# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 15:55:57 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 6-{[3-(dimethylamino)benzyl]amino}pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1cccc(CNc2ccc(cn2)C(N)=O)c1
#
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
 4G0  4G0  6-{[3-(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_4G0
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
 4G0  C4   C  CR16  0  -0.228   4.0711   2.2570  -0.1976
 4G0  C10  C  CR16  0  -0.150  -3.5256   0.1294   1.1573
 4G0  C5   C  CR16  0  -0.348   2.7429   2.2920   0.2087
 4G0  C3   C  CR16  0  -0.366   4.7524   1.0605  -0.3286
 4G0  C9   C  CR16  0  -0.400  -2.1867   0.4314   1.1479
 4G0  C14  C  CR16  0  -0.390   2.7724  -0.1131   0.3643
 4G0  C12  C  CR16  0  -0.074  -3.4104  -0.2250  -1.1823
 4G0  C11  C  CR6   0  -0.165  -4.1818  -0.2306  -0.0245
 4G0  C6   C  CR6   0   0.091   2.0985   1.0948   0.4929
 4G0  C2   C  CR6   0   0.409   4.1132  -0.1659  -0.0557
 4G0  C8   C  CR6   0   0.516  -1.4960   0.3766  -0.0805
 4G0  C7   C  CH2   0  -0.343   0.6533   1.0872   0.9140
 4G0  N2   N  N     0  -0.463  -2.1231   0.0655  -1.2222
 4G0  N3   N  NH2   0  -0.822  -6.1550  -1.1444  -1.0689
 4G0  N1   N  NH1   0  -0.645  -0.1759   0.6262  -0.1783
 4G0  N    N  NT    0  -0.505   4.7701  -1.3593  -0.1941
 4G0  O    O  O     0  -0.491  -6.3134  -0.2525   0.9912
 4G0  H1   H  HCR6  0   0.251   4.5919   3.1814  -0.4142
 4G0  H2   H  HCR6  0   0.269  -4.0744   0.1682   2.0892
 4G0  H3   H  HCR6  0   0.243   2.2209   3.2348   0.3122
 4G0  H4   H  HCR6  0   0.266   5.7883   1.0861  -0.6366
 4G0  H5   H  HCR6  0   0.278  -1.6844   0.7106   2.0629
 4G0  H6   H  HCR6  0   0.262   2.2397  -1.0244   0.6024
 4G0  H7   H  HCR6  0   0.255  -3.8526  -0.4480  -2.1483
 4G0  H8   H  HCH3  0   0.226   6.7756  -0.8765   0.3183
 4G0  H9   H  HCH3  0   0.254   6.5336  -2.3911  -0.5515
 4G0  H10  H  HCH3  0   0.237   6.4176  -0.8685  -1.4128
 4G0  H11  H  HCH3  0   0.227   3.9217  -2.5549   1.3429
 4G0  H12  H  HCH3  0   0.237   3.2109  -2.7777  -0.2590
 4G0  H13  H  HCH3  0   0.255   4.8085  -3.4144   0.0842
 4G0  H14  H  HCH2  0   0.253   0.5245   0.4204   1.7713
 4G0  H15  H  HCH2  0   0.251   0.3545   2.0894   1.2414
 4G0  H16  H  HNH2  0   0.409  -5.5889  -1.5438  -1.7964
 4G0  H17  H  HNH2  0   0.402  -7.1268  -1.4077  -1.0612
 4G0  H18  H  HNH1  0   0.389   0.1939   0.6951  -1.1133
 4G0  C13  C  C     0   0.486  -5.6316  -0.5430   0.0146
 4G0  C    C  CH3   0  -0.536   6.1877  -1.3644  -0.4671
 4G0  C1   C  CH3   0  -0.538   4.1447  -2.5746   0.2704

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
 4G0  C    N    single    1.444  0.020  1.444
 4G0  C3   C4   aromatic  1.383  0.020  1.383
 4G0  C3   C2   aromatic  1.410  0.020  1.410
 4G0  C4   C5   aromatic  1.389  0.020  1.389
 4G0  N    C2   single    1.369  0.020  1.369
 4G0  N    C1   single    1.444  0.020  1.444
 4G0  C2   C14  aromatic  1.406  0.020  1.406
 4G0  C5   C6   aromatic  1.389  0.020  1.389
 4G0  C14  C6   aromatic  1.389  0.020  1.389
 4G0  C6   C7   single    1.505  0.020  1.505
 4G0  C7   N1   single    1.447  0.020  1.447
 4G0  N1   C8   single    1.347  0.020  1.347
 4G0  C9   C8   aromatic  1.410  0.020  1.410
 4G0  C9   C10  aromatic  1.373  0.020  1.373
 4G0  C8   N2   aromatic  1.339  0.020  1.339
 4G0  C10  C11  aromatic  1.399  0.020  1.399
 4G0  N2   C12  aromatic  1.320  0.020  1.320
 4G0  C11  C12  aromatic  1.391  0.020  1.391
 4G0  C11  C13  single    1.484  0.020  1.484
 4G0  C13  O    double    1.226  0.020  1.226
 4G0  C13  N3   single    1.345  0.020  1.345
 4G0  C4   H1   single    0.930  0.020  1.080
 4G0  C10  H2   single    0.930  0.020  1.080
 4G0  C5   H3   single    0.930  0.020  1.080
 4G0  C3   H4   single    0.930  0.020  1.080
 4G0  C9   H5   single    0.930  0.020  1.080
 4G0  C14  H6   single    0.930  0.020  1.080
 4G0  C12  H7   single    0.930  0.020  1.080
 4G0  C    H8   single    0.970  0.020  1.090
 4G0  C    H9   single    0.970  0.020  1.090
 4G0  C    H10  single    0.970  0.020  1.090
 4G0  C1   H11  single    0.970  0.020  1.090
 4G0  C1   H12  single    0.970  0.020  1.090
 4G0  C1   H13  single    0.970  0.020  1.090
 4G0  C7   H14  single    0.970  0.020  1.090
 4G0  C7   H15  single    0.970  0.020  1.090
 4G0  N3   H16  single    0.860  0.020  1.020
 4G0  N3   H17  single    0.860  0.020  1.020
 4G0  N1   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
 4G0  H1   C4   C3   118.86  3.000
 4G0  H1   C4   C5   119.78  3.000
 4G0  C3   C4   C5   121.35  3.000
 4G0  H2   C10  C11  119.92  3.000
 4G0  H2   C10  C9   119.52  3.000
 4G0  C11  C10  C9   120.56  3.000
 4G0  H3   C5   C6   120.49  3.000
 4G0  H3   C5   C4   120.71  3.000
 4G0  C6   C5   C4   118.79  3.000
 4G0  H4   C3   C2   120.68  3.000
 4G0  H4   C3   C4   118.59  3.000
 4G0  C2   C3   C4   120.73  3.000
 4G0  H5   C9   C8   121.33  3.000
 4G0  H5   C9   C10  120.30  3.000
 4G0  C8   C9   C10  118.37  3.000
 4G0  H6   C14  C2   120.24  3.000
 4G0  H6   C14  C6   118.24  3.000
 4G0  C2   C14  C6   121.52  3.000
 4G0  H7   C12  N2   114.55  3.000
 4G0  H7   C12  C11  120.92  3.000
 4G0  N2   C12  C11  124.52  3.000
 4G0  C13  C11  C12  124.37  3.000
 4G0  C13  C11  C10  119.36  3.000
 4G0  C12  C11  C10  116.23  3.000
 4G0  C7   C6   C14  119.16  3.000
 4G0  C7   C6   C5   120.47  3.000
 4G0  C14  C6   C5   120.36  3.000
 4G0  N    C2   C14  121.36  3.000
 4G0  C14  C2   C3   117.23  3.000
 4G0  N    C2   C3   121.41  3.000
 4G0  N1   C8   N2   116.11  3.000
 4G0  N2   C8   C9   121.48  3.000
 4G0  N1   C8   C9   122.41  3.000
 4G0  H15  C7   H14  106.93  3.000
 4G0  H15  C7   N1   111.14  3.000
 4G0  H14  C7   N1   109.27  3.000
 4G0  H15  C7   C6   109.92  3.000
 4G0  H14  C7   C6   109.60  3.000
 4G0  N1   C7   C6   109.92  3.000
 4G0  C8   N2   C12  118.81  3.000
 4G0  H17  N3   H16  116.45  3.000
 4G0  H17  N3   C13  119.09  3.000
 4G0  H16  N3   C13  122.81  3.000
 4G0  H18  N1   C7   117.93  3.000
 4G0  H18  N1   C8   116.07  3.000
 4G0  C7   N1   C8   124.47  3.000
 4G0  C1   N    C    118.90  3.000
 4G0  C1   N    C2   119.56  3.000
 4G0  C    N    C2   119.56  3.000
 4G0  O    C13  N3   122.08  3.000
 4G0  N3   C13  C11  116.95  3.000
 4G0  O    C13  C11  120.97  3.000
 4G0  H10  C    H9   107.14  3.000
 4G0  H10  C    H8   107.79  3.000
 4G0  H9   C    H8   107.80  3.000
 4G0  H10  C    N    111.64  3.000
 4G0  H9   C    N    109.31  3.000
 4G0  H8   C    N    112.94  3.000
 4G0  H13  C1   H12  107.19  3.000
 4G0  H13  C1   H11  107.82  3.000
 4G0  H12  C1   H11  107.68  3.000
 4G0  H13  C1   N    109.32  3.000
 4G0  H12  C1   N    111.77  3.000
 4G0  H11  C1   N    112.83  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
 4G0  CONST_01  C14  C2   C3   C4     0.00   0.0  0
 4G0  CONST_02  C14  C6   C5   C4     0.00   0.0  0
 4G0  CONST_03  N2   C8   C9   C10    0.00   0.0  0
 4G0  CONST_04  N2   C12  C11  C10    0.00   0.0  0
 4G0  CONST_05  C2   C3   C4   C5     0.00   0.0  0
 4G0  CONST_06  C2   C14  C6   C5     0.00   0.0  0
 4G0  CONST_07  C6   C5   C4   C3     0.00   0.0  0
 4G0  CONST_08  C6   C14  C2   C3     0.00   0.0  0
 4G0  CONST_09  C12  N2   C8   C9     0.00   0.0  0
 4G0  CONST_10  C12  C11  C10  C9     0.00   0.0  0
 4G0  CONST_11  C8   C9   C10  C11    0.00   0.0  0
 4G0  CONST_12  C8   N2   C12  C11    0.00   0.0  0
 4G0  CONST_13  N    C2   C3   C4   180.00   0.0  0
 4G0  CONST_14  C7   C6   C5   C4   180.00   0.0  0
 4G0  CONST_15  N1   C8   C9   C10  180.00   0.0  0
 4G0  CONST_16  C13  C11  C10  C9   180.00   0.0  0
 4G0  CONST_17  N1   C8   N2   C12  180.00   0.0  0
 4G0  CONST_18  N    C2   C14  C6   180.00   0.0  0
 4G0  CONST_19  C7   C6   C14  C2   180.00   0.0  0
 4G0  CONST_20  N2   C12  C11  C13  180.00   0.0  0
 4G0  CONST_21  H7   C12  C11  C10  180.00   0.0  0
 4G0  CONST_22  H4   C3   C4   C5   180.00   0.0  0
 4G0  CONST_23  H6   C14  C6   C5   180.00   0.0  0
 4G0  CONST_24  H3   C5   C4   C3   180.00   0.0  0
 4G0  CONST_25  H2   C10  C11  C12  180.00   0.0  0
 4G0  CONST_26  H5   C9   C10  C11  180.00   0.0  0
 4G0  CONST_27  H1   C4   C5   C6   180.00   0.0  0
 4G0  CONST_28  C    N    C2   C3     0.00   0.0  0
 4G0  CONST_29  C1   N    C2   C3   180.00   0.0  0
 4G0  CONST_30  C7   N1   C8   C9     0.00   0.0  0
 4G0  CONST_31  C    N    C2   C14  180.00   0.0  0
 4G0  CONST_32  C1   N    C2   C14    0.00   0.0  0
 4G0  CONST_33  N2   C8   N1   C7   180.00   0.0  0
 4G0  CONST_34  H18  N1   C8   C9   180.00   0.0  0
 4G0  CONST_35  H16  N3   C13  C11    0.00   0.0  0
 4G0  CONST_36  H17  N3   C13  C11  180.00   0.0  0
 4G0  Var_01    O    C13  C11  C10   13.91  30.0  2
 4G0  Var_02    N1   C7   C6   C5   105.26  30.0  2
 4G0  Var_03    C8   N1   C7   C6   172.97  30.0  3
 4G0  Var_04    H8   C    N    C2    60.42  30.0  3
 4G0  Var_05    H11  C1   N    C2   -59.76  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
 4G0  plan-1  C4   0.020
 4G0  plan-1  C5   0.020
 4G0  plan-1  C3   0.020
 4G0  plan-1  C14  0.020
 4G0  plan-1  C6   0.020
 4G0  plan-1  C2   0.020
 4G0  plan-1  C7   0.020
 4G0  plan-1  N    0.020
 4G0  plan-1  H1   0.020
 4G0  plan-1  H3   0.020
 4G0  plan-1  H4   0.020
 4G0  plan-1  H6   0.020
 4G0  plan-2  C10  0.020
 4G0  plan-2  C9   0.020
 4G0  plan-2  C12  0.020
 4G0  plan-2  C11  0.020
 4G0  plan-2  C8   0.020
 4G0  plan-2  N2   0.020
 4G0  plan-2  N1   0.020
 4G0  plan-2  H2   0.020
 4G0  plan-2  H5   0.020
 4G0  plan-2  H7   0.020
 4G0  plan-2  C13  0.020
 4G0  plan-3  C11  0.020
 4G0  plan-3  N3   0.020
 4G0  plan-3  O    0.020
 4G0  plan-3  H16  0.020
 4G0  plan-3  H17  0.020
 4G0  plan-3  C13  0.020
 4G0  plan-4  C8   0.020
 4G0  plan-4  C7   0.020
 4G0  plan-4  N1   0.020
 4G0  plan-4  H18  0.020
 4G0  plan-5  C2   0.020
 4G0  plan-5  N    0.020
 4G0  plan-5  C    0.020
 4G0  plan-5  C1   0.020

