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Jungfraujoch/image_analysis/structure_refinement/monomers/DC.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
DC DC "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" DNA 32 20 .
#
data_comp_DC
#
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
DC OP3 O OP -1 4.759 -6.216 1.740
DC P P P 0 5.427 -6.783 0.501
DC OP1 O O 0 5.450 -8.300 0.487
DC OP2 O OP -1 6.788 -6.171 0.232
DC "O5'" O O2 0 4.494 -6.346 -0.742
DC "C5'" C CH2 0 3.097 -6.734 -0.736
DC "C4'" C CH1 0 2.438 -6.261 -2.009
DC "O4'" O O2 0 2.537 -4.821 -2.097
DC "C3'" C CH1 0 3.044 -6.825 -3.297
DC "O3'" O OH1 0 2.035 -7.363 -4.147
DC "C2'" C CH2 0 3.705 -5.618 -3.951
DC "C1'" C CH1 0 2.890 -4.454 -3.414
DC N1 N NR6 0 3.622 -3.158 -3.358
DC C2 C CR6 0 3.233 -2.087 -4.185
DC O2 O O 0 2.273 -2.221 -4.961
DC N3 N NRD6 0 3.923 -0.917 -4.114
DC C4 C CR6 0 4.961 -0.779 -3.274
DC N4 N NH2 0 5.596 0.387 -3.250
DC C5 C CR16 0 5.371 -1.854 -2.432
DC C6 C CR16 0 4.683 -3.007 -2.507
DC "H5'" H H 0 2.640 -6.331 0.044
DC "H5''" H H 0 3.022 -7.718 -0.669
DC "H4'" H H 0 1.482 -6.507 -1.967
DC "H3'" H H 0 3.719 -7.516 -3.087
DC "HO3'" H H 0 1.460 -6.765 -4.330
DC "H2'" H H 0 3.647 -5.668 -4.930
DC "H2''" H H 0 4.648 -5.546 -3.691
DC "H1'" H H 0 2.063 -4.358 -3.951
DC H41 H H 0 5.385 1.014 -3.827
DC H42 H H 0 6.226 0.528 -2.656
DC H5 H H 0 6.097 -1.763 -1.841
DC H6 H H 0 4.929 -3.731 -1.969
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
DC OP3 P SINGLE n 1.517 0.0192 1.517 0.0192
DC P OP1 DOUBLE n 1.517 0.0192 1.517 0.0192
DC P OP2 SINGLE n 1.517 0.0192 1.517 0.0192
DC P "O5'" SINGLE n 1.614 0.0178 1.614 0.0178
DC "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166
DC "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100
DC "C4'" "O4'" SINGLE n 1.445 0.0100 1.445 0.0100
DC "C4'" "C3'" SINGLE n 1.526 0.0115 1.526 0.0115
DC "O4'" "C1'" SINGLE n 1.413 0.0100 1.413 0.0100
DC "C3'" "O3'" SINGLE n 1.424 0.0100 1.424 0.0100
DC "C3'" "C2'" SINGLE n 1.522 0.0100 1.522 0.0100
DC "C2'" "C1'" SINGLE n 1.520 0.0100 1.520 0.0100
DC "C1'" N1 SINGLE n 1.480 0.0115 1.480 0.0115
DC N1 C2 SINGLE y 1.397 0.0100 1.397 0.0100
DC N1 C6 SINGLE y 1.360 0.0118 1.360 0.0118
DC C2 O2 DOUBLE n 1.241 0.0100 1.241 0.0100
DC C2 N3 SINGLE y 1.355 0.0119 1.355 0.0119
DC N3 C4 DOUBLE y 1.339 0.0110 1.339 0.0110
DC C4 N4 SINGLE n 1.325 0.0109 1.325 0.0109
DC C4 C5 SINGLE y 1.422 0.0123 1.422 0.0123
DC C5 C6 DOUBLE y 1.342 0.0100 1.342 0.0100
DC "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200
DC "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200
DC "C4'" "H4'" SINGLE n 1.089 0.0100 0.987 0.0170
DC "C3'" "H3'" SINGLE n 1.089 0.0100 0.988 0.0189
DC "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
DC "C2'" "H2'" SINGLE n 1.089 0.0100 0.982 0.0200
DC "C2'" "H2''" SINGLE n 1.089 0.0100 0.982 0.0200
DC "C1'" "H1'" SINGLE n 1.089 0.0100 0.991 0.0103
DC N4 H41 SINGLE n 1.016 0.0100 0.877 0.0200
DC N4 H42 SINGLE n 1.016 0.0100 0.877 0.0200
DC C5 H5 SINGLE n 1.082 0.0130 0.941 0.0174
DC C6 H6 SINGLE n 1.082 0.0130 0.935 0.0143
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
DC OP3 P OP1 112.864 1.69
DC OP3 P OP2 112.864 1.69
DC OP3 P "O5'" 105.808 2.07
DC OP1 P OP2 112.864 1.69
DC OP1 P "O5'" 105.808 2.07
DC OP2 P "O5'" 105.808 2.07
DC P "O5'" "C5'" 118.783 1.50
DC "O5'" "C5'" "C4'" 109.342 1.50
DC "O5'" "C5'" "H5'" 109.845 1.50
DC "O5'" "C5'" "H5''" 109.845 1.50
DC "C4'" "C5'" "H5'" 109.624 1.50
DC "C4'" "C5'" "H5''" 109.624 1.50
DC "H5'" "C5'" "H5''" 108.472 1.50
DC "C5'" "C4'" "O4'" 109.615 1.50
DC "C5'" "C4'" "C3'" 114.866 1.63
DC "C5'" "C4'" "H4'" 108.268 1.50
DC "O4'" "C4'" "C3'" 105.770 1.50
DC "O4'" "C4'" "H4'" 108.698 1.50
DC "C3'" "C4'" "H4'" 109.069 1.50
DC "C4'" "O4'" "C1'" 109.692 1.50
DC "C4'" "C3'" "O3'" 110.527 2.37
DC "C4'" "C3'" "C2'" 102.800 1.50
DC "C4'" "C3'" "H3'" 110.775 1.50
DC "O3'" "C3'" "C2'" 110.636 2.59
DC "O3'" "C3'" "H3'" 110.713 1.50
DC "C2'" "C3'" "H3'" 110.862 1.50
DC "C3'" "O3'" "HO3'" 109.026 2.38
DC "C3'" "C2'" "C1'" 102.834 1.50
DC "C3'" "C2'" "H2'" 111.310 1.50
DC "C3'" "C2'" "H2''" 111.310 1.50
DC "C1'" "C2'" "H2'" 111.187 1.50
DC "C1'" "C2'" "H2''" 111.187 1.50
DC "H2'" "C2'" "H2''" 108.952 1.50
DC "O4'" "C1'" "C2'" 106.308 1.50
DC "O4'" "C1'" N1 107.584 1.50
DC "O4'" "C1'" "H1'" 109.550 1.50
DC "C2'" "C1'" N1 114.268 1.50
DC "C2'" "C1'" "H1'" 109.741 1.50
DC N1 "C1'" "H1'" 109.342 1.50
DC "C1'" N1 C2 118.777 1.50
DC "C1'" N1 C6 120.713 1.50
DC C2 N1 C6 120.510 1.50
DC N1 C2 O2 118.710 1.50
DC N1 C2 N3 118.927 1.50
DC O2 C2 N3 122.370 1.50
DC C2 N3 C4 120.266 1.50
DC N3 C4 N4 117.855 1.50
DC N3 C4 C5 121.269 1.50
DC N4 C4 C5 120.876 1.50
DC C4 N4 H41 119.818 1.59
DC C4 N4 H42 119.818 1.59
DC H41 N4 H42 120.363 1.85
DC C4 C5 C6 117.808 1.50
DC C4 C5 H5 121.350 1.50
DC C6 C5 H5 120.848 1.50
DC N1 C6 C5 121.215 1.50
DC N1 C6 H6 118.510 1.50
DC C5 C6 H6 120.275 1.75
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
DC C2e-chi "O4'" "C1'" N1 C2 210.000 10.000 6
DC C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1
DC C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1
DC C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1
DC C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1
DC C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1
DC C3e-chi "O4'" "C1'" N1 C2 210.000 10.000 6
DC C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1
DC C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1
DC C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1
DC C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1
DC C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1
DC alpha "C5'" "O5'" P OP3 -60.000 10.00 3
DC beta P "O5'" "C5'" "C4'" 180.000 10.00 3
DC epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3
DC gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3
DC const_sp2_sp2_4 O2 C2 N1 "C1'" 0.000 5.0 2
DC const_18 C5 C6 N1 "C1'" 180.000 10.0 2
DC const_sp2_sp2_6 O2 C2 N3 C4 180.000 5.0 2
DC const_sp2_sp2_8 N4 C4 N3 C2 180.000 5.0 2
DC sp2_sp2_3 N3 C4 N4 H41 0.000 5.0 2
DC const_11 N4 C4 C5 C6 180.000 10.0 2
DC const_13 C4 C5 C6 N1 0.000 10.0 2
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
DC chir_1 P "O5'" OP3 OP2 both
DC chir_2 "C4'" "O4'" "C3'" "C5'" negative
DC chir_3 "C3'" "O3'" "C4'" "C2'" positive
DC chir_4 "C1'" "O4'" N1 "C2'" 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
DC plan-1 "C1'" 0.020
DC plan-1 C2 0.020
DC plan-1 C4 0.020
DC plan-1 C5 0.020
DC plan-1 C6 0.020
DC plan-1 H5 0.020
DC plan-1 H6 0.020
DC plan-1 N1 0.020
DC plan-1 N3 0.020
DC plan-1 N4 0.020
DC plan-1 O2 0.020
DC plan-2 C4 0.020
DC plan-2 H41 0.020
DC plan-2 H42 0.020
DC plan-2 N4 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
DC SMILES ACDLabs 10.04 O=C1N=C(N)C=CN1C2OC(C(O)C2)COP(=O)(O)O
DC SMILES_CANONICAL CACTVS 3.341 NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2
DC SMILES CACTVS 3.341 NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2
DC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)O)O
DC SMILES "OpenEye OEToolkits" 1.5.0 C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)O)O
DC InChI InChI 1.03 InChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
DC InChIKey InChI 1.03 NCMVOABPESMRCP-SHYZEUOFSA-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
DC acedrg 243 "dictionary generator"
DC acedrg_database 11 "data source"
DC rdkit 2017.03.2 "Chemoinformatics tool"
DC refmac5 5.8.0238 "optimization tool"
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