# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 21:45:20 2020
#   Inital geometry file: a 42 line input string
#   Ligand name: pyridin-3-ylmethanethiol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: SCc1cccnc1
#
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
 PY2  PY2  'pyridin-3-ylmethanethiol '  ligand  15  8  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PY2
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
 PY2  N1   N  N     0  -0.400   1.2087  -0.0901  -1.9816
 PY2  C2   C  CR16  0  -0.086   1.1827   0.3275  -0.7222
 PY2  C3   C  CR6   0   0.019   0.0169   0.4941   0.0175
 PY2  C4   C  CR16  0  -0.167  -1.1874   0.1931  -0.6099
 PY2  C5   C  CR16  0  -0.319  -1.1733  -0.2430  -1.9241
 PY2  C6   C  CR16  0  -0.067   0.0504  -0.3689  -2.5665
 PY2  C    C  CH2   0  -0.627   0.0675   0.9506   1.4413
 PY2  S    S  S2    0  -0.237  -0.1336  -0.5184   2.5138
 PY2  H2   H  HCR6  0   0.262   2.1432   0.5503  -0.2670
 PY2  H4   H  HCR6  0   0.273  -2.1245   0.3032  -0.0775
 PY2  H5   H  HCR6  0   0.274  -2.0906  -0.4804  -2.4448
 PY2  H6   H  HCR6  0   0.266   0.0949  -0.7077  -3.5956
 PY2  H1   H  HCH2  0   0.294  -0.7329   1.6588   1.6513
 PY2  H2A  H  HCH2  0   0.289   1.0200   1.4315   1.6595
 PY2  HS   H  HSH1  0   0.227  -0.1463   0.1213   3.6896

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
 PY2  N1  C2   aromatic  1.327  0.020  1.327
 PY2  N1  C6   aromatic  1.327  0.020  1.327
 PY2  C2  C3   aromatic  1.391  0.020  1.391
 PY2  C2  H2   single    0.930  0.020  1.080
 PY2  C3  C4   aromatic  1.391  0.020  1.391
 PY2  C3  C    single    1.496  0.020  1.496
 PY2  C4  C5   aromatic  1.385  0.020  1.385
 PY2  C4  H4   single    0.930  0.020  1.080
 PY2  C5  C6   aromatic  1.388  0.020  1.388
 PY2  C5  H5   single    0.930  0.020  1.080
 PY2  C6  H6   single    0.930  0.020  1.080
 PY2  C   S    single    1.830  0.020  1.830
 PY2  C   H1   single    0.970  0.020  1.090
 PY2  C   H2A  single    0.970  0.020  1.090
 PY2  S   HS   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
 PY2  C6   N1  C2  117.86  3.000
 PY2  H2   C2  C3  119.60  3.000
 PY2  H2   C2  N1  116.42  3.000
 PY2  C3   C2  N1  123.98  3.000
 PY2  C    C3  C4  121.65  3.000
 PY2  C    C3  C2  120.96  3.000
 PY2  C4   C3  C2  117.38  3.000
 PY2  H4   C4  C5  120.48  3.000
 PY2  H4   C4  C3  120.34  3.000
 PY2  C5   C4  C3  119.17  3.000
 PY2  H5   C5  C6  120.35  3.000
 PY2  H5   C5  C4  121.17  3.000
 PY2  C6   C5  C4  118.49  3.000
 PY2  H6   C6  C5  120.26  3.000
 PY2  H6   C6  N1  116.62  3.000
 PY2  C5   C6  N1  123.12  3.000
 PY2  H2A  C   H1  108.49  3.000
 PY2  H2A  C   S   109.46  3.000
 PY2  H1   C   S   109.16  3.000
 PY2  H2A  C   C3  110.79  3.000
 PY2  H1   C   C3  110.91  3.000
 PY2  S    C   C3  108.00  3.000
 PY2  HS   S   C    97.60  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
 PY2  CONST_01  C4  C3  C2  N1     0.00   0.0  0
 PY2  CONST_02  C4  C5  C6  N1     0.00   0.0  0
 PY2  CONST_03  C5  C6  N1  C2     0.00   0.0  0
 PY2  CONST_04  C5  C4  C3  C2     0.00   0.0  0
 PY2  CONST_05  C6  N1  C2  C3     0.00   0.0  0
 PY2  CONST_06  C6  C5  C4  C3     0.00   0.0  0
 PY2  CONST_07  C   C3  C2  N1   180.00   0.0  0
 PY2  CONST_08  C   C3  C4  C5   180.00   0.0  0
 PY2  CONST_09  H5  C5  C6  N1   180.00   0.0  0
 PY2  CONST_10  H6  C6  N1  C2   180.00   0.0  0
 PY2  CONST_11  H4  C4  C3  C2   180.00   0.0  0
 PY2  CONST_12  H2  C2  C3  C4   180.00   0.0  0
 PY2  Var_01    S   C   C3  C2  -100.51  30.0  2

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
 PY2  plan-1  N1  0.020
 PY2  plan-1  C2  0.020
 PY2  plan-1  C3  0.020
 PY2  plan-1  C4  0.020
 PY2  plan-1  C5  0.020
 PY2  plan-1  C6  0.020
 PY2  plan-1  C   0.020
 PY2  plan-1  H2  0.020
 PY2  plan-1  H4  0.020
 PY2  plan-1  H5  0.020
 PY2  plan-1  H6  0.020

