# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 06:13:17 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 1-[5-({4-[3-(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)c4cccc(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
 OKV  OKV  1-[5-({4-[3-(trifluoromethyl)phenyl]piperazin-1-yl}sulfonyl)-2,3-dihydro-1H-indol-1-yl]ethan-1-one  ligand  53  31  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OKV
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
 OKV  C13  C  CR16  0  -0.237  -3.4879  -1.7045   0.2485
 OKV  C15  C  CR56  0   0.437  -4.6013   0.4069   0.2720
 OKV  C17  C  CR16  0  -0.298  -3.1799  -0.1594  -1.5923
 OKV  C24  C  CR16  0  -0.369   3.7300   0.7195   0.2867
 OKV  C26  C  CR16  0  -0.313   5.7007   0.3566   1.6377
 OKV  C28  C  CT    0   1.048   5.3951   2.5567   0.5011
 OKV  C01  C  CR16  0  -0.350   4.0274  -1.3712   1.4197
 OKV  C02  C  CR6   0   0.403   3.2491  -0.5631   0.5836
 OKV  C04  C  CH2   0  -0.309   1.4749  -2.2347   0.5359
 OKV  C05  C  CH2   0  -0.311  -0.0164  -2.3021   0.2609
 OKV  C07  C  CH2   0  -0.316   0.2628  -0.7979  -1.6126
 OKV  C08  C  CH2   0  -0.302   1.7508  -0.7516  -1.3331
 OKV  C12  C  CR6   0  -0.211  -2.9132  -1.3816  -0.9738
 OKV  C14  C  CR16  0  -0.289  -4.3396  -0.8137   0.8874
 OKV  C16  C  CR56  0  -0.020  -4.0215   0.7249  -0.9588
 OKV  C18  C  CH2   0  -0.500  -4.4419   2.0937  -1.3966
 OKV  C19  C  CH2   0  -0.288  -5.4655   2.5144  -0.3334
 OKV  C23  C  CH3   0  -0.800  -6.9458   2.7533   2.0583
 OKV  C25  C  CR6   0  -0.175   4.9387   1.1618   0.7969
 OKV  C27  C  CR16  0  -0.229   5.2257  -0.9068   1.9421
 OKV  F29  F  F     0  -0.307   4.9363   3.0120  -0.6706
 OKV  F30  F  F     0  -0.315   4.9776   3.4227   1.4386
 OKV  F31  F  F     0  -0.309   6.7296   2.6535   0.4605
 OKV  N03  N  NT    0  -0.527   2.0188  -0.9742   0.0791
 OKV  N06  N  N     0  -0.567  -0.2655  -2.0843  -1.1622
 OKV  N20  N  NR5   0  -0.591  -5.4132   1.4570   0.6907
 OKV  O10  O  OS    0  -0.652  -2.0470  -3.8386  -1.2248
 OKV  O11  O  OS    0  -0.652  -1.7645  -2.2570  -3.1552
 OKV  O22  O  O     0  -0.467  -6.0597   0.6278   2.6940
 OKV  S09  S  S     0   1.375  -1.7724  -2.5004  -1.7219
 OKV  H1   H  HCR6  0   0.284  -3.2882  -2.6589   0.7158
 OKV  H2   H  HCR6  0   0.282  -2.7441   0.0935  -2.5501
 OKV  H3   H  HCR6  0   0.279   3.1389   1.3788  -0.3336
 OKV  H4   H  HCR6  0   0.267   6.6431   0.6933   2.0465
 OKV  H5   H  HCR6  0   0.278   3.7179  -2.3766   1.6672
 OKV  H6   H  HCH2  0   0.270   1.5991  -2.3221   1.6150
 OKV  H7   H  HCH2  0   0.233   1.9759  -3.0950   0.0698
 OKV  H8   H  HCH2  0   0.281  -0.3728  -3.2868   0.5557
 OKV  H9   H  HCH2  0   0.243  -0.5307  -1.5488   0.8709
 OKV  H10  H  HCH2  0   0.244  -0.2325   0.0366  -1.1001
 OKV  H11  H  HCH2  0   0.281   0.1098  -0.6857  -2.6836
 OKV  H12  H  HCH2  0   0.237   2.2612  -1.5036  -1.9503
 OKV  H13  H  HCH2  0   0.271   2.1127   0.2254  -1.6442
 OKV  H14  H  HCR6  0   0.289  -4.7785  -1.0834   1.8322
 OKV  H15  H  HCH2  0   0.278  -3.5885   2.7731  -1.4182
 OKV  H16  H  HCH2  0   0.272  -5.2162   3.4789   0.1054
 OKV  H17  H  HCH3  0   0.274  -6.3258   3.6506   2.0866
 OKV  H18  H  HCH3  0   0.271  -7.6658   2.8838   1.2491
 OKV  H19  H  HCH3  0   0.277  -7.4876   2.6775   2.9973
 OKV  H20  H  HCR6  0   0.267   5.8036  -1.5549   2.5874
 OKV  H21  H  HCH2  0   0.279  -4.8768   2.0903  -2.3957
 OKV  H22  H  HCH2  0   0.271  -6.4717   2.5806  -0.7482
 OKV  C21  C  C     0   0.512  -6.1117   1.5168   1.8624

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
 OKV  O11  S09  double    1.454  0.020  1.454
 OKV  C18  C16  single    1.497  0.020  1.497
 OKV  C18  C19  single    1.535  0.020  1.535
 OKV  C17  C16  aromatic  1.375  0.020  1.375
 OKV  C17  C12  aromatic  1.396  0.020  1.396
 OKV  C16  C15  aromatic  1.397  0.020  1.397
 OKV  S09  O10  double    1.454  0.020  1.454
 OKV  S09  C12  single    1.764  0.020  1.764
 OKV  S09  N06  single    1.660  0.020  1.660
 OKV  C19  N20  single    1.473  0.020  1.473
 OKV  C12  C13  aromatic  1.389  0.020  1.389
 OKV  C15  N20  single    1.392  0.020  1.392
 OKV  C15  C14  aromatic  1.392  0.020  1.392
 OKV  N20  C21  single    1.365  0.020  1.365
 OKV  C13  C14  aromatic  1.388  0.020  1.388
 OKV  N06  C05  single    1.461  0.020  1.461
 OKV  N06  C07  single    1.462  0.020  1.462
 OKV  C05  C04  single    1.518  0.020  1.518
 OKV  C23  C21  single    1.504  0.020  1.504
 OKV  C21  O22  double    1.218  0.020  1.218
 OKV  C04  N03  single    1.447  0.020  1.447
 OKV  C07  C08  single    1.515  0.020  1.515
 OKV  C08  N03  single    1.454  0.020  1.454
 OKV  N03  C02  single    1.392  0.020  1.392
 OKV  C24  C02  aromatic  1.402  0.020  1.402
 OKV  C24  C25  aromatic  1.385  0.020  1.385
 OKV  C02  C01  aromatic  1.399  0.020  1.399
 OKV  F31  C28  single    1.339  0.020  1.339
 OKV  F29  C28  single    1.338  0.020  1.338
 OKV  C28  C25  single    1.497  0.020  1.497
 OKV  C28  F30  single    1.343  0.020  1.343
 OKV  C25  C26  aromatic  1.391  0.020  1.391
 OKV  C01  C27  aromatic  1.387  0.020  1.387
 OKV  C26  C27  aromatic  1.384  0.020  1.384
 OKV  C13  H1   single    0.930  0.020  1.080
 OKV  C17  H2   single    0.930  0.020  1.080
 OKV  C24  H3   single    0.930  0.020  1.080
 OKV  C26  H4   single    0.930  0.020  1.080
 OKV  C01  H5   single    0.930  0.020  1.080
 OKV  C04  H6   single    0.970  0.020  1.090
 OKV  C04  H7   single    0.970  0.020  1.090
 OKV  C05  H8   single    0.970  0.020  1.090
 OKV  C05  H9   single    0.970  0.020  1.090
 OKV  C07  H10  single    0.970  0.020  1.090
 OKV  C07  H11  single    0.970  0.020  1.090
 OKV  C08  H12  single    0.970  0.020  1.090
 OKV  C08  H13  single    0.970  0.020  1.090
 OKV  C14  H14  single    0.930  0.020  1.080
 OKV  C18  H15  single    0.970  0.020  1.090
 OKV  C19  H16  single    0.970  0.020  1.090
 OKV  C23  H17  single    0.970  0.020  1.090
 OKV  C23  H18  single    0.970  0.020  1.090
 OKV  C23  H19  single    0.970  0.020  1.090
 OKV  C27  H20  single    0.930  0.020  1.080
 OKV  C18  H21  single    0.970  0.020  1.090
 OKV  C19  H22  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
 OKV  H1   C13  C14  118.74  3.000
 OKV  H1   C13  C12  120.61  3.000
 OKV  C14  C13  C12  120.65  3.000
 OKV  N20  C15  C16  109.59  3.000
 OKV  N20  C15  C14  129.67  3.000
 OKV  C16  C15  C14  120.74  3.000
 OKV  H2   C17  C16  120.25  3.000
 OKV  H2   C17  C12  121.33  3.000
 OKV  C16  C17  C12  118.41  3.000
 OKV  H3   C24  C25  119.60  3.000
 OKV  H3   C24  C02  119.47  3.000
 OKV  C25  C24  C02  120.92  3.000
 OKV  H4   C26  C27  120.03  3.000
 OKV  H4   C26  C25  121.71  3.000
 OKV  C27  C26  C25  118.25  3.000
 OKV  F31  C28  F30  106.53  3.000
 OKV  F30  C28  F29  106.58  3.000
 OKV  F31  C28  F29  106.90  3.000
 OKV  F30  C28  C25  111.60  3.000
 OKV  F29  C28  C25  112.67  3.000
 OKV  F31  C28  C25  112.16  3.000
 OKV  H5   C01  C27  118.20  3.000
 OKV  H5   C01  C02  120.98  3.000
 OKV  C27  C01  C02  120.81  3.000
 OKV  N03  C02  C01  122.53  3.000
 OKV  C01  C02  C24  117.66  3.000
 OKV  N03  C02  C24  119.79  3.000
 OKV  H7   C04  H6   107.77  3.000
 OKV  H7   C04  N03  112.13  3.000
 OKV  H6   C04  N03  109.86  3.000
 OKV  H7   C04  C05  109.64  3.000
 OKV  H6   C04  C05  106.72  3.000
 OKV  N03  C04  C05  110.54  3.000
 OKV  H9   C05  H8   108.49  3.000
 OKV  H9   C05  N06  111.05  3.000
 OKV  H8   C05  N06  110.07  3.000
 OKV  H9   C05  C04  109.22  3.000
 OKV  H8   C05  C04  108.24  3.000
 OKV  N06  C05  C04  109.71  3.000
 OKV  H11  C07  H10  108.53  3.000
 OKV  H11  C07  N06  110.08  3.000
 OKV  H10  C07  N06  111.24  3.000
 OKV  H11  C07  C08  108.47  3.000
 OKV  H10  C07  C08  109.50  3.000
 OKV  N06  C07  C08  108.97  3.000
 OKV  H13  C08  H12  107.44  3.000
 OKV  H13  C08  N03  110.73  3.000
 OKV  H12  C08  N03  110.80  3.000
 OKV  H13  C08  C07  107.56  3.000
 OKV  H12  C08  C07  109.38  3.000
 OKV  N03  C08  C07  110.82  3.000
 OKV  S09  C12  C17  119.40  3.000
 OKV  S09  C12  C13  119.56  3.000
 OKV  C17  C12  C13  120.98  3.000
 OKV  H14  C14  C15  122.10  3.000
 OKV  H14  C14  C13  119.57  3.000
 OKV  C15  C14  C13  118.33  3.000
 OKV  C18  C16  C17  128.67  3.000
 OKV  C17  C16  C15  120.89  3.000
 OKV  C18  C16  C15  110.43  3.000
 OKV  H21  C18  H15  107.22  3.000
 OKV  H21  C18  C19  111.71  3.000
 OKV  H15  C18  C19  111.39  3.000
 OKV  H21  C18  C16  112.16  3.000
 OKV  H15  C18  C16  110.82  3.000
 OKV  C19  C18  C16  103.61  3.000
 OKV  H22  C19  H16  108.11  3.000
 OKV  H22  C19  N20  109.93  3.000
 OKV  H16  C19  N20  110.35  3.000
 OKV  H22  C19  C18  111.62  3.000
 OKV  H16  C19  C18  111.68  3.000
 OKV  N20  C19  C18  105.14  3.000
 OKV  H19  C23  H18  108.68  3.000
 OKV  H19  C23  H17  108.56  3.000
 OKV  H18  C23  H17  107.22  3.000
 OKV  H19  C23  C21  109.36  3.000
 OKV  H18  C23  C21  111.57  3.000
 OKV  H17  C23  C21  111.36  3.000
 OKV  C28  C25  C26  119.45  3.000
 OKV  C26  C25  C24  121.06  3.000
 OKV  C28  C25  C24  119.40  3.000
 OKV  H20  C27  C01  119.04  3.000
 OKV  H20  C27  C26  119.66  3.000
 OKV  C01  C27  C26  121.29  3.000
 OKV  C08  N03  C04  111.75  3.000
 OKV  C08  N03  C02  118.01  3.000
 OKV  C04  N03  C02  118.37  3.000
 OKV  S09  N06  C07  116.40  3.000
 OKV  C07  N06  C05  111.70  3.000
 OKV  S09  N06  C05  116.47  3.000
 OKV  C19  N20  C21  123.16  3.000
 OKV  C21  N20  C15  126.13  3.000
 OKV  C19  N20  C15  110.68  3.000
 OKV  O11  S09  O10  119.49  3.000
 OKV  O10  S09  N06  106.67  3.000
 OKV  O11  S09  N06  106.59  3.000
 OKV  N06  S09  C12  106.56  3.000
 OKV  O10  S09  C12  108.45  3.000
 OKV  O11  S09  C12  108.38  3.000
 OKV  O22  C21  N20  122.13  3.000
 OKV  O22  C21  C23  122.31  3.000
 OKV  N20  C21  C23  115.56  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
 OKV  CONST_01  C16  C17  C12  C13     0.00   0.0  0
 OKV  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 OKV  CONST_03  C12  C17  C16  C15     0.00   0.0  0
 OKV  CONST_04  C12  C13  C14  C15     0.00   0.0  0
 OKV  CONST_05  C14  C15  C16  C17     0.00   0.0  0
 OKV  CONST_06  C14  C13  C12  C17     0.00   0.0  0
 OKV  CONST_07  C27  C01  C02  C24     0.00   0.0  0
 OKV  CONST_08  C27  C26  C25  C24     0.00   0.0  0
 OKV  CONST_09  C02  C24  C25  C26     0.00   0.0  0
 OKV  CONST_10  C02  C01  C27  C26     0.00   0.0  0
 OKV  CONST_11  C25  C24  C02  C01     0.00   0.0  0
 OKV  CONST_12  C25  C26  C27  C01     0.00   0.0  0
 OKV  CONST_13  N03  C02  C24  C25   180.00   0.0  0
 OKV  CONST_14  N03  C02  C01  C27   180.00   0.0  0
 OKV  CONST_15  C02  C24  C25  C28   180.00   0.0  0
 OKV  CONST_16  C27  C26  C25  C28   180.00   0.0  0
 OKV  CONST_17  S09  C12  C13  C14   180.00   0.0  0
 OKV  CONST_18  S09  C12  C17  C16   180.00   0.0  0
 OKV  CONST_19  H2   C17  C12  C13   180.00   0.0  0
 OKV  CONST_20  H1   C13  C14  C15   180.00   0.0  0
 OKV  CONST_21  H5   C01  C02  C24   180.00   0.0  0
 OKV  CONST_22  H4   C26  C25  C24   180.00   0.0  0
 OKV  CONST_23  H3   C24  C25  C26   180.00   0.0  0
 OKV  CONST_24  H20  C27  C01  C02   180.00   0.0  0
 OKV  CONST_25  H14  C14  C13  C12   180.00   0.0  0
 OKV  CONST_26  C23  C21  N20  C15   180.00   0.0  0
 OKV  CONST_27  O22  C21  N20  C15     0.00   0.0  0
 OKV  CONST_28  C23  C21  N20  C19     0.00   0.0  0
 OKV  CONST_29  O22  C21  N20  C19   180.00   0.0  0
 OKV  Var_01    C19  C18  C16  C15    -5.33  30.0  1
 OKV  Var_02    C18  C19  N20  C15    -6.88  30.0  1
 OKV  Var_03    C04  N03  C02  C24  -172.47  30.0  2
 OKV  Var_04    C05  C04  N03  C02   161.31  30.0  1
 OKV  Var_05    C07  C08  N03  C02  -160.39  30.0  1
 OKV  Var_06    C07  N06  C05  C04   -58.03  30.0  1
 OKV  Var_07    C08  C07  N06  C05    58.21  30.0  1
 OKV  Var_08    C19  N20  C15  C14  -175.82  30.0  1
 OKV  Var_09    N20  C19  C18  C16     7.11  30.0  1
 OKV  Var_10    N06  C05  C04  N03    56.10  30.0  1
 OKV  Var_11    N06  C07  C08  N03   -56.89  30.0  1
 OKV  Var_12    N06  S09  C12  C13   -89.76  30.0  3
 OKV  Var_13    C12  S09  N06  C05    67.01  30.0  1
 OKV  Var_14    F31  C28  C25  C24  -149.76  30.0  2
 OKV  Var_15    H17  C23  C21  N20   -62.38  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
 OKV  plan-1  C24  0.020
 OKV  plan-1  C26  0.020
 OKV  plan-1  C28  0.020
 OKV  plan-1  C01  0.020
 OKV  plan-1  C02  0.020
 OKV  plan-1  C25  0.020
 OKV  plan-1  C27  0.020
 OKV  plan-1  N03  0.020
 OKV  plan-1  H3   0.020
 OKV  plan-1  H4   0.020
 OKV  plan-1  H5   0.020
 OKV  plan-1  H20  0.020
 OKV  plan-2  C13  0.020
 OKV  plan-2  C15  0.020
 OKV  plan-2  C17  0.020
 OKV  plan-2  C12  0.020
 OKV  plan-2  C14  0.020
 OKV  plan-2  C16  0.020
 OKV  plan-2  C18  0.020
 OKV  plan-2  N20  0.020
 OKV  plan-2  S09  0.020
 OKV  plan-2  H1   0.020
 OKV  plan-2  H2   0.020
 OKV  plan-2  H14  0.020
 OKV  plan-3  C15  0.020
 OKV  plan-3  C19  0.020
 OKV  plan-3  C23  0.020
 OKV  plan-3  N20  0.020
 OKV  plan-3  O22  0.020
 OKV  plan-3  C21  0.020

