# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 02:11:03 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: 2-amino-N-methylpyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1cccnc1N
#
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
 8UD  8UD  2-amino-N-methylpyridine-3-carboxamide  ligand  20  11  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8UD
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
 8UD  N1  N  NH1   0  -0.630  -2.1579   0.8333  -0.1709
 8UD  C4  C  CR16  0  -0.180   0.6235   1.4205   0.2448
 8UD  C5  C  CR16  0  -0.356   1.9844   1.6695   0.1564
 8UD  C6  C  CR16  0  -0.053   2.8092   0.5830  -0.0777
 8UD  C7  C  CR6   0   0.447   1.0663  -0.9106  -0.1058
 8UD  C1  C  CH3   0  -0.513  -3.5939   0.7033  -0.0908
 8UD  C2  C  C     0   0.543  -1.3313  -0.1508   0.2083
 8UD  C3  C  CR6   0  -0.189   0.1257   0.1335   0.1021
 8UD  N2  N  N     0  -0.456   2.3754  -0.6609  -0.2030
 8UD  O1  O  O     0  -0.508  -1.7586  -1.2259   0.6267
 8UD  H1  H  HNH1  0   0.411  -1.7874   1.6453  -0.6339
 8UD  H2  H  HNH2  0   0.401  -0.2087  -2.4814   0.0767
 8UD  H3  H  HNH2  0   0.385   1.4268  -2.8873  -0.2492
 8UD  H4  H  HCR6  0   0.271  -0.0491   2.2446   0.4484
 8UD  H5  H  HCR6  0   0.264   2.3881   2.6647   0.2721
 8UD  H6  H  HCR6  0   0.263   3.8824   0.7207  -0.1591
 8UD  H7  H  HCH3  0   0.242  -3.9189   0.4932   0.9279
 8UD  H8  H  HCH3  0   0.252  -4.0394   1.6428  -0.4045
 8UD  H9  H  HCH3  0   0.238  -3.9685  -0.0891  -0.7405
 8UD  N3  N  NH2   0  -0.831   0.6931  -2.1994  -0.2689

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
 8UD  N2  C6  aromatic  1.323  0.020  1.323
 8UD  N2  C7  aromatic  1.336  0.020  1.336
 8UD  C6  C5  aromatic  1.384  0.020  1.384
 8UD  N3  C7  single    1.352  0.020  1.352
 8UD  C7  C3  aromatic  1.421  0.020  1.421
 8UD  C5  C4  aromatic  1.386  0.020  1.386
 8UD  C3  C4  aromatic  1.387  0.020  1.387
 8UD  C3  C2  single    1.488  0.020  1.488
 8UD  O1  C2  double    1.230  0.020  1.230
 8UD  C2  N1  single    1.340  0.020  1.340
 8UD  N1  C1  single    1.444  0.020  1.444
 8UD  N1  H1  single    0.860  0.020  1.020
 8UD  N3  H2  single    0.890  0.020  1.040
 8UD  N3  H3  single    0.890  0.020  1.040
 8UD  C4  H4  single    0.930  0.020  1.080
 8UD  C5  H5  single    0.930  0.020  1.080
 8UD  C6  H6  single    0.930  0.020  1.080
 8UD  C1  H7  single    0.970  0.020  1.090
 8UD  C1  H8  single    0.970  0.020  1.090
 8UD  C1  H9  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
 8UD  H1  N1  C2  119.74  3.000
 8UD  H1  N1  C1  117.69  3.000
 8UD  C2  N1  C1  122.12  3.000
 8UD  H4  C4  C3  120.15  3.000
 8UD  H4  C4  C5  119.01  3.000
 8UD  C3  C4  C5  120.82  3.000
 8UD  H5  C5  C6  121.24  3.000
 8UD  H5  C5  C4  121.71  3.000
 8UD  C6  C5  C4  117.05  3.000
 8UD  H6  C6  N2  115.87  3.000
 8UD  H6  C6  C5  120.17  3.000
 8UD  N2  C6  C5  123.95  3.000
 8UD  N2  C7  C3  121.46  3.000
 8UD  C3  C7  N3  122.39  3.000
 8UD  N2  C7  N3  116.10  3.000
 8UD  H9  C1  H8  108.39  3.000
 8UD  H9  C1  H7  108.32  3.000
 8UD  H8  C1  H7  108.33  3.000
 8UD  H9  C1  N1  111.95  3.000
 8UD  H8  C1  N1  108.30  3.000
 8UD  H7  C1  N1  111.45  3.000
 8UD  O1  C2  C3  122.09  3.000
 8UD  O1  C2  N1  121.59  3.000
 8UD  C3  C2  N1  116.32  3.000
 8UD  C2  C3  C7  121.21  3.000
 8UD  C2  C3  C4  121.42  3.000
 8UD  C7  C3  C4  117.34  3.000
 8UD  C7  N2  C6  119.34  3.000
 8UD  H3  N3  H2  117.08  3.000
 8UD  H3  N3  C7  116.64  3.000
 8UD  H2  N3  C7  118.25  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
 8UD  CONST_01  N2  C6  C5  C4     0.00   0.0  0
 8UD  CONST_02  N2  C7  C3  C4     0.00   0.0  0
 8UD  CONST_03  C7  N2  C6  C5     0.00   0.0  0
 8UD  CONST_04  C7  C3  C4  C5     0.00   0.0  0
 8UD  CONST_05  C3  C7  N2  C6     0.00   0.0  0
 8UD  CONST_06  C3  C4  C5  C6     0.00   0.0  0
 8UD  CONST_07  C6  N2  C7  N3   180.00   0.0  0
 8UD  CONST_08  C4  C3  C7  N3   180.00   0.0  0
 8UD  CONST_09  C2  C3  C4  C5   180.00   0.0  0
 8UD  CONST_10  N2  C7  C3  C2   180.00   0.0  0
 8UD  CONST_11  H6  C6  C5  C4   180.00   0.0  0
 8UD  CONST_12  H4  C4  C5  C6   180.00   0.0  0
 8UD  CONST_13  H5  C5  C4  C3   180.00   0.0  0
 8UD  CONST_15  H3  N3  C7  C3   180.00   0.0  0
 8UD  CONST_16  C3  C2  N1  C1   180.00   0.0  0
 8UD  CONST_17  H1  N1  C2  C3     0.00   0.0  0
 8UD  CONST_18  O1  C2  N1  C1     0.00   0.0  0
 8UD  Var_01    C7  C3  C2  N1  -152.03  30.0  2
 8UD  Var_02    H7  C1  N1  C2    58.10  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
 8UD  plan-1  C4  0.020
 8UD  plan-1  C5  0.020
 8UD  plan-1  C6  0.020
 8UD  plan-1  C7  0.020
 8UD  plan-1  C2  0.020
 8UD  plan-1  C3  0.020
 8UD  plan-1  N2  0.020
 8UD  plan-1  H4  0.020
 8UD  plan-1  H5  0.020
 8UD  plan-1  H6  0.020
 8UD  plan-1  N3  0.020
 8UD  plan-2  N1  0.020
 8UD  plan-2  C1  0.020
 8UD  plan-2  C2  0.020
 8UD  plan-2  C3  0.020
 8UD  plan-2  O1  0.020
 8UD  plan-2  H1  0.020
 8UD  plan-3  C7  0.020
 8UD  plan-3  H2  0.020
 8UD  plan-3  H3  0.020
 8UD  plan-3  N3  0.020

