# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 12:03:34 2020
#   Inital geometry file: a 33 line input string
#   Ligand name: propane-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCCO
#
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
 PDO  PDO  'propane-1,3-diol         '  ligand  13  5  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PDO
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
 PDO  C1   C  CH2   0  -0.144  -1.2331  -0.5093   0.0078
 PDO  O1   O  OH1   0  -0.673  -2.3690   0.3282   0.0257
 PDO  C2   C  CH2   0  -0.491   0.0133   0.3546   0.0385
 PDO  C3   C  CH2   0  -0.144   1.2703  -0.4945   0.0251
 PDO  O3   O  OH1   0  -0.673   2.3957   0.3567   0.0551
 PDO  H11  H  HCH2  0   0.191  -1.2257  -1.1895   0.8699
 PDO  H12  H  HCH2  0   0.191  -1.2165  -1.1400  -0.8909
 PDO  HO1  H  HOH1  0   0.452  -3.1512  -0.2300   0.0089
 PDO  H21  H  HCH2  0   0.228   0.0153   1.0241  -0.8268
 PDO  H22  H  HCH2  0   0.228   0.0033   0.9786   0.9372
 PDO  H31  H  HCH2  0   0.191   1.2599  -1.1731   0.8885
 PDO  H32  H  HCH2  0   0.191   1.2723  -1.1275  -0.8724
 PDO  HO3  H  HOH1  0   0.452   3.1848  -0.1920   0.0423

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
 PDO  C1  O1   single  1.411  0.020  1.411
 PDO  C1  C2   single  1.517  0.020  1.517
 PDO  C1  H11  single  0.970  0.020  1.090
 PDO  C1  H12  single  0.970  0.020  1.090
 PDO  O1  HO1  single  0.850  0.020  0.980
 PDO  C2  C3   single  1.517  0.020  1.517
 PDO  C2  H21  single  0.970  0.020  1.090
 PDO  C2  H22  single  0.970  0.020  1.090
 PDO  C3  O3   single  1.411  0.020  1.411
 PDO  C3  H31  single  0.970  0.020  1.090
 PDO  C3  H32  single  0.970  0.020  1.090
 PDO  O3  HO3  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
 PDO  H12  C1  H11  106.65  3.000
 PDO  H12  C1  C2   109.35  3.000
 PDO  H11  C1  C2   109.35  3.000
 PDO  H12  C1  O1   111.31  3.000
 PDO  H11  C1  O1   111.29  3.000
 PDO  C2   C1  O1   108.85  3.000
 PDO  HO1  O1  C1   108.07  3.000
 PDO  H22  C2  H21  107.50  3.000
 PDO  H22  C2  C3   109.51  3.000
 PDO  H21  C2  C3   109.51  3.000
 PDO  H22  C2  C1   109.51  3.000
 PDO  H21  C2  C1   109.51  3.000
 PDO  C3   C2  C1   111.22  3.000
 PDO  H32  C3  H31  106.64  3.000
 PDO  H32  C3  O3   111.31  3.000
 PDO  H31  C3  O3   111.32  3.000
 PDO  H32  C3  C2   109.35  3.000
 PDO  H31  C3  C2   109.33  3.000
 PDO  O3   C3  C2   108.85  3.000
 PDO  HO3  O3  C3   108.07  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
 PDO  Var_01  O3  C3  C2  C1  -179.98  30.0  3
 PDO  Var_02  C3  C2  C1  O1   179.83  30.0  3

