# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 00:18:54 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: 1-(pyridin-3-yl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cccnc1
#
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
 0YC  0YC  1-(pyridin-3-yl)methanamine  ligand  16  8  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_0YC
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
 0YC  N16  N  NH2   0  -0.796  -2.7277  -0.6288  -0.3728
 0YC  C17  C  CH2   0  -0.337  -1.9688   0.2611   0.4859
 0YC  C18  C  CR6   0  -0.002  -0.4894   0.1989   0.2089
 0YC  C22  C  CR16  0  -0.089   0.1223  -0.9531  -0.2782
 0YC  N23  N  N     0  -0.403   1.4272  -1.0631  -0.5038
 0YC  C24  C  CR16  0  -0.079   2.1961  -0.0110  -0.2505
 0YC  C25  C  CR16  0  -0.318   1.6958   1.1898   0.2301
 0YC  C26  C  CR16  0  -0.193   0.3330   1.2919   0.4582
 0YC  H13  H  HNH2  0   0.357  -3.6902  -0.6501  -0.0631
 0YC  H14  H  HCH2  0   0.218  -2.2862   1.3116   0.4357
 0YC  H15  H  HCH2  0   0.248  -2.1371  -0.0484   1.5216
 0YC  H22  H  HCR6  0   0.255  -0.4819  -1.8250  -0.5015
 0YC  H23  H  HCR6  0   0.260   3.2576  -0.1255  -0.4412
 0YC  H24  H  HCR6  0   0.268   2.3593   2.0234   0.4155
 0YC  H25  H  HCR6  0   0.264  -0.0906   2.2193   0.8259
 0YC  H2   H  HNH2  0   0.346  -2.7440  -0.2610  -1.3158

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
 0YC  C17  N16  single    1.451  0.020  1.451
 0YC  C17  C18  single    1.506  0.020  1.506
 0YC  C18  C26  aromatic  1.390  0.020  1.390
 0YC  C18  C22  aromatic  1.392  0.020  1.392
 0YC  C26  C25  aromatic  1.386  0.020  1.386
 0YC  C22  N23  aromatic  1.329  0.020  1.329
 0YC  C25  C24  aromatic  1.387  0.020  1.387
 0YC  N23  C24  aromatic  1.328  0.020  1.328
 0YC  N16  H13  single    0.890  0.020  1.040
 0YC  C17  H14  single    0.970  0.020  1.090
 0YC  C17  H15  single    0.970  0.020  1.090
 0YC  C22  H22  single    0.930  0.020  1.080
 0YC  C24  H23  single    0.930  0.020  1.080
 0YC  C25  H24  single    0.930  0.020  1.080
 0YC  C26  H25  single    0.930  0.020  1.080
 0YC  N16  H2   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
 0YC  H2   N16  H13  106.11  3.000
 0YC  H2   N16  C17  109.69  3.000
 0YC  H13  N16  C17  109.24  3.000
 0YC  H15  C17  H14  105.63  3.000
 0YC  H15  C17  C18  108.27  3.000
 0YC  H14  C17  C18  108.36  3.000
 0YC  H15  C17  N16  107.83  3.000
 0YC  H14  C17  N16  114.10  3.000
 0YC  C18  C17  N16  112.30  3.000
 0YC  C26  C18  C22  116.95  3.000
 0YC  C22  C18  C17  122.01  3.000
 0YC  C26  C18  C17  121.03  3.000
 0YC  H22  C22  N23  116.47  3.000
 0YC  H22  C22  C18  119.51  3.000
 0YC  N23  C22  C18  124.01  3.000
 0YC  C24  N23  C22  118.08  3.000
 0YC  H23  C24  C25  120.36  3.000
 0YC  H23  C24  N23  116.72  3.000
 0YC  C25  C24  N23  122.92  3.000
 0YC  H24  C25  C26  121.23  3.000
 0YC  H24  C25  C24  120.37  3.000
 0YC  C26  C25  C24  118.41  3.000
 0YC  H25  C26  C25  120.21  3.000
 0YC  H25  C26  C18  120.16  3.000
 0YC  C25  C26  C18  119.63  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
 0YC  CONST_01  C24  C25  C26  C18    0.00   0.0  0
 0YC  CONST_02  C24  N23  C22  C18    0.00   0.0  0
 0YC  CONST_03  C25  C26  C18  C22    0.00   0.0  0
 0YC  CONST_04  C25  C24  N23  C22    0.00   0.0  0
 0YC  CONST_05  C26  C18  C22  N23    0.00   0.0  0
 0YC  CONST_06  C26  C25  C24  N23    0.00   0.0  0
 0YC  CONST_07  C25  C26  C18  C17  180.00   0.0  0
 0YC  CONST_08  N23  C22  C18  C17  180.00   0.0  0
 0YC  CONST_09  H24  C25  C26  C18  180.00   0.0  0
 0YC  CONST_10  H25  C26  C18  C22  180.00   0.0  0
 0YC  CONST_11  H23  C24  N23  C22  180.00   0.0  0
 0YC  CONST_12  H22  C22  N23  C24  180.00   0.0  0
 0YC  Var_01    C26  C18  C17  N16  152.31  30.0  2
 0YC  Var_02    H13  N16  C17  C18  172.02  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
 0YC  plan-1  C17  0.020
 0YC  plan-1  C18  0.020
 0YC  plan-1  C22  0.020
 0YC  plan-1  N23  0.020
 0YC  plan-1  C24  0.020
 0YC  plan-1  C25  0.020
 0YC  plan-1  C26  0.020
 0YC  plan-1  H22  0.020
 0YC  plan-1  H23  0.020
 0YC  plan-1  H24  0.020
 0YC  plan-1  H25  0.020

