# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jun 24 04:52:04 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: (1S)-2-amino-1-phenylethyl 6-O-beta-L-glucopyranosyl-alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@H](O[C@H]1O[C@H](CO[C@H]2O[C@@H](CO)[C@H](O)[C@@H](O)[C@@H]2O)[C@@H](O)[C@H](O)[C@@H]1O)c3ccccc3
#
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
 BAD  BAD  '(1S)-2-amino-1-phenylethyl 6-O-beta-L-glucopyranosyl-alpha-D-mannopyranoside'  ligand  63  32  .  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_BAD
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
 BAD  C1    C  CR16  0  -0.241   4.4100  -3.2904  -2.3354
 BAD  C2    C  CR16  0  -0.305   3.4059  -2.7183  -1.5659
 BAD  C3    C  CR6   0   0.094   3.7038  -1.7427  -0.6191
 BAD  C4    C  CR16  0  -0.300   5.0276  -1.3430  -0.4575
 BAD  C5    C  CR16  0  -0.239   6.0332  -1.9102  -1.2293
 BAD  C6    C  CR16  0  -0.268   5.7281  -2.8857  -2.1696
 BAD  C13   C  CH1   0  -0.033   2.6030  -1.1664   0.2415
 BAD  C15   C  CH2   0  -0.280   2.4405  -1.9692   1.5253
 BAD  N17   N  NH2   0  -0.787   1.3067  -1.4989   2.3019
 BAD  O19   O  O2    0  -0.499   2.8667   0.1820   0.5734
 BAD  C21   C  CH1   0   0.240   2.4294   1.1066  -0.3721
 BAD  O23   O  O2    0  -0.499   1.0356   1.2038  -0.4021
 BAD  C25   C  CH1   0  -0.036   0.4367   1.6465   0.8064
 BAD  C27   C  CH1   0   0.031   0.9459   3.0430   1.1620
 BAD  C29   C  CH1   0  -0.029   3.0700   2.4592  -0.0454
 BAD  C31   C  CH1   0   0.003   2.4690   3.0010   1.2483
 BAD  C34   C  CH2   0  -0.164  -1.0603   1.6113   0.6014
 BAD  O36   O  O2    0  -0.502  -1.4744   0.2549   0.6134
 BAD  C38   C  CH1   0   0.299  -2.8268   0.0534   0.4440
 BAD  O40   O  O2    0  -0.493  -3.1013   0.0130  -0.9319
 BAD  C42   C  CH1   0  -0.016  -4.4759  -0.1308  -1.2231
 BAD  C44   C  CH1   0   0.034  -4.9826  -1.4616  -0.6615
 BAD  C46   C  CH1   0  -0.011  -4.6787  -1.5428   0.8303
 BAD  C48   C  CH1   0  -0.029  -3.2036  -1.2765   1.0897
 BAD  O51   O  OH1   0  -0.669   2.8080   3.3800  -1.0740
 BAD  O53   O  OH1   0  -0.673   2.9169   4.3017   1.5487
 BAD  O55   O  OH1   0  -0.676   0.3808   3.4050   2.3995
 BAD  O57   O  OH1   0  -0.665  -3.0090  -1.2458   2.4817
 BAD  O59   O  OH1   0  -0.672  -5.0783  -2.8179   1.2731
 BAD  O61   O  OH1   0  -0.672  -6.3651  -1.5420  -0.9030
 BAD  C63   C  CH2   0  -0.156  -4.6425  -0.0589  -2.7260
 BAD  O65   O  OH1   0  -0.669  -4.2420   1.2155  -3.1685
 BAD  H1    H  HCR6  0   0.255   4.1625  -4.0459  -3.0701
 BAD  H2    H  HCR6  0   0.249   2.3775  -3.0316  -1.7070
 BAD  H4    H  HCR6  0   0.250   5.2781  -0.5798   0.2684
 BAD  H5    H  HCR6  0   0.254   7.0577  -1.5866  -1.0972
 BAD  H6    H  HCR6  0   0.255   6.5115  -3.3235  -2.7747
 BAD  H13   H  HCH1  0   0.236   1.6568  -1.2400  -0.3121
 BAD  H15   H  HCH2  0   0.210   2.3713  -3.0261   1.2341
 BAD  H15A  H  HCH2  0   0.226   3.3493  -1.8738   2.1272
 BAD  HN17  H  HNH2  0   0.335   0.4612  -1.5999   1.7535
 BAD  HN1A  H  HNH2  0   0.354   1.1871  -2.0947   3.1113
 BAD  H21   H  HCH1  0   0.236   2.7164   0.7957  -1.3872
 BAD  H25   H  HCH1  0   0.244   0.6884   0.9649   1.6304
 BAD  H27   H  HCH1  0   0.213   0.6463   3.7479   0.3722
 BAD  H29   H  HCH1  0   0.232   4.1505   2.3083   0.0890
 BAD  H31   H  HCH1  0   0.228   2.7329   2.3042   2.0553
 BAD  H34   H  HCH2  0   0.231  -1.5580   2.1589   1.4079
 BAD  H34A  H  HCH2  0   0.219  -1.3218   2.0974  -0.3453
 BAD  H38   H  HCH1  0   0.187  -3.4104   0.8648   0.9186
 BAD  H42   H  HCH1  0   0.223  -5.0499   0.6874  -0.7565
 BAD  H44   H  HCH1  0   0.212  -4.4442  -2.2773  -1.1708
 BAD  H46   H  HCH1  0   0.218  -5.2624  -0.7547   1.3331
 BAD  H48   H  HCH1  0   0.221  -2.6062  -2.0721   0.6170
 BAD  HO51  H  HOH1  0   0.455   3.3037   3.1159  -1.8553
 BAD  HO53  H  HOH1  0   0.457   3.7859   4.2426   1.9566
 BAD  HO55  H  HOH1  0   0.452   0.7506   4.2575   2.6519
 BAD  HO57  H  HOH1  0   0.449  -2.0694  -1.1315   2.6556
 BAD  HO59  H  HOH1  0   0.458  -5.0818  -2.8234   2.2353
 BAD  HO61  H  HOH1  0   0.454  -6.6912  -2.3570  -0.5067
 BAD  H63   H  HCH2  0   0.197  -4.0444  -0.8587  -3.1849
 BAD  H63A  H  HCH2  0   0.213  -5.6909  -0.2615  -2.9681
 BAD  HO65  H  HOH1  0   0.457  -4.4027   1.2640  -4.1150

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
 BAD  C1   C2    aromatic  1.388  0.020  1.388
 BAD  C1   C6    aromatic  1.389  0.020  1.389
 BAD  C2   C3    aromatic  1.392  0.020  1.392
 BAD  C3   C4    aromatic  1.392  0.020  1.392
 BAD  C3   C13   single    1.511  0.020  1.511
 BAD  C4   C5    aromatic  1.389  0.020  1.389
 BAD  C5   C6    aromatic  1.389  0.020  1.389
 BAD  C13  C15   single    1.523  0.020  1.523
 BAD  C13  O19   single    1.413  0.020  1.413
 BAD  C15  N17   single    1.452  0.020  1.452
 BAD  O19  C21   single    1.393  0.020  1.393
 BAD  C21  O23   single    1.398  0.020  1.398
 BAD  C21  C29   single    1.532  0.020  1.532
 BAD  O23  C25   single    1.420  0.020  1.420
 BAD  C25  C27   single    1.528  0.020  1.528
 BAD  C25  C34   single    1.511  0.020  1.511
 BAD  C27  C31   single    1.526  0.020  1.526
 BAD  C27  O55   single    1.408  0.020  1.408
 BAD  C29  C31   single    1.526  0.020  1.526
 BAD  C29  O51   single    1.405  0.020  1.405
 BAD  C31  O53   single    1.408  0.020  1.408
 BAD  C34  O36   single    1.418  0.020  1.418
 BAD  O36  C38   single    1.378  0.020  1.378
 BAD  C38  O40   single    1.404  0.020  1.404
 BAD  C38  C48   single    1.526  0.020  1.526
 BAD  O40  C42   single    1.412  0.020  1.412
 BAD  C42  C44   single    1.531  0.020  1.531
 BAD  C42  C63   single    1.514  0.020  1.514
 BAD  C44  C46   single    1.525  0.020  1.525
 BAD  C44  O61   single    1.406  0.020  1.406
 BAD  C46  C48   single    1.521  0.020  1.521
 BAD  C46  O59   single    1.408  0.020  1.408
 BAD  C48  O57   single    1.406  0.020  1.406
 BAD  C63  O65   single    1.407  0.020  1.407
 BAD  C1   H1    single    0.930  0.020  1.080
 BAD  C2   H2    single    0.930  0.020  1.080
 BAD  C4   H4    single    0.930  0.020  1.080
 BAD  C5   H5    single    0.930  0.020  1.080
 BAD  C6   H6    single    0.930  0.020  1.080
 BAD  C13  H13   single    0.970  0.020  1.090
 BAD  C15  H15   single    0.970  0.020  1.090
 BAD  C15  H15A  single    0.970  0.020  1.090
 BAD  N17  HN17  single    0.890  0.020  1.040
 BAD  N17  HN1A  single    0.890  0.020  1.040
 BAD  C21  H21   single    0.970  0.020  1.090
 BAD  C25  H25   single    0.970  0.020  1.090
 BAD  C27  H27   single    0.970  0.020  1.090
 BAD  C29  H29   single    0.970  0.020  1.090
 BAD  C31  H31   single    0.970  0.020  1.090
 BAD  C34  H34   single    0.970  0.020  1.090
 BAD  C34  H34A  single    0.970  0.020  1.090
 BAD  C38  H38   single    0.970  0.020  1.090
 BAD  C42  H42   single    0.970  0.020  1.090
 BAD  C44  H44   single    0.970  0.020  1.090
 BAD  C46  H46   single    0.970  0.020  1.090
 BAD  C48  H48   single    0.970  0.020  1.090
 BAD  O51  HO51  single    0.850  0.020  0.980
 BAD  O53  HO53  single    0.850  0.020  0.980
 BAD  O55  HO55  single    0.850  0.020  0.980
 BAD  O57  HO57  single    0.850  0.020  0.980
 BAD  O59  HO59  single    0.850  0.020  0.980
 BAD  O61  HO61  single    0.850  0.020  0.980
 BAD  C63  H63   single    0.970  0.020  1.090
 BAD  C63  H63A  single    0.970  0.020  1.090
 BAD  O65  HO65  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
 BAD  H1    C1   C6    120.09  3.000
 BAD  H1    C1   C2    119.90  3.000
 BAD  C6    C1   C2    120.01  3.000
 BAD  H2    C2   C3    119.61  3.000
 BAD  H2    C2   C1    119.65  3.000
 BAD  C3    C2   C1    120.74  3.000
 BAD  C13   C3   C4    121.13  3.000
 BAD  C13   C3   C2    119.92  3.000
 BAD  C4    C3   C2    118.92  3.000
 BAD  H4    C4   C5    119.54  3.000
 BAD  H4    C4   C3    120.01  3.000
 BAD  C5    C4   C3    120.45  3.000
 BAD  H5    C5   C6    120.03  3.000
 BAD  H5    C5   C4    119.70  3.000
 BAD  C6    C5   C4    120.27  3.000
 BAD  H6    C6   C5    120.24  3.000
 BAD  H6    C6   C1    120.16  3.000
 BAD  C5    C6   C1    119.60  3.000
 BAD  H13   C13  O19   110.05  3.000
 BAD  H13   C13  C15   107.31  3.000
 BAD  O19   C13  C15   108.96  3.000
 BAD  H13   C13  C3    108.34  3.000
 BAD  O19   C13  C3    111.20  3.000
 BAD  C15   C13  C3    110.90  3.000
 BAD  H15A  C15  H15   106.38  3.000
 BAD  H15A  C15  N17   109.02  3.000
 BAD  H15   C15  N17   113.84  3.000
 BAD  H15A  C15  C13   109.21  3.000
 BAD  H15   C15  C13   106.89  3.000
 BAD  N17   C15  C13   111.31  3.000
 BAD  HN1A  N17  HN17  106.00  3.000
 BAD  HN1A  N17  C15   109.23  3.000
 BAD  HN17  N17  C15   109.26  3.000
 BAD  C21   O19  C13   114.54  3.000
 BAD  H21   C21  C29   109.72  3.000
 BAD  H21   C21  O23   105.08  3.000
 BAD  C29   C21  O23   111.12  3.000
 BAD  H21   C21  O19   110.91  3.000
 BAD  C29   C21  O19   108.06  3.000
 BAD  O23   C21  O19   111.95  3.000
 BAD  C25   O23  C21   115.10  3.000
 BAD  H25   C25  C34   108.31  3.000
 BAD  H25   C25  C27   108.43  3.000
 BAD  C34   C25  C27   112.51  3.000
 BAD  H25   C25  O23   110.39  3.000
 BAD  C34   C25  O23   107.16  3.000
 BAD  C27   C25  O23   110.03  3.000
 BAD  H27   C27  O55   110.91  3.000
 BAD  H27   C27  C31   109.27  3.000
 BAD  O55   C27  C31   110.97  3.000
 BAD  H27   C27  C25   109.13  3.000
 BAD  O55   C27  C25   107.80  3.000
 BAD  C31   C27  C25   108.70  3.000
 BAD  H29   C29  O51   111.27  3.000
 BAD  H29   C29  C31   109.41  3.000
 BAD  O51   C29  C31   108.33  3.000
 BAD  H29   C29  C21   108.42  3.000
 BAD  O51   C29  C21   110.15  3.000
 BAD  C31   C29  C21   109.25  3.000
 BAD  H31   C31  O53   110.66  3.000
 BAD  H31   C31  C29   107.63  3.000
 BAD  O53   C31  C29   112.55  3.000
 BAD  H31   C31  C27   107.39  3.000
 BAD  O53   C31  C27   107.71  3.000
 BAD  C29   C31  C27   110.79  3.000
 BAD  H34A  C34  H34   107.82  3.000
 BAD  H34A  C34  O36   111.22  3.000
 BAD  H34   C34  O36   109.85  3.000
 BAD  H34A  C34  C25   110.07  3.000
 BAD  H34   C34  C25   109.80  3.000
 BAD  O36   C34  C25   108.08  3.000
 BAD  C38   O36  C34   115.18  3.000
 BAD  H38   C38  C48   109.11  3.000
 BAD  H38   C38  O40   109.78  3.000
 BAD  C48   C38  O40   109.97  3.000
 BAD  H38   C38  O36   110.97  3.000
 BAD  C48   C38  O36   108.53  3.000
 BAD  O40   C38  O36   108.46  3.000
 BAD  C42   O40  C38   113.29  3.000
 BAD  H42   C42  C63   109.12  3.000
 BAD  H42   C42  C44   108.51  3.000
 BAD  C63   C42  C44   111.66  3.000
 BAD  H42   C42  O40   110.10  3.000
 BAD  C63   C42  O40   107.88  3.000
 BAD  C44   C42  O40   109.57  3.000
 BAD  H44   C44  O61   111.02  3.000
 BAD  H44   C44  C46   108.39  3.000
 BAD  O61   C44  C46   111.16  3.000
 BAD  H44   C44  C42   108.19  3.000
 BAD  O61   C44  C42   108.19  3.000
 BAD  C46   C44  C42   109.83  3.000
 BAD  H46   C46  O59   110.72  3.000
 BAD  H46   C46  C48   108.10  3.000
 BAD  O59   C46  C48   112.35  3.000
 BAD  H46   C46  C44   107.62  3.000
 BAD  O59   C46  C44   107.42  3.000
 BAD  C48   C46  C44   110.54  3.000
 BAD  H48   C48  O57   111.44  3.000
 BAD  H48   C48  C46   109.04  3.000
 BAD  O57   C48  C46   107.87  3.000
 BAD  H48   C48  C38   108.30  3.000
 BAD  O57   C48  C38   111.46  3.000
 BAD  C46   C48  C38   108.66  3.000
 BAD  HO51  O51  C29   108.57  3.000
 BAD  HO53  O53  C31   108.74  3.000
 BAD  HO55  O55  C27   107.69  3.000
 BAD  HO57  O57  C48   108.46  3.000
 BAD  HO59  O59  C46   108.71  3.000
 BAD  HO61  O61  C44   108.10  3.000
 BAD  H63A  C63  H63   107.10  3.000
 BAD  H63A  C63  O65   111.75  3.000
 BAD  H63   C63  O65   111.89  3.000
 BAD  H63A  C63  C42   108.43  3.000
 BAD  H63   C63  C42   108.67  3.000
 BAD  O65   C63  C42   108.90  3.000
 BAD  HO65  O65  C63   107.92  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
 BAD  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 BAD  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 BAD  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 BAD  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 BAD  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 BAD  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 BAD  CONST_07  C13   C3   C2   C1   180.00   0.0  0
 BAD  CONST_08  C13   C3   C4   C5   180.00   0.0  0
 BAD  CONST_09  H5    C5   C6   C1   180.00   0.0  0
 BAD  CONST_10  H6    C6   C1   C2   180.00   0.0  0
 BAD  CONST_11  H4    C4   C3   C2   180.00   0.0  0
 BAD  CONST_12  H1    C1   C2   C3   180.00   0.0  0
 BAD  CONST_13  H2    C2   C3   C4   180.00   0.0  0
 BAD  Var_01    H34   C34  O36  C38   59.89  30.0  1
 BAD  Var_02    HN17  N17  C15  C13   60.39  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
 BAD  chir_01  C13  C3   C15  O19  negativ
 BAD  chir_02  C21  O19  O23  C29  negativ
 BAD  chir_03  C25  O23  C34  C27  positiv
 BAD  chir_04  C27  O55  C25  C31  positiv
 BAD  chir_05  C29  O51  C31  C21  negativ
 BAD  chir_06  C31  O53  C29  C27  positiv
 BAD  chir_07  C38  O36  O40  C48  negativ
 BAD  chir_08  C42  O40  C63  C44  negativ
 BAD  chir_09  C44  O61  C42  C46  negativ
 BAD  chir_10  C46  O59  C48  C44  negativ
 BAD  chir_11  C48  O57  C46  C38  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
 BAD  plan-1  C1   0.020
 BAD  plan-1  C2   0.020
 BAD  plan-1  C3   0.020
 BAD  plan-1  C4   0.020
 BAD  plan-1  C5   0.020
 BAD  plan-1  C6   0.020
 BAD  plan-1  C13  0.020
 BAD  plan-1  H1   0.020
 BAD  plan-1  H2   0.020
 BAD  plan-1  H4   0.020
 BAD  plan-1  H5   0.020
 BAD  plan-1  H6   0.020

