# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 03:02:58 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: (2E)-2-[(3-fluoro-4-methoxyphenyl)imino]-1-[2-(trifluoromethyl)benzyl]-2,3-dihydro-1H-benzimidazole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1F)N=C2Nc3cc(ccc3N2Cc4ccccc4C(F)(F)F)C(O)=O
#
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
 4A2  4A2  '(2E)-2-[(3-fluoro-4-methoxyphenyl)imino]-1-[2-(trifluoromethyl)benzyl]-2,3-dihydro-1H-benzimidazole-5-carboxylic acid'  ligand  50  33  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4A2
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
 4A2  FAA   F  F     0  -0.295   5.1203  -3.2749  -0.6478
 4A2  CAC   C  CT    0   1.057   4.0023  -2.5611  -0.7878
 4A2  FAB   F  F     0  -0.316   4.3382  -1.4608  -1.4848
 4A2  FAG   F  F     0  -0.315   3.1848  -3.2788  -1.5732
 4A2  CAD   C  CR6   0  -0.248   3.3650  -2.2176   0.5262
 4A2  CAE   C  CR16  0  -0.283   4.0322  -2.5568   1.6993
 4A2  CAF   C  CR16  0  -0.251   3.4858  -2.2519   2.9349
 4A2  CAK   C  CR16  0  -0.227   2.2624  -1.6065   2.9990
 4A2  CAJ   C  CR16  0  -0.276   1.5984  -1.2658   1.8312
 4A2  CAI   C  CR6   0   0.106   2.1307  -1.5571   0.5797
 4A2  CAH   C  CH2   0  -0.394   1.3272  -1.1836  -0.6521
 4A2  NAP   N  NR5   0  -0.598   0.5968   0.0434  -0.4719
 4A2  CAO   C  CR56  0   0.353   1.1576   1.2917  -0.3749
 4A2  CAN   C  CR16  0  -0.299   2.4738   1.7085  -0.4156
 4A2  CAM   C  CR16  0  -0.275   2.7185   3.0711  -0.2870
 4A2  CAW   C  CR6   0  -0.110   1.6750   3.9844  -0.1241
 4A2  CAV   C  C     0   0.535   1.9211   5.4370   0.0057
 4A2  OAL   O  OH1   0  -0.597   3.2088   5.7570  -0.0192
 4A2  OBG   O  O     0  -0.446   1.0427   6.2605   0.1217
 4A2  CAX   C  CR16  0  -0.337   0.3424   3.5503  -0.0820
 4A2  CAY   C  CR56  0   0.357   0.1081   2.2032  -0.2066
 4A2  NAZ   N  NR15  0  -0.760  -1.0541   1.4626  -0.2018
 4A2  CBA   C  CR5   0   0.671  -0.7781   0.1317  -0.3701
 4A2  NBB   N  N     0  -0.541  -1.5465  -0.8852  -0.4554
 4A2  CBC   C  CR6   0   0.229  -2.9169  -0.7631  -0.2531
 4A2  CBD   C  CR16  0  -0.473  -3.7849  -1.3316  -1.1940
 4A2  CBE   C  CR6   0   0.474  -5.1430  -1.2776  -0.9990
 4A2  FBF   F  F     0  -0.315  -5.9609  -1.8204  -1.9153
 4A2  CAS   C  CR6   0   0.218  -5.7227  -0.6764   0.1199
 4A2  OAT   O  O2    0  -0.468  -7.0666  -0.6942   0.1918
 4A2  CAU   C  CH3   0  -0.436  -7.6734  -0.0902   1.3167
 4A2  CAR   C  CR16  0  -0.369  -4.8602  -0.1249   1.0572
 4A2  CAQ   C  CR16  0  -0.331  -3.4811  -0.1695   0.8754
 4A2  HAE   H  HCR6  0   0.275   4.9869  -3.0619   1.6631
 4A2  HAF   H  HCR6  0   0.271   4.0162  -2.5186   3.8387
 4A2  HAK   H  HCR6  0   0.271   1.8197  -1.3672   3.9565
 4A2  HAJ   H  HCR6  0   0.264   0.6450  -0.7593   1.9048
 4A2  HAH1  H  HCH2  0   0.281   1.9412  -1.0786  -1.5441
 4A2  HAH2  H  HCH2  0   0.312   0.5938  -1.9631  -0.8620
 4A2  HAN   H  HCR6  0   0.268   3.2903   1.0111  -0.5420
 4A2  HAM   H  HCR6  0   0.270   3.7433   3.4121  -0.3172
 4A2  HAX   H  HCR6  0   0.278  -0.4709   4.2520   0.0419
 4A2  HAL   H  HOH1  0   0.486   3.3098   6.7170   0.0606
 4A2  HAZ   H  HNR5  0   0.427  -1.9869   1.8368  -0.1343
 4A2  HBD   H  HCR6  0   0.274  -3.3879  -1.8113  -2.0797
 4A2  HAQ   H  HCR6  0   0.270  -2.8472   0.2466   1.6489
 4A2  HAR   H  HCR6  0   0.290  -5.2446   0.3418   1.9538
 4A2  HAU1  H  HCH3  0   0.261  -8.7467  -0.2024   1.1859
 4A2  HAU2  H  HCH3  0   0.229  -7.3808  -0.5783   2.2502
 4A2  HAU3  H  HCH3  0   0.229  -7.4357   0.9746   1.3857

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
 4A2  FAA  CAC   single    1.334  0.020  1.334
 4A2  CAC  FAB   single    1.345  0.020  1.345
 4A2  CAC  FAG   single    1.342  0.020  1.342
 4A2  CAC  CAD   single    1.500  0.020  1.500
 4A2  CAD  CAE   aromatic  1.392  0.020  1.392
 4A2  CAD  CAI   aromatic  1.401  0.020  1.401
 4A2  CAE  CAF   aromatic  1.385  0.020  1.385
 4A2  CAF  CAK   aromatic  1.385  0.020  1.385
 4A2  CAK  CAJ   aromatic  1.386  0.020  1.386
 4A2  CAJ  CAI   aromatic  1.391  0.020  1.391
 4A2  CAI  CAH   single    1.517  0.020  1.517
 4A2  CAH  NAP   single    1.439  0.020  1.439
 4A2  NAP  CAO   single    1.372  0.020  1.372
 4A2  NAP  CBA   single    1.381  0.020  1.381
 4A2  CAO  CAN   aromatic  1.381  0.020  1.381
 4A2  CAO  CAY   aromatic  1.400  0.020  1.400
 4A2  CAN  CAM   aromatic  1.390  0.020  1.390
 4A2  CAM  CAW   aromatic  1.396  0.020  1.396
 4A2  CAW  CAV   single    1.479  0.020  1.479
 4A2  CAW  CAX   aromatic  1.402  0.020  1.402
 4A2  CAV  OAL   single    1.327  0.020  1.327
 4A2  CAV  OBG   double    1.210  0.020  1.210
 4A2  CAX  CAY   aromatic  1.373  0.020  1.373
 4A2  CAY  NAZ   single    1.378  0.020  1.378
 4A2  NAZ  CBA   single    1.370  0.020  1.370
 4A2  CBA  NBB   double    1.277  0.020  1.277
 4A2  NBB  CBC   single    1.391  0.020  1.391
 4A2  CBC  CBD   aromatic  1.401  0.020  1.401
 4A2  CBC  CAQ   aromatic  1.394  0.020  1.394
 4A2  CBD  CBE   aromatic  1.373  0.020  1.373
 4A2  CBE  FBF   single    1.343  0.020  1.343
 4A2  CBE  CAS   aromatic  1.396  0.020  1.396
 4A2  CAS  OAT   single    1.346  0.020  1.346
 4A2  CAS  CAR   aromatic  1.388  0.020  1.388
 4A2  OAT  CAU   single    1.414  0.020  1.414
 4A2  CAR  CAQ   aromatic  1.392  0.020  1.392
 4A2  CAE  HAE   single    0.930  0.020  1.080
 4A2  CAF  HAF   single    0.930  0.020  1.080
 4A2  CAK  HAK   single    0.930  0.020  1.080
 4A2  CAJ  HAJ   single    0.930  0.020  1.080
 4A2  CAH  HAH1  single    0.970  0.020  1.090
 4A2  CAH  HAH2  single    0.970  0.020  1.090
 4A2  CAN  HAN   single    0.930  0.020  1.080
 4A2  CAM  HAM   single    0.930  0.020  1.080
 4A2  CAX  HAX   single    0.930  0.020  1.080
 4A2  OAL  HAL   single    0.850  0.020  0.980
 4A2  NAZ  HAZ   single    0.860  0.020  1.020
 4A2  CBD  HBD   single    0.930  0.020  1.080
 4A2  CAQ  HAQ   single    0.930  0.020  1.080
 4A2  CAR  HAR   single    0.930  0.020  1.080
 4A2  CAU  HAU1  single    0.970  0.020  1.090
 4A2  CAU  HAU2  single    0.970  0.020  1.090
 4A2  CAU  HAU3  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
 4A2  CAD   CAC  FAG   112.11  3.000
 4A2  CAD   CAC  FAB   111.88  3.000
 4A2  FAG   CAC  FAB   106.64  3.000
 4A2  CAD   CAC  FAA   112.75  3.000
 4A2  FAG   CAC  FAA   106.61  3.000
 4A2  FAB   CAC  FAA   106.43  3.000
 4A2  CAI   CAD  CAE   120.34  3.000
 4A2  CAI   CAD  CAC   121.04  3.000
 4A2  CAE   CAD  CAC   118.61  3.000
 4A2  HAE   CAE  CAF   118.77  3.000
 4A2  HAE   CAE  CAD   120.62  3.000
 4A2  CAF   CAE  CAD   120.61  3.000
 4A2  HAF   CAF  CAK   120.64  3.000
 4A2  HAF   CAF  CAE   119.86  3.000
 4A2  CAK   CAF  CAE   119.50  3.000
 4A2  HAK   CAK  CAJ   119.69  3.000
 4A2  HAK   CAK  CAF   120.38  3.000
 4A2  CAJ   CAK  CAF   119.93  3.000
 4A2  HAJ   CAJ  CAI   119.76  3.000
 4A2  HAJ   CAJ  CAK   118.68  3.000
 4A2  CAI   CAJ  CAK   121.55  3.000
 4A2  CAH   CAI  CAJ   118.44  3.000
 4A2  CAH   CAI  CAD   123.47  3.000
 4A2  CAJ   CAI  CAD   118.06  3.000
 4A2  HAH2  CAH  HAH1  106.90  3.000
 4A2  HAH2  CAH  NAP   106.98  3.000
 4A2  HAH1  CAH  NAP   107.86  3.000
 4A2  HAH2  CAH  CAI   109.66  3.000
 4A2  HAH1  CAH  CAI   112.99  3.000
 4A2  NAP   CAH  CAI   112.14  3.000
 4A2  CBA   NAP  CAO   110.09  3.000
 4A2  CBA   NAP  CAH   124.67  3.000
 4A2  CAO   NAP  CAH   125.24  3.000
 4A2  CAY   CAO  CAN   121.42  3.000
 4A2  CAY   CAO  NAP   107.12  3.000
 4A2  CAN   CAO  NAP   131.46  3.000
 4A2  HAN   CAN  CAM   120.67  3.000
 4A2  HAN   CAN  CAO   121.89  3.000
 4A2  CAM   CAN  CAO   117.44  3.000
 4A2  HAM   CAM  CAW   120.37  3.000
 4A2  HAM   CAM  CAN   118.28  3.000
 4A2  CAW   CAM  CAN   121.35  3.000
 4A2  CAX   CAW  CAV   117.36  3.000
 4A2  CAX   CAW  CAM   120.74  3.000
 4A2  CAV   CAW  CAM   121.89  3.000
 4A2  OBG   CAV  OAL   122.83  3.000
 4A2  OBG   CAV  CAW   123.80  3.000
 4A2  OAL   CAV  CAW   113.37  3.000
 4A2  HAL   OAL  CAV   109.80  3.000
 4A2  HAX   CAX  CAY   121.25  3.000
 4A2  HAX   CAX  CAW   121.15  3.000
 4A2  CAY   CAX  CAW   117.60  3.000
 4A2  NAZ   CAY  CAX   132.13  3.000
 4A2  NAZ   CAY  CAO   106.42  3.000
 4A2  CAX   CAY  CAO   121.45  3.000
 4A2  HAZ   NAZ  CBA   123.77  3.000
 4A2  HAZ   NAZ  CAY   125.56  3.000
 4A2  CBA   NAZ  CAY   110.60  3.000
 4A2  NBB   CBA  NAZ   131.34  3.000
 4A2  NBB   CBA  NAP   122.88  3.000
 4A2  NAZ   CBA  NAP   105.77  3.000
 4A2  CBC   NBB  CBA   120.88  3.000
 4A2  CAQ   CBC  CBD   117.75  3.000
 4A2  CAQ   CBC  NBB   123.63  3.000
 4A2  CBD   CBC  NBB   118.51  3.000
 4A2  HBD   CBD  CBE   119.75  3.000
 4A2  HBD   CBD  CBC   120.14  3.000
 4A2  CBE   CBD  CBC   120.11  3.000
 4A2  CAS   CBE  FBF   117.91  3.000
 4A2  CAS   CBE  CBD   122.78  3.000
 4A2  FBF   CBE  CBD   119.32  3.000
 4A2  CAR   CAS  OAT   126.13  3.000
 4A2  CAR   CAS  CBE   117.02  3.000
 4A2  OAT   CAS  CBE   116.85  3.000
 4A2  CAU   OAT  CAS   117.74  3.000
 4A2  HAU3  CAU  HAU2  108.83  3.000
 4A2  HAU3  CAU  HAU1  108.84  3.000
 4A2  HAU2  CAU  HAU1  108.72  3.000
 4A2  HAU3  CAU  OAT   111.90  3.000
 4A2  HAU2  CAU  OAT   111.95  3.000
 4A2  HAU1  CAU  OAT   106.50  3.000
 4A2  HAR   CAR  CAQ   118.32  3.000
 4A2  HAR   CAR  CAS   120.69  3.000
 4A2  CAQ   CAR  CAS   120.98  3.000
 4A2  HAQ   CAQ  CAR   118.31  3.000
 4A2  HAQ   CAQ  CBC   120.31  3.000
 4A2  CAR   CAQ  CBC   121.36  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
 4A2  CONST_01  CAK   CAF  CAE  CAD     0.00   0.0  0
 4A2  CONST_02  CAK   CAJ  CAI  CAD     0.00   0.0  0
 4A2  CONST_03  CAJ   CAI  CAD  CAE     0.00   0.0  0
 4A2  CONST_04  CAJ   CAK  CAF  CAE     0.00   0.0  0
 4A2  CONST_05  CAI   CAD  CAE  CAF     0.00   0.0  0
 4A2  CONST_06  CAI   CAJ  CAK  CAF     0.00   0.0  0
 4A2  CONST_07  CAW   CAM  CAN  CAO     0.00   0.0  0
 4A2  CONST_08  CAW   CAX  CAY  CAO     0.00   0.0  0
 4A2  CONST_09  CAX   CAY  CAO  CAN     0.00   0.0  0
 4A2  CONST_10  CAX   CAW  CAM  CAN     0.00   0.0  0
 4A2  CONST_11  CAY   CAO  CAN  CAM     0.00   0.0  0
 4A2  CONST_12  CAY   CAX  CAW  CAM     0.00   0.0  0
 4A2  CONST_13  CAS   CBE  CBD  CBC     0.00   0.0  0
 4A2  CONST_14  CAS   CAR  CAQ  CBC     0.00   0.0  0
 4A2  CONST_15  CAR   CAQ  CBC  CBD     0.00   0.0  0
 4A2  CONST_16  CAR   CAS  CBE  CBD     0.00   0.0  0
 4A2  CONST_17  CAQ   CBC  CBD  CBE     0.00   0.0  0
 4A2  CONST_18  CAQ   CAR  CAS  CBE     0.00   0.0  0
 4A2  CONST_19  NAZ   CAY  CAO  NAP     0.00   0.0  0
 4A2  CONST_20  CAY   NAZ  CBA  NAP     0.00   0.0  0
 4A2  CONST_21  NAZ   CBA  NAP  CAO     0.00   0.0  0
 4A2  CONST_22  CBA   NAZ  CAY  CAO     0.00   0.0  0
 4A2  CONST_23  CBA   NAP  CAO  CAY     0.00   0.0  0
 4A2  CONST_24  CAF   CAE  CAD  CAC   180.00   0.0  0
 4A2  CONST_25  CAJ   CAI  CAD  CAC   180.00   0.0  0
 4A2  CONST_26  CAH   CAI  CAD  CAE   180.00   0.0  0
 4A2  CONST_27  CAH   CAI  CAJ  CAK   180.00   0.0  0
 4A2  CONST_28  CAV   CAW  CAM  CAN   180.00   0.0  0
 4A2  CONST_29  CAY   CAX  CAW  CAV   180.00   0.0  0
 4A2  CONST_30  CBE   CBD  CBC  NBB   180.00   0.0  0
 4A2  CONST_31  CAR   CAQ  CBC  NBB   180.00   0.0  0
 4A2  CONST_32  FBF   CBE  CBD  CBC   180.00   0.0  0
 4A2  CONST_33  OAT   CAS  CBE  CBD   180.00   0.0  0
 4A2  CONST_34  CAR   CAS  CBE  FBF   180.00   0.0  0
 4A2  CONST_35  CAQ   CAR  CAS  OAT   180.00   0.0  0
 4A2  CONST_36  CAY   CAO  NAP  CAH   180.00   0.0  0
 4A2  CONST_37  NAZ   CBA  NAP  CAH   180.00   0.0  0
 4A2  CONST_38  CBC   NBB  CBA  NAP   180.00   0.0  0
 4A2  CONST_39  NBB   CBA  NAP  CAO   180.00   0.0  0
 4A2  CONST_40  NBB   CBA  NAZ  CAY   180.00   0.0  0
 4A2  CONST_41  CBC   NBB  CBA  NAZ     0.00   0.0  0
 4A2  CONST_42  HAF   CAF  CAE  CAD   180.00   0.0  0
 4A2  CONST_43  HAJ   CAJ  CAI  CAD   180.00   0.0  0
 4A2  CONST_44  HAK   CAK  CAF  CAE   180.00   0.0  0
 4A2  CONST_45  HAE   CAE  CAF  CAK   180.00   0.0  0
 4A2  CONST_46  HAN   CAN  CAO  NAP     0.00   0.0  0
 4A2  CONST_47  HAM   CAM  CAN  CAO   180.00   0.0  0
 4A2  CONST_48  HAX   CAX  CAY  CAO   180.00   0.0  0
 4A2  CONST_49  HAR   CAR  CAQ  CBC   180.00   0.0  0
 4A2  CONST_50  HAQ   CAQ  CBC  CBD   180.00   0.0  0
 4A2  CONST_51  HBD   CBD  CBE  CAS   180.00   0.0  0
 4A2  CONST_52  HAZ   NAZ  CBA  NAP   180.00   0.0  0
 4A2  CONST_53  NBB   CBA  NAP  CAH     0.00   0.0  0
 4A2  CONST_54  HAL   OAL  CAV  CAW   180.00   0.0  0
 4A2  Var_01    NAP   CAH  CAI  CAD  -146.73  30.0  2
 4A2  Var_02    CAO   NAP  CAH  CAI    69.29  30.0  3
 4A2  Var_03    CBD   CBC  NBB  CBA   131.10  30.0  2
 4A2  Var_04    CAE   CAD  CAC  FAA     5.41  30.0  2
 4A2  Var_05    OAL   CAV  CAW  CAM    -1.41  30.0  2
 4A2  Var_06    CAR   CAS  OAT  CAU     0.48  30.0  2
 4A2  Var_07    HAU1  CAU  OAT  CAS   179.64  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
 4A2  plan-1  CAC  0.020
 4A2  plan-1  CAD  0.020
 4A2  plan-1  CAE  0.020
 4A2  plan-1  CAF  0.020
 4A2  plan-1  CAK  0.020
 4A2  plan-1  CAJ  0.020
 4A2  plan-1  CAI  0.020
 4A2  plan-1  CAH  0.020
 4A2  plan-1  HAE  0.020
 4A2  plan-1  HAF  0.020
 4A2  plan-1  HAK  0.020
 4A2  plan-1  HAJ  0.020
 4A2  plan-2  NBB  0.020
 4A2  plan-2  CBC  0.020
 4A2  plan-2  CBD  0.020
 4A2  plan-2  CBE  0.020
 4A2  plan-2  FBF  0.020
 4A2  plan-2  CAS  0.020
 4A2  plan-2  OAT  0.020
 4A2  plan-2  CAR  0.020
 4A2  plan-2  CAQ  0.020
 4A2  plan-2  HBD  0.020
 4A2  plan-2  HAQ  0.020
 4A2  plan-2  HAR  0.020
 4A2  plan-3  CAH  0.020
 4A2  plan-3  NAP  0.020
 4A2  plan-3  CAO  0.020
 4A2  plan-3  CAN  0.020
 4A2  plan-3  CAM  0.020
 4A2  plan-3  CAW  0.020
 4A2  plan-3  CAV  0.020
 4A2  plan-3  CAX  0.020
 4A2  plan-3  CAY  0.020
 4A2  plan-3  NAZ  0.020
 4A2  plan-3  CBA  0.020
 4A2  plan-3  NBB  0.020
 4A2  plan-3  CBC  0.020
 4A2  plan-3  HAN  0.020
 4A2  plan-3  HAM  0.020
 4A2  plan-3  HAX  0.020
 4A2  plan-3  HAZ  0.020
 4A2  plan-4  CAW  0.020
 4A2  plan-4  CAV  0.020
 4A2  plan-4  OAL  0.020
 4A2  plan-4  OBG  0.020
 4A2  plan-4  HAL  0.020

