# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 17:05:41 2021
#   Inital geometry file: a 91 line input string
#   Ligand name: 3,4-di-O-methyl-2,6-di-O-sulfo-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1[C@@H](CO[S](O)(=O)=O)O[C@H](O)[C@H](O[S](O)(=O)=O)[C@H]1OC
#
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
 Z9H  Z9H  3,4-di-O-methyl-2,6-di-O-sulfo-alpha-D-glucopyranose  D-saccharide  38  22  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Z9H
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
 Z9H  O4    O  O2    0  -0.494  53.8382  -3.2107   -8.9403
 Z9H  C7    C  CH3   0  -0.413  52.5563  -3.5045   -8.4292
 Z9H  C4    C  CH1   0   0.022  54.0195  -1.8863   -9.3657
 Z9H  C5    C  CH1   0  -0.015  54.4863  -1.8790  -10.8269
 Z9H  O5    O  O2    0  -0.497  54.7915  -0.5610  -11.2414
 Z9H  C6    C  CH2   0  -0.203  53.3885  -2.3809  -11.7333
 Z9H  O6    O  OC2   0  -0.573  53.9457  -2.4780  -13.0638
 Z9H  S1    S  S     0   1.659  52.9786  -2.3834  -14.3119
 Z9H  O7    O  OS    0  -0.704  52.5194  -0.8662  -14.2983
 Z9H  O8    O  OS    0  -0.633  51.7710  -3.1266  -14.0732
 Z9H  O12   O  OS    0  -0.619  53.8153  -2.6526  -15.4482
 Z9H  C3    C  CH1   0   0.026  55.0647  -1.2056   -8.4827
 Z9H  O3    O  O2    0  -0.489  54.5659  -1.0515   -7.1831
 Z9H  C8    C  CH3   0  -0.408  55.2887  -1.7302   -6.1808
 Z9H  C2    C  CH1   0  -0.053  55.3853   0.1647   -9.0612
 Z9H  O2    O  OC2   0  -0.576  56.4596   0.7273   -8.2841
 Z9H  S2    S  S     0   1.654  56.3247   2.1668   -7.6421
 Z9H  O9    O  OS    0  -0.628  55.0631   2.3189   -6.9643
 Z9H  O10   O  OS    0  -0.707  56.3372   3.0923   -8.9340
 Z9H  O11   O  OS    0  -0.616  57.5688   2.3637   -6.9564
 Z9H  C1    C  CH1   0   0.254  55.8145   0.0767  -10.5245
 Z9H  O1    O  OH1   0  -0.656  57.0238  -0.5910  -10.5830
 Z9H  HO1   H  HOH1  0   0.472  57.4166  -0.4620  -11.4533
 Z9H  H11   H  HCH3  0   0.238  52.5576  -4.5517   -8.1309
 Z9H  H12   H  HCH3  0   0.221  52.3107  -2.8947   -7.5557
 Z9H  H13   H  HCH3  0   0.212  51.7713  -3.3626   -9.1799
 Z9H  H4    H  HCH1  0   0.241  53.0835  -1.3123   -9.2959
 Z9H  H5    H  HCH1  0   0.256  55.3605  -2.5365  -10.9194
 Z9H  H61   H  HCH2  0   0.278  53.0527  -3.3701  -11.4242
 Z9H  H62   H  HCH2  0   0.263  52.5409  -1.6912  -11.7144
 Z9H  HO7   H  H     0   0.512  53.2358  -0.2522  -14.5364
 Z9H  H3    H  HCH1  0   0.251  55.9739  -1.8222   -8.4879
 Z9H  H6    H  HCH3  0   0.235  54.8107  -1.5064   -5.2281
 Z9H  H7    H  HCH3  0   0.214  55.2772  -2.8141   -6.3272
 Z9H  H63   H  HCH3  0   0.213  56.3308  -1.4000   -6.1282
 Z9H  H2    H  HCH1  0   0.294  54.4907   0.7927   -9.0017
 Z9H  HO10  H  H     0   0.515  55.4953   3.5601   -9.0640
 Z9H  H1    H  HCH1  0   0.255  55.8804   1.0779  -10.9625

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
 Z9H  O4   C7    single  1.411  0.020  1.411
 Z9H  O4   C4    single  1.403  0.020  1.403
 Z9H  C7   H11   single  0.970  0.020  1.090
 Z9H  C7   H12   single  0.970  0.020  1.090
 Z9H  C7   H13   single  0.970  0.020  1.090
 Z9H  C4   C5    single  1.534  0.020  1.534
 Z9H  C4   C3    single  1.528  0.020  1.528
 Z9H  C4   H4    single  0.970  0.020  1.090
 Z9H  C5   O5    single  1.415  0.020  1.415
 Z9H  C5   C6    single  1.510  0.020  1.510
 Z9H  C5   H5    single  0.970  0.020  1.090
 Z9H  O5   C1    single  1.403  0.020  1.403
 Z9H  C6   O6    single  1.446  0.020  1.446
 Z9H  C6   H61   single  0.970  0.020  1.090
 Z9H  C6   H62   single  0.970  0.020  1.090
 Z9H  O6   S1    single  1.582  0.020  1.582
 Z9H  S1   O7    single  1.585  0.020  1.585
 Z9H  S1   O8    double  1.438  0.020  1.438
 Z9H  S1   O12   double  1.437  0.020  1.437
 Z9H  O7   HO7   single  0.850  0.020  0.980
 Z9H  C3   O3    single  1.400  0.020  1.400
 Z9H  C3   C2    single  1.522  0.020  1.522
 Z9H  C3   H3    single  0.970  0.020  1.090
 Z9H  O3   C8    single  1.410  0.020  1.410
 Z9H  C8   H6    single  0.970  0.020  1.090
 Z9H  C8   H7    single  0.970  0.020  1.090
 Z9H  C8   H63   single  0.970  0.020  1.090
 Z9H  C2   O2    single  1.440  0.020  1.440
 Z9H  C2   C1    single  1.528  0.020  1.528
 Z9H  C2   H2    single  0.970  0.020  1.090
 Z9H  O2   S2    single  1.582  0.020  1.582
 Z9H  S2   O9    double  1.440  0.020  1.440
 Z9H  S2   O10   single  1.589  0.020  1.589
 Z9H  S2   O11   double  1.434  0.020  1.434
 Z9H  O10  HO10  single  0.850  0.020  0.980
 Z9H  C1   O1    single  1.383  0.020  1.383
 Z9H  C1   H1    single  0.970  0.020  1.090
 Z9H  HO1  O1    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
 Z9H  C4    O4   C7   115.08  3.000
 Z9H  H13   C7   H12  108.32  3.000
 Z9H  H13   C7   H11  108.25  3.000
 Z9H  H12   C7   H11  108.53  3.000
 Z9H  H13   C7   O4   112.08  3.000
 Z9H  H12   C7   O4   112.18  3.000
 Z9H  H11   C7   O4   107.36  3.000
 Z9H  H4    C4   C3   108.23  3.000
 Z9H  H4    C4   C5   108.47  3.000
 Z9H  C3    C4   C5   109.89  3.000
 Z9H  H4    C4   O4   111.31  3.000
 Z9H  C3    C4   O4   109.49  3.000
 Z9H  C5    C4   O4   109.43  3.000
 Z9H  H5    C5   C6   109.23  3.000
 Z9H  H5    C5   O5   111.19  3.000
 Z9H  C6    C5   O5   106.90  3.000
 Z9H  H5    C5   C4   108.65  3.000
 Z9H  C6    C5   C4   110.43  3.000
 Z9H  O5    C5   C4   110.44  3.000
 Z9H  C1    O5   C5   115.54  3.000
 Z9H  H62   C6   H61  109.22  3.000
 Z9H  H62   C6   O6   110.93  3.000
 Z9H  H61   C6   O6   108.60  3.000
 Z9H  H62   C6   C5   110.11  3.000
 Z9H  H61   C6   C5   110.84  3.000
 Z9H  O6    C6   C5   107.13  3.000
 Z9H  S1    O6   C6   119.11  3.000
 Z9H  O12   S1   O8   121.58  3.000
 Z9H  O12   S1   O7   110.78  3.000
 Z9H  O8    S1   O7   104.48  3.000
 Z9H  O12   S1   O6   104.88  3.000
 Z9H  O8    S1   O6   110.59  3.000
 Z9H  O7    S1   O6   103.16  3.000
 Z9H  HO7   O7   S1   112.86  3.000
 Z9H  H3    C3   C2   109.22  3.000
 Z9H  H3    C3   O3   111.16  3.000
 Z9H  C2    C3   O3   109.19  3.000
 Z9H  H3    C3   C4   108.25  3.000
 Z9H  C2    C3   C4   109.00  3.000
 Z9H  O3    C3   C4   109.98  3.000
 Z9H  C8    O3   C3   115.10  3.000
 Z9H  H63   C8   H7   108.39  3.000
 Z9H  H63   C8   H6   108.29  3.000
 Z9H  H7    C8   H6   108.43  3.000
 Z9H  H63   C8   O3   112.16  3.000
 Z9H  H7    C8   O3   112.12  3.000
 Z9H  H6    C8   O3   107.33  3.000
 Z9H  H2    C2   C1   108.34  3.000
 Z9H  H2    C2   O2   110.87  3.000
 Z9H  C1    C2   O2   109.25  3.000
 Z9H  H2    C2   C3   108.89  3.000
 Z9H  C1    C2   C3   111.81  3.000
 Z9H  O2    C2   C3   107.69  3.000
 Z9H  S2    O2   C2   120.71  3.000
 Z9H  O11   S2   O10  107.57  3.000
 Z9H  O11   S2   O9   121.36  3.000
 Z9H  O10   S2   O9   109.15  3.000
 Z9H  O11   S2   O2   104.18  3.000
 Z9H  O10   S2   O2   101.50  3.000
 Z9H  O9    S2   O2   111.21  3.000
 Z9H  HO10  O10  S2   112.47  3.000
 Z9H  H1    C1   O1   111.84  3.000
 Z9H  H1    C1   C2   110.33  3.000
 Z9H  O1    C1   C2   108.31  3.000
 Z9H  H1    C1   O5   104.79  3.000
 Z9H  O1    C1   O5   113.38  3.000
 Z9H  C2    C1   O5   108.12  3.000
 Z9H  HO1   O1   C1   109.28  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
 Z9H  Var_01  O9   S2  O2  C2    47.35  30.0  3
 Z9H  Var_02  H11  C7  O4  C4  -179.47  30.0  3
 Z9H  Var_03  H6   C8  O3  C3   178.67  30.0  3
 Z9H  Var_04  O7   S1  O6  C6    69.75  30.0  3
 Z9H  Var_05  H61  C6  O6  S1    85.47  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
 Z9H  chir_01  C4  O4  C5  C3  positiv
 Z9H  chir_02  C5  O5  C4  C6  negativ
 Z9H  chir_03  C3  O3  C4  C2  negativ
 Z9H  chir_04  C2  O2  C3  C1  positiv
 Z9H  chir_05  C1  O5  O1  C2  positiv

