# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 18:34:11 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: 3,4-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)[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
 5LT  5LT  3,4-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 OK
;

data_comp_5LT
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
 5LT  C1   C  CH1    0   0.288  102.4034   98.2197  -37.5204
 5LT  C2   C  CH1    0  -0.008  103.4105   99.2512  -37.0123
 5LT  O2   O  OH1    0  -0.658  104.6647   98.6329  -36.9278
 5LT  C3   C  CH1    0  -0.070  102.9298   99.7895  -35.6565
 5LT  O3   O  OC2    0  -0.627  101.7651  100.5721  -35.8851
 5LT  C4   C  CH1    0   0.021  102.5613   98.6687  -34.6780
 5LT  O4   O  OC2    0  -0.623  103.7769   98.1176  -34.1841
 5LT  C5   C  CH1    0  -0.041  101.7326   97.5582  -35.3334
 5LT  O5   O  O2     0  -0.487  102.2518   97.1834  -36.5942
 5LT  C6   C  CH2    0  -0.175  100.2429   97.8808  -35.3778
 5LT  O6   O  OH1    0  -0.665   99.5703   96.7460  -35.8712
 5LT  S1   S  S      0   1.566  101.8744  102.2077  -35.6579
 5LT  S2   S  S      0   1.560  103.9688   98.0088  -32.5512
 5LT  O13  O  OS    -1  -0.731  102.2368  102.3739  -34.2491
 5LT  O11  O  OS     0  -0.731  102.9021  102.6630  -36.5964
 5LT  O12  O  OS     0  -0.721  100.5165  102.6150  -35.9980
 5LT  O23  O  OS    -1  -0.736  103.8184   99.3770  -32.0479
 5LT  O21  O  OS     0  -0.726  105.3247   97.4739  -32.4791
 5LT  O22  O  OS     0  -0.736  102.9244   97.0909  -32.0885
 5LT  H1   H  HCH1   0   0.193  101.4472   98.7374  -37.6975
 5LT  H2   H  HCH1   0   0.221  103.4248  100.0979  -37.7153
 5LT  HO2  H  HOH1   0   0.450  105.2880   99.2572  -36.5438
 5LT  H3   H  HCH1   0   0.261  103.7239  100.3893  -35.1952
 5LT  H4   H  HCH1   0   0.254  101.9764   99.1153  -33.8664
 5LT  H5   H  HCH1   0   0.255  101.8391   96.6676  -34.7070
 5LT  H61  H  HCH2   0   0.206   99.9315   98.1259  -34.3535
 5LT  H62  H  HCH2   0   0.211  100.0344   98.7655  -35.9875
 5LT  O1   O  OH1    0  -0.658  102.8273   97.5756  -38.6778
 5LT  HO1  H  HOH1   0   0.456  102.7103   98.1739  -39.4227
 5LT  HO6  H  HOH1   0   0.453   98.6421   96.9730  -35.9745

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
 5LT  C1  O5   single  1.398  0.020  1.398
 5LT  C1  C2   single  1.529  0.020  1.529
 5LT  C2  C3   single  1.536  0.020  1.536
 5LT  C2  O2   single  1.401  0.020  1.401
 5LT  C3  O3   single  1.422  0.020  1.422
 5LT  C3  C4   single  1.533  0.020  1.533
 5LT  O3  S1   single  1.655  0.020  1.655
 5LT  C4  C5   single  1.533  0.020  1.533
 5LT  C4  O4   single  1.423  0.020  1.423
 5LT  O4  S2   single  1.648  0.020  1.648
 5LT  C5  O5   single  1.414  0.020  1.414
 5LT  C5  C6   single  1.525  0.020  1.525
 5LT  C6  O6   single  1.408  0.020  1.408
 5LT  S1  O12  deloc   1.458  0.020  1.458
 5LT  S1  O11  deloc   1.464  0.020  1.464
 5LT  S1  O13  deloc   1.464  0.020  1.464
 5LT  S2  O22  deloc   1.465  0.020  1.465
 5LT  S2  O21  deloc   1.459  0.020  1.459
 5LT  S2  O23  deloc   1.466  0.020  1.466
 5LT  C1  H1   single  0.970  0.020  1.090
 5LT  C2  H2   single  0.970  0.020  1.090
 5LT  O2  HO2  single  0.850  0.020  0.980
 5LT  C3  H3   single  0.970  0.020  1.090
 5LT  C4  H4   single  0.970  0.020  1.090
 5LT  C5  H5   single  0.970  0.020  1.090
 5LT  C6  H61  single  0.970  0.020  1.090
 5LT  C6  H62  single  0.970  0.020  1.090
 5LT  C1  O1   single  1.391  0.020  1.391
 5LT  O1  HO1  single  0.850  0.020  0.980
 5LT  O6  HO6  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
 5LT  O1   C1  H1   110.39  3.000
 5LT  O1   C1  O5   103.95  3.000
 5LT  H1   C1  O5   111.14  3.000
 5LT  O1   C1  C2   112.85  3.000
 5LT  H1   C1  C2   107.95  3.000
 5LT  O5   C1  C2   110.58  3.000
 5LT  H2   C2  C3   107.35  3.000
 5LT  H2   C2  O2   111.50  3.000
 5LT  C3   C2  O2   112.43  3.000
 5LT  H2   C2  C1   108.39  3.000
 5LT  O2   C2  C1   108.18  3.000
 5LT  C3   C2  C1   108.89  3.000
 5LT  HO2  O2  C2   108.52  3.000
 5LT  H3   C3  C4   107.79  3.000
 5LT  H3   C3  O3   111.08  3.000
 5LT  C4   C3  O3   107.95  3.000
 5LT  H3   C3  C2   109.65  3.000
 5LT  C4   C3  C2   112.49  3.000
 5LT  O3   C3  C2   107.90  3.000
 5LT  S1   O3  C3   117.90  3.000
 5LT  H4   C4  C5   108.87  3.000
 5LT  H4   C4  O4   110.90  3.000
 5LT  C5   C4  O4   109.25  3.000
 5LT  H4   C4  C3   107.64  3.000
 5LT  O4   C4  C3   107.42  3.000
 5LT  C5   C4  C3   112.76  3.000
 5LT  S2   O4  C4   117.97  3.000
 5LT  H5   C5  C6   106.51  3.000
 5LT  H5   C5  O5   105.01  3.000
 5LT  C6   C5  O5   112.88  3.000
 5LT  H5   C5  C4   107.00  3.000
 5LT  C6   C5  C4   112.79  3.000
 5LT  O5   C5  C4   112.00  3.000
 5LT  C5   O5  C1   115.72  3.000
 5LT  H62  C6  H61  106.57  3.000
 5LT  H62  C6  O6   111.42  3.000
 5LT  H61  C6  O6   111.78  3.000
 5LT  H62  C6  C5   111.92  3.000
 5LT  H61  C6  C5   107.28  3.000
 5LT  O6   C6  C5   107.83  3.000
 5LT  HO6  O6  C6   107.97  3.000
 5LT  O12  S1  O11  114.67  3.000
 5LT  O11  S1  O13  114.06  3.000
 5LT  O12  S1  O13  115.04  3.000
 5LT  O13  S1  O3   105.10  3.000
 5LT  O11  S1  O3   105.41  3.000
 5LT  O12  S1  O3   100.52  3.000
 5LT  O22  S2  O21  114.65  3.000
 5LT  O21  S2  O23  114.87  3.000
 5LT  O22  S2  O23  113.78  3.000
 5LT  O23  S2  O4   105.47  3.000
 5LT  O21  S2  O4   100.45  3.000
 5LT  O22  S2  O4   105.74  3.000
 5LT  HO1  O1  C1   108.61  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
 5LT  Var_01  O12  S1  O3  C3  179.51  30.0  3
 5LT  Var_02  O22  S2  O4  C4   63.16  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
 5LT  chir_01  C1  O5  C2  O1  negativ
 5LT  chir_02  C2  O2  C1  C3  negativ
 5LT  chir_03  C3  O3  C4  C2  negativ
 5LT  chir_04  C4  O4  C3  C5  negativ
 5LT  chir_05  C5  O5  C4  C6  negativ

