# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 16:53:40 2022
#   Inital geometry file: a 63 line input string
#   Ligand name: [(1~{S},2~{R},3~{R},4~{R},5~{R})-2-(hydroxymethyl)-3,4,5-tris(oxidanyl)cyclohexyl]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+][C@H]1C[C@@H](O)[C@@H](O)[C@H](O)[C@H]1CO
#
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
 VKH  VKH  "(1~{R},2~{R},3~{S},4~{R},5~{R},6~{R})-5-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3,4-triol"
  ligand  28  12  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VKH
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
 VKH  N1   N  NT3   1  -0.817  -19.3364  59.6705  50.2113
 VKH  C2   C  CH1   0  -0.041  -19.9523  57.5265  48.1016
 VKH  C4   C  CH1   0   0.051  -19.3041  59.7529  47.0923
 VKH  C5   C  CH1   0  -0.334  -18.0953  59.8099  48.0455
 VKH  C6   C  CH2   0  -0.176  -17.5971  61.2239  48.3091
 VKH  O2   O  OH1   0  -0.667  -21.1040  58.0888  48.7173
 VKH  C7   C  CH1   0  -0.131  -18.3153  59.0089  49.3304
 VKH  O6   O  OH1   0  -0.671  -18.6259  61.9750  48.9346
 VKH  O4   O  OH1   0  -0.667  -18.9856  60.3602  45.8620
 VKH  C3   C  CH1   0   0.057  -19.6716  58.2980  46.8110
 VKH  O3   O  OH1   0  -0.662  -20.7687  58.2861  45.9379
 VKH  C1   C  CH2   0  -0.485  -18.7433  57.5799  49.0314
 VKH  H1   H  HNT3  0   0.462  -19.2425  59.3671  51.1798
 VKH  H4   H  HCH1  0   0.260  -20.1446  56.4787  47.8380
 VKH  H5   H  HCH1  0   0.227  -20.1700  60.2526  47.5459
 VKH  H6   H  HCH1  0   0.282  -17.2664  59.3006  47.5392
 VKH  H7   H  HCH2  0   0.234  -16.7035  61.1714  48.9419
 VKH  H8   H  HCH2  0   0.233  -17.2913  61.6862  47.3657
 VKH  H9   H  HOH1  0   0.467  -21.4673  57.4450  49.3353
 VKH  H10  H  HCH1  0   0.315  -17.3890  59.0082  49.9058
 VKH  H11  H  HOH1  0   0.473  -18.2713  62.8253  49.2141
 VKH  H12  H  HOH1  0   0.456  -19.1885  61.2981  45.9155
 VKH  H13  H  HCH1  0   0.215  -18.7930  57.8187  46.3502
 VKH  H14  H  HOH1  0   0.450  -20.9371  57.3770  45.6702
 VKH  H15  H  HCH2  0   0.278  -18.9497  57.0376  49.9581
 VKH  H2   H  HNT3  0   0.464  -19.2322  60.6940  50.1670
 VKH  H16  H  HCH2  0   0.273  -17.9003  57.0717  48.5584
 VKH  H3   H  HNT3  0   0.457  -20.2827  59.4224  49.8987

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
 VKH  O4  C4   single  1.408  0.020  1.408
 VKH  O3  C3   single  1.402  0.020  1.402
 VKH  C3  C4   single  1.527  0.020  1.527
 VKH  C3  C2   single  1.530  0.020  1.530
 VKH  C4  C5   single  1.540  0.020  1.540
 VKH  C5  C6   single  1.522  0.020  1.522
 VKH  C5  C7   single  1.530  0.020  1.530
 VKH  C2  O2   single  1.422  0.020  1.422
 VKH  C2  C1   single  1.526  0.020  1.526
 VKH  O6  C6   single  1.419  0.020  1.419
 VKH  C1  C7   single  1.521  0.020  1.521
 VKH  C7  N1   single  1.502  0.020  1.502
 VKH  N1  H1   single  0.890  0.020  1.040
 VKH  C2  H4   single  0.970  0.020  1.090
 VKH  C4  H5   single  0.970  0.020  1.090
 VKH  C5  H6   single  0.970  0.020  1.090
 VKH  C6  H7   single  0.970  0.020  1.090
 VKH  C6  H8   single  0.970  0.020  1.090
 VKH  O2  H9   single  0.850  0.020  0.980
 VKH  C7  H10  single  0.970  0.020  1.090
 VKH  O6  H11  single  0.850  0.020  0.980
 VKH  O4  H12  single  0.850  0.020  0.980
 VKH  C3  H13  single  0.970  0.020  1.090
 VKH  O3  H14  single  0.850  0.020  0.980
 VKH  C1  H15  single  0.970  0.020  1.090
 VKH  H2  N1   single  0.890  0.020  1.040
 VKH  C1  H16  single  0.970  0.020  1.090
 VKH  H3  N1   single  0.890  0.020  1.040

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
 VKH  H3   N1  H2   108.68  3.000
 VKH  H3   N1  H1   107.59  3.000
 VKH  H2   N1  H1   109.11  3.000
 VKH  H3   N1  C7   109.97  3.000
 VKH  H2   N1  C7   110.11  3.000
 VKH  H1   N1  C7   111.31  3.000
 VKH  H4   C2  C1   108.58  3.000
 VKH  H4   C2  C3   108.13  3.000
 VKH  C1   C2  C3   110.55  3.000
 VKH  H4   C2  O2   109.85  3.000
 VKH  C1   C2  O2   111.35  3.000
 VKH  C3   C2  O2   108.33  3.000
 VKH  H5   C4  C3   108.66  3.000
 VKH  H5   C4  O4   110.06  3.000
 VKH  C3   C4  O4   107.72  3.000
 VKH  H5   C4  C5   110.27  3.000
 VKH  C3   C4  C5   109.76  3.000
 VKH  O4   C4  C5   110.31  3.000
 VKH  H6   C5  C7   104.67  3.000
 VKH  H6   C5  C6   105.31  3.000
 VKH  C7   C5  C6   112.83  3.000
 VKH  H6   C5  C4   106.87  3.000
 VKH  C7   C5  C4   112.79  3.000
 VKH  C6   C5  C4   113.48  3.000
 VKH  H8   C6  H7   106.87  3.000
 VKH  H8   C6  O6   111.04  3.000
 VKH  H7   C6  O6   111.21  3.000
 VKH  H8   C6  C5   109.55  3.000
 VKH  H7   C6  C5   108.80  3.000
 VKH  O6   C6  C5   109.31  3.000
 VKH  H9   O2  C2   108.60  3.000
 VKH  H10  C7  C1   110.00  3.000
 VKH  H10  C7  C5   108.74  3.000
 VKH  C1   C7  C5   111.54  3.000
 VKH  H10  C7  N1   105.56  3.000
 VKH  C1   C7  N1   109.74  3.000
 VKH  C5   C7  N1   111.08  3.000
 VKH  H11  O6  C6   109.17  3.000
 VKH  H12  O4  C4   108.93  3.000
 VKH  H13  C3  O3   111.09  3.000
 VKH  H13  C3  C4   107.44  3.000
 VKH  O3   C3  C4   108.13  3.000
 VKH  H13  C3  C2   106.25  3.000
 VKH  C4   C3  C2   111.68  3.000
 VKH  O3   C3  C2   112.18  3.000
 VKH  H14  O3  C3   108.54  3.000
 VKH  H16  C1  H15  106.38  3.000
 VKH  H16  C1  C7   107.77  3.000
 VKH  H15  C1  C7   110.63  3.000
 VKH  H16  C1  C2   109.35  3.000
 VKH  H15  C1  C2   110.46  3.000
 VKH  C7   C1  C2   112.05  3.000

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
 VKH  chir_01  C2  C3  O2  C1  positiv
 VKH  chir_02  C4  O4  C5  C3  positiv
 VKH  chir_03  C5  C4  C6  C7  negativ
 VKH  chir_04  C7  N1  C5  C1  positiv
 VKH  chir_05  C3  O3  C4  C2  negativ

