# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 01:46:56 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 1-nitrocyclohexene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)C1=CCCCC1
#
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
 NYH  NYH  '1-nitrocyclohexene       '  ligand  18  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_NYH
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
 NYH  C1A   C  C      0   0.254  -0.2574   0.0133  -0.0007
 NYH  N1A   N  N      1   0.354  -1.7100  -0.0167   0.0555
 NYH  O1N   O  O      0  -0.402  -2.3398   1.0038  -0.1140
 NYH  O2N   O  O     -1  -0.389  -2.2285  -1.0878   0.2831
 NYH  C2A   C  C1     0  -0.238   0.3480   1.1988  -0.0731
 NYH  C3A   C  CH2    0  -0.484   1.8307   1.3397  -0.0682
 NYH  C4A   C  CH2    0  -0.452   2.5441   0.0560   0.3342
 NYH  C5A   C  CH2    0  -0.453   1.9078  -1.1440  -0.3520
 NYH  C6A   C  CH2    0  -0.495   0.4459  -1.3065   0.0570
 NYH  H2A   H  H      0   0.293  -0.2376   2.1076  -0.1312
 NYH  H3A   H  HCH2   0   0.264   2.1396   1.6608  -1.0697
 NYH  H3AA  H  HCH2   0   0.267   2.0997   2.1665   0.5939
 NYH  H4A   H  HCH2   0   0.247   3.6035   0.1268   0.0843
 NYH  H4AA  H  HCH2   0   0.232   2.4831  -0.0696   1.4190
 NYH  H5A   H  HCH2   0   0.232   1.9709  -1.0190  -1.4370
 NYH  H5AA  H  HCH2   0   0.248   2.4498  -2.0585  -0.1084
 NYH  H6A   H  HCH2   0   0.259   0.3823  -1.7192   1.0682
 NYH  H6AA  H  HCH2   0   0.266  -0.0418  -2.0276  -0.6010

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
 NYH  C1A  N1A   single  1.454  0.020  1.454
 NYH  C1A  C2A   double  1.333  0.020  1.333
 NYH  C1A  C6A   single  1.497  0.020  1.497
 NYH  N1A  O1N   double  1.211  0.020  1.211
 NYH  N1A  O2N   single  1.212  0.020  1.212
 NYH  C2A  C3A   single  1.489  0.020  1.489
 NYH  C3A  C4A   single  1.523  0.020  1.523
 NYH  C4A  C5A   single  1.522  0.020  1.522
 NYH  C5A  C6A   single  1.527  0.020  1.527
 NYH  C2A  H2A   single  0.930  0.020  1.080
 NYH  C3A  H3A   single  0.970  0.020  1.090
 NYH  C3A  H3AA  single  0.970  0.020  1.090
 NYH  C4A  H4A   single  0.970  0.020  1.090
 NYH  C4A  H4AA  single  0.970  0.020  1.090
 NYH  C5A  H5A   single  0.970  0.020  1.090
 NYH  C5A  H5AA  single  0.970  0.020  1.090
 NYH  C6A  H6A   single  0.970  0.020  1.090
 NYH  C6A  H6AA  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
 NYH  C6A   C1A  C2A  124.96  3.000
 NYH  C6A   C1A  N1A  116.73  3.000
 NYH  C2A   C1A  N1A  118.30  3.000
 NYH  O2N   N1A  O1N  123.28  3.000
 NYH  O2N   N1A  C1A  116.94  3.000
 NYH  O1N   N1A  C1A  119.79  3.000
 NYH  H2A   C2A  C3A  117.33  3.000
 NYH  H2A   C2A  C1A  120.25  3.000
 NYH  C3A   C2A  C1A  122.41  3.000
 NYH  H3AA  C3A  H3A  105.22  3.000
 NYH  H3AA  C3A  C4A  111.25  3.000
 NYH  H3A   C3A  C4A  110.88  3.000
 NYH  H3AA  C3A  C2A  108.58  3.000
 NYH  H3A   C3A  C2A  107.77  3.000
 NYH  C4A   C3A  C2A  112.80  3.000
 NYH  H4AA  C4A  H4A  106.80  3.000
 NYH  H4AA  C4A  C5A  109.48  3.000
 NYH  H4A   C4A  C5A  110.73  3.000
 NYH  H4AA  C4A  C3A  109.43  3.000
 NYH  H4A   C4A  C3A  109.86  3.000
 NYH  C5A   C4A  C3A  110.47  3.000
 NYH  H5AA  C5A  H5A  106.77  3.000
 NYH  H5AA  C5A  C6A  109.07  3.000
 NYH  H5A   C5A  C6A  109.46  3.000
 NYH  H5AA  C5A  C4A  110.65  3.000
 NYH  H5A   C5A  C4A  109.45  3.000
 NYH  C6A   C5A  C4A  111.32  3.000
 NYH  H6AA  C6A  H6A  106.38  3.000
 NYH  H6AA  C6A  C5A  109.68  3.000
 NYH  H6A   C6A  C5A  110.08  3.000
 NYH  H6AA  C6A  C1A  110.46  3.000
 NYH  H6A   C6A  C1A  109.94  3.000
 NYH  C5A   C6A  C1A  110.23  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
 NYH  Var_01  C4A  C3A  C2A  C1A  -12.77  30.0  1
 NYH  Var_02  C4A  C5A  C6A  C1A   46.00  30.0  1
 NYH  Var_03  C5A  C6A  C1A  C2A  -15.20  30.0  1
 NYH  Var_04  C5A  C4A  C3A  C2A   43.37  30.0  1
 NYH  Var_05  C6A  C1A  C2A  C3A   -1.68  30.0  1
 NYH  Var_06  C6A  C5A  C4A  C3A  -61.59  30.0  1
 NYH  Var_07  C2A  C1A  N1A  O1N    8.23  30.0  2

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
 NYH  plan-1  C1A  0.020
 NYH  plan-1  N1A  0.020
 NYH  plan-1  O1N  0.020
 NYH  plan-1  O2N  0.020

