diff --git a/docs/CPU_DATA_ANALYSIS_REFINEMENT.md b/docs/CPU_DATA_ANALYSIS_REFINEMENT.md index 6abf3ebe2..e63f0e730 100644 --- a/docs/CPU_DATA_ANALYSIS_REFINEMENT.md +++ b/docs/CPU_DATA_ANALYSIS_REFINEMENT.md @@ -127,10 +127,16 @@ merit (the mean over the working reflections) to about 0.01 on most depositions. The restraints are those of the **CCP4 Monomer Library**, a subset of which is compiled into rugnux (`image_analysis/structure_refinement/monomers/`, regenerated by `update_monomers.py`; nothing is read from disk, and `$CLIBD` is never consulted): the 20 standard amino acids and MSE; the DNA and RNA nucleotides -(DA, DC, DG, DT, A, C, G, U); ATP, ADP, AMP, GTP, GDP and GMP; DMSO; the PEG fragments PEG, PGE, PG4 and 1PE; -glycerol, ethylene glycol, MPD, acetate, sulfate and phosphate; water; and the ions Na, K, Mg, Ca, Mn, Fe²⁺, -Fe³⁺, Co, Ni, Cu, Zn, Cd, Cl, Br and I - 62 compounds - with the library's links and modifications and the -energy types those compounds use. +(DA, DC, DG, DT, A, C, G, U); the modified nucleotides of tRNA and rRNA met most often - pseudouridine (PSU), +5-methylcytidine (5MC), 1-methyladenosine (1MA), the 2'-O-methyl nucleotides OMG, OMC and OMU, dihydrouridine +(H2U), N2-methyl- and N2,N2-dimethylguanosine (2MG, M2G), 7-methylguanosine (7MG) and ribothymidine (5MU), polymer +residues joined by the same backbone link; ATP, ADP, AMP, GTP, GDP and GMP; the cofactors NAD⁺ (NAD), NADH (NAI), +NADP⁺ (NAP), NADPH (NDP), FAD, FMN, heme (HEM), heme C (HEC), S-adenosylmethionine (SAM) and +S-adenosylhomocysteine (SAH), and dioxygen (OXY); DMSO; the PEG fragments PEG, PGE, PG4 and 1PE; glycerol, +ethylene glycol, MPD, acetate, sulfate and phosphate; water; and the ions Na, K, Mg, Ca, Mn, Fe²⁺, Fe³⁺, Co, Ni, +Cu, Zn, Cd, Cl, Br and I - 84 compounds - with the library's links and modifications that apply to them (among +them heme C's two thioethers to its cysteines, HEC-CYS1 and HEC-CYS2, and the covalent links of heme and FAD to +the protein) and the energy types those compounds use. The model's topology is built from it by GEMMI (`prepare_topology`): the links between residues (the peptide and cis-peptide, the nucleic-acid backbone, disulfides, and the model's LINK records where the library @@ -160,17 +166,18 @@ analytic derivatives: above it, $d_0$ the sum of the energy types' van der Waals radii, 2.6 Å where both atoms can hydrogen-bond and 1.9 Å between a metal and N, O or S. The list is rebuilt at every macro-cycle. -**Metal sites.** A metal ion is restrained to the donor atoms (O, N or S) that the model's LINK / -`_struct_conn` records bind it to. Where the library has a link for the pair - its ZN-CYS, ZN-HISND, +**Metal sites.** A metal - an ion, or a metal atom of a ligand such as a heme's iron - is restrained to the +donor atoms (O, N or S) that the model's LINK / `_struct_conn` records bind it to. Where the library has a link for the pair - its ZN-CYS, ZN-HISND, ZN-HISNE, FE-CYS, FE-HISND and FE-HISNE - that link is used as it is, with the modification it makes to the donor's residue (the proton the bond replaces). Every other record becomes a link of one bond at the distance of the library's own statistics of metal sites (its `metals.json`, carried as `monomers/metals.cif`) -for the metal, the donor element and the site's coordination number - the number of such records the ion -has - interpolated linearly between two tabulated coordination numbers (rows resting on at least 20 sites +for the metal, the donor element and the site's coordination number - the number of such records the metal +has, plus the bonds its own residue's dictionary gives it (a heme iron's four pyrrole nitrogens) - interpolated linearly between two tabulated coordination numbers (rows resting on at least 20 sites count; σ is the row's standard deviation, at least 0.02 Å). Only the bond is restrained, not the angles at the metal. A contact without a record stays a repulsion, and a record to a symmetry mate is -left out, as every bond to a symmetry mate is. The rmsd of these bonds is reported apart from the covalent -bonds' (`REFINE_RMSD_METAL_BONDS`). +left out, as every bond to a symmetry mate is. The rmsd of these bonds - with the dictionary's own bonds of +a metal within a ligand, a heme iron's to its porphyrin - is reported apart from the covalent bonds' +(`REFINE_RMSD_METAL_BONDS`). **B restraints.** The B factors of two atoms are restrained to each other in proportion to their size, by the symmetric Kullback-Leibler divergence of two isotropic Gaussians of variances $B_i$ and $B_j$: @@ -289,7 +296,7 @@ GPU, typically 2-15 minutes on the CPU). What the refinement does not do yet - each a known gap, not a design choice: -- **Custom ligands and other monomer libraries.** Only the 62 compounds of §15.4 are restrained. Any other +- **Custom ligands and other monomer libraries.** Only the 84 compounds of §15.4 are restrained. Any other residue is held fixed (it stays in $F_\mathrm{calc}$, the mask and the repulsions); no restraints are generated for a new ligand, and neither a user's restraint CIF nor an external monomer library can be given. - **TLS** refinement. diff --git a/docs/RUGNUX_MODEL_AND_REFERENCE.md b/docs/RUGNUX_MODEL_AND_REFERENCE.md index 615b5e84f..caf6d1542 100644 --- a/docs/RUGNUX_MODEL_AND_REFERENCE.md +++ b/docs/RUGNUX_MODEL_AND_REFERENCE.md @@ -260,12 +260,14 @@ other key outside `REFINE_` stay those of the model as placed, and `.mtz in the same way (see [Rugnux live mode](JFJOCH_BROKER.md#rugnux-live-mode)). What the dictionary restrains is fixed at build time: the 20 standard amino acids and MSE, the DNA/RNA -nucleotides, ATP/ADP/AMP/GTP/GDP/GMP, DMSO, PEG fragments (PEG, PGE, PG4, 1PE), glycerol, ethylene glycol, -sulfate, phosphate, acetate, MPD, water and common ions (a subset of the CCP4 Monomer Library compiled into +nucleotides and the common modified RNA nucleotides (PSU, 5MC, 1MA, OMG, OMC, OMU, H2U, 2MG, M2G, 7MG, 5MU), +ATP/ADP/AMP/GTP/GDP/GMP, the cofactors NAD, NAI, NAP, NDP, FAD, FMN, HEM, HEC, SAM and SAH, dioxygen (OXY), +DMSO, PEG fragments (PEG, PGE, PG4, 1PE), glycerol, ethylene glycol, sulfate, phosphate, acetate, MPD, water +and common ions (a subset of the CCP4 Monomer Library compiled into rugnux; nothing is read from disk). Any other residue is held fixed: it stays in the structure factors and the bulk-solvent mask, and the refined atoms are kept from clashing with it; `REFINE_RESIDUES_FIXED_NAMES` -lists them. The dictionary's hydrogens are added and ride on their parents. Metal ions are restrained to the -donor atoms (O, N, S) the model's LINK / `_struct_conn` records bind them to: by the dictionary's own Zn and Fe +lists them. The dictionary's hydrogens are added and ride on their parents. Metal ions, and the iron of a heme, are +restrained to the donor atoms (O, N, S) the model's LINK / `_struct_conn` records bind them to: by the dictionary's own Zn and Fe links to Cys and His where they apply, otherwise at the library's typical distance for the metal, the donor element and the number of such records of the ion (Mg-O 2.07 A, Na-O 2.42 A, K-O 2.82 A at their usual coordination). A contact without a record, or one to a symmetry mate, is not restrained as a bond. The B factors of bonded atoms and of @@ -300,7 +302,7 @@ the weight trials - are described in [§15](CPU_DATA_ANALYSIS_REFINEMENT.md), an **What it does not do yet.** The refinement is a first, automatic pass on a placed model, not a replacement for a refinement program. Not implemented yet: -- custom ligands or a monomer library beyond the embedded one: other residues are held fixed (they stay in +- custom ligands or a monomer library beyond the embedded compounds above: other residues are held fixed (they stay in Fcalc, the solvent mask and the clash terms), and no restraints are generated for a new ligand; - TLS; - anisotropic ADPs: an ANISOU record is turned into its isotropic B, and only isotropic B is refined; diff --git a/image_analysis/structure_refinement/MonomerLibrary.h b/image_analysis/structure_refinement/MonomerLibrary.h index ec0e944d9..a856f7430 100644 --- a/image_analysis/structure_refinement/MonomerLibrary.h +++ b/image_analysis/structure_refinement/MonomerLibrary.h @@ -9,9 +9,10 @@ #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. +// LGPL-3.0) carried in the binary - the standard amino acids and nucleotides, the common modified RNA nucleotides, +// their links and modifications, the common cofactors (NAD(P)(H), FAD, FMN, hemes, SAM/SAH), a few other 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(); // The ideal distance and its sigma of a bond from a metal ion to a donor atom (O, N, S) at a site of `coordination` diff --git a/image_analysis/structure_refinement/RefinementRestraints.cpp b/image_analysis/structure_refinement/RefinementRestraints.cpp index 5d4c5ae10..5859a9dc5 100644 --- a/image_analysis/structure_refinement/RefinementRestraints.cpp +++ b/image_analysis/structure_refinement/RefinementRestraints.cpp @@ -100,9 +100,15 @@ V3 FromImage(const RestraintRecord &r, V3 g) { r.rot[2] * g.x + r.rot[5] * g.y + r.rot[8] * g.z}; } -// A metal ion: a residue of one atom, of a metal element. -bool IsMetalIon(const gemmi::CRA &cra) { - return cra.residue->atoms.size() == 1 && IsMetal(cra.atom->element); +// The bonds the dictionary gives a metal atom within its own residue: none for an ion, four for a heme's iron. +int DictionaryMetalBonds(const gemmi::MonLib &monlib, const gemmi::CRA &metal) { + auto cc = monlib.monomers.find(metal.residue->name); + if (cc == monlib.monomers.end()) + return 0; + int n = 0; + for (const gemmi::Restraints::Bond &b : cc->second.rt.bonds) + n += b.id1.atom == metal.atom->name || b.id2.atom == metal.atom->name; + return n; } bool IsMetalDonor(const gemmi::Element &el) { @@ -121,11 +127,12 @@ std::string MetalDonorModification(const std::string &resname, const std::string return ""; } -// The model's LINK / struct_conn records between a metal ion and an O, N or S that no link of the dictionary -// describes (its ZN-CYS, ZN-HISND, ZN-HISNE, FE-CYS, FE-HISND and FE-HISNE are taken as they are): a link of -// one bond is made for each in `monlib`, at the distance of the library's statistics of metal sites -// (EmbeddedMetalDistance) for the two elements and the site's coordination - the number of records between the -// ion and an O, N or S - and the record is pointed at it, so that prepare_topology() restrains it like any other link. +// The model's LINK / struct_conn records between a metal atom (an ion, or the iron of a heme) and an O, N or S +// that no link of the dictionary describes (its ZN-CYS, ZN-HISND, ZN-HISNE, FE-CYS, FE-HISND and FE-HISNE are +// taken as they are): a link of one bond is made for each in `monlib`, at the distance of the library's statistics +// of metal sites (EmbeddedMetalDistance) for the two elements and the site's coordination - the number of records +// between the metal and an O, N or S, plus the bonds its own residue's dictionary gives it (a heme's four pyrrole +// N) - and the record is pointed at it, so that prepare_topology() restrains it like any other link. // Only the bond: no angles at the metal. Sites are taken from the records alone, as REFMAC takes links from // the coordinate file; a contact without a record stays a repulsion (BuildRepulsions, METAL_CONTACT). // Records to a symmetry mate are left out, as every bond to a symmetry mate is (BuildRefinementTopology). @@ -145,13 +152,15 @@ int AddMetalLinks(gemmi::Structure &st, gemmi::MonLib &monlib) { gemmi::CRA a = model.find_cra(conn.partner1, true), b = model.find_cra(conn.partner2, true); if (!a.atom || !b.atom) continue; - const bool a_metal = IsMetalIon(a), b_metal = IsMetalIon(b); + const bool a_metal = IsMetal(a.atom->element), b_metal = IsMetal(b.atom->element); if (a_metal == b_metal) continue; const gemmi::CRA &metal = a_metal ? a : b, &donor = a_metal ? b : a; if (!IsMetalDonor(donor.atom->element)) continue; - // the site's coordination: every record of the ion, a symmetry mate's or one the dictionary describes too + // the site's coordination: every record of the metal, a symmetry mate's or one the dictionary describes too + if (coordination.count(metal.atom) == 0) + coordination[metal.atom] = DictionaryMetalBonds(monlib, metal); coordination[metal.atom]++; if (!conn.link_id.empty() || conn.asu == gemmi::Asu::Different || std::get<0>(monlib.match_link(*a.residue, a.atom->name, conn.partner1.altloc, *b.residue, b.atom->name, @@ -410,7 +419,7 @@ RefinementTopology BuildRefinementTopology(gemmi::Structure &st, bool hydrogens) out.refinable[i] = known && a.occ > 0 && !a.is_hydrogen(); out.vdw_radius[i] = VdwRadius(monlib, res.name, a); out.hbond[i] = res.is_water() || CanHydrogenBond(monlib, res.name, a); - out.metal[i] = res.atoms.size() == 1 && IsMetal(a.element); + out.metal[i] = IsMetal(a.element); out.altloc[i] = a.altloc; out.element[i] = a.element.elem; } diff --git a/image_analysis/structure_refinement/RefinementRestraints.h b/image_analysis/structure_refinement/RefinementRestraints.h index 572dbbc7c..335a511bc 100644 --- a/image_analysis/structure_refinement/RefinementRestraints.h +++ b/image_analysis/structure_refinement/RefinementRestraints.h @@ -52,14 +52,14 @@ std::vector BRestraintCurvature(const RestraintSet &set, const std::vect // What refinement knows of a model's chemistry. struct RefinementTopology { RestraintSet geometry; // bonds, angles, torsions, chiral volumes, planes - RestraintSet metal_bonds; // the bonds of metal ions to their donors (LINK records), apart from the rest + RestraintSet metal_bonds; // the bonds of metals (ions, a heme's iron) to their donors, apart from the rest RestraintSet adp; // B of bonded and angle-related atoms alike std::vector refinable; // per atom: its residue is described by the dictionary // Per atom: the atoms the repulsion leaves out - itself and those up to three bonds away (sorted). std::vector> excluded; std::vector vdw_radius; // A std::vector hbond; // donor, acceptor or both (water included) - std::vector metal; // a metal ion + std::vector metal; // a metal atom: an ion, or a metal within a ligand (a heme's iron) std::vector altloc; std::vector element; // Per atom: the heavy atom a hydrogen rides on, -1 for every other atom. @@ -77,9 +77,10 @@ struct RefinementTopology { // The topology of the first model of `st` (hydrogens already removed) from the embedded monomer library // (MonomerLibrary.h), through gemmi's prepare_topology(): links between residues (peptide, cis-peptide, // nucleic-acid backbone, disulfides, the model's LINK records the library describes) and their -// modifications included; the LINK records of metal ions the library has no link for are restrained at the -// library's metal-site distances (RefinementRestraints.cpp, AddMetalLinks). A residue the library does not describe, or with an atom it does not know, is -// held fixed: it stays in the structure factors and the bulk-solvent mask, and it is restrained against. +// modifications included; the LINK records of metals (ions, a heme's iron) the library has no link for are +// restrained at the library's metal-site distances (RefinementRestraints.cpp, AddMetalLinks). A residue the library +// does not describe, or with an atom it does not know, is held fixed: it stays in the structure factors and the +// bulk-solvent mask, and it is restrained against. // Torsions: those with an esd, except the main-chain phi/psi and the sugar puckers given as alternatives. // With `hydrogens`, the dictionary's hydrogens are added to the residues it describes (waters excepted) and // placed; they ride on their parent atoms and take part in no restraint. diff --git a/image_analysis/structure_refinement/monomers/1MA.cif b/image_analysis/structure_refinement/monomers/1MA.cif new file mode 100644 index 000000000..256d8c361 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/1MA.cif @@ -0,0 +1,288 @@ +# +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 +1MA 1MA "6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE" RNA 38 24 . +# +data_comp_1MA +# +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 +1MA P P P 0 46.199 22.985 33.948 +1MA OP1 O O 0 45.612 23.494 35.251 +1MA OP2 O OP -1 45.300 23.247 32.755 +1MA OP3 O OP -1 47.626 23.448 33.724 +1MA "O5'" O O2 0 46.275 21.379 34.098 +1MA "C5'" C CH2 0 46.795 20.601 32.990 +1MA "C4'" C CH1 0 46.838 19.142 33.374 +1MA "O4'" O O2 0 47.700 18.984 34.533 +1MA "C3'" C CH1 0 45.487 18.504 33.742 +1MA "O3'" O OH1 0 45.334 17.241 33.106 +1MA "C2'" C CH1 0 45.552 18.382 35.269 +1MA "O2'" O OH1 0 44.831 17.281 35.781 +1MA "C1'" C CH1 0 47.059 18.182 35.494 +1MA N9 N NR5 0 47.526 18.600 36.823 +1MA C8 C CR15 0 47.503 19.881 37.308 +1MA N7 N NRD5 0 47.981 19.974 38.529 +1MA C5 C CR56 0 48.339 18.679 38.866 +1MA C6 C CR6 0 48.912 18.172 40.064 +1MA N6 N NH1 0 49.200 18.794 41.137 +1MA N1 N NR6 0 49.184 16.766 39.984 +1MA CM1 C CH3 0 49.814 16.095 41.139 +1MA C2 C CR16 0 48.871 16.031 38.868 +1MA N3 N NRD6 0 48.283 16.491 37.799 +1MA C4 C CR56 0 48.059 17.831 37.814 +1MA "H5'" H H 0 47.706 20.911 32.761 +1MA "H5''" H H 0 46.216 20.718 32.197 +1MA "H4'" H H 0 47.231 18.646 32.624 +1MA "H3'" H H 0 44.746 19.109 33.479 +1MA "HO3'" H H 0 44.509 17.042 33.090 +1MA "H2'" H H 0 45.240 19.223 35.696 +1MA "HO2'" H H 0 44.907 17.268 36.626 +1MA "H1'" H H 0 47.295 17.228 35.362 +1MA H8 H H 0 47.164 20.641 36.793 +1MA HN61 H H 0 50.024 19.033 41.188 +1MA HM11 H H 0 49.949 15.154 40.947 +1MA HM12 H H 0 49.240 16.184 41.916 +1MA HM13 H H 0 50.672 16.510 41.324 +1MA H2 H H 0 49.096 15.129 38.869 +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 +1MA P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192 +1MA P OP2 SINGLE n 1.517 0.0192 1.517 0.0192 +1MA P OP3 SINGLE n 1.517 0.0192 1.517 0.0192 +1MA P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 +1MA "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +1MA "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +1MA "C4'" "O4'" SINGLE n 1.451 0.0100 1.451 0.0100 +1MA "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 +1MA "O4'" "C1'" SINGLE n 1.408 0.0100 1.408 0.0100 +1MA "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +1MA "C3'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100 +1MA "C2'" "O2'" SINGLE n 1.411 0.0100 1.411 0.0100 +1MA "C2'" "C1'" SINGLE n 1.539 0.0100 1.539 0.0100 +1MA "C1'" N9 SINGLE n 1.468 0.0100 1.468 0.0100 +1MA N9 C8 SINGLE y 1.369 0.0100 1.369 0.0100 +1MA N9 C4 SINGLE y 1.364 0.0100 1.364 0.0100 +1MA C8 N7 DOUBLE y 1.313 0.0100 1.313 0.0100 +1MA N7 C5 SINGLE y 1.384 0.0100 1.384 0.0100 +1MA C5 C6 SINGLE n 1.410 0.0200 1.410 0.0200 +1MA C5 C4 DOUBLE y 1.379 0.0109 1.379 0.0109 +1MA C6 N6 DOUBLE n 1.272 0.0100 1.272 0.0100 +1MA C6 N1 SINGLE n 1.406 0.0200 1.406 0.0200 +1MA N1 CM1 SINGLE n 1.471 0.0118 1.471 0.0118 +1MA N1 C2 SINGLE n 1.366 0.0100 1.366 0.0100 +1MA C2 N3 DOUBLE n 1.299 0.0100 1.299 0.0100 +1MA N3 C4 SINGLE n 1.355 0.0100 1.355 0.0100 +1MA "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +1MA "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 +1MA "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 +1MA "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +1MA "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +1MA "C2'" "H2'" SINGLE n 1.089 0.0100 0.994 0.0200 +1MA "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 +1MA "C1'" "H1'" SINGLE n 1.089 0.0100 0.992 0.0200 +1MA C8 H8 SINGLE n 1.082 0.0130 0.979 0.0200 +1MA N6 HN61 SINGLE n 1.016 0.0100 0.860 0.0100 +1MA CM1 HM11 SINGLE n 1.089 0.0100 0.970 0.0158 +1MA CM1 HM12 SINGLE n 1.089 0.0100 0.970 0.0158 +1MA CM1 HM13 SINGLE n 1.089 0.0100 0.970 0.0158 +1MA C2 H2 SINGLE n 1.082 0.0130 0.930 0.0100 +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 +1MA OP1 P OP2 112.864 1.69 +1MA OP1 P OP3 112.864 1.69 +1MA OP1 P "O5'" 105.808 2.07 +1MA OP2 P OP3 112.864 1.69 +1MA OP2 P "O5'" 105.808 2.07 +1MA OP3 P "O5'" 105.808 2.07 +1MA P "O5'" "C5'" 118.783 1.50 +1MA "O5'" "C5'" "C4'" 109.342 1.50 +1MA "O5'" "C5'" "H5'" 109.845 1.50 +1MA "O5'" "C5'" "H5''" 109.845 1.50 +1MA "C4'" "C5'" "H5'" 109.624 1.50 +1MA "C4'" "C5'" "H5''" 109.624 1.50 +1MA "H5'" "C5'" "H5''" 108.472 1.50 +1MA "C5'" "C4'" "O4'" 109.123 1.50 +1MA "C5'" "C4'" "C3'" 116.008 1.52 +1MA "C5'" "C4'" "H4'" 108.268 1.50 +1MA "O4'" "C4'" "C3'" 105.388 1.50 +1MA "O4'" "C4'" "H4'" 108.947 1.50 +1MA "C3'" "C4'" "H4'" 109.363 1.86 +1MA "C4'" "O4'" "C1'" 109.426 1.50 +1MA "C4'" "C3'" "O3'" 111.281 2.46 +1MA "C4'" "C3'" "C2'" 102.602 1.50 +1MA "C4'" "C3'" "H3'" 110.452 2.54 +1MA "O3'" "C3'" "C2'" 111.581 2.83 +1MA "O3'" "C3'" "H3'" 110.380 1.67 +1MA "C2'" "C3'" "H3'" 110.504 1.75 +1MA "C3'" "O3'" "HO3'" 108.744 3.00 +1MA "C3'" "C2'" "O2'" 112.782 2.45 +1MA "C3'" "C2'" "C1'" 101.779 1.50 +1MA "C3'" "C2'" "H2'" 110.596 1.51 +1MA "O2'" "C2'" "C1'" 110.620 3.00 +1MA "O2'" "C2'" "H2'" 110.448 1.97 +1MA "C1'" "C2'" "H2'" 110.803 1.50 +1MA "C2'" "O2'" "HO2'" 109.103 2.13 +1MA "O4'" "C1'" "C2'" 106.588 1.50 +1MA "O4'" "C1'" N9 107.830 1.50 +1MA "O4'" "C1'" "H1'" 110.469 1.59 +1MA "C2'" "C1'" N9 113.810 1.50 +1MA "C2'" "C1'" "H1'" 109.847 1.50 +1MA N9 "C1'" "H1'" 108.233 1.86 +1MA "C1'" N9 C8 125.615 2.25 +1MA "C1'" N9 C4 127.393 3.00 +1MA C8 N9 C4 106.992 1.50 +1MA N9 C8 N7 112.621 1.50 +1MA N9 C8 H8 123.218 1.50 +1MA N7 C8 H8 124.162 1.50 +1MA C8 N7 C5 103.718 1.50 +1MA N7 C5 C6 129.894 1.50 +1MA N7 C5 C4 109.368 1.50 +1MA C6 C5 C4 120.738 1.50 +1MA C5 C6 N6 129.510 1.50 +1MA C5 C6 N1 112.223 1.50 +1MA N6 C6 N1 118.267 1.50 +1MA C6 N6 HN61 113.739 3.00 +1MA C6 N1 CM1 118.703 1.50 +1MA C6 N1 C2 122.333 1.50 +1MA CM1 N1 C2 118.965 1.66 +1MA N1 CM1 HM11 109.481 1.50 +1MA N1 CM1 HM12 109.481 1.50 +1MA N1 CM1 HM13 109.481 1.50 +1MA HM11 CM1 HM12 109.428 1.50 +1MA HM11 CM1 HM13 109.428 1.50 +1MA HM12 CM1 HM13 109.428 1.50 +1MA N1 C2 N3 125.328 1.50 +1MA N1 C2 H2 117.343 1.50 +1MA N3 C2 H2 117.329 1.50 +1MA C2 N3 C4 113.724 1.50 +1MA N9 C4 C5 107.302 1.96 +1MA N9 C4 N3 127.043 1.50 +1MA C5 C4 N3 125.654 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 +1MA C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +1MA C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +1MA C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +1MA C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +1MA C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +1MA C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +1MA C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +1MA C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +1MA C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +1MA C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +1MA C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +1MA C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +1MA alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +1MA beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +1MA epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +1MA gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +1MA sp3_sp3_52 "C3'" "C2'" "O2'" "HO2'" 180.000 10.00 3 +1MA const_sp2_sp2_2 N7 C8 N9 "C1'" 180.000 5.0 2 +1MA const_14 C5 C4 N9 "C1'" 180.000 10.0 2 +1MA const_sp2_sp2_5 N9 C8 N7 C5 0.000 5.0 2 +1MA const_sp2_sp2_8 C6 C5 N7 C8 180.000 5.0 2 +1MA sp2_sp2_4 N7 C5 C6 N6 0.000 5.0 2 +1MA const_sp2_sp2_9 N9 C4 C5 N7 0.000 5.0 2 +1MA sp2_sp2_17 C5 C6 N6 HN61 180.000 5.0 2 +1MA sp2_sp2_8 N6 C6 N1 CM1 0.000 5.0 2 +1MA sp2_sp3_7 C6 N1 CM1 HM11 150.000 10.0 6 +1MA sp2_sp2_10 N3 C2 N1 CM1 180.000 5.0 2 +1MA sp2_sp2_13 N1 C2 N3 C4 0.000 5.0 2 +1MA sp2_sp2_16 N9 C4 N3 C2 180.000 5.0 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 +1MA chir_1 P "O5'" OP2 OP3 both +1MA chir_2 "C4'" "O4'" "C3'" "C5'" negative +1MA chir_3 "C3'" "O3'" "C4'" "C2'" positive +1MA chir_4 "C2'" "O2'" "C1'" "C3'" negative +1MA 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 +1MA plan-1 "C1'" 0.020 +1MA plan-1 C4 0.020 +1MA plan-1 C5 0.020 +1MA plan-1 C6 0.020 +1MA plan-1 C8 0.020 +1MA plan-1 H8 0.020 +1MA plan-1 N3 0.020 +1MA plan-1 N7 0.020 +1MA plan-1 N9 0.020 +1MA plan-2 C5 0.020 +1MA plan-2 C6 0.020 +1MA plan-2 N1 0.020 +1MA plan-2 N6 0.020 +1MA plan-3 C2 0.020 +1MA plan-3 C6 0.020 +1MA plan-3 CM1 0.020 +1MA plan-3 N1 0.020 +1MA plan-4 C2 0.020 +1MA plan-4 H2 0.020 +1MA plan-4 N1 0.020 +1MA plan-4 N3 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 +1MA SMILES ACDLabs 12.01 P(=O)(O)(O)OCC1OC(C(C1O)O)n2cnc3\C(=N)N(C)C=Nc23 +1MA InChI InChI 1.03 InChI=1S/C11H16N5O7P/c1-15-3-14-10-6(9(15)12)13-4-16(10)11-8(18)7(17)5(23-11)2-22-24(19,20)21/h3-5,7-8,11-12,17-18H,2H2,1H3,(H2,19,20,21)/b12-9-/t5-,7-,8-,11-/m1/s1 +1MA InChIKey InChI 1.03 BKBYKEWNXKDACS-JOLDIKRXSA-N +1MA SMILES_CANONICAL CACTVS 3.385 CN1C=Nc2n(cnc2C1=N)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O +1MA SMILES CACTVS 3.385 CN1C=Nc2n(cnc2C1=N)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O +1MA SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "[H]/N=C\1/c2c(n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=CN1C" +1MA SMILES "OpenEye OEToolkits" 1.7.6 CN1C=Nc2c(ncn2C3C(C(C(O3)COP(=O)(O)O)O)O)C1=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 +1MA acedrg 243 "dictionary generator" +1MA acedrg_database 11 "data source" +1MA rdkit 2017.03.2 "Chemoinformatics tool" +1MA refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/2MG.cif b/image_analysis/structure_refinement/monomers/2MG.cif new file mode 100644 index 000000000..4603d5a4c --- /dev/null +++ b/image_analysis/structure_refinement/monomers/2MG.cif @@ -0,0 +1,294 @@ +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 +2MG 2MG "2N-METHYLGUANOSINE-5'-MONOPHOSPHATE" RNA 39 25 . + +data_comp_2MG +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 +2MG P P P 0 33.727 6.946 21.647 +2MG OP1 O O 0 33.329 6.945 23.111 +2MG OP2 O OP -1 32.927 7.934 20.820 +2MG OP3 O OP -1 35.224 7.082 21.443 +2MG "O5'" O O2 0 33.337 5.484 21.085 +2MG "C5'" C CH2 0 31.942 5.086 21.079 +2MG "C4'" C CH1 0 31.822 3.646 20.642 +2MG "O4'" O O2 0 32.464 3.473 19.354 +2MG "C3'" C CH1 0 32.490 2.602 21.543 +2MG "O3'" O OH1 0 31.638 2.231 22.620 +2MG "C2'" C CH1 0 32.737 1.450 20.564 +2MG "O2'" O OH1 0 31.625 0.591 20.413 +2MG "C1'" C CH1 0 33.058 2.195 19.266 +2MG N9 N NR5 0 34.492 2.337 19.018 +2MG C8 C CR15 0 35.255 3.479 19.051 +2MG N7 N NRD5 0 36.521 3.268 18.782 +2MG C5 C CR56 0 36.603 1.900 18.557 +2MG C6 C CR6 0 37.720 1.084 18.223 +2MG O6 O O 0 38.896 1.435 18.058 +2MG N1 N NR16 0 37.361 -0.264 18.084 +2MG C2 C CR6 0 36.088 -0.759 18.253 +2MG N2 N NH1 0 35.917 -2.084 18.070 +2MG CM2 C CH3 0 34.985 -2.901 18.830 +2MG N3 N NRD6 0 35.044 0.005 18.552 +2MG C4 C CR56 0 35.359 1.317 18.698 +2MG "H5'" H H 0 31.432 5.664 20.459 +2MG "H5''" H H 0 31.561 5.189 21.986 +2MG "H4'" H H 0 30.869 3.432 20.553 +2MG "H3'" H H 0 33.352 2.945 21.893 +2MG "HO3'" H H 0 32.005 1.601 23.055 +2MG "H2'" H H 0 33.522 0.917 20.859 +2MG "HO2'" H H 0 30.963 1.025 20.105 +2MG "H1'" H H 0 32.654 1.702 18.516 +2MG H8 H H 0 34.907 4.331 19.245 +2MG HN1 H H 0 38.016 -0.841 17.874 +2MG HN2 H H 0 36.394 -2.476 17.453 +2MG HM21 H H 0 34.406 -2.341 19.371 +2MG HM22 H H 0 35.480 -3.500 19.410 +2MG HM23 H H 0 34.443 -3.423 18.218 + +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 +2MG P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192 +2MG P OP2 SINGLE n 1.517 0.0192 1.517 0.0192 +2MG P OP3 SINGLE n 1.517 0.0192 1.517 0.0192 +2MG P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 +2MG "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +2MG "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +2MG "C4'" "O4'" SINGLE n 1.451 0.0100 1.451 0.0100 +2MG "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 +2MG "O4'" "C1'" SINGLE n 1.409 0.0100 1.409 0.0100 +2MG "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +2MG "C3'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100 +2MG "C2'" "O2'" SINGLE n 1.411 0.0100 1.411 0.0100 +2MG "C2'" "C1'" SINGLE n 1.525 0.0100 1.525 0.0100 +2MG "C1'" N9 SINGLE n 1.458 0.0100 1.458 0.0100 +2MG N9 C8 SINGLE y 1.372 0.0100 1.372 0.0100 +2MG N9 C4 SINGLE y 1.375 0.0100 1.375 0.0100 +2MG C8 N7 DOUBLE y 1.312 0.0100 1.312 0.0100 +2MG N7 C5 SINGLE y 1.390 0.0100 1.390 0.0100 +2MG C5 C6 SINGLE y 1.417 0.0103 1.417 0.0103 +2MG C5 C4 DOUBLE y 1.377 0.0100 1.377 0.0100 +2MG C6 O6 DOUBLE n 1.239 0.0100 1.239 0.0100 +2MG C6 N1 SINGLE y 1.396 0.0107 1.396 0.0107 +2MG N1 C2 SINGLE y 1.372 0.0100 1.372 0.0100 +2MG C2 N2 SINGLE n 1.342 0.0119 1.342 0.0119 +2MG C2 N3 DOUBLE y 1.324 0.0127 1.324 0.0127 +2MG N2 CM2 SINGLE n 1.450 0.0100 1.450 0.0100 +2MG N3 C4 SINGLE y 1.355 0.0100 1.355 0.0100 +2MG "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +2MG "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 +2MG "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 +2MG "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +2MG "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +2MG "C2'" "H2'" SINGLE n 1.089 0.0100 0.994 0.0200 +2MG "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 +2MG "C1'" "H1'" SINGLE n 1.089 0.0100 0.984 0.0200 +2MG C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170 +2MG N1 HN1 SINGLE n 1.016 0.0100 0.897 0.0200 +2MG N2 HN2 SINGLE n 1.016 0.0100 0.873 0.0200 +2MG CM2 HM21 SINGLE n 1.089 0.0100 0.970 0.0159 +2MG CM2 HM22 SINGLE n 1.089 0.0100 0.970 0.0159 +2MG CM2 HM23 SINGLE n 1.089 0.0100 0.970 0.0159 + +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 +2MG OP1 P OP2 112.864 1.69 +2MG OP1 P OP3 112.864 1.69 +2MG OP1 P "O5'" 105.808 2.07 +2MG OP2 P OP3 112.864 1.69 +2MG OP2 P "O5'" 105.808 2.07 +2MG OP3 P "O5'" 105.808 2.07 +2MG P "O5'" "C5'" 118.783 1.50 +2MG "O5'" "C5'" "C4'" 109.342 1.50 +2MG "O5'" "C5'" "H5'" 109.845 1.50 +2MG "O5'" "C5'" "H5''" 109.845 1.50 +2MG "C4'" "C5'" "H5'" 109.624 1.50 +2MG "C4'" "C5'" "H5''" 109.624 1.50 +2MG "H5'" "C5'" "H5''" 108.472 1.50 +2MG "C5'" "C4'" "O4'" 109.123 1.50 +2MG "C5'" "C4'" "C3'" 116.008 1.52 +2MG "C5'" "C4'" "H4'" 108.268 1.50 +2MG "O4'" "C4'" "C3'" 105.388 1.50 +2MG "O4'" "C4'" "H4'" 108.947 1.50 +2MG "C3'" "C4'" "H4'" 109.363 1.86 +2MG "C4'" "O4'" "C1'" 109.903 1.50 +2MG "C4'" "C3'" "O3'" 111.281 2.46 +2MG "C4'" "C3'" "C2'" 102.602 1.50 +2MG "C4'" "C3'" "H3'" 110.452 2.54 +2MG "O3'" "C3'" "C2'" 111.581 2.83 +2MG "O3'" "C3'" "H3'" 110.380 1.67 +2MG "C2'" "C3'" "H3'" 110.504 1.75 +2MG "C3'" "O3'" "HO3'" 108.744 3.00 +2MG "C3'" "C2'" "O2'" 112.782 2.45 +2MG "C3'" "C2'" "C1'" 101.239 1.50 +2MG "C3'" "C2'" "H2'" 110.596 1.51 +2MG "O2'" "C2'" "C1'" 111.715 2.69 +2MG "O2'" "C2'" "H2'" 110.448 1.97 +2MG "C1'" "C2'" "H2'" 110.636 1.70 +2MG "C2'" "O2'" "HO2'" 109.103 2.13 +2MG "O4'" "C1'" "C2'" 106.047 1.50 +2MG "O4'" "C1'" N9 108.477 1.50 +2MG "O4'" "C1'" "H1'" 109.807 1.50 +2MG "C2'" "C1'" N9 113.824 1.50 +2MG "C2'" "C1'" "H1'" 109.015 1.50 +2MG N9 "C1'" "H1'" 109.561 1.50 +2MG "C1'" N9 C8 126.829 1.91 +2MG "C1'" N9 C4 127.440 1.80 +2MG C8 N9 C4 105.731 1.50 +2MG N9 C8 N7 113.507 1.50 +2MG N9 C8 H8 123.187 1.50 +2MG N7 C8 H8 123.307 1.50 +2MG C8 N7 C5 104.778 1.50 +2MG N7 C5 C6 130.614 1.50 +2MG N7 C5 C4 110.574 1.50 +2MG C6 C5 C4 118.812 1.50 +2MG C5 C6 O6 128.536 1.50 +2MG C5 C6 N1 110.783 1.50 +2MG O6 C6 N1 120.681 1.50 +2MG C6 N1 C2 124.695 1.50 +2MG C6 N1 HN1 117.267 2.44 +2MG C2 N1 HN1 118.037 1.50 +2MG N1 C2 N2 116.538 1.50 +2MG N1 C2 N3 124.501 1.50 +2MG N2 C2 N3 118.961 1.50 +2MG C2 N2 CM2 121.703 2.30 +2MG C2 N2 HN2 119.049 1.68 +2MG CM2 N2 HN2 119.248 1.66 +2MG N2 CM2 HM21 109.503 1.50 +2MG N2 CM2 HM22 109.503 1.50 +2MG N2 CM2 HM23 109.503 1.50 +2MG HM21 CM2 HM22 109.396 1.50 +2MG HM21 CM2 HM23 109.396 1.50 +2MG HM22 CM2 HM23 109.396 1.50 +2MG C2 N3 C4 113.582 1.50 +2MG N9 C4 C5 105.411 1.50 +2MG N9 C4 N3 126.963 1.50 +2MG C5 C4 N3 127.627 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 +2MG C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +2MG C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +2MG C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +2MG C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +2MG C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +2MG C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +2MG C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +2MG C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +2MG C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +2MG C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +2MG C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +2MG C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +2MG alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +2MG beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +2MG epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +2MG gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +2MG sp3_sp3_52 "C3'" "C2'" "O2'" "HO2'" 180.000 10.00 3 +2MG const_18 N7 C8 N9 "C1'" 180.000 10.0 2 +2MG const_30 C5 C4 N9 "C1'" 180.000 10.0 2 +2MG const_21 N9 C8 N7 C5 0.000 10.0 2 +2MG const_24 C6 C5 N7 C8 180.000 10.0 2 +2MG const_sp2_sp2_4 N7 C5 C6 O6 0.000 5.0 2 +2MG const_25 N9 C4 C5 N7 0.000 10.0 2 +2MG const_sp2_sp2_7 O6 C6 N1 C2 180.000 5.0 2 +2MG const_11 N2 C2 N1 C6 180.000 10.0 2 +2MG sp2_sp2_1 N1 C2 N2 CM2 180.000 5.0 2 +2MG const_14 N2 C2 N3 C4 180.000 10.0 2 +2MG sp2_sp3_7 C2 N2 CM2 HM21 0.000 10.0 6 +2MG 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 +2MG chir_1 P "O5'" OP2 OP3 both +2MG chir_2 "C4'" "O4'" "C3'" "C5'" negative +2MG chir_3 "C3'" "O3'" "C4'" "C2'" positive +2MG chir_4 "C2'" "O2'" "C1'" "C3'" negative +2MG 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 +2MG plan-1 "C1'" 0.020 +2MG plan-1 C2 0.020 +2MG plan-1 C4 0.020 +2MG plan-1 C5 0.020 +2MG plan-1 C6 0.020 +2MG plan-1 C8 0.020 +2MG plan-1 H8 0.020 +2MG plan-1 HN1 0.020 +2MG plan-1 N1 0.020 +2MG plan-1 N2 0.020 +2MG plan-1 N3 0.020 +2MG plan-1 N7 0.020 +2MG plan-1 N9 0.020 +2MG plan-1 O6 0.020 +2MG plan-2 C2 0.020 +2MG plan-2 CM2 0.020 +2MG plan-2 HN2 0.020 +2MG 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 +2MG SMILES ACDLabs 10.04 O=C1c2ncn(c2N=C(NC)N1)C3OC(C(O)C3O)COP(=O)(O)O +2MG SMILES_CANONICAL CACTVS 3.341 CNC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O +2MG SMILES CACTVS 3.341 CNC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O +2MG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CNC1=Nc2c(ncn2[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)C(=O)N1 +2MG SMILES "OpenEye OEToolkits" 1.5.0 CNC1=Nc2c(ncn2C3C(C(C(O3)COP(=O)(O)O)O)O)C(=O)N1 +2MG InChI InChI 1.03 InChI=1S/C11H16N5O8P/c1-12-11-14-8-5(9(19)15-11)13-3-16(8)10-7(18)6(17)4(24-10)2-23-25(20,21)22/h3-4,6-7,10,17-18H,2H2,1H3,(H2,20,21,22)(H2,12,14,15,19)/t4-,6-,7-,10-/m1/s1 +2MG InChIKey InChI 1.03 ZSKBUUXHFBEFIJ-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 +2MG acedrg 243 "dictionary generator" +2MG acedrg_database 11 "data source" +2MG rdkit 2017.03.2 "Chemoinformatics tool" +2MG refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/5MC.cif b/image_analysis/structure_refinement/monomers/5MC.cif new file mode 100644 index 000000000..1358828fc --- /dev/null +++ b/image_analysis/structure_refinement/monomers/5MC.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 +5MC 5MC "5-METHYLCYTIDINE-5'-MONOPHOSPHATE" RNA 36 22 . +# +data_comp_5MC +# +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 +5MC P P P 0 50.440 -8.664 9.985 +5MC OP1 O O 0 48.933 -8.494 10.029 +5MC OP2 O OP -1 51.110 -8.329 11.305 +5MC OP3 O OP -1 50.865 -10.012 9.434 +5MC "O5'" O O2 0 50.976 -7.568 8.928 +5MC "C5'" C CH2 0 52.398 -7.502 8.649 +5MC "C4'" C CH1 0 52.685 -6.336 7.734 +5MC "O4'" O O2 0 51.869 -6.428 6.541 +5MC "C3'" C CH1 0 52.360 -4.941 8.282 +5MC "O3'" O OH1 0 53.402 -4.481 9.135 +5MC "C2'" C CH1 0 52.217 -4.110 6.997 +5MC "O2'" O OH1 0 53.434 -3.537 6.561 +5MC "C1'" C CH1 0 51.731 -5.144 5.969 +5MC N1 N NR6 0 50.307 -4.941 5.576 +5MC C2 C CR6 0 49.973 -4.500 4.284 +5MC O2 O O 0 50.870 -4.281 3.453 +5MC N3 N NRD6 0 48.663 -4.323 3.969 +5MC C4 C CR6 0 47.697 -4.561 4.872 +5MC N4 N NH2 0 46.429 -4.359 4.472 +5MC C5 C CR6 0 48.009 -5.004 6.186 +5MC C6 C CR16 0 49.309 -5.173 6.486 +5MC CM5 C CH3 0 46.922 -5.266 7.189 +5MC "H5'" H H 0 52.694 -8.342 8.219 +5MC "H5''" H H 0 52.900 -7.390 9.494 +5MC "H4'" H H 0 53.630 -6.373 7.473 +5MC "H3'" H H 0 51.499 -4.954 8.773 +5MC "HO3'" H H 0 53.276 -3.658 9.306 +5MC "H2'" H H 0 51.542 -3.413 7.124 +5MC "HO2'" H H 0 54.035 -4.136 6.511 +5MC "H1'" H H 0 52.305 -5.099 5.170 +5MC HN41 H H 0 46.115 -4.796 3.779 +5MC HN42 H H 0 45.920 -3.791 4.905 +5MC H6 H H 0 49.548 -5.468 7.358 +5MC HM51 H H 0 47.279 -5.777 7.934 +5MC HM52 H H 0 46.206 -5.770 6.770 +5MC HM53 H H 0 46.572 -4.422 7.518 +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 +5MC P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192 +5MC P OP2 SINGLE n 1.517 0.0192 1.517 0.0192 +5MC P OP3 SINGLE n 1.517 0.0192 1.517 0.0192 +5MC P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 +5MC "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +5MC "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +5MC "C4'" "O4'" SINGLE n 1.451 0.0111 1.451 0.0111 +5MC "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 +5MC "O4'" "C1'" SINGLE n 1.411 0.0100 1.411 0.0100 +5MC "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +5MC "C3'" "C2'" SINGLE n 1.533 0.0109 1.533 0.0109 +5MC "C2'" "O2'" SINGLE n 1.412 0.0100 1.412 0.0100 +5MC "C2'" "C1'" SINGLE n 1.532 0.0100 1.532 0.0100 +5MC "C1'" N1 SINGLE n 1.485 0.0100 1.485 0.0100 +5MC N1 C2 SINGLE y 1.395 0.0100 1.395 0.0100 +5MC N1 C6 SINGLE y 1.364 0.0100 1.364 0.0100 +5MC C2 O2 DOUBLE n 1.241 0.0100 1.241 0.0100 +5MC C2 N3 SINGLE y 1.353 0.0117 1.353 0.0117 +5MC N3 C4 DOUBLE y 1.341 0.0100 1.341 0.0100 +5MC C4 N4 SINGLE n 1.343 0.0151 1.343 0.0151 +5MC C4 C5 SINGLE y 1.416 0.0131 1.416 0.0131 +5MC C5 C6 DOUBLE y 1.342 0.0102 1.342 0.0102 +5MC C5 CM5 SINGLE n 1.501 0.0100 1.501 0.0100 +5MC "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +5MC "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 +5MC "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 +5MC "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +5MC "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +5MC "C2'" "H2'" SINGLE n 1.089 0.0100 0.978 0.0200 +5MC "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 +5MC "C1'" "H1'" SINGLE n 1.089 0.0100 0.985 0.0100 +5MC N4 HN41 SINGLE n 1.016 0.0100 0.877 0.0200 +5MC N4 HN42 SINGLE n 1.016 0.0100 0.877 0.0200 +5MC C6 H6 SINGLE n 1.082 0.0130 0.951 0.0200 +5MC CM5 HM51 SINGLE n 1.089 0.0100 0.971 0.0135 +5MC CM5 HM52 SINGLE n 1.089 0.0100 0.971 0.0135 +5MC CM5 HM53 SINGLE n 1.089 0.0100 0.971 0.0135 +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 +5MC OP1 P OP2 112.864 1.69 +5MC OP1 P OP3 112.864 1.69 +5MC OP1 P "O5'" 105.808 2.07 +5MC OP2 P OP3 112.864 1.69 +5MC OP2 P "O5'" 105.808 2.07 +5MC OP3 P "O5'" 105.808 2.07 +5MC P "O5'" "C5'" 118.783 1.50 +5MC "O5'" "C5'" "C4'" 109.342 1.50 +5MC "O5'" "C5'" "H5'" 109.845 1.50 +5MC "O5'" "C5'" "H5''" 109.845 1.50 +5MC "C4'" "C5'" "H5'" 109.624 1.50 +5MC "C4'" "C5'" "H5''" 109.624 1.50 +5MC "H5'" "C5'" "H5''" 108.472 1.50 +5MC "C5'" "C4'" "O4'" 109.615 1.50 +5MC "C5'" "C4'" "C3'" 116.008 1.52 +5MC "C5'" "C4'" "H4'" 108.268 1.50 +5MC "O4'" "C4'" "C3'" 104.439 1.50 +5MC "O4'" "C4'" "H4'" 108.698 1.50 +5MC "C3'" "C4'" "H4'" 109.363 1.86 +5MC "C4'" "O4'" "C1'" 109.578 1.50 +5MC "C4'" "C3'" "O3'" 111.281 2.46 +5MC "C4'" "C3'" "C2'" 102.071 1.50 +5MC "C4'" "C3'" "H3'" 110.452 2.54 +5MC "O3'" "C3'" "C2'" 111.993 3.00 +5MC "O3'" "C3'" "H3'" 110.380 1.67 +5MC "C2'" "C3'" "H3'" 110.108 1.66 +5MC "C3'" "O3'" "HO3'" 108.744 3.00 +5MC "C3'" "C2'" "O2'" 112.861 2.52 +5MC "C3'" "C2'" "C1'" 101.269 1.50 +5MC "C3'" "C2'" "H2'" 110.799 1.82 +5MC "O2'" "C2'" "C1'" 109.476 3.00 +5MC "O2'" "C2'" "H2'" 111.022 1.77 +5MC "C1'" "C2'" "H2'" 110.760 1.63 +5MC "C2'" "O2'" "HO2'" 109.449 1.85 +5MC "O4'" "C1'" "C2'" 106.825 1.50 +5MC "O4'" "C1'" N1 108.667 1.50 +5MC "O4'" "C1'" "H1'" 109.327 1.50 +5MC "C2'" "C1'" N1 112.859 1.50 +5MC "C2'" "C1'" "H1'" 109.776 1.83 +5MC N1 "C1'" "H1'" 109.166 1.50 +5MC "C1'" N1 C2 118.572 2.26 +5MC "C1'" N1 C6 121.186 1.50 +5MC C2 N1 C6 120.242 1.50 +5MC N1 C2 O2 118.953 1.50 +5MC N1 C2 N3 118.440 1.50 +5MC O2 C2 N3 122.606 1.50 +5MC C2 N3 C4 119.913 1.50 +5MC N3 C4 N4 117.013 1.55 +5MC N3 C4 C5 121.550 1.50 +5MC N4 C4 C5 121.437 1.50 +5MC C4 N4 HN41 119.860 1.50 +5MC C4 N4 HN42 119.860 1.50 +5MC HN41 N4 HN42 120.280 1.85 +5MC C4 C5 C6 117.857 1.50 +5MC C4 C5 CM5 120.410 1.50 +5MC C6 C5 CM5 121.734 1.50 +5MC N1 C6 C5 121.998 1.50 +5MC N1 C6 H6 118.660 1.56 +5MC C5 C6 H6 119.342 1.50 +5MC C5 CM5 HM51 109.580 1.50 +5MC C5 CM5 HM52 109.580 1.50 +5MC C5 CM5 HM53 109.580 1.50 +5MC HM51 CM5 HM52 109.348 1.50 +5MC HM51 CM5 HM53 109.348 1.50 +5MC HM52 CM5 HM53 109.348 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 +5MC C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +5MC C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +5MC C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +5MC C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +5MC C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +5MC C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +5MC C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +5MC C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +5MC C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +5MC C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +5MC C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +5MC C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +5MC alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +5MC beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +5MC epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +5MC gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +5MC sp3_sp3_52 "C3'" "C2'" "O2'" "HO2'" 180.000 10.00 3 +5MC const_sp2_sp2_4 O2 C2 N1 "C1'" 0.000 5.0 2 +5MC const_18 C5 C6 N1 "C1'" 180.000 10.0 2 +5MC const_sp2_sp2_6 O2 C2 N3 C4 180.000 5.0 2 +5MC const_sp2_sp2_8 N4 C4 N3 C2 180.000 5.0 2 +5MC sp2_sp2_3 N3 C4 N4 HN41 0.000 5.0 2 +5MC const_12 N4 C4 C5 CM5 0.000 10.0 2 +5MC const_15 CM5 C5 C6 N1 180.000 10.0 2 +5MC sp2_sp3_7 C4 C5 CM5 HM51 150.000 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 +5MC chir_1 P "O5'" OP2 OP3 both +5MC chir_2 "C4'" "O4'" "C3'" "C5'" negative +5MC chir_3 "C3'" "O3'" "C4'" "C2'" positive +5MC chir_4 "C2'" "O2'" "C1'" "C3'" negative +5MC 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 +5MC plan-1 "C1'" 0.020 +5MC plan-1 C2 0.020 +5MC plan-1 C4 0.020 +5MC plan-1 C5 0.020 +5MC plan-1 C6 0.020 +5MC plan-1 CM5 0.020 +5MC plan-1 H6 0.020 +5MC plan-1 N1 0.020 +5MC plan-1 N3 0.020 +5MC plan-1 N4 0.020 +5MC plan-1 O2 0.020 +5MC plan-2 C4 0.020 +5MC plan-2 HN41 0.020 +5MC plan-2 HN42 0.020 +5MC 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 +5MC SMILES ACDLabs 10.04 O=C1N=C(N)C(=CN1C2OC(C(O)C2O)COP(=O)(O)O)C +5MC SMILES_CANONICAL CACTVS 3.341 CC1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=O)N=C1N +5MC SMILES CACTVS 3.341 CC1=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=O)N=C1N +5MC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O +5MC SMILES "OpenEye OEToolkits" 1.5.0 CC1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O +5MC InChI InChI 1.03 InChI=1S/C10H16N3O8P/c1-4-2-13(10(16)12-8(4)11)9-7(15)6(14)5(21-9)3-20-22(17,18)19/h2,5-7,9,14-15H,3H2,1H3,(H2,11,12,16)(H2,17,18,19)/t5-,6-,7-,9-/m1/s1 +5MC InChIKey InChI 1.03 NJQONZSFUKNYOY-JXOAFFINSA-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 +5MC acedrg 243 "dictionary generator" +5MC acedrg_database 11 "data source" +5MC rdkit 2017.03.2 "Chemoinformatics tool" +5MC refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/5MU.cif b/image_analysis/structure_refinement/monomers/5MU.cif new file mode 100644 index 000000000..cec03d0f6 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/5MU.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 +5MU 5MU "5-METHYLURIDINE 5'-MONOPHOSPHATE" RNA 35 22 . + +data_comp_5MU +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 +5MU N1 N NR6 0 45.964 22.742 42.610 +5MU C2 C CR6 0 46.310 21.509 42.078 +5MU N3 N NR16 0 45.881 21.292 40.788 +5MU C4 C CR6 0 45.162 22.161 39.983 +5MU C5 C CR6 0 44.836 23.436 40.589 +5MU C5M C CH3 0 44.058 24.436 39.786 +5MU C6 C CR16 0 45.249 23.665 41.851 +5MU O2 O O 0 46.944 20.657 42.690 +5MU O4 O O 0 44.849 21.819 38.838 +5MU "C1'" C CH1 0 46.396 23.062 43.999 +5MU "C2'" C CH1 0 47.646 23.950 44.041 +5MU "O2'" O OH1 0 48.573 23.414 44.962 +5MU "C3'" C CH1 0 47.081 25.308 44.482 +5MU "C4'" C CH1 0 45.911 24.881 45.376 +5MU "O3'" O OH1 0 48.020 26.094 45.207 +5MU "O4'" O O2 0 45.356 23.744 44.672 +5MU "C5'" C CH2 0 44.839 25.915 45.625 +5MU "O5'" O O2 0 44.216 26.287 44.368 +5MU P P P 0 43.153 27.501 44.357 +5MU OP1 O O 0 42.658 27.605 42.927 +5MU OP2 O OP -1 43.921 28.730 44.805 +5MU OP3 O OP -1 42.060 27.102 45.331 +5MU HN3 H H 0 46.097 20.497 40.440 +5MU H71 H H 0 43.917 25.242 40.310 +5MU H72 H H 0 43.197 24.059 39.541 +5MU H73 H H 0 44.550 24.660 38.980 +5MU H6 H H 0 45.037 24.501 42.250 +5MU "H1'" H H 0 46.577 22.230 44.486 +5MU "H2'" H H 0 48.047 24.022 43.151 +5MU "HO2'" H H 0 49.240 23.936 45.028 +5MU "H3'" H H 0 46.752 25.810 43.693 +5MU "H4'" H H 0 46.255 24.578 46.244 +5MU "HO3'" H H 0 47.644 26.816 45.448 +5MU "H5'" H H 0 45.241 26.713 46.049 +5MU "H5''" H H 0 44.158 25.544 46.239 + +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 +5MU N1 C2 SINGLE y 1.376 0.0100 1.376 0.0100 +5MU N1 C6 SINGLE y 1.386 0.0100 1.386 0.0100 +5MU N1 "C1'" SINGLE n 1.476 0.0133 1.476 0.0133 +5MU C2 N3 SINGLE y 1.373 0.0100 1.373 0.0100 +5MU C2 O2 DOUBLE n 1.224 0.0111 1.224 0.0111 +5MU N3 C4 SINGLE y 1.383 0.0100 1.383 0.0100 +5MU C4 C5 SINGLE y 1.446 0.0100 1.446 0.0100 +5MU C4 O4 DOUBLE n 1.234 0.0141 1.234 0.0141 +5MU C5 C5M SINGLE n 1.500 0.0100 1.500 0.0100 +5MU C5 C6 DOUBLE y 1.343 0.0112 1.343 0.0112 +5MU "C1'" "C2'" SINGLE n 1.529 0.0100 1.529 0.0100 +5MU "C1'" "O4'" SINGLE n 1.412 0.0100 1.412 0.0100 +5MU "C2'" "O2'" SINGLE n 1.412 0.0100 1.412 0.0100 +5MU "C2'" "C3'" SINGLE n 1.533 0.0109 1.533 0.0109 +5MU "C3'" "C4'" SINGLE n 1.535 0.0100 1.535 0.0100 +5MU "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +5MU "C4'" "O4'" SINGLE n 1.451 0.0111 1.451 0.0111 +5MU "C4'" "C5'" SINGLE n 1.509 0.0100 1.509 0.0100 +5MU "C5'" "O5'" SINGLE n 1.450 0.0166 1.450 0.0166 +5MU "O5'" P SINGLE n 1.614 0.0178 1.614 0.0178 +5MU P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192 +5MU P OP2 SINGLE n 1.517 0.0192 1.517 0.0192 +5MU P OP3 SINGLE n 1.517 0.0192 1.517 0.0192 +5MU N3 HN3 SINGLE n 1.016 0.0100 0.893 0.0200 +5MU C5M H71 SINGLE n 1.089 0.0100 0.971 0.0135 +5MU C5M H72 SINGLE n 1.089 0.0100 0.971 0.0135 +5MU C5M H73 SINGLE n 1.089 0.0100 0.971 0.0135 +5MU C6 H6 SINGLE n 1.082 0.0130 0.951 0.0200 +5MU "C1'" "H1'" SINGLE n 1.089 0.0100 0.981 0.0118 +5MU "C2'" "H2'" SINGLE n 1.089 0.0100 0.978 0.0200 +5MU "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 +5MU "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +5MU "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 +5MU "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +5MU "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +5MU "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 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 +5MU C2 N1 C6 121.243 1.50 +5MU C2 N1 "C1'" 117.446 1.50 +5MU C6 N1 "C1'" 121.311 1.50 +5MU N1 C2 N3 114.786 1.50 +5MU N1 C2 O2 122.872 1.50 +5MU N3 C2 O2 122.342 1.50 +5MU C2 N3 C4 127.106 1.50 +5MU C2 N3 HN3 115.584 1.79 +5MU C4 N3 HN3 117.311 1.81 +5MU N3 C4 C5 115.265 1.50 +5MU N3 C4 O4 119.787 1.50 +5MU C5 C4 O4 124.948 1.50 +5MU C4 C5 C5M 118.650 1.50 +5MU C4 C5 C6 118.305 1.50 +5MU C5M C5 C6 123.045 1.50 +5MU C5 C5M H71 109.652 1.50 +5MU C5 C5M H72 109.652 1.50 +5MU C5 C5M H73 109.652 1.50 +5MU H71 C5M H72 109.348 1.50 +5MU H71 C5M H73 109.348 1.50 +5MU H72 C5M H73 109.348 1.50 +5MU N1 C6 C5 123.296 1.50 +5MU N1 C6 H6 117.926 1.56 +5MU C5 C6 H6 118.779 1.68 +5MU N1 "C1'" "C2'" 112.859 1.50 +5MU N1 "C1'" "O4'" 108.667 1.50 +5MU N1 "C1'" "H1'" 109.166 1.50 +5MU "C2'" "C1'" "O4'" 106.825 1.50 +5MU "C2'" "C1'" "H1'" 109.776 1.83 +5MU "O4'" "C1'" "H1'" 109.327 1.50 +5MU "C1'" "C2'" "O2'" 109.476 3.00 +5MU "C1'" "C2'" "C3'" 101.269 1.50 +5MU "C1'" "C2'" "H2'" 110.760 1.63 +5MU "O2'" "C2'" "C3'" 112.861 2.52 +5MU "O2'" "C2'" "H2'" 111.022 1.77 +5MU "C3'" "C2'" "H2'" 110.799 1.82 +5MU "C2'" "O2'" "HO2'" 109.449 1.85 +5MU "C2'" "C3'" "C4'" 102.071 1.50 +5MU "C2'" "C3'" "O3'" 111.993 3.00 +5MU "C2'" "C3'" "H3'" 110.108 1.66 +5MU "C4'" "C3'" "O3'" 111.281 2.46 +5MU "C4'" "C3'" "H3'" 110.452 2.54 +5MU "O3'" "C3'" "H3'" 110.380 1.67 +5MU "C3'" "C4'" "O4'" 104.439 1.50 +5MU "C3'" "C4'" "C5'" 116.008 1.52 +5MU "C3'" "C4'" "H4'" 109.363 1.86 +5MU "O4'" "C4'" "C5'" 109.615 1.50 +5MU "O4'" "C4'" "H4'" 108.698 1.50 +5MU "C5'" "C4'" "H4'" 108.268 1.50 +5MU "C3'" "O3'" "HO3'" 108.744 3.00 +5MU "C1'" "O4'" "C4'" 109.578 1.50 +5MU "C4'" "C5'" "O5'" 109.342 1.50 +5MU "C4'" "C5'" "H5'" 109.624 1.50 +5MU "C4'" "C5'" "H5''" 109.624 1.50 +5MU "O5'" "C5'" "H5'" 109.845 1.50 +5MU "O5'" "C5'" "H5''" 109.845 1.50 +5MU "H5'" "C5'" "H5''" 108.472 1.50 +5MU "C5'" "O5'" P 118.783 1.50 +5MU "O5'" P OP1 105.808 2.07 +5MU "O5'" P OP2 105.808 2.07 +5MU "O5'" P OP3 105.808 2.07 +5MU OP1 P OP2 112.864 1.69 +5MU OP1 P OP3 112.864 1.69 +5MU OP2 P OP3 112.864 1.69 + +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 +5MU C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +5MU C2e-nyu0 "C4'" "O4'" "C1'" "C2" 340.700 6.300 1 +5MU C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +5MU C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +5MU C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +5MU C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +5MU C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +5MU C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +5MU C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +5MU C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +5MU C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +5MU C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +5MU alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +5MU beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +5MU epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +5MU gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +5MU const_sp2_sp2_3 O2 C2 N1 C6 180.000 5.0 2 +5MU const_21 C5 C6 N1 C2 0.000 10.0 2 +5MU sp3_sp3_34 "C1'" "C2'" "O2'" "HO2'" 180.000 10.0 3 +5MU const_sp2_sp2_7 O2 C2 N3 C4 180.000 5.0 2 +5MU const_11 O4 C4 N3 C2 180.000 10.0 2 +5MU const_16 O4 C4 C5 C5M 0.000 10.0 2 +5MU sp2_sp3_7 C4 C5 C5M H71 150.000 10.0 6 +5MU const_19 C5M 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 +5MU chir_1 "C1'" "O4'" N1 "C2'" negative +5MU chir_2 "C2'" "O2'" "C1'" "C3'" negative +5MU chir_3 "C3'" "O3'" "C4'" "C2'" positive +5MU chir_4 "C4'" "O4'" "C3'" "C5'" negative +5MU chir_5 P "O5'" OP2 OP3 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 +5MU plan-1 "C1'" 0.020 +5MU plan-1 C2 0.020 +5MU plan-1 C4 0.020 +5MU plan-1 C5 0.020 +5MU plan-1 C5M 0.020 +5MU plan-1 C6 0.020 +5MU plan-1 H6 0.020 +5MU plan-1 HN3 0.020 +5MU plan-1 N1 0.020 +5MU plan-1 N3 0.020 +5MU plan-1 O2 0.020 +5MU 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 +5MU SMILES ACDLabs 10.04 O=C1NC(=O)N(C=C1C)C2OC(C(O)C2O)COP(=O)(O)O +5MU SMILES_CANONICAL CACTVS 3.341 CC1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=O)NC1=O +5MU SMILES CACTVS 3.341 CC1=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=O)NC1=O +5MU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O +5MU SMILES "OpenEye OEToolkits" 1.5.0 CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O +5MU InChI InChI 1.03 InChI=1S/C10H15N2O9P/c1-4-2-12(10(16)11-8(4)15)9-7(14)6(13)5(21-9)3-20-22(17,18)19/h2,5-7,9,13-14H,3H2,1H3,(H,11,15,16)(H2,17,18,19)/t5-,6-,7-,9-/m1/s1 +5MU InChIKey InChI 1.03 IGWHDMPTQKSDTL-JXOAFFINSA-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 +5MU acedrg 243 "dictionary generator" +5MU acedrg_database 11 "data source" +5MU rdkit 2017.03.2 "Chemoinformatics tool" +5MU refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/7MG.cif b/image_analysis/structure_refinement/monomers/7MG.cif new file mode 100644 index 000000000..17dafc8c9 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/7MG.cif @@ -0,0 +1,308 @@ +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 +7MG 7MG "7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE" RNA 41 25 . + +data_comp_7MG +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 +7MG P P P 0 36.755 11.551 18.304 +7MG OP1 O O 0 37.842 12.410 17.686 +7MG OP2 O OP -1 35.360 12.088 18.045 +7MG OP3 O OP -1 36.894 10.081 17.952 +7MG "O5'" O O2 0 36.974 11.645 19.900 +7MG "C5'" C CH2 0 36.067 10.924 20.772 +7MG "C4'" C CH1 0 36.506 11.088 22.207 +7MG "O4'" O O2 0 37.856 10.573 22.349 +7MG "C3'" C CH1 0 36.546 12.531 22.736 +7MG "O3'" O OH1 0 35.933 12.618 24.017 +7MG "C2'" C CH1 0 38.028 12.882 22.708 +7MG "O2'" O OH1 0 38.387 13.794 23.729 +7MG "C1'" C CH1 0 38.659 11.524 23.021 +7MG N9 N NR5 0 40.065 11.364 22.595 +7MG C8 C CH2 0 40.895 12.383 21.944 +7MG N7 N NR5 0 42.179 11.711 21.783 +7MG C5 C CR56 0 42.096 10.393 22.267 +7MG C6 C CR6 0 43.053 9.354 22.315 +7MG O6 O O 0 44.218 9.367 21.927 +7MG N1 N NR16 0 42.512 8.199 22.893 +7MG C2 C CR6 0 41.228 8.062 23.362 +7MG N2 N NH2 0 40.894 6.876 23.884 +7MG N3 N NRD6 0 40.334 9.040 23.317 +7MG C4 C CR56 0 40.795 10.194 22.764 +7MG CM7 C CH3 0 43.334 12.377 21.203 +7MG "H5'" H H 0 36.065 9.964 20.533 +7MG "H5''" H H 0 35.148 11.275 20.664 +7MG "H4'" H H 0 35.901 10.557 22.768 +7MG "H3'" H H 0 36.091 13.140 22.099 +7MG "HO3'" H H 0 36.051 13.402 24.323 +7MG "H2'" H H 0 38.278 13.222 21.823 +7MG "HO2'" H H 0 39.220 13.942 23.778 +7MG "H1'" H H 0 38.572 11.340 23.987 +7MG H81 H H 0 40.524 12.630 21.083 +7MG H82 H H 0 40.988 13.166 22.507 +7MG HN1 H H 0 43.041 7.506 22.961 +7MG HN21 H H 0 40.414 6.841 24.617 +7MG HN22 H H 0 41.156 6.137 23.490 +7MG HM71 H H 0 44.116 11.808 21.264 +7MG HM72 H H 0 43.505 13.205 21.682 +7MG HM73 H H 0 43.157 12.579 20.269 + +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 +7MG P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192 +7MG P OP2 SINGLE n 1.517 0.0192 1.517 0.0192 +7MG P OP3 SINGLE n 1.517 0.0192 1.517 0.0192 +7MG P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 +7MG "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +7MG "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +7MG "C4'" "O4'" SINGLE n 1.450 0.0100 1.450 0.0100 +7MG "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 +7MG "O4'" "C1'" SINGLE n 1.416 0.0117 1.416 0.0117 +7MG "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +7MG "C3'" "C2'" SINGLE n 1.517 0.0200 1.517 0.0200 +7MG "C2'" "O2'" SINGLE n 1.412 0.0200 1.412 0.0200 +7MG "C2'" "C1'" SINGLE n 1.529 0.0100 1.529 0.0100 +7MG "C1'" N9 SINGLE n 1.466 0.0175 1.466 0.0175 +7MG N9 C8 SINGLE n 1.461 0.0141 1.461 0.0141 +7MG N9 C4 SINGLE n 1.376 0.0200 1.376 0.0200 +7MG C8 N7 SINGLE n 1.461 0.0141 1.461 0.0141 +7MG N7 C5 SINGLE n 1.405 0.0200 1.405 0.0200 +7MG N7 CM7 SINGLE n 1.453 0.0100 1.453 0.0100 +7MG C5 C6 SINGLE y 1.393 0.0169 1.393 0.0169 +7MG C5 C4 DOUBLE y 1.389 0.0200 1.389 0.0200 +7MG C6 O6 DOUBLE n 1.228 0.0131 1.228 0.0131 +7MG C6 N1 SINGLE y 1.394 0.0121 1.394 0.0121 +7MG N1 C2 SINGLE y 1.371 0.0108 1.371 0.0108 +7MG C2 N2 SINGLE n 1.337 0.0113 1.337 0.0113 +7MG C2 N3 DOUBLE y 1.323 0.0117 1.323 0.0117 +7MG N3 C4 SINGLE y 1.348 0.0185 1.348 0.0185 +7MG "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +7MG "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 +7MG "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 +7MG "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +7MG "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +7MG "C2'" "H2'" SINGLE n 1.089 0.0100 0.981 0.0200 +7MG "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 +7MG "C1'" "H1'" SINGLE n 1.089 0.0100 0.987 0.0200 +7MG C8 H81 SINGLE n 1.089 0.0100 0.970 0.0140 +7MG C8 H82 SINGLE n 1.089 0.0100 0.970 0.0140 +7MG N1 HN1 SINGLE n 1.016 0.0100 0.873 0.0200 +7MG N2 HN21 SINGLE n 1.016 0.0100 0.877 0.0200 +7MG N2 HN22 SINGLE n 1.016 0.0100 0.877 0.0200 +7MG CM7 HM71 SINGLE n 1.089 0.0100 0.972 0.0143 +7MG CM7 HM72 SINGLE n 1.089 0.0100 0.972 0.0143 +7MG CM7 HM73 SINGLE n 1.089 0.0100 0.972 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 +7MG OP1 P OP2 112.864 1.69 +7MG OP1 P OP3 112.864 1.69 +7MG OP1 P "O5'" 105.808 2.07 +7MG OP2 P OP3 112.864 1.69 +7MG OP2 P "O5'" 105.808 2.07 +7MG OP3 P "O5'" 105.808 2.07 +7MG P "O5'" "C5'" 118.783 1.50 +7MG "O5'" "C5'" "C4'" 109.342 1.50 +7MG "O5'" "C5'" "H5'" 109.845 1.50 +7MG "O5'" "C5'" "H5''" 109.845 1.50 +7MG "C4'" "C5'" "H5'" 109.624 1.50 +7MG "C4'" "C5'" "H5''" 109.624 1.50 +7MG "H5'" "C5'" "H5''" 108.472 1.50 +7MG "C5'" "C4'" "O4'" 109.123 1.50 +7MG "C5'" "C4'" "C3'" 116.008 1.52 +7MG "C5'" "C4'" "H4'" 108.268 1.50 +7MG "O4'" "C4'" "C3'" 104.641 1.82 +7MG "O4'" "C4'" "H4'" 110.466 2.90 +7MG "C3'" "C4'" "H4'" 109.363 1.86 +7MG "C4'" "O4'" "C1'" 109.585 1.50 +7MG "C4'" "C3'" "O3'" 111.281 2.46 +7MG "C4'" "C3'" "C2'" 101.879 2.07 +7MG "C4'" "C3'" "H3'" 110.452 2.54 +7MG "O3'" "C3'" "C2'" 114.431 3.00 +7MG "O3'" "C3'" "H3'" 110.380 1.67 +7MG "C2'" "C3'" "H3'" 107.880 2.97 +7MG "C3'" "O3'" "HO3'" 108.744 3.00 +7MG "C3'" "C2'" "O2'" 112.637 3.00 +7MG "C3'" "C2'" "C1'" 101.599 1.50 +7MG "C3'" "C2'" "H2'" 111.559 3.00 +7MG "O2'" "C2'" "C1'" 107.625 3.00 +7MG "O2'" "C2'" "H2'" 111.144 3.00 +7MG "C1'" "C2'" "H2'" 111.470 3.00 +7MG "C2'" "O2'" "HO2'" 112.841 3.00 +7MG "O4'" "C1'" "C2'" 106.883 1.50 +7MG "O4'" "C1'" N9 109.703 1.83 +7MG "O4'" "C1'" "H1'" 108.522 3.00 +7MG "C2'" "C1'" N9 113.039 1.91 +7MG "C2'" "C1'" "H1'" 111.147 3.00 +7MG N9 "C1'" "H1'" 110.672 1.50 +7MG "C1'" N9 C8 124.243 2.92 +7MG "C1'" N9 C4 126.514 3.00 +7MG C8 N9 C4 109.243 1.81 +7MG N9 C8 N7 102.166 2.68 +7MG N9 C8 H81 111.296 1.50 +7MG N9 C8 H82 111.296 1.50 +7MG N7 C8 H81 111.296 1.50 +7MG N7 C8 H82 111.296 1.50 +7MG H81 C8 H82 111.548 2.37 +7MG C8 N7 C5 111.115 1.81 +7MG C8 N7 CM7 122.962 1.87 +7MG C5 N7 CM7 125.923 1.74 +7MG N7 C5 C6 130.345 1.50 +7MG N7 C5 C4 109.346 2.06 +7MG C6 C5 C4 120.309 1.50 +7MG C5 C6 O6 128.640 1.50 +7MG C5 C6 N1 110.185 1.50 +7MG O6 C6 N1 121.175 1.50 +7MG C6 N1 C2 125.932 1.50 +7MG C6 N1 HN1 116.880 1.50 +7MG C2 N1 HN1 117.188 1.50 +7MG N1 C2 N2 116.451 1.50 +7MG N1 C2 N3 123.751 1.50 +7MG N2 C2 N3 119.799 1.50 +7MG C2 N2 HN21 119.815 1.50 +7MG C2 N2 HN22 119.815 1.50 +7MG HN21 N2 HN22 120.371 1.96 +7MG C2 N3 C4 114.279 1.50 +7MG N9 C4 C5 107.842 2.06 +7MG N9 C4 N3 126.614 1.94 +7MG C5 C4 N3 125.545 1.50 +7MG N7 CM7 HM71 109.783 1.50 +7MG N7 CM7 HM72 109.783 1.50 +7MG N7 CM7 HM73 109.783 1.50 +7MG HM71 CM7 HM72 109.459 1.50 +7MG HM71 CM7 HM73 109.459 1.50 +7MG HM72 CM7 HM73 109.459 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 +7MG C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +7MG C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +7MG C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +7MG C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +7MG C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +7MG C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +7MG C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +7MG C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +7MG C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +7MG C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +7MG C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +7MG C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +7MG alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +7MG beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +7MG epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +7MG gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +7MG sp3_sp3_52 "C3'" "C2'" "O2'" "HO2'" 180.000 10.00 3 +7MG sp2_sp3_4 "C1'" N9 C8 N7 180.000 10.0 6 +7MG sp2_sp2_6 C5 C4 N9 "C1'" 180.000 5.0 2 +7MG sp2_sp3_10 CM7 N7 C8 N9 180.000 10.0 6 +7MG sp2_sp2_4 C6 C5 N7 CM7 0.000 5.0 2 +7MG sp2_sp3_19 C8 N7 CM7 HM71 150.000 10.0 6 +7MG const_sp2_sp2_4 N7 C5 C6 O6 0.000 5.0 2 +7MG const_17 N9 C4 C5 N7 0.000 10.0 2 +7MG const_sp2_sp2_7 O6 C6 N1 C2 180.000 5.0 2 +7MG const_11 N2 C2 N1 C6 180.000 10.0 2 +7MG sp2_sp2_9 N1 C2 N2 HN21 180.000 5.0 2 +7MG const_14 N2 C2 N3 C4 180.000 10.0 2 +7MG 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 +7MG chir_1 P "O5'" OP2 OP3 both +7MG chir_2 "C4'" "O4'" "C3'" "C5'" negative +7MG chir_3 "C3'" "O3'" "C4'" "C2'" positive +7MG chir_4 "C2'" "O2'" "C1'" "C3'" negative +7MG 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 +7MG plan-1 C2 0.020 +7MG plan-1 C4 0.020 +7MG plan-1 C5 0.020 +7MG plan-1 C6 0.020 +7MG plan-1 HN1 0.020 +7MG plan-1 N1 0.020 +7MG plan-1 N2 0.020 +7MG plan-1 N3 0.020 +7MG plan-1 N7 0.020 +7MG plan-1 N9 0.020 +7MG plan-1 O6 0.020 +7MG plan-2 "C1'" 0.020 +7MG plan-2 C4 0.020 +7MG plan-2 C8 0.020 +7MG plan-2 N9 0.020 +7MG plan-3 C5 0.020 +7MG plan-3 C8 0.020 +7MG plan-3 CM7 0.020 +7MG plan-3 N7 0.020 +7MG plan-4 C2 0.020 +7MG plan-4 HN21 0.020 +7MG plan-4 HN22 0.020 +7MG plan-4 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 +7MG SMILES ACDLabs 10.04 O=C1C=2N(CN(C=2N=C(N)N1)C3OC(C(O)C3O)COP(=O)(O)O)C +7MG SMILES_CANONICAL CACTVS 3.341 CN1CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C3=C1C(=O)NC(=N3)N +7MG SMILES CACTVS 3.341 CN1CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C3=C1C(=O)NC(=N3)N +7MG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CN1CN(C2=C1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O +7MG SMILES "OpenEye OEToolkits" 1.5.0 CN1CN(C2=C1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(O)O)O)O +7MG InChI InChI 1.03 InChI=1S/C11H18N5O8P/c1-15-3-16(8-5(15)9(19)14-11(12)13-8)10-7(18)6(17)4(24-10)2-23-25(20,21)22/h4,6-7,10,17-18H,2-3H2,1H3,(H2,20,21,22)(H3,12,13,14,19)/t4-,6-,7-,10-/m1/s1 +7MG InChIKey InChI 1.03 ZMWJGXGSWZFZPJ-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 +7MG acedrg 243 "dictionary generator" +7MG acedrg_database 11 "data source" +7MG rdkit 2017.03.2 "Chemoinformatics tool" +7MG refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/FAD.cif b/image_analysis/structure_refinement/monomers/FAD.cif new file mode 100644 index 000000000..9952352d8 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/FAD.cif @@ -0,0 +1,619 @@ +# +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 +FAD FAD "FLAVIN-ADENINE DINUCLEOTIDE" NON-POLYMER 84 53 . +# +data_comp_FAD +# +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 +FAD PA P P 0 20.714 1.770 23.791 +FAD O1A O O 0 19.737 0.994 22.985 +FAD O2A O OP -1 20.556 3.244 23.868 +FAD O5B O O2 0 20.784 1.154 25.265 +FAD C5B C CH2 0 21.508 1.920 26.259 +FAD C4B C CH1 0 21.685 1.088 27.506 +FAD O4B O O2 0 22.496 1.819 28.451 +FAD C3B C CH1 0 20.398 0.757 28.265 +FAD O3B O OH1 0 20.556 -0.451 28.999 +FAD C2B C CH1 0 20.243 1.982 29.172 +FAD O2B O OH1 0 19.475 1.727 30.330 +FAD C1B C CH1 0 21.699 2.264 29.545 +FAD N9A N NR5 0 21.959 3.685 29.781 +FAD C8A C CR15 0 22.300 4.646 28.862 +FAD N7A N NRD5 0 22.466 5.839 29.380 +FAD C5A C CR56 0 22.214 5.654 30.732 +FAD C6A C CR6 0 22.225 6.545 31.827 +FAD N6A N NH2 0 22.509 7.843 31.720 +FAD N1A N NRD6 0 21.925 6.038 33.053 +FAD C2A C CR16 0 21.639 4.731 33.155 +FAD N3A N NRD6 0 21.600 3.805 32.197 +FAD C4A C CR56 0 21.899 4.330 30.993 +FAD N1 N NRD6 0 21.477 -2.068 14.310 +FAD C2 C CR6 0 21.990 -3.170 13.678 +FAD O2 O O 0 23.119 -3.600 13.933 +FAD N3 N NR16 0 21.215 -3.824 12.720 +FAD C4 C CR6 0 19.939 -3.467 12.324 +FAD O4 O O 0 19.331 -4.099 11.476 +FAD C4X C CR66 0 19.428 -2.318 12.997 +FAD N5 N NRD6 0 18.223 -1.922 12.672 +FAD C5X C CR66 0 17.708 -0.822 13.305 +FAD C6 C CR16 0 16.407 -0.419 12.939 +FAD C7 C CR6 0 15.794 0.671 13.514 +FAD C7M C CH3 0 14.398 1.039 13.068 +FAD C8 C CR6 0 16.505 1.416 14.514 +FAD C8M C CH3 0 15.889 2.619 15.180 +FAD C9 C CR16 0 17.784 1.024 14.876 +FAD C9A C CR66 0 18.422 -0.094 14.291 +FAD N10 N NR6 0 19.717 -0.536 14.620 +FAD C10 C CR66 0 20.261 -1.663 13.986 +FAD "C1'" C CH2 0 20.546 0.156 15.638 +FAD "C2'" C CH1 0 20.455 -0.488 17.014 +FAD "O2'" O OH1 0 19.095 -0.421 17.451 +FAD "C3'" C CH1 0 21.373 0.159 18.058 +FAD "O3'" O OH1 0 22.723 0.097 17.602 +FAD "C4'" C CH1 0 21.301 -0.479 19.449 +FAD "O4'" O OH1 0 19.957 -0.463 19.936 +FAD "C5'" C CH2 0 22.167 0.224 20.481 +FAD "O5'" O O2 0 22.110 -0.483 21.743 +FAD P P P 0 22.951 0.052 22.986 +FAD O1P O O 0 22.742 -0.871 24.130 +FAD O2P O OP -1 24.340 0.346 22.551 +FAD O3P O O2 0 22.191 1.429 23.280 +FAD H51A H H 0 21.005 2.745 26.481 +FAD H52A H H 0 22.397 2.180 25.905 +FAD H4B H H 0 22.151 0.249 27.259 +FAD H3B H H 0 19.629 0.687 27.645 +FAD HO3A H H 0 19.777 -0.616 29.334 +FAD H2B H H 0 19.868 2.745 28.663 +FAD HO2A H H 0 19.501 2.350 30.867 +FAD H1B H H 0 21.939 1.734 30.378 +FAD H8A H H 0 22.407 4.462 27.944 +FAD H61A H H 0 22.502 8.360 32.433 +FAD H62A H H 0 22.705 8.186 30.933 +FAD H2A H H 0 21.438 4.425 34.027 +FAD HN3 H H 0 21.567 -4.529 12.329 +FAD H6 H H 0 15.940 -0.918 12.276 +FAD HM71 H H 0 14.059 1.787 13.584 +FAD HM72 H H 0 13.809 0.276 13.191 +FAD HM73 H H 0 14.414 1.282 12.127 +FAD HM81 H H 0 16.515 3.008 15.814 +FAD HM82 H H 0 15.082 2.352 15.651 +FAD HM83 H H 0 15.664 3.283 14.507 +FAD H9 H H 0 18.238 1.530 15.543 +FAD "H1'1" H H 0 20.293 1.095 15.702 +FAD "H1'2" H H 0 21.480 0.169 15.345 +FAD "H2'" H H 0 20.705 -1.452 16.929 +FAD "HO2'" H H 0 19.029 -0.034 18.222 +FAD "H3'" H H 0 21.118 1.116 18.145 +FAD "HO3'" H H 0 23.179 -0.185 18.222 +FAD "H4'" H H 0 21.600 -1.422 19.381 +FAD "HO4'" H H 0 19.930 -0.056 20.740 +FAD "H5'1" H H 0 21.854 1.142 20.606 +FAD "H5'2" H H 0 23.095 0.252 20.176 +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +FAD PA P(OC)(OP)(O)2 +FAD O1A O(PO3) +FAD O2A O(PO3) +FAD O5B O(CC[5]HH)(PO3) +FAD C5B C(C[5]C[5]O[5]H)(OP)(H)2 +FAD C4B C[5](C[5]C[5]HO)(O[5]C[5])(CHHO)(H){1|N<3>,1|O<2>,2|H<1>} +FAD O4B O[5](C[5]N[5a]C[5]H)(C[5]C[5]CH){2|C<3>,2|H<1>,2|O<2>} +FAD C3B C[5](C[5]C[5]HO)(C[5]O[5]CH)(OH)(H){1|H<1>,1|N<3>} +FAD O3B O(C[5]C[5]2H)(H) +FAD C2B C[5](C[5]N[5a]O[5]H)(C[5]C[5]HO)(OH)(H){1|C<4>,1|H<1>,2|C<3>} +FAD O2B O(C[5]C[5]2H)(H) +FAD C1B C[5](N[5a]C[5a,6a]C[5a])(C[5]C[5]HO)(O[5]C[5])(H){1|C<3>,1|C<4>,1|O<2>,2|N<2>,3|H<1>} +FAD N9A N[5a](C[5a,6a]C[5a,6a]N[6a])(C[5]C[5]O[5]H)(C[5a]N[5a]H){1|H<1>,1|O<2>,2|C<3>,2|C<4>} +FAD C8A C[5a](N[5a]C[5a,6a]C[5])(N[5a]C[5a,6a])(H){1|C<3>,1|C<4>,1|H<1>,1|N<2>,1|O<2>} +FAD N7A N[5a](C[5a,6a]C[5a,6a]C[6a])(C[5a]N[5a]H){1|C<4>,1|N<3>,2|N<2>} +FAD C5A C[5a,6a](C[5a,6a]N[5a]N[6a])(C[6a]N[6a]N)(N[5a]C[5a]){1|C<3>,1|C<4>,1|H<1>} +FAD C6A C[6a](C[5a,6a]C[5a,6a]N[5a])(N[6a]C[6a])(NHH){1|C<3>,1|H<1>,1|N<2>,1|N<3>} +FAD N6A N(C[6a]C[5a,6a]N[6a])(H)2 +FAD N1A N[6a](C[6a]C[5a,6a]N)(C[6a]N[6a]H){1|C<3>,1|N<2>} +FAD C2A C[6a](N[6a]C[5a,6a])(N[6a]C[6a])(H){1|C<3>,2|N<3>} +FAD N3A N[6a](C[5a,6a]C[5a,6a]N[5a])(C[6a]N[6a]H){1|C<4>,1|N<2>,2|C<3>} +FAD C4A C[5a,6a](C[5a,6a]C[6a]N[5a])(N[5a]C[5a]C[5])(N[6a]C[6a]){1|C<4>,1|N<2>,1|N<3>,1|O<2>,3|H<1>} +FAD N1 N[6a](C[6a,6a]C[6a,6a]N[6a])(C[6a]N[6a]O){1|C<4>,1|H<1>,1|N<2>,2|C<3>} +FAD C2 C[6a](N[6a]C[6a,6a])(N[6a]C[6a]H)(O){1|C<3>,1|N<3>,1|O<1>} +FAD O2 O(C[6a]N[6a]2) +FAD N3 N[6a](C[6a]C[6a,6a]O)(C[6a]N[6a]O)(H){1|C<3>,1|N<2>} +FAD C4 C[6a](C[6a,6a]C[6a,6a]N[6a])(N[6a]C[6a]H)(O){1|C<3>,1|N<2>,1|N<3>,1|O<1>} +FAD O4 O(C[6a]C[6a,6a]N[6a]) +FAD C4X C[6a,6a](C[6a,6a]N[6a]2)(N[6a]C[6a,6a])(C[6a]N[6a]O){1|C<4>,1|H<1>,3|C<3>} +FAD N5 N[6a](C[6a,6a]C[6a,6a]C[6a])2{1|H<1>,1|N<2>,1|O<1>,2|C<3>,2|N<3>} +FAD C5X C[6a,6a](C[6a,6a]C[6a]N[6a])(N[6a]C[6a,6a])(C[6a]C[6a]H){1|H<1>,2|C<4>,3|C<3>} +FAD C6 C[6a](C[6a,6a]C[6a,6a]N[6a])(C[6a]C[6a]C)(H){1|C<4>,1|N<3>,2|C<3>} +FAD C7 C[6a](C[6a]C[6a,6a]H)(C[6a]C[6a]C)(CH3){1|C<3>,1|H<1>,1|N<2>} +FAD C7M C(C[6a]C[6a]2)(H)3 +FAD C8 C[6a](C[6a]C[6a,6a]H)(C[6a]C[6a]C)(CH3){1|C<3>,1|H<1>,1|N<3>} +FAD C8M C(C[6a]C[6a]2)(H)3 +FAD C9 C[6a](C[6a,6a]C[6a,6a]N[6a])(C[6a]C[6a]C)(H){1|N<2>,2|C<3>,2|C<4>} +FAD C9A C[6a,6a](C[6a,6a]C[6a]N[6a])(N[6a]C[6a,6a]C)(C[6a]C[6a]H){1|C<4>,1|H<1>,1|N<2>,2|C<3>} +FAD N10 N[6a](C[6a,6a]C[6a,6a]C[6a])(C[6a,6a]C[6a,6a]N[6a])(CCHH){1|H<1>,1|N<2>,4|C<3>} +FAD C10 C[6a,6a](C[6a,6a]C[6a]N[6a])(N[6a]C[6a,6a]C)(N[6a]C[6a]){1|N<3>,2|C<3>,2|O<1>} +FAD "C1'" C(N[6a]C[6a,6a]2)(CCHO)(H)2 +FAD "C2'" C(CN[6a]HH)(CCHO)(OH)(H) +FAD "O2'" O(CCCH)(H) +FAD "C3'" C(CCHO)2(OH)(H) +FAD "O3'" O(CCCH)(H) +FAD "C4'" C(CCHO)(CHHO)(OH)(H) +FAD "O4'" O(CCCH)(H) +FAD "C5'" C(CCHO)(OP)(H)2 +FAD "O5'" O(CCHH)(PO3) +FAD P P(OC)(OP)(O)2 +FAD O1P O(PO3) +FAD O2P O(PO3) +FAD O3P O(PO3)2 +FAD H51A H(CC[5]HO) +FAD H52A H(CC[5]HO) +FAD H4B H(C[5]C[5]O[5]C) +FAD H3B H(C[5]C[5]2O) +FAD HO3A H(OC[5]) +FAD H2B H(C[5]C[5]2O) +FAD HO2A H(OC[5]) +FAD H1B H(C[5]N[5a]C[5]O[5]) +FAD H8A H(C[5a]N[5a]2) +FAD H61A H(NC[6a]H) +FAD H62A H(NC[6a]H) +FAD H2A H(C[6a]N[6a]2) +FAD HN3 H(N[6a]C[6a]2) +FAD H6 H(C[6a]C[6a,6a]C[6a]) +FAD HM71 H(CC[6a]HH) +FAD HM72 H(CC[6a]HH) +FAD HM73 H(CC[6a]HH) +FAD HM81 H(CC[6a]HH) +FAD HM82 H(CC[6a]HH) +FAD HM83 H(CC[6a]HH) +FAD H9 H(C[6a]C[6a,6a]C[6a]) +FAD "H1'1" H(CN[6a]CH) +FAD "H1'2" H(CN[6a]CH) +FAD "H2'" H(CCCO) +FAD "HO2'" H(OC) +FAD "H3'" H(CCCO) +FAD "HO3'" H(OC) +FAD "H4'" H(CCCO) +FAD "HO4'" H(OC) +FAD "H5'1" H(CCHO) +FAD "H5'2" H(CCHO) +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 +FAD PA O1A DOUBLE n 1.485 0.0100 1.485 0.0100 +FAD PA O2A SINGLE n 1.485 0.0100 1.485 0.0100 +FAD PA O5B SINGLE n 1.598 0.0100 1.598 0.0100 +FAD PA O3P SINGLE n 1.600 0.0185 1.600 0.0185 +FAD O5B C5B SINGLE n 1.445 0.0200 1.445 0.0200 +FAD C5B C4B SINGLE n 1.509 0.0100 1.509 0.0100 +FAD C4B O4B SINGLE n 1.444 0.0100 1.444 0.0100 +FAD C4B C3B SINGLE n 1.532 0.0100 1.532 0.0100 +FAD O4B C1B SINGLE n 1.423 0.0100 1.423 0.0100 +FAD C3B O3B SINGLE n 1.422 0.0100 1.422 0.0100 +FAD C3B C2B SINGLE n 1.532 0.0103 1.532 0.0103 +FAD C2B O2B SINGLE n 1.412 0.0100 1.412 0.0100 +FAD C2B C1B SINGLE n 1.528 0.0100 1.528 0.0100 +FAD C1B N9A SINGLE n 1.462 0.0102 1.462 0.0102 +FAD N9A C8A SINGLE y 1.371 0.0100 1.371 0.0100 +FAD N9A C4A SINGLE y 1.374 0.0101 1.374 0.0101 +FAD C8A N7A DOUBLE y 1.311 0.0100 1.311 0.0100 +FAD N7A C5A SINGLE y 1.388 0.0100 1.388 0.0100 +FAD C5A C6A SINGLE y 1.407 0.0100 1.407 0.0100 +FAD C5A C4A DOUBLE y 1.382 0.0100 1.382 0.0100 +FAD C6A N6A SINGLE n 1.332 0.0107 1.332 0.0107 +FAD C6A N1A DOUBLE y 1.355 0.0106 1.355 0.0106 +FAD N1A C2A SINGLE y 1.338 0.0100 1.338 0.0100 +FAD C2A N3A DOUBLE y 1.329 0.0100 1.329 0.0100 +FAD N3A C4A SINGLE y 1.344 0.0100 1.344 0.0100 +FAD N1 C2 SINGLE y 1.369 0.0100 1.369 0.0100 +FAD N1 C10 DOUBLE y 1.317 0.0100 1.317 0.0100 +FAD C2 O2 DOUBLE n 1.235 0.0100 1.235 0.0100 +FAD C2 N3 SINGLE y 1.393 0.0104 1.393 0.0104 +FAD N3 C4 SINGLE y 1.377 0.0130 1.377 0.0130 +FAD C4 O4 DOUBLE n 1.218 0.0100 1.218 0.0100 +FAD C4 C4X SINGLE y 1.398 0.0190 1.398 0.0190 +FAD C4X N5 DOUBLE y 1.308 0.0122 1.308 0.0122 +FAD C4X C10 SINGLE y 1.443 0.0100 1.443 0.0100 +FAD N5 C5X SINGLE y 1.368 0.0100 1.368 0.0100 +FAD C5X C6 SINGLE y 1.409 0.0100 1.409 0.0100 +FAD C5X C9A DOUBLE y 1.410 0.0100 1.410 0.0100 +FAD C6 C7 DOUBLE y 1.376 0.0100 1.376 0.0100 +FAD C7 C7M SINGLE n 1.507 0.0100 1.507 0.0100 +FAD C7 C8 SINGLE y 1.417 0.0165 1.417 0.0165 +FAD C8 C8M SINGLE n 1.504 0.0100 1.504 0.0100 +FAD C8 C9 DOUBLE y 1.379 0.0100 1.379 0.0100 +FAD C9 C9A SINGLE y 1.403 0.0100 1.403 0.0100 +FAD C9A N10 SINGLE y 1.392 0.0100 1.392 0.0100 +FAD N10 C10 SINGLE y 1.385 0.0119 1.385 0.0119 +FAD N10 "C1'" SINGLE n 1.475 0.0100 1.475 0.0100 +FAD "C1'" "C2'" SINGLE n 1.518 0.0148 1.518 0.0148 +FAD "C2'" "O2'" SINGLE n 1.429 0.0132 1.429 0.0132 +FAD "C2'" "C3'" SINGLE n 1.529 0.0130 1.529 0.0130 +FAD "C3'" "O3'" SINGLE n 1.426 0.0100 1.426 0.0100 +FAD "C3'" "C4'" SINGLE n 1.528 0.0126 1.528 0.0126 +FAD "C4'" "O4'" SINGLE n 1.429 0.0111 1.429 0.0111 +FAD "C4'" "C5'" SINGLE n 1.518 0.0135 1.518 0.0135 +FAD "C5'" "O5'" SINGLE n 1.445 0.0200 1.445 0.0200 +FAD "O5'" P SINGLE n 1.592 0.0137 1.592 0.0137 +FAD P O1P DOUBLE n 1.485 0.0100 1.485 0.0100 +FAD P O2P SINGLE n 1.485 0.0100 1.485 0.0100 +FAD P O3P SINGLE n 1.600 0.0185 1.600 0.0185 +FAD C5B H51A SINGLE n 1.089 0.0100 0.991 0.0200 +FAD C5B H52A SINGLE n 1.089 0.0100 0.991 0.0200 +FAD C4B H4B SINGLE n 1.089 0.0100 0.990 0.0200 +FAD C3B H3B SINGLE n 1.089 0.0100 0.991 0.0200 +FAD O3B HO3A SINGLE n 0.970 0.0120 0.839 0.0200 +FAD C2B H2B SINGLE n 1.089 0.0100 0.991 0.0200 +FAD O2B HO2A SINGLE n 0.970 0.0120 0.839 0.0200 +FAD C1B H1B SINGLE n 1.089 0.0100 1.016 0.0200 +FAD C8A H8A SINGLE n 1.082 0.0130 0.942 0.0168 +FAD N6A H61A SINGLE n 1.016 0.0100 0.880 0.0200 +FAD N6A H62A SINGLE n 1.016 0.0100 0.880 0.0200 +FAD C2A H2A SINGLE n 1.082 0.0130 0.946 0.0200 +FAD N3 HN3 SINGLE n 1.016 0.0100 0.880 0.0100 +FAD C6 H6 SINGLE n 1.082 0.0130 0.952 0.0100 +FAD C7M HM71 SINGLE n 1.089 0.0100 0.972 0.0144 +FAD C7M HM72 SINGLE n 1.089 0.0100 0.972 0.0144 +FAD C7M HM73 SINGLE n 1.089 0.0100 0.972 0.0144 +FAD C8M HM81 SINGLE n 1.089 0.0100 0.972 0.0144 +FAD C8M HM82 SINGLE n 1.089 0.0100 0.972 0.0144 +FAD C8M HM83 SINGLE n 1.089 0.0100 0.972 0.0144 +FAD C9 H9 SINGLE n 1.082 0.0130 0.954 0.0100 +FAD "C1'" "H1'1" SINGLE n 1.089 0.0100 0.980 0.0162 +FAD "C1'" "H1'2" SINGLE n 1.089 0.0100 0.980 0.0162 +FAD "C2'" "H2'" SINGLE n 1.089 0.0100 1.000 0.0200 +FAD "O2'" "HO2'" SINGLE n 0.970 0.0120 0.864 0.0200 +FAD "C3'" "H3'" SINGLE n 1.089 0.0100 0.994 0.0118 +FAD "O3'" "HO3'" SINGLE n 0.970 0.0120 0.864 0.0200 +FAD "C4'" "H4'" SINGLE n 1.089 0.0100 0.991 0.0117 +FAD "O4'" "HO4'" SINGLE n 0.970 0.0120 0.864 0.0200 +FAD "C5'" "H5'1" SINGLE n 1.089 0.0100 0.978 0.0200 +FAD "C5'" "H5'2" SINGLE n 1.089 0.0100 0.978 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 +FAD O1A PA O2A 118.805 3.00 +FAD O1A PA O5B 109.340 2.31 +FAD O1A PA O3P 109.053 3.00 +FAD O2A PA O5B 109.340 2.31 +FAD O2A PA O3P 109.053 3.00 +FAD O5B PA O3P 100.137 3.00 +FAD PA O5B C5B 116.362 1.50 +FAD O5B C5B C4B 109.454 1.61 +FAD O5B C5B H51A 109.882 1.50 +FAD O5B C5B H52A 109.882 1.50 +FAD C4B C5B H51A 109.589 1.50 +FAD C4B C5B H52A 109.589 1.50 +FAD H51A C5B H52A 108.471 1.50 +FAD C5B C4B O4B 109.154 1.50 +FAD C5B C4B C3B 115.288 1.50 +FAD C5B C4B H4B 108.351 1.59 +FAD O4B C4B C3B 105.318 1.50 +FAD O4B C4B H4B 109.120 1.50 +FAD C3B C4B H4B 109.322 2.54 +FAD C4B O4B C1B 109.502 2.85 +FAD C4B C3B O3B 110.713 3.00 +FAD C4B C3B C2B 102.593 1.50 +FAD C4B C3B H3B 110.577 3.00 +FAD O3B C3B C2B 111.671 3.00 +FAD O3B C3B H3B 110.541 2.08 +FAD C2B C3B H3B 110.454 1.85 +FAD C3B O3B HO3A 109.389 3.00 +FAD C3B C2B O2B 112.677 3.00 +FAD C3B C2B C1B 101.406 1.50 +FAD C3B C2B H2B 110.788 1.91 +FAD O2B C2B C1B 110.814 3.00 +FAD O2B C2B H2B 110.904 1.50 +FAD C1B C2B H2B 110.342 1.91 +FAD C2B O2B HO2A 109.217 3.00 +FAD O4B C1B C2B 106.114 1.65 +FAD O4B C1B N9A 108.577 1.50 +FAD O4B C1B H1B 109.833 2.53 +FAD C2B C1B N9A 113.380 2.77 +FAD C2B C1B H1B 109.222 1.50 +FAD N9A C1B H1B 109.411 1.50 +FAD C1B N9A C8A 127.072 3.00 +FAD C1B N9A C4A 126.969 2.94 +FAD C8A N9A C4A 105.958 1.50 +FAD N9A C8A N7A 113.692 1.50 +FAD N9A C8A H8A 122.949 1.50 +FAD N7A C8A H8A 123.359 1.50 +FAD C8A N7A C5A 103.906 1.50 +FAD N7A C5A C6A 131.998 1.50 +FAD N7A C5A C4A 110.646 1.50 +FAD C6A C5A C4A 117.356 1.50 +FAD C5A C6A N6A 123.773 1.50 +FAD C5A C6A N1A 117.375 1.50 +FAD N6A C6A N1A 118.852 1.50 +FAD C6A N6A H61A 119.818 3.00 +FAD C6A N6A H62A 119.818 3.00 +FAD H61A N6A H62A 120.363 3.00 +FAD C6A N1A C2A 118.603 1.50 +FAD N1A C2A N3A 129.210 1.50 +FAD N1A C2A H2A 115.363 1.50 +FAD N3A C2A H2A 115.427 1.50 +FAD C2A N3A C4A 111.101 1.50 +FAD N9A C4A C5A 105.797 1.50 +FAD N9A C4A N3A 127.848 1.50 +FAD C5A C4A N3A 126.355 1.50 +FAD C2 N1 C10 118.461 1.50 +FAD N1 C2 O2 121.468 1.50 +FAD N1 C2 N3 119.897 1.50 +FAD O2 C2 N3 118.636 1.50 +FAD C2 N3 C4 126.347 1.50 +FAD C2 N3 HN3 117.238 1.50 +FAD C4 N3 HN3 116.415 2.90 +FAD N3 C4 O4 122.539 1.50 +FAD N3 C4 C4X 112.794 1.50 +FAD O4 C4 C4X 124.668 1.50 +FAD C4 C4X N5 117.421 1.50 +FAD C4 C4X C10 117.741 1.50 +FAD N5 C4X C10 124.838 1.50 +FAD C4X N5 C5X 117.454 1.50 +FAD N5 C5X C6 118.145 1.50 +FAD N5 C5X C9A 122.298 1.50 +FAD C6 C5X C9A 119.556 1.50 +FAD C5X C6 C7 121.774 1.50 +FAD C5X C6 H6 118.910 1.63 +FAD C7 C6 H6 119.325 1.50 +FAD C6 C7 C7M 119.966 1.50 +FAD C6 C7 C8 119.488 1.50 +FAD C7M C7 C8 120.546 1.50 +FAD C7 C7M HM71 109.566 1.50 +FAD C7 C7M HM72 109.566 1.50 +FAD C7 C7M HM73 109.566 1.50 +FAD HM71 C7M HM72 109.334 1.91 +FAD HM71 C7M HM73 109.334 1.91 +FAD HM72 C7M HM73 109.334 1.91 +FAD C7 C8 C8M 120.546 1.50 +FAD C7 C8 C9 119.488 1.50 +FAD C8M C8 C9 119.966 1.50 +FAD C8 C8M HM81 109.566 1.50 +FAD C8 C8M HM82 109.566 1.50 +FAD C8 C8M HM83 109.566 1.50 +FAD HM81 C8M HM82 109.334 1.91 +FAD HM81 C8M HM83 109.334 1.91 +FAD HM82 C8M HM83 109.334 1.91 +FAD C8 C9 C9A 120.779 1.50 +FAD C8 C9 H9 119.551 1.50 +FAD C9A C9 H9 119.670 1.50 +FAD C5X C9A C9 118.907 1.50 +FAD C5X C9A N10 118.199 1.50 +FAD C9 C9A N10 122.894 1.50 +FAD C9A N10 C10 120.671 1.50 +FAD C9A N10 "C1'" 120.592 1.50 +FAD C10 N10 "C1'" 118.737 1.50 +FAD N1 C10 C4X 124.761 1.50 +FAD N1 C10 N10 118.699 1.50 +FAD C4X C10 N10 116.541 1.50 +FAD N10 "C1'" "C2'" 112.123 2.65 +FAD N10 "C1'" "H1'1" 108.981 1.50 +FAD N10 "C1'" "H1'2" 108.981 1.50 +FAD "C2'" "C1'" "H1'1" 109.180 1.50 +FAD "C2'" "C1'" "H1'2" 109.180 1.50 +FAD "H1'1" "C1'" "H1'2" 107.924 2.79 +FAD "C1'" "C2'" "O2'" 109.718 2.99 +FAD "C1'" "C2'" "C3'" 111.239 3.00 +FAD "C1'" "C2'" "H2'" 108.435 1.50 +FAD "O2'" "C2'" "C3'" 109.426 3.00 +FAD "O2'" "C2'" "H2'" 108.176 3.00 +FAD "C3'" "C2'" "H2'" 108.439 2.58 +FAD "C2'" "O2'" "HO2'" 109.126 3.00 +FAD "C2'" "C3'" "O3'" 109.426 3.00 +FAD "C2'" "C3'" "C4'" 113.599 3.00 +FAD "C2'" "C3'" "H3'" 108.439 2.58 +FAD "O3'" "C3'" "C4'" 109.190 2.87 +FAD "O3'" "C3'" "H3'" 108.315 1.83 +FAD "C4'" "C3'" "H3'" 108.171 1.50 +FAD "C3'" "O3'" "HO3'" 108.910 3.00 +FAD "C3'" "C4'" "O4'" 109.920 2.94 +FAD "C3'" "C4'" "C5'" 112.050 2.78 +FAD "C3'" "C4'" "H4'" 108.859 1.50 +FAD "O4'" "C4'" "C5'" 109.162 3.00 +FAD "O4'" "C4'" "H4'" 108.709 1.50 +FAD "C5'" "C4'" "H4'" 108.615 1.79 +FAD "C4'" "O4'" "HO4'" 109.757 3.00 +FAD "C4'" "C5'" "O5'" 109.303 3.00 +FAD "C4'" "C5'" "H5'1" 109.594 1.50 +FAD "C4'" "C5'" "H5'2" 109.594 1.50 +FAD "O5'" "C5'" "H5'1" 108.621 3.00 +FAD "O5'" "C5'" "H5'2" 108.621 3.00 +FAD "H5'1" "C5'" "H5'2" 108.315 1.66 +FAD "C5'" "O5'" P 119.008 2.40 +FAD "O5'" P O1P 108.662 3.00 +FAD "O5'" P O2P 108.662 3.00 +FAD "O5'" P O3P 100.260 3.00 +FAD O1P P O2P 118.805 3.00 +FAD O1P P O3P 109.053 3.00 +FAD O2P P O3P 109.053 3.00 +FAD PA O3P P 133.108 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 +FAD sp3_sp3_27 C5B O5B PA O1A 60.000 10.0 3 +FAD sp3_sp3_30 P O3P PA O1A 60.000 10.0 3 +FAD sp2_sp3_1 C8A N9A C1B O4B 150.000 10.0 6 +FAD const_48 N7A C8A N9A C1B 180.000 0.0 2 +FAD const_80 C5A C4A N9A C1B 180.000 0.0 2 +FAD const_51 N9A C8A N7A C5A 0.000 0.0 2 +FAD const_54 C6A C5A N7A C8A 180.000 0.0 2 +FAD const_38 N7A C5A C6A N6A 0.000 0.0 2 +FAD const_55 N9A C4A C5A N7A 0.000 0.0 2 +FAD sp2_sp2_83 C5A C6A N6A H61A 180.000 20 2 +FAD const_40 N6A C6A N1A C2A 180.000 0.0 2 +FAD const_41 N3A C2A N1A C6A 0.000 0.0 2 +FAD const_43 N1A C2A N3A C4A 0.000 0.0 2 +FAD const_46 N9A C4A N3A C2A 180.000 0.0 2 +FAD const_sp2_sp2_2 O2 C2 N1 C10 180.000 0.0 2 +FAD const_87 C4X C10 N1 C2 0.000 0.0 2 +FAD const_sp2_sp2_5 O2 C2 N3 C4 180.000 0.0 2 +FAD const_sp2_sp2_9 O4 C4 N3 C2 180.000 0.0 2 +FAD const_14 O4 C4 C4X N5 0.000 0.0 2 +FAD const_20 C4 C4X N5 C5X 180.000 0.0 2 +FAD const_15 N1 C10 C4X C4 0.000 0.0 2 +FAD const_22 C6 C5X N5 C4X 180.000 0.0 2 +FAD const_61 N5 C5X C6 C7 180.000 0.0 2 +FAD const_24 N5 C5X C9A C9 180.000 0.0 2 +FAD const_64 C5X C6 C7 C7M 180.000 0.0 2 +FAD sp2_sp3_7 C6 C7 C7M HM71 150.000 10.0 6 +FAD const_70 C7M C7 C8 C8M 0.000 0.0 2 +FAD sp2_sp3_13 C7 C8 C8M HM81 150.000 10.0 6 +FAD const_73 C8M C8 C9 C9A 180.000 0.0 2 +FAD const_75 C8 C9 C9A C5X 0.000 0.0 2 +FAD const_28 C5X C9A N10 "C1'" 180.000 0.0 2 +FAD const_34 N1 C10 N10 "C1'" 0.000 0.0 2 +FAD sp2_sp3_20 C9A N10 "C1'" "C2'" -90.000 10.0 6 +FAD sp3_sp3_31 C4B C5B O5B PA 180.000 10.0 3 +FAD sp3_sp3_58 N10 "C1'" "C2'" "O2'" 180.000 10.0 3 +FAD sp3_sp3_67 "C1'" "C2'" "O2'" "HO2'" 180.000 10.0 3 +FAD sp3_sp3_70 "C1'" "C2'" "C3'" "O3'" 180.000 10.0 3 +FAD sp3_sp3_79 "C2'" "C3'" "O3'" "HO3'" 180.000 10.0 3 +FAD sp3_sp3_82 "C2'" "C3'" "C4'" "O4'" 180.000 10.0 3 +FAD sp3_sp3_91 "C3'" "C4'" "O4'" "HO4'" 180.000 10.0 3 +FAD sp3_sp3_94 "C3'" "C4'" "C5'" "O5'" 180.000 10.0 3 +FAD sp3_sp3_103 "C4'" "C5'" "O5'" P 180.000 10.0 3 +FAD sp3_sp3_108 "C5'" "O5'" P O1P 60.000 10.0 3 +FAD sp3_sp3_110 PA O3P P "O5'" -60.000 10.0 3 +FAD sp3_sp3_34 O4B C4B C5B O5B 180.000 10.0 3 +FAD sp3_sp3_2 C5B C4B O4B C1B -60.000 10.0 3 +FAD sp3_sp3_47 O3B C3B C4B C5B 180.000 10.0 3 +FAD sp3_sp3_4 C2B C1B O4B C4B -60.000 10.0 3 +FAD sp3_sp3_52 C4B C3B O3B HO3A 180.000 10.0 3 +FAD sp3_sp3_20 O2B C2B C3B O3B -60.000 10.0 3 +FAD sp3_sp3_55 C3B C2B O2B HO2A 180.000 10.0 3 +FAD sp3_sp3_8 O4B C1B C2B O2B 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 +FAD chir_1 PA O3P O5B O2A both +FAD chir_2 C4B O4B C3B C5B negative +FAD chir_3 C3B O3B C4B C2B positive +FAD chir_4 C2B O2B C1B C3B negative +FAD chir_5 C1B O4B N9A C2B negative +FAD chir_6 "C2'" "O2'" "C3'" "C1'" positive +FAD chir_7 "C3'" "O3'" "C4'" "C2'" positive +FAD chir_8 "C4'" "O4'" "C3'" "C5'" negative +FAD chir_9 P O3P "O5'" O2P 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 +FAD plan-1 C1B 0.020 +FAD plan-1 C4A 0.020 +FAD plan-1 C5A 0.020 +FAD plan-1 C6A 0.020 +FAD plan-1 C8A 0.020 +FAD plan-1 H8A 0.020 +FAD plan-1 N3A 0.020 +FAD plan-1 N7A 0.020 +FAD plan-1 N9A 0.020 +FAD plan-2 C2A 0.020 +FAD plan-2 C4A 0.020 +FAD plan-2 C5A 0.020 +FAD plan-2 C6A 0.020 +FAD plan-2 H2A 0.020 +FAD plan-2 N1A 0.020 +FAD plan-2 N3A 0.020 +FAD plan-2 N6A 0.020 +FAD plan-2 N7A 0.020 +FAD plan-2 N9A 0.020 +FAD plan-3 C10 0.020 +FAD plan-3 C2 0.020 +FAD plan-3 C4 0.020 +FAD plan-3 C4X 0.020 +FAD plan-3 HN3 0.020 +FAD plan-3 N1 0.020 +FAD plan-3 N10 0.020 +FAD plan-3 N3 0.020 +FAD plan-3 N5 0.020 +FAD plan-3 O2 0.020 +FAD plan-3 O4 0.020 +FAD plan-4 "C1'" 0.020 +FAD plan-4 C10 0.020 +FAD plan-4 C4 0.020 +FAD plan-4 C4X 0.020 +FAD plan-4 C5X 0.020 +FAD plan-4 C6 0.020 +FAD plan-4 C9 0.020 +FAD plan-4 C9A 0.020 +FAD plan-4 N1 0.020 +FAD plan-4 N10 0.020 +FAD plan-4 N5 0.020 +FAD plan-5 C5X 0.020 +FAD plan-5 C6 0.020 +FAD plan-5 C7 0.020 +FAD plan-5 C7M 0.020 +FAD plan-5 C8 0.020 +FAD plan-5 C8M 0.020 +FAD plan-5 C9 0.020 +FAD plan-5 C9A 0.020 +FAD plan-5 H6 0.020 +FAD plan-5 H9 0.020 +FAD plan-5 N10 0.020 +FAD plan-5 N5 0.020 +FAD plan-6 C6A 0.020 +FAD plan-6 H61A 0.020 +FAD plan-6 H62A 0.020 +FAD plan-6 N6A 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 +FAD SMILES ACDLabs 10.04 "O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C" +FAD SMILES_CANONICAL CACTVS 3.341 "Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C" +FAD SMILES CACTVS 3.341 "Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C" +FAD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O" +FAD SMILES "OpenEye OEToolkits" 1.5.0 "Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O" +FAD InChI InChI 1.03 "InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1" +FAD InChIKey InChI 1.03 VWWQXMAJTJZDQX-UYBVJOGSSA-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 +FAD acedrg 275 "dictionary generator" +FAD acedrg_database 12 "data source" +FAD rdkit 2019.09.1 "Chemoinformatics tool" +FAD refmac5 5.8.0405 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/FMN.cif b/image_analysis/structure_refinement/monomers/FMN.cif new file mode 100644 index 000000000..220ed4327 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/FMN.cif @@ -0,0 +1,337 @@ +# +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 +FMN FMN "FLAVIN MONONUCLEOTIDE" NON-POLYMER 50 31 . +# +data_comp_FMN +# +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 +FMN N1 N NRD6 0 33.067 6.557 14.888 +FMN C2 C CR6 0 32.180 5.530 15.005 +FMN O2 O O 0 32.567 4.383 15.250 +FMN N3 N NR6 0 30.830 5.721 14.860 +FMN C4 C CR6 0 30.302 6.963 14.585 +FMN O4 O O 0 29.090 7.087 14.463 +FMN C4A C CR66 0 31.209 8.062 14.453 +FMN N5 N NRD6 0 30.723 9.250 14.191 +FMN C5A C CR66 0 31.604 10.293 14.068 +FMN C6 C CR16 0 31.061 11.563 13.788 +FMN C7 C CR6 0 31.851 12.681 13.648 +FMN C7M C CH3 0 31.199 14.009 13.347 +FMN C8 C CR6 0 33.272 12.544 13.787 +FMN C8M C CH3 0 34.190 13.733 13.641 +FMN C9 C CR16 0 33.814 11.292 14.063 +FMN C9A C CR66 0 33.007 10.140 14.210 +FMN N10 N NR6 0 33.500 8.849 14.490 +FMN C10 C CR66 0 32.615 7.770 14.622 +FMN "C1'" C CH2 0 34.953 8.600 14.655 +FMN "C2'" C CH1 0 35.393 8.656 16.119 +FMN "O2'" O OH1 0 34.975 9.887 16.712 +FMN "C3'" C CH1 0 36.908 8.505 16.320 +FMN "O3'" O OH1 0 37.577 9.611 15.699 +FMN "C4'" C CH1 0 37.505 7.182 15.823 +FMN "O4'" O OH1 0 36.840 6.086 16.455 +FMN "C5'" C CH2 0 38.990 7.063 16.085 +FMN "O5'" O O2 0 39.268 7.119 17.512 +FMN P P P 0 40.802 7.026 18.006 +FMN O1P O O 0 40.755 7.133 19.519 +FMN O2P O OP -1 41.519 8.194 17.355 +FMN O3P O OP -1 41.310 5.680 17.526 +FMN HN3 H H 0 30.294 5.027 14.946 +FMN H6 H H 0 30.115 11.646 13.696 +FMN HM71 H H 0 31.765 14.737 13.647 +FMN HM72 H H 0 30.346 14.059 13.808 +FMN HM73 H H 0 31.051 14.088 12.391 +FMN HM81 H H 0 35.116 13.445 13.677 +FMN HM82 H H 0 34.022 14.362 14.361 +FMN HM83 H H 0 34.023 14.169 12.789 +FMN H9 H H 0 34.761 11.223 14.156 +FMN "H1'1" H H 0 35.460 9.245 14.138 +FMN "H1'2" H H 0 35.168 7.720 14.292 +FMN "H2'" H H 0 34.941 7.923 16.609 +FMN "HO2'" H H 0 35.387 10.537 16.354 +FMN "H3'" H H 0 37.078 8.565 17.295 +FMN "HO3'" H H 0 37.689 9.467 14.871 +FMN "H4'" H H 0 37.357 7.113 14.833 +FMN "HO4'" H H 0 36.918 6.118 17.299 +FMN "H5'1" H H 0 39.467 7.788 15.630 +FMN "H5'2" H H 0 39.317 6.211 15.727 +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 +FMN N1 C2 SINGLE y 1.349 0.0188 1.349 0.0188 +FMN N1 C10 DOUBLE y 1.316 0.0100 1.316 0.0100 +FMN C2 O2 DOUBLE n 1.233 0.0164 1.233 0.0164 +FMN C2 N3 SINGLE y 1.354 0.0200 1.354 0.0200 +FMN N3 C4 SINGLE y 1.372 0.0117 1.372 0.0117 +FMN C4 O4 DOUBLE n 1.223 0.0119 1.223 0.0119 +FMN C4 C4A SINGLE y 1.412 0.0200 1.412 0.0200 +FMN C4A N5 DOUBLE y 1.309 0.0135 1.309 0.0135 +FMN C4A C10 SINGLE y 1.442 0.0100 1.442 0.0100 +FMN N5 C5A SINGLE y 1.369 0.0100 1.369 0.0100 +FMN C5A C6 SINGLE y 1.407 0.0100 1.407 0.0100 +FMN C5A C9A DOUBLE y 1.409 0.0100 1.409 0.0100 +FMN C6 C7 DOUBLE y 1.375 0.0100 1.375 0.0100 +FMN C7 C7M SINGLE n 1.507 0.0100 1.507 0.0100 +FMN C7 C8 SINGLE y 1.415 0.0183 1.415 0.0183 +FMN C8 C8M SINGLE n 1.507 0.0100 1.507 0.0100 +FMN C8 C9 DOUBLE y 1.378 0.0152 1.378 0.0152 +FMN C9 C9A SINGLE y 1.404 0.0100 1.404 0.0100 +FMN C9A N10 SINGLE y 1.393 0.0100 1.393 0.0100 +FMN N10 C10 SINGLE y 1.383 0.0127 1.383 0.0127 +FMN N10 "C1'" SINGLE n 1.474 0.0100 1.474 0.0100 +FMN "C1'" "C2'" SINGLE n 1.517 0.0189 1.517 0.0189 +FMN "C2'" "O2'" SINGLE n 1.424 0.0199 1.424 0.0199 +FMN "C2'" "C3'" SINGLE n 1.531 0.0100 1.531 0.0100 +FMN "C3'" "O3'" SINGLE n 1.424 0.0199 1.424 0.0199 +FMN "C3'" "C4'" SINGLE n 1.530 0.0100 1.530 0.0100 +FMN "C4'" "O4'" SINGLE n 1.429 0.0100 1.429 0.0100 +FMN "C4'" "C5'" SINGLE n 1.511 0.0100 1.511 0.0100 +FMN "C5'" "O5'" SINGLE n 1.454 0.0165 1.454 0.0165 +FMN "O5'" P SINGLE n 1.614 0.0178 1.614 0.0178 +FMN P O1P DOUBLE n 1.517 0.0192 1.517 0.0192 +FMN P O2P SINGLE n 1.517 0.0192 1.517 0.0192 +FMN P O3P SINGLE n 1.517 0.0192 1.517 0.0192 +FMN N3 HN3 SINGLE n 1.016 0.0100 0.880 0.0200 +FMN C6 H6 SINGLE n 1.082 0.0130 0.954 0.0100 +FMN C7M HM71 SINGLE n 1.089 0.0100 0.971 0.0135 +FMN C7M HM72 SINGLE n 1.089 0.0100 0.971 0.0135 +FMN C7M HM73 SINGLE n 1.089 0.0100 0.971 0.0135 +FMN C8M HM81 SINGLE n 1.089 0.0100 0.971 0.0135 +FMN C8M HM82 SINGLE n 1.089 0.0100 0.971 0.0135 +FMN C8M HM83 SINGLE n 1.089 0.0100 0.971 0.0135 +FMN C9 H9 SINGLE n 1.082 0.0130 0.956 0.0118 +FMN "C1'" "H1'1" SINGLE n 1.089 0.0100 0.978 0.0200 +FMN "C1'" "H1'2" SINGLE n 1.089 0.0100 0.978 0.0200 +FMN "C2'" "H2'" SINGLE n 1.089 0.0100 0.992 0.0184 +FMN "O2'" "HO2'" SINGLE n 0.970 0.0120 0.848 0.0200 +FMN "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0184 +FMN "O3'" "HO3'" SINGLE n 0.970 0.0120 0.848 0.0200 +FMN "C4'" "H4'" SINGLE n 1.089 0.0100 1.004 0.0200 +FMN "O4'" "HO4'" SINGLE n 0.970 0.0120 0.848 0.0200 +FMN "C5'" "H5'1" SINGLE n 1.089 0.0100 0.980 0.0146 +FMN "C5'" "H5'2" SINGLE n 1.089 0.0100 0.980 0.0146 +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 +FMN C2 N1 C10 118.131 1.50 +FMN N1 C2 O2 121.177 1.50 +FMN N1 C2 N3 121.483 2.18 +FMN O2 C2 N3 117.340 1.50 +FMN C2 N3 C4 121.560 1.50 +FMN C2 N3 HN3 118.500 2.31 +FMN C4 N3 HN3 119.939 1.50 +FMN N3 C4 O4 119.688 1.50 +FMN N3 C4 C4A 118.005 1.65 +FMN O4 C4 C4A 122.306 1.50 +FMN C4 C4A N5 118.186 1.50 +FMN C4 C4A C10 116.947 1.50 +FMN N5 C4A C10 124.867 1.50 +FMN C4A N5 C5A 117.421 1.50 +FMN N5 C5A C6 118.199 1.50 +FMN N5 C5A C9A 122.273 1.50 +FMN C6 C5A C9A 119.529 1.50 +FMN C5A C6 C7 121.879 1.50 +FMN C5A C6 H6 118.690 1.50 +FMN C7 C6 H6 119.431 1.50 +FMN C6 C7 C7M 120.045 1.50 +FMN C6 C7 C8 119.399 1.50 +FMN C7M C7 C8 120.556 1.50 +FMN C7 C7M HM71 109.535 1.50 +FMN C7 C7M HM72 109.535 1.50 +FMN C7 C7M HM73 109.535 1.50 +FMN HM71 C7M HM72 109.348 1.50 +FMN HM71 C7M HM73 109.348 1.50 +FMN HM72 C7M HM73 109.348 1.50 +FMN C7 C8 C8M 120.556 1.50 +FMN C7 C8 C9 119.399 1.50 +FMN C8M C8 C9 120.045 1.50 +FMN C8 C8M HM81 109.535 1.50 +FMN C8 C8M HM82 109.535 1.50 +FMN C8 C8M HM83 109.535 1.50 +FMN HM81 C8M HM82 109.348 1.50 +FMN HM81 C8M HM83 109.348 1.50 +FMN HM82 C8M HM83 109.348 1.50 +FMN C8 C9 C9A 120.818 1.51 +FMN C8 C9 H9 119.507 1.50 +FMN C9A C9 H9 119.676 1.64 +FMN C5A C9A C9 118.977 1.50 +FMN C5A C9A N10 118.178 1.50 +FMN C9 C9A N10 122.846 1.50 +FMN C9A N10 C10 120.732 1.50 +FMN C9A N10 "C1'" 119.696 1.50 +FMN C10 N10 "C1'" 119.572 1.50 +FMN N1 C10 C4A 123.873 1.50 +FMN N1 C10 N10 119.597 1.50 +FMN C4A C10 N10 116.530 1.50 +FMN N10 "C1'" "C2'" 112.079 1.50 +FMN N10 "C1'" "H1'1" 108.897 1.50 +FMN N10 "C1'" "H1'2" 108.897 1.50 +FMN "C2'" "C1'" "H1'1" 109.291 1.50 +FMN "C2'" "C1'" "H1'2" 109.291 1.50 +FMN "H1'1" "C1'" "H1'2" 107.893 1.50 +FMN "C1'" "C2'" "O2'" 109.698 2.33 +FMN "C1'" "C2'" "C3'" 110.999 2.33 +FMN "C1'" "C2'" "H2'" 108.757 1.75 +FMN "O2'" "C2'" "C3'" 109.320 2.01 +FMN "O2'" "C2'" "H2'" 108.183 1.96 +FMN "C3'" "C2'" "H2'" 108.450 1.83 +FMN "C2'" "O2'" "HO2'" 109.265 3.00 +FMN "C2'" "C3'" "O3'" 109.320 2.01 +FMN "C2'" "C3'" "C4'" 113.695 2.13 +FMN "C2'" "C3'" "H3'" 108.450 1.83 +FMN "O3'" "C3'" "C4'" 109.164 1.97 +FMN "O3'" "C3'" "H3'" 108.243 1.50 +FMN "C4'" "C3'" "H3'" 108.336 1.50 +FMN "C3'" "O3'" "HO3'" 108.564 3.00 +FMN "C3'" "C4'" "O4'" 109.549 1.85 +FMN "C3'" "C4'" "C5'" 112.503 1.50 +FMN "C3'" "C4'" "H4'" 108.777 1.50 +FMN "O4'" "C4'" "C5'" 109.314 1.96 +FMN "O4'" "C4'" "H4'" 108.591 1.50 +FMN "C5'" "C4'" "H4'" 108.656 1.50 +FMN "C4'" "O4'" "HO4'" 111.202 3.00 +FMN "C4'" "C5'" "O5'" 109.438 2.56 +FMN "C4'" "C5'" "H5'1" 109.582 1.50 +FMN "C4'" "C5'" "H5'2" 109.582 1.50 +FMN "O5'" "C5'" "H5'1" 109.393 1.91 +FMN "O5'" "C5'" "H5'2" 109.393 1.91 +FMN "H5'1" "C5'" "H5'2" 108.319 1.50 +FMN "C5'" "O5'" P 118.671 1.50 +FMN "O5'" P O1P 105.795 2.09 +FMN "O5'" P O2P 105.795 2.09 +FMN "O5'" P O3P 105.795 2.09 +FMN O1P P O2P 112.864 1.69 +FMN O1P P O3P 112.864 1.69 +FMN O2P P O3P 112.864 1.69 +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 +FMN const_sp2_sp2_2 O2 C2 N1 C10 180.000 5.0 2 +FMN const_55 C4A C10 N1 C2 0.000 10.0 2 +FMN sp2_sp3_1 C6 C7 C7M HM71 150.000 10.0 6 +FMN const_46 C7M C7 C8 C8M 0.000 10.0 2 +FMN sp2_sp3_7 C7 C8 C8M HM81 150.000 10.0 6 +FMN const_49 C8M C8 C9 C9A 180.000 10.0 2 +FMN const_51 C8 C9 C9A C5A 0.000 10.0 2 +FMN const_28 C5A C9A N10 "C1'" 180.000 10.0 2 +FMN const_34 N1 C10 N10 "C1'" 0.000 10.0 2 +FMN sp2_sp3_14 C9A N10 "C1'" "C2'" -90.000 10.0 6 +FMN sp3_sp3_1 N10 "C1'" "C2'" "O2'" 180.000 10.0 3 +FMN sp3_sp3_10 "C1'" "C2'" "O2'" "HO2'" 180.000 10.0 3 +FMN sp3_sp3_13 "C1'" "C2'" "C3'" "O3'" 180.000 10.0 3 +FMN const_sp2_sp2_5 O2 C2 N3 C4 180.000 5.0 2 +FMN sp3_sp3_22 "C2'" "C3'" "O3'" "HO3'" 180.000 10.0 3 +FMN sp3_sp3_25 "C2'" "C3'" "C4'" "O4'" 180.000 10.0 3 +FMN sp3_sp3_34 "C3'" "C4'" "O4'" "HO4'" 180.000 10.0 3 +FMN sp3_sp3_37 "C3'" "C4'" "C5'" "O5'" 180.000 10.0 3 +FMN sp3_sp3_46 "C4'" "C5'" "O5'" P 180.000 10.0 3 +FMN sp3_sp3_51 "C5'" "O5'" P O1P 60.000 10.0 3 +FMN const_sp2_sp2_9 O4 C4 N3 C2 180.000 5.0 2 +FMN const_14 O4 C4 C4A N5 0.000 10.0 2 +FMN const_15 N1 C10 C4A C4 0.000 10.0 2 +FMN const_20 C4 C4A N5 C5A 180.000 10.0 2 +FMN const_22 C6 C5A N5 C4A 180.000 10.0 2 +FMN const_24 N5 C5A C9A C9 180.000 10.0 2 +FMN const_37 N5 C5A C6 C7 180.000 10.0 2 +FMN const_40 C5A C6 C7 C7M 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 +FMN chir_1 "C2'" "O2'" "C3'" "C1'" positive +FMN chir_2 "C3'" "O3'" "C4'" "C2'" positive +FMN chir_3 "C4'" "O4'" "C3'" "C5'" negative +FMN chir_4 P "O5'" O2P O3P 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 +FMN plan-1 "C1'" 0.020 +FMN plan-1 C10 0.020 +FMN plan-1 C2 0.020 +FMN plan-1 C4 0.020 +FMN plan-1 C4A 0.020 +FMN plan-1 C5A 0.020 +FMN plan-1 C6 0.020 +FMN plan-1 C9 0.020 +FMN plan-1 C9A 0.020 +FMN plan-1 HN3 0.020 +FMN plan-1 N1 0.020 +FMN plan-1 N10 0.020 +FMN plan-1 N3 0.020 +FMN plan-1 N5 0.020 +FMN plan-1 O2 0.020 +FMN plan-1 O4 0.020 +FMN plan-2 C5A 0.020 +FMN plan-2 C6 0.020 +FMN plan-2 C7 0.020 +FMN plan-2 C7M 0.020 +FMN plan-2 C8 0.020 +FMN plan-2 C8M 0.020 +FMN plan-2 C9 0.020 +FMN plan-2 C9A 0.020 +FMN plan-2 H6 0.020 +FMN plan-2 H9 0.020 +FMN plan-2 N10 0.020 +FMN plan-2 N5 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 +FMN SMILES ACDLabs 12.01 N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)COP(=O)(O)O +FMN InChI InChI 1.03 InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1 +FMN InChIKey InChI 1.03 FVTCRASFADXXNN-SCRDCRAPSA-N +FMN SMILES_CANONICAL CACTVS 3.385 Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C +FMN SMILES CACTVS 3.385 Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C +FMN SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O +FMN SMILES "OpenEye OEToolkits" 1.7.6 Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)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 +FMN acedrg 243 "dictionary generator" +FMN acedrg_database 11 "data source" +FMN rdkit 2017.03.2 "Chemoinformatics tool" +FMN refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/H2U.cif b/image_analysis/structure_refinement/monomers/H2U.cif new file mode 100644 index 000000000..4e8fff729 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/H2U.cif @@ -0,0 +1,267 @@ +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 +H2U H2U "5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE" RNA 34 21 . + +data_comp_H2U +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 +H2U P P P 0 50.726 5.590 34.203 +H2U OP1 O O 0 49.785 6.717 34.586 +H2U OP2 O OP -1 50.408 4.289 34.915 +H2U OP3 O OP -1 50.864 5.422 32.702 +H2U "O5'" O O2 0 52.185 6.036 34.731 +H2U "C5'" C CH2 0 52.783 7.247 34.201 +H2U "C4'" C CH1 0 54.080 7.529 34.920 +H2U "O4'" O O2 0 53.820 7.636 36.343 +H2U "C3'" C CH1 0 55.180 6.469 34.768 +H2U "O3'" O OH1 0 56.455 7.077 34.600 +H2U "C1'" C CH1 0 54.676 6.785 37.073 +H2U "C2'" C CH1 0 55.056 5.687 36.077 +H2U "O2'" O OH1 0 56.271 5.034 36.427 +H2U N1 N NR6 0 53.958 6.335 38.328 +H2U C2 C CR6 0 53.665 7.317 39.260 +H2U O2 O O 0 54.100 8.459 39.144 +H2U N3 N NR16 0 52.842 7.004 40.287 +H2U C4 C CR6 0 52.614 5.723 40.737 +H2U O4 O O 0 51.852 5.514 41.665 +H2U C5 C CH2 0 53.341 4.623 40.030 +H2U C6 C CH2 0 53.582 4.925 38.551 +H2U "H5'" H H 0 52.163 8.008 34.324 +H2U "H5''" H H 0 52.957 7.139 33.234 +H2U "H4'" H H 0 54.420 8.393 34.602 +H2U "H3'" H H 0 54.979 5.876 33.998 +H2U "HO3'" H H 0 57.050 6.470 34.603 +H2U "H1'" H H 0 55.490 7.284 37.333 +H2U "H2'" H H 0 54.331 5.025 35.984 +H2U "HO2'" H H 0 56.337 4.943 37.269 +H2U HN3 H H 0 52.424 7.661 40.692 +H2U H51 H H 0 52.822 3.807 40.107 +H2U H52 H H 0 54.195 4.483 40.469 +H2U H61 H H 0 54.297 4.331 38.228 +H2U H62 H H 0 52.764 4.720 38.043 + +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 +H2U P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192 +H2U P OP2 SINGLE n 1.517 0.0192 1.517 0.0192 +H2U P OP3 SINGLE n 1.517 0.0192 1.517 0.0192 +H2U P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 +H2U "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +H2U "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +H2U "C4'" "O4'" SINGLE n 1.449 0.0100 1.449 0.0100 +H2U "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 +H2U "O4'" "C1'" SINGLE n 1.409 0.0106 1.409 0.0106 +H2U "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +H2U "C3'" "C2'" SINGLE n 1.530 0.0134 1.530 0.0134 +H2U "C1'" "C2'" SINGLE n 1.527 0.0119 1.527 0.0119 +H2U "C1'" N1 SINGLE n 1.489 0.0155 1.489 0.0155 +H2U "C2'" "O2'" SINGLE n 1.420 0.0122 1.420 0.0122 +H2U N1 C2 SINGLE n 1.343 0.0200 1.343 0.0200 +H2U N1 C6 SINGLE n 1.467 0.0100 1.467 0.0100 +H2U C2 O2 DOUBLE n 1.226 0.0110 1.226 0.0110 +H2U C2 N3 SINGLE n 1.343 0.0163 1.343 0.0163 +H2U N3 C4 SINGLE n 1.377 0.0101 1.377 0.0101 +H2U C4 O4 DOUBLE n 1.218 0.0100 1.218 0.0100 +H2U C4 C5 SINGLE n 1.497 0.0100 1.497 0.0100 +H2U C5 C6 SINGLE n 1.525 0.0128 1.525 0.0128 +H2U "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +H2U "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 +H2U "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 +H2U "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +H2U "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +H2U "C1'" "H1'" SINGLE n 1.089 0.0100 0.989 0.0200 +H2U "C2'" "H2'" SINGLE n 1.089 0.0100 0.988 0.0200 +H2U "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 +H2U N3 HN3 SINGLE n 1.016 0.0100 0.876 0.0200 +H2U C5 H51 SINGLE n 1.089 0.0100 0.970 0.0100 +H2U C5 H52 SINGLE n 1.089 0.0100 0.970 0.0100 +H2U C6 H61 SINGLE n 1.089 0.0100 0.985 0.0100 +H2U C6 H62 SINGLE n 1.089 0.0100 0.985 0.0100 + +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 +H2U OP1 P OP2 112.864 1.69 +H2U OP1 P OP3 112.864 1.69 +H2U OP1 P "O5'" 105.808 2.07 +H2U OP2 P OP3 112.864 1.69 +H2U OP2 P "O5'" 105.808 2.07 +H2U OP3 P "O5'" 105.808 2.07 +H2U P "O5'" "C5'" 118.783 1.50 +H2U "O5'" "C5'" "C4'" 109.342 1.50 +H2U "O5'" "C5'" "H5'" 109.845 1.50 +H2U "O5'" "C5'" "H5''" 109.845 1.50 +H2U "C4'" "C5'" "H5'" 109.624 1.50 +H2U "C4'" "C5'" "H5''" 109.624 1.50 +H2U "H5'" "C5'" "H5''" 108.472 1.50 +H2U "C5'" "C4'" "O4'" 109.123 1.50 +H2U "C5'" "C4'" "C3'" 116.008 1.52 +H2U "C5'" "C4'" "H4'" 108.268 1.50 +H2U "O4'" "C4'" "C3'" 105.508 1.50 +H2U "O4'" "C4'" "H4'" 108.642 1.50 +H2U "C3'" "C4'" "H4'" 109.363 1.86 +H2U "C4'" "O4'" "C1'" 109.926 1.50 +H2U "C4'" "C3'" "O3'" 111.281 2.46 +H2U "C4'" "C3'" "C2'" 102.352 1.50 +H2U "C4'" "C3'" "H3'" 110.452 2.54 +H2U "O3'" "C3'" "C2'" 112.463 2.73 +H2U "O3'" "C3'" "H3'" 110.380 1.67 +H2U "C2'" "C3'" "H3'" 110.255 2.04 +H2U "C3'" "O3'" "HO3'" 108.744 3.00 +H2U "O4'" "C1'" "C2'" 106.204 2.50 +H2U "O4'" "C1'" N1 108.858 1.71 +H2U "O4'" "C1'" "H1'" 109.395 1.50 +H2U "C2'" "C1'" N1 112.110 1.66 +H2U "C2'" "C1'" "H1'" 109.914 1.68 +H2U N1 "C1'" "H1'" 108.795 2.24 +H2U "C3'" "C2'" "C1'" 104.443 2.26 +H2U "C3'" "C2'" "O2'" 112.463 2.73 +H2U "C3'" "C2'" "H2'" 110.255 2.04 +H2U "C1'" "C2'" "O2'" 111.164 2.38 +H2U "C1'" "C2'" "H2'" 110.518 1.74 +H2U "O2'" "C2'" "H2'" 110.259 1.63 +H2U "C2'" "O2'" "HO2'" 109.104 3.00 +H2U "C1'" N1 C2 118.428 3.00 +H2U "C1'" N1 C6 119.226 3.00 +H2U C2 N1 C6 122.347 2.69 +H2U N1 C2 O2 121.078 1.61 +H2U N1 C2 N3 117.002 2.84 +H2U O2 C2 N3 121.921 1.50 +H2U C2 N3 C4 123.512 2.15 +H2U C2 N3 HN3 118.376 1.92 +H2U C4 N3 HN3 118.112 1.50 +H2U N3 C4 O4 120.553 1.50 +H2U N3 C4 C5 116.998 1.50 +H2U O4 C4 C5 122.450 1.72 +H2U C4 C5 C6 112.021 2.38 +H2U C4 C5 H51 108.560 1.50 +H2U C4 C5 H52 108.560 1.50 +H2U C6 C5 H51 108.959 1.50 +H2U C6 C5 H52 108.959 1.50 +H2U H51 C5 H52 108.118 1.50 +H2U N1 C6 C5 110.160 1.50 +H2U N1 C6 H61 109.581 1.50 +H2U N1 C6 H62 109.581 1.50 +H2U C5 C6 H61 109.272 1.50 +H2U C5 C6 H62 109.272 1.50 +H2U H61 C6 H62 108.112 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 +H2U C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +H2U C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +H2U C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +H2U C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +H2U C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +H2U C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +H2U C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +H2U C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +H2U C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +H2U C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +H2U C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +H2U C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +H2U alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +H2U beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +H2U epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +H2U gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +H2U sp3_sp3_52 "C3'" "C2'" "O2'" "HO2'" 180.000 10.00 3 +H2U sp2_sp2_4 O2 C2 N1 "C1'" 0.000 5.0 2 +H2U sp2_sp3_16 "C1'" N1 C6 C5 180.000 10.0 6 +H2U sp2_sp2_7 O2 C2 N3 C4 180.000 5.0 2 +H2U sp2_sp2_11 O4 C4 N3 C2 180.000 5.0 2 +H2U sp2_sp3_4 O4 C4 C5 C6 180.000 10.0 6 +H2U sp3_sp3_25 C4 C5 C6 N1 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 +H2U chir_1 P "O5'" OP2 OP3 both +H2U chir_2 "C4'" "O4'" "C3'" "C5'" negative +H2U chir_3 "C3'" "O3'" "C4'" "C2'" positive +H2U chir_4 "C1'" "O4'" N1 "C2'" negative +H2U chir_5 "C2'" "O2'" "C1'" "C3'" 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 +H2U plan-1 "C1'" 0.020 +H2U plan-1 C2 0.020 +H2U plan-1 C6 0.020 +H2U plan-1 N1 0.020 +H2U plan-2 C2 0.020 +H2U plan-2 N1 0.020 +H2U plan-2 N3 0.020 +H2U plan-2 O2 0.020 +H2U plan-3 C2 0.020 +H2U plan-3 C4 0.020 +H2U plan-3 HN3 0.020 +H2U plan-3 N3 0.020 +H2U plan-4 C4 0.020 +H2U plan-4 C5 0.020 +H2U plan-4 N3 0.020 +H2U plan-4 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 +H2U SMILES ACDLabs 10.04 O=C1N(CCC(=O)N1)C2OC(C(O)C2O)COP(=O)(O)O +H2U SMILES_CANONICAL CACTVS 3.341 O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2CCC(=O)NC2=O +H2U SMILES CACTVS 3.341 O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2CCC(=O)NC2=O +H2U SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O +H2U SMILES "OpenEye OEToolkits" 1.5.0 C1CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O +H2U InChI InChI 1.03 InChI=1S/C9H15N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h4,6-8,13-14H,1-3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1 +H2U InChIKey InChI 1.03 NBWDKGJHOHJBRJ-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 +H2U acedrg 243 "dictionary generator" +H2U acedrg_database 11 "data source" +H2U rdkit 2017.03.2 "Chemoinformatics tool" +H2U refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/HEC.cif b/image_analysis/structure_refinement/monomers/HEC.cif new file mode 100644 index 000000000..95ec1620f --- /dev/null +++ b/image_analysis/structure_refinement/monomers/HEC.cif @@ -0,0 +1,689 @@ +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 +HEC HEC "HEME C" NON-POLYMER 74 42 . + +data_comp_HEC +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 +HEC FE FE FE FE 2.00 -0.636 0.011 0.178 +HEC CHA CHA C C1 0 2.705 0.563 -0.191 +HEC CHB CHB C C1 0 -1.246 3.264 -0.651 +HEC CHC CHC C C1 0 -3.983 -0.606 0.238 +HEC CHD CHD C C1 0 -0.013 -3.313 0.643 +HEC NA NA N NRD5 -1 0.536 1.644 -0.354 +HEC C1A C1A C CR5 0 1.894 1.679 -0.418 +HEC C2A C2A C CR5 0 2.308 2.957 -0.744 +HEC C3A C3A C CR5 0 1.186 3.724 -0.874 +HEC C4A C4A C CR5 0 0.106 2.908 -0.630 +HEC CMA CMA C CH3 0 1.153 5.194 -1.212 +HEC CAA CAA C CH2 0 3.737 3.412 -0.906 +HEC CBA CBA C CH2 0 4.414 3.848 0.391 +HEC CGA CGA C C 0 4.256 5.326 0.738 +HEC O1A O1A O O 0 5.052 6.137 0.220 +HEC O2A O2A O OC -1 3.339 5.649 1.522 +HEC NB NB N NRD5 0 -2.344 1.145 -0.176 +HEC C1B C1B C CR5 0 -2.390 2.485 -0.453 +HEC C2B C2B C CR5 0 -3.695 2.917 -0.499 +HEC C3B C3B C CR5 0 -4.521 1.785 -0.231 +HEC C4B C4B C CR5 0 -3.632 0.716 -0.043 +HEC CMB CMB C CH3 0 -4.205 4.311 -0.764 +HEC CAB CAB C CH1 -1 -5.944 1.794 -0.181 +HEC CBB CBB C CH3 0 -6.457 1.964 1.230 +HEC NC NC N NRD5 -1 -1.812 -1.692 0.391 +HEC C1C C1C C CR5 0 -3.180 -1.736 0.415 +HEC C2C C2C C CR5 0 -3.614 -3.025 0.618 +HEC C3C C3C C CR5 0 -2.443 -3.843 0.743 +HEC C4C C4C C CR5 0 -1.365 -2.963 0.597 +HEC CMC CMC C CH3 0 -5.039 -3.509 0.709 +HEC CAC CAC C CH1 -1 -2.369 -5.248 0.970 +HEC CBC CBC C CH3 0 -2.389 -6.034 -0.319 +HEC ND ND N NRD5 0 1.066 -1.186 0.196 +HEC C1D C1D C CR5 0 1.125 -2.521 0.464 +HEC C2D C2D C CR5 0 2.438 -2.923 0.528 +HEC C3D C3D C CR5 0 3.211 -1.822 0.301 +HEC C4D C4D C CR5 0 2.353 -0.759 0.089 +HEC CMD CMD C CH3 0 2.947 -4.314 0.810 +HEC CAD CAD C CH2 0 4.718 -1.775 0.271 +HEC CBD CBD C CH2 0 5.319 -1.958 -1.119 +HEC CGD CGD C C 0 6.842 -1.867 -1.168 +HEC O1D O1D O O 0 7.354 -0.784 -1.521 +HEC O2D O2D O OC -1 7.499 -2.881 -0.852 +HEC HHA HHA H H 0 3.635 0.731 -0.226 +HEC HHB HHB H H 0 -1.412 4.181 -0.802 +HEC HHC HHC H H 0 -4.913 -0.752 0.339 +HEC HHD HHD H H 0 0.158 -4.224 0.834 +HEC HMA1 HMA1 H H 0 0.311 5.421 -1.635 +HEC HMA2 HMA2 H H 0 1.871 5.414 -1.827 +HEC HMA3 HMA3 H H 0 1.255 5.717 -0.400 +HEC HAA1 HAA1 H H 0 3.782 4.153 -1.549 +HEC HAA2 HAA2 H H 0 4.266 2.686 -1.303 +HEC HBA1 HBA1 H H 0 5.376 3.645 0.328 +HEC HBA2 HBA2 H H 0 4.050 3.313 1.134 +HEC HMB1 HMB1 H H 0 -5.042 4.275 -1.254 +HEC HMB2 HMB2 H H 0 -3.561 4.806 -1.294 +HEC HMB3 HMB3 H H 0 -4.346 4.770 0.080 +HEC HAB HAB H H 0 -6.300 1.007 -0.566 +HEC HBB1 HBB1 H H 0 -7.428 1.953 1.202 +HEC HBB2 HBB2 H H 0 -6.133 2.815 1.569 +HEC HBB3 HBB3 H H 0 -6.120 1.229 1.767 +HEC HMC1 HMC1 H H 0 -5.098 -4.434 0.423 +HEC HMC2 HMC2 H H 0 -5.609 -2.971 0.136 +HEC HMC3 HMC3 H H 0 -5.349 -3.437 1.627 +HEC HAC HAC H H 0 -3.040 -5.552 1.562 +HEC HBC1 HBC1 H H 0 -2.345 -6.978 -0.098 +HEC HBC2 HBC2 H H 0 -1.619 -5.768 -0.848 +HEC HBC3 HBC3 H H 0 -3.215 -5.828 -0.786 +HEC HMD1 HMD1 H H 0 3.793 -4.460 0.359 +HEC HMD2 HMD2 H H 0 2.311 -4.973 0.490 +HEC HMD3 HMD3 H H 0 3.070 -4.427 1.767 +HEC HAD1 HAD1 H H 0 5.084 -2.466 0.865 +HEC HAD2 HAD2 H H 0 5.025 -0.915 0.634 +HEC HBD1 HBD1 H H 0 4.945 -1.271 -1.719 +HEC HBD2 HBD2 H H 0 5.046 -2.837 -1.469 + +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 +HEC O2D n/a CGD START +HEC CGD O2D CBD . +HEC O1D CGD . . +HEC CBD CGD CAD . +HEC HBD1 CBD . . +HEC HBD2 CBD . . +HEC CAD CBD C3D . +HEC HAD1 CAD . . +HEC HAD2 CAD . . +HEC C3D CAD C4D . +HEC C2D C3D C1D . +HEC CMD C2D HMD1 . +HEC HMD3 CMD . . +HEC HMD2 CMD . . +HEC HMD1 CMD . . +HEC C1D C2D CHD . +HEC CHD C1D HHD . +HEC HHD CHD . . +HEC C4D C3D ND . +HEC CHA C4D HHA . +HEC HHA CHA . . +HEC ND C4D FE . +HEC FE ND NA . +HEC NB FE C4B . +HEC C4B NB C3B . +HEC C3B C4B C2B . +HEC CAB C3B CBB . +HEC HAB CAB . . +HEC CBB CAB HBB1 . +HEC HBB3 CBB . . +HEC HBB2 CBB . . +HEC HBB1 CBB . . +HEC C2B C3B C1B . +HEC CMB C2B HMB1 . +HEC HMB3 CMB . . +HEC HMB2 CMB . . +HEC HMB1 CMB . . +HEC C1B C2B CHB . +HEC CHB C1B HHB . +HEC HHB CHB . . +HEC NC FE C4C . +HEC C4C NC C3C . +HEC C3C C4C C2C . +HEC CAC C3C CBC . +HEC HAC CAC . . +HEC CBC CAC HBC1 . +HEC HBC3 CBC . . +HEC HBC2 CBC . . +HEC HBC1 CBC . . +HEC C2C C3C C1C . +HEC CMC C2C HMC1 . +HEC HMC3 CMC . . +HEC HMC2 CMC . . +HEC HMC1 CMC . . +HEC C1C C2C CHC . +HEC CHC C1C HHC . +HEC HHC CHC . . +HEC NA FE C4A . +HEC C4A NA C3A . +HEC C3A C4A C2A . +HEC CMA C3A HMA1 . +HEC HMA3 CMA . . +HEC HMA2 CMA . . +HEC HMA1 CMA . . +HEC C2A C3A CAA . +HEC C1A C2A . . +HEC CAA C2A CBA . +HEC HAA1 CAA . . +HEC HAA2 CAA . . +HEC CBA CAA CGA . +HEC HBA1 CBA . . +HEC HBA2 CBA . . +HEC CGA CBA O2A . +HEC O1A CGA . . +HEC O2A CGA . END +HEC CHA C1A . ADD +HEC CHB C4A . ADD +HEC CHC C4B . ADD +HEC CHD C4C . ADD +HEC NA C1A . ADD +HEC NB C1B . ADD +HEC NC C1C . ADD +HEC ND C1D . ADD + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +HEC CHA C(C[5a]C[5a]N[5a])2(H) +HEC CHB C(C[5a]C[5a]N[5a])2(H) +HEC CHC C(C[5a]C[5a]N[5a])2(H) +HEC CHD C(C[5a]C[5a]N[5a])2(H) +HEC NA N[5a](C[5a]C[5a]C)2{2|C<4>} +HEC C1A C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>} +HEC C2A C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CCHH){1|C<3>} +HEC C3A C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CH3){1|C<3>} +HEC C4A C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>} +HEC CMA C(C[5a]C[5a]2)(H)3 +HEC CAA C(C[5a]C[5a]2)(CCHH)(H)2 +HEC CBA C(CC[5a]HH)(COO)(H)2 +HEC CGA C(CCHH)(O)2 +HEC O1A O(CCO) +HEC O2A O(CCO) +HEC NB N[5a](C[5a]C[5a]C)2{1|C<3>,1|C<4>} +HEC C1B C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){2|C<3>} +HEC C2B C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CH3){1|C<3>} +HEC C3B C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CCH){1|C<3>} +HEC C4B C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>} +HEC CMB C(C[5a]C[5a]2)(H)3 +HEC CAB C(C[5a]C[5a]2)(CH3)(H) +HEC CBB C(CC[5a]H)(H)3 +HEC NC N[5a](C[5a]C[5a]C)2{1|C<3>,1|C<4>} +HEC C1C C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){2|C<3>} +HEC C2C C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CH3){1|C<3>} +HEC C3C C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CCH){1|C<3>} +HEC C4C C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>} +HEC CMC C(C[5a]C[5a]2)(H)3 +HEC CAC C(C[5a]C[5a]2)(CH3)(H) +HEC CBC C(CC[5a]H)(H)3 +HEC ND N[5a](C[5a]C[5a]C)2{2|C<4>} +HEC C1D C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>} +HEC C2D C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CH3){1|C<3>} +HEC C3D C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CCHH){1|C<3>} +HEC C4D C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>} +HEC CMD C(C[5a]C[5a]2)(H)3 +HEC CAD C(C[5a]C[5a]2)(CCHH)(H)2 +HEC CBD C(CC[5a]HH)(COO)(H)2 +HEC CGD C(CCHH)(O)2 +HEC O1D O(CCO) +HEC O2D O(CCO) +HEC HHA H(CC[5a]2) +HEC HHB H(CC[5a]2) +HEC HHC H(CC[5a]2) +HEC HHD H(CC[5a]2) +HEC HMA1 H(CC[5a]HH) +HEC HMA2 H(CC[5a]HH) +HEC HMA3 H(CC[5a]HH) +HEC HAA1 H(CC[5a]CH) +HEC HAA2 H(CC[5a]CH) +HEC HBA1 H(CCCH) +HEC HBA2 H(CCCH) +HEC HMB1 H(CC[5a]HH) +HEC HMB2 H(CC[5a]HH) +HEC HMB3 H(CC[5a]HH) +HEC HAB H(CC[5a]C) +HEC HBB1 H(CCHH) +HEC HBB2 H(CCHH) +HEC HBB3 H(CCHH) +HEC HMC1 H(CC[5a]HH) +HEC HMC2 H(CC[5a]HH) +HEC HMC3 H(CC[5a]HH) +HEC HAC H(CC[5a]C) +HEC HBC1 H(CCHH) +HEC HBC2 H(CCHH) +HEC HBC3 H(CCHH) +HEC HMD1 H(CC[5a]HH) +HEC HMD2 H(CC[5a]HH) +HEC HMD3 H(CC[5a]HH) +HEC HAD1 H(CC[5a]CH) +HEC HAD2 H(CC[5a]CH) +HEC HBD1 H(CCCH) +HEC HBD2 H(CCCH) + +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 +HEC FE NA SINGLE n 1.9 0.06 1.9 0.06 +HEC FE NB SINGLE n 1.9 0.06 1.9 0.06 +HEC FE NC SINGLE n 1.9 0.06 1.9 0.06 +HEC FE ND SINGLE n 1.9 0.06 1.9 0.06 +HEC CHA C1A DOUBLE n 1.393 0.0200 1.393 0.0200 +HEC CHA C4D SINGLE n 1.393 0.0200 1.393 0.0200 +HEC CHB C4A DOUBLE n 1.393 0.0200 1.393 0.0200 +HEC CHB C1B SINGLE n 1.393 0.0200 1.393 0.0200 +HEC CHC C4B DOUBLE n 1.393 0.0200 1.393 0.0200 +HEC CHC C1C SINGLE n 1.393 0.0200 1.393 0.0200 +HEC CHD C4C SINGLE n 1.393 0.0200 1.393 0.0200 +HEC CHD C1D DOUBLE n 1.393 0.0200 1.393 0.0200 +HEC NA C1A SINGLE y 1.350 0.0200 1.350 0.0200 +HEC NA C4A SINGLE y 1.350 0.0200 1.350 0.0200 +HEC C1A C2A SINGLE y 1.374 0.0147 1.374 0.0147 +HEC C2A C3A DOUBLE y 1.361 0.0149 1.361 0.0149 +HEC C2A CAA SINGLE n 1.502 0.0100 1.502 0.0100 +HEC C3A C4A SINGLE y 1.361 0.0165 1.361 0.0165 +HEC C3A CMA SINGLE n 1.501 0.0106 1.501 0.0106 +HEC CAA CBA SINGLE n 1.526 0.0100 1.526 0.0100 +HEC CBA CGA SINGLE n 1.526 0.0100 1.526 0.0100 +HEC CGA O1A DOUBLE n 1.249 0.0161 1.249 0.0161 +HEC CGA O2A SINGLE n 1.249 0.0161 1.249 0.0161 +HEC NB C1B DOUBLE y 1.350 0.0200 1.350 0.0200 +HEC NB C4B SINGLE y 1.350 0.0200 1.350 0.0200 +HEC C1B C2B SINGLE y 1.361 0.0165 1.361 0.0165 +HEC C2B C3B DOUBLE y 1.436 0.0200 1.436 0.0200 +HEC C2B CMB SINGLE n 1.501 0.0106 1.501 0.0106 +HEC C3B C4B SINGLE y 1.393 0.0200 1.393 0.0200 +HEC C3B CAB SINGLE n 1.407 0.0200 1.407 0.0200 +HEC CAB CBB SINGLE n 1.506 0.0200 1.506 0.0200 +HEC NC C1C SINGLE y 1.350 0.0200 1.350 0.0200 +HEC NC C4C SINGLE y 1.350 0.0200 1.350 0.0200 +HEC C1C C2C DOUBLE y 1.361 0.0165 1.361 0.0165 +HEC C2C C3C SINGLE y 1.436 0.0200 1.436 0.0200 +HEC C2C CMC SINGLE n 1.501 0.0106 1.501 0.0106 +HEC C3C C4C DOUBLE y 1.393 0.0200 1.393 0.0200 +HEC C3C CAC SINGLE n 1.407 0.0200 1.407 0.0200 +HEC CAC CBC SINGLE n 1.506 0.0200 1.506 0.0200 +HEC ND C1D SINGLE y 1.350 0.0200 1.350 0.0200 +HEC ND C4D DOUBLE y 1.350 0.0200 1.350 0.0200 +HEC C1D C2D SINGLE y 1.361 0.0165 1.361 0.0165 +HEC C2D C3D DOUBLE y 1.361 0.0149 1.361 0.0149 +HEC C2D CMD SINGLE n 1.501 0.0106 1.501 0.0106 +HEC C3D C4D SINGLE y 1.374 0.0147 1.374 0.0147 +HEC C3D CAD SINGLE n 1.502 0.0100 1.502 0.0100 +HEC CAD CBD SINGLE n 1.526 0.0100 1.526 0.0100 +HEC CBD CGD SINGLE n 1.526 0.0100 1.526 0.0100 +HEC CGD O1D DOUBLE n 1.249 0.0161 1.249 0.0161 +HEC CGD O2D SINGLE n 1.249 0.0161 1.249 0.0161 +HEC CHA HHA SINGLE n 1.085 0.0150 0.948 0.0107 +HEC CHB HHB SINGLE n 1.085 0.0150 0.948 0.0107 +HEC CHC HHC SINGLE n 1.085 0.0150 0.948 0.0107 +HEC CHD HHD SINGLE n 1.085 0.0150 0.948 0.0107 +HEC CMA HMA1 SINGLE n 1.092 0.0100 0.971 0.0135 +HEC CMA HMA2 SINGLE n 1.092 0.0100 0.971 0.0135 +HEC CMA HMA3 SINGLE n 1.092 0.0100 0.971 0.0135 +HEC CAA HAA1 SINGLE n 1.092 0.0100 0.983 0.0149 +HEC CAA HAA2 SINGLE n 1.092 0.0100 0.983 0.0149 +HEC CBA HBA1 SINGLE n 1.092 0.0100 0.985 0.0125 +HEC CBA HBA2 SINGLE n 1.092 0.0100 0.985 0.0125 +HEC CMB HMB1 SINGLE n 1.092 0.0100 0.971 0.0135 +HEC CMB HMB2 SINGLE n 1.092 0.0100 0.971 0.0135 +HEC CMB HMB3 SINGLE n 1.092 0.0100 0.971 0.0135 +HEC CAB HAB SINGLE n 1.092 0.0100 0.945 0.0129 +HEC CBB HBB1 SINGLE n 1.092 0.0100 0.971 0.0160 +HEC CBB HBB2 SINGLE n 1.092 0.0100 0.971 0.0160 +HEC CBB HBB3 SINGLE n 1.092 0.0100 0.971 0.0160 +HEC CMC HMC1 SINGLE n 1.092 0.0100 0.971 0.0135 +HEC CMC HMC2 SINGLE n 1.092 0.0100 0.971 0.0135 +HEC CMC HMC3 SINGLE n 1.092 0.0100 0.971 0.0135 +HEC CAC HAC SINGLE n 1.092 0.0100 0.945 0.0129 +HEC CBC HBC1 SINGLE n 1.092 0.0100 0.971 0.0160 +HEC CBC HBC2 SINGLE n 1.092 0.0100 0.971 0.0160 +HEC CBC HBC3 SINGLE n 1.092 0.0100 0.971 0.0160 +HEC CMD HMD1 SINGLE n 1.092 0.0100 0.971 0.0135 +HEC CMD HMD2 SINGLE n 1.092 0.0100 0.971 0.0135 +HEC CMD HMD3 SINGLE n 1.092 0.0100 0.971 0.0135 +HEC CAD HAD1 SINGLE n 1.092 0.0100 0.983 0.0149 +HEC CAD HAD2 SINGLE n 1.092 0.0100 0.983 0.0149 +HEC CBD HBD1 SINGLE n 1.092 0.0100 0.985 0.0125 +HEC CBD HBD2 SINGLE n 1.092 0.0100 0.985 0.0125 + +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 +HEC FE NA C1A 127.3755 5.0 +HEC FE NA C4A 127.3755 5.0 +HEC FE NB C1B 127.1020 5.0 +HEC FE NB C4B 127.1020 5.0 +HEC FE NC C1C 127.1020 5.0 +HEC FE NC C4C 127.1020 5.0 +HEC FE ND C1D 127.3755 5.0 +HEC FE ND C4D 127.3755 5.0 +HEC C1A CHA C4D 124.237 3.00 +HEC C1A CHA HHA 117.882 3.00 +HEC C4D CHA HHA 117.882 3.00 +HEC C4A CHB C1B 124.237 3.00 +HEC C4A CHB HHB 117.882 3.00 +HEC C1B CHB HHB 117.882 3.00 +HEC C4B CHC C1C 124.237 3.00 +HEC C4B CHC HHC 117.882 3.00 +HEC C1C CHC HHC 117.882 3.00 +HEC C4C CHD C1D 124.237 3.00 +HEC C4C CHD HHD 117.882 3.00 +HEC C1D CHD HHD 117.882 3.00 +HEC C1A NA C4A 105.249 3.00 +HEC CHA C1A NA 122.751 3.00 +HEC CHA C1A C2A 128.506 3.00 +HEC NA C1A C2A 108.743 1.50 +HEC C1A C2A C3A 108.632 3.00 +HEC C1A C2A CAA 125.377 3.00 +HEC C3A C2A CAA 125.990 1.50 +HEC C2A C3A C4A 108.632 3.00 +HEC C2A C3A CMA 124.744 3.00 +HEC C4A C3A CMA 126.624 1.50 +HEC CHB C4A NA 122.751 3.00 +HEC CHB C4A C3A 128.506 3.00 +HEC NA C4A C3A 108.743 1.50 +HEC C3A CMA HMA1 109.572 1.50 +HEC C3A CMA HMA2 109.572 1.50 +HEC C3A CMA HMA3 109.572 1.50 +HEC HMA1 CMA HMA2 109.322 1.87 +HEC HMA1 CMA HMA3 109.322 1.87 +HEC HMA2 CMA HMA3 109.322 1.87 +HEC C2A CAA CBA 113.932 3.00 +HEC C2A CAA HAA1 109.001 1.50 +HEC C2A CAA HAA2 109.001 1.50 +HEC CBA CAA HAA1 108.631 1.50 +HEC CBA CAA HAA2 108.631 1.50 +HEC HAA1 CAA HAA2 107.419 2.31 +HEC CAA CBA CGA 114.716 3.00 +HEC CAA CBA HBA1 108.790 1.50 +HEC CAA CBA HBA2 108.790 1.50 +HEC CGA CBA HBA1 108.586 1.50 +HEC CGA CBA HBA2 108.586 1.50 +HEC HBA1 CBA HBA2 107.505 1.50 +HEC CBA CGA O1A 117.968 3.00 +HEC CBA CGA O2A 117.968 3.00 +HEC O1A CGA O2A 124.063 1.82 +HEC C1B NB C4B 105.796 3.00 +HEC CHB C1B NB 122.477 3.00 +HEC CHB C1B C2B 128.232 3.00 +HEC NB C1B C2B 109.291 1.50 +HEC C1B C2B C3B 108.186 3.00 +HEC C1B C2B CMB 126.778 1.50 +HEC C3B C2B CMB 125.036 3.00 +HEC C2B C3B C4B 107.432 3.00 +HEC C2B C3B CAB 126.284 3.00 +HEC C4B C3B CAB 126.284 3.00 +HEC CHC C4B NB 121.757 3.00 +HEC CHC C4B C3B 128.949 3.00 +HEC NB C4B C3B 109.294 2.29 +HEC C2B CMB HMB1 109.572 1.50 +HEC C2B CMB HMB2 109.572 1.50 +HEC C2B CMB HMB3 109.572 1.50 +HEC HMB1 CMB HMB2 109.322 1.87 +HEC HMB1 CMB HMB3 109.322 1.87 +HEC HMB2 CMB HMB3 109.322 1.87 +HEC C3B CAB CBB 109.471 3.00 +HEC C3B CAB HAB 109.471 3.00 +HEC CBB CAB HAB 109.471 3.00 +HEC CAB CBB HBB1 109.211 1.50 +HEC CAB CBB HBB2 109.211 1.50 +HEC CAB CBB HBB3 109.211 1.50 +HEC HBB1 CBB HBB2 111.860 1.50 +HEC HBB1 CBB HBB3 111.860 1.50 +HEC HBB2 CBB HBB3 111.860 1.50 +HEC C1C NC C4C 105.796 3.00 +HEC CHC C1C NC 122.477 3.00 +HEC CHC C1C C2C 128.232 3.00 +HEC NC C1C C2C 109.291 1.50 +HEC C1C C2C C3C 108.186 3.00 +HEC C1C C2C CMC 126.778 1.50 +HEC C3C C2C CMC 125.036 3.00 +HEC C2C C3C C4C 107.432 3.00 +HEC C2C C3C CAC 126.284 3.00 +HEC C4C C3C CAC 126.284 3.00 +HEC CHD C4C NC 121.757 3.00 +HEC CHD C4C C3C 128.949 3.00 +HEC NC C4C C3C 109.294 2.29 +HEC C2C CMC HMC1 109.572 1.50 +HEC C2C CMC HMC2 109.572 1.50 +HEC C2C CMC HMC3 109.572 1.50 +HEC HMC1 CMC HMC2 109.322 1.87 +HEC HMC1 CMC HMC3 109.322 1.87 +HEC HMC2 CMC HMC3 109.322 1.87 +HEC C3C CAC CBC 109.471 3.00 +HEC C3C CAC HAC 109.471 3.00 +HEC CBC CAC HAC 109.471 3.00 +HEC CAC CBC HBC1 109.211 1.50 +HEC CAC CBC HBC2 109.211 1.50 +HEC CAC CBC HBC3 109.211 1.50 +HEC HBC1 CBC HBC2 111.860 1.50 +HEC HBC1 CBC HBC3 111.860 1.50 +HEC HBC2 CBC HBC3 111.860 1.50 +HEC C1D ND C4D 105.249 3.00 +HEC CHD C1D ND 122.751 3.00 +HEC CHD C1D C2D 128.506 3.00 +HEC ND C1D C2D 108.743 1.50 +HEC C1D C2D C3D 108.632 3.00 +HEC C1D C2D CMD 126.624 1.50 +HEC C3D C2D CMD 124.744 3.00 +HEC C2D C3D C4D 108.632 3.00 +HEC C2D C3D CAD 125.990 1.50 +HEC C4D C3D CAD 125.377 3.00 +HEC CHA C4D ND 122.751 3.00 +HEC CHA C4D C3D 128.506 3.00 +HEC ND C4D C3D 108.743 1.50 +HEC C2D CMD HMD1 109.572 1.50 +HEC C2D CMD HMD2 109.572 1.50 +HEC C2D CMD HMD3 109.572 1.50 +HEC HMD1 CMD HMD2 109.322 1.87 +HEC HMD1 CMD HMD3 109.322 1.87 +HEC HMD2 CMD HMD3 109.322 1.87 +HEC C3D CAD CBD 113.932 3.00 +HEC C3D CAD HAD1 109.001 1.50 +HEC C3D CAD HAD2 109.001 1.50 +HEC CBD CAD HAD1 108.631 1.50 +HEC CBD CAD HAD2 108.631 1.50 +HEC HAD1 CAD HAD2 107.419 2.31 +HEC CAD CBD CGD 114.716 3.00 +HEC CAD CBD HBD1 108.790 1.50 +HEC CAD CBD HBD2 108.790 1.50 +HEC CGD CBD HBD1 108.586 1.50 +HEC CGD CBD HBD2 108.586 1.50 +HEC HBD1 CBD HBD2 107.505 1.50 +HEC CBD CGD O1D 117.968 3.00 +HEC CBD CGD O2D 117.968 3.00 +HEC O1D CGD O2D 124.063 1.82 +HEC NA FE NB 87.8 5.52 +HEC NA FE NC 157.26 7.8 +HEC NA FE ND 87.8 5.52 +HEC NB FE NC 87.8 5.52 +HEC NB FE ND 157.26 7.8 +HEC NC FE ND 87.8 5.52 + +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 +HEC sp2_sp2_1 ND C4D CHA C1A 0.000 5.0 2 +HEC sp2_sp2_2 NA C1A CHA C4D 0.000 5.0 2 +HEC sp3_sp3_1 C2A CAA CBA CGA 180.000 10.0 3 +HEC sp2_sp3_1 O1A CGA CBA CAA 120.000 20.0 6 +HEC const_0 CHB C1B NB C4B 180.000 0.0 1 +HEC const_1 CHC C4B NB C1B 180.000 0.0 1 +HEC const_2 CHB C1B C2B CMB 0.000 0.0 1 +HEC const_3 CMB C2B C3B CAB 0.000 0.0 1 +HEC sp2_sp3_2 C1B C2B CMB HMB1 150.000 20.0 6 +HEC const_4 CAB C3B C4B CHC 0.000 0.0 1 +HEC sp2_sp3_3 C2B C3B CAB CBB -90.000 20.0 6 +HEC sp2_sp2_3 NB C1B CHB C4A 0.000 5.0 2 +HEC sp2_sp2_4 NA C4A CHB C1B 0.000 5.0 2 +HEC sp3_sp3_2 C3B CAB CBB HBB1 180.000 10.0 3 +HEC const_5 CHC C1C NC C4C 180.000 0.0 1 +HEC const_6 CHD C4C NC C1C 180.000 0.0 1 +HEC const_7 CHC C1C C2C CMC 0.000 0.0 1 +HEC const_8 CMC C2C C3C CAC 0.000 0.0 1 +HEC sp2_sp3_4 C1C C2C CMC HMC1 150.000 20.0 6 +HEC const_9 CAC C3C C4C CHD 0.000 0.0 1 +HEC sp2_sp3_5 C2C C3C CAC CBC -90.000 20.0 6 +HEC sp3_sp3_3 C3C CAC CBC HBC1 180.000 10.0 3 +HEC sp2_sp2_5 NB C4B CHC C1C 0.000 5.0 2 +HEC sp2_sp2_6 NC C1C CHC C4B 0.000 5.0 2 +HEC const_10 CHD C1D ND C4D 180.000 0.0 1 +HEC const_11 CHA C4D ND C1D 180.000 0.0 1 +HEC const_12 CHD C1D C2D CMD 0.000 0.0 1 +HEC const_13 CMD C2D C3D CAD 0.000 0.0 1 +HEC sp2_sp3_6 C1D C2D CMD HMD1 150.000 20.0 6 +HEC const_14 CAD C3D C4D CHA 0.000 0.0 1 +HEC sp2_sp3_7 C2D C3D CAD CBD -90.000 20.0 6 +HEC sp3_sp3_4 C3D CAD CBD CGD 180.000 10.0 3 +HEC sp2_sp3_8 O1D CGD CBD CAD 120.000 20.0 6 +HEC sp2_sp2_7 NC C4C CHD C1D 0.000 5.0 2 +HEC sp2_sp2_8 ND C1D CHD C4C 0.000 5.0 2 +HEC const_15 CHA C1A NA C4A 180.000 0.0 1 +HEC const_16 CHB C4A NA C1A 180.000 0.0 1 +HEC const_17 CHA C1A C2A CAA 0.000 0.0 1 +HEC sp2_sp3_9 C1A C2A CAA CBA -90.000 20.0 6 +HEC const_18 CAA C2A C3A CMA 0.000 0.0 1 +HEC const_19 CMA C3A C4A CHB 0.000 0.0 1 +HEC sp2_sp3_10 C2A C3A CMA HMA1 150.000 20.0 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 +HEC plan-11 FE 0.060 +HEC plan-11 NA 0.060 +HEC plan-11 C1A 0.060 +HEC plan-11 C4A 0.060 +HEC plan-12 FE 0.060 +HEC plan-12 NB 0.060 +HEC plan-12 C1B 0.060 +HEC plan-12 C4B 0.060 +HEC plan-13 FE 0.060 +HEC plan-13 NC 0.060 +HEC plan-13 C1C 0.060 +HEC plan-13 C4C 0.060 +HEC plan-14 FE 0.060 +HEC plan-14 ND 0.060 +HEC plan-14 C1D 0.060 +HEC plan-14 C4D 0.060 +HEC plan-1 C1B 0.020 +HEC plan-1 C2B 0.020 +HEC plan-1 C3B 0.020 +HEC plan-1 C4B 0.020 +HEC plan-1 CAB 0.020 +HEC plan-1 CHB 0.020 +HEC plan-1 CHC 0.020 +HEC plan-1 CMB 0.020 +HEC plan-1 NB 0.020 +HEC plan-2 C1C 0.020 +HEC plan-2 C2C 0.020 +HEC plan-2 C3C 0.020 +HEC plan-2 C4C 0.020 +HEC plan-2 CAC 0.020 +HEC plan-2 CHC 0.020 +HEC plan-2 CHD 0.020 +HEC plan-2 CMC 0.020 +HEC plan-2 NC 0.020 +HEC plan-3 C1D 0.020 +HEC plan-3 C2D 0.020 +HEC plan-3 C3D 0.020 +HEC plan-3 C4D 0.020 +HEC plan-3 CAD 0.020 +HEC plan-3 CHA 0.020 +HEC plan-3 CHD 0.020 +HEC plan-3 CMD 0.020 +HEC plan-3 ND 0.020 +HEC plan-4 C1A 0.020 +HEC plan-4 C2A 0.020 +HEC plan-4 C3A 0.020 +HEC plan-4 C4A 0.020 +HEC plan-4 CAA 0.020 +HEC plan-4 CHA 0.020 +HEC plan-4 CHB 0.020 +HEC plan-4 CMA 0.020 +HEC plan-4 NA 0.020 +HEC plan-5 C1A 0.020 +HEC plan-5 C4D 0.020 +HEC plan-5 CHA 0.020 +HEC plan-5 HHA 0.020 +HEC plan-6 C1B 0.020 +HEC plan-6 C4A 0.020 +HEC plan-6 CHB 0.020 +HEC plan-6 HHB 0.020 +HEC plan-7 C1C 0.020 +HEC plan-7 C4B 0.020 +HEC plan-7 CHC 0.020 +HEC plan-7 HHC 0.020 +HEC plan-8 C1D 0.020 +HEC plan-8 C4C 0.020 +HEC plan-8 CHD 0.020 +HEC plan-8 HHD 0.020 +HEC plan-9 CBA 0.020 +HEC plan-9 CGA 0.020 +HEC plan-9 O1A 0.020 +HEC plan-9 O2A 0.020 +HEC plan-10 CBD 0.020 +HEC plan-10 CGD 0.020 +HEC plan-10 O1D 0.020 +HEC plan-10 O2D 0.020 + +loop_ +_chem_comp_ring_atom.comp_id +_chem_comp_ring_atom.ring_serial_number +_chem_comp_ring_atom.atom_id +_chem_comp_ring_atom.is_aromatic_ring +HEC ring-1 NB YES +HEC ring-1 C1B YES +HEC ring-1 C2B YES +HEC ring-1 C3B YES +HEC ring-1 C4B YES +HEC ring-2 NC YES +HEC ring-2 C1C YES +HEC ring-2 C2C YES +HEC ring-2 C3C YES +HEC ring-2 C4C YES +HEC ring-3 ND YES +HEC ring-3 C1D YES +HEC ring-3 C2D YES +HEC ring-3 C3D YES +HEC ring-3 C4D YES +HEC ring-4 NA YES +HEC ring-4 C1A YES +HEC ring-4 C2A YES +HEC ring-4 C3A YES +HEC ring-4 C4A YES + +loop_ +_acedrg_chem_comp_descriptor.comp_id +_acedrg_chem_comp_descriptor.program_name +_acedrg_chem_comp_descriptor.program_version +_acedrg_chem_comp_descriptor.type +HEC acedrg 314 'dictionary generator' +HEC 'acedrg_database' 12 'data source' +HEC rdkit 2023.03.3 'Chemoinformatics tool' +HEC servalcat 0.4.99 'optimization tool' +HEC metalCoord 0.1.77 'metal coordination analysis' diff --git a/image_analysis/structure_refinement/monomers/HEM.cif b/image_analysis/structure_refinement/monomers/HEM.cif new file mode 100644 index 000000000..a0dfd75e5 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/HEM.cif @@ -0,0 +1,691 @@ +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 +HEM HEM "PROTOPORPHYRIN IX CONTAINING FE" NON-POLYMER 72 42 . + +data_comp_HEM +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 +HEM FE FE FE FE 2.00 2.113 -20.686 36.710 +HEM CHA CHA C C1 0 2.720 -19.528 39.866 +HEM CHB CHB C C1 0 3.392 -17.792 35.417 +HEM CHC CHC C C1 0 1.647 -21.910 33.552 +HEM CHD CHD C C1 0 0.970 -23.635 38.034 +HEM C1A C1A C CR5 0 3.084 -18.642 38.839 +HEM C2A C2A C CR5 0 3.624 -17.376 38.970 +HEM C3A C3A C CR5 0 3.821 -16.888 37.707 +HEM C4A C4A C CR5 0 3.395 -17.851 36.822 +HEM CMA CMA C CH3 0 4.397 -15.536 37.368 +HEM CAA CAA C CH2 0 3.948 -16.673 40.264 +HEM CBA CBA C CH2 0 5.335 -16.990 40.817 +HEM CGA CGA C C 0 5.753 -16.132 42.008 +HEM O1A O1A O O 0 6.478 -15.139 41.789 +HEM O2A O2A O OC -1 5.350 -16.467 43.141 +HEM C1B C1B C CR5 0 3.012 -18.742 34.450 +HEM C2B C2B C CR5 0 3.088 -18.615 33.063 +HEM C3B C3B C CR5 0 2.602 -19.823 32.491 +HEM C4B C4B C CR5 0 2.223 -20.612 33.577 +HEM CMB CMB C CH3 0 3.637 -17.437 32.305 +HEM CAB CAB C C1 0 2.444 -20.228 31.062 +HEM CBB CBB C C2 0 2.468 -19.589 29.912 +HEM C1C C1C C CR5 0 1.305 -22.806 34.583 +HEM C2C C2C C CR5 0 0.791 -24.096 34.439 +HEM C3C C3C C CR5 0 0.605 -24.635 35.742 +HEM C4C C4C C CR5 0 0.990 -23.616 36.614 +HEM CMC CMC C CH3 0 0.531 -24.813 33.142 +HEM CAC CAC C C1 0 0.071 -25.962 36.177 +HEM CBC CBC C C2 0 -0.577 -26.940 35.580 +HEM C1D C1D C CR5 0 1.386 -22.691 38.991 +HEM C2D C2D C CR5 0 1.361 -22.807 40.363 +HEM C3D C3D C CR5 0 1.858 -21.643 40.882 +HEM C4D C4D C CR5 0 2.180 -20.824 39.815 +HEM CMD CMD C CH3 0 0.875 -23.984 41.171 +HEM CAD CAD C CH2 0 2.015 -21.306 42.343 +HEM CBD CBD C CH2 0 0.815 -20.581 42.946 +HEM CGD CGD C C 0 0.988 -20.172 44.406 +HEM O1D O1D O O 0 1.599 -19.110 44.648 +HEM O2D O2D O OC -1 0.509 -20.920 45.284 +HEM NA NA N NRD5 -1 2.940 -18.925 37.520 +HEM NB NB N NRD5 1 2.476 -19.944 34.769 +HEM NC NC N NRD5 -1 1.417 -22.504 35.897 +HEM ND ND N NRD5 1 1.887 -21.472 38.658 +HEM HHA HHA H H 0 2.859 -19.193 40.740 +HEM HHB HHB H H 0 3.670 -16.961 35.061 +HEM HHC HHC H H 0 1.422 -22.211 32.685 +HEM HHD HHD H H 0 0.585 -24.416 38.400 +HEM HMA HMA H H 0 4.826 -15.566 36.499 +HEM HMAA HMAA H H 0 5.058 -15.279 38.029 +HEM HMAB HMAB H H 0 3.686 -14.875 37.351 +HEM HAA HAA H H 0 3.279 -16.915 40.942 +HEM HAAA HAAA H H 0 3.873 -15.702 40.143 +HEM HBA HBA H H 0 5.997 -16.872 40.097 +HEM HBAA HBAA H H 0 5.359 -17.937 41.089 +HEM HMB HMB H H 0 4.047 -17.740 31.479 +HEM HMBA HMBA H H 0 4.310 -16.982 32.835 +HEM HMBB HMBB H H 0 2.918 -16.818 32.099 +HEM HAB HAB H H 0 2.329 -21.154 30.922 +HEM HBB HBB H H 0 2.384 -20.072 29.107 +HEM HBBA HBBA H H 0 2.536 -18.650 29.889 +HEM HMC HMC H H 0 0.678 -25.764 33.258 +HEM HMCA HMCA H H 0 1.133 -24.489 32.454 +HEM HMCB HMCB H H 0 -0.387 -24.660 32.864 +HEM HAC HAC H H 0 0.253 -26.188 37.076 +HEM HBC HBC H H 0 -0.782 -27.725 36.060 +HEM HBCA HBCA H H 0 -0.864 -26.848 34.688 +HEM HMD HMD H H 0 1.479 -24.149 41.913 +HEM HMDA HMDA H H 0 0.841 -24.780 40.620 +HEM HMDB HMDB H H 0 -0.013 -23.796 41.516 +HEM HAD HAD H H 0 2.812 -20.745 42.464 +HEM HADA HADA H H 0 2.181 -22.124 42.860 +HEM HBD HBD H H 0 0.025 -21.165 42.876 +HEM HBDA HBDA H H 0 0.633 -19.773 42.413 + +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 +HEM O2D n/a CGD START +HEM CGD O2D CBD . +HEM O1D CGD . . +HEM CBD CGD CAD . +HEM HBD CBD . . +HEM HBDA CBD . . +HEM CAD CBD C3D . +HEM HAD CAD . . +HEM HADA CAD . . +HEM C3D CAD C4D . +HEM C2D C3D CMD . +HEM CMD C2D HMD . +HEM HMDB CMD . . +HEM HMDA CMD . . +HEM HMD CMD . . +HEM C4D C3D ND . +HEM CHA C4D HHA . +HEM HHA CHA . . +HEM ND C4D FE . +HEM C1D ND CHD . +HEM CHD C1D HHD . +HEM HHD CHD . . +HEM FE ND NA . +HEM NB FE C1B . +HEM C4B NB C3B . +HEM C3B C4B C2B . +HEM CAB C3B CBB . +HEM HAB CAB . . +HEM CBB CAB HBB . +HEM HBBA CBB . . +HEM HBB CBB . . +HEM C2B C3B CMB . +HEM CMB C2B HMB . +HEM HMBB CMB . . +HEM HMBA CMB . . +HEM HMB CMB . . +HEM C1B NB CHB . +HEM CHB C1B HHB . +HEM HHB CHB . . +HEM NC FE C1C . +HEM C4C NC C3C . +HEM C3C C4C C2C . +HEM CAC C3C CBC . +HEM HAC CAC . . +HEM CBC CAC HBC . +HEM HBCA CBC . . +HEM HBC CBC . . +HEM C2C C3C CMC . +HEM CMC C2C HMC . +HEM HMCB CMC . . +HEM HMCA CMC . . +HEM HMC CMC . . +HEM C1C NC CHC . +HEM CHC C1C HHC . +HEM HHC CHC . . +HEM NA FE C4A . +HEM C1A NA . . +HEM C4A NA C3A . +HEM C3A C4A C2A . +HEM CMA C3A HMA . +HEM HMAB CMA . . +HEM HMAA CMA . . +HEM HMA CMA . . +HEM C2A C3A CAA . +HEM CAA C2A CBA . +HEM HAA CAA . . +HEM HAAA CAA . . +HEM CBA CAA CGA . +HEM HBA CBA . . +HEM HBAA CBA . . +HEM CGA CBA O2A . +HEM O1A CGA . . +HEM O2A CGA . END +HEM CHA C1A . ADD +HEM CHB C4A . ADD +HEM CHC C4B . ADD +HEM CHD C4C . ADD +HEM C1A C2A . ADD +HEM C1B C2B . ADD +HEM C1C C2C . ADD +HEM C1D C2D . ADD + +loop_ +_chem_comp_acedrg.comp_id +_chem_comp_acedrg.atom_id +_chem_comp_acedrg.atom_type +HEM CHA C(C[5a]C[5a]N[5a])2(H) +HEM CHB C(C[5a]C[5a]N[5a])2(H) +HEM CHC C(C[5a]C[5a]N[5a])2(H) +HEM CHD C(C[5a]C[5a]N[5a])2(H) +HEM C1A C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>} +HEM C2A C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CCHH){1|C<3>} +HEM C3A C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CH3){1|C<3>} +HEM C4A C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>} +HEM CMA C(C[5a]C[5a]2)(H)3 +HEM CAA C(C[5a]C[5a]2)(CCHH)(H)2 +HEM CBA C(CC[5a]HH)(COO)(H)2 +HEM CGA C(CCHH)(O)2 +HEM O1A O(CCO) +HEM O2A O(CCO) +HEM C1B C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){2|C<3>} +HEM C2B C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CH3){1|C<3>} +HEM C3B C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CCH){1|C<3>} +HEM C4B C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>} +HEM CMB C(C[5a]C[5a]2)(H)3 +HEM CAB C(C[5a]C[5a]2)(CHH)(H) +HEM CBB C(CC[5a]H)(H)2 +HEM C1C C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){2|C<3>} +HEM C2C C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CH3){1|C<3>} +HEM C3C C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CCH){1|C<3>} +HEM C4C C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>} +HEM CMC C(C[5a]C[5a]2)(H)3 +HEM CAC C(C[5a]C[5a]2)(CHH)(H) +HEM CBC C(CC[5a]H)(H)2 +HEM C1D C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>} +HEM C2D C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CH3){1|C<3>} +HEM C3D C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CCHH){1|C<3>} +HEM C4D C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>} +HEM CMD C(C[5a]C[5a]2)(H)3 +HEM CAD C(C[5a]C[5a]2)(CCHH)(H)2 +HEM CBD C(CC[5a]HH)(COO)(H)2 +HEM CGD C(CCHH)(O)2 +HEM O1D O(CCO) +HEM O2D O(CCO) +HEM NA N[5a](C[5a]C[5a]C)2{2|C<4>} +HEM NB N[5a](C[5a]C[5a]C)2{1|C<3>,1|C<4>} +HEM NC N[5a](C[5a]C[5a]C)2{1|C<3>,1|C<4>} +HEM ND N[5a](C[5a]C[5a]C)2{2|C<4>} +HEM HHA H(CC[5a]2) +HEM HHB H(CC[5a]2) +HEM HHC H(CC[5a]2) +HEM HHD H(CC[5a]2) +HEM HMA H(CC[5a]HH) +HEM HMAA H(CC[5a]HH) +HEM HMAB H(CC[5a]HH) +HEM HAA H(CC[5a]CH) +HEM HAAA H(CC[5a]CH) +HEM HBA H(CCCH) +HEM HBAA H(CCCH) +HEM HMB H(CC[5a]HH) +HEM HMBA H(CC[5a]HH) +HEM HMBB H(CC[5a]HH) +HEM HAB H(CC[5a]C) +HEM HBB H(CCH) +HEM HBBA H(CCH) +HEM HMC H(CC[5a]HH) +HEM HMCA H(CC[5a]HH) +HEM HMCB H(CC[5a]HH) +HEM HAC H(CC[5a]C) +HEM HBC H(CCH) +HEM HBCA H(CCH) +HEM HMD H(CC[5a]HH) +HEM HMDA H(CC[5a]HH) +HEM HMDB H(CC[5a]HH) +HEM HAD H(CC[5a]CH) +HEM HADA H(CC[5a]CH) +HEM HBD H(CCCH) +HEM HBDA H(CCCH) + +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 +HEM FE NA SINGLE n 2.04 0.09 2.04 0.09 +HEM FE NB SINGLE n 2.04 0.09 2.04 0.09 +HEM FE NC SINGLE n 2.04 0.09 2.04 0.09 +HEM FE ND SINGLE n 2.04 0.09 2.04 0.09 +HEM CHA C1A DOUBLE n 1.393 0.0200 1.393 0.0200 +HEM CHA C4D SINGLE n 1.393 0.0200 1.393 0.0200 +HEM CHB C4A DOUBLE n 1.393 0.0200 1.393 0.0200 +HEM CHB C1B SINGLE n 1.393 0.0200 1.393 0.0200 +HEM CHC C4B DOUBLE n 1.407 0.0200 1.407 0.0200 +HEM CHC C1C SINGLE n 1.393 0.0200 1.393 0.0200 +HEM CHD C4C SINGLE n 1.407 0.0200 1.407 0.0200 +HEM CHD C1D DOUBLE n 1.393 0.0200 1.393 0.0200 +HEM C1A C2A SINGLE y 1.374 0.0147 1.374 0.0147 +HEM C1A NA SINGLE y 1.350 0.0200 1.350 0.0200 +HEM C2A C3A DOUBLE y 1.361 0.0149 1.361 0.0149 +HEM C2A CAA SINGLE n 1.502 0.0100 1.502 0.0100 +HEM C3A C4A SINGLE y 1.361 0.0165 1.361 0.0165 +HEM C3A CMA SINGLE n 1.501 0.0106 1.501 0.0106 +HEM C4A NA SINGLE y 1.350 0.0200 1.350 0.0200 +HEM CAA CBA SINGLE n 1.526 0.0100 1.526 0.0100 +HEM CBA CGA SINGLE n 1.526 0.0100 1.526 0.0100 +HEM CGA O1A DOUBLE n 1.249 0.0161 1.249 0.0161 +HEM CGA O2A SINGLE n 1.249 0.0161 1.249 0.0161 +HEM C1B C2B SINGLE y 1.379 0.0175 1.379 0.0175 +HEM C1B NB DOUBLE y 1.350 0.0200 1.350 0.0200 +HEM C2B C3B DOUBLE y 1.401 0.0200 1.401 0.0200 +HEM C2B CMB SINGLE n 1.500 0.0100 1.500 0.0100 +HEM C3B C4B SINGLE y 1.388 0.0111 1.388 0.0111 +HEM C3B CAB SINGLE n 1.456 0.0200 1.456 0.0200 +HEM C4B NB SINGLE y 1.388 0.0142 1.388 0.0142 +HEM CAB CBB DOUBLE n 1.306 0.0200 1.306 0.0200 +HEM C1C C2C DOUBLE y 1.379 0.0175 1.379 0.0175 +HEM C1C NC SINGLE y 1.350 0.0200 1.350 0.0200 +HEM C2C C3C SINGLE y 1.401 0.0200 1.401 0.0200 +HEM C2C CMC SINGLE n 1.500 0.0100 1.500 0.0100 +HEM C3C C4C DOUBLE y 1.388 0.0111 1.388 0.0111 +HEM C3C CAC SINGLE n 1.456 0.0200 1.456 0.0200 +HEM C4C NC SINGLE y 1.388 0.0142 1.388 0.0142 +HEM CAC CBC DOUBLE n 1.306 0.0200 1.306 0.0200 +HEM C1D C2D SINGLE y 1.361 0.0165 1.361 0.0165 +HEM C1D ND SINGLE y 1.350 0.0200 1.350 0.0200 +HEM C2D C3D DOUBLE y 1.361 0.0149 1.361 0.0149 +HEM C2D CMD SINGLE n 1.501 0.0106 1.501 0.0106 +HEM C3D C4D SINGLE y 1.374 0.0147 1.374 0.0147 +HEM C3D CAD SINGLE n 1.502 0.0100 1.502 0.0100 +HEM C4D ND DOUBLE y 1.350 0.0200 1.350 0.0200 +HEM CAD CBD SINGLE n 1.526 0.0100 1.526 0.0100 +HEM CBD CGD SINGLE n 1.526 0.0100 1.526 0.0100 +HEM CGD O1D DOUBLE n 1.249 0.0161 1.249 0.0161 +HEM CGD O2D SINGLE n 1.249 0.0161 1.249 0.0161 +HEM CHA HHA SINGLE n 1.085 0.0150 0.948 0.0107 +HEM CHB HHB SINGLE n 1.085 0.0150 0.948 0.0107 +HEM CHC HHC SINGLE n 1.085 0.0150 0.948 0.0107 +HEM CHD HHD SINGLE n 1.085 0.0150 0.948 0.0107 +HEM CMA HMA SINGLE n 1.092 0.0100 0.971 0.0135 +HEM CMA HMAA SINGLE n 1.092 0.0100 0.971 0.0135 +HEM CMA HMAB SINGLE n 1.092 0.0100 0.971 0.0135 +HEM CAA HAA SINGLE n 1.092 0.0100 0.983 0.0149 +HEM CAA HAAA SINGLE n 1.092 0.0100 0.983 0.0149 +HEM CBA HBA SINGLE n 1.092 0.0100 0.985 0.0125 +HEM CBA HBAA SINGLE n 1.092 0.0100 0.985 0.0125 +HEM CMB HMB SINGLE n 1.092 0.0100 0.971 0.0135 +HEM CMB HMBA SINGLE n 1.092 0.0100 0.971 0.0135 +HEM CMB HMBB SINGLE n 1.092 0.0100 0.971 0.0135 +HEM CAB HAB SINGLE n 1.085 0.0150 0.945 0.0100 +HEM CBB HBB SINGLE n 1.085 0.0150 0.943 0.0100 +HEM CBB HBBA SINGLE n 1.085 0.0150 0.943 0.0100 +HEM CMC HMC SINGLE n 1.092 0.0100 0.971 0.0135 +HEM CMC HMCA SINGLE n 1.092 0.0100 0.971 0.0135 +HEM CMC HMCB SINGLE n 1.092 0.0100 0.971 0.0135 +HEM CAC HAC SINGLE n 1.085 0.0150 0.945 0.0100 +HEM CBC HBC SINGLE n 1.085 0.0150 0.943 0.0100 +HEM CBC HBCA SINGLE n 1.085 0.0150 0.943 0.0100 +HEM CMD HMD SINGLE n 1.092 0.0100 0.971 0.0135 +HEM CMD HMDA SINGLE n 1.092 0.0100 0.971 0.0135 +HEM CMD HMDB SINGLE n 1.092 0.0100 0.971 0.0135 +HEM CAD HAD SINGLE n 1.092 0.0100 0.983 0.0149 +HEM CAD HADA SINGLE n 1.092 0.0100 0.983 0.0149 +HEM CBD HBD SINGLE n 1.092 0.0100 0.985 0.0125 +HEM CBD HBDA SINGLE n 1.092 0.0100 0.985 0.0125 + +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 +HEM FE NA C1A 127.3755 5.0 +HEM FE NA C4A 127.3755 5.0 +HEM FE NB C1B 127.1020 5.0 +HEM FE NB C4B 127.1020 5.0 +HEM FE NC C1C 127.1020 5.0 +HEM FE NC C4C 127.1020 5.0 +HEM FE ND C1D 127.3755 5.0 +HEM FE ND C4D 127.3755 5.0 +HEM C1A CHA C4D 124.237 3.00 +HEM C1A CHA HHA 117.882 3.00 +HEM C4D CHA HHA 117.882 3.00 +HEM C4A CHB C1B 124.237 3.00 +HEM C4A CHB HHB 117.882 3.00 +HEM C1B CHB HHB 117.882 3.00 +HEM C4B CHC C1C 124.237 3.00 +HEM C4B CHC HHC 117.882 3.00 +HEM C1C CHC HHC 117.882 3.00 +HEM C4C CHD C1D 124.237 3.00 +HEM C4C CHD HHD 117.882 3.00 +HEM C1D CHD HHD 117.882 3.00 +HEM CHA C1A C2A 128.506 3.00 +HEM CHA C1A NA 122.751 3.00 +HEM C2A C1A NA 108.743 1.50 +HEM C1A C2A C3A 108.632 3.00 +HEM C1A C2A CAA 125.377 3.00 +HEM C3A C2A CAA 125.990 1.50 +HEM C2A C3A C4A 108.632 3.00 +HEM C2A C3A CMA 124.744 3.00 +HEM C4A C3A CMA 126.624 1.50 +HEM CHB C4A C3A 128.506 3.00 +HEM CHB C4A NA 122.751 3.00 +HEM C3A C4A NA 108.743 1.50 +HEM C3A CMA HMA 109.572 1.50 +HEM C3A CMA HMAA 109.572 1.50 +HEM C3A CMA HMAB 109.572 1.50 +HEM HMA CMA HMAA 109.322 1.87 +HEM HMA CMA HMAB 109.322 1.87 +HEM HMAA CMA HMAB 109.322 1.87 +HEM C2A CAA CBA 113.932 3.00 +HEM C2A CAA HAA 109.001 1.50 +HEM C2A CAA HAAA 109.001 1.50 +HEM CBA CAA HAA 108.631 1.50 +HEM CBA CAA HAAA 108.631 1.50 +HEM HAA CAA HAAA 107.419 2.31 +HEM CAA CBA CGA 114.716 3.00 +HEM CAA CBA HBA 108.790 1.50 +HEM CAA CBA HBAA 108.790 1.50 +HEM CGA CBA HBA 108.586 1.50 +HEM CGA CBA HBAA 108.586 1.50 +HEM HBA CBA HBAA 107.505 1.50 +HEM CBA CGA O1A 117.968 3.00 +HEM CBA CGA O2A 117.968 3.00 +HEM O1A CGA O2A 124.063 1.82 +HEM CHB C1B C2B 128.232 3.00 +HEM CHB C1B NB 122.477 3.00 +HEM C2B C1B NB 109.291 1.50 +HEM C1B C2B C3B 108.186 3.00 +HEM C1B C2B CMB 126.778 1.50 +HEM C3B C2B CMB 125.036 3.00 +HEM C2B C3B C4B 107.432 3.00 +HEM C2B C3B CAB 125.770 3.00 +HEM C4B C3B CAB 126.798 3.00 +HEM CHC C4B C3B 128.949 3.00 +HEM CHC C4B NB 121.757 3.00 +HEM C3B C4B NB 109.294 2.29 +HEM C2B CMB HMB 109.572 1.50 +HEM C2B CMB HMBA 109.572 1.50 +HEM C2B CMB HMBB 109.572 1.50 +HEM HMB CMB HMBA 109.322 1.87 +HEM HMB CMB HMBB 109.322 1.87 +HEM HMBA CMB HMBB 109.322 1.87 +HEM C3B CAB CBB 127.109 3.00 +HEM C3B CAB HAB 116.019 1.61 +HEM CBB CAB HAB 116.872 2.59 +HEM CAB CBB HBB 119.970 1.50 +HEM CAB CBB HBBA 119.970 1.50 +HEM HBB CBB HBBA 120.061 1.50 +HEM CHC C1C C2C 128.232 3.00 +HEM CHC C1C NC 122.477 3.00 +HEM C2C C1C NC 109.291 1.50 +HEM C1C C2C C3C 108.186 3.00 +HEM C1C C2C CMC 126.778 1.50 +HEM C3C C2C CMC 125.036 3.00 +HEM C2C C3C C4C 107.432 3.00 +HEM C2C C3C CAC 125.770 3.00 +HEM C4C C3C CAC 126.798 3.00 +HEM CHD C4C C3C 128.949 3.00 +HEM CHD C4C NC 121.757 3.00 +HEM C3C C4C NC 109.294 2.29 +HEM C2C CMC HMC 109.572 1.50 +HEM C2C CMC HMCA 109.572 1.50 +HEM C2C CMC HMCB 109.572 1.50 +HEM HMC CMC HMCA 109.322 1.87 +HEM HMC CMC HMCB 109.322 1.87 +HEM HMCA CMC HMCB 109.322 1.87 +HEM C3C CAC CBC 127.109 3.00 +HEM C3C CAC HAC 116.019 1.61 +HEM CBC CAC HAC 116.872 2.59 +HEM CAC CBC HBC 119.970 1.50 +HEM CAC CBC HBCA 119.970 1.50 +HEM HBC CBC HBCA 120.061 1.50 +HEM CHD C1D C2D 128.506 3.00 +HEM CHD C1D ND 122.751 3.00 +HEM C2D C1D ND 108.743 1.50 +HEM C1D C2D C3D 108.632 3.00 +HEM C1D C2D CMD 126.624 1.50 +HEM C3D C2D CMD 124.744 3.00 +HEM C2D C3D C4D 108.632 3.00 +HEM C2D C3D CAD 125.990 1.50 +HEM C4D C3D CAD 125.377 3.00 +HEM CHA C4D C3D 128.506 3.00 +HEM CHA C4D ND 122.751 3.00 +HEM C3D C4D ND 108.743 1.50 +HEM C2D CMD HMD 109.572 1.50 +HEM C2D CMD HMDA 109.572 1.50 +HEM C2D CMD HMDB 109.572 1.50 +HEM HMD CMD HMDA 109.322 1.87 +HEM HMD CMD HMDB 109.322 1.87 +HEM HMDA CMD HMDB 109.322 1.87 +HEM C3D CAD CBD 113.932 3.00 +HEM C3D CAD HAD 109.001 1.50 +HEM C3D CAD HADA 109.001 1.50 +HEM CBD CAD HAD 108.631 1.50 +HEM CBD CAD HADA 108.631 1.50 +HEM HAD CAD HADA 107.419 2.31 +HEM CAD CBD CGD 114.716 3.00 +HEM CAD CBD HBD 108.790 1.50 +HEM CAD CBD HBDA 108.790 1.50 +HEM CGD CBD HBD 108.586 1.50 +HEM CGD CBD HBDA 108.586 1.50 +HEM HBD CBD HBDA 107.505 1.50 +HEM CBD CGD O1D 117.968 3.00 +HEM CBD CGD O2D 117.968 3.00 +HEM O1D CGD O2D 124.063 1.82 +HEM C1A NA C4A 105.249 3.00 +HEM C1B NB C4B 105.796 3.00 +HEM C1C NC C4C 105.796 3.00 +HEM C1D ND C4D 105.249 3.00 +HEM NA FE ND 89.77 6.92 +HEM NA FE NB 89.77 6.92 +HEM NA FE NC 172.48 12.51 +HEM ND FE NB 172.48 12.51 +HEM ND FE NC 89.77 6.92 +HEM NB FE NC 89.77 6.92 + +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 +HEM sp2_sp2_1 C3D C4D CHA C1A 180.000 5.0 2 +HEM sp2_sp2_2 C2A C1A CHA C4D 180.000 5.0 2 +HEM sp2_sp3_1 O1A CGA CBA CAA 120.000 20.0 6 +HEM const_0 CHB C1B C2B CMB 0.000 0.0 1 +HEM const_1 CHB C1B NB C4B 180.000 0.0 1 +HEM const_2 CMB C2B C3B CAB 0.000 0.0 1 +HEM sp2_sp3_2 C1B C2B CMB HMB 150.000 20.0 6 +HEM const_3 CAB C3B C4B CHC 0.000 0.0 1 +HEM sp2_sp2_3 C2B C3B CAB CBB 180.000 5.0 2 +HEM const_4 CHC C4B NB C1B 180.000 0.0 1 +HEM sp2_sp2_4 C3B CAB CBB HBB 180.000 5.0 2 +HEM sp2_sp2_5 C2B C1B CHB C4A 180.000 5.0 2 +HEM sp2_sp2_6 C3A C4A CHB C1B 180.000 5.0 2 +HEM const_5 CHC C1C C2C CMC 0.000 0.0 1 +HEM const_6 CHC C1C NC C4C 180.000 0.0 1 +HEM const_7 CMC C2C C3C CAC 0.000 0.0 1 +HEM sp2_sp3_3 C1C C2C CMC HMC 150.000 20.0 6 +HEM const_8 CAC C3C C4C CHD 0.000 0.0 1 +HEM sp2_sp2_7 C2C C3C CAC CBC 180.000 5.0 2 +HEM const_9 CHD C4C NC C1C 180.000 0.0 1 +HEM sp2_sp2_8 C3C CAC CBC HBC 180.000 5.0 2 +HEM const_10 CHD C1D C2D CMD 0.000 0.0 1 +HEM const_11 CHD C1D ND C4D 180.000 0.0 1 +HEM const_12 CMD C2D C3D CAD 0.000 0.0 1 +HEM sp2_sp3_4 C1D C2D CMD HMD 150.000 20.0 6 +HEM sp2_sp2_9 C3B C4B CHC C1C 180.000 5.0 2 +HEM sp2_sp2_10 C2C C1C CHC C4B 180.000 5.0 2 +HEM const_13 CAD C3D C4D CHA 0.000 0.0 1 +HEM sp2_sp3_5 C2D C3D CAD CBD -90.000 20.0 6 +HEM const_14 CHA C4D ND C1D 180.000 0.0 1 +HEM sp3_sp3_1 C3D CAD CBD CGD 180.000 10.0 3 +HEM sp2_sp3_6 O1D CGD CBD CAD 120.000 20.0 6 +HEM sp2_sp2_11 C3C C4C CHD C1D 180.000 5.0 2 +HEM sp2_sp2_12 C2D C1D CHD C4C 180.000 5.0 2 +HEM const_15 CHA C1A NA C4A 180.000 0.0 1 +HEM const_16 CHA C1A C2A CAA 0.000 0.0 1 +HEM const_17 CAA C2A C3A CMA 0.000 0.0 1 +HEM sp2_sp3_7 C1A C2A CAA CBA -90.000 20.0 6 +HEM const_18 CMA C3A C4A CHB 0.000 0.0 1 +HEM sp2_sp3_8 C2A C3A CMA HMA 150.000 20.0 6 +HEM const_19 CHB C4A NA C1A 180.000 0.0 1 +HEM sp3_sp3_2 C2A CAA CBA CGA 180.000 10.0 3 + +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 +HEM plan-15 FE 0.060 +HEM plan-15 NA 0.060 +HEM plan-15 C1A 0.060 +HEM plan-15 C4A 0.060 +HEM plan-16 FE 0.060 +HEM plan-16 NB 0.060 +HEM plan-16 C1B 0.060 +HEM plan-16 C4B 0.060 +HEM plan-17 FE 0.060 +HEM plan-17 NC 0.060 +HEM plan-17 C1C 0.060 +HEM plan-17 C4C 0.060 +HEM plan-18 FE 0.060 +HEM plan-18 ND 0.060 +HEM plan-18 C1D 0.060 +HEM plan-18 C4D 0.060 +HEM plan-1 C1B 0.020 +HEM plan-1 C2B 0.020 +HEM plan-1 C3B 0.020 +HEM plan-1 C4B 0.020 +HEM plan-1 CAB 0.020 +HEM plan-1 CHB 0.020 +HEM plan-1 CHC 0.020 +HEM plan-1 CMB 0.020 +HEM plan-1 NB 0.020 +HEM plan-2 C1C 0.020 +HEM plan-2 C2C 0.020 +HEM plan-2 C3C 0.020 +HEM plan-2 C4C 0.020 +HEM plan-2 CAC 0.020 +HEM plan-2 CHC 0.020 +HEM plan-2 CHD 0.020 +HEM plan-2 CMC 0.020 +HEM plan-2 NC 0.020 +HEM plan-3 C1D 0.020 +HEM plan-3 C2D 0.020 +HEM plan-3 C3D 0.020 +HEM plan-3 C4D 0.020 +HEM plan-3 CAD 0.020 +HEM plan-3 CHA 0.020 +HEM plan-3 CHD 0.020 +HEM plan-3 CMD 0.020 +HEM plan-3 ND 0.020 +HEM plan-4 C1A 0.020 +HEM plan-4 C2A 0.020 +HEM plan-4 C3A 0.020 +HEM plan-4 C4A 0.020 +HEM plan-4 CAA 0.020 +HEM plan-4 CHA 0.020 +HEM plan-4 CHB 0.020 +HEM plan-4 CMA 0.020 +HEM plan-4 NA 0.020 +HEM plan-5 C1A 0.020 +HEM plan-5 C4D 0.020 +HEM plan-5 CHA 0.020 +HEM plan-5 HHA 0.020 +HEM plan-6 C1B 0.020 +HEM plan-6 C4A 0.020 +HEM plan-6 CHB 0.020 +HEM plan-6 HHB 0.020 +HEM plan-7 C1C 0.020 +HEM plan-7 C4B 0.020 +HEM plan-7 CHC 0.020 +HEM plan-7 HHC 0.020 +HEM plan-8 C1D 0.020 +HEM plan-8 C4C 0.020 +HEM plan-8 CHD 0.020 +HEM plan-8 HHD 0.020 +HEM plan-9 CBA 0.020 +HEM plan-9 CGA 0.020 +HEM plan-9 O1A 0.020 +HEM plan-9 O2A 0.020 +HEM plan-10 C3B 0.020 +HEM plan-10 CAB 0.020 +HEM plan-10 CBB 0.020 +HEM plan-10 HAB 0.020 +HEM plan-11 CAB 0.020 +HEM plan-11 CBB 0.020 +HEM plan-11 HBB 0.020 +HEM plan-11 HBBA 0.020 +HEM plan-12 C3C 0.020 +HEM plan-12 CAC 0.020 +HEM plan-12 CBC 0.020 +HEM plan-12 HAC 0.020 +HEM plan-13 CAC 0.020 +HEM plan-13 CBC 0.020 +HEM plan-13 HBC 0.020 +HEM plan-13 HBCA 0.020 +HEM plan-14 CBD 0.020 +HEM plan-14 CGD 0.020 +HEM plan-14 O1D 0.020 +HEM plan-14 O2D 0.020 + +loop_ +_chem_comp_ring_atom.comp_id +_chem_comp_ring_atom.ring_serial_number +_chem_comp_ring_atom.atom_id +_chem_comp_ring_atom.is_aromatic_ring +HEM ring-1 C1B YES +HEM ring-1 C2B YES +HEM ring-1 C3B YES +HEM ring-1 C4B YES +HEM ring-1 NB YES +HEM ring-2 C1C YES +HEM ring-2 C2C YES +HEM ring-2 C3C YES +HEM ring-2 C4C YES +HEM ring-2 NC YES +HEM ring-3 C1D YES +HEM ring-3 C2D YES +HEM ring-3 C3D YES +HEM ring-3 C4D YES +HEM ring-3 ND YES +HEM ring-4 C1A YES +HEM ring-4 C2A YES +HEM ring-4 C3A YES +HEM ring-4 C4A YES +HEM ring-4 NA YES + +loop_ +_acedrg_chem_comp_descriptor.comp_id +_acedrg_chem_comp_descriptor.program_name +_acedrg_chem_comp_descriptor.program_version +_acedrg_chem_comp_descriptor.type +HEM acedrg 311 'dictionary generator' +HEM 'acedrg_database' 12 'data source' +HEM rdkit 2019.09.1 'Chemoinformatics tool' +HEM servalcat 0.4.93 'optimization tool' +HEM metalCoord 0.1.63 'metal coordination analysis' diff --git a/image_analysis/structure_refinement/monomers/M2G.cif b/image_analysis/structure_refinement/monomers/M2G.cif new file mode 100644 index 000000000..f08ed483a --- /dev/null +++ b/image_analysis/structure_refinement/monomers/M2G.cif @@ -0,0 +1,307 @@ +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 +M2G M2G "N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE" RNA 42 26 . + +data_comp_M2G +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 +M2G P P P 0 39.624 -6.580 13.186 +M2G OP1 O O 0 40.880 -5.814 12.816 +M2G OP2 O OP -1 38.958 -7.232 11.988 +M2G OP3 O OP -1 39.838 -7.543 14.338 +M2G "O5'" O O2 0 38.577 -5.476 13.725 +M2G "C5'" C CH2 0 37.276 -5.917 14.192 +M2G "C4'" C CH1 0 36.420 -4.719 14.527 +M2G "O4'" O O2 0 37.113 -3.873 15.478 +M2G "C3'" C CH1 0 36.075 -3.781 13.366 +M2G "O3'" O OH1 0 34.949 -4.254 12.637 +M2G "C2'" C CH1 0 35.793 -2.465 14.098 +M2G "O2'" O OH1 0 34.465 -2.359 14.571 +M2G "C1'" C CH1 0 36.802 -2.514 15.248 +M2G N9 N NR5 0 38.030 -1.769 14.978 +M2G C8 C CR15 0 39.306 -2.257 14.820 +M2G N7 N NRD5 0 40.197 -1.323 14.584 +M2G C5 C CR56 0 39.465 -0.144 14.588 +M2G C6 C CR6 0 39.880 1.200 14.389 +M2G O6 O O 0 41.026 1.613 14.162 +M2G N1 N NR16 0 38.812 2.107 14.473 +M2G C2 C CR6 0 37.498 1.761 14.720 +M2G N2 N N 0 36.512 2.761 14.782 +M2G N3 N NRD6 0 37.123 0.497 14.909 +M2G C4 C CR56 0 38.134 -0.404 14.831 +M2G CM1 C CH3 0 35.097 2.452 14.595 +M2G CM2 C CH3 0 36.840 4.157 15.050 +M2G "H5'" H H 0 37.383 -6.482 14.996 +M2G "H5''" H H 0 36.833 -6.454 13.489 +M2G "H4'" H H 0 35.589 -5.043 14.937 +M2G "H3'" H H 0 36.854 -3.676 12.761 +M2G "HO3'" H H 0 34.740 -3.675 12.052 +M2G "H2'" H H 0 35.987 -1.696 13.500 +M2G "HO2'" H H 0 34.306 -2.977 15.131 +M2G "H1'" H H 0 36.375 -2.140 16.053 +M2G H8 H H 0 39.523 -3.172 14.874 +M2G HN1 H H 0 39.016 2.969 14.353 +M2G HM11 H H 0 34.999 1.706 13.981 +M2G HM12 H H 0 34.637 3.225 14.228 +M2G HM13 H H 0 34.702 2.219 15.451 +M2G HM21 H H 0 37.546 4.202 15.715 +M2G HM22 H H 0 36.057 4.624 15.385 +M2G HM23 H H 0 37.142 4.581 14.230 + +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 +M2G P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192 +M2G P OP2 SINGLE n 1.517 0.0192 1.517 0.0192 +M2G P OP3 SINGLE n 1.517 0.0192 1.517 0.0192 +M2G P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 +M2G "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +M2G "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +M2G "C4'" "O4'" SINGLE n 1.451 0.0100 1.451 0.0100 +M2G "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 +M2G "O4'" "C1'" SINGLE n 1.409 0.0100 1.409 0.0100 +M2G "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +M2G "C3'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100 +M2G "C2'" "O2'" SINGLE n 1.411 0.0100 1.411 0.0100 +M2G "C2'" "C1'" SINGLE n 1.525 0.0100 1.525 0.0100 +M2G "C1'" N9 SINGLE n 1.458 0.0100 1.458 0.0100 +M2G N9 C8 SINGLE y 1.372 0.0100 1.372 0.0100 +M2G N9 C4 SINGLE y 1.375 0.0100 1.375 0.0100 +M2G C8 N7 DOUBLE y 1.312 0.0100 1.312 0.0100 +M2G N7 C5 SINGLE y 1.390 0.0100 1.390 0.0100 +M2G C5 C6 SINGLE y 1.417 0.0103 1.417 0.0103 +M2G C5 C4 DOUBLE y 1.377 0.0100 1.377 0.0100 +M2G C6 O6 DOUBLE n 1.239 0.0100 1.239 0.0100 +M2G C6 N1 SINGLE y 1.396 0.0107 1.396 0.0107 +M2G N1 C2 SINGLE y 1.372 0.0100 1.372 0.0100 +M2G C2 N2 SINGLE n 1.370 0.0200 1.370 0.0200 +M2G C2 N3 DOUBLE y 1.324 0.0127 1.324 0.0127 +M2G N2 CM1 SINGLE n 1.453 0.0119 1.453 0.0119 +M2G N2 CM2 SINGLE n 1.453 0.0119 1.453 0.0119 +M2G N3 C4 SINGLE y 1.355 0.0100 1.355 0.0100 +M2G "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +M2G "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 +M2G "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 +M2G "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +M2G "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +M2G "C2'" "H2'" SINGLE n 1.089 0.0100 0.994 0.0200 +M2G "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 +M2G "C1'" "H1'" SINGLE n 1.089 0.0100 0.984 0.0200 +M2G C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170 +M2G N1 HN1 SINGLE n 1.016 0.0100 0.897 0.0200 +M2G CM1 HM11 SINGLE n 1.089 0.0100 0.971 0.0181 +M2G CM1 HM12 SINGLE n 1.089 0.0100 0.971 0.0181 +M2G CM1 HM13 SINGLE n 1.089 0.0100 0.971 0.0181 +M2G CM2 HM21 SINGLE n 1.089 0.0100 0.971 0.0181 +M2G CM2 HM22 SINGLE n 1.089 0.0100 0.971 0.0181 +M2G CM2 HM23 SINGLE n 1.089 0.0100 0.971 0.0181 + +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 +M2G OP1 P OP2 112.864 1.69 +M2G OP1 P OP3 112.864 1.69 +M2G OP1 P "O5'" 105.808 2.07 +M2G OP2 P OP3 112.864 1.69 +M2G OP2 P "O5'" 105.808 2.07 +M2G OP3 P "O5'" 105.808 2.07 +M2G P "O5'" "C5'" 118.783 1.50 +M2G "O5'" "C5'" "C4'" 109.342 1.50 +M2G "O5'" "C5'" "H5'" 109.845 1.50 +M2G "O5'" "C5'" "H5''" 109.845 1.50 +M2G "C4'" "C5'" "H5'" 109.624 1.50 +M2G "C4'" "C5'" "H5''" 109.624 1.50 +M2G "H5'" "C5'" "H5''" 108.472 1.50 +M2G "C5'" "C4'" "O4'" 109.123 1.50 +M2G "C5'" "C4'" "C3'" 116.008 1.52 +M2G "C5'" "C4'" "H4'" 108.268 1.50 +M2G "O4'" "C4'" "C3'" 105.388 1.50 +M2G "O4'" "C4'" "H4'" 108.947 1.50 +M2G "C3'" "C4'" "H4'" 109.363 1.86 +M2G "C4'" "O4'" "C1'" 109.903 1.50 +M2G "C4'" "C3'" "O3'" 111.281 2.46 +M2G "C4'" "C3'" "C2'" 102.602 1.50 +M2G "C4'" "C3'" "H3'" 110.452 2.54 +M2G "O3'" "C3'" "C2'" 111.581 2.83 +M2G "O3'" "C3'" "H3'" 110.380 1.67 +M2G "C2'" "C3'" "H3'" 110.504 1.75 +M2G "C3'" "O3'" "HO3'" 108.744 3.00 +M2G "C3'" "C2'" "O2'" 112.782 2.45 +M2G "C3'" "C2'" "C1'" 101.239 1.50 +M2G "C3'" "C2'" "H2'" 110.596 1.51 +M2G "O2'" "C2'" "C1'" 111.715 2.69 +M2G "O2'" "C2'" "H2'" 110.448 1.97 +M2G "C1'" "C2'" "H2'" 110.636 1.70 +M2G "C2'" "O2'" "HO2'" 109.103 2.13 +M2G "O4'" "C1'" "C2'" 106.047 1.50 +M2G "O4'" "C1'" N9 108.477 1.50 +M2G "O4'" "C1'" "H1'" 109.807 1.50 +M2G "C2'" "C1'" N9 113.824 1.50 +M2G "C2'" "C1'" "H1'" 109.015 1.50 +M2G N9 "C1'" "H1'" 109.561 1.50 +M2G "C1'" N9 C8 126.829 1.91 +M2G "C1'" N9 C4 127.440 1.80 +M2G C8 N9 C4 105.731 1.50 +M2G N9 C8 N7 113.507 1.50 +M2G N9 C8 H8 123.187 1.50 +M2G N7 C8 H8 123.307 1.50 +M2G C8 N7 C5 104.778 1.50 +M2G N7 C5 C6 130.048 1.50 +M2G N7 C5 C4 110.574 1.50 +M2G C6 C5 C4 119.378 1.50 +M2G C5 C6 O6 128.253 1.50 +M2G C5 C6 N1 111.349 1.50 +M2G O6 C6 N1 120.398 1.50 +M2G C6 N1 C2 123.973 1.50 +M2G C6 N1 HN1 117.776 2.44 +M2G C2 N1 HN1 118.251 1.59 +M2G N1 C2 N2 118.650 1.50 +M2G N1 C2 N3 122.959 1.50 +M2G N2 C2 N3 118.391 2.18 +M2G C2 N2 CM1 121.373 2.30 +M2G C2 N2 CM2 121.373 2.30 +M2G CM1 N2 CM2 117.254 1.50 +M2G C2 N3 C4 114.148 1.50 +M2G N9 C4 C5 105.411 1.50 +M2G N9 C4 N3 126.396 1.50 +M2G C5 C4 N3 128.193 1.50 +M2G N2 CM1 HM11 109.468 1.50 +M2G N2 CM1 HM12 109.468 1.50 +M2G N2 CM1 HM13 109.468 1.50 +M2G HM11 CM1 HM12 109.352 1.56 +M2G HM11 CM1 HM13 109.352 1.56 +M2G HM12 CM1 HM13 109.352 1.56 +M2G N2 CM2 HM21 109.468 1.50 +M2G N2 CM2 HM22 109.468 1.50 +M2G N2 CM2 HM23 109.468 1.50 +M2G HM21 CM2 HM22 109.352 1.56 +M2G HM21 CM2 HM23 109.352 1.56 +M2G HM22 CM2 HM23 109.352 1.56 + +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 +M2G C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +M2G C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +M2G C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +M2G C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +M2G C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +M2G C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +M2G C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +M2G C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +M2G C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +M2G C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +M2G C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +M2G C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +M2G alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +M2G beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +M2G epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +M2G gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +M2G sp3_sp3_52 "C3'" "C2'" "O2'" "HO2'" 180.000 10.00 3 +M2G const_18 N7 C8 N9 "C1'" 180.000 10.0 2 +M2G const_30 C5 C4 N9 "C1'" 180.000 10.0 2 +M2G const_21 N9 C8 N7 C5 0.000 10.0 2 +M2G const_24 C6 C5 N7 C8 180.000 10.0 2 +M2G const_sp2_sp2_4 N7 C5 C6 O6 0.000 5.0 2 +M2G const_25 N9 C4 C5 N7 0.000 10.0 2 +M2G const_sp2_sp2_7 O6 C6 N1 C2 180.000 5.0 2 +M2G const_11 N2 C2 N1 C6 180.000 10.0 2 +M2G sp2_sp2_1 N1 C2 N2 CM1 180.000 5.0 2 +M2G const_14 N2 C2 N3 C4 180.000 10.0 2 +M2G sp2_sp3_10 CM2 N2 CM1 HM11 180.000 10.0 6 +M2G sp2_sp3_16 CM1 N2 CM2 HM21 180.000 10.0 6 +M2G 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 +M2G chir_1 P "O5'" OP2 OP3 both +M2G chir_2 "C4'" "O4'" "C3'" "C5'" negative +M2G chir_3 "C3'" "O3'" "C4'" "C2'" positive +M2G chir_4 "C2'" "O2'" "C1'" "C3'" negative +M2G 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 +M2G plan-1 "C1'" 0.020 +M2G plan-1 C2 0.020 +M2G plan-1 C4 0.020 +M2G plan-1 C5 0.020 +M2G plan-1 C6 0.020 +M2G plan-1 C8 0.020 +M2G plan-1 H8 0.020 +M2G plan-1 HN1 0.020 +M2G plan-1 N1 0.020 +M2G plan-1 N2 0.020 +M2G plan-1 N3 0.020 +M2G plan-1 N7 0.020 +M2G plan-1 N9 0.020 +M2G plan-1 O6 0.020 +M2G plan-2 C2 0.020 +M2G plan-2 CM1 0.020 +M2G plan-2 CM2 0.020 +M2G 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 +M2G SMILES ACDLabs 10.04 O=C1c2ncn(c2N=C(N(C)C)N1)C3OC(C(O)C3O)COP(=O)(O)O +M2G SMILES_CANONICAL CACTVS 3.341 CN(C)C1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O +M2G SMILES CACTVS 3.341 CN(C)C1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O +M2G SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CN(C)C1=Nc2c(ncn2[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)C(=O)N1 +M2G SMILES "OpenEye OEToolkits" 1.5.0 CN(C)C1=Nc2c(ncn2C3C(C(C(O3)COP(=O)(O)O)O)O)C(=O)N1 +M2G InChI InChI 1.03 InChI=1S/C12H18N5O8P/c1-16(2)12-14-9-6(10(20)15-12)13-4-17(9)11-8(19)7(18)5(25-11)3-24-26(21,22)23/h4-5,7-8,11,18-19H,3H2,1-2H3,(H,14,15,20)(H2,21,22,23)/t5-,7-,8-,11-/m1/s1 +M2G InChIKey InChI 1.03 IWJFVRMOIKWYNZ-IOSLPCCCSA-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 +M2G acedrg 243 "dictionary generator" +M2G acedrg_database 11 "data source" +M2G rdkit 2017.03.2 "Chemoinformatics tool" +M2G refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/NAD.cif b/image_analysis/structure_refinement/monomers/NAD.cif new file mode 100644 index 000000000..e61090f17 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/NAD.cif @@ -0,0 +1,447 @@ +# +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 +NAD NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE NON-POLYMER 70 44 . +# +data_comp_NAD +# +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 +NAD PA P P 0 18.626 51.830 -19.907 +NAD O1A O O 0 18.239 51.977 -21.341 +NAD O2A O OP -1 17.725 52.411 -18.868 +NAD O5B O O2 0 20.113 52.394 -19.696 +NAD C5B C CH2 0 21.139 52.018 -20.649 +NAD C4B C CH1 0 22.468 52.578 -20.205 +NAD O4B O O2 0 23.527 51.931 -20.956 +NAD C3B C CH1 0 22.679 54.079 -20.440 +NAD O3B O OH1 0 23.576 54.623 -19.479 +NAD C2B C CH1 0 23.256 54.094 -21.858 +NAD O2B O OH1 0 24.009 55.255 -22.137 +NAD C1B C CH1 0 24.142 52.850 -21.831 +NAD N9A N NR5 0 24.299 52.206 -23.131 +NAD C8A C CR15 0 23.301 51.647 -23.891 +NAD N7A N NRD5 0 23.726 51.133 -25.017 +NAD C5A C CR56 0 25.095 51.358 -25.002 +NAD C6A C CR6 0 26.120 51.044 -25.921 +NAD N6A N NH2 0 25.907 50.413 -27.073 +NAD N1A N NRD6 0 27.387 51.412 -25.601 +NAD C2A C CR16 0 27.594 52.049 -24.438 +NAD N3A N NRD6 0 26.710 52.394 -23.501 +NAD C4A C CR56 0 25.462 52.019 -23.841 +NAD O3 O O2 0 18.840 50.272 -19.588 +NAD PN P P 0 18.864 49.438 -18.218 +NAD O1N O O 0 17.461 49.265 -17.740 +NAD O2N O OP -1 19.853 50.066 -17.293 +NAD O5D O O2 0 19.431 48.023 -18.723 +NAD C5D C CH2 0 20.701 47.984 -19.424 +NAD C4D C CH1 0 21.194 46.559 -19.494 +NAD O4D O O2 0 21.428 46.064 -18.157 +NAD C3D C CH1 0 20.242 45.551 -20.164 +NAD O3D O OH1 0 20.944 44.677 -21.042 +NAD C2D C CH1 0 19.601 44.823 -18.973 +NAD O2D O OH1 0 19.219 43.486 -19.258 +NAD C1D C CH1 0 20.764 44.819 -17.978 +NAD N1N N NR6 1 20.354 44.692 -16.557 +NAD C2N C CR16 0 19.658 45.714 -15.942 +NAD C3N C CR6 0 19.271 45.586 -14.608 +NAD C7N C C 0 18.519 46.700 -13.946 +NAD O7N O O 0 18.970 47.210 -12.908 +NAD N7N N NH2 0 17.384 47.110 -14.499 +NAD C4N C CR16 0 19.587 44.433 -13.901 +NAD C5N C CR16 0 20.283 43.414 -14.527 +NAD C6N C CR16 0 20.661 43.549 -15.851 +NAD H51A H H 0 20.912 52.372 -21.544 +NAD H52A H H 0 21.197 51.032 -20.708 +NAD H4B H H 0 22.584 52.377 -19.252 +NAD H3B H H 0 21.811 54.559 -20.413 +NAD HO3A H H 0 23.564 55.469 -19.544 +NAD H2B H H 0 22.529 53.992 -22.526 +NAD HO2A H H 0 24.306 55.209 -22.931 +NAD H1B H H 0 25.026 53.099 -21.478 +NAD H8A H H 0 22.396 51.641 -23.629 +NAD H61A H H 0 26.528 49.888 -27.403 +NAD H62A H H 0 25.147 50.524 -27.495 +NAD H2A H H 0 28.491 52.285 -24.258 +NAD H51N H H 0 21.366 48.541 -18.948 +NAD H52N H H 0 20.590 48.342 -20.339 +NAD H4D H H 0 22.048 46.560 -19.977 +NAD H3D H H 0 19.542 46.042 -20.668 +NAD HO3N H H 0 21.584 44.301 -20.630 +NAD H2D H H 0 18.837 45.341 -18.621 +NAD HO2N H H 0 18.872 43.138 -18.566 +NAD H1D H H 0 21.389 44.085 -18.205 +NAD H2N H H 0 19.441 46.498 -16.419 +NAD H71N H H 0 16.923 47.775 -14.126 +NAD H72N H H 0 17.069 46.727 -15.240 +NAD H4N H H 0 19.329 44.343 -13.000 +NAD H5N H H 0 20.502 42.627 -14.056 +NAD H6N H H 0 21.135 42.856 -16.280 +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 +NAD PA O1A DOUBLE n 1.493 0.0122 1.493 0.0122 +NAD PA O2A SINGLE n 1.493 0.0122 1.493 0.0122 +NAD PA O5B SINGLE n 1.604 0.0133 1.604 0.0133 +NAD PA O3 SINGLE n 1.604 0.0133 1.604 0.0133 +NAD O5B C5B SINGLE n 1.450 0.0166 1.450 0.0166 +NAD C5B C4B SINGLE n 1.509 0.0100 1.509 0.0100 +NAD C4B O4B SINGLE n 1.451 0.0100 1.451 0.0100 +NAD C4B C3B SINGLE n 1.535 0.0100 1.535 0.0100 +NAD O4B C1B SINGLE n 1.409 0.0100 1.409 0.0100 +NAD C3B O3B SINGLE n 1.422 0.0100 1.422 0.0100 +NAD C3B C2B SINGLE n 1.531 0.0100 1.531 0.0100 +NAD C2B O2B SINGLE n 1.411 0.0100 1.411 0.0100 +NAD C2B C1B SINGLE n 1.525 0.0100 1.525 0.0100 +NAD C1B N9A SINGLE n 1.458 0.0100 1.458 0.0100 +NAD N9A C8A SINGLE y 1.372 0.0100 1.372 0.0100 +NAD N9A C4A SINGLE y 1.374 0.0101 1.374 0.0101 +NAD C8A N7A DOUBLE y 1.310 0.0100 1.310 0.0100 +NAD N7A C5A SINGLE y 1.388 0.0100 1.388 0.0100 +NAD C5A C6A SINGLE y 1.408 0.0100 1.408 0.0100 +NAD C5A C4A DOUBLE y 1.381 0.0100 1.381 0.0100 +NAD C6A N6A SINGLE n 1.330 0.0100 1.330 0.0100 +NAD C6A N1A DOUBLE y 1.354 0.0100 1.354 0.0100 +NAD N1A C2A SINGLE y 1.339 0.0100 1.339 0.0100 +NAD C2A N3A DOUBLE y 1.330 0.0100 1.330 0.0100 +NAD N3A C4A SINGLE y 1.343 0.0100 1.343 0.0100 +NAD O3 PN SINGLE n 1.604 0.0133 1.604 0.0133 +NAD PN O1N DOUBLE n 1.493 0.0122 1.493 0.0122 +NAD PN O2N SINGLE n 1.493 0.0122 1.493 0.0122 +NAD PN O5D SINGLE n 1.604 0.0133 1.604 0.0133 +NAD O5D C5D SINGLE n 1.450 0.0166 1.450 0.0166 +NAD C5D C4D SINGLE n 1.509 0.0100 1.509 0.0100 +NAD C4D O4D SINGLE n 1.443 0.0107 1.443 0.0107 +NAD C4D C3D SINGLE n 1.535 0.0100 1.535 0.0100 +NAD O4D C1D SINGLE n 1.425 0.0141 1.425 0.0141 +NAD C3D O3D SINGLE n 1.422 0.0100 1.422 0.0100 +NAD C3D C2D SINGLE n 1.533 0.0100 1.533 0.0100 +NAD C2D O2D SINGLE n 1.419 0.0101 1.419 0.0101 +NAD C2D C1D SINGLE n 1.533 0.0100 1.533 0.0100 +NAD C1D N1N SINGLE n 1.477 0.0138 1.477 0.0138 +NAD N1N C2N DOUBLE y 1.377 0.0105 1.377 0.0105 +NAD N1N C6N SINGLE y 1.375 0.0105 1.375 0.0105 +NAD C2N C3N SINGLE y 1.390 0.0105 1.390 0.0105 +NAD C3N C7N SINGLE n 1.497 0.0100 1.497 0.0100 +NAD C3N C4N DOUBLE y 1.385 0.0100 1.385 0.0100 +NAD C7N O7N DOUBLE n 1.241 0.0105 1.241 0.0105 +NAD C7N N7N SINGLE n 1.326 0.0100 1.326 0.0100 +NAD C4N C5N SINGLE y 1.380 0.0100 1.380 0.0100 +NAD C5N C6N DOUBLE y 1.380 0.0128 1.380 0.0128 +NAD C5B H51A SINGLE n 1.089 0.0100 0.989 0.0200 +NAD C5B H52A SINGLE n 1.089 0.0100 0.989 0.0200 +NAD C4B H4B SINGLE n 1.089 0.0100 0.981 0.0200 +NAD C3B H3B SINGLE n 1.089 0.0100 0.992 0.0200 +NAD O3B HO3A SINGLE n 0.970 0.0120 0.849 0.0200 +NAD C2B H2B SINGLE n 1.089 0.0100 0.994 0.0200 +NAD O2B HO2A SINGLE n 0.970 0.0120 0.849 0.0200 +NAD C1B H1B SINGLE n 1.089 0.0100 0.984 0.0200 +NAD C8A H8A SINGLE n 1.082 0.0130 0.942 0.0170 +NAD N6A H61A SINGLE n 1.016 0.0100 0.877 0.0200 +NAD N6A H62A SINGLE n 1.016 0.0100 0.877 0.0200 +NAD C2A H2A SINGLE n 1.082 0.0130 0.945 0.0200 +NAD C5D H51N SINGLE n 1.089 0.0100 0.989 0.0200 +NAD C5D H52N SINGLE n 1.089 0.0100 0.989 0.0200 +NAD C4D H4D SINGLE n 1.089 0.0100 0.981 0.0200 +NAD C3D H3D SINGLE n 1.089 0.0100 0.992 0.0200 +NAD O3D HO3N SINGLE n 0.970 0.0120 0.849 0.0200 +NAD C2D H2D SINGLE n 1.089 0.0100 0.989 0.0200 +NAD O2D HO2N SINGLE n 0.970 0.0120 0.849 0.0200 +NAD C1D H1D SINGLE n 1.089 0.0100 0.990 0.0173 +NAD C2N H2N SINGLE n 1.082 0.0130 0.943 0.0170 +NAD N7N H71N SINGLE n 1.016 0.0100 0.891 0.0200 +NAD N7N H72N SINGLE n 1.016 0.0100 0.891 0.0200 +NAD C4N H4N SINGLE n 1.082 0.0130 0.941 0.0168 +NAD C5N H5N SINGLE n 1.082 0.0130 0.943 0.0190 +NAD C6N H6N SINGLE n 1.082 0.0130 0.943 0.0169 +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 +NAD O1A PA O2A 118.411 2.35 +NAD O1A PA O5B 109.410 1.50 +NAD O1A PA O3 108.816 2.14 +NAD O2A PA O5B 109.410 1.50 +NAD O2A PA O3 108.816 2.14 +NAD O5B PA O3 101.065 1.97 +NAD PA O5B C5B 118.553 2.41 +NAD O5B C5B C4B 109.342 1.50 +NAD O5B C5B H51A 109.845 1.50 +NAD O5B C5B H52A 109.845 1.50 +NAD C4B C5B H51A 109.624 1.50 +NAD C4B C5B H52A 109.624 1.50 +NAD H51A C5B H52A 108.472 1.50 +NAD C5B C4B O4B 109.123 1.50 +NAD C5B C4B C3B 116.008 1.52 +NAD C5B C4B H4B 108.268 1.50 +NAD O4B C4B C3B 105.388 1.50 +NAD O4B C4B H4B 108.947 1.50 +NAD C3B C4B H4B 109.363 1.86 +NAD C4B O4B C1B 109.903 1.50 +NAD C4B C3B O3B 111.281 2.46 +NAD C4B C3B C2B 102.602 1.50 +NAD C4B C3B H3B 110.452 2.54 +NAD O3B C3B C2B 111.581 2.83 +NAD O3B C3B H3B 110.380 1.67 +NAD C2B C3B H3B 110.504 1.75 +NAD C3B O3B HO3A 108.744 3.00 +NAD C3B C2B O2B 112.782 2.45 +NAD C3B C2B C1B 101.239 1.50 +NAD C3B C2B H2B 110.596 1.51 +NAD O2B C2B C1B 111.715 2.69 +NAD O2B C2B H2B 110.448 1.97 +NAD C1B C2B H2B 110.636 1.70 +NAD C2B O2B HO2A 109.103 2.13 +NAD O4B C1B C2B 106.047 1.50 +NAD O4B C1B N9A 108.477 1.50 +NAD O4B C1B H1B 109.807 1.50 +NAD C2B C1B N9A 113.824 1.50 +NAD C2B C1B H1B 109.015 1.50 +NAD N9A C1B H1B 109.561 1.50 +NAD C1B N9A C8A 126.848 1.91 +NAD C1B N9A C4A 127.459 1.80 +NAD C8A N9A C4A 105.693 1.50 +NAD N9A C8A N7A 113.469 1.50 +NAD N9A C8A H8A 123.206 1.50 +NAD N7A C8A H8A 123.326 1.50 +NAD C8A N7A C5A 104.739 1.50 +NAD N7A C5A C6A 132.250 1.50 +NAD N7A C5A C4A 110.483 1.50 +NAD C6A C5A C4A 117.267 1.50 +NAD C5A C6A N6A 123.792 1.50 +NAD C5A C6A N1A 117.409 1.50 +NAD N6A C6A N1A 118.799 1.50 +NAD C6A N6A H61A 119.723 1.50 +NAD C6A N6A H62A 119.723 1.50 +NAD H61A N6A H62A 120.554 1.88 +NAD C6A N1A C2A 118.521 1.50 +NAD N1A C2A N3A 129.332 1.50 +NAD N1A C2A H2A 115.313 1.50 +NAD N3A C2A H2A 115.355 1.50 +NAD C2A N3A C4A 110.982 1.50 +NAD N9A C4A C5A 105.616 1.50 +NAD N9A C4A N3A 127.895 1.50 +NAD C5A C4A N3A 126.489 1.50 +NAD PA O3 PN 132.542 3.00 +NAD O3 PN O1N 108.816 2.14 +NAD O3 PN O2N 108.816 2.14 +NAD O3 PN O5D 101.065 1.97 +NAD O1N PN O2N 118.411 2.35 +NAD O1N PN O5D 109.410 1.50 +NAD O2N PN O5D 109.410 1.50 +NAD PN O5D C5D 118.553 2.41 +NAD O5D C5D C4D 109.342 1.50 +NAD O5D C5D H51N 109.845 1.50 +NAD O5D C5D H52N 109.845 1.50 +NAD C4D C5D H51N 109.624 1.50 +NAD C4D C5D H52N 109.624 1.50 +NAD H51N C5D H52N 108.472 1.50 +NAD C5D C4D O4D 109.615 1.50 +NAD C5D C4D C3D 116.008 1.52 +NAD C5D C4D H4D 108.268 1.50 +NAD O4D C4D C3D 104.439 1.50 +NAD O4D C4D H4D 108.698 1.50 +NAD C3D C4D H4D 109.363 1.86 +NAD C4D O4D C1D 109.578 1.50 +NAD C4D C3D O3D 111.281 2.46 +NAD C4D C3D C2D 102.071 1.50 +NAD C4D C3D H3D 110.452 2.54 +NAD O3D C3D C2D 111.993 3.00 +NAD O3D C3D H3D 110.380 1.67 +NAD C2D C3D H3D 110.108 1.66 +NAD C3D O3D HO3N 108.744 3.00 +NAD C3D C2D O2D 112.861 2.52 +NAD C3D C2D C1D 101.269 1.50 +NAD C3D C2D H2D 110.799 1.82 +NAD O2D C2D C1D 109.476 3.00 +NAD O2D C2D H2D 111.022 1.77 +NAD C1D C2D H2D 110.760 1.63 +NAD C2D O2D HO2N 109.449 1.85 +NAD O4D C1D C2D 106.825 1.50 +NAD O4D C1D N1N 108.092 1.50 +NAD O4D C1D H1D 109.327 1.50 +NAD C2D C1D N1N 113.620 1.99 +NAD C2D C1D H1D 109.776 1.83 +NAD N1N C1D H1D 108.901 1.50 +NAD C1D N1N C2N 119.705 1.50 +NAD C1D N1N C6N 119.705 1.50 +NAD C2N N1N C6N 120.590 1.50 +NAD N1N C2N C3N 119.549 3.00 +NAD N1N C2N H2N 120.430 1.53 +NAD C3N C2N H2N 120.021 1.50 +NAD C2N C3N C7N 119.660 2.75 +NAD C2N C3N C4N 119.402 1.64 +NAD C7N C3N C4N 120.938 2.50 +NAD C3N C7N O7N 119.730 1.50 +NAD C3N C7N N7N 118.032 1.50 +NAD O7N C7N N7N 122.238 1.50 +NAD C7N N7N H71N 120.236 2.75 +NAD C7N N7N H72N 120.236 2.75 +NAD H71N N7N H72N 119.529 2.83 +NAD C3N C4N C5N 119.166 1.50 +NAD C3N C4N H4N 120.513 1.50 +NAD C5N C4N H4N 120.320 1.50 +NAD C4N C5N C6N 120.016 1.50 +NAD C4N C5N H5N 120.300 1.50 +NAD C6N C5N H5N 119.683 1.50 +NAD N1N C6N C5N 121.277 1.50 +NAD N1N C6N H6N 118.693 1.53 +NAD C5N C6N H6N 120.031 1.59 +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 +NAD sp3_sp3_54 PN O3 PA O1A 60.000 10.0 3 +NAD sp3_sp3_51 C5B O5B PA O1A 60.000 10.0 3 +NAD sp2_sp3_1 C8A N9A C1B O4B 150.000 10.0 6 +NAD const_34 N7A C8A N9A C1B 180.000 10.0 2 +NAD const_46 C5A C4A N9A C1B 180.000 10.0 2 +NAD const_37 N9A C8A N7A C5A 0.000 10.0 2 +NAD const_40 C6A C5A N7A C8A 180.000 10.0 2 +NAD const_sp2_sp2_4 N7A C5A C6A N6A 0.000 5.0 2 +NAD const_41 N9A C4A C5A N7A 0.000 10.0 2 +NAD sp2_sp2_1 C5A C6A N6A H61A 180.000 5.0 2 +NAD const_sp2_sp2_6 N6A C6A N1A C2A 180.000 5.0 2 +NAD const_sp2_sp2_7 N3A C2A N1A C6A 0.000 5.0 2 +NAD const_sp2_sp2_9 N1A C2A N3A C4A 0.000 5.0 2 +NAD const_12 N9A C4A N3A C2A 180.000 10.0 2 +NAD sp3_sp3_84 PA O3 PN O1N 60.000 10.0 3 +NAD sp3_sp3_85 C5D O5D PN O3 180.000 10.0 3 +NAD sp3_sp3_88 C4D C5D O5D PN 180.000 10.0 3 +NAD sp3_sp3_91 O4D C4D C5D O5D 180.000 10.0 3 +NAD sp3_sp3_26 C5D C4D O4D C1D -60.000 10.0 3 +NAD sp3_sp3_104 O3D C3D C4D C5D 180.000 10.0 3 +NAD sp3_sp3_28 C2D C1D O4D C4D -60.000 10.0 3 +NAD sp3_sp3_109 C4D C3D O3D HO3N 180.000 10.0 3 +NAD sp3_sp3_44 O2D C2D C3D O3D -60.000 10.0 3 +NAD sp3_sp3_112 C3D C2D O2D HO2N 180.000 10.0 3 +NAD sp3_sp3_32 O4D C1D C2D O2D 180.000 10.0 3 +NAD sp2_sp3_7 C2N N1N C1D O4D 150.000 10.0 6 +NAD const_14 C3N C2N N1N C1D 180.000 10.0 2 +NAD const_50 C5N C6N N1N C1D 180.000 10.0 2 +NAD const_18 N1N C2N C3N C7N 180.000 10.0 2 +NAD sp2_sp2_6 C2N C3N C7N O7N 0.000 5.0 2 +NAD const_23 C7N C3N C4N C5N 180.000 10.0 2 +NAD sp2_sp2_11 O7N C7N N7N H71N 0.000 5.0 2 +NAD sp3_sp3_55 C4B C5B O5B PA 180.000 10.0 3 +NAD const_25 C3N C4N C5N C6N 0.000 10.0 2 +NAD const_29 C4N C5N C6N N1N 0.000 10.0 2 +NAD sp3_sp3_58 O4B C4B C5B O5B 180.000 10.0 3 +NAD sp3_sp3_2 C5B C4B O4B C1B -60.000 10.0 3 +NAD sp3_sp3_71 O3B C3B C4B C5B 180.000 10.0 3 +NAD sp3_sp3_4 C2B C1B O4B C4B -60.000 10.0 3 +NAD sp3_sp3_76 C4B C3B O3B HO3A 180.000 10.0 3 +NAD sp3_sp3_20 O2B C2B C3B O3B -60.000 10.0 3 +NAD sp3_sp3_79 C3B C2B O2B HO2A 180.000 10.0 3 +NAD sp3_sp3_8 O4B C1B C2B O2B 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 +NAD chir_1 PA O3 O5B O2A both +NAD chir_2 C4B O4B C3B C5B negative +NAD chir_3 C3B O3B C4B C2B positive +NAD chir_4 C2B O2B C1B C3B negative +NAD chir_5 C1B O4B N9A C2B negative +NAD chir_6 PN O3 O5D O2N both +NAD chir_7 C4D O4D C3D C5D negative +NAD chir_8 C3D O3D C4D C2D positive +NAD chir_9 C2D O2D C1D C3D negative +NAD chir_10 C1D O4D N1N C2D 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 +NAD plan-1 C1B 0.020 +NAD plan-1 C2A 0.020 +NAD plan-1 C4A 0.020 +NAD plan-1 C5A 0.020 +NAD plan-1 C6A 0.020 +NAD plan-1 C8A 0.020 +NAD plan-1 H2A 0.020 +NAD plan-1 H8A 0.020 +NAD plan-1 N1A 0.020 +NAD plan-1 N3A 0.020 +NAD plan-1 N6A 0.020 +NAD plan-1 N7A 0.020 +NAD plan-1 N9A 0.020 +NAD plan-2 C1D 0.020 +NAD plan-2 C2N 0.020 +NAD plan-2 C3N 0.020 +NAD plan-2 C4N 0.020 +NAD plan-2 C5N 0.020 +NAD plan-2 C6N 0.020 +NAD plan-2 C7N 0.020 +NAD plan-2 H2N 0.020 +NAD plan-2 H4N 0.020 +NAD plan-2 H5N 0.020 +NAD plan-2 H6N 0.020 +NAD plan-2 N1N 0.020 +NAD plan-3 C6A 0.020 +NAD plan-3 H61A 0.020 +NAD plan-3 H62A 0.020 +NAD plan-3 N6A 0.020 +NAD plan-4 C3N 0.020 +NAD plan-4 C7N 0.020 +NAD plan-4 N7N 0.020 +NAD plan-4 O7N 0.020 +NAD plan-5 C7N 0.020 +NAD plan-5 H71N 0.020 +NAD plan-5 H72N 0.020 +NAD plan-5 N7N 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 +NAD SMILES_CANONICAL CACTVS 3.341 NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O +NAD SMILES CACTVS 3.341 NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O +NAD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N +NAD SMILES "OpenEye OEToolkits" 1.5.0 c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N +NAD InChI InChI 1.03 InChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1 +NAD InChIKey InChI 1.03 BAWFJGJZGIEFAR-NNYOXOHSSA-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 +NAD acedrg 243 "dictionary generator" +NAD acedrg_database 11 "data source" +NAD rdkit 2017.03.2 "Chemoinformatics tool" +NAD refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/NAI.cif b/image_analysis/structure_refinement/monomers/NAI.cif new file mode 100644 index 000000000..5fea12fc9 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/NAI.cif @@ -0,0 +1,460 @@ +# +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 +NAI NAI "1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE" NON-POLYMER 71 44 . +# +data_comp_NAI +# +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 +NAI PA P P 0 32.123 21.120 42.561 +NAI O1A O O 0 30.870 21.929 42.623 +NAI O2A O OP -1 32.361 20.105 43.629 +NAI O5B O O2 0 33.388 22.102 42.470 +NAI C5B C CH2 0 33.354 23.194 41.515 +NAI C4B C CH1 0 34.654 23.958 41.578 +NAI O4B O O2 0 34.715 24.875 40.456 +NAI C3B C CH1 0 34.861 24.837 42.817 +NAI O3B O OH1 0 36.244 24.979 43.116 +NAI C2B C CH1 0 34.216 26.154 42.376 +NAI O2B O OH1 0 34.702 27.273 43.085 +NAI C1B C CH1 0 34.624 26.209 40.905 +NAI N9A N NR5 0 33.672 26.910 40.050 +NAI C8A C CR15 0 32.354 26.580 39.853 +NAI N7A N NRD5 0 31.731 27.382 39.026 +NAI C5A C CR56 0 32.699 28.299 38.644 +NAI C6A C CR6 0 32.662 29.411 37.773 +NAI N6A N NH2 0 31.572 29.792 37.111 +NAI N1A N NRD6 0 33.809 30.121 37.612 +NAI C2A C CR16 0 34.903 29.730 38.283 +NAI N3A N NRD6 0 35.053 28.706 39.124 +NAI C4A C CR56 0 33.903 28.018 39.267 +NAI O3 O O2 0 32.194 20.391 41.133 +NAI PN P P 0 33.045 19.141 40.598 +NAI O1N O OP -1 32.494 17.894 41.207 +NAI O2N O O 0 34.496 19.434 40.787 +NAI O5D O O2 0 32.695 19.167 39.032 +NAI C5D C CH2 0 32.931 20.381 38.272 +NAI C4D C CH1 0 32.960 20.056 36.798 +NAI O4D O O2 0 34.097 19.197 36.527 +NAI C3D C CH1 0 31.723 19.330 36.245 +NAI O3D O OH1 0 31.277 19.932 35.035 +NAI C2D C CH1 0 32.229 17.899 36.048 +NAI O2D O OH1 0 31.575 17.210 34.992 +NAI C1D C CH1 0 33.704 18.112 35.723 +NAI N1N N NR6 0 34.553 16.920 36.041 +NAI C2N C CR16 0 34.762 16.547 37.347 +NAI C3N C CR6 0 35.558 15.478 37.694 +NAI C7N C C 0 35.808 15.235 39.136 +NAI O7N O O 0 36.965 15.266 39.567 +NAI N7N N NH2 0 34.772 14.990 39.928 +NAI C4N C CH2 0 36.124 14.625 36.604 +NAI C5N C CR16 0 35.864 15.118 35.233 +NAI C6N C CR16 0 35.119 16.184 35.007 +NAI H51A H H 0 32.603 23.801 41.726 +NAI H52A H H 0 33.223 22.838 40.602 +NAI H4B H H 0 35.393 23.316 41.506 +NAI H3B H H 0 34.377 24.457 43.595 +NAI HO3A H H 0 36.323 25.360 43.870 +NAI H2B H H 0 33.229 26.100 42.466 +NAI HO2A H H 0 34.323 27.974 42.792 +NAI H1B H H 0 35.506 26.639 40.838 +NAI H8A H H 0 31.936 25.850 40.278 +NAI H61A H H 0 31.623 30.443 36.523 +NAI H62A H H 0 30.806 29.392 37.264 +NAI H2A H H 0 35.676 30.255 38.140 +NAI H51N H H 0 33.794 20.784 38.539 +NAI H52N H H 0 32.211 21.035 38.453 +NAI H4D H H 0 33.085 20.897 36.307 +NAI H3D H H 0 30.994 19.339 36.918 +NAI HO3N H H 0 30.631 19.477 34.725 +NAI H2D H H 0 32.129 17.394 36.890 +NAI HO2N H H 0 31.893 16.425 34.933 +NAI H1D H H 0 33.809 18.353 34.773 +NAI H2N H H 0 34.340 17.035 38.031 +NAI H71N H H 0 34.898 14.848 40.795 +NAI H72N H H 0 33.947 14.963 39.600 +NAI H4N H H 0 35.759 13.720 36.687 +NAI H42N H H 0 37.093 14.548 36.731 +NAI H5N H H 0 36.247 14.649 34.492 +NAI H6N H H 0 34.963 16.456 34.120 +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 +NAI PA O1A DOUBLE n 1.493 0.0122 1.493 0.0122 +NAI PA O2A SINGLE n 1.493 0.0122 1.493 0.0122 +NAI PA O5B SINGLE n 1.604 0.0133 1.604 0.0133 +NAI PA O3 SINGLE n 1.604 0.0133 1.604 0.0133 +NAI O5B C5B SINGLE n 1.450 0.0166 1.450 0.0166 +NAI C5B C4B SINGLE n 1.509 0.0100 1.509 0.0100 +NAI C4B O4B SINGLE n 1.451 0.0100 1.451 0.0100 +NAI C4B C3B SINGLE n 1.535 0.0100 1.535 0.0100 +NAI O4B C1B SINGLE n 1.409 0.0100 1.409 0.0100 +NAI C3B O3B SINGLE n 1.422 0.0100 1.422 0.0100 +NAI C3B C2B SINGLE n 1.531 0.0100 1.531 0.0100 +NAI C2B O2B SINGLE n 1.411 0.0100 1.411 0.0100 +NAI C2B C1B SINGLE n 1.525 0.0100 1.525 0.0100 +NAI C1B N9A SINGLE n 1.458 0.0100 1.458 0.0100 +NAI N9A C8A SINGLE y 1.372 0.0100 1.372 0.0100 +NAI N9A C4A SINGLE y 1.374 0.0101 1.374 0.0101 +NAI C8A N7A DOUBLE y 1.310 0.0100 1.310 0.0100 +NAI N7A C5A SINGLE y 1.388 0.0100 1.388 0.0100 +NAI C5A C6A SINGLE y 1.408 0.0100 1.408 0.0100 +NAI C5A C4A DOUBLE y 1.381 0.0100 1.381 0.0100 +NAI C6A N6A SINGLE n 1.330 0.0100 1.330 0.0100 +NAI C6A N1A DOUBLE y 1.354 0.0100 1.354 0.0100 +NAI N1A C2A SINGLE y 1.339 0.0100 1.339 0.0100 +NAI C2A N3A DOUBLE y 1.330 0.0100 1.330 0.0100 +NAI N3A C4A SINGLE y 1.343 0.0100 1.343 0.0100 +NAI O3 PN SINGLE n 1.604 0.0133 1.604 0.0133 +NAI PN O1N SINGLE n 1.493 0.0122 1.493 0.0122 +NAI PN O2N DOUBLE n 1.493 0.0122 1.493 0.0122 +NAI PN O5D SINGLE n 1.604 0.0133 1.604 0.0133 +NAI O5D C5D SINGLE n 1.450 0.0166 1.450 0.0166 +NAI C5D C4D SINGLE n 1.509 0.0100 1.509 0.0100 +NAI C4D O4D SINGLE n 1.449 0.0100 1.449 0.0100 +NAI C4D C3D SINGLE n 1.535 0.0100 1.535 0.0100 +NAI O4D C1D SINGLE n 1.407 0.0132 1.407 0.0132 +NAI C3D O3D SINGLE n 1.422 0.0100 1.422 0.0100 +NAI C3D C2D SINGLE n 1.530 0.0134 1.530 0.0134 +NAI C2D O2D SINGLE n 1.420 0.0122 1.420 0.0122 +NAI C2D C1D SINGLE n 1.527 0.0119 1.527 0.0119 +NAI C1D N1N SINGLE n 1.492 0.0124 1.492 0.0124 +NAI N1N C2N SINGLE n 1.367 0.0104 1.367 0.0104 +NAI N1N C6N SINGLE n 1.374 0.0156 1.374 0.0156 +NAI C2N C3N DOUBLE n 1.365 0.0175 1.365 0.0175 +NAI C3N C7N SINGLE n 1.480 0.0169 1.480 0.0169 +NAI C3N C4N SINGLE n 1.491 0.0200 1.491 0.0200 +NAI C7N O7N DOUBLE n 1.235 0.0110 1.235 0.0110 +NAI C7N N7N SINGLE n 1.325 0.0100 1.325 0.0100 +NAI C4N C5N SINGLE n 1.477 0.0200 1.477 0.0200 +NAI C5N C6N DOUBLE n 1.315 0.0139 1.315 0.0139 +NAI C5B H51A SINGLE n 1.089 0.0100 0.989 0.0200 +NAI C5B H52A SINGLE n 1.089 0.0100 0.989 0.0200 +NAI C4B H4B SINGLE n 1.089 0.0100 0.981 0.0200 +NAI C3B H3B SINGLE n 1.089 0.0100 0.992 0.0200 +NAI O3B HO3A SINGLE n 0.970 0.0120 0.849 0.0200 +NAI C2B H2B SINGLE n 1.089 0.0100 0.994 0.0200 +NAI O2B HO2A SINGLE n 0.970 0.0120 0.849 0.0200 +NAI C1B H1B SINGLE n 1.089 0.0100 0.984 0.0200 +NAI C8A H8A SINGLE n 1.082 0.0130 0.942 0.0170 +NAI N6A H61A SINGLE n 1.016 0.0100 0.877 0.0200 +NAI N6A H62A SINGLE n 1.016 0.0100 0.877 0.0200 +NAI C2A H2A SINGLE n 1.082 0.0130 0.945 0.0200 +NAI C5D H51N SINGLE n 1.089 0.0100 0.989 0.0200 +NAI C5D H52N SINGLE n 1.089 0.0100 0.989 0.0200 +NAI C4D H4D SINGLE n 1.089 0.0100 0.981 0.0200 +NAI C3D H3D SINGLE n 1.089 0.0100 0.992 0.0200 +NAI O3D HO3N SINGLE n 0.970 0.0120 0.849 0.0200 +NAI C2D H2D SINGLE n 1.089 0.0100 0.988 0.0200 +NAI O2D HO2N SINGLE n 0.970 0.0120 0.849 0.0200 +NAI C1D H1D SINGLE n 1.089 0.0100 0.986 0.0200 +NAI C2N H2N SINGLE n 1.082 0.0130 0.940 0.0112 +NAI N7N H71N SINGLE n 1.016 0.0100 0.887 0.0200 +NAI N7N H72N SINGLE n 1.016 0.0100 0.887 0.0200 +NAI C4N H4N SINGLE n 1.089 0.0100 0.980 0.0113 +NAI C4N H42N SINGLE n 1.089 0.0100 0.980 0.0113 +NAI C5N H5N SINGLE n 1.082 0.0130 0.957 0.0130 +NAI C6N H6N SINGLE n 1.082 0.0130 0.941 0.0198 +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 +NAI O1A PA O2A 118.411 2.35 +NAI O1A PA O5B 109.410 1.50 +NAI O1A PA O3 108.816 2.14 +NAI O2A PA O5B 109.410 1.50 +NAI O2A PA O3 108.816 2.14 +NAI O5B PA O3 101.065 1.97 +NAI PA O5B C5B 118.553 2.41 +NAI O5B C5B C4B 109.342 1.50 +NAI O5B C5B H51A 109.845 1.50 +NAI O5B C5B H52A 109.845 1.50 +NAI C4B C5B H51A 109.624 1.50 +NAI C4B C5B H52A 109.624 1.50 +NAI H51A C5B H52A 108.472 1.50 +NAI C5B C4B O4B 109.123 1.50 +NAI C5B C4B C3B 116.008 1.52 +NAI C5B C4B H4B 108.268 1.50 +NAI O4B C4B C3B 105.388 1.50 +NAI O4B C4B H4B 108.947 1.50 +NAI C3B C4B H4B 109.363 1.86 +NAI C4B O4B C1B 109.903 1.50 +NAI C4B C3B O3B 111.281 2.46 +NAI C4B C3B C2B 102.602 1.50 +NAI C4B C3B H3B 110.452 2.54 +NAI O3B C3B C2B 111.581 2.83 +NAI O3B C3B H3B 110.380 1.67 +NAI C2B C3B H3B 110.504 1.75 +NAI C3B O3B HO3A 108.744 3.00 +NAI C3B C2B O2B 112.782 2.45 +NAI C3B C2B C1B 101.239 1.50 +NAI C3B C2B H2B 110.596 1.51 +NAI O2B C2B C1B 111.715 2.69 +NAI O2B C2B H2B 110.448 1.97 +NAI C1B C2B H2B 110.636 1.70 +NAI C2B O2B HO2A 109.103 2.13 +NAI O4B C1B C2B 106.047 1.50 +NAI O4B C1B N9A 108.477 1.50 +NAI O4B C1B H1B 109.807 1.50 +NAI C2B C1B N9A 113.824 1.50 +NAI C2B C1B H1B 109.015 1.50 +NAI N9A C1B H1B 109.561 1.50 +NAI C1B N9A C8A 126.848 1.91 +NAI C1B N9A C4A 127.459 1.80 +NAI C8A N9A C4A 105.693 1.50 +NAI N9A C8A N7A 113.469 1.50 +NAI N9A C8A H8A 123.206 1.50 +NAI N7A C8A H8A 123.326 1.50 +NAI C8A N7A C5A 104.739 1.50 +NAI N7A C5A C6A 132.250 1.50 +NAI N7A C5A C4A 110.483 1.50 +NAI C6A C5A C4A 117.267 1.50 +NAI C5A C6A N6A 123.792 1.50 +NAI C5A C6A N1A 117.409 1.50 +NAI N6A C6A N1A 118.799 1.50 +NAI C6A N6A H61A 119.723 1.50 +NAI C6A N6A H62A 119.723 1.50 +NAI H61A N6A H62A 120.554 1.88 +NAI C6A N1A C2A 118.521 1.50 +NAI N1A C2A N3A 129.332 1.50 +NAI N1A C2A H2A 115.313 1.50 +NAI N3A C2A H2A 115.355 1.50 +NAI C2A N3A C4A 110.982 1.50 +NAI N9A C4A C5A 105.616 1.50 +NAI N9A C4A N3A 127.895 1.50 +NAI C5A C4A N3A 126.489 1.50 +NAI PA O3 PN 132.542 3.00 +NAI O3 PN O1N 108.816 2.14 +NAI O3 PN O2N 108.816 2.14 +NAI O3 PN O5D 101.065 1.97 +NAI O1N PN O2N 118.411 2.35 +NAI O1N PN O5D 109.410 1.50 +NAI O2N PN O5D 109.410 1.50 +NAI PN O5D C5D 118.553 2.41 +NAI O5D C5D C4D 109.342 1.50 +NAI O5D C5D H51N 109.845 1.50 +NAI O5D C5D H52N 109.845 1.50 +NAI C4D C5D H51N 109.624 1.50 +NAI C4D C5D H52N 109.624 1.50 +NAI H51N C5D H52N 108.472 1.50 +NAI C5D C4D O4D 109.123 1.50 +NAI C5D C4D C3D 116.008 1.52 +NAI C5D C4D H4D 108.268 1.50 +NAI O4D C4D C3D 105.508 1.50 +NAI O4D C4D H4D 108.642 1.50 +NAI C3D C4D H4D 109.363 1.86 +NAI C4D O4D C1D 109.926 1.50 +NAI C4D C3D O3D 111.281 2.46 +NAI C4D C3D C2D 102.352 1.50 +NAI C4D C3D H3D 110.452 2.54 +NAI O3D C3D C2D 112.463 2.73 +NAI O3D C3D H3D 110.380 1.67 +NAI C2D C3D H3D 110.255 2.04 +NAI C3D O3D HO3N 108.744 3.00 +NAI C3D C2D O2D 112.463 2.73 +NAI C3D C2D C1D 104.443 2.26 +NAI C3D C2D H2D 110.255 2.04 +NAI O2D C2D C1D 111.164 2.38 +NAI O2D C2D H2D 110.259 1.63 +NAI C1D C2D H2D 110.518 1.74 +NAI C2D O2D HO2N 109.104 3.00 +NAI O4D C1D C2D 106.204 2.50 +NAI O4D C1D N1N 108.278 1.50 +NAI O4D C1D H1D 109.395 1.50 +NAI C2D C1D N1N 112.110 1.66 +NAI C2D C1D H1D 109.914 1.68 +NAI N1N C1D H1D 109.209 1.50 +NAI C1D N1N C2N 120.851 1.78 +NAI C1D N1N C6N 120.851 1.78 +NAI C2N N1N C6N 118.299 1.80 +NAI N1N C2N C3N 121.110 1.66 +NAI N1N C2N H2N 119.532 1.52 +NAI C3N C2N H2N 119.358 1.50 +NAI C2N C3N C7N 117.781 1.96 +NAI C2N C3N C4N 118.007 1.50 +NAI C7N C3N C4N 124.211 3.00 +NAI C3N C7N O7N 119.878 1.50 +NAI C3N C7N N7N 118.037 3.00 +NAI O7N C7N N7N 122.085 1.50 +NAI C7N N7N H71N 120.214 2.13 +NAI C7N N7N H72N 120.224 2.13 +NAI H71N N7N H72N 119.583 2.34 +NAI C3N C4N C5N 114.356 2.46 +NAI C3N C4N H4N 108.993 1.50 +NAI C3N C4N H42N 108.993 1.50 +NAI C5N C4N H4N 108.815 3.00 +NAI C5N C4N H42N 108.815 3.00 +NAI H4N C4N H42N 106.630 2.58 +NAI C4N C5N C6N 121.257 2.14 +NAI C4N C5N H5N 119.218 1.70 +NAI C6N C5N H5N 119.525 1.50 +NAI N1N C6N C5N 120.771 1.66 +NAI N1N C6N H6N 119.193 1.52 +NAI C5N C6N H6N 120.036 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 +NAI sp3_sp3_54 PN O3 PA O1A 60.000 10.0 3 +NAI sp3_sp3_51 C5B O5B PA O1A 60.000 10.0 3 +NAI sp2_sp3_13 C8A N9A C1B O4B 150.000 10.0 6 +NAI const_14 N7A C8A N9A C1B 180.000 10.0 2 +NAI const_26 C5A C4A N9A C1B 180.000 10.0 2 +NAI const_17 N9A C8A N7A C5A 0.000 10.0 2 +NAI const_20 C6A C5A N7A C8A 180.000 10.0 2 +NAI const_sp2_sp2_4 N7A C5A C6A N6A 0.000 5.0 2 +NAI const_21 N9A C4A C5A N7A 0.000 10.0 2 +NAI sp2_sp2_13 C5A C6A N6A H61A 180.000 5.0 2 +NAI const_sp2_sp2_6 N6A C6A N1A C2A 180.000 5.0 2 +NAI const_sp2_sp2_7 N3A C2A N1A C6A 0.000 5.0 2 +NAI const_sp2_sp2_9 N1A C2A N3A C4A 0.000 5.0 2 +NAI const_12 N9A C4A N3A C2A 180.000 10.0 2 +NAI sp3_sp3_82 PA O3 PN O1N 180.000 10.0 3 +NAI sp3_sp3_85 C5D O5D PN O3 180.000 10.0 3 +NAI sp3_sp3_88 C4D C5D O5D PN 180.000 10.0 3 +NAI sp3_sp3_91 O4D C4D C5D O5D 180.000 10.0 3 +NAI sp3_sp3_26 C5D C4D O4D C1D -60.000 10.0 3 +NAI sp3_sp3_104 O3D C3D C4D C5D 180.000 10.0 3 +NAI sp3_sp3_28 C2D C1D O4D C4D -60.000 10.0 3 +NAI sp3_sp3_109 C4D C3D O3D HO3N 180.000 10.0 3 +NAI sp3_sp3_44 O2D C2D C3D O3D -60.000 10.0 3 +NAI sp3_sp3_112 C3D C2D O2D HO2N 180.000 10.0 3 +NAI sp3_sp3_32 O4D C1D C2D O2D 180.000 10.0 3 +NAI sp2_sp3_19 C2N N1N C1D O4D 150.000 10.0 6 +NAI sp2_sp2_2 C3N C2N N1N C1D 180.000 5.0 2 +NAI sp2_sp2_18 C5N C6N N1N C1D 180.000 5.0 2 +NAI sp2_sp2_6 N1N C2N C3N C7N 180.000 5.0 2 +NAI sp2_sp2_24 C2N C3N C7N O7N 180.000 5.0 2 +NAI sp2_sp3_4 C7N C3N C4N C5N 180.000 10.0 6 +NAI sp2_sp2_27 O7N C7N N7N H71N 0.000 5.0 2 +NAI sp3_sp3_55 C4B C5B O5B PA 180.000 10.0 3 +NAI sp2_sp3_7 C6N C5N C4N C3N 0.000 10.0 6 +NAI sp2_sp2_9 C4N C5N C6N N1N 0.000 5.0 2 +NAI sp3_sp3_58 O4B C4B C5B O5B 180.000 10.0 3 +NAI sp3_sp3_2 C5B C4B O4B C1B -60.000 10.0 3 +NAI sp3_sp3_71 O3B C3B C4B C5B 180.000 10.0 3 +NAI sp3_sp3_4 C2B C1B O4B C4B -60.000 10.0 3 +NAI sp3_sp3_76 C4B C3B O3B HO3A 180.000 10.0 3 +NAI sp3_sp3_20 O2B C2B C3B O3B -60.000 10.0 3 +NAI sp3_sp3_79 C3B C2B O2B HO2A 180.000 10.0 3 +NAI sp3_sp3_8 O4B C1B C2B O2B 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 +NAI chir_1 PA O3 O5B O2A both +NAI chir_2 C4B O4B C3B C5B negative +NAI chir_3 C3B O3B C4B C2B positive +NAI chir_4 C2B O2B C1B C3B negative +NAI chir_5 C1B O4B N9A C2B negative +NAI chir_6 PN O3 O5D O1N both +NAI chir_7 C4D O4D C3D C5D negative +NAI chir_8 C3D O3D C4D C2D positive +NAI chir_9 C2D O2D C1D C3D negative +NAI chir_10 C1D O4D N1N C2D 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 +NAI plan-1 C1B 0.020 +NAI plan-1 C2A 0.020 +NAI plan-1 C4A 0.020 +NAI plan-1 C5A 0.020 +NAI plan-1 C6A 0.020 +NAI plan-1 C8A 0.020 +NAI plan-1 H2A 0.020 +NAI plan-1 H8A 0.020 +NAI plan-1 N1A 0.020 +NAI plan-1 N3A 0.020 +NAI plan-1 N6A 0.020 +NAI plan-1 N7A 0.020 +NAI plan-1 N9A 0.020 +NAI plan-2 C6A 0.020 +NAI plan-2 H61A 0.020 +NAI plan-2 H62A 0.020 +NAI plan-2 N6A 0.020 +NAI plan-3 C1D 0.020 +NAI plan-3 C2N 0.020 +NAI plan-3 C6N 0.020 +NAI plan-3 N1N 0.020 +NAI plan-4 C2N 0.020 +NAI plan-4 C3N 0.020 +NAI plan-4 H2N 0.020 +NAI plan-4 N1N 0.020 +NAI plan-5 C2N 0.020 +NAI plan-5 C3N 0.020 +NAI plan-5 C4N 0.020 +NAI plan-5 C7N 0.020 +NAI plan-6 C3N 0.020 +NAI plan-6 C7N 0.020 +NAI plan-6 N7N 0.020 +NAI plan-6 O7N 0.020 +NAI plan-7 C7N 0.020 +NAI plan-7 H71N 0.020 +NAI plan-7 H72N 0.020 +NAI plan-7 N7N 0.020 +NAI plan-8 C4N 0.020 +NAI plan-8 C5N 0.020 +NAI plan-8 C6N 0.020 +NAI plan-8 H5N 0.020 +NAI plan-9 C5N 0.020 +NAI plan-9 C6N 0.020 +NAI plan-9 H6N 0.020 +NAI plan-9 N1N 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 +NAI SMILES_CANONICAL CACTVS 3.341 NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O +NAI SMILES CACTVS 3.341 NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O +NAI 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)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N +NAI SMILES "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N +NAI InChI InChI 1.03 InChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1 +NAI InChIKey InChI 1.03 BOPGDPNILDQYTO-NNYOXOHSSA-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 +NAI acedrg 243 "dictionary generator" +NAI acedrg_database 11 "data source" +NAI rdkit 2017.03.2 "Chemoinformatics tool" +NAI refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/NAP.cif b/image_analysis/structure_refinement/monomers/NAP.cif new file mode 100644 index 000000000..02a6ea31e --- /dev/null +++ b/image_analysis/structure_refinement/monomers/NAP.cif @@ -0,0 +1,460 @@ +# +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 +NAP NAP "NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE" NON-POLYMER 73 48 . +# +data_comp_NAP +# +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 +NAP PA P P 0 14.707 24.447 12.480 +NAP O1A O O 0 13.458 23.637 12.602 +NAP O2A O OP -1 16.014 23.726 12.475 +NAP O5B O O2 0 14.609 25.379 11.174 +NAP C5B C CH2 0 15.409 26.589 11.081 +NAP C4B C CH1 0 15.737 26.871 9.636 +NAP O4B O O2 0 16.491 28.107 9.568 +NAP C3B C CH1 0 16.601 25.819 8.930 +NAP O3B O OH1 0 15.781 24.855 8.281 +NAP C2B C CH1 0 17.440 26.644 7.958 +NAP O2B O O2 0 16.792 26.811 6.691 +NAP C1B C CH1 0 17.572 27.988 8.672 +NAP N9A N NR5 0 18.813 28.129 9.426 +NAP C8A C CR15 0 19.226 27.352 10.480 +NAP N7A N NRD5 0 20.388 27.707 10.967 +NAP C5A C CR56 0 20.773 28.787 10.187 +NAP C6A C CR6 0 21.921 29.609 10.202 +NAP N6A N NH2 0 22.922 29.462 11.067 +NAP N1A N NRD6 0 21.993 30.607 9.282 +NAP C2A C CR16 0 20.979 30.751 8.415 +NAP N3A N NRD6 0 19.857 30.039 8.308 +NAP C4A C CR56 0 19.809 29.058 9.231 +NAP O3 O O2 0 14.727 25.535 13.659 +NAP PN P P 0 15.006 25.433 15.236 +NAP O1N O O 0 14.417 24.159 15.744 +NAP O2N O OP -1 14.583 26.712 15.880 +NAP O5D O O2 0 16.607 25.326 15.265 +NAP C5D C CH2 0 17.397 26.371 14.640 +NAP C4D C CH1 0 18.836 26.241 15.075 +NAP O4D O O2 0 19.679 27.018 14.196 +NAP C3D C CH1 0 19.161 26.751 16.486 +NAP O3D O OH1 0 20.269 26.050 17.038 +NAP C2D C CH1 0 19.461 28.232 16.227 +NAP O2D O OH1 0 20.299 28.821 17.209 +NAP C1D C CH1 0 20.213 28.142 14.894 +NAP N1N N NR6 1 20.068 29.345 14.038 +NAP C2N C CR16 0 18.841 29.658 13.486 +NAP C3N C CR6 0 18.708 30.789 12.681 +NAP C7N C C 0 17.375 31.126 12.085 +NAP O7N O O 0 16.914 32.269 12.231 +NAP N7N N NH2 0 16.721 30.182 11.419 +NAP C4N C CR16 0 19.808 31.604 12.444 +NAP C5N C CR16 0 21.032 31.285 13.005 +NAP C6N C CR16 0 21.155 30.158 13.797 +NAP P2B P P 0 17.807 26.912 5.431 +NAP O1X O O 0 18.385 25.523 5.232 +NAP O2X O OP -1 16.970 27.355 4.247 +NAP O3X O OP -1 18.878 27.929 5.783 +NAP H51A H H 0 16.247 26.480 11.592 +NAP H52A H H 0 14.907 27.351 11.463 +NAP H4B H H 0 14.895 26.984 9.146 +NAP H3B H H 0 17.191 25.370 9.588 +NAP HO3A H H 0 16.276 24.329 7.835 +NAP H2B H H 0 18.322 26.219 7.847 +NAP H1B H H 0 17.517 28.708 8.003 +NAP H8A H H 0 18.721 26.635 10.822 +NAP H61A H H 0 23.626 29.985 11.016 +NAP H62A H H 0 22.876 28.841 11.686 +NAP H2A H H 0 21.074 31.456 7.793 +NAP H51N H H 0 17.050 27.259 14.903 +NAP H52N H H 0 17.341 26.291 13.658 +NAP H4D H H 0 19.094 25.297 15.004 +NAP H3D H H 0 18.368 26.662 17.076 +NAP HO3N H H 0 20.386 26.311 17.838 +NAP H2D H H 0 18.621 28.744 16.127 +NAP HO2N H H 0 20.439 29.635 17.009 +NAP H1D H H 0 21.174 27.982 15.071 +NAP H2N H H 0 18.092 29.108 13.647 +NAP H71N H H 0 17.067 29.367 11.311 +NAP H72N H H 0 15.919 30.359 11.072 +NAP H4N H H 0 19.723 32.370 11.903 +NAP H5N H H 0 21.785 31.830 12.847 +NAP H6N H H 0 21.988 29.938 14.181 +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 +NAP PA O1A DOUBLE n 1.493 0.0122 1.493 0.0122 +NAP PA O2A SINGLE n 1.493 0.0122 1.493 0.0122 +NAP PA O5B SINGLE n 1.604 0.0133 1.604 0.0133 +NAP PA O3 SINGLE n 1.604 0.0133 1.604 0.0133 +NAP O5B C5B SINGLE n 1.450 0.0166 1.450 0.0166 +NAP C5B C4B SINGLE n 1.509 0.0100 1.509 0.0100 +NAP C4B O4B SINGLE n 1.451 0.0100 1.451 0.0100 +NAP C4B C3B SINGLE n 1.535 0.0100 1.535 0.0100 +NAP O4B C1B SINGLE n 1.409 0.0100 1.409 0.0100 +NAP C3B O3B SINGLE n 1.422 0.0100 1.422 0.0100 +NAP C3B C2B SINGLE n 1.523 0.0106 1.523 0.0106 +NAP C2B O2B SINGLE n 1.425 0.0152 1.425 0.0152 +NAP C2B C1B SINGLE n 1.524 0.0100 1.524 0.0100 +NAP O2B P2B SINGLE n 1.614 0.0178 1.614 0.0178 +NAP C1B N9A SINGLE n 1.458 0.0100 1.458 0.0100 +NAP N9A C8A SINGLE y 1.372 0.0100 1.372 0.0100 +NAP N9A C4A SINGLE y 1.374 0.0101 1.374 0.0101 +NAP C8A N7A DOUBLE y 1.310 0.0100 1.310 0.0100 +NAP N7A C5A SINGLE y 1.388 0.0100 1.388 0.0100 +NAP C5A C6A SINGLE y 1.408 0.0100 1.408 0.0100 +NAP C5A C4A DOUBLE y 1.381 0.0100 1.381 0.0100 +NAP C6A N6A SINGLE n 1.330 0.0100 1.330 0.0100 +NAP C6A N1A DOUBLE y 1.354 0.0100 1.354 0.0100 +NAP N1A C2A SINGLE y 1.339 0.0100 1.339 0.0100 +NAP C2A N3A DOUBLE y 1.330 0.0100 1.330 0.0100 +NAP N3A C4A SINGLE y 1.343 0.0100 1.343 0.0100 +NAP O3 PN SINGLE n 1.604 0.0133 1.604 0.0133 +NAP PN O1N DOUBLE n 1.493 0.0122 1.493 0.0122 +NAP PN O2N SINGLE n 1.493 0.0122 1.493 0.0122 +NAP PN O5D SINGLE n 1.604 0.0133 1.604 0.0133 +NAP O5D C5D SINGLE n 1.450 0.0166 1.450 0.0166 +NAP C5D C4D SINGLE n 1.509 0.0100 1.509 0.0100 +NAP C4D O4D SINGLE n 1.443 0.0107 1.443 0.0107 +NAP C4D C3D SINGLE n 1.535 0.0100 1.535 0.0100 +NAP O4D C1D SINGLE n 1.425 0.0141 1.425 0.0141 +NAP C3D O3D SINGLE n 1.422 0.0100 1.422 0.0100 +NAP C3D C2D SINGLE n 1.533 0.0100 1.533 0.0100 +NAP C2D O2D SINGLE n 1.419 0.0101 1.419 0.0101 +NAP C2D C1D SINGLE n 1.533 0.0100 1.533 0.0100 +NAP C1D N1N SINGLE n 1.477 0.0138 1.477 0.0138 +NAP N1N C2N DOUBLE y 1.377 0.0105 1.377 0.0105 +NAP N1N C6N SINGLE y 1.375 0.0105 1.375 0.0105 +NAP C2N C3N SINGLE y 1.390 0.0105 1.390 0.0105 +NAP C3N C7N SINGLE n 1.497 0.0100 1.497 0.0100 +NAP C3N C4N DOUBLE y 1.385 0.0100 1.385 0.0100 +NAP C7N O7N DOUBLE n 1.241 0.0105 1.241 0.0105 +NAP C7N N7N SINGLE n 1.326 0.0100 1.326 0.0100 +NAP C4N C5N SINGLE y 1.380 0.0100 1.380 0.0100 +NAP C5N C6N DOUBLE y 1.380 0.0128 1.380 0.0128 +NAP P2B O1X DOUBLE n 1.517 0.0192 1.517 0.0192 +NAP P2B O2X SINGLE n 1.517 0.0192 1.517 0.0192 +NAP P2B O3X SINGLE n 1.517 0.0192 1.517 0.0192 +NAP C5B H51A SINGLE n 1.089 0.0100 0.989 0.0200 +NAP C5B H52A SINGLE n 1.089 0.0100 0.989 0.0200 +NAP C4B H4B SINGLE n 1.089 0.0100 0.981 0.0200 +NAP C3B H3B SINGLE n 1.089 0.0100 0.992 0.0200 +NAP O3B HO3A SINGLE n 0.970 0.0120 0.849 0.0200 +NAP C2B H2B SINGLE n 1.089 0.0100 0.985 0.0119 +NAP C1B H1B SINGLE n 1.089 0.0100 0.984 0.0200 +NAP C8A H8A SINGLE n 1.082 0.0130 0.942 0.0170 +NAP N6A H61A SINGLE n 1.016 0.0100 0.877 0.0200 +NAP N6A H62A SINGLE n 1.016 0.0100 0.877 0.0200 +NAP C2A H2A SINGLE n 1.082 0.0130 0.945 0.0200 +NAP C5D H51N SINGLE n 1.089 0.0100 0.989 0.0200 +NAP C5D H52N SINGLE n 1.089 0.0100 0.989 0.0200 +NAP C4D H4D SINGLE n 1.089 0.0100 0.981 0.0200 +NAP C3D H3D SINGLE n 1.089 0.0100 0.992 0.0200 +NAP O3D HO3N SINGLE n 0.970 0.0120 0.849 0.0200 +NAP C2D H2D SINGLE n 1.089 0.0100 0.989 0.0200 +NAP O2D HO2N SINGLE n 0.970 0.0120 0.849 0.0200 +NAP C1D H1D SINGLE n 1.089 0.0100 0.990 0.0173 +NAP C2N H2N SINGLE n 1.082 0.0130 0.943 0.0170 +NAP N7N H71N SINGLE n 1.016 0.0100 0.891 0.0200 +NAP N7N H72N SINGLE n 1.016 0.0100 0.891 0.0200 +NAP C4N H4N SINGLE n 1.082 0.0130 0.941 0.0168 +NAP C5N H5N SINGLE n 1.082 0.0130 0.943 0.0190 +NAP C6N H6N SINGLE n 1.082 0.0130 0.943 0.0169 +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 +NAP O1A PA O2A 118.411 2.35 +NAP O1A PA O5B 109.410 1.50 +NAP O1A PA O3 108.816 2.14 +NAP O2A PA O5B 109.410 1.50 +NAP O2A PA O3 108.816 2.14 +NAP O5B PA O3 101.065 1.97 +NAP PA O5B C5B 118.553 2.41 +NAP O5B C5B C4B 109.342 1.50 +NAP O5B C5B H51A 109.845 1.50 +NAP O5B C5B H52A 109.845 1.50 +NAP C4B C5B H51A 109.624 1.50 +NAP C4B C5B H52A 109.624 1.50 +NAP H51A C5B H52A 108.472 1.50 +NAP C5B C4B O4B 109.123 1.50 +NAP C5B C4B C3B 116.008 1.52 +NAP C5B C4B H4B 108.268 1.50 +NAP O4B C4B C3B 105.388 1.50 +NAP O4B C4B H4B 108.947 1.50 +NAP C3B C4B H4B 109.363 1.86 +NAP C4B O4B C1B 109.903 1.50 +NAP C4B C3B O3B 111.281 2.46 +NAP C4B C3B C2B 102.352 1.50 +NAP C4B C3B H3B 110.452 2.54 +NAP O3B C3B C2B 112.463 2.73 +NAP O3B C3B H3B 110.380 1.67 +NAP C2B C3B H3B 110.255 2.04 +NAP C3B O3B HO3A 108.744 3.00 +NAP C3B C2B O2B 110.766 3.00 +NAP C3B C2B C1B 101.388 1.50 +NAP C3B C2B H2B 110.255 2.04 +NAP O2B C2B C1B 110.738 2.44 +NAP O2B C2B H2B 110.343 1.64 +NAP C1B C2B H2B 111.050 1.62 +NAP C2B O2B P2B 109.471 3.00 +NAP O4B C1B C2B 106.416 1.50 +NAP O4B C1B N9A 108.477 1.50 +NAP O4B C1B H1B 109.807 1.50 +NAP C2B C1B N9A 113.659 1.50 +NAP C2B C1B H1B 109.319 1.50 +NAP N9A C1B H1B 109.561 1.50 +NAP C1B N9A C8A 126.848 1.91 +NAP C1B N9A C4A 127.459 1.80 +NAP C8A N9A C4A 105.693 1.50 +NAP N9A C8A N7A 113.469 1.50 +NAP N9A C8A H8A 123.206 1.50 +NAP N7A C8A H8A 123.326 1.50 +NAP C8A N7A C5A 104.739 1.50 +NAP N7A C5A C6A 132.250 1.50 +NAP N7A C5A C4A 110.483 1.50 +NAP C6A C5A C4A 117.267 1.50 +NAP C5A C6A N6A 123.792 1.50 +NAP C5A C6A N1A 117.409 1.50 +NAP N6A C6A N1A 118.799 1.50 +NAP C6A N6A H61A 119.723 1.50 +NAP C6A N6A H62A 119.723 1.50 +NAP H61A N6A H62A 120.554 1.88 +NAP C6A N1A C2A 118.521 1.50 +NAP N1A C2A N3A 129.332 1.50 +NAP N1A C2A H2A 115.313 1.50 +NAP N3A C2A H2A 115.355 1.50 +NAP C2A N3A C4A 110.982 1.50 +NAP N9A C4A C5A 105.616 1.50 +NAP N9A C4A N3A 127.895 1.50 +NAP C5A C4A N3A 126.489 1.50 +NAP PA O3 PN 132.542 3.00 +NAP O3 PN O1N 108.816 2.14 +NAP O3 PN O2N 108.816 2.14 +NAP O3 PN O5D 101.065 1.97 +NAP O1N PN O2N 118.411 2.35 +NAP O1N PN O5D 109.410 1.50 +NAP O2N PN O5D 109.410 1.50 +NAP PN O5D C5D 118.553 2.41 +NAP O5D C5D C4D 109.342 1.50 +NAP O5D C5D H51N 109.845 1.50 +NAP O5D C5D H52N 109.845 1.50 +NAP C4D C5D H51N 109.624 1.50 +NAP C4D C5D H52N 109.624 1.50 +NAP H51N C5D H52N 108.472 1.50 +NAP C5D C4D O4D 109.615 1.50 +NAP C5D C4D C3D 116.008 1.52 +NAP C5D C4D H4D 108.268 1.50 +NAP O4D C4D C3D 104.439 1.50 +NAP O4D C4D H4D 108.698 1.50 +NAP C3D C4D H4D 109.363 1.86 +NAP C4D O4D C1D 109.578 1.50 +NAP C4D C3D O3D 111.281 2.46 +NAP C4D C3D C2D 102.071 1.50 +NAP C4D C3D H3D 110.452 2.54 +NAP O3D C3D C2D 111.993 3.00 +NAP O3D C3D H3D 110.380 1.67 +NAP C2D C3D H3D 110.108 1.66 +NAP C3D O3D HO3N 108.744 3.00 +NAP C3D C2D O2D 112.861 2.52 +NAP C3D C2D C1D 101.269 1.50 +NAP C3D C2D H2D 110.799 1.82 +NAP O2D C2D C1D 109.476 3.00 +NAP O2D C2D H2D 111.022 1.77 +NAP C1D C2D H2D 110.760 1.63 +NAP C2D O2D HO2N 109.449 1.85 +NAP O4D C1D C2D 106.825 1.50 +NAP O4D C1D N1N 108.092 1.50 +NAP O4D C1D H1D 109.327 1.50 +NAP C2D C1D N1N 113.620 1.99 +NAP C2D C1D H1D 109.776 1.83 +NAP N1N C1D H1D 108.901 1.50 +NAP C1D N1N C2N 119.705 1.50 +NAP C1D N1N C6N 119.705 1.50 +NAP C2N N1N C6N 120.590 1.50 +NAP N1N C2N C3N 119.549 3.00 +NAP N1N C2N H2N 120.430 1.53 +NAP C3N C2N H2N 120.021 1.50 +NAP C2N C3N C7N 119.660 2.75 +NAP C2N C3N C4N 119.402 1.64 +NAP C7N C3N C4N 120.938 2.50 +NAP C3N C7N O7N 119.730 1.50 +NAP C3N C7N N7N 118.032 1.50 +NAP O7N C7N N7N 122.238 1.50 +NAP C7N N7N H71N 120.236 2.75 +NAP C7N N7N H72N 120.236 2.75 +NAP H71N N7N H72N 119.529 2.83 +NAP C3N C4N C5N 119.166 1.50 +NAP C3N C4N H4N 120.513 1.50 +NAP C5N C4N H4N 120.320 1.50 +NAP C4N C5N C6N 120.016 1.50 +NAP C4N C5N H5N 120.300 1.50 +NAP C6N C5N H5N 119.683 1.50 +NAP N1N C6N C5N 121.277 1.50 +NAP N1N C6N H6N 118.693 1.53 +NAP C5N C6N H6N 120.031 1.59 +NAP O2B P2B O1X 106.518 3.00 +NAP O2B P2B O2X 106.518 3.00 +NAP O2B P2B O3X 106.518 3.00 +NAP O1X P2B O2X 112.139 1.52 +NAP O1X P2B O3X 112.139 1.52 +NAP O2X P2B O3X 112.139 1.52 +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 +NAP sp3_sp3_54 PN O3 PA O1A 60.000 10.0 3 +NAP sp3_sp3_51 C5B O5B PA O1A 60.000 10.0 3 +NAP sp3_sp3_82 C2B O2B P2B O1X 180.000 10.0 3 +NAP sp2_sp3_1 C8A N9A C1B O4B 150.000 10.0 6 +NAP const_34 N7A C8A N9A C1B 180.000 10.0 2 +NAP const_46 C5A C4A N9A C1B 180.000 10.0 2 +NAP const_37 N9A C8A N7A C5A 0.000 10.0 2 +NAP const_40 C6A C5A N7A C8A 180.000 10.0 2 +NAP const_sp2_sp2_4 N7A C5A C6A N6A 0.000 5.0 2 +NAP const_41 N9A C4A C5A N7A 0.000 10.0 2 +NAP sp2_sp2_1 C5A C6A N6A H61A 180.000 5.0 2 +NAP const_sp2_sp2_6 N6A C6A N1A C2A 180.000 5.0 2 +NAP const_sp2_sp2_7 N3A C2A N1A C6A 0.000 5.0 2 +NAP const_sp2_sp2_9 N1A C2A N3A C4A 0.000 5.0 2 +NAP const_12 N9A C4A N3A C2A 180.000 10.0 2 +NAP sp3_sp3_87 PA O3 PN O1N 60.000 10.0 3 +NAP sp3_sp3_88 C5D O5D PN O3 180.000 10.0 3 +NAP sp3_sp3_91 C4D C5D O5D PN 180.000 10.0 3 +NAP sp3_sp3_94 O4D C4D C5D O5D 180.000 10.0 3 +NAP sp3_sp3_26 C5D C4D O4D C1D -60.000 10.0 3 +NAP sp3_sp3_107 O3D C3D C4D C5D 180.000 10.0 3 +NAP sp3_sp3_28 C2D C1D O4D C4D -60.000 10.0 3 +NAP sp3_sp3_112 C4D C3D O3D HO3N 180.000 10.0 3 +NAP sp3_sp3_44 O2D C2D C3D O3D -60.000 10.0 3 +NAP sp3_sp3_115 C3D C2D O2D HO2N 180.000 10.0 3 +NAP sp3_sp3_32 O4D C1D C2D O2D 180.000 10.0 3 +NAP sp2_sp3_7 C2N N1N C1D O4D 150.000 10.0 6 +NAP const_14 C3N C2N N1N C1D 180.000 10.0 2 +NAP const_50 C5N C6N N1N C1D 180.000 10.0 2 +NAP const_18 N1N C2N C3N C7N 180.000 10.0 2 +NAP sp2_sp2_6 C2N C3N C7N O7N 0.000 5.0 2 +NAP const_23 C7N C3N C4N C5N 180.000 10.0 2 +NAP sp2_sp2_11 O7N C7N N7N H71N 0.000 5.0 2 +NAP sp3_sp3_55 C4B C5B O5B PA 180.000 10.0 3 +NAP const_25 C3N C4N C5N C6N 0.000 10.0 2 +NAP const_29 C4N C5N C6N N1N 0.000 10.0 2 +NAP sp3_sp3_58 O4B C4B C5B O5B 180.000 10.0 3 +NAP sp3_sp3_2 C5B C4B O4B C1B -60.000 10.0 3 +NAP sp3_sp3_71 O3B C3B C4B C5B 180.000 10.0 3 +NAP sp3_sp3_4 C2B C1B O4B C4B -60.000 10.0 3 +NAP sp3_sp3_76 C4B C3B O3B HO3A 180.000 10.0 3 +NAP sp3_sp3_20 O2B C2B C3B O3B -60.000 10.0 3 +NAP sp3_sp3_79 C3B C2B O2B P2B 180.000 10.0 3 +NAP sp3_sp3_8 O4B C1B C2B O2B 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 +NAP chir_1 PA O3 O5B O2A both +NAP chir_2 C4B O4B C3B C5B negative +NAP chir_3 C3B O3B C2B C4B negative +NAP chir_4 C2B O2B C1B C3B negative +NAP chir_5 C1B O4B N9A C2B negative +NAP chir_6 PN O3 O5D O2N both +NAP chir_7 C4D O4D C3D C5D negative +NAP chir_8 C3D O3D C4D C2D positive +NAP chir_9 C2D O2D C1D C3D negative +NAP chir_10 C1D O4D N1N C2D 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 +NAP plan-1 C1B 0.020 +NAP plan-1 C2A 0.020 +NAP plan-1 C4A 0.020 +NAP plan-1 C5A 0.020 +NAP plan-1 C6A 0.020 +NAP plan-1 C8A 0.020 +NAP plan-1 H2A 0.020 +NAP plan-1 H8A 0.020 +NAP plan-1 N1A 0.020 +NAP plan-1 N3A 0.020 +NAP plan-1 N6A 0.020 +NAP plan-1 N7A 0.020 +NAP plan-1 N9A 0.020 +NAP plan-2 C1D 0.020 +NAP plan-2 C2N 0.020 +NAP plan-2 C3N 0.020 +NAP plan-2 C4N 0.020 +NAP plan-2 C5N 0.020 +NAP plan-2 C6N 0.020 +NAP plan-2 C7N 0.020 +NAP plan-2 H2N 0.020 +NAP plan-2 H4N 0.020 +NAP plan-2 H5N 0.020 +NAP plan-2 H6N 0.020 +NAP plan-2 N1N 0.020 +NAP plan-3 C6A 0.020 +NAP plan-3 H61A 0.020 +NAP plan-3 H62A 0.020 +NAP plan-3 N6A 0.020 +NAP plan-4 C3N 0.020 +NAP plan-4 C7N 0.020 +NAP plan-4 N7N 0.020 +NAP plan-4 O7N 0.020 +NAP plan-5 C7N 0.020 +NAP plan-5 H71N 0.020 +NAP plan-5 H72N 0.020 +NAP plan-5 N7N 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 +NAP SMILES_CANONICAL CACTVS 3.341 NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O +NAP SMILES CACTVS 3.341 NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O +NAP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N +NAP SMILES "OpenEye OEToolkits" 1.5.0 c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N +NAP InChI InChI 1.03 InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1 +NAP InChIKey InChI 1.03 XJLXINKUBYWONI-NNYOXOHSSA-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 +NAP acedrg 243 "dictionary generator" +NAP acedrg_database 11 "data source" +NAP rdkit 2017.03.2 "Chemoinformatics tool" +NAP refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/NDP.cif b/image_analysis/structure_refinement/monomers/NDP.cif new file mode 100644 index 000000000..c3eae3816 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/NDP.cif @@ -0,0 +1,473 @@ +# +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 +NDP NDP "NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE" NON-POLYMER 74 48 . +# +data_comp_NDP +# +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 +NDP PA P P 0 14.746 11.568 81.367 +NDP O1A O O 0 14.846 12.116 82.752 +NDP O2A O OP -1 15.219 10.173 81.123 +NDP O5B O O2 0 15.480 12.564 80.346 +NDP C5B C CH2 0 15.269 13.993 80.484 +NDP C4B C CH1 0 15.682 14.683 79.207 +NDP O4B O O2 0 15.216 16.056 79.244 +NDP C3B C CH1 0 17.194 14.748 78.938 +NDP O3B O OH1 0 17.492 14.414 77.587 +NDP C2B C CH1 0 17.556 16.184 79.308 +NDP O2B O O2 0 18.652 16.694 78.540 +NDP C1B C CH1 0 16.277 16.931 78.947 +NDP N9A N NR5 0 16.067 18.164 79.699 +NDP C8A C CR15 0 16.031 18.293 81.065 +NDP N7A N NRD5 0 15.816 19.519 81.470 +NDP C5A C CR56 0 15.691 20.250 80.299 +NDP C6A C CR6 0 15.449 21.620 80.056 +NDP N6A N NH2 0 15.287 22.522 81.021 +NDP N1A N NRD6 0 15.382 22.028 78.762 +NDP C2A C CR16 0 15.546 21.113 77.794 +NDP N3A N NRD6 0 15.777 19.804 77.905 +NDP C4A C CR56 0 15.840 19.425 79.196 +NDP O3 O O2 0 13.226 11.692 80.871 +NDP PN P P 0 12.518 11.379 79.466 +NDP O1N O O 0 13.514 10.727 78.565 +NDP O2N O OP -1 11.231 10.667 79.724 +NDP O5D O O2 0 12.213 12.863 78.935 +NDP C5D C CH2 0 11.328 13.716 79.706 +NDP C4D C CH1 0 11.023 14.974 78.929 +NDP O4D O O2 0 12.257 15.648 78.585 +NDP C3D C CH1 0 10.306 14.797 77.585 +NDP O3D O OH1 0 8.904 14.643 77.770 +NDP C2D C CH1 0 10.697 16.089 76.857 +NDP O2D O OH1 0 9.719 17.111 76.999 +NDP C1D C CH1 0 12.016 16.522 77.506 +NDP N1N N NR6 0 13.173 16.451 76.558 +NDP C2N C CR16 0 13.593 15.236 76.075 +NDP C3N C CR6 0 14.740 15.096 75.322 +NDP C7N C C 0 15.161 13.734 74.898 +NDP O7N O O 0 15.511 13.557 73.727 +NDP N7N N NH2 0 15.161 12.736 75.773 +NDP C4N C CH2 0 15.493 16.332 74.936 +NDP C5N C CR16 0 14.940 17.593 75.478 +NDP C6N C CR16 0 13.806 17.617 76.151 +NDP P2B P P 0 20.124 16.448 79.172 +NDP O1X O O 0 20.271 14.965 79.456 +NDP O2X O OP -1 20.204 17.281 80.438 +NDP O3X O OP -1 21.106 16.923 78.118 +NDP H51A H H 0 15.806 14.341 81.239 +NDP H52A H H 0 14.314 14.177 80.667 +NDP H4B H H 0 15.242 14.224 78.463 +NDP H3B H H 0 17.664 14.123 79.548 +NDP HO3A H H 0 17.093 14.951 77.068 +NDP H2B H H 0 17.743 16.245 80.273 +NDP H1B H H 0 16.282 17.128 77.984 +NDP H8A H H 0 16.159 17.569 81.654 +NDP H61A H H 0 14.828 23.253 80.863 +NDP H62A H H 0 15.640 22.380 81.812 +NDP H2A H H 0 15.491 21.442 76.910 +NDP H51N H H 0 11.757 13.954 80.565 +NDP H52N H H 0 10.485 13.237 79.901 +NDP H4D H H 0 10.493 15.568 79.503 +NDP H3D H H 0 10.672 14.015 77.099 +NDP HO3N H H 0 8.534 14.576 77.009 +NDP H2D H H 0 10.834 15.895 75.897 +NDP HO2N H H 0 9.885 17.733 76.446 +NDP H1D H H 0 11.933 17.443 77.851 +NDP H2N H H 0 13.079 14.471 76.264 +NDP H71N H H 0 14.910 12.863 76.612 +NDP H72N H H 0 15.415 11.924 75.519 +NDP H41N H H 0 15.516 16.397 73.959 +NDP H42N H H 0 16.424 16.244 75.229 +NDP H5N H H 0 15.417 18.410 75.332 +NDP H6N H H 0 13.411 18.445 76.360 +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 +NDP PA O1A DOUBLE n 1.493 0.0122 1.493 0.0122 +NDP PA O2A SINGLE n 1.493 0.0122 1.493 0.0122 +NDP PA O5B SINGLE n 1.604 0.0133 1.604 0.0133 +NDP PA O3 SINGLE n 1.604 0.0133 1.604 0.0133 +NDP O5B C5B SINGLE n 1.450 0.0166 1.450 0.0166 +NDP C5B C4B SINGLE n 1.509 0.0100 1.509 0.0100 +NDP C4B O4B SINGLE n 1.451 0.0100 1.451 0.0100 +NDP C4B C3B SINGLE n 1.535 0.0100 1.535 0.0100 +NDP O4B C1B SINGLE n 1.409 0.0100 1.409 0.0100 +NDP C3B O3B SINGLE n 1.422 0.0100 1.422 0.0100 +NDP C3B C2B SINGLE n 1.523 0.0106 1.523 0.0106 +NDP C2B O2B SINGLE n 1.425 0.0152 1.425 0.0152 +NDP C2B C1B SINGLE n 1.524 0.0100 1.524 0.0100 +NDP O2B P2B SINGLE n 1.614 0.0178 1.614 0.0178 +NDP C1B N9A SINGLE n 1.458 0.0100 1.458 0.0100 +NDP N9A C8A SINGLE y 1.372 0.0100 1.372 0.0100 +NDP N9A C4A SINGLE y 1.374 0.0101 1.374 0.0101 +NDP C8A N7A DOUBLE y 1.310 0.0100 1.310 0.0100 +NDP N7A C5A SINGLE y 1.388 0.0100 1.388 0.0100 +NDP C5A C6A SINGLE y 1.408 0.0100 1.408 0.0100 +NDP C5A C4A DOUBLE y 1.381 0.0100 1.381 0.0100 +NDP C6A N6A SINGLE n 1.330 0.0100 1.330 0.0100 +NDP C6A N1A DOUBLE y 1.354 0.0100 1.354 0.0100 +NDP N1A C2A SINGLE y 1.339 0.0100 1.339 0.0100 +NDP C2A N3A DOUBLE y 1.330 0.0100 1.330 0.0100 +NDP N3A C4A SINGLE y 1.343 0.0100 1.343 0.0100 +NDP O3 PN SINGLE n 1.604 0.0133 1.604 0.0133 +NDP PN O1N DOUBLE n 1.493 0.0122 1.493 0.0122 +NDP PN O2N SINGLE n 1.493 0.0122 1.493 0.0122 +NDP PN O5D SINGLE n 1.604 0.0133 1.604 0.0133 +NDP O5D C5D SINGLE n 1.450 0.0166 1.450 0.0166 +NDP C5D C4D SINGLE n 1.509 0.0100 1.509 0.0100 +NDP C4D O4D SINGLE n 1.449 0.0100 1.449 0.0100 +NDP C4D C3D SINGLE n 1.535 0.0100 1.535 0.0100 +NDP O4D C1D SINGLE n 1.407 0.0132 1.407 0.0132 +NDP C3D O3D SINGLE n 1.422 0.0100 1.422 0.0100 +NDP C3D C2D SINGLE n 1.530 0.0134 1.530 0.0134 +NDP C2D O2D SINGLE n 1.420 0.0122 1.420 0.0122 +NDP C2D C1D SINGLE n 1.527 0.0119 1.527 0.0119 +NDP C1D N1N SINGLE n 1.492 0.0124 1.492 0.0124 +NDP N1N C2N SINGLE n 1.367 0.0104 1.367 0.0104 +NDP N1N C6N SINGLE n 1.374 0.0156 1.374 0.0156 +NDP C2N C3N DOUBLE n 1.365 0.0175 1.365 0.0175 +NDP C3N C7N SINGLE n 1.480 0.0169 1.480 0.0169 +NDP C3N C4N SINGLE n 1.491 0.0200 1.491 0.0200 +NDP C7N O7N DOUBLE n 1.235 0.0110 1.235 0.0110 +NDP C7N N7N SINGLE n 1.325 0.0100 1.325 0.0100 +NDP C4N C5N SINGLE n 1.477 0.0200 1.477 0.0200 +NDP C5N C6N DOUBLE n 1.315 0.0139 1.315 0.0139 +NDP P2B O1X DOUBLE n 1.517 0.0192 1.517 0.0192 +NDP P2B O2X SINGLE n 1.517 0.0192 1.517 0.0192 +NDP P2B O3X SINGLE n 1.517 0.0192 1.517 0.0192 +NDP C5B H51A SINGLE n 1.089 0.0100 0.989 0.0200 +NDP C5B H52A SINGLE n 1.089 0.0100 0.989 0.0200 +NDP C4B H4B SINGLE n 1.089 0.0100 0.981 0.0200 +NDP C3B H3B SINGLE n 1.089 0.0100 0.992 0.0200 +NDP O3B HO3A SINGLE n 0.970 0.0120 0.849 0.0200 +NDP C2B H2B SINGLE n 1.089 0.0100 0.985 0.0119 +NDP C1B H1B SINGLE n 1.089 0.0100 0.984 0.0200 +NDP C8A H8A SINGLE n 1.082 0.0130 0.942 0.0170 +NDP N6A H61A SINGLE n 1.016 0.0100 0.877 0.0200 +NDP N6A H62A SINGLE n 1.016 0.0100 0.877 0.0200 +NDP C2A H2A SINGLE n 1.082 0.0130 0.945 0.0200 +NDP C5D H51N SINGLE n 1.089 0.0100 0.989 0.0200 +NDP C5D H52N SINGLE n 1.089 0.0100 0.989 0.0200 +NDP C4D H4D SINGLE n 1.089 0.0100 0.981 0.0200 +NDP C3D H3D SINGLE n 1.089 0.0100 0.992 0.0200 +NDP O3D HO3N SINGLE n 0.970 0.0120 0.849 0.0200 +NDP C2D H2D SINGLE n 1.089 0.0100 0.988 0.0200 +NDP O2D HO2N SINGLE n 0.970 0.0120 0.849 0.0200 +NDP C1D H1D SINGLE n 1.089 0.0100 0.986 0.0200 +NDP C2N H2N SINGLE n 1.082 0.0130 0.940 0.0112 +NDP N7N H71N SINGLE n 1.016 0.0100 0.887 0.0200 +NDP N7N H72N SINGLE n 1.016 0.0100 0.887 0.0200 +NDP C4N H41N SINGLE n 1.089 0.0100 0.980 0.0113 +NDP C4N H42N SINGLE n 1.089 0.0100 0.980 0.0113 +NDP C5N H5N SINGLE n 1.082 0.0130 0.957 0.0130 +NDP C6N H6N SINGLE n 1.082 0.0130 0.941 0.0198 +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 +NDP O1A PA O2A 118.411 2.35 +NDP O1A PA O5B 109.410 1.50 +NDP O1A PA O3 108.816 2.14 +NDP O2A PA O5B 109.410 1.50 +NDP O2A PA O3 108.816 2.14 +NDP O5B PA O3 101.065 1.97 +NDP PA O5B C5B 118.553 2.41 +NDP O5B C5B C4B 109.342 1.50 +NDP O5B C5B H51A 109.845 1.50 +NDP O5B C5B H52A 109.845 1.50 +NDP C4B C5B H51A 109.624 1.50 +NDP C4B C5B H52A 109.624 1.50 +NDP H51A C5B H52A 108.472 1.50 +NDP C5B C4B O4B 109.123 1.50 +NDP C5B C4B C3B 116.008 1.52 +NDP C5B C4B H4B 108.268 1.50 +NDP O4B C4B C3B 105.388 1.50 +NDP O4B C4B H4B 108.947 1.50 +NDP C3B C4B H4B 109.363 1.86 +NDP C4B O4B C1B 109.903 1.50 +NDP C4B C3B O3B 111.281 2.46 +NDP C4B C3B C2B 102.352 1.50 +NDP C4B C3B H3B 110.452 2.54 +NDP O3B C3B C2B 112.463 2.73 +NDP O3B C3B H3B 110.380 1.67 +NDP C2B C3B H3B 110.255 2.04 +NDP C3B O3B HO3A 108.744 3.00 +NDP C3B C2B O2B 110.766 3.00 +NDP C3B C2B C1B 101.388 1.50 +NDP C3B C2B H2B 110.255 2.04 +NDP O2B C2B C1B 110.738 2.44 +NDP O2B C2B H2B 110.343 1.64 +NDP C1B C2B H2B 111.050 1.62 +NDP C2B O2B P2B 109.471 3.00 +NDP O4B C1B C2B 106.416 1.50 +NDP O4B C1B N9A 108.477 1.50 +NDP O4B C1B H1B 109.807 1.50 +NDP C2B C1B N9A 113.659 1.50 +NDP C2B C1B H1B 109.319 1.50 +NDP N9A C1B H1B 109.561 1.50 +NDP C1B N9A C8A 126.848 1.91 +NDP C1B N9A C4A 127.459 1.80 +NDP C8A N9A C4A 105.693 1.50 +NDP N9A C8A N7A 113.469 1.50 +NDP N9A C8A H8A 123.206 1.50 +NDP N7A C8A H8A 123.326 1.50 +NDP C8A N7A C5A 104.739 1.50 +NDP N7A C5A C6A 132.250 1.50 +NDP N7A C5A C4A 110.483 1.50 +NDP C6A C5A C4A 117.267 1.50 +NDP C5A C6A N6A 123.792 1.50 +NDP C5A C6A N1A 117.409 1.50 +NDP N6A C6A N1A 118.799 1.50 +NDP C6A N6A H61A 119.723 1.50 +NDP C6A N6A H62A 119.723 1.50 +NDP H61A N6A H62A 120.554 1.88 +NDP C6A N1A C2A 118.521 1.50 +NDP N1A C2A N3A 129.332 1.50 +NDP N1A C2A H2A 115.313 1.50 +NDP N3A C2A H2A 115.355 1.50 +NDP C2A N3A C4A 110.982 1.50 +NDP N9A C4A C5A 105.616 1.50 +NDP N9A C4A N3A 127.895 1.50 +NDP C5A C4A N3A 126.489 1.50 +NDP PA O3 PN 132.542 3.00 +NDP O3 PN O1N 108.816 2.14 +NDP O3 PN O2N 108.816 2.14 +NDP O3 PN O5D 101.065 1.97 +NDP O1N PN O2N 118.411 2.35 +NDP O1N PN O5D 109.410 1.50 +NDP O2N PN O5D 109.410 1.50 +NDP PN O5D C5D 118.553 2.41 +NDP O5D C5D C4D 109.342 1.50 +NDP O5D C5D H51N 109.845 1.50 +NDP O5D C5D H52N 109.845 1.50 +NDP C4D C5D H51N 109.624 1.50 +NDP C4D C5D H52N 109.624 1.50 +NDP H51N C5D H52N 108.472 1.50 +NDP C5D C4D O4D 109.123 1.50 +NDP C5D C4D C3D 116.008 1.52 +NDP C5D C4D H4D 108.268 1.50 +NDP O4D C4D C3D 105.508 1.50 +NDP O4D C4D H4D 108.642 1.50 +NDP C3D C4D H4D 109.363 1.86 +NDP C4D O4D C1D 109.926 1.50 +NDP C4D C3D O3D 111.281 2.46 +NDP C4D C3D C2D 102.352 1.50 +NDP C4D C3D H3D 110.452 2.54 +NDP O3D C3D C2D 112.463 2.73 +NDP O3D C3D H3D 110.380 1.67 +NDP C2D C3D H3D 110.255 2.04 +NDP C3D O3D HO3N 108.744 3.00 +NDP C3D C2D O2D 112.463 2.73 +NDP C3D C2D C1D 104.443 2.26 +NDP C3D C2D H2D 110.255 2.04 +NDP O2D C2D C1D 111.164 2.38 +NDP O2D C2D H2D 110.259 1.63 +NDP C1D C2D H2D 110.518 1.74 +NDP C2D O2D HO2N 109.104 3.00 +NDP O4D C1D C2D 106.204 2.50 +NDP O4D C1D N1N 108.278 1.50 +NDP O4D C1D H1D 109.395 1.50 +NDP C2D C1D N1N 112.110 1.66 +NDP C2D C1D H1D 109.914 1.68 +NDP N1N C1D H1D 109.209 1.50 +NDP C1D N1N C2N 120.851 1.78 +NDP C1D N1N C6N 120.851 1.78 +NDP C2N N1N C6N 118.299 1.80 +NDP N1N C2N C3N 121.110 1.66 +NDP N1N C2N H2N 119.532 1.52 +NDP C3N C2N H2N 119.358 1.50 +NDP C2N C3N C7N 117.781 1.96 +NDP C2N C3N C4N 118.007 1.50 +NDP C7N C3N C4N 124.211 3.00 +NDP C3N C7N O7N 119.878 1.50 +NDP C3N C7N N7N 118.037 3.00 +NDP O7N C7N N7N 122.085 1.50 +NDP C7N N7N H71N 120.214 2.13 +NDP C7N N7N H72N 120.224 2.13 +NDP H71N N7N H72N 119.583 2.34 +NDP C3N C4N C5N 114.356 2.46 +NDP C3N C4N H41N 108.993 1.50 +NDP C3N C4N H42N 108.993 1.50 +NDP C5N C4N H41N 108.815 3.00 +NDP C5N C4N H42N 108.815 3.00 +NDP H41N C4N H42N 106.630 2.58 +NDP C4N C5N C6N 121.257 2.14 +NDP C4N C5N H5N 119.218 1.70 +NDP C6N C5N H5N 119.525 1.50 +NDP N1N C6N C5N 120.771 1.66 +NDP N1N C6N H6N 119.193 1.52 +NDP C5N C6N H6N 120.036 1.50 +NDP O2B P2B O1X 106.518 3.00 +NDP O2B P2B O2X 106.518 3.00 +NDP O2B P2B O3X 106.518 3.00 +NDP O1X P2B O2X 112.139 1.52 +NDP O1X P2B O3X 112.139 1.52 +NDP O2X P2B O3X 112.139 1.52 +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 +NDP sp3_sp3_54 PN O3 PA O1A 60.000 10.0 3 +NDP sp3_sp3_51 C5B O5B PA O1A 60.000 10.0 3 +NDP sp3_sp3_82 C2B O2B P2B O1X 180.000 10.0 3 +NDP sp2_sp3_13 C8A N9A C1B O4B 150.000 10.0 6 +NDP const_14 N7A C8A N9A C1B 180.000 10.0 2 +NDP const_26 C5A C4A N9A C1B 180.000 10.0 2 +NDP const_17 N9A C8A N7A C5A 0.000 10.0 2 +NDP const_20 C6A C5A N7A C8A 180.000 10.0 2 +NDP const_sp2_sp2_4 N7A C5A C6A N6A 0.000 5.0 2 +NDP const_21 N9A C4A C5A N7A 0.000 10.0 2 +NDP sp2_sp2_13 C5A C6A N6A H61A 180.000 5.0 2 +NDP const_sp2_sp2_6 N6A C6A N1A C2A 180.000 5.0 2 +NDP const_sp2_sp2_7 N3A C2A N1A C6A 0.000 5.0 2 +NDP const_sp2_sp2_9 N1A C2A N3A C4A 0.000 5.0 2 +NDP const_12 N9A C4A N3A C2A 180.000 10.0 2 +NDP sp3_sp3_87 PA O3 PN O1N 60.000 10.0 3 +NDP sp3_sp3_88 C5D O5D PN O3 180.000 10.0 3 +NDP sp3_sp3_91 C4D C5D O5D PN 180.000 10.0 3 +NDP sp3_sp3_94 O4D C4D C5D O5D 180.000 10.0 3 +NDP sp3_sp3_26 C5D C4D O4D C1D -60.000 10.0 3 +NDP sp3_sp3_107 O3D C3D C4D C5D 180.000 10.0 3 +NDP sp3_sp3_28 C2D C1D O4D C4D -60.000 10.0 3 +NDP sp3_sp3_112 C4D C3D O3D HO3N 180.000 10.0 3 +NDP sp3_sp3_44 O2D C2D C3D O3D -60.000 10.0 3 +NDP sp3_sp3_115 C3D C2D O2D HO2N 180.000 10.0 3 +NDP sp3_sp3_32 O4D C1D C2D O2D 180.000 10.0 3 +NDP sp2_sp3_19 C2N N1N C1D O4D 150.000 10.0 6 +NDP sp2_sp2_2 C3N C2N N1N C1D 180.000 5.0 2 +NDP sp2_sp2_18 C5N C6N N1N C1D 180.000 5.0 2 +NDP sp2_sp2_6 N1N C2N C3N C7N 180.000 5.0 2 +NDP sp2_sp2_24 C2N C3N C7N O7N 180.000 5.0 2 +NDP sp2_sp3_4 C7N C3N C4N C5N 180.000 10.0 6 +NDP sp2_sp2_27 O7N C7N N7N H71N 0.000 5.0 2 +NDP sp3_sp3_55 C4B C5B O5B PA 180.000 10.0 3 +NDP sp2_sp3_7 C6N C5N C4N C3N 0.000 10.0 6 +NDP sp2_sp2_9 C4N C5N C6N N1N 0.000 5.0 2 +NDP sp3_sp3_58 O4B C4B C5B O5B 180.000 10.0 3 +NDP sp3_sp3_2 C5B C4B O4B C1B -60.000 10.0 3 +NDP sp3_sp3_71 O3B C3B C4B C5B 180.000 10.0 3 +NDP sp3_sp3_4 C2B C1B O4B C4B -60.000 10.0 3 +NDP sp3_sp3_76 C4B C3B O3B HO3A 180.000 10.0 3 +NDP sp3_sp3_20 O2B C2B C3B O3B -60.000 10.0 3 +NDP sp3_sp3_79 C3B C2B O2B P2B 180.000 10.0 3 +NDP sp3_sp3_8 O4B C1B C2B O2B 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 +NDP chir_1 PA O3 O5B O2A both +NDP chir_2 C4B O4B C3B C5B negative +NDP chir_3 C3B O3B C2B C4B negative +NDP chir_4 C2B O2B C1B C3B negative +NDP chir_5 C1B O4B N9A C2B negative +NDP chir_6 PN O3 O5D O2N both +NDP chir_7 C4D O4D C3D C5D negative +NDP chir_8 C3D O3D C4D C2D positive +NDP chir_9 C2D O2D C1D C3D negative +NDP chir_10 C1D O4D N1N C2D 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 +NDP plan-1 C1B 0.020 +NDP plan-1 C2A 0.020 +NDP plan-1 C4A 0.020 +NDP plan-1 C5A 0.020 +NDP plan-1 C6A 0.020 +NDP plan-1 C8A 0.020 +NDP plan-1 H2A 0.020 +NDP plan-1 H8A 0.020 +NDP plan-1 N1A 0.020 +NDP plan-1 N3A 0.020 +NDP plan-1 N6A 0.020 +NDP plan-1 N7A 0.020 +NDP plan-1 N9A 0.020 +NDP plan-2 C6A 0.020 +NDP plan-2 H61A 0.020 +NDP plan-2 H62A 0.020 +NDP plan-2 N6A 0.020 +NDP plan-3 C1D 0.020 +NDP plan-3 C2N 0.020 +NDP plan-3 C6N 0.020 +NDP plan-3 N1N 0.020 +NDP plan-4 C2N 0.020 +NDP plan-4 C3N 0.020 +NDP plan-4 H2N 0.020 +NDP plan-4 N1N 0.020 +NDP plan-5 C2N 0.020 +NDP plan-5 C3N 0.020 +NDP plan-5 C4N 0.020 +NDP plan-5 C7N 0.020 +NDP plan-6 C3N 0.020 +NDP plan-6 C7N 0.020 +NDP plan-6 N7N 0.020 +NDP plan-6 O7N 0.020 +NDP plan-7 C7N 0.020 +NDP plan-7 H71N 0.020 +NDP plan-7 H72N 0.020 +NDP plan-7 N7N 0.020 +NDP plan-8 C4N 0.020 +NDP plan-8 C5N 0.020 +NDP plan-8 C6N 0.020 +NDP plan-8 H5N 0.020 +NDP plan-9 C5N 0.020 +NDP plan-9 C6N 0.020 +NDP plan-9 H6N 0.020 +NDP plan-9 N1N 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 +NDP SMILES_CANONICAL CACTVS 3.341 NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O +NDP SMILES CACTVS 3.341 NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O +NDP 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)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N +NDP SMILES "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N +NDP InChI InChI 1.03 InChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1 +NDP InChIKey InChI 1.03 ACFIXJIJDZMPPO-NNYOXOHSSA-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 +NDP acedrg 243 "dictionary generator" +NDP acedrg_database 11 "data source" +NDP rdkit 2017.03.2 "Chemoinformatics tool" +NDP refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/OMC.cif b/image_analysis/structure_refinement/monomers/OMC.cif new file mode 100644 index 000000000..47bb94cb7 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/OMC.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 +OMC OMC "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" RNA 36 22 . +# +data_comp_OMC +# +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 +OMC N1 N NR6 0 47.593 -6.375 -2.504 +OMC C2 C CR6 0 46.926 -6.660 -1.298 +OMC N3 N NRD6 0 45.724 -6.070 -1.053 +OMC C4 C CR6 0 45.173 -5.232 -1.946 +OMC C5 C CR16 0 45.830 -4.936 -3.175 +OMC C6 C CR16 0 47.017 -5.523 -3.411 +OMC O2 O O 0 47.439 -7.436 -0.475 +OMC N4 N NH2 0 43.999 -4.688 -1.651 +OMC "C1'" C CH1 0 48.910 -7.010 -2.809 +OMC "C2'" C CH1 0 48.823 -8.062 -3.926 +OMC "O2'" O O2 0 49.366 -9.304 -3.486 +OMC CM2 C CH3 0 48.416 -10.158 -2.852 +OMC "C3'" C CH1 0 49.625 -7.429 -5.073 +OMC "C4'" C CH1 0 50.603 -6.511 -4.332 +OMC "O4'" O O2 0 49.817 -6.011 -3.225 +OMC "O3'" O OH1 0 50.326 -8.382 -5.862 +OMC "C5'" C CH2 0 51.176 -5.361 -5.125 +OMC "O5'" O O2 0 50.108 -4.463 -5.525 +OMC P P P 0 50.445 -3.257 -6.544 +OMC OP1 O O 0 49.150 -2.486 -6.714 +OMC OP2 O OP -1 50.910 -3.918 -7.829 +OMC OP3 O OP -1 51.534 -2.441 -5.874 +OMC H5 H H 0 45.449 -4.350 -3.805 +OMC H6 H H 0 47.471 -5.349 -4.209 +OMC HN41 H H 0 43.650 -4.086 -2.185 +OMC HN42 H H 0 43.572 -4.931 -0.922 +OMC "H1'" H H 0 49.270 -7.434 -1.997 +OMC "H2'" H H 0 47.883 -8.180 -4.213 +OMC HM21 H H 0 48.873 -10.933 -2.488 +OMC HM22 H H 0 47.756 -10.447 -3.504 +OMC HM23 H H 0 47.974 -9.675 -2.135 +OMC "H3'" H H 0 49.020 -6.893 -5.647 +OMC "H4'" H H 0 51.347 -7.043 -3.976 +OMC "HO3'" H H 0 50.750 -7.973 -6.473 +OMC "H5'" H H 0 51.639 -5.709 -5.926 +OMC "H5''" H H 0 51.834 -4.872 -4.571 +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 +OMC N1 C2 SINGLE y 1.397 0.0100 1.397 0.0100 +OMC N1 C6 SINGLE y 1.364 0.0108 1.364 0.0108 +OMC N1 "C1'" SINGLE n 1.487 0.0100 1.487 0.0100 +OMC C2 N3 SINGLE y 1.355 0.0119 1.355 0.0119 +OMC C2 O2 DOUBLE n 1.241 0.0100 1.241 0.0100 +OMC N3 C4 DOUBLE y 1.339 0.0110 1.339 0.0110 +OMC C4 C5 SINGLE y 1.422 0.0123 1.422 0.0123 +OMC C4 N4 SINGLE n 1.325 0.0109 1.325 0.0109 +OMC C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 +OMC "C1'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100 +OMC "C1'" "O4'" SINGLE n 1.411 0.0100 1.411 0.0100 +OMC "C2'" "O2'" SINGLE n 1.423 0.0100 1.423 0.0100 +OMC "C2'" "C3'" SINGLE n 1.530 0.0134 1.530 0.0134 +OMC "O2'" CM2 SINGLE n 1.423 0.0131 1.423 0.0131 +OMC "C3'" "C4'" SINGLE n 1.535 0.0100 1.535 0.0100 +OMC "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +OMC "C4'" "O4'" SINGLE n 1.451 0.0111 1.451 0.0111 +OMC "C4'" "C5'" SINGLE n 1.509 0.0100 1.509 0.0100 +OMC "C5'" "O5'" SINGLE n 1.450 0.0166 1.450 0.0166 +OMC "O5'" P SINGLE n 1.614 0.0178 1.614 0.0178 +OMC P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192 +OMC P OP2 SINGLE n 1.517 0.0192 1.517 0.0192 +OMC P OP3 SINGLE n 1.517 0.0192 1.517 0.0192 +OMC C5 H5 SINGLE n 1.082 0.0130 0.941 0.0174 +OMC C6 H6 SINGLE n 1.082 0.0130 0.935 0.0143 +OMC N4 HN41 SINGLE n 1.016 0.0100 0.877 0.0200 +OMC N4 HN42 SINGLE n 1.016 0.0100 0.877 0.0200 +OMC "C1'" "H1'" SINGLE n 1.089 0.0100 0.985 0.0100 +OMC "C2'" "H2'" SINGLE n 1.089 0.0100 0.988 0.0200 +OMC CM2 HM21 SINGLE n 1.089 0.0100 0.971 0.0146 +OMC CM2 HM22 SINGLE n 1.089 0.0100 0.971 0.0146 +OMC CM2 HM23 SINGLE n 1.089 0.0100 0.971 0.0146 +OMC "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +OMC "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 +OMC "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +OMC "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +OMC "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 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 +OMC C2 N1 C6 120.510 1.50 +OMC C2 N1 "C1'" 118.189 2.26 +OMC C6 N1 "C1'" 121.301 1.52 +OMC N1 C2 N3 118.920 1.50 +OMC N1 C2 O2 118.716 1.50 +OMC N3 C2 O2 122.370 1.50 +OMC C2 N3 C4 120.266 1.50 +OMC N3 C4 C5 121.269 1.50 +OMC N3 C4 N4 117.855 1.50 +OMC C5 C4 N4 120.876 1.50 +OMC C4 C5 C6 117.808 1.50 +OMC C4 C5 H5 121.350 1.50 +OMC C6 C5 H5 120.848 1.50 +OMC N1 C6 C5 121.215 1.50 +OMC N1 C6 H6 118.510 1.50 +OMC C5 C6 H6 120.275 1.75 +OMC C4 N4 HN41 119.818 1.59 +OMC C4 N4 HN42 119.818 1.59 +OMC HN41 N4 HN42 120.363 1.85 +OMC N1 "C1'" "C2'" 113.620 1.99 +OMC N1 "C1'" "O4'" 108.667 1.50 +OMC N1 "C1'" "H1'" 109.166 1.50 +OMC "C2'" "C1'" "O4'" 106.391 1.51 +OMC "C2'" "C1'" "H1'" 109.527 1.54 +OMC "O4'" "C1'" "H1'" 109.327 1.50 +OMC "C1'" "C2'" "O2'" 110.738 2.44 +OMC "C1'" "C2'" "C3'" 101.207 1.50 +OMC "C1'" "C2'" "H2'" 110.561 1.96 +OMC "O2'" "C2'" "C3'" 112.623 3.00 +OMC "O2'" "C2'" "H2'" 110.257 1.68 +OMC "C3'" "C2'" "H2'" 110.255 2.04 +OMC "C2'" "O2'" CM2 113.084 1.50 +OMC "O2'" CM2 HM21 109.434 1.50 +OMC "O2'" CM2 HM22 109.434 1.50 +OMC "O2'" CM2 HM23 109.434 1.50 +OMC HM21 CM2 HM22 109.541 1.50 +OMC HM21 CM2 HM23 109.541 1.50 +OMC HM22 CM2 HM23 109.541 1.50 +OMC "C2'" "C3'" "C4'" 102.352 1.50 +OMC "C2'" "C3'" "O3'" 112.463 2.73 +OMC "C2'" "C3'" "H3'" 110.255 2.04 +OMC "C4'" "C3'" "O3'" 111.281 2.46 +OMC "C4'" "C3'" "H3'" 110.452 2.54 +OMC "O3'" "C3'" "H3'" 110.380 1.67 +OMC "C3'" "C4'" "O4'" 104.439 1.50 +OMC "C3'" "C4'" "C5'" 116.008 1.52 +OMC "C3'" "C4'" "H4'" 109.363 1.86 +OMC "O4'" "C4'" "C5'" 109.615 1.50 +OMC "O4'" "C4'" "H4'" 108.698 1.50 +OMC "C5'" "C4'" "H4'" 108.268 1.50 +OMC "C1'" "O4'" "C4'" 109.578 1.50 +OMC "C3'" "O3'" "HO3'" 108.744 3.00 +OMC "C4'" "C5'" "O5'" 109.342 1.50 +OMC "C4'" "C5'" "H5'" 109.624 1.50 +OMC "C4'" "C5'" "H5''" 109.624 1.50 +OMC "O5'" "C5'" "H5'" 109.845 1.50 +OMC "O5'" "C5'" "H5''" 109.845 1.50 +OMC "H5'" "C5'" "H5''" 108.472 1.50 +OMC "C5'" "O5'" P 118.783 1.50 +OMC "O5'" P OP1 105.808 2.07 +OMC "O5'" P OP2 105.808 2.07 +OMC "O5'" P OP3 105.808 2.07 +OMC OP1 P OP2 112.864 1.69 +OMC OP1 P OP3 112.864 1.69 +OMC OP2 P OP3 112.864 1.69 +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 +OMC C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +OMC C2e-nyu0 "C4'" "O4'" "C1'" "C2" 340.700 6.300 1 +OMC C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +OMC C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +OMC C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +OMC C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +OMC C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +OMC C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +OMC C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +OMC C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +OMC C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +OMC C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +OMC alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +OMC beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +OMC epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +OMC gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +OMC const_sp2_sp2_3 O2 C2 N1 C6 180.000 5.0 2 +OMC const_17 C5 C6 N1 C2 0.000 10.0 2 +OMC sp3_sp3_37 HM21 CM2 "O2'" "C2'" 180.000 10.0 3 +OMC const_sp2_sp2_6 O2 C2 N3 C4 180.000 5.0 2 +OMC const_sp2_sp2_8 N4 C4 N3 C2 180.000 5.0 2 +OMC const_11 N4 C4 C5 C6 180.000 10.0 2 +OMC sp2_sp2_3 N3 C4 N4 HN41 0.000 5.0 2 +OMC const_13 C4 C5 C6 N1 0.000 10.0 2 +OMC sp3_sp3_34 "C1'" "C2'" "O2'" CM2 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 +OMC chir_1 "C1'" "O4'" N1 "C2'" negative +OMC chir_2 "C2'" "O2'" "C1'" "C3'" negative +OMC chir_3 "C3'" "O3'" "C2'" "C4'" negative +OMC chir_4 "C4'" "O4'" "C3'" "C5'" negative +OMC chir_5 P "O5'" OP2 OP3 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 +OMC plan-1 "C1'" 0.020 +OMC plan-1 C2 0.020 +OMC plan-1 C4 0.020 +OMC plan-1 C5 0.020 +OMC plan-1 C6 0.020 +OMC plan-1 H5 0.020 +OMC plan-1 H6 0.020 +OMC plan-1 N1 0.020 +OMC plan-1 N3 0.020 +OMC plan-1 N4 0.020 +OMC plan-1 O2 0.020 +OMC plan-2 C4 0.020 +OMC plan-2 HN41 0.020 +OMC plan-2 HN42 0.020 +OMC 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 +OMC SMILES ACDLabs 10.04 O=C1N=C(N)C=CN1C2OC(C(O)C2OC)COP(=O)(O)O +OMC SMILES_CANONICAL CACTVS 3.341 CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=NC2=O)N +OMC SMILES CACTVS 3.341 CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=NC2=O)N +OMC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)O)O +OMC SMILES "OpenEye OEToolkits" 1.5.0 COC1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)O)O +OMC InChI InChI 1.03 InChI=1S/C10H16N3O8P/c1-19-8-7(14)5(4-20-22(16,17)18)21-9(8)13-3-2-6(11)12-10(13)15/h2-3,5,7-9,14H,4H2,1H3,(H2,11,12,15)(H2,16,17,18)/t5-,7-,8-,9-/m1/s1 +OMC InChIKey InChI 1.03 USRXKJOTSNCJMA-ZOQUXTDFSA-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 +OMC acedrg 243 "dictionary generator" +OMC acedrg_database 11 "data source" +OMC rdkit 2017.03.2 "Chemoinformatics tool" +OMC refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/OMG.cif b/image_analysis/structure_refinement/monomers/OMG.cif new file mode 100644 index 000000000..f0bb41e3a --- /dev/null +++ b/image_analysis/structure_refinement/monomers/OMG.cif @@ -0,0 +1,294 @@ +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 +OMG OMG "O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE" RNA 39 25 . + +data_comp_OMG +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 +OMG P P P 0 46.680 -11.593 -10.172 +OMG OP1 O O 0 46.840 -10.158 -9.706 +OMG OP2 O OP -1 47.443 -11.887 -11.449 +OMG OP3 O OP -1 46.957 -12.602 -9.074 +OMG "O5'" O O2 0 45.118 -11.766 -10.543 +OMG "C5'" C CH2 0 44.556 -10.952 -11.605 +OMG "C4'" C CH1 0 43.054 -11.106 -11.627 +OMG "O4'" O O2 0 42.713 -12.507 -11.779 +OMG "C3'" C CH1 0 42.306 -10.664 -10.364 +OMG "O3'" O OH1 0 42.080 -9.260 -10.371 +OMG "C2'" C CH1 0 41.018 -11.485 -10.465 +OMG "O2'" O O2 0 40.048 -10.870 -11.308 +OMG CM2 C CH3 0 38.711 -11.301 -11.064 +OMG "C1'" C CH1 0 41.518 -12.794 -11.083 +OMG N9 N NR5 0 41.769 -13.832 -10.083 +OMG C8 C CR15 0 42.971 -14.402 -9.735 +OMG N7 N NRD5 0 42.865 -15.317 -8.802 +OMG C5 C CR56 0 41.507 -15.358 -8.517 +OMG C6 C CR6 0 40.790 -16.159 -7.588 +OMG O6 O O 0 41.238 -17.015 -6.813 +OMG N1 N NR16 0 39.417 -15.883 -7.616 +OMG C2 C CR6 0 38.813 -14.955 -8.435 +OMG N2 N NH2 0 37.484 -14.824 -8.326 +OMG N3 N NRD6 0 39.486 -14.200 -9.310 +OMG C4 C CR56 0 40.821 -14.453 -9.301 +OMG "H5'" H H 0 44.931 -11.234 -12.476 +OMG "H5''" H H 0 44.789 -10.002 -11.458 +OMG "H4'" H H 0 42.707 -10.610 -12.398 +OMG "H3'" H H 0 42.809 -10.925 -9.551 +OMG "HO3'" H H 0 41.566 -9.062 -9.725 +OMG "H2'" H H 0 40.648 -11.625 -9.558 +OMG HM21 H H 0 38.118 -10.894 -11.717 +OMG HM22 H H 0 38.441 -11.032 -10.171 +OMG HM23 H H 0 38.663 -12.267 -11.141 +OMG "H1'" H H 0 40.844 -13.122 -11.720 +OMG H8 H H 0 43.793 -14.159 -10.125 +OMG HN1 H H 0 38.896 -16.352 -7.054 +OMG HN21 H H 0 37.121 -14.025 -8.337 +OMG HN22 H H 0 36.980 -15.537 -8.245 + +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 +OMG P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192 +OMG P OP2 SINGLE n 1.517 0.0192 1.517 0.0192 +OMG P OP3 SINGLE n 1.517 0.0192 1.517 0.0192 +OMG P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178 +OMG "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166 +OMG "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100 +OMG "C4'" "O4'" SINGLE n 1.451 0.0100 1.451 0.0100 +OMG "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100 +OMG "O4'" "C1'" SINGLE n 1.409 0.0100 1.409 0.0100 +OMG "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +OMG "C3'" "C2'" SINGLE n 1.530 0.0134 1.530 0.0134 +OMG "C2'" "O2'" SINGLE n 1.423 0.0100 1.423 0.0100 +OMG "C2'" "C1'" SINGLE n 1.527 0.0100 1.527 0.0100 +OMG "O2'" CM2 SINGLE n 1.423 0.0131 1.423 0.0131 +OMG "C1'" N9 SINGLE n 1.458 0.0100 1.458 0.0100 +OMG N9 C8 SINGLE y 1.372 0.0100 1.372 0.0100 +OMG N9 C4 SINGLE y 1.375 0.0100 1.375 0.0100 +OMG C8 N7 DOUBLE y 1.312 0.0100 1.312 0.0100 +OMG N7 C5 SINGLE y 1.390 0.0100 1.390 0.0100 +OMG C5 C6 SINGLE y 1.417 0.0103 1.417 0.0103 +OMG C5 C4 DOUBLE y 1.377 0.0100 1.377 0.0100 +OMG C6 O6 DOUBLE n 1.239 0.0100 1.239 0.0100 +OMG C6 N1 SINGLE y 1.396 0.0107 1.396 0.0107 +OMG N1 C2 SINGLE y 1.374 0.0100 1.374 0.0100 +OMG C2 N2 SINGLE n 1.340 0.0101 1.340 0.0101 +OMG C2 N3 DOUBLE y 1.333 0.0104 1.333 0.0104 +OMG N3 C4 SINGLE y 1.355 0.0100 1.355 0.0100 +OMG "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +OMG "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200 +OMG "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 +OMG "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +OMG "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +OMG "C2'" "H2'" SINGLE n 1.089 0.0100 0.988 0.0200 +OMG CM2 HM21 SINGLE n 1.089 0.0100 0.971 0.0146 +OMG CM2 HM22 SINGLE n 1.089 0.0100 0.971 0.0146 +OMG CM2 HM23 SINGLE n 1.089 0.0100 0.971 0.0146 +OMG "C1'" "H1'" SINGLE n 1.089 0.0100 0.984 0.0200 +OMG C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170 +OMG N1 HN1 SINGLE n 1.016 0.0100 0.897 0.0200 +OMG N2 HN21 SINGLE n 1.016 0.0100 0.877 0.0200 +OMG 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 +OMG OP1 P OP2 112.864 1.69 +OMG OP1 P OP3 112.864 1.69 +OMG OP1 P "O5'" 105.808 2.07 +OMG OP2 P OP3 112.864 1.69 +OMG OP2 P "O5'" 105.808 2.07 +OMG OP3 P "O5'" 105.808 2.07 +OMG P "O5'" "C5'" 118.783 1.50 +OMG "O5'" "C5'" "C4'" 109.342 1.50 +OMG "O5'" "C5'" "H5'" 109.845 1.50 +OMG "O5'" "C5'" "H5''" 109.845 1.50 +OMG "C4'" "C5'" "H5'" 109.624 1.50 +OMG "C4'" "C5'" "H5''" 109.624 1.50 +OMG "H5'" "C5'" "H5''" 108.472 1.50 +OMG "C5'" "C4'" "O4'" 109.123 1.50 +OMG "C5'" "C4'" "C3'" 116.008 1.52 +OMG "C5'" "C4'" "H4'" 108.268 1.50 +OMG "O4'" "C4'" "C3'" 105.388 1.50 +OMG "O4'" "C4'" "H4'" 108.947 1.50 +OMG "C3'" "C4'" "H4'" 109.363 1.86 +OMG "C4'" "O4'" "C1'" 109.903 1.50 +OMG "C4'" "C3'" "O3'" 111.281 2.46 +OMG "C4'" "C3'" "C2'" 102.352 1.50 +OMG "C4'" "C3'" "H3'" 110.452 2.54 +OMG "O3'" "C3'" "C2'" 112.463 2.73 +OMG "O3'" "C3'" "H3'" 110.380 1.67 +OMG "C2'" "C3'" "H3'" 110.255 2.04 +OMG "C3'" "O3'" "HO3'" 108.744 3.00 +OMG "C3'" "C2'" "O2'" 112.623 3.00 +OMG "C3'" "C2'" "C1'" 101.388 1.50 +OMG "C3'" "C2'" "H2'" 110.255 2.04 +OMG "O2'" "C2'" "C1'" 110.738 2.44 +OMG "O2'" "C2'" "H2'" 110.257 1.68 +OMG "C1'" "C2'" "H2'" 111.584 1.94 +OMG "C2'" "O2'" CM2 113.084 1.50 +OMG "O2'" CM2 HM21 109.434 1.50 +OMG "O2'" CM2 HM22 109.434 1.50 +OMG "O2'" CM2 HM23 109.434 1.50 +OMG HM21 CM2 HM22 109.541 1.50 +OMG HM21 CM2 HM23 109.541 1.50 +OMG HM22 CM2 HM23 109.541 1.50 +OMG "O4'" "C1'" "C2'" 106.765 1.50 +OMG "O4'" "C1'" N9 108.477 1.50 +OMG "O4'" "C1'" "H1'" 109.807 1.50 +OMG "C2'" "C1'" N9 112.584 1.50 +OMG "C2'" "C1'" "H1'" 109.263 1.50 +OMG N9 "C1'" "H1'" 109.561 1.50 +OMG "C1'" N9 C8 126.829 1.91 +OMG "C1'" N9 C4 127.440 1.80 +OMG C8 N9 C4 105.731 1.50 +OMG N9 C8 N7 113.507 1.50 +OMG N9 C8 H8 123.187 1.50 +OMG N7 C8 H8 123.307 1.50 +OMG C8 N7 C5 104.778 1.50 +OMG N7 C5 C6 130.030 1.50 +OMG N7 C5 C4 110.574 1.50 +OMG C6 C5 C4 119.397 1.50 +OMG C5 C6 O6 128.244 1.50 +OMG C5 C6 N1 111.367 1.50 +OMG O6 C6 N1 120.389 1.50 +OMG C6 N1 C2 125.351 1.50 +OMG C6 N1 HN1 116.978 2.44 +OMG C2 N1 HN1 117.677 2.71 +OMG N1 C2 N2 116.576 1.50 +OMG N1 C2 N3 123.602 1.50 +OMG N2 C2 N3 119.821 1.50 +OMG C2 N2 HN21 119.868 1.50 +OMG C2 N2 HN22 119.868 1.50 +OMG HN21 N2 HN22 120.263 1.96 +OMG C2 N3 C4 112.066 1.50 +OMG N9 C4 C5 105.411 1.50 +OMG N9 C4 N3 126.378 1.50 +OMG 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 +OMG C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +OMG C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1 +OMG C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +OMG C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +OMG C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +OMG C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +OMG C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6 +OMG C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +OMG C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +OMG C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +OMG C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +OMG C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +OMG alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +OMG beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +OMG epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +OMG gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +OMG sp3_sp3_52 "C3'" "C2'" "O2'" CM2 180.000 10.0 3 +OMG sp3_sp3_55 HM21 CM2 "O2'" "C2'" 180.000 10.0 3 +OMG const_18 N7 C8 N9 "C1'" 180.000 10.0 2 +OMG const_30 C5 C4 N9 "C1'" 180.000 10.0 2 +OMG const_21 N9 C8 N7 C5 0.000 10.0 2 +OMG const_24 C6 C5 N7 C8 180.000 10.0 2 +OMG const_sp2_sp2_4 N7 C5 C6 O6 0.000 5.0 2 +OMG const_25 N9 C4 C5 N7 0.000 10.0 2 +OMG const_sp2_sp2_7 O6 C6 N1 C2 180.000 5.0 2 +OMG const_11 N2 C2 N1 C6 180.000 10.0 2 +OMG sp2_sp2_1 N1 C2 N2 HN21 180.000 5.0 2 +OMG const_14 N2 C2 N3 C4 180.000 10.0 2 +OMG 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 +OMG chir_1 P "O5'" OP2 OP3 both +OMG chir_2 "C4'" "O4'" "C3'" "C5'" negative +OMG chir_3 "C3'" "O3'" "C2'" "C4'" negative +OMG chir_4 "C2'" "O2'" "C1'" "C3'" negative +OMG 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 +OMG plan-1 "C1'" 0.020 +OMG plan-1 C2 0.020 +OMG plan-1 C4 0.020 +OMG plan-1 C5 0.020 +OMG plan-1 C6 0.020 +OMG plan-1 C8 0.020 +OMG plan-1 H8 0.020 +OMG plan-1 HN1 0.020 +OMG plan-1 N1 0.020 +OMG plan-1 N2 0.020 +OMG plan-1 N3 0.020 +OMG plan-1 N7 0.020 +OMG plan-1 N9 0.020 +OMG plan-1 O6 0.020 +OMG plan-2 C2 0.020 +OMG plan-2 HN21 0.020 +OMG plan-2 HN22 0.020 +OMG 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 +OMG SMILES ACDLabs 10.04 O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3OC)COP(=O)(O)O +OMG SMILES_CANONICAL CACTVS 3.341 CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1n2cnc3C(=O)NC(=Nc23)N +OMG SMILES CACTVS 3.341 CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1n2cnc3C(=O)NC(=Nc23)N +OMG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CO[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2N=C(NC3=O)N)COP(=O)(O)O)O +OMG SMILES "OpenEye OEToolkits" 1.5.0 COC1C(C(OC1n2cnc3c2N=C(NC3=O)N)COP(=O)(O)O)O +OMG InChI InChI 1.03 InChI=1S/C11H16N5O8P/c1-22-7-6(17)4(2-23-25(19,20)21)24-10(7)16-3-13-5-8(16)14-11(12)15-9(5)18/h3-4,6-7,10,17H,2H2,1H3,(H2,19,20,21)(H3,12,14,15,18)/t4-,6-,7-,10-/m1/s1 +OMG InChIKey InChI 1.03 YPMKZCOIEXUDSS-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 +OMG acedrg 243 "dictionary generator" +OMG acedrg_database 11 "data source" +OMG rdkit 2017.03.2 "Chemoinformatics tool" +OMG refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/OMU.cif b/image_analysis/structure_refinement/monomers/OMU.cif new file mode 100644 index 000000000..4fff76f20 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/OMU.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 +OMU OMU "O2'-METHYLURIDINE 5'-MONOPHOSPHATE" RNA 35 22 . + +data_comp_OMU +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 +OMU N1 N NR6 0 7.321 3.277 -7.800 +OMU C2 C CR6 0 6.703 4.284 -8.539 +OMU N3 N NR16 0 5.357 4.097 -8.759 +OMU C4 C CR6 0 4.576 3.040 -8.325 +OMU C5 C CR16 0 5.282 2.046 -7.565 +OMU C6 C CR16 0 6.597 2.199 -7.332 +OMU O2 O O 0 7.289 5.268 -8.976 +OMU O4 O O 0 3.377 3.016 -8.605 +OMU "C1'" C CH1 0 8.775 3.398 -7.507 +OMU "C2'" C CH1 0 9.066 3.720 -6.033 +OMU "O2'" O O2 0 9.918 4.857 -5.928 +OMU CM2 C CH3 0 9.221 6.100 -5.894 +OMU "C3'" C CH1 0 9.716 2.430 -5.513 +OMU "C4'" C CH1 0 10.361 1.849 -6.776 +OMU "O3'" O OH1 0 10.695 2.660 -4.506 +OMU "O4'" O O2 0 9.408 2.172 -7.816 +OMU "C5'" C CH2 0 10.637 0.365 -6.768 +OMU "O5'" O O2 0 9.387 -0.365 -6.663 +OMU P P P 0 9.434 -1.955 -6.390 +OMU OP1 O O 0 10.088 -2.124 -5.032 +OMU OP2 O OP -1 7.990 -2.420 -6.410 +OMU OP3 O OP -1 10.258 -2.544 -7.519 +OMU HN3 H H 0 4.952 4.733 -9.234 +OMU H5 H H 0 4.828 1.299 -7.235 +OMU H6 H H 0 7.045 1.542 -6.834 +OMU "H1'" H H 0 9.170 4.096 -8.070 +OMU "H2'" H H 0 8.220 3.878 -5.544 +OMU HM21 H H 0 9.861 6.830 -5.932 +OMU HM22 H H 0 8.710 6.162 -5.071 +OMU HM23 H H 0 8.620 6.157 -6.654 +OMU "H3'" H H 0 9.016 1.816 -5.172 +OMU "H4'" H H 0 11.202 2.320 -6.961 +OMU "HO3'" H H 0 11.018 1.914 -4.263 +OMU "H5'" H H 0 11.221 0.141 -6.002 +OMU "H5''" H H 0 11.104 0.110 -7.601 + +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 +OMU N1 C2 SINGLE y 1.383 0.0100 1.383 0.0100 +OMU N1 C6 SINGLE y 1.375 0.0106 1.375 0.0106 +OMU N1 "C1'" SINGLE n 1.476 0.0133 1.476 0.0133 +OMU C2 N3 SINGLE y 1.372 0.0112 1.372 0.0112 +OMU C2 O2 DOUBLE n 1.224 0.0111 1.224 0.0111 +OMU N3 C4 SINGLE y 1.381 0.0100 1.381 0.0100 +OMU C4 C5 SINGLE y 1.434 0.0100 1.434 0.0100 +OMU C4 O4 DOUBLE n 1.231 0.0100 1.231 0.0100 +OMU C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100 +OMU "C1'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100 +OMU "C1'" "O4'" SINGLE n 1.412 0.0100 1.412 0.0100 +OMU "C2'" "O2'" SINGLE n 1.423 0.0100 1.423 0.0100 +OMU "C2'" "C3'" SINGLE n 1.530 0.0134 1.530 0.0134 +OMU "O2'" CM2 SINGLE n 1.423 0.0131 1.423 0.0131 +OMU "C3'" "C4'" SINGLE n 1.535 0.0100 1.535 0.0100 +OMU "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +OMU "C4'" "O4'" SINGLE n 1.451 0.0111 1.451 0.0111 +OMU "C4'" "C5'" SINGLE n 1.509 0.0100 1.509 0.0100 +OMU "C5'" "O5'" SINGLE n 1.450 0.0166 1.450 0.0166 +OMU "O5'" P SINGLE n 1.614 0.0178 1.614 0.0178 +OMU P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192 +OMU P OP2 SINGLE n 1.517 0.0192 1.517 0.0192 +OMU P OP3 SINGLE n 1.517 0.0192 1.517 0.0192 +OMU N3 HN3 SINGLE n 1.016 0.0100 0.889 0.0200 +OMU C5 H5 SINGLE n 1.082 0.0130 0.935 0.0100 +OMU C6 H6 SINGLE n 1.082 0.0130 0.938 0.0107 +OMU "C1'" "H1'" SINGLE n 1.089 0.0100 0.981 0.0118 +OMU "C2'" "H2'" SINGLE n 1.089 0.0100 0.988 0.0200 +OMU CM2 HM21 SINGLE n 1.089 0.0100 0.971 0.0146 +OMU CM2 HM22 SINGLE n 1.089 0.0100 0.971 0.0146 +OMU CM2 HM23 SINGLE n 1.089 0.0100 0.971 0.0146 +OMU "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +OMU "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200 +OMU "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +OMU "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +OMU "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 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 +OMU C2 N1 C6 121.419 1.50 +OMU C2 N1 "C1'" 117.109 1.50 +OMU C6 N1 "C1'" 121.471 1.52 +OMU N1 C2 N3 114.848 1.50 +OMU N1 C2 O2 122.841 1.50 +OMU N3 C2 O2 122.311 1.50 +OMU C2 N3 C4 126.992 1.50 +OMU C2 N3 HN3 115.772 1.79 +OMU C4 N3 HN3 117.236 1.73 +OMU N3 C4 C5 114.659 1.50 +OMU N3 C4 O4 119.401 1.50 +OMU C5 C4 O4 125.940 1.50 +OMU C4 C5 C6 119.525 1.50 +OMU C4 C5 H5 120.151 1.50 +OMU C6 C5 H5 120.325 1.50 +OMU N1 C6 C5 122.557 1.50 +OMU N1 C6 H6 118.477 1.50 +OMU C5 C6 H6 118.966 1.50 +OMU N1 "C1'" "C2'" 113.620 1.99 +OMU N1 "C1'" "O4'" 108.667 1.50 +OMU N1 "C1'" "H1'" 109.166 1.50 +OMU "C2'" "C1'" "O4'" 106.391 1.51 +OMU "C2'" "C1'" "H1'" 109.527 1.54 +OMU "O4'" "C1'" "H1'" 109.327 1.50 +OMU "C1'" "C2'" "O2'" 110.738 2.44 +OMU "C1'" "C2'" "C3'" 101.207 1.50 +OMU "C1'" "C2'" "H2'" 110.561 1.96 +OMU "O2'" "C2'" "C3'" 112.623 3.00 +OMU "O2'" "C2'" "H2'" 110.257 1.68 +OMU "C3'" "C2'" "H2'" 110.255 2.04 +OMU "C2'" "O2'" CM2 113.084 1.50 +OMU "O2'" CM2 HM21 109.434 1.50 +OMU "O2'" CM2 HM22 109.434 1.50 +OMU "O2'" CM2 HM23 109.434 1.50 +OMU HM21 CM2 HM22 109.541 1.50 +OMU HM21 CM2 HM23 109.541 1.50 +OMU HM22 CM2 HM23 109.541 1.50 +OMU "C2'" "C3'" "C4'" 102.352 1.50 +OMU "C2'" "C3'" "O3'" 112.463 2.73 +OMU "C2'" "C3'" "H3'" 110.255 2.04 +OMU "C4'" "C3'" "O3'" 111.281 2.46 +OMU "C4'" "C3'" "H3'" 110.452 2.54 +OMU "O3'" "C3'" "H3'" 110.380 1.67 +OMU "C3'" "C4'" "O4'" 104.439 1.50 +OMU "C3'" "C4'" "C5'" 116.008 1.52 +OMU "C3'" "C4'" "H4'" 109.363 1.86 +OMU "O4'" "C4'" "C5'" 109.615 1.50 +OMU "O4'" "C4'" "H4'" 108.698 1.50 +OMU "C5'" "C4'" "H4'" 108.268 1.50 +OMU "C3'" "O3'" "HO3'" 108.744 3.00 +OMU "C1'" "O4'" "C4'" 109.578 1.50 +OMU "C4'" "C5'" "O5'" 109.342 1.50 +OMU "C4'" "C5'" "H5'" 109.624 1.50 +OMU "C4'" "C5'" "H5''" 109.624 1.50 +OMU "O5'" "C5'" "H5'" 109.845 1.50 +OMU "O5'" "C5'" "H5''" 109.845 1.50 +OMU "H5'" "C5'" "H5''" 108.472 1.50 +OMU "C5'" "O5'" P 118.783 1.50 +OMU "O5'" P OP1 105.808 2.07 +OMU "O5'" P OP2 105.808 2.07 +OMU "O5'" P OP3 105.808 2.07 +OMU OP1 P OP2 112.864 1.69 +OMU OP1 P OP3 112.864 1.69 +OMU OP2 P OP3 112.864 1.69 + +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 +OMU C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +OMU C2e-nyu0 "C4'" "O4'" "C1'" "C2" 340.700 6.300 1 +OMU C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1 +OMU C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +OMU C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +OMU C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +OMU C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6 +OMU C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1 +OMU C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1 +OMU C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +OMU C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +OMU C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +OMU alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +OMU beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +OMU epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +OMU gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +OMU const_sp2_sp2_3 O2 C2 N1 C6 180.000 5.0 2 +OMU const_21 C5 C6 N1 C2 0.000 10.0 2 +OMU sp3_sp3_37 HM21 CM2 "O2'" "C2'" 180.000 10.0 3 +OMU const_sp2_sp2_7 O2 C2 N3 C4 180.000 5.0 2 +OMU const_11 O4 C4 N3 C2 180.000 10.0 2 +OMU const_15 O4 C4 C5 C6 180.000 10.0 2 +OMU const_17 C4 C5 C6 N1 0.000 10.0 2 +OMU sp3_sp3_34 "C1'" "C2'" "O2'" CM2 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 +OMU chir_1 "C1'" "O4'" N1 "C2'" negative +OMU chir_2 "C2'" "O2'" "C1'" "C3'" negative +OMU chir_3 "C3'" "O3'" "C2'" "C4'" negative +OMU chir_4 "C4'" "O4'" "C3'" "C5'" negative +OMU chir_5 P "O5'" OP2 OP3 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 +OMU plan-1 "C1'" 0.020 +OMU plan-1 C2 0.020 +OMU plan-1 C4 0.020 +OMU plan-1 C5 0.020 +OMU plan-1 C6 0.020 +OMU plan-1 H5 0.020 +OMU plan-1 H6 0.020 +OMU plan-1 HN3 0.020 +OMU plan-1 N1 0.020 +OMU plan-1 N3 0.020 +OMU plan-1 O2 0.020 +OMU 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 +OMU SMILES ACDLabs 10.04 O=C1NC(=O)N(C=C1)C2OC(C(O)C2OC)COP(=O)(O)O +OMU SMILES_CANONICAL CACTVS 3.341 CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=O)NC2=O +OMU SMILES CACTVS 3.341 CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)NC2=O +OMU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O +OMU SMILES "OpenEye OEToolkits" 1.5.0 COC1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O +OMU InChI InChI 1.03 InChI=1S/C10H15N2O9P/c1-19-8-7(14)5(4-20-22(16,17)18)21-9(8)12-3-2-6(13)11-10(12)15/h2-3,5,7-9,14H,4H2,1H3,(H,11,13,15)(H2,16,17,18)/t5-,7-,8-,9-/m1/s1 +OMU InChIKey InChI 1.03 FHMMECZNEPGJSJ-ZOQUXTDFSA-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 +OMU acedrg 243 "dictionary generator" +OMU acedrg_database 11 "data source" +OMU rdkit 2017.03.2 "Chemoinformatics tool" +OMU refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/OXY.cif b/image_analysis/structure_refinement/monomers/OXY.cif new file mode 100644 index 000000000..2bc6ecfc7 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/OXY.cif @@ -0,0 +1,57 @@ +# +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 +OXY OXY "OXYGEN MOLECULE" NON-POLYMER 2 2 . +# +data_comp_OXY +# +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 +OXY O1 O O 0 27.236 26.922 33.744 +OXY O2 O O 0 26.684 27.385 32.771 +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 +OXY O1 O2 DOUBLE n 1.210 0.0200 1.210 0.0200 +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 +OXY SMILES_CANONICAL CACTVS 3.341 O=O +OXY SMILES CACTVS 3.341 O=O +OXY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 O=O +OXY SMILES "OpenEye OEToolkits" 1.5.0 O=O +OXY InChI InChI 1.03 InChI=1S/O2/c1-2 +OXY InChIKey InChI 1.03 MYMOFIZGZYHOMD-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 +OXY acedrg 243 "dictionary generator" +OXY acedrg_database 11 "data source" +OXY rdkit 2017.03.2 "Chemoinformatics tool" +OXY refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/PSU.cif b/image_analysis/structure_refinement/monomers/PSU.cif new file mode 100644 index 000000000..4a2fa8af7 --- /dev/null +++ b/image_analysis/structure_refinement/monomers/PSU.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 +PSU PSU "PSEUDOURIDINE-5'-MONOPHOSPHATE" RNA 32 21 . + +data_comp_PSU +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 +PSU N1 N NR16 0 46.164 -7.762 4.833 +PSU C2 C CR6 0 46.590 -7.315 3.610 +PSU N3 N NR16 0 47.833 -7.748 3.219 +PSU C4 C CR6 0 48.652 -8.579 3.959 +PSU C5 C CR6 0 48.162 -9.023 5.229 +PSU C6 C CR16 0 46.903 -8.584 5.636 +PSU O2 O O 0 45.910 -6.578 2.906 +PSU O4 O O 0 49.759 -8.895 3.485 +PSU "C1'" C CH1 0 48.988 -9.928 6.111 +PSU "C2'" C CH1 0 49.724 -9.224 7.265 +PSU "O2'" O OH1 0 51.104 -9.536 7.260 +PSU "C3'" C CH1 0 48.969 -9.682 8.522 +PSU "C4'" C CH1 0 48.520 -11.085 8.105 +PSU "O3'" O OH1 0 49.839 -9.721 9.649 +PSU "O4'" O O2 0 48.167 -10.942 6.712 +PSU "C5'" C CH2 0 47.359 -11.677 8.866 +PSU "O5'" O O2 0 46.178 -10.856 8.677 +PSU P P P 0 44.847 -11.206 9.521 +PSU OP1 O O 0 43.790 -10.223 9.054 +PSU OP2 O OP -1 45.222 -11.019 10.980 +PSU OP3 O OP -1 44.507 -12.644 9.180 +PSU HN1 H H 0 45.353 -7.490 5.108 +PSU HN3 H H 0 48.133 -7.472 2.427 +PSU H6 H H 0 46.552 -8.857 6.469 +PSU "H1'" H H 0 49.672 -10.378 5.553 +PSU "H2'" H H 0 49.616 -8.252 7.170 +PSU "HO2'" H H 0 51.463 -9.174 7.939 +PSU "H3'" H H 0 48.194 -9.103 8.707 +PSU "H4'" H H 0 49.285 -11.706 8.179 +PSU "HO3'" H H 0 49.417 -10.046 10.310 +PSU "H5'" H H 0 47.583 -11.723 9.829 +PSU "H5''" H H 0 47.184 -12.595 8.543 + +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 +PSU N1 C2 SINGLE y 1.365 0.0100 1.365 0.0100 +PSU N1 C6 SINGLE y 1.355 0.0148 1.355 0.0148 +PSU C2 N3 SINGLE y 1.370 0.0100 1.370 0.0100 +PSU C2 O2 DOUBLE n 1.225 0.0100 1.225 0.0100 +PSU N3 C4 SINGLE y 1.379 0.0122 1.379 0.0122 +PSU C4 C5 SINGLE y 1.418 0.0200 1.418 0.0200 +PSU C4 O4 DOUBLE n 1.242 0.0172 1.242 0.0172 +PSU C5 C6 DOUBLE y 1.389 0.0100 1.389 0.0100 +PSU C5 "C1'" SINGLE n 1.506 0.0100 1.506 0.0100 +PSU "C1'" "C2'" SINGLE n 1.532 0.0100 1.532 0.0100 +PSU "C1'" "O4'" SINGLE n 1.434 0.0100 1.434 0.0100 +PSU "C2'" "O2'" SINGLE n 1.414 0.0100 1.414 0.0100 +PSU "C2'" "C3'" SINGLE n 1.533 0.0100 1.533 0.0100 +PSU "C3'" "C4'" SINGLE n 1.535 0.0100 1.535 0.0100 +PSU "C3'" "O3'" SINGLE n 1.423 0.0100 1.423 0.0100 +PSU "C4'" "O4'" SINGLE n 1.448 0.0100 1.448 0.0100 +PSU "C4'" "C5'" SINGLE n 1.509 0.0100 1.509 0.0100 +PSU "C5'" "O5'" SINGLE n 1.450 0.0166 1.450 0.0166 +PSU "O5'" P SINGLE n 1.614 0.0178 1.614 0.0178 +PSU P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192 +PSU P OP2 SINGLE n 1.517 0.0192 1.517 0.0192 +PSU P OP3 SINGLE n 1.517 0.0192 1.517 0.0192 +PSU N1 HN1 SINGLE n 1.016 0.0100 0.898 0.0200 +PSU N3 HN3 SINGLE n 1.016 0.0100 0.889 0.0200 +PSU C6 H6 SINGLE n 1.082 0.0130 0.945 0.0200 +PSU "C1'" "H1'" SINGLE n 1.089 0.0100 0.991 0.0119 +PSU "C2'" "H2'" SINGLE n 1.089 0.0100 0.982 0.0200 +PSU "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 +PSU "C3'" "H3'" SINGLE n 1.089 0.0100 0.985 0.0200 +PSU "C4'" "H4'" SINGLE n 1.089 0.0100 0.988 0.0200 +PSU "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +PSU "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200 +PSU "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 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 +PSU C2 N1 C6 122.342 1.50 +PSU C2 N1 HN1 117.656 2.18 +PSU C6 N1 HN1 120.002 2.19 +PSU N1 C2 N3 115.268 1.50 +PSU N1 C2 O2 122.598 1.50 +PSU N3 C2 O2 122.134 1.50 +PSU C2 N3 C4 125.337 1.50 +PSU C2 N3 HN3 117.319 2.30 +PSU C4 N3 HN3 117.344 1.50 +PSU N3 C4 C5 118.938 3.00 +PSU N3 C4 O4 117.999 1.50 +PSU C5 C4 O4 123.064 1.50 +PSU C4 C5 C6 119.178 1.66 +PSU C4 C5 "C1'" 120.411 1.56 +PSU C6 C5 "C1'" 120.411 1.56 +PSU N1 C6 C5 118.938 3.00 +PSU N1 C6 H6 120.523 1.97 +PSU C5 C6 H6 120.539 1.50 +PSU C5 "C1'" "C2'" 115.040 1.80 +PSU C5 "C1'" "O4'" 110.287 1.50 +PSU C5 "C1'" "H1'" 108.843 1.50 +PSU "C2'" "C1'" "O4'" 104.658 1.50 +PSU "C2'" "C1'" "H1'" 108.221 2.17 +PSU "O4'" "C1'" "H1'" 109.373 1.78 +PSU "C1'" "C2'" "O2'" 111.625 2.24 +PSU "C1'" "C2'" "C3'" 102.060 1.50 +PSU "C1'" "C2'" "H2'" 108.984 1.81 +PSU "O2'" "C2'" "C3'" 114.225 2.57 +PSU "O2'" "C2'" "H2'" 109.642 2.25 +PSU "C3'" "C2'" "H2'" 109.242 2.24 +PSU "C2'" "O2'" "HO2'" 108.353 3.00 +PSU "C2'" "C3'" "C4'" 101.721 1.50 +PSU "C2'" "C3'" "O3'" 109.895 1.81 +PSU "C2'" "C3'" "H3'" 111.377 1.50 +PSU "C4'" "C3'" "O3'" 111.281 2.46 +PSU "C4'" "C3'" "H3'" 110.452 2.54 +PSU "O3'" "C3'" "H3'" 110.380 1.67 +PSU "C3'" "C4'" "O4'" 106.192 1.50 +PSU "C3'" "C4'" "C5'" 116.008 1.52 +PSU "C3'" "C4'" "H4'" 109.363 1.86 +PSU "O4'" "C4'" "C5'" 109.123 1.50 +PSU "O4'" "C4'" "H4'" 108.995 1.50 +PSU "C5'" "C4'" "H4'" 108.268 1.50 +PSU "C3'" "O3'" "HO3'" 108.744 3.00 +PSU "C1'" "O4'" "C4'" 109.937 1.50 +PSU "C4'" "C5'" "O5'" 109.342 1.50 +PSU "C4'" "C5'" "H5'" 109.624 1.50 +PSU "C4'" "C5'" "H5''" 109.624 1.50 +PSU "O5'" "C5'" "H5'" 109.845 1.50 +PSU "O5'" "C5'" "H5''" 109.845 1.50 +PSU "H5'" "C5'" "H5''" 108.472 1.50 +PSU "C5'" "O5'" P 118.783 1.50 +PSU "O5'" P OP1 105.808 2.07 +PSU "O5'" P OP2 105.808 2.07 +PSU "O5'" P OP3 105.808 2.07 +PSU OP1 P OP2 112.864 1.69 +PSU OP1 P OP3 112.864 1.69 +PSU OP2 P OP3 112.864 1.69 + +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 +PSU C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1 +PSU C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1 +PSU C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1 +PSU C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1 +PSU C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1 +PSU C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1 +PSU alpha "C5'" "O5'" P OP3 -60.000 10.00 3 +PSU beta P "O5'" "C5'" "C4'" 180.000 10.00 3 +PSU epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3 +PSU gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3 +PSU const_sp2_sp2_3 O2 C2 N1 C6 180.000 5.0 2 +PSU const_21 C5 C6 N1 C2 0.000 10.0 2 +PSU const_sp2_sp2_7 O2 C2 N3 C4 180.000 5.0 2 +PSU const_11 O4 C4 N3 C2 180.000 10.0 2 +PSU const_15 O4 C4 C5 C6 180.000 10.0 2 +PSU const_17 C4 C5 C6 N1 0.000 10.0 2 +PSU sp2_sp3_1 C4 C5 "C1'" "C2'" 150.000 10.0 6 +PSU sp3_sp3_32 C5 "C1'" "O4'" "C4'" 60.000 10.0 3 +PSU sp3_sp3_5 C5 "C1'" "C2'" "O2'" 60.000 10.0 3 +PSU sp3_sp3_34 "C1'" "C2'" "O2'" "HO2'" 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 +PSU chir_1 "C1'" "O4'" "C2'" C5 positive +PSU chir_2 "C2'" "O2'" "C1'" "C3'" negative +PSU chir_3 "C3'" "O3'" "C4'" "C2'" positive +PSU chir_4 "C4'" "O4'" "C3'" "C5'" negative +PSU chir_5 P "O5'" OP2 OP3 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 +PSU plan-1 "C1'" 0.020 +PSU plan-1 C2 0.020 +PSU plan-1 C4 0.020 +PSU plan-1 C5 0.020 +PSU plan-1 C6 0.020 +PSU plan-1 H6 0.020 +PSU plan-1 HN1 0.020 +PSU plan-1 HN3 0.020 +PSU plan-1 N1 0.020 +PSU plan-1 N3 0.020 +PSU plan-1 O2 0.020 +PSU 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 +PSU SMILES ACDLabs 10.04 O=P(OCC2OC(C1=CNC(=O)NC1=O)C(O)C2O)(O)O +PSU SMILES_CANONICAL CACTVS 3.341 O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)C2=CNC(=O)NC2=O +PSU SMILES CACTVS 3.341 O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)C2=CNC(=O)NC2=O +PSU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1=C(C(=O)NC(=O)N1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O +PSU SMILES "OpenEye OEToolkits" 1.5.0 C1=C(C(=O)NC(=O)N1)C2C(C(C(O2)COP(=O)(O)O)O)O +PSU InChI InChI 1.03 InChI=1S/C9H13N2O9P/c12-5-4(2-19-21(16,17)18)20-7(6(5)13)3-1-10-9(15)11-8(3)14/h1,4-7,12-13H,2H2,(H2,16,17,18)(H2,10,11,14,15)/t4-,5-,6-,7+/m1/s1 +PSU InChIKey InChI 1.03 MOBMOJGXNHLLIR-GBNDHIKLSA-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 +PSU acedrg 243 "dictionary generator" +PSU acedrg_database 11 "data source" +PSU rdkit 2017.03.2 "Chemoinformatics tool" +PSU refmac5 5.8.0238 "optimization tool" diff --git a/image_analysis/structure_refinement/monomers/SAH.cif b/image_analysis/structure_refinement/monomers/SAH.cif new file mode 100644 index 000000000..9f1abc9cb --- /dev/null +++ b/image_analysis/structure_refinement/monomers/SAH.cif @@ -0,0 +1,329 @@ +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 +SAH SAH S-ADENOSYL-L-HOMOCYSTEINE NON-POLYMER 46 26 . + +data_comp_SAH +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 +SAH N N NT3 1 -2.642 13.710 24.335 +SAH CA C CH1 0 -3.261 12.686 25.223 +SAH CB C CH2 0 -2.531 11.342 25.110 +SAH CG C CH2 0 -2.701 10.665 23.762 +SAH SD S S2 0 -1.875 9.057 23.667 +SAH C C C 0 -3.207 13.172 26.677 +SAH O O O 0 -4.296 13.351 27.259 +SAH OXT O OC -1 -2.078 13.355 27.173 +SAH "C5'" C CH2 0 -2.426 8.439 22.058 +SAH "C4'" C CH1 0 -3.830 7.882 22.065 +SAH "O4'" O O2 0 -4.295 7.751 20.701 +SAH "C3'" C CH1 0 -3.966 6.491 22.682 +SAH "O3'" O OH1 0 -5.239 6.333 23.297 +SAH "C2'" C CH1 0 -3.790 5.584 21.462 +SAH "O2'" O OH1 0 -4.370 4.309 21.628 +SAH "C1'" C CH1 0 -4.519 6.393 20.394 +SAH N9 N NR5 0 -4.045 6.148 19.035 +SAH C8 C CR15 0 -2.777 6.375 18.561 +SAH N7 N NRD5 0 -2.628 6.068 17.297 +SAH C5 C CR56 0 -3.878 5.613 16.905 +SAH C6 C CR6 0 -4.372 5.137 15.671 +SAH N6 N NH2 0 -3.632 5.040 14.570 +SAH N1 N NRD6 0 -5.675 4.759 15.617 +SAH C2 C CR16 0 -6.417 4.859 16.731 +SAH N3 N NRD6 0 -6.060 5.290 17.942 +SAH C4 C CR56 0 -4.764 5.658 17.969 +SAH HN1 H H 0 -2.972 14.538 24.529 +SAH HN2 H H 0 -2.828 13.522 23.464 +SAH H3 H H 0 -1.739 13.719 24.450 +SAH HA H H 0 -4.203 12.573 24.958 +SAH HB1 H H 0 -2.865 10.744 25.808 +SAH HB2 H H 0 -1.578 11.488 25.274 +SAH HG1 H H 0 -2.337 11.245 23.060 +SAH HG2 H H 0 -3.657 10.538 23.583 +SAH "H5'1" H H 0 -1.829 7.752 21.772 +SAH "H5'2" H H 0 -2.386 9.152 21.425 +SAH "H4'" H H 0 -4.421 8.511 22.548 +SAH "H3'" H H 0 -3.243 6.329 23.342 +SAH "HO3'" H H 0 -5.240 5.609 23.740 +SAH "H2'" H H 0 -2.826 5.493 21.237 +SAH "HO2'" H H 0 -4.231 3.847 20.929 +SAH "H1'" H H 0 -5.481 6.197 20.448 +SAH H8 H H 0 -2.079 6.715 19.096 +SAH HN61 H H 0 -3.998 5.178 13.785 +SAH HN62 H H 0 -2.780 4.840 14.635 +SAH H2 H H 0 -7.317 4.585 16.646 + +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 +SAH N CA SINGLE n 1.488 0.0100 1.488 0.0100 +SAH CA CB SINGLE n 1.532 0.0100 1.532 0.0100 +SAH CA C SINGLE n 1.533 0.0100 1.533 0.0100 +SAH CB CG SINGLE n 1.517 0.0200 1.517 0.0200 +SAH CG SD SINGLE n 1.810 0.0200 1.810 0.0200 +SAH SD "C5'" SINGLE n 1.810 0.0169 1.810 0.0169 +SAH C O DOUBLE n 1.247 0.0187 1.247 0.0187 +SAH C OXT SINGLE n 1.247 0.0187 1.247 0.0187 +SAH "C5'" "C4'" SINGLE n 1.510 0.0135 1.510 0.0135 +SAH "C4'" "O4'" SINGLE n 1.446 0.0100 1.446 0.0100 +SAH "C4'" "C3'" SINGLE n 1.528 0.0117 1.528 0.0117 +SAH "O4'" "C1'" SINGLE n 1.409 0.0100 1.409 0.0100 +SAH "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +SAH "C3'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100 +SAH "C2'" "O2'" SINGLE n 1.411 0.0100 1.411 0.0100 +SAH "C2'" "C1'" SINGLE n 1.525 0.0100 1.525 0.0100 +SAH "C1'" N9 SINGLE n 1.458 0.0100 1.458 0.0100 +SAH N9 C8 SINGLE y 1.372 0.0100 1.372 0.0100 +SAH N9 C4 SINGLE y 1.374 0.0101 1.374 0.0101 +SAH C8 N7 DOUBLE y 1.310 0.0100 1.310 0.0100 +SAH N7 C5 SINGLE y 1.388 0.0100 1.388 0.0100 +SAH C5 C6 SINGLE y 1.408 0.0100 1.408 0.0100 +SAH C5 C4 DOUBLE y 1.381 0.0100 1.381 0.0100 +SAH C6 N6 SINGLE n 1.330 0.0100 1.330 0.0100 +SAH C6 N1 DOUBLE y 1.354 0.0100 1.354 0.0100 +SAH N1 C2 SINGLE y 1.339 0.0100 1.339 0.0100 +SAH C2 N3 DOUBLE y 1.330 0.0100 1.330 0.0100 +SAH N3 C4 SINGLE y 1.343 0.0100 1.343 0.0100 +SAH N HN1 SINGLE n 1.036 0.0160 0.911 0.0200 +SAH N HN2 SINGLE n 1.036 0.0160 0.911 0.0200 +SAH N H3 SINGLE n 1.036 0.0160 0.911 0.0200 +SAH CA HA SINGLE n 1.089 0.0100 0.985 0.0200 +SAH CB HB1 SINGLE n 1.089 0.0100 0.978 0.0200 +SAH CB HB2 SINGLE n 1.089 0.0100 0.978 0.0200 +SAH CG HG1 SINGLE n 1.089 0.0100 0.981 0.0122 +SAH CG HG2 SINGLE n 1.089 0.0100 0.981 0.0122 +SAH "C5'" "H5'1" SINGLE n 1.089 0.0100 0.954 0.0200 +SAH "C5'" "H5'2" SINGLE n 1.089 0.0100 0.954 0.0200 +SAH "C4'" "H4'" SINGLE n 1.089 0.0100 0.989 0.0197 +SAH "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +SAH "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +SAH "C2'" "H2'" SINGLE n 1.089 0.0100 0.994 0.0200 +SAH "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 +SAH "C1'" "H1'" SINGLE n 1.089 0.0100 0.984 0.0200 +SAH C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170 +SAH N6 HN61 SINGLE n 1.016 0.0100 0.877 0.0200 +SAH N6 HN62 SINGLE n 1.016 0.0100 0.877 0.0200 +SAH 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 +SAH CA N HN1 110.062 1.93 +SAH CA N HN2 110.062 1.93 +SAH CA N H3 110.062 1.93 +SAH HN1 N HN2 109.028 2.41 +SAH HN1 N H3 109.028 2.41 +SAH HN2 N H3 109.028 2.41 +SAH N CA CB 110.906 1.50 +SAH N CA C 109.241 1.50 +SAH N CA HA 108.487 1.50 +SAH CB CA C 109.344 1.50 +SAH CB CA HA 109.670 1.50 +SAH C CA HA 108.824 1.50 +SAH CA CB CG 113.476 1.50 +SAH CA CB HB1 108.666 1.50 +SAH CA CB HB2 108.666 1.50 +SAH CG CB HB1 108.955 1.50 +SAH CG CB HB2 108.955 1.50 +SAH HB1 CB HB2 107.698 1.50 +SAH CB CG SD 113.263 2.33 +SAH CB CG HG1 109.206 1.50 +SAH CB CG HG2 109.206 1.50 +SAH SD CG HG1 108.654 1.50 +SAH SD CG HG2 108.654 1.50 +SAH HG1 CG HG2 107.939 1.50 +SAH CG SD "C5'" 102.171 1.96 +SAH CA C O 117.124 1.50 +SAH CA C OXT 117.124 1.50 +SAH O C OXT 125.752 1.50 +SAH SD "C5'" "C4'" 113.180 3.00 +SAH SD "C5'" "H5'1" 108.574 1.50 +SAH SD "C5'" "H5'2" 108.574 1.50 +SAH "C4'" "C5'" "H5'1" 108.376 1.50 +SAH "C4'" "C5'" "H5'2" 108.376 1.50 +SAH "H5'1" "C5'" "H5'2" 108.127 1.50 +SAH "C5'" "C4'" "O4'" 109.275 1.50 +SAH "C5'" "C4'" "C3'" 114.880 1.64 +SAH "C5'" "C4'" "H4'" 109.000 1.62 +SAH "O4'" "C4'" "C3'" 105.508 1.50 +SAH "O4'" "C4'" "H4'" 109.115 1.50 +SAH "C3'" "C4'" "H4'" 109.143 1.50 +SAH "C4'" "O4'" "C1'" 109.426 1.50 +SAH "C4'" "C3'" "O3'" 110.985 2.41 +SAH "C4'" "C3'" "C2'" 102.352 1.50 +SAH "C4'" "C3'" "H3'" 110.624 1.81 +SAH "O3'" "C3'" "C2'" 111.581 2.83 +SAH "O3'" "C3'" "H3'" 110.380 1.67 +SAH "C2'" "C3'" "H3'" 110.504 1.75 +SAH "C3'" "O3'" "HO3'" 108.744 3.00 +SAH "C3'" "C2'" "O2'" 112.782 2.45 +SAH "C3'" "C2'" "C1'" 101.239 1.50 +SAH "C3'" "C2'" "H2'" 110.596 1.51 +SAH "O2'" "C2'" "C1'" 111.715 2.69 +SAH "O2'" "C2'" "H2'" 110.448 1.97 +SAH "C1'" "C2'" "H2'" 110.636 1.70 +SAH "C2'" "O2'" "HO2'" 109.103 2.13 +SAH "O4'" "C1'" "C2'" 106.047 1.50 +SAH "O4'" "C1'" N9 108.477 1.50 +SAH "O4'" "C1'" "H1'" 109.807 1.50 +SAH "C2'" "C1'" N9 113.824 1.50 +SAH "C2'" "C1'" "H1'" 109.015 1.50 +SAH N9 "C1'" "H1'" 109.561 1.50 +SAH "C1'" N9 C8 126.848 1.91 +SAH "C1'" N9 C4 127.459 1.80 +SAH C8 N9 C4 105.693 1.50 +SAH N9 C8 N7 113.469 1.50 +SAH N9 C8 H8 123.206 1.50 +SAH N7 C8 H8 123.326 1.50 +SAH C8 N7 C5 104.739 1.50 +SAH N7 C5 C6 132.250 1.50 +SAH N7 C5 C4 110.483 1.50 +SAH C6 C5 C4 117.267 1.50 +SAH C5 C6 N6 123.792 1.50 +SAH C5 C6 N1 117.409 1.50 +SAH N6 C6 N1 118.799 1.50 +SAH C6 N6 HN61 119.723 1.50 +SAH C6 N6 HN62 119.723 1.50 +SAH HN61 N6 HN62 120.554 1.88 +SAH C6 N1 C2 118.521 1.50 +SAH N1 C2 N3 129.332 1.50 +SAH N1 C2 H2 115.313 1.50 +SAH N3 C2 H2 115.355 1.50 +SAH C2 N3 C4 110.982 1.50 +SAH N9 C4 C5 105.616 1.50 +SAH N9 C4 N3 127.895 1.50 +SAH 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 +SAH sp3_sp3_25 CB CA N HN1 180.000 10.0 3 +SAH sp3_sp3_4 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3 +SAH sp3_sp3_76 "C4'" "C3'" "O3'" "HO3'" 180.000 10.0 3 +SAH sp3_sp3_20 "O2'" "C2'" "C3'" "O3'" -60.000 10.0 3 +SAH sp3_sp3_79 "C3'" "C2'" "O2'" "HO2'" 180.000 10.0 3 +SAH sp3_sp3_8 "O4'" "C1'" "C2'" "O2'" 180.000 10.0 3 +SAH sp2_sp3_7 C8 N9 "C1'" "O4'" 150.000 10.0 6 +SAH const_14 N7 C8 N9 "C1'" 180.000 10.0 2 +SAH const_26 C5 C4 N9 "C1'" 180.000 10.0 2 +SAH const_17 N9 C8 N7 C5 0.000 10.0 2 +SAH const_20 C6 C5 N7 C8 180.000 10.0 2 +SAH const_sp2_sp2_4 N7 C5 C6 N6 0.000 5.0 2 +SAH const_21 N9 C4 C5 N7 0.000 10.0 2 +SAH sp3_sp3_34 N CA CB CG 180.000 10.0 3 +SAH sp2_sp3_1 O C CA N 0.000 10.0 6 +SAH sp2_sp2_1 C5 C6 N6 HN61 180.000 5.0 2 +SAH const_sp2_sp2_6 N6 C6 N1 C2 180.000 5.0 2 +SAH const_sp2_sp2_7 N3 C2 N1 C6 0.000 5.0 2 +SAH const_sp2_sp2_9 N1 C2 N3 C4 0.000 5.0 2 +SAH const_12 N9 C4 N3 C2 180.000 10.0 2 +SAH sp3_sp3_43 CA CB CG SD 180.000 10.0 3 +SAH sp3_sp3_52 CB CG SD "C5'" 180.000 10.0 3 +SAH sp3_sp3_55 "C4'" "C5'" SD CG 180.000 10.0 3 +SAH sp3_sp3_58 "O4'" "C4'" "C5'" SD 180.000 10.0 3 +SAH sp3_sp3_2 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3 +SAH sp3_sp3_71 "O3'" "C3'" "C4'" "C5'" 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 +SAH chir_1 CA N C CB positive +SAH chir_2 "C4'" "O4'" "C5'" "C3'" positive +SAH chir_3 "C3'" "O3'" "C4'" "C2'" positive +SAH chir_4 "C2'" "O2'" "C1'" "C3'" negative +SAH 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 +SAH plan-1 "C1'" 0.020 +SAH plan-1 C2 0.020 +SAH plan-1 C4 0.020 +SAH plan-1 C5 0.020 +SAH plan-1 C6 0.020 +SAH plan-1 C8 0.020 +SAH plan-1 H2 0.020 +SAH plan-1 H8 0.020 +SAH plan-1 N1 0.020 +SAH plan-1 N3 0.020 +SAH plan-1 N6 0.020 +SAH plan-1 N7 0.020 +SAH plan-1 N9 0.020 +SAH plan-2 C 0.020 +SAH plan-2 CA 0.020 +SAH plan-2 O 0.020 +SAH plan-2 OXT 0.020 +SAH plan-3 C6 0.020 +SAH plan-3 HN61 0.020 +SAH plan-3 HN62 0.020 +SAH plan-3 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 +SAH SMILES ACDLabs 10.04 O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O +SAH SMILES_CANONICAL CACTVS 3.341 N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O +SAH SMILES CACTVS 3.341 N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O +SAH SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N +SAH SMILES "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N +SAH InChI InChI 1.03 InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1 +SAH InChIKey InChI 1.03 ZJUKTBDSGOFHSH-WFMPWKQPSA-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 +SAH acedrg 243 "dictionary generator" +SAH acedrg_database 11 "data source" +SAH rdkit 2017.03.2 "Chemoinformatics tool" +SAH 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 +SAH peptide HN1 H +SAH peptide HN2 H2 diff --git a/image_analysis/structure_refinement/monomers/SAM.cif b/image_analysis/structure_refinement/monomers/SAM.cif new file mode 100644 index 000000000..5feded1da --- /dev/null +++ b/image_analysis/structure_refinement/monomers/SAM.cif @@ -0,0 +1,347 @@ +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 +SAM SAM S-ADENOSYLMETHIONINE NON-POLYMER 50 27 . + +data_comp_SAM +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 +SAM N N NT3 1 -27.592 29.068 46.677 +SAM CA C CH1 0 -28.803 28.395 46.134 +SAM C C C 0 -29.252 27.303 47.112 +SAM O O O 0 -28.390 26.481 47.482 +SAM OXT O OC -1 -30.447 27.315 47.469 +SAM CB C CH2 0 -28.507 27.780 44.760 +SAM CG C CH2 0 -29.706 27.205 44.008 +SAM SD S S3 1 -30.917 28.471 43.547 +SAM CE C CH3 0 -32.145 27.508 42.679 +SAM "C5'" C CH2 0 -30.019 29.269 42.194 +SAM "C4'" C CH1 0 -29.862 30.762 42.411 +SAM "O4'" O O2 0 -29.159 30.988 43.651 +SAM "C3'" C CH1 0 -29.042 31.494 41.354 +SAM "O3'" O OH1 0 -29.880 31.908 40.281 +SAM "C2'" C CH1 0 -28.448 32.677 42.130 +SAM "O2'" O OH1 0 -29.235 33.845 42.037 +SAM "C1'" C CH1 0 -28.400 32.173 43.575 +SAM N9 N NR5 0 -27.055 31.878 44.061 +SAM C8 C CR15 0 -26.399 32.530 45.075 +SAM N7 N NRD5 0 -25.203 32.054 45.314 +SAM C5 C CR56 0 -25.057 31.017 44.404 +SAM C6 C CR6 0 -24.001 30.114 44.153 +SAM N6 N NH2 0 -22.853 30.119 44.825 +SAM N1 N NRD6 0 -24.177 29.196 43.169 +SAM C2 C CR16 0 -25.338 29.196 42.495 +SAM N3 N NRD6 0 -26.395 29.994 42.645 +SAM C4 C CR56 0 -26.195 30.896 43.625 +SAM HN1 H H 0 -27.310 29.714 46.100 +SAM HN2 H H 0 -26.921 28.461 46.790 +SAM H3 H H 0 -27.781 29.453 47.481 +SAM HA H H 0 -29.519 29.065 46.056 +SAM HB1 H H 0 -27.851 27.065 44.879 +SAM HB2 H H 0 -28.094 28.464 44.200 +SAM HG1 H H 0 -30.155 26.532 44.561 +SAM HG2 H H 0 -29.394 26.764 43.189 +SAM HE1 H H 0 -32.772 28.106 42.242 +SAM HE2 H H 0 -32.619 26.946 43.314 +SAM HE3 H H 0 -31.707 26.952 42.015 +SAM "H5'1" H H 0 -30.506 29.113 41.356 +SAM "H5'2" H H 0 -29.133 28.858 42.111 +SAM "H4'" H H 0 -30.759 31.175 42.468 +SAM "H3'" H H 0 -28.320 30.910 41.010 +SAM "HO3'" H H 0 -29.420 32.372 39.739 +SAM "H2'" H H 0 -27.528 32.871 41.805 +SAM "HO2'" H H 0 -28.800 34.500 42.358 +SAM "H1'" H H 0 -28.805 32.854 44.158 +SAM H8 H H 0 -26.773 33.252 45.550 +SAM HN61 H H 0 -22.410 29.370 44.938 +SAM HN62 H H 0 -22.544 30.872 45.153 +SAM H2 H H 0 -25.416 28.540 41.820 + +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 +SAM N CA SINGLE n 1.488 0.0100 1.488 0.0100 +SAM CA C SINGLE n 1.533 0.0100 1.533 0.0100 +SAM CA CB SINGLE n 1.532 0.0100 1.532 0.0100 +SAM C O DOUBLE n 1.247 0.0187 1.247 0.0187 +SAM C OXT SINGLE n 1.247 0.0187 1.247 0.0187 +SAM CB CG SINGLE n 1.516 0.0200 1.516 0.0200 +SAM CG SD SINGLE n 1.807 0.0171 1.807 0.0171 +SAM SD CE SINGLE n 1.786 0.0143 1.786 0.0143 +SAM SD "C5'" SINGLE n 1.807 0.0171 1.807 0.0171 +SAM "C5'" "C4'" SINGLE n 1.516 0.0120 1.516 0.0120 +SAM "C4'" "O4'" SINGLE n 1.446 0.0100 1.446 0.0100 +SAM "C4'" "C3'" SINGLE n 1.528 0.0117 1.528 0.0117 +SAM "O4'" "C1'" SINGLE n 1.409 0.0100 1.409 0.0100 +SAM "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100 +SAM "C3'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100 +SAM "C2'" "O2'" SINGLE n 1.411 0.0100 1.411 0.0100 +SAM "C2'" "C1'" SINGLE n 1.525 0.0100 1.525 0.0100 +SAM "C1'" N9 SINGLE n 1.458 0.0100 1.458 0.0100 +SAM N9 C8 SINGLE y 1.372 0.0100 1.372 0.0100 +SAM N9 C4 SINGLE y 1.374 0.0101 1.374 0.0101 +SAM C8 N7 DOUBLE y 1.310 0.0100 1.310 0.0100 +SAM N7 C5 SINGLE y 1.388 0.0100 1.388 0.0100 +SAM C5 C6 SINGLE y 1.408 0.0100 1.408 0.0100 +SAM C5 C4 DOUBLE y 1.381 0.0100 1.381 0.0100 +SAM C6 N6 SINGLE n 1.330 0.0100 1.330 0.0100 +SAM C6 N1 DOUBLE y 1.354 0.0100 1.354 0.0100 +SAM N1 C2 SINGLE y 1.339 0.0100 1.339 0.0100 +SAM C2 N3 DOUBLE y 1.330 0.0100 1.330 0.0100 +SAM N3 C4 SINGLE y 1.343 0.0100 1.343 0.0100 +SAM N HN1 SINGLE n 1.036 0.0160 0.911 0.0200 +SAM N HN2 SINGLE n 1.036 0.0160 0.911 0.0200 +SAM N H3 SINGLE n 1.036 0.0160 0.911 0.0200 +SAM CA HA SINGLE n 1.089 0.0100 0.985 0.0200 +SAM CB HB1 SINGLE n 1.089 0.0100 0.978 0.0200 +SAM CB HB2 SINGLE n 1.089 0.0100 0.978 0.0200 +SAM CG HG1 SINGLE n 1.089 0.0100 0.981 0.0150 +SAM CG HG2 SINGLE n 1.089 0.0100 0.981 0.0150 +SAM CE HE1 SINGLE n 1.089 0.0100 0.971 0.0165 +SAM CE HE2 SINGLE n 1.089 0.0100 0.971 0.0165 +SAM CE HE3 SINGLE n 1.089 0.0100 0.971 0.0165 +SAM "C5'" "H5'1" SINGLE n 1.089 0.0100 0.981 0.0150 +SAM "C5'" "H5'2" SINGLE n 1.089 0.0100 0.981 0.0150 +SAM "C4'" "H4'" SINGLE n 1.089 0.0100 0.989 0.0197 +SAM "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200 +SAM "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200 +SAM "C2'" "H2'" SINGLE n 1.089 0.0100 0.994 0.0200 +SAM "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200 +SAM "C1'" "H1'" SINGLE n 1.089 0.0100 0.984 0.0200 +SAM C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170 +SAM N6 HN61 SINGLE n 1.016 0.0100 0.877 0.0200 +SAM N6 HN62 SINGLE n 1.016 0.0100 0.877 0.0200 +SAM 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 +SAM CA N HN1 110.062 1.93 +SAM CA N HN2 110.062 1.93 +SAM CA N H3 110.062 1.93 +SAM HN1 N HN2 109.028 2.41 +SAM HN1 N H3 109.028 2.41 +SAM HN2 N H3 109.028 2.41 +SAM N CA C 109.241 1.50 +SAM N CA CB 110.906 1.50 +SAM N CA HA 108.487 1.50 +SAM C CA CB 109.344 1.50 +SAM C CA HA 108.824 1.50 +SAM CB CA HA 109.670 1.50 +SAM CA C O 117.124 1.50 +SAM CA C OXT 117.124 1.50 +SAM O C OXT 125.752 1.50 +SAM CA CB CG 113.808 1.88 +SAM CA CB HB1 108.666 1.50 +SAM CA CB HB2 108.666 1.50 +SAM CG CB HB1 108.557 1.50 +SAM CG CB HB2 108.557 1.50 +SAM HB1 CB HB2 107.698 1.50 +SAM CB CG SD 108.220 3.00 +SAM CB CG HG1 109.481 1.50 +SAM CB CG HG2 109.481 1.50 +SAM SD CG HG1 108.504 1.57 +SAM SD CG HG2 108.504 1.57 +SAM HG1 CG HG2 108.193 1.50 +SAM CG SD CE 102.026 1.83 +SAM CG SD "C5'" 98.345 1.79 +SAM CE SD "C5'" 102.487 1.89 +SAM SD CE HE1 109.268 1.50 +SAM SD CE HE2 109.268 1.50 +SAM SD CE HE3 109.268 1.50 +SAM HE1 CE HE2 109.605 1.50 +SAM HE1 CE HE3 109.605 1.50 +SAM HE2 CE HE3 109.605 1.50 +SAM SD "C5'" "C4'" 111.142 2.46 +SAM SD "C5'" "H5'1" 108.544 1.50 +SAM SD "C5'" "H5'2" 108.544 1.50 +SAM "C4'" "C5'" "H5'1" 109.065 1.50 +SAM "C4'" "C5'" "H5'2" 109.065 1.50 +SAM "H5'1" "C5'" "H5'2" 107.808 1.50 +SAM "C5'" "C4'" "O4'" 109.393 1.53 +SAM "C5'" "C4'" "C3'" 115.549 1.59 +SAM "C5'" "C4'" "H4'" 109.003 1.50 +SAM "O4'" "C4'" "C3'" 105.508 1.50 +SAM "O4'" "C4'" "H4'" 109.115 1.50 +SAM "C3'" "C4'" "H4'" 109.143 1.50 +SAM "C4'" "O4'" "C1'" 109.426 1.50 +SAM "C4'" "C3'" "O3'" 110.985 2.41 +SAM "C4'" "C3'" "C2'" 102.352 1.50 +SAM "C4'" "C3'" "H3'" 110.624 1.81 +SAM "O3'" "C3'" "C2'" 111.581 2.83 +SAM "O3'" "C3'" "H3'" 110.380 1.67 +SAM "C2'" "C3'" "H3'" 110.504 1.75 +SAM "C3'" "O3'" "HO3'" 108.744 3.00 +SAM "C3'" "C2'" "O2'" 112.782 2.45 +SAM "C3'" "C2'" "C1'" 101.239 1.50 +SAM "C3'" "C2'" "H2'" 110.596 1.51 +SAM "O2'" "C2'" "C1'" 111.715 2.69 +SAM "O2'" "C2'" "H2'" 110.448 1.97 +SAM "C1'" "C2'" "H2'" 110.636 1.70 +SAM "C2'" "O2'" "HO2'" 109.103 2.13 +SAM "O4'" "C1'" "C2'" 106.047 1.50 +SAM "O4'" "C1'" N9 108.477 1.50 +SAM "O4'" "C1'" "H1'" 109.807 1.50 +SAM "C2'" "C1'" N9 113.824 1.50 +SAM "C2'" "C1'" "H1'" 109.015 1.50 +SAM N9 "C1'" "H1'" 109.561 1.50 +SAM "C1'" N9 C8 126.848 1.91 +SAM "C1'" N9 C4 127.459 1.80 +SAM C8 N9 C4 105.693 1.50 +SAM N9 C8 N7 113.469 1.50 +SAM N9 C8 H8 123.206 1.50 +SAM N7 C8 H8 123.326 1.50 +SAM C8 N7 C5 104.739 1.50 +SAM N7 C5 C6 132.250 1.50 +SAM N7 C5 C4 110.483 1.50 +SAM C6 C5 C4 117.267 1.50 +SAM C5 C6 N6 123.792 1.50 +SAM C5 C6 N1 117.409 1.50 +SAM N6 C6 N1 118.799 1.50 +SAM C6 N6 HN61 119.723 1.50 +SAM C6 N6 HN62 119.723 1.50 +SAM HN61 N6 HN62 120.554 1.88 +SAM C6 N1 C2 118.521 1.50 +SAM N1 C2 N3 129.332 1.50 +SAM N1 C2 H2 115.313 1.50 +SAM N3 C2 H2 115.355 1.50 +SAM C2 N3 C4 110.982 1.50 +SAM N9 C4 C5 105.616 1.50 +SAM N9 C4 N3 127.895 1.50 +SAM 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 +SAM sp3_sp3_25 C CA N HN1 180.000 10.0 3 +SAM sp3_sp3_2 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3 +SAM sp3_sp3_83 "O3'" "C3'" "C4'" "C5'" 180.000 10.0 3 +SAM sp3_sp3_4 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3 +SAM sp3_sp3_88 "C4'" "C3'" "O3'" "HO3'" 180.000 10.0 3 +SAM sp3_sp3_20 "O2'" "C2'" "C3'" "O3'" -60.000 10.0 3 +SAM sp3_sp3_91 "C3'" "C2'" "O2'" "HO2'" 180.000 10.0 3 +SAM sp3_sp3_8 "O4'" "C1'" "C2'" "O2'" 180.000 10.0 3 +SAM sp2_sp3_7 C8 N9 "C1'" "O4'" 150.000 10.0 6 +SAM const_14 N7 C8 N9 "C1'" 180.000 10.0 2 +SAM const_26 C5 C4 N9 "C1'" 180.000 10.0 2 +SAM const_17 N9 C8 N7 C5 0.000 10.0 2 +SAM const_20 C6 C5 N7 C8 180.000 10.0 2 +SAM sp2_sp3_1 O C CA N 0.000 10.0 6 +SAM sp3_sp3_34 N CA CB CG 180.000 10.0 3 +SAM const_sp2_sp2_4 N7 C5 C6 N6 0.000 5.0 2 +SAM const_21 N9 C4 C5 N7 0.000 10.0 2 +SAM sp2_sp2_1 C5 C6 N6 HN61 180.000 5.0 2 +SAM const_sp2_sp2_6 N6 C6 N1 C2 180.000 5.0 2 +SAM const_sp2_sp2_7 N3 C2 N1 C6 0.000 5.0 2 +SAM const_sp2_sp2_9 N1 C2 N3 C4 0.000 5.0 2 +SAM const_12 N9 C4 N3 C2 180.000 10.0 2 +SAM sp3_sp3_43 CA CB CG SD 180.000 10.0 3 +SAM sp3_sp3_52 CB CG SD CE 180.000 10.0 3 +SAM sp3_sp3_58 HE1 CE SD CG 180.000 10.0 3 +SAM sp3_sp3_64 "C4'" "C5'" SD CG 180.000 10.0 3 +SAM sp3_sp3_70 "O4'" "C4'" "C5'" SD 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 +SAM chir_1 CA N C CB positive +SAM chir_2 SD "C5'" CG CE positive +SAM chir_3 "C4'" "O4'" "C5'" "C3'" positive +SAM chir_4 "C3'" "O3'" "C4'" "C2'" positive +SAM chir_5 "C2'" "O2'" "C1'" "C3'" negative +SAM 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 +SAM plan-1 "C1'" 0.020 +SAM plan-1 C2 0.020 +SAM plan-1 C4 0.020 +SAM plan-1 C5 0.020 +SAM plan-1 C6 0.020 +SAM plan-1 C8 0.020 +SAM plan-1 H2 0.020 +SAM plan-1 H8 0.020 +SAM plan-1 N1 0.020 +SAM plan-1 N3 0.020 +SAM plan-1 N6 0.020 +SAM plan-1 N7 0.020 +SAM plan-1 N9 0.020 +SAM plan-2 C 0.020 +SAM plan-2 CA 0.020 +SAM plan-2 O 0.020 +SAM plan-2 OXT 0.020 +SAM plan-3 C6 0.020 +SAM plan-3 HN61 0.020 +SAM plan-3 HN62 0.020 +SAM plan-3 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 +SAM SMILES ACDLabs 10.04 "[O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O" +SAM SMILES_CANONICAL CACTVS 3.341 C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23 +SAM SMILES CACTVS 3.341 C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23 +SAM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O +SAM SMILES "OpenEye OEToolkits" 1.5.0 C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O +SAM InChI InChI 1.03 InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1 +SAM InChIKey InChI 1.03 MEFKEPWMEQBLKI-FCKMPRQPSA-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 +SAM acedrg 243 "dictionary generator" +SAM acedrg_database 11 "data source" +SAM rdkit 2017.03.2 "Chemoinformatics tool" +SAM 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 +SAM peptide HN1 H +SAM peptide HN2 H2 diff --git a/image_analysis/structure_refinement/monomers/links_and_mods.cif b/image_analysis/structure_refinement/monomers/links_and_mods.cif index 6747c388d..132bf6afb 100644 --- a/image_analysis/structure_refinement/monomers/links_and_mods.cif +++ b/image_analysis/structure_refinement/monomers/links_and_mods.cif @@ -24,11 +24,18 @@ 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 +HEC-CYS1 CYS CYSmod1 peptide HEC HECmod1 NON-POLYMER HEC_CAC-CYS1 +HEC-CYS2 CYS CYSmod1 peptide HEC HECmod2 NON-POLYMER HEC_CAB-CYS2 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 +CYS-FAD CYS CYSmod2 peptide FAD FADmod1 NON-POLYMER CYS-FAD +HIS-FAD1 HIS HISmod1 peptide FAD FADmod2 NON-POLYMER HIS-FAD1 +HIS-FAD2 HIS HISmod2 peptide FAD FADmod3 NON-POLYMER HIS-FAD2 GTP-p GTP GTPmod1 NON-POLYMER . DEL_OP3 DNA/RNA GTP-p +CYS-HEMB CYS CYSmod1 peptide HEM HEMmod2 NON-POLYMER CYS-HEMB +CYS-HEMC CYS CYSmod1 peptide HEM HEMmod3 NON-POLYMER CYS-HEMC 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 @@ -86,9 +93,16 @@ 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 +HECmod1 'HEME C CAB-C3B bond order ' HEC NON-POLYMER +HECmod2 'HEME C CAC-C3C bond order ' HEC NON-POLYMER +FADmod1 "FLAVIN-ADENINE DINUCLEOTIDE" FAD NON-POLYMER HISmod1 HISTIDINE HIS peptide +FADmod2 "FLAVIN-ADENINE DINUCLEOTIDE" FAD NON-POLYMER HISmod2 HISTIDINE HIS peptide +FADmod3 "FLAVIN-ADENINE DINUCLEOTIDE" FAD NON-POLYMER GTPmod1 "GUANOSINE-5'-TRIPHOSPHATE" GTP NON-POLYMER +HEMmod2 "PROTOPORPHYRIN IX CONTAINING FE" HEM NON-POLYMER +HEMmod3 "PROTOPORPHYRIN IX CONTAINING FE" HEM NON-POLYMER TYRmod1 TYROSINE TYR peptide HISmod3 HISTIDINE HIS peptide TYRmod2 TYROSINE TYR peptide @@ -855,6 +869,122 @@ _chem_link_angle.value_angle_esd ZN-HISNE 1 ZN 2 NE2 2 CD2 125.500 3.000 ZN-HISNE 1 ZN 2 NE2 2 CE1 125.500 3.000 +data_link_HEC-CYS1 +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 +HEC-CYS1 1 SG 2 CAC SINGLE 1.824 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 +HEC-CYS1 1 CB 1 SG 2 CAC 101.808 3.00 +HEC-CYS1 2 C3C 2 CAC 1 SG 111.652 3.00 +HEC-CYS1 2 CBC 2 CAC 1 SG 110.252 3.00 +HEC-CYS1 1 SG 2 CAC 2 HAC 107.856 1.89 + +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 +HEC-CYS1 sp3_sp3_1 2 CBC 2 CAC 1 SG 1 CB 60.000 10.0 3 +HEC-CYS1 sp3_sp3_2 1 SG 2 CAC 2 CBC 2 HBC1 60.000 10.0 3 +HEC-CYS1 sp3_sp3_3 1 CA 1 CB 1 SG 2 CAC 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 +HEC-CYS1 2 CAC 1 SG 2 C3C 2 CBC both + +data_link_HEC-CYS2 +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 +HEC-CYS2 1 SG 2 CAB SINGLE 1.824 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 +HEC-CYS2 1 CB 1 SG 2 CAB 101.808 3.00 +HEC-CYS2 2 C3B 2 CAB 1 SG 111.652 3.00 +HEC-CYS2 2 CBB 2 CAB 1 SG 110.252 3.00 +HEC-CYS2 1 SG 2 CAB 2 HAB 107.856 1.89 + +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 +HEC-CYS2 sp3_sp3_1 2 CBB 2 CAB 1 SG 1 CB 60.000 10.0 3 +HEC-CYS2 sp3_sp3_2 1 SG 2 CAB 2 CBB 2 HBB1 60.000 10.0 3 +HEC-CYS2 sp3_sp3_3 1 CA 1 CB 1 SG 2 CAB 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 +HEC-CYS2 2 CAB 1 SG 2 C3B 2 CBB both + data_link_FE-CYS loop_ _chem_link_bond.link_id @@ -941,6 +1071,177 @@ _chem_link_bond.value_dist _chem_link_bond.value_dist_esd symmetry 0 . 0 . . .000 .020 +data_link_CYS-FAD +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 +CYS-FAD 1 SG 2 C8M SINGLE 1.820 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 +CYS-FAD 1 CB 1 SG 2 C8M 101.044 3.00 +CYS-FAD 2 C8 2 C8M 1 SG 113.672 3.00 +CYS-FAD 1 SG 2 C8M 2 HM81 108.732 1.50 +CYS-FAD 1 SG 2 C8M 2 HM82 108.732 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 +CYS-FAD sp3_sp3_1 2 C8 2 C8M 1 SG 1 CB 180.000 10.0 3 +CYS-FAD sp2_sp3_1 2 C7 2 C8 2 C8M 1 SG -90.000 10.0 6 +CYS-FAD sp3_sp3_2 1 CA 1 CB 1 SG 2 C8M 180.000 10.0 3 + +data_link_HIS-FAD1 +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 +HIS-FAD1 1 ND1 2 C8M SINGLE 1.467 0.0125 + +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 +HIS-FAD1 1 CG 1 ND1 2 C8M 125.176 2.51 +HIS-FAD1 1 CE1 1 ND1 2 C8M 126.099 1.66 +HIS-FAD1 2 C8 2 C8M 1 ND1 112.614 2.48 +HIS-FAD1 1 ND1 2 C8M 2 HM81 108.931 1.50 +HIS-FAD1 1 ND1 2 C8M 2 HM82 108.931 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 +HIS-FAD1 sp2_sp3_1 1 CG 1 ND1 2 C8M 2 C8 -90.000 10.0 6 +HIS-FAD1 sp2_sp3_2 2 C7 2 C8 2 C8M 1 ND1 -90.000 10.0 6 +HIS-FAD1 const_82_1 1 CB 1 CG 1 ND1 2 C8M 0.000 0.0 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 +HIS-FAD1 plan-6 1 CB 0.020 +HIS-FAD1 plan-6 2 C8M 0.020 +HIS-FAD1 plan-6 1 CG 0.020 +HIS-FAD1 plan-6 1 CD2 0.020 +HIS-FAD1 plan-6 1 CE1 0.020 +HIS-FAD1 plan-6 1 HD2 0.020 +HIS-FAD1 plan-6 1 HE1 0.020 +HIS-FAD1 plan-6 1 HE2 0.020 +HIS-FAD1 plan-6 1 NE2 0.020 +HIS-FAD1 plan-6 1 ND1 0.020 + +data_link_HIS-FAD2 +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 +HIS-FAD2 1 NE2 2 C8M SINGLE 1.477 0.0113 + +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 +HIS-FAD2 1 CD2 1 NE2 2 C8M 125.649 2.86 +HIS-FAD2 1 CE1 1 NE2 2 C8M 126.201 1.50 +HIS-FAD2 2 C8 2 C8M 1 NE2 112.614 2.48 +HIS-FAD2 1 NE2 2 C8M 2 HM81 109.095 1.50 +HIS-FAD2 1 NE2 2 C8M 2 HM82 109.095 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 +HIS-FAD2 sp2_sp3_1 1 CD2 1 NE2 2 C8M 2 C8 -90.000 10.0 6 +HIS-FAD2 sp2_sp3_2 2 C7 2 C8 2 C8M 1 NE2 -90.000 10.0 6 +HIS-FAD2 const_92_1 1 CG 1 CD2 1 NE2 2 C8M 180.000 0.0 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 +HIS-FAD2 plan-6 1 CB 0.020 +HIS-FAD2 plan-6 2 C8M 0.020 +HIS-FAD2 plan-6 1 CG 0.020 +HIS-FAD2 plan-6 1 CD2 0.020 +HIS-FAD2 plan-6 1 CE1 0.020 +HIS-FAD2 plan-6 1 HD1 0.020 +HIS-FAD2 plan-6 1 HD2 0.020 +HIS-FAD2 plan-6 1 HE1 0.020 +HIS-FAD2 plan-6 1 NE2 0.020 +HIS-FAD2 plan-6 1 ND1 0.020 + data_link_GTP-p loop_ _chem_link_bond.link_id @@ -998,6 +1299,122 @@ _chem_link_chir.atom_id_3 _chem_link_chir.volume_sign GTP-p 2 P 2 "O5'" 1 "O3'" 2 OP2 both +data_link_CYS-HEMB +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 +CYS-HEMB 1 SG 2 CAB SINGLE 1.824 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 +CYS-HEMB 1 CB 1 SG 2 CAB 101.808 3.00 +CYS-HEMB 2 C3B 2 CAB 1 SG 111.652 3.00 +CYS-HEMB 2 CBB 2 CAB 1 SG 110.252 3.00 +CYS-HEMB 1 SG 2 CAB 2 HAB 107.856 1.89 + +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 +CYS-HEMB sp3_sp3_1 2 CBB 2 CAB 1 SG 1 CB 60.000 10.0 3 +CYS-HEMB sp3_sp3_2 1 SG 2 CAB 2 CBB 2 HBB 60.000 10.0 3 +CYS-HEMB sp3_sp3_3 1 CA 1 CB 1 SG 2 CAB 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 +CYS-HEMB 2 CAB 1 SG 2 C3B 2 CBB both + +data_link_CYS-HEMC +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 +CYS-HEMC 1 SG 2 CAC SINGLE 1.824 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 +CYS-HEMC 1 CB 1 SG 2 CAC 101.808 3.00 +CYS-HEMC 2 C3C 2 CAC 1 SG 111.652 3.00 +CYS-HEMC 2 CBC 2 CAC 1 SG 110.252 3.00 +CYS-HEMC 1 SG 2 CAC 2 HAC 107.856 1.89 + +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 +CYS-HEMC sp3_sp3_1 2 CBC 2 CAC 1 SG 1 CB 60.000 10.0 3 +CYS-HEMC sp3_sp3_2 1 SG 2 CAC 2 CBC 2 HBC 60.000 10.0 3 +CYS-HEMC sp3_sp3_3 1 CA 1 CB 1 SG 2 CAC 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 +CYS-HEMC 2 CAC 1 SG 2 C3C 2 CBC both + data_link_HIS_TYR1 loop_ _chem_link_bond.link_id @@ -3332,6 +3749,161 @@ _chem_mod_tor.new_value_angle_esd _chem_mod_tor.new_period DEL-HG1 delete CA CB OG1 HG1 . . . 3 +data_mod_HECmod1 +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 +HECmod1 change CAC . 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 +HECmod1 change C2C C3C single 1.375 0.0200 1.375 0.0200 +HECmod1 change C3C CAC single 1.503 0.0100 1.503 0.0100 +HECmod1 change CAC CBC single 1.513 0.0121 1.513 0.0121 +HECmod1 change CAC HAC single 0.990 0.0200 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 +HECmod1 change NC C4C C3C 108.743 1.50 +HECmod1 change C3C CAC CBC 112.400 1.50 +HECmod1 change C3C CAC HAC 108.177 1.50 +HECmod1 change CBC CAC HAC 108.549 2.04 +HECmod1 change HBC1 CBC HBC2 109.460 1.50 +HECmod1 change HBC1 CBC HBC3 109.460 1.50 +HECmod1 change HBC2 CBC HBC3 109.460 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 +HECmod1 delete C3C CAC CBC HBC1 . . . 3 +HECmod1 change C2C C3C CAC CBC sp2_sp3_8 150.000 20.0 6 + +data_mod_HECmod2 +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 +HECmod2 change CAB . 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 +HECmod2 change C2B C3B double 1.375 0.0200 1.375 0.0200 +HECmod2 change C3B CAB single 1.503 0.0100 1.503 0.0100 +HECmod2 change CAB CBB single 1.513 0.0121 1.513 0.0121 +HECmod2 change CAB HAB single 0.990 0.0200 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 +HECmod2 change NB C4B C3B 108.743 1.50 +HECmod2 change C3B CAB CBB 112.400 1.50 +HECmod2 change C3B CAB HAB 108.177 1.50 +HECmod2 change CBB CAB HAB 108.549 2.04 +HECmod2 change HBB1 CBB HBB2 109.460 1.50 +HECmod2 change HBB1 CBB HBB3 109.460 1.50 +HECmod2 change HBB2 CBB HBB3 109.460 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 +HECmod2 delete C3B CAB CBB HBB1 . . . 3 +HECmod2 change C2B C3B CAB CBB sp2_sp3_6 150.000 20.0 6 + +data_mod_FADmod1 +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 +FADmod1 delete HM83 . H H 0 +FADmod1 change C8M . C CH2 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 +FADmod1 delete C8M HM83 single . . . . +FADmod1 change C7 C8 single 1.401 0.0100 1.401 0.0100 +FADmod1 change C8 C8M single 1.516 0.0100 1.516 0.0100 +FADmod1 change C8 C9 double 1.377 0.0162 1.377 0.0162 +FADmod1 change C8M HM81 single 0.982 0.0200 1.089 0.0100 +FADmod1 change C8M HM82 single 0.982 0.0200 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 +FADmod1 delete C8 C8M HM83 . . +FADmod1 delete HM81 C8M HM83 . . +FADmod1 delete HM82 C8M HM83 . . +FADmod1 change C7 C8 C8M 120.426 2.23 +FADmod1 change C8M C8 C9 120.074 3.00 + data_mod_HISmod1 loop_ _chem_mod_atom.mod_id @@ -3392,6 +3964,46 @@ HISmod1 delete plan-1 HE2 0.020 HISmod1 delete plan-1 ND1 0.020 HISmod1 delete plan-1 NE2 0.020 +data_mod_FADmod2 +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 +FADmod2 delete HM83 . H H 0 +FADmod2 change C8M . C CH2 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 +FADmod2 delete C8M HM83 single . . . . +FADmod2 change C7 C8 single 1.398 0.0119 1.398 0.0119 +FADmod2 change C8 C8M single 1.514 0.0100 1.514 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 +FADmod2 delete C8 C8M HM83 . . +FADmod2 delete HM81 C8M HM83 . . +FADmod2 delete HM82 C8M HM83 . . +FADmod2 change C7 C8 C8M 120.918 3.00 +FADmod2 change C8M C8 C9 119.582 3.00 + data_mod_HISmod2 loop_ _chem_mod_atom.mod_id @@ -3450,6 +4062,46 @@ HISmod2 delete plan-1 HE2 0.020 HISmod2 delete plan-1 ND1 0.020 HISmod2 delete plan-1 NE2 0.020 +data_mod_FADmod3 +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 +FADmod3 delete HM83 . H H 0 +FADmod3 change C8M . C CH2 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 +FADmod3 delete C8M HM83 single . . . . +FADmod3 change C7 C8 single 1.398 0.0119 1.398 0.0119 +FADmod3 change C8 C8M single 1.514 0.0100 1.514 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 +FADmod3 delete C8 C8M HM83 . . +FADmod3 delete HM81 C8M HM83 . . +FADmod3 delete HM82 C8M HM83 . . +FADmod3 change C7 C8 C8M 120.918 3.00 +FADmod3 change C8M C8 C9 119.582 3.00 + data_mod_GTPmod1 loop_ _chem_mod_atom.mod_id @@ -3501,6 +4153,162 @@ _chem_mod_tor.new_value_angle_esd _chem_mod_tor.new_period GTPmod1 delete "C4'" "C3'" "O3'" "HO3'" . . . 0 +data_mod_HEMmod2 +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 +HEMmod2 change CAB . C CH1 0 +HEMmod2 change CBB . C CH3 0 +HEMmod2 add . H31 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 +HEMmod2 change C2B C3B double 1.375 0.0200 1.375 0.0200 +HEMmod2 change C3B C4B single 1.381 0.0200 1.381 0.0200 +HEMmod2 change C3B CAB single 1.503 0.0100 1.503 0.0100 +HEMmod2 change CAB CBB single 1.513 0.0121 1.513 0.0121 +HEMmod2 change CAB HAB single 0.990 0.0200 1.092 0.0100 +HEMmod2 add CBB H31 single 0.960 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 +HEMmod2 change C3B C4B NB 108.743 1.50 +HEMmod2 change C3B CAB CBB 112.400 1.50 +HEMmod2 change C3B CAB HAB 108.177 1.50 +HEMmod2 change CBB CAB HAB 108.549 2.04 +HEMmod2 change CAB CBB HBB 109.518 1.50 +HEMmod2 change CAB CBB HBBA 109.518 1.50 +HEMmod2 change HBB CBB HBBA 109.460 1.50 +HEMmod2 add CAB CBB H31 109.518 1.50 +HEMmod2 add HBB CBB H31 109.460 1.50 +HEMmod2 add HBBA CBB H31 109.460 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 +HEMmod2 delete C3B CAB CBB HBB . . . 2 +HEMmod2 change C2B C3B CAB CBB sp2_sp3_9 150.000 20.0 6 + +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 +HEMmod2 delete plan-10 C3B 0.020 +HEMmod2 delete plan-10 CAB 0.020 +HEMmod2 delete plan-10 CBB 0.020 +HEMmod2 delete plan-10 HAB 0.020 +HEMmod2 delete plan-11 CAB 0.020 +HEMmod2 delete plan-11 CBB 0.020 +HEMmod2 delete plan-11 HBB 0.020 +HEMmod2 delete plan-11 HBBA 0.020 + +data_mod_HEMmod3 +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 +HEMmod3 change CAC . C CH1 0 +HEMmod3 change CBC . C CH3 0 +HEMmod3 add . H32 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 +HEMmod3 change C2C C3C single 1.375 0.0200 1.375 0.0200 +HEMmod3 change C3C C4C double 1.381 0.0200 1.381 0.0200 +HEMmod3 change C3C CAC single 1.503 0.0100 1.503 0.0100 +HEMmod3 change CAC CBC single 1.513 0.0121 1.513 0.0121 +HEMmod3 change CAC HAC single 0.990 0.0200 1.092 0.0100 +HEMmod3 add CBC H32 single 0.960 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 +HEMmod3 change C3C C4C NC 108.743 1.50 +HEMmod3 change C3C CAC CBC 112.400 1.50 +HEMmod3 change C3C CAC HAC 108.177 1.50 +HEMmod3 change CBC CAC HAC 108.549 2.04 +HEMmod3 change CAC CBC HBC 109.518 1.50 +HEMmod3 change CAC CBC HBCA 109.518 1.50 +HEMmod3 change HBC CBC HBCA 109.460 1.50 +HEMmod3 add CAC CBC H32 109.518 1.50 +HEMmod3 add HBC CBC H32 109.460 1.50 +HEMmod3 add HBCA CBC H32 109.460 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 +HEMmod3 delete C3C CAC CBC HBC . . . 2 +HEMmod3 change C2C C3C CAC CBC sp2_sp3_9 150.000 20.0 6 + +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 +HEMmod3 delete plan-12 C3C 0.020 +HEMmod3 delete plan-12 CAC 0.020 +HEMmod3 delete plan-12 CBC 0.020 +HEMmod3 delete plan-12 HAC 0.020 +HEMmod3 delete plan-13 CAC 0.020 +HEMmod3 delete plan-13 CBC 0.020 +HEMmod3 delete plan-13 HBC 0.020 +HEMmod3 delete plan-13 HBCA 0.020 + data_mod_TYRmod1 loop_ _chem_mod_atom.mod_id diff --git a/image_analysis/structure_refinement/monomers/update_monomers.py b/image_analysis/structure_refinement/monomers/update_monomers.py index 1e13afc30..dfd8a3a04 100644 --- a/image_analysis/structure_refinement/monomers/update_monomers.py +++ b/image_analysis/structure_refinement/monomers/update_monomers.py @@ -28,11 +28,17 @@ 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"] +# The modified nucleotides of tRNA and rRNA most often met, polymer residues joined by the same backbone link. +MODIFIED_NUCLEOTIDES = ["PSU", "5MC", "1MA", "OMG", "OMC", "OMU", "H2U", "M2G", "7MG", "2MG", "5MU"] NUCLEOTIDE_LIGANDS = ["ATP", "ADP", "AMP", "GTP", "GDP", "GMP"] +# The cofactors most often met, and the oxygen a heme iron binds. (Not carbon monoxide: CMO.cif has C-O at 1.25 A, +# where bound CO is near 1.15 A.) +COFACTORS = ["NAD", "NAI", "NAP", "NDP", "FAD", "FMN", "HEM", "HEC", "SAM", "SAH", "OXY"] 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 +COMPOUNDS = (AMINO_ACIDS + NUCLEOTIDES + MODIFIED_NUCLEOTIDES + NUCLEOTIDE_LIGANDS + COFACTORS + ADDITIVES + + WATER_AND_IONS) # The donor elements of metal sites whose distances metals.cif carries. METAL_LIGANDS = ["O", "N", "S"] diff --git a/tests/RefinementTest.cpp b/tests/RefinementTest.cpp index 826087805..ca0135827 100644 --- a/tests/RefinementTest.cpp +++ b/tests/RefinementTest.cpp @@ -10,6 +10,7 @@ #include #include +#include #include #include "../common/CUDAWrapper.h" @@ -332,6 +333,103 @@ TEST_CASE("RefinementRestraints_metal_links", "[Refinement]") { CHECK(RestraintValue(metal_bonds, r, xyzb) == Catch::Approx(r.ideal).margin(0.005)); } +// Deposited models cut down to a ligand and the residues within 4.2 A of it (test_data/ligands, from the PDB entries +// their names start with; the tRNA as its modified nucleotides and their neighbours in the chain): every ligand is +// restrained, its own restraints included, the deposited geometry agrees with the dictionary, and the links the +// ligands need are made - the RNA backbone to and from each modified nucleotide, the iron of a heme to its histidine +// (and a heme C's to its methionine) from the LINK records, and a heme C's two thioethers to its cysteines. +TEST_CASE("RefinementRestraints_deposited_ligands", "[Refinement]") { + const std::vector modified_nucleotides = {"PSU", "5MC", "1MA", "OMG", "OMC", "H2U", "M2G", "7MG", + "2MG", "5MU"}; + const std::vector>> cases = { + {"1ehz_psu", modified_nucleotides}, {"8bkh_hem", {"HEM"}}, {"6k9i_hec", {"HEC"}}, {"2w3v_ndp", {"NDP"}}, + {"5vml_nap", {"NAP"}}, {"6f3p_nad", {"NAD"}}, {"8con_nai", {"NAI"}}, {"3tk0_fad", {"FAD"}}, + {"7tcd_fmn", {"FMN"}}, {"6w4h_sam", {"SAM"}}, {"5epe_sah", {"SAH"}}}; + for (const auto &[name, ligands] : cases) { + DYNAMIC_SECTION(name) { + gemmi::Structure st = gemmi::read_structure_gz("../../tests/test_data/ligands/" + name + ".pdb.gz"); + const RefinementTopology topo = BuildRefinementTopology(st); + std::vector atoms = atoms_of(st.models[0]); + std::vector residue_of; + for (const gemmi::Chain &ch : st.models[0].chains) + for (const gemmi::Residue &r : ch.residues) + for (size_t k = 0; k < r.atoms.size(); k++) + residue_of.push_back(&r); + auto index_of = [&](const gemmi::Residue &r, const char *atom) { + const gemmi::Atom *a = r.find_atom(atom, '*'); + return a == nullptr ? -1 : static_cast(std::find(atoms.begin(), atoms.end(), a) - atoms.begin()); + }; + auto bonded = [&](const RestraintSet &set, int i, int j) { + for (const RestraintRecord &r : set.records) + if (r.kind == static_cast(RestraintKind::Bond) && + ((r.atom[0] == i && r.atom[1] == j) || (r.atom[0] == j && r.atom[1] == i))) + return true; + return false; + }; + + std::map restraints, found; + for (const RestraintRecord &r : topo.geometry.records) + if (r.kind != static_cast(RestraintKind::Plane)) + restraints[residue_of[r.atom[0]]->name]++; + for (size_t i = 0; i < atoms.size(); i++) + if (std::find(ligands.begin(), ligands.end(), residue_of[i]->name) != ligands.end()) { + found[residue_of[i]->name]++; + CHECK(topo.refinable[i]); + } + for (const std::string &code : ligands) { + INFO(code); + CHECK(found[code] > 0); + CHECK(restraints[code] > 0); + CHECK(std::find(topo.fixed_names.begin(), topo.fixed_names.end(), code) == topo.fixed_names.end()); + } + + std::vector> xyzb; + for (gemmi::Atom *a : atoms) + xyzb.push_back({a->pos.x, a->pos.y, a->pos.z, a->b_iso}); + const GeometryStatistics g = MeasureGeometry(topo.geometry, {}, xyzb, &topo.metal_bonds); + CHECK(g.rmsd_bonds < 0.03); + CHECK(g.rmsd_angles < 3.0); + CHECK(g.rmsd_metal < 0.1); + + if (name == "1ehz_psu") { + // each modified nucleotide bonded to the residue before it in the chain, where that one is there + int links = 0; + for (const gemmi::Residue &r : st.models[0].chains[0].residues) { + const gemmi::Residue *prev = &r == &st.models[0].chains[0].residues.front() ? nullptr : &r - 1; + if (prev == nullptr || prev->seqid.num != r.seqid.num - 1 || + std::find(ligands.begin(), ligands.end(), r.name) == ligands.end()) + continue; + INFO(r.name << " " << *r.seqid.num); + CHECK(bonded(topo.geometry, index_of(*prev, "O3'"), index_of(r, "P"))); + links++; + } + CHECK(links >= 10); + } + if (name == "8bkh_hem" || name == "6k9i_hec") { + const gemmi::Residue *heme = nullptr, *his = nullptr; + for (const gemmi::Residue &r : st.models[0].chains[0].residues) { + if (r.name == ligands[0]) + heme = &r; + if (r.name == "HIS" && r.seqid.num == (name == "8bkh_hem" ? 93 : 18)) + his = &r; + } + REQUIRE(heme != nullptr); + REQUIRE(his != nullptr); + const int fe = index_of(*heme, "FE"); + CHECK(topo.metal[fe]); + CHECK(topo.metal_links == (name == "8bkh_hem" ? 1 : 2)); // the histidine; and the methionine + CHECK(bonded(topo.metal_bonds, fe, index_of(*his, "NE2"))); + CHECK(bonded(topo.metal_bonds, fe, index_of(*heme, "NA"))); // the porphyrin's own, among the metal's + if (name == "6k9i_hec") + for (auto [cys, carbon] : {std::pair{14, "CAB"}, std::pair{17, "CAC"}}) + for (const gemmi::Residue &r : st.models[0].chains[0].residues) + if (r.name == "CYS" && r.seqid.num == cys) + CHECK(bonded(topo.geometry, index_of(r, "SG"), index_of(*heme, carbon))); + } + } + } +} + TEST_CASE("RefinementRestraints_gradient", "[Refinement]") { const gemmi::UnitCell cell(14, 15, 16, 90, 90, 90); gemmi::Structure st = residue_crystal({"TYR", "DG"}, cell, "P 21 21 21", 5); diff --git a/tests/test_data/ligands/1ehz_psu.pdb.gz b/tests/test_data/ligands/1ehz_psu.pdb.gz new file mode 100644 index 000000000..24966d5db Binary files /dev/null and b/tests/test_data/ligands/1ehz_psu.pdb.gz differ diff --git a/tests/test_data/ligands/2w3v_ndp.pdb.gz b/tests/test_data/ligands/2w3v_ndp.pdb.gz new file mode 100644 index 000000000..5b4aa2a3c Binary files /dev/null and b/tests/test_data/ligands/2w3v_ndp.pdb.gz differ diff --git a/tests/test_data/ligands/3tk0_fad.pdb.gz b/tests/test_data/ligands/3tk0_fad.pdb.gz new file mode 100644 index 000000000..dfb558cae Binary files /dev/null and b/tests/test_data/ligands/3tk0_fad.pdb.gz differ diff --git a/tests/test_data/ligands/5epe_sah.pdb.gz b/tests/test_data/ligands/5epe_sah.pdb.gz new file mode 100644 index 000000000..f6f99fa94 Binary files /dev/null and b/tests/test_data/ligands/5epe_sah.pdb.gz differ diff --git a/tests/test_data/ligands/5vml_nap.pdb.gz b/tests/test_data/ligands/5vml_nap.pdb.gz new file mode 100644 index 000000000..0eafacceb Binary files /dev/null and b/tests/test_data/ligands/5vml_nap.pdb.gz differ diff --git a/tests/test_data/ligands/6f3p_nad.pdb.gz b/tests/test_data/ligands/6f3p_nad.pdb.gz new file mode 100644 index 000000000..a910bb1ff Binary files /dev/null and b/tests/test_data/ligands/6f3p_nad.pdb.gz differ diff --git a/tests/test_data/ligands/6k9i_hec.pdb.gz b/tests/test_data/ligands/6k9i_hec.pdb.gz new file mode 100644 index 000000000..8ce3b8364 Binary files /dev/null and b/tests/test_data/ligands/6k9i_hec.pdb.gz differ diff --git a/tests/test_data/ligands/6w4h_sam.pdb.gz b/tests/test_data/ligands/6w4h_sam.pdb.gz new file mode 100644 index 000000000..67c476fb0 Binary files /dev/null and b/tests/test_data/ligands/6w4h_sam.pdb.gz differ diff --git a/tests/test_data/ligands/7tcd_fmn.pdb.gz b/tests/test_data/ligands/7tcd_fmn.pdb.gz new file mode 100644 index 000000000..58da6ca00 Binary files /dev/null and b/tests/test_data/ligands/7tcd_fmn.pdb.gz differ diff --git a/tests/test_data/ligands/8bkh_hem.pdb.gz b/tests/test_data/ligands/8bkh_hem.pdb.gz new file mode 100644 index 000000000..4057dd29c Binary files /dev/null and b/tests/test_data/ligands/8bkh_hem.pdb.gz differ diff --git a/tests/test_data/ligands/8con_nai.pdb.gz b/tests/test_data/ligands/8con_nai.pdb.gz new file mode 100644 index 000000000..db2a34f00 Binary files /dev/null and b/tests/test_data/ligands/8con_nai.pdb.gz differ