# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 06:33:12 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: methyl 2-azanylpyridine-4-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1ccnc(N)c1
#
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
 J9T  J9T  'methyl 2-azanylpyridine-4-carboxylate'  ligand  19  11  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J9T
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
 J9T  C01  C  CH3   0  -0.424   3.8245  -0.1430  -0.0131
 J9T  O02  O  O2    0  -0.450   2.4443  -0.5110   0.0065
 J9T  C03  C  C     0   0.600   1.5518   0.4600  -0.0022
 J9T  O04  O  O     0  -0.438   1.8316   1.6330  -0.0220
 J9T  C05  C  CR6   0   0.025   0.1509  -0.0545   0.0166
 J9T  C06  C  CR16  0  -0.384  -0.1489  -1.4193   0.0160
 J9T  C07  C  CR16  0  -0.052  -1.4844  -1.7717   0.0291
 J9T  N08  N  N     0  -0.451  -2.4898  -0.9038   0.0441
 J9T  C09  C  CR6   0   0.479  -2.2033   0.3966   0.0498
 J9T  N10  N  NH2   0  -0.836  -3.2446   1.2662   0.1136
 J9T  C11  C  CR16  0  -0.400  -0.8765   0.8646   0.0339
 J9T  H1   H  HCH3  0   0.256   4.3797  -1.0759   0.0004
 J9T  H2   H  HCH3  0   0.244   4.0724   0.4143  -0.9160
 J9T  H3   H  HCH3  0   0.244   4.0891   0.4499   0.8619
 J9T  H4   H  HCR6  0   0.267   0.6137  -2.1828   0.0029
 J9T  H5   H  HCR6  0   0.264  -1.7627  -2.8199   0.0262
 J9T  H6   H  HNH2  0   0.387  -4.1573   0.9090  -0.1147
 J9T  H7   H  HNH2  0   0.395  -3.0863   2.2265  -0.1397
 J9T  H8   H  HCR6  0   0.274  -0.6779   1.9282   0.0353

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
 J9T  N08  C07  aromatic  1.328  0.020  1.328
 J9T  N08  C09  aromatic  1.332  0.020  1.332
 J9T  N10  C09  single    1.358  0.020  1.358
 J9T  C07  C06  aromatic  1.381  0.020  1.381
 J9T  C09  C11  aromatic  1.407  0.020  1.407
 J9T  C06  C05  aromatic  1.397  0.020  1.397
 J9T  C11  C05  aromatic  1.379  0.020  1.379
 J9T  C05  C03  single    1.493  0.020  1.493
 J9T  C03  O02  single    1.319  0.020  1.319
 J9T  C03  O04  double    1.206  0.020  1.206
 J9T  O02  C01  single    1.429  0.020  1.429
 J9T  C01  H1   single    0.970  0.020  1.090
 J9T  C01  H2   single    0.970  0.020  1.090
 J9T  C01  H3   single    0.970  0.020  1.090
 J9T  C06  H4   single    0.930  0.020  1.080
 J9T  C07  H5   single    0.930  0.020  1.080
 J9T  N10  H6   single    0.890  0.020  1.040
 J9T  N10  H7   single    0.890  0.020  1.040
 J9T  C11  H8   single    0.930  0.020  1.080

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
 J9T  H3   C01  H2   109.39  3.000
 J9T  H3   C01  H1   109.47  3.000
 J9T  H2   C01  H1   109.47  3.000
 J9T  H3   C01  O02  111.33  3.000
 J9T  H2   C01  O02  111.28  3.000
 J9T  H1   C01  O02  105.82  3.000
 J9T  C03  O02  C01  117.65  3.000
 J9T  C05  C03  O04  123.59  3.000
 J9T  O04  C03  O02  124.00  3.000
 J9T  C05  C03  O02  112.42  3.000
 J9T  C11  C05  C06  119.43  3.000
 J9T  C11  C05  C03  118.03  3.000
 J9T  C06  C05  C03  122.55  3.000
 J9T  H4   C06  C07  120.19  3.000
 J9T  H4   C06  C05  122.64  3.000
 J9T  C07  C06  C05  117.17  3.000
 J9T  H5   C07  N08  115.93  3.000
 J9T  H5   C07  C06  119.65  3.000
 J9T  N08  C07  C06  124.42  3.000
 J9T  C09  N08  C07  118.38  3.000
 J9T  C11  C09  N10  120.70  3.000
 J9T  C11  C09  N08  121.84  3.000
 J9T  N10  C09  N08  117.42  3.000
 J9T  H7   N10  H6   115.13  3.000
 J9T  H7   N10  C09  118.61  3.000
 J9T  H6   N10  C09  117.22  3.000
 J9T  H8   C11  C09  120.00  3.000
 J9T  H8   C11  C05  121.23  3.000
 J9T  C09  C11  C05  118.76  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
 J9T  CONST_01  N08  C07  C06  C05    0.00   0.0  0
 J9T  CONST_02  N08  C09  C11  C05    0.00   0.0  0
 J9T  CONST_03  C09  N08  C07  C06    0.00   0.0  0
 J9T  CONST_04  C09  C11  C05  C06    0.00   0.0  0
 J9T  CONST_05  C11  C09  N08  C07    0.00   0.0  0
 J9T  CONST_06  C11  C05  C06  C07    0.00   0.0  0
 J9T  CONST_07  C07  C06  C05  C03  180.00   0.0  0
 J9T  CONST_08  C09  C11  C05  C03  180.00   0.0  0
 J9T  CONST_09  N10  C09  C11  C05  180.00   0.0  0
 J9T  CONST_10  N10  C09  N08  C07  180.00   0.0  0
 J9T  CONST_11  H5   C07  C06  C05  180.00   0.0  0
 J9T  CONST_12  H8   C11  C05  C06  180.00   0.0  0
 J9T  CONST_13  H4   C06  C07  N08  180.00   0.0  0
 J9T  Var_01    C06  C05  C03  O02   -1.20  30.0  2
 J9T  Var_02    C05  C03  O02  C01  179.85  30.0  1
 J9T  Var_03    H1   C01  O02  C03  179.88  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
 J9T  plan-1  C03  0.020
 J9T  plan-1  C05  0.020
 J9T  plan-1  C06  0.020
 J9T  plan-1  C07  0.020
 J9T  plan-1  N08  0.020
 J9T  plan-1  C09  0.020
 J9T  plan-1  N10  0.020
 J9T  plan-1  C11  0.020
 J9T  plan-1  H4   0.020
 J9T  plan-1  H5   0.020
 J9T  plan-1  H8   0.020
 J9T  plan-2  C09  0.020
 J9T  plan-2  N10  0.020
 J9T  plan-2  H6   0.020
 J9T  plan-2  H7   0.020
 J9T  plan-3  O02  0.020
 J9T  plan-3  C03  0.020
 J9T  plan-3  O04  0.020
 J9T  plan-3  C05  0.020

