# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 09:55:11 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (6R)-3-(methylsulfanyl)-6-phenyl-1-(1H-pyrazol-3-yl)-6,7-dihydrothieno[3,4-c]pyridin-4(5H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1sc(c2C[C@@H](NC(=O)c12)c3ccccc3)c4cc[nH]n4
#
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
 69C  69C  (6R)-3-(methylsulfanyl)-6-phenyl-1-(1H-pyrazol-3-yl)-6,7-dihydrothieno[3,4-c]pyridin-4(5H)-one  ligand  38  23  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_69C
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
 69C  S1   S  S2    0   0.117  -3.5419  -1.3794   0.1097
 69C  C2   C  CR5   0   0.247   0.2171  -0.3642  -0.8812
 69C  C3   C  CR5   0   0.047  -1.1965  -0.2123  -0.8174
 69C  C5   C  CR5   0  -0.416  -1.8331  -1.2322  -0.1555
 69C  C7   C  CR5   0   0.255   1.9938  -2.0281  -0.1098
 69C  C9   C  CR15  0   0.017   3.7858  -3.1176   0.5593
 69C  C10  C  CH3   0  -0.804  -3.6182  -2.8453   1.1628
 69C  C11  C  CR6   0   0.161   0.6460   2.6617  -0.1048
 69C  C12  C  CR16  0  -0.301   1.8514   3.3405   0.0623
 69C  C13  C  CR16  0  -0.241   2.1995   3.8893   1.2877
 69C  C15  C  CR16  0  -0.235   0.1351   3.0972   2.2151
 69C  C4   C  C     0   0.492  -1.8818   0.9525  -1.3821
 69C  N    N  NH1   0  -0.627  -1.0683   1.9615  -1.7590
 69C  S    S  S2    0   0.258  -0.6875  -2.3887   0.3966
 69C  C6   C  CR5   0  -0.338   0.6515  -1.4987  -0.2639
 69C  N2   N  N     0  -0.303   2.9829  -1.6440  -0.9068
 69C  N1   N  NR15  0  -0.411   4.0464  -2.3077  -0.4781
 69C  C8   C  CR15  0  -0.514   2.4496  -2.9686   0.8399
 69C  C1   C  CH2   0  -0.502   1.0106   0.6701  -1.6055
 69C  C    C  CH1   0  -0.189   0.3487   2.0456  -1.4597
 69C  C16  C  CR16  0  -0.314  -0.2112   2.5507   0.9849
 69C  C14  C  CR16  0  -0.270   1.3394   3.7678   2.3721
 69C  H1   H  HCR5  0   0.296   4.5489  -3.7270   1.0140
 69C  H2   H  HCH3  0   0.280  -3.2479  -3.7325   0.6514
 69C  H3   H  HCH3  0   0.281  -3.0826  -2.6966   2.0991
 69C  H4   H  HCH3  0   0.301  -4.6727  -2.9936   1.3870
 69C  H5   H  HCR6  0   0.252   2.5274   3.4430  -0.7797
 69C  H6   H  HCR6  0   0.256   3.1378   4.4183   1.3938
 69C  H7   H  HCR6  0   0.256  -0.5441   2.9987   3.0521
 69C  H8   H  HNH1  0   0.402  -1.5190   2.8060  -2.0801
 69C  H10  H  HCR5  0   0.270   1.8904  -3.4525   1.6237
 69C  H11  H  HCH2  0   0.270   2.0381   0.7153  -1.2491
 69C  H12  H  HCH2  0   0.273   1.0588   0.4110  -2.6675
 69C  H13  H  HCH1  0   0.287   0.7871   2.6958  -2.2189
 69C  H14  H  HCR6  0   0.250  -1.1624   2.0425   0.8955
 69C  H15  H  HCR6  0   0.256   1.6047   4.1968   3.3297
 69C  H9   H  HNR5  0   0.425   4.9323  -2.1809  -0.9410
 69C  O    O  O     0  -0.483  -3.1023   0.9963  -1.4984

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
 69C  C14  C13  aromatic  1.389  0.020  1.389
 69C  C14  C15  aromatic  1.387  0.020  1.387
 69C  C13  C12  aromatic  1.387  0.020  1.387
 69C  C15  C16  aromatic  1.390  0.020  1.390
 69C  C12  C11  aromatic  1.393  0.020  1.393
 69C  C16  C11  aromatic  1.391  0.020  1.391
 69C  C11  C    single    1.518  0.020  1.518
 69C  C    N    single    1.451  0.020  1.451
 69C  C    C1   single    1.533  0.020  1.533
 69C  N    C4   single    1.350  0.020  1.350
 69C  C1   C2   single    1.491  0.020  1.491
 69C  C4   O    double    1.227  0.020  1.227
 69C  C4   C3   single    1.465  0.020  1.465
 69C  C8   C9   aromatic  1.373  0.020  1.373
 69C  C8   C7   aromatic  1.412  0.020  1.412
 69C  C2   C3   aromatic  1.423  0.020  1.423
 69C  C2   C6   aromatic  1.363  0.020  1.363
 69C  C9   N1   aromatic  1.342  0.020  1.342
 69C  C3   C5   aromatic  1.372  0.020  1.372
 69C  C7   C6   single    1.451  0.020  1.451
 69C  C7   N2   aromatic  1.327  0.020  1.327
 69C  C6   S    aromatic  1.738  0.020  1.738
 69C  N1   N2   aromatic  1.325  0.020  1.325
 69C  C5   S    aromatic  1.719  0.020  1.719
 69C  C5   S1   single    1.736  0.020  1.736
 69C  S1   C10  single    1.807  0.020  1.807
 69C  C9   H1   single    0.930  0.020  1.080
 69C  C10  H2   single    0.970  0.020  1.090
 69C  C10  H3   single    0.970  0.020  1.090
 69C  C10  H4   single    0.970  0.020  1.090
 69C  C12  H5   single    0.930  0.020  1.080
 69C  C13  H6   single    0.930  0.020  1.080
 69C  C15  H7   single    0.930  0.020  1.080
 69C  N    H8   single    0.860  0.020  1.020
 69C  C8   H10  single    0.930  0.020  1.080
 69C  C1   H11  single    0.970  0.020  1.090
 69C  C1   H12  single    0.970  0.020  1.090
 69C  C    H13  single    0.970  0.020  1.090
 69C  C16  H14  single    0.930  0.020  1.080
 69C  C14  H15  single    0.930  0.020  1.080
 69C  N1   H9   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
 69C  C10  S1   C5   101.51  3.000
 69C  C1   C2   C6   128.89  3.000
 69C  C6   C2   C3   112.66  3.000
 69C  C1   C2   C3   118.44  3.000
 69C  C4   C3   C5   124.05  3.000
 69C  C5   C3   C2   113.76  3.000
 69C  C4   C3   C2   122.17  3.000
 69C  S    C5   C3   110.23  3.000
 69C  S    C5   S1   123.37  3.000
 69C  C3   C5   S1   126.40  3.000
 69C  C8   C7   N2   110.86  3.000
 69C  N2   C7   C6   121.33  3.000
 69C  C8   C7   C6   127.80  3.000
 69C  H1   C9   C8   131.63  3.000
 69C  H1   C9   N1   122.02  3.000
 69C  C8   C9   N1   106.34  3.000
 69C  H4   C10  H3   108.55  3.000
 69C  H4   C10  H2   108.38  3.000
 69C  H3   C10  H2   110.35  3.000
 69C  H4   C10  S1   105.76  3.000
 69C  H3   C10  S1   111.70  3.000
 69C  H2   C10  S1   111.90  3.000
 69C  C16  C11  C    123.11  3.000
 69C  C    C11  C12  118.31  3.000
 69C  C16  C11  C12  118.56  3.000
 69C  H5   C12  C13  119.47  3.000
 69C  H5   C12  C11  119.48  3.000
 69C  C13  C12  C11  121.04  3.000
 69C  H6   C13  C14  120.19  3.000
 69C  H6   C13  C12  119.84  3.000
 69C  C14  C13  C12  119.97  3.000
 69C  H7   C15  C14  120.08  3.000
 69C  H7   C15  C16  119.50  3.000
 69C  C14  C15  C16  120.42  3.000
 69C  N    C4   O    123.13  3.000
 69C  O    C4   C3   122.03  3.000
 69C  N    C4   C3   114.84  3.000
 69C  H8   N    C    116.94  3.000
 69C  H8   N    C4   116.43  3.000
 69C  C    N    C4   125.06  3.000
 69C  C6   S    C5    92.68  3.000
 69C  S    C6   C7   119.04  3.000
 69C  S    C6   C2   110.66  3.000
 69C  C7   C6   C2   130.30  3.000
 69C  N1   N2   C7   105.01  3.000
 69C  H9   N1   N2   119.61  3.000
 69C  H9   N1   C9   127.01  3.000
 69C  N2   N1   C9   113.37  3.000
 69C  H10  C8   C9   127.21  3.000
 69C  H10  C8   C7   128.37  3.000
 69C  C9   C8   C7   104.41  3.000
 69C  H12  C1   H11  106.62  3.000
 69C  H12  C1   C    108.89  3.000
 69C  H11  C1   C    109.82  3.000
 69C  H12  C1   C2   109.30  3.000
 69C  H11  C1   C2   111.85  3.000
 69C  C    C1   C2   110.26  3.000
 69C  H13  C    C1   107.15  3.000
 69C  H13  C    N    106.46  3.000
 69C  C1   C    N    110.48  3.000
 69C  H13  C    C11  107.48  3.000
 69C  C1   C    C11  111.37  3.000
 69C  N    C    C11  113.52  3.000
 69C  H14  C16  C15  118.47  3.000
 69C  H14  C16  C11  120.96  3.000
 69C  C15  C16  C11  120.57  3.000
 69C  H15  C14  C15  120.29  3.000
 69C  H15  C14  C13  120.28  3.000
 69C  C15  C14  C13  119.43  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
 69C  CONST_01  S    C5   C3   C2     0.00   0.0  0
 69C  CONST_04  C5   S    C6   C2     0.00   0.0  0
 69C  CONST_05  C7   C6   C2   C3   180.00   0.0  0
 69C  CONST_06  S    C6   C2   C3     0.00   0.0  0
 69C  CONST_07  C6   S    C5   C3     0.00   0.0  0
 69C  CONST_08  C6   C2   C3   C5     0.00   0.0  0
 69C  CONST_09  C7   C6   S    C5   180.00   0.0  0
 69C  CONST_10  N1   C9   C8   C7     0.00   0.0  0
 69C  CONST_11  C9   N1   N2   C7     0.00   0.0  0
 69C  CONST_12  C6   C7   C8   C9   180.00   0.0  0
 69C  CONST_13  N2   C7   C8   C9     0.00   0.0  0
 69C  CONST_14  C14  C13  C12  C11    0.00   0.0  0
 69C  CONST_15  C14  C15  C16  C11    0.00   0.0  0
 69C  CONST_16  C15  C14  C13  C12    0.00   0.0  0
 69C  CONST_17  C15  C16  C11  C12    0.00   0.0  0
 69C  CONST_18  C16  C15  C14  C13    0.00   0.0  0
 69C  CONST_19  C16  C11  C12  C13    0.00   0.0  0
 69C  CONST_22  N1   N2   C7   C6   180.00   0.0  0
 69C  CONST_23  C8   C9   N1   N2     0.00   0.0  0
 69C  CONST_24  C8   C7   N2   N1     0.00   0.0  0
 69C  CONST_25  C1   C2   C6   C7     0.00   0.0  0
 69C  CONST_26  C    C11  C12  C13  180.00   0.0  0
 69C  CONST_27  C    C11  C16  C15  180.00   0.0  0
 69C  CONST_28  C    N    C4   C3     0.00   0.0  0
 69C  CONST_29  C4   C3   C5   S1     0.00   0.0  0
 69C  CONST_30  C2   C3   C5   S1   180.00   0.0  0
 69C  CONST_31  C6   S    C5   S1   180.00   0.0  0
 69C  CONST_32  C    N    C4   O    180.00   0.0  0
 69C  CONST_33  H1   C9   C8   C7   180.00   0.0  0
 69C  CONST_34  H9   N1   N2   C7   180.00   0.0  0
 69C  CONST_35  H6   C13  C12  C11  180.00   0.0  0
 69C  CONST_36  H7   C15  C16  C11  180.00   0.0  0
 69C  CONST_37  H15  C14  C13  C12  180.00   0.0  0
 69C  CONST_38  H14  C16  C11  C12  180.00   0.0  0
 69C  CONST_39  H10  C8   C7   C6     0.00   0.0  0
 69C  CONST_40  H5   C12  C11  C      0.00   0.0  0
 69C  CONST_41  H8   N    C4   C3   180.00   0.0  0
 69C  Var_01    N    C4   C3   C2   -10.63  30.0  1
 69C  Var_02    C    C1   C2   C3    32.76  30.0  1
 69C  Var_03    S    C5   S1   C10    5.37  30.0  1
 69C  Var_04    H2   C10  S1   C5   -63.06  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 69C  chir_01  C  C11  N  C1  positiv

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
 69C  plan-1  C7   0.020
 69C  plan-1  C9   0.020
 69C  plan-1  C6   0.020
 69C  plan-1  N2   0.020
 69C  plan-1  N1   0.020
 69C  plan-1  C8   0.020
 69C  plan-1  H1   0.020
 69C  plan-1  H10  0.020
 69C  plan-1  H9   0.020
 69C  plan-2  C11  0.020
 69C  plan-2  C12  0.020
 69C  plan-2  C13  0.020
 69C  plan-2  C15  0.020
 69C  plan-2  C    0.020
 69C  plan-2  C16  0.020
 69C  plan-2  C14  0.020
 69C  plan-2  H5   0.020
 69C  plan-2  H6   0.020
 69C  plan-2  H7   0.020
 69C  plan-2  H14  0.020
 69C  plan-2  H15  0.020
 69C  plan-3  S1   0.020
 69C  plan-3  C2   0.020
 69C  plan-3  C3   0.020
 69C  plan-3  C5   0.020
 69C  plan-3  C7   0.020
 69C  plan-3  C4   0.020
 69C  plan-3  S    0.020
 69C  plan-3  C6   0.020
 69C  plan-3  C1   0.020
 69C  plan-4  C3   0.020
 69C  plan-4  C4   0.020
 69C  plan-4  N    0.020
 69C  plan-4  C    0.020
 69C  plan-4  H8   0.020
 69C  plan-4  O    0.020

