# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 08:18:30 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 1-hydroxy-5-methylpyridine-2(1H)-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN(O)C(=S)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
 5MH  5MH  1-hydroxy-5-methylpyridine-2(1H)-thione  ligand  16  9  .  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_5MH
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
 5MH  S1  S  S1    0  -0.408   2.5387  -0.4629  -0.0509
 5MH  C1  C  CR6   0   0.199   0.8445  -0.4127  -0.0426
 5MH  C2  C  CR16  0  -0.372  -0.0271  -1.5157  -0.0289
 5MH  C3  C  CR16  0  -0.131  -1.3889  -1.3550  -0.0241
 5MH  C4  C  CR6   0  -0.064  -1.9691  -0.0768  -0.0314
 5MH  C6  C  CH3   0  -0.719  -3.4525   0.1352  -0.0213
 5MH  C5  C  CR16  0   0.038  -1.1101   0.9899  -0.0455
 5MH  N1  N  NR6   0  -0.159   0.2200   0.7993  -0.0507
 5MH  O1  O  OH1   0  -0.518   0.9689   1.9190  -0.0678
 5MH  H1  H  HCR6  0   0.293   0.4132  -2.5022  -0.0224
 5MH  H2  H  HCR6  0   0.283  -2.0279  -2.2289  -0.0145
 5MH  H3  H  HCH3  0   0.255  -3.9791  -0.8166  -0.0525
 5MH  H4  H  HCH3  0   0.259  -3.7721   0.6624   0.8778
 5MH  H5  H  HCH3  0   0.259  -3.7773   0.7233  -0.8796
 5MH  H6  H  HCR6  0   0.331  -1.4379   2.0203  -0.0527
 5MH  H7  H  HOH1  0   0.454   1.8979   1.5731  -0.0678

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
 5MH  C6  C4  single  1.499  0.020  1.499
 5MH  C5  C4  double  1.370  0.020  1.370
 5MH  C5  N1  single  1.344  0.020  1.344
 5MH  C4  C3  single  1.404  0.020  1.404
 5MH  O1  N1  single  1.347  0.020  1.347
 5MH  N1  C1  single  1.364  0.020  1.364
 5MH  C3  C2  double  1.371  0.020  1.371
 5MH  C1  C2  single  1.406  0.020  1.406
 5MH  C1  S1  double  1.695  0.020  1.695
 5MH  C2  H1  single  0.930  0.020  1.080
 5MH  C3  H2  single  0.930  0.020  1.080
 5MH  C6  H3  single  0.970  0.020  1.090
 5MH  C6  H4  single  0.970  0.020  1.090
 5MH  C6  H5  single  0.970  0.020  1.090
 5MH  C5  H6  single  0.930  0.020  1.080
 5MH  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
 5MH  N1  C1  C2  114.42  3.000
 5MH  C2  C1  S1  126.62  3.000
 5MH  N1  C1  S1  118.95  3.000
 5MH  H1  C2  C3  120.78  3.000
 5MH  H1  C2  C1  117.63  3.000
 5MH  C3  C2  C1  121.59  3.000
 5MH  H2  C3  C4  119.41  3.000
 5MH  H2  C3  C2  119.44  3.000
 5MH  C4  C3  C2  121.14  3.000
 5MH  C5  C4  C6  120.71  3.000
 5MH  C5  C4  C3  116.74  3.000
 5MH  C6  C4  C3  122.54  3.000
 5MH  H5  C6  H4  107.53  3.000
 5MH  H5  C6  H3  107.77  3.000
 5MH  H4  C6  H3  107.74  3.000
 5MH  H5  C6  C4  111.47  3.000
 5MH  H4  C6  C4  111.36  3.000
 5MH  H3  C6  C4  110.80  3.000
 5MH  H6  C5  N1  115.80  3.000
 5MH  H6  C5  C4  123.51  3.000
 5MH  N1  C5  C4  120.69  3.000
 5MH  O1  N1  C5  115.62  3.000
 5MH  O1  N1  C1  118.97  3.000
 5MH  C5  N1  C1  125.41  3.000
 5MH  H7  O1  N1  103.36  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
 5MH  Var_01  H3  C6  C4  C3  -2.50  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
 5MH  plan-1  S1  0.020
 5MH  plan-1  C1  0.020
 5MH  plan-1  C2  0.020
 5MH  plan-1  C3  0.020
 5MH  plan-1  C4  0.020
 5MH  plan-1  C6  0.020
 5MH  plan-1  C5  0.020
 5MH  plan-1  N1  0.020
 5MH  plan-1  O1  0.020
 5MH  plan-1  H1  0.020
 5MH  plan-1  H2  0.020
 5MH  plan-1  H6  0.020

