# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 13:32:03 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 1-hydroxy-3-methylpyridine-2(1H)-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC=CN(O)C1=S
#
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
 3MH  3MH  1-hydroxy-3-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_3MH
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
 3MH  S1  S  S1    0  -0.386   1.9797   0.3515   0.0996
 3MH  C1  C  CR6   0   0.234   0.3274   0.0566  -0.0367
 3MH  C2  C  CR6   0  -0.058  -0.2785  -1.2325  -0.0424
 3MH  C6  C  CH3   0  -0.715   0.6011  -2.4376   0.0236
 3MH  C3  C  CR16  0  -0.107  -1.6461  -1.3417  -0.1028
 3MH  C4  C  CR16  0  -0.373  -2.4696  -0.2078  -0.1426
 3MH  C5  C  CR16  0  -0.006  -1.8833   1.0197  -0.1346
 3MH  N1  N  NR6   0  -0.177  -0.5401   1.1093  -0.1067
 3MH  O1  O  OH1   0  -0.526  -0.0421   2.3624  -0.1878
 3MH  H1  H  HCH3  0   0.251   1.1904  -2.4413   0.9416
 3MH  H2  H  HCH3  0   0.248   0.0094  -3.3508  -0.0109
 3MH  H3  H  HCH3  0   0.227   1.3108  -2.4517  -0.8045
 3MH  H4  H  HCR6  0   0.291  -2.0986  -2.3250  -0.1099
 3MH  H5  H  HCR6  0   0.253  -3.5453  -0.2867  -0.1731
 3MH  H6  H  HCR6  0   0.346  -2.4260   1.9524  -0.1626
 3MH  H7  H  HOH1  0   0.497   0.7582   2.3608   0.3718

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
 3MH  C5  C4  double  1.360  0.020  1.360
 3MH  C5  N1  single  1.346  0.020  1.346
 3MH  C4  C3  single  1.402  0.020  1.402
 3MH  O1  N1  single  1.351  0.020  1.351
 3MH  N1  C1  single  1.366  0.020  1.366
 3MH  C3  C2  double  1.373  0.020  1.373
 3MH  C1  C2  single  1.424  0.020  1.424
 3MH  C1  S1  double  1.684  0.020  1.684
 3MH  C2  C6  single  1.493  0.020  1.493
 3MH  C6  H1  single  0.970  0.020  1.090
 3MH  C6  H2  single  0.970  0.020  1.090
 3MH  C6  H3  single  0.970  0.020  1.090
 3MH  C3  H4  single  0.930  0.020  1.080
 3MH  C4  H5  single  0.930  0.020  1.080
 3MH  C5  H6  single  0.930  0.020  1.080
 3MH  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
 3MH  N1  C1  C2  115.29  3.000
 3MH  C2  C1  S1  125.18  3.000
 3MH  N1  C1  S1  119.50  3.000
 3MH  C3  C2  C6  121.62  3.000
 3MH  C6  C2  C1  118.66  3.000
 3MH  C3  C2  C1  119.72  3.000
 3MH  H3  C6  H2  108.58  3.000
 3MH  H3  C6  H1  106.70  3.000
 3MH  H2  C6  H1  108.50  3.000
 3MH  H3  C6  C2  111.11  3.000
 3MH  H2  C6  C2  110.82  3.000
 3MH  H1  C6  C2  110.98  3.000
 3MH  H4  C3  C4  119.28  3.000
 3MH  H4  C3  C2  119.26  3.000
 3MH  C4  C3  C2  121.46  3.000
 3MH  H5  C4  C5  119.72  3.000
 3MH  H5  C4  C3  121.82  3.000
 3MH  C5  C4  C3  118.46  3.000
 3MH  H6  C5  N1  116.40  3.000
 3MH  H6  C5  C4  124.25  3.000
 3MH  N1  C5  C4  119.35  3.000
 3MH  O1  N1  C5  115.36  3.000
 3MH  O1  N1  C1  118.94  3.000
 3MH  C5  N1  C1  125.69  3.000
 3MH  H7  O1  N1  105.44  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
 3MH  Var_01  H1  C6  C2  C1  60.63  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
 3MH  plan-1  S1  0.020
 3MH  plan-1  C1  0.020
 3MH  plan-1  C2  0.020
 3MH  plan-1  C6  0.020
 3MH  plan-1  C3  0.020
 3MH  plan-1  C4  0.020
 3MH  plan-1  C5  0.020
 3MH  plan-1  N1  0.020
 3MH  plan-1  O1  0.020
 3MH  plan-1  H4  0.020
 3MH  plan-1  H5  0.020
 3MH  plan-1  H6  0.020

