# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 14:30:35 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  30  20  .  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_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   0.240  -1.8194  -0.5493   1.0558
 PDX  C2    C  CH1    0  -0.003  -0.8585   0.0601   0.0362
 PDX  C3    C  CH1    0   0.008   0.5846  -0.0300   0.5198
 PDX  C4    C  CH1    0   0.011   0.6858   0.6055   1.9035
 PDX  C5    C  CH1    0  -0.018  -0.3459  -0.0279   2.8483
 PDX  C6    C  CH2    0  -0.161  -0.3708   0.6688   4.1921
 PDX  O1    O  OH1    0  -0.664  -1.5955  -1.9190   1.1058
 PDX  O2    O  OC2    0  -0.608  -0.9883  -0.6120  -1.1975
 PDX  O3    O  OC2    0  -0.617   1.4148   0.6964  -0.3668
 PDX  O4    O  OH1    0  -0.657   1.9932   0.4230   2.3830
 PDX  O5    O  O2     0  -0.501  -1.6484   0.0750   2.2987
 PDX  O6    O  OH1    0  -0.670  -1.2401  -0.0267   5.0528
 PDX  O1S   O  OS     0  -0.736  -1.7086  -0.8509  -3.4648
 PDX  O2S   O  OS     0  -0.748  -3.0718   0.5055  -1.9268
 PDX  O3S   O  OS    -1  -0.735  -0.9197   1.3615  -2.7127
 PDX  O1X   O  OS     0  -0.743   3.4105  -0.7801  -0.2505
 PDX  O2X   O  OS     0  -0.746   3.2186   1.0560  -1.8804
 PDX  O3X   O  OS    -1  -0.730   1.8796  -0.9940  -2.1437
 PDX  S     S  S      0   1.572  -1.7311   0.1782  -2.4290
 PDX  S'    S  S      0   1.565   2.5737  -0.0858  -1.2324
 PDX  H1    H  HCH1   0   0.237  -2.8498  -0.3217   0.7627
 PDX  H2    H  HCH1   0   0.248  -1.1145   1.1226  -0.0563
 PDX  H3    H  HCH1   0   0.241   0.8924  -1.0805   0.5896
 PDX  H4    H  HCH1   0   0.222   0.4458   1.6744   1.7988
 PDX  H5    H  HCH1   0   0.223  -0.0717  -1.0809   3.0037
 PDX  H6C1  H  HCH2   0   0.198  -0.6837   1.7125   4.0488
 PDX  H6C2  H  HCH2   0   0.199   0.6501   0.6914   4.5903
 PDX  HA    H  HOH1   0   0.463  -2.3317  -2.3407   1.5618
 PDX  HB    H  HOH1   0   0.456   2.2194   1.1611   2.9548
 PDX  H6    H  HOH1   0   0.456  -1.2130   0.4035   5.9120

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  1.528  0.020  1.528
 PDX  C1   O1    single  1.389  0.020  1.389
 PDX  C1   O5    single  1.401  0.020  1.401
 PDX  C1   H1    single  0.970  0.020  1.090
 PDX  C2   C3    single  1.525  0.020  1.525
 PDX  C2   O2    single  1.411  0.020  1.411
 PDX  C2   H2    single  0.970  0.020  1.090
 PDX  C3   C4    single  1.526  0.020  1.526
 PDX  C3   O3    single  1.415  0.020  1.415
 PDX  C3   H3    single  0.970  0.020  1.090
 PDX  C4   C5    single  1.536  0.020  1.536
 PDX  C4   O4    single  1.404  0.020  1.404
 PDX  C4   H4    single  0.970  0.020  1.090
 PDX  C5   C6    single  1.514  0.020  1.514
 PDX  C5   O5    single  1.417  0.020  1.417
 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  1.641  0.020  1.641
 PDX  O3   S'    single  1.644  0.020  1.644
 PDX  O4   HB    single  0.850  0.020  0.980
 PDX  O6   H6    single  0.850  0.020  0.980
 PDX  O1S  S     deloc   1.460  0.020  1.460
 PDX  O2S  S     deloc   1.469  0.020  1.469
 PDX  O3S  S     deloc   1.463  0.020  1.463
 PDX  O1X  S'    deloc   1.465  0.020  1.465
 PDX  O2X  S'    deloc   1.463  0.020  1.463
 PDX  O3X  S'    deloc   1.462  0.020  1.462

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    105.04  3.000
 PDX  H1    C1  O1    111.49  3.000
 PDX  O5    C1  O1    112.82  3.000
 PDX  H1    C1  C2    109.28  3.000
 PDX  O5    C1  C2    109.72  3.000
 PDX  O1    C1  C2    108.42  3.000
 PDX  H2    C2  O2    111.48  3.000
 PDX  H2    C2  C3    107.75  3.000
 PDX  O2    C2  C3    109.65  3.000
 PDX  H2    C2  C1    107.21  3.000
 PDX  O2    C2  C1    109.61  3.000
 PDX  C3    C2  C1    111.11  3.000
 PDX  H3    C3  O3    111.52  3.000
 PDX  H3    C3  C4    108.81  3.000
 PDX  O3    C3  C4    108.39  3.000
 PDX  H3    C3  C2    110.02  3.000
 PDX  O3    C3  C2    109.04  3.000
 PDX  C4    C3  C2    109.01  3.000
 PDX  H4    C4  O4    111.21  3.000
 PDX  H4    C4  C5    108.21  3.000
 PDX  O4    C4  C5    111.21  3.000
 PDX  H4    C4  C3    107.68  3.000
 PDX  O4    C4  C3    108.49  3.000
 PDX  C5    C4  C3    109.97  3.000
 PDX  H5    C5  O5    110.71  3.000
 PDX  H5    C5  C6    108.63  3.000
 PDX  O5    C5  C6    107.20  3.000
 PDX  H5    C5  C4    108.33  3.000
 PDX  O5    C5  C4    110.42  3.000
 PDX  C6    C5  C4    111.55  3.000
 PDX  H6C2  C6  H6C1  107.03  3.000
 PDX  H6C2  C6  O6    111.31  3.000
 PDX  H6C1  C6  O6    111.92  3.000
 PDX  H6C2  C6  C5    108.46  3.000
 PDX  H6C1  C6  C5    109.02  3.000
 PDX  O6    C6  C5    109.01  3.000
 PDX  HA    O1  C1    109.00  3.000
 PDX  S     O2  C2    117.94  3.000
 PDX  S'    O3  C3    119.94  3.000
 PDX  HB    O4  C4    108.82  3.000
 PDX  C5    O5  C1    115.07  3.000
 PDX  H6    O6  C6    107.95  3.000
 PDX  O3S   S   O2S   113.11  3.000
 PDX  O3S   S   O1S   115.09  3.000
 PDX  O2S   S   O1S   114.44  3.000
 PDX  O3S   S   O2    106.50  3.000
 PDX  O2S   S   O2    105.30  3.000
 PDX  O1S   S   O2    100.72  3.000
 PDX  O3X   S'  O2X   114.72  3.000
 PDX  O3X   S'  O1X   113.24  3.000
 PDX  O2X   S'  O1X   114.52  3.000
 PDX  O3X   S'  O3    106.80  3.000
 PDX  O2X   S'  O3     99.94  3.000
 PDX  O1X   S'  O3    105.97  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  -177.76  30.0  3
 PDX  Var_02  O1X  S'  O3  C3   -56.04  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

