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)
284 lines
17 KiB
Plaintext
284 lines
17 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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ADP ADP "ADENOSINE-5'-DIPHOSPHATE" NON-POLYMER 39 27 .
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#
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data_comp_ADP
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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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ADP PB P P 0 46.212 2.934 41.132
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ADP O1B O O 0 47.352 3.648 41.816
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ADP O2B O OP -1 46.188 3.167 39.642
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ADP O3B O OP -1 46.138 1.471 41.495
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ADP PA P P 0 43.308 3.312 41.426
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ADP O1A O O 0 42.947 3.885 40.095
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ADP O2A O OP -1 43.043 1.862 41.663
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ADP O3A O O2 0 44.860 3.603 41.708
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ADP "O5'" O O2 0 42.611 4.176 42.585
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ADP "C5'" C CH2 0 42.803 5.614 42.612
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ADP "C4'" C CH1 0 41.916 6.217 43.675
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ADP "O4'" O O2 0 42.237 5.618 44.957
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ADP "C3'" C CH1 0 42.060 7.727 43.896
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ADP "O3'" O OH1 0 40.836 8.295 44.347
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ADP "C2'" C CH1 0 43.161 7.787 44.958
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ADP "O2'" O OH1 0 43.139 8.979 45.714
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ADP "C1'" C CH1 0 42.808 6.577 45.819
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ADP N9 N NR5 0 43.956 5.966 46.481
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ADP C8 C CR15 0 45.032 5.373 45.867
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ADP N7 N NRD5 0 45.919 4.902 46.707
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ADP C5 C CR56 0 45.398 5.197 47.958
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ADP C6 C CR6 0 45.872 4.953 49.266
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ADP N6 N NH2 0 47.020 4.334 49.530
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ADP N1 N NRD6 0 45.104 5.379 50.303
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ADP C2 C CR16 0 43.948 6.003 50.029
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ADP N3 N NRD6 0 43.405 6.285 48.844
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ADP C4 C CR56 0 44.184 5.853 47.833
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ADP "H5'1" H H 0 42.575 6.001 41.731
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ADP "H5'2" H H 0 43.749 5.824 42.811
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ADP "H4'" H H 0 40.984 6.008 43.451
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ADP "H3'" H H 0 42.359 8.172 43.061
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ADP "HO3'" H H 0 40.903 9.141 44.325
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ADP "H2'" H H 0 44.053 7.669 44.537
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ADP "HO2'" H H 0 43.755 8.950 46.297
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ADP "H1'" H H 0 42.146 6.850 46.493
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ADP H8 H H 0 45.124 5.315 44.932
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ADP HN61 H H 0 47.233 4.142 50.360
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ADP HN62 H H 0 47.561 4.119 48.873
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ADP H2 H H 0 43.448 6.281 50.782
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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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ADP PB O1B DOUBLE n 1.509 0.0200 1.509 0.0200
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ADP PB O2B SINGLE n 1.509 0.0200 1.509 0.0200
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ADP PB O3B SINGLE n 1.509 0.0200 1.509 0.0200
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ADP PB O3A SINGLE n 1.614 0.0178 1.614 0.0178
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ADP PA O1A DOUBLE n 1.493 0.0122 1.493 0.0122
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ADP PA O2A SINGLE n 1.493 0.0122 1.493 0.0122
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ADP PA O3A SINGLE n 1.604 0.0133 1.604 0.0133
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ADP PA "O5'" SINGLE n 1.604 0.0133 1.604 0.0133
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ADP "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166
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ADP "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100
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ADP "C4'" "O4'" SINGLE n 1.451 0.0100 1.451 0.0100
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ADP "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100
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ADP "O4'" "C1'" SINGLE n 1.409 0.0100 1.409 0.0100
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ADP "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100
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ADP "C3'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100
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ADP "C2'" "O2'" SINGLE n 1.411 0.0100 1.411 0.0100
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ADP "C2'" "C1'" SINGLE n 1.525 0.0100 1.525 0.0100
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ADP "C1'" N9 SINGLE n 1.458 0.0100 1.458 0.0100
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ADP N9 C8 SINGLE y 1.372 0.0100 1.372 0.0100
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ADP N9 C4 SINGLE y 1.374 0.0101 1.374 0.0101
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ADP C8 N7 DOUBLE y 1.310 0.0100 1.310 0.0100
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ADP N7 C5 SINGLE y 1.388 0.0100 1.388 0.0100
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ADP C5 C6 SINGLE y 1.408 0.0100 1.408 0.0100
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ADP C5 C4 DOUBLE y 1.381 0.0100 1.381 0.0100
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ADP C6 N6 SINGLE n 1.330 0.0100 1.330 0.0100
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ADP C6 N1 DOUBLE y 1.354 0.0100 1.354 0.0100
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ADP N1 C2 SINGLE y 1.339 0.0100 1.339 0.0100
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ADP C2 N3 DOUBLE y 1.330 0.0100 1.330 0.0100
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ADP N3 C4 SINGLE y 1.343 0.0100 1.343 0.0100
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ADP "C5'" "H5'1" SINGLE n 1.089 0.0100 0.989 0.0200
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ADP "C5'" "H5'2" SINGLE n 1.089 0.0100 0.989 0.0200
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ADP "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200
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ADP "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200
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ADP "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
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ADP "C2'" "H2'" SINGLE n 1.089 0.0100 0.994 0.0200
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ADP "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200
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ADP "C1'" "H1'" SINGLE n 1.089 0.0100 0.984 0.0200
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ADP C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170
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ADP N6 HN61 SINGLE n 1.016 0.0100 0.877 0.0200
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ADP N6 HN62 SINGLE n 1.016 0.0100 0.877 0.0200
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ADP C2 H2 SINGLE n 1.082 0.0130 0.945 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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ADP O1B PB O2B 112.716 1.50
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ADP O1B PB O3B 112.716 1.50
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ADP O1B PB O3A 105.965 2.38
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ADP O2B PB O3B 112.716 1.50
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ADP O2B PB O3A 105.965 2.38
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ADP O3B PB O3A 105.965 2.38
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ADP O1A PA O2A 118.411 2.35
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ADP O1A PA O3A 108.816 2.14
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ADP O1A PA "O5'" 109.410 1.50
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ADP O2A PA O3A 108.816 2.14
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ADP O2A PA "O5'" 109.410 1.50
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ADP O3A PA "O5'" 101.065 1.97
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ADP PB O3A PA 132.584 3.00
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ADP PA "O5'" "C5'" 118.553 2.41
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ADP "O5'" "C5'" "C4'" 109.342 1.50
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ADP "O5'" "C5'" "H5'1" 109.845 1.50
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ADP "O5'" "C5'" "H5'2" 109.845 1.50
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ADP "C4'" "C5'" "H5'1" 109.624 1.50
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ADP "C4'" "C5'" "H5'2" 109.624 1.50
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ADP "H5'1" "C5'" "H5'2" 108.472 1.50
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ADP "C5'" "C4'" "O4'" 109.123 1.50
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ADP "C5'" "C4'" "C3'" 116.008 1.52
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ADP "C5'" "C4'" "H4'" 108.268 1.50
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ADP "O4'" "C4'" "C3'" 105.388 1.50
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ADP "O4'" "C4'" "H4'" 108.947 1.50
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ADP "C3'" "C4'" "H4'" 109.363 1.86
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ADP "C4'" "O4'" "C1'" 109.903 1.50
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ADP "C4'" "C3'" "O3'" 111.281 2.46
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ADP "C4'" "C3'" "C2'" 102.602 1.50
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ADP "C4'" "C3'" "H3'" 110.452 2.54
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ADP "O3'" "C3'" "C2'" 111.581 2.83
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ADP "O3'" "C3'" "H3'" 110.380 1.67
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ADP "C2'" "C3'" "H3'" 110.504 1.75
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ADP "C3'" "O3'" "HO3'" 108.744 3.00
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ADP "C3'" "C2'" "O2'" 112.782 2.45
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ADP "C3'" "C2'" "C1'" 101.239 1.50
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ADP "C3'" "C2'" "H2'" 110.596 1.51
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ADP "O2'" "C2'" "C1'" 111.715 2.69
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ADP "O2'" "C2'" "H2'" 110.448 1.97
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ADP "C1'" "C2'" "H2'" 110.636 1.70
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ADP "C2'" "O2'" "HO2'" 109.103 2.13
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ADP "O4'" "C1'" "C2'" 106.047 1.50
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ADP "O4'" "C1'" N9 108.477 1.50
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ADP "O4'" "C1'" "H1'" 109.807 1.50
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ADP "C2'" "C1'" N9 113.824 1.50
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ADP "C2'" "C1'" "H1'" 109.015 1.50
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ADP N9 "C1'" "H1'" 109.561 1.50
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ADP "C1'" N9 C8 126.848 1.91
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ADP "C1'" N9 C4 127.459 1.80
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ADP C8 N9 C4 105.693 1.50
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ADP N9 C8 N7 113.469 1.50
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ADP N9 C8 H8 123.206 1.50
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ADP N7 C8 H8 123.326 1.50
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ADP C8 N7 C5 104.739 1.50
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ADP N7 C5 C6 132.250 1.50
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ADP N7 C5 C4 110.483 1.50
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ADP C6 C5 C4 117.267 1.50
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ADP C5 C6 N6 123.792 1.50
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ADP C5 C6 N1 117.409 1.50
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ADP N6 C6 N1 118.799 1.50
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ADP C6 N6 HN61 119.723 1.50
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ADP C6 N6 HN62 119.723 1.50
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ADP HN61 N6 HN62 120.554 1.88
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ADP C6 N1 C2 118.521 1.50
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ADP N1 C2 N3 129.332 1.50
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ADP N1 C2 H2 115.313 1.50
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ADP N3 C2 H2 115.355 1.50
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ADP C2 N3 C4 110.982 1.50
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ADP N9 C4 C5 105.616 1.50
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ADP N9 C4 N3 127.895 1.50
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ADP C5 C4 N3 126.489 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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ADP sp3_sp3_27 PA O3A PB O1B 60.000 10.0 3
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ADP sp3_sp3_2 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3
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ADP sp3_sp3_50 "O3'" "C3'" "C4'" "C5'" 180.000 10.0 3
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ADP sp3_sp3_4 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3
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ADP sp3_sp3_55 "C4'" "C3'" "O3'" "HO3'" 180.000 10.0 3
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ADP sp3_sp3_20 "O2'" "C2'" "C3'" "O3'" -60.000 10.0 3
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ADP sp3_sp3_58 "C3'" "C2'" "O2'" "HO2'" 180.000 10.0 3
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ADP sp3_sp3_8 "O4'" "C1'" "C2'" "O2'" 180.000 10.0 3
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ADP sp2_sp3_1 C8 N9 "C1'" "O4'" 150.000 10.0 6
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ADP const_14 N7 C8 N9 "C1'" 180.000 10.0 2
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ADP const_26 C5 C4 N9 "C1'" 180.000 10.0 2
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ADP const_17 N9 C8 N7 C5 0.000 10.0 2
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ADP const_20 C6 C5 N7 C8 180.000 10.0 2
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ADP const_sp2_sp2_4 N7 C5 C6 N6 0.000 5.0 2
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ADP const_21 N9 C4 C5 N7 0.000 10.0 2
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ADP sp2_sp2_1 C5 C6 N6 HN61 180.000 5.0 2
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ADP const_sp2_sp2_6 N6 C6 N1 C2 180.000 5.0 2
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ADP const_sp2_sp2_7 N3 C2 N1 C6 0.000 5.0 2
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ADP const_sp2_sp2_9 N1 C2 N3 C4 0.000 5.0 2
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ADP const_12 N9 C4 N3 C2 180.000 10.0 2
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ADP sp3_sp3_30 PB O3A PA O1A 60.000 10.0 3
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ADP sp3_sp3_33 "C5'" "O5'" PA O1A 60.000 10.0 3
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ADP sp3_sp3_34 "C4'" "C5'" "O5'" PA 180.000 10.0 3
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ADP sp3_sp3_37 "O4'" "C4'" "C5'" "O5'" 180.000 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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ADP chir_1 PB O3A O2B O3B both
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ADP chir_2 PA O3A "O5'" O2A both
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ADP chir_3 "C4'" "O4'" "C3'" "C5'" negative
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ADP chir_4 "C3'" "O3'" "C4'" "C2'" positive
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ADP chir_5 "C2'" "O2'" "C1'" "C3'" negative
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ADP chir_6 "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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ADP plan-1 "C1'" 0.020
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ADP plan-1 C2 0.020
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ADP plan-1 C4 0.020
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ADP plan-1 C5 0.020
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ADP plan-1 C6 0.020
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ADP plan-1 C8 0.020
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ADP plan-1 H2 0.020
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ADP plan-1 H8 0.020
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ADP plan-1 N1 0.020
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ADP plan-1 N3 0.020
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ADP plan-1 N6 0.020
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ADP plan-1 N7 0.020
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ADP plan-1 N9 0.020
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ADP plan-2 C6 0.020
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ADP plan-2 HN61 0.020
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ADP plan-2 HN62 0.020
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ADP plan-2 N6 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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ADP SMILES ACDLabs 10.04 O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
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ADP SMILES_CANONICAL CACTVS 3.341 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
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ADP SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
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ADP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
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ADP SMILES "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
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ADP InChI InChI 1.03 InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
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ADP InChIKey InChI 1.03 XTWYTFMLZFPYCI-KQYNXXCUSA-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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ADP acedrg 243 "dictionary generator"
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ADP acedrg_database 11 "data source"
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ADP rdkit 2017.03.2 "Chemoinformatics tool"
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ADP refmac5 5.8.0238 "optimization tool"
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