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Jungfraujoch/image_analysis/structure_refinement/monomers/PRO.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
PRO PRO PROLINE P-peptide 17 8 .
data_comp_PRO
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_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
PRO N N N NT2 1 39.160 37.649 83.026
PRO CA CA C CH1 0 38.550 38.680 82.125
PRO C C C C 0 37.155 39.077 82.602
PRO O O O O 0 36.450 38.196 83.146
PRO CB CB C CH2 0 38.553 38.007 80.756
PRO CG CG C CH2 0 38.265 36.558 81.098
PRO CD CD C CH2 0 38.934 36.298 82.416
PRO OXT OXT O OC -1 36.821 40.268 82.409
PRO H H H H 0 40.054 37.806 83.097
PRO H2 H2 H H 0 38.800 37.681 83.862
PRO HA HA H H 0 39.125 39.473 82.102
PRO HB3 HB3 H H 0 39.422 38.100 80.320
PRO HB2 HB2 H H 0 37.858 38.378 80.178
PRO HG3 HG3 H H 0 38.625 35.964 80.410
PRO HG2 HG2 H H 0 37.302 36.406 81.169
PRO HD3 HD3 H H 0 38.363 35.755 82.994
PRO HD2 HD2 H H 0 39.785 35.835 82.289
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
PRO N n/a CA START
PRO CA N C .
PRO HA CA . .
PRO CB CA CG .
PRO HB3 CB . .
PRO HB2 CB . .
PRO CG CB CD .
PRO HG3 CG . .
PRO HG2 CG . .
PRO CD CG HD2 .
PRO HD3 CD . .
PRO HD2 CD . .
PRO C CA . END
PRO O C . .
PRO OXT C . .
PRO H N . .
PRO H2 N . .
PRO CD N . ADD
loop_
_chem_comp_acedrg.comp_id
_chem_comp_acedrg.atom_id
_chem_comp_acedrg.atom_type
PRO N N[5](C[5]C[5]CH)(C[5]C[5]HH)(H)2{4|H<1>}
PRO CA C[5](C[5]C[5]HH)(N[5]C[5]HH)(COO)(H){4|H<1>}
PRO C C(C[5]C[5]N[5]H)(O)2
PRO O O(CC[5]O)
PRO CB C[5](C[5]C[5]HH)(C[5]N[5]CH)(H)2{4|H<1>}
PRO CG C[5](C[5]C[5]HH)(C[5]N[5]HH)(H)2{1|C<3>,3|H<1>}
PRO CD C[5](C[5]C[5]HH)(N[5]C[5]HH)(H)2{1|C<3>,3|H<1>}
PRO OXT O(CC[5]O)
PRO H H(N[5]C[5]2H)
PRO H2 H(N[5]C[5]2H)
PRO HA H(C[5]C[5]N[5]C)
PRO HB3 H(C[5]C[5]2H)
PRO HB2 H(C[5]C[5]2H)
PRO HG3 H(C[5]C[5]2H)
PRO HG2 H(C[5]C[5]2H)
PRO HD3 H(C[5]C[5]N[5]H)
PRO HD2 H(C[5]C[5]N[5]H)
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.value_dist_nucleus
_chem_comp_bond.value_dist_nucleus_esd
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
PRO N CA SINGLE n 1.496 0.0142 1.496 0.0142
PRO N CD SINGLE n 1.499 0.0135 1.499 0.0135
PRO CA C SINGLE n 1.525 0.0103 1.525 0.0103
PRO CA CB SINGLE n 1.526 0.0157 1.526 0.0157
PRO C O DOUBLE n 1.252 0.0117 1.252 0.0117
PRO C OXT SINGLE n 1.252 0.0117 1.252 0.0117
PRO CB CG SINGLE n 1.516 0.0179 1.516 0.0179
PRO CG CD SINGLE n 1.497 0.0200 1.497 0.0200
PRO N H SINGLE n 1.018 0.0520 0.910 0.0200
PRO N H2 SINGLE n 1.018 0.0520 0.910 0.0200
PRO CA HA SINGLE n 1.092 0.0100 0.980 0.0200
PRO CB HB3 SINGLE n 1.092 0.0100 0.977 0.0145
PRO CB HB2 SINGLE n 1.092 0.0100 0.977 0.0145
PRO CG HG3 SINGLE n 1.092 0.0100 0.978 0.0181
PRO CG HG2 SINGLE n 1.092 0.0100 0.978 0.0181
PRO CD HD3 SINGLE n 1.092 0.0100 0.977 0.0199
PRO CD HD2 SINGLE n 1.092 0.0100 0.977 0.0199
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
PRO CA N CD 107.978 1.50
PRO CA N H 109.889 3.00
PRO CA N H2 109.889 3.00
PRO CD N H 110.257 3.00
PRO CD N H2 110.257 3.00
PRO H N H2 108.772 3.00
PRO N CA C 110.397 1.50
PRO N CA CB 103.994 1.50
PRO N CA HA 109.579 1.50
PRO C CA CB 113.159 3.00
PRO C CA HA 109.687 1.50
PRO CB CA HA 109.910 1.89
PRO CA C O 116.979 3.00
PRO CA C OXT 116.979 3.00
PRO O C OXT 126.043 1.52
PRO CA CB CG 101.701 3.00
PRO CA CB HB3 110.865 1.50
PRO CA CB HB2 110.865 1.50
PRO CG CB HB3 110.891 1.59
PRO CG CB HB2 110.891 1.59
PRO HB3 CB HB2 108.880 2.25
PRO CB CG CD 105.541 3.00
PRO CB CG HG3 110.897 1.50
PRO CB CG HG2 110.897 1.50
PRO CD CG HG3 110.621 1.50
PRO CD CG HG2 110.621 1.50
PRO HG3 CG HG2 108.871 1.50
PRO N CD CG 104.386 2.30
PRO N CD HD3 110.569 1.50
PRO N CD HD2 110.569 1.50
PRO CG CD HD3 111.131 1.62
PRO CG CD HD2 111.131 1.62
PRO HD3 CD HD2 109.116 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
PRO chi1 N CA CB CG -60.000 10.0 3
PRO chi2 CA CB CG CD 180.000 10.0 3
PRO sp3_sp3_1 CB CA N CD 60.000 10.0 3
PRO sp3_sp3_28 N CD CG CB -60.000 10.0 3
PRO sp3_sp3_37 CG CD N CA 180.000 10.0 3
PRO 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
PRO 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
PRO plan-1 C 0.020
PRO plan-1 CA 0.020
PRO plan-1 O 0.020
PRO 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
PRO SMILES ACDLabs 10.04 "O=C(O)C1NCCC1"
PRO SMILES_CANONICAL CACTVS 3.341 "OC(=O)[C@@H]1CCCN1"
PRO SMILES CACTVS 3.341 "OC(=O)[CH]1CCCN1"
PRO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1C[C@H](NC1)C(=O)O"
PRO SMILES "OpenEye OEToolkits" 1.5.0 "C1CC(NC1)C(=O)O"
PRO InChI InChI 1.03 "InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1"
PRO InChIKey InChI 1.03 ONIBWKKTOPOVIA-BYPYZUCNSA-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
PRO acedrg 281 "dictionary generator"
PRO acedrg_database 12 "data source"
PRO rdkit 2019.09.1 "Chemoinformatics tool"
PRO refmac5 5.8.0419 "optimization tool"
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