# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 05:34:42 2022
#   Inital geometry file: a 100 line input string
#   Ligand name: 6-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-7-oxidanyl-chromen-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](Oc2cc3C=CC(=O)Oc3cc2O)[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
 7OU  7OU  "6-[(2S,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-7-oxidanyl-chromen-2-one"
  ligand  40  24  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7OU
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
 7OU  O1   O  O2    0  -0.516  18.3368  -35.9534  37.4325
 7OU  O2   O  O2    0  -0.487  19.9856  -36.1999  35.9127
 7OU  O3   O  O     0  -0.467  19.8357  -39.5614  41.2788
 7OU  O4   O  OH1   0  -0.663  16.4726  -35.4920  35.3091
 7OU  O5   O  OH1   0  -0.662  17.6800  -34.7110  32.8634
 7OU  O6   O  OH1   0  -0.666  20.0442  -36.0622  32.2650
 7OU  C1   C  CH1   0   0.291  18.6102  -36.3074  36.1097
 7OU  C2   C  CH1   0  -0.038  17.8646  -35.3475  35.1921
 7OU  C3   C  CR6   0   0.297  18.6921  -36.8748  38.3752
 7OU  C4   C  CH1   0   0.011  18.2348  -35.6534  33.7426
 7OU  C5   C  CH1   0   0.025  19.7470  -35.6405  33.5727
 7OU  C6   C  CH1   0  -0.015  20.3840  -36.5803  34.6086
 7OU  C7   C  CR66  0  -0.016  18.3137  -38.9510  39.5451
 7OU  C8   C  CR66  0   0.395  19.4388  -38.6904  40.3245
 7OU  C9   C  CR6   0   0.303  19.8231  -36.6229  39.1781
 7OU  C10  C  CR16  0  -0.381  17.9535  -38.0171  38.5675
 7OU  C11  C  CR16  0  -0.469  20.1884  -37.5377  40.1567
 7OU  C12  C  CR16  0  -0.117  17.5944  -40.1593  39.8032
 7OU  C13  C  CR6   0   0.539  19.1779  -40.7226  41.5589
 7OU  C14  C  CH2   0  -0.194  21.8963  -36.6024  34.5685
 7OU  C15  C  CR16  0  -0.478  18.0036  -41.0092  40.7640
 7OU  H1   H  HOH1  0   0.458  16.1801  -35.0681  36.1217
 7OU  H3   H  HOH1  0   0.457  20.9086  -35.7213  32.0183
 7OU  H4   H  HOH1  0   0.484  21.2329  -35.4072  39.5733
 7OU  H5   H  HOH1  0   0.458  23.3522  -35.3266  34.6505
 7OU  H6   H  HCH1  0   0.205  18.2759  -37.3426  35.9137
 7OU  H7   H  HCH1  0   0.229  18.1893  -34.3231  35.4284
 7OU  H8   H  HCH1  0   0.209  17.8737  -36.6704  33.5110
 7OU  H9   H  HCH1  0   0.227  20.1026  -34.6176  33.7540
 7OU  H10  H  HCH1  0   0.229  20.0444  -37.6070  34.3959
 7OU  H11  H  HCR6  0   0.286  17.0760  -38.1967  37.9567
 7OU  H12  H  HCR6  0   0.300  21.0537  -37.3593  40.7847
 7OU  H13  H  HCR6  0   0.291  16.7140  -40.3824  39.2127
 7OU  H14  H  HCH2  0   0.209  22.2049  -37.0504  33.6163
 7OU  H15  H  HCH2  0   0.221  22.2515  -37.2765  35.3587
 7OU  H16  H  HCR6  0   0.287  17.4767  -41.9279  40.9781
 7OU  H2   H  HOH1  0   0.448  16.7228  -34.7346  32.9672
 7OU  O7   O  OH1   0  -0.598  20.4902  -35.4885  38.9626
 7OU  O8   O  O     0  -0.424  19.6279  -41.4095  42.4406
 7OU  O9   O  OH1   0  -0.666  22.3946  -35.2962  34.7282

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
 7OU  O6   C5   single    1.406  0.020  1.406
 7OU  O5   C4   single    1.403  0.020  1.403
 7OU  C5   C4   single    1.522  0.020  1.522
 7OU  C5   C6   single    1.537  0.020  1.537
 7OU  C4   C2   single    1.527  0.020  1.527
 7OU  C14  O9   single    1.407  0.020  1.407
 7OU  C14  C6   single    1.513  0.020  1.513
 7OU  C6   O2   single    1.416  0.020  1.416
 7OU  C2   O4   single    1.404  0.020  1.404
 7OU  C2   C1   single    1.523  0.020  1.523
 7OU  O2   C1   single    1.394  0.020  1.394
 7OU  C1   O1   single    1.396  0.020  1.396
 7OU  O1   C3   single    1.365  0.020  1.365
 7OU  C3   C10  aromatic  1.374  0.020  1.374
 7OU  C3   C9   aromatic  1.410  0.020  1.410
 7OU  C10  C7   aromatic  1.399  0.020  1.399
 7OU  O7   C9   single    1.334  0.020  1.334
 7OU  C9   C11  aromatic  1.389  0.020  1.389
 7OU  C7   C12  single    1.430  0.020  1.430
 7OU  C7   C8   aromatic  1.393  0.020  1.393
 7OU  C12  C15  double    1.346  0.020  1.346
 7OU  C11  C8   aromatic  1.385  0.020  1.385
 7OU  C8   O3   single    1.352  0.020  1.352
 7OU  C15  C13  single    1.447  0.020  1.447
 7OU  O3   C13  single    1.364  0.020  1.364
 7OU  C13  O8   double    1.205  0.020  1.205
 7OU  O4   H1   single    0.850  0.020  0.980
 7OU  O5   H2   single    0.850  0.020  0.980
 7OU  O6   H3   single    0.850  0.020  0.980
 7OU  O7   H4   single    0.850  0.020  0.980
 7OU  O9   H5   single    0.850  0.020  0.980
 7OU  C1   H6   single    0.970  0.020  1.090
 7OU  C2   H7   single    0.970  0.020  1.090
 7OU  C4   H8   single    0.970  0.020  1.090
 7OU  C5   H9   single    0.970  0.020  1.090
 7OU  C6   H10  single    0.970  0.020  1.090
 7OU  C10  H11  single    0.930  0.020  1.080
 7OU  C11  H12  single    0.930  0.020  1.080
 7OU  C12  H13  single    0.930  0.020  1.080
 7OU  C14  H14  single    0.970  0.020  1.090
 7OU  C14  H15  single    0.970  0.020  1.090
 7OU  C15  H16  single    0.930  0.020  1.080

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
 7OU  C3   O1   C1   115.60  3.000
 7OU  C6   O2   C1   112.78  3.000
 7OU  C13  O3   C8   123.51  3.000
 7OU  H1   O4   C2   109.04  3.000
 7OU  H2   O5   C4   108.00  3.000
 7OU  H3   O6   C5   108.81  3.000
 7OU  H6   C1   C2   109.60  3.000
 7OU  H6   C1   O2   110.22  3.000
 7OU  C2   C1   O2   110.45  3.000
 7OU  H6   C1   O1   110.26  3.000
 7OU  O2   C1   O1   107.92  3.000
 7OU  C2   C1   O1   108.37  3.000
 7OU  H7   C2   C4   108.59  3.000
 7OU  H7   C2   C1   108.24  3.000
 7OU  C4   C2   C1   109.09  3.000
 7OU  H7   C2   O4   111.74  3.000
 7OU  C1   C2   O4   111.73  3.000
 7OU  C4   C2   O4   107.38  3.000
 7OU  C10  C3   C9   120.01  3.000
 7OU  C9   C3   O1   118.79  3.000
 7OU  C10  C3   O1   121.19  3.000
 7OU  H8   C4   C5   108.03  3.000
 7OU  H8   C4   C2   107.73  3.000
 7OU  C5   C4   C2   110.19  3.000
 7OU  H8   C4   O5   110.98  3.000
 7OU  C2   C4   O5   111.37  3.000
 7OU  C5   C4   O5   108.50  3.000
 7OU  H9   C5   C6   108.91  3.000
 7OU  H9   C5   C4   108.14  3.000
 7OU  C6   C5   C4   109.35  3.000
 7OU  H9   C5   O6   111.38  3.000
 7OU  C6   C5   O6   110.85  3.000
 7OU  C4   C5   O6   108.14  3.000
 7OU  H10  C6   C14  106.81  3.000
 7OU  H10  C6   C5   108.17  3.000
 7OU  C14  C6   C5   113.91  3.000
 7OU  H10  C6   O2   109.96  3.000
 7OU  C14  C6   O2   108.04  3.000
 7OU  C5   C6   O2   109.88  3.000
 7OU  C12  C7   C10  124.10  3.000
 7OU  C12  C7   C8   117.60  3.000
 7OU  C10  C7   C8   118.29  3.000
 7OU  C11  C8   C7   121.66  3.000
 7OU  C11  C8   O3   117.57  3.000
 7OU  C7   C8   O3   120.77  3.000
 7OU  C11  C9   C3   119.66  3.000
 7OU  C11  C9   O7   122.87  3.000
 7OU  C3   C9   O7   117.47  3.000
 7OU  H11  C10  C7   119.44  3.000
 7OU  H11  C10  C3   119.61  3.000
 7OU  C7   C10  C3   120.95  3.000
 7OU  H12  C11  C9   120.66  3.000
 7OU  H12  C11  C8   119.92  3.000
 7OU  C9   C11  C8   119.42  3.000
 7OU  H13  C12  C15  120.40  3.000
 7OU  H13  C12  C7   118.98  3.000
 7OU  C15  C12  C7   120.62  3.000
 7OU  C15  C13  O8   126.32  3.000
 7OU  O8   C13  O3   117.11  3.000
 7OU  C15  C13  O3   116.57  3.000
 7OU  H15  C14  H14  106.45  3.000
 7OU  H15  C14  C6   108.26  3.000
 7OU  H14  C14  C6   108.07  3.000
 7OU  H15  C14  O9   111.95  3.000
 7OU  H14  C14  O9   112.22  3.000
 7OU  C6   C14  O9   109.71  3.000
 7OU  H16  C15  C13  117.09  3.000
 7OU  H16  C15  C12  122.00  3.000
 7OU  C13  C15  C12  120.91  3.000
 7OU  H4   O7   C9   110.76  3.000
 7OU  H5   O9   C14  108.31  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
 7OU  CONST_01  C8   C7   C10  C3      0.00   0.0  0
 7OU  CONST_02  C8   C11  C9   C3      0.00   0.0  0
 7OU  CONST_03  C9   C3   C10  C7      0.00   0.0  0
 7OU  CONST_04  C9   C11  C8   C7      0.00   0.0  0
 7OU  CONST_05  C11  C9   C3   C10     0.00   0.0  0
 7OU  CONST_06  C11  C8   C7   C10     0.00   0.0  0
 7OU  CONST_07  C7   C10  C3   O1    180.00   0.0  0
 7OU  CONST_08  C11  C9   C3   O1    180.00   0.0  0
 7OU  CONST_09  C10  C3   C9   O7    180.00   0.0  0
 7OU  CONST_10  C8   C11  C9   O7    180.00   0.0  0
 7OU  CONST_11  H12  C11  C8   O3      0.00   0.0  0
 7OU  CONST_12  H12  C11  C9   C3    180.00   0.0  0
 7OU  CONST_13  H12  C11  C8   C7    180.00   0.0  0
 7OU  CONST_14  H11  C10  C7   C8    180.00   0.0  0
 7OU  CONST_15  H11  C10  C3   C9    180.00   0.0  0
 7OU  CONST_16  H11  C10  C7   C12     0.00   0.0  0
 7OU  Var_01    C12  C15  C13  O3     -0.15  30.0  1
 7OU  Var_02    C13  C15  C12  C7      0.05  30.0  1
 7OU  Var_03    C13  O3   C8   C7     -0.81  30.0  1
 7OU  Var_04    C15  C12  C7   C8     -0.29  30.0  1
 7OU  Var_05    C15  C13  O3   C8      0.54  30.0  1
 7OU  Var_06    C15  C12  C7   C10  -179.94  30.0  1
 7OU  Var_07    C13  O3   C8   C11   179.08  30.0  1
 7OU  Var_08    C12  C15  C13  O8    179.86  30.0  1
 7OU  Var_09    C8   O3   C13  O8   -179.48  30.0  1
 7OU  Var_10    C10  C3   O1   C1    -75.23  30.0  2
 7OU  Var_11    C9   C3   O1   C1    106.14  30.0  2
 7OU  Var_12    H16  C15  C13  O3    179.92  30.0  1
 7OU  Var_13    H16  C15  C12  C7    179.97  30.0  1
 7OU  Var_14    H13  C12  C7   C8    179.78  30.0  1
 7OU  Var_15    H13  C12  C7   C10     0.14  30.0  1
 7OU  Var_16    H13  C12  C15  C13   179.98  30.0  1
 7OU  Var_17    H16  C15  C13  O8     -0.06  30.0  1

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
 7OU  chir_01  C1  C2  O2  O1   negativ
 7OU  chir_02  C2  O4  C1  C4   negativ
 7OU  chir_03  C4  O5  C2  C5   positiv
 7OU  chir_04  C5  O6  C6  C4   positiv
 7OU  chir_05  C6  O2  C5  C14  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
 7OU  plan-1  O3   0.020
 7OU  plan-1  C13  0.020
 7OU  plan-1  C15  0.020
 7OU  plan-1  O8   0.020
 7OU  plan-2  O1   0.020
 7OU  plan-2  O3   0.020
 7OU  plan-2  C3   0.020
 7OU  plan-2  C7   0.020
 7OU  plan-2  C8   0.020
 7OU  plan-2  C9   0.020
 7OU  plan-2  C10  0.020
 7OU  plan-2  C11  0.020
 7OU  plan-2  C12  0.020
 7OU  plan-2  H11  0.020
 7OU  plan-2  H12  0.020
 7OU  plan-2  O7   0.020

