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Jungfraujoch/image_analysis/structure_refinement/monomers/THR.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
THR THR THREONINE peptide 17 8 .
data_comp_THR
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
THR N N NT3 1 36.284 31.964 31.738
THR CA C CH1 0 35.016 31.199 31.745
THR C C C 0 34.952 30.333 30.501
THR O O O 0 35.086 30.909 29.398
THR CB C CH1 0 33.833 32.166 31.829
THR OG1 O OH1 0 34.044 32.962 32.993
THR CG2 C CH3 0 32.493 31.457 31.927
THR OXT O OC -1 34.770 29.107 30.668
THR H H H 0 36.319 32.492 31.007
THR H2 H H 0 36.984 31.395 31.731
THR H3 H H 0 36.331 32.480 32.477
THR HA H H 0 35.006 30.619 32.537
THR HB H H 0 33.830 32.749 31.033
THR HG1 H H 0 34.002 32.475 33.707
THR HG21 H H 0 32.588 30.657 32.470
THR HG22 H H 0 32.191 31.210 31.037
THR HG23 H H 0 31.841 32.050 32.336
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
THR N n/a CA START
THR H N . .
THR H2 N . .
THR H3 N . .
THR CA N C .
THR HA CA . .
THR CB CA CG2 .
THR HB CB . .
THR OG1 CB HG1 .
THR HG1 OG1 . .
THR CG2 CB HG23 .
THR HG21 CG2 . .
THR HG22 CG2 . .
THR HG23 CG2 . .
THR C CA . END
THR O C . .
THR OXT C . .
loop_
_chem_comp_acedrg.comp_id
_chem_comp_acedrg.atom_id
_chem_comp_acedrg.atom_type
THR N N(CCCH)(H)3
THR CA C(CCHO)(NH3)(COO)(H)
THR C C(CCHN)(O)2
THR O O(CCO)
THR CB C(CCHN)(CH3)(OH)(H)
THR OG1 O(CCCH)(H)
THR CG2 C(CCHO)(H)3
THR OXT O(CCO)
THR H H(NCHH)
THR H2 H(NCHH)
THR H3 H(NCHH)
THR HA H(CCCN)
THR HB H(CCCO)
THR HG1 H(OC)
THR HG21 H(CCHH)
THR HG22 H(CCHH)
THR HG23 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
THR N CA SINGLE n 1.480 0.0122 1.480 0.0122
THR CA C SINGLE n 1.515 0.0129 1.515 0.0129
THR CA CB SINGLE n 1.528 0.0100 1.528 0.0100
THR C O DOUBLE n 1.251 0.0183 1.251 0.0183
THR C OXT SINGLE n 1.251 0.0183 1.251 0.0183
THR CB OG1 SINGLE n 1.424 0.0100 1.424 0.0100
THR CB CG2 SINGLE n 1.518 0.0100 1.518 0.0100
THR N H SINGLE n 1.018 0.0520 0.902 0.0102
THR N H2 SINGLE n 1.018 0.0520 0.902 0.0102
THR N H3 SINGLE n 1.018 0.0520 0.902 0.0102
THR CA HA SINGLE n 1.092 0.0100 0.982 0.0200
THR CB HB SINGLE n 1.092 0.0100 0.987 0.0100
THR OG1 HG1 SINGLE n 0.972 0.0180 0.864 0.0200
THR CG2 HG21 SINGLE n 1.092 0.0100 0.972 0.0156
THR CG2 HG22 SINGLE n 1.092 0.0100 0.972 0.0156
THR CG2 HG23 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
THR CA N H 109.577 1.50
THR CA N H2 109.577 1.50
THR CA N H3 109.577 1.50
THR H N H2 109.032 3.00
THR H N H3 109.032 3.00
THR H2 N H3 109.032 3.00
THR N CA C 109.121 1.50
THR N CA CB 109.645 1.84
THR N CA HA 108.639 1.50
THR C CA CB 111.778 1.58
THR C CA HA 109.055 1.50
THR CB CA HA 108.870 1.50
THR CA C O 117.098 1.50
THR CA C OXT 117.098 1.50
THR O C OXT 125.804 1.50
THR CA CB OG1 105.245 3.00
THR CA CB CG2 112.544 1.50
THR CA CB HB 109.595 2.39
THR OG1 CB CG2 109.974 3.00
THR OG1 CB HB 109.323 1.86
THR CG2 CB HB 109.170 2.61
THR CB OG1 HG1 109.544 3.00
THR CB CG2 HG21 109.532 1.50
THR CB CG2 HG22 109.532 1.50
THR CB CG2 HG23 109.532 1.50
THR HG21 CG2 HG22 109.425 1.50
THR HG21 CG2 HG23 109.425 1.50
THR HG22 CG2 HG23 109.425 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
THR chi1 N CA CB CG2 -60.000 10.0 3
THR hh1 CA CB OG1 HG1 -60.000 10.0 3
THR hh2 CA CB CG2 HG23 -60.000 10.0 3
THR sp3_sp3_1 C CA N H 180.000 10.0 3
THR 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
THR chir_1 CA N C CB positive
THR chir_2 CB OG1 CA CG2 negative
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
THR plan-1 C 0.020
THR plan-1 CA 0.020
THR plan-1 O 0.020
THR 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
THR SMILES ACDLabs 10.04 O=C(O)C(N)C(O)C
THR SMILES_CANONICAL CACTVS 3.341 C[C@@H](O)[C@H](N)C(O)=O
THR SMILES CACTVS 3.341 C[CH](O)[CH](N)C(O)=O
THR SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[C@H]([C@@H](C(=O)O)N)O
THR SMILES "OpenEye OEToolkits" 1.5.0 CC(C(C(=O)O)N)O
THR InChI InChI 1.03 InChI=1S/C4H9NO3/c1-2(6)3(5)4(7)8/h2-3,6H,5H2,1H3,(H,7,8)/t2-,3+/m1/s1
THR InChIKey InChI 1.03 AYFVYJQAPQTCCC-GBXIJSLDSA-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
THR acedrg 278 "dictionary generator"
THR acedrg_database 12 "data source"
THR rdkit 2019.09.1 "Chemoinformatics tool"
THR refmac5 5.8.0419 "optimization tool"
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