# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 15:22:37 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: 1-nitrohexane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC[N+]([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
 N6C  N6C  '1-nitrohexane            '  ligand  22  9  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_N6C
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
 N6C  O1   O  O      0  -0.385   2.8703  -1.0783   0.4856
 N6C  N1   N  N      1   0.438   2.8193   0.0164  -0.0170
 N6C  O2   O  O     -1  -0.393   3.7898   0.6649  -0.3286
 N6C  C1   C  CH2    0  -0.318   1.4856   0.6371  -0.2771
 N6C  C2   C  CH2    0  -0.456   0.3048  -0.2339   0.0860
 N6C  C3   C  CH2    0  -0.425  -0.9962   0.5101  -0.2039
 N6C  C4   C  CH2    0  -0.406  -2.2285  -0.3196   0.1333
 N6C  C5   C  CH2    0  -0.418  -3.5350   0.4149  -0.1419
 N6C  C6   C  CH3    0  -0.661  -4.7635  -0.4137   0.2081
 N6C  H1   H  HCH2   0   0.297   1.4941   1.5698   0.2888
 N6C  H1A  H  HCH2   0   0.296   1.4929   0.8951  -1.3367
 N6C  H2   H  HCH2   0   0.243   0.3300  -1.1622  -0.4882
 N6C  H2A  H  HCH2   0   0.243   0.3423  -0.5007   1.1439
 N6C  H3   H  HCH2   0   0.221  -1.0185   1.4424   0.3692
 N6C  H3A  H  HCH2   0   0.221  -1.0292   0.7959  -1.2600
 N6C  H4   H  HCH2   0   0.211  -2.2085  -1.2504  -0.4430
 N6C  H4A  H  HCH2   0   0.211  -2.1920  -0.6115   1.1881
 N6C  H5   H  HCH2   0   0.211  -3.5511   1.3498   0.4262
 N6C  H5A  H  HCH2   0   0.212  -3.5742   0.6994  -1.1978
 N6C  H6   H  HCH3   0   0.216  -4.7929  -1.3401  -0.3685
 N6C  H6A  H  HCH3   0   0.216  -4.7687  -0.6841   1.2656
 N6C  H6B  H  HCH3   0   0.226  -5.6854   0.1316   0.0027

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
 N6C  O1  N1   double  1.206  0.020  1.206
 N6C  N1  O2   single  1.208  0.020  1.208
 N6C  N1  C1   single  1.494  0.020  1.494
 N6C  C1  C2   single  1.512  0.020  1.512
 N6C  C2  C3   single  1.526  0.020  1.526
 N6C  C3  C4   single  1.523  0.020  1.523
 N6C  C4  C5   single  1.524  0.020  1.524
 N6C  C5  C6   single  1.523  0.020  1.523
 N6C  C1  H1   single  0.970  0.020  1.090
 N6C  C1  H1A  single  0.970  0.020  1.090
 N6C  C2  H2   single  0.970  0.020  1.090
 N6C  C2  H2A  single  0.970  0.020  1.090
 N6C  C3  H3   single  0.970  0.020  1.090
 N6C  C3  H3A  single  0.970  0.020  1.090
 N6C  C4  H4   single  0.970  0.020  1.090
 N6C  C4  H4A  single  0.970  0.020  1.090
 N6C  C5  H5   single  0.970  0.020  1.090
 N6C  C5  H5A  single  0.970  0.020  1.090
 N6C  C6  H6   single  0.970  0.020  1.090
 N6C  C6  H6A  single  0.970  0.020  1.090
 N6C  C6  H6B  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
 N6C  C1   N1  O2   116.70  3.000
 N6C  C1   N1  O1   119.19  3.000
 N6C  O2   N1  O1   124.11  3.000
 N6C  H1A  C1  H1   107.56  3.000
 N6C  H1A  C1  C2   112.02  3.000
 N6C  H1   C1  C2   111.96  3.000
 N6C  H1A  C1  N1   105.16  3.000
 N6C  H1   C1  N1   104.95  3.000
 N6C  C2   C1  N1   114.59  3.000
 N6C  H2A  C2  H2   107.52  3.000
 N6C  H2A  C2  C3   109.42  3.000
 N6C  H2   C2  C3   109.52  3.000
 N6C  H2A  C2  C1   110.29  3.000
 N6C  H2   C2  C1   110.21  3.000
 N6C  C3   C2  C1   109.84  3.000
 N6C  H3A  C3  H3   106.39  3.000
 N6C  H3A  C3  C4   109.35  3.000
 N6C  H3   C3  C4   109.36  3.000
 N6C  H3A  C3  C2   109.65  3.000
 N6C  H3   C3  C2   109.45  3.000
 N6C  C4   C3  C2   112.46  3.000
 N6C  H4A  C4  H4   106.25  3.000
 N6C  H4A  C4  C5   109.34  3.000
 N6C  H4   C4  C5   109.29  3.000
 N6C  H4A  C4  C3   109.35  3.000
 N6C  H4   C4  C3   109.37  3.000
 N6C  C5   C4  C3   113.02  3.000
 N6C  H5A  C5  H5   106.17  3.000
 N6C  H5A  C5  C6   109.54  3.000
 N6C  H5   C5  C6   109.50  3.000
 N6C  H5A  C5  C4   109.29  3.000
 N6C  H5   C5  C4   109.31  3.000
 N6C  C6   C5  C4   112.82  3.000
 N6C  H6B  C6  H6A  107.59  3.000
 N6C  H6B  C6  H6   107.59  3.000
 N6C  H6A  C6  H6   107.54  3.000
 N6C  H6B  C6  C5   111.51  3.000
 N6C  H6A  C6  C5   111.18  3.000
 N6C  H6   C6  C5   111.23  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
 N6C  Var_01  C2  C1  N1  O1    -2.27  30.0  3
 N6C  Var_02  C3  C2  C1  N1   179.20  30.0  3
 N6C  Var_03  C4  C3  C2  C1   179.63  30.0  3
 N6C  Var_04  C5  C4  C3  C2   179.59  30.0  3
 N6C  Var_05  C6  C5  C4  C3  -179.49  30.0  3
 N6C  Var_06  H6  C6  C5  C4   -59.89  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
 N6C  plan-1  O1  0.020
 N6C  plan-1  N1  0.020
 N6C  plan-1  O2  0.020
 N6C  plan-1  C1  0.020

