# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 11:04:49 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 3-{[(1S,2S,3R)-2,3-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)c3[C@@H](F)[C@@H](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
 72Q  72Q  3-{[(1S,2S,3R)-2,3-difluoro-1-hydroxy-7-(methylsulfonyl)-2,3-dihydro-1H-inden-4-yl]oxy}-5-fluorobenzonitrile  ligand  38  26  .  2021-08-05  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_72Q
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
 72Q  N1   N  NS    0  -0.236  -5.5293  -0.8245   3.3669
 72Q  C16  C  CSP   0   0.071  -5.0890  -0.5724   2.3335
 72Q  C11  C  CR6   0   0.024  -4.5445  -0.2590   1.0506
 72Q  C12  C  CR16  0  -0.296  -3.2560   0.2609   0.9680
 72Q  C13  C  CR6   0   0.336  -2.7523   0.5652  -0.2849
 72Q  C14  C  CR16  0  -0.438  -3.4937   0.3614  -1.4375
 72Q  C15  C  CR6   0   0.560  -4.7704  -0.1528  -1.3080
 72Q  F3   F  F     0  -0.297  -5.4942  -0.3484  -2.4109
 72Q  C10  C  CR16  0  -0.400  -5.3212  -0.4746  -0.0854
 72Q  O4   O  O2    0  -0.493  -1.5099   1.1271  -0.3949
 72Q  C2   C  CR6   0   0.335  -0.4132   0.3400  -0.3298
 72Q  C3   C  CR16  0  -0.338  -0.4469  -1.0474  -0.3502
 72Q  C4   C  CR16  0  -0.240   0.7414  -1.7603  -0.3446
 72Q  C8   C  CR56  0  -0.078   0.8157   0.9857  -0.2686
 72Q  C9   C  CR15  0   0.184   1.0782   2.4619  -0.2759
 72Q  F2   F  F     0  -0.355   0.2228   3.1758   0.5357
 72Q  C5   C  CR15  0   0.091   2.5151   2.5437   0.2230
 72Q  F1   F  F     0  -0.365   2.4983   2.4792   1.6043
 72Q  C7   C  CR56  0   0.177   2.0055   0.2739  -0.2583
 72Q  C6   C  CR15  0  -0.050   3.1553   1.2565  -0.3129
 72Q  O1   O  OH1   0  -0.647   4.2679   0.8393   0.4058
 72Q  C1   C  CR6   0  -0.324   1.9746  -1.1195  -0.3109
 72Q  S1   S  S     0   1.211   3.4117  -2.1800  -0.2920
 72Q  O2   O  OS    0  -0.659   4.1400  -2.0122   0.9591
 72Q  O3   O  OS    0  -0.673   2.9396  -3.5272  -0.6170
 72Q  C17  C  CH3   0  -0.802   4.4144  -1.6424  -1.6567
 72Q  H1   H  HCR6  0   0.310  -2.6684   0.4309   1.8602
 72Q  H2   H  HCR6  0   0.317  -3.0888   0.6046  -2.4115
 72Q  H3   H  HCR6  0   0.312  -6.3224  -0.8767  -0.0147
 72Q  H4   H  HCR6  0   0.301  -1.3798  -1.5930  -0.3918
 72Q  H5   H  HCR6  0   0.297   0.6876  -2.8388  -0.3812
 72Q  H6   H  HCR5  0   0.259   1.0052   2.8696  -1.2885
 72Q  H7   H  HCR5  0   0.254   3.0417   3.4514  -0.0744
 72Q  H8   H  HCR5  0   0.274   3.3909   1.4257  -1.3738
 72Q  H9   H  HOH1  0   0.469   5.0298   1.3558   0.1231
 72Q  H10  H  HCH3  0   0.295   4.8142  -0.6516  -1.4712
 72Q  H11  H  HCH3  0   0.316   5.2325  -2.3581  -1.7348
 72Q  H12  H  HCH3  0   0.297   3.8187  -1.6605  -2.5663

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
 72Q  F1   C5   single    1.383  0.020  1.383
 72Q  F2   C9   single    1.378  0.020  1.378
 72Q  C5   C9   single    1.523  0.020  1.523
 72Q  C5   C6   single    1.534  0.020  1.534
 72Q  C9   C8   single    1.499  0.020  1.499
 72Q  O1   C6   single    1.389  0.020  1.389
 72Q  C6   C7   single    1.513  0.020  1.513
 72Q  O4   C13  single    1.368  0.020  1.368
 72Q  O4   C2   single    1.351  0.020  1.351
 72Q  C8   C2   aromatic  1.390  0.020  1.390
 72Q  C8   C7   aromatic  1.387  0.020  1.387
 72Q  C14  C13  aromatic  1.385  0.020  1.385
 72Q  C14  C15  aromatic  1.382  0.020  1.382
 72Q  C13  C12  aromatic  1.384  0.020  1.384
 72Q  F3   C15  single    1.334  0.020  1.334
 72Q  C15  C10  aromatic  1.379  0.020  1.379
 72Q  C2   C3   aromatic  1.388  0.020  1.388
 72Q  C7   C1   aromatic  1.395  0.020  1.395
 72Q  C12  C11  aromatic  1.392  0.020  1.392
 72Q  C10  C11  aromatic  1.393  0.020  1.393
 72Q  C11  C16  single    1.429  0.020  1.429
 72Q  O2   S1   double    1.457  0.020  1.457
 72Q  C3   C4   aromatic  1.386  0.020  1.386
 72Q  C1   C4   aromatic  1.390  0.020  1.390
 72Q  C1   S1   single    1.786  0.020  1.786
 72Q  C16  N1   triple    1.151  0.020  1.151
 72Q  S1   C17  single    1.777  0.020  1.777
 72Q  S1   O3   double    1.464  0.020  1.464
 72Q  C12  H1   single    0.930  0.020  1.080
 72Q  C14  H2   single    0.930  0.020  1.080
 72Q  C10  H3   single    0.930  0.020  1.080
 72Q  C3   H4   single    0.930  0.020  1.080
 72Q  C4   H5   single    0.930  0.020  1.080
 72Q  C9   H6   single    0.970  0.020  1.090
 72Q  C5   H7   single    0.970  0.020  1.090
 72Q  C6   H8   single    0.970  0.020  1.090
 72Q  O1   H9   single    0.850  0.020  0.980
 72Q  C17  H10  single    0.970  0.020  1.090
 72Q  C17  H11  single    0.970  0.020  1.090
 72Q  C17  H12  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
 72Q  C11  C16  N1   180.00  3.000
 72Q  C10  C11  C12  121.71  3.000
 72Q  C10  C11  C16  119.07  3.000
 72Q  C12  C11  C16  119.21  3.000
 72Q  H1   C12  C13  120.96  3.000
 72Q  H1   C12  C11  120.84  3.000
 72Q  C13  C12  C11  118.20  3.000
 72Q  O4   C13  C14  118.65  3.000
 72Q  C14  C13  C12  121.73  3.000
 72Q  O4   C13  C12  119.57  3.000
 72Q  H2   C14  C15  120.88  3.000
 72Q  H2   C14  C13  121.02  3.000
 72Q  C15  C14  C13  118.10  3.000
 72Q  C10  C15  F3   118.83  3.000
 72Q  C10  C15  C14  122.60  3.000
 72Q  F3   C15  C14  118.58  3.000
 72Q  H3   C10  C15  120.97  3.000
 72Q  H3   C10  C11  121.37  3.000
 72Q  C15  C10  C11  117.66  3.000
 72Q  C2   O4   C13  119.60  3.000
 72Q  C8   C2   C3   119.11  3.000
 72Q  C3   C2   O4   124.18  3.000
 72Q  C8   C2   O4   116.69  3.000
 72Q  H4   C3   C4   118.71  3.000
 72Q  H4   C3   C2   121.72  3.000
 72Q  C4   C3   C2   119.56  3.000
 72Q  H5   C4   C1   120.34  3.000
 72Q  H5   C4   C3   118.08  3.000
 72Q  C1   C4   C3   121.58  3.000
 72Q  C7   C8   C9   110.81  3.000
 72Q  C7   C8   C2   121.38  3.000
 72Q  C9   C8   C2   127.74  3.000
 72Q  H6   C9   C5   110.25  3.000
 72Q  H6   C9   F2   108.09  3.000
 72Q  C5   C9   F2   111.39  3.000
 72Q  H6   C9   C8   111.09  3.000
 72Q  C5   C9   C8   102.50  3.000
 72Q  F2   C9   C8   113.48  3.000
 72Q  H7   C5   C6   113.67  3.000
 72Q  H7   C5   F1   108.48  3.000
 72Q  C6   C5   F1   108.35  3.000
 72Q  H7   C5   C9   114.26  3.000
 72Q  C6   C5   C9   103.54  3.000
 72Q  F1   C5   C9   108.25  3.000
 72Q  C1   C7   C6   131.61  3.000
 72Q  C1   C7   C8   119.58  3.000
 72Q  C6   C7   C8   108.56  3.000
 72Q  H8   C6   O1   111.95  3.000
 72Q  H8   C6   C7   107.30  3.000
 72Q  O1   C6   C7   113.27  3.000
 72Q  H8   C6   C5   107.29  3.000
 72Q  C7   C6   C5   102.42  3.000
 72Q  O1   C6   C5   113.93  3.000
 72Q  H9   O1   C6   108.71  3.000
 72Q  S1   C1   C7   125.10  3.000
 72Q  S1   C1   C4   116.13  3.000
 72Q  C7   C1   C4   118.75  3.000
 72Q  C17  S1   O3   106.85  3.000
 72Q  O3   S1   O2   117.24  3.000
 72Q  C17  S1   O2   110.03  3.000
 72Q  O3   S1   C1   106.53  3.000
 72Q  C17  S1   C1   105.44  3.000
 72Q  O2   S1   C1   110.05  3.000
 72Q  H12  C17  H11  109.90  3.000
 72Q  H12  C17  H10  111.11  3.000
 72Q  H11  C17  H10  109.61  3.000
 72Q  H12  C17  S1   109.17  3.000
 72Q  H11  C17  S1   106.26  3.000
 72Q  H10  C17  S1   110.68  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
 72Q  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 72Q  CONST_02  C14  C15  C10  C11     0.00   0.0  0
 72Q  CONST_03  C15  C14  C13  C12     0.00   0.0  0
 72Q  CONST_04  C15  C10  C11  C12     0.00   0.0  0
 72Q  CONST_05  C10  C15  C14  C13     0.00   0.0  0
 72Q  CONST_06  C10  C11  C12  C13     0.00   0.0  0
 72Q  CONST_07  C1   C7   C8   C2      0.00   0.0  0
 72Q  CONST_08  C1   C4   C3   C2      0.00   0.0  0
 72Q  CONST_09  C7   C8   C2   C3      0.00   0.0  0
 72Q  CONST_10  C7   C1   C4   C3      0.00   0.0  0
 72Q  CONST_11  C8   C2   C3   C4      0.00   0.0  0
 72Q  CONST_12  C8   C7   C1   C4      0.00   0.0  0
 72Q  CONST_13  C13  C12  C11  C16   180.00   0.0  0
 72Q  CONST_14  C15  C10  C11  C16   180.00   0.0  0
 72Q  CONST_15  O4   C13  C12  C11   180.00   0.0  0
 72Q  CONST_16  F3   C15  C10  C11   180.00   0.0  0
 72Q  CONST_17  F3   C15  C14  C13   180.00   0.0  0
 72Q  CONST_18  O4   C13  C14  C15   180.00   0.0  0
 72Q  CONST_19  C9   C8   C2   O4      0.00   0.0  0
 72Q  CONST_20  C7   C8   C2   O4    180.00   0.0  0
 72Q  CONST_21  C4   C3   C2   O4    180.00   0.0  0
 72Q  CONST_22  S1   C1   C4   C3    180.00   0.0  0
 72Q  CONST_23  S1   C1   C7   C8    180.00   0.0  0
 72Q  CONST_24  S1   C1   C7   C6      0.00   0.0  0
 72Q  CONST_25  H2   C14  C13  C12   180.00   0.0  0
 72Q  CONST_26  H3   C10  C11  C12   180.00   0.0  0
 72Q  CONST_27  H1   C12  C13  C14   180.00   0.0  0
 72Q  CONST_28  H5   C4   C3   C2    180.00   0.0  0
 72Q  CONST_29  H4   C3   C2   C8    180.00   0.0  0
 72Q  Var_01    C8   C2   O4   C13  -171.67  30.0  2
 72Q  Var_02    O2   S1   C1   C4   -115.74  30.0  2
 72Q  Var_03    H10  C17  S1   C1     67.98  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
 72Q  chir_01  C9  F2  C5  C8  negativ
 72Q  chir_02  C5  F1  C9  C6  positiv
 72Q  chir_03  C6  O1  C5  C7  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
 72Q  plan-1  N1   0.020
 72Q  plan-1  C16  0.020
 72Q  plan-1  C11  0.020
 72Q  plan-1  C12  0.020
 72Q  plan-1  C13  0.020
 72Q  plan-1  C14  0.020
 72Q  plan-1  C15  0.020
 72Q  plan-1  F3   0.020
 72Q  plan-1  C10  0.020
 72Q  plan-1  O4   0.020
 72Q  plan-1  H1   0.020
 72Q  plan-1  H2   0.020
 72Q  plan-1  H3   0.020
 72Q  plan-2  O4   0.020
 72Q  plan-2  C2   0.020
 72Q  plan-2  C3   0.020
 72Q  plan-2  C4   0.020
 72Q  plan-2  C8   0.020
 72Q  plan-2  C9   0.020
 72Q  plan-2  C7   0.020
 72Q  plan-2  C6   0.020
 72Q  plan-2  C1   0.020
 72Q  plan-2  S1   0.020
 72Q  plan-2  H4   0.020
 72Q  plan-2  H5   0.020

