# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 17:33:38 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: 4,6-dimethylpyridin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)c(N)cn1
#
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
 8NF  8NF  "5-amino-2,4-dimethylpyridine"
  ligand  19  9  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8NF
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
 8NF  C01  C  CH3   0  -0.741  13.0979  20.0317  41.1202
 8NF  C02  C  CR6   0   0.152  14.1926  21.0404  41.2742
 8NF  C03  C  CR16  0  -0.371  15.3853  20.7316  41.9056
 8NF  C04  C  CR6   0   0.211  16.4023  21.6772  42.0277
 8NF  C06  C  CR16  0  -0.164  15.1109  23.2210  40.9431
 8NF  C07  C  CR6   0   0.180  14.0421  22.3433  40.7694
 8NF  C08  C  CH3   0  -0.726  17.6930  21.3402  42.7161
 8NF  N05  N  N     0  -0.417  16.2508  22.9039  41.5439
 8NF  N71  N  NH2   0  -0.857  12.9079  22.7190  40.0737
 8NF  H1   H  HCH3  0   0.250  12.8405  19.8847  40.0689
 8NF  H2   H  HCH3  0   0.257  13.3881  19.0679  41.5340
 8NF  H3   H  HCH3  0   0.249  12.1840  20.3483  41.6295
 8NF  H4   H  HCR6  0   0.248  15.5308  19.7344  42.3059
 8NF  H5   H  HCR6  0   0.248  15.0295  24.2373  40.5656
 8NF  H6   H  HCH3  0   0.241  18.3950  22.1686  42.6416
 8NF  H7   H  HCH3  0   0.241  17.5368  21.1258  43.7752
 8NF  H8   H  HCH3  0   0.240  18.1623  20.4571  42.2794
 8NF  H9   H  HNH2  0   0.381  12.0479  22.2899  40.3789
 8NF  H10  H  HNH2  0   0.377  12.7890  23.7150  39.9694

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
 8NF  N71  C07  single    1.383  0.020  1.383
 8NF  C07  C06  aromatic  1.394  0.020  1.394
 8NF  C07  C02  aromatic  1.405  0.020  1.405
 8NF  C06  N05  aromatic  1.327  0.020  1.327
 8NF  C01  C02  single    1.497  0.020  1.497
 8NF  C02  C03  aromatic  1.384  0.020  1.384
 8NF  N05  C04  aromatic  1.327  0.020  1.327
 8NF  C03  C04  aromatic  1.394  0.020  1.394
 8NF  C04  C08  single    1.501  0.020  1.501
 8NF  C01  H1   single    0.970  0.020  1.090
 8NF  C01  H2   single    0.970  0.020  1.090
 8NF  C01  H3   single    0.970  0.020  1.090
 8NF  C03  H4   single    0.930  0.020  1.080
 8NF  C06  H5   single    0.930  0.020  1.080
 8NF  C08  H6   single    0.970  0.020  1.090
 8NF  C08  H7   single    0.970  0.020  1.090
 8NF  C08  H8   single    0.970  0.020  1.090
 8NF  N71  H9   single    0.890  0.020  1.040
 8NF  N71  H10  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
 8NF  H3   C01  H2   107.60  3.000
 8NF  H3   C01  H1   106.88  3.000
 8NF  H2   C01  H1   108.04  3.000
 8NF  H3   C01  C02  111.62  3.000
 8NF  H2   C01  C02  111.27  3.000
 8NF  H1   C01  C02  111.23  3.000
 8NF  C07  C02  C03  117.57  3.000
 8NF  C03  C02  C01  121.79  3.000
 8NF  C07  C02  C01  120.64  3.000
 8NF  H4   C03  C04  119.58  3.000
 8NF  H4   C03  C02  119.28  3.000
 8NF  C04  C03  C02  121.14  3.000
 8NF  N05  C04  C08  118.22  3.000
 8NF  C08  C04  C03  121.01  3.000
 8NF  N05  C04  C03  120.77  3.000
 8NF  H5   C06  N05  116.42  3.000
 8NF  H5   C06  C07  119.21  3.000
 8NF  N05  C06  C07  124.38  3.000
 8NF  N71  C07  C06  121.38  3.000
 8NF  C06  C07  C02  117.19  3.000
 8NF  N71  C07  C02  121.36  3.000
 8NF  H8   C08  H7   106.91  3.000
 8NF  H8   C08  H6   108.13  3.000
 8NF  H7   C08  H6   107.94  3.000
 8NF  H8   C08  C04  111.59  3.000
 8NF  H7   C08  C04  111.47  3.000
 8NF  H6   C08  C04  110.63  3.000
 8NF  C06  N05  C04  118.94  3.000
 8NF  H10  N71  H9   110.55  3.000
 8NF  H10  N71  C07  114.65  3.000
 8NF  H9   N71  C07  115.58  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
 8NF  CONST_01  N05  C06  C07  C02     0.00   0.0  0
 8NF  CONST_02  N05  C04  C03  C02     0.00   0.0  0
 8NF  CONST_03  C06  C07  C02  C03     0.00   0.0  0
 8NF  CONST_04  C06  N05  C04  C03     0.00   0.0  0
 8NF  CONST_05  C07  C06  N05  C04     0.00   0.0  0
 8NF  CONST_06  C07  C02  C03  C04     0.00   0.0  0
 8NF  CONST_07  C06  C07  C02  C01   180.00   0.0  0
 8NF  CONST_08  C04  C03  C02  C01   180.00   0.0  0
 8NF  CONST_09  C08  C04  C03  C02   180.00   0.0  0
 8NF  CONST_10  N71  C07  C02  C03   180.00   0.0  0
 8NF  CONST_11  C08  C04  N05  C06   180.00   0.0  0
 8NF  CONST_12  N71  C07  C06  N05   180.00   0.0  0
 8NF  CONST_13  H5   C06  C07  C02   180.00   0.0  0
 8NF  CONST_14  H5   C06  N05  C04   180.00   0.0  0
 8NF  CONST_15  H4   C03  C02  C07   180.00   0.0  0
 8NF  CONST_16  H4   C03  C04  N05   180.00   0.0  0
 8NF  Var_01    H1   C01  C02  C03  -122.12  30.0  2
 8NF  Var_02    H2   C01  C02  C03    -1.61  30.0  2
 8NF  Var_03    H3   C01  C02  C03   118.61  30.0  2
 8NF  Var_04    H6   C08  C04  C03   175.20  30.0  2
 8NF  Var_05    H7   C08  C04  C03   -64.69  30.0  2
 8NF  Var_06    H8   C08  C04  C03    54.77  30.0  2
 8NF  Var_07    H1   C01  C02  C07    57.52  30.0  2
 8NF  Var_08    H2   C01  C02  C07   178.03  30.0  2
 8NF  Var_09    H3   C01  C02  C07   -61.76  30.0  2
 8NF  Var_10    H6   C08  C04  N05    -5.18  30.0  2
 8NF  Var_11    H7   C08  C04  N05   114.94  30.0  2
 8NF  Var_12    H8   C08  C04  N05  -125.61  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
 8NF  plan-1  C01  0.020
 8NF  plan-1  C02  0.020
 8NF  plan-1  C03  0.020
 8NF  plan-1  C04  0.020
 8NF  plan-1  C06  0.020
 8NF  plan-1  C07  0.020
 8NF  plan-1  C08  0.020
 8NF  plan-1  N05  0.020
 8NF  plan-1  N71  0.020
 8NF  plan-1  H4   0.020
 8NF  plan-1  H5   0.020
 8NF  plan-2  C07  0.020
 8NF  plan-2  N71  0.020
 8NF  plan-2  H9   0.020
 8NF  plan-2  H10  0.020

