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)
222 lines
5.7 KiB
Plaintext
222 lines
5.7 KiB
Plaintext
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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VAL VAL VALINE peptide 19 8 .
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data_comp_VAL
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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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VAL N N NT3 1 11.307 2.990 48.522
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VAL CA C CH1 0 10.346 4.137 48.590
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VAL C C C 0 9.715 4.163 49.994
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VAL O O O 0 9.179 3.107 50.398
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VAL CB C CH1 0 9.259 4.073 47.494
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VAL CG1 C CH3 0 8.396 5.334 47.475
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VAL CG2 C CH3 0 9.849 3.802 46.112
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VAL OXT O OC -1 9.782 5.237 50.630
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VAL H H H 0 11.930 3.145 47.888
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VAL H2 H H 0 10.867 2.229 48.319
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VAL H3 H H 0 11.735 2.877 49.308
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VAL HA H H 0 10.853 4.963 48.468
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VAL HB H H 0 8.670 3.315 47.717
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VAL HG11 H H 0 8.964 6.117 47.567
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VAL HG12 H H 0 7.763 5.306 48.212
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VAL HG13 H H 0 7.907 5.387 46.637
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VAL HG21 H H 0 10.555 4.444 45.928
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VAL HG22 H H 0 9.155 3.884 45.436
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VAL HG23 H H 0 10.217 2.902 46.084
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loop_
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_chem_comp_tree.comp_id
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_chem_comp_tree.atom_id
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_chem_comp_tree.atom_back
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_chem_comp_tree.atom_forward
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_chem_comp_tree.connect_type
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VAL N n/a CA START
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VAL H N . .
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VAL H2 N . .
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VAL H3 N . .
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VAL CA N C .
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VAL HA CA . .
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VAL CB CA CG2 .
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VAL HB CB . .
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VAL CG1 CB HG13 .
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VAL HG11 CG1 . .
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VAL HG12 CG1 . .
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VAL HG13 CG1 . .
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VAL CG2 CB HG23 .
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VAL HG21 CG2 . .
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VAL HG22 CG2 . .
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VAL HG23 CG2 . .
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VAL C CA . END
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VAL O C . .
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VAL OXT C . .
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loop_
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_chem_comp_acedrg.comp_id
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_chem_comp_acedrg.atom_id
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_chem_comp_acedrg.atom_type
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VAL N N(CCCH)(H)3
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VAL CA C(CCCH)(NH3)(COO)(H)
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VAL C C(CCHN)(O)2
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VAL O O(CCO)
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VAL CB C(CCHN)(CH3)2(H)
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VAL CG1 C(CCCH)(H)3
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VAL CG2 C(CCCH)(H)3
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VAL OXT O(CCO)
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VAL H H(NCHH)
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VAL H2 H(NCHH)
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VAL H3 H(NCHH)
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VAL HA H(CCCN)
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VAL HB H(CC3)
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VAL HG11 H(CCHH)
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VAL HG12 H(CCHH)
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VAL HG13 H(CCHH)
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VAL HG21 H(CCHH)
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VAL HG22 H(CCHH)
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VAL HG23 H(CCHH)
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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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VAL N CA SINGLE n 1.495 0.0100 1.495 0.0100
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VAL CA C SINGLE n 1.538 0.0100 1.538 0.0100
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VAL CA CB SINGLE n 1.541 0.0101 1.541 0.0101
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VAL C O DOUBLE n 1.251 0.0183 1.251 0.0183
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VAL C OXT SINGLE n 1.251 0.0183 1.251 0.0183
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VAL CB CG1 SINGLE n 1.524 0.0131 1.524 0.0131
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VAL CB CG2 SINGLE n 1.524 0.0131 1.524 0.0131
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VAL N H SINGLE n 1.018 0.0520 0.902 0.0102
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VAL N H2 SINGLE n 1.018 0.0520 0.902 0.0102
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VAL N H3 SINGLE n 1.018 0.0520 0.902 0.0102
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VAL CA HA SINGLE n 1.092 0.0100 0.977 0.0200
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VAL CB HB SINGLE n 1.092 0.0100 0.986 0.0184
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VAL CG1 HG11 SINGLE n 1.092 0.0100 0.972 0.0156
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VAL CG1 HG12 SINGLE n 1.092 0.0100 0.972 0.0156
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VAL CG1 HG13 SINGLE n 1.092 0.0100 0.972 0.0156
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VAL CG2 HG21 SINGLE n 1.092 0.0100 0.972 0.0156
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VAL CG2 HG22 SINGLE n 1.092 0.0100 0.972 0.0156
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VAL CG2 HG23 SINGLE n 1.092 0.0100 0.972 0.0156
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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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VAL CA N H 109.990 2.80
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VAL CA N H2 109.990 2.80
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VAL CA N H3 109.990 2.80
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VAL H N H2 109.032 3.00
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VAL H N H3 109.032 3.00
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VAL H2 N H3 109.032 3.00
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VAL N CA C 108.738 1.50
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VAL N CA CB 111.627 2.88
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VAL N CA HA 108.328 1.50
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VAL C CA CB 111.231 1.50
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VAL C CA HA 108.550 1.50
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VAL CB CA HA 108.536 1.50
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VAL CA C O 117.155 1.50
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VAL CA C OXT 117.155 1.50
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VAL O C OXT 125.690 1.50
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VAL CA CB CG1 111.834 1.50
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VAL CA CB CG2 111.834 1.50
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VAL CA CB HB 107.069 1.50
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VAL CG1 CB CG2 110.700 1.76
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VAL CG1 CB HB 107.681 2.06
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VAL CG2 CB HB 107.681 2.06
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VAL CB CG1 HG11 109.510 1.50
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VAL CB CG1 HG12 109.510 1.50
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VAL CB CG1 HG13 109.510 1.50
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VAL HG11 CG1 HG12 109.390 1.50
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VAL HG11 CG1 HG13 109.390 1.50
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VAL HG12 CG1 HG13 109.390 1.50
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VAL CB CG2 HG21 109.510 1.50
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VAL CB CG2 HG22 109.510 1.50
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VAL CB CG2 HG23 109.510 1.50
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VAL HG21 CG2 HG22 109.390 1.50
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VAL HG21 CG2 HG23 109.390 1.50
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VAL HG22 CG2 HG23 109.390 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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VAL chi1 N CA CB CG2 -60.000 10.0 3
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VAL hh1 CA CB CG1 HG13 180.000 10.0 3
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VAL hh2 CA CB CG2 HG23 -60.000 10.0 3
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VAL sp3_sp3_1 C CA N H 180.000 10.0 3
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VAL sp2_sp3_1 O C CA N 0.000 10.0 6
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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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VAL chir_1 CA N C CB positive
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VAL chir_2 CB CA CG1 CG2 both
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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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VAL plan-1 C 0.020
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VAL plan-1 CA 0.020
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VAL plan-1 O 0.020
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VAL plan-1 OXT 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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VAL SMILES ACDLabs 10.04 O=C(O)C(N)C(C)C
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VAL SMILES_CANONICAL CACTVS 3.341 CC(C)[C@H](N)C(O)=O
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VAL SMILES CACTVS 3.341 CC(C)[CH](N)C(O)=O
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VAL SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC(C)[C@@H](C(=O)O)N
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VAL SMILES "OpenEye OEToolkits" 1.5.0 CC(C)C(C(=O)O)N
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VAL InChI InChI 1.03 InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1
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VAL InChIKey InChI 1.03 KZSNJWFQEVHDMF-BYPYZUCNSA-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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VAL acedrg 278 "dictionary generator"
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VAL acedrg_database 12 "data source"
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VAL rdkit 2019.09.1 "Chemoinformatics tool"
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VAL refmac5 5.8.0419 "optimization tool"
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