# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 14:16:40 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: 1-(4-chloropyridin-2-yl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cc(Cl)ccn1
#
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
 NNY  NNY  1-(4-chloropyridin-2-yl)methanamine  ligand  16  9  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NNY
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
 NNY  C12   C   CH2   0  -0.348   2.4692   0.7747  -0.4913
 NNY  C13   C   CR6   0   0.251   1.1890   0.0182  -0.2567
 NNY  C17   C   CR16  0  -0.072   0.1754  -1.9611   0.2507
 NNY  C18   C   CR16  0  -0.304  -1.0971  -1.4067   0.2145
 NNY  C19   C   CR6   0   0.078  -1.1852  -0.0591  -0.0796
 NNY  C20   C   CR16  0  -0.316  -0.0350   0.6740  -0.3197
 NNY  N23   N   NH2   0  -0.791   3.2409   0.8587   0.7390
 NNY  N24   N   N     0  -0.412   1.2878  -1.2792   0.0252
 NNY  CL27  CL  CL    0  -0.102  -2.7260   0.7142  -0.1470
 NNY  H12   H   HCH2  0   0.244   3.0614   0.2268  -1.2279
 NNY  H12A  H   HCH2  0   0.217   2.2299   1.7472  -0.9396
 NNY  H17   H   HCR6  0   0.273   0.2878  -3.0167   0.4716
 NNY  H18   H   HCR6  0   0.292  -1.9721  -2.0111   0.4057
 NNY  H20   H   HCR6  0   0.291  -0.0815   1.7302  -0.5478
 NNY  HN23  H   HNH2  0   0.355   4.1374   1.2821   0.5358
 NNY  HN2A  H   HNH2  0   0.343   2.7795   1.4879   1.3843

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
 NNY  C12  C13   single    1.505  0.020  1.505
 NNY  C12  N23   single    1.455  0.020  1.455
 NNY  C13  C20   aromatic  1.390  0.020  1.390
 NNY  C13  N24   aromatic  1.331  0.020  1.331
 NNY  C17  C18   aromatic  1.388  0.020  1.388
 NNY  C17  N24   aromatic  1.324  0.020  1.324
 NNY  C18  C19   aromatic  1.382  0.020  1.382
 NNY  C19  C20   aromatic  1.385  0.020  1.385
 NNY  C19  CL27  single    1.725  0.020  1.725
 NNY  C12  H12   single    0.970  0.020  1.090
 NNY  C12  H12A  single    0.970  0.020  1.090
 NNY  C17  H17   single    0.930  0.020  1.080
 NNY  C18  H18   single    0.930  0.020  1.080
 NNY  C20  H20   single    0.930  0.020  1.080
 NNY  N23  HN23  single    0.890  0.020  1.040
 NNY  N23  HN2A  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
 NNY  H12A  C12  H12   106.69  3.000
 NNY  H12A  C12  N23   114.21  3.000
 NNY  H12   C12  N23   108.16  3.000
 NNY  H12A  C12  C13   108.88  3.000
 NNY  H12   C12  C13   108.31  3.000
 NNY  N23   C12  C13   110.38  3.000
 NNY  N24   C13  C20   122.32  3.000
 NNY  N24   C13  C12   117.36  3.000
 NNY  C20   C13  C12   120.31  3.000
 NNY  H17   C17  N24   116.67  3.000
 NNY  H17   C17  C18   119.28  3.000
 NNY  N24   C17  C18   124.05  3.000
 NNY  H18   C18  C19   122.10  3.000
 NNY  H18   C18  C17   120.95  3.000
 NNY  C19   C18  C17   116.95  3.000
 NNY  CL27  C19  C20   119.84  3.000
 NNY  CL27  C19  C18   120.15  3.000
 NNY  C20   C19  C18   120.00  3.000
 NNY  H20   C20  C19   121.18  3.000
 NNY  H20   C20  C13   120.54  3.000
 NNY  C19   C20  C13   118.27  3.000
 NNY  HN2A  N23  HN23  105.77  3.000
 NNY  HN2A  N23  C12   109.46  3.000
 NNY  HN23  N23  C12   108.92  3.000
 NNY  C17   N24  C13   118.40  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
 NNY  CONST_01  C18   C19  C20  C13    0.00   0.0  0
 NNY  CONST_02  C18   C17  N24  C13    0.00   0.0  0
 NNY  CONST_03  C20   C19  C18  C17    0.00   0.0  0
 NNY  CONST_04  C20   C13  N24  C17    0.00   0.0  0
 NNY  CONST_05  N24   C17  C18  C19    0.00   0.0  0
 NNY  CONST_06  N24   C13  C20  C19    0.00   0.0  0
 NNY  CONST_07  C19   C20  C13  C12  180.00   0.0  0
 NNY  CONST_08  C17   N24  C13  C12  180.00   0.0  0
 NNY  CONST_09  CL27  C19  C20  C13  180.00   0.0  0
 NNY  CONST_10  CL27  C19  C18  C17  180.00   0.0  0
 NNY  CONST_11  H17   C17  N24  C13  180.00   0.0  0
 NNY  CONST_12  H20   C20  C19  C18  180.00   0.0  0
 NNY  CONST_13  H18   C18  C19  C20  180.00   0.0  0
 NNY  Var_01    N23   C12  C13  C20  111.94  30.0  1
 NNY  Var_02    HN23  N23  C12  C13  174.00  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
 NNY  plan-1  C12   0.020
 NNY  plan-1  C13   0.020
 NNY  plan-1  C17   0.020
 NNY  plan-1  C18   0.020
 NNY  plan-1  C19   0.020
 NNY  plan-1  C20   0.020
 NNY  plan-1  N24   0.020
 NNY  plan-1  CL27  0.020
 NNY  plan-1  H17   0.020
 NNY  plan-1  H18   0.020
 NNY  plan-1  H20   0.020

