# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 12:44:33 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: 1-methyl-1,6-dihydropyridin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CC=CC(=C1)N
#
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
 LG5  LG5  1-methyl-1,6-dihydropyridin-3-amine  ligand  18  8  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LG5
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
 LG5  C1    C  C1    0  -0.285   0.1767   1.6422   0.2234
 LG5  C2    C  CH2   0  -0.324   1.1349   0.9920  -0.7333
 LG5  N3    N  NT    0  -0.430   1.2071  -0.4458  -0.5433
 LG5  C4    C  C1    0  -0.170  -0.0607  -1.0517  -0.4404
 LG5  C5    C  C     0   0.196  -1.1307  -0.3875   0.0428
 LG5  C6    C  C1    0  -0.231  -0.9265   0.9663   0.5533
 LG5  C7    C  CH3   0  -0.518   2.1471  -0.8999   0.4667
 LG5  N8    N  NH2   0  -0.859  -2.4011  -0.9463   0.2052
 LG5  H1    H  H     0   0.249   0.3845   2.6244   0.6299
 LG5  H21   H  HCH2  0   0.241   2.1383   1.4085  -0.6363
 LG5  H22   H  HCH2  0   0.238   0.8099   1.1920  -1.7638
 LG5  H4    H  H     0   0.242  -0.1125  -2.1057  -0.7022
 LG5  H6    H  H     0   0.254  -1.6668   1.3804   1.2283
 LG5  H71   H  HCH3  0   0.204   1.8691  -0.6183   1.4902
 LG5  H72   H  HCH3  0   0.234   2.2126  -1.9885   0.4300
 LG5  H73   H  HCH3  0   0.230   3.1409  -0.5011   0.2578
 LG5  HN81  H  HNH2  0   0.365  -3.1438  -0.3341  -0.1021
 LG5  HN82  H  HNH2  0   0.362  -2.5030  -1.8381  -0.2567

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
 LG5  C1  C2    single  1.502  0.020  1.502
 LG5  C1  C6    double  1.335  0.020  1.335
 LG5  C1  H1    single  0.930  0.020  1.080
 LG5  C2  N3    single  1.452  0.020  1.452
 LG5  C2  H21   single  0.970  0.020  1.090
 LG5  C2  H22   single  0.970  0.020  1.090
 LG5  N3  C4    single  1.409  0.020  1.409
 LG5  N3  C7    single  1.453  0.020  1.453
 LG5  C4  C5    double  1.349  0.020  1.349
 LG5  C4  H4    single  0.930  0.020  1.080
 LG5  C5  C6    single  1.461  0.020  1.461
 LG5  C5  N8    single  1.397  0.020  1.397
 LG5  C6  H6    single  0.930  0.020  1.080
 LG5  C7  H71   single  0.970  0.020  1.090
 LG5  C7  H72   single  0.970  0.020  1.090
 LG5  C7  H73   single  0.970  0.020  1.090
 LG5  N8  HN81  single  0.890  0.020  1.040
 LG5  N8  HN82  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
 LG5  H1    C1  C6    121.66  3.000
 LG5  H1    C1  C2    120.61  3.000
 LG5  C6    C1  C2    117.73  3.000
 LG5  H22   C2  H21   106.62  3.000
 LG5  H22   C2  N3    108.52  3.000
 LG5  H21   C2  N3    108.71  3.000
 LG5  H22   C2  C1    109.26  3.000
 LG5  H21   C2  C1    111.40  3.000
 LG5  N3    C2  C1    112.15  3.000
 LG5  C7    N3  C4    113.39  3.000
 LG5  C7    N3  C2    115.64  3.000
 LG5  C4    N3  C2    113.00  3.000
 LG5  H4    C4  C5    121.72  3.000
 LG5  H4    C4  N3    116.25  3.000
 LG5  C5    C4  N3    121.88  3.000
 LG5  N8    C5  C6    117.19  3.000
 LG5  N8    C5  C4    124.46  3.000
 LG5  C6    C5  C4    118.07  3.000
 LG5  H6    C6  C5    118.43  3.000
 LG5  H6    C6  C1    121.65  3.000
 LG5  C5    C6  C1    119.88  3.000
 LG5  H73   C7  H72   107.67  3.000
 LG5  H73   C7  H71   108.39  3.000
 LG5  H72   C7  H71   107.61  3.000
 LG5  H73   C7  N3    110.00  3.000
 LG5  H72   C7  N3    109.11  3.000
 LG5  H71   C7  N3    113.86  3.000
 LG5  HN82  N8  HN81  108.78  3.000
 LG5  HN82  N8  C5    113.07  3.000
 LG5  HN81  N8  C5    112.99  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
 LG5  Var_01  C4    N3  C2  C1    46.98  30.0  1
 LG5  Var_02  C4    C5  C6  C1    17.66  30.0  1
 LG5  Var_03  C5    C6  C1  C2     3.27  30.0  1
 LG5  Var_04  C5    C4  N3  C2   -28.57  30.0  1
 LG5  Var_05  C6    C1  C2  N3   -35.44  30.0  1
 LG5  Var_06  C6    C5  C4  N3    -4.26  30.0  1
 LG5  Var_07  H71   C7  N3  C2    67.19  30.0  3
 LG5  Var_08  HN81  N8  C5  C4  -136.60  30.0  2

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
 LG5  plan-1  C2  0.020
 LG5  plan-1  N3  0.020
 LG5  plan-1  C4  0.020
 LG5  plan-1  C7  0.020

