# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 15:31:17 2020
#   Inital geometry file: a 48 line input string
#   Ligand name: 4-methylpyridine-2(1H)-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC(=S)NC=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
 4H2  4H2  4-methylpyridine-2(1H)-thione  ligand  15  8  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4H2
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
 4H2  C6  C  CH3   0  -0.722   2.7159   1.4342  -0.0086
 4H2  C3  C  CR6   0   0.230   1.5691   0.4769  -0.0068
 4H2  C2  C  CR16  0  -0.416   0.2692   0.9158  -0.0692
 4H2  C1  C  CR6   0   0.220  -0.8295   0.0244  -0.0708
 4H2  S1  S  S1    0  -0.444  -2.4466   0.4888  -0.1455
 4H2  N1  N  NR16  0  -0.610  -0.4993  -1.2938  -0.0059
 4H2  C5  C  CR16  0   0.066   0.7613  -1.7674   0.0571
 4H2  C4  C  CR16  0  -0.412   1.8184  -0.9143   0.0588
 4H2  H1  H  HCH3  0   0.262   3.3292   1.3004   0.8835
 4H2  H2  H  HCH3  0   0.262   3.3628   1.2547  -0.8687
 4H2  H3  H  HCH3  0   0.256   2.3798   2.4681  -0.0426
 4H2  H4  H  HCR6  0   0.276   0.0537   1.9741  -0.1202
 4H2  H6  H  HCR6  0   0.323   0.8604  -2.8413   0.1038
 4H2  H7  H  HCR6  0   0.281   2.8252  -1.3028   0.1100
 4H2  H5  H  HNR6  0   0.426  -1.2637  -1.9559  -0.0059

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
 4H2  C5  C4  double  1.358  0.020  1.358
 4H2  C5  N1  single  1.348  0.020  1.348
 4H2  C4  C3  single  1.415  0.020  1.415
 4H2  N1  C1  single  1.360  0.020  1.360
 4H2  C3  C6  single  1.494  0.020  1.494
 4H2  C3  C2  double  1.373  0.020  1.373
 4H2  C1  C2  single  1.415  0.020  1.415
 4H2  C1  S1  double  1.684  0.020  1.684
 4H2  C6  H1  single  0.970  0.020  1.090
 4H2  C6  H2  single  0.970  0.020  1.090
 4H2  C6  H3  single  0.970  0.020  1.090
 4H2  C2  H4  single  0.930  0.020  1.080
 4H2  C5  H6  single  0.930  0.020  1.080
 4H2  C4  H7  single  0.930  0.020  1.080
 4H2  N1  H5  single  0.860  0.020  1.020

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
 4H2  H3  C6  H2  108.36  3.000
 4H2  H3  C6  H1  108.42  3.000
 4H2  H2  C6  H1  106.93  3.000
 4H2  H3  C6  C3  111.83  3.000
 4H2  H2  C6  C3  110.53  3.000
 4H2  H1  C6  C3  110.61  3.000
 4H2  C4  C3  C2  118.89  3.000
 4H2  C2  C3  C6  121.45  3.000
 4H2  C4  C3  C6  119.66  3.000
 4H2  H4  C2  C1  117.51  3.000
 4H2  H4  C2  C3  120.23  3.000
 4H2  C1  C2  C3  122.26  3.000
 4H2  N1  C1  S1  120.15  3.000
 4H2  S1  C1  C2  124.89  3.000
 4H2  N1  C1  C2  114.96  3.000
 4H2  H5  N1  C5  118.48  3.000
 4H2  H5  N1  C1  116.80  3.000
 4H2  C5  N1  C1  124.72  3.000
 4H2  H6  C5  C4  123.59  3.000
 4H2  H6  C5  N1  115.93  3.000
 4H2  C4  C5  N1  120.48  3.000
 4H2  H7  C4  C5  119.96  3.000
 4H2  H7  C4  C3  121.33  3.000
 4H2  C5  C4  C3  118.71  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
 4H2  Var_01  H1  C6  C3  C2  122.14  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
 4H2  plan-1  C6  0.020
 4H2  plan-1  C3  0.020
 4H2  plan-1  C2  0.020
 4H2  plan-1  C1  0.020
 4H2  plan-1  S1  0.020
 4H2  plan-1  N1  0.020
 4H2  plan-1  C5  0.020
 4H2  plan-1  C4  0.020
 4H2  plan-1  H4  0.020
 4H2  plan-1  H6  0.020
 4H2  plan-1  H7  0.020
 4H2  plan-1  H5  0.020

