# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 17:56:02 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 2-amino-5-[3-(piperazin-1-yl)phenyl]-N-(pyridin-4-yl)pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncc(cc1C(=O)Nc2ccncc2)c3cccc(c3)N4CCNCC4
#
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
 AFU  AFU  2-amino-5-[3-(piperazin-1-yl)phenyl]-N-(pyridin-4-yl)pyridine-3-carboxamide  ligand  50  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AFU
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
 AFU  CAA  C  CR16  0  -0.070   7.0849  -0.9332   1.2760
 AFU  CAC  C  CR16  0  -0.061   6.4484  -2.6281  -0.0750
 AFU  CAD  C  CR16  0  -0.422   5.2563  -2.0036  -0.3835
 AFU  CAE  C  CR6   0   0.475   4.9723  -0.7581   0.1816
 AFU  CAF  C  CR16  0  -0.372   5.9247  -0.2113   1.0419
 AFU  CAH  C  C     0   0.558   3.3397   1.1039   0.0903
 AFU  CAI  C  CR6   0  -0.192   1.9397   1.3799  -0.3124
 AFU  CAK  C  CR6   0   0.460   1.5439   2.6708  -0.7508
 AFU  CAM  C  CR16  0  -0.092  -0.6068   1.9354  -1.0786
 AFU  CAN  C  CR6   0  -0.005  -0.3548   0.6505  -0.6005
 AFU  CAO  C  CR16  0  -0.247   0.9612   0.4000  -0.2284
 AFU  CAQ  C  CR6   0   0.121  -1.4109  -0.3723  -0.5025
 AFU  CAR  C  CR16  0  -0.358  -1.1179  -1.7219  -0.7154
 AFU  CAS  C  CR16  0  -0.225  -2.1323  -2.6571  -0.6167
 AFU  CAT  C  CR16  0  -0.375  -3.4349  -2.2834  -0.3152
 AFU  CAU  C  CR6   0   0.404  -3.7595  -0.9349  -0.1166
 AFU  CAV  C  CR16  0  -0.423  -2.7179   0.0007  -0.2069
 AFU  CAX  C  CH2   0  -0.301  -6.1274  -1.4944   0.0883
 AFU  CAY  C  CH2   0  -0.297  -7.4751  -0.8072  -0.0477
 AFU  CBA  C  CH2   0  -0.299  -6.6356   1.1422   1.0132
 AFU  CBB  C  CH2   0  -0.299  -5.2752   0.4906   1.1697
 AFU  NAB  N  N     0  -0.416   7.3644  -2.1148   0.7408
 AFU  NAG  N  NH1   0  -0.753   3.7548  -0.1755  -0.1400
 AFU  NAL  N  N     0  -0.448   0.2883   2.9009  -1.1472
 AFU  NAP  N  NH2   0  -0.828   2.3961   3.7084  -0.8510
 AFU  NAW  N  NT    0  -0.525  -5.0613  -0.5110   0.1318
 AFU  NAZ  N  NH1   0  -0.598  -7.6670   0.1256   1.0439
 AFU  OAJ  O  O     0  -0.461   4.0650   1.9582   0.5725
 AFU  H1   H  HCR6  0   0.266   7.8305  -0.5168   1.9445
 AFU  H2   H  HCR6  0   0.268   6.6724  -3.5940  -0.5135
 AFU  H3   H  HCR6  0   0.285   4.5570  -2.4812  -1.0579
 AFU  H4   H  HCR6  0   0.290   5.7895   0.7403   1.5276
 AFU  H5   H  HCR6  0   0.265  -1.5991   2.1948  -1.4339
 AFU  H6   H  HCR6  0   0.276   1.2160  -0.5735   0.1740
 AFU  H7   H  HCR6  0   0.244  -0.1156  -2.0358  -0.9773
 AFU  H8   H  HCR6  0   0.254  -1.9110  -3.7053  -0.7732
 AFU  H9   H  HCR6  0   0.267  -4.1832  -3.0578  -0.2284
 AFU  H10  H  HCR6  0   0.257  -2.9288   1.0497  -0.0473
 AFU  H12  H  HCH2  0   0.249  -5.9901  -2.1433  -0.7773
 AFU  H13  H  HCH2  0   0.195  -7.5193  -0.3220  -1.0357
 AFU  H14  H  HCH2  0   0.239  -8.2588  -1.5662  -0.0224
 AFU  H15  H  HCH2  0   0.238  -6.7857   1.8415   1.8379
 AFU  H16  H  HCH2  0   0.196  -6.6396   1.7286   0.0806
 AFU  H17  H  HCH2  0   0.253  -4.5158   1.2664   1.1148
 AFU  H18  H  HCH2  0   0.216  -5.2035   0.0335   2.1674
 AFU  H19  H  HNH1  0   0.426   3.1551  -0.7480  -0.7150
 AFU  H20  H  HNH2  0   0.407   3.2643   3.6911  -0.3449
 AFU  H21  H  HNH2  0   0.392   1.9970   4.6114  -1.0443
 AFU  H22  H  HNH1  0   0.356  -8.5788   0.5571   0.9722
 AFU  H11  H  HCH2  0   0.212  -6.1296  -2.1340   0.9838

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
 AFU  NAB  CAA  aromatic  1.327  0.020  1.327
 AFU  NAB  CAC  aromatic  1.330  0.020  1.330
 AFU  CAA  CAF  aromatic  1.386  0.020  1.386
 AFU  NAZ  CAY  single    1.449  0.020  1.449
 AFU  NAZ  CBA  single    1.449  0.020  1.449
 AFU  CAY  CAX  single    1.519  0.020  1.519
 AFU  CAC  CAD  aromatic  1.381  0.020  1.381
 AFU  CAF  CAE  aromatic  1.395  0.020  1.395
 AFU  CBA  CBB  single    1.516  0.020  1.516
 AFU  CAX  NAW  single    1.451  0.020  1.451
 AFU  CAE  CAD  aromatic  1.397  0.020  1.397
 AFU  CAE  NAG  single    1.388  0.020  1.388
 AFU  NAG  CAH  single    1.365  0.020  1.365
 AFU  NAW  CBB  single    1.458  0.020  1.458
 AFU  NAW  CAU  single    1.391  0.020  1.391
 AFU  CAH  OAJ  double    1.220  0.020  1.220
 AFU  CAH  CAI  single    1.483  0.020  1.483
 AFU  CAU  CAV  aromatic  1.403  0.020  1.403
 AFU  CAU  CAT  aromatic  1.401  0.020  1.401
 AFU  CAV  CAQ  aromatic  1.391  0.020  1.391
 AFU  CAO  CAI  aromatic  1.387  0.020  1.387
 AFU  CAO  CAN  aromatic  1.390  0.020  1.390
 AFU  CAI  CAK  aromatic  1.420  0.020  1.420
 AFU  CAT  CAS  aromatic  1.388  0.020  1.388
 AFU  CAQ  CAN  single    1.473  0.020  1.473
 AFU  CAQ  CAR  aromatic  1.397  0.020  1.397
 AFU  CAN  CAM  aromatic  1.394  0.020  1.394
 AFU  CAK  NAP  single    1.346  0.020  1.346
 AFU  CAK  NAL  aromatic  1.337  0.020  1.337
 AFU  CAS  CAR  aromatic  1.383  0.020  1.383
 AFU  CAM  NAL  aromatic  1.318  0.020  1.318
 AFU  CAA  H1   single    0.930  0.020  1.080
 AFU  CAC  H2   single    0.930  0.020  1.080
 AFU  CAD  H3   single    0.930  0.020  1.080
 AFU  CAF  H4   single    0.930  0.020  1.080
 AFU  CAM  H5   single    0.930  0.020  1.080
 AFU  CAO  H6   single    0.930  0.020  1.080
 AFU  CAR  H7   single    0.930  0.020  1.080
 AFU  CAS  H8   single    0.930  0.020  1.080
 AFU  CAT  H9   single    0.930  0.020  1.080
 AFU  CAV  H10  single    0.930  0.020  1.080
 AFU  CAX  H11  single    0.970  0.020  1.090
 AFU  CAX  H12  single    0.970  0.020  1.090
 AFU  CAY  H13  single    0.970  0.020  1.090
 AFU  CAY  H14  single    0.970  0.020  1.090
 AFU  CBA  H15  single    0.970  0.020  1.090
 AFU  CBA  H16  single    0.970  0.020  1.090
 AFU  CBB  H17  single    0.970  0.020  1.090
 AFU  CBB  H18  single    0.970  0.020  1.090
 AFU  NAG  H19  single    0.860  0.020  1.020
 AFU  NAP  H20  single    0.890  0.020  1.040
 AFU  NAP  H21  single    0.890  0.020  1.040
 AFU  NAZ  H22  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
 AFU  H1   CAA  NAB  116.47  3.000
 AFU  H1   CAA  CAF  118.65  3.000
 AFU  NAB  CAA  CAF  124.88  3.000
 AFU  H2   CAC  NAB  116.72  3.000
 AFU  H2   CAC  CAD  119.40  3.000
 AFU  NAB  CAC  CAD  123.87  3.000
 AFU  H3   CAD  CAE  120.94  3.000
 AFU  H3   CAD  CAC  119.82  3.000
 AFU  CAE  CAD  CAC  119.23  3.000
 AFU  NAG  CAE  CAF  125.27  3.000
 AFU  NAG  CAE  CAD  117.32  3.000
 AFU  CAF  CAE  CAD  117.40  3.000
 AFU  H4   CAF  CAE  122.60  3.000
 AFU  H4   CAF  CAA  119.29  3.000
 AFU  CAE  CAF  CAA  118.12  3.000
 AFU  OAJ  CAH  NAG  122.85  3.000
 AFU  OAJ  CAH  CAI  122.57  3.000
 AFU  NAG  CAH  CAI  114.58  3.000
 AFU  CAO  CAI  CAK  117.67  3.000
 AFU  CAK  CAI  CAH  121.09  3.000
 AFU  CAO  CAI  CAH  121.21  3.000
 AFU  NAP  CAK  NAL  116.10  3.000
 AFU  NAL  CAK  CAI  120.66  3.000
 AFU  NAP  CAK  CAI  123.18  3.000
 AFU  H5   CAM  NAL  115.38  3.000
 AFU  H5   CAM  CAN  119.85  3.000
 AFU  NAL  CAM  CAN  124.76  3.000
 AFU  CAQ  CAN  CAO  122.39  3.000
 AFU  CAQ  CAN  CAM  122.21  3.000
 AFU  CAO  CAN  CAM  115.40  3.000
 AFU  H6   CAO  CAN  118.93  3.000
 AFU  H6   CAO  CAI  119.41  3.000
 AFU  CAN  CAO  CAI  121.61  3.000
 AFU  CAV  CAQ  CAR  119.24  3.000
 AFU  CAR  CAQ  CAN  120.66  3.000
 AFU  CAV  CAQ  CAN  120.10  3.000
 AFU  H7   CAR  CAS  120.02  3.000
 AFU  H7   CAR  CAQ  120.74  3.000
 AFU  CAS  CAR  CAQ  119.23  3.000
 AFU  H8   CAS  CAT  118.93  3.000
 AFU  H8   CAS  CAR  119.62  3.000
 AFU  CAT  CAS  CAR  121.44  3.000
 AFU  H9   CAT  CAU  121.20  3.000
 AFU  H9   CAT  CAS  118.32  3.000
 AFU  CAU  CAT  CAS  120.48  3.000
 AFU  NAW  CAU  CAV  120.19  3.000
 AFU  CAV  CAU  CAT  117.43  3.000
 AFU  NAW  CAU  CAT  122.36  3.000
 AFU  H10  CAV  CAU  119.50  3.000
 AFU  H10  CAV  CAQ  118.34  3.000
 AFU  CAU  CAV  CAQ  122.17  3.000
 AFU  H12  CAX  H11  107.48  3.000
 AFU  H12  CAX  NAW  109.55  3.000
 AFU  H11  CAX  NAW  111.78  3.000
 AFU  H12  CAX  CAY  108.05  3.000
 AFU  H11  CAX  CAY  109.51  3.000
 AFU  NAW  CAX  CAY  110.36  3.000
 AFU  H14  CAY  H13  107.36  3.000
 AFU  H14  CAY  NAZ  109.59  3.000
 AFU  H13  CAY  NAZ  112.76  3.000
 AFU  H14  CAY  CAX  108.69  3.000
 AFU  H13  CAY  CAX  108.37  3.000
 AFU  NAZ  CAY  CAX  109.96  3.000
 AFU  H16  CBA  H15  107.34  3.000
 AFU  H16  CBA  NAZ  112.89  3.000
 AFU  H15  CBA  NAZ  109.61  3.000
 AFU  H16  CBA  CBB  108.62  3.000
 AFU  H15  CBA  CBB  108.70  3.000
 AFU  NAZ  CBA  CBB  109.57  3.000
 AFU  H18  CBB  H17  107.27  3.000
 AFU  H18  CBB  NAW  110.52  3.000
 AFU  H17  CBB  NAW  110.60  3.000
 AFU  H18  CBB  CBA  109.31  3.000
 AFU  H17  CBB  CBA  108.35  3.000
 AFU  NAW  CBB  CBA  110.69  3.000
 AFU  CAC  NAB  CAA  116.49  3.000
 AFU  H19  NAG  CAH  116.57  3.000
 AFU  H19  NAG  CAE  114.55  3.000
 AFU  CAH  NAG  CAE  128.42  3.000
 AFU  CAM  NAL  CAK  119.75  3.000
 AFU  H21  NAP  H20  117.06  3.000
 AFU  H21  NAP  CAK  117.05  3.000
 AFU  H20  NAP  CAK  119.74  3.000
 AFU  CBB  NAW  CAX  112.28  3.000
 AFU  CBB  NAW  CAU  118.27  3.000
 AFU  CAX  NAW  CAU  118.39  3.000
 AFU  H22  NAZ  CBA  109.94  3.000
 AFU  H22  NAZ  CAY  109.92  3.000
 AFU  CBA  NAZ  CAY  109.98  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
 AFU  CONST_01  CAD  CAC  NAB  CAA     0.00   0.0  0
 AFU  CONST_02  CAD  CAE  CAF  CAA     0.00   0.0  0
 AFU  CONST_03  CAF  CAA  NAB  CAC     0.00   0.0  0
 AFU  CONST_04  CAF  CAE  CAD  CAC     0.00   0.0  0
 AFU  CONST_05  NAB  CAA  CAF  CAE     0.00   0.0  0
 AFU  CONST_06  NAB  CAC  CAD  CAE     0.00   0.0  0
 AFU  CONST_07  CAQ  CAN  CAO  CAI   180.00   0.0  0
 AFU  CONST_08  CAM  CAN  CAO  CAI     0.00   0.0  0
 AFU  CONST_09  CAM  NAL  CAK  CAI     0.00   0.0  0
 AFU  CONST_10  CAN  CAO  CAI  CAK     0.00   0.0  0
 AFU  CONST_11  CAN  CAM  NAL  CAK     0.00   0.0  0
 AFU  CONST_14  CAU  CAV  CAQ  CAN   180.00   0.0  0
 AFU  CONST_15  CAS  CAR  CAQ  CAN   180.00   0.0  0
 AFU  CONST_16  NAL  CAK  CAI  CAO     0.00   0.0  0
 AFU  CONST_19  NAL  CAM  CAN  CAO     0.00   0.0  0
 AFU  CONST_20  CAT  CAU  CAV  CAQ     0.00   0.0  0
 AFU  CONST_21  NAL  CAM  CAN  CAQ   180.00   0.0  0
 AFU  CONST_22  CAT  CAS  CAR  CAQ     0.00   0.0  0
 AFU  CONST_23  CAU  CAV  CAQ  CAR     0.00   0.0  0
 AFU  CONST_24  CAU  CAT  CAS  CAR     0.00   0.0  0
 AFU  CONST_25  CAV  CAU  CAT  CAS     0.00   0.0  0
 AFU  CONST_26  CAV  CAQ  CAR  CAS     0.00   0.0  0
 AFU  CONST_27  NAW  CAU  CAV  CAQ   180.00   0.0  0
 AFU  CONST_28  NAW  CAU  CAT  CAS   180.00   0.0  0
 AFU  CONST_29  NAG  CAE  CAF  CAA   180.00   0.0  0
 AFU  CONST_30  NAG  CAE  CAD  CAC   180.00   0.0  0
 AFU  CONST_31  CAN  CAO  CAI  CAH   180.00   0.0  0
 AFU  CONST_32  NAL  CAK  CAI  CAH   180.00   0.0  0
 AFU  CONST_33  NAP  CAK  NAL  CAM   180.00   0.0  0
 AFU  CONST_34  NAP  CAK  CAI  CAO   180.00   0.0  0
 AFU  CONST_35  H2   CAC  NAB  CAA   180.00   0.0  0
 AFU  CONST_36  H1   CAA  NAB  CAC   180.00   0.0  0
 AFU  CONST_37  H4   CAF  CAE  CAD   180.00   0.0  0
 AFU  CONST_38  H3   CAD  CAE  CAF   180.00   0.0  0
 AFU  CONST_39  H6   CAO  CAI  CAK   180.00   0.0  0
 AFU  CONST_40  H5   CAM  NAL  CAK   180.00   0.0  0
 AFU  CONST_41  H10  CAV  CAQ  CAN     0.00   0.0  0
 AFU  CONST_42  H7   CAR  CAQ  CAN     0.00   0.0  0
 AFU  CONST_43  H8   CAS  CAR  CAQ   180.00   0.0  0
 AFU  CONST_44  H9   CAT  CAS  CAR   180.00   0.0  0
 AFU  CONST_45  CAI  CAH  NAG  CAE   180.00   0.0  0
 AFU  CONST_46  CAH  NAG  CAE  CAD   180.00   0.0  0
 AFU  CONST_47  CAH  NAG  CAE  CAF     0.00   0.0  0
 AFU  CONST_48  H19  NAG  CAE  CAD     0.00   0.0  0
 AFU  CONST_50  H21  NAP  CAK  CAI   180.00   0.0  0
 AFU  CONST_51  OAJ  CAH  NAG  CAE     0.00   0.0  0
 AFU  Var_01    CAX  NAW  CAU  CAT    -4.44  30.0  2
 AFU  Var_02    CAY  CAX  NAW  CAU  -162.49  30.0  1
 AFU  Var_03    CBA  CBB  NAW  CAU   162.19  30.0  1
 AFU  Var_04    CBA  NAZ  CAY  CAX    60.95  30.0  1
 AFU  Var_05    CBB  CBA  NAZ  CAY   -60.79  30.0  1
 AFU  Var_06    NAZ  CAY  CAX  NAW   -56.96  30.0  1
 AFU  Var_07    NAZ  CBA  CBB  NAW    56.94  30.0  1
 AFU  Var_08    NAG  CAH  CAI  CAK  -149.42  30.0  1

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
 AFU  plan-1  CAH  0.020
 AFU  plan-1  CAI  0.020
 AFU  plan-1  CAK  0.020
 AFU  plan-1  CAM  0.020
 AFU  plan-1  CAN  0.020
 AFU  plan-1  CAO  0.020
 AFU  plan-1  CAQ  0.020
 AFU  plan-1  NAL  0.020
 AFU  plan-1  NAP  0.020
 AFU  plan-1  H5   0.020
 AFU  plan-1  H6   0.020
 AFU  plan-2  CAN  0.020
 AFU  plan-2  CAQ  0.020
 AFU  plan-2  CAR  0.020
 AFU  plan-2  CAS  0.020
 AFU  plan-2  CAT  0.020
 AFU  plan-2  CAU  0.020
 AFU  plan-2  CAV  0.020
 AFU  plan-2  NAW  0.020
 AFU  plan-2  H7   0.020
 AFU  plan-2  H8   0.020
 AFU  plan-2  H9   0.020
 AFU  plan-2  H10  0.020
 AFU  plan-3  CAA  0.020
 AFU  plan-3  CAC  0.020
 AFU  plan-3  CAD  0.020
 AFU  plan-3  CAE  0.020
 AFU  plan-3  CAF  0.020
 AFU  plan-3  NAB  0.020
 AFU  plan-3  NAG  0.020
 AFU  plan-3  H1   0.020
 AFU  plan-3  H2   0.020
 AFU  plan-3  H3   0.020
 AFU  plan-3  H4   0.020
 AFU  plan-4  CAE  0.020
 AFU  plan-4  CAH  0.020
 AFU  plan-4  CAI  0.020
 AFU  plan-4  NAG  0.020
 AFU  plan-4  OAJ  0.020
 AFU  plan-4  H19  0.020
 AFU  plan-5  CAK  0.020
 AFU  plan-5  NAP  0.020
 AFU  plan-5  H20  0.020
 AFU  plan-5  H21  0.020

