leonarski_f
e58453a693
A restraint dictionary carried in the binary, so refinement reads nothing from disk and needs no CLIBD_MON: the 20 amino acids and MSE, the DNA/RNA nucleotides, ATP/ADP/AMP/GTP/GDP/GMP, DMSO, PEG fragments (PEG, PGE, PG4, 1PE), GOL, EDO, SO4, PO4, ACT, MPD, water and common ions - copied verbatim from the CCP4 Monomer Library (LGPL-3.0) - plus links_and_mods.cif cut down to the links and modifications those compounds can take (peptide, cis-peptide, proline, N-methyl, disulfide, nucleic-acid backbone, termini, metal-Cys/His) and ener_lib.cif cut to its atom-type table. monomers/update_monomers.py holds the compound list and regenerates the subset; CMake embeds every .cif of the directory as string pieces under MSVC's literal limit; EmbeddedMonomerLibrary() parses them from memory into a gemmi::MonLib once per process. About 0.7 MB of text in the binary. gemmi v0.7.5's monlib.cpp, topo.cpp and riding_h.cpp vendored verbatim (prepare_topology). Licence text in licenses/, rows and a note in THIRD_PARTY_NOTICES.md. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 38034718052c4a300691393b5b817f476c83dfc2)
189 lines
4.8 KiB
Plaintext
189 lines
4.8 KiB
Plaintext
data_comp_list
|
|
loop_
|
|
_chem_comp.id
|
|
_chem_comp.three_letter_code
|
|
_chem_comp.name
|
|
_chem_comp.group
|
|
_chem_comp.number_atoms_all
|
|
_chem_comp.number_atoms_nh
|
|
_chem_comp.desc_level
|
|
SER SER SERINE peptide 14 7 .
|
|
|
|
data_comp_SER
|
|
loop_
|
|
_chem_comp_atom.comp_id
|
|
_chem_comp_atom.atom_id
|
|
_chem_comp_atom.type_symbol
|
|
_chem_comp_atom.type_energy
|
|
_chem_comp_atom.charge
|
|
_chem_comp_atom.x
|
|
_chem_comp_atom.y
|
|
_chem_comp_atom.z
|
|
SER N N NT3 1 88.105 -7.500 -9.831
|
|
SER CA C CH1 0 87.822 -7.221 -11.265
|
|
SER C C C 0 88.475 -5.896 -11.689
|
|
SER O O O 0 88.336 -4.918 -10.921
|
|
SER CB C CH2 0 86.337 -7.203 -11.533
|
|
SER OG O OH1 0 85.742 -8.447 -11.190
|
|
SER OXT O OC -1 89.099 -5.887 -12.773
|
|
SER H H H 0 87.553 -7.016 -9.304
|
|
SER H2 H H 0 88.960 -7.295 -9.626
|
|
SER H3 H H 0 87.971 -8.377 -9.665
|
|
SER HA H H 0 88.226 -7.948 -11.803
|
|
SER HB3 H H 0 86.182 -7.019 -12.479
|
|
SER HB2 H H 0 85.923 -6.490 -11.011
|
|
SER HG H H 0 84.904 -8.380 -11.287
|
|
|
|
loop_
|
|
_chem_comp_tree.comp_id
|
|
_chem_comp_tree.atom_id
|
|
_chem_comp_tree.atom_back
|
|
_chem_comp_tree.atom_forward
|
|
_chem_comp_tree.connect_type
|
|
SER N n/a CA START
|
|
SER H N . .
|
|
SER H2 N . .
|
|
SER H3 N . .
|
|
SER CA N C .
|
|
SER HA CA . .
|
|
SER CB CA OG .
|
|
SER HB3 CB . .
|
|
SER HB2 CB . .
|
|
SER OG CB HG .
|
|
SER HG OG . .
|
|
SER C CA . END
|
|
SER O C . .
|
|
SER OXT C . .
|
|
|
|
loop_
|
|
_chem_comp_acedrg.comp_id
|
|
_chem_comp_acedrg.atom_id
|
|
_chem_comp_acedrg.atom_type
|
|
SER N N(CCCH)(H)3
|
|
SER CA C(CHHO)(NH3)(COO)(H)
|
|
SER C C(CCHN)(O)2
|
|
SER O O(CCO)
|
|
SER CB C(CCHN)(OH)(H)2
|
|
SER OG O(CCHH)(H)
|
|
SER OXT O(CCO)
|
|
SER H H(NCHH)
|
|
SER H2 H(NCHH)
|
|
SER H3 H(NCHH)
|
|
SER HA H(CCCN)
|
|
SER HB3 H(CCHO)
|
|
SER HB2 H(CCHO)
|
|
SER HG H(OC)
|
|
|
|
loop_
|
|
_chem_comp_bond.comp_id
|
|
_chem_comp_bond.atom_id_1
|
|
_chem_comp_bond.atom_id_2
|
|
_chem_comp_bond.type
|
|
_chem_comp_bond.aromatic
|
|
_chem_comp_bond.value_dist_nucleus
|
|
_chem_comp_bond.value_dist_nucleus_esd
|
|
_chem_comp_bond.value_dist
|
|
_chem_comp_bond.value_dist_esd
|
|
SER N CA SINGLE n 1.487 0.0100 1.487 0.0100
|
|
SER CA C SINGLE n 1.536 0.0100 1.536 0.0100
|
|
SER CA CB SINGLE n 1.508 0.0190 1.508 0.0190
|
|
SER C O DOUBLE n 1.251 0.0183 1.251 0.0183
|
|
SER C OXT SINGLE n 1.251 0.0183 1.251 0.0183
|
|
SER CB OG SINGLE n 1.421 0.0108 1.421 0.0108
|
|
SER N H SINGLE n 1.018 0.0520 0.902 0.0102
|
|
SER N H2 SINGLE n 1.018 0.0520 0.902 0.0102
|
|
SER N H3 SINGLE n 1.018 0.0520 0.902 0.0102
|
|
SER CA HA SINGLE n 1.092 0.0100 0.991 0.0200
|
|
SER CB HB3 SINGLE n 1.092 0.0100 0.976 0.0180
|
|
SER CB HB2 SINGLE n 1.092 0.0100 0.976 0.0180
|
|
SER OG HG SINGLE n 0.972 0.0180 0.846 0.0200
|
|
|
|
loop_
|
|
_chem_comp_angle.comp_id
|
|
_chem_comp_angle.atom_id_1
|
|
_chem_comp_angle.atom_id_2
|
|
_chem_comp_angle.atom_id_3
|
|
_chem_comp_angle.value_angle
|
|
_chem_comp_angle.value_angle_esd
|
|
SER CA N H 109.696 3.00
|
|
SER CA N H2 109.696 3.00
|
|
SER CA N H3 109.696 3.00
|
|
SER H N H2 109.032 3.00
|
|
SER H N H3 109.032 3.00
|
|
SER H2 N H3 109.032 3.00
|
|
SER N CA C 109.839 1.50
|
|
SER N CA CB 111.152 1.50
|
|
SER N CA HA 108.129 1.50
|
|
SER C CA CB 111.300 1.50
|
|
SER C CA HA 108.235 1.50
|
|
SER CB CA HA 108.445 1.50
|
|
SER CA C O 117.199 1.50
|
|
SER CA C OXT 117.189 1.50
|
|
SER O C OXT 125.593 1.50
|
|
SER CA CB OG 110.934 1.86
|
|
SER CA CB HB3 109.238 1.50
|
|
SER CA CB HB2 109.238 1.50
|
|
SER OG CB HB3 109.353 1.50
|
|
SER OG CB HB2 109.353 1.50
|
|
SER HB3 CB HB2 108.095 1.88
|
|
SER CB OG HG 108.539 3.00
|
|
|
|
loop_
|
|
_chem_comp_tor.comp_id
|
|
_chem_comp_tor.id
|
|
_chem_comp_tor.atom_id_1
|
|
_chem_comp_tor.atom_id_2
|
|
_chem_comp_tor.atom_id_3
|
|
_chem_comp_tor.atom_id_4
|
|
_chem_comp_tor.value_angle
|
|
_chem_comp_tor.value_angle_esd
|
|
_chem_comp_tor.period
|
|
SER chi1 N CA CB OG -60.000 10.0 3
|
|
SER hh1 CA CB OG HG 180.000 10.0 3
|
|
SER sp3_sp3_1 C CA N H 180.000 10.0 3
|
|
SER sp2_sp3_1 O C CA N 0.000 10.0 6
|
|
|
|
loop_
|
|
_chem_comp_chir.comp_id
|
|
_chem_comp_chir.id
|
|
_chem_comp_chir.atom_id_centre
|
|
_chem_comp_chir.atom_id_1
|
|
_chem_comp_chir.atom_id_2
|
|
_chem_comp_chir.atom_id_3
|
|
_chem_comp_chir.volume_sign
|
|
SER chir_1 CA N C CB positive
|
|
|
|
loop_
|
|
_chem_comp_plane_atom.comp_id
|
|
_chem_comp_plane_atom.plane_id
|
|
_chem_comp_plane_atom.atom_id
|
|
_chem_comp_plane_atom.dist_esd
|
|
SER plan-1 C 0.020
|
|
SER plan-1 CA 0.020
|
|
SER plan-1 O 0.020
|
|
SER plan-1 OXT 0.020
|
|
|
|
loop_
|
|
_pdbx_chem_comp_descriptor.comp_id
|
|
_pdbx_chem_comp_descriptor.type
|
|
_pdbx_chem_comp_descriptor.program
|
|
_pdbx_chem_comp_descriptor.program_version
|
|
_pdbx_chem_comp_descriptor.descriptor
|
|
SER SMILES ACDLabs 10.04 O=C(O)C(N)CO
|
|
SER SMILES_CANONICAL CACTVS 3.341 N[C@@H](CO)C(O)=O
|
|
SER SMILES CACTVS 3.341 N[CH](CO)C(O)=O
|
|
SER SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@@H](C(=O)O)N)O
|
|
SER SMILES "OpenEye OEToolkits" 1.5.0 C(C(C(=O)O)N)O
|
|
SER InChI InChI 1.03 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m0/s1
|
|
SER InChIKey InChI 1.03 MTCFGRXMJLQNBG-REOHCLBHSA-N
|
|
|
|
loop_
|
|
_pdbx_chem_comp_description_generator.comp_id
|
|
_pdbx_chem_comp_description_generator.program_name
|
|
_pdbx_chem_comp_description_generator.program_version
|
|
_pdbx_chem_comp_description_generator.descriptor
|
|
SER acedrg 278 "dictionary generator"
|
|
SER acedrg_database 12 "data source"
|
|
SER rdkit 2019.09.1 "Chemoinformatics tool"
|
|
SER refmac5 5.8.0419 "optimization tool"
|