# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 20:55:23 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 3-{4-[2-(beta-D-glucopyranosyloxy)ethyl]piperazin-1-yl}propane-1-sulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](OCCN2CCN(CCC[S](O)(=O)=O)CC2)[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
 GBE  GBE  '3-{4-[2-(beta-D-glucopyranosyloxy)ethyl]piperazin-1-yl}propane-1-sulfonic acid'  ligand  56  27  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GBE
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
 GBE  C1    C  CH1    0   0.262  -3.3353  -1.0722  -0.0295
 GBE  O1    O  O2     0  -0.491  -3.3397  -2.4292  -0.2771
 GBE  C2    C  CH1    0  -0.003  -3.1351  -0.2822  -1.3194
 GBE  O2    O  OH1    0  -0.710  -1.9333  -0.5821  -1.9751
 GBE  C3    C  CH1    0  -0.015  -3.1785   1.1985  -0.9526
 GBE  O3    O  OH1    0  -0.675  -3.0746   2.0308  -2.0830
 GBE  C4    C  CH1    0   0.033  -4.4843   1.5385  -0.2448
 GBE  O4    O  OH1    0  -0.673  -4.4893   2.8616   0.2330
 GBE  C5    C  CH1    0  -0.018  -4.6754   0.6020   0.9512
 GBE  O5    O  O2     0  -0.492  -4.5790  -0.7444   0.5308
 GBE  C6    C  CH2    0  -0.157  -6.0313   0.7865   1.5983
 GBE  O6    O  OH1    0  -0.671  -6.1049  -0.0290   2.7432
 GBE  OAA   O  OS    -1  -0.770   6.8453   3.2267  -0.0050
 GBE  OAB   O  OS     0  -0.772   6.5943   1.2219   1.4074
 GBE  OAG   O  OS     0  -0.772   4.9924   3.0821   1.6119
 GBE  CAH   C  CH2    0  -0.456   3.8684   0.6055   0.0061
 GBE  CAJ   C  CH2    0  -0.221  -2.4997  -3.2330   0.5317
 GBE  CAL   C  CH2    0  -0.283  -1.2042  -3.5813  -0.1788
 GBE  CAM   C  CH2    0  -0.294   1.5171  -1.6477  -1.8801
 GBE  CAN   C  CH2    0  -0.292   1.1117  -0.6353   0.2271
 GBE  CAO   C  CH2    0  -0.293   0.6578  -2.8306  -1.4838
 GBE  CAP   C  CH2    0  -0.302   0.2647  -1.8258   0.6359
 GBE  CAQ   C  CH2    0  -0.632   4.8864   1.5902  -0.5460
 GBE  NAY   N  NT     0  -0.423   2.1344  -1.0352  -0.7195
 GBE  NAZ   N  NT     0  -0.475  -0.3720  -2.4362  -0.5264
 GBE  SBA   S  S      0   1.403   5.9145   2.3423   0.7256
 GBE  H1    H  HCH1   0   0.186  -2.5342  -0.8060   0.6854
 GBE  H2    H  HCH1   0   0.213  -3.9792  -0.5068  -1.9894
 GBE  HO2   H  HOH1   0   0.463  -1.3881  -1.2053  -1.4390
 GBE  H3    H  HCH1   0   0.202  -2.3503   1.3953  -0.2499
 GBE  HO3   H  HOH1   0   0.454  -2.2006   1.9048  -2.4663
 GBE  H4    H  HCH1   0   0.210  -5.3135   1.3702  -0.9510
 GBE  HO4   H  HOH1   0   0.454  -4.2948   3.4473  -0.5062
 GBE  H5    H  HCH1   0   0.224  -3.8886   0.8195   1.6922
 GBE  H6    H  HCH2   0   0.211  -6.1556   1.8457   1.8465
 GBE  H6A   H  HCH2   0   0.198  -6.8099   0.5339   0.8648
 GBE  HO6   H  HOH1   0   0.457  -6.9770   0.0836   3.1310
 GBE  HAH   H  HCH2   0   0.236   3.2554   1.1104   0.7555
 GBE  HAHA  H  HCH2   0   0.233   4.3796  -0.2198   0.5055
 GBE  HAJ   H  HCH2   0   0.228  -2.3158  -2.7562   1.5003
 GBE  HAJA  H  HCH2   0   0.252  -3.0290  -4.1656   0.7382
 GBE  HAK   H  HCH2   0   0.191   2.4307   0.8824  -1.5761
 GBE  HAKA  H  HCH2   0   0.227   3.6604  -0.3300  -1.9058
 GBE  HAL   H  HCH2   0   0.220  -0.6547  -4.2984   0.4501
 GBE  HALA  H  HCH2   0   0.249  -1.4543  -4.1042  -1.1050
 GBE  HAM   H  HCH2   0   0.244   2.2998  -1.9994  -2.5563
 GBE  HAMA  H  HCH2   0   0.197   0.9071  -0.9237  -2.4466
 GBE  HAN   H  HCH2   0   0.190   0.4584   0.1526  -0.1881
 GBE  HANA  H  HCH2   0   0.250   1.5741  -0.2260   1.1260
 GBE  HAO   H  HCH2   0   0.251   0.1741  -3.2374  -2.3739
 GBE  HAOA  H  HCH2   0   0.217   1.2967  -3.6217  -1.0631
 GBE  HAP   H  HCH2   0   0.220   0.8911  -2.5600   1.1651
 GBE  HAPA  H  HCH2   0   0.248  -0.4945  -1.4840   1.3407
 GBE  HAQ   H  HCH2   0   0.259   5.5617   1.0984  -1.2502
 GBE  HAQA  H  HCH2   0   0.258   4.3911   2.4050  -1.0793
 GBE  CAK   C  CH2    0  -0.247   3.0032   0.0553  -1.1204

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
 GBE  C1   O1    single  1.379  0.020  1.379
 GBE  C1   C2    single  1.526  0.020  1.526
 GBE  C1   O5    single  1.403  0.020  1.403
 GBE  O1   CAJ   single  1.416  0.020  1.416
 GBE  C2   O2    single  1.401  0.020  1.401
 GBE  C2   C3    single  1.526  0.020  1.526
 GBE  C3   O3    single  1.408  0.020  1.408
 GBE  C3   C4    single  1.524  0.020  1.524
 GBE  C4   O4    single  1.407  0.020  1.407
 GBE  C4   C5    single  1.531  0.020  1.531
 GBE  C5   O5    single  1.414  0.020  1.414
 GBE  C5   C6    single  1.514  0.020  1.514
 GBE  C6   O6    single  1.408  0.020  1.408
 GBE  OAA  SBA   deloc   1.477  0.020  1.477
 GBE  OAB  SBA   deloc   1.477  0.020  1.477
 GBE  OAG  SBA   deloc   1.478  0.020  1.478
 GBE  CAH  CAK   single  1.523  0.020  1.523
 GBE  CAH  CAQ   single  1.520  0.020  1.520
 GBE  CAJ  CAL   single  1.518  0.020  1.518
 GBE  CAK  NAY   single  1.451  0.020  1.451
 GBE  CAL  NAZ   single  1.458  0.020  1.458
 GBE  CAM  CAO   single  1.515  0.020  1.515
 GBE  CAM  NAY   single  1.450  0.020  1.450
 GBE  CAN  CAP   single  1.517  0.020  1.517
 GBE  CAN  NAY   single  1.450  0.020  1.450
 GBE  CAO  NAZ   single  1.460  0.020  1.460
 GBE  CAP  NAZ   single  1.459  0.020  1.459
 GBE  CAQ  SBA   single  1.800  0.020  1.800
 GBE  C1   H1    single  0.970  0.020  1.090
 GBE  C2   H2    single  0.970  0.020  1.090
 GBE  O2   HO2   single  0.850  0.020  0.980
 GBE  C3   H3    single  0.970  0.020  1.090
 GBE  O3   HO3   single  0.850  0.020  0.980
 GBE  C4   H4    single  0.970  0.020  1.090
 GBE  O4   HO4   single  0.850  0.020  0.980
 GBE  C5   H5    single  0.970  0.020  1.090
 GBE  C6   H6    single  0.970  0.020  1.090
 GBE  C6   H6A   single  0.970  0.020  1.090
 GBE  O6   HO6   single  0.850  0.020  0.980
 GBE  CAH  HAH   single  0.970  0.020  1.090
 GBE  CAH  HAHA  single  0.970  0.020  1.090
 GBE  CAJ  HAJ   single  0.970  0.020  1.090
 GBE  CAJ  HAJA  single  0.970  0.020  1.090
 GBE  CAK  HAK   single  0.970  0.020  1.090
 GBE  CAK  HAKA  single  0.970  0.020  1.090
 GBE  CAL  HAL   single  0.970  0.020  1.090
 GBE  CAL  HALA  single  0.970  0.020  1.090
 GBE  CAM  HAM   single  0.970  0.020  1.090
 GBE  CAM  HAMA  single  0.970  0.020  1.090
 GBE  CAN  HAN   single  0.970  0.020  1.090
 GBE  CAN  HANA  single  0.970  0.020  1.090
 GBE  CAO  HAO   single  0.970  0.020  1.090
 GBE  CAO  HAOA  single  0.970  0.020  1.090
 GBE  CAP  HAP   single  0.970  0.020  1.090
 GBE  CAP  HAPA  single  0.970  0.020  1.090
 GBE  CAQ  HAQ   single  0.970  0.020  1.090
 GBE  CAQ  HAQA  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
 GBE  H1    C1   O5   109.13  3.000
 GBE  H1    C1   C2   109.08  3.000
 GBE  O5    C1   C2   109.45  3.000
 GBE  H1    C1   O1   110.80  3.000
 GBE  O5    C1   O1   107.38  3.000
 GBE  C2    C1   O1   110.98  3.000
 GBE  CAJ   O1   C1   116.99  3.000
 GBE  H2    C2   C3   108.81  3.000
 GBE  H2    C2   O2   109.22  3.000
 GBE  C3    C2   O2   110.15  3.000
 GBE  H2    C2   C1   107.95  3.000
 GBE  C3    C2   C1   107.18  3.000
 GBE  O2    C2   C1   113.41  3.000
 GBE  HO2   O2   C2   110.79  3.000
 GBE  H3    C3   C4   107.91  3.000
 GBE  H3    C3   O3   110.52  3.000
 GBE  C4    C3   O3   107.72  3.000
 GBE  H3    C3   C2   107.74  3.000
 GBE  C4    C3   C2   110.64  3.000
 GBE  O3    C3   C2   112.24  3.000
 GBE  HO3   O3   C3   108.02  3.000
 GBE  H4    C4   C5   108.26  3.000
 GBE  H4    C4   O4   111.02  3.000
 GBE  C5    C4   O4   108.03  3.000
 GBE  H4    C4   C3   108.24  3.000
 GBE  C5    C4   C3   109.47  3.000
 GBE  O4    C4   C3   111.76  3.000
 GBE  HO4   O4   C4   108.10  3.000
 GBE  H5    C5   C6   109.14  3.000
 GBE  H5    C5   O5   109.82  3.000
 GBE  C6    C5   O5   107.71  3.000
 GBE  H5    C5   C4   108.38  3.000
 GBE  C6    C5   C4   111.79  3.000
 GBE  O5    C5   C4   109.98  3.000
 GBE  C5    O5   C1   113.68  3.000
 GBE  H6A   C6   H6   107.05  3.000
 GBE  H6A   C6   O6   111.88  3.000
 GBE  H6    C6   O6   111.73  3.000
 GBE  H6A   C6   C5   108.74  3.000
 GBE  H6    C6   C5   108.44  3.000
 GBE  O6    C6   C5   108.90  3.000
 GBE  HO6   O6   C6   107.92  3.000
 GBE  HAHA  CAH  HAH  107.37  3.000
 GBE  HAHA  CAH  CAQ  110.01  3.000
 GBE  HAH   CAH  CAQ  109.01  3.000
 GBE  HAHA  CAH  CAK  109.34  3.000
 GBE  HAH   CAH  CAK  110.84  3.000
 GBE  CAQ   CAH  CAK  110.23  3.000
 GBE  HAJA  CAJ  HAJ  106.61  3.000
 GBE  HAJA  CAJ  CAL  107.83  3.000
 GBE  HAJ   CAJ  CAL  111.75  3.000
 GBE  HAJA  CAJ  O1   107.77  3.000
 GBE  HAJ   CAJ  O1   110.96  3.000
 GBE  CAL   CAJ  O1   111.66  3.000
 GBE  HALA  CAL  HAL  106.67  3.000
 GBE  HALA  CAL  NAZ  107.73  3.000
 GBE  HAL   CAL  NAZ  111.28  3.000
 GBE  HALA  CAL  CAJ  108.14  3.000
 GBE  HAL   CAL  CAJ  107.95  3.000
 GBE  NAZ   CAL  CAJ  114.74  3.000
 GBE  HAMA  CAM  HAM  106.83  3.000
 GBE  HAMA  CAM  NAY  111.66  3.000
 GBE  HAM   CAM  NAY  109.05  3.000
 GBE  HAMA  CAM  CAO  109.46  3.000
 GBE  HAM   CAM  CAO  108.48  3.000
 GBE  NAY   CAM  CAO  111.21  3.000
 GBE  HANA  CAN  HAN  107.03  3.000
 GBE  HANA  CAN  NAY  110.03  3.000
 GBE  HAN   CAN  NAY  111.63  3.000
 GBE  HANA  CAN  CAP  108.00  3.000
 GBE  HAN   CAN  CAP  109.32  3.000
 GBE  NAY   CAN  CAP  110.69  3.000
 GBE  HAOA  CAO  HAO  107.52  3.000
 GBE  HAOA  CAO  NAZ  110.67  3.000
 GBE  HAO   CAO  NAZ  108.83  3.000
 GBE  HAOA  CAO  CAM  109.39  3.000
 GBE  HAO   CAO  CAM  109.21  3.000
 GBE  NAZ   CAO  CAM  111.14  3.000
 GBE  HAPA  CAP  HAP  107.13  3.000
 GBE  HAPA  CAP  NAZ  110.01  3.000
 GBE  HAP   CAP  NAZ  110.62  3.000
 GBE  HAPA  CAP  CAN  108.47  3.000
 GBE  HAP   CAP  CAN  109.59  3.000
 GBE  NAZ   CAP  CAN  110.93  3.000
 GBE  HAQA  CAQ  HAQ  107.53  3.000
 GBE  HAQA  CAQ  SBA  106.99  3.000
 GBE  HAQ   CAQ  SBA  106.88  3.000
 GBE  HAQA  CAQ  CAH  110.91  3.000
 GBE  HAQ   CAQ  CAH  110.88  3.000
 GBE  SBA   CAQ  CAH  113.37  3.000
 GBE  CAN   NAY  CAM  109.80  3.000
 GBE  CAN   NAY  CAK  113.30  3.000
 GBE  CAM   NAY  CAK  110.56  3.000
 GBE  CAP   NAZ  CAO  109.12  3.000
 GBE  CAP   NAZ  CAL  112.82  3.000
 GBE  CAO   NAZ  CAL  110.29  3.000
 GBE  CAQ   SBA  OAG  106.05  3.000
 GBE  CAQ   SBA  OAB  105.78  3.000
 GBE  OAG   SBA  OAB  112.96  3.000
 GBE  CAQ   SBA  OAA  105.11  3.000
 GBE  OAG   SBA  OAA  112.96  3.000
 GBE  OAB   SBA  OAA  113.10  3.000
 GBE  HAKA  CAK  HAK  106.19  3.000
 GBE  HAKA  CAK  NAY  107.06  3.000
 GBE  HAK   CAK  NAY  111.51  3.000
 GBE  HAKA  CAK  CAH  108.47  3.000
 GBE  HAK   CAK  CAH  109.21  3.000
 GBE  NAY   CAK  CAH  114.04  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
 GBE  Var_01  CAP  NAZ  CAO  CAM   -56.69  30.0  1
 GBE  Var_02  CAP  CAN  NAY  CAM    57.49  30.0  1
 GBE  Var_03  CAO  NAZ  CAP  CAN    57.40  30.0  1
 GBE  Var_04  CAO  CAM  NAY  CAN   -56.96  30.0  1
 GBE  Var_05  NAZ  CAO  CAM  NAY    57.35  30.0  1
 GBE  Var_06  NAZ  CAP  CAN  NAY   -58.70  30.0  1
 GBE  Var_07  CAM  NAY  CAK  CAH  -170.39  30.0  3
 GBE  Var_08  CAL  CAJ  O1   C1    -99.70  30.0  3
 GBE  Var_09  NAZ  CAL  CAJ  O1     61.88  30.0  3
 GBE  Var_10  NAY  CAK  CAH  CAQ   171.47  30.0  3
 GBE  Var_11  CAH  CAQ  SBA  OAA   178.63  30.0  3
 GBE  Var_12  SBA  CAQ  CAH  CAK   177.76  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
 GBE  chir_01  C1  O1  C2  O5  negativ
 GBE  chir_02  C2  O2  C1  C3  negativ
 GBE  chir_03  C3  O3  C2  C4  positiv
 GBE  chir_04  C4  O4  C5  C3  positiv
 GBE  chir_05  C5  O5  C4  C6  negativ

