# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun 21 22:48:27 2020
#   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  48  29  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.318   -6.7721  -0.9729   0.1214
 R3X  CAA  C  CR16   0  -0.381   -8.0957  -0.5602   0.1614
 R3X  CAF  C  CR6    0   0.284   -8.3996   0.7929   0.0920
 R3X  OAP  O  OH1    0  -0.661   -9.6845   1.2608   0.0934
 R3X  CAE  C  CR16   0  -0.324   -7.3689   1.7222  -0.0049
 R3X  CAD  C  CR16   0  -0.305   -6.0538   1.2937  -0.0518
 R3X  CAC  C  CR6    0   0.184   -5.7144  -0.0653   0.0117
 R3X  CAG  C  C1     0  -0.295   -4.3521  -0.5703  -0.0528
 R3X  CAH  C  C1     0  -0.254   -3.2292   0.1597   0.0168
 R3X  CAI  C  CR6    0   0.212   -1.8688  -0.3481  -0.0899
 R3X  CAN  C  CR16   0  -0.420   -0.8241   0.4910   0.2948
 R3X  CAJ  C  CR16   0  -0.423   -1.5986  -1.6283  -0.5774
 R3X  CAK  C  CR6    0   0.455   -0.2832  -2.0590  -0.6502
 R3X  OAO  O  OH1    0  -0.620   -0.0348  -3.2931  -1.1182
 R3X  CAL  C  CR16   0  -0.520    0.7636  -1.2356  -0.2455
 R3X  CAM  C  CR6    0   0.389    0.4928   0.0444   0.2242
 R3X  O1   O  O2     0  -0.516    1.4504   0.9098   0.6448
 R3X  C1   C  CH1    0   0.306    2.7033   0.8559   0.0067
 R3X  C2   C  CH1    0  -0.039    3.6072   1.9545   0.5488
 R3X  C3   C  CH1    0   0.025    5.0016   1.8208  -0.0837
 R3X  C4   C  CH1    0   0.075    5.5350   0.3915   0.0251
 R3X  C5   C  CH1    0  -0.178    4.4520  -0.5499  -0.5052
 R3X  C6   C  C      0   0.489    4.8032  -2.0590  -0.5320
 R3X  O2   O  OH1    0  -0.649    3.1308   3.2502   0.2572
 R3X  O3   O  OH1    0  -0.630    5.8986   2.7107   0.5261
 R3X  O4   O  OH1    0  -0.667    6.7092   0.2669  -0.7110
 R3X  O5   O  O2     0  -0.470    3.2908  -0.3591   0.2740
 R3X  O6A  O  OC    -1  -0.563    6.0216  -2.3050  -0.6476
 R3X  O6B  O  O      0  -0.544    3.8462  -2.8407  -0.4907
 R3X  HAB  H  HCR6   0   0.259   -6.5574  -2.0336   0.1762
 R3X  HAA  H  HCR6   0   0.247   -8.8882  -1.2978   0.2418
 R3X  HAP  H  HOH1   0   0.449  -10.2881   0.5426   0.3086
 R3X  HAE  H  HCR6   0   0.253   -7.5935   2.7803  -0.0749
 R3X  HAD  H  HCR6   0   0.248   -5.2758   2.0384  -0.1543
 R3X  HAG  H  H      0   0.221   -4.2673  -1.6469  -0.1527
 R3X  HAH  H  H      0   0.207   -3.3039   1.2310   0.1804
 R3X  HAN  H  HCR6   0   0.208   -1.0291   1.4900   0.6596
 R3X  HAJ  H  HCR6   0   0.207   -2.3883  -2.2842  -0.9192
 R3X  HAO  H  HOH1   0   0.467    0.9171  -3.4577  -1.1042
 R3X  HAL  H  HCR6   0   0.378    1.7775  -1.6219  -0.2770
 R3X  H1   H  HCH1   0   0.171    2.5525   0.9907  -1.0823
 R3X  H2   H  HCH1   0   0.209    3.7069   1.7987   1.6337
 R3X  H3   H  HCH1   0   0.180    4.8986   2.0409  -1.1611
 R3X  HA   H  HOH1   0   0.423    2.3471   3.4040   0.7888
 R3X  H4   H  HCH1   0   0.179    5.6908   0.1613   1.0938
 R3X  HB   H  HOH1   0   0.417    5.5610   3.5996   0.3911
 R3X  H5   H  HCH1   0   0.194    4.2486  -0.2667  -1.5559
 R3X  HC   H  HOH1   0   0.440    6.8124  -0.7087  -0.7856

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  1.387  0.020  1.387
 R3X  CAB  CAC  aromatic  1.398  0.020  1.398
 R3X  CAA  CAF  aromatic  1.389  0.020  1.389
 R3X  CAF  OAP  single    1.367  0.020  1.367
 R3X  CAF  CAE  aromatic  1.391  0.020  1.391
 R3X  CAE  CAD  aromatic  1.384  0.020  1.384
 R3X  CAD  CAC  aromatic  1.402  0.020  1.402
 R3X  CAC  CAG  single    1.454  0.020  1.454
 R3X  CAG  CAH  double    1.341  0.020  1.341
 R3X  CAH  CAI  single    1.456  0.020  1.456
 R3X  CAI  CAN  aromatic  1.394  0.020  1.394
 R3X  CAI  CAJ  aromatic  1.396  0.020  1.396
 R3X  CAN  CAM  aromatic  1.392  0.020  1.392
 R3X  CAJ  CAK  aromatic  1.386  0.020  1.386
 R3X  CAK  OAO  single    1.343  0.020  1.343
 R3X  CAK  CAL  aromatic  1.392  0.020  1.392
 R3X  CAL  CAM  aromatic  1.390  0.020  1.390
 R3X  CAM  O1   single    1.358  0.020  1.358
 R3X  O1   C1   single    1.407  0.020  1.407
 R3X  C1   C2   single    1.522  0.020  1.522
 R3X  C1   O5   single    1.376  0.020  1.376
 R3X  C2   C3   single    1.537  0.020  1.537
 R3X  C2   O2   single    1.411  0.020  1.411
 R3X  C3   C4   single    1.529  0.020  1.529
 R3X  C3   O3   single    1.403  0.020  1.403
 R3X  C4   C5   single    1.530  0.020  1.530
 R3X  C4   O4   single    1.391  0.020  1.391
 R3X  C5   C6   single    1.550  0.020  1.550
 R3X  C5   O5   single    1.411  0.020  1.411
 R3X  C6   O6A  deloc     1.248  0.020  1.248
 R3X  C6   O6B  deloc     1.236  0.020  1.236
 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

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  119.31  3.000
 R3X  HAB  CAB  CAA  118.61  3.000
 R3X  CAC  CAB  CAA  122.08  3.000
 R3X  HAA  CAA  CAF  120.39  3.000
 R3X  HAA  CAA  CAB  119.78  3.000
 R3X  CAF  CAA  CAB  119.83  3.000
 R3X  CAE  CAF  OAP  117.88  3.000
 R3X  CAE  CAF  CAA  119.49  3.000
 R3X  OAP  CAF  CAA  122.62  3.000
 R3X  HAP  OAP  CAF  109.52  3.000
 R3X  HAE  CAE  CAD  119.80  3.000
 R3X  HAE  CAE  CAF  120.20  3.000
 R3X  CAD  CAE  CAF  119.97  3.000
 R3X  HAD  CAD  CAC  119.82  3.000
 R3X  HAD  CAD  CAE  118.26  3.000
 R3X  CAC  CAD  CAE  121.91  3.000
 R3X  CAG  CAC  CAD  124.15  3.000
 R3X  CAG  CAC  CAB  119.13  3.000
 R3X  CAD  CAC  CAB  116.72  3.000
 R3X  HAG  CAG  CAH  118.66  3.000
 R3X  HAG  CAG  CAC  114.97  3.000
 R3X  CAH  CAG  CAC  126.37  3.000
 R3X  HAH  CAH  CAI  114.79  3.000
 R3X  HAH  CAH  CAG  119.14  3.000
 R3X  CAI  CAH  CAG  126.06  3.000
 R3X  CAJ  CAI  CAN  120.22  3.000
 R3X  CAJ  CAI  CAH  121.75  3.000
 R3X  CAN  CAI  CAH  118.03  3.000
 R3X  HAN  CAN  CAM  119.47  3.000
 R3X  HAN  CAN  CAI  120.42  3.000
 R3X  CAM  CAN  CAI  120.11  3.000
 R3X  HAJ  CAJ  CAK  119.19  3.000
 R3X  HAJ  CAJ  CAI  121.66  3.000
 R3X  CAK  CAJ  CAI  119.14  3.000
 R3X  CAL  CAK  OAO  120.38  3.000
 R3X  CAL  CAK  CAJ  120.97  3.000
 R3X  OAO  CAK  CAJ  118.65  3.000
 R3X  HAO  OAO  CAK  109.50  3.000
 R3X  HAL  CAL  CAM  121.29  3.000
 R3X  HAL  CAL  CAK  118.91  3.000
 R3X  CAM  CAL  CAK  119.77  3.000
 R3X  O1   CAM  CAL  123.66  3.000
 R3X  O1   CAM  CAN  116.55  3.000
 R3X  CAL  CAM  CAN  119.78  3.000
 R3X  C1   O1   CAM  117.59  3.000
 R3X  H1   C1   O5   110.90  3.000
 R3X  H1   C1   C2   110.06  3.000
 R3X  O5   C1   C2   108.33  3.000
 R3X  H1   C1   O1   108.66  3.000
 R3X  O5   C1   O1   109.03  3.000
 R3X  C2   C1   O1   109.85  3.000
 R3X  H2   C2   O2   111.36  3.000
 R3X  H2   C2   C3   108.13  3.000
 R3X  O2   C2   C3   107.52  3.000
 R3X  H2   C2   C1   107.62  3.000
 R3X  O2   C2   C1   112.87  3.000
 R3X  C3   C2   C1   109.23  3.000
 R3X  H3   C3   O3   110.93  3.000
 R3X  H3   C3   C4   106.74  3.000
 R3X  O3   C3   C4   109.81  3.000
 R3X  H3   C3   C2   107.43  3.000
 R3X  O3   C3   C2   110.24  3.000
 R3X  C4   C3   C2   111.61  3.000
 R3X  H4   C4   O4   111.98  3.000
 R3X  H4   C4   C5   107.88  3.000
 R3X  O4   C4   C5   111.03  3.000
 R3X  H4   C4   C3   108.23  3.000
 R3X  O4   C4   C3   109.90  3.000
 R3X  C5   C4   C3   107.67  3.000
 R3X  H5   C5   O5   109.77  3.000
 R3X  H5   C5   C6   105.92  3.000
 R3X  O5   C5   C6   109.13  3.000
 R3X  H5   C5   C4   107.56  3.000
 R3X  O5   C5   C4   107.93  3.000
 R3X  C6   C5   C4   116.41  3.000
 R3X  O6B  C6   O6A  129.35  3.000
 R3X  O6B  C6   C5   116.08  3.000
 R3X  O6A  C6   C5   114.50  3.000
 R3X  HA   O2   C2   107.97  3.000
 R3X  HB   O3   C3   107.53  3.000
 R3X  HC   O4   C4   102.56  3.000
 R3X  C5   O5   C1   111.31  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  Var_01    CAI  CAH  CAG  CAC  -177.97   0.0  2
 R3X  Var_02    CAH  CAG  CAC  CAB  -170.68  30.0  2
 R3X  Var_03    CAN  CAI  CAH  CAG  -166.12  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-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

