# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 04:59:23 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: (1~{R},2~{S},4~{S},5~{R})-cyclohexane-1,2,3,4,5-pentol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1C[C@@H](O)[C@H](O)C(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
 HQ8  HQ8  (1~{R},2~{S},4~{S},5~{R})-cyclohexane-1,2,3,4,5-pentol  ligand  23  11  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_HQ8
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
 HQ8  C1   C  CH1   0   0.031   1.3321   0.5700  -0.0291
 HQ8  C2   C  CH1   0   0.034   0.7882  -0.8419   0.1723
 HQ8  C4   C  CH1   0   0.039  -0.6001  -0.9579  -0.4425
 HQ8  C5   C  CH1   0  -0.025  -1.5598   0.0793   0.1452
 HQ8  C6   C  CH1   0  -0.009  -1.0140   1.4990  -0.0350
 HQ8  C7   C  CH2   0  -0.514   0.3868   1.6123   0.5546
 HQ8  O1   O  OH1   0  -0.682   2.6058   0.6057   0.5882
 HQ8  O3   O  OH1   0  -0.673  -1.0622  -2.2715  -0.2374
 HQ8  O4   O  OH1   0  -0.678   1.6194  -1.7972  -0.4452
 HQ8  O5   O  OH1   0  -0.672  -1.0402   1.7745  -1.4209
 HQ8  O2   O  OH1   0  -0.668  -1.7405  -0.2117   1.5107
 HQ8  H1   H  HCH1  0   0.208   1.4341   0.7414  -1.1095
 HQ8  H2   H  HCH1  0   0.203   0.7192  -1.0307   1.2551
 HQ8  H3   H  HCH1  0   0.214  -0.5072  -0.7443  -1.5169
 HQ8  H4   H  HCH1  0   0.230  -2.5153   0.0079  -0.3978
 HQ8  H5   H  HCH1  0   0.227  -1.6805   2.1910   0.5014
 HQ8  H6   H  HCH2  0   0.234   0.3282   1.4880   1.6393
 HQ8  H7   H  HCH2  0   0.247   0.7814   2.6184   0.3774
 HQ8  H8   H  HOH1  0   0.455   3.1074   1.3344   0.2114
 HQ8  H9   H  HOH1  0   0.449  -1.8750  -2.3847  -0.7398
 HQ8  H10  H  HOH1  0   0.444   2.5156  -1.6435  -0.1276
 HQ8  H11  H  HOH1  0   0.454  -0.7092   2.6675  -1.5582
 HQ8  H12  H  HOH1  0   0.453  -2.4075   0.3869   1.8613

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
 HQ8  C6  C5   single  1.532  0.020  1.532
 HQ8  C6  C7   single  1.524  0.020  1.524
 HQ8  C6  O5   single  1.413  0.020  1.413
 HQ8  C5  C4   single  1.530  0.020  1.530
 HQ8  C7  C1   single  1.523  0.020  1.523
 HQ8  C4  O3   single  1.407  0.020  1.407
 HQ8  C4  C2   single  1.523  0.020  1.523
 HQ8  C1  C2   single  1.526  0.020  1.526
 HQ8  C1  O1   single  1.416  0.020  1.416
 HQ8  C2  O4   single  1.409  0.020  1.409
 HQ8  C5  O2   single  1.408  0.020  1.408
 HQ8  C1  H1   single  0.970  0.020  1.090
 HQ8  C2  H2   single  0.970  0.020  1.090
 HQ8  C4  H3   single  0.970  0.020  1.090
 HQ8  C5  H4   single  0.970  0.020  1.090
 HQ8  C6  H5   single  0.970  0.020  1.090
 HQ8  C7  H6   single  0.970  0.020  1.090
 HQ8  C7  H7   single  0.970  0.020  1.090
 HQ8  O1  H8   single  0.850  0.020  0.980
 HQ8  O3  H9   single  0.850  0.020  0.980
 HQ8  O4  H10  single  0.850  0.020  0.980
 HQ8  O5  H11  single  0.850  0.020  0.980
 HQ8  O2  H12  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
 HQ8  H1   C1  O1  109.96  3.000
 HQ8  H1   C1  C7  109.13  3.000
 HQ8  O1   C1  C7  111.95  3.000
 HQ8  H1   C1  C2  107.89  3.000
 HQ8  O1   C1  C2  106.64  3.000
 HQ8  C7   C1  C2  111.17  3.000
 HQ8  H2   C2  O4  110.59  3.000
 HQ8  H2   C2  C4  109.07  3.000
 HQ8  O4   C2  C4  108.01  3.000
 HQ8  H2   C2  C1  108.10  3.000
 HQ8  O4   C2  C1  111.05  3.000
 HQ8  C4   C2  C1  110.00  3.000
 HQ8  H3   C4  O3  110.58  3.000
 HQ8  H3   C4  C5  107.25  3.000
 HQ8  O3   C4  C5  111.75  3.000
 HQ8  H3   C4  C2  107.62  3.000
 HQ8  O3   C4  C2  108.15  3.000
 HQ8  C5   C4  C2  111.41  3.000
 HQ8  H4   C5  O2  110.70  3.000
 HQ8  H4   C5  C6  108.13  3.000
 HQ8  O2   C5  C6  110.57  3.000
 HQ8  H4   C5  C4  108.11  3.000
 HQ8  O2   C5  C4  108.24  3.000
 HQ8  C6   C5  C4  111.08  3.000
 HQ8  H5   C6  O5  110.14  3.000
 HQ8  H5   C6  C7  108.74  3.000
 HQ8  O5   C6  C7  112.45  3.000
 HQ8  H5   C6  C5  108.05  3.000
 HQ8  O5   C6  C5  106.83  3.000
 HQ8  C7   C6  C5  110.54  3.000
 HQ8  H7   C7  H6  106.52  3.000
 HQ8  H7   C7  C6  109.69  3.000
 HQ8  H6   C7  C6  109.03  3.000
 HQ8  H7   C7  C1  110.06  3.000
 HQ8  H6   C7  C1  109.61  3.000
 HQ8  C6   C7  C1  111.79  3.000
 HQ8  H8   O1  C1  108.51  3.000
 HQ8  H9   O3  C4  108.12  3.000
 HQ8  H10  O4  C2  107.23  3.000
 HQ8  H11  O5  C6  108.33  3.000
 HQ8  H12  O2  C5  108.29  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
 HQ8  chir_01  C1  C7  C2  O1  positiv
 HQ8  chir_02  C2  O4  C1  C4  negativ
 HQ8  chir_03  C4  O3  C2  C5  positiv
 HQ8  chir_04  C5  O2  C4  C6  positiv
 HQ8  chir_05  C6  O5  C5  C7  negativ

