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)
218 lines
5.6 KiB
Plaintext
218 lines
5.6 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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GLU GLU "GLUTAMIC ACID" peptide 18 10 .
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data_comp_GLU
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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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GLU N N NT3 1 88.319 -7.751 -10.089
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GLU CA C CH1 0 87.677 -7.162 -11.296
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GLU C C C 0 88.359 -5.826 -11.640
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GLU O O O 0 88.389 -4.954 -10.744
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GLU CB C CH2 0 86.177 -6.950 -11.080
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GLU CG C CH2 0 85.390 -8.247 -10.908
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GLU CD C C 0 83.891 -8.048 -10.773
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GLU OE1 O O 0 83.281 -7.495 -11.711
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GLU OE2 O OC -1 83.334 -8.447 -9.728
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GLU OXT O OC -1 88.836 -5.708 -12.790
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GLU H H H 0 88.066 -7.298 -9.352
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GLU H2 H H 0 89.218 -7.717 -10.158
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GLU H3 H H 0 88.077 -8.615 -9.999
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GLU HA H H 0 87.806 -7.788 -12.054
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GLU HB3 H H 0 85.814 -6.460 -11.847
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GLU HB2 H H 0 86.049 -6.394 -10.284
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GLU HG3 H H 0 85.714 -8.714 -10.110
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GLU HG2 H H 0 85.559 -8.827 -11.681
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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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GLU N n/a CA START
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GLU H N . .
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GLU H2 N . .
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GLU H3 N . .
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GLU CA N C .
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GLU HA CA . .
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GLU CB CA CG .
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GLU HB3 CB . .
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GLU HB2 CB . .
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GLU CG CB CD .
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GLU HG3 CG . .
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GLU HG2 CG . .
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GLU CD CG OE2 .
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GLU OE1 CD . .
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GLU OE2 CD . .
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GLU C CA . END
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GLU O C . .
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GLU 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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GLU N N(CCCH)(H)3
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GLU CA C(CCHH)(NH3)(COO)(H)
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GLU C C(CCHN)(O)2
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GLU O O(CCO)
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GLU CB C(CCHH)(CCHN)(H)2
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GLU CG C(CCHH)(COO)(H)2
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GLU CD C(CCHH)(O)2
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GLU OE1 O(CCO)
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GLU OE2 O(CCO)
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GLU OXT O(CCO)
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GLU H H(NCHH)
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GLU H2 H(NCHH)
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GLU H3 H(NCHH)
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GLU HA H(CCCN)
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GLU HB3 H(CCCH)
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GLU HB2 H(CCCH)
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GLU HG3 H(CCCH)
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GLU HG2 H(CCCH)
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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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GLU N CA SINGLE n 1.487 0.0100 1.487 0.0100
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GLU CA C SINGLE n 1.538 0.0113 1.538 0.0113
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GLU CA CB SINGLE n 1.529 0.0100 1.529 0.0100
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GLU C O DOUBLE n 1.251 0.0183 1.251 0.0183
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GLU C OXT SINGLE n 1.251 0.0183 1.251 0.0183
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GLU CB CG SINGLE n 1.526 0.0100 1.526 0.0100
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GLU CG CD SINGLE n 1.518 0.0135 1.518 0.0135
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GLU CD OE1 DOUBLE n 1.249 0.0161 1.249 0.0161
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GLU CD OE2 SINGLE n 1.249 0.0161 1.249 0.0161
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GLU N H SINGLE n 1.018 0.0520 0.902 0.0102
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GLU N H2 SINGLE n 1.018 0.0520 0.902 0.0102
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GLU N H3 SINGLE n 1.018 0.0520 0.902 0.0102
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GLU CA HA SINGLE n 1.092 0.0100 0.991 0.0200
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GLU CB HB3 SINGLE n 1.092 0.0100 0.980 0.0168
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GLU CB HB2 SINGLE n 1.092 0.0100 0.980 0.0168
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GLU CG HG3 SINGLE n 1.092 0.0100 0.981 0.0172
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GLU CG HG2 SINGLE n 1.092 0.0100 0.981 0.0172
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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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GLU CA N H 109.990 3.00
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GLU CA N H2 109.990 3.00
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GLU CA N H3 109.990 3.00
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GLU H N H2 109.032 3.00
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GLU H N H3 109.032 3.00
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GLU H2 N H3 109.032 3.00
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GLU N CA C 109.258 1.50
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GLU N CA CB 110.440 2.46
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GLU N CA HA 108.387 1.58
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GLU C CA CB 111.059 3.00
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GLU C CA HA 108.774 1.79
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GLU CB CA HA 109.080 2.33
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GLU CA C O 117.148 1.60
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GLU CA C OXT 117.148 1.60
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GLU O C OXT 125.704 1.50
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GLU CA CB CG 113.294 1.61
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GLU CA CB HB3 108.677 1.74
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GLU CA CB HB2 108.677 1.74
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GLU CG CB HB3 108.696 2.80
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GLU CG CB HB2 108.696 2.80
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GLU HB3 CB HB2 107.655 1.50
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GLU CB CG CD 114.140 3.00
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GLU CB CG HG3 108.968 1.50
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GLU CB CG HG2 108.968 1.50
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GLU CD CG HG3 108.472 1.50
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GLU CD CG HG2 108.472 1.50
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GLU HG3 CG HG2 107.541 1.92
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GLU CG CD OE1 118.251 3.00
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GLU CG CD OE2 118.251 3.00
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GLU OE1 CD OE2 123.498 1.82
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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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GLU chi1 N CA CB CG -60.000 10.0 3
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GLU chi2 CA CB CG CD 180.000 10.0 3
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GLU chi3 CB CG CD OE1 180.000 10.0 6
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GLU sp3_sp3_1 C CA N H 180.000 10.0 3
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GLU 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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GLU chir_1 CA N C CB positive
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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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GLU plan-1 C 0.020
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GLU plan-1 CA 0.020
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GLU plan-1 O 0.020
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GLU plan-1 OXT 0.020
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GLU plan-2 CD 0.020
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GLU plan-2 CG 0.020
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GLU plan-2 OE1 0.020
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GLU plan-2 OE2 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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GLU SMILES ACDLabs 12.01 O=C(O)C(N)CCC(=O)O
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GLU SMILES_CANONICAL CACTVS 3.370 N[C@@H](CCC(O)=O)C(O)=O
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GLU SMILES CACTVS 3.370 N[CH](CCC(O)=O)C(O)=O
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GLU SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 C(CC(=O)O)[C@@H](C(=O)O)N
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GLU SMILES "OpenEye OEToolkits" 1.7.0 C(CC(=O)O)C(C(=O)O)N
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GLU InChI InChI 1.03 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/t3-/m0/s1
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GLU InChIKey InChI 1.03 WHUUTDBJXJRKMK-VKHMYHEASA-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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GLU acedrg 278 "dictionary generator"
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GLU acedrg_database 12 "data source"
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GLU rdkit 2019.09.1 "Chemoinformatics tool"
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GLU refmac5 5.8.0419 "optimization tool"
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