# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 17:22:54 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 6-{[2-(dimethylamino)benzyl]amino}pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1ccccc1CNc2ccc(cn2)C(N)=O
#
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
 4G4  4G4  6-{[2-(dimethylamino)benzyl]amino}pyridine-3-carboxamide  ligand  38  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4G4
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
 4G4  C7   C  CR16  0  -0.261   4.3507   2.1468   0.5359
 4G4  C6   C  CR16  0  -0.258   5.2041   1.0548   0.5116
 4G4  C14  C  CR16  0  -0.151  -3.1110   0.0364  -1.0074
 4G4  C8   C  CR16  0  -0.288   3.0317   1.9753   0.1426
 4G4  C5   C  CR16  0  -0.311   4.7340  -0.1902   0.1203
 4G4  C13  C  CR16  0  -0.396  -1.7493   0.2077  -0.9799
 4G4  C16  C  CR16  0  -0.073  -3.1470   0.3619   1.3397
 4G4  C15  C  CR6   0  -0.165  -3.8576   0.0941   0.1738
 4G4  C9   C  CR6   0   0.049   2.5449   0.7375  -0.2641
 4G4  C4   C  CR6   0   0.272   3.4033  -0.3775  -0.2637
 4G4  C12  C  CR6   0   0.519  -1.1302   0.4533   0.2629
 4G4  C10  C  CH2   0  -0.364   1.1200   0.6516  -0.7381
 4G4  N17  N  N     0  -0.462  -1.8395   0.5380   1.3950
 4G4  N19  N  NH2   0  -0.822  -5.9625  -0.3161   1.2752
 4G4  N11  N  NH1   0  -0.652   0.2027   0.6079   0.3819
 4G4  N2   N  NT    0  -0.495   2.9248  -1.6329  -0.6819
 4G4  O20  O  O     0  -0.491  -5.9314   0.0061  -0.9521
 4G4  H1   H  HCR6  0   0.253   4.7086   3.1215   0.8394
 4G4  H2   H  HCR6  0   0.256   6.2409   1.1650   0.8030
 4G4  H3   H  HCR6  0   0.269  -3.6057  -0.1522  -1.9512
 4G4  H4   H  HCR6  0   0.252   2.3648   2.8298   0.1255
 4G4  H5   H  HCR6  0   0.262   5.4188  -1.0276   0.1209
 4G4  H6   H  HCR6  0   0.278  -1.1724   0.1567  -1.8925
 4G4  H7   H  HCR6  0   0.255  -3.6582   0.4617   2.2927
 4G4  H8   H  HCH3  0   0.207   4.5359  -3.0232  -0.4285
 4G4  H9   H  HCH3  0   0.247   3.3854  -3.3680  -1.7193
 4G4  H10  H  HCH3  0   0.245   4.5556  -2.0680  -1.9224
 4G4  H11  H  HCH3  0   0.254   1.2470  -1.5978   0.5952
 4G4  H12  H  HCH3  0   0.235   1.5117  -3.1136  -0.2592
 4G4  H13  H  HCH3  0   0.213   2.5343  -2.6888   1.1225
 4G4  H14  H  HCH2  0   0.261   0.9032   1.5173  -1.3746
 4G4  H15  H  HCH2  0   0.262   0.9940  -0.2381  -1.3594
 4G4  H16  H  HNH2  0   0.410  -5.4768  -0.5200   2.1304
 4G4  H17  H  HNH2  0   0.403  -6.9611  -0.4418   1.2788
 4G4  H18  H  HNH1  0   0.392   0.5422   0.8827   1.2901
 4G4  C18  C  C     0   0.486  -5.3305  -0.0768   0.1134
 4G4  C1   C  CH3   0  -0.547   3.9054  -2.5615  -1.2007
 4G4  C3   C  CH3   0  -0.544   2.0129  -2.2855   0.2437

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
 4G4  C6   C7   aromatic  1.386  0.020  1.386
 4G4  C6   C5   aromatic  1.387  0.020  1.387
 4G4  C7   C8   aromatic  1.387  0.020  1.387
 4G4  C5   C4   aromatic  1.398  0.020  1.398
 4G4  C8   C9   aromatic  1.391  0.020  1.391
 4G4  C4   C9   aromatic  1.407  0.020  1.407
 4G4  C4   N2   single    1.407  0.020  1.407
 4G4  C9   C10  single    1.504  0.020  1.504
 4G4  N2   C3   single    1.454  0.020  1.454
 4G4  N2   C1   single    1.447  0.020  1.447
 4G4  C10  N11  single    1.448  0.020  1.448
 4G4  N11  C12  single    1.347  0.020  1.347
 4G4  C13  C12  aromatic  1.410  0.020  1.410
 4G4  C13  C14  aromatic  1.373  0.020  1.373
 4G4  C12  N17  aromatic  1.339  0.020  1.339
 4G4  C14  C15  aromatic  1.399  0.020  1.399
 4G4  N17  C16  aromatic  1.320  0.020  1.320
 4G4  C15  C16  aromatic  1.391  0.020  1.391
 4G4  C15  C18  single    1.484  0.020  1.484
 4G4  C18  O20  double    1.226  0.020  1.226
 4G4  C18  N19  single    1.344  0.020  1.344
 4G4  C7   H1   single    0.930  0.020  1.080
 4G4  C6   H2   single    0.930  0.020  1.080
 4G4  C14  H3   single    0.930  0.020  1.080
 4G4  C8   H4   single    0.930  0.020  1.080
 4G4  C5   H5   single    0.930  0.020  1.080
 4G4  C13  H6   single    0.930  0.020  1.080
 4G4  C16  H7   single    0.930  0.020  1.080
 4G4  C1   H8   single    0.970  0.020  1.090
 4G4  C1   H9   single    0.970  0.020  1.090
 4G4  C1   H10  single    0.970  0.020  1.090
 4G4  C3   H11  single    0.970  0.020  1.090
 4G4  C3   H12  single    0.970  0.020  1.090
 4G4  C3   H13  single    0.970  0.020  1.090
 4G4  C10  H14  single    0.970  0.020  1.090
 4G4  C10  H15  single    0.970  0.020  1.090
 4G4  N19  H16  single    0.860  0.020  1.020
 4G4  N19  H17  single    0.860  0.020  1.020
 4G4  N11  H18  single    0.860  0.020  1.020

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
 4G4  H1   C7   C8   120.37  3.000
 4G4  H1   C7   C6   120.73  3.000
 4G4  C8   C7   C6   118.89  3.000
 4G4  H2   C6   C5   119.46  3.000
 4G4  H2   C6   C7   120.31  3.000
 4G4  C5   C6   C7   120.23  3.000
 4G4  H3   C14  C15  119.98  3.000
 4G4  H3   C14  C13  119.52  3.000
 4G4  C15  C14  C13  120.49  3.000
 4G4  H4   C8   C9   118.79  3.000
 4G4  H4   C8   C7   119.47  3.000
 4G4  C9   C8   C7   121.72  3.000
 4G4  H5   C5   C4   119.94  3.000
 4G4  H5   C5   C6   118.70  3.000
 4G4  C4   C5   C6   121.36  3.000
 4G4  H6   C13  C12  121.20  3.000
 4G4  H6   C13  C14  120.44  3.000
 4G4  C12  C13  C14  118.36  3.000
 4G4  H7   C16  N17  114.65  3.000
 4G4  H7   C16  C15  120.84  3.000
 4G4  N17  C16  C15  124.51  3.000
 4G4  C18  C15  C16  124.27  3.000
 4G4  C18  C15  C14  119.39  3.000
 4G4  C16  C15  C14  116.30  3.000
 4G4  C10  C9   C4   122.19  3.000
 4G4  C10  C9   C8   118.33  3.000
 4G4  C4   C9   C8   119.45  3.000
 4G4  N2   C4   C9   119.96  3.000
 4G4  N2   C4   C5   121.67  3.000
 4G4  C9   C4   C5   118.34  3.000
 4G4  N11  C12  N17  116.25  3.000
 4G4  N17  C12  C13  121.59  3.000
 4G4  N11  C12  C13  122.16  3.000
 4G4  H15  C10  H14  106.87  3.000
 4G4  H15  C10  N11  110.01  3.000
 4G4  H14  C10  N11  110.34  3.000
 4G4  H15  C10  C9   109.57  3.000
 4G4  H14  C10  C9   108.98  3.000
 4G4  N11  C10  C9   110.98  3.000
 4G4  C12  N17  C16  118.74  3.000
 4G4  H17  N19  H16  116.83  3.000
 4G4  H17  N19  C18  119.46  3.000
 4G4  H16  N19  C18  123.01  3.000
 4G4  H18  N11  C10  118.38  3.000
 4G4  H18  N11  C12  116.37  3.000
 4G4  C10  N11  C12  124.18  3.000
 4G4  C3   N2   C1   111.43  3.000
 4G4  C1   N2   C4   116.66  3.000
 4G4  C3   N2   C4   115.13  3.000
 4G4  O20  C18  N19  122.20  3.000
 4G4  N19  C18  C15  116.87  3.000
 4G4  O20  C18  C15  120.93  3.000
 4G4  H10  C1   H9   107.73  3.000
 4G4  H10  C1   H8   108.27  3.000
 4G4  H9   C1   H8   107.28  3.000
 4G4  H10  C1   N2   110.57  3.000
 4G4  H9   C1   N2   108.78  3.000
 4G4  H8   C1   N2   113.99  3.000
 4G4  H13  C3   H12  107.95  3.000
 4G4  H13  C3   H11  107.92  3.000
 4G4  H12  C3   H11  107.79  3.000
 4G4  H13  C3   N2   112.10  3.000
 4G4  H12  C3   N2   109.60  3.000
 4G4  H11  C3   N2   111.32  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
 4G4  CONST_01  C4   C5   C6   C7      0.00   0.0  0
 4G4  CONST_02  C4   C9   C8   C7      0.00   0.0  0
 4G4  CONST_03  C9   C8   C7   C6      0.00   0.0  0
 4G4  CONST_04  C9   C4   C5   C6      0.00   0.0  0
 4G4  CONST_05  N17  C12  C13  C14     0.00   0.0  0
 4G4  CONST_06  N17  C16  C15  C14     0.00   0.0  0
 4G4  CONST_07  C5   C6   C7   C8      0.00   0.0  0
 4G4  CONST_08  C5   C4   C9   C8      0.00   0.0  0
 4G4  CONST_09  C16  N17  C12  C13     0.00   0.0  0
 4G4  CONST_10  C16  C15  C14  C13     0.00   0.0  0
 4G4  CONST_11  C12  C13  C14  C15     0.00   0.0  0
 4G4  CONST_12  C12  N17  C16  C15     0.00   0.0  0
 4G4  CONST_13  C10  C9   C8   C7    180.00   0.0  0
 4G4  CONST_14  N2   C4   C5   C6    180.00   0.0  0
 4G4  CONST_15  N11  C12  C13  C14   180.00   0.0  0
 4G4  CONST_16  N2   C4   C9   C8    180.00   0.0  0
 4G4  CONST_17  C10  C9   C4   C5    180.00   0.0  0
 4G4  CONST_18  C18  C15  C14  C13   180.00   0.0  0
 4G4  CONST_19  N11  C12  N17  C16   180.00   0.0  0
 4G4  CONST_20  N17  C16  C15  C18   180.00   0.0  0
 4G4  CONST_21  H5   C5   C6   C7    180.00   0.0  0
 4G4  CONST_22  H4   C8   C7   C6    180.00   0.0  0
 4G4  CONST_23  H7   C16  C15  C14   180.00   0.0  0
 4G4  CONST_24  H2   C6   C7   C8    180.00   0.0  0
 4G4  CONST_25  H1   C7   C6   C5    180.00   0.0  0
 4G4  CONST_26  H3   C14  C15  C16   180.00   0.0  0
 4G4  CONST_27  H6   C13  C14  C15   180.00   0.0  0
 4G4  CONST_30  C10  N11  C12  C13     0.00   0.0  0
 4G4  CONST_33  N17  C12  N11  C10   180.00   0.0  0
 4G4  CONST_34  H18  N11  C12  C13   180.00   0.0  0
 4G4  CONST_35  H16  N19  C18  C15     0.00   0.0  0
 4G4  CONST_36  H17  N19  C18  C15   180.00   0.0  0
 4G4  Var_01    O20  C18  C15  C14   -15.04  30.0  2
 4G4  Var_02    N11  C10  C9   C8    -79.66  30.0  2
 4G4  Var_03    C12  N11  C10  C9   -176.05  30.0  3
 4G4  Var_04    H11  C3   N2   C4     47.01  30.0  3
 4G4  Var_05    H8   C1   N2   C4     74.98  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
 4G4  plan-1  C7   0.020
 4G4  plan-1  C6   0.020
 4G4  plan-1  C8   0.020
 4G4  plan-1  C5   0.020
 4G4  plan-1  C9   0.020
 4G4  plan-1  C4   0.020
 4G4  plan-1  C10  0.020
 4G4  plan-1  N2   0.020
 4G4  plan-1  H1   0.020
 4G4  plan-1  H2   0.020
 4G4  plan-1  H4   0.020
 4G4  plan-1  H5   0.020
 4G4  plan-2  C14  0.020
 4G4  plan-2  C13  0.020
 4G4  plan-2  C16  0.020
 4G4  plan-2  C15  0.020
 4G4  plan-2  C12  0.020
 4G4  plan-2  N17  0.020
 4G4  plan-2  N11  0.020
 4G4  plan-2  H3   0.020
 4G4  plan-2  H6   0.020
 4G4  plan-2  H7   0.020
 4G4  plan-2  C18  0.020
 4G4  plan-3  C15  0.020
 4G4  plan-3  N19  0.020
 4G4  plan-3  O20  0.020
 4G4  plan-3  H16  0.020
 4G4  plan-3  H17  0.020
 4G4  plan-3  C18  0.020
 4G4  plan-4  C12  0.020
 4G4  plan-4  C10  0.020
 4G4  plan-4  N11  0.020
 4G4  plan-4  H18  0.020
 4G4  plan-5  C4   0.020
 4G4  plan-5  N2   0.020
 4G4  plan-5  C1   0.020
 4G4  plan-5  C3   0.020

