# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 10:49:28 2020
#   Inital geometry file: a 41 line input string
#   Ligand name: (1~{R},2~{R})-cyclopentane-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CCC[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
 6VV  6VV  (1~{R},2~{R})-cyclopentane-1,2-diol  ligand  17  7  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6VV
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
 6VV  O01  O  OH1   0  -0.678  -1.9341  -0.7603  -0.3925
 6VV  C02  C  CH1   0   0.055  -0.8276  -0.2521   0.3214
 6VV  C03  C  CH2   0  -0.492  -0.7521   1.2836   0.3551
 6VV  C04  C  CH2   0  -0.449   0.7390   1.5945   0.2547
 6VV  C05  C  CH2   0  -0.476   1.2048   0.5585  -0.7639
 6VV  C06  C  CH1   0   0.021   0.4865  -0.7256  -0.3398
 6VV  O07  O  OH1   0  -0.681   1.2155  -1.4506   0.6342
 6VV  H1   H  HOH1  0   0.449  -2.7353  -0.4525   0.0420
 6VV  H2   H  HCH1  0   0.206  -0.8325  -0.6305   1.3525
 6VV  H3   H  HCH2  0   0.225  -1.2657   1.6838  -0.5243
 6VV  H4   H  HCH2  0   0.238  -1.2306   1.7082   1.2390
 6VV  H5   H  HCH2  0   0.236   0.9425   2.6229  -0.0453
 6VV  H6   H  HCH2  0   0.222   1.2319   1.4308   1.2165
 6VV  H7   H  HCH2  0   0.224   0.8570   0.8493  -1.7594
 6VV  H8   H  HCH2  0   0.239   2.2890   0.4368  -0.8243
 6VV  H9   H  HCH1  0   0.214   0.2649  -1.3619  -1.2060
 6VV  H10  H  HOH1  0   0.447   2.0524  -1.7169   0.2411

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
 6VV  C03  C04  single  1.526  0.020  1.526
 6VV  C03  C02  single  1.538  0.020  1.538
 6VV  O07  C06  single  1.416  0.020  1.416
 6VV  C04  C05  single  1.526  0.020  1.526
 6VV  C02  C06  single  1.545  0.020  1.545
 6VV  C02  O01  single  1.411  0.020  1.411
 6VV  C06  C05  single  1.531  0.020  1.531
 6VV  O01  H1   single  0.850  0.020  0.980
 6VV  C02  H2   single  0.970  0.020  1.090
 6VV  C03  H3   single  0.970  0.020  1.090
 6VV  C03  H4   single  0.970  0.020  1.090
 6VV  C04  H5   single  0.970  0.020  1.090
 6VV  C04  H6   single  0.970  0.020  1.090
 6VV  C05  H7   single  0.970  0.020  1.090
 6VV  C05  H8   single  0.970  0.020  1.090
 6VV  C06  H9   single  0.970  0.020  1.090
 6VV  O07  H10  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
 6VV  H1   O01  C02  108.02  3.000
 6VV  H2   C02  C06  107.45  3.000
 6VV  H2   C02  C03  108.89  3.000
 6VV  C06  C02  C03  105.88  3.000
 6VV  H2   C02  O01  110.32  3.000
 6VV  C06  C02  O01  109.87  3.000
 6VV  C03  C02  O01  114.15  3.000
 6VV  H4   C03  H3   107.63  3.000
 6VV  H4   C03  C04  113.73  3.000
 6VV  H3   C03  C04  109.34  3.000
 6VV  H4   C03  C02  112.63  3.000
 6VV  H3   C03  C02  108.94  3.000
 6VV  C04  C03  C02  104.47  3.000
 6VV  H6   C04  H5   107.41  3.000
 6VV  H6   C04  C05  110.38  3.000
 6VV  H5   C04  C05  113.57  3.000
 6VV  H6   C04  C03  110.61  3.000
 6VV  H5   C04  C03  113.10  3.000
 6VV  C05  C04  C03  101.76  3.000
 6VV  H8   C05  H7   107.14  3.000
 6VV  H8   C05  C06  112.79  3.000
 6VV  H7   C05  C06  109.02  3.000
 6VV  H8   C05  C04  114.55  3.000
 6VV  H7   C05  C04  109.27  3.000
 6VV  C06  C05  C04  103.97  3.000
 6VV  H9   C06  O07  110.49  3.000
 6VV  H9   C06  C05  111.24  3.000
 6VV  O07  C06  C05  112.23  3.000
 6VV  H9   C06  C02  110.10  3.000
 6VV  C05  C06  C02  105.10  3.000
 6VV  O07  C06  C02  107.48  3.000
 6VV  H10  O07  C06  107.96  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
 6VV  Var_01  C05  C04  C03  C02   39.77  30.0  1
 6VV  Var_02  C06  C05  C04  C03  -42.86  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
 6VV  chir_01  C02  C03  C06  O01  positiv
 6VV  chir_02  C06  O07  C02  C05  negativ

