# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun  4 01:50:01 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (6R)-5-O-acetyl-2,6-anhydro-6-{[4-(sulfamoyloxy)piperidin-1-yl]sulfonyl}-L-glucitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)O[C@@H]1[C@H](O)[C@@H](O)[C@@H](CO)O[C@@H]1[S](=O)(=O)N2CC[C@@H](CC2)O[S](N)(=O)=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
 5L3  5L3  (6R)-5-O-acetyl-2,6-anhydro-6-{[4-(sulfamoyloxy)piperidin-1-yl]sulfonyl}-L-glucitol  D-saccharide  52  28  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5L3
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
 5L3  C1   C  CH1   0  -0.176  -1.5651   0.0240  -0.2871
 5L3  O2   O  O2    0  -0.459  -3.8016   0.4942   0.3758
 5L3  C5   C  CH1   0  -0.068  -1.4935  -2.1045   0.7433
 5L3  CBI  C  CH3   0  -0.777  -5.4686   1.8382   1.3316
 5L3  CBE  C  C     0   0.575  -4.8089   1.3212   0.0892
 5L3  OBH  O  O     0  -0.446  -5.1303   1.6285  -1.0287
 5L3  C2   C  CH1   0  -0.032  -3.0326  -0.0763  -0.6746
 5L3  C3   C  CH1   0   0.034  -3.3966  -1.5494  -0.8259
 5L3  O3   O  OH1   0  -0.659  -4.7742  -1.6285  -1.0592
 5L3  C4   C  CH1   0  -0.009  -2.9800  -2.3322   0.4173
 5L3  O4   O  OH1   0  -0.665  -3.2697  -3.6860   0.1683
 5L3  C6   C  CH2   0  -0.164  -0.5406  -2.7983  -0.2185
 5L3  O6   O  OH1   0  -0.654   0.7748  -2.5403   0.2085
 5L3  O5   O  O2    0  -0.470  -1.2504  -0.7034   0.8506
 5L3  SAG  S  S     0   1.387  -1.0985   1.7471   0.0841
 5L3  OAH  O  OS    0  -0.656  -1.5620   2.5121  -1.0647
 5L3  OAJ  O  OS    0  -0.641  -1.5645   2.0869   1.4162
 5L3  NAB  N  N     0  -0.570   0.5271   1.7755   0.1064
 5L3  CAC  C  CH2   0  -0.331   1.3019   1.7522  -1.1290
 5L3  CAD  C  CH2   0  -0.448   2.2263   0.5421  -1.1734
 5L3  CAA  C  CH2   0  -0.309   1.3035   1.6917   1.3375
 5L3  CAF  C  CH2   0  -0.461   2.2257   0.4804   1.3258
 5L3  CAE  C  CH1   0   0.010   3.0844   0.5027   0.0763
 5L3  OAK  O  OC2   0  -0.580   3.8920  -0.6990   0.0700
 5L3  SAL  S  S     0   1.561   5.4597  -0.5855  -0.2212
 5L3  OAN  O  OS    0  -0.642   5.9025  -1.9565  -0.1798
 5L3  OAO  O  OS    0  -0.652   5.6686   0.2296  -1.3967
 5L3  NAM  N  NC2   0  -0.897   6.1332   0.2052   1.0326
 5L3  H1   H  HCH1  0   0.294  -0.9598  -0.2534  -1.1636
 5L3  H2   H  HCH1  0   0.270  -1.2932  -2.4889   1.7471
 5L3  H3   H  HCH3  0   0.262  -5.0903   1.3740   2.2376
 5L3  H4   H  HCH3  0   0.278  -5.3059   2.9148   1.3958
 5L3  H5   H  HCH3  0   0.274  -6.5442   1.6790   1.2666
 5L3  H6   H  HCH1  0   0.301  -3.2052   0.4445  -1.6177
 5L3  H7   H  HCH1  0   0.232  -2.8292  -1.9255  -1.6913
 5L3  H8   H  HOH1  0   0.457  -5.0147  -2.5598  -1.1156
 5L3  H9   H  HCH1  0   0.253  -3.5664  -1.9620   1.2680
 5L3  H10  H  HOH1  0   0.464  -3.3573  -4.1478   1.0079
 5L3  H11  H  HCH2  0   0.227  -0.7701  -3.8686  -0.1997
 5L3  H12  H  HCH2  0   0.205  -0.6968  -2.4676  -1.2533
 5L3  H13  H  HOH1  0   0.459   1.3815  -2.9090  -0.4394
 5L3  H16  H  HCH2  0   0.284   0.6415   1.7494  -1.9937
 5L3  H17  H  HCH2  0   0.265   1.8868   2.6759  -1.1828
 5L3  H18  H  HCH2  0   0.248   1.6372  -0.3761  -1.2314
 5L3  H19  H  HCH2  0   0.265   2.8477   0.6038  -2.0679
 5L3  H20  H  HCH2  0   0.252   1.8909   2.6111   1.4264
 5L3  H21  H  HCH2  0   0.257   2.8511   0.5058   2.2207
 5L3  H22  H  HCH2  0   0.267   1.6319  -0.4346   1.3434
 5L3  H23  H  HCH1  0   0.245   3.7290   1.3900   0.1023
 5L3  H24  H  HNC2  0   0.428   5.9878  -0.2216   1.9402
 5L3  H25  H  HNC2  0   0.428   5.9978   1.2089   1.0438
 5L3  H14  H  HCH2  0   0.285   0.6423   1.6515   2.1980

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
 5L3  C1   C2   single  1.521  0.020  1.521
 5L3  C1   O5   single  1.387  0.020  1.387
 5L3  C1   SAG  single  1.823  0.020  1.823
 5L3  O2   CBE  single  1.334  0.020  1.334
 5L3  O2   C2   single  1.421  0.020  1.421
 5L3  C5   C4   single  1.539  0.020  1.539
 5L3  C5   C6   single  1.521  0.020  1.521
 5L3  C5   O5   single  1.426  0.020  1.426
 5L3  CBI  CBE  single  1.499  0.020  1.499
 5L3  CBE  OBH  double  1.203  0.020  1.203
 5L3  C2   C3   single  1.525  0.020  1.525
 5L3  C3   O3   single  1.399  0.020  1.399
 5L3  C3   C4   single  1.527  0.020  1.527
 5L3  C4   O4   single  1.407  0.020  1.407
 5L3  C6   O6   single  1.407  0.020  1.407
 5L3  SAG  OAH  double  1.456  0.020  1.456
 5L3  SAG  OAJ  double  1.452  0.020  1.452
 5L3  SAG  NAB  single  1.626  0.020  1.626
 5L3  NAB  CAC  single  1.458  0.020  1.458
 5L3  NAB  CAA  single  1.458  0.020  1.458
 5L3  CAC  CAD  single  1.523  0.020  1.523
 5L3  CAD  CAE  single  1.516  0.020  1.516
 5L3  CAA  CAF  single  1.522  0.020  1.522
 5L3  CAF  CAE  single  1.516  0.020  1.516
 5L3  CAE  OAK  single  1.448  0.020  1.448
 5L3  OAK  SAL  single  1.598  0.020  1.598
 5L3  SAL  OAN  deloc   1.441  0.020  1.441
 5L3  SAL  OAO  deloc   1.446  0.020  1.446
 5L3  SAL  NAM  single  1.628  0.020  1.628
 5L3  C1   H1   single  0.970  0.020  1.090
 5L3  C5   H2   single  0.970  0.020  1.090
 5L3  CBI  H3   single  0.970  0.020  1.090
 5L3  CBI  H4   single  0.970  0.020  1.090
 5L3  CBI  H5   single  0.970  0.020  1.090
 5L3  C2   H6   single  0.970  0.020  1.090
 5L3  C3   H7   single  0.970  0.020  1.090
 5L3  O3   H8   single  0.850  0.020  0.980
 5L3  C4   H9   single  0.970  0.020  1.090
 5L3  O4   H10  single  0.850  0.020  0.980
 5L3  C6   H11  single  0.970  0.020  1.090
 5L3  C6   H12  single  0.970  0.020  1.090
 5L3  O6   H13  single  0.850  0.020  0.980
 5L3  CAC  H16  single  0.970  0.020  1.090
 5L3  CAC  H17  single  0.970  0.020  1.090
 5L3  CAD  H18  single  0.970  0.020  1.090
 5L3  CAD  H19  single  0.970  0.020  1.090
 5L3  CAA  H20  single  0.970  0.020  1.090
 5L3  CAF  H21  single  0.970  0.020  1.090
 5L3  CAF  H22  single  0.970  0.020  1.090
 5L3  CAE  H23  single  0.970  0.020  1.090
 5L3  NAM  H24  single  0.890  0.020  1.040
 5L3  NAM  H25  single  0.890  0.020  1.040
 5L3  CAA  H14  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
 5L3  H1   C1   SAG  105.05  3.000
 5L3  H1   C1   O5   113.35  3.000
 5L3  SAG  C1   O5   105.70  3.000
 5L3  H1   C1   C2   108.12  3.000
 5L3  SAG  C1   C2   111.16  3.000
 5L3  O5   C1   C2   113.17  3.000
 5L3  C2   O2   CBE  119.90  3.000
 5L3  H2   C5   O5   104.18  3.000
 5L3  H2   C5   C6   107.78  3.000
 5L3  O5   C5   C6   112.88  3.000
 5L3  H2   C5   C4   108.63  3.000
 5L3  O5   C5   C4   109.03  3.000
 5L3  C6   C5   C4   113.81  3.000
 5L3  H5   CBI  H4   107.17  3.000
 5L3  H5   CBI  H3   109.34  3.000
 5L3  H4   CBI  H3   108.71  3.000
 5L3  H5   CBI  CBE  109.56  3.000
 5L3  H4   CBI  CBE  108.88  3.000
 5L3  H3   CBI  CBE  113.00  3.000
 5L3  OBH  CBE  CBI  124.37  3.000
 5L3  OBH  CBE  O2   124.02  3.000
 5L3  CBI  CBE  O2   111.60  3.000
 5L3  H6   C2   C3   109.72  3.000
 5L3  H6   C2   O2   111.20  3.000
 5L3  C3   C2   O2   109.39  3.000
 5L3  H6   C2   C1   109.96  3.000
 5L3  C3   C2   C1   108.62  3.000
 5L3  O2   C2   C1   107.89  3.000
 5L3  H7   C3   C4   108.91  3.000
 5L3  H7   C3   O3   110.91  3.000
 5L3  C4   C3   O3   112.05  3.000
 5L3  H7   C3   C2   106.56  3.000
 5L3  C4   C3   C2   110.44  3.000
 5L3  O3   C3   C2   107.82  3.000
 5L3  H8   O3   C3   108.06  3.000
 5L3  H9   C4   O4   110.60  3.000
 5L3  H9   C4   C3   108.20  3.000
 5L3  O4   C4   C3   107.04  3.000
 5L3  H9   C4   C5   107.58  3.000
 5L3  O4   C4   C5   112.26  3.000
 5L3  C3   C4   C5   111.11  3.000
 5L3  H10  O4   C4   109.04  3.000
 5L3  H12  C6   H11  106.32  3.000
 5L3  H12  C6   O6   111.35  3.000
 5L3  H11  C6   O6   111.72  3.000
 5L3  H12  C6   C5   111.68  3.000
 5L3  H11  C6   C5   107.68  3.000
 5L3  O6   C6   C5   108.07  3.000
 5L3  H13  O6   C6   108.37  3.000
 5L3  C5   O5   C1   114.52  3.000
 5L3  NAB  SAG  OAJ  107.71  3.000
 5L3  NAB  SAG  OAH  108.66  3.000
 5L3  OAJ  SAG  OAH  119.93  3.000
 5L3  NAB  SAG  C1   105.97  3.000
 5L3  OAJ  SAG  C1   109.02  3.000
 5L3  OAH  SAG  C1   104.74  3.000
 5L3  CAA  NAB  CAC  115.56  3.000
 5L3  CAA  NAB  SAG  122.89  3.000
 5L3  CAC  NAB  SAG  121.28  3.000
 5L3  H17  CAC  H16  106.70  3.000
 5L3  H17  CAC  CAD  110.16  3.000
 5L3  H16  CAC  CAD  110.07  3.000
 5L3  H17  CAC  NAB  108.18  3.000
 5L3  H16  CAC  NAB  110.54  3.000
 5L3  CAD  CAC  NAB  111.08  3.000
 5L3  H19  CAD  H18  108.13  3.000
 5L3  H19  CAD  CAE  110.79  3.000
 5L3  H18  CAD  CAE  109.09  3.000
 5L3  H19  CAD  CAC  108.94  3.000
 5L3  H18  CAD  CAC  110.00  3.000
 5L3  CAE  CAD  CAC  109.88  3.000
 5L3  H14  CAA  H20  107.06  3.000
 5L3  H14  CAA  CAF  110.21  3.000
 5L3  H20  CAA  CAF  110.12  3.000
 5L3  H14  CAA  NAB  110.30  3.000
 5L3  H20  CAA  NAB  107.83  3.000
 5L3  CAF  CAA  NAB  111.21  3.000
 5L3  H22  CAF  H21  108.54  3.000
 5L3  H22  CAF  CAE  109.51  3.000
 5L3  H21  CAF  CAE  110.52  3.000
 5L3  H22  CAF  CAA  109.73  3.000
 5L3  H21  CAF  CAA  108.79  3.000
 5L3  CAE  CAF  CAA  109.73  3.000
 5L3  H23  CAE  OAK  110.10  3.000
 5L3  H23  CAE  CAF  108.98  3.000
 5L3  OAK  CAE  CAF  107.90  3.000
 5L3  H23  CAE  CAD  109.33  3.000
 5L3  OAK  CAE  CAD  109.49  3.000
 5L3  CAF  CAE  CAD  111.04  3.000
 5L3  SAL  OAK  CAE  119.27  3.000
 5L3  NAM  SAL  OAO  107.01  3.000
 5L3  NAM  SAL  OAN  108.22  3.000
 5L3  OAO  SAL  OAN  121.01  3.000
 5L3  NAM  SAL  OAK  107.45  3.000
 5L3  OAO  SAL  OAK  109.26  3.000
 5L3  OAN  SAL  OAK  103.21  3.000
 5L3  H25  NAM  H24  112.84  3.000
 5L3  H25  NAM  SAL  115.75  3.000
 5L3  H24  NAM  SAL  115.20  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
 5L3  Var_01  CAE  CAD  CAC  NAB   -53.71  30.0  1
 5L3  Var_02  CAE  CAF  CAA  NAB    53.88  30.0  1
 5L3  Var_03  CAF  CAA  NAB  CAC   -53.77  30.0  1
 5L3  Var_04  CAA  NAB  CAC  CAD    53.61  30.0  1
 5L3  Var_05  CAC  NAB  SAG  C1     76.31  30.0  3
 5L3  Var_06  OAN  SAL  OAK  CAE  -178.55  30.0  3
 5L3  Var_07  H3   CBI  CBE  O2     -6.22  30.0  3
 5L3  Var_08  H24  NAM  SAL  OAK    57.68  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
 5L3  chir_01  C1   C2   O5   SAG  positiv
 5L3  chir_02  C5   O5   C6   C4   positiv
 5L3  chir_03  C2   O2   C1   C3   negativ
 5L3  chir_04  C3   O3   C2   C4   negativ
 5L3  chir_05  C4   O4   C5   C3   negativ
 5L3  chir_06  CAE  CAD  CAF  OAK  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
 5L3  plan-1  O2   0.020
 5L3  plan-1  CBI  0.020
 5L3  plan-1  CBE  0.020
 5L3  plan-1  OBH  0.020

