# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 19:09:40 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: (1~{R},2~{S},4~{S},5~{R})-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1[C@@H](O)[C@H](O)[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
 VKN  VKN  "(1R,2S,4S,5R)-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol"  saccharide  27  13  .  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_VKN
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
 VKN  C1   C  CH1   0   0.007  45.5815  101.5123  18.5522
 VKN  C2   C  CH1   0  -0.024  44.6496  101.7583  19.7452
 VKN  C7   C  CH1   0   0.059  46.5690  100.3619  18.7689
 VKN  C5   C  CH1   0  -0.377  47.2943  100.4785  20.1180
 VKN  C6   C  CH2   0  -0.167  48.2887   99.3473  20.3303
 VKN  O6   O  OH1   0  -0.674  47.5843   98.1222  20.4696
 VKN  C4   C  CH1   0   0.052  46.3063  100.6328  21.2765
 VKN  O4   O  OH1   0  -0.681  47.0068  100.8045  22.4981
 VKN  C3   C  CH1   0   0.034  45.4447  101.8700  21.0425
 VKN  O3   O  OH1   0  -0.679  44.5196  102.0750  22.0859
 VKN  O2   O  OH1   0  -0.662  43.6954  100.7267  19.8015
 VKN  O5   O  OH1   0  -0.689  45.8666   99.1510  18.6152
 VKN  H1   H  HCH1  0   0.226  44.9614  101.2662  17.6783
 VKN  O1   O  OH1   0  -0.669  46.3602  102.6628  18.2994
 VKN  H2   H  HCH1  0   0.219  44.1445  102.7236  19.5710
 VKN  H6   H  HCH1  0   0.207  47.3361  100.4554  17.9829
 VKN  H5   H  HCH1  0   0.251  47.8984  101.3928  20.0738
 VKN  H61  H  HCH2  0   0.218  48.9722   99.3098  19.4730
 VKN  H62  H  HCH2  0   0.222  48.8960   99.5461  21.2185
 VKN  HO6  H  HOH1  0   0.466  48.2164   97.3994  20.5315
 VKN  H4   H  HCH1  0   0.221  45.6559   99.7543  21.3358
 VKN  HO4  H  HOH1  0   0.456  46.7856  100.0829  23.0914
 VKN  H3   H  HCH1  0   0.198  46.1180  102.7356  20.9504
 VKN  HO3  H  HOH1  0   0.444  44.9906  101.9731  22.9203
 VKN  HO2  H  HOH1  0   0.444  43.1540  100.8755  20.5840
 VKN  HO5  H  HOH1  0   0.446  46.3398   98.4729  19.1198
 VKN  H7   H  HOH1  0   0.452  45.7673  103.3982  18.1151

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
 VKN  C1  C7   single  1.531  0.020  1.531
 VKN  C1  C2   single  1.534  0.020  1.534
 VKN  C7  O5   single  1.408  0.020  1.408
 VKN  C7  C5   single  1.536  0.020  1.536
 VKN  C2  O2   single  1.406  0.020  1.406
 VKN  C2  C3   single  1.526  0.020  1.526
 VKN  C5  C6   single  1.521  0.020  1.521
 VKN  C5  C4   single  1.530  0.020  1.530
 VKN  C6  O6   single  1.420  0.020  1.420
 VKN  C3  C4   single  1.526  0.020  1.526
 VKN  C3  O3   single  1.409  0.020  1.409
 VKN  C4  O4   single  1.419  0.020  1.419
 VKN  C1  H1   single  0.970  0.020  1.090
 VKN  C1  O1   single  1.412  0.020  1.412
 VKN  C2  H2   single  0.970  0.020  1.090
 VKN  C7  H6   single  0.970  0.020  1.090
 VKN  C5  H5   single  0.970  0.020  1.090
 VKN  C6  H61  single  0.970  0.020  1.090
 VKN  C6  H62  single  0.970  0.020  1.090
 VKN  O6  HO6  single  0.850  0.020  0.980
 VKN  C4  H4   single  0.970  0.020  1.090
 VKN  O4  HO4  single  0.850  0.020  0.980
 VKN  C3  H3   single  0.970  0.020  1.090
 VKN  O3  HO3  single  0.850  0.020  0.980
 VKN  O2  HO2  single  0.850  0.020  0.980
 VKN  O5  HO5  single  0.850  0.020  0.980
 VKN  O1  H7   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
 VKN  O1   C1  H1   110.56  3.000
 VKN  O1   C1  C7   106.37  3.000
 VKN  H1   C1  C7   107.94  3.000
 VKN  O1   C1  C2   110.10  3.000
 VKN  H1   C1  C2   108.15  3.000
 VKN  C7   C1  C2   113.72  3.000
 VKN  H2   C2  O2   109.72  3.000
 VKN  H2   C2  C3   107.99  3.000
 VKN  O2   C2  C3   111.92  3.000
 VKN  H2   C2  C1   107.20  3.000
 VKN  C3   C2  C1   110.88  3.000
 VKN  O2   C2  C1   109.01  3.000
 VKN  H6   C7  O5   110.02  3.000
 VKN  H6   C7  C5   106.93  3.000
 VKN  O5   C7  C5   113.37  3.000
 VKN  H6   C7  C1   106.50  3.000
 VKN  C5   C7  C1   111.82  3.000
 VKN  O5   C7  C1   107.99  3.000
 VKN  H5   C5  C4   107.58  3.000
 VKN  H5   C5  C6   105.40  3.000
 VKN  C4   C5  C6   113.04  3.000
 VKN  H5   C5  C7   106.74  3.000
 VKN  C4   C5  C7   111.57  3.000
 VKN  C6   C5  C7   112.02  3.000
 VKN  H62  C6  H61  107.15  3.000
 VKN  H62  C6  O6   110.63  3.000
 VKN  H61  C6  O6   110.86  3.000
 VKN  H62  C6  C5   109.95  3.000
 VKN  H61  C6  C5   108.88  3.000
 VKN  O6   C6  C5   109.33  3.000
 VKN  HO6  O6  C6   109.18  3.000
 VKN  H4   C4  C3   108.88  3.000
 VKN  H4   C4  O4   110.12  3.000
 VKN  C3   C4  O4   108.23  3.000
 VKN  H4   C4  C5   110.10  3.000
 VKN  O4   C4  C5   110.20  3.000
 VKN  C3   C4  C5   109.28  3.000
 VKN  HO4  O4  C4   109.11  3.000
 VKN  H3   C3  O3   110.44  3.000
 VKN  H3   C3  C4   107.77  3.000
 VKN  O3   C3  C4   112.03  3.000
 VKN  H3   C3  C2   107.77  3.000
 VKN  O3   C3  C2   107.34  3.000
 VKN  C4   C3  C2   111.43  3.000
 VKN  HO3  O3  C3   107.75  3.000
 VKN  HO2  O2  C2   107.49  3.000
 VKN  HO5  O5  C7   107.54  3.000
 VKN  H7   O1  C1   108.49  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
 VKN  chir_01  C1  C7  C2  O1  negativ
 VKN  chir_02  C2  O2  C1  C3  positiv
 VKN  chir_03  C7  O5  C1  C5  negativ
 VKN  chir_04  C5  C7  C6  C4  positiv
 VKN  chir_05  C4  O4  C5  C3  positiv
 VKN  chir_06  C3  O3  C4  C2  negativ

