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Jungfraujoch/image_analysis/structure_refinement/monomers/TYR.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
TYR TYR TYROSINE peptide 24 13 .
data_comp_TYR
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
TYR N N NT3 1 5.311 5.160 15.589
TYR CA C CH1 0 5.358 6.374 16.456
TYR C C C 0 4.823 7.578 15.662
TYR O O O 0 3.988 8.305 16.245
TYR CB C CH2 0 6.763 6.679 16.994
TYR CG C CR6 0 7.348 5.630 17.938
TYR CD1 C CR16 0 7.096 5.672 19.314
TYR CD2 C CR16 0 8.161 4.597 17.458
TYR CE1 C CR16 0 7.628 4.720 20.176
TYR CE2 C CR16 0 8.697 3.641 18.313
TYR CZ C CR6 0 8.431 3.702 19.674
TYR OH O OH1 0 8.982 2.738 20.476
TYR OXT O OC -1 5.248 7.759 14.496
TYR H H H 0 5.552 4.421 16.046
TYR H2 H H 0 5.856 5.257 14.876
TYR H3 H H 0 4.470 5.038 15.288
TYR HA H H 0 4.756 6.220 17.232
TYR HB3 H H 0 6.733 7.543 17.464
TYR HB2 H H 0 7.369 6.788 16.227
TYR HD1 H H 0 6.552 6.358 19.667
TYR HD2 H H 0 8.350 4.543 16.534
TYR HE1 H H 0 7.444 4.765 21.099
TYR HE2 H H 0 9.240 2.953 17.971
TYR HH H H 0 8.782 2.828 21.308
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
TYR N n/a CA START
TYR H N . .
TYR H2 N . .
TYR H3 N . .
TYR CA N C .
TYR HA CA . .
TYR CB CA CG .
TYR HB3 CB . .
TYR HB2 CB . .
TYR CG CB CD1 .
TYR CD1 CG CE1 .
TYR HD1 CD1 . .
TYR CE1 CD1 CZ .
TYR HE1 CE1 . .
TYR CZ CE1 CE2 .
TYR OH CZ HH .
TYR HH OH . .
TYR CE2 CZ CD2 .
TYR HE2 CE2 . .
TYR CD2 CE2 HD2 .
TYR HD2 CD2 . .
TYR C CA . END
TYR O C . .
TYR OXT C . .
TYR CD2 CG . ADD
loop_
_chem_comp_acedrg.comp_id
_chem_comp_acedrg.atom_id
_chem_comp_acedrg.atom_type
TYR N N(CCCH)(H)3
TYR CA C(CC[6a]HH)(NH3)(COO)(H)
TYR C C(CCHN)(O)2
TYR O O(CCO)
TYR CB C(C[6a]C[6a]2)(CCHN)(H)2
TYR CG C[6a](C[6a]C[6a]H)2(CCHH){1|C<3>,2|H<1>}
TYR CD1 C[6a](C[6a]C[6a]C)(C[6a]C[6a]H)(H){1|C<3>,1|H<1>,1|O<2>}
TYR CD2 C[6a](C[6a]C[6a]C)(C[6a]C[6a]H)(H){1|C<3>,1|H<1>,1|O<2>}
TYR CE1 C[6a](C[6a]C[6a]H)(C[6a]C[6a]O)(H){1|C<3>,1|C<4>,1|H<1>}
TYR CE2 C[6a](C[6a]C[6a]H)(C[6a]C[6a]O)(H){1|C<3>,1|C<4>,1|H<1>}
TYR CZ C[6a](C[6a]C[6a]H)2(OH){1|C<3>,2|H<1>}
TYR OH O(C[6a]C[6a]2)(H)
TYR OXT O(CCO)
TYR H H(NCHH)
TYR H2 H(NCHH)
TYR H3 H(NCHH)
TYR HA H(CCCN)
TYR HB3 H(CC[6a]CH)
TYR HB2 H(CC[6a]CH)
TYR HD1 H(C[6a]C[6a]2)
TYR HD2 H(C[6a]C[6a]2)
TYR HE1 H(C[6a]C[6a]2)
TYR HE2 H(C[6a]C[6a]2)
TYR HH H(OC[6a])
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
TYR N CA SINGLE n 1.489 0.0100 1.489 0.0100
TYR CA C SINGLE n 1.531 0.0171 1.531 0.0171
TYR CA CB SINGLE n 1.532 0.0100 1.532 0.0100
TYR C O DOUBLE n 1.251 0.0183 1.251 0.0183
TYR C OXT SINGLE n 1.251 0.0183 1.251 0.0183
TYR CB CG SINGLE n 1.523 0.0100 1.523 0.0100
TYR CG CD1 DOUBLE y 1.390 0.0116 1.390 0.0116
TYR CG CD2 SINGLE y 1.390 0.0116 1.390 0.0116
TYR CD1 CE1 SINGLE y 1.385 0.0100 1.385 0.0100
TYR CD2 CE2 DOUBLE y 1.385 0.0100 1.385 0.0100
TYR CE1 CZ DOUBLE y 1.383 0.0100 1.383 0.0100
TYR CE2 CZ SINGLE y 1.383 0.0100 1.383 0.0100
TYR CZ OH SINGLE n 1.365 0.0137 1.365 0.0137
TYR N H SINGLE n 1.018 0.0520 0.902 0.0102
TYR N H2 SINGLE n 1.018 0.0520 0.902 0.0102
TYR N H3 SINGLE n 1.018 0.0520 0.902 0.0102
TYR CA HA SINGLE n 1.092 0.0100 0.994 0.0200
TYR CB HB3 SINGLE n 1.092 0.0100 0.983 0.0163
TYR CB HB2 SINGLE n 1.092 0.0100 0.983 0.0163
TYR CD1 HD1 SINGLE n 1.085 0.0150 0.944 0.0143
TYR CD2 HD2 SINGLE n 1.085 0.0150 0.944 0.0143
TYR CE1 HE1 SINGLE n 1.085 0.0150 0.942 0.0174
TYR CE2 HE2 SINGLE n 1.085 0.0150 0.942 0.0174
TYR OH HH SINGLE n 0.966 0.0059 0.858 0.0200
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
TYR CA N H 109.791 3.00
TYR CA N H2 109.791 3.00
TYR CA N H3 109.791 3.00
TYR H N H2 109.032 3.00
TYR H N H3 109.032 3.00
TYR H2 N H3 109.032 3.00
TYR N CA C 109.085 1.50
TYR N CA CB 109.965 3.00
TYR N CA HA 108.547 1.50
TYR C CA CB 111.980 3.00
TYR C CA HA 108.746 1.50
TYR CB CA HA 108.686 1.50
TYR CA C O 117.219 3.00
TYR CA C OXT 117.219 3.00
TYR O C OXT 125.562 1.50
TYR CA CB CG 114.693 2.05
TYR CA CB HB3 108.494 1.50
TYR CA CB HB2 108.494 1.50
TYR CG CB HB3 108.859 1.50
TYR CG CB HB2 108.859 1.50
TYR HB3 CB HB2 107.843 2.16
TYR CB CG CD1 121.060 1.50
TYR CB CG CD2 121.060 1.50
TYR CD1 CG CD2 117.879 1.50
TYR CG CD1 CE1 121.468 1.50
TYR CG CD1 HD1 119.327 1.50
TYR CE1 CD1 HD1 119.205 1.50
TYR CG CD2 CE2 121.468 1.50
TYR CG CD2 HD2 119.327 1.50
TYR CE2 CD2 HD2 119.205 1.50
TYR CD1 CE1 CZ 119.794 1.50
TYR CD1 CE1 HE1 120.177 1.50
TYR CZ CE1 HE1 120.029 1.50
TYR CD2 CE2 CZ 119.794 1.50
TYR CD2 CE2 HE2 120.177 1.50
TYR CZ CE2 HE2 120.029 1.50
TYR CE1 CZ CE2 119.597 1.50
TYR CE1 CZ OH 120.202 3.00
TYR CE2 CZ OH 120.202 3.00
TYR CZ OH HH 109.970 3.00
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
TYR chi1 N CA CB CG -60.000 10.0 3
TYR chi2 CA CB CG CD1 90.000 10.0 6
TYR CONST_1 CB CG CD1 CE1 0.000 0.0 1
TYR CONST_2 CG CD1 CE1 CZ 0.000 0.0 1
TYR CONST_3 CZ CE2 CD2 CG 0.000 0.0 1
TYR CONST_4 CD1 CE1 CZ CE2 0.000 0.0 1
TYR CONST_5 CE1 CZ CE2 CD2 0.000 0.0 1
TYR hh1 CE1 CZ OH HH 0.000 5.0 2
TYR sp3_sp3_1 C CA N H 180.000 10.0 3
TYR const_21 CE2 CD2 CG CD1 0.000 0.0 1
TYR 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
TYR 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
TYR plan-1 CB 0.020
TYR plan-1 CD1 0.020
TYR plan-1 CD2 0.020
TYR plan-1 CE1 0.020
TYR plan-1 CE2 0.020
TYR plan-1 CG 0.020
TYR plan-1 CZ 0.020
TYR plan-1 HD1 0.020
TYR plan-1 HD2 0.020
TYR plan-1 HE1 0.020
TYR plan-1 HE2 0.020
TYR plan-1 OH 0.020
TYR plan-2 C 0.020
TYR plan-2 CA 0.020
TYR plan-2 O 0.020
TYR plan-2 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
TYR SMILES ACDLabs 10.04 "O=C(O)C(N)Cc1ccc(O)cc1"
TYR SMILES_CANONICAL CACTVS 3.341 "N[C@@H](Cc1ccc(O)cc1)C(O)=O"
TYR SMILES CACTVS 3.341 "N[CH](Cc1ccc(O)cc1)C(O)=O"
TYR SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1cc(ccc1C[C@@H](C(=O)O)N)O"
TYR SMILES "OpenEye OEToolkits" 1.5.0 "c1cc(ccc1CC(C(=O)O)N)O"
TYR InChI InChI 1.03 "InChI=1S/C9H11NO3/c10-8(9(12)13)5-6-1-3-7(11)4-2-6/h1-4,8,11H,5,10H2,(H,12,13)/t8-/m0/s1"
TYR InChIKey InChI 1.03 OUYCCCASQSFEME-QMMMGPOBSA-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
TYR acedrg 278 "dictionary generator"
TYR acedrg_database 12 "data source"
TYR rdkit 2019.09.1 "Chemoinformatics tool"
TYR refmac5 5.8.0419 "optimization tool"
TYR servalcat 0.4.57 'optimization tool'
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