# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 18:48:10 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (2S)-3-phenyl-2-[4-(2-phenylethyl)phenoxy]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](Cc1ccccc1)Oc2ccc(CCc3ccccc3)cc2
#
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
 DKD  DKD  '(2S)-3-phenyl-2-[4-(2-phenylethyl)phenoxy]propanoic acid'  ligand  47  26  .  2022-07-24  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_DKD
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
 DKD  CAK   C  CR16   0  -0.305  -4.5963  -1.7815   1.1162
 DKD  CAG   C  CR16   0  -0.244  -4.5979  -3.1703   1.0905
 DKD  CAD   C  CR16   0  -0.275  -4.6236  -3.8457  -0.1225
 DKD  CAH   C  CR16   0  -0.241  -4.6523  -3.1220  -1.3083
 DKD  CAL   C  CR16   0  -0.310  -4.6550  -1.7342  -1.2761
 DKD  CAX   C  CR6    0   0.150  -4.6277  -1.0455  -0.0649
 DKD  CAS   C  CH2    0  -0.547  -4.5996   0.4570  -0.0454
 DKD  CAZ   C  CH1    0  -0.088  -3.2012   1.0175  -0.3022
 DKD  CAU   C  C      0   0.386  -3.2348   2.5654  -0.3002
 DKD  OAB   O  O      0  -0.582  -2.7538   3.1483   0.6829
 DKD  OAA   O  OC    -1  -0.612  -3.7788   3.0693  -1.3025
 DKD  OAT   O  O2     0  -0.475  -2.3648   0.4856   0.7056
 DKD  CAY   C  CR6    0   0.392  -1.0324   0.6067   0.5895
 DKD  CAP   C  CR16   0  -0.348  -0.2714   0.0829   1.6367
 DKD  CAN   C  CR16   0  -0.296   1.1108   0.1362   1.5972
 DKD  CAO   C  CR16   0  -0.362  -0.3716   1.1807  -0.4957
 DKD  CAM   C  CR16   0  -0.302   1.0174   1.2217  -0.5163
 DKD  CAW   C  CR6    0   0.105   1.7872   0.7080   0.5205
 DKD  CAR   C  CH2    0  -0.502   3.2887   0.7226   0.4620
 DKD  CAQ   C  CH2    0  -0.503   3.8536  -0.5163  -0.2484
 DKD  CAV   C  CR6    0   0.132   5.3550  -0.4969  -0.3043
 DKD  CAI   C  CR16   0  -0.309   6.1147  -0.9865   0.7567
 DKD  CAE   C  CR16   0  -0.241   7.5016  -0.9320   0.7268
 DKD  CAC   C  CR16   0  -0.274   8.1547  -0.3833  -0.3699
 DKD  CAF   C  CR16   0  -0.240   7.4089   0.1095  -1.4327
 DKD  CAJ   C  CR16   0  -0.312   6.0216   0.0530  -1.3971
 DKD  HAK   H  HCR6   0   0.241  -4.5758  -1.2621   2.0669
 DKD  HAG   H  HCR6   0   0.251  -4.5780  -3.7266   2.0191
 DKD  HAD   H  HCR6   0   0.252  -4.6244  -4.9278  -0.1443
 DKD  HAH   H  HCR6   0   0.251  -4.6776  -3.6395  -2.2590
 DKD  HAL   H  HCR6   0   0.244  -4.6825  -1.1756  -2.2054
 DKD  HAS   H  HCH2   0   0.258  -5.2579   0.8558  -0.8186
 DKD  HASA  H  HCH2   0   0.250  -4.9711   0.8285   0.9139
 DKD  HAZ   H  HCH1   0   0.224  -2.8706   0.6656  -1.2892
 DKD  HAP   H  HCR6   0   0.252  -0.7748  -0.3648   2.4849
 DKD  HAN   H  HCR6   0   0.242   1.6740  -0.2758   2.4271
 DKD  HAO   H  HCR6   0   0.266  -0.9113   1.6057  -1.3305
 DKD  HAM   H  HCR6   0   0.244   1.5084   1.6760  -1.3696
 DKD  HAR   H  HCH2   0   0.245   3.6363   1.6193  -0.0575
 DKD  HARA  H  HCH2   0   0.244   3.6985   0.7723   1.4742
 DKD  HAQ   H  HCH2   0   0.246   3.5087  -1.4139   0.2715
 DKD  HAQA  H  HCH2   0   0.246   3.4456  -0.5644  -1.2610
 DKD  HAI   H  HCR6   0   0.245   5.6140  -1.4194   1.6150
 DKD  HAE   H  HCR6   0   0.252   8.0729  -1.3222   1.5596
 DKD  HAC   H  HCR6   0   0.252   9.2361  -0.3432  -0.3975
 DKD  HAF   H  HCR6   0   0.252   7.9070   0.5372  -2.2933
 DKD  HAJ   H  HCR6   0   0.245   5.4491   0.4384  -2.2332

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
 DKD  CAK  CAG   aromatic  1.389  0.020  1.389
 DKD  CAK  CAX   aromatic  1.392  0.020  1.392
 DKD  CAG  CAD   aromatic  1.389  0.020  1.389
 DKD  CAD  CAH   aromatic  1.389  0.020  1.389
 DKD  CAH  CAL   aromatic  1.388  0.020  1.388
 DKD  CAL  CAX   aromatic  1.394  0.020  1.394
 DKD  CAX  CAS   single    1.503  0.020  1.503
 DKD  CAS  CAZ   single    1.528  0.020  1.528
 DKD  CAZ  CAU   single    1.548  0.020  1.548
 DKD  CAZ  OAT   single    1.414  0.020  1.414
 DKD  CAU  OAB   deloc     1.240  0.020  1.240
 DKD  CAU  OAA   deloc     1.247  0.020  1.247
 DKD  OAT  CAY   single    1.343  0.020  1.343
 DKD  CAY  CAP   aromatic  1.396  0.020  1.396
 DKD  CAY  CAO   aromatic  1.394  0.020  1.394
 DKD  CAP  CAN   aromatic  1.384  0.020  1.384
 DKD  CAN  CAW   aromatic  1.394  0.020  1.394
 DKD  CAO  CAM   aromatic  1.390  0.020  1.390
 DKD  CAM  CAW   aromatic  1.390  0.020  1.390
 DKD  CAW  CAR   single    1.503  0.020  1.503
 DKD  CAR  CAQ   single    1.536  0.020  1.536
 DKD  CAQ  CAV   single    1.503  0.020  1.503
 DKD  CAV  CAI   aromatic  1.394  0.020  1.394
 DKD  CAV  CAJ   aromatic  1.393  0.020  1.393
 DKD  CAI  CAE   aromatic  1.388  0.020  1.388
 DKD  CAE  CAC   aromatic  1.389  0.020  1.389
 DKD  CAC  CAF   aromatic  1.389  0.020  1.389
 DKD  CAF  CAJ   aromatic  1.389  0.020  1.389
 DKD  CAK  HAK   single    0.930  0.020  1.080
 DKD  CAG  HAG   single    0.930  0.020  1.080
 DKD  CAD  HAD   single    0.930  0.020  1.080
 DKD  CAH  HAH   single    0.930  0.020  1.080
 DKD  CAL  HAL   single    0.930  0.020  1.080
 DKD  CAS  HAS   single    0.970  0.020  1.090
 DKD  CAS  HASA  single    0.970  0.020  1.090
 DKD  CAZ  HAZ   single    0.970  0.020  1.090
 DKD  CAP  HAP   single    0.930  0.020  1.080
 DKD  CAN  HAN   single    0.930  0.020  1.080
 DKD  CAO  HAO   single    0.930  0.020  1.080
 DKD  CAM  HAM   single    0.930  0.020  1.080
 DKD  CAR  HAR   single    0.970  0.020  1.090
 DKD  CAR  HARA  single    0.970  0.020  1.090
 DKD  CAQ  HAQ   single    0.970  0.020  1.090
 DKD  CAQ  HAQA  single    0.970  0.020  1.090
 DKD  CAI  HAI   single    0.930  0.020  1.080
 DKD  CAE  HAE   single    0.930  0.020  1.080
 DKD  CAC  HAC   single    0.930  0.020  1.080
 DKD  CAF  HAF   single    0.930  0.020  1.080
 DKD  CAJ  HAJ   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
 DKD  HAK   CAK  CAX  119.43  3.000
 DKD  HAK   CAK  CAG  119.71  3.000
 DKD  CAX   CAK  CAG  120.86  3.000
 DKD  HAG   CAG  CAD  119.98  3.000
 DKD  HAG   CAG  CAK  119.85  3.000
 DKD  CAD   CAG  CAK  120.17  3.000
 DKD  HAD   CAD  CAH  120.24  3.000
 DKD  HAD   CAD  CAG  120.26  3.000
 DKD  CAH   CAD  CAG  119.50  3.000
 DKD  HAH   CAH  CAL  119.88  3.000
 DKD  HAH   CAH  CAD  120.06  3.000
 DKD  CAL   CAH  CAD  120.07  3.000
 DKD  HAL   CAL  CAX  119.39  3.000
 DKD  HAL   CAL  CAH  119.67  3.000
 DKD  CAX   CAL  CAH  120.94  3.000
 DKD  CAS   CAX  CAL  120.38  3.000
 DKD  CAS   CAX  CAK  121.14  3.000
 DKD  CAL   CAX  CAK  118.46  3.000
 DKD  HASA  CAS  HAS  107.01  3.000
 DKD  HASA  CAS  CAZ  109.49  3.000
 DKD  HAS   CAS  CAZ  107.39  3.000
 DKD  HASA  CAS  CAX  110.16  3.000
 DKD  HAS   CAS  CAX  110.18  3.000
 DKD  CAZ   CAS  CAX  112.43  3.000
 DKD  HAZ   CAZ  OAT  109.99  3.000
 DKD  HAZ   CAZ  CAU  109.14  3.000
 DKD  OAT   CAZ  CAU  112.84  3.000
 DKD  HAZ   CAZ  CAS  107.99  3.000
 DKD  OAT   CAZ  CAS  106.48  3.000
 DKD  CAU   CAZ  CAS  110.28  3.000
 DKD  OAA   CAU  OAB  128.07  3.000
 DKD  OAA   CAU  CAZ  114.36  3.000
 DKD  OAB   CAU  CAZ  117.55  3.000
 DKD  CAY   OAT  CAZ  119.44  3.000
 DKD  CAO   CAY  CAP  118.68  3.000
 DKD  CAO   CAY  OAT  125.07  3.000
 DKD  CAP   CAY  OAT  116.23  3.000
 DKD  HAP   CAP  CAN  120.16  3.000
 DKD  HAP   CAP  CAY  119.28  3.000
 DKD  CAN   CAP  CAY  120.56  3.000
 DKD  HAN   CAN  CAW  119.67  3.000
 DKD  HAN   CAN  CAP  118.84  3.000
 DKD  CAW   CAN  CAP  121.49  3.000
 DKD  HAO   CAO  CAM  118.42  3.000
 DKD  HAO   CAO  CAY  121.75  3.000
 DKD  CAM   CAO  CAY  119.83  3.000
 DKD  HAM   CAM  CAW  119.42  3.000
 DKD  HAM   CAM  CAO  118.47  3.000
 DKD  CAW   CAM  CAO  122.11  3.000
 DKD  CAR   CAW  CAM  121.39  3.000
 DKD  CAR   CAW  CAN  121.25  3.000
 DKD  CAM   CAW  CAN  117.33  3.000
 DKD  HARA  CAR  HAR  106.48  3.000
 DKD  HARA  CAR  CAQ  109.09  3.000
 DKD  HAR   CAR  CAQ  108.96  3.000
 DKD  HARA  CAR  CAW  109.82  3.000
 DKD  HAR   CAR  CAW  110.13  3.000
 DKD  CAQ   CAR  CAW  112.19  3.000
 DKD  HAQA  CAQ  HAQ  106.66  3.000
 DKD  HAQA  CAQ  CAV  109.82  3.000
 DKD  HAQ   CAQ  CAV  110.10  3.000
 DKD  HAQA  CAQ  CAR  109.08  3.000
 DKD  HAQ   CAQ  CAR  109.05  3.000
 DKD  CAV   CAQ  CAR  111.99  3.000
 DKD  CAJ   CAV  CAI  118.36  3.000
 DKD  CAJ   CAV  CAQ  120.82  3.000
 DKD  CAI   CAV  CAQ  120.79  3.000
 DKD  HAI   CAI  CAE  119.61  3.000
 DKD  HAI   CAI  CAV  119.43  3.000
 DKD  CAE   CAI  CAV  120.96  3.000
 DKD  HAE   CAE  CAC  120.10  3.000
 DKD  HAE   CAE  CAI  119.77  3.000
 DKD  CAC   CAE  CAI  120.13  3.000
 DKD  HAC   CAC  CAF  120.25  3.000
 DKD  HAC   CAC  CAE  120.29  3.000
 DKD  CAF   CAC  CAE  119.46  3.000
 DKD  HAF   CAF  CAJ  119.74  3.000
 DKD  HAF   CAF  CAC  120.10  3.000
 DKD  CAJ   CAF  CAC  120.16  3.000
 DKD  HAJ   CAJ  CAF  119.55  3.000
 DKD  HAJ   CAJ  CAV  119.51  3.000
 DKD  CAF   CAJ  CAV  120.93  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
 DKD  CONST_01  CAH  CAD  CAG  CAK    0.00   0.0  0
 DKD  CONST_02  CAH  CAL  CAX  CAK    0.00   0.0  0
 DKD  CONST_03  CAL  CAX  CAK  CAG    0.00   0.0  0
 DKD  CONST_04  CAL  CAH  CAD  CAG    0.00   0.0  0
 DKD  CONST_05  CAX  CAK  CAG  CAD    0.00   0.0  0
 DKD  CONST_06  CAX  CAL  CAH  CAD    0.00   0.0  0
 DKD  CONST_07  CAW  CAN  CAP  CAY    0.00   0.0  0
 DKD  CONST_08  CAW  CAM  CAO  CAY    0.00   0.0  0
 DKD  CONST_09  CAM  CAO  CAY  CAP    0.00   0.0  0
 DKD  CONST_10  CAM  CAW  CAN  CAP    0.00   0.0  0
 DKD  CONST_11  CAO  CAY  CAP  CAN    0.00   0.0  0
 DKD  CONST_12  CAO  CAM  CAW  CAN    0.00   0.0  0
 DKD  CONST_13  CAC  CAE  CAI  CAV    0.00   0.0  0
 DKD  CONST_14  CAC  CAF  CAJ  CAV    0.00   0.0  0
 DKD  CONST_15  CAF  CAJ  CAV  CAI    0.00   0.0  0
 DKD  CONST_16  CAF  CAC  CAE  CAI    0.00   0.0  0
 DKD  CONST_17  CAJ  CAV  CAI  CAE    0.00   0.0  0
 DKD  CONST_18  CAJ  CAF  CAC  CAE    0.00   0.0  0
 DKD  CONST_19  CAS  CAX  CAK  CAG  180.00   0.0  0
 DKD  CONST_20  CAS  CAX  CAL  CAH  180.00   0.0  0
 DKD  CONST_21  CAN  CAP  CAY  OAT  180.00   0.0  0
 DKD  CONST_22  CAM  CAO  CAY  OAT  180.00   0.0  0
 DKD  CONST_23  CAR  CAW  CAN  CAP  180.00   0.0  0
 DKD  CONST_24  CAR  CAW  CAM  CAO  180.00   0.0  0
 DKD  CONST_25  CAE  CAI  CAV  CAQ  180.00   0.0  0
 DKD  CONST_26  CAF  CAJ  CAV  CAQ  180.00   0.0  0
 DKD  CONST_27  HAD  CAD  CAG  CAK  180.00   0.0  0
 DKD  CONST_28  HAL  CAL  CAX  CAK  180.00   0.0  0
 DKD  CONST_29  HAH  CAH  CAD  CAG  180.00   0.0  0
 DKD  CONST_30  HAK  CAK  CAG  CAD  180.00   0.0  0
 DKD  CONST_31  HAG  CAG  CAD  CAH  180.00   0.0  0
 DKD  CONST_32  HAN  CAN  CAP  CAY  180.00   0.0  0
 DKD  CONST_33  HAM  CAM  CAO  CAY  180.00   0.0  0
 DKD  CONST_34  HAO  CAO  CAY  CAP  180.00   0.0  0
 DKD  CONST_35  HAP  CAP  CAY  CAO  180.00   0.0  0
 DKD  CONST_36  HAE  CAE  CAI  CAV  180.00   0.0  0
 DKD  CONST_37  HAF  CAF  CAJ  CAV  180.00   0.0  0
 DKD  CONST_38  HAJ  CAJ  CAV  CAI  180.00   0.0  0
 DKD  CONST_39  HAC  CAC  CAE  CAI  180.00   0.0  0
 DKD  CONST_40  HAI  CAI  CAE  CAC  180.00   0.0  0
 DKD  Var_01    CAZ  CAS  CAX  CAK   98.62  30.0  2
 DKD  Var_02    CAP  CAY  OAT  CAZ  178.67  30.0  2
 DKD  Var_03    CAQ  CAR  CAW  CAN   90.64  30.0  2
 DKD  Var_04    CAV  CAQ  CAR  CAW  179.99  30.0  3
 DKD  Var_05    CAI  CAV  CAQ  CAR   85.69  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
 DKD  chir_01  CAZ  CAS  CAU  OAT  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
 DKD  plan-1  CAK  0.020
 DKD  plan-1  CAG  0.020
 DKD  plan-1  CAD  0.020
 DKD  plan-1  CAH  0.020
 DKD  plan-1  CAL  0.020
 DKD  plan-1  CAX  0.020
 DKD  plan-1  CAS  0.020
 DKD  plan-1  HAK  0.020
 DKD  plan-1  HAG  0.020
 DKD  plan-1  HAD  0.020
 DKD  plan-1  HAH  0.020
 DKD  plan-1  HAL  0.020
 DKD  plan-2  OAT  0.020
 DKD  plan-2  CAY  0.020
 DKD  plan-2  CAP  0.020
 DKD  plan-2  CAN  0.020
 DKD  plan-2  CAO  0.020
 DKD  plan-2  CAM  0.020
 DKD  plan-2  CAW  0.020
 DKD  plan-2  CAR  0.020
 DKD  plan-2  HAP  0.020
 DKD  plan-2  HAN  0.020
 DKD  plan-2  HAO  0.020
 DKD  plan-2  HAM  0.020
 DKD  plan-3  CAQ  0.020
 DKD  plan-3  CAV  0.020
 DKD  plan-3  CAI  0.020
 DKD  plan-3  CAE  0.020
 DKD  plan-3  CAC  0.020
 DKD  plan-3  CAF  0.020
 DKD  plan-3  CAJ  0.020
 DKD  plan-3  HAI  0.020
 DKD  plan-3  HAE  0.020
 DKD  plan-3  HAC  0.020
 DKD  plan-3  HAF  0.020
 DKD  plan-3  HAJ  0.020
 DKD  plan-4  CAZ  0.020
 DKD  plan-4  CAU  0.020
 DKD  plan-4  OAB  0.020
 DKD  plan-4  OAA  0.020

