# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun 20 14:32:49 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: octyl 3-amino-3-deoxy-2-O-(2,6-dideoxy-alpha-L-lyxo-hexopyranosyl)-beta-D-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCO[C@@H]1O[C@H](CO)[C@H](O)[C@H](N)[C@H]1O[C@H]2C[C@H](O)[C@H](O)[C@H](C)O2
#
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
 AD7  AD7  'octyl 3-amino-3-deoxy-2-O-(2,6-dideoxy-alpha-L-lyxo-hexopyranosyl)-beta-D-galactopyranoside'  ligand  68  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AD7
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
 AD7  CBA   C  CH2   0  -0.406   7.3117   0.0099  -0.2492
 AD7  CAZ   C  CH2   0  -0.411   6.1081  -0.7227   0.3293
 AD7  CAY   C  CH2   0  -0.409   4.7790  -0.2506  -0.2464
 AD7  CAX   C  CH2   0  -0.419   3.5830  -0.9988   0.3280
 AD7  CAW   C  CH2   0  -0.485   2.2516  -0.5214  -0.2388
 AD7  CAV   C  CH2   0  -0.171   1.0905  -1.2981   0.3441
 AD7  OAK   O  O2    0  -0.493  -0.1247  -0.8266  -0.2158
 AD7  CAJ   C  CH1   0   0.288  -1.2544  -1.3809   0.3371
 AD7  OAS   O  O2    0  -0.502  -1.3864  -2.6886  -0.1652
 AD7  CAR   C  CH1   0  -0.014  -2.4863  -3.3949   0.3641
 AD7  CAT   C  CH2   0  -0.171  -2.4240  -4.8226  -0.1318
 AD7  OAU   O  OH1   0  -0.658  -1.2942  -5.4491   0.4265
 AD7  CAP   C  CH1   0  -0.009  -3.7946  -2.6953  -0.0096
 AD7  OAQ   O  OH1   0  -0.660  -4.0144  -2.6651  -1.3998
 AD7  CAN   C  CH1   0  -0.125  -3.7299  -1.2628   0.5126
 AD7  NAO   N  NH2   0  -0.793  -4.9286  -0.5187   0.1693
 AD7  CAL   C  CH1   0   0.026  -2.4864  -0.5588  -0.0362
 AD7  OAM   O  O2    0  -0.524  -2.3877   0.7275   0.5404
 AD7  CAA   C  CH1   0   0.257  -2.6461   1.8056  -0.3209
 AD7  CAB   C  CH2   0  -0.509  -2.9319   3.0356   0.5299
 AD7  OAI   O  O2    0  -0.493  -1.5991   2.0221  -1.2186
 AD7  CAE   C  CH1   0   0.014  -0.3896   2.5094  -0.6559
 AD7  CAF   C  CH3   0  -0.697   0.6220   2.6008  -1.7787
 AD7  CAD   C  CH1   0   0.016  -0.6185   3.8390   0.0664
 AD7  OAH   O  OH1   0  -0.660  -1.0792   4.8569  -0.7899
 AD7  CAC   C  CH1   0   0.052  -1.6605   3.6062   1.1491
 AD7  OAG   O  OH1   0  -0.655  -1.8955   4.8163   1.8301
 AD7  HBA   H  HCH2  0   0.206   7.2037   1.0858  -0.0720
 AD7  C19   C  CH2   0  -0.411   8.6396  -0.4645   0.3283
 AD7  HBAA  H  HCH2  0   0.206   7.3246  -0.1160  -1.3377
 AD7  HAZ   H  HCH2  0   0.206   6.2176  -1.7982   0.1509
 AD7  HAZA  H  HCH2  0   0.206   6.0962  -0.5975   1.4178
 AD7  HAY   H  HCH2  0   0.206   4.6622   0.8224  -0.0592
 AD7  HAYA  H  HCH2  0   0.208   4.7911  -0.3680  -1.3355
 AD7  HAX   H  HCH2  0   0.209   3.6992  -2.0706   0.1343
 AD7  HAXA  H  HCH2  0   0.208   3.5768  -0.8868   1.4177
 AD7  HAW   H  HCH2  0   0.219   2.1246   0.5445  -0.0280
 AD7  HAWA  H  HCH2  0   0.249   2.2540  -0.6290  -1.3280
 AD7  HAV   H  HCH2  0   0.228   1.2214  -2.3676   0.1428
 AD7  HAVA  H  HCH2  0   0.231   1.0677  -1.1770   1.4358
 AD7  HAJ   H  HCH1  0   0.228  -1.1686  -1.4209   1.4412
 AD7  HAR   H  HCH1  0   0.268  -2.4336  -3.4177   1.4648
 AD7  HAT   H  HCH2  0   0.197  -3.3546  -5.3224   0.1689
 AD7  HATA  H  HCH2  0   0.193  -2.3881  -4.8360  -1.2287
 AD7  HOAU  H  HOH1  0   0.441  -1.2647  -6.3531   0.1011
 AD7  HAP   H  HCH1  0   0.222  -4.6156  -3.2124   0.5092
 AD7  HOAQ  H  HOH1  0   0.439  -4.3255  -3.5277  -1.6879
 AD7  HAN   H  HCH1  0   0.237  -3.5967  -1.3535   1.6036
 AD7  HNAO  H  HNH2  0   0.337  -5.7434  -1.0569   0.4407
 AD7  HNAA  H  HNH2  0   0.340  -4.9689   0.3201   0.7347
 AD7  HAL   H  HCH1  0   0.237  -2.5516  -0.4977  -1.1290
 AD7  HAA   H  HCH1  0   0.237  -3.5128   1.5778  -0.9516
 AD7  HAB   H  HCH2  0   0.241  -3.3987   3.7909  -0.1056
 AD7  HABA  H  HCH2  0   0.223  -3.6589   2.7823   1.3062
 AD7  HAE   H  HCH1  0   0.228  -0.0078   1.8018   0.0888
 AD7  HAF   H  HCH3  0   0.207   0.2808   3.2434  -2.5926
 AD7  HAFA  H  HCH3  0   0.220   1.5676   2.9953  -1.4051
 AD7  HAFB  H  HCH3  0   0.260   0.8198   1.6134  -2.1953
 AD7  HAD   H  HCH1  0   0.212   0.3316   4.1226   0.5443
 AD7  HOAH  H  HOH1  0   0.434  -0.3778   5.0767  -1.4100
 AD7  HAC   H  HCH1  0   0.208  -1.2303   2.8607   1.8323
 AD7  HOAG  H  HOH1  0   0.428  -2.4756   4.6295   2.5748
 AD7  H35   H  HCH2  0   0.203   8.6282  -0.3344   1.4150
 AD7  H36   H  HCH2  0   0.205   8.7444  -1.5400   0.1546
 AD7  C20   C  CH3   0  -0.647   9.8382   0.2673  -0.2593
 AD7  H37   H  HCH3  0   0.220  10.7757  -0.0886   0.1693
 AD7  H38   H  HCH3  0   0.210   9.8947   0.1277  -1.3406
 AD7  H39   H  HCH3  0   0.211   9.7756   1.3409  -0.0711

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
 AD7  CBA  CAZ   single  1.523  0.020  1.523
 AD7  CBA  HBA   single  0.970  0.020  1.090
 AD7  CBA  C19   single  1.524  0.020  1.524
 AD7  CBA  HBAA  single  0.970  0.020  1.090
 AD7  CAZ  CAY   single  1.523  0.020  1.523
 AD7  CAZ  HAZ   single  0.970  0.020  1.090
 AD7  CAZ  HAZA  single  0.970  0.020  1.090
 AD7  CAY  CAX   single  1.523  0.020  1.523
 AD7  CAY  HAY   single  0.970  0.020  1.090
 AD7  CAY  HAYA  single  0.970  0.020  1.090
 AD7  CAX  CAW   single  1.524  0.020  1.524
 AD7  CAX  HAX   single  0.970  0.020  1.090
 AD7  CAX  HAXA  single  0.970  0.020  1.090
 AD7  CAW  CAV   single  1.514  0.020  1.514
 AD7  CAW  HAW   single  0.970  0.020  1.090
 AD7  CAW  HAWA  single  0.970  0.020  1.090
 AD7  CAV  OAK   single  1.419  0.020  1.419
 AD7  CAV  HAV   single  0.970  0.020  1.090
 AD7  CAV  HAVA  single  0.970  0.020  1.090
 AD7  OAK  CAJ   single  1.374  0.020  1.374
 AD7  CAJ  OAS   single  1.407  0.020  1.407
 AD7  CAJ  CAL   single  1.527  0.020  1.527
 AD7  CAJ  HAJ   single  0.970  0.020  1.090
 AD7  OAS  CAR   single  1.410  0.020  1.410
 AD7  CAR  CAT   single  1.513  0.020  1.513
 AD7  CAR  CAP   single  1.530  0.020  1.530
 AD7  CAR  HAR   single  0.970  0.020  1.090
 AD7  CAT  OAU   single  1.407  0.020  1.407
 AD7  CAT  HAT   single  0.970  0.020  1.090
 AD7  CAT  HATA  single  0.970  0.020  1.090
 AD7  OAU  HOAU  single  0.850  0.020  0.980
 AD7  CAP  OAQ   single  1.408  0.020  1.408
 AD7  CAP  CAN   single  1.526  0.020  1.526
 AD7  CAP  HAP   single  0.970  0.020  1.090
 AD7  OAQ  HOAQ  single  0.850  0.020  0.980
 AD7  CAN  NAO   single  1.452  0.020  1.452
 AD7  CAN  CAL   single  1.531  0.020  1.531
 AD7  CAN  HAN   single  0.970  0.020  1.090
 AD7  NAO  HNAO  single  0.890  0.020  1.040
 AD7  NAO  HNAA  single  0.890  0.020  1.040
 AD7  CAL  OAM   single  1.413  0.020  1.413
 AD7  CAL  HAL   single  0.970  0.020  1.090
 AD7  OAM  CAA   single  1.404  0.020  1.404
 AD7  CAA  CAB   single  1.523  0.020  1.523
 AD7  CAA  OAI   single  1.396  0.020  1.396
 AD7  CAA  HAA   single  0.970  0.020  1.090
 AD7  CAB  CAC   single  1.525  0.020  1.525
 AD7  CAB  HAB   single  0.970  0.020  1.090
 AD7  CAB  HABA  single  0.970  0.020  1.090
 AD7  OAI  CAE   single  1.420  0.020  1.420
 AD7  CAE  CAF   single  1.514  0.020  1.514
 AD7  CAE  CAD   single  1.530  0.020  1.530
 AD7  CAE  HAE   single  0.970  0.020  1.090
 AD7  CAF  HAF   single  0.970  0.020  1.090
 AD7  CAF  HAFA  single  0.970  0.020  1.090
 AD7  CAF  HAFB  single  0.970  0.020  1.090
 AD7  CAD  OAH   single  1.408  0.020  1.408
 AD7  CAD  CAC   single  1.521  0.020  1.521
 AD7  CAD  HAD   single  0.970  0.020  1.090
 AD7  OAH  HOAH  single  0.850  0.020  0.980
 AD7  CAC  OAG   single  1.408  0.020  1.408
 AD7  CAC  HAC   single  0.970  0.020  1.090
 AD7  OAG  HOAG  single  0.850  0.020  0.980
 AD7  C19  H35   single  0.970  0.020  1.090
 AD7  C19  H36   single  0.970  0.020  1.090
 AD7  C19  C20   single  1.522  0.020  1.522
 AD7  C20  H37   single  0.970  0.020  1.090
 AD7  C20  H38   single  0.970  0.020  1.090
 AD7  C20  H39   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
 AD7  HBAA  CBA  C19   109.30  3.000
 AD7  HBAA  CBA  HBA   105.94  3.000
 AD7  C19   CBA  HBA   109.29  3.000
 AD7  HBAA  CBA  CAZ   109.34  3.000
 AD7  C19   CBA  CAZ   113.27  3.000
 AD7  HBA   CBA  CAZ   109.44  3.000
 AD7  HAZA  CAZ  HAZ   105.95  3.000
 AD7  HAZA  CAZ  CAY   109.30  3.000
 AD7  HAZ   CAZ  CAY   109.26  3.000
 AD7  HAZA  CAZ  CBA   109.32  3.000
 AD7  HAZ   CAZ  CBA   109.35  3.000
 AD7  CAY   CAZ  CBA   113.39  3.000
 AD7  HAYA  CAY  HAY   106.03  3.000
 AD7  HAYA  CAY  CAX   109.33  3.000
 AD7  HAY   CAY  CAX   109.45  3.000
 AD7  HAYA  CAY  CAZ   109.44  3.000
 AD7  HAY   CAY  CAZ   109.39  3.000
 AD7  CAX   CAY  CAZ   112.97  3.000
 AD7  HAXA  CAX  HAX   106.05  3.000
 AD7  HAXA  CAX  CAW   109.45  3.000
 AD7  HAX   CAX  CAW   109.48  3.000
 AD7  HAXA  CAX  CAY   109.23  3.000
 AD7  HAX   CAX  CAY   109.31  3.000
 AD7  CAW   CAX  CAY   113.07  3.000
 AD7  HAWA  CAW  HAW   106.73  3.000
 AD7  HAWA  CAW  CAV   109.54  3.000
 AD7  HAW   CAW  CAV   109.68  3.000
 AD7  HAWA  CAW  CAX   109.72  3.000
 AD7  HAW   CAW  CAX   109.57  3.000
 AD7  CAV   CAW  CAX   111.48  3.000
 AD7  HAVA  CAV  HAV   107.01  3.000
 AD7  HAVA  CAV  OAK   109.74  3.000
 AD7  HAV   CAV  OAK   110.74  3.000
 AD7  HAVA  CAV  CAW   110.00  3.000
 AD7  HAV   CAV  CAW   109.77  3.000
 AD7  OAK   CAV  CAW   109.54  3.000
 AD7  CAJ   OAK  CAV   114.28  3.000
 AD7  HAJ   CAJ  CAL   108.99  3.000
 AD7  HAJ   CAJ  OAS   109.23  3.000
 AD7  CAL   CAJ  OAS   109.71  3.000
 AD7  HAJ   CAJ  OAK   110.60  3.000
 AD7  CAL   CAJ  OAK   110.34  3.000
 AD7  OAS   CAJ  OAK   107.96  3.000
 AD7  CAR   OAS  CAJ   113.87  3.000
 AD7  HAR   CAR  CAP   107.12  3.000
 AD7  HAR   CAR  CAT   107.81  3.000
 AD7  CAP   CAR  CAT   112.75  3.000
 AD7  HAR   CAR  OAS   110.36  3.000
 AD7  CAP   CAR  OAS   110.26  3.000
 AD7  CAT   CAR  OAS   108.51  3.000
 AD7  HATA  CAT  HAT   107.20  3.000
 AD7  HATA  CAT  OAU   111.39  3.000
 AD7  HAT   CAT  OAU   111.66  3.000
 AD7  HATA  CAT  CAR   109.91  3.000
 AD7  HAT   CAT  CAR   107.75  3.000
 AD7  OAU   CAT  CAR   108.86  3.000
 AD7  HOAU  OAU  CAT   108.00  3.000
 AD7  HAP   CAP  CAN   108.15  3.000
 AD7  HAP   CAP  OAQ   111.06  3.000
 AD7  CAN   CAP  OAQ   108.93  3.000
 AD7  HAP   CAP  CAR   107.94  3.000
 AD7  CAN   CAP  CAR   108.02  3.000
 AD7  OAQ   CAP  CAR   112.61  3.000
 AD7  HOAQ  OAQ  CAP   109.10  3.000
 AD7  HAN   CAN  CAL   107.12  3.000
 AD7  HAN   CAN  NAO   112.07  3.000
 AD7  CAL   CAN  NAO   110.49  3.000
 AD7  HAN   CAN  CAP   105.46  3.000
 AD7  CAL   CAN  CAP   110.09  3.000
 AD7  NAO   CAN  CAP   111.41  3.000
 AD7  HNAA  NAO  HNAO  104.98  3.000
 AD7  HNAA  NAO  CAN   108.99  3.000
 AD7  HNAO  NAO  CAN   109.16  3.000
 AD7  HAL   CAL  OAM   111.11  3.000
 AD7  HAL   CAL  CAN   109.56  3.000
 AD7  OAM   CAL  CAN   109.21  3.000
 AD7  HAL   CAL  CAJ   108.76  3.000
 AD7  OAM   CAL  CAJ   109.50  3.000
 AD7  CAN   CAL  CAJ   108.67  3.000
 AD7  CAA   OAM  CAL   115.84  3.000
 AD7  HAA   CAA  OAI   104.80  3.000
 AD7  HAA   CAA  CAB   109.94  3.000
 AD7  OAI   CAA  CAB   112.01  3.000
 AD7  HAA   CAA  OAM   109.82  3.000
 AD7  OAI   CAA  OAM   112.06  3.000
 AD7  CAB   CAA  OAM   108.18  3.000
 AD7  HABA  CAB  HAB   106.81  3.000
 AD7  HABA  CAB  CAC   110.66  3.000
 AD7  HAB   CAB  CAC   109.51  3.000
 AD7  HABA  CAB  CAA   109.54  3.000
 AD7  HAB   CAB  CAA   108.29  3.000
 AD7  CAC   CAB  CAA   111.88  3.000
 AD7  CAE   OAI  CAA   115.92  3.000
 AD7  HAE   CAE  CAD   107.00  3.000
 AD7  HAE   CAE  CAF   108.07  3.000
 AD7  CAD   CAE  CAF   113.42  3.000
 AD7  HAE   CAE  OAI   110.14  3.000
 AD7  CAD   CAE  OAI   110.96  3.000
 AD7  CAF   CAE  OAI   107.21  3.000
 AD7  HAFB  CAF  HAFA  107.54  3.000
 AD7  HAFB  CAF  HAF   107.76  3.000
 AD7  HAFA  CAF  HAF   108.27  3.000
 AD7  HAFB  CAF  CAE   110.49  3.000
 AD7  HAFA  CAF  CAE   110.31  3.000
 AD7  HAF   CAF  CAE   112.31  3.000
 AD7  HAD   CAD  CAC   108.77  3.000
 AD7  HAD   CAD  OAH   111.12  3.000
 AD7  CAC   CAD  OAH   108.63  3.000
 AD7  HAD   CAD  CAE   107.44  3.000
 AD7  CAC   CAD  CAE   107.79  3.000
 AD7  OAH   CAD  CAE   112.96  3.000
 AD7  HOAH  OAH  CAD   108.59  3.000
 AD7  HAC   CAC  OAG   110.34  3.000
 AD7  HAC   CAC  CAD   106.16  3.000
 AD7  OAG   CAC  CAD   109.10  3.000
 AD7  HAC   CAC  CAB   108.96  3.000
 AD7  OAG   CAC  CAB   112.25  3.000
 AD7  CAD   CAC  CAB   109.85  3.000
 AD7  HOAG  OAG  CAC   107.95  3.000
 AD7  C20   C19  H36   109.62  3.000
 AD7  C20   C19  H35   109.53  3.000
 AD7  H36   C19  H35   105.99  3.000
 AD7  C20   C19  CBA   112.97  3.000
 AD7  H36   C19  CBA   109.22  3.000
 AD7  H35   C19  CBA   109.28  3.000
 AD7  H39   C20  H38   107.43  3.000
 AD7  H39   C20  H37   107.61  3.000
 AD7  H38   C20  H37   107.64  3.000
 AD7  H39   C20  C19   111.16  3.000
 AD7  H38   C20  C19   111.20  3.000
 AD7  H37   C20  C19   111.61  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
 AD7  Var_01  HAV  CAV  OAK  CAJ    64.50  30.0  1
 AD7  Var_02  CAX  CAY  CAZ  CBA   179.42  30.0  3
 AD7  Var_03  C20  C19  CBA  CAZ   179.72  30.0  3
 AD7  Var_04  CAW  CAX  CAY  CAZ   179.58  30.0  3
 AD7  Var_05  C19  CBA  CAZ  CAY  -179.99  30.0  1
 AD7  Var_06  CAV  CAW  CAX  CAY   179.37  30.0  3
 AD7  Var_07  OAK  CAV  CAW  CAX  -179.67  30.0  3
 AD7  Var_08  H37  C20  C19  CBA   179.97  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
 AD7  chir_01  CAJ  OAK  OAS  CAL  positiv
 AD7  chir_02  CAR  OAS  CAP  CAT  negativ
 AD7  chir_03  CAP  OAQ  CAR  CAN  negativ
 AD7  chir_04  CAN  NAO  CAL  CAP  positiv
 AD7  chir_05  CAL  OAM  CAN  CAJ  positiv
 AD7  chir_06  CAA  OAI  OAM  CAB  negativ
 AD7  chir_07  CAE  OAI  CAF  CAD  negativ
 AD7  chir_08  CAD  OAH  CAE  CAC  positiv
 AD7  chir_09  CAC  OAG  CAD  CAB  positiv

