# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 22:40:52 2020
#   Inital geometry file: a 36 line input string
#   Ligand name: pyridine-2-thiol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Sc1ccccn1
#
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
 PYS  PYS  'pyridine-2-thiol         '  ligand  12  7  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PYS
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
 PYS  N1   N  N     0  -0.410  -1.0418   0.2916  -0.0846
 PYS  C2   C  CR6   0   0.060   0.1682   0.2208   0.4442
 PYS  C3   C  CR16  0  -0.298   1.3234   0.0098  -0.3081
 PYS  C4   C  CR16  0  -0.145   1.1877  -0.1312  -1.6764
 PYS  C5   C  CR16  0  -0.334  -0.0785  -0.0574  -2.2451
 PYS  C6   C  CR16  0  -0.065  -1.1559   0.1543  -1.4031
 PYS  S2   S  S2    0  -0.161   0.3354   0.4030   2.1924
 PYS  H3   H  HCR6  0   0.282   2.2948  -0.0431   0.1655
 PYS  H4   H  HCR6  0   0.279   2.0612  -0.2979  -2.2927
 PYS  H5   H  HCR6  0   0.273  -0.2264  -0.1609  -3.3106
 PYS  H6   H  HCR6  0   0.270  -2.1618   0.2178  -1.8022
 PYS  HS2  H  HSH1  0   0.249  -0.9675   0.5557   2.4515

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
 PYS  N1  C2   aromatic  1.322  0.020  1.322
 PYS  N1  C6   aromatic  1.330  0.020  1.330
 PYS  C2  C3   aromatic  1.395  0.020  1.395
 PYS  C2  S2   single    1.766  0.020  1.766
 PYS  C3  C4   aromatic  1.382  0.020  1.382
 PYS  C3  H3   single    0.930  0.020  1.080
 PYS  C4  C5   aromatic  1.390  0.020  1.390
 PYS  C4  H4   single    0.930  0.020  1.080
 PYS  C5  C6   aromatic  1.384  0.020  1.384
 PYS  C5  H5   single    0.930  0.020  1.080
 PYS  C6  H6   single    0.930  0.020  1.080
 PYS  S2  HS2  single    1.200  0.020  1.300

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
 PYS  C6   N1  C2  117.98  3.000
 PYS  S2   C2  C3  118.12  3.000
 PYS  S2   C2  N1  118.49  3.000
 PYS  C3   C2  N1  123.39  3.000
 PYS  H3   C3  C4  121.09  3.000
 PYS  H3   C3  C2  121.00  3.000
 PYS  C4   C3  C2  117.91  3.000
 PYS  H4   C4  C5  120.70  3.000
 PYS  H4   C4  C3  120.02  3.000
 PYS  C5   C4  C3  119.28  3.000
 PYS  H5   C5  C6  120.54  3.000
 PYS  H5   C5  C4  121.53  3.000
 PYS  C6   C5  C4  117.93  3.000
 PYS  H6   C6  C5  120.49  3.000
 PYS  H6   C6  N1  116.00  3.000
 PYS  C5   C6  N1  123.51  3.000
 PYS  HS2  S2  C2   96.40  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
 PYS  CONST_01  C4  C3  C2  N1    0.00  0.0  0
 PYS  CONST_02  C4  C5  C6  N1    0.00  0.0  0
 PYS  CONST_03  C5  C6  N1  C2    0.00  0.0  0
 PYS  CONST_04  C5  C4  C3  C2    0.00  0.0  0
 PYS  CONST_05  C6  N1  C2  C3    0.00  0.0  0
 PYS  CONST_06  C6  C5  C4  C3    0.00  0.0  0
 PYS  CONST_07  S2  C2  C3  C4  180.00  0.0  0
 PYS  CONST_08  S2  C2  N1  C6  180.00  0.0  0
 PYS  CONST_09  H3  C3  C2  N1  180.00  0.0  0
 PYS  CONST_10  H5  C5  C6  N1  180.00  0.0  0
 PYS  CONST_11  H6  C6  N1  C2  180.00  0.0  0
 PYS  CONST_12  H4  C4  C3  C2  180.00  0.0  0

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
 PYS  plan-1  N1  0.020
 PYS  plan-1  C2  0.020
 PYS  plan-1  C3  0.020
 PYS  plan-1  C4  0.020
 PYS  plan-1  C5  0.020
 PYS  plan-1  C6  0.020
 PYS  plan-1  S2  0.020
 PYS  plan-1  H3  0.020
 PYS  plan-1  H4  0.020
 PYS  plan-1  H5  0.020
 PYS  plan-1  H6  0.020

