# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 03:41:27 2021
#   Inital geometry file: a 65 line input string
#   Ligand name: N,N-dimethyl-2-(methylsulfanyl)pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1ncccc1C(=O)N(C)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
 PJY  PJY  N,N-dimethyl-2-(methylsulfanyl)pyridine-3-carboxamide  ligand  25  13  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PJY
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
 PJY  C1   C  CH3   0  -0.760   1.8484  20.5461  -15.8509
 PJY  C3   C  CR6   0   0.084   1.7877  18.7049  -13.7828
 PJY  C12  C  CH3   0  -0.521   4.0784  16.3888  -14.4247
 PJY  C13  C  CH3   0  -0.523   5.9727  17.1651  -13.1044
 PJY  C5   C  CR16  0  -0.057  -0.3748  18.2276  -13.2377
 PJY  C6   C  CR16  0  -0.337   0.0005  17.4128  -12.1862
 PJY  C7   C  CR16  0  -0.143   1.3575  17.2573  -11.9379
 PJY  C8   C  CR6   0  -0.121   2.2801  17.8890  -12.7533
 PJY  C9   C  C     0   0.477   3.7402  17.8033  -12.4238
 PJY  N11  N  NT    0  -0.424   4.5403  17.1931  -13.3132
 PJY  N4   N  N     0  -0.413   0.4971  18.8656  -14.0122
 PJY  O10  O  O     0  -0.478   4.1395  18.2991  -11.3782
 PJY  S2   S  S2    0   0.044   2.9382  19.5686  -14.8004
 PJY  H1   H  HCH3  0   0.280   2.5067  21.1321  -16.4889
 PJY  H2   H  HCH3  0   0.275   1.2203  19.9113  -16.4695
 PJY  H3   H  HCH3  0   0.274   1.2286  21.2171  -15.2622
 PJY  H4   H  HCH3  0   0.264   2.9949  16.3522  -14.4718
 PJY  H5   H  HCH3  0   0.247   4.4547  16.7859  -15.3676
 PJY  H6   H  HCH3  0   0.253   4.4425  15.3659  -14.3117
 PJY  H7   H  HCH3  0   0.259   6.2727  17.9240  -12.3894
 PJY  H8   H  HCH3  0   0.245   6.2952  16.1882  -12.7374
 PJY  H9   H  HCH3  0   0.247   6.4769  17.3571  -14.0518
 PJY  H10  H  HCR6  0   0.273  -1.4219  18.3825  -13.4704
 PJY  H11  H  HCR6  0   0.276  -0.7413  16.9184  -11.5756
 PJY  H12  H  HCR6  0   0.282   1.6961  16.6377  -11.1171

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
 PJY  C1   S2   single    1.802  0.020  1.802
 PJY  S2   C3   single    1.762  0.020  1.762
 PJY  C12  N11  single    1.448  0.020  1.448
 PJY  N4   C3   aromatic  1.321  0.020  1.321
 PJY  N4   C5   aromatic  1.329  0.020  1.329
 PJY  C3   C8   aromatic  1.403  0.020  1.403
 PJY  C5   C6   aromatic  1.382  0.020  1.382
 PJY  N11  C13  single    1.448  0.020  1.448
 PJY  N11  C9   single    1.343  0.020  1.343
 PJY  C8   C9   single    1.499  0.020  1.499
 PJY  C8   C7   aromatic  1.384  0.020  1.384
 PJY  C9   O10  double    1.224  0.020  1.224
 PJY  C6   C7   aromatic  1.388  0.020  1.388
 PJY  C1   H1   single    0.970  0.020  1.090
 PJY  C1   H2   single    0.970  0.020  1.090
 PJY  C1   H3   single    0.970  0.020  1.090
 PJY  C12  H4   single    0.970  0.020  1.090
 PJY  C12  H5   single    0.970  0.020  1.090
 PJY  C12  H6   single    0.970  0.020  1.090
 PJY  C13  H7   single    0.970  0.020  1.090
 PJY  C13  H8   single    0.970  0.020  1.090
 PJY  C13  H9   single    0.970  0.020  1.090
 PJY  C5   H10  single    0.930  0.020  1.080
 PJY  C6   H11  single    0.930  0.020  1.080
 PJY  C7   H12  single    0.930  0.020  1.080

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
 PJY  H3   C1   H2   109.85  3.000
 PJY  H3   C1   H1   109.28  3.000
 PJY  H2   C1   H1   109.30  3.000
 PJY  H3   C1   S2   111.35  3.000
 PJY  H2   C1   S2   111.39  3.000
 PJY  H1   C1   S2   105.55  3.000
 PJY  S2   C3   N4   118.57  3.000
 PJY  N4   C3   C8   122.77  3.000
 PJY  S2   C3   C8   118.66  3.000
 PJY  H6   C12  H5   108.40  3.000
 PJY  H6   C12  H4   107.81  3.000
 PJY  H5   C12  H4   108.63  3.000
 PJY  H6   C12  N11  109.55  3.000
 PJY  H5   C12  N11  110.58  3.000
 PJY  H4   C12  N11  111.76  3.000
 PJY  H9   C13  H8   108.24  3.000
 PJY  H9   C13  H7   108.76  3.000
 PJY  H8   C13  H7   108.82  3.000
 PJY  H9   C13  N11  109.19  3.000
 PJY  H8   C13  N11  110.97  3.000
 PJY  H7   C13  N11  110.80  3.000
 PJY  H10  C5   N4   116.10  3.000
 PJY  H10  C5   C6   120.66  3.000
 PJY  N4   C5   C6   123.24  3.000
 PJY  H11  C6   C7   121.25  3.000
 PJY  H11  C6   C5   120.88  3.000
 PJY  C7   C6   C5   117.87  3.000
 PJY  H12  C7   C8   119.96  3.000
 PJY  H12  C7   C6   120.36  3.000
 PJY  C8   C7   C6   119.68  3.000
 PJY  C9   C8   C7   119.58  3.000
 PJY  C7   C8   C3   117.63  3.000
 PJY  C9   C8   C3   122.44  3.000
 PJY  O10  C9   N11  123.73  3.000
 PJY  O10  C9   C8   118.83  3.000
 PJY  N11  C9   C8   117.43  3.000
 PJY  C9   N11  C13  120.18  3.000
 PJY  C9   N11  C12  124.81  3.000
 PJY  C13  N11  C12  114.56  3.000
 PJY  C5   N4   C3   118.78  3.000
 PJY  C3   S2   C1   101.98  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
 PJY  CONST_01  C6   C5   N4   C3     0.00   0.0  0
 PJY  CONST_02  C6   C7   C8   C3     0.00   0.0  0
 PJY  CONST_03  C8   C3   N4   C5     0.00   0.0  0
 PJY  CONST_04  C8   C7   C6   C5     0.00   0.0  0
 PJY  CONST_05  N4   C3   C8   C7     0.00   0.0  0
 PJY  CONST_06  N4   C5   C6   C7     0.00   0.0  0
 PJY  CONST_07  S2   C3   N4   C5   180.00   0.0  0
 PJY  CONST_08  C9   C8   C7   C6   180.00   0.0  0
 PJY  CONST_09  S2   C3   C8   C7   180.00   0.0  0
 PJY  CONST_10  N4   C3   C8   C9   180.00   0.0  0
 PJY  CONST_11  H10  C5   N4   C3   180.00   0.0  0
 PJY  CONST_12  H12  C7   C8   C3   180.00   0.0  0
 PJY  CONST_13  H11  C6   C7   C8   180.00   0.0  0
 PJY  CONST_14  C8   C9   N11  C12    0.00   0.0  0
 PJY  CONST_15  C8   C9   N11  C13  180.00   0.0  0
 PJY  CONST_16  O10  C9   N11  C12  180.00   0.0  0
 PJY  CONST_17  O10  C9   N11  C13    0.00   0.0  0
 PJY  Var_01    N4   C3   S2   C1     3.41  30.0  2
 PJY  Var_02    N11  C9   C8   C3   -69.72  30.0  2
 PJY  Var_03    H1   C1   S2   C3   178.29  30.0  3
 PJY  Var_04    H7   C13  N11  C12  169.21  30.0  3
 PJY  Var_05    H4   C12  N11  C13  173.55  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
 PJY  plan-1  C3   0.020
 PJY  plan-1  C5   0.020
 PJY  plan-1  C6   0.020
 PJY  plan-1  C7   0.020
 PJY  plan-1  C8   0.020
 PJY  plan-1  C9   0.020
 PJY  plan-1  N4   0.020
 PJY  plan-1  S2   0.020
 PJY  plan-1  H10  0.020
 PJY  plan-1  H11  0.020
 PJY  plan-1  H12  0.020
 PJY  plan-2  C12  0.020
 PJY  plan-2  C13  0.020
 PJY  plan-2  C8   0.020
 PJY  plan-2  C9   0.020
 PJY  plan-2  N11  0.020
 PJY  plan-2  O10  0.020

