# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 18:48:27 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 1-methyl-5-oxidanyl-4-oxidanylidene-pyridine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C=C(O)C(=O)C=C1C(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
 E7Z  E7Z  '1-methyl-5-oxidanyl-4-oxidanylidene-pyridine-2-carboxylic acid'  ligand  19  12  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E7Z
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
 E7Z  C4  C  CR6   0   0.361   1.5346   0.9997  -0.0498
 E7Z  C5  C  CR16  0  -0.470   0.1201   1.1942  -0.0411
 E7Z  C6  C  CR6   0   0.285  -0.7608   0.1460  -0.0213
 E7Z  C7  C  C     0   0.508  -2.2272   0.4186  -0.1446
 E7Z  N   N  NR6   0  -0.495  -0.3319  -1.1352   0.0219
 E7Z  C1  C  CH3   0  -0.527  -1.2288  -2.2910   0.1041
 E7Z  C2  C  CR16  0  -0.102   1.0078  -1.3826   0.0285
 E7Z  C3  C  CR6   0   0.188   1.9311  -0.3883  -0.0144
 E7Z  O1  O  O     0  -0.523   2.3917   1.8975  -0.0781
 E7Z  O2  O  O     0  -0.412  -2.9807  -0.2495  -0.8028
 E7Z  O3  O  OH1   0  -0.573  -2.5725   1.5026   0.5217
 E7Z  O4  O  OH1   0  -0.626   3.2403  -0.6710  -0.0117
 E7Z  H1  H  HCR6  0   0.289  -0.2591   2.2061  -0.0749
 E7Z  H2  H  HCH3  0   0.274  -1.6479  -2.5322  -0.8685
 E7Z  H3  H  HCH3  0   0.270  -0.6527  -3.1382   0.4616
 E7Z  H4  H  HCH3  0   0.271  -2.0286  -2.1094   0.8149
 E7Z  H5  H  HCR6  0   0.316   1.3036  -2.4208   0.0788
 E7Z  H7  H  HOH1  0   0.496  -3.5084   1.7072   0.3693
 E7Z  H8  H  HOH1  0   0.467   3.7143   0.1751  -0.0386

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
 E7Z  C1  N   single  1.465  0.020  1.465
 E7Z  C2  N   single  1.362  0.020  1.362
 E7Z  C2  C3  double  1.358  0.020  1.358
 E7Z  N   C6  single  1.352  0.020  1.352
 E7Z  O4  C3  single  1.339  0.020  1.339
 E7Z  C3  C4  single  1.444  0.020  1.444
 E7Z  O2  C7  double  1.203  0.020  1.203
 E7Z  C6  C7  single  1.497  0.020  1.497
 E7Z  C6  C5  double  1.369  0.020  1.369
 E7Z  C7  O3  single  1.318  0.020  1.318
 E7Z  C4  C5  single  1.428  0.020  1.428
 E7Z  C4  O1  double  1.242  0.020  1.242
 E7Z  C5  H1  single  0.930  0.020  1.080
 E7Z  C1  H2  single  0.970  0.020  1.090
 E7Z  C1  H3  single  0.970  0.020  1.090
 E7Z  C1  H4  single  0.970  0.020  1.090
 E7Z  C2  H5  single  0.930  0.020  1.080
 E7Z  O3  H7  single  0.850  0.020  0.980
 E7Z  O4  H8  single  0.850  0.020  0.980

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
 E7Z  O1  C4  C3  120.41  3.000
 E7Z  O1  C4  C5  125.84  3.000
 E7Z  C3  C4  C5  113.75  3.000
 E7Z  H1  C5  C6  119.43  3.000
 E7Z  H1  C5  C4  118.34  3.000
 E7Z  C6  C5  C4  122.21  3.000
 E7Z  N   C6  C7  119.09  3.000
 E7Z  C7  C6  C5  119.32  3.000
 E7Z  N   C6  C5  121.46  3.000
 E7Z  O3  C7  O2  124.68  3.000
 E7Z  O3  C7  C6  111.39  3.000
 E7Z  O2  C7  C6  123.89  3.000
 E7Z  C2  N   C1  117.29  3.000
 E7Z  C2  N   C6  118.96  3.000
 E7Z  C1  N   C6  123.73  3.000
 E7Z  H4  C1  H3  107.83  3.000
 E7Z  H4  C1  H2  109.84  3.000
 E7Z  H3  C1  H2  109.05  3.000
 E7Z  H4  C1  N   110.84  3.000
 E7Z  H3  C1  N   108.02  3.000
 E7Z  H2  C1  N   111.17  3.000
 E7Z  H5  C2  C3  121.26  3.000
 E7Z  H5  C2  N   116.35  3.000
 E7Z  C3  C2  N   122.39  3.000
 E7Z  O4  C3  C2  120.67  3.000
 E7Z  O4  C3  C4  118.12  3.000
 E7Z  C2  C3  C4  121.21  3.000
 E7Z  H7  O3  C7  110.29  3.000
 E7Z  H8  O4  C3  107.06  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
 E7Z  CONST_01  H7  O3  C7  C6  180.00   0.0  0
 E7Z  Var_01    O2  C7  C6  C5  139.10  30.0  2
 E7Z  Var_02    H2  C1  N   C6   79.52  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
 E7Z  plan-1  C4  0.020
 E7Z  plan-1  C5  0.020
 E7Z  plan-1  C6  0.020
 E7Z  plan-1  C7  0.020
 E7Z  plan-1  N   0.020
 E7Z  plan-1  C1  0.020
 E7Z  plan-1  C2  0.020
 E7Z  plan-1  C3  0.020
 E7Z  plan-1  O1  0.020
 E7Z  plan-1  O4  0.020
 E7Z  plan-1  H1  0.020
 E7Z  plan-1  H5  0.020
 E7Z  plan-2  C6  0.020
 E7Z  plan-2  C7  0.020
 E7Z  plan-2  O2  0.020
 E7Z  plan-2  O3  0.020
 E7Z  plan-2  H7  0.020

