# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 08:23:31 2020
#   Inital geometry file: a 41 line input string
#   Ligand name: (1R,2S)-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
 17Y  17Y  (1R,2S)-cyclopentane-1,2-diol  ligand  17  7  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_17Y
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
 17Y  OAA  O  OH1   0  -0.672  -1.8818  -0.7640   0.1758
 17Y  CAF  C  CH1   0   0.054  -0.5325  -0.5534   0.5043
 17Y  CAD  C  CH2   0  -0.483   0.4855  -1.2690  -0.3943
 17Y  CAC  C  CH2   0  -0.443   1.7661  -0.4137  -0.3038
 17Y  CAE  C  CH2   0  -0.493   1.3704   0.8366   0.5077
 17Y  CAG  C  CH1   0  -0.001  -0.1470   0.9154   0.3884
 17Y  OAB  O  OH1   0  -0.675  -0.5601   1.3733  -0.8816
 17Y  H1   H  HOH1  0   0.449  -2.0766  -1.6961   0.3107
 17Y  H2   H  HCH1  0   0.201  -0.3380  -0.8423   1.5481
 17Y  H3   H  HCH2  0   0.232   0.6464  -2.3014  -0.0802
 17Y  H4   H  HCH2  0   0.228   0.1075  -1.2986  -1.4178
 17Y  H5   H  HCH2  0   0.231   2.5841  -0.9496   0.1777
 17Y  H6   H  HCH2  0   0.232   2.1165  -0.1393  -1.2988
 17Y  H7   H  HCH2  0   0.231   1.6385   0.7123   1.5598
 17Y  H8   H  HCH2  0   0.244   1.8668   1.7475   0.1663
 17Y  H9   H  HCH1  0   0.216  -0.5925   1.5204   1.1898
 17Y  H10  H  HOH1  0   0.448  -0.1845   2.2483  -1.0177

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
 17Y  CAF  OAA  single  1.405  0.020  1.405
 17Y  CAF  CAG  single  1.523  0.020  1.523
 17Y  CAF  CAD  single  1.535  0.020  1.535
 17Y  CAG  CAE  single  1.524  0.020  1.524
 17Y  CAG  OAB  single  1.412  0.020  1.412
 17Y  CAE  CAC  single  1.542  0.020  1.542
 17Y  CAD  CAC  single  1.543  0.020  1.543
 17Y  OAA  H1   single  0.850  0.020  0.980
 17Y  CAF  H2   single  0.970  0.020  1.090
 17Y  CAD  H3   single  0.970  0.020  1.090
 17Y  CAD  H4   single  0.970  0.020  1.090
 17Y  CAC  H5   single  0.970  0.020  1.090
 17Y  CAC  H6   single  0.970  0.020  1.090
 17Y  CAE  H7   single  0.970  0.020  1.090
 17Y  CAE  H8   single  0.970  0.020  1.090
 17Y  CAG  H9   single  0.970  0.020  1.090
 17Y  OAB  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
 17Y  H1   OAA  CAF  107.88  3.000
 17Y  H2   CAF  CAG  106.29  3.000
 17Y  H2   CAF  CAD  108.40  3.000
 17Y  CAG  CAF  CAD  103.72  3.000
 17Y  H2   CAF  OAA  110.63  3.000
 17Y  CAD  CAF  OAA  115.49  3.000
 17Y  CAG  CAF  OAA  111.71  3.000
 17Y  H4   CAD  H3   107.18  3.000
 17Y  H4   CAD  CAC  110.94  3.000
 17Y  H3   CAD  CAC  112.66  3.000
 17Y  H4   CAD  CAF  109.39  3.000
 17Y  H3   CAD  CAF  111.74  3.000
 17Y  CAC  CAD  CAF  104.94  3.000
 17Y  H6   CAC  H5   106.61  3.000
 17Y  H6   CAC  CAE  111.03  3.000
 17Y  H5   CAC  CAE  111.02  3.000
 17Y  H6   CAC  CAD  110.67  3.000
 17Y  H5   CAC  CAD  112.10  3.000
 17Y  CAE  CAC  CAD  105.50  3.000
 17Y  H8   CAE  H7   106.52  3.000
 17Y  H8   CAE  CAG  112.64  3.000
 17Y  H7   CAE  CAG  109.00  3.000
 17Y  H8   CAE  CAC  113.27  3.000
 17Y  H7   CAE  CAC  110.58  3.000
 17Y  CAG  CAE  CAC  104.84  3.000
 17Y  H9   CAG  OAB  111.03  3.000
 17Y  H9   CAG  CAE  112.03  3.000
 17Y  OAB  CAG  CAE  112.24  3.000
 17Y  H9   CAG  CAF  111.90  3.000
 17Y  OAB  CAG  CAF  107.89  3.000
 17Y  CAE  CAG  CAF  101.31  3.000
 17Y  H10  OAB  CAG  107.95  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
 17Y  Var_01  CAE  CAC  CAD  CAF   -6.45  30.0  1
 17Y  Var_02  CAG  CAE  CAC  CAD  -20.77  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
 17Y  chir_01  CAF  OAA  CAG  CAD  positiv
 17Y  chir_02  CAG  OAB  CAF  CAE  negativ

