# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 15:53:04 2021
#   Inital geometry file: a 124 line input string
#   Ligand name: (2S,3S,4S,5R,6S)-6-[3-[(E)-2-(4-hydroxyphenyl)ethenyl]-5-oxidanyl-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)Oc2cc(O)cc(/C=C/c3ccc(O)cc3)c2
#
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
 R3X  R3X  '(2S,3S,4S,5R,6S)-6-[3-[(E)-2-(4-hydroxyphenyl)ethenyl]-5-oxidanyl-phenoxy]-3,4,5-tris(oxidanyl)oxane-2-carboxylic acid'  ligand  49  29  .  2021-08-23  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_R3X
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
 R3X  CAB  C  CR16  0  -0.301  22.2688  41.7292  55.0006
 R3X  CAA  C  CR16  0  -0.327  22.3668  41.8210  53.6237
 R3X  CAF  C  CR6   0   0.347  21.8497  42.9345  52.9665
 R3X  OAP  O  OH1   0  -0.627  21.9593  42.9871  51.6268
 R3X  CAE  C  CR16  0  -0.359  21.2428  43.9458  53.7125
 R3X  CAD  C  CR16  0  -0.320  21.1526  43.8393  55.0874
 R3X  CAC  C  CR6   0   0.148  21.6599  42.7274  55.7677
 R3X  CAG  C  C1    0  -0.300  21.5820  42.5583  57.2147
 R3X  CAH  C  C1    0  -0.326  20.9894  43.3873  58.0851
 R3X  CAI  C  CR6   0   0.208  20.9065  43.2041  59.5336
 R3X  CAN  C  CR16  0  -0.481  21.5373  42.1526  60.2013
 R3X  CAJ  C  CR16  0  -0.441  20.1495  44.1204  60.2640
 R3X  CAK  C  CR6   0   0.412  20.0255  43.9849  61.6413
 R3X  OAO  O  OH1   0  -0.633  19.2830  44.8998  62.2926
 R3X  CAL  C  CR16  0  -0.515  20.6608  42.9445  62.3138
 R3X  CAM  C  CR6   0   0.427  21.4091  42.0302  61.5765
 R3X  O1   O  O2    0  -0.495  22.0633  40.9760  62.1332
 R3X  C1   C  CH1   0   0.270  21.7610  40.5804  63.4257
 R3X  C2   C  CH1   0   0.007  22.2175  39.1410  63.6102
 R3X  C3   C  CH1   0  -0.016  21.9985  38.7507  65.0678
 R3X  C4   C  CH1   0   0.001  22.6751  39.7368  66.0176
 R3X  C5   C  CH1   0  -0.083  22.1969  41.1613  65.6520
 R3X  C6   C  C     0   0.504  22.9217  42.2289  66.4434
 R3X  O2   O  OH1   0  -0.665  21.4709  38.3393  62.7377
 R3X  O3   O  OH1   0  -0.666  22.5012  37.4492  65.2265
 R3X  O4   O  OH1   0  -0.660  22.3167  39.3656  67.3193
 R3X  O5   O  O2    0  -0.491  22.4663  41.4195  64.3000
 R3X  O6A  O  OH1   0  -0.587  22.5241  42.2436  67.7061
 R3X  O6B  O  O     0  -0.419  23.7617  42.9560  65.9866
 R3X  HAB  H  HCR6  0   0.256  22.6753  40.8550  55.4951
 R3X  HAA  H  HCR6  0   0.266  22.8423  41.0310  53.0561
 R3X  HAP  H  HOH1  0   0.476  21.5587  43.7948  51.2858
 R3X  HAE  H  HCR6  0   0.275  20.8382  44.8202  53.2156
 R3X  HAD  H  HCR6  0   0.258  20.6768  44.6456  55.6306
 R3X  HAG  H  H     0   0.253  22.0533  41.6523  57.5848
 R3X  HAH  H  H     0   0.250  20.5037  44.2858  57.7176
 R3X  HAN  H  HCR6  0   0.258  22.1273  41.4206  59.6657
 R3X  HAJ  H  HCR6  0   0.259  19.6547  44.9426  59.7612
 R3X  HAO  H  HOH1  0   0.476  19.2514  44.7016  63.2352
 R3X  HAL  H  HCR6  0   0.297  20.5794  42.8829  63.3915
 R3X  H1   H  HCH1  0   0.223  20.6757  40.6527  63.6130
 R3X  H2   H  HCH1  0   0.230  23.2954  39.0911  63.3886
 R3X  H3   H  HCH1  0   0.227  20.9154  38.7807  65.2703
 R3X  HA   H  HOH1  0   0.458  21.7142  37.4201  62.8907
 R3X  H4   H  HCH1  0   0.244  23.7624  39.6878  65.8651
 R3X  HB   H  HOH1  0   0.459  22.1951  37.1024  66.0705
 R3X  H5   H  HCH1  0   0.274  21.1192  41.2336  65.8676
 R3X  HC   H  HOH1  0   0.463  22.9833  39.6750  67.9390
 R3X  H6A  H  HOH1  0   0.490  23.0203  42.9098  68.2065

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
 R3X  CAB  CAA  aromatic  1.383  0.020  1.383
 R3X  CAB  CAC  aromatic  1.398  0.020  1.398
 R3X  CAA  CAF  aromatic  1.393  0.020  1.393
 R3X  CAF  OAP  single    1.345  0.020  1.345
 R3X  CAF  CAE  aromatic  1.396  0.020  1.396
 R3X  CAE  CAD  aromatic  1.382  0.020  1.382
 R3X  CAD  CAC  aromatic  1.399  0.020  1.399
 R3X  CAC  CAG  single    1.459  0.020  1.459
 R3X  CAG  CAH  double    1.340  0.020  1.340
 R3X  CAH  CAI  single    1.462  0.020  1.462
 R3X  CAI  CAN  aromatic  1.396  0.020  1.396
 R3X  CAI  CAJ  aromatic  1.395  0.020  1.395
 R3X  CAN  CAM  aromatic  1.387  0.020  1.387
 R3X  CAJ  CAK  aromatic  1.389  0.020  1.389
 R3X  CAK  OAO  single    1.346  0.020  1.346
 R3X  CAK  CAL  aromatic  1.392  0.020  1.392
 R3X  CAL  CAM  aromatic  1.393  0.020  1.393
 R3X  CAM  O1   single    1.360  0.020  1.360
 R3X  O1   C1   single    1.385  0.020  1.385
 R3X  C1   C2   single    1.521  0.020  1.521
 R3X  C1   O5   single    1.402  0.020  1.402
 R3X  C2   C3   single    1.525  0.020  1.525
 R3X  C2   O2   single    1.400  0.020  1.400
 R3X  C3   C4   single    1.527  0.020  1.527
 R3X  C3   O3   single    1.404  0.020  1.404
 R3X  C4   C5   single    1.546  0.020  1.546
 R3X  C4   O4   single    1.400  0.020  1.400
 R3X  C5   C6   single    1.514  0.020  1.514
 R3X  C5   O5   single    1.402  0.020  1.402
 R3X  C6   O6A  single    1.324  0.020  1.324
 R3X  C6   O6B  double    1.201  0.020  1.201
 R3X  CAB  HAB  single    0.930  0.020  1.080
 R3X  CAA  HAA  single    0.930  0.020  1.080
 R3X  OAP  HAP  single    0.850  0.020  0.980
 R3X  CAE  HAE  single    0.930  0.020  1.080
 R3X  CAD  HAD  single    0.930  0.020  1.080
 R3X  CAG  HAG  single    0.930  0.020  1.080
 R3X  CAH  HAH  single    0.930  0.020  1.080
 R3X  CAN  HAN  single    0.930  0.020  1.080
 R3X  CAJ  HAJ  single    0.930  0.020  1.080
 R3X  OAO  HAO  single    0.850  0.020  0.980
 R3X  CAL  HAL  single    0.930  0.020  1.080
 R3X  C1   H1   single    0.970  0.020  1.090
 R3X  C2   H2   single    0.970  0.020  1.090
 R3X  C3   H3   single    0.970  0.020  1.090
 R3X  O2   HA   single    0.850  0.020  0.980
 R3X  C4   H4   single    0.970  0.020  1.090
 R3X  O3   HB   single    0.850  0.020  0.980
 R3X  C5   H5   single    0.970  0.020  1.090
 R3X  O4   HC   single    0.850  0.020  0.980
 R3X  O6A  H6A  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
 R3X  HAB  CAB  CAC  119.27  3.000
 R3X  HAB  CAB  CAA  118.77  3.000
 R3X  CAC  CAB  CAA  121.96  3.000
 R3X  HAA  CAA  CAF  119.94  3.000
 R3X  HAA  CAA  CAB  120.29  3.000
 R3X  CAF  CAA  CAB  119.77  3.000
 R3X  CAE  CAF  OAP  122.65  3.000
 R3X  CAE  CAF  CAA  119.25  3.000
 R3X  OAP  CAF  CAA  118.10  3.000
 R3X  HAP  OAP  CAF  110.57  3.000
 R3X  HAE  CAE  CAD  119.59  3.000
 R3X  HAE  CAE  CAF  120.12  3.000
 R3X  CAD  CAE  CAF  120.29  3.000
 R3X  HAD  CAD  CAC  120.50  3.000
 R3X  HAD  CAD  CAE  118.07  3.000
 R3X  CAC  CAD  CAE  121.43  3.000
 R3X  CAG  CAC  CAD  123.72  3.000
 R3X  CAG  CAC  CAB  118.98  3.000
 R3X  CAD  CAC  CAB  117.30  3.000
 R3X  HAG  CAG  CAH  119.11  3.000
 R3X  HAG  CAG  CAC  114.29  3.000
 R3X  CAH  CAG  CAC  126.59  3.000
 R3X  HAH  CAH  CAI  114.44  3.000
 R3X  HAH  CAH  CAG  119.34  3.000
 R3X  CAI  CAH  CAG  126.22  3.000
 R3X  CAJ  CAI  CAN  119.30  3.000
 R3X  CAJ  CAI  CAH  117.85  3.000
 R3X  CAN  CAI  CAH  122.85  3.000
 R3X  HAN  CAN  CAM  118.79  3.000
 R3X  HAN  CAN  CAI  121.28  3.000
 R3X  CAM  CAN  CAI  119.94  3.000
 R3X  HAJ  CAJ  CAK  119.56  3.000
 R3X  HAJ  CAJ  CAI  120.22  3.000
 R3X  CAK  CAJ  CAI  120.22  3.000
 R3X  CAL  CAK  OAO  121.72  3.000
 R3X  CAL  CAK  CAJ  120.73  3.000
 R3X  OAO  CAK  CAJ  117.55  3.000
 R3X  HAO  OAO  CAK  110.58  3.000
 R3X  HAL  CAL  CAM  122.01  3.000
 R3X  HAL  CAL  CAK  119.28  3.000
 R3X  CAM  CAL  CAK  118.69  3.000
 R3X  O1   CAM  CAL  123.42  3.000
 R3X  O1   CAM  CAN  115.47  3.000
 R3X  CAL  CAM  CAN  121.11  3.000
 R3X  C1   O1   CAM  119.89  3.000
 R3X  H1   C1   O5   110.46  3.000
 R3X  H1   C1   C2   109.66  3.000
 R3X  O5   C1   C2   109.85  3.000
 R3X  H1   C1   O1   110.75  3.000
 R3X  O5   C1   O1   107.53  3.000
 R3X  C2   C1   O1   108.53  3.000
 R3X  H2   C2   O2   111.75  3.000
 R3X  H2   C2   C3   108.74  3.000
 R3X  O2   C2   C3   111.87  3.000
 R3X  H2   C2   C1   108.18  3.000
 R3X  O2   C2   C1   107.82  3.000
 R3X  C3   C2   C1   108.36  3.000
 R3X  H3   C3   O3   110.87  3.000
 R3X  H3   C3   C4   107.67  3.000
 R3X  O3   C3   C4   111.69  3.000
 R3X  H3   C3   C2   108.04  3.000
 R3X  O3   C3   C2   107.09  3.000
 R3X  C4   C3   C2   111.44  3.000
 R3X  H4   C4   O4   111.74  3.000
 R3X  H4   C4   C5   108.31  3.000
 R3X  O4   C4   C5   112.63  3.000
 R3X  H4   C4   C3   108.86  3.000
 R3X  O4   C4   C3   107.07  3.000
 R3X  C5   C4   C3   108.11  3.000
 R3X  H5   C5   O5   111.38  3.000
 R3X  H5   C5   C6   108.65  3.000
 R3X  O5   C5   C6   106.39  3.000
 R3X  H5   C5   C4   108.47  3.000
 R3X  O5   C5   C4   109.76  3.000
 R3X  C6   C5   C4   112.21  3.000
 R3X  O6B  C6   O6A  124.47  3.000
 R3X  O6B  C6   C5   124.26  3.000
 R3X  O6A  C6   C5   111.27  3.000
 R3X  HA   O2   C2   108.22  3.000
 R3X  HB   O3   C3   108.62  3.000
 R3X  HC   O4   C4   109.66  3.000
 R3X  C5   O5   C1   113.22  3.000
 R3X  H6A  O6A  C6   110.25  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
 R3X  CONST_01  CAE  CAF  CAA  CAB     0.00   0.0  0
 R3X  CONST_02  CAE  CAD  CAC  CAB     0.00   0.0  0
 R3X  CONST_03  CAD  CAC  CAB  CAA     0.00   0.0  0
 R3X  CONST_04  CAD  CAE  CAF  CAA     0.00   0.0  0
 R3X  CONST_05  CAC  CAB  CAA  CAF     0.00   0.0  0
 R3X  CONST_06  CAC  CAD  CAE  CAF     0.00   0.0  0
 R3X  CONST_07  CAL  CAM  CAN  CAI     0.00   0.0  0
 R3X  CONST_08  CAL  CAK  CAJ  CAI     0.00   0.0  0
 R3X  CONST_09  CAK  CAJ  CAI  CAN     0.00   0.0  0
 R3X  CONST_10  CAK  CAL  CAM  CAN     0.00   0.0  0
 R3X  CONST_11  CAM  CAN  CAI  CAJ     0.00   0.0  0
 R3X  CONST_12  CAM  CAL  CAK  CAJ     0.00   0.0  0
 R3X  CONST_13  OAP  CAF  CAA  CAB   180.00   0.0  0
 R3X  CONST_14  CAG  CAC  CAB  CAA   180.00   0.0  0
 R3X  CONST_15  CAD  CAE  CAF  OAP   180.00   0.0  0
 R3X  CONST_16  CAG  CAC  CAD  CAE   180.00   0.0  0
 R3X  CONST_17  CAM  CAN  CAI  CAH   180.00   0.0  0
 R3X  CONST_18  CAK  CAJ  CAI  CAH   180.00   0.0  0
 R3X  CONST_19  O1   CAM  CAN  CAI   180.00   0.0  0
 R3X  CONST_20  OAO  CAK  CAJ  CAI   180.00   0.0  0
 R3X  CONST_21  O1   CAM  CAL  CAK   180.00   0.0  0
 R3X  CONST_22  CAM  CAL  CAK  OAO   180.00   0.0  0
 R3X  CONST_23  HAD  CAD  CAC  CAB   180.00   0.0  0
 R3X  CONST_24  HAE  CAE  CAF  CAA   180.00   0.0  0
 R3X  CONST_25  HAB  CAB  CAA  CAF   180.00   0.0  0
 R3X  CONST_26  HAA  CAA  CAF  CAE   180.00   0.0  0
 R3X  CONST_27  HAJ  CAJ  CAI  CAN   180.00   0.0  0
 R3X  CONST_28  HAL  CAL  CAM  CAN   180.00   0.0  0
 R3X  CONST_29  HAN  CAN  CAI  CAJ   180.00   0.0  0
 R3X  CONST_30  H6A  O6A  C6   C5    180.00   0.0  0
 R3X  Var_01    CAI  CAH  CAG  CAC   179.46   0.0  2
 R3X  Var_02    CAH  CAG  CAC  CAB  -177.17  30.0  2
 R3X  Var_03    CAN  CAI  CAH  CAG     4.63  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
 R3X  chir_01  C1  O1  C2  O5  negativ
 R3X  chir_02  C2  O2  C1  C3  negativ
 R3X  chir_03  C3  O3  C2  C4  positiv
 R3X  chir_04  C4  O4  C3  C5  negativ
 R3X  chir_05  C5  O5  C4  C6  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
 R3X  plan-1  CAB  0.020
 R3X  plan-1  CAA  0.020
 R3X  plan-1  CAF  0.020
 R3X  plan-1  OAP  0.020
 R3X  plan-1  CAE  0.020
 R3X  plan-1  CAD  0.020
 R3X  plan-1  CAC  0.020
 R3X  plan-1  CAG  0.020
 R3X  plan-1  HAB  0.020
 R3X  plan-1  HAA  0.020
 R3X  plan-1  HAE  0.020
 R3X  plan-1  HAD  0.020
 R3X  plan-2  CAH  0.020
 R3X  plan-2  CAI  0.020
 R3X  plan-2  CAN  0.020
 R3X  plan-2  CAJ  0.020
 R3X  plan-2  CAK  0.020
 R3X  plan-2  OAO  0.020
 R3X  plan-2  CAL  0.020
 R3X  plan-2  CAM  0.020
 R3X  plan-2  O1   0.020
 R3X  plan-2  HAN  0.020
 R3X  plan-2  HAJ  0.020
 R3X  plan-2  HAL  0.020
 R3X  plan-3  C5   0.020
 R3X  plan-3  C6   0.020
 R3X  plan-3  O6A  0.020
 R3X  plan-3  O6B  0.020
 R3X  plan-3  H6A  0.020
 R3X  plan-4  CAC  0.020
 R3X  plan-4  CAG  0.020
 R3X  plan-4  CAH  0.020
 R3X  plan-4  CAI  0.020
 R3X  plan-4  HAG  0.020
 R3X  plan-4  HAH  0.020

