# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 15:52:22 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: N,N-dimethylpyridin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1ccncc1
#
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
 JGD  JGD  N,N-dimethylpyridin-4-amine  ligand  19  9  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JGD
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
 JGD  C01   C  CH3   0  -0.539   2.3455   1.2192   0.1108
 JGD  N02   N  NT    0  -0.495   1.6236  -0.0303   0.0280
 JGD  C03   C  CH3   0  -0.539   2.3451  -1.2805  -0.0453
 JGD  C04   C  CR6   0   0.476   0.2716  -0.0296   0.0228
 JGD  C05   C  CR16  0  -0.417  -0.4792   1.1631   0.0684
 JGD  C06   C  CR16  0  -0.079  -1.8575   1.0973   0.0587
 JGD  N07   N  N     0  -0.439  -2.5673  -0.0279   0.0100
 JGD  C08   C  CR16  0  -0.079  -1.8585  -1.1540  -0.0320
 JGD  C09   C  CR16  0  -0.417  -0.4802  -1.2215  -0.0287
 JGD  H011  H  HCH3  0   0.240   2.0981   1.7728   1.0199
 JGD  H012  H  HCH3  0   0.260   3.4127   1.0192   0.1254
 JGD  H013  H  HCH3  0   0.239   2.1414   1.8696  -0.7438
 JGD  H032  H  HCH3  0   0.240   2.1017  -1.8378  -0.9532
 JGD  H033  H  HCH3  0   0.260   3.4126  -1.0815  -0.0560
 JGD  H031  H  HCH3  0   0.239   2.1363  -1.9273   0.8110
 JGD  H051  H  HCR6  0   0.272  -0.0042   2.1331   0.1088
 JGD  H061  H  HCR6  0   0.252  -2.4243   2.0224   0.0925
 JGD  H081  H  HCR6  0   0.252  -2.4261  -2.0785  -0.0713
 JGD  H091  H  HCR6  0   0.272  -0.0061  -2.1921  -0.0647

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
 JGD  C03  N02   single    1.445  0.020  1.445
 JGD  C09  C08   aromatic  1.380  0.020  1.380
 JGD  C09  C04   aromatic  1.410  0.020  1.410
 JGD  C08  N07   aromatic  1.331  0.020  1.331
 JGD  N02  C04   single    1.352  0.020  1.352
 JGD  N02  C01   single    1.445  0.020  1.445
 JGD  C04  C05   aromatic  1.410  0.020  1.410
 JGD  N07  C06   aromatic  1.331  0.020  1.331
 JGD  C05  C06   aromatic  1.380  0.020  1.380
 JGD  C01  H011  single    0.970  0.020  1.090
 JGD  C01  H012  single    0.970  0.020  1.090
 JGD  C01  H013  single    0.970  0.020  1.090
 JGD  C03  H032  single    0.970  0.020  1.090
 JGD  C03  H033  single    0.970  0.020  1.090
 JGD  C03  H031  single    0.970  0.020  1.090
 JGD  C05  H051  single    0.930  0.020  1.080
 JGD  C06  H061  single    0.930  0.020  1.080
 JGD  C08  H081  single    0.930  0.020  1.080
 JGD  C09  H091  single    0.930  0.020  1.080

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
 JGD  H013  C01  H012  107.67  3.000
 JGD  H013  C01  H011  107.86  3.000
 JGD  H012  C01  H011  107.73  3.000
 JGD  H013  C01  N02   112.11  3.000
 JGD  H012  C01  N02   109.42  3.000
 JGD  H011  C01  N02   111.87  3.000
 JGD  C04   N02  C03   119.96  3.000
 JGD  C04   N02  C01   119.95  3.000
 JGD  C03   N02  C01   120.09  3.000
 JGD  H031  C03  H033  107.69  3.000
 JGD  H031  C03  H032  107.85  3.000
 JGD  H033  C03  H032  107.71  3.000
 JGD  H031  C03  N02   112.13  3.000
 JGD  H033  C03  N02   109.43  3.000
 JGD  H032  C03  N02   111.85  3.000
 JGD  C09   C04  C05   115.61  3.000
 JGD  C05   C04  N02   122.19  3.000
 JGD  C09   C04  N02   122.19  3.000
 JGD  H051  C05  C06   118.82  3.000
 JGD  H051  C05  C04   121.76  3.000
 JGD  C06   C05  C04   119.42  3.000
 JGD  H061  C06  N07   116.30  3.000
 JGD  H061  C06  C05   118.73  3.000
 JGD  N07   C06  C05   124.97  3.000
 JGD  C08   N07  C06   115.61  3.000
 JGD  H081  C08  C09   118.73  3.000
 JGD  H081  C08  N07   116.30  3.000
 JGD  C09   C08  N07   124.97  3.000
 JGD  H091  C09  C08   118.82  3.000
 JGD  H091  C09  C04   121.77  3.000
 JGD  C08   C09  C04   119.42  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
 JGD  CONST_01  N07   C08  C09  C04    0.00   0.0  0
 JGD  CONST_02  N07   C06  C05  C04    0.00   0.0  0
 JGD  CONST_03  C08   C09  C04  C05    0.00   0.0  0
 JGD  CONST_04  C08   N07  C06  C05    0.00   0.0  0
 JGD  CONST_05  C09   C08  N07  C06    0.00   0.0  0
 JGD  CONST_06  C09   C04  C05  C06    0.00   0.0  0
 JGD  CONST_07  C08   C09  C04  N02  180.00   0.0  0
 JGD  CONST_08  C06   C05  C04  N02  180.00   0.0  0
 JGD  CONST_09  H081  C08  C09  C04  180.00   0.0  0
 JGD  CONST_10  H061  C06  C05  C04  180.00   0.0  0
 JGD  CONST_11  H091  C09  C04  C05  180.00   0.0  0
 JGD  CONST_12  H051  C05  C06  N07  180.00   0.0  0
 JGD  CONST_13  C09   C04  N02  C01  180.00   0.0  0
 JGD  CONST_14  C05   C04  N02  C01    0.00   0.0  0
 JGD  CONST_15  C09   C04  N02  C03    0.00   0.0  0
 JGD  CONST_16  C05   C04  N02  C03  180.00   0.0  0
 JGD  Var_01    H032  C03  N02  C04   59.22  30.0  3
 JGD  Var_02    H011  C01  N02  C04   59.39  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
 JGD  plan-1  N02   0.020
 JGD  plan-1  C04   0.020
 JGD  plan-1  C05   0.020
 JGD  plan-1  C06   0.020
 JGD  plan-1  N07   0.020
 JGD  plan-1  C08   0.020
 JGD  plan-1  C09   0.020
 JGD  plan-1  H051  0.020
 JGD  plan-1  H061  0.020
 JGD  plan-1  H081  0.020
 JGD  plan-1  H091  0.020
 JGD  plan-2  C01   0.020
 JGD  plan-2  N02   0.020
 JGD  plan-2  C03   0.020
 JGD  plan-2  C04   0.020

