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)
105 lines
4.3 KiB
Plaintext
105 lines
4.3 KiB
Plaintext
#
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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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ACT ACT "ACETATE ION" NON-POLYMER 7 4 .
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#
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data_comp_ACT
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#
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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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ACT C C C 0 50.652 -7.080 41.537
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ACT O O O 0 50.915 -7.323 42.732
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ACT OXT O OC -1 51.516 -6.945 40.648
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ACT CH3 C CH3 0 49.181 -6.939 41.139
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ACT H1 H H 0 49.117 -6.760 40.187
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ACT H2 H H 0 48.780 -6.205 41.632
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ACT H3 H H 0 48.708 -7.761 41.345
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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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ACT C O DOUBLE n 1.247 0.0187 1.247 0.0187
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ACT C OXT SINGLE n 1.247 0.0187 1.247 0.0187
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ACT C CH3 SINGLE n 1.530 0.0200 1.530 0.0200
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ACT CH3 H1 SINGLE n 1.089 0.0100 0.971 0.0140
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ACT CH3 H2 SINGLE n 1.089 0.0100 0.971 0.0140
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ACT CH3 H3 SINGLE n 1.089 0.0100 0.971 0.0140
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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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ACT O C OXT 123.884 1.50
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ACT O C CH3 118.052 1.94
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ACT OXT C CH3 118.052 1.94
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ACT C CH3 H1 109.670 1.50
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ACT C CH3 H2 109.670 1.50
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ACT C CH3 H3 109.670 1.50
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ACT H1 CH3 H2 109.424 1.50
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ACT H1 CH3 H3 109.424 1.50
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ACT H2 CH3 H3 109.424 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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ACT sp2_sp3_1 O C CH3 H1 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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ACT plan-1 C 0.020
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ACT plan-1 CH3 0.020
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ACT plan-1 O 0.020
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ACT 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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ACT SMILES ACDLabs 10.04 "[O-]C(=O)C"
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ACT SMILES_CANONICAL CACTVS 3.341 CC([O-])=O
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ACT SMILES CACTVS 3.341 CC([O-])=O
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ACT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC(=O)[O-]
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ACT SMILES "OpenEye OEToolkits" 1.5.0 CC(=O)[O-]
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ACT InChI InChI 1.03 InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
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ACT InChIKey InChI 1.03 QTBSBXVTEAMEQO-UHFFFAOYSA-M
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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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ACT acedrg 243 "dictionary generator"
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ACT acedrg_database 11 "data source"
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ACT rdkit 2017.03.2 "Chemoinformatics tool"
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ACT refmac5 5.8.0238 "optimization tool"
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