# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 14:21:04 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 2,3,4,6-tetra-O-acetyl-1-thio-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)OC[C@H]1O[C@@H](S)[C@H](OC(C)=O)[C@@H](OC(C)=O)[C@@H]1OC(C)=O
#
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
 TS8  TS8  2,3,4,6-tetra-O-acetyl-1-thio-beta-D-glucopyranose  D-saccharide  44  24  .  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_TS8
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
 TS8  S     S  S2    0  -0.184  -0.9763   3.3981  -0.2442
 TS8  C1    C  CH1   0  -0.152  -0.4563   1.7671   0.3291
 TS8  C2    C  CH1   0   0.019  -1.4146   0.7038  -0.2109
 TS8  O2    O  O2    0  -0.464  -2.6989   0.8816   0.3577
 TS8  C3    C  CH1   0  -0.011  -0.9168  -0.6653   0.2286
 TS8  O3    O  O2    0  -0.467  -1.7078  -1.6600  -0.4014
 TS8  C4    C  CH1   0   0.001   0.5300  -0.8691  -0.1958
 TS8  O4    O  O2    0  -0.470   0.9559  -2.0930   0.3871
 TS8  C5    C  CH1   0  -0.027   1.3802   0.2920   0.3292
 TS8  O5    O  O2    0  -0.465   0.8353   1.5026  -0.1525
 TS8  C6    C  CH2   0  -0.178   2.8085   0.2108  -0.1620
 TS8  O6    O  O2    0  -0.453   3.5064   1.3052   0.4253
 TS8  CAD   C  CH3   0  -0.770   5.3924   2.6337   0.8201
 TS8  CAE   C  CH3   0  -0.772   1.8471  -4.2527   0.4318
 TS8  CAF   C  CH3   0  -0.773  -4.9566   1.4763   0.4154
 TS8  CAG   C  C     0   0.560  -2.4676  -2.4836   0.3366
 TS8  OAH   O  O     0  -0.450   5.4027   0.6571  -0.5537
 TS8  OAI   O  O     0  -0.432   1.8302  -2.8587  -1.5293
 TS8  OAJ   O  O     0  -0.433  -3.6093   1.5623  -1.5749
 TS8  OAK   O  O     0  -0.432  -2.5347  -2.4361   1.5351
 TS8  CAW   C  C     0   0.569   4.8039   1.4283   0.1522
 TS8  CAX   C  C     0   0.562   1.5608  -3.0218  -0.3696
 TS8  CAY   C  C     0   0.570  -3.7132   1.3216  -0.4028
 TS8  CAZ   C  CH3   0  -0.776  -3.1999  -3.4516  -0.5399
 TS8  HS    H  HSH1  0   0.244  -0.3641   4.1004   0.7150
 TS8  H1    H  HCH1  0   0.286  -0.4756   1.7609   1.4260
 TS8  H2    H  HCH1  0   0.291  -1.4482   0.7599  -1.3030
 TS8  H3    H  HCH1  0   0.286  -0.9885  -0.7416   1.3182
 TS8  H4    H  HCH1  0   0.284   0.5995  -0.9099  -1.2868
 TS8  H5    H  HCH1  0   0.259   1.3804   0.2717   1.4278
 TS8  H6    H  HCH2  0   0.253   3.2612  -0.7323   0.1492
 TS8  H6A   H  HCH2  0   0.253   2.8472   0.2697  -1.2529
 TS8  HAD   H  HCH3  0   0.264   6.4632   2.6790   0.6443
 TS8  HADA  H  HCH3  0   0.276   4.9307   3.5412   0.4291
 TS8  HADB  H  HCH3  0   0.273   5.2043   2.6120   1.8934
 TS8  HAE   H  HCH3  0   0.276   0.9177  -4.6985   0.7882
 TS8  HAEA  H  HCH3  0   0.268   2.3827  -4.9809  -0.1698
 TS8  HAEB  H  HCH3  0   0.279   2.4423  -4.0036   1.3104
 TS8  HAF   H  HCH3  0   0.271  -5.1463   0.5876   1.0164
 TS8  HAFA  H  HCH3  0   0.280  -4.8371   2.3137   1.1048
 TS8  HAFB  H  HCH3  0   0.267  -5.8113   1.6705  -0.2258
 TS8  HAZ   H  HCH3  0   0.276  -2.4961  -4.0427  -1.1262
 TS8  HAZA  H  HCH3  0   0.268  -3.8105  -4.1183   0.0615
 TS8  HAZB  H  HCH3  0   0.277  -3.8388  -2.9205  -1.2461

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
 TS8  S    C1    single  1.805  0.020  1.805
 TS8  S    HS    single  1.200  0.020  1.300
 TS8  O5   C1    single  1.404  0.020  1.404
 TS8  C1   C2    single  1.530  0.020  1.530
 TS8  C1   H1    single  0.970  0.020  1.090
 TS8  C3   C2    single  1.522  0.020  1.522
 TS8  C2   O2    single  1.416  0.020  1.416
 TS8  C2   H2    single  0.970  0.020  1.090
 TS8  O2   CAY   single  1.342  0.020  1.342
 TS8  O3   C3    single  1.418  0.020  1.418
 TS8  C4   C3    single  1.521  0.020  1.521
 TS8  C3   H3    single  0.970  0.020  1.090
 TS8  CAG  O3    single  1.342  0.020  1.342
 TS8  C5   C4    single  1.532  0.020  1.532
 TS8  C4   O4    single  1.421  0.020  1.421
 TS8  C4   H4    single  0.970  0.020  1.090
 TS8  O4   CAX   single  1.342  0.020  1.342
 TS8  C6   C5    single  1.513  0.020  1.513
 TS8  O5   C5    single  1.412  0.020  1.412
 TS8  C5   H5    single  0.970  0.020  1.090
 TS8  O6   C6    single  1.425  0.020  1.425
 TS8  C6   H6    single  0.970  0.020  1.090
 TS8  C6   H6A   single  0.970  0.020  1.090
 TS8  CAW  O6    single  1.332  0.020  1.332
 TS8  CAD  CAW   single  1.498  0.020  1.498
 TS8  CAD  HAD   single  0.970  0.020  1.090
 TS8  CAD  HADA  single  0.970  0.020  1.090
 TS8  CAD  HADB  single  0.970  0.020  1.090
 TS8  CAX  CAE   single  1.496  0.020  1.496
 TS8  CAE  HAE   single  0.970  0.020  1.090
 TS8  CAE  HAEA  single  0.970  0.020  1.090
 TS8  CAE  HAEB  single  0.970  0.020  1.090
 TS8  CAY  CAF   single  1.496  0.020  1.496
 TS8  CAF  HAF   single  0.970  0.020  1.090
 TS8  CAF  HAFA  single  0.970  0.020  1.090
 TS8  CAF  HAFB  single  0.970  0.020  1.090
 TS8  CAZ  CAG   single  1.497  0.020  1.497
 TS8  CAG  OAK   double  1.201  0.020  1.201
 TS8  OAH  CAW   double  1.205  0.020  1.205
 TS8  OAI  CAX   double  1.202  0.020  1.202
 TS8  CAY  OAJ   double  1.201  0.020  1.201
 TS8  CAZ  HAZ   single  0.970  0.020  1.090
 TS8  CAZ  HAZA  single  0.970  0.020  1.090
 TS8  CAZ  HAZB  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
 TS8  HS    S    C1     96.59  3.000
 TS8  H1    C1   O5    110.98  3.000
 TS8  H1    C1   C2    109.75  3.000
 TS8  O5    C1   C2    108.92  3.000
 TS8  H1    C1   S     108.52  3.000
 TS8  C2    C1   S     109.60  3.000
 TS8  O5    C1   S     109.05  3.000
 TS8  H2    C2   C3    110.15  3.000
 TS8  H2    C2   O2    111.50  3.000
 TS8  C3    C2   O2    107.09  3.000
 TS8  H2    C2   C1    109.63  3.000
 TS8  O2    C2   C1    109.83  3.000
 TS8  C3    C2   C1    108.57  3.000
 TS8  CAY   O2   C2    119.95  3.000
 TS8  H3    C3   C4    109.31  3.000
 TS8  H3    C3   O3    110.89  3.000
 TS8  C4    C3   O3    108.21  3.000
 TS8  H3    C3   C2    109.19  3.000
 TS8  C4    C3   C2    110.55  3.000
 TS8  O3    C3   C2    108.68  3.000
 TS8  CAG   O3   C3    120.13  3.000
 TS8  H4    C4   C5    109.56  3.000
 TS8  H4    C4   O4    110.97  3.000
 TS8  C5    C4   O4    110.24  3.000
 TS8  H4    C4   C3    110.09  3.000
 TS8  O4    C4   C3    106.62  3.000
 TS8  C5    C4   C3    109.31  3.000
 TS8  CAX   O4   C4    119.99  3.000
 TS8  H5    C5   C6    108.87  3.000
 TS8  H5    C5   O5    110.91  3.000
 TS8  C6    C5   O5    107.43  3.000
 TS8  H5    C5   C4    109.20  3.000
 TS8  O5    C5   C4    108.58  3.000
 TS8  C6    C5   C4    111.85  3.000
 TS8  C5    O5   C1    113.55  3.000
 TS8  H6A   C6   H6    108.44  3.000
 TS8  H6A   C6   O6    110.65  3.000
 TS8  H6    C6   O6    110.06  3.000
 TS8  H6A   C6   C5    110.77  3.000
 TS8  H6    C6   C5    110.21  3.000
 TS8  O6    C6   C5    106.71  3.000
 TS8  CAW   O6   C6    117.64  3.000
 TS8  HADB  CAD  HADA  107.25  3.000
 TS8  HADB  CAD  HAD   109.30  3.000
 TS8  HADA  CAD  HAD   108.94  3.000
 TS8  HADB  CAD  CAW   110.80  3.000
 TS8  HADA  CAD  CAW   110.08  3.000
 TS8  HAD   CAD  CAW   110.40  3.000
 TS8  HAEB  CAE  HAEA  109.30  3.000
 TS8  HAEB  CAE  HAE   107.18  3.000
 TS8  HAEA  CAE  HAE   109.10  3.000
 TS8  HAEB  CAE  CAX   110.37  3.000
 TS8  HAEA  CAE  CAX   110.44  3.000
 TS8  HAE   CAE  CAX   110.38  3.000
 TS8  HAFB  CAF  HAFA  108.78  3.000
 TS8  HAFB  CAF  HAF   109.54  3.000
 TS8  HAFA  CAF  HAF   107.25  3.000
 TS8  HAFB  CAF  CAY   110.46  3.000
 TS8  HAFA  CAF  CAY   109.50  3.000
 TS8  HAF   CAF  CAY   111.22  3.000
 TS8  CAZ   CAG  OAK   125.62  3.000
 TS8  OAK   CAG  O3    123.78  3.000
 TS8  CAZ   CAG  O3    110.60  3.000
 TS8  OAH   CAW  CAD   125.52  3.000
 TS8  OAH   CAW  O6    123.04  3.000
 TS8  CAD   CAW  O6    111.45  3.000
 TS8  OAI   CAX  CAE   125.85  3.000
 TS8  OAI   CAX  O4    123.45  3.000
 TS8  CAE   CAX  O4    110.70  3.000
 TS8  OAJ   CAY  CAF   125.79  3.000
 TS8  OAJ   CAY  O2    123.60  3.000
 TS8  CAF   CAY  O2    110.61  3.000
 TS8  HAZB  CAZ  HAZA  109.16  3.000
 TS8  HAZB  CAZ  HAZ   107.10  3.000
 TS8  HAZA  CAZ  HAZ   109.15  3.000
 TS8  HAZB  CAZ  CAG   110.54  3.000
 TS8  HAZA  CAZ  CAG   110.35  3.000
 TS8  HAZ   CAZ  CAG   110.46  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
 TS8  Var_01  CAF  CAY  O2   C2   -178.11  30.0  3
 TS8  Var_02  CAZ  CAG  O3   C3   -179.52  30.0  1
 TS8  Var_03  CAE  CAX  O4   C4   -176.66  30.0  3
 TS8  Var_04  CAD  CAW  O6   C6    179.05  30.0  1
 TS8  Var_05  HAF  CAF  CAY  O2    -48.70  30.0  3
 TS8  Var_06  HAZ  CAZ  CAG  O3     59.01  30.0  3
 TS8  Var_07  HAE  CAE  CAX  O4     62.23  30.0  3
 TS8  Var_08  HAD  CAD  CAW  O6    176.00  30.0  3
 TS8  Var_09  H6   C6   O6   CAW    59.30  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
 TS8  chir_01  C1  S   O5  C2  positiv
 TS8  chir_02  C2  O2  C3  C1  positiv
 TS8  chir_03  C3  O3  C4  C2  negativ
 TS8  chir_04  C4  O4  C5  C3  positiv
 TS8  chir_05  C5  O5  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
 TS8  plan-1  O3   0.020
 TS8  plan-1  CAG  0.020
 TS8  plan-1  OAK  0.020
 TS8  plan-1  CAZ  0.020
 TS8  plan-2  O6   0.020
 TS8  plan-2  CAD  0.020
 TS8  plan-2  OAH  0.020
 TS8  plan-2  CAW  0.020
 TS8  plan-3  O4   0.020
 TS8  plan-3  CAE  0.020
 TS8  plan-3  OAI  0.020
 TS8  plan-3  CAX  0.020
 TS8  plan-4  O2   0.020
 TS8  plan-4  CAF  0.020
 TS8  plan-4  OAJ  0.020
 TS8  plan-4  CAY  0.020

