# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 05:00:44 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: (2S)-2-(4-chlorophenyl)-2-(pyridin-3-yl)-1-{4-[4-(trifluoromethyl)phenyl]piperazin-1-yl}ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1ccc(cc1)N2CCN(CC2)C(=O)[C@@H](c3ccc(Cl)cc3)c4cccnc4
#
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
 UDO  UDO  (2S)-2-(4-chlorophenyl)-2-(pyridin-3-yl)-1-{4-[4-(trifluoromethyl)phenyl]piperazin-1-yl}ethanone  ligand  53  32  .  2021-08-24  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_UDO
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
 UDO  CAM   C   CR16  0  -0.329  -4.3188  -0.6523  -0.5749
 UDO  CAO   C   CR16  0  -0.259  -5.6411  -0.3855  -0.8591
 UDO  CBB   C   CR6   0  -0.235  -6.2867   0.7110  -0.2918
 UDO  CBF   C   CT    0   1.049  -7.7307   0.9473  -0.5676
 UDO  FAC   F   F     0  -0.319  -8.5248   0.1778   0.1996
 UDO  FAD   F   F     0  -0.308  -8.0986   2.2145  -0.3398
 UDO  FAB   F   F     0  -0.313  -8.0563   0.6655  -1.8378
 UDO  CAP   C   CR16  0  -0.256  -5.5709   1.5307   0.5677
 UDO  CAN   C   CR16  0  -0.341  -4.2401   1.2728   0.8508
 UDO  CBA   C   CR6   0   0.398  -3.5797   0.1677   0.2956
 UDO  NBE   N   NT    0  -0.526  -2.2652  -0.1382   0.6067
 UDO  CAU   C   CH2   0  -0.300  -1.5769   0.6682   1.5957
 UDO  CAS   C   CH2   0  -0.311  -0.3593  -0.0632   2.1363
 UDO  CAT   C   CH2   0  -0.282  -1.3872  -0.6021  -0.4564
 UDO  CAR   C   CH2   0  -0.317  -0.1786  -1.3252   0.1108
 UDO  NBD   N   NT    0  -0.452   0.5159  -0.4745   1.0554
 UDO  CAW   C   C     0   0.588   1.7842  -0.0246   0.9756
 UDO  OAA   O   O     0  -0.469   2.2770   0.7067   1.8182
 UDO  CBC   C   CH1   0  -0.605   2.6188  -0.4994  -0.2222
 UDO  CAY   C   CR6   0   0.237   3.8252   0.3886  -0.4134
 UDO  CAK   C   CR16  0  -0.299   3.8286   1.3400  -1.4249
 UDO  CAI   C   CR16  0  -0.176   4.9177   2.1767  -1.6249
 UDO  CAX   C   CR6   0  -0.053   6.0187   2.0547  -0.7959
 UDO  CLA   CL  CL    0  -0.123   7.3893   3.0852  -1.0352
 UDO  CAJ   C   CR16  0  -0.179   6.0421   1.1104   0.2202
 UDO  CAL   C   CR16  0  -0.279   4.9457   0.2854   0.4042
 UDO  CAZ   C   CR6   0   0.059   3.0053  -1.9556  -0.0868
 UDO  CAH   C   CR16  0  -0.155   3.2139  -2.7354  -1.2189
 UDO  CAF   C   CR16  0  -0.291   3.6013  -4.0553  -1.0742
 UDO  CAG   C   CR16  0  -0.051   3.7695  -4.5563   0.2082
 UDO  NAV   N   N     0  -0.394   3.5745  -3.8287   1.2989
 UDO  CAQ   C   CR16  0  -0.079   3.2023  -2.5643   1.1482
 UDO  HAM   H   HCR6  0   0.280  -3.8694  -1.5281  -1.0206
 UDO  HAO   H   HCR6  0   0.273  -6.1696  -1.0542  -1.5263
 UDO  HAP   H   HCR6  0   0.257  -6.0296   2.3986   1.0219
 UDO  HAN   H   HCR6  0   0.265  -3.7225   1.9642   1.4993
 UDO  HAU1  H   HCH2  0   0.228  -1.2727   1.6431   1.1888
 UDO  HAU2  H   HCH2  0   0.259  -2.2388   0.8555   2.4409
 UDO  HAT1  H   HCH2  0   0.270  -1.9080  -1.2928  -1.1150
 UDO  HAT2  H   HCH2  0   0.225  -1.0469   0.2428  -1.0717
 UDO  HAS1  H   HCH2  0   0.279   0.1770   0.5813   2.8263
 UDO  HAS2  H   HCH2  0   0.249  -0.6833  -0.9533   2.6840
 UDO  HAR1  H   HCH2  0   0.262  -0.5011  -2.2340   0.6273
 UDO  HAR2  H   HCH2  0   0.263   0.4587  -1.6413  -0.7093
 UDO  HBC   H   HCH1  0   0.270   2.0115  -0.4043  -1.1268
 UDO  HAK   H   HCR6  0   0.231   2.9711   1.4408  -2.0787
 UDO  HAL   H   HCR6  0   0.246   4.9843  -0.4517   1.1949
 UDO  HAI   H   HCR6  0   0.259   4.9036   2.9092  -2.4195
 UDO  HAJ   H   HCR6  0   0.258   6.9070   1.0171   0.8621
 UDO  HAH   H   HCR6  0   0.247   3.0711  -2.3170  -2.2079
 UDO  HAQ   H   HCR6  0   0.246   3.0569  -2.0065   2.0681
 UDO  HAF   H   HCR6  0   0.253   3.7676  -4.6858  -1.9358
 UDO  HAG   H   HCR6  0   0.250   4.0711  -5.5864   0.3579

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
 UDO  CAM  CAO   aromatic  1.379  0.020  1.379
 UDO  CAM  CBA   aromatic  1.406  0.020  1.406
 UDO  CAO  CBB   aromatic  1.393  0.020  1.393
 UDO  CBB  CBF   single    1.489  0.020  1.489
 UDO  CBB  CAP   aromatic  1.387  0.020  1.387
 UDO  CBF  FAC   single    1.346  0.020  1.346
 UDO  CBF  FAD   single    1.339  0.020  1.339
 UDO  CBF  FAB   single    1.341  0.020  1.341
 UDO  CAP  CAN   aromatic  1.385  0.020  1.385
 UDO  CAN  CBA   aromatic  1.402  0.020  1.402
 UDO  CBA  NBE   single    1.385  0.020  1.385
 UDO  NBE  CAU   single    1.450  0.020  1.450
 UDO  NBE  CAT   single    1.455  0.020  1.455
 UDO  CAU  CAS   single    1.520  0.020  1.520
 UDO  CAS  NBD   single    1.450  0.020  1.450
 UDO  CAT  CAR   single    1.518  0.020  1.518
 UDO  CAR  NBD   single    1.449  0.020  1.449
 UDO  NBD  CAW   single    1.348  0.020  1.348
 UDO  CAW  OAA   double    1.220  0.020  1.220
 UDO  CAW  CBC   single    1.535  0.020  1.535
 UDO  CBC  CAY   single    1.510  0.020  1.510
 UDO  CBC  CAZ   single    1.513  0.020  1.513
 UDO  CAY  CAK   aromatic  1.389  0.020  1.389
 UDO  CAY  CAL   aromatic  1.391  0.020  1.391
 UDO  CAK  CAI   aromatic  1.388  0.020  1.388
 UDO  CAI  CAX   aromatic  1.384  0.020  1.384
 UDO  CAX  CLA   single    1.731  0.020  1.731
 UDO  CAX  CAJ   aromatic  1.387  0.020  1.387
 UDO  CAJ  CAL   aromatic  1.384  0.020  1.384
 UDO  CAZ  CAH   aromatic  1.390  0.020  1.390
 UDO  CAZ  CAQ   aromatic  1.391  0.020  1.391
 UDO  CAH  CAF   aromatic  1.383  0.020  1.383
 UDO  CAF  CAG   aromatic  1.387  0.020  1.387
 UDO  CAG  NAV   aromatic  1.326  0.020  1.326
 UDO  NAV  CAQ   aromatic  1.327  0.020  1.327
 UDO  CAM  HAM   single    0.930  0.020  1.080
 UDO  CAO  HAO   single    0.930  0.020  1.080
 UDO  CAP  HAP   single    0.930  0.020  1.080
 UDO  CAN  HAN   single    0.930  0.020  1.080
 UDO  CAU  HAU1  single    0.970  0.020  1.090
 UDO  CAU  HAU2  single    0.970  0.020  1.090
 UDO  CAT  HAT1  single    0.970  0.020  1.090
 UDO  CAT  HAT2  single    0.970  0.020  1.090
 UDO  CAS  HAS1  single    0.970  0.020  1.090
 UDO  CAS  HAS2  single    0.970  0.020  1.090
 UDO  CAR  HAR1  single    0.970  0.020  1.090
 UDO  CAR  HAR2  single    0.970  0.020  1.090
 UDO  CBC  HBC   single    0.970  0.020  1.090
 UDO  CAK  HAK   single    0.930  0.020  1.080
 UDO  CAL  HAL   single    0.930  0.020  1.080
 UDO  CAI  HAI   single    0.930  0.020  1.080
 UDO  CAJ  HAJ   single    0.930  0.020  1.080
 UDO  CAH  HAH   single    0.930  0.020  1.080
 UDO  CAQ  HAQ   single    0.930  0.020  1.080
 UDO  CAF  HAF   single    0.930  0.020  1.080
 UDO  CAG  HAG   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
 UDO  HAM   CAM  CBA   120.62  3.000
 UDO  HAM   CAM  CAO   118.08  3.000
 UDO  CBA   CAM  CAO   121.27  3.000
 UDO  HAO   CAO  CBB   120.73  3.000
 UDO  HAO   CAO  CAM   118.42  3.000
 UDO  CBB   CAO  CAM   120.85  3.000
 UDO  CAP   CBB  CBF   121.44  3.000
 UDO  CAP   CBB  CAO   118.59  3.000
 UDO  CBF   CBB  CAO   119.93  3.000
 UDO  FAB   CBF  FAD   107.05  3.000
 UDO  FAB   CBF  FAC   106.05  3.000
 UDO  FAD   CBF  FAC   106.38  3.000
 UDO  FAB   CBF  CBB   112.18  3.000
 UDO  FAD   CBF  CBB   112.65  3.000
 UDO  FAC   CBF  CBB   112.08  3.000
 UDO  HAP   CAP  CAN   118.11  3.000
 UDO  HAP   CAP  CBB   121.04  3.000
 UDO  CAN   CAP  CBB   120.84  3.000
 UDO  HAN   CAN  CBA   121.11  3.000
 UDO  HAN   CAN  CAP   117.65  3.000
 UDO  CBA   CAN  CAP   121.23  3.000
 UDO  NBE   CBA  CAN   122.15  3.000
 UDO  NBE   CBA  CAM   120.62  3.000
 UDO  CAN   CBA  CAM   117.21  3.000
 UDO  CAT   NBE  CAU   112.92  3.000
 UDO  CAT   NBE  CBA   118.63  3.000
 UDO  CAU   NBE  CBA   118.74  3.000
 UDO  HAU2  CAU  HAU1  107.63  3.000
 UDO  HAU2  CAU  CAS   107.06  3.000
 UDO  HAU1  CAU  CAS   109.67  3.000
 UDO  HAU2  CAU  NBE   109.65  3.000
 UDO  HAU1  CAU  NBE   111.85  3.000
 UDO  CAS   CAU  NBE   110.81  3.000
 UDO  HAS2  CAS  HAS1  108.12  3.000
 UDO  HAS2  CAS  NBD   108.72  3.000
 UDO  HAS1  CAS  NBD   110.11  3.000
 UDO  HAS2  CAS  CAU   109.41  3.000
 UDO  HAS1  CAS  CAU   109.64  3.000
 UDO  NBD   CAS  CAU   110.79  3.000
 UDO  HAT2  CAT  HAT1  107.31  3.000
 UDO  HAT2  CAT  CAR   109.19  3.000
 UDO  HAT1  CAT  CAR   107.76  3.000
 UDO  HAT2  CAT  NBE   110.53  3.000
 UDO  HAT1  CAT  NBE   110.86  3.000
 UDO  CAR   CAT  NBE   111.06  3.000
 UDO  HAR2  CAR  HAR1  106.73  3.000
 UDO  HAR2  CAR  NBD   112.47  3.000
 UDO  HAR1  CAR  NBD   108.74  3.000
 UDO  HAR2  CAR  CAT   108.89  3.000
 UDO  HAR1  CAR  CAT   109.72  3.000
 UDO  NBD   CAR  CAT   110.22  3.000
 UDO  CAW   NBD  CAR   127.48  3.000
 UDO  CAW   NBD  CAS   121.15  3.000
 UDO  CAR   NBD  CAS   111.30  3.000
 UDO  CBC   CAW  OAA   120.32  3.000
 UDO  CBC   CAW  NBD   117.03  3.000
 UDO  OAA   CAW  NBD   122.64  3.000
 UDO  HBC   CBC  CAZ   107.44  3.000
 UDO  HBC   CBC  CAY   106.72  3.000
 UDO  CAZ   CBC  CAY   111.92  3.000
 UDO  HBC   CBC  CAW   108.46  3.000
 UDO  CAZ   CBC  CAW   111.52  3.000
 UDO  CAY   CBC  CAW   110.56  3.000
 UDO  CAL   CAY  CAK   118.49  3.000
 UDO  CAL   CAY  CBC   121.70  3.000
 UDO  CAK   CAY  CBC   119.81  3.000
 UDO  HAK   CAK  CAI   118.57  3.000
 UDO  HAK   CAK  CAY   120.10  3.000
 UDO  CAI   CAK  CAY   121.33  3.000
 UDO  HAI   CAI  CAX   120.71  3.000
 UDO  HAI   CAI  CAK   120.29  3.000
 UDO  CAX   CAI  CAK   119.01  3.000
 UDO  CAJ   CAX  CLA   119.54  3.000
 UDO  CAJ   CAX  CAI   120.81  3.000
 UDO  CLA   CAX  CAI   119.65  3.000
 UDO  HAJ   CAJ  CAL   120.21  3.000
 UDO  HAJ   CAJ  CAX   120.47  3.000
 UDO  CAL   CAJ  CAX   119.32  3.000
 UDO  HAL   CAL  CAJ   118.36  3.000
 UDO  HAL   CAL  CAY   120.59  3.000
 UDO  CAJ   CAL  CAY   121.04  3.000
 UDO  CAQ   CAZ  CAH   117.15  3.000
 UDO  CAQ   CAZ  CBC   122.47  3.000
 UDO  CAH   CAZ  CBC   120.36  3.000
 UDO  HAH   CAH  CAF   120.06  3.000
 UDO  HAH   CAH  CAZ   120.46  3.000
 UDO  CAF   CAH  CAZ   119.48  3.000
 UDO  HAF   CAF  CAG   120.51  3.000
 UDO  HAF   CAF  CAH   121.11  3.000
 UDO  CAG   CAF  CAH   118.38  3.000
 UDO  HAG   CAG  NAV   116.68  3.000
 UDO  HAG   CAG  CAF   120.32  3.000
 UDO  NAV   CAG  CAF   123.00  3.000
 UDO  CAQ   NAV  CAG   118.10  3.000
 UDO  HAQ   CAQ  NAV   115.54  3.000
 UDO  HAQ   CAQ  CAZ   120.57  3.000
 UDO  NAV   CAQ  CAZ   123.89  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
 UDO  CONST_01  CAP  CBB  CAO  CAM     0.00   0.0  0
 UDO  CONST_02  CAP  CAN  CBA  CAM     0.00   0.0  0
 UDO  CONST_03  CAN  CBA  CAM  CAO     0.00   0.0  0
 UDO  CONST_04  CAN  CAP  CBB  CAO     0.00   0.0  0
 UDO  CONST_05  CBA  CAM  CAO  CBB     0.00   0.0  0
 UDO  CONST_06  CBA  CAN  CAP  CBB     0.00   0.0  0
 UDO  CONST_07  CAX  CAI  CAK  CAY     0.00   0.0  0
 UDO  CONST_08  CAX  CAJ  CAL  CAY     0.00   0.0  0
 UDO  CONST_09  CAJ  CAL  CAY  CAK     0.00   0.0  0
 UDO  CONST_10  CAJ  CAX  CAI  CAK     0.00   0.0  0
 UDO  CONST_11  CAL  CAY  CAK  CAI     0.00   0.0  0
 UDO  CONST_12  CAL  CAJ  CAX  CAI     0.00   0.0  0
 UDO  CONST_13  CAG  CAF  CAH  CAZ     0.00   0.0  0
 UDO  CONST_14  CAG  NAV  CAQ  CAZ     0.00   0.0  0
 UDO  CONST_15  NAV  CAQ  CAZ  CAH     0.00   0.0  0
 UDO  CONST_16  NAV  CAG  CAF  CAH     0.00   0.0  0
 UDO  CONST_17  CAQ  CAZ  CAH  CAF     0.00   0.0  0
 UDO  CONST_18  CAQ  NAV  CAG  CAF     0.00   0.0  0
 UDO  CONST_19  NBE  CBA  CAM  CAO   180.00   0.0  0
 UDO  CONST_20  NBE  CBA  CAN  CAP   180.00   0.0  0
 UDO  CONST_21  CBF  CBB  CAO  CAM   180.00   0.0  0
 UDO  CONST_22  CAN  CAP  CBB  CBF   180.00   0.0  0
 UDO  CONST_23  CAI  CAK  CAY  CBC   180.00   0.0  0
 UDO  CONST_24  CAJ  CAL  CAY  CBC   180.00   0.0  0
 UDO  CONST_25  CAF  CAH  CAZ  CBC   180.00   0.0  0
 UDO  CONST_26  NAV  CAQ  CAZ  CBC   180.00   0.0  0
 UDO  CONST_27  CLA  CAX  CAI  CAK   180.00   0.0  0
 UDO  CONST_28  CAL  CAJ  CAX  CLA   180.00   0.0  0
 UDO  CONST_29  HAN  CAN  CBA  CAM   180.00   0.0  0
 UDO  CONST_30  HAP  CAP  CBB  CAO   180.00   0.0  0
 UDO  CONST_31  HAM  CAM  CAO  CBB   180.00   0.0  0
 UDO  CONST_32  HAO  CAO  CBB  CAP   180.00   0.0  0
 UDO  CONST_33  HAI  CAI  CAK  CAY   180.00   0.0  0
 UDO  CONST_34  HAJ  CAJ  CAL  CAY   180.00   0.0  0
 UDO  CONST_35  HAL  CAL  CAY  CAK   180.00   0.0  0
 UDO  CONST_36  HAK  CAK  CAI  CAX   180.00   0.0  0
 UDO  CONST_37  HAF  CAF  CAH  CAZ   180.00   0.0  0
 UDO  CONST_38  HAQ  CAQ  CAZ  CAH   180.00   0.0  0
 UDO  CONST_39  HAG  CAG  CAF  CAH   180.00   0.0  0
 UDO  CONST_40  HAH  CAH  CAF  CAG   180.00   0.0  0
 UDO  CONST_41  OAA  CAW  NBD  CAS     0.00   0.0  0
 UDO  CONST_42  CBC  CAW  NBD  CAS   180.00   0.0  0
 UDO  CONST_43  OAA  CAW  NBD  CAR   180.00   0.0  0
 UDO  CONST_44  CBC  CAW  NBD  CAR     0.00   0.0  0
 UDO  Var_01    CAU  NBE  CBA  CAM  -174.79  30.0  2
 UDO  Var_02    CAS  CAU  NBE  CBA   161.17  30.0  1
 UDO  Var_03    CAR  CAT  NBE  CBA  -160.56  30.0  1
 UDO  Var_04    NBD  CAS  CAU  NBE    54.64  30.0  1
 UDO  Var_05    NBD  CAR  CAT  NBE   -55.29  30.0  1
 UDO  Var_06    CAR  NBD  CAS  CAU   -57.94  30.0  1
 UDO  Var_07    CAT  CAR  NBD  CAS    58.06  30.0  1
 UDO  Var_08    FAC  CBF  CBB  CAO    80.54  30.0  2

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
 UDO  chir_01  CBC  CAW  CAY  CAZ  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
 UDO  plan-1  CAM  0.020
 UDO  plan-1  CAO  0.020
 UDO  plan-1  CBB  0.020
 UDO  plan-1  CBF  0.020
 UDO  plan-1  CAP  0.020
 UDO  plan-1  CAN  0.020
 UDO  plan-1  CBA  0.020
 UDO  plan-1  NBE  0.020
 UDO  plan-1  HAM  0.020
 UDO  plan-1  HAO  0.020
 UDO  plan-1  HAP  0.020
 UDO  plan-1  HAN  0.020
 UDO  plan-2  CBC  0.020
 UDO  plan-2  CAY  0.020
 UDO  plan-2  CAK  0.020
 UDO  plan-2  CAI  0.020
 UDO  plan-2  CAX  0.020
 UDO  plan-2  CLA  0.020
 UDO  plan-2  CAJ  0.020
 UDO  plan-2  CAL  0.020
 UDO  plan-2  HAK  0.020
 UDO  plan-2  HAL  0.020
 UDO  plan-2  HAI  0.020
 UDO  plan-2  HAJ  0.020
 UDO  plan-3  CBC  0.020
 UDO  plan-3  CAZ  0.020
 UDO  plan-3  CAH  0.020
 UDO  plan-3  CAF  0.020
 UDO  plan-3  CAG  0.020
 UDO  plan-3  NAV  0.020
 UDO  plan-3  CAQ  0.020
 UDO  plan-3  HAH  0.020
 UDO  plan-3  HAQ  0.020
 UDO  plan-3  HAF  0.020
 UDO  plan-3  HAG  0.020
 UDO  plan-4  CAS  0.020
 UDO  plan-4  CAR  0.020
 UDO  plan-4  NBD  0.020
 UDO  plan-4  CAW  0.020
 UDO  plan-4  OAA  0.020
 UDO  plan-4  CBC  0.020

