# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 21:15:04 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: (2R,3S)-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(O)c2C[C@H](OC(=O)c3cc(O)c(O)c(O)c3)[C@H](Oc2c1)c4ccc(O)c(O)c4
#
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
 XEG  XEG  '(2R,3S)-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate'  ligand  50  32  .  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_XEG
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
 XEG  OAA   O  O     0  -0.435   0.7967  -0.8008  -2.1484
 XEG  OAC   O  OH1   0  -0.634   1.9997   4.3728  -1.6537
 XEG  OAD   O  OH1   0  -0.643   2.4933   3.1767   0.7294
 XEG  OAF   O  OH1   0  -0.642   4.3974  -0.7200   2.6537
 XEG  OAG   O  OH1   0  -0.623  -4.1372  -3.7250   0.7569
 XEG  OAH   O  OH1   0  -0.632   6.3732  -0.6023   0.8041
 XEG  CAI   C  CR16  0  -0.331  -0.0151   3.1594  -1.8661
 XEG  CAJ   C  CR16  0  -0.305  -0.9230   2.2244  -1.3865
 XEG  CAK   C  CR16  0  -0.496  -5.8457  -2.0641   0.6069
 XEG  CAL   C  CR16  0  -0.384   3.4916  -0.7858  -1.3704
 XEG  CAM   C  CR16  0  -0.436   2.7200  -0.8357   0.9184
 XEG  CAN   C  CR16  0  -0.526  -5.1792   0.2256   0.2360
 XEG  CAO   C  CR16  0  -0.416   0.4343   1.9295   0.5645
 XEG  CAP   C  C     0  -0.477  -2.0426  -1.9543   0.3191
 XEG  OAQ   O  O2    0  -0.486   0.1636  -1.0844  -0.0178
 XEG  OAR   O  O     0  -0.493  -2.9339   0.7939   0.0239
 XEG  CAS   C  C     0   0.614   1.0716  -0.9017  -0.9786
 XEG  CAT   C  CR6   0   0.377  -6.1734  -0.7227   0.4228
 XEG  CAU   C  CR6   0   0.284   1.1311   3.4707  -1.1506
 XEG  CAV   C  CR6   0   0.283   1.3558   2.8399   0.0786
 XEG  CAW   C  CR6   0   0.324   4.8034  -0.7069  -0.9326
 XEG  CAX   C  CR6   0   0.298   4.0313  -0.7494   1.3543
 XEG  CAY   C  CR6   0   0.342  -4.5114  -2.4434   0.5865
 XEG  CAZ   C  CR6   0  -0.080   2.4515  -0.8519  -0.4499
 XEG  CBA   C  CR6   0   0.050  -0.7050   1.6030  -0.1651
 XEG  CBB   C  CR6   0   0.194   5.0801  -0.6861   0.4347
 XEG  CBC   C  CR66  0   0.417  -3.8485  -0.1856   0.2205
 XEG  CBD   C  CR66  0  -0.156  -3.4814  -1.5175   0.3828
 XEG  CBE   C  CR16  0   0.006  -1.2119  -0.8479  -0.2959
 XEG  CBF   C  CR16  0  -0.014  -1.5857   0.4974   0.3372
 XEG  HOAB  H  HOH1  0   0.476  -7.5934   0.5496   0.3176
 XEG  HOAC  H  HOH1  0   0.473   2.7524   4.4837  -1.0611
 XEG  HOAD  H  HOH1  0   0.476   2.6030   2.6427   1.5234
 XEG  HOAE  H  HOH1  0   0.474   6.6552  -0.6203  -1.4139
 XEG  HOAF  H  HOH1  0   0.485   3.6307  -0.7983   3.2321
 XEG  HOAG  H  HOH1  0   0.478  -4.9092  -4.2899   0.8745
 XEG  HOAH  H  HOH1  0   0.485   6.4656  -0.6305   1.7641
 XEG  HAI   H  HCR6  0   0.264  -0.1893   3.6466  -2.8175
 XEG  HAJ   H  HCR6  0   0.249  -1.7943   1.9867  -1.9821
 XEG  HAK   H  HCR6  0   0.273  -6.6291  -2.7979   0.7581
 XEG  HAL   H  HCR6  0   0.268   3.2925  -0.7960  -2.4338
 XEG  HAM   H  HCR6  0   0.281   1.9215  -0.8776   1.6478
 XEG  HAN   H  HCR6  0   0.273  -5.4183   1.2741   0.1019
 XEG  HAO   H  HCR6  0   0.270   0.6145   1.4593   1.5255
 XEG  HAP   H  H     0   0.260  -1.6627  -2.1870   1.3193
 XEG  HAPA  H  H     0   0.268  -1.9423  -2.8629  -0.2782
 XEG  HBE   H  HCR6  0   0.273  -1.3826  -0.7946  -1.3739
 XEG  HBF   H  HCR6  0   0.261  -1.4769   0.4074   1.4272
 XEG  OAE   O  OH1   0  -0.633   5.7931  -0.6506  -1.8454
 XEG  OAB   O  OH1   0  -0.633  -7.4802  -0.3991   0.4450

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
 XEG  OAA  CAS   double    1.206  0.020  1.206
 XEG  CAT  OAB   single    1.347  0.020  1.347
 XEG  OAB  HOAB  single    0.850  0.020  0.980
 XEG  CAU  OAC   single    1.350  0.020  1.350
 XEG  OAC  HOAC  single    0.850  0.020  0.980
 XEG  CAV  OAD   single    1.353  0.020  1.353
 XEG  OAD  HOAD  single    0.850  0.020  0.980
 XEG  OAE  CAW   single    1.348  0.020  1.348
 XEG  OAE  HOAE  single    0.850  0.020  0.980
 XEG  CAX  OAF   single    1.350  0.020  1.350
 XEG  OAF  HOAF  single    0.850  0.020  0.980
 XEG  OAG  CAY   single    1.346  0.020  1.346
 XEG  OAG  HOAG  single    0.850  0.020  0.980
 XEG  CBB  OAH   single    1.347  0.020  1.347
 XEG  OAH  HOAH  single    0.850  0.020  0.980
 XEG  CAJ  CAI   aromatic  1.389  0.020  1.389
 XEG  CAI  CAU   aromatic  1.387  0.020  1.387
 XEG  CAI  HAI   single    0.930  0.020  1.080
 XEG  CAJ  CBA   aromatic  1.388  0.020  1.388
 XEG  CAJ  HAJ   single    0.930  0.020  1.080
 XEG  CAY  CAK   aromatic  1.387  0.020  1.387
 XEG  CAK  CAT   aromatic  1.393  0.020  1.393
 XEG  CAK  HAK   single    0.930  0.020  1.080
 XEG  CAL  CAW   aromatic  1.385  0.020  1.385
 XEG  CAL  CAZ   aromatic  1.390  0.020  1.390
 XEG  CAL  HAL   single    0.930  0.020  1.080
 XEG  CAZ  CAM   aromatic  1.395  0.020  1.395
 XEG  CAM  CAX   aromatic  1.385  0.020  1.385
 XEG  CAM  HAM   single    0.930  0.020  1.080
 XEG  CBC  CAN   aromatic  1.393  0.020  1.393
 XEG  CAN  CAT   aromatic  1.386  0.020  1.386
 XEG  CAN  HAN   single    0.930  0.020  1.080
 XEG  CBA  CAO   aromatic  1.392  0.020  1.392
 XEG  CAO  CAV   aromatic  1.383  0.020  1.383
 XEG  CAO  HAO   single    0.930  0.020  1.080
 XEG  CBE  CAP   single    1.514  0.020  1.514
 XEG  CAP  CBD   single    1.505  0.020  1.505
 XEG  CAP  HAP   single    0.970  0.020  1.090
 XEG  CAP  HAPA  single    0.970  0.020  1.090
 XEG  CAS  OAQ   single    1.335  0.020  1.335
 XEG  OAQ  CBE   single    1.423  0.020  1.423
 XEG  CBF  OAR   single    1.416  0.020  1.416
 XEG  OAR  CBC   single    1.354  0.020  1.354
 XEG  CAS  CAZ   single    1.479  0.020  1.479
 XEG  CAU  CAV   aromatic  1.400  0.020  1.400
 XEG  CAW  CBB   aromatic  1.395  0.020  1.395
 XEG  CBB  CAX   aromatic  1.396  0.020  1.396
 XEG  CBD  CAY   aromatic  1.400  0.020  1.400
 XEG  CBF  CBA   single    1.500  0.020  1.500
 XEG  CBD  CBC   aromatic  1.391  0.020  1.391
 XEG  CBE  CBF   single    1.533  0.020  1.533
 XEG  CBE  HBE   single    0.970  0.020  1.090
 XEG  CBF  HBF   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
 XEG  HOAC  OAC  CAU  110.49  3.000
 XEG  HOAD  OAD  CAV  110.75  3.000
 XEG  HOAF  OAF  CAX  111.11  3.000
 XEG  HOAG  OAG  CAY  110.54  3.000
 XEG  HOAH  OAH  CBB  111.28  3.000
 XEG  HAI   CAI  CAU  119.03  3.000
 XEG  HAI   CAI  CAJ  120.07  3.000
 XEG  CAU   CAI  CAJ  120.89  3.000
 XEG  HAJ   CAJ  CBA  120.85  3.000
 XEG  HAJ   CAJ  CAI  118.96  3.000
 XEG  CBA   CAJ  CAI  120.19  3.000
 XEG  HAK   CAK  CAY  120.80  3.000
 XEG  HAK   CAK  CAT  120.02  3.000
 XEG  CAY   CAK  CAT  119.18  3.000
 XEG  HAL   CAL  CAZ  120.84  3.000
 XEG  HAL   CAL  CAW  119.04  3.000
 XEG  CAZ   CAL  CAW  120.12  3.000
 XEG  HAM   CAM  CAZ  121.26  3.000
 XEG  HAM   CAM  CAX  119.27  3.000
 XEG  CAZ   CAM  CAX  119.47  3.000
 XEG  HAN   CAN  CBC  119.67  3.000
 XEG  HAN   CAN  CAT  121.35  3.000
 XEG  CBC   CAN  CAT  118.99  3.000
 XEG  HAO   CAO  CBA  119.92  3.000
 XEG  HAO   CAO  CAV  119.05  3.000
 XEG  CBA   CAO  CAV  121.03  3.000
 XEG  HAPA  CAP  HAP  106.92  3.000
 XEG  HAPA  CAP  CBE  109.60  3.000
 XEG  HAP   CAP  CBE  109.63  3.000
 XEG  HAPA  CAP  CBD  110.64  3.000
 XEG  HAP   CAP  CBD  110.77  3.000
 XEG  CBE   CAP  CBD  109.24  3.000
 XEG  CBE   OAQ  CAS  119.61  3.000
 XEG  CBF   OAR  CBC  117.36  3.000
 XEG  CAZ   CAS  OAQ  112.47  3.000
 XEG  CAZ   CAS  OAA  123.83  3.000
 XEG  OAQ   CAS  OAA  123.70  3.000
 XEG  CAN   CAT  CAK  120.51  3.000
 XEG  CAN   CAT  OAB  122.26  3.000
 XEG  CAK   CAT  OAB  117.23  3.000
 XEG  CAV   CAU  CAI  118.99  3.000
 XEG  CAV   CAU  OAC  121.69  3.000
 XEG  CAI   CAU  OAC  119.32  3.000
 XEG  CAU   CAV  CAO  119.87  3.000
 XEG  CAU   CAV  OAD  116.43  3.000
 XEG  CAO   CAV  OAD  123.70  3.000
 XEG  CBB   CAW  CAL  119.90  3.000
 XEG  CBB   CAW  OAE  121.17  3.000
 XEG  CAL   CAW  OAE  118.94  3.000
 XEG  CBB   CAX  CAM  120.46  3.000
 XEG  CBB   CAX  OAF  115.41  3.000
 XEG  CAM   CAX  OAF  124.13  3.000
 XEG  CBD   CAY  CAK  121.94  3.000
 XEG  CBD   CAY  OAG  116.34  3.000
 XEG  CAK   CAY  OAG  121.73  3.000
 XEG  CAS   CAZ  CAM  122.06  3.000
 XEG  CAS   CAZ  CAL  117.58  3.000
 XEG  CAM   CAZ  CAL  120.34  3.000
 XEG  CBF   CBA  CAO  118.55  3.000
 XEG  CBF   CBA  CAJ  122.18  3.000
 XEG  CAO   CBA  CAJ  119.01  3.000
 XEG  CAX   CBB  CAW  119.72  3.000
 XEG  CAX   CBB  OAH  122.90  3.000
 XEG  CAW   CBB  OAH  117.38  3.000
 XEG  CBD   CBC  OAR  122.08  3.000
 XEG  CBD   CBC  CAN  122.24  3.000
 XEG  OAR   CBC  CAN  115.68  3.000
 XEG  CBC   CBD  CAY  117.13  3.000
 XEG  CBC   CBD  CAP  121.69  3.000
 XEG  CAY   CBD  CAP  121.17  3.000
 XEG  HBE   CBE  CBF  109.05  3.000
 XEG  HBE   CBE  OAQ  110.61  3.000
 XEG  CBF   CBE  OAQ  107.50  3.000
 XEG  HBE   CBE  CAP  110.53  3.000
 XEG  CBF   CBE  CAP  109.86  3.000
 XEG  OAQ   CBE  CAP  109.24  3.000
 XEG  HBF   CBF  CBE  108.27  3.000
 XEG  HBF   CBF  CBA  109.53  3.000
 XEG  CBE   CBF  CBA  111.43  3.000
 XEG  HBF   CBF  OAR  109.32  3.000
 XEG  CBE   CBF  OAR  108.94  3.000
 XEG  CBA   CBF  OAR  109.31  3.000
 XEG  HOAE  OAE  CAW  110.78  3.000
 XEG  HOAB  OAB  CAT  110.38  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
 XEG  CONST_01  CAO  CBA  CAJ  CAI    0.00   0.0  0
 XEG  CONST_02  CAO  CAV  CAU  CAI    0.00   0.0  0
 XEG  CONST_03  CAV  CAU  CAI  CAJ    0.00   0.0  0
 XEG  CONST_04  CAV  CAO  CBA  CAJ    0.00   0.0  0
 XEG  CONST_05  CBC  CBD  CAY  CAK    0.00   0.0  0
 XEG  CONST_06  CBC  CAN  CAT  CAK    0.00   0.0  0
 XEG  CONST_07  CAX  CBB  CAW  CAL    0.00   0.0  0
 XEG  CONST_08  CAX  CAM  CAZ  CAL    0.00   0.0  0
 XEG  CONST_09  CAW  CAL  CAZ  CAM    0.00   0.0  0
 XEG  CONST_10  CAW  CBB  CAX  CAM    0.00   0.0  0
 XEG  CONST_11  CAY  CBD  CBC  CAN    0.00   0.0  0
 XEG  CONST_12  CAY  CAK  CAT  CAN    0.00   0.0  0
 XEG  CONST_13  CBD  CAY  CAK  CAT    0.00   0.0  0
 XEG  CONST_14  CBD  CBC  CAN  CAT    0.00   0.0  0
 XEG  CONST_15  CBA  CAJ  CAI  CAU    0.00   0.0  0
 XEG  CONST_16  CBA  CAO  CAV  CAU    0.00   0.0  0
 XEG  CONST_17  CBB  CAW  CAL  CAZ    0.00   0.0  0
 XEG  CONST_18  CBB  CAX  CAM  CAZ    0.00   0.0  0
 XEG  CONST_19  CBF  CBA  CAJ  CAI  180.00   0.0  0
 XEG  CONST_20  CBF  CBA  CAO  CAV  180.00   0.0  0
 XEG  CONST_21  CAY  CAK  CAT  OAB  180.00   0.0  0
 XEG  CONST_22  CBC  CAN  CAT  OAB  180.00   0.0  0
 XEG  CONST_23  CAJ  CAI  CAU  OAC  180.00   0.0  0
 XEG  CONST_24  CAO  CAV  CAU  OAC  180.00   0.0  0
 XEG  CONST_25  CBA  CAO  CAV  OAD  180.00   0.0  0
 XEG  CONST_26  CAI  CAU  CAV  OAD  180.00   0.0  0
 XEG  CONST_27  CAZ  CAL  CAW  OAE  180.00   0.0  0
 XEG  CONST_28  CAX  CBB  CAW  OAE  180.00   0.0  0
 XEG  CONST_29  CAZ  CAM  CAX  OAF  180.00   0.0  0
 XEG  CONST_30  CAW  CBB  CAX  OAF  180.00   0.0  0
 XEG  CONST_31  CAT  CAK  CAY  OAG  180.00   0.0  0
 XEG  CONST_32  CAP  CBD  CAY  OAG    0.00   0.0  0
 XEG  CONST_33  CBC  CBD  CAY  OAG  180.00   0.0  0
 XEG  CONST_34  CAL  CAW  CBB  OAH  180.00   0.0  0
 XEG  CONST_35  CAM  CAX  CBB  OAH  180.00   0.0  0
 XEG  CONST_36  CAW  CAL  CAZ  CAS  180.00   0.0  0
 XEG  CONST_37  CAX  CAM  CAZ  CAS  180.00   0.0  0
 XEG  CONST_38  HAO  CAO  CBA  CAJ  180.00   0.0  0
 XEG  CONST_39  HAN  CAN  CAT  CAK  180.00   0.0  0
 XEG  CONST_40  HAM  CAM  CAZ  CAL  180.00   0.0  0
 XEG  CONST_41  HAL  CAL  CAZ  CAM  180.00   0.0  0
 XEG  CONST_42  HAK  CAK  CAT  CAN  180.00   0.0  0
 XEG  CONST_43  HAJ  CAJ  CBA  CAO  180.00   0.0  0
 XEG  CONST_44  HAI  CAI  CAU  CAV  180.00   0.0  0
 XEG  Var_01    CBE  CAP  CBD  CAY  163.74  30.0  1
 XEG  Var_02    CAL  CAZ  CAS  OAA   -5.02  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
 XEG  chir_01  CBE  CAP  OAQ  CBF  positiv
 XEG  chir_02  CBF  OAR  CBE  CBA  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
 XEG  plan-1  OAC  0.020
 XEG  plan-1  OAD  0.020
 XEG  plan-1  CAI  0.020
 XEG  plan-1  CAJ  0.020
 XEG  plan-1  CAO  0.020
 XEG  plan-1  CAU  0.020
 XEG  plan-1  CAV  0.020
 XEG  plan-1  CBA  0.020
 XEG  plan-1  CBF  0.020
 XEG  plan-1  HAI  0.020
 XEG  plan-1  HAJ  0.020
 XEG  plan-1  HAO  0.020
 XEG  plan-2  OAF  0.020
 XEG  plan-2  OAH  0.020
 XEG  plan-2  CAL  0.020
 XEG  plan-2  CAM  0.020
 XEG  plan-2  CAS  0.020
 XEG  plan-2  CAW  0.020
 XEG  plan-2  CAX  0.020
 XEG  plan-2  CAZ  0.020
 XEG  plan-2  CBB  0.020
 XEG  plan-2  HAL  0.020
 XEG  plan-2  HAM  0.020
 XEG  plan-2  OAE  0.020
 XEG  plan-3  OAG  0.020
 XEG  plan-3  CAK  0.020
 XEG  plan-3  CAN  0.020
 XEG  plan-3  CAP  0.020
 XEG  plan-3  OAR  0.020
 XEG  plan-3  CAT  0.020
 XEG  plan-3  CAY  0.020
 XEG  plan-3  CBC  0.020
 XEG  plan-3  CBD  0.020
 XEG  plan-3  HAK  0.020
 XEG  plan-3  HAN  0.020
 XEG  plan-3  OAB  0.020
 XEG  plan-4  OAA  0.020
 XEG  plan-4  OAQ  0.020
 XEG  plan-4  CAS  0.020
 XEG  plan-4  CAZ  0.020

