# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 20:06:12 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: (1R,2R)-cyclohexane-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CCCC[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
 40O  40O  (1R,2R)-cyclohexane-1,2-diol  ligand  20  8  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_40O
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
 40O  C4   C  CH2   0  -0.484  -0.6764   1.4450   0.1306
 40O  C5   C  CH1   0   0.060   0.5990   0.7127  -0.2781
 40O  C6   C  CH1   0   0.061   0.5981  -0.7007   0.2816
 40O  C1   C  CH2   0  -0.485  -0.6481  -1.4515  -0.1804
 40O  C2   C  CH2   0  -0.441  -1.9290  -0.7266   0.2158
 40O  C3   C  CH2   0  -0.440  -1.9294   0.7014  -0.3166
 40O  O7   O  OH1   0  -0.676   1.7835  -1.3431  -0.1384
 40O  O8   O  OH1   0  -0.676   1.7546   1.3731   0.1938
 40O  H1   H  HCH2  0   0.219  -0.6863   1.5580   1.2205
 40O  H2   H  HCH2  0   0.237  -0.6634   2.4553  -0.2898
 40O  H3   H  HCH1  0   0.187   0.6192   0.6391  -1.3782
 40O  H4   H  HCH1  0   0.186   0.5690  -0.6265   1.3816
 40O  H5   H  HCH2  0   0.220  -0.6109  -1.5647  -1.2697
 40O  H6   H  HCH2  0   0.237  -0.6381  -2.4614   0.2412
 40O  H7   H  HCH2  0   0.235  -2.7965  -1.2743  -0.1581
 40O  H8   H  HCH2  0   0.217  -2.0202  -0.7097   1.3069
 40O  H9   H  HCH2  0   0.235  -2.8188   1.2354   0.0243
 40O  H10  H  HCH2  0   0.216  -1.9784   0.6843  -1.4104
 40O  H11  H  HOH1  0   0.446   1.7434  -2.2578   0.1575
 40O  H12  H  HOH1  0   0.446   1.7257   2.2807  -0.1250

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
 40O  O7  C6   single  1.412  0.020  1.412
 40O  C6  C1   single  1.526  0.020  1.526
 40O  C6  C5   single  1.520  0.020  1.520
 40O  C1  C2   single  1.524  0.020  1.524
 40O  C5  C4   single  1.526  0.020  1.526
 40O  C5  O8   single  1.412  0.020  1.412
 40O  C4  C3   single  1.524  0.020  1.524
 40O  C2  C3   single  1.524  0.020  1.524
 40O  C4  H1   single  0.970  0.020  1.090
 40O  C4  H2   single  0.970  0.020  1.090
 40O  C5  H3   single  0.970  0.020  1.090
 40O  C6  H4   single  0.970  0.020  1.090
 40O  C1  H5   single  0.970  0.020  1.090
 40O  C1  H6   single  0.970  0.020  1.090
 40O  C2  H7   single  0.970  0.020  1.090
 40O  C2  H8   single  0.970  0.020  1.090
 40O  C3  H9   single  0.970  0.020  1.090
 40O  C3  H10  single  0.970  0.020  1.090
 40O  O7  H11  single  0.850  0.020  0.980
 40O  O8  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
 40O  H2   C4  H1  106.67  3.000
 40O  H2   C4  C3  110.33  3.000
 40O  H1   C4  C3  109.56  3.000
 40O  H2   C4  C5  109.28  3.000
 40O  H1   C4  C5  108.86  3.000
 40O  C3   C4  C5  111.98  3.000
 40O  H3   C5  O8  110.46  3.000
 40O  H3   C5  C6  107.77  3.000
 40O  O8   C5  C6  108.20  3.000
 40O  H3   C5  C4  108.32  3.000
 40O  O8   C5  C4  111.72  3.000
 40O  C6   C5  C4  110.30  3.000
 40O  H4   C6  O7  110.46  3.000
 40O  H4   C6  C1  108.27  3.000
 40O  O7   C6  C1  111.81  3.000
 40O  H4   C6  C5  107.73  3.000
 40O  C1   C6  C5  110.27  3.000
 40O  O7   C6  C5  108.23  3.000
 40O  H6   C1  H5  106.70  3.000
 40O  H6   C1  C2  110.27  3.000
 40O  H5   C1  C2  109.63  3.000
 40O  H6   C1  C6  109.26  3.000
 40O  H5   C1  C6  108.91  3.000
 40O  C2   C1  C6  111.93  3.000
 40O  H8   C2  H7  106.42  3.000
 40O  H8   C2  C3  109.49  3.000
 40O  H7   C2  C3  110.50  3.000
 40O  H8   C2  C1  109.66  3.000
 40O  H7   C2  C1  109.88  3.000
 40O  C3   C2  C1  110.80  3.000
 40O  H10  C3  H9  106.44  3.000
 40O  H10  C3  C2  109.53  3.000
 40O  H9   C3  C2  110.45  3.000
 40O  H10  C3  C4  109.73  3.000
 40O  H9   C3  C4  109.84  3.000
 40O  C2   C3  C4  110.76  3.000
 40O  H11  O7  C6  107.82  3.000
 40O  H12  O8  C5  107.80  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
 40O  Var_01  C1  C2  C3  C4  -54.44  30.0  1
 40O  Var_02  C2  C3  C4  C5   55.68  30.0  1
 40O  Var_03  C3  C2  C1  C6   55.80  30.0  1

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
 40O  chir_01  C5  C6  C4  O8  negativ
 40O  chir_02  C6  O7  C5  C1  negativ

