# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 11:12:48 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: heptyl 1-thio-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCS[C@@H]1O[C@H](CO)[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
 HTG  HTG  'heptyl 1-thio-beta-D-glucopyranoside'  D-saccharide  45  19  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_HTG
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
 HTG  C1    C  CH1   0  -0.132  -1.4671   0.3281  -0.0455
 HTG  S1    S  S2    0  -0.014  -0.0295   0.9678  -0.9270
 HTG  C2    C  CH1   0   0.017  -2.5881   1.3704  -0.0903
 HTG  O2    O  OH1   0  -0.662  -2.2431   2.5404   0.6030
 HTG  C3    C  CH1   0  -0.002  -3.8228   0.7873   0.5853
 HTG  O3    O  OH1   0  -0.671  -4.9481   1.6206   0.4428
 HTG  C4    C  CH1   0   0.033  -4.1813  -0.5682  -0.0134
 HTG  O4    O  OH1   0  -0.671  -5.2179  -1.1853   0.7083
 HTG  C5    C  CH1   0  -0.012  -2.9603  -1.4877   0.0260
 HTG  O5    O  O2    0  -0.471  -1.8800  -0.8686  -0.6478
 HTG  C6    C  CH2   0  -0.157  -3.2257  -2.8145  -0.6520
 HTG  O6    O  OH1   0  -0.670  -2.0935  -3.6371  -0.5000
 HTG  C1'   C  CH2   0  -0.547   1.3177   0.1108  -0.0554
 HTG  C2'   C  CH2   0  -0.425   2.6641   0.6195  -0.5458
 HTG  C3'   C  CH2   0  -0.411   3.8184  -0.0705   0.1722
 HTG  C4'   C  CH2   0  -0.413   5.1840   0.4205  -0.2912
 HTG  C5'   C  CH2   0  -0.407   6.3385  -0.2650   0.4278
 HTG  C6'   C  CH2   0  -0.419   7.7082   0.2219  -0.0292
 HTG  C7'   C  CH3   0  -0.663   8.8540  -0.4678   0.6981
 HTG  H1    H  HCH1  0   0.254  -1.1708   0.1608   1.0015
 HTG  H2    H  HCH1  0   0.224  -2.8268   1.5783  -1.1450
 HTG  HO2   H  HOH1  0   0.450  -1.4761   2.9362   0.1730
 HTG  H3    H  HCH1  0   0.217  -3.5823   0.6340   1.6497
 HTG  HO3   H  HOH1  0   0.458  -4.8267   2.3994   0.9945
 HTG  H4    H  HCH1  0   0.213  -4.4673  -0.4182  -1.0669
 HTG  HO4   H  HOH1  0   0.455  -5.9864  -0.6055   0.6849
 HTG  H5    H  HCH1  0   0.223  -2.6932  -1.6688   1.0802
 HTG  H61   H  HCH2  0   0.214  -4.1155  -3.2627  -0.1983
 HTG  H62   H  HCH2  0   0.197  -3.4603  -2.6342  -1.7106
 HTG  HO6   H  HOH1  0   0.457  -2.3094  -4.5041  -0.8545
 HTG  H1'1  H  HCH2  0   0.267   1.2257  -0.9620  -0.2301
 HTG  H1'2  H  HCH2  0   0.267   1.2061   0.2918   1.0152
 HTG  H2'1  H  HCH2  0   0.230   2.7282   1.7001  -0.3877
 HTG  H2'2  H  HCH2  0   0.231   2.7525   0.4544  -1.6237
 HTG  H3'1  H  HCH2  0   0.216   3.7483  -1.1524   0.0168
 HTG  H3'2  H  HCH2  0   0.216   3.7214   0.0892   1.2512
 HTG  H4'1  H  HCH2  0   0.210   5.2523   1.5031  -0.1378
 HTG  H4'2  H  HCH2  0   0.210   5.2800   0.2610  -1.3707
 HTG  H5'1  H  HCH2  0   0.207   6.2694  -1.3479   0.2754
 HTG  H5'2  H  HCH2  0   0.207   6.2396  -0.1056   1.5073
 HTG  H6'1  H  HCH2  0   0.210   7.7757   1.3038   0.1221
 HTG  H6'2  H  HCH2  0   0.210   7.8072   0.0610  -1.1072
 HTG  H7'1  H  HCH3  0   0.216   8.7982  -0.2950   1.7746
 HTG  H7'2  H  HCH3  0   0.216   8.8291  -1.5474   0.5382
 HTG  H7'3  H  HCH3  0   0.226   9.8236  -0.1053   0.3552

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
 HTG  C1   S1    single  1.804  0.020  1.804
 HTG  C1   C2    single  1.531  0.020  1.531
 HTG  C1   O5    single  1.402  0.020  1.402
 HTG  C1   H1    single  0.970  0.020  1.090
 HTG  S1   C1'   single  1.819  0.020  1.819
 HTG  C2   O2    single  1.403  0.020  1.403
 HTG  C2   C3    single  1.523  0.020  1.523
 HTG  C2   H2    single  0.970  0.020  1.090
 HTG  O2   HO2   single  0.850  0.020  0.980
 HTG  C3   O3    single  1.407  0.020  1.407
 HTG  C3   C4    single  1.525  0.020  1.525
 HTG  C3   H3    single  0.970  0.020  1.090
 HTG  O3   HO3   single  0.850  0.020  0.980
 HTG  C4   O4    single  1.406  0.020  1.406
 HTG  C4   C5    single  1.529  0.020  1.529
 HTG  C4   H4    single  0.970  0.020  1.090
 HTG  O4   HO4   single  0.850  0.020  0.980
 HTG  C5   O5    single  1.416  0.020  1.416
 HTG  C5   C6    single  1.513  0.020  1.513
 HTG  C5   H5    single  0.970  0.020  1.090
 HTG  C6   O6    single  1.408  0.020  1.408
 HTG  C6   H61   single  0.970  0.020  1.090
 HTG  C6   H62   single  0.970  0.020  1.090
 HTG  O6   HO6   single  0.850  0.020  0.980
 HTG  C1'  C2'   single  1.521  0.020  1.521
 HTG  C1'  H1'1  single  0.970  0.020  1.090
 HTG  C1'  H1'2  single  0.970  0.020  1.090
 HTG  C2'  C3'   single  1.525  0.020  1.525
 HTG  C2'  H2'1  single  0.970  0.020  1.090
 HTG  C2'  H2'2  single  0.970  0.020  1.090
 HTG  C3'  C4'   single  1.523  0.020  1.523
 HTG  C3'  H3'1  single  0.970  0.020  1.090
 HTG  C3'  H3'2  single  0.970  0.020  1.090
 HTG  C4'  C5'   single  1.523  0.020  1.523
 HTG  C4'  H4'1  single  0.970  0.020  1.090
 HTG  C4'  H4'2  single  0.970  0.020  1.090
 HTG  C5'  C6'   single  1.524  0.020  1.524
 HTG  C5'  H5'1  single  0.970  0.020  1.090
 HTG  C5'  H5'2  single  0.970  0.020  1.090
 HTG  C6'  C7'   single  1.522  0.020  1.522
 HTG  C6'  H6'1  single  0.970  0.020  1.090
 HTG  C6'  H6'2  single  0.970  0.020  1.090
 HTG  C7'  H7'1  single  0.970  0.020  1.090
 HTG  C7'  H7'2  single  0.970  0.020  1.090
 HTG  C7'  H7'3  single  0.970  0.020  1.090

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
 HTG  H1    C1   O5    110.99  3.000
 HTG  H1    C1   C2    109.17  3.000
 HTG  O5    C1   C2    110.66  3.000
 HTG  H1    C1   S1    107.71  3.000
 HTG  O5    C1   S1    109.12  3.000
 HTG  C2    C1   S1    109.13  3.000
 HTG  C1'   S1   C1    100.89  3.000
 HTG  H2    C2   C3    108.75  3.000
 HTG  H2    C2   O2    111.66  3.000
 HTG  C3    C2   O2    107.42  3.000
 HTG  H2    C2   C1    108.37  3.000
 HTG  C3    C2   C1    108.65  3.000
 HTG  O2    C2   C1    111.91  3.000
 HTG  HO2   O2   C2    108.52  3.000
 HTG  H3    C3   C4    107.88  3.000
 HTG  H3    C3   O3    110.77  3.000
 HTG  C4    C3   O3    107.38  3.000
 HTG  H3    C3   C2    107.74  3.000
 HTG  C4    C3   C2    110.90  3.000
 HTG  O3    C3   C2    112.11  3.000
 HTG  HO3   O3   C3    108.68  3.000
 HTG  H4    C4   C5    108.29  3.000
 HTG  H4    C4   O4    111.05  3.000
 HTG  C5    C4   O4    108.16  3.000
 HTG  H4    C4   C3    108.39  3.000
 HTG  C5    C4   C3    109.68  3.000
 HTG  O4    C4   C3    111.22  3.000
 HTG  HO4   O4   C4    108.16  3.000
 HTG  H5    C5   C6    109.07  3.000
 HTG  H5    C5   O5    110.00  3.000
 HTG  C6    C5   O5    107.70  3.000
 HTG  H5    C5   C4    108.48  3.000
 HTG  C6    C5   C4    112.06  3.000
 HTG  O5    C5   C4    109.52  3.000
 HTG  C5    O5   C1    113.18  3.000
 HTG  H62   C6   H61   107.03  3.000
 HTG  H62   C6   O6    111.81  3.000
 HTG  H61   C6   O6    111.70  3.000
 HTG  H62   C6   C5    108.97  3.000
 HTG  H61   C6   C5    108.41  3.000
 HTG  O6    C6   C5    108.84  3.000
 HTG  HO6   O6   C6    107.85  3.000
 HTG  H1'2  C1'  H1'1  108.15  3.000
 HTG  H1'2  C1'  C2'   110.57  3.000
 HTG  H1'1  C1'  C2'   110.61  3.000
 HTG  H1'2  C1'  S1    108.43  3.000
 HTG  H1'1  C1'  S1    108.92  3.000
 HTG  C2'   C1'  S1    110.10  3.000
 HTG  H2'2  C2'  H2'1  106.66  3.000
 HTG  H2'2  C2'  C3'   109.54  3.000
 HTG  H2'1  C2'  C3'   109.55  3.000
 HTG  H2'2  C2'  C1'   109.80  3.000
 HTG  H2'1  C2'  C1'   109.62  3.000
 HTG  C3'   C2'  C1'   111.54  3.000
 HTG  H3'2  C3'  H3'1  106.15  3.000
 HTG  H3'2  C3'  C4'   109.39  3.000
 HTG  H3'1  C3'  C4'   109.43  3.000
 HTG  H3'2  C3'  C2'   109.33  3.000
 HTG  H3'1  C3'  C2'   109.38  3.000
 HTG  C4'   C3'  C2'   112.93  3.000
 HTG  H4'2  C4'  H4'1  106.05  3.000
 HTG  H4'2  C4'  C5'   109.46  3.000
 HTG  H4'1  C4'  C5'   109.35  3.000
 HTG  H4'2  C4'  C3'   109.35  3.000
 HTG  H4'1  C4'  C3'   109.38  3.000
 HTG  C5'   C4'  C3'   113.01  3.000
 HTG  H5'2  C5'  H5'1  105.96  3.000
 HTG  H5'2  C5'  C6'   109.28  3.000
 HTG  H5'1  C5'  C6'   109.32  3.000
 HTG  H5'2  C5'  C4'   109.34  3.000
 HTG  H5'1  C5'  C4'   109.35  3.000
 HTG  C6'   C5'  C4'   113.33  3.000
 HTG  H6'2  C6'  H6'1  106.01  3.000
 HTG  H6'2  C6'  C7'   109.63  3.000
 HTG  H6'1  C6'  C7'   109.60  3.000
 HTG  H6'2  C6'  C5'   109.25  3.000
 HTG  H6'1  C6'  C5'   109.25  3.000
 HTG  C7'   C6'  C5'   112.87  3.000
 HTG  H7'3  C7'  H7'2  107.64  3.000
 HTG  H7'3  C7'  H7'1  107.63  3.000
 HTG  H7'2  C7'  H7'1  107.44  3.000
 HTG  H7'3  C7'  C6'   111.62  3.000
 HTG  H7'2  C7'  C6'   111.15  3.000
 HTG  H7'1  C7'  C6'   111.16  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
 HTG  Var_01  C2'   C1'  S1   C1   -174.00  30.0  3
 HTG  Var_02  C3'   C2'  C1'  S1    179.56  30.0  3
 HTG  Var_03  C4'   C3'  C2'  C1'  -179.75  30.0  3
 HTG  Var_04  C5'   C4'  C3'  C2'   179.84  30.0  3
 HTG  Var_05  C6'   C5'  C4'  C3'  -179.94  30.0  3
 HTG  Var_06  C7'   C6'  C5'  C4'   179.87  30.0  3
 HTG  Var_07  H7'1  C7'  C6'  C5'   -59.87  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
 HTG  chir_01  C1  S1  C2  O5  negativ
 HTG  chir_02  C2  O2  C1  C3  negativ
 HTG  chir_03  C3  O3  C2  C4  positiv
 HTG  chir_04  C4  O4  C5  C3  positiv
 HTG  chir_05  C5  O5  C4  C6  negativ

