# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 14:49:17 2021
#   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  39  25  .  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_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  -0.656  69.2631   0.8917  -18.0667
 Z9L  C4    C  CH1   0   0.027  68.7615   1.1274  -19.3500
 Z9L  C5    C  CH1   0  -0.011  69.8893   0.8872  -20.3585
 Z9L  O5    O  O2    0  -0.495  69.4541   1.1974  -21.6687
 Z9L  C6    C  CH2   0  -0.242  70.3909  -0.5350  -20.3611
 Z9L  O6    O  OC2   0  -0.576  69.3140  -1.4317  -20.7221
 Z9L  S1    S  S     0   1.652  68.9932  -2.6483  -19.7519
 Z9L  O7    O  OS    0  -0.625  68.2389  -2.1887  -18.6164
 Z9L  O11   O  OS    0  -0.626  70.1887  -3.4274  -19.5493
 Z9L  O15   O  OS    0  -0.691  67.9592  -3.3972  -20.6721
 Z9L  C3    C  CH1   0  -0.039  68.2802   2.5688  -19.4897
 Z9L  O3    O  OC2   0  -0.588  67.0904   2.7252  -18.6942
 Z9L  S2    S  S     0   1.647  67.0679   3.8225  -17.5340
 Z9L  O8    O  OS    0  -0.621  68.0189   3.4550  -16.5173
 Z9L  O9    O  OS    0  -0.690  65.5896   3.5769  -17.0537
 Z9L  O10   O  OS    0  -0.617  67.0931   5.1422  -18.0993
 Z9L  C2    C  CH1   0  -0.051  67.9112   2.8580  -20.9308
 Z9L  O2    O  OC2   0  -0.570  67.5919   4.2501  -21.0408
 Z9L  S3    S  S     0   1.656  66.2335   4.7123  -21.7241
 Z9L  O12   O  OS    0  -0.697  65.1440   4.3411  -20.6385
 Z9L  O13   O  OS    0  -0.627  66.0073   3.9419  -22.9209
 Z9L  O14   O  OS    0  -0.611  66.3193   6.1418  -21.7442
 Z9L  C1    C  CH1   0   0.275  69.0772   2.5310  -21.8652
 Z9L  O1    O  O2    0  -0.488  70.0906   3.4288  -21.6058
 Z9L  C7    C  CH3   0  -0.413  71.1377   3.4233  -22.5600
 Z9L  H4    H  HCH1  0   0.258  67.9223   0.4630  -19.5884
 Z9L  H5    H  HCH1  0   0.268  70.7538   1.5023  -20.0706
 Z9L  H61   H  HCH2  0   0.292  71.1764  -0.6605  -21.1055
 Z9L  H62   H  HCH2  0   0.278  70.8101  -0.7723  -19.3830
 Z9L  H6O   H  H     0   0.518  68.3778  -3.8771  -21.4078
 Z9L  H3    H  HCH1  0   0.298  69.0714   3.2479  -19.1538
 Z9L  H9O   H  H     0   0.518  65.4985   2.7935  -16.4834
 Z9L  H2    H  HCH1  0   0.307  67.0630   2.2303  -21.2226
 Z9L  H12O  H  H     0   0.515  64.6743   3.5136  -20.8357
 Z9L  H1    H  HCH1  0   0.263  68.7464   2.5862  -22.9104
 Z9L  H71   H  HCH3  0   0.246  71.7634   4.2895  -22.3572
 Z9L  H72   H  HCH3  0   0.225  71.7542   2.5240  -22.4937
 Z9L  H73   H  HCH3  0   0.223  70.7456   3.5030  -23.5784
 Z9L  HO4   H  HOH1  0   0.466  68.5881   0.4643  -17.5332

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  1.398  0.020  1.398
 Z9L  C4   C5    single  1.532  0.020  1.532
 Z9L  C4   C3    single  1.526  0.020  1.526
 Z9L  C4   H4    single  0.970  0.020  1.090
 Z9L  C5   O5    single  1.415  0.020  1.415
 Z9L  C5   C6    single  1.508  0.020  1.508
 Z9L  C5   H5    single  0.970  0.020  1.090
 Z9L  O5   C1    single  1.400  0.020  1.400
 Z9L  C6   O6    single  1.447  0.020  1.447
 Z9L  C6   H61   single  0.970  0.020  1.090
 Z9L  C6   H62   single  0.970  0.020  1.090
 Z9L  O6   S1    single  1.589  0.020  1.589
 Z9L  S1   O7    double  1.439  0.020  1.439
 Z9L  S1   O11   double  1.441  0.020  1.441
 Z9L  S1   O15   single  1.574  0.020  1.574
 Z9L  O15  H6O   single  0.850  0.020  0.980
 Z9L  C3   O3    single  1.440  0.020  1.440
 Z9L  C3   C2    single  1.515  0.020  1.515
 Z9L  C3   H3    single  0.970  0.020  1.090
 Z9L  O3   S2    single  1.597  0.020  1.597
 Z9L  S2   O8    double  1.440  0.020  1.440
 Z9L  S2   O9    single  1.574  0.020  1.574
 Z9L  S2   O10   double  1.436  0.020  1.436
 Z9L  O9   H9O   single  0.850  0.020  0.980
 Z9L  C2   O2    single  1.433  0.020  1.433
 Z9L  C2   C1    single  1.530  0.020  1.530
 Z9L  C2   H2    single  0.970  0.020  1.090
 Z9L  O2   S3    single  1.589  0.020  1.589
 Z9L  S3   O12   single  1.582  0.020  1.582
 Z9L  S3   O13   double  1.441  0.020  1.441
 Z9L  S3   O14   double  1.432  0.020  1.432
 Z9L  O12  H12O  single  0.850  0.020  0.980
 Z9L  C1   O1    single  1.379  0.020  1.379
 Z9L  C1   H1    single  0.970  0.020  1.090
 Z9L  O1   C7    single  1.417  0.020  1.417
 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   109.43  3.000
 Z9L  H4    C4   C3   108.12  3.000
 Z9L  H4    C4   C5   108.98  3.000
 Z9L  C3    C4   C5   108.66  3.000
 Z9L  H4    C4   O4   111.84  3.000
 Z9L  C3    C4   O4   110.89  3.000
 Z9L  C5    C4   O4   108.29  3.000
 Z9L  H5    C5   C6   105.46  3.000
 Z9L  H5    C5   O5   111.20  3.000
 Z9L  C6    C5   O5   107.90  3.000
 Z9L  H5    C5   C4   108.59  3.000
 Z9L  C6    C5   C4   113.20  3.000
 Z9L  O5    C5   C4   110.41  3.000
 Z9L  C1    O5   C5   114.94  3.000
 Z9L  H62   C6   H61  108.10  3.000
 Z9L  H62   C6   O6   112.03  3.000
 Z9L  H61   C6   O6   107.14  3.000
 Z9L  H62   C6   C5   109.36  3.000
 Z9L  H61   C6   C5   110.47  3.000
 Z9L  O6    C6   C5   109.71  3.000
 Z9L  S1    O6   C6   118.19  3.000
 Z9L  O15   S1   O11  111.71  3.000
 Z9L  O15   S1   O7   105.61  3.000
 Z9L  O11   S1   O7   119.78  3.000
 Z9L  O15   S1   O6    98.04  3.000
 Z9L  O11   S1   O6   109.41  3.000
 Z9L  O7    S1   O6   110.07  3.000
 Z9L  H6O   O15  S1   113.21  3.000
 Z9L  H3    C3   C2   110.44  3.000
 Z9L  H3    C3   O3   111.10  3.000
 Z9L  C2    C3   O3   107.67  3.000
 Z9L  H3    C3   C4   109.25  3.000
 Z9L  C2    C3   C4   110.13  3.000
 Z9L  O3    C3   C4   108.22  3.000
 Z9L  S2    O3   C3   119.19  3.000
 Z9L  O10   S2   O9   106.27  3.000
 Z9L  O10   S2   O8   120.06  3.000
 Z9L  O9    S2   O8   111.42  3.000
 Z9L  O10   S2   O3   110.19  3.000
 Z9L  O9    S2   O3    97.34  3.000
 Z9L  O8    S2   O3   109.16  3.000
 Z9L  H9O   O9   S2   113.10  3.000
 Z9L  H2    C2   C1   107.77  3.000
 Z9L  H2    C2   O2   111.34  3.000
 Z9L  C1    C2   O2   109.31  3.000
 Z9L  H2    C2   C3   109.43  3.000
 Z9L  C1    C2   C3   110.77  3.000
 Z9L  O2    C2   C3   108.23  3.000
 Z9L  S3    O2   C2   120.41  3.000
 Z9L  O14   S3   O13  122.10  3.000
 Z9L  O14   S3   O12  106.56  3.000
 Z9L  O13   S3   O12  109.65  3.000
 Z9L  O14   S3   O2   104.19  3.000
 Z9L  O13   S3   O2   109.62  3.000
 Z9L  O12   S3   O2   103.02  3.000
 Z9L  H12O  O12  S3   113.17  3.000
 Z9L  H1    C1   O1   111.59  3.000
 Z9L  H1    C1   C2   109.95  3.000
 Z9L  O1    C1   C2   107.83  3.000
 Z9L  H1    C1   O5   105.23  3.000
 Z9L  O1    C1   O5   113.34  3.000
 Z9L  C2    C1   O5   108.86  3.000
 Z9L  C7    O1   C1   114.46  3.000
 Z9L  H73   C7   H72  108.59  3.000
 Z9L  H73   C7   H71  108.77  3.000
 Z9L  H72   C7   H71  108.64  3.000
 Z9L  H73   C7   O1   111.21  3.000
 Z9L  H72   C7   O1   112.30  3.000
 Z9L  H71   C7   O1   107.25  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  -65.38  30.0  3
 Z9L  Var_02  O12  S3  O2  C2   73.31  30.0  3
 Z9L  Var_03  H71  C7  O1  C1  169.20  30.0  3
 Z9L  Var_04  O7   S1  O6  C6   78.37  30.0  3
 Z9L  Var_05  H61  C6  O6  S1  113.47  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
 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

