# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 14:02:51 2021
#   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  49  29  .  2021-08-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.440  20.4913  43.6540  54.7454
 R4G  CAK  C  CR6   0   0.392  20.8167  43.8082  53.3992
 R4G  OAP  O  OH1   0  -0.633  19.9701  44.5236  52.6347
 R4G  CAL  C  CR16  0  -0.487  21.9734  43.2390  52.8853
 R4G  CAM  C  CR6   0   0.415  22.8074  42.5099  53.7329
 R4G  OAO  O  OH1   0  -0.634  23.9145  41.9751  53.1830
 R4G  CAN  C  CR16  0  -0.519  22.4951  42.3520  55.0751
 R4G  CAI  C  CR6   0   0.206  21.3280  42.9271  55.5890
 R4G  CAH  C  C1    0  -0.316  20.9362  42.8000  56.9924
 R4G  CAG  C  C1    0  -0.305  21.6153  42.1545  57.9495
 R4G  CAC  C  CR6   0   0.167  21.2273  42.0286  59.3519
 R4G  CAD  C  CR16  0  -0.311  22.0565  41.3119  60.2180
 R4G  CAE  C  CR16  0  -0.313  21.7475  41.1664  61.5604
 R4G  CAB  C  CR16  0  -0.328  20.0605  42.5869  59.8849
 R4G  CAA  C  CR16  0  -0.291  19.7349  42.4419  61.2214
 R4G  CAF  C  CR6   0   0.309  20.5834  41.7283  62.0656
 R4G  O1   O  O2    0  -0.508  20.2909  41.5112  63.3855
 R4G  C1   C  CH1   0   0.267  20.2387  42.5934  64.2576
 R4G  O5   O  O2    0  -0.490  19.0036  43.2390  64.0715
 R4G  C5   C  CH1   0  -0.055  18.7656  44.2783  64.9810
 R4G  C6   C  C     0   0.511  17.3855  44.8226  64.6677
 R4G  OBC  O  OH1   0  -0.580  16.7814  45.2831  65.7484
 R4G  O6   O  O     0  -0.423  16.9190  44.8462  63.5601
 R4G  C4   C  CH1   0   0.023  19.8194  45.3807  64.8178
 R4G  O4   O  OH1   0  -0.663  19.5307  46.3966  65.7361
 R4G  C3   C  CH1   0  -0.013  21.1914  44.7577  65.0419
 R4G  O3   O  OH1   0  -0.668  22.1540  45.7613  64.8381
 R4G  C2   C  CH1   0  -0.052  21.3879  43.5866  64.0818
 R4G  O2   O  OH1   0  -0.667  22.5983  42.9231  64.3494
 R4G  HAJ  H  HCR6  0   0.258  19.5838  44.1027  55.1307
 R4G  HAP  H  HOH1  0   0.476  20.2848  44.5578  51.7245
 R4G  HAL  H  HCR6  0   0.277  22.2354  43.3534  51.8392
 R4G  HAO  H  HOH1  0   0.475  24.4194  41.4925  53.8471
 R4G  HAN  H  HCR6  0   0.265  23.1592  41.7795  55.7116
 R4G  HAH  H  H     0   0.253  20.0005  43.2893  57.2438
 R4G  HAG  H  H     0   0.254  22.5517  41.6660  57.6982
 R4G  HAD  H  HCR6  0   0.259  22.9681  40.8675  59.8370
 R4G  HAB  H  HCR6  0   0.259  19.3832  43.1471  59.2533
 R4G  HAE  H  HCR6  0   0.269  22.4051  40.6092  62.2151
 R4G  HAA  H  HCR6  0   0.278  18.8210  42.8788  61.5992
 R4G  H1   H  HCH1  0   0.246  20.2840  42.1529  65.2640
 R4G  H2   H  HCH1  0   0.249  21.3650  43.9839  63.0582
 R4G  H5   H  HCH1  0   0.266  18.7922  43.9107  66.0174
 R4G  H4   H  HCH1  0   0.230  19.7666  45.7492  63.7812
 R4G  HBC  H  HOH1  0   0.488  15.9254  45.6734  65.5134
 R4G  HA   H  HOH1  0   0.459  20.2071  47.0772  65.6515
 R4G  H3   H  HCH1  0   0.225  21.2333  44.3801  66.0757
 R4G  HB   H  HOH1  0   0.460  22.9875  45.4708  65.2211
 R4G  HC   H  HOH1  0   0.465  23.2098  43.0754  63.6250

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    1.463  0.020  1.463
 R4G  CAH  CAG  double    1.339  0.020  1.339
 R4G  CAG  CAC  single    1.461  0.020  1.461
 R4G  CAC  CAD  aromatic  1.397  0.020  1.397
 R4G  CAC  CAB  aromatic  1.399  0.020  1.399
 R4G  CAD  CAE  aromatic  1.385  0.020  1.385
 R4G  CAE  CAF  aromatic  1.388  0.020  1.388
 R4G  CAB  CAA  aromatic  1.383  0.020  1.383
 R4G  CAA  CAF  aromatic  1.394  0.020  1.394
 R4G  CAF  O1   single    1.369  0.020  1.369
 R4G  O1   C1   single    1.391  0.020  1.391
 R4G  C1   O5   single    1.406  0.020  1.406
 R4G  C1   C2   single    1.529  0.020  1.529
 R4G  O5   C5   single    1.401  0.020  1.401
 R4G  C5   C6   single    1.516  0.020  1.516
 R4G  C5   C4   single    1.534  0.020  1.534
 R4G  C6   OBC  single    1.321  0.020  1.321
 R4G  C6   O6   double    1.202  0.020  1.202
 R4G  C4   O4   single    1.400  0.020  1.400
 R4G  C4   C3   single    1.523  0.020  1.523
 R4G  C3   O3   single    1.405  0.020  1.405
 R4G  C3   C2   single    1.527  0.020  1.527
 R4G  C2   O2   single    1.406  0.020  1.406
 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  OBC  HBC  single    0.850  0.020  0.980
 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  119.57  3.000
 R4G  CAI  CAJ  CAK  120.17  3.000
 R4G  CAL  CAK  OAP  122.12  3.000
 R4G  CAL  CAK  CAJ  120.46  3.000
 R4G  OAP  CAK  CAJ  117.42  3.000
 R4G  HAP  OAP  CAK  110.47  3.000
 R4G  HAL  CAL  CAM  119.79  3.000
 R4G  HAL  CAL  CAK  121.02  3.000
 R4G  CAM  CAL  CAK  119.19  3.000
 R4G  CAN  CAM  OAO  122.34  3.000
 R4G  CAN  CAM  CAL  120.86  3.000
 R4G  OAO  CAM  CAL  116.81  3.000
 R4G  HAO  OAO  CAM  110.38  3.000
 R4G  HAN  CAN  CAI  120.85  3.000
 R4G  HAN  CAN  CAM  119.38  3.000
 R4G  CAI  CAN  CAM  119.77  3.000
 R4G  CAH  CAI  CAN  122.70  3.000
 R4G  CAH  CAI  CAJ  117.75  3.000
 R4G  CAN  CAI  CAJ  119.55  3.000
 R4G  HAH  CAH  CAG  119.26  3.000
 R4G  HAH  CAH  CAI  114.46  3.000
 R4G  CAG  CAH  CAI  126.28  3.000
 R4G  HAG  CAG  CAC  114.37  3.000
 R4G  HAG  CAG  CAH  119.26  3.000
 R4G  CAC  CAG  CAH  126.37  3.000
 R4G  CAB  CAC  CAD  117.62  3.000
 R4G  CAB  CAC  CAG  123.57  3.000
 R4G  CAD  CAC  CAG  118.81  3.000
 R4G  HAD  CAD  CAE  119.05  3.000
 R4G  HAD  CAD  CAC  119.46  3.000
 R4G  CAE  CAD  CAC  121.49  3.000
 R4G  HAE  CAE  CAF  119.86  3.000
 R4G  HAE  CAE  CAD  120.32  3.000
 R4G  CAF  CAE  CAD  119.83  3.000
 R4G  HAB  CAB  CAA  118.08  3.000
 R4G  HAB  CAB  CAC  120.41  3.000
 R4G  CAA  CAB  CAC  121.51  3.000
 R4G  HAA  CAA  CAF  120.66  3.000
 R4G  HAA  CAA  CAB  119.62  3.000
 R4G  CAF  CAA  CAB  119.72  3.000
 R4G  O1   CAF  CAA  122.35  3.000
 R4G  O1   CAF  CAE  117.77  3.000
 R4G  CAA  CAF  CAE  119.84  3.000
 R4G  C1   O1   CAF  119.27  3.000
 R4G  H1   C1   C2   109.55  3.000
 R4G  H1   C1   O5   109.95  3.000
 R4G  C2   C1   O5   110.29  3.000
 R4G  H1   C1   O1   105.10  3.000
 R4G  C2   C1   O1   113.90  3.000
 R4G  O5   C1   O1   107.89  3.000
 R4G  C5   O5   C1   113.81  3.000
 R4G  H5   C5   C4   108.90  3.000
 R4G  H5   C5   C6   109.67  3.000
 R4G  C4   C5   C6   110.20  3.000
 R4G  H5   C5   O5   111.07  3.000
 R4G  C4   C5   O5   110.32  3.000
 R4G  C6   C5   O5   106.66  3.000
 R4G  O6   C6   OBC  124.71  3.000
 R4G  O6   C6   C5   123.42  3.000
 R4G  OBC  C6   C5   111.86  3.000
 R4G  HBC  OBC  C6   110.23  3.000
 R4G  H4   C4   C3   108.57  3.000
 R4G  H4   C4   O4   111.39  3.000
 R4G  C3   C4   O4   112.71  3.000
 R4G  H4   C4   C5   107.92  3.000
 R4G  C3   C4   C5   108.01  3.000
 R4G  O4   C4   C5   108.07  3.000
 R4G  HA   O4   C4   108.09  3.000
 R4G  H3   C3   C2   108.80  3.000
 R4G  H3   C3   O3   110.79  3.000
 R4G  C2   C3   O3   111.61  3.000
 R4G  H3   C3   C4   108.21  3.000
 R4G  C2   C3   C4   109.69  3.000
 R4G  O3   C3   C4   107.67  3.000
 R4G  HB   O3   C3   108.66  3.000
 R4G  H2   C2   O2   111.47  3.000
 R4G  H2   C2   C3   107.81  3.000
 R4G  O2   C2   C3   110.67  3.000
 R4G  H2   C2   C1   109.06  3.000
 R4G  O2   C2   C1   108.58  3.000
 R4G  C3   C2   C1   109.22  3.000
 R4G  HC   O2   C2   109.26  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  CONST_30  HBC  OBC  C6   C5    180.00   0.0  0
 R4G  Var_01    CAC  CAG  CAH  CAI   179.87   0.0  2
 R4G  Var_02    CAG  CAH  CAI  CAJ  -179.32  30.0  2
 R4G  Var_03    CAD  CAC  CAG  CAH   179.79  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-3  HBC  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

