# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 17:02:36 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: 5-(pyridin-2-yl)thiophene-2-carbothioamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=S)c1sc(cc1)c2ccccn2
#
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
 H0J  H0J  5-(pyridin-2-yl)thiophene-2-carbothioamide  ligand  22  14  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H0J
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
 H0J  N1   N  N     0  -0.428   2.9055   1.2213   0.1269
 H0J  C4   C  CR6   0   0.257   2.1526   0.1233   0.0640
 H0J  C5   C  CR16  0  -0.329   2.7058  -1.1492  -0.0721
 H0J  C6   C  CR5   0  -0.219   0.7082   0.3431   0.1479
 H0J  C7   C  CR15  0  -0.186   0.0639   1.5434   0.3124
 H0J  C8   C  CR15  0  -0.171  -1.3370   1.4171   0.3373
 H0J  C1   C  CR16  0  -0.151   4.0830  -1.2725  -0.1473
 H0J  C2   C  CR16  0  -0.320   4.8645  -0.1301  -0.0822
 H0J  C3   C  CR16  0  -0.071   4.2207   1.0927   0.0561
 H0J  C9   C  CR5   0  -0.205  -1.7647   0.1219   0.1987
 H0J  S1   S  S2    0   0.254  -0.4189  -0.9476   0.0231
 H0J  S2   S  S1    0  -0.351  -4.4128   0.6982  -0.0656
 H0J  N2   N  NH2   0  -0.752  -3.3376  -1.6496   0.3972
 H0J  H1   H  HCR6  0   0.274   2.0820  -2.0329  -0.1167
 H0J  H2   H  HCR5  0   0.274   0.5900   2.4809   0.4105
 H0J  H3   H  HCR5  0   0.278  -2.0207   2.2437   0.4613
 H0J  H4   H  HCR6  0   0.281   4.5355  -2.2491  -0.2549
 H0J  H5   H  HCR6  0   0.277   5.9430  -0.1786  -0.1352
 H0J  H6   H  HCR6  0   0.268   4.7970   2.0095   0.1110
 H0J  H7   H  HNH2  0   0.421  -4.2746  -2.0202   0.3894
 H0J  H8   H  HNH2  0   0.422  -2.6053  -2.2852   0.6748
 H0J  C10  C  C     0   0.179  -3.1453  -0.3535   0.1963

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
 H0J  C1   C5   aromatic  1.385  0.020  1.385
 H0J  C1   C2   aromatic  1.386  0.020  1.386
 H0J  C5   C4   aromatic  1.394  0.020  1.394
 H0J  C2   C3   aromatic  1.389  0.020  1.389
 H0J  C4   C6   single    1.463  0.020  1.463
 H0J  C4   N1   aromatic  1.333  0.020  1.333
 H0J  C7   C6   aromatic  1.372  0.020  1.372
 H0J  C7   C8   aromatic  1.407  0.020  1.407
 H0J  C3   N1   aromatic  1.323  0.020  1.323
 H0J  C6   S1   aromatic  1.718  0.020  1.718
 H0J  C8   C9   aromatic  1.371  0.020  1.371
 H0J  C9   S1   aromatic  1.728  0.020  1.728
 H0J  C9   C10  single    1.460  0.020  1.460
 H0J  N2   C10  single    1.326  0.020  1.326
 H0J  C10  S2   double    1.668  0.020  1.668
 H0J  C5   H1   single    0.930  0.020  1.080
 H0J  C7   H2   single    0.930  0.020  1.080
 H0J  C8   H3   single    0.930  0.020  1.080
 H0J  C1   H4   single    0.930  0.020  1.080
 H0J  C2   H5   single    0.930  0.020  1.080
 H0J  C3   H6   single    0.930  0.020  1.080
 H0J  N2   H7   single    0.860  0.020  1.020
 H0J  N2   H8   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
 H0J  C3   N1   C4   118.61  3.000
 H0J  C6   C4   C5   122.29  3.000
 H0J  C6   C4   N1   115.54  3.000
 H0J  C5   C4   N1   122.16  3.000
 H0J  H1   C5   C1   119.88  3.000
 H0J  H1   C5   C4   121.36  3.000
 H0J  C1   C5   C4   118.76  3.000
 H0J  S1   C6   C7   110.97  3.000
 H0J  S1   C6   C4   122.04  3.000
 H0J  C7   C6   C4   126.99  3.000
 H0J  H2   C7   C8   124.17  3.000
 H0J  H2   C7   C6   122.80  3.000
 H0J  C8   C7   C6   113.03  3.000
 H0J  H3   C8   C9   122.49  3.000
 H0J  H3   C8   C7   124.32  3.000
 H0J  C9   C8   C7   113.19  3.000
 H0J  H4   C1   C2   120.87  3.000
 H0J  H4   C1   C5   120.12  3.000
 H0J  C2   C1   C5   119.01  3.000
 H0J  H5   C2   C3   120.46  3.000
 H0J  H5   C2   C1   121.56  3.000
 H0J  C3   C2   C1   117.98  3.000
 H0J  H6   C3   C2   120.21  3.000
 H0J  H6   C3   N1   116.31  3.000
 H0J  C2   C3   N1   123.48  3.000
 H0J  S1   C9   C10  122.33  3.000
 H0J  C10  C9   C8   127.06  3.000
 H0J  S1   C9   C8   110.61  3.000
 H0J  C9   S1   C6    92.21  3.000
 H0J  H8   N2   H7   116.45  3.000
 H0J  H8   N2   C10  123.54  3.000
 H0J  H7   N2   C10  119.56  3.000
 H0J  N2   C10  S2   122.01  3.000
 H0J  S2   C10  C9   120.90  3.000
 H0J  N2   C10  C9   117.08  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
 H0J  CONST_01  C1   C5   C4   N1     0.00   0.0  0
 H0J  CONST_02  C7   C6   C4   N1     0.00   0.0  0
 H0J  CONST_03  S1   C6   C4   N1   180.00   0.0  0
 H0J  CONST_04  C1   C2   C3   N1     0.00   0.0  0
 H0J  CONST_05  C2   C1   C5   C4     0.00   0.0  0
 H0J  CONST_06  C8   C7   C6   C4   180.00   0.0  0
 H0J  CONST_07  C9   S1   C6   C4   180.00   0.0  0
 H0J  CONST_08  C2   C3   N1   C4     0.00   0.0  0
 H0J  CONST_09  C3   C2   C1   C5     0.00   0.0  0
 H0J  CONST_10  C7   C6   C4   C5   180.00   0.0  0
 H0J  CONST_11  S1   C6   C4   C5     0.00   0.0  0
 H0J  CONST_12  C3   N1   C4   C5     0.00   0.0  0
 H0J  CONST_13  C1   C5   C4   C6   180.00   0.0  0
 H0J  CONST_14  C3   N1   C4   C6   180.00   0.0  0
 H0J  CONST_15  C9   C8   C7   C6     0.00   0.0  0
 H0J  CONST_16  C8   C9   S1   C6     0.00   0.0  0
 H0J  CONST_17  C9   S1   C6   C7     0.00   0.0  0
 H0J  CONST_18  S1   C9   C8   C7     0.00   0.0  0
 H0J  CONST_19  S1   C6   C7   C8     0.00   0.0  0
 H0J  CONST_20  C10  C9   S1   C6   180.00   0.0  0
 H0J  CONST_21  C10  C9   C8   C7   180.00   0.0  0
 H0J  CONST_22  H1   C5   C4   N1   180.00   0.0  0
 H0J  CONST_23  H5   C2   C3   N1   180.00   0.0  0
 H0J  CONST_24  H4   C1   C5   C4   180.00   0.0  0
 H0J  CONST_25  H2   C7   C6   C4     0.00   0.0  0
 H0J  CONST_26  H6   C3   N1   C4   180.00   0.0  0
 H0J  CONST_27  H3   C8   C7   C6   180.00   0.0  0
 H0J  Var_01    N2   C10  C9   C8  -162.94  30.0  2
 H0J  Var_02    H7   N2   C10  C9  -179.10  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
 H0J  plan-1  C4   0.020
 H0J  plan-1  C6   0.020
 H0J  plan-1  C7   0.020
 H0J  plan-1  C8   0.020
 H0J  plan-1  C9   0.020
 H0J  plan-1  S1   0.020
 H0J  plan-1  H2   0.020
 H0J  plan-1  H3   0.020
 H0J  plan-1  C10  0.020
 H0J  plan-2  N1   0.020
 H0J  plan-2  C4   0.020
 H0J  plan-2  C5   0.020
 H0J  plan-2  C6   0.020
 H0J  plan-2  C1   0.020
 H0J  plan-2  C2   0.020
 H0J  plan-2  C3   0.020
 H0J  plan-2  H1   0.020
 H0J  plan-2  H4   0.020
 H0J  plan-2  H5   0.020
 H0J  plan-2  H6   0.020
 H0J  plan-3  C9   0.020
 H0J  plan-3  S2   0.020
 H0J  plan-3  N2   0.020
 H0J  plan-3  C10  0.020

