# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 05:09:00 2022
#   Inital geometry file: a 81 line input string
#   Ligand name: (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-phenoxy-oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](Oc2ccccc2)[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
 7OL  7OL  "(2R,3S,4S,5R,6R)-2-(hydroxymethyl)-6-phenoxy-oxane-3,4,5-triol"
  ligand  34  18  .  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_7OL
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
 7OL  O6   O  OH1   0  -0.666  23.0807  -35.4003  34.9443
 7OL  C6   C  CH2   0  -0.197  22.6215  -36.7280  35.0217
 7OL  C4   C  CH1   0  -0.021  21.1122  -36.7504  35.1133
 7OL  C2   C  CH1   0   0.023  20.4068  -36.0313  33.9555
 7OL  O3   O  OH1   0  -0.667  20.6970  -36.6634  32.7329
 7OL  C1   C  CH1   0   0.015  18.9033  -36.0799  34.1787
 7OL  O2   O  OH1   0  -0.664  18.2757  -35.3391  33.1632
 7OL  C3   C  CH1   0  -0.020  18.5825  -35.5033  35.5555
 7OL  O5   O  OH1   0  -0.661  17.1982  -35.6089  35.7616
 7OL  C5   C  CH1   0   0.211  19.3903  -36.2028  36.6512
 7OL  O1   O  O2    0  -0.494  20.7477  -36.1655  36.3587
 7OL  O4   O  O2    0  -0.494  18.9044  -37.5150  36.7595
 7OL  C7   C  CR6   0   0.391  19.2778  -38.2989  37.8004
 7OL  C9   C  CR16  0  -0.348  18.7166  -39.5757  37.8221
 7OL  C11  C  CR16  0  -0.239  19.0218  -40.4541  38.8480
 7OL  C12  C  CR16  0  -0.278  19.8891  -40.0758  39.8665
 7OL  C10  C  CR16  0  -0.241  20.4464  -38.8072  39.8380
 7OL  C8   C  CR16  0  -0.365  20.1551  -37.9150  38.8116
 7OL  H11  H  HOH1  0   0.457  24.0223  -35.4179  34.7523
 7OL  H6   H  HCH2  0   0.210  22.9152  -37.3181  34.1457
 7OL  H7   H  HCH2  0   0.219  23.0261  -37.2517  35.8980
 7OL  H4   H  HCH1  0   0.235  20.8185  -37.8091  35.0867
 7OL  H2   H  HCH1  0   0.225  20.7168  -34.9780  33.9431
 7OL  H9   H  HOH1  0   0.456  21.5230  -36.3099  32.3904
 7OL  H1   H  HCH1  0   0.212  18.5807  -37.1330  34.1477
 7OL  H8   H  HOH1  0   0.447  17.3298  -35.3338  33.3445
 7OL  H3   H  HCH1  0   0.236  18.9047  -34.4525  35.5625
 7OL  H10  H  HOH1  0   0.460  16.9260  -34.9497  36.4074
 7OL  H5   H  HCH1  0   0.256  19.2696  -35.6706  37.6027
 7OL  H13  H  HCR6  0   0.261  18.0388  -39.8703  37.0304
 7OL  H15  H  HCR6  0   0.256  18.5765  -41.4407  38.8500
 7OL  H16  H  HCR6  0   0.251  20.1277  -40.7627  40.6674
 7OL  H14  H  HCR6  0   0.257  21.1285  -38.4979  40.6197
 7OL  H12  H  HCR6  0   0.279  20.6277  -36.9434  38.8218

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
 7OL  O3   C2   single    1.407  0.020  1.407
 7OL  O2   C1   single    1.405  0.020  1.405
 7OL  C2   C1   single    1.521  0.020  1.521
 7OL  C2   C4   single    1.535  0.020  1.535
 7OL  C1   C3   single    1.527  0.020  1.527
 7OL  O6   C6   single    1.407  0.020  1.407
 7OL  C6   C4   single    1.512  0.020  1.512
 7OL  C4   O1   single    1.423  0.020  1.423
 7OL  C3   O5   single    1.404  0.020  1.404
 7OL  C3   C5   single    1.530  0.020  1.530
 7OL  O1   C5   single    1.389  0.020  1.389
 7OL  C5   O4   single    1.404  0.020  1.404
 7OL  O4   C7   single    1.355  0.020  1.355
 7OL  C7   C9   aromatic  1.395  0.020  1.395
 7OL  C7   C8   aromatic  1.393  0.020  1.393
 7OL  C9   C11  aromatic  1.385  0.020  1.385
 7OL  C8   C10  aromatic  1.391  0.020  1.391
 7OL  C11  C12  aromatic  1.390  0.020  1.390
 7OL  C10  C12  aromatic  1.386  0.020  1.386
 7OL  O6   H11  single    0.850  0.020  0.980
 7OL  C6   H6   single    0.970  0.020  1.090
 7OL  C6   H7   single    0.970  0.020  1.090
 7OL  C4   H4   single    0.970  0.020  1.090
 7OL  C2   H2   single    0.970  0.020  1.090
 7OL  O3   H9   single    0.850  0.020  0.980
 7OL  C1   H1   single    0.970  0.020  1.090
 7OL  O2   H8   single    0.850  0.020  0.980
 7OL  C3   H3   single    0.970  0.020  1.090
 7OL  O5   H10  single    0.850  0.020  0.980
 7OL  C5   H5   single    0.970  0.020  1.090
 7OL  C9   H13  single    0.930  0.020  1.080
 7OL  C11  H15  single    0.930  0.020  1.080
 7OL  C12  H16  single    0.930  0.020  1.080
 7OL  C10  H14  single    0.930  0.020  1.080
 7OL  C8   H12  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
 7OL  H11  O6   C6   108.27  3.000
 7OL  H7   C6   H6   106.39  3.000
 7OL  H7   C6   C4   108.20  3.000
 7OL  H6   C6   C4   107.93  3.000
 7OL  H7   C6   O6   111.94  3.000
 7OL  H6   C6   O6   112.12  3.000
 7OL  C4   C6   O6   110.06  3.000
 7OL  H4   C4   O1   110.40  3.000
 7OL  H4   C4   C2   108.08  3.000
 7OL  O1   C4   C2   110.48  3.000
 7OL  H4   C4   C6   106.23  3.000
 7OL  O1   C4   C6   107.60  3.000
 7OL  C2   C4   C6   113.96  3.000
 7OL  H2   C2   C1   108.15  3.000
 7OL  H2   C2   O3   111.28  3.000
 7OL  C1   C2   O3   108.49  3.000
 7OL  H2   C2   C4   109.16  3.000
 7OL  C1   C2   C4   109.19  3.000
 7OL  O3   C2   C4   110.51  3.000
 7OL  H9   O3   C2   108.76  3.000
 7OL  H1   C1   C3   108.95  3.000
 7OL  H1   C1   O2   110.66  3.000
 7OL  C3   C1   O2   111.02  3.000
 7OL  H1   C1   C2   108.41  3.000
 7OL  C3   C1   C2   109.15  3.000
 7OL  O2   C1   C2   108.59  3.000
 7OL  H8   O2   C1   107.79  3.000
 7OL  H3   C3   C5   106.12  3.000
 7OL  H3   C3   O5   111.11  3.000
 7OL  C5   C3   O5   112.40  3.000
 7OL  H3   C3   C1   107.77  3.000
 7OL  C5   C3   C1   111.23  3.000
 7OL  O5   C3   C1   108.13  3.000
 7OL  H10  O5   C3   109.03  3.000
 7OL  H5   C5   O4   110.40  3.000
 7OL  H5   C5   O1   106.09  3.000
 7OL  O4   C5   O1   112.31  3.000
 7OL  H5   C5   C3   109.95  3.000
 7OL  O4   C5   C3   107.45  3.000
 7OL  O1   C5   C3   110.66  3.000
 7OL  C5   O1   C4   115.05  3.000
 7OL  C7   O4   C5   120.31  3.000
 7OL  C8   C7   C9   119.63  3.000
 7OL  C8   C7   O4   124.87  3.000
 7OL  C9   C7   O4   115.50  3.000
 7OL  H13  C9   C11  120.47  3.000
 7OL  H13  C9   C7   119.30  3.000
 7OL  C11  C9   C7   120.23  3.000
 7OL  H15  C11  C12  120.22  3.000
 7OL  H15  C11  C9   119.27  3.000
 7OL  C12  C11  C9   120.51  3.000
 7OL  H16  C12  C10  120.52  3.000
 7OL  H16  C12  C11  120.48  3.000
 7OL  C10  C12  C11  119.00  3.000
 7OL  H14  C10  C8   118.79  3.000
 7OL  H14  C10  C12  120.00  3.000
 7OL  C8   C10  C12  121.21  3.000
 7OL  H12  C8   C10  118.57  3.000
 7OL  H12  C8   C7   122.02  3.000
 7OL  C10  C8   C7   119.40  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
 7OL  CONST_01  C12  C11  C9   C7     0.00   0.0  0
 7OL  CONST_02  C12  C10  C8   C7     0.00   0.0  0
 7OL  CONST_03  C10  C8   C7   C9     0.00   0.0  0
 7OL  CONST_04  C10  C12  C11  C9     0.00   0.0  0
 7OL  CONST_05  C8   C7   C9   C11    0.00   0.0  0
 7OL  CONST_06  C8   C10  C12  C11    0.00   0.0  0
 7OL  CONST_07  C11  C9   C7   O4   180.00   0.0  0
 7OL  CONST_08  C10  C8   C7   O4   180.00   0.0  0
 7OL  CONST_09  H15  C11  C9   C7   180.00   0.0  0
 7OL  CONST_10  H14  C10  C8   C7   180.00   0.0  0
 7OL  CONST_11  H12  C8   C7   C9   180.00   0.0  0
 7OL  CONST_12  H16  C12  C11  C9   180.00   0.0  0
 7OL  CONST_13  H14  C10  C12  C11  180.00   0.0  0
 7OL  CONST_14  H13  C9   C11  C12  180.00   0.0  0
 7OL  CONST_15  H12  C8   C10  C12  180.00   0.0  0
 7OL  CONST_16  H15  C11  C12  C10  180.00   0.0  0
 7OL  CONST_17  H13  C9   C7   C8   180.00   0.0  0
 7OL  CONST_18  H16  C12  C10  C8   180.00   0.0  0
 7OL  Var_01    C9   C7   O4   C5   178.88  30.0  2
 7OL  Var_02    C8   C7   O4   C5    -1.02  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
 7OL  chir_01  C4  C2  C6  O1  negativ
 7OL  chir_02  C2  O3  C4  C1  positiv
 7OL  chir_03  C1  O2  C2  C3  negativ
 7OL  chir_04  C3  O5  C1  C5  positiv
 7OL  chir_05  C5  O4  O1  C3  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
 7OL  plan-1  O4   0.020
 7OL  plan-1  C7   0.020
 7OL  plan-1  C9   0.020
 7OL  plan-1  C11  0.020
 7OL  plan-1  C12  0.020
 7OL  plan-1  C10  0.020
 7OL  plan-1  C8   0.020
 7OL  plan-1  H13  0.020
 7OL  plan-1  H15  0.020
 7OL  plan-1  H16  0.020
 7OL  plan-1  H14  0.020
 7OL  plan-1  H12  0.020

