# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 10:29:33 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 1-hydroxy-4,6-dimethylpyridine-2(1H)-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC(=S)N(O)C(=C1)C
#
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
 7MH  7MH  1-hydroxy-4,6-dimethylpyridine-2(1H)-thione  ligand  19  10  .  2022-07-23  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_7MH
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
 7MH  C7  C  CH3   0  -0.708   0.9043   2.7798   0.0470
 7MH  C5  C  CR6   0   0.401   0.7834   1.2962   0.0016
 7MH  C4  C  CR16  0  -0.454   1.8582   0.4477   0.0358
 7MH  C3  C  CR6   0   0.249   1.6775  -0.9435  -0.0073
 7MH  C6  C  CH3   0  -0.722   2.8617  -1.8545   0.0273
 7MH  C2  C  CR16  0  -0.434   0.3943  -1.4343  -0.0839
 7MH  C1  C  CR6   0   0.200  -0.7241  -0.5883  -0.1202
 7MH  S1  S  S1    0  -0.408  -2.3430  -1.0846  -0.2109
 7MH  N1  N  NR6   0  -0.215  -0.4518   0.7501  -0.0763
 7MH  O1  O  OH1   0  -0.517  -1.4830   1.6194  -0.1071
 7MH  H1  H  HCH3  0   0.274   0.5054   3.2420  -0.8567
 7MH  H2  H  HCH3  0   0.273   0.3677   3.1993   0.8983
 7MH  H3  H  HCH3  0   0.267   1.9524   3.0530   0.1356
 7MH  H4  H  HCR6  0   0.281   2.8500   0.8734   0.0988
 7MH  H5  H  HCH3  0   0.262   3.4673  -1.6682   0.9150
 7MH  H6  H  HCH3  0   0.255   2.5642  -2.9009   0.0296
 7MH  H7  H  HCH3  0   0.263   3.5028  -1.6839  -0.8387
 7MH  H8  H  HCR6  0   0.281   0.2113  -2.4992  -0.1163
 7MH  H9  H  HOH1  0   0.453  -2.2774   1.0272  -0.1558

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
 7MH  C7  C5  single  1.489  0.020  1.489
 7MH  C5  C4  double  1.370  0.020  1.370
 7MH  C5  N1  single  1.353  0.020  1.353
 7MH  C4  C3  single  1.404  0.020  1.404
 7MH  O1  N1  single  1.349  0.020  1.349
 7MH  N1  C1  single  1.367  0.020  1.367
 7MH  C3  C6  single  1.495  0.020  1.495
 7MH  C3  C2  double  1.376  0.020  1.376
 7MH  C1  C2  single  1.403  0.020  1.403
 7MH  C1  S1  double  1.696  0.020  1.696
 7MH  C7  H1  single  0.970  0.020  1.090
 7MH  C7  H2  single  0.970  0.020  1.090
 7MH  C7  H3  single  0.970  0.020  1.090
 7MH  C4  H4  single  0.930  0.020  1.080
 7MH  C6  H5  single  0.970  0.020  1.090
 7MH  C6  H6  single  0.970  0.020  1.090
 7MH  C6  H7  single  0.970  0.020  1.090
 7MH  C2  H8  single  0.930  0.020  1.080
 7MH  O1  H9  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
 7MH  H3  C7  H2  108.33  3.000
 7MH  H3  C7  H1  108.28  3.000
 7MH  H2  C7  H1  107.70  3.000
 7MH  H3  C7  C5  109.34  3.000
 7MH  H2  C7  C5  111.54  3.000
 7MH  H1  C7  C5  111.54  3.000
 7MH  N1  C5  C4  117.89  3.000
 7MH  N1  C5  C7  118.56  3.000
 7MH  C4  C5  C7  123.55  3.000
 7MH  H4  C4  C3  120.68  3.000
 7MH  H4  C4  C5  118.51  3.000
 7MH  C3  C4  C5  120.81  3.000
 7MH  C2  C3  C6  121.52  3.000
 7MH  C2  C3  C4  118.38  3.000
 7MH  C6  C3  C4  120.10  3.000
 7MH  H7  C6  H6  108.23  3.000
 7MH  H7  C6  H5  107.04  3.000
 7MH  H6  C6  H5  108.33  3.000
 7MH  H7  C6  C3  110.61  3.000
 7MH  H6  C6  C3  111.70  3.000
 7MH  H5  C6  C3  110.77  3.000
 7MH  H8  C2  C1  117.28  3.000
 7MH  H8  C2  C3  120.72  3.000
 7MH  C1  C2  C3  121.99  3.000
 7MH  N1  C1  S1  118.60  3.000
 7MH  S1  C1  C2  125.87  3.000
 7MH  N1  C1  C2  115.53  3.000
 7MH  O1  N1  C1  118.56  3.000
 7MH  C1  N1  C5  125.39  3.000
 7MH  O1  N1  C5  116.05  3.000
 7MH  H9  O1  N1  103.22  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
 7MH  Var_01  H1  C7  C5  C4  118.27  30.0  3
 7MH  Var_02  H5  C6  C3  C4   56.74  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
 7MH  plan-1  C7  0.020
 7MH  plan-1  C5  0.020
 7MH  plan-1  C4  0.020
 7MH  plan-1  C3  0.020
 7MH  plan-1  C6  0.020
 7MH  plan-1  C2  0.020
 7MH  plan-1  C1  0.020
 7MH  plan-1  S1  0.020
 7MH  plan-1  N1  0.020
 7MH  plan-1  O1  0.020
 7MH  plan-1  H4  0.020
 7MH  plan-1  H8  0.020

