# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 18:43:36 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: nonanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCC(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
 KNA  KNA  'nonanoic acid            '  ligand  28  11  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KNA
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
 KNA  C1   C  C      0   0.409   4.0639  -0.0449  -0.0404
 KNA  O1   O  OC    -1  -0.635   5.0730   0.6766  -0.1939
 KNA  C2   C  CH2    0  -0.581   2.7097   0.6861  -0.0170
 KNA  O2   O  O      0  -0.610   4.0610  -1.2836   0.1023
 KNA  C3   C  CH2    0  -0.402   1.4722  -0.1964   0.0087
 KNA  C4   C  CH2    0  -0.409   0.1754   0.6044   0.0139
 KNA  C5   C  CH2    0  -0.410  -1.0724  -0.2699   0.0193
 KNA  C6   C  CH2    0  -0.411  -2.3699   0.5286   0.0213
 KNA  C7   C  CH2    0  -0.406  -3.6164  -0.3477   0.0141
 KNA  C8   C  CH2    0  -0.419  -4.9163   0.4477   0.0172
 KNA  C9   C  CH3    0  -0.662  -6.1512  -0.4429   0.0038
 KNA  H2   H  HCH2   0   0.217   2.7008   1.3521   0.8552
 KNA  H2A  H  HCH2   0   0.212   2.6656   1.3578  -0.8821
 KNA  H3   H  HCH2   0   0.199   1.4770  -0.8657  -0.8575
 KNA  H3A  H  HCH2   0   0.200   1.4985  -0.8466   0.8881
 KNA  H4   H  HCH2   0   0.202   0.1573   1.2666   0.8874
 KNA  H4A  H  HCH2   0   0.201   0.1488   1.2640  -0.8616
 KNA  H5   H  HCH2   0   0.204  -1.0548  -0.9297  -0.8557
 KNA  H5A  H  HCH2   0   0.204  -1.0499  -0.9296   0.8942
 KNA  H6   H  HCH2   0   0.205  -2.3920   1.1849   0.8987
 KNA  H6A  H  HCH2   0   0.205  -2.3887   1.1914  -0.8514
 KNA  H7   H  HCH2   0   0.205  -3.5947  -1.0011  -0.8658
 KNA  H7A  H  HCH2   0   0.205  -3.5975  -1.0140   0.8842
 KNA  H8   H  HCH2   0   0.210  -4.9410   1.0975   0.8977
 KNA  H8A  H  HCH2   0   0.210  -4.9344   1.1142  -0.8509
 KNA  H9   H  HCH3   0   0.215  -6.1662  -1.0793  -0.8832
 KNA  H9A  H  HCH3   0   0.215  -6.1734  -1.0969   0.8776
 KNA  H9B  H  HCH3   0   0.225  -7.0718   0.1418   0.0056

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
 KNA  O2  C1   deloc   1.247  0.020  1.247
 KNA  C1  C2   single  1.539  0.020  1.539
 KNA  C1  O1   deloc   1.250  0.020  1.250
 KNA  C3  C2   single  1.520  0.020  1.520
 KNA  C2  H2   single  0.970  0.020  1.090
 KNA  C2  H2A  single  0.970  0.020  1.090
 KNA  C3  C4   single  1.524  0.020  1.524
 KNA  C3  H3   single  0.970  0.020  1.090
 KNA  C3  H3A  single  0.970  0.020  1.090
 KNA  C5  C4   single  1.524  0.020  1.524
 KNA  C4  H4   single  0.970  0.020  1.090
 KNA  C4  H4A  single  0.970  0.020  1.090
 KNA  C5  C6   single  1.524  0.020  1.524
 KNA  C5  H5   single  0.970  0.020  1.090
 KNA  C5  H5A  single  0.970  0.020  1.090
 KNA  C6  C7   single  1.524  0.020  1.524
 KNA  C6  H6   single  0.970  0.020  1.090
 KNA  C6  H6A  single  0.970  0.020  1.090
 KNA  C7  C8   single  1.524  0.020  1.524
 KNA  C7  H7   single  0.970  0.020  1.090
 KNA  C7  H7A  single  0.970  0.020  1.090
 KNA  C8  C9   single  1.523  0.020  1.523
 KNA  C8  H8   single  0.970  0.020  1.090
 KNA  C8  H8A  single  0.970  0.020  1.090
 KNA  C9  H9   single  0.970  0.020  1.090
 KNA  C9  H9A  single  0.970  0.020  1.090
 KNA  C9  H9B  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
 KNA  O2   C1  C2   117.91  3.000
 KNA  C2   C1  O1   115.98  3.000
 KNA  O2   C1  O1   126.11  3.000
 KNA  H2A  C2  H2   104.78  3.000
 KNA  H2A  C2  C3   109.65  3.000
 KNA  H2   C2  C3   109.40  3.000
 KNA  H2A  C2  C1   108.33  3.000
 KNA  H2   C2  C1   107.91  3.000
 KNA  C3   C2  C1   116.16  3.000
 KNA  H3A  C3  H3   105.82  3.000
 KNA  H3A  C3  C4   109.27  3.000
 KNA  H3   C3  C4   109.13  3.000
 KNA  H3A  C3  C2   109.82  3.000
 KNA  H3   C3  C2   109.75  3.000
 KNA  C4   C3  C2   112.81  3.000
 KNA  H4A  C4  H4   105.81  3.000
 KNA  H4A  C4  C5   109.15  3.000
 KNA  H4   C4  C5   109.29  3.000
 KNA  H4A  C4  C3   109.52  3.000
 KNA  H4   C4  C3   109.52  3.000
 KNA  C5   C4  C3   113.28  3.000
 KNA  H5A  C5  H5   105.94  3.000
 KNA  H5A  C5  C6   109.38  3.000
 KNA  H5   C5  C6   109.28  3.000
 KNA  H5A  C5  C4   109.35  3.000
 KNA  H5   C5  C4   109.24  3.000
 KNA  C6   C5  C4   113.37  3.000
 KNA  H6A  C6  H6   105.96  3.000
 KNA  H6A  C6  C7   109.27  3.000
 KNA  H6   C6  C7   109.38  3.000
 KNA  H6A  C6  C5   109.30  3.000
 KNA  H6   C6  C5   109.40  3.000
 KNA  C7   C6  C5   113.28  3.000
 KNA  H7A  C7  H7   105.94  3.000
 KNA  H7A  C7  C8   109.29  3.000
 KNA  H7   C7  C8   109.25  3.000
 KNA  H7A  C7  C6   109.38  3.000
 KNA  H7   C7  C6   109.30  3.000
 KNA  C8   C7  C6   113.43  3.000
 KNA  H8A  C8  H8   106.02  3.000
 KNA  H8A  C8  C9   109.62  3.000
 KNA  H8   C8  C9   109.64  3.000
 KNA  H8A  C8  C7   109.29  3.000
 KNA  H8   C8  C7   109.32  3.000
 KNA  C9   C8  C7   112.74  3.000
 KNA  H9B  C9  H9A  107.62  3.000
 KNA  H9B  C9  H9   107.59  3.000
 KNA  H9A  C9  H9   107.51  3.000
 KNA  H9B  C9  C8   111.78  3.000
 KNA  H9A  C9  C8   111.09  3.000
 KNA  H9   C9  C8   111.06  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
 KNA  Var_01  C4  C3  C2  C1  -179.31  30.0  1
 KNA  Var_02  C3  C2  C1  O1   173.23  30.0  3
 KNA  Var_03  C5  C4  C3  C2   179.17  30.0  3
 KNA  Var_04  C6  C5  C4  C3  -179.87  30.0  1
 KNA  Var_05  C7  C6  C5  C4   179.48  30.0  3
 KNA  Var_06  C8  C7  C6  C5   179.95  30.0  3
 KNA  Var_07  C9  C8  C7  C6   179.75  30.0  3
 KNA  Var_08  H9  C9  C8  C7   -59.79  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 KNA  plan-1  C1  0.020
 KNA  plan-1  O1  0.020
 KNA  plan-1  C2  0.020
 KNA  plan-1  O2  0.020

