# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 14:17:02 2021
#   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  19  11  .  2021-08-25  2022-11-18
;
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  -0.433  35.5892  45.9137  8.0633
 ZY9  C    C  C     0   0.520  36.7607  45.7001  7.8637
 ZY9  C10  C  CR6   0   0.085  37.7263  46.7691  7.4686
 ZY9  N11  N  N     0  -0.425  38.9941  46.4181  7.2790
 ZY9  C9   C  CR16  0  -0.296  37.2632  48.0664  7.3193
 ZY9  C8   C  CR16  0  -0.142  38.1808  49.0421  6.9537
 ZY9  C6   C  CR16  0  -0.311  39.4985  48.6793  6.7539
 ZY9  C7   C  CR6   0   0.234  39.8697  47.3438  6.9252
 ZY9  C2   C  CH2   0  -0.344  41.3048  46.9192  6.7616
 ZY9  N    N  NH2   0  -0.794  41.4178  45.5227  6.3936
 ZY9  O1   O  OH1   0  -0.579  37.3202  44.5090  7.9689
 ZY9  H1   H  HCR6  0   0.278  36.2231  48.3095  7.4818
 ZY9  H2   H  HCR6  0   0.280  37.8670  50.0689  6.8228
 ZY9  H3   H  HCR6  0   0.273  40.2379  49.4153  6.4648
 ZY9  H4   H  HCH2  0   0.228  41.8285  47.1825  7.6938
 ZY9  H5   H  HCH2  0   0.242  41.7637  47.5336  5.9838
 ZY9  H6   H  HNH2  0   0.352  42.3977  45.2763  6.3475
 ZY9  H7   H  HNH2  0   0.346  41.0162  44.9508  7.1251
 ZY9  H9   H  HOH1  0   0.487  36.6479  43.8582  8.2212

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    1.449  0.020  1.449
 ZY9  C2   C7   single    1.506  0.020  1.506
 ZY9  C6   C7   aromatic  1.397  0.020  1.397
 ZY9  C6   C8   aromatic  1.381  0.020  1.381
 ZY9  C7   N11  aromatic  1.322  0.020  1.322
 ZY9  C8   C9   aromatic  1.388  0.020  1.388
 ZY9  N11  C10  aromatic  1.329  0.020  1.329
 ZY9  C9   C10  aromatic  1.386  0.020  1.386
 ZY9  C10  C    single    1.494  0.020  1.494
 ZY9  C    O    double    1.207  0.020  1.207
 ZY9  C    O1   single    1.320  0.020  1.320
 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
 ZY9  O1   H9   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
 ZY9  O1   C    C10  113.13  3.000
 ZY9  O1   C    O    123.89  3.000
 ZY9  C10  C    O    122.97  3.000
 ZY9  C9   C10  N11  123.41  3.000
 ZY9  C9   C10  C    118.85  3.000
 ZY9  N11  C10  C    117.73  3.000
 ZY9  C7   N11  C10  119.00  3.000
 ZY9  H1   C9   C8   121.18  3.000
 ZY9  H1   C9   C10  121.08  3.000
 ZY9  C8   C9   C10  117.74  3.000
 ZY9  H2   C8   C6   120.57  3.000
 ZY9  H2   C8   C9   120.48  3.000
 ZY9  C6   C8   C9   118.95  3.000
 ZY9  H3   C6   C7   120.09  3.000
 ZY9  H3   C6   C8   120.77  3.000
 ZY9  C7   C6   C8   119.14  3.000
 ZY9  C2   C7   C6   120.64  3.000
 ZY9  C6   C7   N11  121.75  3.000
 ZY9  C2   C7   N11  117.57  3.000
 ZY9  H5   C2   H4   105.58  3.000
 ZY9  H5   C2   N    109.19  3.000
 ZY9  H4   C2   N    114.11  3.000
 ZY9  H5   C2   C7   108.61  3.000
 ZY9  H4   C2   C7   107.09  3.000
 ZY9  N    C2   C7   111.95  3.000
 ZY9  H7   N    H6   106.24  3.000
 ZY9  H7   N    C2   109.29  3.000
 ZY9  H6   N    C2   108.78  3.000
 ZY9  H9   O1   C    109.43  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  CONST_14  H9   O1   C    C10   180.00   0.0  0
 ZY9  Var_01    N11  C10  C    O     179.80  30.0  2
 ZY9  Var_02    N    C2   C7   N11    27.66  30.0  2
 ZY9  Var_03    H6   N    C2   C7   -176.85  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
 ZY9  plan-2  H9   0.020

