# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 01:54:20 2022
#   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  36  22  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  53.7233  -3.1297   -9.2000
 Z9H  C7   C  CH3    0  -0.406  52.5134  -3.4147   -8.5370
 Z9H  C4   C  CH1    0   0.029  53.9552  -1.7697   -9.4703
 Z9H  C5   C  CH1    0  -0.011  54.4079  -1.6329  -10.9270
 Z9H  O5   O  O2     0  -0.493  54.7410  -0.2853  -11.2114
 Z9H  C6   C  CH2    0  -0.168  53.3172  -2.0286  -11.8981
 Z9H  O6   O  OC2    0  -0.615  53.8636  -1.9648  -13.2061
 Z9H  S1   S  S      0   1.569  53.0758  -2.7812  -14.3972
 Z9H  O7   O  OS    -1  -0.729  53.8857  -2.4206  -15.5573
 Z9H  O8   O  OS     0  -0.742  51.7134  -2.2429  -14.4047
 Z9H  O12  O  OS     0  -0.742  53.1500  -4.1938  -14.0156
 Z9H  C3   C  CH1    0   0.040  55.0427  -1.2286   -8.5433
 Z9H  O3   O  O2     0  -0.492  54.5701  -1.2668   -7.2214
 Z9H  C8   C  CH3    0  -0.405  55.4902  -1.7332   -6.2618
 Z9H  C2   C  CH1    0  -0.052  55.4037   0.1941   -8.9545
 Z9H  O2   O  OC2    0  -0.629  56.5258   0.6151   -8.1938
 Z9H  S2   S  S      0   1.567  56.5327   2.1612   -7.5960
 Z9H  O9   O  OS     0  -0.730  55.4802   2.1835   -6.5804
 Z9H  O10  O  OS    -1  -0.727  56.2638   3.0197   -8.7517
 Z9H  O11  O  OS     0  -0.722  57.8911   2.2336   -7.0702
 Z9H  C1   C  CH1    0   0.263  55.7554   0.2693  -10.4450
 Z9H  O1   O  OH1    0  -0.665  56.9502  -0.3987  -10.7304
 Z9H  HO1  H  HOH1   0   0.453  57.6136  -0.1302  -10.0839
 Z9H  H11  H  HCH3   0   0.230  52.4498  -4.4970   -8.4279
 Z9H  H12  H  HCH3   0   0.214  52.4657  -2.9634   -7.5430
 Z9H  H13  H  HCH3   0   0.208  51.6422  -3.0785   -9.1101
 Z9H  H4   H  HCH1   0   0.226  53.0378  -1.1770   -9.3305
 Z9H  H5   H  HCH1   0   0.232  55.2709  -2.2928  -11.0870
 Z9H  H61  H  HCH2   0   0.230  52.9795  -3.0397  -11.6556
 Z9H  H62  H  HCH2   0   0.219  52.4614  -1.3513  -11.8002
 Z9H  H3   H  HCH1   0   0.222  55.9280  -1.8722   -8.6546
 Z9H  H6   H  HCH3   0   0.228  54.9519  -1.8443   -5.3210
 Z9H  H7   H  HCH3   0   0.207  55.9039  -2.7099   -6.5351
 Z9H  H63  H  HCH3   0   0.210  56.3222  -1.0430   -6.1030
 Z9H  H2   H  HCH1   0   0.248  54.5324   0.8361   -8.7753
 Z9H  H1   H  HCH1   0   0.227  55.8108   1.3209  -10.7498

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  1.409  0.020  1.409
 Z9H  O4   C4   single  1.406  0.020  1.406
 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  1.532  0.020  1.532
 Z9H  C4   C3   single  1.528  0.020  1.528
 Z9H  C4   H4   single  0.970  0.020  1.090
 Z9H  C5   O5   single  1.417  0.020  1.417
 Z9H  C5   C6   single  1.513  0.020  1.513
 Z9H  C5   H5   single  0.970  0.020  1.090
 Z9H  O5   C1   single  1.387  0.020  1.387
 Z9H  C6   O6   single  1.419  0.020  1.419
 Z9H  C6   H61  single  0.970  0.020  1.090
 Z9H  C6   H62  single  0.970  0.020  1.090
 Z9H  O6   S1   single  1.645  0.020  1.645
 Z9H  S1   O7   deloc   1.460  0.020  1.460
 Z9H  S1   O8   deloc   1.465  0.020  1.465
 Z9H  S1   O12  deloc   1.465  0.020  1.465
 Z9H  C3   O3   single  1.404  0.020  1.404
 Z9H  C3   C2   single  1.524  0.020  1.524
 Z9H  C3   H3   single  0.970  0.020  1.090
 Z9H  O3   C8   single  1.409  0.020  1.409
 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  1.420  0.020  1.420
 Z9H  C2   C1   single  1.533  0.020  1.533
 Z9H  C2   H2   single  0.970  0.020  1.090
 Z9H  O2   S2   single  1.658  0.020  1.658
 Z9H  S2   O9   deloc   1.463  0.020  1.463
 Z9H  S2   O10  deloc   1.465  0.020  1.465
 Z9H  S2   O11  deloc   1.458  0.020  1.458
 Z9H  C1   O1   single  1.398  0.020  1.398
 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   115.33  3.000
 Z9H  H13  C7  H12  108.32  3.000
 Z9H  H13  C7  H11  108.10  3.000
 Z9H  H12  C7  H11  108.46  3.000
 Z9H  H13  C7  O4   112.00  3.000
 Z9H  H12  C7  O4   112.46  3.000
 Z9H  H11  C7  O4   107.35  3.000
 Z9H  H4   C4  C3   108.99  3.000
 Z9H  H4   C4  C5   108.60  3.000
 Z9H  C3   C4  C5   109.57  3.000
 Z9H  H4   C4  O4   111.03  3.000
 Z9H  C3   C4  O4   110.08  3.000
 Z9H  C5   C4  O4   108.55  3.000
 Z9H  H5   C5  C6   108.41  3.000
 Z9H  H5   C5  O5   110.95  3.000
 Z9H  C6   C5  O5   106.82  3.000
 Z9H  H5   C5  C4   108.49  3.000
 Z9H  C6   C5  C4   111.96  3.000
 Z9H  O5   C5  C4   110.21  3.000
 Z9H  C1   O5  C5   116.18  3.000
 Z9H  H62  C6  H61  108.10  3.000
 Z9H  H62  C6  O6   110.81  3.000
 Z9H  H61  C6  O6   111.41  3.000
 Z9H  H62  C6  C5   110.12  3.000
 Z9H  H61  C6  C5   108.80  3.000
 Z9H  O6   C6  C5   107.59  3.000
 Z9H  S1   O6  C6   117.43  3.000
 Z9H  O12  S1  O8   113.75  3.000
 Z9H  O12  S1  O7   114.65  3.000
 Z9H  O8   S1  O7   114.90  3.000
 Z9H  O12  S1  O6   105.41  3.000
 Z9H  O8   S1  O6   105.47  3.000
 Z9H  O7   S1  O6   100.78  3.000
 Z9H  H3   C3  C2   109.15  3.000
 Z9H  H3   C3  O3   110.49  3.000
 Z9H  C2   C3  O3   111.04  3.000
 Z9H  H3   C3  C4   107.71  3.000
 Z9H  C2   C3  C4   109.60  3.000
 Z9H  O3   C3  C4   108.78  3.000
 Z9H  C8   O3  C3   115.49  3.000
 Z9H  H63  C8  H7   108.18  3.000
 Z9H  H63  C8  H6   108.37  3.000
 Z9H  H7   C8  H6   108.13  3.000
 Z9H  H63  C8  O3   112.78  3.000
 Z9H  H7   C8  O3   111.83  3.000
 Z9H  H6   C8  O3   107.41  3.000
 Z9H  H2   C2  C1   108.19  3.000
 Z9H  H2   C2  O2   111.52  3.000
 Z9H  C1   C2  O2   108.97  3.000
 Z9H  H2   C2  C3   108.31  3.000
 Z9H  C1   C2  C3   111.24  3.000
 Z9H  O2   C2  C3   108.63  3.000
 Z9H  S2   O2  C2   118.24  3.000
 Z9H  O11  S2  O10  115.24  3.000
 Z9H  O11  S2  O9   114.78  3.000
 Z9H  O10  S2  O9   114.01  3.000
 Z9H  O11  S2  O2   100.38  3.000
 Z9H  O10  S2  O2   105.15  3.000
 Z9H  O9   S2  O2   105.17  3.000
 Z9H  H1   C1  O1   110.99  3.000
 Z9H  H1   C1  C2   109.20  3.000
 Z9H  O1   C1  C2   111.78  3.000
 Z9H  H1   C1  O5   105.48  3.000
 Z9H  O1   C1  O5   108.73  3.000
 Z9H  C2   C1  O5   110.48  3.000
 Z9H  HO1  O1  C1   108.54  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    68.19  30.0  3
 Z9H  Var_02  H11  C7  O4  C4   177.91  30.0  3
 Z9H  Var_03  H6   C8  O3  C3  -172.04  30.0  3
 Z9H  Var_04  O7   S1  O6  C6   177.32  30.0  3
 Z9H  Var_05  H61  C6  O6  S1    41.95  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

