# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 04:29:56 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: (2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-(4-oxidanylphenoxy)oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](Oc2ccc(O)cc2)[C@H](O)[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
 7OQ  7OQ  "(2R,3S,4S,5R,6S)-2-(hydroxymethyl)-6-(4-oxidanylphenoxy)oxane-3,4,5-triol"
  ligand  35  19  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_7OQ
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
 7OQ  O7   O  OH1   0  -0.635  20.2216  -39.2669  42.4157
 7OQ  C12  C  CR6   0   0.337  20.0217  -38.4656  41.3458
 7OQ  C10  C  CR16  0  -0.327  20.4564  -38.9090  40.1022
 7OQ  C8   C  CR16  0  -0.341  20.2911  -38.1239  38.9685
 7OQ  C11  C  CR16  0  -0.366  19.4072  -37.2196  41.4385
 7OQ  C9   C  CR16  0  -0.329  19.2300  -36.4406  40.3070
 7OQ  C7   C  CR6   0   0.345  19.6706  -36.8833  39.0654
 7OQ  O4   O  O2    0  -0.503  19.4619  -36.0340  38.0181
 7OQ  C5   C  CH1   0   0.274  19.5558  -36.5007  36.7148
 7OQ  O1   O  O2    0  -0.498  20.9071  -36.5144  36.3545
 7OQ  C3   C  CH1   0  -0.031  18.7800  -35.5335  35.8251
 7OQ  O5   O  OH1   0  -0.663  17.4025  -35.5735  36.0994
 7OQ  C1   C  CH1   0   0.012  18.9677  -35.9080  34.3578
 7OQ  O2   O  OH1   0  -0.662  18.3953  -34.9444  33.5122
 7OQ  C2   C  CH1   0   0.028  20.4501  -36.0204  34.0341
 7OQ  O3   O  OH1   0  -0.667  20.5803  -36.4974  32.7180
 7OQ  C4   C  CH1   0  -0.017  21.1108  -36.9826  35.0330
 7OQ  C6   C  CH2   0  -0.194  22.5966  -37.1654  34.8129
 7OQ  O6   O  OH1   0  -0.666  23.2364  -35.9127  34.8294
 7OQ  H16  H  HOH1  0   0.471  19.8739  -38.8534  43.2136
 7OQ  H14  H  HCR6  0   0.264  20.9396  -39.8741  40.0156
 7OQ  H12  H  HCR6  0   0.283  20.6675  -38.4997  38.0269
 7OQ  H15  H  HCR6  0   0.272  19.0569  -36.8510  42.3961
 7OQ  H13  H  HCR6  0   0.266  18.7438  -35.4766  40.3892
 7OQ  H5   H  HCH1  0   0.206  19.1225  -37.5133  36.6279
 7OQ  H3   H  HCH1  0   0.228  19.1941  -34.5256  35.9790
 7OQ  H10  H  HOH1  0   0.458  17.2297  -35.0662  36.8983
 7OQ  H1   H  HCH1  0   0.209  18.5071  -36.8977  34.1960
 7OQ  H8   H  HOH1  0   0.448  17.4566  -34.8875  33.7196
 7OQ  H2   H  HCH1  0   0.226  20.9019  -35.0262  34.1465
 7OQ  H9   H  HOH1  0   0.456  21.4360  -36.2238  32.3746
 7OQ  H4   H  HCH1  0   0.228  20.6503  -37.9766  34.9098
 7OQ  H6   H  HCH2  0   0.220  22.9817  -37.8354  35.5930
 7OQ  H7   H  HCH2  0   0.210  22.7355  -37.6880  33.8595
 7OQ  H11  H  HOH1  0   0.458  24.1601  -36.0419  34.5972

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
 7OQ  O3   C2   single    1.406  0.020  1.406
 7OQ  O2   C1   single    1.404  0.020  1.404
 7OQ  C2   C1   single    1.521  0.020  1.521
 7OQ  C2   C4   single    1.536  0.020  1.536
 7OQ  C1   C3   single    1.526  0.020  1.526
 7OQ  C6   C4   single    1.513  0.020  1.513
 7OQ  C6   O6   single    1.407  0.020  1.407
 7OQ  C4   O1   single    1.417  0.020  1.417
 7OQ  C3   O5   single    1.405  0.020  1.405
 7OQ  C3   C5   single    1.526  0.020  1.526
 7OQ  O1   C5   single    1.399  0.020  1.399
 7OQ  C5   O4   single    1.388  0.020  1.388
 7OQ  O4   C7   single    1.364  0.020  1.364
 7OQ  C8   C7   aromatic  1.390  0.020  1.390
 7OQ  C8   C10  aromatic  1.389  0.020  1.389
 7OQ  C7   C9   aromatic  1.390  0.020  1.390
 7OQ  C10  C12  aromatic  1.390  0.020  1.390
 7OQ  C9   C11  aromatic  1.385  0.020  1.385
 7OQ  C12  C11  aromatic  1.392  0.020  1.392
 7OQ  C12  O7   single    1.352  0.020  1.352
 7OQ  O7   H16  single    0.850  0.020  0.980
 7OQ  C10  H14  single    0.930  0.020  1.080
 7OQ  C8   H12  single    0.930  0.020  1.080
 7OQ  C11  H15  single    0.930  0.020  1.080
 7OQ  C9   H13  single    0.930  0.020  1.080
 7OQ  C5   H5   single    0.970  0.020  1.090
 7OQ  C3   H3   single    0.970  0.020  1.090
 7OQ  O5   H10  single    0.850  0.020  0.980
 7OQ  C1   H1   single    0.970  0.020  1.090
 7OQ  O2   H8   single    0.850  0.020  0.980
 7OQ  C2   H2   single    0.970  0.020  1.090
 7OQ  O3   H9   single    0.850  0.020  0.980
 7OQ  C4   H4   single    0.970  0.020  1.090
 7OQ  C6   H6   single    0.970  0.020  1.090
 7OQ  C6   H7   single    0.970  0.020  1.090
 7OQ  O6   H11  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
 7OQ  H16  O7   C12  110.35  3.000
 7OQ  C11  C12  C10  118.88  3.000
 7OQ  C11  C12  O7   122.90  3.000
 7OQ  C10  C12  O7   118.22  3.000
 7OQ  H14  C10  C8   119.45  3.000
 7OQ  H14  C10  C12  119.70  3.000
 7OQ  C8   C10  C12  120.85  3.000
 7OQ  H12  C8   C7   121.74  3.000
 7OQ  H12  C8   C10  118.22  3.000
 7OQ  C7   C8   C10  120.04  3.000
 7OQ  H15  C11  C9   119.27  3.000
 7OQ  H15  C11  C12  120.37  3.000
 7OQ  C9   C11  C12  120.35  3.000
 7OQ  H13  C9   C7   119.58  3.000
 7OQ  H13  C9   C11  119.75  3.000
 7OQ  C7   C9   C11  120.67  3.000
 7OQ  O4   C7   C9   116.04  3.000
 7OQ  C9   C7   C8   119.20  3.000
 7OQ  O4   C7   C8   124.76  3.000
 7OQ  C5   O4   C7   120.08  3.000
 7OQ  H5   C5   C3   109.61  3.000
 7OQ  H5   C5   O1   110.47  3.000
 7OQ  C3   C5   O1   110.32  3.000
 7OQ  H5   C5   O4   110.83  3.000
 7OQ  O1   C5   O4   108.10  3.000
 7OQ  C3   C5   O4   107.46  3.000
 7OQ  C4   O1   C5   112.48  3.000
 7OQ  H3   C3   C1   108.24  3.000
 7OQ  H3   C3   O5   111.57  3.000
 7OQ  C1   C3   O5   107.54  3.000
 7OQ  H3   C3   C5   107.92  3.000
 7OQ  O5   C3   C5   111.50  3.000
 7OQ  C1   C3   C5   110.03  3.000
 7OQ  H10  O5   C3   108.85  3.000
 7OQ  H1   C1   C2   108.01  3.000
 7OQ  H1   C1   O2   110.92  3.000
 7OQ  C2   C1   O2   108.65  3.000
 7OQ  H1   C1   C3   108.04  3.000
 7OQ  C2   C1   C3   110.03  3.000
 7OQ  O2   C1   C3   111.14  3.000
 7OQ  H8   O2   C1   107.96  3.000
 7OQ  H2   C2   C4   108.88  3.000
 7OQ  H2   C2   O3   111.41  3.000
 7OQ  C4   C2   O3   110.87  3.000
 7OQ  H2   C2   C1   108.20  3.000
 7OQ  C4   C2   C1   109.08  3.000
 7OQ  O3   C2   C1   108.33  3.000
 7OQ  H9   O3   C2   108.67  3.000
 7OQ  H4   C4   C6   106.56  3.000
 7OQ  H4   C4   C2   108.20  3.000
 7OQ  C6   C4   C2   113.79  3.000
 7OQ  H4   C4   O1   110.02  3.000
 7OQ  C6   C4   O1   108.47  3.000
 7OQ  C2   C4   O1   109.74  3.000
 7OQ  H7   C6   H6   106.42  3.000
 7OQ  H7   C6   O6   112.16  3.000
 7OQ  H6   C6   O6   112.06  3.000
 7OQ  H7   C6   C4   107.97  3.000
 7OQ  H6   C6   C4   108.35  3.000
 7OQ  O6   C6   C4   109.71  3.000
 7OQ  H11  O6   C6   108.33  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
 7OQ  CONST_01  C7   C8   C10  C12     0.00   0.0  0
 7OQ  CONST_02  C7   C9   C11  C12     0.00   0.0  0
 7OQ  CONST_03  C9   C7   C8   C10     0.00   0.0  0
 7OQ  CONST_04  C9   C11  C12  C10     0.00   0.0  0
 7OQ  CONST_05  C11  C9   C7   C8      0.00   0.0  0
 7OQ  CONST_06  C11  C12  C10  C8      0.00   0.0  0
 7OQ  CONST_07  C8   C10  C12  O7    180.00   0.0  0
 7OQ  CONST_08  C9   C11  C12  O7    180.00   0.0  0
 7OQ  CONST_09  O4   C7   C8   C10   180.00   0.0  0
 7OQ  CONST_10  O4   C7   C9   C11   180.00   0.0  0
 7OQ  CONST_11  H12  C8   C10  C12   180.00   0.0  0
 7OQ  CONST_12  H13  C9   C11  C12   180.00   0.0  0
 7OQ  CONST_13  H15  C11  C12  C10   180.00   0.0  0
 7OQ  CONST_14  H13  C9   C7   C8    180.00   0.0  0
 7OQ  CONST_15  H14  C10  C12  C11   180.00   0.0  0
 7OQ  CONST_16  H12  C8   C7   C9    180.00   0.0  0
 7OQ  CONST_17  H14  C10  C8   C7    180.00   0.0  0
 7OQ  CONST_18  H15  C11  C9   C7    180.00   0.0  0
 7OQ  Var_01    C5   O4   C7   C8     16.52  30.0  2
 7OQ  Var_02    C5   O4   C7   C9   -164.09  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
 7OQ  chir_01  C5  C3  O1  O4  negativ
 7OQ  chir_02  C3  O5  C5  C1  negativ
 7OQ  chir_03  C1  O2  C3  C2  positiv
 7OQ  chir_04  C2  O3  C4  C1  positiv
 7OQ  chir_05  C4  O1  C2  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
 7OQ  plan-1  O7   0.020
 7OQ  plan-1  C12  0.020
 7OQ  plan-1  C10  0.020
 7OQ  plan-1  C8   0.020
 7OQ  plan-1  C11  0.020
 7OQ  plan-1  C9   0.020
 7OQ  plan-1  C7   0.020
 7OQ  plan-1  O4   0.020
 7OQ  plan-1  H14  0.020
 7OQ  plan-1  H12  0.020
 7OQ  plan-1  H15  0.020
 7OQ  plan-1  H13  0.020

