# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 17:03:43 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  48  26  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.298  -4.5062  -1.7667   1.0952
 DKD  CAG   C  CR16  0  -0.243  -4.4521  -3.1539   1.0652
 DKD  CAD   C  CR16  0  -0.270  -4.4612  -3.8258  -0.1501
 DKD  CAH   C  CR16  0  -0.240  -4.5287  -3.1027  -1.3343
 DKD  CAL   C  CR16  0  -0.304  -4.5883  -1.7163  -1.2994
 DKD  CAX   C  CR6   0   0.141  -4.5779  -1.0335  -0.0854
 DKD  CAS   C  CH2   0  -0.551  -4.6137   0.4691  -0.0610
 DKD  CAZ   C  CH1   0  -0.079  -3.2198   1.0604  -0.2991
 DKD  CAU   C  C     0   0.510  -3.2853   2.5815  -0.2720
 DKD  OAB   O  O     0  -0.417  -2.9293   3.2553   0.6570
 DKD  OAA   O  OH1   0  -0.588  -3.8101   3.0557  -1.3906
 DKD  OAT   O  O2    0  -0.471  -2.3880   0.5974   0.7252
 DKD  CAY   C  CR6   0   0.379  -1.0433   0.6902   0.5930
 DKD  CAP   C  CR16  0  -0.336  -0.2932   0.1600   1.6411
 DKD  CAN   C  CR16  0  -0.294   1.0890   0.1967   1.5952
 DKD  CAO   C  CR16  0  -0.358  -0.3870   1.2542  -0.4961
 DKD  CAM   C  CR16  0  -0.298   1.0030   1.2788  -0.5225
 DKD  CAW   C  CR6   0   0.111   1.7671   0.7572   0.5134
 DKD  CAR   C  CH2   0  -0.503   3.2683   0.7504   0.4490
 DKD  CAQ   C  CH2   0  -0.504   3.8081  -0.4911  -0.2768
 DKD  CAV   C  CR6   0   0.132   5.3098  -0.4984  -0.3361
 DKD  CAI   C  CR16  0  -0.309   6.0626  -1.0095   0.7194
 DKD  CAE   C  CR16  0  -0.241   7.4503  -0.9801   0.6860
 DKD  CAC   C  CR16  0  -0.273   8.1104  -0.4358  -0.4086
 DKD  CAF   C  CR16  0  -0.240   7.3713   0.0776  -1.4663
 DKD  CAJ   C  CR16  0  -0.312   5.9833   0.0463  -1.4272
 DKD  HAK   H  HCR6  0   0.246  -4.4987  -1.2486   2.0466
 DKD  HAG   H  HCR6  0   0.255  -4.4012  -3.7112   1.9919
 DKD  HAD   H  HCR6  0   0.255  -4.4194  -4.9069  -0.1746
 DKD  HAH   H  HCR6  0   0.255  -4.5397  -3.6189  -2.2858
 DKD  HAL   H  HCR6  0   0.250  -4.6491  -1.1575  -2.2268
 DKD  HAS   H  HCH2  0   0.281  -5.2809   0.8422  -0.8397
 DKD  HASA  H  HCH2  0   0.275  -5.0020   0.8275   0.8953
 DKD  HAZ   H  HCH1  0   0.280  -2.8678   0.7301  -1.2849
 DKD  HOAA  H  HOH1  0   0.489  -3.8866   4.0214  -1.3473
 DKD  HAP   H  HCR6  0   0.261  -0.8008  -0.2786   2.4911
 DKD  HAN   H  HCR6  0   0.249   1.6509  -0.2196   2.4232
 DKD  HAO   H  HCR6  0   0.272  -0.9209   1.6813  -1.3346
 DKD  HAM   H  HCR6  0   0.252   1.4957   1.7243  -1.3789
 DKD  HAR   H  HCH2  0   0.248   3.6269   1.6471  -0.0627
 DKD  HARA  H  HCH2  0   0.247   3.6818   0.7819   1.4601
 DKD  HAQ   H  HCH2  0   0.248   3.4482  -1.3879   0.2340
 DKD  HAQA  H  HCH2  0   0.247   3.3973  -0.5203  -1.2889
 DKD  HAI   H  HCR6  0   0.246   5.5561  -1.4394   1.5760
 DKD  HAE   H  HCR6  0   0.253   8.0164  -1.3859   1.5149
 DKD  HAC   H  HCR6  0   0.253   9.1922  -0.4147  -0.4382
 DKD  HAF   H  HCR6  0   0.253   7.8751   0.5015  -2.3256
 DKD  HAJ   H  HCR6  0   0.245   5.4158   0.4475  -2.2593

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  1.393  0.020  1.393
 DKD  CAX  CAS   single    1.503  0.020  1.503
 DKD  CAS  CAZ   single    1.533  0.020  1.533
 DKD  CAZ  CAU   single    1.523  0.020  1.523
 DKD  CAZ  OAT   single    1.398  0.020  1.398
 DKD  CAU  OAB   double    1.202  0.020  1.202
 DKD  CAU  OAA   single    1.323  0.020  1.323
 DKD  OAT  CAY   single    1.354  0.020  1.354
 DKD  CAY  CAP   aromatic  1.394  0.020  1.394
 DKD  CAY  CAO   aromatic  1.391  0.020  1.391
 DKD  CAP  CAN   aromatic  1.383  0.020  1.383
 DKD  CAN  CAW   aromatic  1.394  0.020  1.394
 DKD  CAO  CAM   aromatic  1.391  0.020  1.391
 DKD  CAM  CAW   aromatic  1.389  0.020  1.389
 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  OAA  HOAA  single    0.850  0.020  0.980
 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  119.57  3.000
 DKD  HAK   CAK  CAG  119.77  3.000
 DKD  CAX   CAK  CAG  120.66  3.000
 DKD  HAG   CAG  CAD  120.02  3.000
 DKD  HAG   CAG  CAK  119.85  3.000
 DKD  CAD   CAG  CAK  120.13  3.000
 DKD  HAD   CAD  CAH  120.17  3.000
 DKD  HAD   CAD  CAG  120.19  3.000
 DKD  CAH   CAD  CAG  119.64  3.000
 DKD  HAH   CAH  CAL  119.86  3.000
 DKD  HAH   CAH  CAD  120.10  3.000
 DKD  CAL   CAH  CAD  120.03  3.000
 DKD  HAL   CAL  CAX  119.55  3.000
 DKD  HAL   CAL  CAH  119.71  3.000
 DKD  CAX   CAL  CAH  120.74  3.000
 DKD  CAS   CAX  CAL  120.26  3.000
 DKD  CAS   CAX  CAK  120.94  3.000
 DKD  CAL   CAX  CAK  118.79  3.000
 DKD  HASA  CAS  HAS  107.17  3.000
 DKD  HASA  CAS  CAZ  109.42  3.000
 DKD  HAS   CAS  CAZ  108.26  3.000
 DKD  HASA  CAS  CAX  110.52  3.000
 DKD  HAS   CAS  CAX  110.17  3.000
 DKD  CAZ   CAS  CAX  111.19  3.000
 DKD  HAZ   CAZ  OAT  111.56  3.000
 DKD  HAZ   CAZ  CAU  109.29  3.000
 DKD  OAT   CAZ  CAU  110.08  3.000
 DKD  HAZ   CAZ  CAS  108.36  3.000
 DKD  OAT   CAZ  CAS  107.43  3.000
 DKD  CAU   CAZ  CAS  110.09  3.000
 DKD  OAA   CAU  OAB  124.76  3.000
 DKD  OAA   CAU  CAZ  111.10  3.000
 DKD  OAB   CAU  CAZ  124.13  3.000
 DKD  HOAA  OAA  CAU  110.51  3.000
 DKD  CAY   OAT  CAZ  119.77  3.000
 DKD  CAO   CAY  CAP  119.28  3.000
 DKD  CAO   CAY  OAT  124.93  3.000
 DKD  CAP   CAY  OAT  115.78  3.000
 DKD  HAP   CAP  CAN  120.34  3.000
 DKD  HAP   CAP  CAY  119.48  3.000
 DKD  CAN   CAP  CAY  120.18  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  118.14  3.000
 DKD  HAO   CAO  CAY  122.28  3.000
 DKD  CAM   CAO  CAY  119.58  3.000
 DKD  HAM   CAM  CAW  119.58  3.000
 DKD  HAM   CAM  CAO  118.47  3.000
 DKD  CAW   CAM  CAO  121.95  3.000
 DKD  CAR   CAW  CAM  121.29  3.000
 DKD  CAR   CAW  CAN  121.15  3.000
 DKD  CAM   CAW  CAN  117.52  3.000
 DKD  HARA  CAR  HAR  106.58  3.000
 DKD  HARA  CAR  CAQ  109.12  3.000
 DKD  HAR   CAR  CAQ  109.06  3.000
 DKD  HARA  CAR  CAW  109.77  3.000
 DKD  HAR   CAR  CAW  110.13  3.000
 DKD  CAQ   CAR  CAW  112.03  3.000
 DKD  HAQA  CAQ  HAQ  106.69  3.000
 DKD  HAQA  CAQ  CAV  109.81  3.000
 DKD  HAQ   CAQ  CAV  110.09  3.000
 DKD  HAQA  CAQ  CAR  109.09  3.000
 DKD  HAQ   CAQ  CAR  109.06  3.000
 DKD  CAV   CAQ  CAR  111.95  3.000
 DKD  CAJ   CAV  CAI  118.39  3.000
 DKD  CAJ   CAV  CAQ  120.81  3.000
 DKD  CAI   CAV  CAQ  120.77  3.000
 DKD  HAI   CAI  CAE  119.63  3.000
 DKD  HAI   CAI  CAV  119.44  3.000
 DKD  CAE   CAI  CAV  120.93  3.000
 DKD  HAE   CAE  CAC  120.11  3.000
 DKD  HAE   CAE  CAI  119.76  3.000
 DKD  CAC   CAE  CAI  120.14  3.000
 DKD  HAC   CAC  CAF  120.26  3.000
 DKD  HAC   CAC  CAE  120.27  3.000
 DKD  CAF   CAC  CAE  119.48  3.000
 DKD  HAF   CAF  CAJ  119.75  3.000
 DKD  HAF   CAF  CAC  120.11  3.000
 DKD  CAJ   CAF  CAC  120.14  3.000
 DKD  HAJ   CAJ  CAF  119.55  3.000
 DKD  HAJ   CAJ  CAV  119.52  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  CONST_41  HOAA  OAA  CAU  CAZ   180.00   0.0  0
 DKD  Var_01    CAZ   CAS  CAX  CAK    97.35  30.0  2
 DKD  Var_02    CAP   CAY  OAT  CAZ  -177.76  30.0  2
 DKD  Var_03    CAQ   CAR  CAW  CAN    91.35  30.0  2
 DKD  Var_04    CAV   CAQ  CAR  CAW  -179.81  30.0  3
 DKD  Var_05    CAI   CAV  CAQ  CAR    85.48  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
 DKD  plan-4  HOAA  0.020

