# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 13:54:51 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (2S)-3-[(4-cyanonaphthalen-1-yl)oxy]-N-[4-cyano-3-(trifluoromethyl)phenyl]-2-hydroxy-2-methylpropanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@](O)(COc1ccc(C#N)c2ccccc12)C(=O)Nc3ccc(C#N)c(c3)C(F)(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
 RLL  RLL  (2S)-3-[(4-cyanonaphthalen-1-yl)oxy]-N-[4-cyano-3-(trifluoromethyl)phenyl]-2-hydroxy-2-methylpropanamide  ligand  48  32  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RLL
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
 RLL  CAA   C  CH3   0  -0.663   0.8138   1.5753  -1.9597
 RLL  NAB   N  NS    0  -0.237  -8.2976  -1.4441  -0.5986
 RLL  NAC   N  NS    0  -0.259   8.7749  -2.6578   0.7936
 RLL  OAD   O  O     0  -0.444  -0.7132  -1.0947  -1.7899
 RLL  OAE   O  OH1   0  -0.652   0.4668   1.4694   0.3733
 RLL  FAF   F  F     0  -0.291  -5.8111   2.2691   1.5786
 RLL  FAG   F  F     0  -0.310  -7.0210   0.5167   1.8841
 RLL  FAH   F  F     0  -0.310  -7.3094   1.7304   0.1324
 RLL  CAI   C  CSP   0   0.015  -7.1964  -1.1104  -0.5430
 RLL  CAK   C  CR16  0  -0.237   7.4329   2.1209   0.5942
 RLL  CAL   C  CR16  0  -0.250   6.1880   2.7221   0.3389
 RLL  CAM   C  CR16  0  -0.300  -3.5511  -1.1724  -1.1912
 RLL  CAN   C  CR16  0  -0.229  -4.8955  -1.4967  -1.1926
 RLL  CAO   C  CR16  0  -0.239   5.4082  -2.2554   0.0915
 RLL  CAP   C  CR16  0  -0.412   4.1654  -1.6632  -0.1587
 RLL  CAQ   C  CR16  0  -0.328   7.5555   0.7570   0.5978
 RLL  CAR   C  CR16  0  -0.280   5.0857   1.9477   0.0931
 RLL  CAS   C  CR16  0  -0.417  -4.0486   0.7224   0.2157
 RLL  CAT   C  CH2   0  -0.196   1.7193  -0.3645  -0.6050
 RLL  NAU   N  NH1   0  -0.748  -1.7951   0.3620  -0.4080
 RLL  OAV   O  O2    0  -0.453   2.9099   0.3644  -0.3807
 RLL  CAW   C  C     0   0.539  -0.7039  -0.1406  -1.0385
 RLL  CAX   C  CR6   0   0.446  -3.1137  -0.0537  -0.4831
 RLL  CAY   C  CR6   0   0.027  -5.8246  -0.7274  -0.5017
 RLL  CAZ   C  CR6   0  -0.049   6.5238  -1.4918   0.3400
 RLL  CBA   C  CR6   0   0.403   4.0478  -0.2911  -0.1590
 RLL  CBB   C  CR6   0  -0.150  -5.3848   0.3967   0.2102
 RLL  CBC   C  CR66  0   0.177   6.4387  -0.0676   0.3462
 RLL  CBD   C  CR66  0  -0.032   5.1849   0.5386   0.0914
 RLL  CBE   C  CT    0   0.050   0.5883   0.6522  -0.7637
 RLL  CBF   C  CT    0   1.079  -6.3786   1.2376   0.9578
 RLL  HAA   H  HCH3  0   0.262   1.7225   2.1611  -1.8287
 RLL  HAAA  H  HCH3  0   0.249   0.9043   1.0023  -2.8810
 RLL  HAAB  H  HCH3  0   0.254  -0.0205   2.2689  -2.0721
 RLL  HOAE  H  HOH1  0   0.465   0.5415   0.9367   1.1744
 RLL  HAK   H  HCR6  0   0.270   8.2987   2.7393   0.7902
 RLL  HAL   H  HCR6  0   0.267   6.1015   3.8004   0.3383
 RLL  HAM   H  HCR6  0   0.305  -2.8639  -1.7933  -1.7401
 RLL  HAN   H  HCR6  0   0.297  -5.2268  -2.3675  -1.7412
 RLL  HAO   H  HCR6  0   0.289   5.4821  -3.3344   0.0877
 RLL  HAP   H  HCR6  0   0.300   3.3189  -2.3070  -0.3486
 RLL  HAQ   H  HCR6  0   0.260   8.5200   0.3071   0.7979
 RLL  HAR   H  HCR6  0   0.266   4.1334   2.4208  -0.1008
 RLL  HAS   H  HCR6  0   0.302  -3.7011   1.5916   0.7585
 RLL  HAT   H  HCH2  0   0.262   1.8056  -0.9797  -1.5034
 RLL  HATA  H  HCH2  0   0.264   1.5166  -1.0296   0.2438
 RLL  HNAU  H  HNH1  0   0.428  -1.6174   1.1696   0.1753
 RLL  CAJ   C  CSP   0   0.014   7.7665  -2.1352   0.5907

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
 RLL  CAA  CBE   single    1.528  0.020  1.528
 RLL  NAB  CAI   triple    1.152  0.020  1.152
 RLL  NAC  CAJ   triple    1.154  0.020  1.154
 RLL  OAD  CAW   double    1.215  0.020  1.215
 RLL  OAE  CBE   single    1.405  0.020  1.405
 RLL  FAF  CBF   single    1.331  0.020  1.331
 RLL  FAG  CBF   single    1.338  0.020  1.338
 RLL  FAH  CBF   single    1.338  0.020  1.338
 RLL  CAI  CAY   single    1.425  0.020  1.425
 RLL  CAJ  CAZ   single    1.422  0.020  1.422
 RLL  CAK  CAL   aromatic  1.406  0.020  1.406
 RLL  CAK  CAQ   aromatic  1.369  0.020  1.369
 RLL  CAL  CAR   aromatic  1.369  0.020  1.369
 RLL  CAM  CAN   aromatic  1.383  0.020  1.383
 RLL  CAM  CAX   aromatic  1.394  0.020  1.394
 RLL  CAN  CAY   aromatic  1.390  0.020  1.390
 RLL  CAO  CAP   aromatic  1.399  0.020  1.399
 RLL  CAO  CAZ   aromatic  1.375  0.020  1.375
 RLL  CAP  CBA   aromatic  1.377  0.020  1.377
 RLL  CAQ  CBC   aromatic  1.411  0.020  1.411
 RLL  CAR  CBD   aromatic  1.413  0.020  1.413
 RLL  CAS  CAX   aromatic  1.402  0.020  1.402
 RLL  CAS  CBB   aromatic  1.375  0.020  1.375
 RLL  CAT  OAV   single    1.414  0.020  1.414
 RLL  CAT  CBE   single    1.529  0.020  1.529
 RLL  NAU  CAW   single    1.357  0.020  1.357
 RLL  NAU  CAX   single    1.385  0.020  1.385
 RLL  OAV  CBA   single    1.332  0.020  1.332
 RLL  CAW  CBE   single    1.541  0.020  1.541
 RLL  CAY  CBB   aromatic  1.401  0.020  1.401
 RLL  CAZ  CBC   aromatic  1.427  0.020  1.427
 RLL  CBA  CBD   aromatic  1.430  0.020  1.430
 RLL  CBB  CBF   single    1.501  0.020  1.501
 RLL  CBC  CBD   aromatic  1.416  0.020  1.416
 RLL  CAA  HAA   single    0.970  0.020  1.090
 RLL  CAA  HAAA  single    0.970  0.020  1.090
 RLL  CAA  HAAB  single    0.970  0.020  1.090
 RLL  OAE  HOAE  single    0.850  0.020  0.980
 RLL  CAK  HAK   single    0.930  0.020  1.080
 RLL  CAL  HAL   single    0.930  0.020  1.080
 RLL  CAM  HAM   single    0.930  0.020  1.080
 RLL  CAN  HAN   single    0.930  0.020  1.080
 RLL  CAO  HAO   single    0.930  0.020  1.080
 RLL  CAP  HAP   single    0.930  0.020  1.080
 RLL  CAQ  HAQ   single    0.930  0.020  1.080
 RLL  CAR  HAR   single    0.930  0.020  1.080
 RLL  CAS  HAS   single    0.930  0.020  1.080
 RLL  CAT  HAT   single    0.970  0.020  1.090
 RLL  CAT  HATA  single    0.970  0.020  1.090
 RLL  NAU  HNAU  single    0.860  0.020  1.020

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
 RLL  HAAB  CAA  HAAA  108.12  3.000
 RLL  HAAB  CAA  HAA   107.97  3.000
 RLL  HAAA  CAA  HAA   108.40  3.000
 RLL  HAAB  CAA  CBE   110.61  3.000
 RLL  HAAA  CAA  CBE   110.91  3.000
 RLL  HAA   CAA  CBE   110.73  3.000
 RLL  HOAE  OAE  CBE   110.12  3.000
 RLL  CAY   CAI  NAB   180.00  3.000
 RLL  HAK   CAK  CAQ   119.82  3.000
 RLL  HAK   CAK  CAL   119.80  3.000
 RLL  CAQ   CAK  CAL   120.38  3.000
 RLL  HAL   CAL  CAR   119.95  3.000
 RLL  HAL   CAL  CAK   119.82  3.000
 RLL  CAR   CAL  CAK   120.23  3.000
 RLL  HAM   CAM  CAX   121.42  3.000
 RLL  HAM   CAM  CAN   119.00  3.000
 RLL  CAX   CAM  CAN   119.58  3.000
 RLL  HAN   CAN  CAY   119.55  3.000
 RLL  HAN   CAN  CAM   119.16  3.000
 RLL  CAY   CAN  CAM   121.30  3.000
 RLL  HAO   CAO  CAZ   119.96  3.000
 RLL  HAO   CAO  CAP   118.83  3.000
 RLL  CAZ   CAO  CAP   121.20  3.000
 RLL  HAP   CAP  CBA   121.79  3.000
 RLL  HAP   CAP  CAO   118.37  3.000
 RLL  CBA   CAP  CAO   119.84  3.000
 RLL  HAQ   CAQ  CBC   119.68  3.000
 RLL  HAQ   CAQ  CAK   119.61  3.000
 RLL  CBC   CAQ  CAK   120.71  3.000
 RLL  HAR   CAR  CBD   119.89  3.000
 RLL  HAR   CAR  CAL   119.59  3.000
 RLL  CBD   CAR  CAL   120.52  3.000
 RLL  HAS   CAS  CBB   120.28  3.000
 RLL  HAS   CAS  CAX   118.73  3.000
 RLL  CBB   CAS  CAX   120.99  3.000
 RLL  HATA  CAT  HAT   108.02  3.000
 RLL  HATA  CAT  CBE   110.29  3.000
 RLL  HAT   CAT  CBE   110.34  3.000
 RLL  HATA  CAT  OAV   110.20  3.000
 RLL  HAT   CAT  OAV   110.75  3.000
 RLL  CBE   CAT  OAV   107.25  3.000
 RLL  HNAU  NAU  CAX   115.98  3.000
 RLL  HNAU  NAU  CAW   114.97  3.000
 RLL  CAX   NAU  CAW   129.01  3.000
 RLL  CBA   OAV  CAT   119.48  3.000
 RLL  CBE   CAW  NAU   113.64  3.000
 RLL  CBE   CAW  OAD   121.40  3.000
 RLL  NAU   CAW  OAD   124.92  3.000
 RLL  NAU   CAX  CAS   116.23  3.000
 RLL  NAU   CAX  CAM   124.55  3.000
 RLL  CAS   CAX  CAM   119.22  3.000
 RLL  CBB   CAY  CAN   119.12  3.000
 RLL  CBB   CAY  CAI   122.17  3.000
 RLL  CAN   CAY  CAI   118.70  3.000
 RLL  CBC   CAZ  CAO   120.46  3.000
 RLL  CBC   CAZ  CAJ   120.20  3.000
 RLL  CAO   CAZ  CAJ   119.34  3.000
 RLL  CBD   CBA  OAV   115.03  3.000
 RLL  CBD   CBA  CAP   120.68  3.000
 RLL  OAV   CBA  CAP   124.29  3.000
 RLL  CBF   CBB  CAY   119.64  3.000
 RLL  CBF   CBB  CAS   120.56  3.000
 RLL  CAY   CBB  CAS   119.79  3.000
 RLL  CBD   CBC  CAZ   118.65  3.000
 RLL  CBD   CBC  CAQ   118.87  3.000
 RLL  CAZ   CBC  CAQ   122.48  3.000
 RLL  CBC   CBD  CBA   119.17  3.000
 RLL  CBC   CBD  CAR   119.28  3.000
 RLL  CBA   CBD  CAR   121.55  3.000
 RLL  CAW   CBE  CAT   107.26  3.000
 RLL  CAW   CBE  OAE   111.77  3.000
 RLL  CAT   CBE  OAE   111.51  3.000
 RLL  CAW   CBE  CAA   107.16  3.000
 RLL  CAT   CBE  CAA   111.95  3.000
 RLL  OAE   CBE  CAA   107.15  3.000
 RLL  CBB   CBF  FAH   111.08  3.000
 RLL  CBB   CBF  FAG   111.15  3.000
 RLL  FAH   CBF  FAG   106.95  3.000
 RLL  CBB   CBF  FAF   112.59  3.000
 RLL  FAH   CBF  FAF   107.39  3.000
 RLL  FAG   CBF  FAF   107.42  3.000
 RLL  CAZ   CAJ  NAC   180.00  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
 RLL  CONST_01  CBD   CAR  CAL  CAK     0.00   0.0  0
 RLL  CONST_02  CAZ   CBC  CAQ  CAK   180.00   0.0  0
 RLL  CONST_03  CBD   CBC  CAQ  CAK     0.00   0.0  0
 RLL  CONST_04  CBC   CAQ  CAK  CAL     0.00   0.0  0
 RLL  CONST_05  CBA   CBD  CAR  CAL   180.00   0.0  0
 RLL  CONST_06  CBC   CBD  CAR  CAL     0.00   0.0  0
 RLL  CONST_07  CBB   CAY  CAN  CAM     0.00   0.0  0
 RLL  CONST_08  CBB   CAS  CAX  CAM     0.00   0.0  0
 RLL  CONST_09  CAS   CAX  CAM  CAN     0.00   0.0  0
 RLL  CONST_10  CAS   CBB  CAY  CAN     0.00   0.0  0
 RLL  CONST_11  CBD   CBA  CAP  CAO     0.00   0.0  0
 RLL  CONST_12  CAQ   CBC  CAZ  CAO   180.00   0.0  0
 RLL  CONST_13  CBD   CBC  CAZ  CAO     0.00   0.0  0
 RLL  CONST_14  CBC   CAZ  CAO  CAP     0.00   0.0  0
 RLL  CONST_15  CAR   CBD  CBA  CAP   180.00   0.0  0
 RLL  CONST_16  CBC   CBD  CBA  CAP     0.00   0.0  0
 RLL  CONST_17  CAR   CAL  CAK  CAQ     0.00   0.0  0
 RLL  CONST_18  CAR   CBD  CBC  CAQ     0.00   0.0  0
 RLL  CONST_19  CBA   CBD  CBC  CAQ   180.00   0.0  0
 RLL  CONST_20  CAZ   CBC  CBD  CAR   180.00   0.0  0
 RLL  CONST_21  CAY   CAN  CAM  CAX     0.00   0.0  0
 RLL  CONST_22  CAY   CBB  CAS  CAX     0.00   0.0  0
 RLL  CONST_23  CBA   CAP  CAO  CAZ     0.00   0.0  0
 RLL  CONST_24  CBA   CBD  CBC  CAZ     0.00   0.0  0
 RLL  CONST_25  CAM   CAN  CAY  CAI   180.00   0.0  0
 RLL  CONST_26  CAS   CBB  CAY  CAI   180.00   0.0  0
 RLL  CONST_27  CAP   CAO  CAZ  CAJ   180.00   0.0  0
 RLL  CONST_28  CAQ   CBC  CAZ  CAJ     0.00   0.0  0
 RLL  CONST_29  CBD   CBC  CAZ  CAJ   180.00   0.0  0
 RLL  CONST_30  NAU   CAX  CAM  CAN   180.00   0.0  0
 RLL  CONST_31  CBF   CBB  CAY  CAN   180.00   0.0  0
 RLL  CONST_32  OAV   CBA  CAP  CAO   180.00   0.0  0
 RLL  CONST_33  OAV   CBA  CBD  CAR     0.00   0.0  0
 RLL  CONST_34  CBB   CAS  CAX  NAU   180.00   0.0  0
 RLL  CONST_35  CBC   CBD  CBA  OAV   180.00   0.0  0
 RLL  CONST_36  CBF   CBB  CAS  CAX   180.00   0.0  0
 RLL  CONST_37  HAR   CAR  CAL  CAK   180.00   0.0  0
 RLL  CONST_38  HAQ   CAQ  CAK  CAL   180.00   0.0  0
 RLL  CONST_39  HAS   CAS  CAX  CAM   180.00   0.0  0
 RLL  CONST_40  HAL   CAL  CAK  CAQ   180.00   0.0  0
 RLL  CONST_41  HAK   CAK  CAL  CAR   180.00   0.0  0
 RLL  CONST_42  HAM   CAM  CAX  CAS   180.00   0.0  0
 RLL  CONST_43  HAN   CAN  CAM  CAX   180.00   0.0  0
 RLL  CONST_44  HAP   CAP  CAO  CAZ   180.00   0.0  0
 RLL  CONST_45  HAO   CAO  CAP  CBA   180.00   0.0  0
 RLL  CONST_46  CAW   NAU  CAX  CAM     0.00   0.0  0
 RLL  CONST_47  CAW   NAU  CAX  CAS   180.00   0.0  0
 RLL  CONST_48  HNAU  NAU  CAX  CAM   180.00   0.0  0
 RLL  CONST_49  CAX   NAU  CAW  OAD     0.00   0.0  0
 RLL  CONST_50  CBE   CAW  NAU  CAX   180.00   0.0  0
 RLL  Var_01    CAS   CBB  CBF  FAF     0.05  30.0  3
 RLL  Var_02    CBD   CBA  OAV  CAT  -178.40  30.0  2
 RLL  Var_03    CBE   CAT  OAV  CBA   177.54  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
 RLL  chir_01  CBE  OAE  CAT  CAW  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
 RLL  plan-1  NAB   0.020
 RLL  plan-1  CAI   0.020
 RLL  plan-1  CAM   0.020
 RLL  plan-1  CAN   0.020
 RLL  plan-1  CAS   0.020
 RLL  plan-1  NAU   0.020
 RLL  plan-1  CAX   0.020
 RLL  plan-1  CAY   0.020
 RLL  plan-1  CBB   0.020
 RLL  plan-1  CBF   0.020
 RLL  plan-1  HAM   0.020
 RLL  plan-1  HAN   0.020
 RLL  plan-1  HAS   0.020
 RLL  plan-2  NAC   0.020
 RLL  plan-2  CAK   0.020
 RLL  plan-2  CAL   0.020
 RLL  plan-2  CAO   0.020
 RLL  plan-2  CAP   0.020
 RLL  plan-2  CAQ   0.020
 RLL  plan-2  CAR   0.020
 RLL  plan-2  OAV   0.020
 RLL  plan-2  CAZ   0.020
 RLL  plan-2  CBA   0.020
 RLL  plan-2  CBC   0.020
 RLL  plan-2  CBD   0.020
 RLL  plan-2  HAK   0.020
 RLL  plan-2  HAL   0.020
 RLL  plan-2  HAO   0.020
 RLL  plan-2  HAP   0.020
 RLL  plan-2  HAQ   0.020
 RLL  plan-2  HAR   0.020
 RLL  plan-2  CAJ   0.020
 RLL  plan-3  OAD   0.020
 RLL  plan-3  NAU   0.020
 RLL  plan-3  CAW   0.020
 RLL  plan-3  CAX   0.020
 RLL  plan-3  CBE   0.020
 RLL  plan-3  HNAU  0.020

