# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 19:05:25 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (3S,4R)-3-[(1,3-benzodioxol-5-yloxy)methyl]-4-(4-fluorophenyl)piperidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(cc1)[C@@H]2CCNC[C@H]2COc3ccc4OCOc4c3
#
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
 8PR  8PR  (3S,4R)-3-[(1,3-benzodioxol-5-yloxy)methyl]-4-(4-fluorophenyl)piperidine  ligand  44  24  .  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_8PR
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
 8PR  FAA   F  F     0  -0.319  -3.9662   4.3073   0.4884
 8PR  CAB   C  CR16  0  -0.395  -3.4531   2.5952  -1.0358
 8PR  CAC   C  CR16  0  -0.396  -3.5889   2.1478   1.3330
 8PR  CAD   C  CR16  0  -0.429   2.2096   0.5495  -0.9765
 8PR  CAE   C  CR16  0  -0.311  -3.1445   1.2586  -1.2542
 8PR  CAF   C  CR16  0  -0.296  -3.2811   0.8175   1.0897
 8PR  CAG   C  CR16  0  -0.331   3.4488   1.1520  -1.2495
 8PR  CAH   C  CR16  0  -0.444   3.2277  -0.8836   0.7048
 8PR  CAI   C  CH2   0  -0.318  -3.4982  -3.4853  -0.2990
 8PR  CAJ   C  CH2   0  -0.420  -3.8451  -2.0299  -0.0060
 8PR  CAK   C  CH2   0  -0.290  -1.1434  -3.0250  -0.1256
 8PR  CAL   C  CH2   0   0.068   6.4953   0.5019   0.4727
 8PR  CAM   C  CH2   0  -0.154  -0.2476  -0.6781  -0.3493
 8PR  NAN   N  NH1   0  -0.577  -2.2283  -3.9043   0.2675
 8PR  OAO   O  O2    0  -0.482   0.9465  -1.0742   0.3016
 8PR  OAP   O  O     0  -0.491   5.8396   1.1082  -0.6290
 8PR  OAQ   O  O     0  -0.486   5.6373  -0.5276   0.9522
 8PR  CAR   C  CR6   0   0.506  -3.6692   3.0157   0.2605
 8PR  CAS   C  CR6   0   0.381   2.0996  -0.4504  -0.0179
 8PR  CAT   C  CR6   0   0.162  -3.0516   0.3500  -0.2039
 8PR  CAU   C  CR56  0   0.275   4.5367   0.7216  -0.5411
 8PR  CAV   C  CR56  0   0.316   4.4202  -0.2766   0.4159
 8PR  CAW   C  CH1   0  -0.282  -1.3866  -1.5373   0.1675
 8PR  CAX   C  CH1   0  -0.327  -2.7193  -1.0980  -0.4661
 8PR  HAB   H  HCR6  0   0.277  -3.5218   3.2928  -1.8603
 8PR  HAC   H  HCR6  0   0.277  -3.7657   2.5020   2.3402
 8PR  HAE   H  HCR6  0   0.259  -2.9704   0.9209  -2.2688
 8PR  HAF   H  HCR6  0   0.258  -3.2244   0.1384   1.9316
 8PR  HAG   H  HCR6  0   0.274   3.5257   1.9256  -2.0011
 8PR  HAH   H  HCR6  0   0.277   3.1440  -1.6628   1.4511
 8PR  HAI   H  HCH2  0   0.238  -4.2853  -4.1448   0.0721
 8PR  HAIA  H  HCH2  0   0.216  -3.4510  -3.6311  -1.3840
 8PR  HAJ   H  HCH2  0   0.235  -4.7776  -1.7546  -0.5055
 8PR  HAJA  H  HCH2  0   0.221  -4.0129  -1.9054   1.0693
 8PR  HAK   H  HCH2  0   0.244  -0.2318  -3.3619   0.3693
 8PR  HAKA  H  HCH2  0   0.211  -0.9786  -3.1453  -1.2039
 8PR  HAL   H  HCH2  0   0.245   7.4417   0.0694   0.1500
 8PR  HALA  H  HCH2  0   0.230   6.6607   1.2410   1.2649
 8PR  HAM   H  HCH2  0   0.236  -0.4435   0.3819  -0.1546
 8PR  HAMA  H  HCH2  0   0.214  -0.1514  -0.8012  -1.4369
 8PR  HNAN  H  HNH1  0   0.340  -2.3011  -3.9069   1.2784
 8PR  HAW   H  HCH1  0   0.232  -1.4599  -1.4078   1.2554
 8PR  HAX   H  HCH1  0   0.238  -2.6170  -1.2197  -1.5528
 8PR  HAD   H  HCR6  0   0.319   1.3479   0.8889  -1.5338

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
 8PR  FAA  CAR   single    1.345  0.020  1.345
 8PR  CAR  CAB   aromatic  1.380  0.020  1.380
 8PR  CAB  CAE   aromatic  1.389  0.020  1.389
 8PR  CAB  HAB   single    0.930  0.020  1.080
 8PR  CAR  CAC   aromatic  1.382  0.020  1.382
 8PR  CAC  CAF   aromatic  1.387  0.020  1.387
 8PR  CAC  HAC   single    0.930  0.020  1.080
 8PR  CAS  CAD   aromatic  1.390  0.020  1.390
 8PR  CAD  CAG   aromatic  1.405  0.020  1.405
 8PR  CAD  HAD   single    0.930  0.020  1.080
 8PR  CAE  CAT   aromatic  1.392  0.020  1.392
 8PR  CAE  HAE   single    0.930  0.020  1.080
 8PR  CAF  CAT   aromatic  1.395  0.020  1.395
 8PR  CAF  HAF   single    0.930  0.020  1.080
 8PR  CAU  CAG   aromatic  1.368  0.020  1.368
 8PR  CAG  HAG   single    0.930  0.020  1.080
 8PR  CAH  CAS   aromatic  1.408  0.020  1.408
 8PR  CAH  CAV   aromatic  1.369  0.020  1.369
 8PR  CAH  HAH   single    0.930  0.020  1.080
 8PR  CAJ  CAI   single    1.525  0.020  1.525
 8PR  CAI  NAN   single    1.452  0.020  1.452
 8PR  CAI  HAI   single    0.970  0.020  1.090
 8PR  CAI  HAIA  single    0.970  0.020  1.090
 8PR  CAJ  CAX   single    1.532  0.020  1.532
 8PR  CAJ  HAJ   single    0.970  0.020  1.090
 8PR  CAJ  HAJA  single    0.970  0.020  1.090
 8PR  CAW  CAK   single    1.536  0.020  1.536
 8PR  NAN  CAK   single    1.451  0.020  1.451
 8PR  CAK  HAK   single    0.970  0.020  1.090
 8PR  CAK  HAKA  single    0.970  0.020  1.090
 8PR  OAQ  CAL   single    1.423  0.020  1.423
 8PR  OAP  CAL   single    1.418  0.020  1.418
 8PR  CAL  HAL   single    0.970  0.020  1.090
 8PR  CAL  HALA  single    0.970  0.020  1.090
 8PR  CAW  CAM   single    1.517  0.020  1.517
 8PR  CAM  OAO   single    1.417  0.020  1.417
 8PR  CAM  HAM   single    0.970  0.020  1.090
 8PR  CAM  HAMA  single    0.970  0.020  1.090
 8PR  NAN  HNAN  single    0.890  0.020  1.040
 8PR  OAO  CAS   single    1.349  0.020  1.349
 8PR  CAU  OAP   single    1.362  0.020  1.362
 8PR  CAV  OAQ   single    1.354  0.020  1.354
 8PR  CAT  CAX   single    1.509  0.020  1.509
 8PR  CAV  CAU   aromatic  1.388  0.020  1.388
 8PR  CAX  CAW   single    1.540  0.020  1.540
 8PR  CAW  HAW   single    0.970  0.020  1.090
 8PR  CAX  HAX   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
 8PR  HAB   CAB  CAR  120.62  3.000
 8PR  HAB   CAB  CAE  120.97  3.000
 8PR  CAR   CAB  CAE  118.41  3.000
 8PR  HAC   CAC  CAR  120.48  3.000
 8PR  HAC   CAC  CAF  120.89  3.000
 8PR  CAR   CAC  CAF  118.63  3.000
 8PR  HAD   CAD  CAS  121.23  3.000
 8PR  HAD   CAD  CAG  117.94  3.000
 8PR  CAS   CAD  CAG  120.83  3.000
 8PR  HAE   CAE  CAT  119.50  3.000
 8PR  HAE   CAE  CAB  118.88  3.000
 8PR  CAT   CAE  CAB  121.62  3.000
 8PR  HAF   CAF  CAT  120.14  3.000
 8PR  HAF   CAF  CAC  118.47  3.000
 8PR  CAT   CAF  CAC  121.39  3.000
 8PR  HAG   CAG  CAU  121.91  3.000
 8PR  HAG   CAG  CAD  120.31  3.000
 8PR  CAU   CAG  CAD  117.78  3.000
 8PR  HAH   CAH  CAV  122.16  3.000
 8PR  HAH   CAH  CAS  120.90  3.000
 8PR  CAV   CAH  CAS  116.94  3.000
 8PR  HAIA  CAI  HAI  106.69  3.000
 8PR  HAIA  CAI  NAN  108.07  3.000
 8PR  HAI   CAI  NAN  108.87  3.000
 8PR  HAIA  CAI  CAJ  109.10  3.000
 8PR  HAI   CAI  CAJ  110.32  3.000
 8PR  NAN   CAI  CAJ  113.54  3.000
 8PR  HAJA  CAJ  HAJ  106.81  3.000
 8PR  HAJA  CAJ  CAX  109.77  3.000
 8PR  HAJ   CAJ  CAX  109.66  3.000
 8PR  HAJA  CAJ  CAI  109.39  3.000
 8PR  HAJ   CAJ  CAI  110.28  3.000
 8PR  CAX   CAJ  CAI  110.84  3.000
 8PR  HAKA  CAK  HAK  106.65  3.000
 8PR  HAKA  CAK  CAW  108.52  3.000
 8PR  HAK   CAK  CAW  110.18  3.000
 8PR  HAKA  CAK  NAN  108.19  3.000
 8PR  HAK   CAK  NAN  108.35  3.000
 8PR  CAW   CAK  NAN  114.65  3.000
 8PR  HALA  CAL  HAL  110.54  3.000
 8PR  HALA  CAL  OAQ  109.58  3.000
 8PR  HAL   CAL  OAQ  109.65  3.000
 8PR  HALA  CAL  OAP  110.06  3.000
 8PR  HAL   CAL  OAP  109.96  3.000
 8PR  OAQ   CAL  OAP  106.99  3.000
 8PR  HAMA  CAM  HAM  107.46  3.000
 8PR  HAMA  CAM  CAW  109.84  3.000
 8PR  HAM   CAM  CAW  110.68  3.000
 8PR  HAMA  CAM  OAO  110.47  3.000
 8PR  HAM   CAM  OAO  109.86  3.000
 8PR  CAW   CAM  OAO  108.53  3.000
 8PR  HNAN  NAN  CAK  109.00  3.000
 8PR  HNAN  NAN  CAI  109.09  3.000
 8PR  CAK   NAN  CAI  111.92  3.000
 8PR  CAS   OAO  CAM  118.83  3.000
 8PR  CAU   OAP  CAL  105.72  3.000
 8PR  CAV   OAQ  CAL  105.93  3.000
 8PR  CAC   CAR  CAB  121.91  3.000
 8PR  CAC   CAR  FAA  118.97  3.000
 8PR  CAB   CAR  FAA  119.12  3.000
 8PR  OAO   CAS  CAH  114.89  3.000
 8PR  OAO   CAS  CAD  124.31  3.000
 8PR  CAH   CAS  CAD  120.80  3.000
 8PR  CAX   CAT  CAF  121.28  3.000
 8PR  CAX   CAT  CAE  120.67  3.000
 8PR  CAF   CAT  CAE  118.04  3.000
 8PR  CAV   CAU  OAP  109.21  3.000
 8PR  CAV   CAU  CAG  121.11  3.000
 8PR  OAP   CAU  CAG  129.66  3.000
 8PR  CAU   CAV  OAQ  109.34  3.000
 8PR  CAU   CAV  CAH  122.53  3.000
 8PR  OAQ   CAV  CAH  128.13  3.000
 8PR  HAW   CAW  CAX  108.44  3.000
 8PR  HAW   CAW  CAM  108.71  3.000
 8PR  CAX   CAW  CAM  110.37  3.000
 8PR  HAW   CAW  CAK  108.29  3.000
 8PR  CAX   CAW  CAK  109.56  3.000
 8PR  CAM   CAW  CAK  111.38  3.000
 8PR  HAX   CAX  CAW  107.15  3.000
 8PR  HAX   CAX  CAT  107.38  3.000
 8PR  CAW   CAX  CAT  113.14  3.000
 8PR  HAX   CAX  CAJ  107.36  3.000
 8PR  CAW   CAX  CAJ  109.81  3.000
 8PR  CAT   CAX  CAJ  111.70  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
 8PR  CONST_01  CAF  CAC  CAR  CAB    0.00   0.0  0
 8PR  CONST_02  CAF  CAT  CAE  CAB    0.00   0.0  0
 8PR  CONST_03  CAE  CAB  CAR  CAC    0.00   0.0  0
 8PR  CONST_04  CAE  CAT  CAF  CAC    0.00   0.0  0
 8PR  CONST_05  CAV  CAH  CAS  CAD    0.00   0.0  0
 8PR  CONST_06  CAV  CAU  CAG  CAD    0.00   0.0  0
 8PR  CONST_07  CAH  CAS  CAD  CAG    0.00   0.0  0
 8PR  CONST_08  CAH  CAV  CAU  CAG    0.00   0.0  0
 8PR  CONST_09  CAT  CAE  CAB  CAR    0.00   0.0  0
 8PR  CONST_10  CAT  CAF  CAC  CAR    0.00   0.0  0
 8PR  CONST_11  CAU  CAG  CAD  CAS    0.00   0.0  0
 8PR  CONST_12  CAU  CAV  CAH  CAS    0.00   0.0  0
 8PR  CONST_13  CAX  CAT  CAE  CAB  180.00   0.0  0
 8PR  CONST_14  CAX  CAT  CAF  CAC  180.00   0.0  0
 8PR  CONST_15  CAE  CAB  CAR  FAA  180.00   0.0  0
 8PR  CONST_16  CAF  CAC  CAR  FAA  180.00   0.0  0
 8PR  CONST_17  OAO  CAS  CAD  CAG  180.00   0.0  0
 8PR  CONST_18  CAV  CAH  CAS  OAO  180.00   0.0  0
 8PR  CONST_19  HAC  CAC  CAR  CAB  180.00   0.0  0
 8PR  CONST_20  HAB  CAB  CAR  CAC  180.00   0.0  0
 8PR  CONST_21  HAH  CAH  CAS  CAD  180.00   0.0  0
 8PR  CONST_22  HAF  CAF  CAT  CAE  180.00   0.0  0
 8PR  CONST_23  HAE  CAE  CAT  CAF  180.00   0.0  0
 8PR  CONST_24  HAD  CAD  CAS  CAH  180.00   0.0  0
 8PR  CONST_25  HAG  CAG  CAU  OAP    0.00   0.0  0
 8PR  Var_01    CAW  CAK  NAN  CAI   53.70  30.0  1
 8PR  Var_02    CAK  NAN  CAI  CAJ  -53.54  30.0  1
 8PR  Var_03    CAU  CAV  OAQ  CAL    9.82  30.0  1
 8PR  Var_04    CAV  CAU  OAP  CAL  -10.60  30.0  1
 8PR  Var_05    CAX  CAJ  CAI  NAN   54.96  30.0  1
 8PR  Var_06    HAL  CAL  OAP  CAU  135.47  30.0  1
 8PR  Var_07    CAW  CAM  OAO  CAS  179.21  30.0  1

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
 8PR  chir_01  CAW  CAK  CAM  CAX  negativ
 8PR  chir_02  CAX  CAJ  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
 8PR  plan-1  FAA  0.020
 8PR  plan-1  CAB  0.020
 8PR  plan-1  CAC  0.020
 8PR  plan-1  CAE  0.020
 8PR  plan-1  CAF  0.020
 8PR  plan-1  CAR  0.020
 8PR  plan-1  CAT  0.020
 8PR  plan-1  CAX  0.020
 8PR  plan-1  HAB  0.020
 8PR  plan-1  HAC  0.020
 8PR  plan-1  HAE  0.020
 8PR  plan-1  HAF  0.020
 8PR  plan-2  CAD  0.020
 8PR  plan-2  CAG  0.020
 8PR  plan-2  CAH  0.020
 8PR  plan-2  OAO  0.020
 8PR  plan-2  OAP  0.020
 8PR  plan-2  OAQ  0.020
 8PR  plan-2  CAS  0.020
 8PR  plan-2  CAU  0.020
 8PR  plan-2  CAV  0.020
 8PR  plan-2  HAG  0.020
 8PR  plan-2  HAH  0.020
 8PR  plan-2  HAD  0.020

