# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 05:45:55 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: 1-pyridin-2-ylmethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccccn1
#
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
 APY  APY  1-pyridin-2-ylmethanamine  ligand  16  8  .  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_APY
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
 APY  N    N  NH2   0  -0.796   0.3471   0.3628   2.7314
 APY  CM   C  CH2   0  -0.341  -0.6841  -0.2081   1.8820
 APY  C2   C  CR6   0   0.250  -0.3174  -0.1065   0.4249
 APY  C3   C  CR16  0  -0.339  -1.2823   0.1504  -0.5451
 APY  C4   C  CR16  0  -0.148  -0.9045   0.1878  -1.8773
 APY  C5   C  CR16  0  -0.334   0.4265  -0.0296  -2.2017
 APY  C6   C  CR16  0  -0.075   1.3154  -0.2747  -1.1670
 APY  N1   N  N     0  -0.433   0.9575  -0.3167   0.1108
 APY  HN1  H  HNH2  0   0.343   1.2133  -0.1343   2.5684
 APY  HN2  H  HNH2  0   0.350   0.1045   0.1930   3.6989
 APY  HM1  H  HCH2  0   0.222  -0.8964  -1.2667   2.0952
 APY  HM2  H  HCH2  0   0.236  -1.6224   0.3241   2.0514
 APY  H3   H  HCR6  0   0.264  -2.3111   0.3239  -0.2568
 APY  H4   H  HCR6  0   0.272  -1.6362   0.3875  -2.6494
 APY  H5   H  HCR6  0   0.268   0.7701  -0.0096  -3.2268
 APY  H6   H  HCR6  0   0.261   2.3651  -0.4466  -1.3791

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
 APY  N   CM   single    1.453  0.020  1.453
 APY  N   HN1  single    0.890  0.020  1.040
 APY  N   HN2  single    0.890  0.020  1.040
 APY  CM  C2   single    1.506  0.020  1.506
 APY  CM  HM1  single    0.970  0.020  1.090
 APY  CM  HM2  single    0.970  0.020  1.090
 APY  C2  C3   aromatic  1.392  0.020  1.392
 APY  C2  N1   aromatic  1.330  0.020  1.330
 APY  C3  C4   aromatic  1.385  0.020  1.385
 APY  C3  H3   single    0.930  0.020  1.080
 APY  C4  C5   aromatic  1.387  0.020  1.387
 APY  C4  H4   single    0.930  0.020  1.080
 APY  C5  C6   aromatic  1.386  0.020  1.386
 APY  C5  H5   single    0.930  0.020  1.080
 APY  C6  N1   aromatic  1.328  0.020  1.328
 APY  C6  H6   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
 APY  HN2  N   HN1  106.07  3.000
 APY  HN2  N   CM   108.84  3.000
 APY  HN1  N   CM   108.69  3.000
 APY  HM2  CM  HM1  105.84  3.000
 APY  HM2  CM  C2   109.05  3.000
 APY  HM1  CM  C2   107.41  3.000
 APY  HM2  CM  N    109.13  3.000
 APY  HM1  CM  N    113.68  3.000
 APY  C2   CM  N    111.49  3.000
 APY  N1   C2  C3   121.95  3.000
 APY  N1   C2  CM   116.83  3.000
 APY  C3   C2  CM   121.19  3.000
 APY  H3   C3  C4   120.73  3.000
 APY  H3   C3  C2   120.19  3.000
 APY  C4   C3  C2   119.08  3.000
 APY  H4   C4  C5   120.71  3.000
 APY  H4   C4  C3   120.45  3.000
 APY  C5   C4  C3   118.84  3.000
 APY  H5   C5  C6   120.48  3.000
 APY  H5   C5  C4   121.58  3.000
 APY  C6   C5  C4   117.94  3.000
 APY  H6   C6  N1   116.36  3.000
 APY  H6   C6  C5   120.18  3.000
 APY  N1   C6  C5   123.46  3.000
 APY  C6   N1  C2   118.73  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
 APY  CONST_01  C5   C4  C3  C2     0.00   0.0  0
 APY  CONST_02  C5   C6  N1  C2     0.00   0.0  0
 APY  CONST_03  C6   N1  C2  C3     0.00   0.0  0
 APY  CONST_04  C6   C5  C4  C3     0.00   0.0  0
 APY  CONST_05  N1   C2  C3  C4     0.00   0.0  0
 APY  CONST_06  N1   C6  C5  C4     0.00   0.0  0
 APY  CONST_07  C4   C3  C2  CM   180.00   0.0  0
 APY  CONST_08  C6   N1  C2  CM   180.00   0.0  0
 APY  CONST_09  H4   C4  C3  C2   180.00   0.0  0
 APY  CONST_10  H6   C6  N1  C2   180.00   0.0  0
 APY  CONST_11  H5   C5  C4  C3   180.00   0.0  0
 APY  CONST_12  H3   C3  C4  C5   180.00   0.0  0
 APY  Var_01    C3   C2  CM  N   -143.17  30.0  2
 APY  Var_02    HN1  N   CM  C2   -59.42  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
 APY  plan-1  CM  0.020
 APY  plan-1  C2  0.020
 APY  plan-1  C3  0.020
 APY  plan-1  C4  0.020
 APY  plan-1  C5  0.020
 APY  plan-1  C6  0.020
 APY  plan-1  N1  0.020
 APY  plan-1  H3  0.020
 APY  plan-1  H4  0.020
 APY  plan-1  H5  0.020
 APY  plan-1  H6  0.020

