# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 16:44:36 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: 1-thio-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](S)[C@H](O)[C@@H](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
 GS1  GS1  1-thio-beta-D-glucopyranose  D-saccharide  24  12  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GS1
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
 GS1  C1   C  CH1   0  -0.139  -7.7051  10.3340  60.3091
 GS1  S1   S  S2    0  -0.205  -9.0154  10.3172  59.0597
 GS1  C2   C  CH1   0   0.050  -8.1460   9.4962  61.5055
 GS1  O2   O  OH1   0  -0.659  -9.3052  10.0724  62.0411
 GS1  C3   C  CH1   0  -0.007  -7.0079   9.4653  62.5194
 GS1  O3   O  OH1   0  -0.668  -7.4134   8.6143  63.5653
 GS1  C4   C  CH1   0   0.030  -5.7074   9.0039  61.8725
 GS1  O4   O  OH1   0  -0.682  -4.6956   9.1234  62.8410
 GS1  C5   C  CH1   0  -0.026  -5.4284   9.8478  60.6227
 GS1  O5   O  O2    0  -0.473  -6.5404   9.7937  59.7481
 GS1  C6   C  CH2   0  -0.177  -4.2497   9.3348  59.8068
 GS1  O6   O  OH1   0  -0.671  -3.0936   9.3688  60.6207
 GS1  H1   H  HCH1  0   0.262  -7.5369  11.3721  60.6274
 GS1  HS1  H  HSH1  0   0.233  -8.4797  11.2453  58.2577
 GS1  H2   H  HCH1  0   0.222  -8.3305   8.4682  61.1540
 GS1  HO2  H  HOH1  0   0.453  -9.5411   9.5845  62.8375
 GS1  H3   H  HCH1  0   0.215  -6.8569  10.4934  62.8865
 GS1  HO3  H  HOH1  0   0.456  -6.8243   8.7453  64.3149
 GS1  H4   H  HCH1  0   0.200  -5.8307   7.9567  61.5483
 GS1  HO4  H  HOH1  0   0.450  -3.8496   9.0088  62.3859
 GS1  H5   H  HCH1  0   0.228  -5.2368  10.8879  60.9330
 GS1  H61  H  HCH2  0   0.216  -4.4719   8.3156  59.4684
 GS1  H62  H  HCH2  0   0.225  -4.1277   9.9616  58.9158
 GS1  HO6  H  HOH1  0   0.470  -2.4064   8.8396  60.2049

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
 GS1  C1  S1   single  1.811  0.020  1.811
 GS1  C1  C2   single  1.526  0.020  1.526
 GS1  C1  O5   single  1.401  0.020  1.401
 GS1  C1  H1   single  0.970  0.020  1.090
 GS1  S1  HS1  single  1.200  0.020  1.300
 GS1  C2  O2   single  1.401  0.020  1.401
 GS1  C2  C3   single  1.525  0.020  1.525
 GS1  C2  H2   single  0.970  0.020  1.090
 GS1  O2  HO2  single  0.850  0.020  0.980
 GS1  C3  O3   single  1.408  0.020  1.408
 GS1  C3  C4   single  1.524  0.020  1.524
 GS1  C3  H3   single  0.970  0.020  1.090
 GS1  O3  HO3  single  0.850  0.020  0.980
 GS1  C4  O4   single  1.406  0.020  1.406
 GS1  C4  C5   single  1.534  0.020  1.534
 GS1  C4  H4   single  0.970  0.020  1.090
 GS1  O4  HO4  single  0.850  0.020  0.980
 GS1  C5  O5   single  1.416  0.020  1.416
 GS1  C5  C6   single  1.523  0.020  1.523
 GS1  C5  H5   single  0.970  0.020  1.090
 GS1  C6  O6   single  1.414  0.020  1.414
 GS1  C6  H61  single  0.970  0.020  1.090
 GS1  C6  H62  single  0.970  0.020  1.090
 GS1  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
 GS1  H1   C1  O5   110.68  3.000
 GS1  H1   C1  C2   109.62  3.000
 GS1  O5   C1  C2   110.03  3.000
 GS1  H1   C1  S1   108.62  3.000
 GS1  O5   C1  S1   108.77  3.000
 GS1  C2   C1  S1   109.08  3.000
 GS1  HS1  S1  C1    96.74  3.000
 GS1  H2   C2  C3   108.55  3.000
 GS1  H2   C2  O2   111.54  3.000
 GS1  C3   C2  O2   111.83  3.000
 GS1  H2   C2  C1   108.09  3.000
 GS1  C3   C2  C1   108.47  3.000
 GS1  O2   C2  C1   108.25  3.000
 GS1  HO2  O2  C2   108.08  3.000
 GS1  H3   C3  C4   107.87  3.000
 GS1  H3   C3  O3   110.85  3.000
 GS1  C4   C3  O3   112.21  3.000
 GS1  H3   C3  C2   107.75  3.000
 GS1  C4   C3  C2   111.15  3.000
 GS1  O3   C3  C2   106.93  3.000
 GS1  HO3  O3  C3   108.67  3.000
 GS1  H4   C4  C5   107.65  3.000
 GS1  H4   C4  O4   111.32  3.000
 GS1  C5   C4  O4   112.57  3.000
 GS1  H4   C4  C3   108.47  3.000
 GS1  C5   C4  C3   109.55  3.000
 GS1  O4   C4  C3   107.22  3.000
 GS1  HO4  O4  C4   107.17  3.000
 GS1  H5   C5  C6   109.53  3.000
 GS1  H5   C5  O5   110.27  3.000
 GS1  C6   C5  O5   105.31  3.000
 GS1  H5   C5  C4   108.75  3.000
 GS1  C6   C5  C4   113.09  3.000
 GS1  O5   C5  C4   109.85  3.000
 GS1  C5   O5  C1   113.01  3.000
 GS1  H62  C6  H61  107.65  3.000
 GS1  H62  C6  O6   111.29  3.000
 GS1  H61  C6  O6   111.44  3.000
 GS1  H62  C6  C5   109.21  3.000
 GS1  H61  C6  C5   108.76  3.000
 GS1  O6   C6  C5   108.44  3.000
 GS1  HO6  O6  C6   108.79  3.000

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
 GS1  chir_01  C1  S1  C2  O5  negativ
 GS1  chir_02  C2  O2  C1  C3  negativ
 GS1  chir_03  C3  O3  C2  C4  positiv
 GS1  chir_04  C4  O4  C5  C3  positiv
 GS1  chir_05  C5  O5  C4  C6  negativ

