# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 08:10:18 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: (2R,3R,4S,5R,6R)-2-(hydroxymethyl)-6-(2-sulfanylethoxy)oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](OCCS)[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
 TGA  TGA  (2R,3R,4S,5R,6R)-2-(hydroxymethyl)-6-(2-sulfanylethoxy)oxane-3,4,5-triol  D-saccharide  31  15  .  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_TGA
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
 TGA  O2    O  OH1   0  -0.670  -0.7187   2.7104   0.4477
 TGA  C2    C  CH1   0  -0.025  -1.0488   1.4528  -0.0899
 TGA  C3    C  CH1   0   0.003  -2.3789   1.0283   0.5190
 TGA  O3    O  OH1   0  -0.674  -3.4331   1.8801   0.1443
 TGA  C4    C  CH1   0  -0.002  -2.7426  -0.3864   0.0748
 TGA  O4    O  OH1   0  -0.672  -3.0157  -0.4449  -1.3032
 TGA  C5    C  CH1   0  -0.017  -1.5786  -1.3200   0.3879
 TGA  C6    C  CH2   0  -0.155  -1.8356  -2.7385  -0.0745
 TGA  O6    O  OH1   0  -0.670  -0.8195  -3.5681   0.4369
 TGA  O5    O  O2    0  -0.493  -0.3873  -0.8584  -0.2154
 TGA  C1    C  CH1   0   0.298   0.0062   0.4034   0.2531
 TGA  O1    O  O2    0  -0.497   1.1871   0.7546  -0.3674
 TGA  C13   C  CH2   0  -0.136   2.3477   0.1404   0.1597
 TGA  C14   C  CH2   0  -0.584   3.5462   0.8091  -0.4842
 TGA  S15   S  S2    0  -0.258   5.0541   0.0479   0.2019
 TGA  H     H  HSH1  0   0.232   5.9350   0.7492  -0.5178
 TGA  H2    H  HOH1  0   0.457   0.0069   3.0823  -0.0633
 TGA  HA    H  HCH1  0   0.225  -1.1500   1.4979  -1.1831
 TGA  H3    H  HCH1  0   0.214  -2.2591   1.0119   1.6142
 TGA  H1    H  HCH1  0   0.184   0.1392   0.3678   1.3519
 TGA  HB    H  HOH1  0   0.456  -3.1646   2.7912   0.3036
 TGA  H4    H  HCH1  0   0.235  -3.6085  -0.7211   0.6659
 TGA  HC    H  HOH1  0   0.453  -3.6762   0.2269  -1.5034
 TGA  H5    H  HCH1  0   0.228  -1.4657  -1.3347   1.4844
 TGA  H61C  H  HCH2  0   0.203  -2.8259  -3.0366   0.2939
 TGA  H62C  H  HCH2  0   0.207  -1.8736  -2.7722  -1.1692
 TGA  H6    H  HOH1  0   0.457  -0.9781  -4.4612   0.1189
 TGA  H131  H  HCH2  0   0.223   2.3817   0.2671   1.2490
 TGA  H132  H  HCH2  0   0.227   2.3564  -0.9342  -0.0494
 TGA  H141  H  HCH2  0   0.277   3.5260   0.6665  -1.5643
 TGA  H142  H  HCH2  0   0.274   3.5442   1.8773  -0.2692

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
 TGA  O2   C2    single  1.407  0.020  1.407
 TGA  C2   C3    single  1.523  0.020  1.523
 TGA  C2   C1    single  1.527  0.020  1.527
 TGA  C3   O3    single  1.406  0.020  1.406
 TGA  C3   C4    single  1.527  0.020  1.527
 TGA  C4   O4    single  1.406  0.020  1.406
 TGA  C4   C5    single  1.525  0.020  1.525
 TGA  C5   C6    single  1.514  0.020  1.514
 TGA  C5   O5    single  1.413  0.020  1.413
 TGA  C6   O6    single  1.408  0.020  1.408
 TGA  O5   C1    single  1.402  0.020  1.402
 TGA  C1   O1    single  1.380  0.020  1.380
 TGA  O1   C13   single  1.415  0.020  1.415
 TGA  C13  C14   single  1.516  0.020  1.516
 TGA  C14  S15   single  1.823  0.020  1.823
 TGA  S15  H     single  1.200  0.020  1.300
 TGA  O2   H2    single  0.850  0.020  0.980
 TGA  C2   HA    single  0.970  0.020  1.090
 TGA  C3   H3    single  0.970  0.020  1.090
 TGA  C1   H1    single  0.970  0.020  1.090
 TGA  O3   HB    single  0.850  0.020  0.980
 TGA  C4   H4    single  0.970  0.020  1.090
 TGA  O4   HC    single  0.850  0.020  0.980
 TGA  C5   H5    single  0.970  0.020  1.090
 TGA  C6   H61C  single  0.970  0.020  1.090
 TGA  C6   H62C  single  0.970  0.020  1.090
 TGA  O6   H6    single  0.850  0.020  0.980
 TGA  C13  H131  single  0.970  0.020  1.090
 TGA  C13  H132  single  0.970  0.020  1.090
 TGA  C14  H141  single  0.970  0.020  1.090
 TGA  C14  H142  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
 TGA  H2    O2   C2    108.63  3.000
 TGA  HA    C2   C1    108.38  3.000
 TGA  HA    C2   C3    109.19  3.000
 TGA  C1    C2   C3    108.78  3.000
 TGA  HA    C2   O2    111.41  3.000
 TGA  C1    C2   O2    111.49  3.000
 TGA  C3    C2   O2    107.53  3.000
 TGA  H3    C3   C4    107.53  3.000
 TGA  H3    C3   O3    110.82  3.000
 TGA  C4    C3   O3    107.77  3.000
 TGA  H3    C3   C2    107.85  3.000
 TGA  C4    C3   C2    110.49  3.000
 TGA  O3    C3   C2    112.29  3.000
 TGA  HB    O3   C3    108.66  3.000
 TGA  H4    C4   C5    107.71  3.000
 TGA  H4    C4   O4    111.15  3.000
 TGA  C5    C4   O4    108.90  3.000
 TGA  H4    C4   C3    108.24  3.000
 TGA  C5    C4   C3    109.02  3.000
 TGA  O4    C4   C3    111.71  3.000
 TGA  HC    O4   C4    107.93  3.000
 TGA  H5    C5   O5    110.04  3.000
 TGA  H5    C5   C6    107.98  3.000
 TGA  O5    C5   C6    108.59  3.000
 TGA  H5    C5   C4    106.89  3.000
 TGA  O5    C5   C4    110.85  3.000
 TGA  C6    C5   C4    112.43  3.000
 TGA  H62C  C6   H61C  107.18  3.000
 TGA  H62C  C6   O6    111.70  3.000
 TGA  H61C  C6   O6    111.66  3.000
 TGA  H62C  C6   C5    109.86  3.000
 TGA  H61C  C6   C5    107.76  3.000
 TGA  O6    C6   C5    108.58  3.000
 TGA  H6    O6   C6    107.95  3.000
 TGA  C1    O5   C5    112.83  3.000
 TGA  H1    C1   O1    110.59  3.000
 TGA  H1    C1   O5    109.65  3.000
 TGA  O1    C1   O5    108.60  3.000
 TGA  H1    C1   C2    109.15  3.000
 TGA  O1    C1   C2    108.39  3.000
 TGA  O5    C1   C2    110.45  3.000
 TGA  C13   O1   C1    115.09  3.000
 TGA  H132  C13  H131  107.63  3.000
 TGA  H132  C13  C14   110.22  3.000
 TGA  H131  C13  C14   110.26  3.000
 TGA  H132  C13  O1    111.19  3.000
 TGA  H131  C13  O1    110.19  3.000
 TGA  C14   C13  O1    107.38  3.000
 TGA  H142  C14  H141  108.90  3.000
 TGA  H142  C14  S15   109.67  3.000
 TGA  H141  C14  S15   109.50  3.000
 TGA  H142  C14  C13   110.31  3.000
 TGA  H141  C14  C13   110.40  3.000
 TGA  S15   C14  C13   108.05  3.000
 TGA  H     S15  C14    97.09  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
 TGA  Var_01  C14  C13  O1   C1  -170.92  30.0  3
 TGA  Var_02  S15  C14  C13  O1   179.15  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
 TGA  chir_01  C2  O2  C3  C1  positiv
 TGA  chir_02  C3  O3  C2  C4  positiv
 TGA  chir_03  C4  O4  C5  C3  negativ
 TGA  chir_04  C5  O5  C4  C6  negativ
 TGA  chir_05  C1  O5  O1  C2  negativ

