# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 18:55:31 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  29  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   0.550   4.0083  -0.1306   0.0150
 KNA  O1   O  OH1   0  -0.599   5.0551   0.6897  -0.0361
 KNA  C2   C  CH2   0  -0.580   2.7079   0.6234   0.0130
 KNA  O2   O  O     0  -0.447   4.1193  -1.3308   0.0603
 KNA  C3   C  CH2   0  -0.418   1.4761  -0.2670   0.0194
 KNA  C4   C  CH2   0  -0.415   0.1890   0.5487   0.0200
 KNA  C5   C  CH2   0  -0.412  -1.0624  -0.3203   0.0173
 KNA  C6   C  CH2   0  -0.412  -2.3538   0.4874   0.0161
 KNA  C7   C  CH2   0  -0.407  -3.6054  -0.3815   0.0163
 KNA  C8   C  CH2   0  -0.419  -4.9002   0.4224   0.0130
 KNA  C9   C  CH3   0  -0.662  -6.1404  -0.4610   0.0144
 KNA  HO1  H  HOH1  0   0.478   5.8768   0.1765  -0.0289
 KNA  H2   H  HCH2  0   0.276   2.7030   1.2885   0.8834
 KNA  H2A  H  HCH2  0   0.274   2.6984   1.2866  -0.8580
 KNA  H3   H  HCH2  0   0.224   1.4884  -0.9249  -0.8541
 KNA  H3A  H  HCH2  0   0.225   1.4933  -0.9181   0.8977
 KNA  H4   H  HCH2  0   0.212   0.1728   1.2055   0.8968
 KNA  H4A  H  HCH2  0   0.212   0.1740   1.2094  -0.8541
 KNA  H5   H  HCH2  0   0.209  -1.0445  -0.9783  -0.8588
 KNA  H5A  H  HCH2  0   0.209  -1.0468  -0.9803   0.8919
 KNA  H6   H  HCH2  0   0.207  -2.3700   1.1472   0.8909
 KNA  H6A  H  HCH2  0   0.207  -2.3695   1.1456  -0.8601
 KNA  H7   H  HCH2  0   0.206  -3.5883  -1.0428  -0.8576
 KNA  H7A  H  HCH2  0   0.206  -3.5904  -1.0397   0.8928
 KNA  H8   H  HCH2  0   0.210  -4.9179   1.0831   0.8856
 KNA  H8A  H  HCH2  0   0.210  -4.9165   1.0781  -0.8634
 KNA  H9   H  HCH3  0   0.215  -6.1612  -1.1090  -0.8641
 KNA  H9A  H  HCH3  0   0.216  -6.1639  -1.1028   0.8972
 KNA  H9B  H  HCH3  0   0.226  -7.0576   0.1294   0.0109

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   double  1.206  0.020  1.206
 KNA  C1  C2   single  1.503  0.020  1.503
 KNA  C1  O1   single  1.331  0.020  1.331
 KNA  O1  HO1  single  0.850  0.020  0.980
 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  1.523  0.020  1.523
 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   125.36  3.000
 KNA  C2   C1  O1   111.80  3.000
 KNA  O2   C1  O1   122.84  3.000
 KNA  HO1  O1  C1   109.90  3.000
 KNA  H2A  C2  H2   105.33  3.000
 KNA  H2A  C2  C3   110.57  3.000
 KNA  H2   C2  C3   110.41  3.000
 KNA  H2A  C2  C1   108.20  3.000
 KNA  H2   C2  C1   107.89  3.000
 KNA  C3   C2  C1   114.03  3.000
 KNA  H3A  C3  H3   106.45  3.000
 KNA  H3A  C3  C4   109.38  3.000
 KNA  H3   C3  C4   109.38  3.000
 KNA  H3A  C3  C2   109.84  3.000
 KNA  H3   C3  C2   109.87  3.000
 KNA  C4   C3  C2   111.77  3.000
 KNA  H4A  C4  H4   106.06  3.000
 KNA  H4A  C4  C5   109.34  3.000
 KNA  H4   C4  C5   109.34  3.000
 KNA  H4A  C4  C3   109.51  3.000
 KNA  H4   C4  C3   109.49  3.000
 KNA  C5   C4  C3   112.86  3.000
 KNA  H5A  C5  H5   106.03  3.000
 KNA  H5A  C5  C6   109.39  3.000
 KNA  H5   C5  C6   109.37  3.000
 KNA  H5A  C5  C4   109.30  3.000
 KNA  H5   C5  C4   109.30  3.000
 KNA  C6   C5  C4   113.20  3.000
 KNA  H6A  C6  H6   106.05  3.000
 KNA  H6A  C6  C7   109.32  3.000
 KNA  H6   C6  C7   109.34  3.000
 KNA  H6A  C6  C5   109.34  3.000
 KNA  H6   C6  C5   109.34  3.000
 KNA  C7   C6  C5   113.21  3.000
 KNA  H7A  C7  H7   105.96  3.000
 KNA  H7A  C7  C8   109.27  3.000
 KNA  H7   C7  C8   109.26  3.000
 KNA  H7A  C7  C6   109.34  3.000
 KNA  H7   C7  C6   109.34  3.000
 KNA  C8   C7  C6   113.39  3.000
 KNA  H8A  C8  H8   106.05  3.000
 KNA  H8A  C8  C9   109.63  3.000
 KNA  H8   C8  C9   109.65  3.000
 KNA  H8A  C8  C7   109.29  3.000
 KNA  H8   C8  C7   109.30  3.000
 KNA  C9   C8  C7   112.70  3.000
 KNA  H9B  C9  H9A  107.62  3.000
 KNA  H9B  C9  H9   107.62  3.000
 KNA  H9A  C9  H9   107.54  3.000
 KNA  H9B  C9  C8   111.77  3.000
 KNA  H9A  C9  C8   111.06  3.000
 KNA  H9   C9  C8   111.05  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  CONST_01  HO1  O1  C1  C2   180.00   0.0  0
 KNA  Var_01    C4   C3  C2  C1   179.88  30.0  1
 KNA  Var_02    C3   C2  C1  O1   177.90  30.0  3
 KNA  Var_03    C5   C4  C3  C2   179.63  30.0  3
 KNA  Var_04    C6   C5  C4  C3  -179.93  30.0  1
 KNA  Var_05    C7   C6  C5  C4  -179.88  30.0  3
 KNA  Var_06    C8   C7  C6  C5  -179.91  30.0  3
 KNA  Var_07    C9   C8  C7  C6  -179.95  30.0  3
 KNA  Var_08    H9   C9  C8  C7   -59.75  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
 KNA  plan-1  HO1  0.020

