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Jungfraujoch/image_analysis/structure_refinement/monomers/LEU.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
LEU LEU LEUCINE peptide 22 9 .
data_comp_LEU
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
LEU N N NT3 1 16.397 16.089 52.368
LEU CA C CH1 0 15.211 16.954 52.118
LEU C C C 0 13.931 16.126 52.332
LEU O O O 0 13.023 16.642 53.022
LEU CB C CH2 0 15.230 17.562 50.712
LEU CG C CH1 0 16.388 18.503 50.342
LEU CD1 C CH3 0 16.596 19.599 51.384
LEU CD2 C CH3 0 17.703 17.774 50.057
LEU OXT O OC -1 13.888 14.994 51.800
LEU H H H 0 16.605 15.616 51.628
LEU H2 H H 0 16.242 15.512 53.045
LEU H3 H H 0 17.102 16.600 52.600
LEU HA H H 0 15.218 17.683 52.788
LEU HB3 H H 0 14.387 18.055 50.587
LEU HB2 H H 0 15.214 16.822 50.062
LEU HG H H 0 16.133 18.961 49.500
LEU HD11 H H 0 15.741 20.011 51.596
LEU HD12 H H 0 17.200 20.273 51.030
LEU HD13 H H 0 16.978 19.215 52.192
LEU HD21 H H 0 17.517 16.879 49.726
LEU HD22 H H 0 18.230 17.713 50.871
LEU HD23 H H 0 18.205 18.266 49.386
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
LEU N n/a CA START
LEU H N . .
LEU H2 N . .
LEU H3 N . .
LEU CA N C .
LEU HA CA . .
LEU CB CA CG .
LEU HB3 CB . .
LEU HB2 CB . .
LEU CG CB CD2 .
LEU HG CG . .
LEU CD1 CG HD13 .
LEU HD11 CD1 . .
LEU HD12 CD1 . .
LEU HD13 CD1 . .
LEU CD2 CG HD23 .
LEU HD21 CD2 . .
LEU HD22 CD2 . .
LEU HD23 CD2 . .
LEU C CA . END
LEU O C . .
LEU OXT C . .
loop_
_chem_comp_acedrg.comp_id
_chem_comp_acedrg.atom_id
_chem_comp_acedrg.atom_type
LEU N N(CCCH)(H)3
LEU CA C(CCHH)(NH3)(COO)(H)
LEU C C(CCHN)(O)2
LEU O O(CCO)
LEU CB C(CCCH)(CCHN)(H)2
LEU CG C(CCHH)(CH3)2(H)
LEU CD1 C(CCCH)(H)3
LEU CD2 C(CCCH)(H)3
LEU OXT O(CCO)
LEU H H(NCHH)
LEU H2 H(NCHH)
LEU H3 H(NCHH)
LEU HA H(CCCN)
LEU HB3 H(CCCH)
LEU HB2 H(CCCH)
LEU HG H(CC3)
LEU HD11 H(CCHH)
LEU HD12 H(CCHH)
LEU HD13 H(CCHH)
LEU HD21 H(CCHH)
LEU HD22 H(CCHH)
LEU HD23 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
LEU N CA SINGLE n 1.487 0.0100 1.487 0.0100
LEU CA C SINGLE n 1.538 0.0113 1.538 0.0113
LEU CA CB SINGLE n 1.528 0.0100 1.528 0.0100
LEU C O DOUBLE n 1.251 0.0183 1.251 0.0183
LEU C OXT SINGLE n 1.251 0.0183 1.251 0.0183
LEU CB CG SINGLE n 1.532 0.0100 1.532 0.0100
LEU CG CD1 SINGLE n 1.519 0.0200 1.519 0.0200
LEU CG CD2 SINGLE n 1.519 0.0200 1.519 0.0200
LEU N H SINGLE n 1.018 0.0520 0.902 0.0102
LEU N H2 SINGLE n 1.018 0.0520 0.902 0.0102
LEU N H3 SINGLE n 1.018 0.0520 0.902 0.0102
LEU CA HA SINGLE n 1.092 0.0100 0.991 0.0200
LEU CB HB3 SINGLE n 1.092 0.0100 0.985 0.0129
LEU CB HB2 SINGLE n 1.092 0.0100 0.985 0.0129
LEU CG HG SINGLE n 1.092 0.0100 0.992 0.0164
LEU CD1 HD11 SINGLE n 1.092 0.0100 0.972 0.0156
LEU CD1 HD12 SINGLE n 1.092 0.0100 0.972 0.0156
LEU CD1 HD13 SINGLE n 1.092 0.0100 0.972 0.0156
LEU CD2 HD21 SINGLE n 1.092 0.0100 0.972 0.0156
LEU CD2 HD22 SINGLE n 1.092 0.0100 0.972 0.0156
LEU CD2 HD23 SINGLE n 1.092 0.0100 0.972 0.0156
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
LEU CA N H 109.990 3.00
LEU CA N H2 109.990 3.00
LEU CA N H3 109.990 3.00
LEU H N H2 109.032 3.00
LEU H N H3 109.032 3.00
LEU H2 N H3 109.032 3.00
LEU N CA C 109.258 1.50
LEU N CA CB 109.859 2.63
LEU N CA HA 108.387 1.58
LEU C CA CB 111.627 1.50
LEU C CA HA 108.774 1.79
LEU CB CA HA 109.261 1.50
LEU CA C O 117.148 1.60
LEU CA C OXT 117.148 1.60
LEU O C OXT 125.704 1.50
LEU CA CB CG 115.973 1.50
LEU CA CB HB3 108.172 1.50
LEU CA CB HB2 108.172 1.50
LEU CG CB HB3 108.390 1.50
LEU CG CB HB2 108.390 1.50
LEU HB3 CB HB2 107.673 3.00
LEU CB CG CD1 110.898 3.00
LEU CB CG CD2 110.898 3.00
LEU CB CG HG 108.090 1.50
LEU CD1 CG CD2 110.647 1.82
LEU CD1 CG HG 107.962 1.81
LEU CD2 CG HG 107.962 1.81
LEU CG CD1 HD11 109.527 1.50
LEU CG CD1 HD12 109.527 1.50
LEU CG CD1 HD13 109.527 1.50
LEU HD11 CD1 HD12 109.390 1.50
LEU HD11 CD1 HD13 109.390 1.50
LEU HD12 CD1 HD13 109.390 1.50
LEU CG CD2 HD21 109.527 1.50
LEU CG CD2 HD22 109.527 1.50
LEU CG CD2 HD23 109.527 1.50
LEU HD21 CD2 HD22 109.390 1.50
LEU HD21 CD2 HD23 109.390 1.50
LEU HD22 CD2 HD23 109.390 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
LEU chi1 N CA CB CG -60.000 10.0 3
LEU chi2 CA CB CG CD1 180.000 10.0 3
LEU hh1 CB CG CD1 HD13 60.000 10.0 3
LEU hh2 CB CG CD2 HD23 180.000 10.0 3
LEU sp3_sp3_1 C CA N H 180.000 10.0 3
LEU 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
LEU chir_1 CA N C CB positive
LEU chir_2 CG CB CD1 CD2 both
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
LEU plan-1 C 0.020
LEU plan-1 CA 0.020
LEU plan-1 O 0.020
LEU 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
LEU SMILES ACDLabs 10.04 O=C(O)C(N)CC(C)C
LEU SMILES_CANONICAL CACTVS 3.341 CC(C)C[C@H](N)C(O)=O
LEU SMILES CACTVS 3.341 CC(C)C[CH](N)C(O)=O
LEU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC(C)C[C@@H](C(=O)O)N
LEU SMILES "OpenEye OEToolkits" 1.5.0 CC(C)CC(C(=O)O)N
LEU InChI InChI 1.03 InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t5-/m0/s1
LEU InChIKey InChI 1.03 ROHFNLRQFUQHCH-YFKPBYRVSA-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
LEU acedrg 278 "dictionary generator"
LEU acedrg_database 12 "data source"
LEU rdkit 2019.09.1 "Chemoinformatics tool"
LEU refmac5 5.8.0419 "optimization tool"
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