# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 05:10:45 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (2S)-3-(acetyloxy)-2-hydroxypropyl 6-deoxy-6-sulfo-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)OC[C@@H](O)CO[C@@H]1O[C@H](C[S](O)(=O)=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
 1E2  1E2  '(2S)-3-(acetyloxy)-2-hydroxypropyl 6-deoxy-6-sulfo-beta-D-glucopyranoside'  ligand  42  23  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1E2
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
 1E2  C2   C  CH1    0  -0.025   1.6131  -2.5577  -0.0862
 1E2  C4   C  CH1    0   0.048   3.5720  -0.9838  -0.2579
 1E2  C6   C  CH2    0  -0.673   2.9927   1.4690  -0.5248
 1E2  C5   C  CH1    0   0.024   2.5920   0.1422   0.0819
 1E2  O10  O  O      0  -0.454  -6.0683   1.3279   1.0340
 1E2  C23  C  C      0   0.566  -6.1705   0.3278   0.3684
 1E2  C24  C  CH3    0  -0.770  -7.4582  -0.2421  -0.1463
 1E2  C46  C  CH2    0  -0.181  -3.8284   0.0389   0.3738
 1E2  C45  C  CH1    0  -0.058  -2.8179  -0.9265  -0.2229
 1E2  O47  O  OH1    0  -0.649  -2.9101  -1.0019  -1.6231
 1E2  C44  C  CH2    0  -0.186  -1.4275  -0.5367   0.2501
 1E2  O6   O  O2     0  -0.496  -0.5100  -1.5119  -0.2054
 1E2  C1   C  CH1    0   0.293   0.7779  -1.3256   0.2476
 1E2  O2   O  OH1    0  -0.667   1.1699  -3.7003   0.6024
 1E2  C3   C  CH1    0  -0.011   3.0561  -2.2948   0.3319
 1E2  O3   O  OH1    0  -0.672   3.9225  -3.3197  -0.0928
 1E2  O4   O  OH1    0  -0.671   4.8296  -0.6450   0.2685
 1E2  O5   O  O2     0  -0.507   1.3191  -0.2098  -0.4042
 1E2  S    S  S      0   1.411   1.8985   2.8381  -0.0690
 1E2  O9   O  OS     0  -0.754   0.6399   2.6652  -0.8150
 1E2  O7   O  OS     0  -0.766   1.7342   2.7365   1.3950
 1E2  O8   O  OS    -1  -0.769   2.6432   4.0456  -0.4838
 1E2  H1   H  HCH1   0   0.223   1.5788  -2.7064  -1.1762
 1E2  H2   H  HCH1   0   0.213   3.6139  -1.0856  -1.3538
 1E2  H3   H  HCH2   0   0.281   3.9890   1.7387  -0.1745
 1E2  H4   H  HCH2   0   0.268   3.0228   1.4151  -1.6159
 1E2  H5   H  HCH1   0   0.231   2.5619   0.2526   1.1767
 1E2  H6   H  HCH3   0   0.262  -8.3057   0.2676   0.3029
 1E2  H7   H  HCH3   0   0.277  -7.5096  -0.1178  -1.2293
 1E2  H8   H  HCH3   0   0.270  -7.5263  -1.3096   0.0598
 1E2  H11  H  HCH1   0   0.248  -3.0378  -1.9333   0.1463
 1E2  H12  H  HOH1   0   0.444  -2.6833  -0.1439  -1.9989
 1E2  H13  H  HCH2   0   0.218  -1.1583   0.4586  -0.1247
 1E2  H14  H  HCH2   0   0.226  -1.4127  -0.4856   1.3466
 1E2  H15  H  HCH1   0   0.189   0.7872  -1.1560   1.3424
 1E2  H16  H  HOH1   0   0.457   0.3309  -3.9796   0.2232
 1E2  H17  H  HCH1   0   0.216   3.0811  -2.1947   1.4293
 1E2  H18  H  HOH1   0   0.457   3.7168  -4.1188   0.4022
 1E2  H19  H  HOH1   0   0.456   5.4529  -1.3419   0.0387
 1E2  H9   H  HCH2   0   0.238  -3.6504   1.0576   0.0149
 1E2  O48  O  O2     0  -0.449  -5.1274  -0.4024  -0.0144
 1E2  H10  H  HCH2   0   0.243  -3.7413   0.0490   1.4633

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
 1E2  O7   S    deloc   1.477  0.020  1.477
 1E2  C6   S    single  1.811  0.020  1.811
 1E2  C6   C5   single  1.513  0.020  1.513
 1E2  O9   S    deloc   1.473  0.020  1.473
 1E2  S    O8   deloc   1.478  0.020  1.478
 1E2  O4   C4   single  1.405  0.020  1.405
 1E2  C4   C5   single  1.531  0.020  1.531
 1E2  C4   C3   single  1.527  0.020  1.527
 1E2  C5   O5   single  1.407  0.020  1.407
 1E2  O5   C1   single  1.401  0.020  1.401
 1E2  O3   C3   single  1.408  0.020  1.408
 1E2  C3   C2   single  1.525  0.020  1.525
 1E2  C1   C2   single  1.525  0.020  1.525
 1E2  C1   O6   single  1.378  0.020  1.378
 1E2  C2   O2   single  1.406  0.020  1.406
 1E2  O6   C44  single  1.414  0.020  1.414
 1E2  C24  C23  single  1.499  0.020  1.499
 1E2  C44  C45  single  1.519  0.020  1.519
 1E2  C23  O10  double  1.206  0.020  1.206
 1E2  C23  O48  single  1.330  0.020  1.330
 1E2  O47  C45  single  1.405  0.020  1.405
 1E2  C45  C46  single  1.520  0.020  1.520
 1E2  O48  C46  single  1.426  0.020  1.426
 1E2  C2   H1   single  0.970  0.020  1.090
 1E2  C4   H2   single  0.970  0.020  1.090
 1E2  C6   H3   single  0.970  0.020  1.090
 1E2  C6   H4   single  0.970  0.020  1.090
 1E2  C5   H5   single  0.970  0.020  1.090
 1E2  C24  H6   single  0.970  0.020  1.090
 1E2  C24  H7   single  0.970  0.020  1.090
 1E2  C24  H8   single  0.970  0.020  1.090
 1E2  C46  H9   single  0.970  0.020  1.090
 1E2  C46  H10  single  0.970  0.020  1.090
 1E2  C45  H11  single  0.970  0.020  1.090
 1E2  O47  H12  single  0.850  0.020  0.980
 1E2  C44  H13  single  0.970  0.020  1.090
 1E2  C44  H14  single  0.970  0.020  1.090
 1E2  C1   H15  single  0.970  0.020  1.090
 1E2  O2   H16  single  0.850  0.020  0.980
 1E2  C3   H17  single  0.970  0.020  1.090
 1E2  O3   H18  single  0.850  0.020  0.980
 1E2  O4   H19  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
 1E2  H1   C2   C3   108.92  3.000
 1E2  H1   C2   O2   111.44  3.000
 1E2  C3   C2   O2   107.70  3.000
 1E2  H1   C2   C1   107.98  3.000
 1E2  O2   C2   C1   112.13  3.000
 1E2  C3   C2   C1   108.59  3.000
 1E2  H2   C4   O4   111.17  3.000
 1E2  H2   C4   C3   108.53  3.000
 1E2  O4   C4   C3   111.39  3.000
 1E2  H2   C4   C5   108.25  3.000
 1E2  C3   C4   C5   109.23  3.000
 1E2  O4   C4   C5   108.21  3.000
 1E2  H4   C6   H3   107.93  3.000
 1E2  H4   C6   S    107.77  3.000
 1E2  H3   C6   S    106.52  3.000
 1E2  H4   C6   C5   111.37  3.000
 1E2  H3   C6   C5   109.28  3.000
 1E2  S    C6   C5   113.71  3.000
 1E2  H5   C5   O5   110.11  3.000
 1E2  H5   C5   C6   108.55  3.000
 1E2  O5   C5   C6   108.69  3.000
 1E2  H5   C5   C4   108.18  3.000
 1E2  O5   C5   C4   108.56  3.000
 1E2  C6   C5   C4   112.73  3.000
 1E2  O48  C23  C24  111.49  3.000
 1E2  O48  C23  O10  123.22  3.000
 1E2  C24  C23  O10  125.28  3.000
 1E2  H8   C24  H7   107.25  3.000
 1E2  H8   C24  H6   109.44  3.000
 1E2  H7   C24  H6   108.67  3.000
 1E2  H8   C24  C23  111.17  3.000
 1E2  H7   C24  C23  109.75  3.000
 1E2  H6   C24  C23  110.48  3.000
 1E2  H10  C46  H9   107.78  3.000
 1E2  H10  C46  C45  110.14  3.000
 1E2  H9   C46  C45  110.75  3.000
 1E2  H10  C46  O48  110.29  3.000
 1E2  H9   C46  O48  110.30  3.000
 1E2  C45  C46  O48  107.59  3.000
 1E2  H11  C45  C44  108.35  3.000
 1E2  H11  C45  O47  105.87  3.000
 1E2  C44  C45  O47  112.58  3.000
 1E2  H11  C45  C46  108.56  3.000
 1E2  O47  C45  C46  112.44  3.000
 1E2  C44  C45  C46  108.86  3.000
 1E2  H12  O47  C45  108.98  3.000
 1E2  H14  C44  H13  107.20  3.000
 1E2  H14  C44  O6   110.18  3.000
 1E2  H13  C44  O6   110.87  3.000
 1E2  H14  C44  C45  109.59  3.000
 1E2  H13  C44  C45  110.55  3.000
 1E2  O6   C44  C45  108.45  3.000
 1E2  C1   O6   C44  114.04  3.000
 1E2  H15  C1   O5   109.54  3.000
 1E2  H15  C1   O6   110.70  3.000
 1E2  O5   C1   O6   108.41  3.000
 1E2  H15  C1   C2   109.59  3.000
 1E2  O6   C1   C2   109.31  3.000
 1E2  O5   C1   C2   109.27  3.000
 1E2  H16  O2   C2   108.53  3.000
 1E2  H17  C3   O3   110.65  3.000
 1E2  H17  C3   C4   107.39  3.000
 1E2  O3   C3   C4   107.49  3.000
 1E2  H17  C3   C2   108.06  3.000
 1E2  O3   C3   C2   111.97  3.000
 1E2  C4   C3   C2   111.20  3.000
 1E2  H18  O3   C3   108.53  3.000
 1E2  H19  O4   C4   108.40  3.000
 1E2  C1   O5   C5   112.83  3.000
 1E2  O8   S    O7   112.98  3.000
 1E2  O8   S    O9   112.59  3.000
 1E2  O7   S    O9   113.51  3.000
 1E2  O8   S    C6   104.04  3.000
 1E2  O9   S    C6   107.46  3.000
 1E2  O7   S    C6   105.35  3.000
 1E2  C46  O48  C23  117.81  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
 1E2  Var_01  O7   S    C6   C5     47.74  30.0  3
 1E2  Var_02  H13  C44  O6   C1     63.19  30.0  3
 1E2  Var_03  C45  C46  O48  C23  -177.98  30.0  3
 1E2  Var_04  H6   C24  C23  O10    -9.86  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
 1E2  chir_01  C2   C3   C1   O2   positiv
 1E2  chir_02  C4   O4   C5   C3   positiv
 1E2  chir_03  C5   O5   C4   C6   negativ
 1E2  chir_04  C45  O47  C44  C46  negativ
 1E2  chir_05  C1   O5   O6   C2   negativ
 1E2  chir_06  C3   O3   C2   C4   positiv

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
 1E2  plan-1  O10  0.020
 1E2  plan-1  C23  0.020
 1E2  plan-1  C24  0.020
 1E2  plan-1  O48  0.020

