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)
154 lines
3.8 KiB
Plaintext
154 lines
3.8 KiB
Plaintext
data_comp_list
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loop_
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_chem_comp.id
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_chem_comp.three_letter_code
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_chem_comp.name
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_chem_comp.group
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_chem_comp.number_atoms_all
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_chem_comp.number_atoms_nh
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_chem_comp.desc_level
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GLY GLY GLYCINE peptide 10 5 .
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data_comp_GLY
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loop_
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_chem_comp_atom.comp_id
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_chem_comp_atom.atom_id
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_chem_comp_atom.type_symbol
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_chem_comp_atom.type_energy
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_chem_comp_atom.charge
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_chem_comp_atom.x
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_chem_comp_atom.y
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_chem_comp_atom.z
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GLY N N NT3 1 25.320 35.545 47.014
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GLY CA C CH2 0 25.532 37.001 46.897
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GLY C C C 0 26.039 37.376 45.517
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GLY O O O 0 27.114 36.860 45.146
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GLY OXT O OC -1 25.343 38.172 44.853
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GLY H H H 0 26.098 35.105 46.869
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GLY H2 H H 0 24.710 35.270 46.405
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GLY H3 H H 0 25.019 35.342 47.843
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GLY HA3 H H 0 26.185 37.288 47.578
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GLY HA2 H H 0 24.682 37.467 47.075
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loop_
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_chem_comp_tree.comp_id
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_chem_comp_tree.atom_id
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_chem_comp_tree.atom_back
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_chem_comp_tree.atom_forward
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_chem_comp_tree.connect_type
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GLY N n/a CA START
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GLY H N . .
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GLY H2 N . .
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GLY H3 N . .
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GLY CA N C .
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GLY HA3 CA . .
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GLY HA2 CA . .
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GLY C CA . END
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GLY O C . .
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GLY OXT C . .
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loop_
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_chem_comp_acedrg.comp_id
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_chem_comp_acedrg.atom_id
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_chem_comp_acedrg.atom_type
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GLY N N(CCHH)(H)3
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GLY CA C(NH3)(COO)(H)2
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GLY C C(CHHN)(O)2
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GLY O O(CCO)
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GLY OXT O(CCO)
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GLY H H(NCHH)
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GLY H2 H(NCHH)
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GLY H3 H(NCHH)
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GLY HA3 H(CCHN)
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GLY HA2 H(CCHN)
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loop_
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_chem_comp_bond.comp_id
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_chem_comp_bond.atom_id_1
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_chem_comp_bond.atom_id_2
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_chem_comp_bond.type
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_chem_comp_bond.aromatic
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_chem_comp_bond.value_dist_nucleus
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_chem_comp_bond.value_dist_nucleus_esd
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_chem_comp_bond.value_dist
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_chem_comp_bond.value_dist_esd
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GLY N CA SINGLE n 1.476 0.0106 1.476 0.0106
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GLY CA C SINGLE n 1.517 0.0121 1.517 0.0121
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GLY C O DOUBLE n 1.249 0.0161 1.249 0.0161
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GLY C OXT SINGLE n 1.249 0.0161 1.249 0.0161
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GLY N H SINGLE n 1.018 0.0520 0.905 0.0200
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GLY N H2 SINGLE n 1.018 0.0520 0.905 0.0200
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GLY N H3 SINGLE n 1.018 0.0520 0.905 0.0200
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GLY CA HA3 SINGLE n 1.092 0.0100 0.986 0.0200
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GLY CA HA2 SINGLE n 1.092 0.0100 0.986 0.0200
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loop_
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_chem_comp_angle.comp_id
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_chem_comp_angle.atom_id_1
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_chem_comp_angle.atom_id_2
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_chem_comp_angle.atom_id_3
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_chem_comp_angle.value_angle
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_chem_comp_angle.value_angle_esd
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GLY CA N H 110.151 2.94
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GLY CA N H2 110.151 2.94
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GLY CA N H3 110.151 2.94
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GLY H N H2 109.089 3.00
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GLY H N H3 109.089 3.00
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GLY H2 N H3 109.089 3.00
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GLY N CA C 111.292 1.50
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GLY N CA HA3 109.172 1.50
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GLY N CA HA2 109.172 1.50
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GLY C CA HA3 109.620 1.50
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GLY C CA HA2 109.620 1.50
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GLY HA3 CA HA2 108.054 1.50
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GLY CA C O 117.080 1.50
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GLY CA C OXT 117.080 1.50
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GLY O C OXT 125.839 1.50
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loop_
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_chem_comp_tor.comp_id
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_chem_comp_tor.id
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_chem_comp_tor.atom_id_1
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_chem_comp_tor.atom_id_2
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_chem_comp_tor.atom_id_3
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_chem_comp_tor.atom_id_4
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_chem_comp_tor.value_angle
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_chem_comp_tor.value_angle_esd
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_chem_comp_tor.period
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GLY sp3_sp3_1 C CA N H 180.000 10.0 3
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GLY sp2_sp3_1 O C CA HA3 0.000 10.0 6
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loop_
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_chem_comp_plane_atom.comp_id
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_chem_comp_plane_atom.plane_id
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_chem_comp_plane_atom.atom_id
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_chem_comp_plane_atom.dist_esd
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GLY plan-1 C 0.020
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GLY plan-1 CA 0.020
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GLY plan-1 O 0.020
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GLY plan-1 OXT 0.020
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loop_
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_pdbx_chem_comp_descriptor.comp_id
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_pdbx_chem_comp_descriptor.type
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_pdbx_chem_comp_descriptor.program
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_pdbx_chem_comp_descriptor.program_version
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_pdbx_chem_comp_descriptor.descriptor
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GLY SMILES ACDLabs 10.04 O=C(O)CN
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GLY SMILES_CANONICAL CACTVS 3.341 NCC(O)=O
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GLY SMILES CACTVS 3.341 NCC(O)=O
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GLY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(C(=O)O)N
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GLY SMILES "OpenEye OEToolkits" 1.5.0 C(C(=O)O)N
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GLY InChI InChI 1.03 InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)
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GLY InChIKey InChI 1.03 DHMQDGOQFOQNFH-UHFFFAOYSA-N
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loop_
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_pdbx_chem_comp_description_generator.comp_id
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_pdbx_chem_comp_description_generator.program_name
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_pdbx_chem_comp_description_generator.program_version
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_pdbx_chem_comp_description_generator.descriptor
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GLY acedrg 278 "dictionary generator"
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GLY acedrg_database 12 "data source"
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GLY rdkit 2019.09.1 "Chemoinformatics tool"
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GLY refmac5 5.8.0419 "optimization tool"
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