# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 20:32:41 2021
#   Inital geometry file: a 45 line input string
#   Ligand name: pentane-1,1-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC(O)O
#
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
 DK9  DK9  'pentane-1,1-diol         '  ligand  19  7  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DK9
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
 DK9  O4   O  OH1   0  -0.673  -59.9013  -21.9461  -22.3307
 DK9  C4   C  CH1   0   0.267  -60.3270  -20.8039  -23.0402
 DK9  O3   O  OH1   0  -0.660  -60.1557  -21.0642  -24.3931
 DK9  C5   C  CH2   0  -0.486  -59.5445  -19.5578  -22.6478
 DK9  C6   C  CH2   0  -0.418  -58.0218  -19.6352  -22.7488
 DK9  C7   C  CH2   0  -0.417  -57.4376  -19.5206  -24.1538
 DK9  C8   C  CH3   0  -0.662  -55.9161  -19.4542  -24.1342
 DK9  H1   H  HOH1  0   0.450  -60.1423  -21.8359  -21.4048
 DK9  H2   H  HOH1  0   0.456  -60.7832  -21.7452  -24.6584
 DK9  H3   H  HCH2  0   0.223  -59.9210  -18.7128  -23.2329
 DK9  H4   H  HCH2  0   0.232  -59.8142  -19.3367  -21.6104
 DK9  H5   H  HCH2  0   0.211  -57.6686  -20.5575  -22.2780
 DK9  H6   H  HCH2  0   0.215  -57.6097  -18.8209  -22.1440
 DK9  H7   H  HCH2  0   0.204  -57.8353  -18.6221  -24.6369
 DK9  H8   H  HCH2  0   0.220  -57.7594  -20.3626  -24.7671
 DK9  H9   H  HCH3  0   0.224  -55.5051  -19.3799  -25.1420
 DK9  H10  H  HCH3  0   0.213  -55.5645  -18.5883  -23.5695
 DK9  H11  H  HCH3  0   0.214  -55.4870  -20.3438  -23.6691
 DK9  H12  H  HCH1  0   0.188  -61.3909  -20.6182  -22.8184

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
 DK9  O3  C4   single  1.388  0.020  1.388
 DK9  C8  C7   single  1.523  0.020  1.523
 DK9  C7  C6   single  1.526  0.020  1.526
 DK9  C4  C5   single  1.523  0.020  1.523
 DK9  C4  O4   single  1.410  0.020  1.410
 DK9  C6  C5   single  1.528  0.020  1.528
 DK9  O4  H1   single  0.850  0.020  0.980
 DK9  O3  H2   single  0.850  0.020  0.980
 DK9  C5  H3   single  0.970  0.020  1.090
 DK9  C5  H4   single  0.970  0.020  1.090
 DK9  C6  H5   single  0.970  0.020  1.090
 DK9  C6  H6   single  0.970  0.020  1.090
 DK9  C7  H7   single  0.970  0.020  1.090
 DK9  C7  H8   single  0.970  0.020  1.090
 DK9  C8  H9   single  0.970  0.020  1.090
 DK9  C8  H10  single  0.970  0.020  1.090
 DK9  C8  H11  single  0.970  0.020  1.090
 DK9  C4  H12  single  0.970  0.020  1.090

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
 DK9  H1   O4  C4   108.38  3.000
 DK9  H12  C4  C5   107.83  3.000
 DK9  H12  C4  O3   110.28  3.000
 DK9  C5   C4  O3   109.94  3.000
 DK9  H12  C4  O4   109.05  3.000
 DK9  C5   C4  O4   112.21  3.000
 DK9  O3   C4  O4   107.53  3.000
 DK9  H2   O3  C4   108.69  3.000
 DK9  H4   C5  H3   105.42  3.000
 DK9  H4   C5  C6   108.57  3.000
 DK9  H3   C5  C6   110.27  3.000
 DK9  H4   C5  C4   106.44  3.000
 DK9  H3   C5  C4   108.49  3.000
 DK9  C6   C5  C4   116.98  3.000
 DK9  H6   C6  H5   105.53  3.000
 DK9  H6   C6  C7   107.98  3.000
 DK9  H5   C6  C7   109.63  3.000
 DK9  H6   C6  C5   107.51  3.000
 DK9  H5   C6  C5   109.63  3.000
 DK9  C7   C6  C5   116.02  3.000
 DK9  H8   C7  H7   106.16  3.000
 DK9  H8   C7  C8   109.62  3.000
 DK9  H7   C7  C8   109.44  3.000
 DK9  H8   C7  C6   110.30  3.000
 DK9  H7   C7  C6   109.19  3.000
 DK9  C8   C7  C6   111.96  3.000
 DK9  H11  C8  H10  107.42  3.000
 DK9  H11  C8  H9   107.52  3.000
 DK9  H10  C8  H9   107.61  3.000
 DK9  H11  C8  C7   111.25  3.000
 DK9  H10  C8  C7   111.28  3.000
 DK9  H9   C8  C7   111.56  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
 DK9  Var_01  C6  C5  C4  O4   54.43  30.0  3
 DK9  Var_02  C7  C6  C5  C4   77.15  30.0  1
 DK9  Var_03  C8  C7  C6  C5  173.69  30.0  1
 DK9  Var_04  H9  C8  C7  C6  179.57  30.0  3

