# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 04:45:08 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 2-{4-[2-(beta-D-glucopyranosyloxy)ethyl]piperazin-1-yl}ethanesulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](OCCN2CCN(CC2)CC[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
 GBH  GBH  '2-{4-[2-(beta-D-glucopyranosyloxy)ethyl]piperazin-1-yl}ethanesulfonic acid'  D-saccharide  53  26  .  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_GBH
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
 GBH  C1    C  CH1    0   0.187   3.0392  -0.9997   0.5231
 GBH  O1    O  O2     0  -0.394   2.8696  -2.1322   1.2926
 GBH  C2    C  CH1    0   0.006   2.7175   0.2510   1.3390
 GBH  O2    O  OH1    0  -0.710   1.3970   0.2750   1.8084
 GBH  C3    C  CH1    0  -0.009   2.9950   1.4683   0.4620
 GBH  O3    O  OH1    0  -0.719   2.8125   2.6758   1.1618
 GBH  C4    C  CH1    0   0.015   4.4264   1.4385  -0.0570
 GBH  O4    O  OH1    0  -0.723   4.6687   2.4721  -0.9797
 GBH  C5    C  CH1    0  -0.009   4.6747   0.1031  -0.7634
 GBH  O5    O  O2     0  -0.471   4.3809  -0.9653   0.1148
 GBH  C6    C  CH2    0  -0.155   6.1147  -0.0438  -1.2054
 GBH  O6    O  OH1    0  -0.649   6.2575  -1.2597  -1.9000
 GBH  OAA   O  OS     0  -0.781  -4.8920   3.1957  -0.5546
 GBH  OAB   O  OS    -1  -0.842  -6.8816   1.7421  -0.5614
 GBH  OAG   O  OS     0  -0.726  -5.3926   1.8039  -2.5239
 GBH  CAI   C  CH2    0  -0.211   2.0790  -3.1726   0.7499
 GBH  CAJ   C  CH2    0  -0.305   0.6335  -3.0915   1.2074
 GBH  CAK   C  CH2    0  -0.325  -0.3572  -1.8937  -0.6557
 GBH  CAL   C  CH2    0  -0.296  -1.3314  -1.7496   1.5075
 GBH  CAM   C  CH2    0  -0.267  -1.0774  -0.6221  -1.0559
 GBH  CAN   C  CH2    0  -0.282  -2.0764  -0.4950   1.0906
 GBH  CAO   C  CH2    0  -0.305  -3.0793   0.6651  -0.7778
 GBH  CAP   C  CH2    0  -0.656  -4.5383   0.6050  -0.3531
 GBH  NAX   N  NT     0  -0.466  -0.0768  -1.8943   0.7747
 GBH  NAY   N  NT     0  -0.394  -2.3283  -0.4947  -0.3367
 GBH  SAZ   S  S      0   1.373  -5.5073   1.9509  -1.0583
 GBH  H1    H  HCH1   0   0.169   2.3952  -1.0231  -0.3751
 GBH  H2    H  HCH1   0   0.251   3.4047   0.2747   2.1983
 GBH  HO2   H  HOH1   0   0.454   0.8704  -0.4389   1.3780
 GBH  H3    H  HCH1   0   0.230   2.3204   1.4238  -0.4109
 GBH  HO3   H  HOH1   0   0.443   1.8876   2.7284   1.4247
 GBH  H4    H  HCH1   0   0.231   5.1124   1.5055   0.8029
 GBH  HO4   H  HOH1   0   0.444   4.4707   3.3103  -0.5492
 GBH  H5    H  HCH1   0   0.213   4.0178   0.0541  -1.6482
 GBH  H6    H  HCH2   0   0.205   6.3711   0.8139  -1.8352
 GBH  H6A   H  HCH2   0   0.129   6.7634  -0.0004  -0.3192
 GBH  HO6   H  HOH1   0   0.446   7.1457  -1.2882  -2.2664
 GBH  HAI   H  HCH2   0   0.225   2.1606  -3.2002  -0.3419
 GBH  HAIA  H  HCH2   0   0.299   2.4899  -4.1157   1.1157
 GBH  HAJ   H  HCH2   0   0.241   0.1209  -4.0038   0.8667
 GBH  HAJA  H  HCH2   0   0.245   0.6179  -3.1136   2.2997
 GBH  HAK   H  HCH2   0   0.222  -0.9664  -2.7668  -0.9352
 GBH  HAKA  H  HCH2   0   0.248   0.5720  -1.9590  -1.2233
 GBH  HAL   H  HCH2   0   0.205  -1.1132  -1.6973   2.5761
 GBH  HALA  H  HCH2   0   0.256  -1.9805  -2.6238   1.3481
 GBH  HAM   H  HCH2   0   0.134  -0.4081   0.2398  -0.8854
 GBH  HAMA  H  HCH2   0   0.266  -1.2825  -0.6591  -2.1279
 GBH  HAN   H  HCH2   0   0.245  -3.0202  -0.4754   1.6384
 GBH  HANA  H  HCH2   0   0.225  -1.5106   0.3994   1.4040
 GBH  HAO   H  HCH2   0   0.254  -3.0386   0.6895  -1.8688
 GBH  HAOA  H  HCH2   0   0.211  -2.6283   1.6042  -0.4211
 GBH  HAP   H  HCH2   0   0.303  -4.9951  -0.3286  -0.6841
 GBH  HAPA  H  HCH2   0   0.317  -4.6563   0.6722   0.7299

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
 GBH  C1   O1    single  1.380  0.020  1.380
 GBH  C1   C2    single  1.528  0.020  1.528
 GBH  C1   O5    single  1.403  0.020  1.403
 GBH  O1   CAI   single  1.415  0.020  1.415
 GBH  C2   O2    single  1.402  0.020  1.402
 GBH  C2   C3    single  1.526  0.020  1.526
 GBH  C3   O3    single  1.408  0.020  1.408
 GBH  C3   C4    single  1.523  0.020  1.523
 GBH  C4   O4    single  1.407  0.020  1.407
 GBH  C4   C5    single  1.531  0.020  1.531
 GBH  C5   O5    single  1.414  0.020  1.414
 GBH  C5   C6    single  1.513  0.020  1.513
 GBH  C6   O6    single  1.408  0.020  1.408
 GBH  OAA  SAZ   deloc   1.477  0.020  1.477
 GBH  OAB  SAZ   deloc   1.476  0.020  1.476
 GBH  OAG  SAZ   deloc   1.477  0.020  1.477
 GBH  CAI  CAJ   single  1.518  0.020  1.518
 GBH  CAJ  NAX   single  1.458  0.020  1.458
 GBH  CAK  CAM   single  1.515  0.020  1.515
 GBH  CAK  NAX   single  1.458  0.020  1.458
 GBH  CAL  CAN   single  1.517  0.020  1.517
 GBH  CAL  NAX   single  1.460  0.020  1.460
 GBH  CAM  NAY   single  1.449  0.020  1.449
 GBH  CAN  NAY   single  1.449  0.020  1.449
 GBH  CAO  CAP   single  1.521  0.020  1.521
 GBH  CAO  NAY   single  1.450  0.020  1.450
 GBH  CAP  SAZ   single  1.802  0.020  1.802
 GBH  C1   H1    single  0.970  0.020  1.090
 GBH  C2   H2    single  0.970  0.020  1.090
 GBH  O2   HO2   single  0.850  0.020  0.980
 GBH  C3   H3    single  0.970  0.020  1.090
 GBH  O3   HO3   single  0.850  0.020  0.980
 GBH  C4   H4    single  0.970  0.020  1.090
 GBH  O4   HO4   single  0.850  0.020  0.980
 GBH  C5   H5    single  0.970  0.020  1.090
 GBH  C6   H6    single  0.970  0.020  1.090
 GBH  C6   H6A   single  0.970  0.020  1.090
 GBH  O6   HO6   single  0.850  0.020  0.980
 GBH  CAI  HAI   single  0.970  0.020  1.090
 GBH  CAI  HAIA  single  0.970  0.020  1.090
 GBH  CAJ  HAJ   single  0.970  0.020  1.090
 GBH  CAJ  HAJA  single  0.970  0.020  1.090
 GBH  CAK  HAK   single  0.970  0.020  1.090
 GBH  CAK  HAKA  single  0.970  0.020  1.090
 GBH  CAL  HAL   single  0.970  0.020  1.090
 GBH  CAL  HALA  single  0.970  0.020  1.090
 GBH  CAM  HAM   single  0.970  0.020  1.090
 GBH  CAM  HAMA  single  0.970  0.020  1.090
 GBH  CAN  HAN   single  0.970  0.020  1.090
 GBH  CAN  HANA  single  0.970  0.020  1.090
 GBH  CAO  HAO   single  0.970  0.020  1.090
 GBH  CAO  HAOA  single  0.970  0.020  1.090
 GBH  CAP  HAP   single  0.970  0.020  1.090
 GBH  CAP  HAPA  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
 GBH  H1    C1   O5   108.73  3.000
 GBH  H1    C1   C2   109.18  3.000
 GBH  O5    C1   C2   109.68  3.000
 GBH  H1    C1   O1   111.36  3.000
 GBH  O5    C1   O1   107.46  3.000
 GBH  C2    C1   O1   110.39  3.000
 GBH  CAI   O1   C1   117.28  3.000
 GBH  H2    C2   C3   108.55  3.000
 GBH  H2    C2   O2   109.05  3.000
 GBH  C3    C2   O2   110.50  3.000
 GBH  H2    C2   C1   107.65  3.000
 GBH  C3    C2   C1   107.94  3.000
 GBH  O2    C2   C1   113.03  3.000
 GBH  HO2   O2   C2   110.15  3.000
 GBH  H3    C3   C4   107.70  3.000
 GBH  H3    C3   O3   110.39  3.000
 GBH  C4    C3   O3   107.94  3.000
 GBH  H3    C3   C2   108.13  3.000
 GBH  C4    C3   C2   110.56  3.000
 GBH  O3    C3   C2   112.03  3.000
 GBH  HO3   O3   C3   107.88  3.000
 GBH  H4    C4   C5   108.19  3.000
 GBH  H4    C4   O4   111.10  3.000
 GBH  C5    C4   O4   108.08  3.000
 GBH  H4    C4   C3   108.54  3.000
 GBH  C5    C4   C3   109.07  3.000
 GBH  O4    C4   C3   111.78  3.000
 GBH  HO4   O4   C4   108.12  3.000
 GBH  H5    C5   C6   109.15  3.000
 GBH  H5    C5   O5   109.94  3.000
 GBH  C6    C5   O5   107.81  3.000
 GBH  H5    C5   C4   108.19  3.000
 GBH  C6    C5   C4   111.94  3.000
 GBH  O5    C5   C4   109.80  3.000
 GBH  C5    O5   C1   113.46  3.000
 GBH  H6A   C6   H6   107.14  3.000
 GBH  H6A   C6   O6   111.85  3.000
 GBH  H6    C6   O6   111.67  3.000
 GBH  H6A   C6   C5   108.80  3.000
 GBH  H6    C6   C5   108.35  3.000
 GBH  O6    C6   C5   108.93  3.000
 GBH  HO6   O6   C6   107.90  3.000
 GBH  HAIA  CAI  HAI  106.51  3.000
 GBH  HAIA  CAI  CAJ  107.67  3.000
 GBH  HAI   CAI  CAJ  111.88  3.000
 GBH  HAIA  CAI  O1   107.24  3.000
 GBH  HAI   CAI  O1   111.05  3.000
 GBH  CAJ   CAI  O1   112.16  3.000
 GBH  HAJA  CAJ  HAJ  106.62  3.000
 GBH  HAJA  CAJ  NAX  107.85  3.000
 GBH  HAJ   CAJ  NAX  111.21  3.000
 GBH  HAJA  CAJ  CAI  108.29  3.000
 GBH  HAJ   CAJ  CAI  107.81  3.000
 GBH  NAX   CAJ  CAI  114.73  3.000
 GBH  HAKA  CAK  HAK  106.97  3.000
 GBH  HAKA  CAK  NAX  110.29  3.000
 GBH  HAK   CAK  NAX  110.81  3.000
 GBH  HAKA  CAK  CAM  108.53  3.000
 GBH  HAK   CAK  CAM  109.61  3.000
 GBH  NAX   CAK  CAM  110.55  3.000
 GBH  HALA  CAL  HAL  107.32  3.000
 GBH  HALA  CAL  NAX  110.82  3.000
 GBH  HAL   CAL  NAX  108.92  3.000
 GBH  HALA  CAL  CAN  109.11  3.000
 GBH  HAL   CAL  CAN  109.11  3.000
 GBH  NAX   CAL  CAN  111.46  3.000
 GBH  HAMA  CAM  HAM  106.96  3.000
 GBH  HAMA  CAM  NAY  109.16  3.000
 GBH  HAM   CAM  NAY  112.21  3.000
 GBH  HAMA  CAM  CAK  108.67  3.000
 GBH  HAM   CAM  CAK  109.03  3.000
 GBH  NAY   CAM  CAK  110.68  3.000
 GBH  HANA  CAN  HAN  106.63  3.000
 GBH  HANA  CAN  NAY  111.62  3.000
 GBH  HAN   CAN  NAY  110.12  3.000
 GBH  HANA  CAN  CAL  109.89  3.000
 GBH  HAN   CAN  CAL  107.55  3.000
 GBH  NAY   CAN  CAL  110.86  3.000
 GBH  HAOA  CAO  HAO  106.82  3.000
 GBH  HAOA  CAO  NAY  111.80  3.000
 GBH  HAO   CAO  NAY  107.60  3.000
 GBH  HAOA  CAO  CAP  109.64  3.000
 GBH  HAO   CAO  CAP  108.40  3.000
 GBH  NAY   CAO  CAP  112.35  3.000
 GBH  HAPA  CAP  HAP  107.97  3.000
 GBH  HAPA  CAP  SAZ  106.51  3.000
 GBH  HAP   CAP  SAZ  107.18  3.000
 GBH  HAPA  CAP  CAO  112.23  3.000
 GBH  HAP   CAP  CAO  110.54  3.000
 GBH  SAZ   CAP  CAO  112.15  3.000
 GBH  CAL   NAX  CAK  109.10  3.000
 GBH  CAL   NAX  CAJ  110.56  3.000
 GBH  CAK   NAX  CAJ  112.67  3.000
 GBH  CAO   NAY  CAN  112.94  3.000
 GBH  CAO   NAY  CAM  111.50  3.000
 GBH  CAN   NAY  CAM  109.81  3.000
 GBH  CAP   SAZ  OAG  105.79  3.000
 GBH  CAP   SAZ  OAB  105.26  3.000
 GBH  OAG   SAZ  OAB  113.08  3.000
 GBH  CAP   SAZ  OAA  105.78  3.000
 GBH  OAG   SAZ  OAA  112.94  3.000
 GBH  OAB   SAZ  OAA  113.10  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
 GBH  Var_01  CAN  NAY  CAM  CAK    58.30  30.0  1
 GBH  Var_02  CAN  CAL  NAX  CAK   -56.60  30.0  1
 GBH  Var_03  CAM  NAY  CAN  CAL   -56.84  30.0  1
 GBH  Var_04  CAM  CAK  NAX  CAL    57.62  30.0  1
 GBH  Var_05  NAY  CAM  CAK  NAX   -59.47  30.0  1
 GBH  Var_06  NAY  CAN  CAL  NAX    56.88  30.0  1
 GBH  Var_07  CAK  NAX  CAJ  CAI    70.93  30.0  3
 GBH  Var_08  CAP  CAO  NAY  CAM   163.32  30.0  1
 GBH  Var_09  CAJ  CAI  O1   C1    -94.76  30.0  3
 GBH  Var_10  NAX  CAJ  CAI  O1     63.49  30.0  3
 GBH  Var_11  SAZ  CAP  CAO  NAY  -173.58  30.0  3
 GBH  Var_12  CAO  CAP  SAZ  OAA   -60.40  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
 GBH  chir_01  C1  O1  C2  O5  negativ
 GBH  chir_02  C2  O2  C1  C3  negativ
 GBH  chir_03  C3  O3  C2  C4  positiv
 GBH  chir_04  C4  O4  C5  C3  positiv
 GBH  chir_05  C5  O5  C4  C6  negativ

