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)
215 lines
5.5 KiB
Plaintext
215 lines
5.5 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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ASN ASN ASPARAGINE peptide 17 9 .
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data_comp_ASN
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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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ASN N N NT3 1 14.911 16.808 19.868
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ASN CA C CH1 0 15.816 17.894 20.345
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ASN C C C 0 15.155 18.638 21.512
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ASN O O O 0 15.771 18.659 22.602
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ASN CB C CH2 0 16.178 18.868 19.226
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ASN CG C C 0 16.898 18.214 18.068
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ASN OD1 O O 0 17.108 16.995 18.059
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ASN ND2 N NH2 0 17.282 19.004 17.075
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ASN OXT O OC -1 14.046 19.172 21.292
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ASN H H H 0 14.283 17.146 19.316
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ASN H2 H H 0 14.499 16.402 20.561
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ASN H3 H H 0 15.385 16.183 19.422
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ASN HA H H 0 16.651 17.482 20.665
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ASN HB3 H H 0 16.746 19.574 19.593
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ASN HB2 H H 0 15.359 19.286 18.893
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ASN HD21 H H 0 16.894 19.794 16.957
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ASN HD22 H H 0 17.928 18.741 16.527
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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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ASN N n/a CA START
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ASN H N . .
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ASN H2 N . .
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ASN H3 N . .
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ASN CA N C .
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ASN HA CA . .
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ASN CB CA CG .
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ASN HB3 CB . .
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ASN HB2 CB . .
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ASN CG CB ND2 .
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ASN OD1 CG . .
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ASN ND2 CG HD22 .
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ASN HD21 ND2 . .
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ASN HD22 ND2 . .
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ASN C CA . END
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ASN O C . .
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ASN 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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ASN N N(CCCH)(H)3
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ASN CA C(CCHH)(NH3)(COO)(H)
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ASN C C(CCHN)(O)2
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ASN O O(CCO)
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ASN CB C(CCHN)(CNO)(H)2
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ASN CG C(CCHH)(NHH)(O)
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ASN OD1 O(CCN)
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ASN ND2 N(CCO)(H)2
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ASN OXT O(CCO)
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ASN H H(NCHH)
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ASN H2 H(NCHH)
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ASN H3 H(NCHH)
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ASN HA H(CCCN)
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ASN HB3 H(CCCH)
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ASN HB2 H(CCCH)
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ASN HD21 H(NCH)
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ASN HD22 H(NCH)
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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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ASN N CA SINGLE n 1.490 0.0100 1.490 0.0100
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ASN CA C SINGLE n 1.533 0.0100 1.533 0.0100
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ASN CA CB SINGLE n 1.525 0.0100 1.525 0.0100
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ASN C O DOUBLE n 1.251 0.0183 1.251 0.0183
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ASN C OXT SINGLE n 1.251 0.0183 1.251 0.0183
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ASN CB CG SINGLE n 1.510 0.0100 1.510 0.0100
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ASN CG OD1 DOUBLE n 1.236 0.0100 1.236 0.0100
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ASN CG ND2 SINGLE n 1.325 0.0100 1.325 0.0100
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ASN N H SINGLE n 1.018 0.0520 0.902 0.0102
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ASN N H2 SINGLE n 1.018 0.0520 0.902 0.0102
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ASN N H3 SINGLE n 1.018 0.0520 0.902 0.0102
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ASN CA HA SINGLE n 1.092 0.0100 0.984 0.0200
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ASN CB HB3 SINGLE n 1.092 0.0100 0.978 0.0143
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ASN CB HB2 SINGLE n 1.092 0.0100 0.978 0.0143
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ASN ND2 HD21 SINGLE n 1.013 0.0120 0.887 0.0200
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ASN ND2 HD22 SINGLE n 1.013 0.0120 0.887 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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ASN CA N H 109.990 3.00
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ASN CA N H2 109.990 3.00
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ASN CA N H3 109.990 3.00
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ASN H N H2 109.032 3.00
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ASN H N H3 109.032 3.00
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ASN H2 N H3 109.032 3.00
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ASN N CA C 109.258 1.50
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ASN N CA CB 111.558 1.50
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ASN N CA HA 108.387 1.58
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ASN C CA CB 111.904 3.00
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ASN C CA HA 108.774 1.79
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ASN CB CA HA 107.748 1.50
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ASN CA C O 117.148 1.60
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ASN CA C OXT 117.148 1.60
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ASN O C OXT 125.704 1.50
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ASN CA CB CG 112.193 1.50
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ASN CA CB HB3 109.177 1.50
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ASN CA CB HB2 109.177 1.50
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ASN CG CB HB3 109.132 1.50
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ASN CG CB HB2 109.132 1.50
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ASN HB3 CB HB2 108.039 1.50
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ASN CB CG OD1 120.239 1.50
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ASN CB CG ND2 117.180 1.62
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ASN OD1 CG ND2 122.581 1.50
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ASN CG ND2 HD21 119.917 2.87
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ASN CG ND2 HD22 119.917 2.87
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ASN HD21 ND2 HD22 120.165 3.00
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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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ASN chi1 N CA CB CG -60.000 10.0 3
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ASN chi2 CA CB CG ND2 180.000 10.0 6
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ASN hh1 CB CG ND2 HD22 180.000 5.0 2
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ASN sp3_sp3_1 C CA N H 180.000 10.0 3
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ASN 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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ASN 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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ASN plan-1 C 0.020
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ASN plan-1 CA 0.020
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ASN plan-1 O 0.020
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ASN plan-1 OXT 0.020
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ASN plan-2 CB 0.020
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ASN plan-2 CG 0.020
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ASN plan-2 ND2 0.020
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ASN plan-2 OD1 0.020
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ASN plan-3 CG 0.020
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ASN plan-3 HD21 0.020
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ASN plan-3 HD22 0.020
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ASN plan-3 ND2 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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ASN SMILES ACDLabs 12.01 O=C(N)CC(N)C(=O)O
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ASN InChI InChI 1.03 InChI=1S/C4H8N2O3/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H2,6,7)(H,8,9)/t2-/m0/s1
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ASN InChIKey InChI 1.03 DCXYFEDJOCDNAF-REOHCLBHSA-N
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ASN SMILES_CANONICAL CACTVS 3.370 N[C@@H](CC(N)=O)C(O)=O
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ASN SMILES CACTVS 3.370 N[CH](CC(N)=O)C(O)=O
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ASN SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 C([C@@H](C(=O)O)N)C(=O)N
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ASN SMILES "OpenEye OEToolkits" 1.7.2 C(C(C(=O)O)N)C(=O)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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ASN acedrg 278 "dictionary generator"
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ASN acedrg_database 12 "data source"
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ASN rdkit 2019.09.1 "Chemoinformatics tool"
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ASN refmac5 5.8.0419 "optimization tool"
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