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)
199 lines
5.1 KiB
Plaintext
199 lines
5.1 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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ASP ASP "ASPARTIC ACID" peptide 15 9 .
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data_comp_ASP
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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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ASP N N NT3 1 33.542 17.835 39.145
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ASP CA C CH1 0 34.991 17.614 38.867
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ASP C C C 0 35.178 17.161 37.413
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ASP O O O 0 36.268 17.442 36.867
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ASP CB C CH2 0 35.617 16.650 39.866
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ASP CG C C 0 34.932 15.299 40.037
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ASP OD1 O O 0 35.515 14.435 40.725
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ASP OD2 O OC -1 33.817 15.122 39.501
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ASP OXT O OC -1 34.232 16.542 36.875
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ASP H H H 0 33.408 17.940 40.031
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ASP H2 H H 0 33.045 17.139 38.857
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ASP H3 H H 0 33.263 18.581 38.722
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ASP HA H H 0 35.453 18.476 38.978
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ASP HB3 H H 0 35.641 17.087 40.742
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ASP HB2 H H 0 36.543 16.483 39.592
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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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ASP N n/a CA START
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ASP H N . .
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ASP H2 N . .
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ASP H3 N . .
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ASP CA N C .
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ASP HA CA . .
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ASP CB CA CG .
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ASP HB3 CB . .
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ASP HB2 CB . .
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ASP CG CB OD2 .
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ASP OD1 CG . .
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ASP OD2 CG . .
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ASP C CA . END
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ASP O C . .
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ASP 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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ASP N N(CCCH)(H)3
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ASP CA C(CCHH)(NH3)(COO)(H)
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ASP C C(CCHN)(O)2
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ASP O O(CCO)
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ASP CB C(CCHN)(COO)(H)2
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ASP CG C(CCHH)(O)2
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ASP OD1 O(CCO)
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ASP OD2 O(CCO)
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ASP OXT O(CCO)
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ASP H H(NCHH)
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ASP H2 H(NCHH)
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ASP H3 H(NCHH)
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ASP HA H(CCCN)
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ASP HB3 H(CCCH)
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ASP HB2 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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ASP N CA SINGLE n 1.490 0.0100 1.490 0.0100
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ASP CA C SINGLE n 1.533 0.0100 1.533 0.0100
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ASP CA CB SINGLE n 1.521 0.0100 1.521 0.0100
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ASP C O DOUBLE n 1.251 0.0183 1.251 0.0183
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ASP C OXT SINGLE n 1.251 0.0183 1.251 0.0183
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ASP CB CG SINGLE n 1.522 0.0100 1.522 0.0100
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ASP CG OD1 DOUBLE n 1.249 0.0161 1.249 0.0161
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ASP CG OD2 SINGLE n 1.249 0.0161 1.249 0.0161
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ASP N H SINGLE n 1.018 0.0520 0.902 0.0102
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ASP N H2 SINGLE n 1.018 0.0520 0.902 0.0102
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ASP N H3 SINGLE n 1.018 0.0520 0.902 0.0102
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ASP CA HA SINGLE n 1.092 0.0100 0.984 0.0200
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ASP CB HB3 SINGLE n 1.092 0.0100 0.980 0.0165
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ASP CB HB2 SINGLE n 1.092 0.0100 0.980 0.0165
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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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ASP CA N H 109.990 3.00
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ASP CA N H2 109.990 3.00
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ASP CA N H3 109.990 3.00
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ASP H N H2 109.032 3.00
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ASP H N H3 109.032 3.00
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ASP H2 N H3 109.032 3.00
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ASP N CA C 109.258 1.50
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ASP N CA CB 111.400 1.50
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ASP N CA HA 108.387 1.58
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ASP C CA CB 112.421 3.00
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ASP C CA HA 108.774 1.79
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ASP CB CA HA 108.472 2.65
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ASP CA C O 117.148 1.60
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ASP CA C OXT 117.148 1.60
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ASP O C OXT 125.704 1.50
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ASP CA CB CG 115.436 1.50
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ASP CA CB HB3 108.799 3.00
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ASP CA CB HB2 108.799 3.00
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ASP CG CB HB3 108.242 2.79
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ASP CG CB HB2 108.242 2.79
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ASP HB3 CB HB2 107.976 2.66
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ASP CB CG OD1 117.985 1.50
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ASP CB CG OD2 117.985 1.50
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ASP OD1 CG OD2 124.031 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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ASP chi1 N CA CB CG -60.000 10.0 3
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ASP chi2 CA CB CG OD1 180.000 10.0 6
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ASP sp3_sp3_1 C CA N H 180.000 10.0 3
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ASP 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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ASP 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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ASP plan-1 C 0.020
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ASP plan-1 CA 0.020
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ASP plan-1 O 0.020
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ASP plan-1 OXT 0.020
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ASP plan-2 CB 0.020
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ASP plan-2 CG 0.020
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ASP plan-2 OD1 0.020
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ASP plan-2 OD2 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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ASP SMILES ACDLabs 12.01 O=C(O)CC(N)C(=O)O
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ASP SMILES_CANONICAL CACTVS 3.370 N[C@@H](CC(O)=O)C(O)=O
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ASP SMILES CACTVS 3.370 N[CH](CC(O)=O)C(O)=O
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ASP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 C([C@@H](C(=O)O)N)C(=O)O
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ASP SMILES "OpenEye OEToolkits" 1.7.0 C(C(C(=O)O)N)C(=O)O
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ASP InChI InChI 1.03 InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)/t2-/m0/s1
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ASP InChIKey InChI 1.03 CKLJMWTZIZZHCS-REOHCLBHSA-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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ASP acedrg 278 "dictionary generator"
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ASP acedrg_database 12 "data source"
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ASP rdkit 2019.09.1 "Chemoinformatics tool"
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ASP refmac5 5.8.0419 "optimization tool"
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