# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 14:53:11 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 2-[(1R)-2-carboxy-1-(naphthalen-1-ylmethyl)ethyl]-1,3-dioxo-2,3-dihydro-1H-isoindole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@@H](Cc1cccc2ccccc12)N3C(=O)c4ccc(cc4C3=O)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
 WH6  WH6  '2-[(1R)-2-carboxy-1-(naphthalen-1-ylmethyl)ethyl]-1,3-dioxo-2,3-dihydro-1H-isoindole-5-carboxylic acid'  ligand  45  30  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WH6
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
 WH6  CAZ   C  CR6    0   0.104   3.1361   0.9778  -0.2128
 WH6  CAN   C  CR16   0  -0.337   3.9596   0.2470   0.6781
 WH6  CAH   C  CR16   0  -0.253   4.6846   0.8767   1.6536
 WH6  CAG   C  CR16   0  -0.263   4.6232   2.2772   1.7970
 WH6  CAL   C  CR16   0  -0.311   3.8396   3.0143   0.9526
 WH6  CAY   C  CR6    0   0.110   3.0828   2.3909  -0.0677
 WH6  CAM   C  C1     0  -0.338   2.2767   3.1535  -0.9450
 WH6  CAI   C  C1     0  -0.238   1.5617   2.5380  -1.9322
 WH6  CAJ   C  C1     0  -0.346   1.6179   1.1378  -2.0776
 WH6  CAV   C  C      0   0.139   2.3747   0.3528  -1.2439
 WH6  CAR   C  CH2    0  -0.554   2.3437  -1.1410  -1.4015
 WH6  CBC   C  CH1    0  -0.073   1.4327  -1.8293  -0.3720
 WH6  CAQ   C  CH2    0  -0.590   1.3634  -3.3344  -0.5815
 WH6  CAS   C  C      0   0.415   0.4671  -4.0773   0.4266
 WH6  OAE   O  O      0  -0.597   0.2912  -3.5373   1.5359
 WH6  OAA   O  OC    -1  -0.621   0.0177  -5.1796   0.0540
 WH6  N1    N  NR5    0  -0.603   0.1155  -1.2073  -0.3540
 WH6  CAX   C  CR5    0   0.584  -0.3317  -0.4278   0.7067
 WH6  OAD   O  O      0  -0.401   0.2870  -0.1794   1.7095
 WH6  CBB   C  CR5    0  -0.008  -1.6853   0.0434   0.3341
 WH6  CAP   C  C1     0  -0.353  -2.5742   0.8375   1.0236
 WH6  CAU   C  C      0  -0.092  -3.7960   1.1363   0.4141
 WH6  CAT   C  C      0   0.415  -4.8191   2.0130   1.1368
 WH6  OAF   O  OC    -1  -0.585  -5.8809   2.2387   0.5297
 WH6  OAB   O  O      0  -0.583  -4.4920   2.4184   2.2665
 WH6  CAK   C  C1     0  -0.278  -4.0750   0.6308  -0.8568
 WH6  CAO   C  C1     0  -0.292  -3.1695  -0.1709  -1.5481
 WH6  CBA   C  CR5    0  -0.029  -1.9735  -0.4527  -0.9245
 WH6  CAW   C  CR5    0   0.576  -0.8101  -1.2500  -1.3797
 WH6  OAC   O  O      0  -0.414  -0.6766  -1.8195  -2.4370
 WH6  HAN   H  HCR6   0   0.246   4.0277  -0.8292   0.5897
 WH6  HAH   H  HCR6   0   0.257   5.3080   0.2953   2.3203
 WH6  HAG   H  HCR6   0   0.256   5.1966   2.7654   2.5742
 WH6  HAL   H  HCR6   0   0.253   3.7884   4.0918   1.0551
 WH6  HAM   H  H      0   0.252   2.2383   4.2295  -0.8232
 WH6  HAI   H  H      0   0.255   0.9491   3.1202  -2.6083
 WH6  HAJ   H  H      0   0.248   1.0484   0.6708  -2.8726
 WH6  HAR   H  HCH2   0   0.265   2.0064  -1.3914  -2.4083
 WH6  HARA  H  HCH2   0   0.256   3.3432  -1.5704  -1.3023
 WH6  HBC   H  HCH1   0   0.267   1.8294  -1.6480   0.6258
 WH6  HAQ   H  HCH2   0   0.230   1.0690  -3.5774  -1.6027
 WH6  HAQA  H  HCH2   0   0.247   2.3839  -3.7178  -0.4663
 WH6  HAP   H  H      0   0.259  -2.3436   1.2246   2.0071
 WH6  HAK   H  H      0   0.262  -5.0252   0.8751  -1.3116
 WH6  HAO   H  H      0   0.265  -3.4011  -0.5528  -2.5337

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
 WH6  CAZ  CAN   aromatic  1.416  0.020  1.416
 WH6  CAZ  CAY   aromatic  1.422  0.020  1.422
 WH6  CAZ  CAV   aromatic  1.426  0.020  1.426
 WH6  CAN  CAH   aromatic  1.369  0.020  1.369
 WH6  CAN  HAN   single    0.930  0.020  1.080
 WH6  CAH  CAG   aromatic  1.409  0.020  1.409
 WH6  CAH  HAH   single    0.930  0.020  1.080
 WH6  CAG  CAL   aromatic  1.368  0.020  1.368
 WH6  CAG  HAG   single    0.930  0.020  1.080
 WH6  CAL  CAY   aromatic  1.415  0.020  1.415
 WH6  CAL  HAL   single    0.930  0.020  1.080
 WH6  CAY  CAM   aromatic  1.415  0.020  1.415
 WH6  CAM  CAI   aromatic  1.366  0.020  1.366
 WH6  CAM  HAM   single    0.930  0.020  1.080
 WH6  CAI  CAJ   aromatic  1.409  0.020  1.409
 WH6  CAI  HAI   single    0.930  0.020  1.080
 WH6  CAJ  CAV   aromatic  1.373  0.020  1.373
 WH6  CAJ  HAJ   single    0.930  0.020  1.080
 WH6  CAV  CAR   single    1.502  0.020  1.502
 WH6  CAR  CBC   single    1.537  0.020  1.537
 WH6  CAR  HAR   single    0.970  0.020  1.090
 WH6  CAR  HARA  single    0.970  0.020  1.090
 WH6  CBC  CAQ   single    1.521  0.020  1.521
 WH6  CBC  N1    single    1.457  0.020  1.457
 WH6  CBC  HBC   single    0.970  0.020  1.090
 WH6  CAQ  CAS   single    1.540  0.020  1.540
 WH6  CAQ  HAQ   single    0.970  0.020  1.090
 WH6  CAQ  HAQA  single    0.970  0.020  1.090
 WH6  CAS  OAE   deloc     1.246  0.020  1.246
 WH6  CAS  OAA   deloc     1.247  0.020  1.247
 WH6  N1   CAX   single    1.390  0.020  1.390
 WH6  N1   CAW   single    1.382  0.020  1.382
 WH6  CAX  OAD   double    1.204  0.020  1.204
 WH6  CAX  CBB   single    1.481  0.020  1.481
 WH6  CBB  CAP   aromatic  1.377  0.020  1.377
 WH6  CBB  CBA   aromatic  1.383  0.020  1.383
 WH6  CAP  CAU   aromatic  1.398  0.020  1.398
 WH6  CAP  HAP   single    0.930  0.020  1.080
 WH6  CAU  CAT   single    1.529  0.020  1.529
 WH6  CAU  CAK   aromatic  1.396  0.020  1.396
 WH6  CAT  OAF   deloc     1.244  0.020  1.244
 WH6  CAT  OAB   deloc     1.244  0.020  1.244
 WH6  CAK  CAO   aromatic  1.393  0.020  1.393
 WH6  CAK  HAK   single    0.930  0.020  1.080
 WH6  CAO  CBA   aromatic  1.378  0.020  1.378
 WH6  CAO  HAO   single    0.930  0.020  1.080
 WH6  CBA  CAW   single    1.482  0.020  1.482
 WH6  CAW  OAC   double    1.208  0.020  1.208

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
 WH6  CAV   CAZ  CAY  119.31  3.000
 WH6  CAV   CAZ  CAN  122.62  3.000
 WH6  CAY   CAZ  CAN  118.07  3.000
 WH6  HAN   CAN  CAH  118.85  3.000
 WH6  HAN   CAN  CAZ  119.89  3.000
 WH6  CAH   CAN  CAZ  121.26  3.000
 WH6  HAH   CAH  CAG  119.76  3.000
 WH6  HAH   CAH  CAN  119.80  3.000
 WH6  CAG   CAH  CAN  120.44  3.000
 WH6  HAG   CAG  CAL  120.26  3.000
 WH6  HAG   CAG  CAH  119.89  3.000
 WH6  CAL   CAG  CAH  119.85  3.000
 WH6  HAL   CAL  CAY  118.75  3.000
 WH6  HAL   CAL  CAG  120.30  3.000
 WH6  CAY   CAL  CAG  120.95  3.000
 WH6  CAM   CAY  CAL  120.96  3.000
 WH6  CAM   CAY  CAZ  119.60  3.000
 WH6  CAL   CAY  CAZ  119.44  3.000
 WH6  HAM   CAM  CAI  120.69  3.000
 WH6  HAM   CAM  CAY  119.07  3.000
 WH6  CAI   CAM  CAY  120.25  3.000
 WH6  HAI   CAI  CAJ  119.53  3.000
 WH6  HAI   CAI  CAM  120.36  3.000
 WH6  CAJ   CAI  CAM  120.11  3.000
 WH6  HAJ   CAJ  CAV  119.26  3.000
 WH6  HAJ   CAJ  CAI  118.88  3.000
 WH6  CAV   CAJ  CAI  121.85  3.000
 WH6  CAR   CAV  CAJ  119.58  3.000
 WH6  CAR   CAV  CAZ  121.51  3.000
 WH6  CAJ   CAV  CAZ  118.87  3.000
 WH6  HARA  CAR  HAR  106.05  3.000
 WH6  HARA  CAR  CBC  107.78  3.000
 WH6  HAR   CAR  CBC  109.39  3.000
 WH6  HARA  CAR  CAV  111.26  3.000
 WH6  HAR   CAR  CAV  109.36  3.000
 WH6  CBC   CAR  CAV  112.78  3.000
 WH6  HBC   CBC  N1   104.30  3.000
 WH6  HBC   CBC  CAQ  107.91  3.000
 WH6  N1    CBC  CAQ  112.52  3.000
 WH6  HBC   CBC  CAR  108.86  3.000
 WH6  N1    CBC  CAR  110.67  3.000
 WH6  CAQ   CBC  CAR  112.20  3.000
 WH6  HAQA  CAQ  HAQ  105.78  3.000
 WH6  HAQA  CAQ  CAS  107.72  3.000
 WH6  HAQ   CAQ  CAS  110.40  3.000
 WH6  HAQA  CAQ  CBC  106.81  3.000
 WH6  HAQ   CAQ  CBC  111.21  3.000
 WH6  CAS   CAQ  CBC  114.44  3.000
 WH6  OAA   CAS  OAE  126.72  3.000
 WH6  OAA   CAS  CAQ  116.13  3.000
 WH6  OAE   CAS  CAQ  117.12  3.000
 WH6  CAW   N1   CAX  111.60  3.000
 WH6  CAW   N1   CBC  125.66  3.000
 WH6  CAX   N1   CBC  122.66  3.000
 WH6  CBB   CAX  OAD  127.84  3.000
 WH6  CBB   CAX  N1   106.29  3.000
 WH6  OAD   CAX  N1   125.86  3.000
 WH6  CBA   CBB  CAP  121.87  3.000
 WH6  CBA   CBB  CAX  107.77  3.000
 WH6  CAP   CBB  CAX  130.36  3.000
 WH6  HAP   CAP  CAU  120.41  3.000
 WH6  HAP   CAP  CBB  121.60  3.000
 WH6  CAU   CAP  CBB  117.98  3.000
 WH6  CAK   CAU  CAT  120.28  3.000
 WH6  CAK   CAU  CAP  119.62  3.000
 WH6  CAT   CAU  CAP  120.09  3.000
 WH6  OAB   CAT  OAF  127.48  3.000
 WH6  OAB   CAT  CAU  116.11  3.000
 WH6  OAF   CAT  CAU  116.40  3.000
 WH6  HAK   CAK  CAO  119.50  3.000
 WH6  HAK   CAK  CAU  118.47  3.000
 WH6  CAO   CAK  CAU  122.03  3.000
 WH6  HAO   CAO  CBA  121.72  3.000
 WH6  HAO   CAO  CAK  121.07  3.000
 WH6  CBA   CAO  CAK  117.21  3.000
 WH6  CAW   CBA  CAO  130.72  3.000
 WH6  CAW   CBA  CBB  108.00  3.000
 WH6  CAO   CBA  CBB  121.28  3.000
 WH6  OAC   CAW  CBA  127.52  3.000
 WH6  OAC   CAW  N1   126.15  3.000
 WH6  CBA   CAW  N1   106.32  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
 WH6  CONST_01  CAG  CAH  CAN  CAZ    0.00   0.0  0
 WH6  CONST_02  CAG  CAL  CAY  CAZ    0.00   0.0  0
 WH6  CONST_03  CAI  CAM  CAY  CAZ    0.00   0.0  0
 WH6  CONST_04  CAI  CAJ  CAV  CAZ    0.00   0.0  0
 WH6  CONST_05  CAL  CAY  CAZ  CAN    0.00   0.0  0
 WH6  CONST_06  CAM  CAY  CAZ  CAN  180.00   0.0  0
 WH6  CONST_07  CAJ  CAV  CAZ  CAN  180.00   0.0  0
 WH6  CONST_08  CAL  CAG  CAH  CAN    0.00   0.0  0
 WH6  CONST_09  CAY  CAZ  CAN  CAH    0.00   0.0  0
 WH6  CONST_10  CAV  CAZ  CAN  CAH  180.00   0.0  0
 WH6  CONST_11  CAY  CAL  CAG  CAH    0.00   0.0  0
 WH6  CONST_12  CAM  CAY  CAL  CAG  180.00   0.0  0
 WH6  CONST_13  CAV  CAZ  CAY  CAL  180.00   0.0  0
 WH6  CONST_14  CAI  CAM  CAY  CAL  180.00   0.0  0
 WH6  CONST_15  CAJ  CAV  CAZ  CAY    0.00   0.0  0
 WH6  CONST_16  CAJ  CAI  CAM  CAY    0.00   0.0  0
 WH6  CONST_17  CAV  CAZ  CAY  CAM    0.00   0.0  0
 WH6  CONST_18  CAV  CAJ  CAI  CAM    0.00   0.0  0
 WH6  CONST_19  CAK  CAU  CAP  CBB    0.00   0.0  0
 WH6  CONST_20  CAK  CAO  CBA  CBB    0.00   0.0  0
 WH6  CONST_21  CAO  CBA  CBB  CAP    0.00   0.0  0
 WH6  CONST_22  CAO  CAK  CAU  CAP    0.00   0.0  0
 WH6  CONST_23  CBA  CBB  CAP  CAU    0.00   0.0  0
 WH6  CONST_24  CBA  CAO  CAK  CAU    0.00   0.0  0
 WH6  CONST_25  CAW  N1   CAX  CBB    0.00   0.0  0
 WH6  CONST_26  CAR  CAV  CAZ  CAN    0.00   0.0  0
 WH6  CONST_27  CAR  CAV  CAZ  CAY  180.00   0.0  0
 WH6  CONST_28  CAR  CAV  CAJ  CAI  180.00   0.0  0
 WH6  CONST_29  CAT  CAU  CAP  CBB  180.00   0.0  0
 WH6  CONST_30  CAO  CAK  CAU  CAT  180.00   0.0  0
 WH6  CONST_31  CBB  CAX  N1   CBC  180.00   0.0  0
 WH6  CONST_32  CAW  N1   CAX  OAD  180.00   0.0  0
 WH6  CONST_33  HAH  CAH  CAN  CAZ  180.00   0.0  0
 WH6  CONST_34  HAL  CAL  CAY  CAZ  180.00   0.0  0
 WH6  CONST_35  HAM  CAM  CAY  CAZ  180.00   0.0  0
 WH6  CONST_36  HAJ  CAJ  CAV  CAZ  180.00   0.0  0
 WH6  CONST_37  HAG  CAG  CAH  CAN  180.00   0.0  0
 WH6  CONST_38  HAN  CAN  CAH  CAG  180.00   0.0  0
 WH6  CONST_39  HAI  CAI  CAM  CAY  180.00   0.0  0
 WH6  CONST_40  HAP  CAP  CBB  CAX    0.00   0.0  0
 WH6  CONST_41  HAO  CAO  CBA  CBB  180.00   0.0  0
 WH6  CONST_42  HAK  CAK  CAU  CAP  180.00   0.0  0
 WH6  CONST_43  OAD  CAX  N1   CBC    0.00   0.0  0
 WH6  Var_01    CBC  CAR  CAV  CAZ   77.22  30.0  2
 WH6  Var_02    OAF  CAT  CAU  CAP  179.77  30.0  2
 WH6  Var_03    OAE  CAS  CAQ  CBC  -25.16  30.0  3

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
 WH6  chir_01  CBC  CAR  CAQ  N1  positiv

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
 WH6  plan-1  CBC  0.020
 WH6  plan-1  N1   0.020
 WH6  plan-1  CAX  0.020
 WH6  plan-1  OAD  0.020
 WH6  plan-1  CBB  0.020
 WH6  plan-1  CAP  0.020
 WH6  plan-1  CAU  0.020
 WH6  plan-1  CAT  0.020
 WH6  plan-1  CAK  0.020
 WH6  plan-1  CAO  0.020
 WH6  plan-1  CBA  0.020
 WH6  plan-1  CAW  0.020
 WH6  plan-1  OAC  0.020
 WH6  plan-1  HAP  0.020
 WH6  plan-1  HAK  0.020
 WH6  plan-1  HAO  0.020
 WH6  plan-2  CAZ  0.020
 WH6  plan-2  CAN  0.020
 WH6  plan-2  CAH  0.020
 WH6  plan-2  CAG  0.020
 WH6  plan-2  CAL  0.020
 WH6  plan-2  CAY  0.020
 WH6  plan-2  CAM  0.020
 WH6  plan-2  CAI  0.020
 WH6  plan-2  CAJ  0.020
 WH6  plan-2  CAV  0.020
 WH6  plan-2  CAR  0.020
 WH6  plan-2  HAN  0.020
 WH6  plan-2  HAH  0.020
 WH6  plan-2  HAG  0.020
 WH6  plan-2  HAL  0.020
 WH6  plan-2  HAM  0.020
 WH6  plan-2  HAI  0.020
 WH6  plan-2  HAJ  0.020
 WH6  plan-3  CAQ  0.020
 WH6  plan-3  CAS  0.020
 WH6  plan-3  OAE  0.020
 WH6  plan-3  OAA  0.020
 WH6  plan-4  CAU  0.020
 WH6  plan-4  CAT  0.020
 WH6  plan-4  OAF  0.020
 WH6  plan-4  OAB  0.020

