# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:26:35 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: 6-[(3,5-dichloropyridin-4-yl)methoxy]-1-{[3-(trifluoromethyl)phenyl]sulfonyl}-2,3-dihydro-1H-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cccc(c1)[S](=O)(=O)N2CCc3ccc(OCc4c(Cl)cncc4Cl)cc23
#
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
 L7J  L7J  6-[(3,5-dichloropyridin-4-yl)methoxy]-1-{[3-(trifluoromethyl)phenyl]sulfonyl}-2,3-dihydro-1H-indole  ligand  47  32  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L7J
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
 L7J  CAD  C   CR6   0  -0.170   3.4636   0.1451  -0.6197
 L7J  CAE  C   CR16  0  -0.235   4.6364   0.0030   0.1109
 L7J  CAF  C   CR16  0  -0.229   4.8415  -1.1632   0.8315
 L7J  CAG  C   CR16  0  -0.249   3.8925  -2.1724   0.8157
 L7J  CAH  C   CR6   0  -0.176   2.7311  -2.0225   0.0657
 L7J  CAI  C   CT    0   1.063   1.7022  -3.1125   0.0787
 L7J  CAM  C   CR16  0  -0.271   2.5085  -0.8614  -0.6583
 L7J  CAO  C   CH2   0  -0.303   3.3685   3.3205   0.6308
 L7J  CAP  C   CH2   0  -0.490   2.4013   3.9291   1.6481
 L7J  CAQ  C   CR56  0  -0.021   1.1569   3.1176   1.4513
 L7J  CAR  C   CR16  0  -0.309   0.0215   3.0248   2.2232
 L7J  CAS  C   CR16  0  -0.387  -1.0576   2.2513   1.7972
 L7J  CAT  C   CR6   0   0.399  -0.9844   1.5928   0.5751
 L7J  CAV  C   CH2   0  -0.255  -3.1098   0.5860   0.8743
 L7J  CAW  C   CR6   0   0.362  -3.9541  -0.4078   0.1354
 L7J  CAX  C   CR6   0  -0.202  -5.1668  -0.0922  -0.4670
 L7J  CAZ  C   CR16  0  -0.014  -5.8928  -1.0643  -1.1438
 L7J  CBB  C   CR16  0  -0.015  -4.3206  -2.6469  -0.6946
 L7J  CBC  C   CR6   0  -0.179  -3.5413  -1.7307  -0.0051
 L7J  CBE  C   CR16  0  -0.412   0.1583   1.6826  -0.2280
 L7J  CBF  C   CR56  0   0.421   1.2208   2.4323   0.2377
 L7J  FAJ  F   F     0  -0.300   0.8556  -3.0247  -0.9489
 L7J  FAK  F   F     0  -0.305   2.2603  -4.3260   0.0330
 L7J  FAL  F   F     0  -0.313   0.9676  -3.0680   1.2002
 L7J  NAN  N   NR5   0  -0.710   2.4756   2.6755  -0.3625
 L7J  NBA  N   N     0  -0.393  -5.4737  -2.3126  -1.2503
 L7J  OAA  O   OS    0  -0.631   4.4375   2.2582  -1.8203
 L7J  OAC  O   OS    0  -0.630   2.1718   1.4142  -2.5133
 L7J  SAB  S   S     0   1.387   3.1596   1.6639  -1.4813
 L7J  CLA  CL  CL    0  -0.096  -5.8158   1.5046  -0.4047
 L7J  CLB  CL  CL    0  -0.086  -2.0535  -2.2618   0.6790
 L7J  H1   H   HCR6  0   0.301   5.3931   0.7751   0.1149
 L7J  H2   H   HCR6  0   0.289   5.7514  -1.2881   1.4014
 L7J  H3   H   HCR6  0   0.292   4.0747  -3.0766   1.3816
 L7J  H4   H   HCR6  0   0.296   1.6193  -0.7495  -1.2612
 L7J  H5   H   HCH2  0   0.282   4.0012   4.0579   0.1461
 L7J  H6   H   HCH2  0   0.262   4.0042   2.5758   1.1189
 L7J  H7   H   HCH2  0   0.273   2.8022   3.8750   2.6593
 L7J  H8   H   HCH2  0   0.269   2.2116   4.9814   1.4237
 L7J  H9   H   HCR6  0   0.262  -0.0428   3.5521   3.1666
 L7J  H10  H   HCR6  0   0.286  -1.9365   2.1908   2.4236
 L7J  H11  H   HCH2  0   0.261  -3.6669   1.5035   1.0725
 L7J  H12  H   HCH2  0   0.261  -2.8145   0.1652   1.8413
 L7J  H13  H   HCR6  0   0.298  -6.8379  -0.8117  -1.6094
 L7J  H14  H   HCR6  0   0.297  -3.9952  -3.6753  -0.7954
 L7J  H15  H   HCR6  0   0.285   0.1662   1.1767  -1.1823
 L7J  OAU  O   O2    0  -0.466  -1.9815   0.8390   0.0625

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
 L7J  OAA  SAB  double    1.450  0.020  1.450
 L7J  OAC  SAB  double    1.450  0.020  1.450
 L7J  CLA  CAX  single    1.725  0.020  1.725
 L7J  SAB  NAN  single    1.656  0.020  1.656
 L7J  SAB  CAD  single    1.772  0.020  1.772
 L7J  NAN  CAO  single    1.483  0.020  1.483
 L7J  NAN  CBF  single    1.412  0.020  1.412
 L7J  CAZ  CAX  aromatic  1.389  0.020  1.389
 L7J  CAZ  NBA  aromatic  1.321  0.020  1.321
 L7J  CAX  CAW  aromatic  1.390  0.020  1.390
 L7J  CBE  CBF  aromatic  1.381  0.020  1.381
 L7J  CBE  CAT  aromatic  1.400  0.020  1.400
 L7J  CAD  CAM  aromatic  1.388  0.020  1.388
 L7J  CAD  CAE  aromatic  1.389  0.020  1.389
 L7J  CAO  CAP  single    1.530  0.020  1.530
 L7J  CBF  CAQ  aromatic  1.395  0.020  1.395
 L7J  OAU  CAT  single    1.351  0.020  1.351
 L7J  OAU  CAV  single    1.413  0.020  1.413
 L7J  NBA  CBB  aromatic  1.323  0.020  1.323
 L7J  CAM  CAH  aromatic  1.386  0.020  1.386
 L7J  CAE  CAF  aromatic  1.386  0.020  1.386
 L7J  CAT  CAS  aromatic  1.390  0.020  1.390
 L7J  CAW  CAV  single    1.499  0.020  1.499
 L7J  CAW  CBC  aromatic  1.393  0.020  1.393
 L7J  FAL  CAI  single    1.341  0.020  1.341
 L7J  CAQ  CAP  single    1.499  0.020  1.499
 L7J  CAQ  CAR  aromatic  1.376  0.020  1.376
 L7J  CAH  CAI  single    1.499  0.020  1.499
 L7J  CAH  CAG  aromatic  1.391  0.020  1.391
 L7J  CBB  CBC  aromatic  1.386  0.020  1.386
 L7J  CAF  CAG  aromatic  1.385  0.020  1.385
 L7J  CBC  CLB  single    1.722  0.020  1.722
 L7J  CAS  CAR  aromatic  1.394  0.020  1.394
 L7J  CAI  FAK  single    1.337  0.020  1.337
 L7J  CAI  FAJ  single    1.334  0.020  1.334
 L7J  CAE  H1   single    0.930  0.020  1.080
 L7J  CAF  H2   single    0.930  0.020  1.080
 L7J  CAG  H3   single    0.930  0.020  1.080
 L7J  CAM  H4   single    0.930  0.020  1.080
 L7J  CAO  H5   single    0.970  0.020  1.090
 L7J  CAO  H6   single    0.970  0.020  1.090
 L7J  CAP  H7   single    0.970  0.020  1.090
 L7J  CAP  H8   single    0.970  0.020  1.090
 L7J  CAR  H9   single    0.930  0.020  1.080
 L7J  CAS  H10  single    0.930  0.020  1.080
 L7J  CAV  H11  single    0.970  0.020  1.090
 L7J  CAV  H12  single    0.970  0.020  1.090
 L7J  CAZ  H13  single    0.930  0.020  1.080
 L7J  CBB  H14  single    0.930  0.020  1.080
 L7J  CBE  H15  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
 L7J  SAB  CAD  CAM  119.32  3.000
 L7J  CAM  CAD  CAE  121.43  3.000
 L7J  SAB  CAD  CAE  119.22  3.000
 L7J  H1   CAE  CAF  119.69  3.000
 L7J  H1   CAE  CAD  121.32  3.000
 L7J  CAF  CAE  CAD  118.98  3.000
 L7J  H2   CAF  CAG  119.90  3.000
 L7J  H2   CAF  CAE  119.73  3.000
 L7J  CAG  CAF  CAE  120.37  3.000
 L7J  H3   CAG  CAH  120.84  3.000
 L7J  H3   CAG  CAF  119.17  3.000
 L7J  CAH  CAG  CAF  119.98  3.000
 L7J  CAM  CAH  CAI  120.22  3.000
 L7J  CAI  CAH  CAG  119.36  3.000
 L7J  CAM  CAH  CAG  120.40  3.000
 L7J  FAL  CAI  FAK  106.70  3.000
 L7J  FAK  CAI  FAJ  107.36  3.000
 L7J  FAL  CAI  FAJ  107.12  3.000
 L7J  FAJ  CAI  CAH  112.40  3.000
 L7J  FAK  CAI  CAH  111.92  3.000
 L7J  FAL  CAI  CAH  111.04  3.000
 L7J  H4   CAM  CAH  120.69  3.000
 L7J  H4   CAM  CAD  120.46  3.000
 L7J  CAH  CAM  CAD  118.83  3.000
 L7J  H6   CAO  H5   108.84  3.000
 L7J  H6   CAO  NAN  110.64  3.000
 L7J  H5   CAO  NAN  110.31  3.000
 L7J  H6   CAO  CAP  109.97  3.000
 L7J  H5   CAO  CAP  113.27  3.000
 L7J  NAN  CAO  CAP  103.75  3.000
 L7J  H8   CAP  H7   107.60  3.000
 L7J  H8   CAP  CAQ  110.52  3.000
 L7J  H7   CAP  CAQ  113.62  3.000
 L7J  H8   CAP  CAO  110.88  3.000
 L7J  H7   CAP  CAO  111.40  3.000
 L7J  CAQ  CAP  CAO  102.84  3.000
 L7J  CBF  CAQ  CAR  119.51  3.000
 L7J  CAR  CAQ  CAP  130.39  3.000
 L7J  CBF  CAQ  CAP  110.01  3.000
 L7J  H9   CAR  CAS  119.37  3.000
 L7J  H9   CAR  CAQ  120.33  3.000
 L7J  CAS  CAR  CAQ  120.30  3.000
 L7J  H10  CAS  CAT  121.72  3.000
 L7J  H10  CAS  CAR  118.89  3.000
 L7J  CAT  CAS  CAR  119.38  3.000
 L7J  OAU  CAT  CBE  114.88  3.000
 L7J  OAU  CAT  CAS  123.98  3.000
 L7J  CBE  CAT  CAS  121.14  3.000
 L7J  H12  CAV  H11  107.48  3.000
 L7J  H12  CAV  OAU  111.15  3.000
 L7J  H11  CAV  OAU  111.18  3.000
 L7J  H12  CAV  CAW  109.42  3.000
 L7J  H11  CAV  CAW  111.06  3.000
 L7J  OAU  CAV  CAW  106.58  3.000
 L7J  CBC  CAW  CAX  115.49  3.000
 L7J  CBC  CAW  CAV  120.83  3.000
 L7J  CAX  CAW  CAV  123.67  3.000
 L7J  CLA  CAX  CAZ  117.95  3.000
 L7J  CAZ  CAX  CAW  120.53  3.000
 L7J  CLA  CAX  CAW  121.51  3.000
 L7J  H13  CAZ  NBA  117.55  3.000
 L7J  H13  CAZ  CAX  120.13  3.000
 L7J  NBA  CAZ  CAX  122.32  3.000
 L7J  H14  CBB  NBA  117.55  3.000
 L7J  H14  CBB  CBC  120.32  3.000
 L7J  NBA  CBB  CBC  122.12  3.000
 L7J  CLB  CBC  CBB  118.65  3.000
 L7J  CLB  CBC  CAW  120.60  3.000
 L7J  CBB  CBC  CAW  120.75  3.000
 L7J  H15  CBE  CBF  123.12  3.000
 L7J  H15  CBE  CAT  118.88  3.000
 L7J  CBF  CBE  CAT  117.99  3.000
 L7J  NAN  CBF  CBE  129.33  3.000
 L7J  CBE  CBF  CAQ  121.65  3.000
 L7J  NAN  CBF  CAQ  109.02  3.000
 L7J  SAB  NAN  CBF  123.29  3.000
 L7J  CBF  NAN  CAO  108.98  3.000
 L7J  SAB  NAN  CAO  118.00  3.000
 L7J  CBB  NBA  CAZ  118.78  3.000
 L7J  OAC  SAB  OAA  120.31  3.000
 L7J  OAC  SAB  NAN  107.73  3.000
 L7J  OAA  SAB  NAN  105.76  3.000
 L7J  NAN  SAB  CAD  105.42  3.000
 L7J  OAC  SAB  CAD  108.38  3.000
 L7J  OAA  SAB  CAD  108.29  3.000
 L7J  CAV  OAU  CAT  118.13  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
 L7J  CONST_01  CAG  CAH  CAM  CAD     0.00   0.0  0
 L7J  CONST_02  CAG  CAF  CAE  CAD     0.00   0.0  0
 L7J  CONST_03  CAH  CAM  CAD  CAE     0.00   0.0  0
 L7J  CONST_04  CAH  CAG  CAF  CAE     0.00   0.0  0
 L7J  CONST_05  CAM  CAD  CAE  CAF     0.00   0.0  0
 L7J  CONST_06  CAM  CAH  CAG  CAF     0.00   0.0  0
 L7J  CONST_07  CAT  CBE  CBF  CAQ     0.00   0.0  0
 L7J  CONST_08  CAT  CAS  CAR  CAQ     0.00   0.0  0
 L7J  CONST_09  CBE  CBF  CAQ  CAR     0.00   0.0  0
 L7J  CONST_10  CBE  CAT  CAS  CAR     0.00   0.0  0
 L7J  CONST_11  CBF  CBE  CAT  CAS     0.00   0.0  0
 L7J  CONST_12  CBF  CAQ  CAR  CAS     0.00   0.0  0
 L7J  CONST_13  NBA  CAZ  CAX  CAW     0.00   0.0  0
 L7J  CONST_14  NBA  CBB  CBC  CAW     0.00   0.0  0
 L7J  CONST_15  CBB  NBA  CAZ  CAX     0.00   0.0  0
 L7J  CONST_16  CBB  CBC  CAW  CAX     0.00   0.0  0
 L7J  CONST_17  CBC  CAW  CAX  CAZ     0.00   0.0  0
 L7J  CONST_18  CBC  CBB  NBA  CAZ     0.00   0.0  0
 L7J  CONST_19  CAI  CAH  CAM  CAD   180.00   0.0  0
 L7J  CONST_20  SAB  CAD  CAE  CAF   180.00   0.0  0
 L7J  CONST_21  CAI  CAH  CAG  CAF   180.00   0.0  0
 L7J  CONST_22  SAB  CAD  CAM  CAH   180.00   0.0  0
 L7J  CONST_23  OAU  CAT  CAS  CAR   180.00   0.0  0
 L7J  CONST_24  CAZ  CAX  CAW  CAV   180.00   0.0  0
 L7J  CONST_25  CBB  CBC  CAW  CAV   180.00   0.0  0
 L7J  CONST_26  CLB  CBC  CAW  CAX   180.00   0.0  0
 L7J  CONST_27  CLA  CAX  CAW  CBC   180.00   0.0  0
 L7J  CONST_28  OAU  CAT  CBE  CBF   180.00   0.0  0
 L7J  CONST_29  CLA  CAX  CAZ  NBA   180.00   0.0  0
 L7J  CONST_30  CLB  CBC  CBB  NBA   180.00   0.0  0
 L7J  CONST_31  H2   CAF  CAE  CAD   180.00   0.0  0
 L7J  CONST_32  H4   CAM  CAD  CAE   180.00   0.0  0
 L7J  CONST_33  H3   CAG  CAF  CAE   180.00   0.0  0
 L7J  CONST_34  H1   CAE  CAF  CAG   180.00   0.0  0
 L7J  CONST_35  H9   CAR  CAQ  CAP     0.00   0.0  0
 L7J  CONST_36  H15  CBE  CBF  CAQ   180.00   0.0  0
 L7J  CONST_37  H10  CAS  CAR  CAQ   180.00   0.0  0
 L7J  CONST_38  H13  CAZ  CAX  CAW   180.00   0.0  0
 L7J  CONST_39  H14  CBB  CBC  CAW   180.00   0.0  0
 L7J  Var_01    CBE  CBF  NAN  CAO  -169.32  30.0  1
 L7J  Var_02    CBF  CAQ  CAP  CAO   -16.43  30.0  1
 L7J  Var_03    CBF  NAN  CAO  CAP   -21.74  30.0  1
 L7J  Var_04    NAN  CAO  CAP  CAQ    22.32  30.0  1
 L7J  Var_05    CAO  NAN  SAB  CAD    77.72  30.0  3
 L7J  Var_06    NAN  SAB  CAD  CAE   -84.96  30.0  2
 L7J  Var_07    FAL  CAI  CAH  CAG    78.22  30.0  2
 L7J  Var_08    CAW  CAV  OAU  CAT  -172.61  30.0  3
 L7J  Var_09    CBE  CAT  OAU  CAV   173.49  30.0  2
 L7J  Var_10    OAU  CAV  CAW  CAX  -108.18  30.0  2

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
 L7J  plan-1  CAD  0.020
 L7J  plan-1  CAE  0.020
 L7J  plan-1  CAF  0.020
 L7J  plan-1  CAG  0.020
 L7J  plan-1  CAH  0.020
 L7J  plan-1  CAI  0.020
 L7J  plan-1  CAM  0.020
 L7J  plan-1  SAB  0.020
 L7J  plan-1  H1   0.020
 L7J  plan-1  H2   0.020
 L7J  plan-1  H3   0.020
 L7J  plan-1  H4   0.020
 L7J  plan-2  CAV  0.020
 L7J  plan-2  CAW  0.020
 L7J  plan-2  CAX  0.020
 L7J  plan-2  CAZ  0.020
 L7J  plan-2  CBB  0.020
 L7J  plan-2  CBC  0.020
 L7J  plan-2  NBA  0.020
 L7J  plan-2  CLA  0.020
 L7J  plan-2  CLB  0.020
 L7J  plan-2  H13  0.020
 L7J  plan-2  H14  0.020
 L7J  plan-3  CAP  0.020
 L7J  plan-3  CAQ  0.020
 L7J  plan-3  CAR  0.020
 L7J  plan-3  CAS  0.020
 L7J  plan-3  CAT  0.020
 L7J  plan-3  CBE  0.020
 L7J  plan-3  CBF  0.020
 L7J  plan-3  NAN  0.020
 L7J  plan-3  H9   0.020
 L7J  plan-3  H10  0.020
 L7J  plan-3  H15  0.020
 L7J  plan-3  OAU  0.020

