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)
87 lines
3.4 KiB
Plaintext
87 lines
3.4 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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SO4 SO4 "SULFATE ION" NON-POLYMER 5 5 .
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#
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data_comp_SO4
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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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SO4 S S S3 0 16.537 34.975 5.493
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SO4 O1 O O 0 17.831 34.952 4.866
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SO4 O2 O O 0 16.570 35.855 6.629
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SO4 O3 O OS -1 15.557 35.444 4.551
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SO4 O4 O OS -1 16.190 33.647 5.924
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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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SO4 S O1 DOUBLE n 1.438 0.0156 1.438 0.0156
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SO4 S O2 DOUBLE n 1.438 0.0156 1.438 0.0156
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SO4 S O3 SINGLE n 1.438 0.0156 1.438 0.0156
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SO4 S O4 SINGLE n 1.438 0.0156 1.438 0.0156
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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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SO4 O1 S O2 109.467 1.50
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SO4 O1 S O3 109.467 1.50
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SO4 O1 S O4 109.467 1.50
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SO4 O2 S O3 109.467 1.50
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SO4 O2 S O4 109.467 1.50
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SO4 O3 S O4 109.467 1.50
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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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SO4 chir_1 S O1 O2 O3 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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SO4 SMILES ACDLabs 10.04 "[O-]S([O-])(=O)=O"
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SO4 SMILES_CANONICAL CACTVS 3.341 "[O-][S]([O-])(=O)=O"
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SO4 SMILES CACTVS 3.341 "[O-][S]([O-])(=O)=O"
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SO4 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "[O-]S(=O)(=O)[O-]"
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SO4 SMILES "OpenEye OEToolkits" 1.5.0 "[O-]S(=O)(=O)[O-]"
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SO4 InChI InChI 1.03 InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
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SO4 InChIKey InChI 1.03 QAOWNCQODCNURD-UHFFFAOYSA-L
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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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SO4 acedrg 243 "dictionary generator"
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SO4 acedrg_database 11 "data source"
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SO4 rdkit 2017.03.2 "Chemoinformatics tool"
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SO4 refmac5 5.8.0238 "optimization tool"
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