# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun 21 22:14:33 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (2S,3S,4S,5R,6S)-6-[4-[(E)-2-[3,5-bis(oxidanyl)phenyl]ethenyl]phenoxy]-3,4,5-tris(oxidanyl)oxane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1[C@@H](O)[C@@H](O[C@@H]([C@H]1O)C(O)=O)Oc2ccc(cc2)/C=C/c3cc(O)cc(O)c3
#
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
 R4G  R4G  '(2S,3S,4S,5R,6S)-6-[4-[(E)-2-[3,5-bis(oxidanyl)phenyl]ethenyl]phenoxy]-3,4,5-tris(oxidanyl)oxane-2-carboxylic acid'  ligand  48  29  .  2021-08-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_R4G
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
 R4G  CAJ  C  CR16   0  -0.441  -5.8818  -1.3747  -0.7235
 R4G  CAK  C  CR6    0   0.391  -7.2657  -1.5232  -0.7847
 R4G  OAP  O  OH1    0  -0.633  -7.7432  -2.6613  -1.3237
 R4G  CAL  C  CR16   0  -0.488  -8.1028  -0.5266  -0.3028
 R4G  CAM  C  CR6    0   0.415  -7.5407   0.6266   0.2448
 R4G  OAO  O  OH1    0  -0.634  -8.3967   1.5635   0.6968
 R4G  CAN  C  CR16   0  -0.522  -6.1641   0.7854   0.3115
 R4G  CAI  C  CR6    0   0.207  -5.3240  -0.2212  -0.1768
 R4G  CAH  C  C1     0  -0.321  -3.8654  -0.1217  -0.1434
 R4G  CAG  C  C1     0  -0.303  -3.1503   0.9090   0.3266
 R4G  CAC  C  C      0   0.154  -1.6945   1.0120   0.3561
 R4G  CAD  C  C1     0  -0.299  -1.1084   2.1988   0.8070
 R4G  CAE  C  C1     0  -0.334   0.2636   2.3635   0.8400
 R4G  CAB  C  C1     0  -0.327  -0.8353  -0.0150  -0.0422
 R4G  CAA  C  C1     0  -0.328   0.5413   0.1274  -0.0030
 R4G  CAF  C  C      0   0.361   1.0997   1.3302   0.4278
 R4G  O1   O  O2     0  -0.498   2.4304   1.5816   0.4863
 R4G  C1   C  CH1    0   0.265   3.3274   0.7291  -0.1558
 R4G  O5   O  O2     0  -0.485   3.5459  -0.3658   0.6775
 R4G  C5   C  CH1    0  -0.162   4.4332  -1.3034   0.1117
 R4G  C6   C  C      0   0.439   4.5199  -2.5477   1.0171
 R4G  OBC  O  OC    -1  -0.616   5.4627  -3.3319   0.7269
 R4G  O6   O  O      0  -0.554   3.6854  -2.6902   1.9106
 R4G  C4   C  CH1    0   0.036   5.8179  -0.6669  -0.1149
 R4G  O4   O  OH1    0  -0.702   6.6839  -1.5683  -0.7446
 R4G  C3   C  CH1    0   0.012   5.6670   0.5737  -0.9799
 R4G  O3   O  OH1    0  -0.670   6.9189   1.2039  -1.0856
 R4G  C2   C  CH1    0  -0.030   4.6213   1.5071  -0.3788
 R4G  O2   O  OH1    0  -0.667   4.4364   2.5738  -1.2748
 R4G  HAJ  H  HCR6   0   0.257  -5.2430  -2.1622  -1.1047
 R4G  HAP  H  HOH1   0   0.475  -8.7066  -2.6601  -1.3143
 R4G  HAL  H  HCR6   0   0.276  -9.1812  -0.6338  -0.3451
 R4G  HAO  H  HOH1   0   0.475  -7.9122   2.3093   1.0679
 R4G  HAN  H  HCR6   0   0.265  -5.7528   1.6907   0.7422
 R4G  HAH  H  H      0   0.251  -3.3475  -0.9833  -0.5524
 R4G  HAG  H  H      0   0.253  -3.6684   1.7751   0.7267
 R4G  HAD  H  H      0   0.257  -1.7410   3.0167   1.1306
 R4G  HAB  H  H      0   0.260  -1.2343  -0.9609  -0.3860
 R4G  HAE  H  H      0   0.267   0.6931   3.2962   1.1830
 R4G  HAA  H  H      0   0.286   1.1553  -0.7132  -0.2942
 R4G  H1   H  HCH1   0   0.208   2.9202   0.4075  -1.1311
 R4G  H2   H  HCH1   0   0.228   4.9813   1.8592   0.5994
 R4G  H5   H  HCH1   0   0.231   4.0525  -1.6379  -0.8699
 R4G  H4   H  HCH1   0   0.196   6.2089  -0.3538   0.8693
 R4G  HA   H  HOH1   0   0.439   6.4699  -2.4254  -0.3071
 R4G  H3   H  HCH1   0   0.206   5.3069   0.2497  -1.9711
 R4G  HB   H  HOH1   0   0.450   6.8183   1.9769  -1.6508
 R4G  HC   H  HOH1   0   0.459   3.9707   3.2836  -0.8225

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
 R4G  CAJ  CAK  aromatic  1.393  0.020  1.393
 R4G  CAJ  CAI  aromatic  1.393  0.020  1.393
 R4G  CAK  OAP  single    1.347  0.020  1.347
 R4G  CAK  CAL  aromatic  1.388  0.020  1.388
 R4G  CAL  CAM  aromatic  1.395  0.020  1.395
 R4G  CAM  OAO  single    1.347  0.020  1.347
 R4G  CAM  CAN  aromatic  1.387  0.020  1.387
 R4G  CAN  CAI  aromatic  1.399  0.020  1.399
 R4G  CAI  CAH  single    1.462  0.020  1.462
 R4G  CAH  CAG  double    1.340  0.020  1.340
 R4G  CAG  CAC  single    1.460  0.020  1.460
 R4G  CAC  CAD  aromatic  1.398  0.020  1.398
 R4G  CAC  CAB  aromatic  1.397  0.020  1.397
 R4G  CAD  CAE  aromatic  1.382  0.020  1.382
 R4G  CAE  CAF  aromatic  1.392  0.020  1.392
 R4G  CAB  CAA  aromatic  1.384  0.020  1.384
 R4G  CAA  CAF  aromatic  1.394  0.020  1.394
 R4G  CAF  O1   single    1.356  0.020  1.356
 R4G  O1   C1   single    1.394  0.020  1.394
 R4G  C1   O5   single    1.393  0.020  1.393
 R4G  C1   C2   single    1.526  0.020  1.526
 R4G  O5   C5   single    1.409  0.020  1.409
 R4G  C5   C6   single    1.541  0.020  1.541
 R4G  C5   C4   single    1.541  0.020  1.541
 R4G  C6   OBC  deloc     1.260  0.020  1.260
 R4G  C6   O6   deloc     1.231  0.020  1.231
 R4G  C4   O4   single    1.400  0.020  1.400
 R4G  C4   C3   single    1.520  0.020  1.520
 R4G  C3   O3   single    1.406  0.020  1.406
 R4G  C3   C2   single    1.525  0.020  1.525
 R4G  C2   O2   single    1.405  0.020  1.405
 R4G  CAJ  HAJ  single    0.930  0.020  1.080
 R4G  OAP  HAP  single    0.850  0.020  0.980
 R4G  CAL  HAL  single    0.930  0.020  1.080
 R4G  OAO  HAO  single    0.850  0.020  0.980
 R4G  CAN  HAN  single    0.930  0.020  1.080
 R4G  CAH  HAH  single    0.930  0.020  1.080
 R4G  CAG  HAG  single    0.930  0.020  1.080
 R4G  CAD  HAD  single    0.930  0.020  1.080
 R4G  CAB  HAB  single    0.930  0.020  1.080
 R4G  CAE  HAE  single    0.930  0.020  1.080
 R4G  CAA  HAA  single    0.930  0.020  1.080
 R4G  C1   H1   single    0.970  0.020  1.090
 R4G  C2   H2   single    0.970  0.020  1.090
 R4G  C5   H5   single    0.970  0.020  1.090
 R4G  C4   H4   single    0.970  0.020  1.090
 R4G  O4   HA   single    0.850  0.020  0.980
 R4G  C3   H3   single    0.970  0.020  1.090
 R4G  O3   HB   single    0.850  0.020  0.980
 R4G  O2   HC   single    0.850  0.020  0.980

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
 R4G  HAJ  CAJ  CAI  120.26  3.000
 R4G  HAJ  CAJ  CAK  119.52  3.000
 R4G  CAI  CAJ  CAK  120.21  3.000
 R4G  CAL  CAK  OAP  122.13  3.000
 R4G  CAL  CAK  CAJ  120.49  3.000
 R4G  OAP  CAK  CAJ  117.38  3.000
 R4G  HAP  OAP  CAK  110.46  3.000
 R4G  HAL  CAL  CAM  119.85  3.000
 R4G  HAL  CAL  CAK  121.01  3.000
 R4G  CAM  CAL  CAK  119.14  3.000
 R4G  CAN  CAM  OAO  122.33  3.000
 R4G  CAN  CAM  CAL  120.88  3.000
 R4G  OAO  CAM  CAL  116.79  3.000
 R4G  HAO  OAO  CAM  110.36  3.000
 R4G  HAN  CAN  CAI  120.78  3.000
 R4G  HAN  CAN  CAM  119.43  3.000
 R4G  CAI  CAN  CAM  119.79  3.000
 R4G  CAH  CAI  CAN  122.82  3.000
 R4G  CAH  CAI  CAJ  117.69  3.000
 R4G  CAN  CAI  CAJ  119.49  3.000
 R4G  HAH  CAH  CAG  119.22  3.000
 R4G  HAH  CAH  CAI  114.42  3.000
 R4G  CAG  CAH  CAI  126.36  3.000
 R4G  HAG  CAG  CAC  114.34  3.000
 R4G  HAG  CAG  CAH  119.23  3.000
 R4G  CAC  CAG  CAH  126.43  3.000
 R4G  CAB  CAC  CAD  117.26  3.000
 R4G  CAB  CAC  CAG  123.76  3.000
 R4G  CAD  CAC  CAG  118.98  3.000
 R4G  HAD  CAD  CAE  118.84  3.000
 R4G  HAD  CAD  CAC  119.49  3.000
 R4G  CAE  CAD  CAC  121.66  3.000
 R4G  HAE  CAE  CAF  119.68  3.000
 R4G  HAE  CAE  CAD  120.27  3.000
 R4G  CAF  CAE  CAD  120.05  3.000
 R4G  HAB  CAB  CAA  117.73  3.000
 R4G  HAB  CAB  CAC  120.41  3.000
 R4G  CAA  CAB  CAC  121.85  3.000
 R4G  HAA  CAA  CAF  121.77  3.000
 R4G  HAA  CAA  CAB  118.50  3.000
 R4G  CAF  CAA  CAB  119.72  3.000
 R4G  O1   CAF  CAA  124.51  3.000
 R4G  O1   CAF  CAE  116.06  3.000
 R4G  CAA  CAF  CAE  119.43  3.000
 R4G  C1   O1   CAF  119.89  3.000
 R4G  H1   C1   C2   109.38  3.000
 R4G  H1   C1   O5   110.92  3.000
 R4G  C2   C1   O5   110.79  3.000
 R4G  H1   C1   O1   110.33  3.000
 R4G  C2   C1   O1   107.52  3.000
 R4G  O5   C1   O1   107.82  3.000
 R4G  C5   O5   C1   112.42  3.000
 R4G  H5   C5   C4   107.70  3.000
 R4G  H5   C5   C6   107.28  3.000
 R4G  C4   C5   C6   111.67  3.000
 R4G  H5   C5   O5   109.95  3.000
 R4G  C4   C5   O5   110.49  3.000
 R4G  C6   C5   O5   109.67  3.000
 R4G  O6   C6   OBC  127.04  3.000
 R4G  O6   C6   C5   118.80  3.000
 R4G  OBC  C6   C5   114.16  3.000
 R4G  H4   C4   C3   108.11  3.000
 R4G  H4   C4   O4   111.37  3.000
 R4G  C3   C4   O4   109.34  3.000
 R4G  H4   C4   C5   107.71  3.000
 R4G  C3   C4   C5   109.37  3.000
 R4G  O4   C4   C5   110.87  3.000
 R4G  HA   O4   C4   103.06  3.000
 R4G  H3   C3   C2   108.06  3.000
 R4G  H3   C3   O3   110.78  3.000
 R4G  C2   C3   O3   111.47  3.000
 R4G  H3   C3   C4   107.69  3.000
 R4G  C2   C3   C4   110.08  3.000
 R4G  O3   C3   C4   108.69  3.000
 R4G  HB   O3   C3   108.12  3.000
 R4G  H2   C2   O2   111.54  3.000
 R4G  H2   C2   C3   108.78  3.000
 R4G  O2   C2   C3   107.67  3.000
 R4G  H2   C2   C1   108.09  3.000
 R4G  O2   C2   C1   111.62  3.000
 R4G  C3   C2   C1   109.08  3.000
 R4G  HC   O2   C2   108.91  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
 R4G  CONST_01  CAM  CAL  CAK  CAJ     0.00   0.0  0
 R4G  CONST_02  CAM  CAN  CAI  CAJ     0.00   0.0  0
 R4G  CONST_03  CAN  CAI  CAJ  CAK     0.00   0.0  0
 R4G  CONST_04  CAN  CAM  CAL  CAK     0.00   0.0  0
 R4G  CONST_05  CAI  CAJ  CAK  CAL     0.00   0.0  0
 R4G  CONST_06  CAI  CAN  CAM  CAL     0.00   0.0  0
 R4G  CONST_07  CAF  CAE  CAD  CAC     0.00   0.0  0
 R4G  CONST_08  CAF  CAA  CAB  CAC     0.00   0.0  0
 R4G  CONST_09  CAA  CAB  CAC  CAD     0.00   0.0  0
 R4G  CONST_10  CAA  CAF  CAE  CAD     0.00   0.0  0
 R4G  CONST_11  CAB  CAC  CAD  CAE     0.00   0.0  0
 R4G  CONST_12  CAB  CAA  CAF  CAE     0.00   0.0  0
 R4G  CONST_13  CAH  CAI  CAJ  CAK   180.00   0.0  0
 R4G  CONST_14  OAO  CAM  CAL  CAK   180.00   0.0  0
 R4G  CONST_15  CAI  CAJ  CAK  OAP   180.00   0.0  0
 R4G  CONST_16  CAM  CAL  CAK  OAP   180.00   0.0  0
 R4G  CONST_17  CAH  CAI  CAN  CAM   180.00   0.0  0
 R4G  CONST_18  CAI  CAN  CAM  OAO   180.00   0.0  0
 R4G  CONST_19  CAE  CAD  CAC  CAG   180.00   0.0  0
 R4G  CONST_20  CAA  CAB  CAC  CAG   180.00   0.0  0
 R4G  CONST_21  O1   CAF  CAE  CAD   180.00   0.0  0
 R4G  CONST_22  O1   CAF  CAA  CAB   180.00   0.0  0
 R4G  CONST_23  HAL  CAL  CAK  CAJ   180.00   0.0  0
 R4G  CONST_24  HAN  CAN  CAI  CAJ   180.00   0.0  0
 R4G  CONST_25  HAJ  CAJ  CAK  CAL   180.00   0.0  0
 R4G  CONST_26  HAE  CAE  CAD  CAC   180.00   0.0  0
 R4G  CONST_27  HAA  CAA  CAB  CAC   180.00   0.0  0
 R4G  CONST_28  HAB  CAB  CAC  CAD   180.00   0.0  0
 R4G  CONST_29  HAD  CAD  CAC  CAB   180.00   0.0  0
 R4G  Var_01    CAC  CAG  CAH  CAI  -179.76   0.0  2
 R4G  Var_02    CAG  CAH  CAI  CAJ   179.22  30.0  2
 R4G  Var_03    CAD  CAC  CAG  CAH   176.03  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
 R4G  chir_01  C1  O1  O5  C2  positiv
 R4G  chir_02  C5  O5  C6  C4  positiv
 R4G  chir_03  C4  O4  C5  C3  positiv
 R4G  chir_04  C3  O3  C2  C4  positiv
 R4G  chir_05  C2  O2  C3  C1  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
 R4G  plan-1  CAJ  0.020
 R4G  plan-1  CAK  0.020
 R4G  plan-1  OAP  0.020
 R4G  plan-1  CAL  0.020
 R4G  plan-1  CAM  0.020
 R4G  plan-1  OAO  0.020
 R4G  plan-1  CAN  0.020
 R4G  plan-1  CAI  0.020
 R4G  plan-1  CAH  0.020
 R4G  plan-1  HAJ  0.020
 R4G  plan-1  HAL  0.020
 R4G  plan-1  HAN  0.020
 R4G  plan-2  CAG  0.020
 R4G  plan-2  CAC  0.020
 R4G  plan-2  CAD  0.020
 R4G  plan-2  CAE  0.020
 R4G  plan-2  CAB  0.020
 R4G  plan-2  CAA  0.020
 R4G  plan-2  CAF  0.020
 R4G  plan-2  O1   0.020
 R4G  plan-2  HAD  0.020
 R4G  plan-2  HAB  0.020
 R4G  plan-2  HAE  0.020
 R4G  plan-2  HAA  0.020
 R4G  plan-3  C5   0.020
 R4G  plan-3  C6   0.020
 R4G  plan-3  OBC  0.020
 R4G  plan-3  O6   0.020
 R4G  plan-4  CAI  0.020
 R4G  plan-4  CAH  0.020
 R4G  plan-4  CAG  0.020
 R4G  plan-4  CAC  0.020
 R4G  plan-4  HAH  0.020
 R4G  plan-4  HAG  0.020

