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Jungfraujoch/image_analysis/structure_refinement/monomers/ILE.cif
T
leonarski_f e58453a693 Refinement restraints: the CCP4 Monomer Library subset embedded in rugnux, read through gemmi's MonLib 
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)
2026-10-25 07:20:32 +01:00

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data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
ILE ILE ISOLEUCINE peptide 22 9 .
data_comp_ILE
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
ILE N N NT3 1 52.911 76.465 68.493
ILE CA C CH1 0 53.201 77.811 67.902
ILE C C C 0 51.886 78.441 67.404
ILE O O O 0 51.005 77.667 66.962
ILE CB C CH1 0 54.273 77.728 66.792
ILE CG1 C CH2 0 54.806 79.117 66.415
ILE CG2 C CH3 0 53.775 76.967 65.560
ILE CD1 C CH3 0 55.991 79.094 65.464
ILE OXT O OC -1 51.789 79.686 67.476
ILE H H H 0 53.671 75.992 68.596
ILE H2 H H 0 52.344 75.994 67.973
ILE H3 H H 0 52.530 76.571 69.304
ILE HA H H 0 53.554 78.378 68.615
ILE HB H H 0 55.027 77.224 67.158
ILE HG12 H H 0 55.071 79.584 67.234
ILE HG13 H H 0 54.084 79.629 65.999
ILE HG21 H H 0 53.180 76.249 65.830
ILE HG22 H H 0 54.534 76.591 65.082
ILE HG23 H H 0 53.296 77.576 64.972
ILE HD11 H H 0 56.404 78.209 65.466
ILE HD12 H H 0 56.648 79.757 65.749
ILE HD13 H H 0 55.687 79.307 64.562
loop_
_chem_comp_tree.comp_id
_chem_comp_tree.atom_id
_chem_comp_tree.atom_back
_chem_comp_tree.atom_forward
_chem_comp_tree.connect_type
ILE N n/a CA START
ILE H N . .
ILE H2 N . .
ILE H3 N . .
ILE CA N C .
ILE HA CA . .
ILE CB CA CG2 .
ILE HB CB . .
ILE CG1 CB CD1 .
ILE HG13 CG1 . .
ILE HG12 CG1 . .
ILE CD1 CG1 HD13 .
ILE HD11 CD1 . .
ILE HD12 CD1 . .
ILE HD13 CD1 . .
ILE CG2 CB HG23 .
ILE HG21 CG2 . .
ILE HG22 CG2 . .
ILE HG23 CG2 . .
ILE C CA . END
ILE O C . .
ILE OXT C . .
loop_
_chem_comp_acedrg.comp_id
_chem_comp_acedrg.atom_id
_chem_comp_acedrg.atom_type
ILE N N(CCCH)(H)3
ILE CA C(CCCH)(NH3)(COO)(H)
ILE C C(CCHN)(O)2
ILE O O(CCO)
ILE CB C(CCHH)(CCHN)(CH3)(H)
ILE CG1 C(CCCH)(CH3)(H)2
ILE CG2 C(CCCH)(H)3
ILE CD1 C(CCHH)(H)3
ILE OXT O(CCO)
ILE H H(NCHH)
ILE H2 H(NCHH)
ILE H3 H(NCHH)
ILE HA H(CCCN)
ILE HB H(CC3)
ILE HG12 H(CCCH)
ILE HG13 H(CCCH)
ILE HG21 H(CCHH)
ILE HG22 H(CCHH)
ILE HG23 H(CCHH)
ILE HD11 H(CCHH)
ILE HD12 H(CCHH)
ILE HD13 H(CCHH)
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.aromatic
_chem_comp_bond.value_dist_nucleus
_chem_comp_bond.value_dist_nucleus_esd
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
ILE N CA SINGLE n 1.495 0.0100 1.495 0.0100
ILE CA C SINGLE n 1.538 0.0100 1.538 0.0100
ILE CA CB SINGLE n 1.540 0.0102 1.540 0.0102
ILE C O DOUBLE n 1.251 0.0183 1.251 0.0183
ILE C OXT SINGLE n 1.251 0.0183 1.251 0.0183
ILE CB CG1 SINGLE n 1.529 0.0200 1.529 0.0200
ILE CB CG2 SINGLE n 1.529 0.0119 1.529 0.0119
ILE CG1 CD1 SINGLE n 1.518 0.0129 1.518 0.0129
ILE N H SINGLE n 1.018 0.0520 0.902 0.0102
ILE N H2 SINGLE n 1.018 0.0520 0.902 0.0102
ILE N H3 SINGLE n 1.018 0.0520 0.902 0.0102
ILE CA HA SINGLE n 1.092 0.0100 0.977 0.0200
ILE CB HB SINGLE n 1.092 0.0100 0.978 0.0189
ILE CG1 HG12 SINGLE n 1.092 0.0100 0.979 0.0127
ILE CG1 HG13 SINGLE n 1.092 0.0100 0.979 0.0127
ILE CG2 HG21 SINGLE n 1.092 0.0100 0.972 0.0156
ILE CG2 HG22 SINGLE n 1.092 0.0100 0.972 0.0156
ILE CG2 HG23 SINGLE n 1.092 0.0100 0.972 0.0156
ILE CD1 HD11 SINGLE n 1.092 0.0100 0.976 0.0140
ILE CD1 HD12 SINGLE n 1.092 0.0100 0.976 0.0140
ILE CD1 HD13 SINGLE n 1.092 0.0100 0.976 0.0140
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
ILE CA N H 109.990 2.80
ILE CA N H2 109.990 2.80
ILE CA N H3 109.990 2.80
ILE H N H2 109.032 3.00
ILE H N H3 109.032 3.00
ILE H2 N H3 109.032 3.00
ILE N CA C 108.738 1.50
ILE N CA CB 110.837 1.50
ILE N CA HA 108.328 1.50
ILE C CA CB 111.703 1.50
ILE C CA HA 108.550 1.50
ILE CB CA HA 108.373 1.50
ILE CA C O 117.155 1.50
ILE CA C OXT 117.155 1.50
ILE O C OXT 125.690 1.50
ILE CA CB CG1 111.638 1.50
ILE CA CB CG2 110.951 1.50
ILE CA CB HB 107.422 1.50
ILE CG1 CB CG2 111.728 1.50
ILE CG1 CB HB 107.389 1.50
ILE CG2 CB HB 107.597 1.50
ILE CB CG1 CD1 114.066 1.50
ILE CB CG1 HG12 108.686 1.50
ILE CB CG1 HG13 108.686 1.50
ILE CD1 CG1 HG12 108.722 1.50
ILE CD1 CG1 HG13 108.722 1.50
ILE HG12 CG1 HG13 107.774 1.50
ILE CB CG2 HG21 109.633 1.50
ILE CB CG2 HG22 109.633 1.50
ILE CB CG2 HG23 109.633 1.50
ILE HG21 CG2 HG22 109.390 1.50
ILE HG21 CG2 HG23 109.390 1.50
ILE HG22 CG2 HG23 109.390 1.50
ILE CG1 CD1 HD11 109.644 2.81
ILE CG1 CD1 HD12 109.644 2.81
ILE CG1 CD1 HD13 109.644 2.81
ILE HD11 CD1 HD12 109.381 1.50
ILE HD11 CD1 HD13 109.381 1.50
ILE HD12 CD1 HD13 109.381 1.50
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
ILE chi1 N CA CB CG2 -60.000 10.0 3
ILE chi2 CA CB CG1 CD1 180.000 10.0 3
ILE hh1 CA CB CG2 HG23 -60.000 10.0 3
ILE hh2 CB CG1 CD1 HD13 60.000 10.0 3
ILE sp3_sp3_1 C CA N H 180.000 10.0 3
ILE sp2_sp3_1 O C CA N 0.000 10.0 6
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
ILE chir_1 CA N C CB positive
ILE chir_2 CB CA CG1 CG2 positive
loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
ILE plan-1 C 0.020
ILE plan-1 CA 0.020
ILE plan-1 O 0.020
ILE plan-1 OXT 0.020
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
ILE SMILES ACDLabs 10.04 O=C(O)C(N)C(C)CC
ILE SMILES_CANONICAL CACTVS 3.341 CC[C@H](C)[C@H](N)C(O)=O
ILE SMILES CACTVS 3.341 CC[CH](C)[CH](N)C(O)=O
ILE SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC[C@H](C)[C@@H](C(=O)O)N
ILE SMILES "OpenEye OEToolkits" 1.5.0 CCC(C)C(C(=O)O)N
ILE InChI InChI 1.03 InChI=1S/C6H13NO2/c1-3-4(2)5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t4-,5-/m0/s1
ILE InChIKey InChI 1.03 AGPKZVBTJJNPAG-WHFBIAKZSA-N
loop_
_pdbx_chem_comp_description_generator.comp_id
_pdbx_chem_comp_description_generator.program_name
_pdbx_chem_comp_description_generator.program_version
_pdbx_chem_comp_description_generator.descriptor
ILE acedrg 278 "dictionary generator"
ILE acedrg_database 12 "data source"
ILE rdkit 2019.09.1 "Chemoinformatics tool"
ILE refmac5 5.8.0419 "optimization tool"
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