# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 13:07:10 2021
#   Inital geometry file: a 91 line input string
#   Ligand name: 5-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-ylcarbonyl)-1-methyl-pyridin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C=C(C=CC1=O)C(=O)N2CCc3sccc3C2
#
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
 LEQ  LEQ  5-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-ylcarbonyl)-1-methyl-pyridin-2-one  ligand  33  19  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LEQ
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
 LEQ  C1   C  CH3   0  -0.520  -9.0913   -7.3664  -17.4612
 LEQ  C3   C  CR16  0   0.071  -7.4385   -9.1366  -17.2888
 LEQ  C12  C  CR15  0  -0.471  -1.4438  -14.5810  -15.6837
 LEQ  C13  C  CR15  0  -0.205  -2.6302  -14.5639  -16.3460
 LEQ  C14  C  CR5   0   0.124  -3.3914  -13.3895  -16.0734
 LEQ  C15  C  CH2   0  -0.314  -4.7322  -13.0811  -16.6690
 LEQ  C16  C  CR16  0  -0.115  -5.1812   -8.6897  -16.7019
 LEQ  C17  C  CR16  0  -0.456  -5.4630   -7.3657  -16.6249
 LEQ  C18  C  CR6   0   0.572  -6.7873   -6.8576  -16.8597
 LEQ  N2   N  NR6   0  -0.506  -7.7343   -7.8264  -17.1974
 LEQ  C4   C  CR6   0  -0.225  -6.1930   -9.6274  -17.0290
 LEQ  C5   C  C     0   0.533  -5.9582  -11.0814  -17.2256
 LEQ  O6   O  O     0  -0.485  -6.5039  -11.6700  -18.1504
 LEQ  N7   N  NT    0  -0.479  -5.1013  -11.7044  -16.3815
 LEQ  C8   C  CH2   0  -0.349  -4.8407  -11.2861  -15.0113
 LEQ  C9   C  CH2   0  -0.481  -3.3461  -11.2623  -14.7211
 LEQ  C10  C  CR5   0  -0.234  -2.7659  -12.5482  -15.2049
 LEQ  S11  S  S2    0   0.206  -1.2386  -13.1746  -14.7189
 LEQ  H1   H  HCH3  0   0.265  -9.5106   -6.8896  -16.5782
 LEQ  H2   H  HCH3  0   0.265  -9.0983   -6.6543  -18.2832
 LEQ  H3   H  HCH3  0   0.261  -9.7069   -8.2194  -17.7288
 LEQ  H4   H  HCR6  0   0.312  -8.2549   -9.7869  -17.5710
 LEQ  H5   H  HCR5  0   0.294  -0.6775  -15.3397  -15.7123
 LEQ  H6   H  HCR5  0   0.264  -2.9538  -15.3548  -17.0090
 LEQ  H7   H  HCH2  0   0.273  -4.6975  -13.2240  -17.7484
 LEQ  H8   H  HCH2  0   0.257  -5.4890  -13.7743  -16.2815
 LEQ  H9   H  HCR6  0   0.284  -4.1646   -9.0246  -16.5365
 LEQ  H10  H  HCR6  0   0.278  -4.6922   -6.6438  -16.3925
 LEQ  H11  H  HCH2  0   0.285  -5.2878  -10.3157  -14.8140
 LEQ  H12  H  HCH2  0   0.272  -5.3291  -11.9963  -14.3356
 LEQ  H13  H  HCH2  0   0.267  -3.1939  -11.1321  -13.6481
 LEQ  H14  H  HCH2  0   0.261  -2.8697  -10.4087  -15.2126
 LEQ  O19  O  O     0  -0.502  -7.1165   -5.6796  -16.7914

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
 LEQ  C1   N2   single    1.457  0.020  1.457
 LEQ  O6   C5   double    1.225  0.020  1.225
 LEQ  C3   N2   single    1.346  0.020  1.346
 LEQ  C3   C4   double    1.364  0.020  1.364
 LEQ  N2   C18  single    1.396  0.020  1.396
 LEQ  C5   C4   single    1.486  0.020  1.486
 LEQ  C5   N7   single    1.355  0.020  1.355
 LEQ  C4   C16  single    1.418  0.020  1.418
 LEQ  C18  O19  double    1.225  0.020  1.225
 LEQ  C18  C17  single    1.438  0.020  1.438
 LEQ  C13  C12  aromatic  1.359  0.020  1.359
 LEQ  C13  C14  aromatic  1.426  0.020  1.426
 LEQ  C12  S11  aromatic  1.718  0.020  1.718
 LEQ  C15  C14  single    1.499  0.020  1.499
 LEQ  C15  N7   single    1.454  0.020  1.454
 LEQ  C16  C17  double    1.356  0.020  1.356
 LEQ  C14  C10  aromatic  1.361  0.020  1.361
 LEQ  N7   C8   single    1.456  0.020  1.456
 LEQ  S11  C10  aromatic  1.721  0.020  1.721
 LEQ  C10  C9   single    1.491  0.020  1.491
 LEQ  C8   C9   single    1.523  0.020  1.523
 LEQ  C1   H1   single    0.970  0.020  1.090
 LEQ  C1   H2   single    0.970  0.020  1.090
 LEQ  C1   H3   single    0.970  0.020  1.090
 LEQ  C3   H4   single    0.930  0.020  1.080
 LEQ  C12  H5   single    0.930  0.020  1.080
 LEQ  C13  H6   single    0.930  0.020  1.080
 LEQ  C15  H7   single    0.970  0.020  1.090
 LEQ  C15  H8   single    0.970  0.020  1.090
 LEQ  C16  H9   single    0.930  0.020  1.080
 LEQ  C17  H10  single    0.930  0.020  1.080
 LEQ  C8   H11  single    0.970  0.020  1.090
 LEQ  C8   H12  single    0.970  0.020  1.090
 LEQ  C9   H13  single    0.970  0.020  1.090
 LEQ  C9   H14  single    0.970  0.020  1.090

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
 LEQ  H3   C1   H2   108.94  3.000
 LEQ  H3   C1   H1   109.03  3.000
 LEQ  H2   C1   H1   108.91  3.000
 LEQ  H3   C1   N2   108.96  3.000
 LEQ  H2   C1   N2   110.46  3.000
 LEQ  H1   C1   N2   110.52  3.000
 LEQ  H4   C3   C4   121.52  3.000
 LEQ  H4   C3   N2   115.93  3.000
 LEQ  C4   C3   N2   122.54  3.000
 LEQ  H5   C12  S11  120.39  3.000
 LEQ  H5   C12  C13  128.04  3.000
 LEQ  S11  C12  C13  111.57  3.000
 LEQ  H6   C13  C14  124.04  3.000
 LEQ  H6   C13  C12  123.42  3.000
 LEQ  C14  C13  C12  112.54  3.000
 LEQ  C10  C14  C15  122.49  3.000
 LEQ  C10  C14  C13  112.68  3.000
 LEQ  C15  C14  C13  124.82  3.000
 LEQ  H8   C15  H7   106.80  3.000
 LEQ  H8   C15  N7   110.69  3.000
 LEQ  H7   C15  N7   109.16  3.000
 LEQ  H8   C15  C14  110.28  3.000
 LEQ  H7   C15  C14  109.77  3.000
 LEQ  N7   C15  C14  110.08  3.000
 LEQ  H9   C16  C4   120.04  3.000
 LEQ  H9   C16  C17  119.23  3.000
 LEQ  C4   C16  C17  120.71  3.000
 LEQ  H10  C17  C18  117.11  3.000
 LEQ  H10  C17  C16  121.07  3.000
 LEQ  C18  C17  C16  121.82  3.000
 LEQ  O19  C18  N2   119.90  3.000
 LEQ  O19  C18  C17  125.32  3.000
 LEQ  N2   C18  C17  114.78  3.000
 LEQ  C18  N2   C3   122.87  3.000
 LEQ  C18  N2   C1   117.16  3.000
 LEQ  C3   N2   C1   119.97  3.000
 LEQ  C5   C4   C16  124.40  3.000
 LEQ  C16  C4   C3   117.24  3.000
 LEQ  C5   C4   C3   118.12  3.000
 LEQ  N7   C5   O6   122.10  3.000
 LEQ  N7   C5   C4   117.88  3.000
 LEQ  O6   C5   C4   119.99  3.000
 LEQ  C8   N7   C5   124.57  3.000
 LEQ  C8   N7   C15  114.37  3.000
 LEQ  C5   N7   C15  118.22  3.000
 LEQ  H12  C8   H11  106.48  3.000
 LEQ  H12  C8   C9   109.29  3.000
 LEQ  H11  C8   C9   110.82  3.000
 LEQ  H12  C8   N7   108.33  3.000
 LEQ  H11  C8   N7   110.71  3.000
 LEQ  C9   C8   N7   111.07  3.000
 LEQ  H14  C9   H13  106.73  3.000
 LEQ  H14  C9   C10  110.95  3.000
 LEQ  H13  C9   C10  111.56  3.000
 LEQ  H14  C9   C8   110.73  3.000
 LEQ  H13  C9   C8   109.03  3.000
 LEQ  C10  C9   C8   107.85  3.000
 LEQ  S11  C10  C9   124.58  3.000
 LEQ  C9   C10  C14  124.13  3.000
 LEQ  S11  C10  C14  111.29  3.000
 LEQ  C10  S11  C12   91.91  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
 LEQ  CONST_01  C10  C14  C13  C12     0.00   0.0  0
 LEQ  CONST_02  C14  C10  S11  C12     0.00   0.0  0
 LEQ  CONST_03  C10  S11  C12  C13     0.00   0.0  0
 LEQ  CONST_04  S11  C10  C14  C13     0.00   0.0  0
 LEQ  CONST_05  S11  C12  C13  C14     0.00   0.0  0
 LEQ  CONST_06  C17  C18  N2   C3      0.00   0.0  0
 LEQ  CONST_07  C4   C5   N7   C15   180.00   0.0  0
 LEQ  CONST_09  C17  C18  N2   C1    180.00   0.0  0
 LEQ  CONST_10  O19  C18  N2   C3    180.00   0.0  0
 LEQ  CONST_11  H5   C12  C13  C14   180.00   0.0  0
 LEQ  CONST_12  H6   C13  C14  C15     0.00   0.0  0
 LEQ  CONST_13  O6   C5   N7   C15     0.00   0.0  0
 LEQ  CONST_15  O19  C18  N2   C1      0.00   0.0  0
 LEQ  Var_01    N7   C15  C14  C13  -169.11  30.0  1
 LEQ  Var_02    C8   N7   C15  C14   -43.90  30.0  1
 LEQ  Var_03    C8   C9   C10  C14    16.83  30.0  1
 LEQ  Var_04    C9   C8   N7   C15    66.05  30.0  1
 LEQ  Var_05    C10  C9   C8   N7    -48.08  30.0  1
 LEQ  Var_06    N7   C5   C4   C3   -145.39  30.0  2
 LEQ  Var_07    H1   C1   N2   C3    118.84  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
 LEQ  plan-1  C1   0.020
 LEQ  plan-1  C3   0.020
 LEQ  plan-1  C16  0.020
 LEQ  plan-1  C17  0.020
 LEQ  plan-1  C18  0.020
 LEQ  plan-1  N2   0.020
 LEQ  plan-1  C4   0.020
 LEQ  plan-1  C5   0.020
 LEQ  plan-1  H4   0.020
 LEQ  plan-1  H9   0.020
 LEQ  plan-1  H10  0.020
 LEQ  plan-1  O19  0.020
 LEQ  plan-2  C12  0.020
 LEQ  plan-2  C13  0.020
 LEQ  plan-2  C14  0.020
 LEQ  plan-2  C15  0.020
 LEQ  plan-2  C9   0.020
 LEQ  plan-2  C10  0.020
 LEQ  plan-2  S11  0.020
 LEQ  plan-2  H5   0.020
 LEQ  plan-2  H6   0.020
 LEQ  plan-3  C15  0.020
 LEQ  plan-3  C4   0.020
 LEQ  plan-3  C5   0.020
 LEQ  plan-3  O6   0.020
 LEQ  plan-3  N7   0.020
 LEQ  plan-3  C8   0.020

