# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 14:35:58 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (2E,4E)-2-amino-6-oxohexa-2,4-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=C/C=C/C=O)/C(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
 6OD  6OD  '(2E,4E)-2-amino-6-oxohexa-2,4-dienoic acid'  ligand  16  10  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6OD
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
 6OD  O2  O  O      0  -0.559   1.2945   1.6795   0.0279
 6OD  C5  C  C      0   0.403   2.0869   0.7278   0.0073
 6OD  O1  O  OC    -1  -0.584   3.3287   0.7718   0.0349
 6OD  C4  C  C      0   0.213   1.4966  -0.7039  -0.0635
 6OD  N   N  NH2    0  -0.794   2.4355  -1.6466  -0.1283
 6OD  C3  C  C1     0  -0.400   0.1597  -1.0473  -0.0657
 6OD  C2  C  C1     0  -0.205  -0.9483  -0.1798  -0.0008
 6OD  C1  C  C1     0  -0.391  -2.2563  -0.5812  -0.0037
 6OD  C   C  C1     0   0.106  -3.2939   0.3986   0.0670
 6OD  O   O  O      0  -0.475  -4.5002   0.1823   0.0725
 6OD  H2  H  HNH2   0   0.398   3.4012  -1.3649  -0.1016
 6OD  H3  H  H      0   0.231  -0.0617  -2.1116  -0.1210
 6OD  H5  H  H      0   0.268  -0.7480   0.8835   0.0566
 6OD  H7  H  H      0   0.233  -2.5257  -1.6318  -0.0598
 6OD  H9  H  H      0   0.157  -2.9216   1.4416   0.1201
 6OD  H4  H  HNH2   0   0.399   2.2124  -2.6271  -0.1515

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
 6OD  N   C4  single  1.332  0.020  1.332
 6OD  O2  C5  deloc   1.239  0.020  1.239
 6OD  C4  C5  single  1.550  0.020  1.550
 6OD  C4  C3  double  1.380  0.020  1.380
 6OD  C5  O1  deloc   1.243  0.020  1.243
 6OD  C3  C2  single  1.409  0.020  1.409
 6OD  C2  C1  double  1.368  0.020  1.368
 6OD  C1  C   single  1.429  0.020  1.429
 6OD  O   C   double  1.226  0.020  1.226
 6OD  N   H2  single  0.860  0.020  1.020
 6OD  C3  H3  single  0.930  0.020  1.080
 6OD  C2  H5  single  0.930  0.020  1.080
 6OD  C1  H7  single  0.930  0.020  1.080
 6OD  C   H9  single  0.930  0.020  1.080
 6OD  N   H4  single  0.860  0.020  1.020

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
 6OD  C4  C5  O1  114.47  3.000
 6OD  O1  C5  O2  127.71  3.000
 6OD  C4  C5  O2  117.82  3.000
 6OD  C3  C4  N   120.43  3.000
 6OD  C3  C4  C5  126.78  3.000
 6OD  N   C4  C5  112.79  3.000
 6OD  H4  N   H2  119.10  3.000
 6OD  H4  N   C4  122.32  3.000
 6OD  H2  N   C4  118.49  3.000
 6OD  H3  C3  C2  116.39  3.000
 6OD  H3  C3  C4  116.13  3.000
 6OD  C2  C3  C4  127.48  3.000
 6OD  H5  C2  C1  117.70  3.000
 6OD  H5  C2  C3  117.47  3.000
 6OD  C1  C2  C3  124.83  3.000
 6OD  H7  C1  C   119.06  3.000
 6OD  H7  C1  C2  121.40  3.000
 6OD  C   C1  C2  119.53  3.000
 6OD  H9  C   O   119.76  3.000
 6OD  H9  C   C1  113.81  3.000
 6OD  O   C   C1  126.44  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
 6OD  Var_01  C2  C3  C4  C5    -0.20   0.0  2
 6OD  Var_02  C   C1  C2  C3   179.97   0.0  2
 6OD  Var_03  N   C4  C5  O2   177.77  30.0  2
 6OD  Var_04  C1  C2  C3  C4  -179.84  30.0  2
 6OD  Var_05  O   C   C1  C2   179.97  30.0  2
 6OD  Var_06  H2  N   C4  C5     1.59  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
 6OD  plan-1  O2  0.020
 6OD  plan-1  C5  0.020
 6OD  plan-1  O1  0.020
 6OD  plan-1  C4  0.020
 6OD  plan-2  C5  0.020
 6OD  plan-2  C4  0.020
 6OD  plan-2  N   0.020
 6OD  plan-2  C3  0.020
 6OD  plan-2  C2  0.020
 6OD  plan-2  H3  0.020
 6OD  plan-3  C3  0.020
 6OD  plan-3  C2  0.020
 6OD  plan-3  C1  0.020
 6OD  plan-3  C   0.020
 6OD  plan-3  H5  0.020
 6OD  plan-3  H7  0.020
 6OD  plan-4  C1  0.020
 6OD  plan-4  C   0.020
 6OD  plan-4  O   0.020
 6OD  plan-4  H9  0.020

