# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 07:12:22 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: ~{N}-(2-azanylethyl)-1-methyl-6-oxidanylidene-pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C=C(C=CC1=O)C(=O)NCCN
#
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
 D8Q  D8Q  ~{N}-(2-azanylethyl)-1-methyl-6-oxidanylidene-pyridine-3-carboxamide  ligand  27  14  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D8Q
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
 D8Q  C01  C  CH3   0  -0.532  -3.8200   1.4853  -0.0812
 D8Q  C03  C  CR16  0   0.105  -1.4814   0.9281  -0.0239
 D8Q  C04  C  CR6   0  -0.212  -0.4034   0.0943   0.0185
 D8Q  C05  C  CR16  0  -0.117  -0.6799  -1.2980   0.0682
 D8Q  C06  C  CR16  0  -0.434  -1.9539  -1.7540   0.0747
 D8Q  C07  C  CR6   0   0.549  -3.0916  -0.8688   0.0471
 D8Q  C09  C  C     0   0.546   0.9431   0.7265   0.0418
 D8Q  C12  C  CH2   0  -0.228   3.3623   0.3919   0.0124
 D8Q  C13  C  CH2   0  -0.316   4.3468  -0.7596  -0.0954
 D8Q  N02  N  NR6   0  -0.519  -2.7541   0.4922  -0.0190
 D8Q  N11  N  NH1   0  -0.678   2.0037  -0.1024  -0.0328
 D8Q  N14  N  NH2   0  -0.772   5.7013  -0.2499   0.0138
 D8Q  O08  O  O     0  -0.445  -4.2529  -1.2326   0.0808
 D8Q  O10  O  O     0  -0.443   1.0743   1.9353   0.1337
 D8Q  H1   H  HCH3  0   0.285  -4.7790   0.9913   0.0188
 D8Q  H2   H  HCH3  0   0.252  -3.7050   2.2054   0.7257
 D8Q  H3   H  HCH3  0   0.252  -3.7889   2.0086  -1.0351
 D8Q  H4   H  HCR6  0   0.300  -1.3457   2.0006  -0.0605
 D8Q  H5   H  HCR6  0   0.224   0.1158  -2.0307   0.1165
 D8Q  H6   H  HCR6  0   0.261  -2.1629  -2.8134   0.1219
 D8Q  H7   H  HCH2  0   0.224   3.5242   0.9323   0.9499
 D8Q  H8   H  HCH2  0   0.237   3.5407   1.1014  -0.7987
 D8Q  H9   H  HCH2  0   0.196   4.1010  -1.5228   0.6572
 D8Q  H10  H  HCH2  0   0.223   4.2382  -1.2371  -1.0722
 D8Q  H11  H  HNH1  0   0.375   1.8694  -1.0871  -0.1752
 D8Q  H12  H  HNH2  0   0.329   5.9021  -0.0303   0.9810
 D8Q  H13  H  HNH2  0   0.338   6.3565  -0.9766  -0.2387

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
 D8Q  C06  C05  double  1.353  0.020  1.353
 D8Q  C06  C07  single  1.442  0.020  1.442
 D8Q  O08  C07  double  1.217  0.020  1.217
 D8Q  C05  C04  single  1.420  0.020  1.420
 D8Q  C07  N02  single  1.404  0.020  1.404
 D8Q  C04  C09  single  1.488  0.020  1.488
 D8Q  C04  C03  double  1.363  0.020  1.363
 D8Q  N02  C03  single  1.345  0.020  1.345
 D8Q  N02  C01  single  1.458  0.020  1.458
 D8Q  O10  C09  double  1.219  0.020  1.219
 D8Q  N14  C13  single  1.451  0.020  1.451
 D8Q  C13  C12  single  1.519  0.020  1.519
 D8Q  C09  N11  single  1.348  0.020  1.348
 D8Q  N11  C12  single  1.446  0.020  1.446
 D8Q  C01  H1   single  0.970  0.020  1.090
 D8Q  C01  H2   single  0.970  0.020  1.090
 D8Q  C01  H3   single  0.970  0.020  1.090
 D8Q  C03  H4   single  0.930  0.020  1.080
 D8Q  C05  H5   single  0.930  0.020  1.080
 D8Q  C06  H6   single  0.930  0.020  1.080
 D8Q  C12  H7   single  0.970  0.020  1.090
 D8Q  C12  H8   single  0.970  0.020  1.090
 D8Q  C13  H9   single  0.970  0.020  1.090
 D8Q  C13  H10  single  0.970  0.020  1.090
 D8Q  N11  H11  single  0.860  0.020  1.020
 D8Q  N14  H12  single  0.890  0.020  1.040
 D8Q  N14  H13  single  0.890  0.020  1.040

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
 D8Q  H3   C01  H2   109.19  3.000
 D8Q  H3   C01  H1   108.99  3.000
 D8Q  H2   C01  H1   109.09  3.000
 D8Q  H3   C01  N02  110.12  3.000
 D8Q  H2   C01  N02  110.00  3.000
 D8Q  H1   C01  N02  109.43  3.000
 D8Q  H4   C03  N02  116.11  3.000
 D8Q  H4   C03  C04  120.54  3.000
 D8Q  N02  C03  C04  123.35  3.000
 D8Q  C09  C04  C05  126.31  3.000
 D8Q  C09  C04  C03  117.15  3.000
 D8Q  C05  C04  C03  116.53  3.000
 D8Q  H5   C05  C06  117.62  3.000
 D8Q  H5   C05  C04  121.46  3.000
 D8Q  C06  C05  C04  120.91  3.000
 D8Q  H6   C06  C07  116.75  3.000
 D8Q  H6   C06  C05  120.83  3.000
 D8Q  C07  C06  C05  122.41  3.000
 D8Q  O08  C07  N02  121.36  3.000
 D8Q  N02  C07  C06  113.98  3.000
 D8Q  O08  C07  C06  124.66  3.000
 D8Q  O10  C09  N11  121.94  3.000
 D8Q  N11  C09  C04  116.74  3.000
 D8Q  O10  C09  C04  121.32  3.000
 D8Q  H8   C12  H7   106.94  3.000
 D8Q  H8   C12  N11  110.62  3.000
 D8Q  H7   C12  N11  109.55  3.000
 D8Q  H8   C12  C13  109.50  3.000
 D8Q  H7   C12  C13  109.84  3.000
 D8Q  N11  C12  C13  110.33  3.000
 D8Q  H10  C13  H9   106.63  3.000
 D8Q  H10  C13  N14  108.27  3.000
 D8Q  H9   C13  N14  113.63  3.000
 D8Q  H10  C13  C12  109.29  3.000
 D8Q  H9   C13  C12  109.44  3.000
 D8Q  N14  C13  C12  109.47  3.000
 D8Q  C07  N02  C03  122.80  3.000
 D8Q  C03  N02  C01  118.08  3.000
 D8Q  C07  N02  C01  119.11  3.000
 D8Q  H11  N11  C12  117.73  3.000
 D8Q  H11  N11  C09  120.37  3.000
 D8Q  C12  N11  C09  121.81  3.000
 D8Q  H13  N14  H12  105.44  3.000
 D8Q  H13  N14  C13  109.50  3.000
 D8Q  H12  N14  C13  109.47  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
 D8Q  CONST_01  C06  C07  N02  C03     0.00   0.0  0
 D8Q  CONST_02  C06  C07  N02  C01   180.00   0.0  0
 D8Q  CONST_03  O08  C07  N02  C03   180.00   0.0  0
 D8Q  CONST_04  O08  C07  N02  C01     0.00   0.0  0
 D8Q  CONST_05  C12  N11  C09  C04   180.00   0.0  0
 D8Q  CONST_06  H11  N11  C09  C04     0.00   0.0  0
 D8Q  CONST_07  O10  C09  N11  C12     0.00   0.0  0
 D8Q  Var_01    O10  C09  C04  C03     6.05  30.0  2
 D8Q  Var_02    H1   C01  N02  C03  -175.05  30.0  3
 D8Q  Var_03    C13  C12  N11  C09  -179.84  30.0  3
 D8Q  Var_04    N14  C13  C12  N11  -177.39  30.0  1
 D8Q  Var_05    H12  N14  C13  C12    76.02  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
 D8Q  plan-1  C01  0.020
 D8Q  plan-1  C03  0.020
 D8Q  plan-1  C04  0.020
 D8Q  plan-1  C05  0.020
 D8Q  plan-1  C06  0.020
 D8Q  plan-1  C07  0.020
 D8Q  plan-1  C09  0.020
 D8Q  plan-1  N02  0.020
 D8Q  plan-1  O08  0.020
 D8Q  plan-1  H4   0.020
 D8Q  plan-1  H5   0.020
 D8Q  plan-1  H6   0.020
 D8Q  plan-2  C04  0.020
 D8Q  plan-2  C09  0.020
 D8Q  plan-2  C12  0.020
 D8Q  plan-2  N11  0.020
 D8Q  plan-2  O10  0.020
 D8Q  plan-2  H11  0.020

