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)
257 lines
15 KiB
Plaintext
257 lines
15 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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GMP GMP GUANOSINE NON-POLYMER 33 20 .
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#
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data_comp_GMP
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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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GMP "O5'" O OH1 0 31.023 62.348 13.095
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GMP "C5'" C CH2 0 30.880 60.990 13.491
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GMP "C4'" C CH1 0 32.039 60.141 13.016
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GMP "O4'" O O2 0 32.223 60.322 11.591
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GMP "C3'" C CH1 0 33.402 60.499 13.617
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GMP "O3'" O OH1 0 33.583 59.871 14.880
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GMP "C2'" C CH1 0 34.373 59.978 12.551
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GMP "O2'" O OH1 0 34.741 58.628 12.744
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GMP "C1'" C CH1 0 33.583 60.160 11.252
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GMP N9 N NR5 0 33.999 61.321 10.471
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GMP C8 C CR15 0 33.932 62.634 10.866
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GMP N7 N NRD5 0 34.376 63.473 9.962
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GMP C5 C CR56 0 34.763 62.661 8.903
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GMP C6 C CR6 0 35.321 63.006 7.643
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GMP O6 O O 0 35.589 64.136 7.210
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GMP N1 N NR6 0 35.569 61.874 6.857
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GMP C2 C CR6 0 35.310 60.575 7.237
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GMP N2 N NH2 0 35.612 59.614 6.354
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GMP N3 N NRD6 0 34.785 60.248 8.422
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GMP C4 C CR56 0 34.537 61.332 9.203
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GMP "HO5'" H H 0 30.412 62.808 13.461
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GMP "H5'1" H H 0 30.045 60.632 13.121
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GMP "H5'2" H H 0 30.824 60.943 14.469
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GMP "H4'" H H 0 31.840 59.197 13.196
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GMP "H3'" H H 0 33.489 61.482 13.709
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GMP "HO3'" H H 0 34.374 60.022 15.150
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GMP "H2'" H H 0 35.192 60.542 12.533
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GMP "HO2'" H H 0 34.046 58.141 12.763
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GMP "H1'" H H 0 33.686 59.348 10.707
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GMP H8 H H 0 33.598 62.904 11.704
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GMP HN1 H H 0 35.923 62.012 6.043
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GMP HN21 H H 0 35.993 58.873 6.627
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GMP HN22 H H 0 35.427 59.728 5.504
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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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GMP "O5'" "C5'" SINGLE n 1.421 0.0131 1.421 0.0131
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GMP "C5'" "C4'" SINGLE n 1.511 0.0177 1.511 0.0177
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GMP "C4'" "O4'" SINGLE n 1.451 0.0100 1.451 0.0100
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GMP "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100
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GMP "O4'" "C1'" SINGLE n 1.409 0.0100 1.409 0.0100
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GMP "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100
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GMP "C3'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100
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GMP "C2'" "O2'" SINGLE n 1.411 0.0100 1.411 0.0100
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GMP "C2'" "C1'" SINGLE n 1.525 0.0100 1.525 0.0100
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GMP "C1'" N9 SINGLE n 1.458 0.0100 1.458 0.0100
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GMP N9 C8 SINGLE y 1.372 0.0100 1.372 0.0100
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GMP N9 C4 SINGLE y 1.375 0.0100 1.375 0.0100
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GMP C8 N7 DOUBLE y 1.312 0.0100 1.312 0.0100
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GMP N7 C5 SINGLE y 1.390 0.0100 1.390 0.0100
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GMP C5 C6 SINGLE y 1.417 0.0103 1.417 0.0103
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GMP C5 C4 DOUBLE y 1.377 0.0100 1.377 0.0100
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GMP C6 O6 DOUBLE n 1.239 0.0100 1.239 0.0100
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GMP C6 N1 SINGLE y 1.396 0.0107 1.396 0.0107
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GMP N1 C2 SINGLE y 1.374 0.0100 1.374 0.0100
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GMP C2 N2 SINGLE n 1.340 0.0101 1.340 0.0101
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GMP C2 N3 DOUBLE y 1.333 0.0104 1.333 0.0104
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GMP N3 C4 SINGLE y 1.355 0.0100 1.355 0.0100
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GMP "O5'" "HO5'" SINGLE n 0.970 0.0120 0.848 0.0200
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GMP "C5'" "H5'1" SINGLE n 1.089 0.0100 0.981 0.0200
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GMP "C5'" "H5'2" SINGLE n 1.089 0.0100 0.981 0.0200
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GMP "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200
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GMP "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200
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GMP "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
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GMP "C2'" "H2'" SINGLE n 1.089 0.0100 0.994 0.0200
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GMP "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200
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GMP "C1'" "H1'" SINGLE n 1.089 0.0100 0.984 0.0200
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GMP C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170
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GMP N1 HN1 SINGLE n 1.016 0.0100 0.897 0.0200
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GMP N2 HN21 SINGLE n 1.016 0.0100 0.877 0.0200
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GMP N2 HN22 SINGLE n 1.016 0.0100 0.877 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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GMP "C5'" "O5'" "HO5'" 109.007 3.00
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GMP "O5'" "C5'" "C4'" 111.279 1.98
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GMP "O5'" "C5'" "H5'1" 109.280 1.50
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GMP "O5'" "C5'" "H5'2" 109.280 1.50
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GMP "C4'" "C5'" "H5'1" 109.326 2.00
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GMP "C4'" "C5'" "H5'2" 109.326 2.00
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GMP "H5'1" "C5'" "H5'2" 108.248 2.26
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GMP "C5'" "C4'" "O4'" 109.170 1.50
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GMP "C5'" "C4'" "C3'" 114.598 1.97
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GMP "C5'" "C4'" "H4'" 109.037 1.87
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GMP "O4'" "C4'" "C3'" 105.388 1.50
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GMP "O4'" "C4'" "H4'" 108.947 1.50
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GMP "C3'" "C4'" "H4'" 109.363 1.86
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GMP "C4'" "O4'" "C1'" 109.903 1.50
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GMP "C4'" "C3'" "O3'" 111.281 2.46
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GMP "C4'" "C3'" "C2'" 102.602 1.50
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GMP "C4'" "C3'" "H3'" 110.452 2.54
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GMP "O3'" "C3'" "C2'" 111.581 2.83
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GMP "O3'" "C3'" "H3'" 110.380 1.67
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GMP "C2'" "C3'" "H3'" 110.504 1.75
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GMP "C3'" "O3'" "HO3'" 108.744 3.00
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GMP "C3'" "C2'" "O2'" 112.782 2.45
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GMP "C3'" "C2'" "C1'" 101.239 1.50
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GMP "C3'" "C2'" "H2'" 110.596 1.51
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GMP "O2'" "C2'" "C1'" 111.715 2.69
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GMP "O2'" "C2'" "H2'" 110.448 1.97
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GMP "C1'" "C2'" "H2'" 110.636 1.70
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GMP "C2'" "O2'" "HO2'" 109.103 2.13
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GMP "O4'" "C1'" "C2'" 106.047 1.50
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GMP "O4'" "C1'" N9 108.477 1.50
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GMP "O4'" "C1'" "H1'" 109.807 1.50
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GMP "C2'" "C1'" N9 113.824 1.50
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GMP "C2'" "C1'" "H1'" 109.015 1.50
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GMP N9 "C1'" "H1'" 109.561 1.50
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GMP "C1'" N9 C8 126.829 1.91
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GMP "C1'" N9 C4 127.440 1.80
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GMP C8 N9 C4 105.731 1.50
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GMP N9 C8 N7 113.507 1.50
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GMP N9 C8 H8 123.187 1.50
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GMP N7 C8 H8 123.307 1.50
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GMP C8 N7 C5 104.778 1.50
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GMP N7 C5 C6 130.030 1.50
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GMP N7 C5 C4 110.574 1.50
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GMP C6 C5 C4 119.397 1.50
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GMP C5 C6 O6 128.244 1.50
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GMP C5 C6 N1 111.367 1.50
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GMP O6 C6 N1 120.389 1.50
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GMP C6 N1 C2 125.351 1.50
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GMP C6 N1 HN1 116.978 2.44
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GMP C2 N1 HN1 117.677 2.71
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GMP N1 C2 N2 116.576 1.50
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GMP N1 C2 N3 123.602 1.50
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GMP N2 C2 N3 119.821 1.50
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GMP C2 N2 HN21 119.868 1.50
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GMP C2 N2 HN22 119.868 1.50
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GMP HN21 N2 HN22 120.263 1.96
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GMP C2 N3 C4 112.066 1.50
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GMP N9 C4 C5 105.411 1.50
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GMP N9 C4 N3 126.378 1.50
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GMP C5 C4 N3 128.211 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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GMP sp3_sp3_25 "C4'" "C5'" "O5'" "HO5'" 180.000 10.0 3
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GMP const_21 N9 C8 N7 C5 0.000 10.0 2
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GMP const_24 C6 C5 N7 C8 180.000 10.0 2
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GMP const_sp2_sp2_4 N7 C5 C6 O6 0.000 5.0 2
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GMP const_25 N9 C4 C5 N7 0.000 10.0 2
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GMP const_sp2_sp2_7 O6 C6 N1 C2 180.000 5.0 2
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GMP const_11 N2 C2 N1 C6 180.000 10.0 2
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GMP sp2_sp2_1 N1 C2 N2 HN21 180.000 5.0 2
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GMP const_14 N2 C2 N3 C4 180.000 10.0 2
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GMP const_16 N9 C4 N3 C2 180.000 10.0 2
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GMP sp3_sp3_28 "O4'" "C4'" "C5'" "O5'" 180.000 10.0 3
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GMP sp3_sp3_2 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3
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GMP sp3_sp3_41 "O3'" "C3'" "C4'" "C5'" 180.000 10.0 3
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GMP sp3_sp3_4 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3
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GMP sp3_sp3_46 "C4'" "C3'" "O3'" "HO3'" 180.000 10.0 3
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GMP sp3_sp3_20 "O2'" "C2'" "C3'" "O3'" -60.000 10.0 3
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GMP sp3_sp3_49 "C3'" "C2'" "O2'" "HO2'" 180.000 10.0 3
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GMP sp3_sp3_8 "O4'" "C1'" "C2'" "O2'" 180.000 10.0 3
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GMP sp2_sp3_1 C8 N9 "C1'" "O4'" 150.000 10.0 6
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GMP const_18 N7 C8 N9 "C1'" 180.000 10.0 2
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GMP const_30 C5 C4 N9 "C1'" 180.000 10.0 2
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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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GMP chir_1 "C4'" "O4'" "C3'" "C5'" negative
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GMP chir_2 "C3'" "O3'" "C4'" "C2'" positive
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GMP chir_3 "C2'" "O2'" "C1'" "C3'" negative
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GMP chir_4 "C1'" "O4'" N9 "C2'" negative
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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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GMP plan-1 "C1'" 0.020
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GMP plan-1 C2 0.020
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GMP plan-1 C4 0.020
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GMP plan-1 C5 0.020
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GMP plan-1 C6 0.020
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GMP plan-1 C8 0.020
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GMP plan-1 H8 0.020
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GMP plan-1 HN1 0.020
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GMP plan-1 N1 0.020
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GMP plan-1 N2 0.020
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GMP plan-1 N3 0.020
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GMP plan-1 N7 0.020
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GMP plan-1 N9 0.020
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GMP plan-1 O6 0.020
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GMP plan-2 C2 0.020
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GMP plan-2 HN21 0.020
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GMP plan-2 HN22 0.020
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GMP plan-2 N2 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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GMP SMILES ACDLabs 10.04 O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3O)CO
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GMP InChI InChI 1.03 InChI=1S/C10H13N5O5/c11-10-13-7-4(8(19)14-10)12-2-15(7)9-6(18)5(17)3(1-16)20-9/h2-3,5-6,9,16-18H,1H2,(H3,11,13,14,19)/t3-,5-,6-,9-/m1/s1
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GMP InChIKey InChI 1.03 NYHBQMYGNKIUIF-UUOKFMHZSA-N
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GMP SMILES_CANONICAL CACTVS 3.385 NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
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GMP SMILES CACTVS 3.385 NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO)[CH](O)[CH]3O
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GMP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5 c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N=C(NC2=O)N
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GMP SMILES "OpenEye OEToolkits" 1.7.5 c1nc2c(n1C3C(C(C(O3)CO)O)O)N=C(NC2=O)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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GMP acedrg 243 "dictionary generator"
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GMP acedrg_database 11 "data source"
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GMP rdkit 2017.03.2 "Chemoinformatics tool"
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GMP refmac5 5.8.0238 "optimization tool"
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