# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 19:27:47 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 6-{[2-(4-methylpiperazin-1-yl)benzyl]amino}pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccccc2CNc3ccc(cn3)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
 4H7  4H7  6-{[2-(4-methylpiperazin-1-yl)benzyl]amino}pyridine-3-carboxamide  ligand  47  24  .  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_4H7
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
 4H7  C8   C  CR16  0  -0.249   4.2282   3.4462   0.2567
 4H7  C7   C  CR16  0  -0.267   4.7861   2.2453   0.6699
 4H7  C14  C  CR16  0  -0.165  -2.3970  -0.6230  -1.1765
 4H7  C9   C  CR16  0  -0.320   2.9450   3.4594  -0.2732
 4H7  C6   C  CR16  0  -0.267   4.0559   1.0702   0.5538
 4H7  C13  C  CR16  0  -0.361  -1.4136   0.3295  -1.2294
 4H7  C16  C  CR16  0  -0.089  -2.7897  -0.0238   1.0793
 4H7  C15  C  CR6   0  -0.155  -3.1094  -0.8484   0.0073
 4H7  C10  C  CR6   0   0.060   2.2059   2.2872  -0.3957
 4H7  C5   C  CR6   0   0.268   2.7659   1.0778   0.0285
 4H7  C12  C  CR6   0   0.529  -1.1424   1.0848  -0.0680
 4H7  C2   C  CH2   0  -0.290   2.5887  -1.0973  -0.9927
 4H7  C3   C  CH2   0  -0.295   1.6508  -0.7105   1.1849
 4H7  C1   C  CH2   0  -0.286   1.6264  -2.2531  -1.1864
 4H7  C4   C  CH2   0  -0.294   0.7188  -1.8912   0.9840
 4H7  C11  C  CH2   0  -0.349   0.8201   2.3272  -0.9859
 4H7  N3   N  N     0  -0.468  -1.8535   0.9077   1.0541
 4H7  N1   N  NT    0  -0.498   2.0025  -0.1159  -0.0954
 4H7  N    N  NT    0  -0.414   1.3049  -2.8672   0.0863
 4H7  N4   N  NH2   0  -0.821  -4.5803  -2.2906   1.2548
 4H7  N2   N  NH1   0  -0.648  -0.1933   2.0362  -0.0028
 4H7  O    O  O     0  -0.493  -4.6357  -2.3463  -0.9952
 4H7  H13  H  HCR6  0   0.255   4.7872   4.3684   0.3470
 4H7  H12  H  HCR6  0   0.256   5.7862   2.2213   1.0835
 4H7  H19  H  HCR6  0   0.264  -2.6140  -1.2128  -2.0575
 4H7  H14  H  HCR6  0   0.252   2.5097   4.3973  -0.5976
 4H7  H11  H  HCR6  0   0.254   4.4984   0.1343   0.8739
 4H7  H18  H  HCR6  0   0.267  -0.8649   0.4837  -2.1463
 4H7  H20  H  HCR6  0   0.254  -3.3313  -0.0968   2.0178
 4H7  H6   H  HCH2  0   0.198   3.5491  -1.4896  -0.6202
 4H7  H5   H  HCH2  0   0.239   2.7846  -0.6261  -1.9578
 4H7  H8   H  HCH2  0   0.238   1.1477   0.0391   1.7992
 4H7  H7   H  HCH2  0   0.204   2.5401  -1.0469   1.7422
 4H7  H4   H  HCH2  0   0.196   0.7237  -1.8875  -1.7055
 4H7  H3   H  HCH2  0   0.233   2.0946  -2.9994  -1.8335
 4H7  H10  H  HCH2  0   0.231   0.5369  -2.3632   1.9534
 4H7  H9   H  HCH2  0   0.211  -0.2542  -1.5329   0.6121
 4H7  H1   H  HCH3  0   0.231   0.9256  -4.7563  -0.7205
 4H7  H    H  HCH3  0   0.231   0.2580  -4.4852   0.8895
 4H7  H2   H  HCH3  0   0.189  -0.5313  -3.7687  -0.5233
 4H7  H15  H  HCH2  0   0.255   0.6455   3.3131  -1.4268
 4H7  H16  H  HCH2  0   0.261   0.7534   1.6056  -1.7967
 4H7  H21  H  HNH2  0   0.408  -4.0882  -2.0599   2.0997
 4H7  H22  H  HNH2  0   0.401  -5.2772  -3.0142   1.3215
 4H7  H17  H  HNH1  0   0.383  -0.1212   2.5094   0.8847
 4H7  C17  C  C     0   0.479  -4.1647  -1.8875   0.0401
 4H7  C    C  CH3   0  -0.515   0.4455  -4.0164  -0.0780

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
 4H7  C7   C6   aromatic  1.388  0.020  1.388
 4H7  C7   C8   aromatic  1.387  0.020  1.387
 4H7  C6   C5   aromatic  1.393  0.020  1.393
 4H7  C8   C9   aromatic  1.388  0.020  1.388
 4H7  C2   N1   single    1.453  0.020  1.453
 4H7  C2   C1   single    1.516  0.020  1.516
 4H7  C5   N1   single    1.422  0.020  1.422
 4H7  C5   C10  aromatic  1.399  0.020  1.399
 4H7  C9   C10  aromatic  1.391  0.020  1.391
 4H7  N1   C3   single    1.455  0.020  1.455
 4H7  C1   N    single    1.449  0.020  1.449
 4H7  N    C    single    1.444  0.020  1.444
 4H7  N    C4   single    1.450  0.020  1.450
 4H7  C10  C11  single    1.507  0.020  1.507
 4H7  C3   C4   single    1.518  0.020  1.518
 4H7  C11  N2   single    1.442  0.020  1.442
 4H7  N2   C12  single    1.345  0.020  1.345
 4H7  C13  C12  aromatic  1.412  0.020  1.412
 4H7  C13  C14  aromatic  1.370  0.020  1.370
 4H7  C12  N3   aromatic  1.340  0.020  1.340
 4H7  C14  C15  aromatic  1.400  0.020  1.400
 4H7  N3   C16  aromatic  1.321  0.020  1.321
 4H7  C15  C16  aromatic  1.390  0.020  1.390
 4H7  C15  C17  single    1.481  0.020  1.481
 4H7  C17  O    double    1.226  0.020  1.226
 4H7  C17  N4   single    1.346  0.020  1.346
 4H7  C8   H13  single    0.930  0.020  1.080
 4H7  C7   H12  single    0.930  0.020  1.080
 4H7  C14  H19  single    0.930  0.020  1.080
 4H7  C9   H14  single    0.930  0.020  1.080
 4H7  C6   H11  single    0.930  0.020  1.080
 4H7  C13  H18  single    0.930  0.020  1.080
 4H7  C16  H20  single    0.930  0.020  1.080
 4H7  C2   H6   single    0.970  0.020  1.090
 4H7  C2   H5   single    0.970  0.020  1.090
 4H7  C3   H8   single    0.970  0.020  1.090
 4H7  C3   H7   single    0.970  0.020  1.090
 4H7  C1   H4   single    0.970  0.020  1.090
 4H7  C1   H3   single    0.970  0.020  1.090
 4H7  C4   H10  single    0.970  0.020  1.090
 4H7  C4   H9   single    0.970  0.020  1.090
 4H7  C    H1   single    0.970  0.020  1.090
 4H7  C    H    single    0.970  0.020  1.090
 4H7  C    H2   single    0.970  0.020  1.090
 4H7  C11  H15  single    0.970  0.020  1.090
 4H7  C11  H16  single    0.970  0.020  1.090
 4H7  N4   H21  single    0.860  0.020  1.020
 4H7  N4   H22  single    0.860  0.020  1.020
 4H7  N2   H17  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
 4H7  H13  C8   C9   120.08  3.000
 4H7  H13  C8   C7   120.34  3.000
 4H7  C9   C8   C7   119.58  3.000
 4H7  H12  C7   C6   119.94  3.000
 4H7  H12  C7   C8   120.30  3.000
 4H7  C6   C7   C8   119.76  3.000
 4H7  H19  C14  C15  119.92  3.000
 4H7  H19  C14  C13  119.43  3.000
 4H7  C15  C14  C13  120.65  3.000
 4H7  H14  C9   C10  119.30  3.000
 4H7  H14  C9   C8   119.59  3.000
 4H7  C10  C9   C8   121.11  3.000
 4H7  H11  C6   C5   119.62  3.000
 4H7  H11  C6   C7   119.44  3.000
 4H7  C5   C6   C7   120.93  3.000
 4H7  H18  C13  C12  121.64  3.000
 4H7  H18  C13  C14  119.79  3.000
 4H7  C12  C13  C14  118.56  3.000
 4H7  H20  C16  N3   114.67  3.000
 4H7  H20  C16  C15  120.80  3.000
 4H7  N3   C16  C15  124.52  3.000
 4H7  C17  C15  C16  124.26  3.000
 4H7  C17  C15  C14  119.61  3.000
 4H7  C16  C15  C14  116.09  3.000
 4H7  C11  C10  C5   120.66  3.000
 4H7  C11  C10  C9   120.05  3.000
 4H7  C5   C10  C9   119.28  3.000
 4H7  N1   C5   C10  118.97  3.000
 4H7  C10  C5   C6   119.33  3.000
 4H7  N1   C5   C6   121.70  3.000
 4H7  N2   C12  N3   115.28  3.000
 4H7  N3   C12  C13  121.08  3.000
 4H7  N2   C12  C13  123.63  3.000
 4H7  H5   C2   H6   107.22  3.000
 4H7  H5   C2   N1   109.07  3.000
 4H7  H6   C2   N1   112.53  3.000
 4H7  H5   C2   C1   109.27  3.000
 4H7  H6   C2   C1   108.95  3.000
 4H7  N1   C2   C1   109.74  3.000
 4H7  H7   C3   H8   107.27  3.000
 4H7  H7   C3   N1   112.00  3.000
 4H7  H8   C3   N1   109.02  3.000
 4H7  H7   C3   C4   108.97  3.000
 4H7  H8   C3   C4   109.00  3.000
 4H7  N1   C3   C4   110.49  3.000
 4H7  H3   C1   H4   107.34  3.000
 4H7  H3   C1   N    109.00  3.000
 4H7  H4   C1   N    111.84  3.000
 4H7  H3   C1   C2   108.92  3.000
 4H7  H4   C1   C2   109.07  3.000
 4H7  N    C1   C2   110.58  3.000
 4H7  H9   C4   H10  107.02  3.000
 4H7  H9   C4   N    111.53  3.000
 4H7  H10  C4   N    109.00  3.000
 4H7  H9   C4   C3   109.52  3.000
 4H7  H10  C4   C3   108.70  3.000
 4H7  N    C4   C3   110.94  3.000
 4H7  H16  C11  H15  106.72  3.000
 4H7  H16  C11  N2   109.35  3.000
 4H7  H15  C11  N2   110.16  3.000
 4H7  H16  C11  C10  109.32  3.000
 4H7  H15  C11  C10  109.18  3.000
 4H7  N2   C11  C10  111.97  3.000
 4H7  C12  N3   C16  119.03  3.000
 4H7  C3   N1   C2   111.40  3.000
 4H7  C3   N1   C5   113.34  3.000
 4H7  C2   N1   C5   113.83  3.000
 4H7  C    N    C4   111.44  3.000
 4H7  C4   N    C1   110.38  3.000
 4H7  C    N    C1   111.67  3.000
 4H7  H22  N4   H21  116.64  3.000
 4H7  H22  N4   C17  119.27  3.000
 4H7  H21  N4   C17  122.62  3.000
 4H7  H17  N2   C11  117.08  3.000
 4H7  H17  N2   C12  115.15  3.000
 4H7  C11  N2   C12  127.27  3.000
 4H7  O    C17  N4   122.09  3.000
 4H7  N4   C17  C15  116.75  3.000
 4H7  O    C17  C15  121.16  3.000
 4H7  H2   C    H    107.61  3.000
 4H7  H2   C    H1   107.73  3.000
 4H7  H    C    H1   107.83  3.000
 4H7  H2   C    N    113.25  3.000
 4H7  H    C    N    110.07  3.000
 4H7  H1   C    N    110.16  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
 4H7  CONST_01  C5   C6   C7   C8      0.00   0.0  0
 4H7  CONST_02  C5   C10  C9   C8      0.00   0.0  0
 4H7  CONST_03  C10  C5   C6   C7      0.00   0.0  0
 4H7  CONST_04  C10  C9   C8   C7      0.00   0.0  0
 4H7  CONST_05  N3   C12  C13  C14     0.00   0.0  0
 4H7  CONST_06  N3   C16  C15  C14     0.00   0.0  0
 4H7  CONST_07  C6   C7   C8   C9      0.00   0.0  0
 4H7  CONST_08  C6   C5   C10  C9      0.00   0.0  0
 4H7  CONST_09  C16  N3   C12  C13     0.00   0.0  0
 4H7  CONST_10  C16  C15  C14  C13     0.00   0.0  0
 4H7  CONST_11  C12  C13  C14  C15     0.00   0.0  0
 4H7  CONST_12  C12  N3   C16  C15     0.00   0.0  0
 4H7  CONST_13  N1   C5   C6   C7    180.00   0.0  0
 4H7  CONST_14  N1   C5   C10  C9    180.00   0.0  0
 4H7  CONST_15  C11  C10  C9   C8    180.00   0.0  0
 4H7  CONST_16  N2   C12  C13  C14   180.00   0.0  0
 4H7  CONST_17  C11  C10  C5   C6    180.00   0.0  0
 4H7  CONST_18  C17  C15  C14  C13   180.00   0.0  0
 4H7  CONST_19  N2   C12  N3   C16   180.00   0.0  0
 4H7  CONST_20  N3   C16  C15  C17   180.00   0.0  0
 4H7  CONST_21  N1   C5   C10  C11     0.00   0.0  0
 4H7  CONST_22  H11  C6   C7   C8    180.00   0.0  0
 4H7  CONST_23  H14  C9   C8   C7    180.00   0.0  0
 4H7  CONST_24  H20  C16  C15  C14   180.00   0.0  0
 4H7  CONST_25  H12  C7   C8   C9    180.00   0.0  0
 4H7  CONST_26  H13  C8   C7   C6    180.00   0.0  0
 4H7  CONST_27  H19  C14  C15  C16   180.00   0.0  0
 4H7  CONST_28  H18  C13  C14  C15   180.00   0.0  0
 4H7  CONST_29  C11  N2   C12  C13     0.00   0.0  0
 4H7  CONST_30  N3   C12  N2   C11   180.00   0.0  0
 4H7  CONST_31  H17  N2   C12  C13   180.00   0.0  0
 4H7  CONST_32  H21  N4   C17  C15     0.00   0.0  0
 4H7  CONST_33  H22  N4   C17  C15   180.00   0.0  0
 4H7  Var_01    C2   N1   C5   C6    -62.73  30.0  2
 4H7  Var_02    C1   C2   N1   C5   -173.22  30.0  1
 4H7  Var_03    C4   C3   N1   C5    174.04  30.0  1
 4H7  Var_04    C4   N    C1   C2     58.53  30.0  1
 4H7  Var_05    C1   N    C4   C3    -57.21  30.0  1
 4H7  Var_06    N    C1   C2   N1    -58.21  30.0  1
 4H7  Var_07    N    C4   C3   N1     55.73  30.0  1
 4H7  Var_08    O    C17  C15  C14   -16.38  30.0  2
 4H7  Var_09    N2   C11  C10  C9   -111.65  30.0  2
 4H7  Var_10    C12  N2   C11  C10  -124.93  30.0  3
 4H7  Var_11    H1   C    N    C1     58.60  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
 4H7  plan-1  C8   0.020
 4H7  plan-1  C7   0.020
 4H7  plan-1  C9   0.020
 4H7  plan-1  C6   0.020
 4H7  plan-1  C10  0.020
 4H7  plan-1  C5   0.020
 4H7  plan-1  C11  0.020
 4H7  plan-1  N1   0.020
 4H7  plan-1  H13  0.020
 4H7  plan-1  H12  0.020
 4H7  plan-1  H14  0.020
 4H7  plan-1  H11  0.020
 4H7  plan-2  C14  0.020
 4H7  plan-2  C13  0.020
 4H7  plan-2  C16  0.020
 4H7  plan-2  C15  0.020
 4H7  plan-2  C12  0.020
 4H7  plan-2  N3   0.020
 4H7  plan-2  N2   0.020
 4H7  plan-2  H19  0.020
 4H7  plan-2  H18  0.020
 4H7  plan-2  H20  0.020
 4H7  plan-2  C17  0.020
 4H7  plan-3  C15  0.020
 4H7  plan-3  N4   0.020
 4H7  plan-3  O    0.020
 4H7  plan-3  H21  0.020
 4H7  plan-3  H22  0.020
 4H7  plan-3  C17  0.020
 4H7  plan-4  C12  0.020
 4H7  plan-4  C11  0.020
 4H7  plan-4  N2   0.020
 4H7  plan-4  H17  0.020

