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)
118 lines
5.1 KiB
Plaintext
118 lines
5.1 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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DMS DMS "DIMETHYL SULFOXIDE" NON-POLYMER 10 4 .
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#
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data_comp_DMS
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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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DMS S S S3 0 63.218 46.394 -11.587
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DMS O O O 0 63.732 46.133 -12.975
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DMS C1 C CH3 0 64.619 46.928 -10.638
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DMS C2 C CH3 0 63.010 44.801 -10.834
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DMS H11 H H 0 64.347 47.082 -9.723
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DMS H12 H H 0 64.967 47.748 -11.014
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DMS H13 H H 0 65.302 46.245 -10.662
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DMS H21 H H 0 63.858 44.337 -10.825
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DMS H22 H H 0 62.366 44.288 -11.340
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DMS H23 H H 0 62.693 44.913 -9.927
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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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DMS S O DOUBLE n 1.503 0.0200 1.503 0.0200
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DMS S C1 SINGLE n 1.774 0.0176 1.774 0.0176
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DMS S C2 SINGLE n 1.774 0.0176 1.774 0.0176
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DMS C1 H11 SINGLE n 1.089 0.0100 0.967 0.0136
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DMS C1 H12 SINGLE n 1.089 0.0100 0.967 0.0136
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DMS C1 H13 SINGLE n 1.089 0.0100 0.967 0.0136
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DMS C2 H21 SINGLE n 1.089 0.0100 0.967 0.0136
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DMS C2 H22 SINGLE n 1.089 0.0100 0.967 0.0136
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DMS C2 H23 SINGLE n 1.089 0.0100 0.967 0.0136
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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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DMS O S C1 106.047 1.50
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DMS O S C2 106.047 1.50
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DMS C1 S C2 97.789 1.50
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DMS S C1 H11 109.408 1.50
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DMS S C1 H12 109.408 1.50
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DMS S C1 H13 109.408 1.50
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DMS H11 C1 H12 109.545 1.50
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DMS H11 C1 H13 109.545 1.50
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DMS H12 C1 H13 109.545 1.50
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DMS S C2 H21 109.408 1.50
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DMS S C2 H22 109.408 1.50
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DMS S C2 H23 109.408 1.50
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DMS H21 C2 H22 109.545 1.50
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DMS H21 C2 H23 109.545 1.50
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DMS H22 C2 H23 109.545 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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DMS sp3_sp3_1 H11 C1 S O 180.000 10.0 3
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DMS sp3_sp3_8 H21 C2 S O -60.000 10.0 3
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loop_
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_chem_comp_chir.comp_id
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_chem_comp_chir.id
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_chem_comp_chir.atom_id_centre
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_chem_comp_chir.atom_id_1
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_chem_comp_chir.atom_id_2
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_chem_comp_chir.atom_id_3
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_chem_comp_chir.volume_sign
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DMS chir_1 S O C1 C2 both
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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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DMS SMILES ACDLabs 10.04 sulfinyldimethane
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DMS SMILES_CANONICAL CACTVS 3.341 C[S](C)=O
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DMS SMILES CACTVS 3.341 C[S](C)=O
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DMS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CS(=O)C
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DMS SMILES "OpenEye OEToolkits" 1.5.0 CS(=O)C
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DMS InChI InChI 1.03 InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
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DMS InChIKey InChI 1.03 IAZDPXIOMUYVGZ-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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DMS acedrg 243 "dictionary generator"
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DMS acedrg_database 11 "data source"
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DMS rdkit 2017.03.2 "Chemoinformatics tool"
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DMS refmac5 5.8.0238 "optimization tool"
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