# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 09:31:34 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 2-(pyridin-3-yl)ethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCc1cccnc1
#
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
 45X  45X  2-(pyridin-3-yl)ethanamine  ligand  19  9  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_45X
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
 45X  C1   C  CH2   0  -0.515  -1.4058  -0.0896  -0.7323
 45X  C6   C  CR16  0  -0.108   0.8193  -1.1842  -0.2834
 45X  C5   C  CR16  0  -0.075   2.6971  -0.0412   0.2987
 45X  C4   C  CR16  0  -0.318   2.0344   1.1754   0.2285
 45X  C3   C  CR16  0  -0.191   0.6933   1.1778  -0.1207
 45X  C2   C  CR6   0   0.029   0.0518  -0.0277  -0.3871
 45X  N    N  NH2   0  -0.799  -3.6958  -0.0350   0.1362
 45X  C    C  CH2   0  -0.269  -2.2921   0.0296   0.5072
 45X  N1   N  N     0  -0.402   2.1052  -1.2024   0.0469
 45X  H1   H  HCH2  0   0.244  -1.6519   0.7137  -1.4330
 45X  H2   H  HCH2  0   0.243  -1.6326  -1.0315  -1.2362
 45X  H3   H  HCR6  0   0.254   0.3623  -2.1486  -0.4867
 45X  H4   H  HCR6  0   0.261   3.7477  -0.0775   0.5652
 45X  H5   H  HCR6  0   0.269   2.5602   2.0966   0.4399
 45X  H6   H  HCR6  0   0.265   0.1488   2.1123  -0.1934
 45X  H7   H  HNH2  0   0.349  -4.2640  -0.0802   0.9722
 45X  H8   H  HNH2  0   0.341  -3.9622   0.8245  -0.3281
 45X  H10  H  HCH2  0   0.224  -2.0738  -0.8065   1.1766
 45X  H11  H  HCH2  0   0.200  -2.0192   0.9425   1.0554

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
 45X  N   C    single    1.453  0.020  1.453
 45X  C1  C    single    1.528  0.020  1.528
 45X  C1  C2   single    1.499  0.020  1.499
 45X  C6  C2   aromatic  1.392  0.020  1.392
 45X  C6  N1   aromatic  1.328  0.020  1.328
 45X  C2  C3   aromatic  1.391  0.020  1.391
 45X  N1  C5   aromatic  1.328  0.020  1.328
 45X  C3  C4   aromatic  1.386  0.020  1.386
 45X  C5  C4   aromatic  1.387  0.020  1.387
 45X  C1  H1   single    0.970  0.020  1.090
 45X  C1  H2   single    0.970  0.020  1.090
 45X  C6  H3   single    0.930  0.020  1.080
 45X  C5  H4   single    0.930  0.020  1.080
 45X  C4  H5   single    0.930  0.020  1.080
 45X  C3  H6   single    0.930  0.020  1.080
 45X  N   H7   single    0.890  0.020  1.040
 45X  N   H8   single    0.890  0.020  1.040
 45X  C   H10  single    0.970  0.020  1.090
 45X  C   H11  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
 45X  H2   C1  H1   106.92  3.000
 45X  H2   C1  C    108.73  3.000
 45X  H1   C1  C    109.37  3.000
 45X  H2   C1  C2   110.11  3.000
 45X  H1   C1  C2   109.62  3.000
 45X  C    C1  C2   111.95  3.000
 45X  H3   C6  N1   116.22  3.000
 45X  H3   C6  C2   119.45  3.000
 45X  N1   C6  C2   124.33  3.000
 45X  H4   C5  N1   116.69  3.000
 45X  H4   C5  C4   120.31  3.000
 45X  N1   C5  C4   122.99  3.000
 45X  H5   C4  C3   121.21  3.000
 45X  H5   C4  C5   120.32  3.000
 45X  C3   C4  C5   118.47  3.000
 45X  H6   C3  C2   120.16  3.000
 45X  H6   C3  C4   120.30  3.000
 45X  C2   C3  C4   119.53  3.000
 45X  C3   C2  C6   116.83  3.000
 45X  C3   C2  C1   121.88  3.000
 45X  C6   C2  C1   121.26  3.000
 45X  H8   N   H7   105.61  3.000
 45X  H8   N   C    109.47  3.000
 45X  H7   N   C    109.47  3.000
 45X  H11  C   H10  106.28  3.000
 45X  H11  C   N    113.83  3.000
 45X  H10  C   N    108.37  3.000
 45X  H11  C   C1   108.98  3.000
 45X  H10  C   C1   108.73  3.000
 45X  N    C   C1   110.46  3.000
 45X  C5   N1  C6   117.84  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
 45X  CONST_01  C4  C3  C2  C6     0.00   0.0  0
 45X  CONST_02  C4  C5  N1  C6     0.00   0.0  0
 45X  CONST_03  C2  C6  N1  C5     0.00   0.0  0
 45X  CONST_04  C2  C3  C4  C5     0.00   0.0  0
 45X  CONST_05  N1  C6  C2  C3     0.00   0.0  0
 45X  CONST_06  N1  C5  C4  C3     0.00   0.0  0
 45X  CONST_07  N1  C6  C2  C1   180.00   0.0  0
 45X  CONST_08  C4  C3  C2  C1   180.00   0.0  0
 45X  CONST_09  H6  C3  C2  C6   180.00   0.0  0
 45X  CONST_10  H4  C5  N1  C6   180.00   0.0  0
 45X  CONST_11  H3  C6  N1  C5   180.00   0.0  0
 45X  CONST_12  H5  C4  C3  C2   180.00   0.0  0
 45X  Var_01    C   C1  C2  C6    99.45  30.0  2
 45X  Var_02    N   C   C1  C2  -179.96  30.0  3
 45X  Var_03    H7  N   C   C1   172.45  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
 45X  plan-1  C1  0.020
 45X  plan-1  C6  0.020
 45X  plan-1  C5  0.020
 45X  plan-1  C4  0.020
 45X  plan-1  C3  0.020
 45X  plan-1  C2  0.020
 45X  plan-1  N1  0.020
 45X  plan-1  H3  0.020
 45X  plan-1  H4  0.020
 45X  plan-1  H5  0.020
 45X  plan-1  H6  0.020

