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Jungfraujoch/image_analysis/structure_refinement/monomers/GLN.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
GLN GLN GLUTAMINE peptide 20 10 .
data_comp_GLN
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
GLN N N NT3 1 -13.189 34.859 120.921
GLN CA C CH1 0 -12.155 35.335 119.962
GLN C C C 0 -10.823 35.547 120.705
GLN O O O 0 -9.774 35.259 120.087
GLN CB C CH2 0 -12.610 36.599 119.226
GLN CG C CH2 0 -12.991 37.771 120.127
GLN CD C C 0 -13.453 38.985 119.351
GLN OE1 O O 0 -14.437 38.935 118.605
GLN NE2 N NH2 0 -12.747 40.094 119.519
GLN OXT O OC -1 -10.882 35.991 121.873
GLN H H H 0 -14.005 34.886 120.536
GLN H2 H H 0 -13.202 35.368 121.666
GLN H3 H H 0 -13.012 34.007 121.158
GLN HA H H 0 -12.019 34.624 119.285
GLN HB3 H H 0 -13.381 36.370 118.666
GLN HB2 H H 0 -11.887 36.885 118.629
GLN HG3 H H 0 -12.221 38.023 120.680
GLN HG2 H H 0 -13.713 37.495 120.731
GLN HE21 H H 0 -11.862 40.066 119.472
GLN HE22 H H 0 -13.160 40.862 119.679
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
GLN N n/a CA START
GLN H N . .
GLN H2 N . .
GLN H3 N . .
GLN CA N C .
GLN HA CA . .
GLN CB CA CG .
GLN HB3 CB . .
GLN HB2 CB . .
GLN CG CB CD .
GLN HG3 CG . .
GLN HG2 CG . .
GLN CD CG NE2 .
GLN OE1 CD . .
GLN NE2 CD HE22 .
GLN HE21 NE2 . .
GLN HE22 NE2 . .
GLN C CA . END
GLN O C . .
GLN OXT C . .
loop_
_chem_comp_acedrg.comp_id
_chem_comp_acedrg.atom_id
_chem_comp_acedrg.atom_type
GLN N N(CCCH)(H)3
GLN CA C(CCHH)(NH3)(COO)(H)
GLN C C(CCHN)(O)2
GLN O O(CCO)
GLN CB C(CCHH)(CCHN)(H)2
GLN CG C(CCHH)(CNO)(H)2
GLN CD C(CCHH)(NHH)(O)
GLN OE1 O(CCN)
GLN NE2 N(CCO)(H)2
GLN OXT O(CCO)
GLN H H(NCHH)
GLN H2 H(NCHH)
GLN H3 H(NCHH)
GLN HA H(CCCN)
GLN HB3 H(CCCH)
GLN HB2 H(CCCH)
GLN HG3 H(CCCH)
GLN HG2 H(CCCH)
GLN HE21 H(NCH)
GLN HE22 H(NCH)
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
GLN N CA SINGLE n 1.487 0.0100 1.487 0.0100
GLN CA C SINGLE n 1.538 0.0113 1.538 0.0113
GLN CA CB SINGLE n 1.529 0.0100 1.529 0.0100
GLN C O DOUBLE n 1.251 0.0183 1.251 0.0183
GLN C OXT SINGLE n 1.251 0.0183 1.251 0.0183
GLN CB CG SINGLE n 1.525 0.0100 1.525 0.0100
GLN CG CD SINGLE n 1.513 0.0100 1.513 0.0100
GLN CD OE1 DOUBLE n 1.236 0.0100 1.236 0.0100
GLN CD NE2 SINGLE n 1.325 0.0100 1.325 0.0100
GLN N H SINGLE n 1.018 0.0520 0.902 0.0102
GLN N H2 SINGLE n 1.018 0.0520 0.902 0.0102
GLN N H3 SINGLE n 1.018 0.0520 0.902 0.0102
GLN CA HA SINGLE n 1.092 0.0100 0.991 0.0200
GLN CB HB3 SINGLE n 1.092 0.0100 0.980 0.0168
GLN CB HB2 SINGLE n 1.092 0.0100 0.980 0.0168
GLN CG HG3 SINGLE n 1.092 0.0100 0.981 0.0172
GLN CG HG2 SINGLE n 1.092 0.0100 0.981 0.0172
GLN NE2 HE21 SINGLE n 1.013 0.0120 0.887 0.0200
GLN NE2 HE22 SINGLE n 1.013 0.0120 0.887 0.0200
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
GLN CA N H 109.990 3.00
GLN CA N H2 109.990 3.00
GLN CA N H3 109.990 3.00
GLN H N H2 109.032 3.00
GLN H N H3 109.032 3.00
GLN H2 N H3 109.032 3.00
GLN N CA C 109.258 1.50
GLN N CA CB 110.440 2.46
GLN N CA HA 108.387 1.58
GLN C CA CB 111.059 3.00
GLN C CA HA 108.774 1.79
GLN CB CA HA 109.080 2.33
GLN CA C O 117.148 1.60
GLN CA C OXT 117.148 1.60
GLN O C OXT 125.704 1.50
GLN CA CB CG 113.998 1.50
GLN CA CB HB3 108.677 1.74
GLN CA CB HB2 108.677 1.74
GLN CG CB HB3 108.907 1.50
GLN CG CB HB2 108.907 1.50
GLN HB3 CB HB2 107.655 1.50
GLN CB CG CD 113.265 1.50
GLN CB CG HG3 109.355 1.50
GLN CB CG HG2 109.355 1.50
GLN CD CG HG3 108.958 1.89
GLN CD CG HG2 108.958 1.89
GLN HG3 CG HG2 107.827 1.56
GLN CG CD OE1 121.487 1.50
GLN CG CD NE2 116.074 1.76
GLN OE1 CD NE2 122.439 1.50
GLN CD NE2 HE21 119.917 2.87
GLN CD NE2 HE22 119.917 2.87
GLN HE21 NE2 HE22 120.165 3.00
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
GLN chi1 N CA CB CG -60.000 10.0 3
GLN chi2 CA CB CG CD 180.000 10.0 3
GLN chi3 CB CG CD NE2 180.000 10.0 6
GLN hh1 CG CD NE2 HE22 180.000 5.0 2
GLN sp3_sp3_1 C CA N H 180.000 10.0 3
GLN 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
GLN chir_1 CA N C CB 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
GLN plan-1 C 0.020
GLN plan-1 CA 0.020
GLN plan-1 O 0.020
GLN plan-1 OXT 0.020
GLN plan-2 CD 0.020
GLN plan-2 CG 0.020
GLN plan-2 NE2 0.020
GLN plan-2 OE1 0.020
GLN plan-3 CD 0.020
GLN plan-3 HE21 0.020
GLN plan-3 HE22 0.020
GLN plan-3 NE2 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
GLN SMILES ACDLabs 10.04 O=C(N)CCC(N)C(=O)O
GLN SMILES_CANONICAL CACTVS 3.341 N[C@@H](CCC(N)=O)C(O)=O
GLN SMILES CACTVS 3.341 N[CH](CCC(N)=O)C(O)=O
GLN SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(CC(=O)N)[C@@H](C(=O)O)N
GLN SMILES "OpenEye OEToolkits" 1.5.0 C(CC(=O)N)C(C(=O)O)N
GLN InChI InChI 1.03 InChI=1S/C5H10N2O3/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H2,7,8)(H,9,10)/t3-/m0/s1
GLN InChIKey InChI 1.03 ZDXPYRJPNDTMRX-VKHMYHEASA-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
GLN acedrg 278 "dictionary generator"
GLN acedrg_database 12 "data source"
GLN rdkit 2019.09.1 "Chemoinformatics tool"
GLN refmac5 5.8.0419 "optimization tool"
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