# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 13:33:44 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: nonane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCC
#
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
 DD9  DD9  'nonane                   '  ligand  29  9  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DD9
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
 DD9  C1   C  CH3   0  -0.662   5.0814   0.3510  -0.0181
 DD9  C2   C  CH2   0  -0.419   3.8190  -0.5002  -0.0064
 DD9  C3   C  CH2   0  -0.406   2.5452   0.3365  -0.0126
 DD9  C4   C  CH2   0  -0.412   1.2709  -0.4986  -0.0026
 DD9  C5   C  CH2   0  -0.411   0.0018   0.3448  -0.0077
 DD9  C6   C  CH2   0  -0.412  -1.2760  -0.4851   0.0003
 DD9  C7   C  CH2   0  -0.406  -2.5418   0.3631  -0.0045
 DD9  C8   C  CH2   0  -0.419  -3.8241  -0.4606   0.0031
 DD9  C9   C  CH3   0  -0.662  -5.0777   0.4036  -0.0083
 DD9  H1   H  HCH3  0   0.215   5.1193   0.9848  -0.9063
 DD9  H1A  H  HCH3  0   0.215   5.1215   1.0058   0.8548
 DD9  H1B  H  HCH3  0   0.225   5.9833  -0.2623  -0.0121
 DD9  H2   H  HCH2  0   0.210   3.8175  -1.1673  -0.8742
 DD9  H2A  H  HCH2  0   0.210   3.8212  -1.1497   0.8746
 DD9  H3   H  HCH2  0   0.205   2.5478   1.0048   0.8562
 DD9  H3A  H  HCH2  0   0.205   2.5455   0.9881  -0.8940
 DD9  H4   H  HCH2  0   0.206   1.2668  -1.1657  -0.8722
 DD9  H4A  H  HCH2  0   0.206   1.2703  -1.1502   0.8786
 DD9  H5   H  HCH2  0   0.206   0.0065   1.0115   0.8621
 DD9  H5A  H  HCH2  0   0.206   0.0044   0.9973  -0.8882
 DD9  H6   H  HCH2  0   0.206  -1.2819  -1.1510  -0.8702
 DD9  H6A  H  HCH2  0   0.206  -1.2797  -1.1381   0.8805
 DD9  H7   H  HCH2  0   0.206  -2.5356   1.0296   0.8656
 DD9  H7A  H  HCH2  0   0.205  -2.5373   1.0166  -0.8845
 DD9  H8   H  HCH2  0   0.210  -3.8300  -1.1285  -0.8641
 DD9  H8A  H  HCH2  0   0.210  -3.8322  -1.1094   0.8846
 DD9  H9   H  HCH3  0   0.215  -5.1110   1.0586   0.8645
 DD9  H9A  H  HCH3  0   0.215  -5.1089   1.0376  -0.8966
 DD9  H9B  H  HCH3  0   0.225  -5.9857  -0.2005  -0.0021

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
 DD9  C2  C1   single  1.523  0.020  1.523
 DD9  C1  H1   single  0.970  0.020  1.090
 DD9  C1  H1A  single  0.970  0.020  1.090
 DD9  C1  H1B  single  0.970  0.020  1.090
 DD9  C3  C2   single  1.524  0.020  1.524
 DD9  C2  H2   single  0.970  0.020  1.090
 DD9  C2  H2A  single  0.970  0.020  1.090
 DD9  C4  C3   single  1.524  0.020  1.524
 DD9  C3  H3   single  0.970  0.020  1.090
 DD9  C3  H3A  single  0.970  0.020  1.090
 DD9  C5  C4   single  1.524  0.020  1.524
 DD9  C4  H4   single  0.970  0.020  1.090
 DD9  C4  H4A  single  0.970  0.020  1.090
 DD9  C6  C5   single  1.524  0.020  1.524
 DD9  C5  H5   single  0.970  0.020  1.090
 DD9  C5  H5A  single  0.970  0.020  1.090
 DD9  C7  C6   single  1.524  0.020  1.524
 DD9  C6  H6   single  0.970  0.020  1.090
 DD9  C6  H6A  single  0.970  0.020  1.090
 DD9  C8  C7   single  1.524  0.020  1.524
 DD9  C7  H7   single  0.970  0.020  1.090
 DD9  C7  H7A  single  0.970  0.020  1.090
 DD9  C9  C8   single  1.523  0.020  1.523
 DD9  C8  H8   single  0.970  0.020  1.090
 DD9  C8  H8A  single  0.970  0.020  1.090
 DD9  C9  H9   single  0.970  0.020  1.090
 DD9  C9  H9A  single  0.970  0.020  1.090
 DD9  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
 DD9  H1B  C1  H1A  107.60  3.000
 DD9  H1B  C1  H1   107.59  3.000
 DD9  H1A  C1  H1   107.52  3.000
 DD9  H1B  C1  C2   111.79  3.000
 DD9  H1A  C1  C2   111.07  3.000
 DD9  H1   C1  C2   111.07  3.000
 DD9  H2A  C2  H2   106.05  3.000
 DD9  H2A  C2  C3   109.31  3.000
 DD9  H2   C2  C3   109.28  3.000
 DD9  H2A  C2  C1   109.65  3.000
 DD9  H2   C2  C1   109.62  3.000
 DD9  C3   C2  C1   112.71  3.000
 DD9  H3A  C3  H3   105.96  3.000
 DD9  H3A  C3  C4   109.35  3.000
 DD9  H3   C3  C4   109.32  3.000
 DD9  H3A  C3  C2   109.23  3.000
 DD9  H3   C3  C2   109.24  3.000
 DD9  C4   C3  C2   113.46  3.000
 DD9  H4A  C4  H4   106.03  3.000
 DD9  H4A  C4  C5   109.35  3.000
 DD9  H4   C4  C5   109.34  3.000
 DD9  H4A  C4  C3   109.37  3.000
 DD9  H4   C4  C3   109.36  3.000
 DD9  C5   C4  C3   113.15  3.000
 DD9  H5A  C5  H5   105.99  3.000
 DD9  H5A  C5  C6   109.30  3.000
 DD9  H5   C5  C6   109.32  3.000
 DD9  H5A  C5  C4   109.28  3.000
 DD9  H5   C5  C4   109.30  3.000
 DD9  C6   C5  C4   113.39  3.000
 DD9  H6A  C6  H6   106.01  3.000
 DD9  H6A  C6  C7   109.36  3.000
 DD9  H6   C6  C7   109.35  3.000
 DD9  H6A  C6  C5   109.36  3.000
 DD9  H6   C6  C5   109.34  3.000
 DD9  C7   C6  C5   113.17  3.000
 DD9  H7A  C7  H7   105.95  3.000
 DD9  H7A  C7  C8   109.25  3.000
 DD9  H7   C7  C8   109.24  3.000
 DD9  H7A  C7  C6   109.33  3.000
 DD9  H7   C7  C6   109.35  3.000
 DD9  C8   C7  C6   113.45  3.000
 DD9  H8A  C8  H8   106.04  3.000
 DD9  H8A  C8  C9   109.65  3.000
 DD9  H8   C8  C9   109.63  3.000
 DD9  H8A  C8  C7   109.31  3.000
 DD9  H8   C8  C7   109.29  3.000
 DD9  C9   C8  C7   112.70  3.000
 DD9  H9B  C9  H9A  107.61  3.000
 DD9  H9B  C9  H9   107.60  3.000
 DD9  H9A  C9  H9   107.53  3.000
 DD9  H9B  C9  C8   111.78  3.000
 DD9  H9A  C9  C8   111.05  3.000
 DD9  H9   C9  C8   111.08  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
 DD9  Var_01  C4  C3  C2  C1   179.94  30.0  1
 DD9  Var_02  C5  C4  C3  C2   179.95  30.0  1
 DD9  Var_03  C6  C5  C4  C3   179.92  30.0  1
 DD9  Var_04  C7  C6  C5  C4   179.99  30.0  1
 DD9  Var_05  C8  C7  C6  C5   179.98  30.0  1
 DD9  Var_06  C9  C8  C7  C6  -179.74  30.0  1
 DD9  Var_07  H1  C1  C2  C3   -59.90  30.0  3
 DD9  Var_08  H9  C9  C8  C7   -59.77  30.0  3

