# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 03:39:30 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 1-hydroxy-4-methylpyridine-2(1H)-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC(=S)N(O)C=C1
#
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
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 2YU  2YU  1-hydroxy-4-methylpyridine-2(1H)-thione  ligand  16  9  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2YU
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.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 2YU  S1  S  S1    0  -0.402   2.0929   1.1851   0.0679
 2YU  C1  C  CR6   0   0.215   0.5980   0.3922   0.0076
 2YU  C2  C  CR16  0  -0.424  -0.6683   1.0065   0.0197
 2YU  C3  C  CR6   0   0.234  -1.8404   0.2889  -0.0306
 2YU  C6  C  CH3   0  -0.720  -3.1739   0.9629  -0.0144
 2YU  C4  C  CR16  0  -0.425  -1.7580  -1.1151  -0.0986
 2YU  C5  C  CR16  0   0.064  -0.5364  -1.7158  -0.1115
 2YU  N1  N  NR6   0  -0.171   0.5800  -0.9694  -0.0590
 2YU  O1  O  OH1   0  -0.521   1.7468  -1.6454  -0.0746
 2YU  H1  H  HCR6  0   0.286  -0.6886   2.0863   0.0709
 2YU  H2  H  HCH3  0   0.263  -3.7372   0.7195  -0.9161
 2YU  H3  H  HCH3  0   0.263  -3.7654   0.6182   0.8346
 2YU  H4  H  HCH3  0   0.257  -3.0779   2.0445   0.0495
 2YU  H5  H  HCR6  0   0.290  -2.6433  -1.7328  -0.1417
 2YU  H6  H  HCR6  0   0.338  -0.3958  -2.7854  -0.1616
 2YU  H7  H  HOH1  0   0.453   2.4269  -0.9268  -0.0301

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.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 2YU  C5  C4  double  1.361  0.020  1.361
 2YU  C5  N1  single  1.344  0.020  1.344
 2YU  C4  C3  single  1.408  0.020  1.408
 2YU  O1  N1  single  1.349  0.020  1.349
 2YU  N1  C1  single  1.363  0.020  1.363
 2YU  C3  C6  single  1.494  0.020  1.494
 2YU  C3  C2  double  1.375  0.020  1.375
 2YU  C1  C2  single  1.407  0.020  1.407
 2YU  C1  S1  double  1.693  0.020  1.693
 2YU  C2  H1  single  0.930  0.020  1.080
 2YU  C6  H2  single  0.970  0.020  1.090
 2YU  C6  H3  single  0.970  0.020  1.090
 2YU  C6  H4  single  0.970  0.020  1.090
 2YU  C4  H5  single  0.930  0.020  1.080
 2YU  C5  H6  single  0.930  0.020  1.080
 2YU  O1  H7  single  0.850  0.020  0.980

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
 2YU  N1  C1  C2  115.12  3.000
 2YU  C2  C1  S1  126.13  3.000
 2YU  N1  C1  S1  118.76  3.000
 2YU  H1  C2  C3  120.45  3.000
 2YU  H1  C2  C1  116.95  3.000
 2YU  C3  C2  C1  122.59  3.000
 2YU  C4  C3  C6  120.17  3.000
 2YU  C6  C3  C2  121.65  3.000
 2YU  C4  C3  C2  118.18  3.000
 2YU  H4  C6  H3  108.44  3.000
 2YU  H4  C6  H2  108.42  3.000
 2YU  H3  C6  H2  107.03  3.000
 2YU  H4  C6  C3  111.75  3.000
 2YU  H3  C6  C3  110.48  3.000
 2YU  H2  C6  C3  110.57  3.000
 2YU  H5  C4  C5  118.86  3.000
 2YU  H5  C4  C3  121.61  3.000
 2YU  C5  C4  C3  119.54  3.000
 2YU  H6  C5  N1  116.34  3.000
 2YU  H6  C5  C4  123.66  3.000
 2YU  N1  C5  C4  119.99  3.000
 2YU  O1  N1  C5  116.09  3.000
 2YU  O1  N1  C1  119.33  3.000
 2YU  C5  N1  C1  124.58  3.000
 2YU  H7  O1  N1  103.29  3.000

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
 2YU  Var_01  H2  C6  C3  C2  120.33  30.0  3

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
 2YU  plan-1  S1  0.020
 2YU  plan-1  C1  0.020
 2YU  plan-1  C2  0.020
 2YU  plan-1  C3  0.020
 2YU  plan-1  C6  0.020
 2YU  plan-1  C4  0.020
 2YU  plan-1  C5  0.020
 2YU  plan-1  N1  0.020
 2YU  plan-1  O1  0.020
 2YU  plan-1  H1  0.020
 2YU  plan-1  H5  0.020
 2YU  plan-1  H6  0.020

