new_dist_esd +HISmod3 delete plan-1 CB 0.020 +HISmod3 delete plan-1 CD2 0.020 +HISmod3 delete plan-1 CE1 0.020 +HISmod3 delete plan-1 CG 0.020 +HISmod3 delete plan-1 HD1 0.020 +HISmod3 delete plan-1 HD2 0.020 +HISmod3 delete plan-1 HE1 0.020 +HISmod3 delete plan-1 HE2 0.020 +HISmod3 delete plan-1 ND1 0.020 +HISmod3 delete plan-1 NE2 0.020 + +data_mod_TYRmod2 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +TYRmod2 delete HE2 . H H 0 +TYRmod2 change CE2 . C CR6 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +TYRmod2 delete CE2 HE2 single . . . . +TYRmod2 change CG CD2 single 1.374 0.0100 1.374 0.0100 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +TYRmod2 delete CD2 CE2 HE2 . . +TYRmod2 delete CZ CE2 HE2 . . +TYRmod2 change CB CG CD2 121.348 2.28 + +loop_ +_chem_mod_plane_atom.mod_id +_chem_mod_plane_atom.function +_chem_mod_plane_atom.plane_id +_chem_mod_plane_atom.atom_id +_chem_mod_plane_atom.new_dist_esd +TYRmod2 delete plan-1 CB 0.020 +TYRmod2 delete plan-1 CD1 0.020 +TYRmod2 delete plan-1 CD2 0.020 +TYRmod2 delete plan-1 CE1 0.020 +TYRmod2 delete plan-1 CE2 0.020 +TYRmod2 delete plan-1 CG 0.020 +TYRmod2 delete plan-1 CZ 0.020 +TYRmod2 delete plan-1 HD1 0.020 +TYRmod2 delete plan-1 HD2 0.020 +TYRmod2 delete plan-1 HE1 0.020 +TYRmod2 delete plan-1 HE2 0.020 +TYRmod2 delete plan-1 OH 0.020 + +data_mod_LYSmod1 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +LYSmod1 delete HZ2 . H H 0 +LYSmod1 delete HZ3 . H H 0 +LYSmod1 change NZ . N NT1 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +LYSmod1 delete NZ HZ2 single . . . . +LYSmod1 delete NZ HZ3 single . . . . +LYSmod1 change CE NZ single 1.468 0.0134 1.468 0.0134 +LYSmod1 change NZ HZ1 single 0.914 0.010 1.036 0.016 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +LYSmod1 delete CE NZ HZ2 . . +LYSmod1 delete CE NZ HZ3 . . +LYSmod1 delete HZ1 NZ HZ2 . . +LYSmod1 delete HZ1 NZ HZ3 . . +LYSmod1 delete HZ2 NZ HZ3 . . +LYSmod1 change CE NZ HZ1 111.861 3.00 + +data_mod_CYSmod2 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +CYSmod2 delete HG . H HSH1 0 +CYSmod2 change SG . S S2 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +CYSmod2 delete SG HG single . . . . +CYSmod2 change CB SG single 1.805 0.0100 1.805 0.0100 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +CYSmod2 delete CB SG HG . . + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +CYSmod2 delete CA CB SG HG . . + +data_mod_LYSmod2 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +LYSmod2 delete HZ1 . H H 0 +LYSmod2 delete HZ2 . H H 0 +LYSmod2 delete HZ3 . H H 0 +LYSmod2 change NZ . N N 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +LYSmod2 delete NZ HZ1 single . . . . +LYSmod2 delete NZ HZ2 single . . . . +LYSmod2 delete NZ HZ3 single . . . . +LYSmod2 change CE NZ single 1.480 0.0168 1.480 0.0168 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +LYSmod2 delete CE NZ HZ1 . . +LYSmod2 delete CE NZ HZ2 . . +LYSmod2 delete CE NZ HZ3 . . +LYSmod2 delete HZ1 NZ HZ2 . . +LYSmod2 delete HZ1 NZ HZ3 . . +LYSmod2 delete HZ2 NZ HZ3 . . + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +LYSmod2 delete CD CE NZ HZ3 . . + +data_mod_LYSmod3 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +LYSmod3 delete HZ2 . H H 0 +LYSmod3 delete HZ3 . H H 0 +LYSmod3 change NZ . N NH1 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +LYSmod3 delete NZ HZ2 single . . . . +LYSmod3 delete NZ HZ3 single . . . . +LYSmod3 change CE NZ single 1.456 0.0109 1.456 0.0109 +LYSmod3 change NZ HZ1 single 0.914 0.010 1.036 0.016 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +LYSmod3 delete CE NZ HZ2 . . +LYSmod3 delete CE NZ HZ3 . . +LYSmod3 delete HZ1 NZ HZ2 . . +LYSmod3 delete HZ1 NZ HZ3 . . +LYSmod3 delete HZ2 NZ HZ3 . . +LYSmod3 change CE NZ HZ1 118.241 1.90 + +data_mod_ASNmod1 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +ASNmod1 delete ND2 . N NH2 0 +ASNmod1 delete HD21 . H H 0 +ASNmod1 delete HD22 . H H 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +ASNmod1 delete CG ND2 single . . . . +ASNmod1 delete ND2 HD21 single . . . . +ASNmod1 delete ND2 HD22 single . . . . +ASNmod1 change CB CG single 1.508 0.0116 1.508 0.0116 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +ASNmod1 delete CB CG ND2 . . +ASNmod1 delete OD1 CG ND2 . . +ASNmod1 delete CG ND2 HD21 . . +ASNmod1 delete CG ND2 HD22 . . +ASNmod1 delete HD21 ND2 HD22 . . +ASNmod1 change CB CG OD1 121.400 1.50 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +ASNmod1 delete CB CG ND2 HD21 . . + +loop_ +_chem_mod_plane_atom.mod_id +_chem_mod_plane_atom.function +_chem_mod_plane_atom.plane_id +_chem_mod_plane_atom.atom_id +_chem_mod_plane_atom.new_dist_esd +ASNmod1 delete plan-2 CB 0.020 +ASNmod1 delete plan-2 CG 0.020 +ASNmod1 delete plan-2 ND2 0.020 +ASNmod1 delete plan-2 OD1 0.020 +ASNmod1 delete plan-3 CG 0.020 +ASNmod1 delete plan-3 HD21 0.020 +ASNmod1 delete plan-3 HD22 0.020 +ASNmod1 delete plan-3 ND2 0.020 + +data_mod_METmod1 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +METmod1 change SD . S S3 1 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +METmod1 change CG SD single 1.808 0.0100 1.808 0.0100 +METmod1 change CE HE3 single 0.967 0.0100 1.089 0.0100 +METmod1 change CE HE2 single 0.967 0.0100 1.089 0.0100 +METmod1 change CE HE1 single 0.967 0.0100 1.089 0.0100 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +METmod1 change CA CB CG 114.058 2.21 +METmod1 change CG CB HB3 108.377 2.40 +METmod1 change CG CB HB2 108.377 2.40 +METmod1 change CB CG SD 110.122 1.50 +METmod1 change CB CG HG3 108.661 3.00 +METmod1 change CB CG HG2 108.661 3.00 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.id +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +_chem_mod_tor.new_period +METmod1 change CA CB CG SD sp3_sp3_19 180.000 10.0 3 +METmod1 change CB CG SD CE sp3_sp3_28 180.000 10.0 3 + +data_mod_TYRmod3 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +TYRmod3 delete HE1 . H H 0 +TYRmod3 change CE1 . C CR6 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +TYRmod3 delete CE1 HE1 single . . . . +TYRmod3 change CE1 CZ double 1.395 0.0152 1.395 0.0152 +TYRmod3 change CD1 HD1 single 0.940 0.0104 1.082 0.0130 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +TYRmod3 delete CD1 CE1 HE1 . . +TYRmod3 delete CZ CE1 HE1 . . +TYRmod3 change CB CG CD1 121.186 2.28 +TYRmod3 change CG CD1 HD1 119.873 2.79 +TYRmod3 change CD1 CE1 CZ 119.634 2.58 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.id +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +_chem_mod_tor.new_period +TYRmod3 change CB CG CD1 CE1 const_sp2_sp2_3 180.000 0.0 2 + +loop_ +_chem_mod_plane_atom.mod_id +_chem_mod_plane_atom.function +_chem_mod_plane_atom.plane_id +_chem_mod_plane_atom.atom_id +_chem_mod_plane_atom.new_dist_esd +TYRmod3 delete plan-1 CB 0.020 +TYRmod3 delete plan-1 CD1 0.020 +TYRmod3 delete plan-1 CD2 0.020 +TYRmod3 delete plan-1 CE1 0.020 +TYRmod3 delete plan-1 CE2 0.020 +TYRmod3 delete plan-1 CG 0.020 +TYRmod3 delete plan-1 CZ 0.020 +TYRmod3 delete plan-1 HD1 0.020 +TYRmod3 delete plan-1 HD2 0.020 +TYRmod3 delete plan-1 HE1 0.020 +TYRmod3 delete plan-1 HE2 0.020 +TYRmod3 delete plan-1 OH 0.020 + +data_mod_LEUmod1 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +LEUmod1 delete OXT . O OC -1 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +LEUmod1 delete C OXT single . . . . +LEUmod1 change CA C single 1.527 0.0100 1.527 0.0100 +LEUmod1 change C O double 1.229 0.0102 1.229 0.0102 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +LEUmod1 delete CA C OXT . . +LEUmod1 delete O C OXT . . +LEUmod1 change CA C O 121.041 1.50 + +loop_ +_chem_mod_plane_atom.mod_id +_chem_mod_plane_atom.function +_chem_mod_plane_atom.plane_id +_chem_mod_plane_atom.atom_id +_chem_mod_plane_atom.new_dist_esd +LEUmod1 delete plan-1 C 0.020 +LEUmod1 delete plan-1 CA 0.020 +LEUmod1 delete plan-1 O 0.020 +LEUmod1 delete plan-1 OXT 0.020 + +data_mod_LYSmod4 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +LYSmod4 delete HZ1 . H H 0 +LYSmod4 delete HZ2 . H H 0 +LYSmod4 delete HZ3 . H H 0 +LYSmod4 change NZ . N N 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +LYSmod4 delete NZ HZ1 single . . . . +LYSmod4 delete NZ HZ2 single . . . . +LYSmod4 delete NZ HZ3 single . . . . +LYSmod4 change CE NZ single 1.462 0.0100 1.462 0.0100 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +LYSmod4 delete CE NZ HZ1 . . +LYSmod4 delete CE NZ HZ2 . . +LYSmod4 delete CE NZ HZ3 . . +LYSmod4 delete HZ1 NZ HZ2 . . +LYSmod4 delete HZ1 NZ HZ3 . . +LYSmod4 delete HZ2 NZ HZ3 . . + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +LYSmod4 delete CD CE NZ HZ1 . . + +data_mod_TRPmod1 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +TRPmod1 delete HH2 . H H 0 +TRPmod1 change CH2 . C CR6 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +TRPmod1 delete CH2 HH2 single . . . . +TRPmod1 change CE2 CZ2 single 1.395 0.0185 1.395 0.0185 +TRPmod1 change CE3 CZ3 double 1.379 0.0158 1.379 0.0158 +TRPmod1 change CZ2 CH2 double 1.391 0.0100 1.391 0.0100 +TRPmod1 change CZ3 CH2 single 1.412 0.0100 1.412 0.0100 +TRPmod1 change CZ2 HZ2 single 0.950 0.0100 1.082 0.0130 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +TRPmod1 delete CZ2 CH2 HH2 . . +TRPmod1 delete CZ3 CH2 HH2 . . +TRPmod1 change CE2 CZ2 CH2 119.258 1.50 +TRPmod1 change CZ2 CH2 CZ3 119.154 1.50 + +loop_ +_chem_mod_plane_atom.mod_id +_chem_mod_plane_atom.function +_chem_mod_plane_atom.plane_id +_chem_mod_plane_atom.atom_id +_chem_mod_plane_atom.new_dist_esd +TRPmod1 delete plan-1 CD2 0.020 +TRPmod1 delete plan-1 CE2 0.020 +TRPmod1 delete plan-1 CE3 0.020 +TRPmod1 delete plan-1 CG 0.020 +TRPmod1 delete plan-1 CH2 0.020 +TRPmod1 delete plan-1 CZ2 0.020 +TRPmod1 delete plan-1 CZ3 0.020 +TRPmod1 delete plan-1 HE3 0.020 +TRPmod1 delete plan-1 HH2 0.020 +TRPmod1 delete plan-1 HZ2 0.020 +TRPmod1 delete plan-1 HZ3 0.020 +TRPmod1 delete plan-1 NE1 0.020 + +data_mod_TYRmod4 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +TYRmod4 delete HE2 . H H 0 +TYRmod4 change CE2 . C CR6 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +TYRmod4 delete CE2 HE2 single . . . . +TYRmod4 change CG CD2 single 1.391 0.0149 1.391 0.0149 +TYRmod4 change CD2 CE2 double 1.396 0.0127 1.396 0.0127 +TYRmod4 change CE2 CZ single 1.400 0.0131 1.400 0.0131 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +TYRmod4 delete CD2 CE2 HE2 . . +TYRmod4 delete CZ CE2 HE2 . . +TYRmod4 change CB CG CD2 121.325 2.28 +TYRmod4 change CD1 CG CD2 117.170 2.83 +TYRmod4 change CG CD2 CE2 123.240 3.00 +TYRmod4 change CD2 CE2 CZ 118.013 1.50 + +loop_ +_chem_mod_plane_atom.mod_id +_chem_mod_plane_atom.function +_chem_mod_plane_atom.plane_id +_chem_mod_plane_atom.atom_id +_chem_mod_plane_atom.new_dist_esd +TYRmod4 delete plan-1 CB 0.020 +TYRmod4 delete plan-1 CD1 0.020 +TYRmod4 delete plan-1 CD2 0.020 +TYRmod4 delete plan-1 CE1 0.020 +TYRmod4 delete plan-1 CE2 0.020 +TYRmod4 delete plan-1 CG 0.020 +TYRmod4 delete plan-1 CZ 0.020 +TYRmod4 delete plan-1 HD1 0.020 +TYRmod4 delete plan-1 HD2 0.020 +TYRmod4 delete plan-1 HE1 0.020 +TYRmod4 delete plan-1 HE2 0.020 +TYRmod4 delete plan-1 OH 0.020 + +data_mod_TYRmod5 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +TYRmod5 delete HH . H H 0 +TYRmod5 change OH . O O 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +TYRmod5 delete OH HH single . . . . +TYRmod5 change CZ OH single 1.410 0.0100 1.410 0.0100 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +TYRmod5 delete CZ OH HH . . +TYRmod5 change CE1 CZ CE2 121.469 1.50 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.id +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +_chem_mod_tor.new_period +TYRmod5 delete CE1 CZ OH HH . . . 0 + +data_mod_LYSmod5 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +LYSmod5 delete HZ2 . H H 0 +LYSmod5 delete HZ3 . H H 0 +LYSmod5 change NZ . N NH1 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +LYSmod5 delete NZ HZ2 single . . . . +LYSmod5 delete NZ HZ3 single . . . . +LYSmod5 change CE NZ single 1.456 0.0109 1.456 0.0109 +LYSmod5 change NZ HZ1 single 0.914 0.010 1.036 0.016 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +LYSmod5 delete CE NZ HZ2 . . +LYSmod5 delete CE NZ HZ3 . . +LYSmod5 delete HZ1 NZ HZ2 . . +LYSmod5 delete HZ1 NZ HZ3 . . +LYSmod5 delete HZ2 NZ HZ3 . . +LYSmod5 change CE NZ HZ1 118.176 1.90 + +data_mod_MS6mod2 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +MS6mod2 delete H2 . H H 0 +MS6mod2 delete H3 . H H 0 +MS6mod2 change N . N NH1 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +MS6mod2 delete N H2 single . . . . +MS6mod2 delete N H3 single . . . . +MS6mod2 change N CA single 1.454 0.0100 1.454 0.0100 +MS6mod2 change N H single 0.871 0.0200 1.016 0.0100 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +MS6mod2 delete CA N H2 . . +MS6mod2 delete CA N H3 . . +MS6mod2 delete H N H2 . . +MS6mod2 delete H N H3 . . +MS6mod2 delete H2 N H3 . . +MS6mod2 change CA N H 119.298 3.00 +MS6mod2 change N CA C 111.439 3.00 + +data_mod_ASPprot +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +ASPprot change OD2 . O OH1 0 +ASPprot add . HD2 H H 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +ASPprot change CB CG single 1.505 0.0100 1.505 0.0100 +ASPprot change CG OD1 double 1.217 0.0198 1.217 0.0198 +ASPprot change CG OD2 single 1.308 0.0191 1.308 0.0191 +ASPprot add OD2 HD2 single 0.876 0.0200 0.966 0.0059 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +ASPprot change CA CB CG 113.488 1.82 +ASPprot change CG CB HB3 108.725 1.50 +ASPprot change CG CB HB2 108.725 1.50 +ASPprot change CB CG OD1 123.540 1.50 +ASPprot change CB CG OD2 113.234 2.02 +ASPprot add CG OD2 HD2 110.209 3.00 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.id +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +_chem_mod_tor.new_period +ASPprot add CB CG OD2 HD2 sp2_sp2_1 180.000 5.0 2 + +data_mod_GLUprot +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +GLUprot change OE2 . O OH1 0 +GLUprot add . HE2 H H 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +GLUprot change CG CD single 1.504 0.0100 1.504 0.0100 +GLUprot change CD OE1 double 1.217 0.0198 1.217 0.0198 +GLUprot change CD OE2 single 1.308 0.0191 1.308 0.0191 +GLUprot add OE2 HE2 single 0.876 0.0200 0.966 0.0059 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +GLUprot change CG CD OE1 123.741 1.99 +GLUprot change CG CD OE2 113.306 2.95 +GLUprot add CD OE2 HE2 110.209 3.00 + +loop_ +_chem_mod_tor.mod_id +_chem_mod_tor.function +_chem_mod_tor.atom_id_1 +_chem_mod_tor.atom_id_2 +_chem_mod_tor.atom_id_3 +_chem_mod_tor.atom_id_4 +_chem_mod_tor.id +_chem_mod_tor.new_value_angle +_chem_mod_tor.new_value_angle_esd +_chem_mod_tor.new_period +GLUprot add CG CD OE2 HE2 sp2_sp2_1 180.000 5.0 2 + +data_mod_HISprot1 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +HISprot1 delete HD1 . H H 0 +HISprot1 change ND1 . N NRD5 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +HISprot1 delete ND1 HD1 single . . . . +HISprot1 change CB CG single 1.491 0.0100 1.491 0.0100 +HISprot1 change CG CD2 double 1.359 0.0100 1.359 0.0100 +HISprot1 change CD2 NE2 single 1.373 0.0100 1.373 0.0100 +HISprot1 change CE1 NE2 single 1.335 0.0127 1.335 0.0127 +HISprot1 change CB HB3 single 0.981 0.0100 1.092 0.0100 +HISprot1 change CB HB2 single 0.981 0.0100 1.092 0.0100 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +HISprot1 delete CG ND1 HD1 . . +HISprot1 delete CE1 ND1 HD1 . . +HISprot1 change CA N H 109.786 3.00 +HISprot1 change CA N H2 109.786 3.00 +HISprot1 change CA N H3 109.786 3.00 +HISprot1 change N CA HA 108.404 1.50 +HISprot1 change CB CA HA 109.001 1.50 +HISprot1 change CA C O 117.155 2.01 +HISprot1 change CA C OXT 117.155 2.01 +HISprot1 change HB3 CB HB2 107.622 1.50 +HISprot1 change CB CG ND1 121.338 1.81 +HISprot1 change ND1 CG CD2 108.617 1.58 +HISprot1 change CG ND1 CE1 105.858 1.50 +HISprot1 change ND1 CE1 NE2 111.595 1.50 +HISprot1 change ND1 CE1 HE1 124.330 1.50 +HISprot1 change NE2 CE1 HE1 124.075 2.88 +HISprot1 change CD2 NE2 CE1 107.204 3.00 + +loop_ +_chem_mod_plane_atom.mod_id +_chem_mod_plane_atom.function +_chem_mod_plane_atom.plane_id +_chem_mod_plane_atom.atom_id +_chem_mod_plane_atom.new_dist_esd +HISprot1 delete plan-1 CB 0.020 +HISprot1 delete plan-1 CD2 0.020 +HISprot1 delete plan-1 CE1 0.020 +HISprot1 delete plan-1 CG 0.020 +HISprot1 delete plan-1 HD1 0.020 +HISprot1 delete plan-1 HD2 0.020 +HISprot1 delete plan-1 HE1 0.020 +HISprot1 delete plan-1 HE2 0.020 +HISprot1 delete plan-1 ND1 0.020 +HISprot1 delete plan-1 NE2 0.020 +HISprot1 add plan-1 CB 0.020 +HISprot1 add plan-1 CD2 0.020 +HISprot1 add plan-1 CE1 0.020 +HISprot1 add plan-1 CG 0.020 +HISprot1 add plan-1 HD2 0.020 +HISprot1 add plan-1 HE1 0.020 +HISprot1 add plan-1 HE2 0.020 +HISprot1 add plan-1 ND1 0.020 +HISprot1 add plan-1 NE2 0.020 + +data_mod_HISprot2 +loop_ +_chem_mod_atom.mod_id +_chem_mod_atom.function +_chem_mod_atom.atom_id +_chem_mod_atom.new_atom_id +_chem_mod_atom.new_type_symbol +_chem_mod_atom.new_type_energy +_chem_mod_atom.new_charge +HISprot2 delete HE2 . H H 0 +HISprot2 change ND1 . N NR15 0 +HISprot2 change NE2 . N NRD5 0 + +loop_ +_chem_mod_bond.mod_id +_chem_mod_bond.function +_chem_mod_bond.atom_id_1 +_chem_mod_bond.atom_id_2 +_chem_mod_bond.new_type +_chem_mod_bond.new_value_dist +_chem_mod_bond.new_value_dist_esd +_chem_mod_bond.new_value_dist_nucleus +_chem_mod_bond.new_value_dist_nucleus_esd +HISprot2 delete NE2 HE2 single . . . . +HISprot2 change CB CG single 1.494 0.0100 1.494 0.0100 +HISprot2 change CG CD2 double 1.356 0.0100 1.356 0.0100 +HISprot2 change ND1 CE1 single 1.346 0.0100 1.346 0.0100 +HISprot2 change CD2 NE2 single 1.380 0.0100 1.380 0.0100 +HISprot2 change CE1 NE2 double 1.308 0.0100 1.308 0.0100 +HISprot2 change CB HB3 single 0.981 0.0100 1.092 0.0100 +HISprot2 change CB HB2 single 0.981 0.0100 1.092 0.0100 +HISprot2 change ND1 HD1 single 0.919 0.0200 1.013 0.0120 +HISprot2 change CD2 HD2 single 0.929 0.0143 1.085 0.0150 + +loop_ +_chem_mod_angle.mod_id +_chem_mod_angle.function +_chem_mod_angle.atom_id_1 +_chem_mod_angle.atom_id_2 +_chem_mod_angle.atom_id_3 +_chem_mod_angle.new_value_angle +_chem_mod_angle.new_value_angle_esd +HISprot2 delete CD2 NE2 HE2 . . +HISprot2 delete CE1 NE2 HE2 . . +HISprot2 change CA N H 109.786 3.00 +HISprot2 change CA N H2 109.786 3.00 +HISprot2 change CA N H3 109.786 3.00 +HISprot2 change N CA HA 108.404 1.50 +HISprot2 change CB CA HA 109.001 1.50 +HISprot2 change CA C O 117.155 2.01 +HISprot2 change CA C OXT 117.155 2.01 +HISprot2 change HB3 CB HB2 107.622 1.50 +HISprot2 change CB CG CD2 132.429 1.50 +HISprot2 change CG ND1 CE1 107.807 1.50 +HISprot2 change CG CD2 NE2 110.147 1.50 +HISprot2 change CG CD2 HD2 124.943 1.50 +HISprot2 change ND1 CE1 NE2 111.530 1.50 +HISprot2 change ND1 CE1 HE1 123.708 1.50 +HISprot2 change NE2 CE1 HE1 124.763 3.00 +HISprot2 change CD2 NE2 CE1 105.756 3.00 + +loop_ +_chem_mod_plane_atom.mod_id +_chem_mod_plane_atom.function +_chem_mod_plane_atom.plane_id +_chem_mod_plane_atom.atom_id +_chem_mod_plane_atom.new_dist_esd +HISprot2 delete plan-1 CB 0.020 +HISprot2 delete plan-1 CD2 0.020 +HISprot2 delete plan-1 CE1 0.020 +HISprot2 delete plan-1 CG 0.020 +HISprot2 delete plan-1 HD1 0.020 +HISprot2 delete plan-1 HD2 0.020 +HISprot2 delete plan-1 HE1 0.020 +HISprot2 delete plan-1 HE2 0.020 +HISprot2 delete plan-1 ND1 0.020 +HISprot2 delete plan-1 NE2 0.020 +HISprot2 add plan-1 CB 0.020 +HISprot2 add plan-1 CD2 0.020 +HISprot2 add plan-1 CE1 0.020 +HISprot2 add plan-1 CG 0.020 +HISprot2 add plan-1 HD1 0.020 +HISprot2 add plan-1 HD2 0.020 +HISprot2 add plan-1 HE1 0.020 +HISprot2 add plan-1 ND1 0.020 +HISprot2 add plan-1 NE2 0.020 diff --git a/image_analysis/structure_refinement/monomers/update_monomers.py b/image_analysis/structure_refinement/monomers/update_monomers.py new file mode 100644 index 000000000..5b0b8d871 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/update_monomers.py @@ -0,0 +1,96 @@ +#!/usr/bin/env python3 +# SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute +# SPDX-License-Identifier: GPL-3.0-only +"""Copy the subset of the CCP4 Monomer Library (https://github.com/MonomerLibrary/monomers, LGPL-3.0) +that rugnux's restrained refinement carries in its binary into this directory. + + update_monomers.py /path/to/monomers + +COMPOUNDS below is THE list: a compound named there is restrained by the refinement, everything else +is held fixed. To add one, add its code and run this again; CMake embeds every .cif of this directory +(MonomerLibrary.cpp), so nothing else needs to change. + +The compound files are copied verbatim. links_and_mods.cif is cut down to the links and modifications +that can apply to these compounds (the polymer links, the termini, the disulfide, ...), and ener_lib.cif +to its atom-type table (_lib_atom: the van der Waals and ion radii and the hydrogen-bond types). +Requires the gemmi Python module.""" + +import os +import shutil +import sys + +import gemmi + +AMINO_ACIDS = ["ALA", "ARG", "ASN", "ASP", "CYS", "GLN", "GLU", "GLY", "HIS", "ILE", + "LEU", "LYS", "MET", "PHE", "PRO", "SER", "THR", "TRP", "TYR", "VAL", "MSE"] +NUCLEOTIDES = ["DA", "DC", "DG", "DT", "A", "C", "G", "U"] +NUCLEOTIDE_LIGANDS = ["ATP", "ADP", "AMP", "GTP", "GDP", "GMP"] +ADDITIVES = ["DMS", "PEG", "PGE", "PG4", "1PE", "GOL", "EDO", "SO4", "PO4", "ACT", "MPD"] +WATER_AND_IONS = ["HOH", "NA", "K", "MG", "CA", "ZN", "MN", "FE", "FE2", "NI", "CU", "CO", "CD", + "CL", "BR", "IOD"] +COMPOUNDS = AMINO_ACIDS + NUCLEOTIDES + NUCLEOTIDE_LIGANDS + ADDITIVES + WATER_AND_IONS + +# Groups of the polymers above; links and modifications of other groups (sugars) are left out. +GROUPS = {".", "peptide", "P-peptide", "M-peptide", "DNA/RNA", "NON-POLYMER"} + + +def compound_path(lib, code): + return os.path.join(lib, code[0].lower(), code + ".cif") + + +def applies(comp, group): + return (comp == "." or comp in COMPOUNDS) and group in GROUPS + + +def trim_links_and_mods(lib, out): + doc = gemmi.cif.read(os.path.join(lib, "links_and_mods.cif")) + links = doc.find_block("link_list").find("_chem_link.", ["id", "comp_id_1", "mod_id_1", "group_comp_1", + "comp_id_2", "mod_id_2", "group_comp_2", "name"]) + mods = doc.find_block("mod_list").find("_chem_mod.", ["id", "name", "comp_id", "group_id"]) + keep_links = [list(r) for r in links if applies(r[1], r[3]) and applies(r[4], r[6])] + keep_mods = [list(r) for r in mods if applies(r[2], r[3])] + keep = {"link_" + r[0] for r in keep_links} | {"mod_" + r[0] for r in keep_mods} + + new = gemmi.cif.Document() + for name, tag, rows in (("link_list", "_chem_link.", keep_links), ("mod_list", "_chem_mod.", keep_mods)): + block = new.add_new_block(name) + old = doc.find_block(name).find_loop_item(tag + "id").loop + loop = block.init_loop(tag, [t[len(tag):] for t in old.tags]) + for r in rows: + loop.add_row(r) + for block in doc: + if block.name in keep: + new.add_copied_block(block) + new.write_file(out) + return len(keep_links), len(keep_mods) + + +def trim_ener_lib(lib, out): + doc = gemmi.cif.read(os.path.join(lib, "ener_lib.cif")) + atoms = doc[0].find_loop_item("_lib_atom.type").loop + new = gemmi.cif.Document() + block = new.add_new_block(doc[0].name) + loop = block.init_loop("_lib_atom.", [t[len("_lib_atom."):] for t in atoms.tags]) + for i in range(atoms.length()): + loop.add_row([atoms[i, j] for j in range(atoms.width())]) + new.write_file(out) + + +def main(): + if len(sys.argv) != 2: + sys.exit(__doc__) + lib = sys.argv[1] + here = os.path.dirname(os.path.abspath(__file__)) + for f in os.listdir(here): + if f.endswith(".cif"): + os.remove(os.path.join(here, f)) + for code in COMPOUNDS: + shutil.copyfile(compound_path(lib, code), os.path.join(here, code + ".cif")) + n_links, n_mods = trim_links_and_mods(lib, os.path.join(here, "links_and_mods.cif")) + trim_ener_lib(lib, os.path.join(here, "ener_lib.cif")) + shutil.copyfile(os.path.join(lib, "COPYING"), os.path.join(here, "COPYING")) + print(f"{len(COMPOUNDS)} compounds, {n_links} links, {n_mods} modifications") + + +if __name__ == "__main__": + main() diff --git a/licenses/COLLECT.sh b/licenses/COLLECT.sh index 772ff0748..d594d75da 100644 --- a/licenses/COLLECT.sh +++ b/licenses/COLLECT.sh @@ -75,6 +75,7 @@ copy_license bitshuffle-hperf.txt compression/bitshuffle_hperf/LICENSE-APACHE copy_license lz4.txt compression/lz4/LICENSE copy_license xilinx-hls-headers.txt fpga/include/LICENSE.HLS_Headers copy_license gemmi.txt gemmi_gph/LICENSE.txt +copy_license ccp4-monomer-library.txt image_analysis/structure_refinement/monomers/COPYING # GEMMI bundles six third-party headers under its own include tree, each under its own licence # (see THIRD_PARTY_NOTICES.md). Only PEGTL ships a LICENSE file; sajson, fast_float, half, pocketfft # and tinydir carry their terms in a comment at the top of the header, so licenses/sajson.txt, diff --git a/licenses/ccp4-monomer-library.txt b/licenses/ccp4-monomer-library.txt new file mode 100644 index 000000000..3f7b8b1e5 --- /dev/null +++ b/licenses/ccp4-monomer-library.txt @@ -0,0 +1,166 @@ + GNU LESSER GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + + This version of the GNU Lesser General Public License incorporates +the terms and conditions of version 3 of the GNU General Public +License, supplemented by the additional permissions listed below. + + 0. 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