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)
267 lines
16 KiB
Plaintext
267 lines
16 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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DA DA "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" DNA 34 22 .
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#
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data_comp_DA
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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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DA OP3 O OP -1 -6.497 8.522 9.951
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DA P P P 0 -5.346 9.062 9.122
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DA OP1 O O 0 -4.898 10.441 9.565
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DA OP2 O OP -1 -5.605 8.977 7.630
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DA "O5'" O O2 0 -4.097 8.080 9.408
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DA "C5'" C CH2 0 -3.640 7.912 10.774
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DA "C4'" C CH1 0 -2.470 6.958 10.801
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DA "O4'" O O2 0 -2.888 5.686 10.260
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DA "C3'" C CH1 0 -1.251 7.408 9.993
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DA "O3'" O OH1 0 -0.049 7.159 10.716
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DA "C2'" C CH2 0 -1.324 6.542 8.739
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DA "C1'" C CH1 0 -1.962 5.267 9.263
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DA N9 N NR5 0 -2.687 4.489 8.258
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DA C8 C CR15 0 -3.753 4.911 7.501
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DA N7 N NRD5 0 -4.206 3.997 6.680
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DA C5 C CR56 0 -3.393 2.896 6.907
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DA C6 C CR6 0 -3.368 1.602 6.342
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DA N6 N NH2 0 -4.214 1.192 5.400
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DA N1 N NRD6 0 -2.423 0.736 6.793
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DA C2 C CR16 0 -1.573 1.156 7.744
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DA N3 N NRD6 0 -1.504 2.345 8.344
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DA C4 C CR56 0 -2.450 3.184 7.880
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DA "H5'" H H 0 -4.373 7.554 11.332
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DA "H5''" H H 0 -3.363 8.786 11.145
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DA "H4'" H H 0 -2.203 6.829 11.743
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DA "H3'" H H 0 -1.322 8.365 9.759
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DA "HO3'" H H 0 0.583 7.601 10.361
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DA "H2'" H H 0 -0.433 6.369 8.376
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DA "H2''" H H 0 -1.875 6.962 8.051
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DA "H1'" H H 0 -1.264 4.700 9.685
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DA H8 H H 0 -4.120 5.776 7.565
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DA H61 H H 0 -4.304 0.334 5.236
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DA H62 H H 0 -4.679 1.782 4.946
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DA H2 H H 0 -0.933 0.520 8.026
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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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DA OP3 P SINGLE n 1.517 0.0192 1.517 0.0192
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DA P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192
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DA P OP2 SINGLE n 1.517 0.0192 1.517 0.0192
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DA P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178
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DA "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166
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DA "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100
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DA "C4'" "O4'" SINGLE n 1.442 0.0100 1.442 0.0100
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DA "C4'" "C3'" SINGLE n 1.526 0.0115 1.526 0.0115
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DA "O4'" "C1'" SINGLE n 1.425 0.0100 1.425 0.0100
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DA "C3'" "O3'" SINGLE n 1.424 0.0100 1.424 0.0100
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DA "C3'" "C2'" SINGLE n 1.526 0.0101 1.526 0.0101
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DA "C2'" "C1'" SINGLE n 1.521 0.0118 1.521 0.0118
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DA "C1'" N9 SINGLE n 1.462 0.0111 1.462 0.0111
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DA N9 C8 SINGLE y 1.373 0.0100 1.373 0.0100
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DA N9 C4 SINGLE y 1.377 0.0100 1.377 0.0100
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DA C8 N7 DOUBLE y 1.310 0.0100 1.310 0.0100
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DA N7 C5 SINGLE y 1.388 0.0100 1.388 0.0100
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DA C5 C6 SINGLE y 1.408 0.0100 1.408 0.0100
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DA C5 C4 DOUBLE y 1.381 0.0100 1.381 0.0100
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DA C6 N6 SINGLE n 1.330 0.0100 1.330 0.0100
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DA C6 N1 DOUBLE y 1.354 0.0100 1.354 0.0100
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DA N1 C2 SINGLE y 1.339 0.0100 1.339 0.0100
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DA C2 N3 DOUBLE y 1.330 0.0100 1.330 0.0100
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DA N3 C4 SINGLE y 1.343 0.0100 1.343 0.0100
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DA "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200
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DA "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200
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DA "C4'" "H4'" SINGLE n 1.089 0.0100 0.987 0.0170
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DA "C3'" "H3'" SINGLE n 1.089 0.0100 0.988 0.0189
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DA "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
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DA "C2'" "H2'" SINGLE n 1.089 0.0100 0.977 0.0113
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DA "C2'" "H2''" SINGLE n 1.089 0.0100 0.977 0.0113
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DA "C1'" "H1'" SINGLE n 1.089 0.0100 0.993 0.0101
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DA C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170
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DA N6 H61 SINGLE n 1.016 0.0100 0.877 0.0200
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DA N6 H62 SINGLE n 1.016 0.0100 0.877 0.0200
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DA 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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DA OP3 P OP1 112.864 1.69
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DA OP3 P OP2 112.864 1.69
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DA OP3 P "O5'" 105.808 2.07
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DA OP1 P OP2 112.864 1.69
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DA OP1 P "O5'" 105.808 2.07
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DA OP2 P "O5'" 105.808 2.07
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DA P "O5'" "C5'" 118.783 1.50
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DA "O5'" "C5'" "C4'" 109.342 1.50
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DA "O5'" "C5'" "H5'" 109.845 1.50
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DA "O5'" "C5'" "H5''" 109.845 1.50
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DA "C4'" "C5'" "H5'" 109.624 1.50
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DA "C4'" "C5'" "H5''" 109.624 1.50
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DA "H5'" "C5'" "H5''" 108.472 1.50
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DA "C5'" "C4'" "O4'" 109.123 1.50
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DA "C5'" "C4'" "C3'" 114.866 1.63
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DA "C5'" "C4'" "H4'" 108.268 1.50
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DA "O4'" "C4'" "C3'" 105.506 1.50
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DA "O4'" "C4'" "H4'" 108.947 1.50
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DA "C3'" "C4'" "H4'" 109.069 1.50
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DA "C4'" "O4'" "C1'" 108.795 1.50
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DA "C4'" "C3'" "O3'" 110.527 2.37
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DA "C4'" "C3'" "C2'" 102.433 1.50
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DA "C4'" "C3'" "H3'" 110.775 1.50
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DA "O3'" "C3'" "C2'" 111.424 1.96
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DA "O3'" "C3'" "H3'" 110.713 1.50
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DA "C2'" "C3'" "H3'" 110.846 1.50
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DA "C3'" "O3'" "HO3'" 109.026 2.38
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DA "C3'" "C2'" "C1'" 102.663 1.50
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DA "C3'" "C2'" "H2'" 111.194 1.50
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DA "C3'" "C2'" "H2''" 111.194 1.50
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DA "C1'" "C2'" "H2'" 111.213 1.50
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DA "C1'" "C2'" "H2''" 111.213 1.50
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DA "H2'" "C2'" "H2''" 109.148 1.50
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DA "O4'" "C1'" "C2'" 106.035 1.50
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DA "O4'" "C1'" N9 108.236 1.50
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DA "O4'" "C1'" "H1'" 109.059 1.50
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DA "C2'" "C1'" N9 114.190 1.67
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DA "C2'" "C1'" "H1'" 109.272 1.50
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DA N9 "C1'" "H1'" 109.282 1.50
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DA "C1'" N9 C8 127.636 2.81
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DA "C1'" N9 C4 126.671 2.93
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DA C8 N9 C4 105.693 1.50
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DA N9 C8 N7 113.469 1.50
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DA N9 C8 H8 123.206 1.50
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DA N7 C8 H8 123.326 1.50
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DA C8 N7 C5 104.739 1.50
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DA N7 C5 C6 132.250 1.50
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DA N7 C5 C4 110.483 1.50
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DA C6 C5 C4 117.267 1.50
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DA C5 C6 N6 123.792 1.50
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DA C5 C6 N1 117.409 1.50
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DA N6 C6 N1 118.799 1.50
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DA C6 N6 H61 119.723 1.50
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DA C6 N6 H62 119.723 1.50
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DA H61 N6 H62 120.554 1.88
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DA C6 N1 C2 118.521 1.50
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DA N1 C2 N3 129.332 1.50
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DA N1 C2 H2 115.313 1.50
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DA N3 C2 H2 115.355 1.50
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DA C2 N3 C4 110.982 1.50
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DA N9 C4 C5 105.616 1.50
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DA N9 C4 N3 127.895 1.50
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DA 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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DA C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6
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DA C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1
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DA C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1
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DA C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1
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DA C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1
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DA C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1
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DA C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6
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DA C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1
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DA C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1
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DA C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1
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DA C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1
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DA C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1
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DA alpha "C5'" "O5'" P OP3 -60.000 10.00 3
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DA beta P "O5'" "C5'" "C4'" 180.000 10.00 3
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DA epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3
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DA gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3
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DA const_14 N7 C8 N9 "C1'" 180.000 10.0 2
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DA const_26 C5 C4 N9 "C1'" 180.000 10.0 2
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DA const_17 N9 C8 N7 C5 0.000 10.0 2
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DA const_20 C6 C5 N7 C8 180.000 10.0 2
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DA const_sp2_sp2_4 N7 C5 C6 N6 0.000 5.0 2
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DA const_21 N9 C4 C5 N7 0.000 10.0 2
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DA sp2_sp2_1 C5 C6 N6 H61 180.000 5.0 2
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DA const_sp2_sp2_6 N6 C6 N1 C2 180.000 5.0 2
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DA const_sp2_sp2_7 N3 C2 N1 C6 0.000 5.0 2
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DA const_sp2_sp2_9 N1 C2 N3 C4 0.000 5.0 2
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DA const_12 N9 C4 N3 C2 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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DA chir_1 P "O5'" OP3 OP2 both
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DA chir_2 "C4'" "O4'" "C3'" "C5'" negative
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DA chir_3 "C3'" "O3'" "C4'" "C2'" positive
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DA 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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DA plan-1 "C1'" 0.020
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DA plan-1 C2 0.020
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DA plan-1 C4 0.020
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DA plan-1 C5 0.020
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DA plan-1 C6 0.020
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DA plan-1 C8 0.020
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DA plan-1 H2 0.020
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DA plan-1 H8 0.020
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DA plan-1 N1 0.020
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DA plan-1 N3 0.020
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DA plan-1 N6 0.020
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DA plan-1 N7 0.020
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DA plan-1 N9 0.020
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DA plan-2 C6 0.020
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DA plan-2 H61 0.020
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DA plan-2 H62 0.020
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DA 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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DA SMILES ACDLabs 10.04 O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
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DA SMILES_CANONICAL CACTVS 3.341 Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3
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DA SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3
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DA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N
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DA SMILES "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)O)O)N
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DA InChI InChI 1.03 InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
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DA InChIKey InChI 1.03 KHWCHTKSEGGWEX-RRKCRQDMSA-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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DA acedrg 243 "dictionary generator"
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DA acedrg_database 11 "data source"
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DA rdkit 2017.03.2 "Chemoinformatics tool"
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DA refmac5 5.8.0238 "optimization tool"
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