# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 11:33:11 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: (2R,5R)-hexane-2,5-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)CC[C@@H](C)O
#
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
 HX2  HX2  '(2R,5R)-hexane-2,5-diol  '  ligand  22  8  .  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_HX2
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
 HX2  C1   C  CH3   0  -0.680   3.1018  -0.7769   0.4219
 HX2  O1   O  OH1   0  -0.670   2.1212   1.1208  -0.7327
 HX2  C2   C  CH1   0   0.031   1.9541   0.2207   0.3499
 HX2  O2   O  OH1   0  -0.670  -2.0916  -1.1766  -0.7258
 HX2  C3   C  CH2   0  -0.441   0.6037  -0.4887   0.3003
 HX2  C4   C  CH2   0  -0.441  -0.5877   0.4606   0.2831
 HX2  C5   C  CH1   0   0.031  -1.9380  -0.2486   0.3353
 HX2  C6   C  CH3   0  -0.680  -3.0872   0.7494   0.3688
 HX2  H1   H  HCH3  0   0.233   4.0653  -0.2682   0.4698
 HX2  H1A  H  HCH3  0   0.224   3.0126  -1.4094   1.3058
 HX2  H1B  H  HCH3  0   0.218   3.1055  -1.4311  -0.4538
 HX2  HO1  H  HOH1  0   0.438   2.0745   0.6126  -1.5498
 HX2  H2   H  HCH1  0   0.213   1.9808   0.8503   1.2460
 HX2  H3   H  HCH2  0   0.216   0.5757  -1.1465  -0.5756
 HX2  H3A  H  HCH2  0   0.218   0.5311  -1.1448   1.1743
 HX2  H4   H  HCH2  0   0.217  -0.5246   1.1359   1.1431
 HX2  H4A  H  HCH2  0   0.216  -0.5510   1.0985  -0.6071
 HX2  H5   H  HCH1  0   0.213  -1.9743  -0.8555   1.2466
 HX2  H6   H  HCH3  0   0.233  -4.0508   0.2412   0.4190
 HX2  H6A  H  HCH3  0   0.225  -3.0078   1.4046   1.2368
 HX2  H6B  H  HCH3  0   0.218  -3.0818   1.3804  -0.5238
 HX2  HO2  H  HOH1  0   0.438  -2.0472  -0.6878  -1.5549

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
 HX2  C1  C2   single  1.522  0.020  1.522
 HX2  O1  C2   single  1.418  0.020  1.418
 HX2  C2  C3   single  1.526  0.020  1.526
 HX2  O2  C5   single  1.418  0.020  1.418
 HX2  C3  C4   single  1.523  0.020  1.523
 HX2  C4  C5   single  1.526  0.020  1.526
 HX2  C5  C6   single  1.522  0.020  1.522
 HX2  C1  H1   single  0.970  0.020  1.090
 HX2  C1  H1A  single  0.970  0.020  1.090
 HX2  C1  H1B  single  0.970  0.020  1.090
 HX2  O1  HO1  single  0.850  0.020  0.980
 HX2  C2  H2   single  0.970  0.020  1.090
 HX2  O2  HO2  single  0.850  0.020  0.980
 HX2  C3  H3   single  0.970  0.020  1.090
 HX2  C3  H3A  single  0.970  0.020  1.090
 HX2  C4  H4   single  0.970  0.020  1.090
 HX2  C4  H4A  single  0.970  0.020  1.090
 HX2  C5  H5   single  0.970  0.020  1.090
 HX2  C6  H6   single  0.970  0.020  1.090
 HX2  C6  H6A  single  0.970  0.020  1.090
 HX2  C6  H6B  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
 HX2  H1B  C1  H1A  107.61  3.000
 HX2  H1B  C1  H1   108.15  3.000
 HX2  H1A  C1  H1   107.89  3.000
 HX2  H1B  C1  C2   110.90  3.000
 HX2  H1A  C1  C2   110.90  3.000
 HX2  H1   C1  C2   111.25  3.000
 HX2  HO1  O1  C2   107.88  3.000
 HX2  H2   C2  C3   108.38  3.000
 HX2  H2   C2  O1   104.89  3.000
 HX2  C3   C2  O1   111.99  3.000
 HX2  H2   C2  C1   108.63  3.000
 HX2  C3   C2  C1   111.35  3.000
 HX2  O1   C2  C1   111.30  3.000
 HX2  HO2  O2  C5   107.88  3.000
 HX2  H3A  C3  H3   106.05  3.000
 HX2  H3A  C3  C4   109.29  3.000
 HX2  H3   C3  C4   110.18  3.000
 HX2  H3A  C3  C2   108.13  3.000
 HX2  H3   C3  C2   109.13  3.000
 HX2  C4   C3  C2   113.75  3.000
 HX2  H4A  C4  H4   106.09  3.000
 HX2  H4A  C4  C5   109.14  3.000
 HX2  H4   C4  C5   108.10  3.000
 HX2  H4A  C4  C3   110.23  3.000
 HX2  H4   C4  C3   109.28  3.000
 HX2  C5   C4  C3   113.70  3.000
 HX2  H5   C5  C6   108.65  3.000
 HX2  H5   C5  C4   108.37  3.000
 HX2  C6   C5  C4   111.34  3.000
 HX2  H5   C5  O2   104.85  3.000
 HX2  C6   C5  O2   111.33  3.000
 HX2  C4   C5  O2   111.99  3.000
 HX2  H6B  C6  H6A  107.63  3.000
 HX2  H6B  C6  H6   108.12  3.000
 HX2  H6A  C6  H6   107.92  3.000
 HX2  H6B  C6  C5   110.90  3.000
 HX2  H6A  C6  C5   110.88  3.000
 HX2  H6   C6  C5   111.25  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
 HX2  Var_01  C5  C4  C3  C2  -175.82  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
 HX2  chir_01  C2  C1  O1  C3  negativ
 HX2  chir_02  C5  O2  C4  C6  negativ

