# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 02:53:40 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: (2S)-3-(biphenyl-4-yl)-2-(biphenyl-4-yloxy)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](Cc1ccc(cc1)c2ccccc2)Oc3ccc(cc3)c4ccccc4
#
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
 AXY  AXY  '(2S)-3-(biphenyl-4-yl)-2-(biphenyl-4-yloxy)propanoic acid'  ligand  51  30  .  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_AXY
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
 AXY  CAK  C  CR16   0  -0.314   4.9305  -2.5039  -0.5838
 AXY  CAE  C  CR16   0  -0.240   5.8180  -3.5663  -0.4923
 AXY  CAC  C  CR16   0  -0.268   6.9072  -3.4959   0.3665
 AXY  CAF  C  CR16   0  -0.240   7.1015  -2.3525   1.1304
 AXY  CAL  C  CR16   0  -0.313   6.2142  -1.2902   1.0370
 AXY  CAZ  C  CR6    0   0.091   5.1135  -1.3489   0.1795
 AXY  CBB  C  CR6    0   0.071   4.1670  -0.2191   0.0855
 AXY  CAR  C  CR16   0  -0.297   3.8375   0.5369   1.2118
 AXY  CAJ  C  CR16   0  -0.294   2.9540   1.6004   1.1212
 AXY  CAQ  C  CR16   0  -0.300   3.5783   0.1305  -1.1304
 AXY  CAI  C  CR16   0  -0.287   2.6924   1.1938  -1.2155
 AXY  CAX  C  CR6    0   0.134   2.3661   1.9486  -0.0928
 AXY  CAU  C  CH2    0  -0.547   1.3808   3.0793  -0.1649
 AXY  CBD  C  CH1    0  -0.093  -0.0282   2.6452   0.2374
 AXY  CAW  C  C      0   0.387  -0.9906   3.8589   0.2468
 AXY  OAB  O  O      0  -0.581  -1.8178   3.9406  -0.6732
 AXY  OAA  O  OC    -1  -0.610  -0.8057   4.6518   1.1899
 AXY  OAV  O  O2     0  -0.472  -0.4142   1.6475  -0.6888
 AXY  CAY  C  CR6    0   0.403  -1.5171   0.9219  -0.4621
 AXY  CAP  C  CR16   0  -0.348  -1.8793   0.0190  -1.4650
 AXY  CAT  C  CR16   0  -0.296  -2.9857  -0.7941  -1.3144
 AXY  CAO  C  CR16   0  -0.361  -2.2902   0.9799   0.6970
 AXY  CAS  C  CR16   0  -0.303  -3.3957   0.1527   0.8339
 AXY  CBC  C  CR6    0   0.061  -3.7731  -0.7474  -0.1606
 AXY  CBA  C  CR6    0   0.097  -4.9602  -1.6103  -0.0082
 AXY  CAM  C  CR16   0  -0.317  -5.3131  -2.1381   1.2363
 AXY  CAG  C  CR16   0  -0.240  -6.4323  -2.9455   1.3777
 AXY  CAD  C  CR16   0  -0.271  -7.2222  -3.2480   0.2762
 AXY  CAH  C  CR16   0  -0.240  -6.8818  -2.7324  -0.9675
 AXY  CAN  C  CR16   0  -0.319  -5.7650  -1.9214  -1.1070
 AXY  H1   H  HCR6   0   0.253   4.0745  -2.5842  -1.2424
 AXY  H2   H  HCR6   0   0.256   5.6520  -4.4550  -1.0876
 AXY  H3   H  HCR6   0   0.256   7.5979  -4.3256   0.4409
 AXY  H4   H  HCR6   0   0.257   7.9512  -2.2831   1.7972
 AXY  H5   H  HCR6   0   0.252   6.3926  -0.3983   1.6252
 AXY  H6   H  HCR6   0   0.250   4.2614   0.2839   2.1759
 AXY  H7   H  HCR6   0   0.247   2.7150   2.1679   2.0138
 AXY  H8   H  HCR6   0   0.249   3.8267  -0.4217  -2.0286
 AXY  H9   H  HCR6   0   0.243   2.2588   1.4475  -2.1752
 AXY  H10  H  HCH2   0   0.260   1.6827   3.8817   0.5095
 AXY  H11  H  HCH2   0   0.252   1.3561   3.5003  -1.1737
 AXY  H12  H  HCH1   0   0.230   0.0261   2.2207   1.2486
 AXY  H14  H  HCR6   0   0.257  -1.2786  -0.0414  -2.3642
 AXY  H15  H  HCR6   0   0.250  -3.2269  -1.4932  -2.1058
 AXY  H16  H  HCR6   0   0.271  -2.0612   1.6674   1.4995
 AXY  H17  H  HCR6   0   0.253  -3.9893   0.2372   1.7358
 AXY  H18  H  HCR6   0   0.250  -4.6968  -1.9314   2.1028
 AXY  H19  H  HCR6   0   0.255  -6.6816  -3.3472   2.3516
 AXY  H20  H  HCR6   0   0.255  -8.0943  -3.8793   0.3860
 AXY  H21  H  HCR6   0   0.255  -7.4928  -2.9542  -1.8332
 AXY  H22  H  HCR6   0   0.251  -5.5283  -1.5104  -2.0808

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
 AXY  CAH  CAD  aromatic  1.389  0.020  1.389
 AXY  CAH  CAN  aromatic  1.387  0.020  1.387
 AXY  CAD  CAG  aromatic  1.389  0.020  1.389
 AXY  CAN  CBA  aromatic  1.397  0.020  1.397
 AXY  CAG  CAM  aromatic  1.387  0.020  1.387
 AXY  CBA  CAM  aromatic  1.397  0.020  1.397
 AXY  CBA  CBC  single    1.475  0.020  1.475
 AXY  CBC  CAT  aromatic  1.398  0.020  1.398
 AXY  CBC  CAS  aromatic  1.393  0.020  1.393
 AXY  CAT  CAP  aromatic  1.381  0.020  1.381
 AXY  CAS  CAO  aromatic  1.387  0.020  1.387
 AXY  CAP  CAY  aromatic  1.397  0.020  1.397
 AXY  CAO  CAY  aromatic  1.395  0.020  1.395
 AXY  CAY  OAV  single    1.339  0.020  1.339
 AXY  CBD  OAV  single    1.415  0.020  1.415
 AXY  CBD  CAW  single    1.549  0.020  1.549
 AXY  CBD  CAU  single    1.528  0.020  1.528
 AXY  OAB  CAW  deloc     1.240  0.020  1.240
 AXY  CAW  OAA  deloc     1.246  0.020  1.246
 AXY  CAU  CAX  single    1.502  0.020  1.502
 AXY  CAX  CAI  aromatic  1.392  0.020  1.392
 AXY  CAX  CAJ  aromatic  1.393  0.020  1.393
 AXY  CAI  CAQ  aromatic  1.387  0.020  1.387
 AXY  CAJ  CAR  aromatic  1.386  0.020  1.386
 AXY  CAQ  CBB  aromatic  1.395  0.020  1.395
 AXY  CAR  CBB  aromatic  1.396  0.020  1.396
 AXY  CBB  CAZ  single    1.477  0.020  1.477
 AXY  CAZ  CAK  aromatic  1.396  0.020  1.396
 AXY  CAZ  CAL  aromatic  1.397  0.020  1.397
 AXY  CAK  CAE  aromatic  1.387  0.020  1.387
 AXY  CAL  CAF  aromatic  1.387  0.020  1.387
 AXY  CAE  CAC  aromatic  1.389  0.020  1.389
 AXY  CAF  CAC  aromatic  1.389  0.020  1.389
 AXY  CAK  H1   single    0.930  0.020  1.080
 AXY  CAE  H2   single    0.930  0.020  1.080
 AXY  CAC  H3   single    0.930  0.020  1.080
 AXY  CAF  H4   single    0.930  0.020  1.080
 AXY  CAL  H5   single    0.930  0.020  1.080
 AXY  CAR  H6   single    0.930  0.020  1.080
 AXY  CAJ  H7   single    0.930  0.020  1.080
 AXY  CAQ  H8   single    0.930  0.020  1.080
 AXY  CAI  H9   single    0.930  0.020  1.080
 AXY  CAU  H10  single    0.970  0.020  1.090
 AXY  CAU  H11  single    0.970  0.020  1.090
 AXY  CBD  H12  single    0.970  0.020  1.090
 AXY  CAP  H14  single    0.930  0.020  1.080
 AXY  CAT  H15  single    0.930  0.020  1.080
 AXY  CAO  H16  single    0.930  0.020  1.080
 AXY  CAS  H17  single    0.930  0.020  1.080
 AXY  CAM  H18  single    0.930  0.020  1.080
 AXY  CAG  H19  single    0.930  0.020  1.080
 AXY  CAD  H20  single    0.930  0.020  1.080
 AXY  CAH  H21  single    0.930  0.020  1.080
 AXY  CAN  H22  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
 AXY  H1   CAK  CAZ  119.82  3.000
 AXY  H1   CAK  CAE  119.28  3.000
 AXY  CAZ  CAK  CAE  120.89  3.000
 AXY  H2   CAE  CAC  120.13  3.000
 AXY  H2   CAE  CAK  119.62  3.000
 AXY  CAC  CAE  CAK  120.25  3.000
 AXY  H3   CAC  CAF  120.28  3.000
 AXY  H3   CAC  CAE  120.28  3.000
 AXY  CAF  CAC  CAE  119.44  3.000
 AXY  H4   CAF  CAL  119.63  3.000
 AXY  H4   CAF  CAC  120.10  3.000
 AXY  CAL  CAF  CAC  120.27  3.000
 AXY  H5   CAL  CAZ  119.86  3.000
 AXY  H5   CAL  CAF  119.25  3.000
 AXY  CAZ  CAL  CAF  120.88  3.000
 AXY  CBB  CAZ  CAL  120.80  3.000
 AXY  CAL  CAZ  CAK  118.27  3.000
 AXY  CBB  CAZ  CAK  120.93  3.000
 AXY  CAQ  CBB  CAR  117.89  3.000
 AXY  CAR  CBB  CAZ  120.95  3.000
 AXY  CAQ  CBB  CAZ  121.16  3.000
 AXY  H6   CAR  CAJ  119.15  3.000
 AXY  H6   CAR  CBB  119.95  3.000
 AXY  CAJ  CAR  CBB  120.89  3.000
 AXY  H7   CAJ  CAX  119.57  3.000
 AXY  H7   CAJ  CAR  119.23  3.000
 AXY  CAX  CAJ  CAR  121.20  3.000
 AXY  H8   CAQ  CAI  119.11  3.000
 AXY  H8   CAQ  CBB  119.87  3.000
 AXY  CAI  CAQ  CBB  121.01  3.000
 AXY  H9   CAI  CAX  119.60  3.000
 AXY  H9   CAI  CAQ  119.32  3.000
 AXY  CAX  CAI  CAQ  121.07  3.000
 AXY  CAU  CAX  CAI  121.56  3.000
 AXY  CAI  CAX  CAJ  117.94  3.000
 AXY  CAU  CAX  CAJ  120.47  3.000
 AXY  H11  CAU  H10  107.06  3.000
 AXY  H11  CAU  CBD  109.36  3.000
 AXY  H10  CAU  CBD  107.54  3.000
 AXY  H11  CAU  CAX  110.43  3.000
 AXY  H10  CAU  CAX  110.03  3.000
 AXY  CBD  CAU  CAX  112.24  3.000
 AXY  H12  CBD  OAV  110.10  3.000
 AXY  H12  CBD  CAW  109.15  3.000
 AXY  OAV  CBD  CAW  112.77  3.000
 AXY  H12  CBD  CAU  107.85  3.000
 AXY  CAW  CBD  CAU  110.60  3.000
 AXY  OAV  CBD  CAU  106.23  3.000
 AXY  OAA  CAW  OAB  128.22  3.000
 AXY  OAA  CAW  CBD  114.27  3.000
 AXY  OAB  CAW  CBD  117.49  3.000
 AXY  CAY  OAV  CBD  119.72  3.000
 AXY  CAO  CAY  CAP  118.67  3.000
 AXY  CAO  CAY  OAV  125.07  3.000
 AXY  CAP  CAY  OAV  116.23  3.000
 AXY  H14  CAP  CAT  120.13  3.000
 AXY  H14  CAP  CAY  119.23  3.000
 AXY  CAT  CAP  CAY  120.65  3.000
 AXY  H15  CAT  CBC  119.95  3.000
 AXY  H15  CAT  CAP  118.59  3.000
 AXY  CBC  CAT  CAP  121.44  3.000
 AXY  H16  CAO  CAS  118.34  3.000
 AXY  H16  CAO  CAY  121.73  3.000
 AXY  CAS  CAO  CAY  119.93  3.000
 AXY  H17  CAS  CBC  119.75  3.000
 AXY  H17  CAS  CAO  118.19  3.000
 AXY  CBC  CAS  CAO  122.04  3.000
 AXY  CBA  CBC  CAS  121.46  3.000
 AXY  CAS  CBC  CAT  117.27  3.000
 AXY  CBA  CBC  CAT  121.27  3.000
 AXY  CAN  CBA  CAM  118.10  3.000
 AXY  CAM  CBA  CBC  121.08  3.000
 AXY  CAN  CBA  CBC  120.83  3.000
 AXY  H18  CAM  CAG  119.24  3.000
 AXY  H18  CAM  CBA  119.79  3.000
 AXY  CAG  CAM  CBA  120.96  3.000
 AXY  H19  CAG  CAD  120.11  3.000
 AXY  H19  CAG  CAM  119.57  3.000
 AXY  CAD  CAG  CAM  120.32  3.000
 AXY  H20  CAD  CAH  120.32  3.000
 AXY  H20  CAD  CAG  120.33  3.000
 AXY  CAH  CAD  CAG  119.34  3.000
 AXY  H21  CAH  CAN  119.59  3.000
 AXY  H21  CAH  CAD  120.12  3.000
 AXY  CAN  CAH  CAD  120.29  3.000
 AXY  H22  CAN  CAH  119.22  3.000
 AXY  H22  CAN  CBA  119.78  3.000
 AXY  CAH  CAN  CBA  120.99  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
 AXY  CONST_03  CAF  CAL  CAZ  CAK    0.00   0.0  0
 AXY  CONST_04  CAF  CAC  CAE  CAK    0.00   0.0  0
 AXY  CONST_05  CBB  CAZ  CAK  CAE  180.00   0.0  0
 AXY  CONST_06  CAL  CAZ  CAK  CAE    0.00   0.0  0
 AXY  CONST_07  CAL  CAF  CAC  CAE    0.00   0.0  0
 AXY  CONST_08  CAZ  CAK  CAE  CAC    0.00   0.0  0
 AXY  CONST_09  CAZ  CAL  CAF  CAC    0.00   0.0  0
 AXY  CONST_10  CBB  CAZ  CAL  CAF  180.00   0.0  0
 AXY  CONST_13  CAI  CAQ  CBB  CAZ  180.00   0.0  0
 AXY  CONST_14  CAJ  CAR  CBB  CAZ  180.00   0.0  0
 AXY  CONST_15  CAX  CAI  CAQ  CBB    0.00   0.0  0
 AXY  CONST_16  CAX  CAJ  CAR  CBB    0.00   0.0  0
 AXY  CONST_17  CAI  CAX  CAJ  CAR    0.00   0.0  0
 AXY  CONST_18  CAI  CAQ  CBB  CAR    0.00   0.0  0
 AXY  CONST_19  CAQ  CAI  CAX  CAJ    0.00   0.0  0
 AXY  CONST_20  CAQ  CBB  CAR  CAJ    0.00   0.0  0
 AXY  CONST_21  CBC  CAT  CAP  CAY    0.00   0.0  0
 AXY  CONST_22  CBC  CAS  CAO  CAY    0.00   0.0  0
 AXY  CONST_23  CBA  CBC  CAT  CAP  180.00   0.0  0
 AXY  CONST_24  CAS  CBC  CAT  CAP    0.00   0.0  0
 AXY  CONST_25  CAS  CAO  CAY  CAP    0.00   0.0  0
 AXY  CONST_28  CAO  CAS  CBC  CAT    0.00   0.0  0
 AXY  CONST_29  CAO  CAY  CAP  CAT    0.00   0.0  0
 AXY  CONST_30  CBA  CBC  CAS  CAO  180.00   0.0  0
 AXY  CONST_33  CAH  CAN  CBA  CBC  180.00   0.0  0
 AXY  CONST_34  CAG  CAM  CBA  CBC  180.00   0.0  0
 AXY  CONST_35  CAD  CAH  CAN  CBA    0.00   0.0  0
 AXY  CONST_36  CAD  CAG  CAM  CBA    0.00   0.0  0
 AXY  CONST_37  CAH  CAD  CAG  CAM    0.00   0.0  0
 AXY  CONST_38  CAH  CAN  CBA  CAM    0.00   0.0  0
 AXY  CONST_39  CAN  CAH  CAD  CAG    0.00   0.0  0
 AXY  CONST_40  CAN  CBA  CAM  CAG    0.00   0.0  0
 AXY  CONST_41  CAU  CAX  CAJ  CAR  180.00   0.0  0
 AXY  CONST_42  CAU  CAX  CAI  CAQ  180.00   0.0  0
 AXY  CONST_43  CAT  CAP  CAY  OAV  180.00   0.0  0
 AXY  CONST_44  CAS  CAO  CAY  OAV  180.00   0.0  0
 AXY  CONST_45  H5   CAL  CAZ  CAK  180.00   0.0  0
 AXY  CONST_46  H3   CAC  CAE  CAK  180.00   0.0  0
 AXY  CONST_47  H4   CAF  CAC  CAE  180.00   0.0  0
 AXY  CONST_48  H1   CAK  CAE  CAC  180.00   0.0  0
 AXY  CONST_49  H2   CAE  CAC  CAF  180.00   0.0  0
 AXY  CONST_50  H8   CAQ  CBB  CAZ    0.00   0.0  0
 AXY  CONST_51  H6   CAR  CBB  CAZ    0.00   0.0  0
 AXY  CONST_52  H9   CAI  CAQ  CBB  180.00   0.0  0
 AXY  CONST_53  H7   CAJ  CAR  CBB  180.00   0.0  0
 AXY  CONST_54  H15  CAT  CAP  CAY  180.00   0.0  0
 AXY  CONST_55  H17  CAS  CAO  CAY  180.00   0.0  0
 AXY  CONST_56  H16  CAO  CAY  CAP  180.00   0.0  0
 AXY  CONST_57  H14  CAP  CAY  CAO  180.00   0.0  0
 AXY  CONST_58  H22  CAN  CBA  CBC    0.00   0.0  0
 AXY  CONST_59  H18  CAM  CBA  CBC    0.00   0.0  0
 AXY  CONST_60  H21  CAH  CAN  CBA  180.00   0.0  0
 AXY  CONST_61  H19  CAG  CAM  CBA  180.00   0.0  0
 AXY  CONST_62  H20  CAD  CAG  CAM  180.00   0.0  0
 AXY  Var_01    CBD  CAU  CAX  CAJ  -82.57  30.0  2
 AXY  Var_02    CAP  CAY  OAV  CBD  175.92  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
 AXY  chir_01  CBD  OAV  CAW  CAU  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
 AXY  plan-1  CAK  0.020
 AXY  plan-1  CAE  0.020
 AXY  plan-1  CAC  0.020
 AXY  plan-1  CAF  0.020
 AXY  plan-1  CAL  0.020
 AXY  plan-1  CAZ  0.020
 AXY  plan-1  CBB  0.020
 AXY  plan-1  H1   0.020
 AXY  plan-1  H2   0.020
 AXY  plan-1  H3   0.020
 AXY  plan-1  H4   0.020
 AXY  plan-1  H5   0.020
 AXY  plan-2  CAZ  0.020
 AXY  plan-2  CBB  0.020
 AXY  plan-2  CAR  0.020
 AXY  plan-2  CAJ  0.020
 AXY  plan-2  CAQ  0.020
 AXY  plan-2  CAI  0.020
 AXY  plan-2  CAX  0.020
 AXY  plan-2  CAU  0.020
 AXY  plan-2  H6   0.020
 AXY  plan-2  H7   0.020
 AXY  plan-2  H8   0.020
 AXY  plan-2  H9   0.020
 AXY  plan-3  OAV  0.020
 AXY  plan-3  CAY  0.020
 AXY  plan-3  CAP  0.020
 AXY  plan-3  CAT  0.020
 AXY  plan-3  CAO  0.020
 AXY  plan-3  CAS  0.020
 AXY  plan-3  CBC  0.020
 AXY  plan-3  CBA  0.020
 AXY  plan-3  H14  0.020
 AXY  plan-3  H15  0.020
 AXY  plan-3  H16  0.020
 AXY  plan-3  H17  0.020
 AXY  plan-4  CBC  0.020
 AXY  plan-4  CBA  0.020
 AXY  plan-4  CAM  0.020
 AXY  plan-4  CAG  0.020
 AXY  plan-4  CAD  0.020
 AXY  plan-4  CAH  0.020
 AXY  plan-4  CAN  0.020
 AXY  plan-4  H18  0.020
 AXY  plan-4  H19  0.020
 AXY  plan-4  H20  0.020
 AXY  plan-4  H21  0.020
 AXY  plan-4  H22  0.020
 AXY  plan-5  CBD  0.020
 AXY  plan-5  CAW  0.020
 AXY  plan-5  OAB  0.020
 AXY  plan-5  OAA  0.020

