# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:17:21 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-5-thio-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1[C@H](O)S[C@H](CO)[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
 0YT  0YT  2-(acetylamino)-2-deoxy-5-thio-beta-D-glucopyranose  D-saccharide  30  15  .  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_0YT
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
 0YT  C1   C  CH1   0  -0.050  -21.5461  27.1913  5.9493
 0YT  C2   C  CH1   0  -0.106  -22.9431  27.7134  5.6153
 0YT  N2   N  NH1   0  -0.612  -23.0356  29.1058  5.9772
 0YT  C7   C  C     0   0.501  -23.1230  30.1212  5.0941
 0YT  O7   O  O     0  -0.488  -23.1778  29.9577  3.8850
 0YT  C8   C  CH3   0  -0.783  -23.1721  31.4896  5.7325
 0YT  C3   C  CH1   0   0.056  -24.0437  26.9198  6.3263
 0YT  O3   O  OH1   0  -0.663  -25.2676  27.4928  5.9484
 0YT  C4   C  CH1   0   0.061  -24.0364  25.4225  6.0024
 0YT  O4   O  OH1   0  -0.674  -25.1373  24.8796  6.7032
 0YT  C5   C  CH1   0  -0.446  -22.7268  24.7580  6.4285
 0YT  C6   C  CH2   0  -0.162  -22.7216  23.2475  6.2979
 0YT  O6   O  OH1   0  -0.662  -22.9373  22.9017  4.9517
 0YT  S5   S  S2    0  -0.027  -21.3781  25.4450  5.4184
 0YT  H3   H  HCH1  0   0.269  -23.0880  27.6379  4.5352
 0YT  H4   H  HNH1  0   0.399  -22.9898  29.3320  6.9597
 0YT  H5   H  HCH3  0   0.258  -23.1064  32.2637  4.9728
 0YT  H6   H  HCH3  0   0.265  -24.1071  31.6184  6.2801
 0YT  H7   H  HCH3  0   0.258  -22.3581  31.6243  6.4455
 0YT  H8   H  HCH1  0   0.203  -23.8839  27.0200  7.4149
 0YT  H9   H  HOH1  0   0.446  -25.9655  26.9513  6.3338
 0YT  H10  H  HCH1  0   0.230  -24.1619  25.2990  4.9200
 0YT  H11  H  HOH1  0   0.462  -25.4724  24.1194  6.2189
 0YT  H12  H  HCH1  0   0.286  -22.5220  24.9898  7.4800
 0YT  H13  H  HCH2  0   0.223  -21.7622  22.8671  6.6702
 0YT  H14  H  HCH2  0   0.221  -23.4977  22.8406  6.9578
 0YT  H15  H  HOH1  0   0.458  -22.9827  21.9434  4.8878
 0YT  O1   O  OH1   0  -0.637  -20.6113  27.9505  5.2610
 0YT  H1   H  HCH1  0   0.249  -21.3957  27.2282  7.0366
 0YT  H2   H  HOH1  0   0.464  -19.7466  27.8290  5.6666

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
 0YT  C2  C1   single  1.528  0.020  1.528
 0YT  C2  N2   single  1.442  0.020  1.442
 0YT  C2  C3   single  1.532  0.020  1.532
 0YT  C2  H3   single  0.970  0.020  1.090
 0YT  N2  H4   single  0.860  0.020  1.020
 0YT  C7  C8   single  1.511  0.020  1.511
 0YT  C7  N2   single  1.349  0.020  1.349
 0YT  O7  C7   double  1.221  0.020  1.221
 0YT  C8  H5   single  0.970  0.020  1.090
 0YT  C8  H6   single  0.970  0.020  1.090
 0YT  C8  H7   single  0.970  0.020  1.090
 0YT  C3  H8   single  0.970  0.020  1.090
 0YT  O3  C3   single  1.403  0.020  1.403
 0YT  O3  H9   single  0.850  0.020  0.980
 0YT  C4  C3   single  1.532  0.020  1.532
 0YT  C4  O4   single  1.413  0.020  1.413
 0YT  C4  C5   single  1.529  0.020  1.529
 0YT  C4  H10  single  0.970  0.020  1.090
 0YT  O4  H11  single  0.850  0.020  0.980
 0YT  C5  H12  single  0.970  0.020  1.090
 0YT  C6  C5   single  1.516  0.020  1.516
 0YT  C6  H13  single  0.970  0.020  1.090
 0YT  C6  H14  single  0.970  0.020  1.090
 0YT  O6  C6   single  1.406  0.020  1.406
 0YT  O6  H15  single  0.850  0.020  0.980
 0YT  S5  C1   single  1.833  0.020  1.833
 0YT  S5  C5   single  1.820  0.020  1.820
 0YT  C1  O1   single  1.387  0.020  1.387
 0YT  C1  H1   single  0.970  0.020  1.090
 0YT  O1  H2   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
 0YT  H1   C1  O1   112.37  3.000
 0YT  H1   C1  S5   107.83  3.000
 0YT  O1   C1  S5   108.42  3.000
 0YT  H1   C1  C2   109.27  3.000
 0YT  O1   C1  C2   108.70  3.000
 0YT  S5   C1  C2   110.24  3.000
 0YT  H3   C2  C3   109.14  3.000
 0YT  H3   C2  N2   107.84  3.000
 0YT  C3   C2  N2   109.74  3.000
 0YT  H3   C2  C1   108.28  3.000
 0YT  C3   C2  C1   112.23  3.000
 0YT  N2   C2  C1   109.49  3.000
 0YT  H4   N2  C7   118.14  3.000
 0YT  C7   N2  C2   124.55  3.000
 0YT  H4   N2  C2   117.25  3.000
 0YT  C8   C7  O7   122.56  3.000
 0YT  O7   C7  N2   123.39  3.000
 0YT  C8   C7  N2   114.04  3.000
 0YT  H7   C8  H6   107.28  3.000
 0YT  H7   C8  H5   108.91  3.000
 0YT  H6   C8  H5   108.57  3.000
 0YT  H7   C8  C7   111.34  3.000
 0YT  H6   C8  C7   110.29  3.000
 0YT  H5   C8  C7   110.35  3.000
 0YT  H8   C3  C4   107.23  3.000
 0YT  C4   C3  O3   110.26  3.000
 0YT  H8   C3  O3   110.76  3.000
 0YT  C4   C3  C2   113.88  3.000
 0YT  O3   C3  C2   106.87  3.000
 0YT  H8   C3  C2   107.85  3.000
 0YT  H9   O3  C3   107.12  3.000
 0YT  H10  C4  C5   108.91  3.000
 0YT  H10  C4  O4   110.92  3.000
 0YT  C5   C4  O4   111.23  3.000
 0YT  H10  C4  C3   108.55  3.000
 0YT  C5   C4  C3   111.71  3.000
 0YT  O4   C4  C3   105.48  3.000
 0YT  H11  O4  C4   108.99  3.000
 0YT  H12  C5  S5   108.31  3.000
 0YT  S5   C5  C6   109.01  3.000
 0YT  H12  C5  C6   107.01  3.000
 0YT  S5   C5  C4   108.43  3.000
 0YT  C6   C5  C4   114.32  3.000
 0YT  H12  C5  C4   109.60  3.000
 0YT  H14  C6  H13  106.61  3.000
 0YT  H14  C6  O6   112.09  3.000
 0YT  H13  C6  O6   111.94  3.000
 0YT  O6   C6  C5   109.07  3.000
 0YT  H14  C6  C5   108.38  3.000
 0YT  H13  C6  C5   108.61  3.000
 0YT  H15  O6  C6   108.41  3.000
 0YT  C5   S5  C1    97.52  3.000
 0YT  H2   O1  C1   109.10  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
 0YT  CONST_01  C8  C7  N2  C2  180.00   0.0  0
 0YT  CONST_02  O7  C7  N2  C2    0.00   0.0  0
 0YT  CONST_03  H4  N2  C7  O7  180.00   0.0  0
 0YT  Var_01    H5  C8  C7  N2  172.37  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
 0YT  chir_01  C1  C2  S5  O1  negativ
 0YT  chir_02  C2  N2  C3  C1  positiv
 0YT  chir_03  C3  O3  C2  C4  positiv
 0YT  chir_04  C4  O4  C5  C3  positiv
 0YT  chir_05  C5  S5  C4  C6  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 0YT  plan-1  C2  0.020
 0YT  plan-1  N2  0.020
 0YT  plan-1  C7  0.020
 0YT  plan-1  O7  0.020
 0YT  plan-1  C8  0.020
 0YT  plan-1  H4  0.020

