# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 00:48:00 2022
#   Inital geometry file: a 97 line input string
#   Ligand name: methyl 2,3,6-tri-O-sulfo-alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1O[C@H](CO[S](O)(=O)=O)[C@@H](O)[C@H](O[S](O)(=O)=O)[C@H]1O[S](O)(=O)=O
#
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
 Z9L  Z9L  'methyl 2,3,6-tri-O-sulfo-alpha-D-glucopyranoside'  D-saccharide  36  25  .  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_Z9L
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
 Z9L  O4   O  OH1    0  -0.699  69.2099   1.1141  -17.9015
 Z9L  C4   C  CH1    0   0.052  68.6367   1.2962  -19.1680
 Z9L  C5   C  CH1    0  -0.014  69.7159   0.9251  -20.1910
 Z9L  O5   O  O2     0  -0.501  69.2797   1.1793  -21.5143
 Z9L  C6   C  CH2    0  -0.192  70.1379  -0.5276  -20.1199
 Z9L  O6   O  OC2    0  -0.615  69.0029  -1.3550  -20.3159
 Z9L  S1   S  S      0   1.574  69.1752  -2.9680  -20.0302
 Z9L  O7   O  OS     0  -0.742  69.6302  -3.0755  -18.6416
 Z9L  O11  O  OS     0  -0.743  70.1591  -3.4375  -21.0091
 Z9L  O15  O  OS    -1  -0.730  67.8094  -3.4293  -20.2636
 Z9L  C3   C  CH1    0  -0.042  68.1544   2.7306  -19.4031
 Z9L  O3   O  OC2    0  -0.618  66.9605   2.9771  -18.6655
 Z9L  S2   S  S      0   1.583  67.0196   3.7222  -17.2069
 Z9L  O8   O  OS     0  -0.743  67.6401   2.7312  -16.3038
 Z9L  O9   O  OS    -1  -0.713  65.6038   3.9456  -16.9489
 Z9L  O10  O  OS     0  -0.721  67.8230   4.9283  -17.3919
 Z9L  C2   C  CH1    0  -0.012  67.7888   2.9343  -20.8660
 Z9L  O2   O  OC2    0  -0.618  67.4730   4.2944  -21.0728
 Z9L  S3   S  S      0   1.560  66.1257   4.6501  -21.9596
 Z9L  O12  O  OS    -1  -0.731  64.9886   4.2403  -21.1356
 Z9L  O13  O  OS     0  -0.734  66.2637   3.8800  -23.1994
 Z9L  O14  O  OS     0  -0.725  66.2830   6.0928  -22.1107
 Z9L  C1   C  CH1    0   0.264  68.9413   2.5125  -21.7740
 Z9L  O1   O  O2     0  -0.489  69.9954   3.3891  -21.5687
 Z9L  C7   C  CH3    0  -0.406  71.0381   3.2894  -22.5133
 Z9L  H4   H  HCH1   0   0.206  67.7672   0.6378  -19.3144
 Z9L  H5   H  HCH1   0   0.234  70.6154   1.5134  -19.9608
 Z9L  H61  H  HCH2   0   0.233  70.8941  -0.7132  -20.8905
 Z9L  H62  H  HCH2   0   0.230  70.6021  -0.7088  -19.1477
 Z9L  H3   H  HCH1   0   0.247  68.9436   3.4363  -19.1175
 Z9L  H2   H  HCH1   0   0.252  66.9400   2.2793  -21.0988
 Z9L  H1   H  HCH1   0   0.236  68.6168   2.5284  -22.8224
 Z9L  H71  H  HCH3   0   0.236  71.7079   4.1317  -22.3489
 Z9L  H72  H  HCH3   0   0.216  71.6142   2.3658  -22.4086
 Z9L  H73  H  HCH3   0   0.213  70.6578   3.3436  -23.5392
 Z9L  HO4  H  HOH1   0   0.450  68.6594   1.5574  -17.2306

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
 Z9L  O4  C4   single  1.402  0.020  1.402
 Z9L  C4  C5   single  1.533  0.020  1.533
 Z9L  C4  C3   single  1.532  0.020  1.532
 Z9L  C4  H4   single  0.970  0.020  1.090
 Z9L  C5  O5   single  1.416  0.020  1.416
 Z9L  C5  C6   single  1.514  0.020  1.514
 Z9L  C5  H5   single  0.970  0.020  1.090
 Z9L  O5  C1   single  1.400  0.020  1.400
 Z9L  C6  O6   single  1.418  0.020  1.418
 Z9L  C6  H61  single  0.970  0.020  1.090
 Z9L  C6  H62  single  0.970  0.020  1.090
 Z9L  O6  S1   single  1.647  0.020  1.647
 Z9L  S1  O7   deloc   1.465  0.020  1.465
 Z9L  S1  O11  deloc   1.465  0.020  1.465
 Z9L  S1  O15  deloc   1.460  0.020  1.460
 Z9L  C3  O3   single  1.425  0.020  1.425
 Z9L  C3  C2   single  1.522  0.020  1.522
 Z9L  C3  H3   single  0.970  0.020  1.090
 Z9L  O3  S2   single  1.639  0.020  1.639
 Z9L  S2  O8   deloc   1.477  0.020  1.477
 Z9L  S2  O9   deloc   1.456  0.020  1.456
 Z9L  S2  O10  deloc   1.461  0.020  1.461
 Z9L  C2  O2   single  1.412  0.020  1.412
 Z9L  C2  C1   single  1.527  0.020  1.527
 Z9L  C2  H2   single  0.970  0.020  1.090
 Z9L  O2  S3   single  1.652  0.020  1.652
 Z9L  S3  O12  deloc   1.463  0.020  1.463
 Z9L  S3  O13  deloc   1.466  0.020  1.466
 Z9L  S3  O14  deloc   1.459  0.020  1.459
 Z9L  C1  O1   single  1.386  0.020  1.386
 Z9L  C1  H1   single  0.970  0.020  1.090
 Z9L  O1  C7   single  1.410  0.020  1.410
 Z9L  C7  H71  single  0.970  0.020  1.090
 Z9L  C7  H72  single  0.970  0.020  1.090
 Z9L  C7  H73  single  0.970  0.020  1.090
 Z9L  O4  HO4  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
 Z9L  HO4  O4  C4   109.39  3.000
 Z9L  H4   C4  C3   106.92  3.000
 Z9L  H4   C4  C5   108.83  3.000
 Z9L  C3   C4  C5   110.25  3.000
 Z9L  H4   C4  O4   111.44  3.000
 Z9L  C3   C4  O4   112.90  3.000
 Z9L  C5   C4  O4   106.48  3.000
 Z9L  H5   C5  C6   105.99  3.000
 Z9L  H5   C5  O5   110.59  3.000
 Z9L  C6   C5  O5   107.57  3.000
 Z9L  H5   C5  C4   107.87  3.000
 Z9L  C6   C5  C4   113.40  3.000
 Z9L  O5   C5  C4   111.31  3.000
 Z9L  C1   O5  C5   114.75  3.000
 Z9L  H62  C6  H61  107.73  3.000
 Z9L  H62  C6  O6   111.49  3.000
 Z9L  H61  C6  O6   110.88  3.000
 Z9L  H62  C6  C5   108.62  3.000
 Z9L  H61  C6  C5   108.77  3.000
 Z9L  O6   C6  C5   109.28  3.000
 Z9L  S1   O6  C6   117.62  3.000
 Z9L  O15  S1  O11  114.84  3.000
 Z9L  O15  S1  O7   114.75  3.000
 Z9L  O11  S1  O7   113.65  3.000
 Z9L  O15  S1  O6   100.59  3.000
 Z9L  O11  S1  O6   105.55  3.000
 Z9L  O7   S1  O6   105.59  3.000
 Z9L  H3   C3  C2   109.71  3.000
 Z9L  H3   C3  O3   110.91  3.000
 Z9L  C2   C3  O3   105.86  3.000
 Z9L  H3   C3  C4   109.64  3.000
 Z9L  C2   C3  C4   110.40  3.000
 Z9L  O3   C3  C4   110.27  3.000
 Z9L  S2   O3  C3   120.61  3.000
 Z9L  O10  S2  O9   115.49  3.000
 Z9L  O10  S2  O8   113.59  3.000
 Z9L  O9   S2  O8   113.76  3.000
 Z9L  O10  S2  O3   106.41  3.000
 Z9L  O9   S2  O3   101.09  3.000
 Z9L  O8   S2  O3   104.72  3.000
 Z9L  H2   C2  C1   107.03  3.000
 Z9L  H2   C2  O2   111.79  3.000
 Z9L  C1   C2  O2   110.36  3.000
 Z9L  H2   C2  C3   108.06  3.000
 Z9L  C1   C2  C3   110.70  3.000
 Z9L  O2   C2  C3   108.88  3.000
 Z9L  S3   O2  C2   117.94  3.000
 Z9L  O14  S3  O13  114.94  3.000
 Z9L  O14  S3  O12  114.78  3.000
 Z9L  O13  S3  O12  113.73  3.000
 Z9L  O14  S3  O2   100.40  3.000
 Z9L  O13  S3  O2   105.31  3.000
 Z9L  O12  S3  O2   105.75  3.000
 Z9L  H1   C1  O1   110.92  3.000
 Z9L  H1   C1  C2   109.93  3.000
 Z9L  O1   C1  C2   108.13  3.000
 Z9L  H1   C1  O5   105.22  3.000
 Z9L  O1   C1  O5   113.02  3.000
 Z9L  C2   C1  O5   109.59  3.000
 Z9L  C7   O1  C1   114.72  3.000
 Z9L  H73  C7  H72  108.32  3.000
 Z9L  H73  C7  H71  108.46  3.000
 Z9L  H72  C7  H71  108.35  3.000
 Z9L  H73  C7  O1   111.53  3.000
 Z9L  H72  C7  O1   112.65  3.000
 Z9L  H71  C7  O1   107.40  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
 Z9L  Var_01  O8   S2  O3  C3  -70.28  30.0  3
 Z9L  Var_02  O12  S3  O2  C2   68.93  30.0  3
 Z9L  Var_03  H71  C7  O1  C1  170.31  30.0  3
 Z9L  Var_04  O7   S1  O6  C6   57.28  30.0  3
 Z9L  Var_05  H61  C6  O6  S1   70.14  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
 Z9L  chir_01  C4  O4  C5  C3  positiv
 Z9L  chir_02  C5  O5  C4  C6  negativ
 Z9L  chir_03  C3  O3  C4  C2  negativ
 Z9L  chir_04  C2  O2  C3  C1  positiv
 Z9L  chir_05  C1  O5  O1  C2  positiv

