# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 11:57:58 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 3-({(1S)-7-[(difluoromethyl)sulfonyl]-2,2-difluoro-1-hydroxy-2,3-dihydro-1H-inden-4-yl}oxy)-5-fluorobenzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1c2c(CC1(F)F)c(Oc3cc(F)cc(c3)C#N)ccc2[S](=O)(=O)C(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
 86D  86D  3-({(1S)-7-[(difluoromethyl)sulfonyl]-2,2-difluoro-1-hydroxy-2,3-dihydro-1H-inden-4-yl}oxy)-5-fluorobenzonitrile  ligand  38  28  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_86D
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
 86D  N1   N  NS    0  -0.236  -6.5955  -0.4530   2.9982
 86D  C17  C  CSP   0   0.072  -5.9364  -0.2675   2.0728
 86D  C6   C  CR6   0   0.023  -5.1193  -0.0365   0.9241
 86D  C7   C  CR16  0  -0.299  -3.8454   0.5006   1.0929
 86D  C8   C  CR6   0   0.332  -3.0761   0.7222  -0.0346
 86D  C9   C  CR16  0  -0.430  -3.5389   0.4206  -1.3059
 86D  C10  C  CR6   0   0.560  -4.8071  -0.1143  -1.4261
 86D  F1   F  F     0  -0.296  -5.2623  -0.4117  -2.6437
 86D  C5   C  CR16  0  -0.399  -5.6179  -0.3548  -0.3361
 86D  O1   O  O2    0  -0.493  -1.8371   1.2893   0.1062
 86D  C1   C  CR6   0   0.338  -0.7459   0.4948   0.1562
 86D  C14  C  CR56  0   0.006   0.4794   1.1479   0.2363
 86D  C15  C  CH2   0  -0.576   0.7209   2.6276   0.2716
 86D  C11  C  CR5   0   0.743   2.2047   2.6803  -0.0494
 86D  F5   F  F     0  -0.329   2.8265   3.7790   0.4355
 86D  F2   F  F     0  -0.344   2.3788   2.7073  -1.4043
 86D  C13  C  CR56  0   0.184   1.6592   0.4262   0.2981
 86D  C12  C  CR15  0  -0.164   2.8199   1.3753   0.4879
 86D  O4   O  OH1   0  -0.647   3.0624   1.4743   1.8610
 86D  C4   C  CR6   0  -0.329   1.6170  -0.9659   0.2759
 86D  C3   C  CR16  0  -0.223   0.3919  -1.6169   0.1917
 86D  C2   C  CR16  0  -0.336  -0.7886  -0.8945   0.1428
 86D  S1   S  S     0   1.150   3.0729  -1.9557   0.2794
 86D  O2   O  OS    0  -0.629   4.1720  -1.2614   0.9297
 86D  O3   O  OS    0  -0.638   2.7279  -3.3147   0.6699
 86D  C16  C  CH1   0   0.402   3.5016  -2.0536  -1.5055
 86D  F3   F  F     0  -0.302   2.4043  -2.4456  -2.1694
 86D  F4   F  F     0  -0.303   3.8416  -0.8247  -1.9246
 86D  H1   H  HCR6  0   0.309  -3.4686   0.7432   2.0771
 86D  H2   H  HCR6  0   0.320  -2.9295   0.6024  -2.1822
 86D  H3   H  HCR6  0   0.313  -6.6061  -0.7775  -0.4596
 86D  H4   H  HCH2  0   0.297   0.1237   3.1912  -0.4464
 86D  H5   H  HCH2  0   0.299   0.5236   3.0340   1.2662
 86D  H6   H  HCR5  0   0.269   3.7140   1.1086  -0.0803
 86D  H7   H  HOH1  0   0.469   3.9749   1.7489   1.9969
 86D  H8   H  HCR6  0   0.301   0.3361  -2.6962   0.1783
 86D  H9   H  HCR6  0   0.304  -1.7244  -1.4336   0.0907
 86D  H12  H  HCH1  0   0.281   4.3216  -2.7616  -1.6453

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
 86D  N1   C17  triple    1.151  0.020  1.151
 86D  C17  C6   single    1.429  0.020  1.429
 86D  C6   C7   aromatic  1.393  0.020  1.393
 86D  C6   C5   aromatic  1.392  0.020  1.392
 86D  C7   C8   aromatic  1.383  0.020  1.383
 86D  C8   C9   aromatic  1.386  0.020  1.386
 86D  C8   O1   single    1.370  0.020  1.370
 86D  C9   C10  aromatic  1.382  0.020  1.382
 86D  C10  F1   single    1.333  0.020  1.333
 86D  C10  C5   aromatic  1.380  0.020  1.380
 86D  O1   C1   single    1.351  0.020  1.351
 86D  C1   C14  aromatic  1.391  0.020  1.391
 86D  C1   C2   aromatic  1.390  0.020  1.390
 86D  C14  C15  single    1.500  0.020  1.500
 86D  C14  C13  aromatic  1.384  0.020  1.384
 86D  C15  C11  single    1.519  0.020  1.519
 86D  C11  F5   single    1.352  0.020  1.352
 86D  C11  F2   single    1.366  0.020  1.366
 86D  C11  C12  single    1.540  0.020  1.540
 86D  C13  C12  single    1.511  0.020  1.511
 86D  C13  C4   aromatic  1.393  0.020  1.393
 86D  C12  O4   single    1.398  0.020  1.398
 86D  C4   C3   aromatic  1.390  0.020  1.390
 86D  C4   S1   single    1.761  0.020  1.761
 86D  C3   C2   aromatic  1.385  0.020  1.385
 86D  S1   O2   double    1.454  0.020  1.454
 86D  S1   O3   double    1.455  0.020  1.455
 86D  S1   C16  single    1.838  0.020  1.838
 86D  C16  F3   single    1.341  0.020  1.341
 86D  C16  F4   single    1.342  0.020  1.342
 86D  C7   H1   single    0.930  0.020  1.080
 86D  C9   H2   single    0.930  0.020  1.080
 86D  C5   H3   single    0.930  0.020  1.080
 86D  C15  H4   single    0.970  0.020  1.090
 86D  C15  H5   single    0.970  0.020  1.090
 86D  C12  H6   single    0.970  0.020  1.090
 86D  O4   H7   single    0.850  0.020  0.980
 86D  C3   H8   single    0.930  0.020  1.080
 86D  C2   H9   single    0.930  0.020  1.080
 86D  C16  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
 86D  C6   C17  N1   180.00  3.000
 86D  C5   C6   C7   121.71  3.000
 86D  C5   C6   C17  119.08  3.000
 86D  C7   C6   C17  119.21  3.000
 86D  H1   C7   C8   120.81  3.000
 86D  H1   C7   C6   121.04  3.000
 86D  C8   C7   C6   118.15  3.000
 86D  O1   C8   C9   119.10  3.000
 86D  O1   C8   C7   119.06  3.000
 86D  C9   C8   C7   121.81  3.000
 86D  H2   C9   C10  120.74  3.000
 86D  H2   C9   C8   121.19  3.000
 86D  C10  C9   C8   118.07  3.000
 86D  C5   C10  F1   118.81  3.000
 86D  C5   C10  C9   122.56  3.000
 86D  F1   C10  C9   118.63  3.000
 86D  H3   C5   C10  120.98  3.000
 86D  H3   C5   C6   121.32  3.000
 86D  C10  C5   C6   117.70  3.000
 86D  C1   O1   C8   119.40  3.000
 86D  C2   C1   C14  119.80  3.000
 86D  C2   C1   O1   124.25  3.000
 86D  C14  C1   O1   115.95  3.000
 86D  C13  C14  C15  112.09  3.000
 86D  C13  C14  C1   120.57  3.000
 86D  C15  C14  C1   127.34  3.000
 86D  H5   C15  H4   107.95  3.000
 86D  H5   C15  C11  110.85  3.000
 86D  H4   C15  C11  112.19  3.000
 86D  H5   C15  C14  111.06  3.000
 86D  H4   C15  C14  113.97  3.000
 86D  C11  C15  C14  100.75  3.000
 86D  C12  C11  F2   108.17  3.000
 86D  C12  C11  F5   112.32  3.000
 86D  F2   C11  F5   106.31  3.000
 86D  C12  C11  C15  106.69  3.000
 86D  F2   C11  C15  109.55  3.000
 86D  F5   C11  C15  113.68  3.000
 86D  C4   C13  C12  130.76  3.000
 86D  C4   C13  C14  119.63  3.000
 86D  C12  C13  C14  109.44  3.000
 86D  H6   C12  O4   112.72  3.000
 86D  H6   C12  C13  114.20  3.000
 86D  O4   C12  C13  107.52  3.000
 86D  H6   C12  C11  110.64  3.000
 86D  O4   C12  C11  110.61  3.000
 86D  C13  C12  C11  100.46  3.000
 86D  H7   O4   C12  108.86  3.000
 86D  S1   C4   C3   117.76  3.000
 86D  S1   C4   C13  122.46  3.000
 86D  C3   C4   C13  119.73  3.000
 86D  H8   C3   C2   118.45  3.000
 86D  H8   C3   C4   120.93  3.000
 86D  C2   C3   C4   120.61  3.000
 86D  H9   C2   C3   118.65  3.000
 86D  H9   C2   C1   121.69  3.000
 86D  C3   C2   C1   119.66  3.000
 86D  C16  S1   O3   105.43  3.000
 86D  C16  S1   O2   106.47  3.000
 86D  O3   S1   O2   120.35  3.000
 86D  C16  S1   C4   102.76  3.000
 86D  O3   S1   C4   109.24  3.000
 86D  O2   S1   C4   110.96  3.000
 86D  H12  C16  F4   111.31  3.000
 86D  H12  C16  F3   111.19  3.000
 86D  F4   C16  F3   108.68  3.000
 86D  H12  C16  S1   109.50  3.000
 86D  F4   C16  S1   108.27  3.000
 86D  F3   C16  S1   107.79  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
 86D  CONST_01  C9   C8   C7   C6      0.00   0.0  0
 86D  CONST_02  C9   C10  C5   C6      0.00   0.0  0
 86D  CONST_03  C10  C5   C6   C7      0.00   0.0  0
 86D  CONST_04  C10  C9   C8   C7      0.00   0.0  0
 86D  CONST_05  C5   C6   C7   C8      0.00   0.0  0
 86D  CONST_06  C5   C10  C9   C8      0.00   0.0  0
 86D  CONST_07  C4   C13  C14  C1      0.00   0.0  0
 86D  CONST_08  C4   C3   C2   C1      0.00   0.0  0
 86D  CONST_09  C3   C2   C1   C14     0.00   0.0  0
 86D  CONST_10  C3   C4   C13  C14     0.00   0.0  0
 86D  CONST_11  C2   C1   C14  C13     0.00   0.0  0
 86D  CONST_12  C2   C3   C4   C13     0.00   0.0  0
 86D  CONST_13  C8   C7   C6   C17   180.00   0.0  0
 86D  CONST_14  C10  C5   C6   C17   180.00   0.0  0
 86D  CONST_15  O1   C8   C7   C6    180.00   0.0  0
 86D  CONST_16  F1   C10  C5   C6    180.00   0.0  0
 86D  CONST_17  F1   C10  C9   C8    180.00   0.0  0
 86D  CONST_18  O1   C8   C9   C10   180.00   0.0  0
 86D  CONST_19  C15  C14  C1   O1      0.00   0.0  0
 86D  CONST_20  C13  C14  C1   O1    180.00   0.0  0
 86D  CONST_21  C3   C2   C1   O1    180.00   0.0  0
 86D  CONST_22  S1   C4   C13  C14   180.00   0.0  0
 86D  CONST_23  S1   C4   C13  C12     0.00   0.0  0
 86D  CONST_24  S1   C4   C3   C2    180.00   0.0  0
 86D  CONST_25  H3   C5   C6   C7    180.00   0.0  0
 86D  CONST_26  H2   C9   C8   C7    180.00   0.0  0
 86D  CONST_27  H1   C7   C8   C9    180.00   0.0  0
 86D  CONST_28  H8   C3   C2   C1    180.00   0.0  0
 86D  CONST_29  H9   C2   C1   C14   180.00   0.0  0
 86D  Var_01    C11  C15  C14  C1   -164.19  30.0  1
 86D  Var_02    C12  C11  C15  C14   -29.71  30.0  1
 86D  Var_03    C14  C1   O1   C8    177.06  30.0  2
 86D  Var_04    O2   S1   C4   C13    27.41  30.0  2
 86D  Var_05    F3   C16  S1   C4    -51.29  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
 86D  chir_01  C12  C11  C13  O4  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
 86D  plan-1  N1   0.020
 86D  plan-1  C17  0.020
 86D  plan-1  C6   0.020
 86D  plan-1  C7   0.020
 86D  plan-1  C8   0.020
 86D  plan-1  C9   0.020
 86D  plan-1  C10  0.020
 86D  plan-1  F1   0.020
 86D  plan-1  C5   0.020
 86D  plan-1  O1   0.020
 86D  plan-1  H1   0.020
 86D  plan-1  H2   0.020
 86D  plan-1  H3   0.020
 86D  plan-2  O1   0.020
 86D  plan-2  C1   0.020
 86D  plan-2  C14  0.020
 86D  plan-2  C15  0.020
 86D  plan-2  C13  0.020
 86D  plan-2  C12  0.020
 86D  plan-2  C4   0.020
 86D  plan-2  C3   0.020
 86D  plan-2  C2   0.020
 86D  plan-2  S1   0.020
 86D  plan-2  H8   0.020
 86D  plan-2  H9   0.020

