# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:38:40 2022
#   Inital geometry file: a 104 line input string
#   Ligand name: 3-{[(1S)-2,2-difluoro-1-hydroxy-7-(methylsulfonyl)-2,3-dihydro-1H-inden-4-yl]oxy}-5-fluorobenzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)c1ccc(Oc2cc(F)cc(c2)C#N)c3CC(F)(F)[C@@H](O)c13
#
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
 79A  79A  3-{[(1S)-2,2-difluoro-1-hydroxy-7-(methylsulfonyl)-2,3-dihydro-1H-inden-4-yl]oxy}-5-fluorobenzonitrile  ligand  38  26  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_79A
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
 79A  N1   N  NS    0  -0.188  -5.0808  -1.1221   3.4122
 79A  C17  C  CSP   0   0.047  -4.8027  -0.6922   2.3810
 79A  C6   C  CR6   0   0.163  -4.4565  -0.1592   1.1017
 79A  C7   C  CR16  0  -0.355  -3.1426   0.2300   0.8630
 79A  C8   C  CR6   0   0.399  -2.8282   0.7481  -0.3837
 79A  C9   C  CR16  0  -0.425  -3.7867   0.8829  -1.3749
 79A  C10  C  CR6   0   0.448  -5.0820   0.4930  -1.0893
 79A  F1   F  F     0  -0.297  -6.0102   0.6235  -2.0378
 79A  C5   C  CR16  0  -0.430  -5.4481  -0.0338   0.1313
 79A  O1   O  O2    0  -0.461  -1.5674   1.1972  -0.6535
 79A  C1   C  CR6   0   0.284  -0.5129   0.3495  -0.5598
 79A  C14  C  CR56  0  -0.027   0.7284   0.9293  -0.3493
 79A  C15  C  CH2   0  -0.625   1.0239   2.3898  -0.1912
 79A  C11  C  CR5   0   0.747   2.4065   2.3415   0.4288
 79A  F3   F  F     0  -0.317   2.3079   2.2548   1.7826
 79A  F2   F  F     0  -0.365   3.1517   3.4482   0.1787
 79A  C13  C  CR56  0   0.180   1.8756   0.1504  -0.2725
 79A  C12  C  CR15  0  -0.165   3.0711   1.0596  -0.1074
 79A  O4   O  OH1   0  -0.664   4.0489   0.5358   0.7249
 79A  C4   C  CR6   0  -0.175   1.7834  -1.2314  -0.4285
 79A  S1   S  S     0   1.220   3.1544  -2.3732  -0.3179
 79A  C16  C  CH3   0  -0.860   4.3533  -1.7973  -1.4963
 79A  O3   O  OS    0  -0.653   3.7170  -2.3428   1.0257
 79A  O2   O  OS    0  -0.669   2.6639  -3.6617  -0.8086
 79A  C3   C  CR16  0  -0.304   0.5330  -1.8035  -0.6392
 79A  C2   C  CR16  0  -0.279  -0.6122  -1.0274  -0.7023
 79A  H1   H  HCR6  0   0.304  -2.3922   0.1384   1.6365
 79A  H2   H  HCR6  0   0.306  -3.5289   1.2878  -2.3451
 79A  H3   H  HCR6  0   0.307  -6.4686  -0.3326   0.3263
 79A  H4   H  HCH2  0   0.285   1.0659   2.8889  -1.1631
 79A  H5   H  HCH2  0   0.294   0.3064   2.9267   0.4303
 79A  H6   H  HCR5  0   0.264   3.4588   1.2914  -1.1114
 79A  H7   H  HOH1  0   0.460   4.8716   1.0179   0.5908
 79A  H8   H  HCH3  0   0.333   4.7823  -0.8530  -1.1804
 79A  H9   H  HCH3  0   0.327   5.1342  -2.5565  -1.5337
 79A  H10  H  HCH3  0   0.320   3.8803  -1.7060  -2.4713
 79A  H11  H  HCR6  0   0.268   0.4361  -2.8717  -0.7681
 79A  H12  H  HCR6  0   0.304  -1.5644  -1.5094  -0.8793

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
 79A  F3   C11  single    1.360  0.020  1.360
 79A  F2   C11  single    1.357  0.020  1.357
 79A  C11  C15  single    1.516  0.020  1.516
 79A  C11  C12  single    1.540  0.020  1.540
 79A  C15  C14  single    1.498  0.020  1.498
 79A  O1   C8   single    1.365  0.020  1.365
 79A  O1   C1   single    1.356  0.020  1.356
 79A  C12  O4   single    1.387  0.020  1.387
 79A  C12  C13  single    1.511  0.020  1.511
 79A  C9   C8   aromatic  1.385  0.020  1.385
 79A  C9   C10  aromatic  1.382  0.020  1.382
 79A  C14  C1   aromatic  1.386  0.020  1.386
 79A  C14  C13  aromatic  1.389  0.020  1.389
 79A  C8   C7   aromatic  1.386  0.020  1.386
 79A  F1   C10  single    1.334  0.020  1.334
 79A  C10  C5   aromatic  1.379  0.020  1.379
 79A  C1   C2   aromatic  1.388  0.020  1.388
 79A  C13  C4   aromatic  1.394  0.020  1.394
 79A  C7   C6   aromatic  1.391  0.020  1.391
 79A  C5   C6   aromatic  1.393  0.020  1.393
 79A  C6   C17  single    1.428  0.020  1.428
 79A  C2   C3   aromatic  1.385  0.020  1.385
 79A  O2   S1   double    1.463  0.020  1.463
 79A  C4   C3   aromatic  1.391  0.020  1.391
 79A  C4   S1   single    1.788  0.020  1.788
 79A  C17  N1   triple    1.151  0.020  1.151
 79A  S1   C16  single    1.777  0.020  1.777
 79A  S1   O3   double    1.457  0.020  1.457
 79A  C7   H1   single    0.930  0.020  1.080
 79A  C9   H2   single    0.930  0.020  1.080
 79A  C5   H3   single    0.930  0.020  1.080
 79A  C15  H4   single    0.970  0.020  1.090
 79A  C15  H5   single    0.970  0.020  1.090
 79A  C12  H6   single    0.970  0.020  1.090
 79A  O4   H7   single    0.850  0.020  0.980
 79A  C16  H8   single    0.970  0.020  1.090
 79A  C16  H9   single    0.970  0.020  1.090
 79A  C16  H10  single    0.970  0.020  1.090
 79A  C3   H11  single    0.930  0.020  1.080
 79A  C2   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
 79A  C6   C17  N1   180.00  3.000
 79A  C5   C6   C7   121.85  3.000
 79A  C5   C6   C17  119.01  3.000
 79A  C7   C6   C17  119.14  3.000
 79A  H1   C7   C8   121.16  3.000
 79A  H1   C7   C6   120.59  3.000
 79A  C8   C7   C6   118.24  3.000
 79A  O1   C8   C9   117.75  3.000
 79A  C9   C8   C7   121.53  3.000
 79A  O1   C8   C7   120.67  3.000
 79A  H2   C9   C10  120.91  3.000
 79A  H2   C9   C8   120.86  3.000
 79A  C10  C9   C8   118.23  3.000
 79A  C5   C10  F1   118.82  3.000
 79A  C5   C10  C9   122.64  3.000
 79A  F1   C10  C9   118.53  3.000
 79A  H3   C5   C10  121.06  3.000
 79A  H3   C5   C6   121.42  3.000
 79A  C10  C5   C6   117.52  3.000
 79A  C1   O1   C8   119.92  3.000
 79A  C2   C1   C14  119.65  3.000
 79A  C2   C1   O1   123.88  3.000
 79A  C14  C1   O1   116.45  3.000
 79A  C13  C14  C15  112.21  3.000
 79A  C13  C14  C1   120.90  3.000
 79A  C15  C14  C1   126.89  3.000
 79A  H5   C15  H4   107.89  3.000
 79A  H5   C15  C11  112.50  3.000
 79A  H4   C15  C11  110.06  3.000
 79A  H5   C15  C14  114.22  3.000
 79A  H4   C15  C14  111.02  3.000
 79A  C11  C15  C14  101.06  3.000
 79A  C12  C11  F2   112.18  3.000
 79A  C12  C11  F3   108.95  3.000
 79A  F2   C11  F3   105.97  3.000
 79A  C12  C11  C15  106.12  3.000
 79A  F2   C11  C15  113.53  3.000
 79A  F3   C11  C15  110.06  3.000
 79A  C4   C13  C12  131.39  3.000
 79A  C4   C13  C14  119.69  3.000
 79A  C12  C13  C14  108.79  3.000
 79A  H6   C12  O4   112.24  3.000
 79A  H6   C12  C13  107.80  3.000
 79A  O4   C12  C13  113.34  3.000
 79A  H6   C12  C11  107.11  3.000
 79A  C13  C12  C11  101.39  3.000
 79A  O4   C12  C11  114.18  3.000
 79A  H7   O4   C12  109.25  3.000
 79A  C3   C4   S1   115.86  3.000
 79A  S1   C4   C13  125.15  3.000
 79A  C3   C4   C13  118.95  3.000
 79A  O2   S1   O3   117.19  3.000
 79A  O3   S1   C16  110.14  3.000
 79A  O2   S1   C16  106.81  3.000
 79A  O3   S1   C4   109.87  3.000
 79A  C16  S1   C4   105.63  3.000
 79A  O2   S1   C4   106.53  3.000
 79A  H10  C16  H9   109.85  3.000
 79A  H10  C16  H8   111.11  3.000
 79A  H9   C16  H8   109.46  3.000
 79A  H10  C16  S1   109.17  3.000
 79A  H9   C16  S1   106.28  3.000
 79A  H8   C16  S1   110.86  3.000
 79A  H11  C3   C2   118.33  3.000
 79A  H11  C3   C4   120.35  3.000
 79A  C2   C3   C4   121.32  3.000
 79A  H12  C2   C3   119.05  3.000
 79A  H12  C2   C1   121.46  3.000
 79A  C3   C2   C1   119.49  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
 79A  CONST_01  C9   C8   C7   C6      0.00   0.0  0
 79A  CONST_02  C9   C10  C5   C6      0.00   0.0  0
 79A  CONST_03  C10  C9   C8   C7      0.00   0.0  0
 79A  CONST_04  C10  C5   C6   C7      0.00   0.0  0
 79A  CONST_05  C5   C10  C9   C8      0.00   0.0  0
 79A  CONST_06  C5   C6   C7   C8      0.00   0.0  0
 79A  CONST_07  C4   C13  C14  C1      0.00   0.0  0
 79A  CONST_08  C4   C3   C2   C1      0.00   0.0  0
 79A  CONST_09  C3   C2   C1   C14     0.00   0.0  0
 79A  CONST_10  C3   C4   C13  C14     0.00   0.0  0
 79A  CONST_11  C2   C1   C14  C13     0.00   0.0  0
 79A  CONST_12  C2   C3   C4   C13     0.00   0.0  0
 79A  CONST_13  C8   C7   C6   C17   180.00   0.0  0
 79A  CONST_14  C10  C5   C6   C17   180.00   0.0  0
 79A  CONST_15  O1   C8   C7   C6    180.00   0.0  0
 79A  CONST_16  F1   C10  C5   C6    180.00   0.0  0
 79A  CONST_17  F1   C10  C9   C8    180.00   0.0  0
 79A  CONST_18  O1   C8   C9   C10   180.00   0.0  0
 79A  CONST_19  C15  C14  C1   O1      0.00   0.0  0
 79A  CONST_20  C13  C14  C1   O1    180.00   0.0  0
 79A  CONST_21  C3   C2   C1   O1    180.00   0.0  0
 79A  CONST_22  S1   C4   C13  C14   180.00   0.0  0
 79A  CONST_23  S1   C4   C13  C12     0.00   0.0  0
 79A  CONST_24  C2   C3   C4   S1    180.00   0.0  0
 79A  CONST_25  H2   C9   C8   C7    180.00   0.0  0
 79A  CONST_26  H3   C5   C6   C7    180.00   0.0  0
 79A  CONST_27  H1   C7   C8   C9    180.00   0.0  0
 79A  CONST_28  H11  C3   C2   C1    180.00   0.0  0
 79A  CONST_29  H12  C2   C1   C14   180.00   0.0  0
 79A  Var_01    C11  C15  C14  C1    162.92  30.0  1
 79A  Var_02    C12  C11  C15  C14    30.05  30.0  1
 79A  Var_03    C14  C1   O1   C8   -156.64  30.0  2
 79A  Var_04    O2   S1   C4   C13  -168.77  30.0  2
 79A  Var_05    H8   C16  S1   C4     68.44  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
 79A  chir_01  C12  C11  O4  C13  negativ

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
 79A  plan-1  N1   0.020
 79A  plan-1  C17  0.020
 79A  plan-1  C6   0.020
 79A  plan-1  C7   0.020
 79A  plan-1  C8   0.020
 79A  plan-1  C9   0.020
 79A  plan-1  C10  0.020
 79A  plan-1  F1   0.020
 79A  plan-1  C5   0.020
 79A  plan-1  O1   0.020
 79A  plan-1  H1   0.020
 79A  plan-1  H2   0.020
 79A  plan-1  H3   0.020
 79A  plan-2  O1   0.020
 79A  plan-2  C1   0.020
 79A  plan-2  C14  0.020
 79A  plan-2  C15  0.020
 79A  plan-2  C13  0.020
 79A  plan-2  C12  0.020
 79A  plan-2  C4   0.020
 79A  plan-2  S1   0.020
 79A  plan-2  C3   0.020
 79A  plan-2  C2   0.020
 79A  plan-2  H11  0.020
 79A  plan-2  H12  0.020

