# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 13:16:40 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: (2~{R},3~{S},4~{S},5~{R})-2-[2-[3,4-bis(oxidanyl)phenyl]ethoxy]-2,5-bis(hydroxymethyl)oxolane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@](CO)(OCCc2ccc(O)c(O)c2)[C@@H](O)[C@@H]1O
#
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
 9OK  9OK  (2~{R},3~{S},4~{S},5~{R})-2-[2-[3,4-bis(oxidanyl)phenyl]ethoxy]-2,5-bis(hydroxymethyl)oxolane-3,4-diol  D-saccharide  42  22  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9OK
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
 9OK  C4   C  CH1   0  -0.032  -2.3551   0.9791   1.4569
 9OK  C5   C  CH1   0  -0.009  -2.6427   1.6145   0.0958
 9OK  C6   C  CH2   0  -0.157  -1.7397   2.7793  -0.2255
 9OK  CAF  C  CR16  0  -0.419   2.8754  -0.0383  -0.9517
 9OK  CAJ  C  CR6   0   0.272   4.0915   0.4816  -0.5405
 9OK  OAC  O  OH1   0  -0.646   4.6902   1.5499  -1.1176
 9OK  CAI  C  CR6   0   0.275   4.7770  -0.1067   0.5305
 9OK  OAB  O  OH1   0  -0.637   5.9680   0.3674   0.9588
 9OK  CAD  C  CR16  0  -0.329   4.2183  -1.2052   1.1630
 9OK  CAE  C  CR16  0  -0.323   2.9965  -1.7193   0.7436
 9OK  CAK  C  CR6   0   0.095   2.3111  -1.1462  -0.3190
 9OK  CAH  C  CH2   0  -0.539   0.9661  -1.6622  -0.7500
 9OK  CAG  C  CH2   0  -0.150  -0.1455  -0.8932  -0.0499
 9OK  OAA  O  O2    0  -0.494  -1.3841  -1.4237  -0.4782
 9OK  C2   C  CT    0   0.478  -2.5502  -0.7034  -0.2560
 9OK  C1   C  CH2   0  -0.168  -3.6733  -1.5077  -0.8967
 9OK  O1   O  OH1   0  -0.668  -3.3786  -1.7422  -2.2474
 9OK  O5   O  O2    0  -0.509  -2.4613   0.5711  -0.8528
 9OK  O6   O  OH1   0  -0.668  -2.1244   3.3414  -1.4555
 9OK  O4   O  OH1   0  -0.663  -3.0225   1.5849   2.5316
 9OK  C3   C  CH1   0  -0.043  -2.8733  -0.4309   1.2292
 9OK  O3   O  OH1   0  -0.654  -2.3464  -1.4311   2.0475
 9OK  H1   H  HCH1  0   0.234  -1.2714   0.9525   1.6368
 9OK  H2   H  HCH1  0   0.231  -3.6888   1.9541   0.0808
 9OK  H3   H  HCH2  0   0.201  -1.8207   3.5036   0.5970
 9OK  H4   H  HCH2  0   0.199  -0.6972   2.4313  -0.2412
 9OK  H6   H  HOH1  0   0.481   4.1510   1.8992  -1.8356
 9OK  H7   H  HOH1  0   0.471   6.2436   1.1210   0.4242
 9OK  H8   H  HCR6  0   0.261   4.7506  -1.6618   1.9886
 9OK  H9   H  HCR6  0   0.246   2.5811  -2.5790   1.2554
 9OK  H10  H  HCH2  0   0.246   0.8490  -1.5608  -1.8317
 9OK  H11  H  HCH2  0   0.249   0.8803  -2.7251  -0.5121
 9OK  H12  H  HCH2  0   0.214  -0.0277  -0.9873   1.0346
 9OK  H13  H  HCH2  0   0.210  -0.0493   0.1681  -0.3034
 9OK  H14  H  HCH2  0   0.204  -3.7990  -2.4422  -0.3315
 9OK  H15  H  HCH2  0   0.206  -4.6017  -0.9360  -0.7741
 9OK  H16  H  HOH1  0   0.458  -4.1640  -2.1113  -2.6608
 9OK  H17  H  HOH1  0   0.458  -1.5212   4.0621  -1.6575
 9OK  H18  H  HOH1  0   0.459  -2.5132   2.3459   2.8256
 9OK  H19  H  HCH1  0   0.235  -3.9705  -0.3823   1.3278
 9OK  H20  H  HOH1  0   0.459  -2.6595  -1.2785   2.9448
 9OK  H5   H  HCR6  0   0.266   2.3557   0.4255  -1.7846

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
 9OK  O6   C6   single    1.406  0.020  1.406
 9OK  O4   C4   single    1.403  0.020  1.403
 9OK  C5   C6   single    1.508  0.020  1.508
 9OK  C5   C4   single    1.529  0.020  1.529
 9OK  C5   O5   single    1.422  0.020  1.422
 9OK  C4   C3   single    1.519  0.020  1.519
 9OK  O5   C2   single    1.410  0.020  1.410
 9OK  C3   C2   single    1.544  0.020  1.544
 9OK  C3   O3   single    1.396  0.020  1.396
 9OK  C1   C2   single    1.523  0.020  1.523
 9OK  C1   O1   single    1.402  0.020  1.402
 9OK  C2   OAA  single    1.389  0.020  1.389
 9OK  OAA  CAG  single    1.414  0.020  1.414
 9OK  CAG  CAH  single    1.522  0.020  1.522
 9OK  CAH  CAK  single    1.504  0.020  1.504
 9OK  CAE  CAK  aromatic  1.388  0.020  1.388
 9OK  CAE  CAD  aromatic  1.390  0.020  1.390
 9OK  CAK  CAF  aromatic  1.395  0.020  1.395
 9OK  CAD  CAI  aromatic  1.385  0.020  1.385
 9OK  CAF  CAJ  aromatic  1.385  0.020  1.385
 9OK  CAI  CAJ  aromatic  1.401  0.020  1.401
 9OK  CAI  OAB  single    1.352  0.020  1.352
 9OK  CAJ  OAC  single    1.354  0.020  1.354
 9OK  C4   H1   single    0.970  0.020  1.090
 9OK  C5   H2   single    0.970  0.020  1.090
 9OK  C6   H3   single    0.970  0.020  1.090
 9OK  C6   H4   single    0.970  0.020  1.090
 9OK  CAF  H5   single    0.930  0.020  1.080
 9OK  OAC  H6   single    0.850  0.020  0.980
 9OK  OAB  H7   single    0.850  0.020  0.980
 9OK  CAD  H8   single    0.930  0.020  1.080
 9OK  CAE  H9   single    0.930  0.020  1.080
 9OK  CAH  H10  single    0.970  0.020  1.090
 9OK  CAH  H11  single    0.970  0.020  1.090
 9OK  CAG  H12  single    0.970  0.020  1.090
 9OK  CAG  H13  single    0.970  0.020  1.090
 9OK  C1   H14  single    0.970  0.020  1.090
 9OK  C1   H15  single    0.970  0.020  1.090
 9OK  O1   H16  single    0.850  0.020  0.980
 9OK  O6   H17  single    0.850  0.020  0.980
 9OK  O4   H18  single    0.850  0.020  0.980
 9OK  C3   H19  single    0.970  0.020  1.090
 9OK  O3   H20  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
 9OK  H1   C4   C3   109.78  3.000
 9OK  H1   C4   O4   110.75  3.000
 9OK  C3   C4   O4   110.70  3.000
 9OK  H1   C4   C5   109.95  3.000
 9OK  C3   C4   C5   100.83  3.000
 9OK  O4   C4   C5   114.40  3.000
 9OK  H2   C5   O5   109.81  3.000
 9OK  H2   C5   C6   109.15  3.000
 9OK  O5   C5   C6   110.37  3.000
 9OK  H2   C5   C4   108.61  3.000
 9OK  O5   C5   C4   105.36  3.000
 9OK  C6   C5   C4   113.44  3.000
 9OK  H4   C6   H3   106.81  3.000
 9OK  H4   C6   O6   111.94  3.000
 9OK  H3   C6   O6   111.78  3.000
 9OK  H4   C6   C5   109.05  3.000
 9OK  H3   C6   C5   107.78  3.000
 9OK  O6   C6   C5   109.34  3.000
 9OK  H5   CAF  CAK  119.57  3.000
 9OK  H5   CAF  CAJ  119.18  3.000
 9OK  CAK  CAF  CAJ  121.24  3.000
 9OK  CAI  CAJ  OAC  116.16  3.000
 9OK  OAC  CAJ  CAF  123.92  3.000
 9OK  CAI  CAJ  CAF  119.92  3.000
 9OK  H6   OAC  CAJ  110.87  3.000
 9OK  CAD  CAI  OAB  119.27  3.000
 9OK  OAB  CAI  CAJ  121.74  3.000
 9OK  CAD  CAI  CAJ  118.99  3.000
 9OK  H7   OAB  CAI  110.51  3.000
 9OK  H8   CAD  CAE  120.39  3.000
 9OK  H8   CAD  CAI  118.95  3.000
 9OK  CAE  CAD  CAI  120.66  3.000
 9OK  H9   CAE  CAK  119.99  3.000
 9OK  H9   CAE  CAD  119.20  3.000
 9OK  CAK  CAE  CAD  120.80  3.000
 9OK  CAH  CAK  CAE  121.29  3.000
 9OK  CAE  CAK  CAF  118.37  3.000
 9OK  CAH  CAK  CAF  120.29  3.000
 9OK  H11  CAH  H10  107.30  3.000
 9OK  H11  CAH  CAG  109.51  3.000
 9OK  H10  CAH  CAG  109.27  3.000
 9OK  H11  CAH  CAK  109.99  3.000
 9OK  H10  CAH  CAK  110.35  3.000
 9OK  CAG  CAH  CAK  110.37  3.000
 9OK  H13  CAG  H12  107.64  3.000
 9OK  H13  CAG  OAA  111.74  3.000
 9OK  H12  CAG  OAA  111.22  3.000
 9OK  H13  CAG  CAH  108.60  3.000
 9OK  H12  CAG  CAH  109.49  3.000
 9OK  OAA  CAG  CAH  108.11  3.000
 9OK  C2   OAA  CAG  119.51  3.000
 9OK  C3   C2   O5   105.12  3.000
 9OK  C3   C2   C1   110.09  3.000
 9OK  O5   C2   C1   110.23  3.000
 9OK  C1   C2   OAA  106.15  3.000
 9OK  C3   C2   OAA  114.91  3.000
 9OK  O5   C2   OAA  110.37  3.000
 9OK  H15  C1   H14  106.78  3.000
 9OK  H15  C1   O1   111.88  3.000
 9OK  H14  C1   O1   112.15  3.000
 9OK  H15  C1   C2   107.57  3.000
 9OK  H14  C1   C2   108.48  3.000
 9OK  O1   C1   C2   109.80  3.000
 9OK  H16  O1   C1   107.87  3.000
 9OK  C2   O5   C5   111.89  3.000
 9OK  H17  O6   C6   108.17  3.000
 9OK  H18  O4   C4   108.91  3.000
 9OK  H19  C3   O3   110.78  3.000
 9OK  H19  C3   C2   107.58  3.000
 9OK  O3   C3   C2   111.01  3.000
 9OK  H19  C3   C4   106.56  3.000
 9OK  O3   C3   C4   116.64  3.000
 9OK  C2   C3   C4   103.68  3.000
 9OK  H20  O3   C3   108.07  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
 9OK  CONST_01  CAD  CAE  CAK  CAF     0.00   0.0  0
 9OK  CONST_02  CAD  CAI  CAJ  CAF     0.00   0.0  0
 9OK  CONST_03  CAE  CAK  CAF  CAJ     0.00   0.0  0
 9OK  CONST_04  CAE  CAD  CAI  CAJ     0.00   0.0  0
 9OK  CONST_05  CAK  CAE  CAD  CAI     0.00   0.0  0
 9OK  CONST_06  CAK  CAF  CAJ  CAI     0.00   0.0  0
 9OK  CONST_07  OAB  CAI  CAJ  CAF   180.00   0.0  0
 9OK  CONST_08  CAH  CAK  CAF  CAJ   180.00   0.0  0
 9OK  CONST_09  CAK  CAF  CAJ  OAC   180.00   0.0  0
 9OK  CONST_10  CAD  CAI  CAJ  OAC   180.00   0.0  0
 9OK  CONST_11  CAE  CAD  CAI  OAB   180.00   0.0  0
 9OK  CONST_12  CAH  CAK  CAE  CAD   180.00   0.0  0
 9OK  CONST_13  H9   CAE  CAK  CAF   180.00   0.0  0
 9OK  CONST_14  H8   CAD  CAI  CAJ   180.00   0.0  0
 9OK  CONST_15  H5   CAF  CAJ  CAI   180.00   0.0  0
 9OK  Var_01    CAG  CAH  CAK  CAF   -84.84  30.0  2
 9OK  Var_02    OAA  CAG  CAH  CAK  -179.44  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
 9OK  chir_01  C4  O4  C5  C3  positiv
 9OK  chir_02  C5  O5  C4  C6  negativ
 9OK  chir_03  C2  O5  C3  C1  negativ
 9OK  chir_04  C3  O3  C2  C4  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
 9OK  plan-1  CAF  0.020
 9OK  plan-1  CAJ  0.020
 9OK  plan-1  OAC  0.020
 9OK  plan-1  CAI  0.020
 9OK  plan-1  OAB  0.020
 9OK  plan-1  CAD  0.020
 9OK  plan-1  CAE  0.020
 9OK  plan-1  CAK  0.020
 9OK  plan-1  CAH  0.020
 9OK  plan-1  H8   0.020
 9OK  plan-1  H9   0.020
 9OK  plan-1  H5   0.020

