# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 03:59:06 2022
#   Inital geometry file: a 85 line input string
#   Ligand name: (1S,2S,3R,4S,5S)-5-[(1,3-dihydroxypropan-2-yl)amino]-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC(CO)N[C@H]1C[C@](O)(CO)[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
 VOG  VOG  (1S,2S,3R,4S,5S)-5-[(1,3-dihydroxypropan-2-yl)amino]-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol  ligand  39  18  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VOG
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
 VOG  C1   C  CT    0   0.178  -1.5704   0.7230   0.5679
 VOG  O1   O  OH1   0  -0.668  -1.0542   1.5758  -0.4261
 VOG  C2   C  CH1   0   0.053  -2.2577  -0.5037  -0.0576
 VOG  O2   O  OH1   0  -0.674  -3.2278  -0.0746  -0.9792
 VOG  C3   C  CH1   0  -0.018  -1.2458  -1.4382  -0.7155
 VOG  O3   O  OH1   0  -0.691  -1.9415  -2.5475  -1.2730
 VOG  C4   C  CH1   0   0.053  -0.2535  -1.9366   0.3282
 VOG  O4   O  OH1   0  -0.680   0.6322  -2.8972  -0.1954
 VOG  C5   C  CH1   0  -0.101   0.5516  -0.7591   0.8737
 VOG  C6   C  CH2   0  -0.485  -0.4314   0.2478   1.4719
 VOG  C7   C  CH2   0  -0.166  -2.5418   1.5196   1.4575
 VOG  O7   O  OH1   0  -0.669  -3.4407   2.2754   0.6748
 VOG  N    N  NH1   0  -0.594   1.3727  -0.2245  -0.1948
 VOG  C8   C  CH1   0  -0.127   2.1459   0.9694   0.0740
 VOG  C9   C  CH2   0  -0.167   3.0722   0.8912   1.2870
 VOG  O9   O  OH1   0  -0.666   3.9188  -0.2316   1.1989
 VOG  C10  C  CH2   0  -0.158   2.8423   1.4014  -1.2074
 VOG  O10  O  OH1   0  -0.669   3.7273   0.4012  -1.6630
 VOG  H1   H  HOH1  0   0.436  -1.8068   2.0634  -0.7830
 VOG  H2   H  HCH1  0   0.185  -2.7341  -1.0647   0.7652
 VOG  H3   H  HOH1  0   0.441  -3.5691  -0.8613  -1.4182
 VOG  H4   H  HCH1  0   0.232  -0.6994  -0.8961  -1.4935
 VOG  H5   H  HOH1  0   0.462  -1.7813  -2.5709  -2.2194
 VOG  H6   H  HCH1  0   0.197  -0.8241  -2.3666   1.1680
 VOG  H7   H  HOH1  0   0.443   0.1069  -3.5524  -0.6679
 VOG  H8   H  HCH1  0   0.219   1.1556  -1.1339   1.7165
 VOG  H9   H  HCH2  0   0.257   0.0979   1.1214   1.8596
 VOG  H10  H  HCH2  0   0.248  -0.8737  -0.2331   2.3510
 VOG  H11  H  HCH2  0   0.198  -3.0810   0.8273   2.1152
 VOG  H12  H  HCH2  0   0.219  -1.9481   2.1766   2.1033
 VOG  H13  H  HOH1  0   0.459  -3.5022   3.1554   1.0531
 VOG  H14  H  HNH1  0   0.338   1.9969  -0.9544  -0.5108
 VOG  H16  H  HCH1  0   0.234   1.4516   1.7881   0.2858
 VOG  H17  H  HCH2  0   0.191   3.6416   1.8300   1.3516
 VOG  H18  H  HCH2  0   0.199   2.4560   0.8464   2.1949
 VOG  H19  H  HOH1  0   0.450   4.3462  -0.3445   2.0520
 VOG  H20  H  HCH2  0   0.203   2.0625   1.6076  -1.9505
 VOG  H21  H  HCH2  0   0.186   3.3685   2.3473  -1.0198
 VOG  H22  H  HOH1  0   0.451   3.9873   0.6245  -2.5608

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
 VOG  O7   C7   single  1.411  0.020  1.411
 VOG  C7   C1   single  1.539  0.020  1.539
 VOG  O3   C3   single  1.423  0.020  1.423
 VOG  C2   O2   single  1.405  0.020  1.405
 VOG  C2   C3   single  1.526  0.020  1.526
 VOG  C2   C1   single  1.539  0.020  1.539
 VOG  C4   C3   single  1.524  0.020  1.524
 VOG  C4   O4   single  1.408  0.020  1.408
 VOG  C4   C5   single  1.527  0.020  1.527
 VOG  C1   C6   single  1.530  0.020  1.530
 VOG  C1   O1   single  1.408  0.020  1.408
 VOG  C6   C5   single  1.529  0.020  1.529
 VOG  C5   N    single  1.450  0.020  1.450
 VOG  N    C8   single  1.448  0.020  1.448
 VOG  C10  C8   single  1.521  0.020  1.521
 VOG  C10  O10  single  1.411  0.020  1.411
 VOG  C8   C9   single  1.528  0.020  1.528
 VOG  C9   O9   single  1.409  0.020  1.409
 VOG  O1   H1   single  0.850  0.020  0.980
 VOG  C2   H2   single  0.970  0.020  1.090
 VOG  O2   H3   single  0.850  0.020  0.980
 VOG  C3   H4   single  0.970  0.020  1.090
 VOG  O3   H5   single  0.850  0.020  0.980
 VOG  C4   H6   single  0.970  0.020  1.090
 VOG  O4   H7   single  0.850  0.020  0.980
 VOG  C5   H8   single  0.970  0.020  1.090
 VOG  C6   H9   single  0.970  0.020  1.090
 VOG  C6   H10  single  0.970  0.020  1.090
 VOG  C7   H11  single  0.970  0.020  1.090
 VOG  C7   H12  single  0.970  0.020  1.090
 VOG  O7   H13  single  0.850  0.020  0.980
 VOG  N    H14  single  0.890  0.020  1.040
 VOG  C8   H16  single  0.970  0.020  1.090
 VOG  C9   H17  single  0.970  0.020  1.090
 VOG  C9   H18  single  0.970  0.020  1.090
 VOG  O9   H19  single  0.850  0.020  0.980
 VOG  C10  H20  single  0.970  0.020  1.090
 VOG  C10  H21  single  0.970  0.020  1.090
 VOG  O10  H22  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
 VOG  C7   C1   C6   106.80  3.000
 VOG  C6   C1   C2   108.97  3.000
 VOG  C7   C1   C2   111.44  3.000
 VOG  C6   C1   O1   109.42  3.000
 VOG  C2   C1   O1   111.08  3.000
 VOG  C7   C1   O1   109.02  3.000
 VOG  H1   O1   C1   106.34  3.000
 VOG  H2   C2   C3   107.23  3.000
 VOG  H2   C2   O2   110.24  3.000
 VOG  C3   C2   O2   111.22  3.000
 VOG  H2   C2   C1   107.15  3.000
 VOG  C3   C2   C1   111.54  3.000
 VOG  O2   C2   C1   109.36  3.000
 VOG  H3   O2   C2   107.10  3.000
 VOG  H4   C3   C4   108.89  3.000
 VOG  H4   C3   O3   110.59  3.000
 VOG  C4   C3   O3   109.37  3.000
 VOG  H4   C3   C2   109.52  3.000
 VOG  C4   C3   C2   109.67  3.000
 VOG  O3   C3   C2   108.78  3.000
 VOG  H5   O3   C3   108.88  3.000
 VOG  H6   C4   C5   107.55  3.000
 VOG  H6   C4   O4   110.05  3.000
 VOG  C5   C4   O4   109.11  3.000
 VOG  H6   C4   C3   108.19  3.000
 VOG  C5   C4   C3   109.62  3.000
 VOG  O4   C4   C3   112.22  3.000
 VOG  H7   O4   C4   107.67  3.000
 VOG  H8   C5   N    112.24  3.000
 VOG  H8   C5   C6   106.08  3.000
 VOG  N    C5   C6   114.18  3.000
 VOG  H8   C5   C4   107.44  3.000
 VOG  N    C5   C4   108.64  3.000
 VOG  C6   C5   C4   107.97  3.000
 VOG  H10  C6   H9   105.18  3.000
 VOG  H10  C6   C5   106.52  3.000
 VOG  H9   C6   C5   110.72  3.000
 VOG  H10  C6   C1   108.06  3.000
 VOG  H9   C6   C1   108.79  3.000
 VOG  C5   C6   C1   116.88  3.000
 VOG  H12  C7   H11  106.95  3.000
 VOG  H12  C7   O7   110.53  3.000
 VOG  H11  C7   O7   110.94  3.000
 VOG  H12  C7   C1   108.00  3.000
 VOG  H11  C7   C1   109.28  3.000
 VOG  O7   C7   C1   111.01  3.000
 VOG  H13  O7   C7   108.25  3.000
 VOG  H14  N    C8   108.89  3.000
 VOG  H14  N    C5   108.28  3.000
 VOG  C8   N    C5   118.02  3.000
 VOG  H16  C8   C10  103.95  3.000
 VOG  H16  C8   C9   105.62  3.000
 VOG  C10  C8   C9   113.94  3.000
 VOG  H16  C8   N    108.31  3.000
 VOG  C9   C8   N    115.40  3.000
 VOG  C10  C8   N    108.80  3.000
 VOG  H18  C9   H17  106.07  3.000
 VOG  H18  C9   O9   110.87  3.000
 VOG  H17  C9   O9   111.89  3.000
 VOG  H18  C9   C8   108.56  3.000
 VOG  H17  C9   C8   108.46  3.000
 VOG  O9   C9   C8   110.81  3.000
 VOG  H19  O9   C9   107.78  3.000
 VOG  H21  C10  H20  107.12  3.000
 VOG  H21  C10  O10  111.41  3.000
 VOG  H20  C10  O10  111.13  3.000
 VOG  H21  C10  C8   108.66  3.000
 VOG  H20  C10  C8   107.38  3.000
 VOG  O10  C10  C8   110.97  3.000
 VOG  H22  O10  C10  107.85  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
 VOG  Var_01  C10  C8   N   C5  -175.91  30.0  3
 VOG  Var_02  O10  C10  C8  N    -61.28  30.0  2
 VOG  Var_03  O9   C9   C8  N     53.66  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
 VOG  chir_01  C1  C2  C6  O1  negativ
 VOG  chir_02  C2  O2  C1  C3  positiv
 VOG  chir_03  C3  O3  C2  C4  negativ
 VOG  chir_04  C4  O4  C3  C5  positiv
 VOG  chir_05  C5  N   C6  C4  negativ

