# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 09:28:25 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 1-[5-({4-[3-chloro-5-(trifluoromethyl)phenyl]piperazin-1-yl}sulfonyl)-2,3-dihydro-1H-indol-1-yl]ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCc2cc(ccc12)[S](=O)(=O)N3CCN(CC3)c4cc(Cl)cc(c4)C(F)(F)F
#
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
 OKY  OKY  1-[5-({4-[3-chloro-5-(trifluoromethyl)phenyl]piperazin-1-yl}sulfonyl)-2,3-dihydro-1H-indol-1-yl]ethan-1-one  ligand  53  32  .  2021-08-17  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OKY
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
 OKY  C13   C   CR16  0  -0.237  -3.8600   1.7178   0.1252
 OKY  C15   C   CR56  0   0.438  -5.1142  -0.2401  -0.4118
 OKY  C17   C   CR16  0  -0.300  -3.6721  -0.2523   1.5228
 OKY  C24   C   CR16  0  -0.370   3.3363  -1.1081  -0.1972
 OKY  C26   C   CR16  0  -0.285   5.3286  -0.5701  -1.4647
 OKY  C01   C   CR16  0  -0.310   3.6826   1.1401  -0.9655
 OKY  C02   C   CR6   0   0.416   2.8808   0.2173  -0.2850
 OKY  C04   C   CH2   0  -0.303   1.3205   0.0835   1.5886
 OKY  C05   C   CH2   0  -0.316  -0.1754   0.1337   1.8237
 OKY  C07   C   CH2   0  -0.313  -0.3408   1.9728   0.2717
 OKY  C08   C   CH2   0  -0.311   1.1557   1.9100   0.0281
 OKY  C12   C   CR6   0  -0.211  -3.3214   1.0656   1.2261
 OKY  C14   C   CR16  0  -0.288  -4.7631   1.0730  -0.7093
 OKY  C16   C   CR56  0  -0.021  -4.5650  -0.8925   0.6958
 OKY  C18   C   CH2   0  -0.497  -5.0746  -2.2986   0.7726
 OKY  C19   C   CH2   0  -0.289  -6.1901  -2.3274  -0.2777
 OKY  C23   C   CH3   0  -0.801  -7.6456  -1.8849  -2.6682
 OKY  C25   C   CR6   0  -0.179   4.5373  -1.4796  -0.7693
 OKY  C27   C   CR6   0  -0.008   4.8705   0.7292  -1.5478
 OKY  C29   C   CT    0   1.054   4.9798  -2.9109  -0.7119
 OKY  F30   F   F     0  -0.302   4.4052  -3.5875   0.2864
 OKY  F31   F   F     0  -0.312   4.6804  -3.5603  -1.8466
 OKY  F32   F   F     0  -0.309   6.3036  -3.0178  -0.5480
 OKY  N03   N   NT    0  -0.529   1.6581   0.5718   0.2600
 OKY  N06   N   N     0  -0.568  -0.6390   1.5033   1.6210
 OKY  N20   N   NR5   0  -0.589  -6.0035  -1.0937  -1.0597
 OKY  O10   O   OS    0  -0.651  -2.2944   3.3258   2.0441
 OKY  O11   O   OS    0  -0.652  -2.1895   1.3340   3.5714
 OKY  O22   O   O     0  -0.466  -6.5209   0.2171  -2.8281
 OKY  S09   S   S     0   1.376  -2.1320   1.8934   2.2308
 OKY  CL28  CL  CL    0  -0.115   5.8262   1.9037  -2.3889
 OKY  H1    H   HCR6  0   0.284  -3.5939   2.7432  -0.0916
 OKY  H2    H   HCR6  0   0.282  -3.2640  -0.7672   2.3824
 OKY  H4    H   HCR6  0   0.290   6.2644  -0.8553  -1.9241
 OKY  H5    H   HCR6  0   0.299   3.4030   2.1808  -1.0381
 OKY  H6    H   HCH2  0   0.243   1.8292   0.6774   2.3593
 OKY  H7    H   HCH2  0   0.274   1.6352  -0.9496   1.7128
 OKY  H8    H   HCH2  0   0.245  -0.6812  -0.5640   1.1444
 OKY  H9    H   HCH2  0   0.283  -0.3695  -0.1813   2.8464
 OKY  H10   H   HCH2  0   0.283  -0.6574   3.0073   0.1542
 OKY  H11   H   HCH2  0   0.245  -0.8593   1.3650  -0.4803
 OKY  H12   H   HCH2  0   0.273   1.3142   2.1908  -1.0127
 OKY  H13   H   HCH2  0   0.239   1.6625   2.6537   0.6582
 OKY  H14   H   HCR6  0   0.288  -5.1756   1.6015  -1.5515
 OKY  H15   H   HCH2  0   0.277  -4.2797  -3.0066   0.5300
 OKY  H16   H   HCH2  0   0.272  -6.1234  -3.2022  -0.9204
 OKY  H17   H   HCH3  0   0.277  -8.1327  -1.5612  -3.5840
 OKY  H18   H   HCH3  0   0.273  -7.1378  -2.8310  -2.8602
 OKY  H19   H   HCH3  0   0.272  -8.4107  -2.0751  -1.9138
 OKY  H20   H   HCH2  0   0.279  -5.4461  -2.5575   1.7632
 OKY  H21   H   HCH2  0   0.270  -7.1766  -2.3221   0.1883
 OKY  C21   C   C     0   0.513  -6.6839  -0.8214  -2.2123
 OKY  H3    H   HCR6  0   0.286   2.7307  -1.8499   0.3025

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
 OKY  O10  S09   double    1.454  0.020  1.454
 OKY  C18  C16   single    1.498  0.020  1.498
 OKY  C18  C19   single    1.532  0.020  1.532
 OKY  C17  C16   aromatic  1.375  0.020  1.375
 OKY  C17  C12   aromatic  1.396  0.020  1.396
 OKY  S09  O11   double    1.454  0.020  1.454
 OKY  S09  C12   single    1.763  0.020  1.763
 OKY  S09  N06   single    1.659  0.020  1.659
 OKY  C16  C15   aromatic  1.398  0.020  1.398
 OKY  C19  N20   single    1.473  0.020  1.473
 OKY  C12  C13   aromatic  1.388  0.020  1.388
 OKY  C15  N20   single    1.393  0.020  1.393
 OKY  C15  C14   aromatic  1.391  0.020  1.391
 OKY  N20  C21   single    1.366  0.020  1.366
 OKY  N06  C07   single    1.459  0.020  1.459
 OKY  N06  C05   single    1.460  0.020  1.460
 OKY  C07  C08   single    1.518  0.020  1.518
 OKY  C13  C14   aromatic  1.388  0.020  1.388
 OKY  C21  C23   single    1.505  0.020  1.505
 OKY  C21  O22   double    1.218  0.020  1.218
 OKY  C08  N03   single    1.448  0.020  1.448
 OKY  C05  C04   single    1.515  0.020  1.515
 OKY  N03  C04   single    1.455  0.020  1.455
 OKY  N03  C02   single    1.385  0.020  1.385
 OKY  F30  C29   single    1.336  0.020  1.336
 OKY  C24  C02   aromatic  1.404  0.020  1.404
 OKY  C24  C25   aromatic  1.381  0.020  1.381
 OKY  C02  C01   aromatic  1.399  0.020  1.399
 OKY  F32  C29   single    1.338  0.020  1.338
 OKY  C29  C25   single    1.499  0.020  1.499
 OKY  C29  F31   single    1.341  0.020  1.341
 OKY  C25  C26   aromatic  1.392  0.020  1.392
 OKY  C01  C27   aromatic  1.385  0.020  1.385
 OKY  C26  C27   aromatic  1.380  0.020  1.380
 OKY  C27  CL28  single    1.732  0.020  1.732
 OKY  C13  H1    single    0.930  0.020  1.080
 OKY  C17  H2    single    0.930  0.020  1.080
 OKY  C24  H3    single    0.930  0.020  1.080
 OKY  C26  H4    single    0.930  0.020  1.080
 OKY  C01  H5    single    0.930  0.020  1.080
 OKY  C04  H6    single    0.970  0.020  1.090
 OKY  C04  H7    single    0.970  0.020  1.090
 OKY  C05  H8    single    0.970  0.020  1.090
 OKY  C05  H9    single    0.970  0.020  1.090
 OKY  C07  H10   single    0.970  0.020  1.090
 OKY  C07  H11   single    0.970  0.020  1.090
 OKY  C08  H12   single    0.970  0.020  1.090
 OKY  C08  H13   single    0.970  0.020  1.090
 OKY  C14  H14   single    0.930  0.020  1.080
 OKY  C18  H15   single    0.970  0.020  1.090
 OKY  C19  H16   single    0.970  0.020  1.090
 OKY  C23  H17   single    0.970  0.020  1.090
 OKY  C23  H18   single    0.970  0.020  1.090
 OKY  C23  H19   single    0.970  0.020  1.090
 OKY  C18  H20   single    0.970  0.020  1.090
 OKY  C19  H21   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
 OKY  H1    C13  C14  118.68  3.000
 OKY  H1    C13  C12  120.60  3.000
 OKY  C14   C13  C12  120.72  3.000
 OKY  N20   C15  C16  109.48  3.000
 OKY  N20   C15  C14  129.80  3.000
 OKY  C16   C15  C14  120.71  3.000
 OKY  H2    C17  C16  120.07  3.000
 OKY  H2    C17  C12  121.57  3.000
 OKY  C16   C17  C12  118.35  3.000
 OKY  H3    C24  C25  119.63  3.000
 OKY  H3    C24  C02  119.68  3.000
 OKY  C25   C24  C02  120.67  3.000
 OKY  H4    C26  C27  120.67  3.000
 OKY  H4    C26  C25  122.16  3.000
 OKY  C27   C26  C25  117.17  3.000
 OKY  H5    C01  C27  118.66  3.000
 OKY  H5    C01  C02  121.32  3.000
 OKY  C27   C01  C02  120.01  3.000
 OKY  N03   C02  C01  121.91  3.000
 OKY  C01   C02  C24  117.84  3.000
 OKY  N03   C02  C24  120.23  3.000
 OKY  H7    C04  H6   107.44  3.000
 OKY  H7    C04  N03  110.86  3.000
 OKY  H6    C04  N03  110.61  3.000
 OKY  H7    C04  C05  107.43  3.000
 OKY  H6    C04  C05  109.30  3.000
 OKY  N03   C04  C05  111.08  3.000
 OKY  H9    C05  H8   108.41  3.000
 OKY  H9    C05  N06  110.21  3.000
 OKY  H8    C05  N06  111.35  3.000
 OKY  H9    C05  C04  108.22  3.000
 OKY  H8    C05  C04  109.76  3.000
 OKY  N06   C05  C04  108.85  3.000
 OKY  H11   C07  H10  108.37  3.000
 OKY  H11   C07  N06  111.03  3.000
 OKY  H10   C07  N06  110.26  3.000
 OKY  H11   C07  C08  109.45  3.000
 OKY  H10   C07  C08  107.99  3.000
 OKY  N06   C07  C08  109.67  3.000
 OKY  H13   C08  H12  107.84  3.000
 OKY  H13   C08  N03  111.94  3.000
 OKY  H12   C08  N03  109.92  3.000
 OKY  H13   C08  C07  109.56  3.000
 OKY  H12   C08  C07  106.63  3.000
 OKY  N03   C08  C07  110.77  3.000
 OKY  S09   C12  C17  119.45  3.000
 OKY  S09   C12  C13  119.53  3.000
 OKY  C17   C12  C13  120.98  3.000
 OKY  H14   C14  C15  122.27  3.000
 OKY  H14   C14  C13  119.44  3.000
 OKY  C15   C14  C13  118.29  3.000
 OKY  C18   C16  C17  128.85  3.000
 OKY  C17   C16  C15  120.95  3.000
 OKY  C18   C16  C15  110.19  3.000
 OKY  H20   C18  H15  107.24  3.000
 OKY  H20   C18  C19  111.76  3.000
 OKY  H15   C18  C19  111.44  3.000
 OKY  H20   C18  C16  112.70  3.000
 OKY  H15   C18  C16  110.47  3.000
 OKY  C19   C18  C16  103.31  3.000
 OKY  H21   C19  H16  108.16  3.000
 OKY  H21   C19  N20  109.71  3.000
 OKY  H16   C19  N20  110.63  3.000
 OKY  H21   C19  C18  111.43  3.000
 OKY  H16   C19  C18  112.05  3.000
 OKY  N20   C19  C18  104.84  3.000
 OKY  H19   C23  H18  107.28  3.000
 OKY  H19   C23  H17  108.68  3.000
 OKY  H18   C23  H17  108.59  3.000
 OKY  H19   C23  C21  111.22  3.000
 OKY  H18   C23  C21  111.65  3.000
 OKY  H17   C23  C21  109.34  3.000
 OKY  C29   C25  C26  118.37  3.000
 OKY  C26   C25  C24  121.71  3.000
 OKY  C29   C25  C24  119.84  3.000
 OKY  CL28  C27  C01  118.43  3.000
 OKY  CL28  C27  C26  118.97  3.000
 OKY  C01   C27  C26  122.58  3.000
 OKY  F32   C29  F31  106.60  3.000
 OKY  F31   C29  F30  106.92  3.000
 OKY  F32   C29  F30  107.07  3.000
 OKY  F31   C29  C25  111.34  3.000
 OKY  F32   C29  C25  111.89  3.000
 OKY  F30   C29  C25  112.66  3.000
 OKY  C08   N03  C04  112.07  3.000
 OKY  C04   N03  C02  118.57  3.000
 OKY  C08   N03  C02  118.68  3.000
 OKY  S09   N06  C07  116.61  3.000
 OKY  C07   N06  C05  111.42  3.000
 OKY  S09   N06  C05  117.09  3.000
 OKY  C19   N20  C21  123.51  3.000
 OKY  C21   N20  C15  126.05  3.000
 OKY  C19   N20  C15  110.32  3.000
 OKY  O11   S09  O10  119.55  3.000
 OKY  O11   S09  N06  106.50  3.000
 OKY  O10   S09  N06  106.57  3.000
 OKY  N06   S09  C12  106.69  3.000
 OKY  O11   S09  C12  108.54  3.000
 OKY  O10   S09  C12  108.31  3.000
 OKY  O22   C21  N20  121.99  3.000
 OKY  O22   C21  C23  122.34  3.000
 OKY  N20   C21  C23  115.67  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
 OKY  CONST_01  C16   C17  C12  C13     0.00   0.0  0
 OKY  CONST_02  C16   C15  C14  C13     0.00   0.0  0
 OKY  CONST_03  C12   C17  C16  C15     0.00   0.0  0
 OKY  CONST_04  C12   C13  C14  C15     0.00   0.0  0
 OKY  CONST_05  C14   C15  C16  C17     0.00   0.0  0
 OKY  CONST_06  C14   C13  C12  C17     0.00   0.0  0
 OKY  CONST_07  C27   C01  C02  C24     0.00   0.0  0
 OKY  CONST_08  C27   C26  C25  C24     0.00   0.0  0
 OKY  CONST_09  C02   C24  C25  C26     0.00   0.0  0
 OKY  CONST_10  C02   C01  C27  C26     0.00   0.0  0
 OKY  CONST_11  C25   C24  C02  C01     0.00   0.0  0
 OKY  CONST_12  C25   C26  C27  C01     0.00   0.0  0
 OKY  CONST_13  N03   C02  C24  C25   180.00   0.0  0
 OKY  CONST_14  N03   C02  C01  C27   180.00   0.0  0
 OKY  CONST_15  C29   C25  C24  C02   180.00   0.0  0
 OKY  CONST_16  CL28  C27  C01  C02   180.00   0.0  0
 OKY  CONST_17  S09   C12  C13  C14   180.00   0.0  0
 OKY  CONST_18  S09   C12  C17  C16   180.00   0.0  0
 OKY  CONST_19  CL28  C27  C26  C25   180.00   0.0  0
 OKY  CONST_20  C29   C25  C26  C27   180.00   0.0  0
 OKY  CONST_21  H2    C17  C12  C13   180.00   0.0  0
 OKY  CONST_22  H1    C13  C14  C15   180.00   0.0  0
 OKY  CONST_23  H5    C01  C02  C24   180.00   0.0  0
 OKY  CONST_24  H4    C26  C25  C24   180.00   0.0  0
 OKY  CONST_25  H3    C24  C25  C26   180.00   0.0  0
 OKY  CONST_26  H14   C14  C13  C12   180.00   0.0  0
 OKY  CONST_27  C23   C21  N20  C15   180.00   0.0  0
 OKY  CONST_28  O22   C21  N20  C15     0.00   0.0  0
 OKY  CONST_29  C23   C21  N20  C19     0.00   0.0  0
 OKY  CONST_30  O22   C21  N20  C19   180.00   0.0  0
 OKY  Var_01    C19   C18  C16  C15    -9.90  30.0  1
 OKY  Var_02    C18   C19  N20  C15   -12.73  30.0  1
 OKY  Var_03    C08   N03  C02  C24  -173.52  30.0  2
 OKY  Var_04    C07   C08  N03  C02   160.72  30.0  1
 OKY  Var_05    C05   C04  N03  C02  -159.85  30.0  1
 OKY  Var_06    C07   N06  C05  C04    59.09  30.0  1
 OKY  Var_07    C08   C07  N06  C05   -58.91  30.0  1
 OKY  Var_08    C19   N20  C15  C14  -172.23  30.0  1
 OKY  Var_09    N20   C19  C18  C16    13.19  30.0  1
 OKY  Var_10    N06   C07  C08  N03    55.88  30.0  1
 OKY  Var_11    N06   C05  C04  N03   -56.77  30.0  1
 OKY  Var_12    N06   S09  C12  C13   -91.83  30.0  2
 OKY  Var_13    C12   S09  N06  C05   -70.99  30.0  2
 OKY  Var_14    F30   C29  C25  C24   -22.61  30.0  2
 OKY  Var_15    H17   C23  C21  N20   179.59  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
 OKY  plan-1  C24   0.020
 OKY  plan-1  C26   0.020
 OKY  plan-1  C01   0.020
 OKY  plan-1  C02   0.020
 OKY  plan-1  C25   0.020
 OKY  plan-1  C27   0.020
 OKY  plan-1  C29   0.020
 OKY  plan-1  N03   0.020
 OKY  plan-1  CL28  0.020
 OKY  plan-1  H4    0.020
 OKY  plan-1  H5    0.020
 OKY  plan-1  H3    0.020
 OKY  plan-2  C13   0.020
 OKY  plan-2  C15   0.020
 OKY  plan-2  C17   0.020
 OKY  plan-2  C12   0.020
 OKY  plan-2  C14   0.020
 OKY  plan-2  C16   0.020
 OKY  plan-2  C18   0.020
 OKY  plan-2  N20   0.020
 OKY  plan-2  S09   0.020
 OKY  plan-2  H1    0.020
 OKY  plan-2  H2    0.020
 OKY  plan-2  H14   0.020
 OKY  plan-3  C15   0.020
 OKY  plan-3  C19   0.020
 OKY  plan-3  C23   0.020
 OKY  plan-3  N20   0.020
 OKY  plan-3  O22   0.020
 OKY  plan-3  C21   0.020

