# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 14:02:42 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: 5-thio-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1S[C@H](O)[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
 GLT  GLT  5-thio-alpha-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 PERFECT
;

data_comp_GLT
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
 GLT  C1   C  CH1   0  -0.125  44.0869  37.6817  -0.4784
 GLT  C2   C  CH1   0   0.065  43.2370  38.8254   0.0543
 GLT  C3   C  CH1   0   0.009  42.7431  38.5800   1.4797
 GLT  C4   C  CH1   0   0.046  41.8636  37.3363   1.6065
 GLT  C5   C  CH1   0  -0.431  42.6069  36.0564   1.2181
 GLT  C6   C  CH2   0  -0.129  41.7289  34.8287   1.3938
 GLT  S5   S  S2    0  -0.027  43.1053  36.1461  -0.5334
 GLT  O1   O  OH1   0  -0.635  45.2360  37.5620   0.2974
 GLT  O2   O  OH1   0  -0.669  44.0102  39.9976  -0.0179
 GLT  O3   O  OH1   0  -0.674  42.0142  39.7343   1.8322
 GLT  O4   O  OH1   0  -0.671  41.4476  37.2910   2.9579
 GLT  O6   O  OH1   0  -0.660  42.4259  33.6945   0.9399
 GLT  H1   H  HCH1  0   0.272  44.3179  37.8798  -1.5334
 GLT  H2   H  HCH1  0   0.218  42.3585  38.8934  -0.6039
 GLT  H3   H  HCH1  0   0.215  43.6125  38.4557   2.1423
 GLT  H4   H  HCH1  0   0.224  40.9993  37.4465   0.9364
 GLT  H5   H  HCH1  0   0.278  43.5076  35.9515   1.8304
 GLT  H61  H  HCH2  0   0.218  41.4712  34.7390   2.4554
 GLT  H62  H  HCH2  0   0.201  40.7899  34.9765   0.8417
 GLT  HO1  H  HOH1  0   0.460  45.7978  36.8801  -0.0858
 GLT  HO2  H  HOH1  0   0.448  43.4978  40.7116   0.3767
 GLT  HO3  H  HOH1  0   0.452  41.7528  39.6520   2.7553
 GLT  HO4  H  HOH1  0   0.460  40.5572  36.9315   3.0039
 GLT  HO6  H  HOH1  0   0.456  41.8536  32.9296   1.0503

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
 GLT  C1  C2   single  1.521  0.020  1.521
 GLT  C1  S5   single  1.823  0.020  1.823
 GLT  C1  O1   single  1.392  0.020  1.392
 GLT  C1  H1   single  0.970  0.020  1.090
 GLT  C2  C3   single  1.528  0.020  1.528
 GLT  C2  O2   single  1.406  0.020  1.406
 GLT  C2  H2   single  0.970  0.020  1.090
 GLT  C3  C4   single  1.529  0.020  1.529
 GLT  C3  O3   single  1.410  0.020  1.410
 GLT  C3  H3   single  0.970  0.020  1.090
 GLT  C4  C5   single  1.530  0.020  1.530
 GLT  C4  O4   single  1.415  0.020  1.415
 GLT  C4  H4   single  0.970  0.020  1.090
 GLT  C5  C6   single  1.520  0.020  1.520
 GLT  C5  S5   single  1.823  0.020  1.823
 GLT  C5  H5   single  0.970  0.020  1.090
 GLT  C6  O6   single  1.406  0.020  1.406
 GLT  C6  H61  single  0.970  0.020  1.090
 GLT  C6  H62  single  0.970  0.020  1.090
 GLT  O1  HO1  single  0.850  0.020  0.980
 GLT  O2  HO2  single  0.850  0.020  0.980
 GLT  O3  HO3  single  0.850  0.020  0.980
 GLT  O4  HO4  single  0.850  0.020  0.980
 GLT  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
 GLT  H1   C1  O1   112.18  3.000
 GLT  H1   C1  S5   103.66  3.000
 GLT  O1   C1  S5   112.89  3.000
 GLT  H1   C1  C2   108.56  3.000
 GLT  O1   C1  C2   109.32  3.000
 GLT  S5   C1  C2   110.05  3.000
 GLT  H2   C2  O2   110.91  3.000
 GLT  H2   C2  C3   108.06  3.000
 GLT  O2   C2  C3   111.07  3.000
 GLT  H2   C2  C1   106.45  3.000
 GLT  O2   C2  C1   107.55  3.000
 GLT  C3   C2  C1   112.73  3.000
 GLT  H3   C3  O3   110.52  3.000
 GLT  H3   C3  C4   108.23  3.000
 GLT  O3   C3  C4   110.36  3.000
 GLT  H3   C3  C2   108.93  3.000
 GLT  O3   C3  C2   105.59  3.000
 GLT  C4   C3  C2   113.20  3.000
 GLT  H4   C4  O4   110.75  3.000
 GLT  H4   C4  C5   108.12  3.000
 GLT  O4   C4  C5   111.01  3.000
 GLT  H4   C4  C3   108.68  3.000
 GLT  O4   C4  C3   105.93  3.000
 GLT  C5   C4  C3   112.34  3.000
 GLT  H5   C5  S5   108.50  3.000
 GLT  H5   C5  C6   109.48  3.000
 GLT  S5   C5  C6   107.98  3.000
 GLT  H5   C5  C4   109.76  3.000
 GLT  S5   C5  C4   109.60  3.000
 GLT  C6   C5  C4   111.45  3.000
 GLT  H62  C6  H61  107.25  3.000
 GLT  H62  C6  O6   111.69  3.000
 GLT  H61  C6  O6   111.29  3.000
 GLT  H62  C6  C5   109.08  3.000
 GLT  H61  C6  C5   108.30  3.000
 GLT  O6   C6  C5   109.14  3.000
 GLT  C5   S5  C1    99.18  3.000
 GLT  HO1  O1  C1   108.71  3.000
 GLT  HO2  O2  C2   107.72  3.000
 GLT  HO3  O3  C3   108.06  3.000
 GLT  HO4  O4  C4   109.27  3.000
 GLT  HO6  O6  C6   108.03  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
 GLT  chir_01  C1  C2  S5  O1  positiv
 GLT  chir_02  C2  O2  C1  C3  negativ
 GLT  chir_03  C3  O3  C2  C4  positiv
 GLT  chir_04  C4  O4  C5  C3  positiv
 GLT  chir_05  C5  S5  C4  C6  negativ

