# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 21:26:20 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 4-(4-aminopiperidin-1-yl)-2-{[(2-aminopyrimidin-5-yl)methyl]amino}-5-nitrobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1CCN(CC1)c2cc(NCc3cnc(N)nc3)c(cc2[N+]([O-])=O)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
 Z14  Z14  4-(4-aminopiperidin-1-yl)-2-{[(2-aminopyrimidin-5-yl)methyl]amino}-5-nitrobenzamide  ligand  50  28  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Z14
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
 Z14  N01   N  NH1    0  -0.686   1.8554  -0.3427   0.0981
 Z14  N02   N  NH2    0  -0.811   0.8050  -4.2926  -0.8629
 Z14  N03   N  N      0  -0.451   5.9229   1.0419  -0.7635
 Z14  N04   N  N      0  -0.452   5.8444   0.9565   1.6114
 Z14  N05   N  NT     0  -0.478  -2.7453   0.9689   0.0026
 Z14  N06   N  NH2    0  -0.791  -5.7621   3.9720   0.1266
 Z14  N07   N  NH2    0  -0.817   7.8432   0.9812   0.4879
 Z14  C09   C  CR16   0  -0.333  -1.1533  -2.3728  -0.1544
 Z14  C10   C  CR6    0  -0.153   0.1924  -2.0692  -0.1638
 Z14  C11   C  CR6    0   0.451   0.5679  -0.7027   0.0213
 Z14  C12   C  CR16   0  -0.525  -0.4459   0.2707   0.0575
 Z14  C13   C  CR6    0   0.438  -1.8019  -0.0294   0.0214
 Z14  C14   C  CR6    0   0.140  -2.1466  -1.4117  -0.0218
 Z14  C16   C  CH2    0  -0.351   2.3224   1.0127   0.3017
 Z14  C17   C  CR6    0  -0.096   3.8166   1.0312   0.3569
 Z14  C18   C  CR16   0  -0.018   4.6041   1.0635  -0.7874
 Z14  C19   C  CR6    0   0.553   6.4988   0.9831   0.4443
 Z14  C20   C  CR16   0  -0.023   4.5256   0.9782   1.5492
 Z14  C21   C  CH2    0  -0.327  -2.3554   2.3096   0.4055
 Z14  C22   C  CH2    0  -0.426  -3.5772   3.1269   0.8019
 Z14  C23   C  CH2    0  -0.322  -3.7096   0.9791  -1.0963
 Z14  C24   C  CH2    0  -0.441  -4.9650   1.7433  -0.7198
 Z14  C25   C  CH1    0  -0.089  -4.6252   3.1721  -0.3000
 Z14  O26   O  O      0  -0.505   2.3757  -2.9835   0.0612
 Z14  O27   O  O      0  -0.410  -3.7513  -3.0225  -0.1711
 Z14  O28   O  O     -1  -0.394  -4.2600  -1.2094   0.8254
 Z14  HN01  H  HNH1   0   0.409   2.5246  -1.0997   0.1350
 Z14  HN02  H  HNH2   0   0.414  -0.0602  -4.3787  -1.3667
 Z14  HN0A  H  HNH2   0   0.407   1.4820  -5.0244  -1.0072
 Z14  HN06  H  HNH2   0   0.343  -6.4475   4.0100  -0.6188
 Z14  HN0B  H  HNH2   0   0.334  -6.2279   3.5090   0.8999
 Z14  HN07  H  HNH2   0   0.398   8.3565   0.8121  -0.3596
 Z14  HN0C  H  HNH2   0   0.398   8.3013   0.7554   1.3537
 Z14  H09   H  HCR6   0   0.287  -1.4610  -3.4085  -0.1867
 Z14  H12   H  HCR6   0   0.303  -0.1496   1.3085   0.0619
 Z14  H16   H  HCH2   0   0.260   1.9747   1.6556  -0.5130
 Z14  H16A  H  HCH2   0   0.260   1.9108   1.4281   1.2283
 Z14  H18   H  HCR6   0   0.270   4.1402   1.1142  -1.7689
 Z14  H20   H  HCR6   0   0.269   3.9968   0.9562   2.4984
 Z14  H21   H  HCH2   0   0.260  -1.6859   2.2451   1.2634
 Z14  H21A  H  HCH2   0   0.219  -1.8073   2.8278  -0.3963
 Z14  H22   H  HCH2   0   0.222  -4.0183   2.6923   1.7053
 Z14  H22A  H  HCH2   0   0.241  -3.2527   4.1383   1.0557
 Z14  H23   H  HCH2   0   0.231  -3.2417   1.4579  -1.9696
 Z14  H23A  H  HCH2   0   0.258  -3.9572  -0.0312  -1.4098
 Z14  H24   H  HCH2   0   0.235  -5.6448   1.7515  -1.5759
 Z14  H24A  H  HCH2   0   0.223  -5.4751   1.2299   0.1009
 Z14  H25   H  HCH1   0   0.214  -4.1814   3.6790  -1.1668
 Z14  C15   C  C      0   0.534   1.2108  -3.1383  -0.3099
 Z14  N08   N  N      1   0.327  -3.4729  -1.9021   0.2155

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
 Z14  N01  C11   single    1.339  0.020  1.339
 Z14  N01  C16   single    1.448  0.020  1.448
 Z14  N01  HN01  single    0.860  0.020  1.020
 Z14  N02  C15   single    1.343  0.020  1.343
 Z14  N02  HN02  single    0.860  0.020  1.020
 Z14  N02  HN0A  single    0.860  0.020  1.020
 Z14  N03  C18   aromatic  1.319  0.020  1.319
 Z14  N03  C19   aromatic  1.339  0.020  1.339
 Z14  N04  C19   aromatic  1.338  0.020  1.338
 Z14  N04  C20   aromatic  1.320  0.020  1.320
 Z14  N05  C13   single    1.374  0.020  1.374
 Z14  N05  C21   single    1.453  0.020  1.453
 Z14  N05  C23   single    1.462  0.020  1.462
 Z14  N06  C25   single    1.454  0.020  1.454
 Z14  N06  HN06  single    0.890  0.020  1.040
 Z14  N06  HN0B  single    0.890  0.020  1.040
 Z14  N07  C19   single    1.345  0.020  1.345
 Z14  N07  HN07  single    0.890  0.020  1.040
 Z14  N07  HN0C  single    0.890  0.020  1.040
 Z14  N08  C14   single    1.434  0.020  1.434
 Z14  N08  O27   double    1.217  0.020  1.217
 Z14  N08  O28   single    1.213  0.020  1.213
 Z14  C09  C10   aromatic  1.380  0.020  1.380
 Z14  C09  C14   aromatic  1.389  0.020  1.389
 Z14  C09  H09   single    0.930  0.020  1.080
 Z14  C10  C11   aromatic  1.429  0.020  1.429
 Z14  C10  C15   single    1.484  0.020  1.484
 Z14  C11  C12   aromatic  1.406  0.020  1.406
 Z14  C12  C13   aromatic  1.389  0.020  1.389
 Z14  C12  H12   single    0.930  0.020  1.080
 Z14  C13  C14   aromatic  1.425  0.020  1.425
 Z14  C15  O26   double    1.232  0.020  1.232
 Z14  C16  C17   single    1.495  0.020  1.495
 Z14  C16  H16   single    0.970  0.020  1.090
 Z14  C16  H16A  single    0.970  0.020  1.090
 Z14  C17  C18   aromatic  1.389  0.020  1.389
 Z14  C17  C20   aromatic  1.388  0.020  1.388
 Z14  C18  H18   single    0.930  0.020  1.080
 Z14  C20  H20   single    0.930  0.020  1.080
 Z14  C21  C22   single    1.522  0.020  1.522
 Z14  C21  H21   single    0.970  0.020  1.090
 Z14  C21  H21A  single    0.970  0.020  1.090
 Z14  C22  C25   single    1.521  0.020  1.521
 Z14  C22  H22   single    0.970  0.020  1.090
 Z14  C22  H22A  single    0.970  0.020  1.090
 Z14  C23  C24   single    1.517  0.020  1.517
 Z14  C23  H23   single    0.970  0.020  1.090
 Z14  C23  H23A  single    0.970  0.020  1.090
 Z14  C24  C25   single    1.527  0.020  1.527
 Z14  C24  H24   single    0.970  0.020  1.090
 Z14  C24  H24A  single    0.970  0.020  1.090
 Z14  C25  H25   single    0.970  0.020  1.090

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
 Z14  HN01  N01  C16   118.83  3.000
 Z14  HN01  N01  C11   115.92  3.000
 Z14  C16   N01  C11   124.74  3.000
 Z14  HN0A  N02  HN02  116.40  3.000
 Z14  HN0A  N02  C15   118.71  3.000
 Z14  HN02  N02  C15   122.71  3.000
 Z14  C19   N03  C18   116.55  3.000
 Z14  C20   N04  C19   116.55  3.000
 Z14  C23   N05  C21   112.26  3.000
 Z14  C23   N05  C13   117.93  3.000
 Z14  C21   N05  C13   118.84  3.000
 Z14  HN0B  N06  HN06  105.50  3.000
 Z14  HN0B  N06  C25   109.36  3.000
 Z14  HN06  N06  C25   109.49  3.000
 Z14  HN0C  N07  HN07  117.11  3.000
 Z14  HN0C  N07  C19   118.93  3.000
 Z14  HN07  N07  C19   118.90  3.000
 Z14  H09   C09  C14   117.55  3.000
 Z14  H09   C09  C10   119.23  3.000
 Z14  C14   C09  C10   123.10  3.000
 Z14  C15   C10  C11   121.42  3.000
 Z14  C15   C10  C09   120.77  3.000
 Z14  C11   C10  C09   117.76  3.000
 Z14  C12   C11  C10   118.41  3.000
 Z14  C12   C11  N01   120.38  3.000
 Z14  C10   C11  N01   121.14  3.000
 Z14  H12   C12  C13   118.41  3.000
 Z14  H12   C12  C11   117.89  3.000
 Z14  C13   C12  C11   123.62  3.000
 Z14  C14   C13  C12   116.51  3.000
 Z14  C14   C13  N05   122.56  3.000
 Z14  C12   C13  N05   120.91  3.000
 Z14  C13   C14  C09   120.08  3.000
 Z14  C13   C14  N08   123.40  3.000
 Z14  C09   C14  N08   116.15  3.000
 Z14  H16A  C16  H16   106.71  3.000
 Z14  H16A  C16  C17   109.84  3.000
 Z14  H16   C16  C17   109.74  3.000
 Z14  H16A  C16  N01   110.65  3.000
 Z14  H16   C16  N01   110.04  3.000
 Z14  C17   C16  N01   109.82  3.000
 Z14  C20   C17  C18   114.76  3.000
 Z14  C20   C17  C16   122.79  3.000
 Z14  C18   C17  C16   122.42  3.000
 Z14  H18   C18  C17   120.19  3.000
 Z14  H18   C18  N03   116.35  3.000
 Z14  C17   C18  N03   123.45  3.000
 Z14  N07   C19  N04   117.42  3.000
 Z14  N07   C19  N03   117.33  3.000
 Z14  N04   C19  N03   125.24  3.000
 Z14  H20   C20  C17   120.16  3.000
 Z14  H20   C20  N04   116.40  3.000
 Z14  C17   C20  N04   123.44  3.000
 Z14  H21A  C21  H21   107.18  3.000
 Z14  H21A  C21  C22   109.66  3.000
 Z14  H21   C21  C22   108.64  3.000
 Z14  H21A  C21  N05   111.47  3.000
 Z14  H21   C21  N05   109.17  3.000
 Z14  C22   C21  N05   110.62  3.000
 Z14  H22A  C22  H22   107.19  3.000
 Z14  H22A  C22  C25   110.21  3.000
 Z14  H22   C22  C25   109.38  3.000
 Z14  H22A  C22  C21   108.62  3.000
 Z14  H22   C22  C21   108.96  3.000
 Z14  C25   C22  C21   112.35  3.000
 Z14  H23A  C23  H23   105.81  3.000
 Z14  H23A  C23  C24   110.57  3.000
 Z14  H23   C23  C24   109.25  3.000
 Z14  H23A  C23  N05   111.14  3.000
 Z14  H23   C23  N05   108.61  3.000
 Z14  C24   C23  N05   111.27  3.000
 Z14  H24A  C24  H24   107.52  3.000
 Z14  H24A  C24  C25   109.66  3.000
 Z14  H24   C24  C25   110.27  3.000
 Z14  H24A  C24  C23   109.61  3.000
 Z14  H24   C24  C23   108.91  3.000
 Z14  C25   C24  C23   110.81  3.000
 Z14  H25   C25  C24   107.75  3.000
 Z14  H25   C25  C22   107.88  3.000
 Z14  C24   C25  C22   108.93  3.000
 Z14  H25   C25  N06   107.08  3.000
 Z14  C24   C25  N06   114.92  3.000
 Z14  C22   C25  N06   110.03  3.000
 Z14  O26   C15  C10   121.92  3.000
 Z14  O26   C15  N02   121.18  3.000
 Z14  C10   C15  N02   116.91  3.000
 Z14  O28   N08  O27   122.47  3.000
 Z14  O28   N08  C14   119.21  3.000
 Z14  O27   N08  C14   118.28  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
 Z14  CONST_01  C20   C17  C18  N03     0.00   0.0  0
 Z14  CONST_02  C20   N04  C19  N03     0.00   0.0  0
 Z14  CONST_03  C18   N03  C19  N04     0.00   0.0  0
 Z14  CONST_04  C18   C17  C20  N04     0.00   0.0  0
 Z14  CONST_05  C12   C11  C10  C09     0.00   0.0  0
 Z14  CONST_06  C12   C13  C14  C09     0.00   0.0  0
 Z14  CONST_07  C13   C14  C09  C10     0.00   0.0  0
 Z14  CONST_08  C13   C12  C11  C10     0.00   0.0  0
 Z14  CONST_09  C14   C09  C10  C11     0.00   0.0  0
 Z14  CONST_10  C14   C13  C12  C11     0.00   0.0  0
 Z14  CONST_11  C19   N03  C18  C17     0.00   0.0  0
 Z14  CONST_12  C19   N04  C20  C17     0.00   0.0  0
 Z14  CONST_13  C11   C12  C13  N05   180.00   0.0  0
 Z14  CONST_14  C09   C14  C13  N05   180.00   0.0  0
 Z14  CONST_15  C09   C10  C11  N01   180.00   0.0  0
 Z14  CONST_16  C13   C12  C11  N01   180.00   0.0  0
 Z14  CONST_17  C16   C17  C18  N03   180.00   0.0  0
 Z14  CONST_18  C16   C17  C20  N04   180.00   0.0  0
 Z14  CONST_19  N08   C14  C13  N05     0.00   0.0  0
 Z14  CONST_20  C18   N03  C19  N07   180.00   0.0  0
 Z14  CONST_21  C20   N04  C19  N07   180.00   0.0  0
 Z14  CONST_22  C10   C09  C14  N08   180.00   0.0  0
 Z14  CONST_23  C12   C13  C14  N08   180.00   0.0  0
 Z14  CONST_24  C15   C10  C11  C12   180.00   0.0  0
 Z14  CONST_25  C15   C10  C09  C14   180.00   0.0  0
 Z14  CONST_26  H12   C12  C13  N05     0.00   0.0  0
 Z14  CONST_27  H09   C09  C10  C11   180.00   0.0  0
 Z14  CONST_28  H20   C20  C17  C18   180.00   0.0  0
 Z14  CONST_29  H18   C18  N03  C19   180.00   0.0  0
 Z14  CONST_32  C16   N01  C11  C10   180.00   0.0  0
 Z14  CONST_33  C16   N01  C11  C12     0.00   0.0  0
 Z14  CONST_36  HN07  N07  C19  N03     0.00   0.0  0
 Z14  CONST_37  HN0C  N07  C19  N03   180.00   0.0  0
 Z14  CONST_38  HN01  N01  C11  C10     0.00   0.0  0
 Z14  CONST_40  HN0A  N02  C15  C10   180.00   0.0  0
 Z14  Var_01    C25   C22  C21  N05   -55.36  30.0  1
 Z14  Var_02    C25   C24  C23  N05    56.91  30.0  1
 Z14  Var_03    C21   N05  C13  C12   -17.64  30.0  2
 Z14  Var_04    C22   C21  N05  C13  -159.49  30.0  1
 Z14  Var_05    C24   C23  N05  C13   157.57  30.0  1
 Z14  Var_06    C18   C17  C16  N01    83.27  30.0  2
 Z14  Var_07    C09   C10  C15  N02    21.53  30.0  2
 Z14  Var_08    C17   C16  N01  C11   179.06  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 Z14  chir_01  C25  N06  C22  C24  negativ

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
 Z14  plan-1  N03   0.020
 Z14  plan-1  N04   0.020
 Z14  plan-1  N07   0.020
 Z14  plan-1  C16   0.020
 Z14  plan-1  C17   0.020
 Z14  plan-1  C18   0.020
 Z14  plan-1  C19   0.020
 Z14  plan-1  C20   0.020
 Z14  plan-1  H18   0.020
 Z14  plan-1  H20   0.020
 Z14  plan-2  N01   0.020
 Z14  plan-2  N05   0.020
 Z14  plan-2  C09   0.020
 Z14  plan-2  C10   0.020
 Z14  plan-2  C11   0.020
 Z14  plan-2  C12   0.020
 Z14  plan-2  C13   0.020
 Z14  plan-2  C14   0.020
 Z14  plan-2  H09   0.020
 Z14  plan-2  H12   0.020
 Z14  plan-2  C15   0.020
 Z14  plan-2  N08   0.020
 Z14  plan-3  N01   0.020
 Z14  plan-3  C11   0.020
 Z14  plan-3  C16   0.020
 Z14  plan-3  HN01  0.020
 Z14  plan-4  N07   0.020
 Z14  plan-4  C19   0.020
 Z14  plan-4  HN07  0.020
 Z14  plan-4  HN0C  0.020
 Z14  plan-5  C14   0.020
 Z14  plan-5  O27   0.020
 Z14  plan-5  O28   0.020
 Z14  plan-5  N08   0.020
 Z14  plan-6  N02   0.020
 Z14  plan-6  C10   0.020
 Z14  plan-6  O26   0.020
 Z14  plan-6  HN02  0.020
 Z14  plan-6  HN0A  0.020
 Z14  plan-6  C15   0.020

