mx/Jungfraujoch
3
2 Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 87 Wiki Activity
Files
128e3bb9aed76abb5de7a03a39793b3e8564d159
Jungfraujoch/image_analysis/structure_refinement/monomers/MPD.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

171 lines
9.1 KiB
Plaintext
Raw Blame History

#
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
MPD MPD (4S)-2-METHYL-2,4-PENTANEDIOL NON-POLYMER 22 8 .
#
data_comp_MPD
#
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
MPD C1 C CH3 0 -2.742 -3.513 8.489
MPD C2 C CT 0 -3.104 -4.028 9.879
MPD O2 O OH1 0 -3.051 -5.468 9.845
MPD CM C CH3 0 -4.531 -3.659 10.262
MPD C3 C CH2 0 -2.100 -3.522 10.924
MPD C4 C CH1 0 -2.174 -4.161 12.300
MPD O4 O OH1 0 -1.753 -5.524 12.217
MPD C5 C CH3 0 -1.373 -3.434 13.348
MPD H11 H H 0 -2.205 -2.707 8.574
MPD H12 H H 0 -3.550 -3.311 7.989
MPD H13 H H 0 -2.231 -4.191 8.014
MPD HO2 H H 0 -2.246 -5.731 9.774
MPD HM1 H H 0 -4.554 -2.734 10.562
MPD HM2 H H 0 -4.831 -4.241 10.980
MPD HM3 H H 0 -5.116 -3.767 9.494
MPD H31 H H 0 -2.230 -2.555 11.026
MPD H32 H H 0 -1.197 -3.662 10.569
MPD H4 H H 0 -3.118 -4.168 12.600
MPD HO4 H H 0 -0.938 -5.565 11.984
MPD H51 H H 0 -0.836 -4.069 13.855
MPD H52 H H 0 -1.976 -2.969 13.955
MPD H53 H H 0 -0.783 -2.784 12.924
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
MPD C1 C2 SINGLE n 1.520 0.0101 1.520 0.0101
MPD C2 O2 SINGLE n 1.437 0.0141 1.437 0.0141
MPD C2 CM SINGLE n 1.520 0.0101 1.520 0.0101
MPD C2 C3 SINGLE n 1.531 0.0100 1.531 0.0100
MPD C3 C4 SINGLE n 1.506 0.0200 1.506 0.0200
MPD C4 O4 SINGLE n 1.424 0.0199 1.424 0.0199
MPD C4 C5 SINGLE n 1.501 0.0160 1.501 0.0160
MPD C1 H11 SINGLE n 1.089 0.0100 0.972 0.0148
MPD C1 H12 SINGLE n 1.089 0.0100 0.972 0.0148
MPD C1 H13 SINGLE n 1.089 0.0100 0.972 0.0148
MPD O2 HO2 SINGLE n 0.970 0.0120 0.848 0.0200
MPD CM HM1 SINGLE n 1.089 0.0100 0.972 0.0148
MPD CM HM2 SINGLE n 1.089 0.0100 0.972 0.0148
MPD CM HM3 SINGLE n 1.089 0.0100 0.972 0.0148
MPD C3 H31 SINGLE n 1.089 0.0100 0.981 0.0160
MPD C3 H32 SINGLE n 1.089 0.0100 0.981 0.0160
MPD C4 H4 SINGLE n 1.089 0.0100 0.992 0.0184
MPD O4 HO4 SINGLE n 0.970 0.0120 0.848 0.0200
MPD C5 H51 SINGLE n 1.089 0.0100 0.974 0.0145
MPD C5 H52 SINGLE n 1.089 0.0100 0.974 0.0145
MPD C5 H53 SINGLE n 1.089 0.0100 0.974 0.0145
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
MPD C2 C1 H11 109.123 1.50
MPD C2 C1 H12 109.123 1.50
MPD C2 C1 H13 109.123 1.50
MPD H11 C1 H12 109.441 1.50
MPD H11 C1 H13 109.441 1.50
MPD H12 C1 H13 109.441 1.50
MPD C1 C2 O2 107.291 2.44
MPD C1 C2 CM 110.915 1.50
MPD C1 C2 C3 111.119 1.58
MPD O2 C2 CM 107.291 2.44
MPD O2 C2 C3 107.760 2.12
MPD CM C2 C3 111.119 1.58
MPD C2 O2 HO2 109.561 1.92
MPD C2 CM HM1 109.123 1.50
MPD C2 CM HM2 109.123 1.50
MPD C2 CM HM3 109.123 1.50
MPD HM1 CM HM2 109.441 1.50
MPD HM1 CM HM3 109.441 1.50
MPD HM2 CM HM3 109.441 1.50
MPD C2 C3 C4 111.094 2.85
MPD C2 C3 H31 108.201 1.50
MPD C2 C3 H32 108.201 1.50
MPD C4 C3 H31 108.468 1.50
MPD C4 C3 H32 108.468 1.50
MPD H31 C3 H32 107.715 1.50
MPD C3 C4 O4 109.024 2.32
MPD C3 C4 C5 113.468 3.00
MPD C3 C4 H4 108.603 1.50
MPD O4 C4 C5 109.534 2.02
MPD O4 C4 H4 107.545 2.92
MPD C5 C4 H4 108.620 2.54
MPD C4 O4 HO4 109.880 2.07
MPD C4 C5 H51 109.852 1.50
MPD C4 C5 H52 109.852 1.50
MPD C4 C5 H53 109.852 1.50
MPD H51 C5 H52 109.425 1.50
MPD H51 C5 H53 109.425 1.50
MPD H52 C5 H53 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
MPD sp3_sp3_2 H11 C1 C2 O2 -60.000 10.0 3
MPD sp3_sp3_10 C1 C2 O2 HO2 180.000 10.0 3
MPD sp3_sp3_19 C1 C2 CM HM1 -60.000 10.0 3
MPD sp3_sp3_25 C1 C2 C3 C4 60.000 10.0 3
MPD sp3_sp3_31 C2 C3 C4 O4 180.000 10.0 3
MPD sp3_sp3_40 C3 C4 O4 HO4 180.000 10.0 3
MPD sp3_sp3_43 C3 C4 C5 H51 180.000 10.0 3
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
MPD chir_1 C2 O2 C3 C1 both
MPD chir_2 C4 O4 C3 C5 positive
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
MPD SMILES ACDLabs 11.02 OC(C)CC(O)(C)C
MPD SMILES_CANONICAL CACTVS 3.352 C[C@H](O)CC(C)(C)O
MPD SMILES CACTVS 3.352 C[CH](O)CC(C)(C)O
MPD SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 C[C@@H](CC(C)(C)O)O
MPD SMILES "OpenEye OEToolkits" 1.7.0 CC(CC(C)(C)O)O
MPD InChI InChI 1.03 InChI=1S/C6H14O2/c1-5(7)4-6(2,3)8/h5,7-8H,4H2,1-3H3/t5-/m0/s1
MPD InChIKey InChI 1.03 SVTBMSDMJJWYQN-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
MPD acedrg 243 "dictionary generator"
MPD acedrg_database 11 "data source"
MPD rdkit 2017.03.2 "Chemoinformatics tool"
MPD refmac5 5.8.0238 "optimization tool"
Reference in new issue View Git Blame Copy Permalink