# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 13:25:04 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (2~{S},3~{R},4~{S},5~{R},6~{S})-2-[(2~{R})-oxiran-2-yl]-6-phenoxy-oxane-3,4,5-triol
#   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]2CO2)[C@@H]1O)Oc3ccccc3
#
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
 7NU  7NU  (2~{S},3~{R},4~{S},5~{R},6~{S})-2-[(2~{R})-oxiran-2-yl]-6-phenoxy-oxane-3,4,5-triol  D-saccharide  35  19  .  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
;

data_comp_7NU
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
 7NU  O2   O  OH1   0  -0.667  -0.7156   2.8949   0.6080
 7NU  C2   C  CH1   0  -0.018  -1.0712   1.7070  -0.0527
 7NU  C3   C  CH1   0   0.004  -2.3513   1.1866   0.5905
 7NU  O3   O  OH1   0  -0.671  -3.4347   2.0593   0.3979
 7NU  C1   C  CH1   0   0.262   0.0146   0.6427   0.0924
 7NU  O5   O  O2    0  -0.498  -0.3940  -0.5615  -0.4927
 7NU  C5   C  CH1   0  -0.033  -1.5391  -1.1105   0.1302
 7NU  C6   C  CH1   0  -0.010  -1.7691  -2.4479  -0.5225
 7NU  O6   O  O2    0  -0.483  -2.6519  -3.3094   0.1668
 7NU  C7   C  CH2   0  -0.249  -1.2772  -3.6670   0.1064
 7NU  C4   C  CH1   0   0.010  -2.7320  -0.1706   0.0030
 7NU  O4   O  OH1   0  -0.669  -3.0835  -0.0787  -1.3536
 7NU  O1   O  O2    0  -0.499   1.1412   1.0897  -0.5858
 7NU  C8   C  CR6   0   0.367   2.3683   0.6057  -0.2510
 7NU  C9   C  CR16  0  -0.341   3.4558   1.3688  -0.6684
 7NU  C10  C  CR16  0  -0.244   4.7448   0.9528  -0.3778
 7NU  C11  C  CR16  0  -0.274   4.9639  -0.2207   0.3344
 7NU  C12  C  CR16  0  -0.245   3.8756  -0.9752   0.7450
 7NU  C13  C  CR16  0  -0.351   2.5761  -0.5769   0.4524
 7NU  H1   H  HOH1  0   0.460  -0.0858   3.3787   0.0652
 7NU  H2   H  HCH1  0   0.235  -1.2486   1.8760  -1.1233
 7NU  H3   H  HCH1  0   0.217  -2.1545   1.0374   1.6645
 7NU  H4   H  HOH1  0   0.456  -3.1773   2.9386   0.6953
 7NU  H5   H  HCH1  0   0.212   0.2416   0.4911   1.1626
 7NU  H6   H  HCH1  0   0.248  -1.3533  -1.2657   1.2047
 7NU  H7   H  HCH1  0   0.270  -1.8858  -2.4310  -1.6043
 7NU  H8   H  HCH2  0   0.248  -1.0393  -4.5290  -0.5096
 7NU  H9   H  HCH2  0   0.244  -0.7318  -3.6063   1.0449
 7NU  H10  H  HCH1  0   0.244  -3.5526  -0.5892   0.6035
 7NU  H11  H  HOH1  0   0.456  -3.8129   0.5447  -1.4358
 7NU  H12  H  HCR6  0   0.265   3.2834   2.2868  -1.2164
 7NU  H13  H  HCR6  0   0.260   5.5827   1.5549  -0.7051
 7NU  H14  H  HCR6  0   0.256   5.9708  -0.5436   0.5617
 7NU  H15  H  HCR6  0   0.261   4.0299  -1.8950   1.2941
 7NU  H16  H  HCR6  0   0.279   1.7524  -1.2052   0.7625

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
 7NU  C12  C11  aromatic  1.386  0.020  1.386
 7NU  C12  C13  aromatic  1.390  0.020  1.390
 7NU  C11  C10  aromatic  1.390  0.020  1.390
 7NU  C13  C8   aromatic  1.392  0.020  1.392
 7NU  C10  C9   aromatic  1.385  0.020  1.385
 7NU  C8   C9   aromatic  1.393  0.020  1.393
 7NU  C8   O1   single    1.361  0.020  1.361
 7NU  O1   C1   single    1.389  0.020  1.389
 7NU  C1   O5   single    1.400  0.020  1.400
 7NU  C1   C2   single    1.527  0.020  1.527
 7NU  O2   C2   single    1.405  0.020  1.405
 7NU  O5   C5   single    1.414  0.020  1.414
 7NU  C2   C3   single    1.524  0.020  1.524
 7NU  O6   C7   single    1.422  0.020  1.422
 7NU  O6   C6   single    1.413  0.020  1.413
 7NU  C5   C6   single    1.506  0.020  1.506
 7NU  C5   C4   single    1.524  0.020  1.524
 7NU  C7   C6   single    1.457  0.020  1.457
 7NU  C3   C4   single    1.527  0.020  1.527
 7NU  C3   O3   single    1.404  0.020  1.404
 7NU  C4   O4   single    1.404  0.020  1.404
 7NU  O2   H1   single    0.850  0.020  0.980
 7NU  C2   H2   single    0.970  0.020  1.090
 7NU  C3   H3   single    0.970  0.020  1.090
 7NU  O3   H4   single    0.850  0.020  0.980
 7NU  C1   H5   single    0.970  0.020  1.090
 7NU  C5   H6   single    0.970  0.020  1.090
 7NU  C6   H7   single    0.970  0.020  1.090
 7NU  C7   H8   single    0.970  0.020  1.090
 7NU  C7   H9   single    0.970  0.020  1.090
 7NU  C4   H10  single    0.970  0.020  1.090
 7NU  O4   H11  single    0.850  0.020  0.980
 7NU  C9   H12  single    0.930  0.020  1.080
 7NU  C10  H13  single    0.930  0.020  1.080
 7NU  C11  H14  single    0.930  0.020  1.080
 7NU  C12  H15  single    0.930  0.020  1.080
 7NU  C13  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
 7NU  H1   O2   C2   109.00  3.000
 7NU  H2   C2   C1   108.33  3.000
 7NU  H2   C2   C3   109.16  3.000
 7NU  C1   C2   C3   108.60  3.000
 7NU  H2   C2   O2   111.67  3.000
 7NU  C3   C2   O2   107.62  3.000
 7NU  C1   C2   O2   111.38  3.000
 7NU  H3   C3   C4   107.41  3.000
 7NU  H3   C3   O3   110.82  3.000
 7NU  C4   C3   O3   107.89  3.000
 7NU  H3   C3   C2   107.91  3.000
 7NU  O3   C3   C2   112.20  3.000
 7NU  C4   C3   C2   110.52  3.000
 7NU  H4   O3   C3   108.59  3.000
 7NU  H5   C1   O1   110.53  3.000
 7NU  H5   C1   O5   110.30  3.000
 7NU  O1   C1   O5   108.03  3.000
 7NU  H5   C1   C2   109.50  3.000
 7NU  O5   C1   C2   110.63  3.000
 7NU  O1   C1   C2   107.82  3.000
 7NU  C5   O5   C1   112.72  3.000
 7NU  H6   C5   C4   107.48  3.000
 7NU  H6   C5   C6   108.87  3.000
 7NU  C4   C5   C6   113.08  3.000
 7NU  H6   C5   O5   110.35  3.000
 7NU  C4   C5   O5   110.95  3.000
 7NU  C6   C5   O5   106.11  3.000
 7NU  H7   C6   C7   118.57  3.000
 7NU  H7   C6   O6   115.30  3.000
 7NU  C7   C6   O6    59.36  3.000
 7NU  H7   C6   C5   115.69  3.000
 7NU  C7   C6   C5   120.29  3.000
 7NU  O6   C6   C5   115.18  3.000
 7NU  C7   O6   C6    61.87  3.000
 7NU  H9   C7   H8   115.09  3.000
 7NU  H9   C7   O6   115.75  3.000
 7NU  H8   C7   O6   115.82  3.000
 7NU  H9   C7   C6   119.68  3.000
 7NU  H8   C7   C6   119.55  3.000
 7NU  O6   C7   C6    58.77  3.000
 7NU  H10  C4   O4   111.45  3.000
 7NU  H10  C4   C5   107.68  3.000
 7NU  O4   C4   C5   108.47  3.000
 7NU  H10  C4   C3   108.32  3.000
 7NU  O4   C4   C3   112.08  3.000
 7NU  C5   C4   C3   108.72  3.000
 7NU  H11  O4   C4   108.33  3.000
 7NU  C8   O1   C1   119.79  3.000
 7NU  C13  C8   C9   120.04  3.000
 7NU  C9   C8   O1   115.82  3.000
 7NU  C13  C8   O1   124.14  3.000
 7NU  H12  C9   C10  120.59  3.000
 7NU  H12  C9   C8   119.47  3.000
 7NU  C10  C9   C8   119.95  3.000
 7NU  H13  C10  C11  120.17  3.000
 7NU  H13  C10  C9   119.32  3.000
 7NU  C11  C10  C9   120.51  3.000
 7NU  H14  C11  C12  120.41  3.000
 7NU  H14  C11  C10  120.43  3.000
 7NU  C12  C11  C10  119.17  3.000
 7NU  H15  C12  C13  118.92  3.000
 7NU  H15  C12  C11  120.05  3.000
 7NU  C13  C12  C11  121.03  3.000
 7NU  H16  C13  C12  119.02  3.000
 7NU  H16  C13  C8   121.67  3.000
 7NU  C12  C13  C8   119.30  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
 7NU  CONST_01  C11  C12  C13  C8     0.00   0.0  0
 7NU  CONST_02  C11  C10  C9   C8     0.00   0.0  0
 7NU  CONST_03  C12  C11  C10  C9     0.00   0.0  0
 7NU  CONST_04  C12  C13  C8   C9     0.00   0.0  0
 7NU  CONST_05  C13  C12  C11  C10    0.00   0.0  0
 7NU  CONST_06  C13  C8   C9   C10    0.00   0.0  0
 7NU  CONST_07  C12  C13  C8   O1   180.00   0.0  0
 7NU  CONST_08  C10  C9   C8   O1   180.00   0.0  0
 7NU  CONST_09  H15  C12  C13  C8   180.00   0.0  0
 7NU  CONST_10  H13  C10  C9   C8   180.00   0.0  0
 7NU  CONST_11  H14  C11  C10  C9   180.00   0.0  0
 7NU  CONST_12  H16  C13  C8   C9   180.00   0.0  0
 7NU  CONST_13  H12  C9   C10  C11  180.00   0.0  0
 7NU  Var_01    C13  C8   O1   C1    19.28  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
 7NU  chir_01  C2  C1  O2  C3  positiv
 7NU  chir_02  C3  O3  C2  C4  positiv
 7NU  chir_03  C1  O1  O5  C2  positiv
 7NU  chir_04  C5  O5  C6  C4  positiv
 7NU  chir_06  C4  C5  C3  O4  negativ
 7NU  chir_07  C6  O6  C5  C7  both

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
 7NU  plan-1  O1   0.020
 7NU  plan-1  C8   0.020
 7NU  plan-1  C9   0.020
 7NU  plan-1  C10  0.020
 7NU  plan-1  C11  0.020
 7NU  plan-1  C12  0.020
 7NU  plan-1  C13  0.020
 7NU  plan-1  H12  0.020
 7NU  plan-1  H13  0.020
 7NU  plan-1  H14  0.020
 7NU  plan-1  H15  0.020
 7NU  plan-1  H16  0.020

