# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jul  9 12:06:12 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: nonyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[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
 ZDM  ZDM  'nonyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside'  saccharide  72  32  .  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_ZDM
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
 ZDM  C1    C  CH1   0  -0.027  -0.0684  -2.0539   0.5388
 ZDM  O1    O  O2    0  -0.494  -5.0220   0.6972   1.1734
 ZDM  C2    C  CH1   0   0.017  -1.4868  -1.7942   0.0567
 ZDM  O2    O  OH1   0  -0.674  -6.8188   1.9960  -1.6929
 ZDM  C3    C  CH1   0   0.015  -2.0263  -0.4850   0.6213
 ZDM  O3    O  OH1   0  -0.701  -4.8388  -2.3084  -0.8980
 ZDM  C4    C  CH1   0  -0.013  -1.0363   0.6568   0.3599
 ZDM  C5    C  CH1   0   0.022  -5.4007  -1.1762  -0.2875
 ZDM  O5    O  O2    0  -0.495   0.2424   0.2970   0.8359
 ZDM  C6    C  CH1   0   0.302   0.7818  -0.8335   0.1985
 ZDM  C7    C  CH1   0  -0.012  -5.8757  -0.2119  -1.3669
 ZDM  O7    O  O2    0  -0.510  -3.2472  -0.1803  -0.0147
 ZDM  C8    C  CH1   0   0.037  -6.4724   1.0342  -0.7272
 ZDM  C9    C  CH1   0  -0.015  -5.4437   1.6560   0.2144
 ZDM  C10   C  CH1   0   0.200  -4.4371  -0.4601   0.6648
 ZDM  C11   C  CH2   0  -0.162  -6.0006   2.8371   0.9794
 ZDM  O16   O  O2    0  -0.503   2.0590  -1.0375   0.6632
 ZDM  C18   C  CH2   0  -0.141   3.0590  -0.2321   0.0552
 ZDM  C19   C  CH2   0  -0.465   4.4224  -0.6991   0.5190
 ZDM  C22   C  CH2   0  -0.426   5.5421   0.0755  -0.1659
 ZDM  C25   C  CH2   0  -0.412   6.9299  -0.3686   0.2786
 ZDM  C28   C  CH2   0  -0.412   8.0511   0.3771  -0.4332
 ZDM  C31   C  CH2   0  -0.412   9.4418  -0.0643   0.0055
 ZDM  C34   C  CH2   0  -0.407  10.5619   0.6727  -0.7174
 ZDM  O49   O  OH1   0  -0.668   0.3892  -3.2134  -0.1092
 ZDM  O55   O  OH1   0  -0.677  -2.3662  -2.8306   0.4435
 ZDM  C57   C  CH2   0  -0.172  -1.4503   1.9314   1.0651
 ZDM  O61   O  OH1   0  -0.670  -0.5808   2.9642   0.6671
 ZDM  C20   C  CH2   0  -0.418  11.9546   0.2341  -0.2814
 ZDM  C21   C  CH3   0  -0.663  13.0645   0.9760  -1.0130
 ZDM  H1    H  HCH1  0   0.230  -0.0727  -2.1777   1.6321
 ZDM  H2    H  HCH1  0   0.229  -1.4634  -1.7020  -1.0404
 ZDM  HO2   H  HOH1  0   0.453  -7.4151   1.5795  -2.3240
 ZDM  H3    H  HCH1  0   0.241  -2.1648  -0.5917   1.7069
 ZDM  HO3   H  HOH1  0   0.456  -4.0462  -2.5914  -0.4135
 ZDM  H4    H  HCH1  0   0.228  -0.9996   0.8401  -0.7263
 ZDM  H6    H  HCH1  0   0.187   0.7801  -0.6785  -0.8978
 ZDM  H101  H  HOH1  0   0.455  -5.2965   4.2339   2.1180
 ZDM  H7    H  HCH1  0   0.216  -5.0107   0.0931  -1.9743
 ZDM  H8    H  HCH1  0   0.209  -7.3529   0.7329  -0.1362
 ZDM  H9    H  HCH1  0   0.226  -4.5902   2.0029  -0.3848
 ZDM  H10   H  HCH1  0   0.254  -4.2425  -1.0916   1.5389
 ZDM  H11   H  HCH2  0   0.194  -6.8158   2.4918   1.6308
 ZDM  H16   H  HCH2  0   0.212  -6.4395   3.5385   0.2623
 ZDM  H18   H  HCH2  0   0.206   2.9855  -0.3159  -1.0370
 ZDM  H18A  H  HCH2  0   0.211   2.9144   0.8237   0.3097
 ZDM  H19   H  HCH2  0   0.226   4.5029  -0.5832   1.6041
 ZDM  H19A  H  HCH2  0   0.223   4.5316  -1.7664   0.3036
 ZDM  H22   H  HCH2  0   0.214   5.4554  -0.0452  -1.2512
 ZDM  H20   H  HCH2  0   0.215   5.4246   1.1464   0.0308
 ZDM  H25   H  HCH2  0   0.210   7.0272  -0.2281   1.3607
 ZDM  H221  H  HCH2  0   0.209   7.0396  -1.4441   0.1014
 ZDM  H28   H  HCH2  0   0.207   7.9507   0.2344  -1.5149
 ZDM  H28A  H  HCH2  0   0.208   7.9407   1.4532  -0.2591
 ZDM  H31   H  HCH2  0   0.207   9.5457   0.0855   1.0859
 ZDM  H26   H  HCH2  0   0.206   9.5491  -1.1419  -0.1617
 ZDM  H34   H  HCH2  0   0.206  10.4574   0.5220  -1.7978
 ZDM  H34A  H  HCH2  0   0.206  10.4541   1.7505  -0.5519
 ZDM  HO49  H  HOH1  0   0.459   1.2049  -3.4994   0.3139
 ZDM  HO55  H  HOH1  0   0.468  -2.0322  -3.6632   0.0891
 ZDM  H57   H  HCH2  0   0.227  -2.4902   2.1579   0.8116
 ZDM  H57A  H  HCH2  0   0.199  -1.4134   1.7626   2.1503
 ZDM  HO61  H  HOH1  0   0.456  -0.8514   3.7700   1.1158
 ZDM  H341  H  HCH2  0   0.210  12.0597   0.3865   0.7973
 ZDM  H35   H  HCH2  0   0.210  12.0618  -0.8426  -0.4462
 ZDM  H36   H  HCH3  0   0.216  13.0027   0.8142  -2.0909
 ZDM  H37   H  HCH3  0   0.216  12.9999   2.0520  -0.8398
 ZDM  H38   H  HCH3  0   0.226  14.0517   0.6479  -0.6861
 ZDM  H5    H  HCH1  0   0.209  -6.2733  -1.4655   0.3187
 ZDM  O4    O  OH1   0  -0.678  -6.8742  -0.7875  -2.1801
 ZDM  O6    O  OH1   0  -0.665  -4.9564   3.4306   1.7142
 ZDM  HO4   H  HOH1  0   0.457  -6.4608  -1.4351  -2.7588

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
 ZDM  C1   C2    single  1.520  0.020  1.520
 ZDM  O1   C9    single  1.420  0.020  1.420
 ZDM  C2   C3    single  1.524  0.020  1.524
 ZDM  C2   O55   single  1.413  0.020  1.413
 ZDM  C3   O7    single  1.410  0.020  1.410
 ZDM  C4   C3    single  1.534  0.020  1.534
 ZDM  C4   C57   single  1.514  0.020  1.514
 ZDM  C5   O3    single  1.404  0.020  1.404
 ZDM  C5   C7    single  1.523  0.020  1.523
 ZDM  O5   C4    single  1.411  0.020  1.411
 ZDM  C6   C1    single  1.526  0.020  1.526
 ZDM  C6   O5    single  1.405  0.020  1.405
 ZDM  O6   C11   single  1.408  0.020  1.408
 ZDM  C7   O4    single  1.411  0.020  1.411
 ZDM  O7   C10   single  1.398  0.020  1.398
 ZDM  C8   O2    single  1.406  0.020  1.406
 ZDM  C8   C7    single  1.523  0.020  1.523
 ZDM  C9   C8    single  1.527  0.020  1.527
 ZDM  C9   C11   single  1.513  0.020  1.513
 ZDM  C10  O1    single  1.393  0.020  1.393
 ZDM  C10  C5    single  1.532  0.020  1.532
 ZDM  O16  C6    single  1.374  0.020  1.374
 ZDM  C18  O16   single  1.421  0.020  1.421
 ZDM  C19  C18   single  1.514  0.020  1.514
 ZDM  C22  C19   single  1.524  0.020  1.524
 ZDM  C25  C22   single  1.523  0.020  1.523
 ZDM  C28  C25   single  1.523  0.020  1.523
 ZDM  C31  C28   single  1.524  0.020  1.524
 ZDM  C34  C31   single  1.523  0.020  1.523
 ZDM  C34  C20   single  1.524  0.020  1.524
 ZDM  O49  C1    single  1.405  0.020  1.405
 ZDM  O61  C57   single  1.408  0.020  1.408
 ZDM  C20  C21   single  1.522  0.020  1.522
 ZDM  C21  H38   single  0.970  0.020  1.090
 ZDM  C1   H1    single  0.970  0.020  1.090
 ZDM  C2   H2    single  0.970  0.020  1.090
 ZDM  O2   HO2   single  0.850  0.020  0.980
 ZDM  C3   H3    single  0.970  0.020  1.090
 ZDM  O3   HO3   single  0.850  0.020  0.980
 ZDM  C4   H4    single  0.970  0.020  1.090
 ZDM  O4   HO4   single  0.850  0.020  0.980
 ZDM  C5   H5    single  0.970  0.020  1.090
 ZDM  C6   H6    single  0.970  0.020  1.090
 ZDM  O6   H101  single  0.850  0.020  0.980
 ZDM  C7   H7    single  0.970  0.020  1.090
 ZDM  C8   H8    single  0.970  0.020  1.090
 ZDM  C9   H9    single  0.970  0.020  1.090
 ZDM  C10  H10   single  0.970  0.020  1.090
 ZDM  C11  H11   single  0.970  0.020  1.090
 ZDM  C11  H16   single  0.970  0.020  1.090
 ZDM  C18  H18   single  0.970  0.020  1.090
 ZDM  C18  H18A  single  0.970  0.020  1.090
 ZDM  C19  H19   single  0.970  0.020  1.090
 ZDM  C19  H19A  single  0.970  0.020  1.090
 ZDM  C22  H22   single  0.970  0.020  1.090
 ZDM  C22  H20   single  0.970  0.020  1.090
 ZDM  C25  H25   single  0.970  0.020  1.090
 ZDM  C25  H221  single  0.970  0.020  1.090
 ZDM  C28  H28   single  0.970  0.020  1.090
 ZDM  C28  H28A  single  0.970  0.020  1.090
 ZDM  C31  H31   single  0.970  0.020  1.090
 ZDM  C31  H26   single  0.970  0.020  1.090
 ZDM  C34  H34   single  0.970  0.020  1.090
 ZDM  C34  H34A  single  0.970  0.020  1.090
 ZDM  O49  HO49  single  0.850  0.020  0.980
 ZDM  O55  HO55  single  0.850  0.020  0.980
 ZDM  C57  H57   single  0.970  0.020  1.090
 ZDM  C57  H57A  single  0.970  0.020  1.090
 ZDM  O61  HO61  single  0.850  0.020  0.980
 ZDM  C20  H341  single  0.970  0.020  1.090
 ZDM  C20  H35   single  0.970  0.020  1.090
 ZDM  C21  H36   single  0.970  0.020  1.090
 ZDM  C21  H37   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
 ZDM  H1    C1   O49   111.51  3.000
 ZDM  H1    C1   C6    108.29  3.000
 ZDM  O49   C1   C6    112.07  3.000
 ZDM  H1    C1   C2    109.31  3.000
 ZDM  O49   C1   C2    107.38  3.000
 ZDM  C6    C1   C2    108.21  3.000
 ZDM  C10   O1   C9    116.05  3.000
 ZDM  H2    C2   O55   110.32  3.000
 ZDM  H2    C2   C3    107.73  3.000
 ZDM  O55   C2   C3    107.95  3.000
 ZDM  H2    C2   C1    108.08  3.000
 ZDM  O55   C2   C1    111.62  3.000
 ZDM  C3    C2   C1    111.06  3.000
 ZDM  HO2   O2   C8    107.86  3.000
 ZDM  H3    C3   O7    110.93  3.000
 ZDM  H3    C3   C4    108.78  3.000
 ZDM  O7    C3   C4    108.73  3.000
 ZDM  H3    C3   C2    109.08  3.000
 ZDM  C4    C3   C2    110.36  3.000
 ZDM  O7    C3   C2    108.96  3.000
 ZDM  HO3   O3   C5    110.17  3.000
 ZDM  H4    C4   C57   109.16  3.000
 ZDM  H4    C4   O5    110.16  3.000
 ZDM  C57   C4   O5    107.77  3.000
 ZDM  H4    C4   C3    108.25  3.000
 ZDM  O5    C4   C3    109.73  3.000
 ZDM  C57   C4   C3    111.76  3.000
 ZDM  H5    C5   C10   106.20  3.000
 ZDM  H5    C5   C7    108.01  3.000
 ZDM  C10   C5   C7    109.91  3.000
 ZDM  H5    C5   O3    110.17  3.000
 ZDM  C10   C5   O3    113.30  3.000
 ZDM  C7    C5   O3    109.10  3.000
 ZDM  C6    O5   C4    113.57  3.000
 ZDM  H6    C6   O16   110.92  3.000
 ZDM  H6    C6   O5    109.63  3.000
 ZDM  O16   C6   O5    108.83  3.000
 ZDM  H6    C6   C1    109.39  3.000
 ZDM  O16   C6   C1    108.89  3.000
 ZDM  O5    C6   C1    109.17  3.000
 ZDM  H7    C7   C8    108.26  3.000
 ZDM  H7    C7   C5    108.75  3.000
 ZDM  C8    C7   C5    110.04  3.000
 ZDM  H7    C7   O4    110.58  3.000
 ZDM  C8    C7   O4    107.38  3.000
 ZDM  C5    C7   O4    111.77  3.000
 ZDM  C10   O7   C3    118.32  3.000
 ZDM  H8    C8   C9    108.59  3.000
 ZDM  H8    C8   C7    108.33  3.000
 ZDM  C9    C8   C7    109.17  3.000
 ZDM  H8    C8   O2    111.00  3.000
 ZDM  C9    C8   O2    108.12  3.000
 ZDM  C7    C8   O2    111.58  3.000
 ZDM  H9    C9   C11   108.36  3.000
 ZDM  H9    C9   C8    108.39  3.000
 ZDM  C11   C9   C8    112.43  3.000
 ZDM  H9    C9   O1    110.53  3.000
 ZDM  C11   C9   O1    107.15  3.000
 ZDM  C8    C9   O1    109.98  3.000
 ZDM  H10   C10  O7    110.60  3.000
 ZDM  H10   C10  C5    109.76  3.000
 ZDM  O7    C10  C5    109.06  3.000
 ZDM  H10   C10  O1    105.20  3.000
 ZDM  C5    C10  O1    110.56  3.000
 ZDM  O7    C10  O1    111.62  3.000
 ZDM  H16   C11  H11   106.98  3.000
 ZDM  H16   C11  C9    108.45  3.000
 ZDM  H11   C11  C9    109.10  3.000
 ZDM  H16   C11  O6    111.66  3.000
 ZDM  H11   C11  O6    111.91  3.000
 ZDM  C9    C11  O6    108.66  3.000
 ZDM  C18   O16  C6    115.17  3.000
 ZDM  H18A  C18  H18   107.21  3.000
 ZDM  H18A  C18  C19   110.18  3.000
 ZDM  H18   C18  C19   109.97  3.000
 ZDM  H18A  C18  O16   110.73  3.000
 ZDM  H18   C18  O16   109.59  3.000
 ZDM  C19   C18  O16   109.14  3.000
 ZDM  H19A  C19  H19   106.92  3.000
 ZDM  H19A  C19  C22   109.51  3.000
 ZDM  H19   C19  C22   109.74  3.000
 ZDM  H19A  C19  C18   109.30  3.000
 ZDM  H19   C19  C18   109.71  3.000
 ZDM  C22   C19  C18   111.54  3.000
 ZDM  H20   C22  H22   106.09  3.000
 ZDM  H20   C22  C25   109.29  3.000
 ZDM  H22   C22  C25   109.22  3.000
 ZDM  H20   C22  C19   109.72  3.000
 ZDM  H22   C22  C19   109.34  3.000
 ZDM  C25   C22  C19   112.95  3.000
 ZDM  H221  C25  H25   106.07  3.000
 ZDM  H221  C25  C28   109.35  3.000
 ZDM  H25   C25  C28   109.48  3.000
 ZDM  H221  C25  C22   109.28  3.000
 ZDM  H25   C25  C22   109.38  3.000
 ZDM  C28   C25  C22   113.05  3.000
 ZDM  H28A  C28  H28   105.99  3.000
 ZDM  H28A  C28  C31   109.31  3.000
 ZDM  H28   C28  C31   109.28  3.000
 ZDM  H28A  C28  C25   109.42  3.000
 ZDM  H28   C28  C25   109.28  3.000
 ZDM  C31   C28  C25   113.30  3.000
 ZDM  H26   C31  H31   106.00  3.000
 ZDM  H26   C31  C34   109.35  3.000
 ZDM  H31   C31  C34   109.40  3.000
 ZDM  H26   C31  C28   109.29  3.000
 ZDM  H31   C31  C28   109.32  3.000
 ZDM  C34   C31  C28   113.23  3.000
 ZDM  H34A  C34  H34   105.95  3.000
 ZDM  H34A  C34  C20   109.26  3.000
 ZDM  H34   C34  C20   109.25  3.000
 ZDM  H34A  C34  C31   109.38  3.000
 ZDM  H34   C34  C31   109.35  3.000
 ZDM  C20   C34  C31   113.39  3.000
 ZDM  HO49  O49  C1    108.58  3.000
 ZDM  HO55  O55  C2    108.48  3.000
 ZDM  H57A  C57  H57   107.01  3.000
 ZDM  H57A  C57  O61   111.79  3.000
 ZDM  H57   C57  O61   111.70  3.000
 ZDM  H57A  C57  C4    108.75  3.000
 ZDM  H57   C57  C4    109.04  3.000
 ZDM  O61   C57  C4    108.48  3.000
 ZDM  HO61  O61  C57   108.01  3.000
 ZDM  H35   C20  H341  106.02  3.000
 ZDM  H35   C20  C21   109.62  3.000
 ZDM  H341  C20  C21   109.62  3.000
 ZDM  H35   C20  C34   109.24  3.000
 ZDM  H341  C20  C34   109.25  3.000
 ZDM  C21   C20  C34   112.87  3.000
 ZDM  H38   C21  H37   107.62  3.000
 ZDM  H37   C21  H36   107.42  3.000
 ZDM  H38   C21  H36   107.62  3.000
 ZDM  H37   C21  C20   111.15  3.000
 ZDM  H36   C21  C20   111.16  3.000
 ZDM  H38   C21  C20   111.67  3.000
 ZDM  HO4   O4   C7    108.50  3.000
 ZDM  H101  O6   C11   108.01  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
 ZDM  Var_01  C19  C18  O16  C6   -172.06  30.0  2
 ZDM  Var_02  C22  C19  C18  O16   176.60  30.0  1
 ZDM  Var_03  C25  C22  C19  C18   179.96  30.0  2
 ZDM  Var_04  C28  C25  C22  C19   178.39  30.0  1
 ZDM  Var_05  C31  C28  C25  C22  -179.90  30.0  1
 ZDM  Var_06  C34  C31  C28  C25   179.43  30.0  1
 ZDM  Var_07  C20  C34  C31  C28   180.00  30.0  1
 ZDM  Var_08  C21  C20  C34  C31   179.89  30.0  3
 ZDM  Var_09  H38  C21  C20  C34   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
 ZDM  chir_01  C1   C2   C6   O49  positiv
 ZDM  chir_02  C2   O55  C1   C3   positiv
 ZDM  chir_03  C3   O7   C4   C2   positiv
 ZDM  chir_04  C4   O5   C3   C57  negativ
 ZDM  chir_05  C5   O3   C10  C7   negativ
 ZDM  chir_06  C6   O5   O16  C1   negativ
 ZDM  chir_07  C7   C5   O4   C8   negativ
 ZDM  chir_08  C8   O2   C9   C7   positiv
 ZDM  chir_09  C9   O1   C8   C11  negativ
 ZDM  chir_10  C10  O7   O1   C5   negativ

