# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 12:56:55 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 2,3-di-O-sulfo-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O)[C@H](O[S](O)(=O)=O)[C@@H](O[S](O)(=O)=O)[C@@H]1O
#
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
 PDX  PDX  2,3-di-O-sulfo-alpha-D-glucopyranose  D-saccharide  32  20  .  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_PDX
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
 PDX  C1    C  CH1   0   0.249  -1.8356  -0.6076   1.0808
 PDX  C2    C  CH1   0  -0.044  -0.8897   0.0401   0.0689
 PDX  C3    C  CH1   0  -0.046   0.5395  -0.0231   0.5660
 PDX  C4    C  CH1   0   0.023   0.6462   0.6130   1.9507
 PDX  C5    C  CH1   0  -0.020  -0.3792  -0.0392   2.8840
 PDX  C6    C  CH2   0  -0.158  -0.4364   0.6710   4.2203
 PDX  O1    O  OH1   0  -0.656  -1.5494  -1.9597   1.1214
 PDX  O2    O  OC2   0  -0.575  -0.9534  -0.6668  -1.1774
 PDX  O3    O  OC2   0  -0.581   1.3535   0.7467  -0.3423
 PDX  O4    O  OH1   0  -0.656   1.9242   0.4220   2.4883
 PDX  O5    O  O2    0  -0.494  -1.6743   0.0384   2.3095
 PDX  O6    O  OH1   0  -0.669  -1.3063  -0.0388   5.0676
 PDX  O1S   O  OS    0  -0.611  -1.6213  -1.0324  -3.4383
 PDX  O2S   O  OS    0  -0.626  -2.9687   0.5231  -1.9973
 PDX  O3S   O  OS    0  -0.699  -0.7322   1.1457  -2.8465
 PDX  O1X   O  OS    0  -0.624   3.3201  -0.7706  -0.2797
 PDX  O2X   O  OS    0  -0.616   3.1718   1.2169  -1.8078
 PDX  O3X   O  OS    0  -0.698   1.8525  -0.7501  -2.2682
 PDX  S     S  S     0   1.657  -1.7062  -0.0274  -2.4209
 PDX  S'    S  S     0   1.651   2.5659   0.1016  -1.1418
 PDX  H1    H  HCH1  0   0.261  -2.8733  -0.4155   0.7893
 PDX  H2    H  HCH1  0   0.305  -1.1834   1.0877  -0.0522
 PDX  H3    H  HCH1  0   0.295   0.8870  -1.0597   0.6195
 PDX  H4    H  HCH1  0   0.249   0.4010   1.6804   1.8558
 PDX  H5    H  HCH1  0   0.242  -0.0906  -1.0861   3.0489
 PDX  H6C1  H  HCH2  0   0.200  -0.7713   1.7055   4.0614
 PDX  H6C2  H  HCH2  0   0.216   0.5783   0.7198   4.6280
 PDX  HA    H  HOH1  0   0.474  -2.2742  -2.4272   1.5513
 PDX  HB    H  HOH1  0   0.464   2.5037   1.1288   2.1904
 PDX  H6    H  HOH1  0   0.458  -1.2909   0.3849   5.9303
 PDX  H3S   H  H     0   0.516  -1.0673   2.0245  -2.6015
 PDX  HO'   H  H     0   0.513   1.7713  -1.6920  -2.0423

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
 PDX  C1   C2    single  1.529  0.020  1.529
 PDX  C1   O1    single  1.383  0.020  1.383
 PDX  C1   O5    single  1.398  0.020  1.398
 PDX  C1   H1    single  0.970  0.020  1.090
 PDX  C2   C3    single  1.514  0.020  1.514
 PDX  C2   O2    single  1.434  0.020  1.434
 PDX  C2   H2    single  0.970  0.020  1.090
 PDX  C3   C4    single  1.528  0.020  1.528
 PDX  C3   O3    single  1.442  0.020  1.442
 PDX  C3   H3    single  0.970  0.020  1.090
 PDX  C4   C5    single  1.532  0.020  1.532
 PDX  C4   O4    single  1.400  0.020  1.400
 PDX  C4   H4    single  0.970  0.020  1.090
 PDX  C5   C6    single  1.514  0.020  1.514
 PDX  C5   O5    single  1.419  0.020  1.419
 PDX  C5   H5    single  0.970  0.020  1.090
 PDX  C6   O6    single  1.407  0.020  1.407
 PDX  C6   H6C1  single  0.970  0.020  1.090
 PDX  C6   H6C2  single  0.970  0.020  1.090
 PDX  O1   HA    single  0.850  0.020  0.980
 PDX  O2   S     single  1.588  0.020  1.588
 PDX  O3   S'    single  1.589  0.020  1.589
 PDX  O4   HB    single  0.850  0.020  0.980
 PDX  O6   H6    single  0.850  0.020  0.980
 PDX  O1S  S     double  1.433  0.020  1.433
 PDX  O2S  S     double  1.441  0.020  1.441
 PDX  O3S  S     single  1.583  0.020  1.583
 PDX  O3S  H3S   single  0.850  0.020  0.980
 PDX  O1X  S'    double  1.440  0.020  1.440
 PDX  O2X  S'    double  1.433  0.020  1.433
 PDX  O3X  S'    single  1.582  0.020  1.582
 PDX  O3X  HO'   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
 PDX  H1    C1   O5    105.21  3.000
 PDX  H1    C1   O1    112.06  3.000
 PDX  O5    C1   O1    113.72  3.000
 PDX  H1    C1   C2    109.62  3.000
 PDX  O5    C1   C2    108.34  3.000
 PDX  O1    C1   C2    107.79  3.000
 PDX  H2    C2   O2    111.32  3.000
 PDX  H2    C2   C3    109.24  3.000
 PDX  O2    C2   C3    107.85  3.000
 PDX  H2    C2   C1    108.22  3.000
 PDX  O2    C2   C1    109.80  3.000
 PDX  C3    C2   C1    110.42  3.000
 PDX  H3    C3   O3    110.92  3.000
 PDX  H3    C3   C4    109.14  3.000
 PDX  O3    C3   C4    108.01  3.000
 PDX  H3    C3   C2    110.80  3.000
 PDX  O3    C3   C2    107.68  3.000
 PDX  C4    C3   C2    110.25  3.000
 PDX  H4    C4   O4    111.67  3.000
 PDX  H4    C4   C5    108.46  3.000
 PDX  O4    C4   C5    108.60  3.000
 PDX  H4    C4   C3    108.09  3.000
 PDX  O4    C4   C3    110.80  3.000
 PDX  C5    C4   C3    109.15  3.000
 PDX  H5    C5   O5    110.66  3.000
 PDX  H5    C5   C6    108.93  3.000
 PDX  O5    C5   C6    107.29  3.000
 PDX  H5    C5   C4    108.74  3.000
 PDX  O5    C5   C4    109.93  3.000
 PDX  C6    C5   C4    111.29  3.000
 PDX  H6C2  C6   H6C1  107.12  3.000
 PDX  H6C2  C6   O6    111.80  3.000
 PDX  H6C1  C6   O6    111.95  3.000
 PDX  H6C2  C6   C5    108.33  3.000
 PDX  H6C1  C6   C5    108.99  3.000
 PDX  O6    C6   C5    108.55  3.000
 PDX  HA    O1   C1    109.38  3.000
 PDX  S     O2   C2    120.20  3.000
 PDX  S'    O3   C3    122.05  3.000
 PDX  HB    O4   C4    109.33  3.000
 PDX  C5    O5   C1    115.85  3.000
 PDX  H6    O6   C6    107.95  3.000
 PDX  H3S   O3S  S     112.96  3.000
 PDX  HO'   O3X  S'    113.19  3.000
 PDX  O3S   S    O2S   109.57  3.000
 PDX  O3S   S    O1S   107.00  3.000
 PDX  O2S   S    O1S   121.92  3.000
 PDX  O3S   S    O2    102.55  3.000
 PDX  O2S   S    O2    109.81  3.000
 PDX  O1S   S    O2    104.21  3.000
 PDX  O3X   S'   O2X   106.18  3.000
 PDX  O3X   S'   O1X   109.66  3.000
 PDX  O2X   S'   O1X   121.88  3.000
 PDX  O3X   S'   O3    103.46  3.000
 PDX  O2X   S'   O3    103.91  3.000
 PDX  O1X   S'   O3    110.14  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
 PDX  Var_01  O1S  S   O2  C2  -177.11  30.0  3
 PDX  Var_02  O1X  S'  O3  C3   -42.41  30.0  3

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
 PDX  chir_01  C1  C2  O1  O5  negativ
 PDX  chir_02  C2  O2  C3  C1  positiv
 PDX  chir_03  C3  O3  C4  C2  negativ
 PDX  chir_04  C4  O4  C5  C3  positiv
 PDX  chir_05  C5  O5  C4  C6  negativ

