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)
302 lines
19 KiB
Plaintext
302 lines
19 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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ATP ATP "ADENOSINE-5'-TRIPHOSPHATE" NON-POLYMER 43 31 .
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#
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data_comp_ATP
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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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ATP PG P P 0 44.662 45.077 58.117
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ATP O1G O O 0 43.261 45.625 58.004
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ATP O2G O OP -1 45.679 45.923 57.392
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ATP O3G O OP -1 45.059 44.781 59.542
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ATP PB P P 0 44.268 43.226 55.860
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ATP O1B O O 0 44.078 41.746 55.818
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ATP O2B O OP -1 43.182 44.124 55.365
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ATP O3B O O2 0 44.645 43.653 57.356
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ATP PA P P 0 46.020 43.596 53.536
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ATP O1A O O 0 47.423 44.087 53.400
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ATP O2A O OP -1 44.948 44.301 52.771
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ATP O3A O O2 0 45.624 43.591 55.090
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ATP "O5'" O O2 0 45.968 42.029 53.199
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ATP "C5'" C CH2 0 46.946 41.148 53.808
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ATP "C4'" C CH1 0 46.681 39.728 53.369
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ATP "O4'" O O2 0 46.924 39.620 51.943
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ATP "C3'" C CH1 0 47.567 38.650 54.004
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ATP "O3'" O OH1 0 46.881 37.406 54.075
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ATP "C2'" C CH1 0 48.756 38.611 53.041
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ATP "O2'" O OH1 0 49.451 37.383 53.067
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ATP "C1'" C CH1 0 48.066 38.829 51.697
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ATP N9 N NT 0 48.916 39.514 50.718
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ATP C8 C CR15 0 48.960 40.860 50.413
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ATP N7 N NRD5 0 49.847 41.139 49.485
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ATP C5 C CR56 0 50.421 39.915 49.166
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ATP C6 C CR6 0 51.429 39.540 48.250
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ATP N6 N NH2 0 52.063 40.400 47.457
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ATP N1 N NRD6 0 51.760 38.223 48.186
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ATP C2 C CR16 0 51.117 37.359 48.990
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ATP N3 N NRD6 0 50.158 37.599 49.885
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ATP C4 C CR56 0 49.852 38.909 49.924
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ATP "H5'1" H H 0 46.885 41.207 54.794
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ATP "H5'2" H H 0 47.858 41.415 53.533
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ATP "H4'" H H 0 45.738 39.523 53.548
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ATP "H3'" H H 0 47.862 38.933 54.908
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ATP "HO3'" H H 0 47.400 36.827 54.416
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ATP "H2'" H H 0 49.382 39.360 53.233
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ATP "HO2'" H H 0 50.094 37.416 52.513
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ATP "H1'" H H 0 47.793 37.957 51.333
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ATP H8 H H 0 48.417 41.517 50.815
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ATP HN61 H H 0 52.825 40.173 47.086
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ATP HN62 H H 0 51.716 41.193 47.308
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ATP H2 H H 0 51.382 36.456 48.909
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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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ATP PG O1G DOUBLE n 1.509 0.0200 1.509 0.0200
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ATP PG O2G SINGLE n 1.509 0.0200 1.509 0.0200
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ATP PG O3G SINGLE n 1.509 0.0200 1.509 0.0200
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ATP PG O3B SINGLE n 1.614 0.0178 1.614 0.0178
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ATP PB O1B DOUBLE n 1.493 0.0157 1.493 0.0157
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ATP PB O2B SINGLE n 1.493 0.0157 1.493 0.0157
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ATP PB O3B SINGLE n 1.601 0.0114 1.601 0.0114
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ATP PB O3A SINGLE n 1.601 0.0114 1.601 0.0114
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ATP PA O1A DOUBLE n 1.493 0.0122 1.493 0.0122
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ATP PA O2A SINGLE n 1.493 0.0122 1.493 0.0122
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ATP PA O3A SINGLE n 1.604 0.0133 1.604 0.0133
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ATP PA "O5'" SINGLE n 1.604 0.0133 1.604 0.0133
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ATP "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166
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ATP "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100
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ATP "C4'" "O4'" SINGLE n 1.451 0.0100 1.451 0.0100
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ATP "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100
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ATP "O4'" "C1'" SINGLE n 1.409 0.0100 1.409 0.0100
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ATP "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100
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ATP "C3'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100
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ATP "C2'" "O2'" SINGLE n 1.411 0.0100 1.411 0.0100
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ATP "C2'" "C1'" SINGLE n 1.525 0.0100 1.525 0.0100
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ATP "C1'" N9 SINGLE n 1.458 0.0200 1.458 0.0200
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ATP N9 C8 SINGLE y 1.372 0.0200 1.372 0.0200
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ATP N9 C4 SINGLE y 1.372 0.0100 1.372 0.0100
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ATP C8 N7 DOUBLE y 1.310 0.0100 1.310 0.0100
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ATP N7 C5 SINGLE y 1.388 0.0100 1.388 0.0100
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ATP C5 C6 SINGLE y 1.408 0.0100 1.408 0.0100
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ATP C5 C4 DOUBLE y 1.381 0.0100 1.381 0.0100
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ATP C6 N6 SINGLE n 1.330 0.0100 1.330 0.0100
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ATP C6 N1 DOUBLE y 1.354 0.0100 1.354 0.0100
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ATP N1 C2 SINGLE y 1.339 0.0100 1.339 0.0100
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ATP C2 N3 DOUBLE y 1.330 0.0100 1.330 0.0100
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ATP N3 C4 SINGLE y 1.343 0.0100 1.343 0.0100
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ATP "C5'" "H5'1" SINGLE n 1.089 0.0100 0.989 0.0200
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ATP "C5'" "H5'2" SINGLE n 1.089 0.0100 0.989 0.0200
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ATP "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200
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ATP "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200
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ATP "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
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ATP "C2'" "H2'" SINGLE n 1.089 0.0100 0.994 0.0200
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ATP "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200
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ATP "C1'" "H1'" SINGLE n 1.089 0.0100 0.984 0.0200
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ATP C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170
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ATP N6 HN61 SINGLE n 1.016 0.0100 0.877 0.0200
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ATP N6 HN62 SINGLE n 1.016 0.0100 0.877 0.0200
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ATP 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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ATP O1G PG O2G 112.716 1.50
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ATP O1G PG O3G 112.716 1.50
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ATP O1G PG O3B 105.965 2.38
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ATP O2G PG O3G 112.716 1.50
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ATP O2G PG O3B 105.965 2.38
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ATP O3G PG O3B 105.965 2.38
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ATP O1B PB O2B 119.630 1.50
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ATP O1B PB O3B 108.678 2.29
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ATP O1B PB O3A 108.678 2.29
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ATP O2B PB O3B 108.678 2.29
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ATP O2B PB O3A 108.678 2.29
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ATP O3B PB O3A 100.890 2.10
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ATP PG O3B PB 132.584 3.00
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ATP O1A PA O2A 118.411 2.35
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ATP O1A PA O3A 108.816 2.14
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ATP O1A PA "O5'" 109.410 1.50
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ATP O2A PA O3A 108.816 2.14
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ATP O2A PA "O5'" 109.410 1.50
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ATP O3A PA "O5'" 101.065 1.97
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ATP PB O3A PA 132.542 3.00
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ATP PA "O5'" "C5'" 118.553 2.41
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ATP "O5'" "C5'" "C4'" 109.342 1.50
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ATP "O5'" "C5'" "H5'1" 109.845 1.50
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ATP "O5'" "C5'" "H5'2" 109.845 1.50
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ATP "C4'" "C5'" "H5'1" 109.624 1.50
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ATP "C4'" "C5'" "H5'2" 109.624 1.50
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ATP "H5'1" "C5'" "H5'2" 108.472 1.50
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ATP "C5'" "C4'" "O4'" 109.123 1.50
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ATP "C5'" "C4'" "C3'" 116.008 1.52
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ATP "C5'" "C4'" "H4'" 108.268 1.50
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ATP "O4'" "C4'" "C3'" 105.388 1.50
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ATP "O4'" "C4'" "H4'" 108.947 1.50
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ATP "C3'" "C4'" "H4'" 109.363 1.86
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ATP "C4'" "O4'" "C1'" 109.903 1.50
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ATP "C4'" "C3'" "O3'" 111.281 2.46
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ATP "C4'" "C3'" "C2'" 102.602 1.50
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ATP "C4'" "C3'" "H3'" 110.452 2.54
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ATP "O3'" "C3'" "C2'" 111.581 2.83
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ATP "O3'" "C3'" "H3'" 110.380 1.67
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ATP "C2'" "C3'" "H3'" 110.504 1.75
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ATP "C3'" "O3'" "HO3'" 108.744 3.00
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ATP "C3'" "C2'" "O2'" 112.782 2.45
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ATP "C3'" "C2'" "C1'" 101.239 1.50
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ATP "C3'" "C2'" "H2'" 110.596 1.51
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ATP "O2'" "C2'" "C1'" 111.715 2.69
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ATP "O2'" "C2'" "H2'" 110.448 1.97
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ATP "C1'" "C2'" "H2'" 110.636 1.70
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ATP "C2'" "O2'" "HO2'" 109.103 2.13
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ATP "O4'" "C1'" "C2'" 106.047 1.50
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ATP "O4'" "C1'" N9 108.167 1.51
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ATP "O4'" "C1'" "H1'" 109.807 1.50
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ATP "C2'" "C1'" N9 113.752 2.20
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ATP "C2'" "C1'" "H1'" 109.015 1.50
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ATP N9 "C1'" "H1'" 109.246 1.50
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ATP "C1'" N9 C8 126.078 2.46
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ATP "C1'" N9 C4 125.158 1.54
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ATP C8 N9 C4 107.594 1.50
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ATP N9 C8 N7 112.130 1.94
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ATP N9 C8 H8 124.701 2.19
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ATP N7 C8 H8 123.170 1.50
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ATP C8 N7 C5 103.927 1.50
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ATP N7 C5 C6 132.145 1.50
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ATP N7 C5 C4 110.588 1.50
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ATP C6 C5 C4 117.267 1.50
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ATP C5 C6 N6 123.792 1.50
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ATP C5 C6 N1 117.409 1.50
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ATP N6 C6 N1 118.799 1.50
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ATP C6 N6 HN61 119.723 1.50
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ATP C6 N6 HN62 119.723 1.50
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ATP HN61 N6 HN62 120.554 1.88
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ATP C6 N1 C2 118.521 1.50
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ATP N1 C2 N3 129.332 1.50
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ATP N1 C2 H2 115.313 1.50
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ATP N3 C2 H2 115.355 1.50
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ATP C2 N3 C4 110.982 1.50
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ATP N9 C4 C5 107.666 1.69
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ATP N9 C4 N3 125.845 1.50
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ATP 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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ATP sp3_sp3_27 PB O3B PG O1G 60.000 10.0 3
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ATP sp3_sp3_40 "C4'" "C5'" "O5'" PA 180.000 10.0 3
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ATP sp3_sp3_43 "O4'" "C4'" "C5'" "O5'" 180.000 10.0 3
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ATP sp3_sp3_2 "C5'" "C4'" "O4'" "C1'" -60.000 10.0 3
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ATP sp3_sp3_56 "O3'" "C3'" "C4'" "C5'" 180.000 10.0 3
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ATP sp3_sp3_4 "C2'" "C1'" "O4'" "C4'" -60.000 10.0 3
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ATP sp3_sp3_61 "C4'" "C3'" "O3'" "HO3'" 180.000 10.0 3
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ATP sp3_sp3_20 "O2'" "C2'" "C3'" "O3'" -60.000 10.0 3
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ATP sp3_sp3_64 "C3'" "C2'" "O2'" "HO2'" 180.000 10.0 3
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ATP sp3_sp3_8 "O4'" "C1'" "C2'" "O2'" 180.000 10.0 3
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ATP sp2_sp3_1 C8 N9 "C1'" "O4'" 150.000 10.0 6
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ATP const_14 N7 C8 N9 "C1'" 180.000 10.0 2
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ATP const_26 C5 C4 N9 "C1'" 180.000 10.0 2
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ATP const_17 N9 C8 N7 C5 0.000 10.0 2
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ATP const_20 C6 C5 N7 C8 180.000 10.0 2
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ATP const_sp2_sp2_4 N7 C5 C6 N6 0.000 5.0 2
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ATP const_21 N9 C4 C5 N7 0.000 10.0 2
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ATP sp2_sp2_1 C5 C6 N6 HN61 180.000 5.0 2
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ATP const_sp2_sp2_6 N6 C6 N1 C2 180.000 5.0 2
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ATP const_sp2_sp2_7 N3 C2 N1 C6 0.000 5.0 2
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ATP const_sp2_sp2_9 N1 C2 N3 C4 0.000 5.0 2
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ATP const_12 N9 C4 N3 C2 180.000 10.0 2
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ATP sp3_sp3_33 PA O3A PB O1B 60.000 10.0 3
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ATP sp3_sp3_30 PG O3B PB O1B 60.000 10.0 3
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ATP sp3_sp3_36 PB O3A PA O1A 60.000 10.0 3
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ATP sp3_sp3_39 "C5'" "O5'" PA O1A 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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ATP chir_1 PG O3B O2G O3G both
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ATP chir_2 PB O3A O3B O2B both
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ATP chir_3 PA O3A "O5'" O2A both
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ATP chir_4 "C4'" "O4'" "C3'" "C5'" negative
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ATP chir_5 "C3'" "O3'" "C4'" "C2'" positive
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ATP chir_6 "C2'" "O2'" "C1'" "C3'" negative
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ATP chir_7 "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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ATP plan-1 "C1'" 0.020
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ATP plan-1 C2 0.020
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ATP plan-1 C4 0.020
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ATP plan-1 C5 0.020
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ATP plan-1 C6 0.020
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ATP plan-1 C8 0.020
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ATP plan-1 H2 0.020
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ATP plan-1 H8 0.020
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ATP plan-1 N1 0.020
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ATP plan-1 N3 0.020
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ATP plan-1 N6 0.020
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ATP plan-1 N7 0.020
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ATP plan-1 N9 0.020
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ATP plan-2 C6 0.020
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ATP plan-2 HN61 0.020
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ATP plan-2 HN62 0.020
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ATP 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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ATP SMILES ACDLabs 10.04 O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
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ATP SMILES_CANONICAL CACTVS 3.341 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
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ATP SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
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ATP 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)O[P@](=O)(O)OP(=O)(O)O)O)O)N
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ATP SMILES "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
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ATP InChI InChI 1.03 InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
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ATP InChIKey InChI 1.03 ZKHQWZAMYRWXGA-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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ATP acedrg 243 "dictionary generator"
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ATP acedrg_database 11 "data source"
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ATP rdkit 2017.03.2 "Chemoinformatics tool"
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ATP refmac5 5.8.0238 "optimization tool"
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