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)
256 lines
15 KiB
Plaintext
256 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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C C "CYTIDINE-5'-MONOPHOSPHATE" RNA 33 21 .
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#
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data_comp_C
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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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C OP3 O OP -1 26.264 21.286 -11.211
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C P P P 0 27.065 20.768 -12.391
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C OP1 O O 0 26.731 21.481 -13.688
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C OP2 O OP -1 27.015 19.258 -12.520
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C "O5'" O O2 0 28.604 21.132 -12.071
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C "C5'" C CH2 0 28.962 22.520 -11.845
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C "C4'" C CH1 0 30.463 22.648 -11.735
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C "O4'" O O2 0 30.967 21.749 -10.719
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C "C3'" C CH1 0 31.273 22.268 -12.980
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C "O3'" O OH1 0 31.285 23.333 -13.923
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C "C2'" C CH1 0 32.660 21.973 -12.387
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C "O2'" O OH1 0 33.494 23.113 -12.311
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C "C1'" C CH1 0 32.329 21.476 -10.970
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C N1 N NR6 0 32.565 20.011 -10.805
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C C2 C CR6 0 33.589 19.539 -9.963
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C O2 O O 0 34.302 20.347 -9.344
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C N3 N NRD6 0 33.778 18.197 -9.840
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C C4 C CR6 0 33.005 17.329 -10.512
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C N4 N NH2 0 33.237 16.032 -10.352
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C C5 C CR16 0 31.965 17.787 -11.373
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C C6 C CR16 0 31.786 19.115 -11.490
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C "H5'" H H 0 28.541 22.842 -11.010
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C "H5''" H H 0 28.636 23.077 -12.594
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C "H4'" H H 0 30.676 23.570 -11.475
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C "H3'" H H 0 30.904 21.447 -13.396
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C "HO3'" H H 0 31.819 23.134 -14.553
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C "H2'" H H 0 33.101 21.267 -12.901
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C "HO2'" H H 0 33.087 23.744 -11.913
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C "H1'" H H 0 32.871 21.976 -10.317
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C H41 H H 0 33.920 15.764 -9.869
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C H42 H H 0 32.707 15.443 -10.731
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C H5 H H 0 31.420 17.183 -11.847
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C H6 H H 0 31.112 19.446 -12.046
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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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C OP3 P SINGLE n 1.517 0.0192 1.517 0.0192
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C P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192
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C P OP2 SINGLE n 1.517 0.0192 1.517 0.0192
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C P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178
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C "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166
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C "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100
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C "C4'" "O4'" SINGLE n 1.451 0.0111 1.451 0.0111
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C "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100
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C "O4'" "C1'" SINGLE n 1.411 0.0100 1.411 0.0100
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C "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100
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C "C3'" "C2'" SINGLE n 1.533 0.0109 1.533 0.0109
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C "C2'" "O2'" SINGLE n 1.412 0.0100 1.412 0.0100
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C "C2'" "C1'" SINGLE n 1.532 0.0100 1.532 0.0100
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C "C1'" N1 SINGLE n 1.487 0.0100 1.487 0.0100
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C N1 C2 SINGLE y 1.397 0.0100 1.397 0.0100
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C N1 C6 SINGLE y 1.364 0.0108 1.364 0.0108
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C C2 O2 DOUBLE n 1.241 0.0100 1.241 0.0100
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C C2 N3 SINGLE y 1.355 0.0119 1.355 0.0119
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C N3 C4 DOUBLE y 1.339 0.0110 1.339 0.0110
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C C4 N4 SINGLE n 1.325 0.0109 1.325 0.0109
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C C4 C5 SINGLE y 1.422 0.0123 1.422 0.0123
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C C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100
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C "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200
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C "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200
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C "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200
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C "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200
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C "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
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C "C2'" "H2'" SINGLE n 1.089 0.0100 0.978 0.0200
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C "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200
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C "C1'" "H1'" SINGLE n 1.089 0.0100 0.985 0.0100
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C N4 H41 SINGLE n 1.016 0.0100 0.877 0.0200
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C N4 H42 SINGLE n 1.016 0.0100 0.877 0.0200
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C C5 H5 SINGLE n 1.082 0.0130 0.941 0.0174
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C C6 H6 SINGLE n 1.082 0.0130 0.935 0.0143
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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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C OP3 P OP1 112.864 1.69
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C OP3 P OP2 112.864 1.69
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C OP3 P "O5'" 105.808 2.07
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C OP1 P OP2 112.864 1.69
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C OP1 P "O5'" 105.808 2.07
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C OP2 P "O5'" 105.808 2.07
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C P "O5'" "C5'" 118.783 1.50
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C "O5'" "C5'" "C4'" 109.342 1.50
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C "O5'" "C5'" "H5'" 109.845 1.50
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C "O5'" "C5'" "H5''" 109.845 1.50
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C "C4'" "C5'" "H5'" 109.624 1.50
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C "C4'" "C5'" "H5''" 109.624 1.50
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C "H5'" "C5'" "H5''" 108.472 1.50
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C "C5'" "C4'" "O4'" 109.615 1.50
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C "C5'" "C4'" "C3'" 116.008 1.52
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C "C5'" "C4'" "H4'" 108.268 1.50
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C "O4'" "C4'" "C3'" 104.439 1.50
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C "O4'" "C4'" "H4'" 108.698 1.50
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C "C3'" "C4'" "H4'" 109.363 1.86
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C "C4'" "O4'" "C1'" 109.578 1.50
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C "C4'" "C3'" "O3'" 111.281 2.46
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C "C4'" "C3'" "C2'" 102.071 1.50
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C "C4'" "C3'" "H3'" 110.452 2.54
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C "O3'" "C3'" "C2'" 111.993 3.00
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C "O3'" "C3'" "H3'" 110.380 1.67
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C "C2'" "C3'" "H3'" 110.108 1.66
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C "C3'" "O3'" "HO3'" 108.744 3.00
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C "C3'" "C2'" "O2'" 112.861 2.52
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C "C3'" "C2'" "C1'" 101.269 1.50
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C "C3'" "C2'" "H2'" 110.799 1.82
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C "O2'" "C2'" "C1'" 109.476 3.00
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C "O2'" "C2'" "H2'" 111.022 1.77
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C "C1'" "C2'" "H2'" 110.760 1.63
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C "C2'" "O2'" "HO2'" 109.449 1.85
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C "O4'" "C1'" "C2'" 106.825 1.50
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C "O4'" "C1'" N1 108.667 1.50
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C "O4'" "C1'" "H1'" 109.327 1.50
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C "C2'" "C1'" N1 112.859 1.50
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C "C2'" "C1'" "H1'" 109.776 1.83
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C N1 "C1'" "H1'" 109.166 1.50
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C "C1'" N1 C2 118.189 2.26
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C "C1'" N1 C6 121.301 1.52
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C C2 N1 C6 120.510 1.50
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C N1 C2 O2 118.710 1.50
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C N1 C2 N3 118.927 1.50
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C O2 C2 N3 122.370 1.50
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C C2 N3 C4 120.266 1.50
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C N3 C4 N4 117.855 1.50
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C N3 C4 C5 121.269 1.50
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C N4 C4 C5 120.876 1.50
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C C4 N4 H41 119.818 1.59
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C C4 N4 H42 119.818 1.59
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C H41 N4 H42 120.363 1.85
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C C4 C5 C6 117.808 1.50
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C C4 C5 H5 121.350 1.50
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C C6 C5 H5 120.848 1.50
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C N1 C6 C5 121.215 1.50
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C N1 C6 H6 118.510 1.50
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C C5 C6 H6 120.275 1.75
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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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C C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6
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C C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1
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C C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1
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C C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1
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C C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1
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C C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1
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C C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6
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C C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1
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C C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1
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C C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1
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C C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1
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C C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1
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C alpha "C5'" "O5'" P OP3 -60.000 10.00 3
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C beta P "O5'" "C5'" "C4'" 180.000 10.00 3
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C epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3
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C gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3
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C sp3_sp3_52 "C3'" "C2'" "O2'" "HO2'" 180.000 10.00 3
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C const_sp2_sp2_4 O2 C2 N1 "C1'" 0.000 5.0 2
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C const_18 C5 C6 N1 "C1'" 180.000 10.0 2
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C const_sp2_sp2_6 O2 C2 N3 C4 180.000 5.0 2
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C const_sp2_sp2_8 N4 C4 N3 C2 180.000 5.0 2
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C sp2_sp2_3 N3 C4 N4 H41 0.000 5.0 2
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C const_11 N4 C4 C5 C6 180.000 10.0 2
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C const_13 C4 C5 C6 N1 0.000 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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C chir_1 P "O5'" OP3 OP2 both
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C chir_2 "C4'" "O4'" "C3'" "C5'" negative
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C chir_3 "C3'" "O3'" "C4'" "C2'" positive
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C chir_4 "C2'" "O2'" "C1'" "C3'" negative
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C chir_5 "C1'" "O4'" N1 "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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C plan-1 "C1'" 0.020
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C plan-1 C2 0.020
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C plan-1 C4 0.020
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C plan-1 C5 0.020
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C plan-1 C6 0.020
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C plan-1 H5 0.020
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C plan-1 H6 0.020
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C plan-1 N1 0.020
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C plan-1 N3 0.020
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C plan-1 N4 0.020
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C plan-1 O2 0.020
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C plan-2 C4 0.020
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C plan-2 H41 0.020
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C plan-2 H42 0.020
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C plan-2 N4 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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C SMILES ACDLabs 10.04 O=C1N=C(N)C=CN1C2OC(C(O)C2O)COP(=O)(O)O
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C SMILES_CANONICAL CACTVS 3.341 NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
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C SMILES CACTVS 3.341 NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
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C SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
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C SMILES "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O
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C InChI InChI 1.03 InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
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C InChIKey InChI 1.03 IERHLVCPSMICTF-XVFCMESISA-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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C acedrg 243 "dictionary generator"
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C acedrg_database 11 "data source"
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C rdkit 2017.03.2 "Chemoinformatics tool"
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C refmac5 5.8.0238 "optimization tool"
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