# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 16:09:48 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 6-(aminomethyl)pyridine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cccc(n1)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
 ZY9  ZY9  '6-(aminomethyl)pyridine-2-carboxylic acid'  ligand  18  11  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ZY9
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
 ZY9  O    O  O      0  -0.592  -3.1269  -0.1282  -0.3399
 ZY9  C    C  C      0   0.383  -2.0917   0.5584  -0.2344
 ZY9  C10  C  CR6    0   0.034  -0.7869  -0.2276  -0.0753
 ZY9  N11  N  N      0  -0.428   0.3446   0.4600   0.0446
 ZY9  C9   C  CR16   0  -0.325  -0.8035  -1.6200  -0.0570
 ZY9  C8   C  CR16   0  -0.145   0.3934  -2.3010   0.0877
 ZY9  C6   C  CR16   0  -0.343   1.5687  -1.5758   0.2057
 ZY9  C7   C  CR6    0   0.230   1.4974  -0.1874   0.1782
 ZY9  C2   C  CH2    0  -0.344   2.7265   0.6714   0.3211
 ZY9  N    N  NH2    0  -0.796   2.7734   1.6751  -0.7314
 ZY9  O1   O  OC    -1  -0.587  -2.0025   1.7957  -0.2451
 ZY9  H1   H  HCR6   0   0.254  -1.7378  -2.1523  -0.1579
 ZY9  H2   H  HCR6   0   0.264   0.4134  -3.3832   0.1028
 ZY9  H3   H  HCR6   0   0.259   2.5234  -2.0741   0.3139
 ZY9  H4   H  HCH2   0   0.214   2.7244   1.0977   1.3354
 ZY9  H5   H  HCH2   0   0.231   3.6164   0.0422   0.2569
 ZY9  H6   H  HNH2   0   0.342   1.9408   2.2472  -0.6632
 ZY9  H7   H  HNH2   0   0.348   3.5539   2.2965  -0.5618

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
 ZY9  N    C2   single    1.455  0.020  1.455
 ZY9  C2   C7   single    1.506  0.020  1.506
 ZY9  C6   C7   aromatic  1.390  0.020  1.390
 ZY9  C6   C8   aromatic  1.386  0.020  1.386
 ZY9  C7   N11  aromatic  1.329  0.020  1.329
 ZY9  C8   C9   aromatic  1.385  0.020  1.385
 ZY9  N11  C10  aromatic  1.329  0.020  1.329
 ZY9  C9   C10  aromatic  1.393  0.020  1.393
 ZY9  C10  C    single    1.531  0.020  1.531
 ZY9  C    O    deloc     1.247  0.020  1.247
 ZY9  C    O1   deloc     1.241  0.020  1.241
 ZY9  C9   H1   single    0.930  0.020  1.080
 ZY9  C8   H2   single    0.930  0.020  1.080
 ZY9  C6   H3   single    0.930  0.020  1.080
 ZY9  C2   H4   single    0.970  0.020  1.090
 ZY9  C2   H5   single    0.970  0.020  1.090
 ZY9  N    H6   single    0.890  0.020  1.040
 ZY9  N    H7   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
 ZY9  O1   C    C10  116.84  3.000
 ZY9  O1   C    O    127.46  3.000
 ZY9  C10  C    O    115.69  3.000
 ZY9  C9   C10  N11  121.74  3.000
 ZY9  C9   C10  C    120.29  3.000
 ZY9  N11  C10  C    117.97  3.000
 ZY9  C7   N11  C10  119.70  3.000
 ZY9  H1   C9   C8   121.00  3.000
 ZY9  H1   C9   C10  120.12  3.000
 ZY9  C8   C9   C10  118.87  3.000
 ZY9  H2   C8   C6   120.41  3.000
 ZY9  H2   C8   C9   120.61  3.000
 ZY9  C6   C8   C9   118.98  3.000
 ZY9  H3   C6   C7   120.46  3.000
 ZY9  H3   C6   C8   121.04  3.000
 ZY9  C7   C6   C8   118.50  3.000
 ZY9  C2   C7   C6   121.71  3.000
 ZY9  C6   C7   N11  122.21  3.000
 ZY9  C2   C7   N11  116.08  3.000
 ZY9  H5   C2   H4   106.20  3.000
 ZY9  H5   C2   N    109.19  3.000
 ZY9  H4   C2   N    113.55  3.000
 ZY9  H5   C2   C7   109.33  3.000
 ZY9  H4   C2   C7   107.87  3.000
 ZY9  N    C2   C7   110.55  3.000
 ZY9  H7   N    H6   106.02  3.000
 ZY9  H7   N    C2   109.10  3.000
 ZY9  H6   N    C2   108.33  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
 ZY9  CONST_01  C6   C7   N11  C10     0.00   0.0  0
 ZY9  CONST_02  C6   C8   C9   C10     0.00   0.0  0
 ZY9  CONST_03  C8   C6   C7   N11     0.00   0.0  0
 ZY9  CONST_04  C8   C9   C10  N11     0.00   0.0  0
 ZY9  CONST_05  C7   C6   C8   C9      0.00   0.0  0
 ZY9  CONST_06  C7   N11  C10  C9      0.00   0.0  0
 ZY9  CONST_07  C7   N11  C10  C     180.00   0.0  0
 ZY9  CONST_08  C8   C9   C10  C     180.00   0.0  0
 ZY9  CONST_09  C2   C7   N11  C10   180.00   0.0  0
 ZY9  CONST_10  C2   C7   C6   C8    180.00   0.0  0
 ZY9  CONST_11  H2   C8   C9   C10   180.00   0.0  0
 ZY9  CONST_12  H3   C6   C7   N11   180.00   0.0  0
 ZY9  CONST_13  H1   C9   C10  N11   180.00   0.0  0
 ZY9  Var_01    N11  C10  C    O    -179.83  30.0  3
 ZY9  Var_02    N    C2   C7   N11   -50.48  30.0  1
 ZY9  Var_03    H6   N    C2   C7     59.37  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
 ZY9  plan-1  C    0.020
 ZY9  plan-1  C10  0.020
 ZY9  plan-1  N11  0.020
 ZY9  plan-1  C9   0.020
 ZY9  plan-1  C8   0.020
 ZY9  plan-1  C6   0.020
 ZY9  plan-1  C7   0.020
 ZY9  plan-1  C2   0.020
 ZY9  plan-1  H1   0.020
 ZY9  plan-1  H2   0.020
 ZY9  plan-1  H3   0.020
 ZY9  plan-2  O    0.020
 ZY9  plan-2  C    0.020
 ZY9  plan-2  C10  0.020
 ZY9  plan-2  O1   0.020

