# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 19:30:48 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: pentane-1,5-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCCCCO
#
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
 9JE  9JE  'pentane-1,5-diol         '  ligand  19  7  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_9JE
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
 9JE  C02  C  CH2   0  -0.137   2.5141  -0.4602   0.0360
 9JE  C03  C  CH2   0  -0.451   1.2670   0.4016   0.0109
 9JE  C04  C  CH2   0  -0.436  -0.0030  -0.4398   0.0240
 9JE  C05  C  CH2   0  -0.451  -1.2721   0.4028  -0.0061
 9JE  C06  C  CH2   0  -0.137  -2.5195  -0.4587   0.0109
 9JE  O01  O  OH1   0  -0.676   3.6548   0.3721   0.0227
 9JE  O07  O  OH1   0  -0.676  -3.6602   0.3727  -0.0306
 9JE  H1   H  HCH2  0   0.187   2.4938  -1.0967   0.9312
 9JE  H2   H  HCH2  0   0.187   2.5021  -1.1355  -0.8303
 9JE  H3   H  HCH2  0   0.220   1.2707   1.0737   0.8754
 9JE  H4   H  HCH2  0   0.220   1.2788   1.0345  -0.8824
 9JE  H5   H  HCH2  0   0.217   0.0024  -1.1199  -0.8346
 9JE  H6   H  HCH2  0   0.217  -0.0092  -1.0756   0.9161
 9JE  H7   H  HCH2  0   0.220  -1.2841   1.0796   0.8541
 9JE  H8   H  HCH2  0   0.220  -1.2744   1.0303  -0.9033
 9JE  H9   H  HCH2  0   0.187  -2.4941  -1.1453  -0.8462
 9JE  H10  H  HCH2  0   0.187  -2.5129  -1.0834   0.9145
 9JE  H11  H  HOH1  0   0.452   4.4352  -0.1887   0.0332
 9JE  H12  H  HOH1  0   0.452  -4.4406  -0.1879  -0.0108

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
 9JE  O01  C02  single  1.412  0.020  1.412
 9JE  C02  C03  single  1.516  0.020  1.516
 9JE  C03  C04  single  1.523  0.020  1.523
 9JE  C04  C05  single  1.524  0.020  1.524
 9JE  C05  C06  single  1.516  0.020  1.516
 9JE  O07  C06  single  1.412  0.020  1.412
 9JE  C02  H1   single  0.970  0.020  1.090
 9JE  C02  H2   single  0.970  0.020  1.090
 9JE  C03  H3   single  0.970  0.020  1.090
 9JE  C03  H4   single  0.970  0.020  1.090
 9JE  C04  H5   single  0.970  0.020  1.090
 9JE  C04  H6   single  0.970  0.020  1.090
 9JE  C05  H7   single  0.970  0.020  1.090
 9JE  C05  H8   single  0.970  0.020  1.090
 9JE  C06  H9   single  0.970  0.020  1.090
 9JE  C06  H10  single  0.970  0.020  1.090
 9JE  O01  H11  single  0.850  0.020  0.980
 9JE  O07  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
 9JE  H2   C02  H1   106.63  3.000
 9JE  H2   C02  O01  111.33  3.000
 9JE  H1   C02  O01  111.35  3.000
 9JE  H2   C02  C03  109.12  3.000
 9JE  H1   C02  C03  109.12  3.000
 9JE  O01  C02  C03  109.23  3.000
 9JE  H4   C03  H3   106.82  3.000
 9JE  H4   C03  C04  109.59  3.000
 9JE  H3   C03  C04  109.57  3.000
 9JE  H4   C03  C02  109.46  3.000
 9JE  H3   C03  C02  109.45  3.000
 9JE  C04  C03  C02  111.82  3.000
 9JE  H6   C04  H5   106.14  3.000
 9JE  H6   C04  C05  109.41  3.000
 9JE  H5   C04  C05  109.39  3.000
 9JE  H6   C04  C03  109.40  3.000
 9JE  H5   C04  C03  109.39  3.000
 9JE  C05  C04  C03  112.88  3.000
 9JE  H8   C05  H7   106.83  3.000
 9JE  H8   C05  C06  109.46  3.000
 9JE  H7   C05  C06  109.49  3.000
 9JE  H8   C05  C04  109.56  3.000
 9JE  H7   C05  C04  109.60  3.000
 9JE  C06  C05  C04  111.77  3.000
 9JE  H10  C06  H9   106.63  3.000
 9JE  H10  C06  O07  111.34  3.000
 9JE  H9   C06  O07  111.32  3.000
 9JE  H10  C06  C05  109.11  3.000
 9JE  H9   C06  C05  109.11  3.000
 9JE  O07  C06  C05  109.26  3.000
 9JE  H11  O01  C02  108.18  3.000
 9JE  H12  O07  C06  108.18  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
 9JE  Var_01  C05  C04  C03  C02  -179.78  30.0  3
 9JE  Var_02  C06  C05  C04  C03  -179.87  30.0  3
 9JE  Var_03  O01  C02  C03  C04  -179.99  30.0  1
 9JE  Var_04  O07  C06  C05  C04  -179.47  30.0  3

