# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 03:29:25 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 2-{[(2-aminopyrimidin-5-yl)methyl]amino}-5-nitro-4-{[2-(piperazin-1-yl)ethyl]amino}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(c(NCCN2CCNCC2)cc1NCc3cnc(N)nc3)[N+]([O-])=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
 18Z  18Z  2-{[(2-aminopyrimidin-5-yl)methyl]amino}-5-nitro-4-{[2-(piperazin-1-yl)ethyl]amino}benzamide  ligand  55  30  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_18Z
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
 18Z  N01   N  NH2    0  -0.812  -3.0130   4.4766   0.4000
 18Z  N02   N  NH1    0  -0.687   2.3915   1.0955  -0.1411
 18Z  N03   N  NH1    0  -0.685  -2.2933   0.3601   0.0438
 18Z  N04   N  N      0  -0.453  -5.3740  -2.6630  -1.0286
 18Z  N05   N  N      0  -0.452  -5.3347  -2.5807   1.3489
 18Z  N06   N  NH2    0  -0.820  -7.1132  -3.4788   0.2182
 18Z  N07   N  NT     0  -0.423   4.5670  -1.8884   0.2105
 18Z  N08   N  NH1    0  -0.579   6.0128  -4.3723  -0.1578
 18Z  N09   N  N      1   0.339   1.9019   3.9903  -0.3832
 18Z  C10   C  CR16   0  -0.357  -0.4314   3.4720  -0.1854
 18Z  C11   C  CR6    0  -0.147  -1.5159   2.6422  -0.0562
 18Z  C12   C  CR6    0   0.453  -1.2726   1.2246  -0.0236
 18Z  C13   C  CR16   0  -0.559   0.0459   0.7672  -0.0374
 18Z  C14   C  CR6    0   0.459   1.1576   1.6131  -0.1362
 18Z  C15   C  CR6    0   0.177   0.8873   3.0174  -0.2374
 18Z  C16   C  C      0   0.533  -2.8913   3.1939   0.0239
 18Z  C17   C  CH2    0  -0.353  -2.1436  -1.0792   0.0537
 18Z  C18   C  CR6    0  -0.096  -3.4850  -1.7379   0.0985
 18Z  C19   C  CR16   0  -0.023  -4.1818  -2.0976  -1.0479
 18Z  C20   C  CR6    0   0.558  -5.9109  -2.8856   0.1782
 18Z  C21   C  CR16   0  -0.021  -4.1435  -2.0167   1.2896
 18Z  C22   C  CH2    0  -0.277   2.6858  -0.3115  -0.0052
 18Z  C23   C  CH2    0  -0.299   4.1961  -0.5102  -0.0237
 18Z  C24   C  CH2    0  -0.289   5.9657  -2.0013   0.5922
 18Z  C25   C  CH2    0  -0.325   6.3159  -3.4457   0.9204
 18Z  C26   C  CH2    0  -0.321   4.6416  -4.1942  -0.6034
 18Z  C27   C  CH2    0  -0.297   4.2863  -2.7493  -0.9280
 18Z  O28   O  O      0  -0.506  -3.8828   2.5129  -0.2453
 18Z  O29   O  O     -1  -0.420   1.5961   5.1638  -0.4912
 18Z  O30   O  O      0  -0.445   3.0753   3.6354  -0.3968
 18Z  HN01  H  HNH2   0   0.414  -2.2602   4.9992   0.8118
 18Z  HN0A  H  HNH2   0   0.407  -3.9355   4.8712   0.4872
 18Z  HN02  H  HNH1   0   0.411   3.1584   1.7439  -0.2136
 18Z  HN03  H  HNH1   0   0.409  -3.2188   0.7546  -0.0598
 18Z  HN06  H  HNH2   0   0.400  -7.6257  -3.6342  -0.6315
 18Z  HN0B  H  HNH2   0   0.400  -7.5964  -3.5796   1.0929
 18Z  HN08  H  HNH1   0   0.339   6.6390  -4.1890  -0.9339
 18Z  H10   H  HCR6   0   0.288  -0.5851   4.5383  -0.2675
 18Z  H13   H  HCR6   0   0.304   0.2186  -0.2962   0.0192
 18Z  H17   H  HCH2   0   0.258  -1.5963  -1.4140  -0.8349
 18Z  H17A  H  HCH2   0   0.259  -1.5515  -1.3900   0.9206
 18Z  H19   H  HCR6   0   0.269  -3.7477  -1.9212  -2.0283
 18Z  H21   H  HCR6   0   0.269  -3.6776  -1.7735   2.2406
 18Z  H22   H  HCH2   0   0.241   2.2859  -0.7026   0.9363
 18Z  H22A  H  HCH2   0   0.240   2.2114  -0.8734  -0.8157
 18Z  H23   H  HCH2   0   0.246   4.6285   0.0969   0.7770
 18Z  H23A  H  HCH2   0   0.208   4.6073  -0.1238  -0.9724
 18Z  H24   H  HCH2   0   0.188   6.6332  -1.6394  -0.2105
 18Z  H24A  H  HCH2   0   0.235   6.1475  -1.3694   1.4654
 18Z  H25   H  HCH2   0   0.219   5.7534  -3.7558   1.8069
 18Z  H25A  H  HCH2   0   0.237   7.3759  -3.5182   1.1710
 18Z  H26   H  HCH2   0   0.237   4.4621  -4.8207  -1.4790
 18Z  H26A  H  HCH2   0   0.219   3.9757  -4.5515   0.1888
 18Z  H27   H  HCH2   0   0.236   3.2262  -2.6950  -1.1840
 18Z  H27A  H  HCH2   0   0.190   4.8471  -2.4216  -1.8223

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
 18Z  N01  C16   single    1.342  0.020  1.342
 18Z  N01  HN01  single    0.860  0.020  1.020
 18Z  N01  HN0A  single    0.860  0.020  1.020
 18Z  N02  C14   single    1.338  0.020  1.338
 18Z  N02  C22   single    1.444  0.020  1.444
 18Z  N02  HN02  single    0.860  0.020  1.020
 18Z  N03  C12   single    1.339  0.020  1.339
 18Z  N03  C17   single    1.447  0.020  1.447
 18Z  N03  HN03  single    0.860  0.020  1.020
 18Z  N04  C19   aromatic  1.320  0.020  1.320
 18Z  N04  C20   aromatic  1.339  0.020  1.339
 18Z  N05  C20   aromatic  1.340  0.020  1.340
 18Z  N05  C21   aromatic  1.319  0.020  1.319
 18Z  N06  C20   single    1.341  0.020  1.341
 18Z  N06  HN06  single    0.860  0.020  1.020
 18Z  N06  HN0B  single    0.860  0.020  1.020
 18Z  N07  C23   single    1.446  0.020  1.446
 18Z  N07  C24   single    1.454  0.020  1.454
 18Z  N07  C27   single    1.455  0.020  1.455
 18Z  N08  C25   single    1.454  0.020  1.454
 18Z  N08  C26   single    1.453  0.020  1.453
 18Z  N08  HN08  single    0.890  0.020  1.040
 18Z  N09  C15   single    1.413  0.020  1.413
 18Z  N09  O29   single    1.218  0.020  1.218
 18Z  N09  O30   double    1.226  0.020  1.226
 18Z  C10  C11   aromatic  1.372  0.020  1.372
 18Z  C10  C15   aromatic  1.396  0.020  1.396
 18Z  C10  H10   single    0.930  0.020  1.080
 18Z  C11  C12   aromatic  1.439  0.020  1.439
 18Z  C11  C16   single    1.484  0.020  1.484
 18Z  C12  C13   aromatic  1.396  0.020  1.396
 18Z  C13  C14   aromatic  1.400  0.020  1.400
 18Z  C13  H13   single    0.930  0.020  1.080
 18Z  C14  C15   aromatic  1.434  0.020  1.434
 18Z  C16  O28   double    1.233  0.020  1.233
 18Z  C17  C18   single    1.495  0.020  1.495
 18Z  C17  H17   single    0.970  0.020  1.090
 18Z  C17  H17A  single    0.970  0.020  1.090
 18Z  C18  C19   aromatic  1.389  0.020  1.389
 18Z  C18  C21   aromatic  1.389  0.020  1.389
 18Z  C19  H19   single    0.930  0.020  1.080
 18Z  C21  H21   single    0.930  0.020  1.080
 18Z  C22  C23   single    1.523  0.020  1.523
 18Z  C22  H22   single    0.970  0.020  1.090
 18Z  C22  H22A  single    0.970  0.020  1.090
 18Z  C23  H23   single    0.970  0.020  1.090
 18Z  C23  H23A  single    0.970  0.020  1.090
 18Z  C24  C25   single    1.522  0.020  1.522
 18Z  C24  H24   single    0.970  0.020  1.090
 18Z  C24  H24A  single    0.970  0.020  1.090
 18Z  C25  H25   single    0.970  0.020  1.090
 18Z  C25  H25A  single    0.970  0.020  1.090
 18Z  C26  C27   single    1.523  0.020  1.523
 18Z  C26  H26   single    0.970  0.020  1.090
 18Z  C26  H26A  single    0.970  0.020  1.090
 18Z  C27  H27   single    0.970  0.020  1.090
 18Z  C27  H27A  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
 18Z  HN0A  N01  HN01  116.55  3.000
 18Z  HN0A  N01  C16   118.80  3.000
 18Z  HN01  N01  C16   122.96  3.000
 18Z  HN02  N02  C22   118.63  3.000
 18Z  HN02  N02  C14   116.97  3.000
 18Z  C22   N02  C14   124.37  3.000
 18Z  HN03  N03  C17   118.91  3.000
 18Z  HN03  N03  C12   116.13  3.000
 18Z  C17   N03  C12   124.30  3.000
 18Z  C20   N04  C19   116.52  3.000
 18Z  C21   N05  C20   116.51  3.000
 18Z  HN0B  N06  HN06  118.41  3.000
 18Z  HN0B  N06  C20   120.11  3.000
 18Z  HN06  N06  C20   120.04  3.000
 18Z  C27   N07  C24   110.19  3.000
 18Z  C27   N07  C23   112.81  3.000
 18Z  C24   N07  C23   111.29  3.000
 18Z  HN08  N08  C26   109.03  3.000
 18Z  HN08  N08  C25   108.89  3.000
 18Z  C26   N08  C25   110.26  3.000
 18Z  O30   N09  O29   121.22  3.000
 18Z  O30   N09  C15   119.28  3.000
 18Z  O29   N09  C15   119.50  3.000
 18Z  H10   C10  C15   116.94  3.000
 18Z  H10   C10  C11   119.45  3.000
 18Z  C15   C10  C11   123.61  3.000
 18Z  C16   C11  C12   121.45  3.000
 18Z  C16   C11  C10   120.86  3.000
 18Z  C12   C11  C10   117.68  3.000
 18Z  C13   C12  C11   118.85  3.000
 18Z  C13   C12  N03   120.59  3.000
 18Z  C11   C12  N03   120.55  3.000
 18Z  H13   C13  C14   118.17  3.000
 18Z  H13   C13  C12   118.27  3.000
 18Z  C14   C13  C12   123.55  3.000
 18Z  C15   C14  C13   116.55  3.000
 18Z  C15   C14  N02   123.54  3.000
 18Z  C13   C14  N02   119.91  3.000
 18Z  C14   C15  C10   119.64  3.000
 18Z  C14   C15  N09   123.11  3.000
 18Z  C10   C15  N09   117.25  3.000
 18Z  O28   C16  C11   121.89  3.000
 18Z  O28   C16  N01   121.09  3.000
 18Z  C11   C16  N01   117.02  3.000
 18Z  H17A  C17  H17   106.56  3.000
 18Z  H17A  C17  C18   109.66  3.000
 18Z  H17   C17  C18   109.74  3.000
 18Z  H17A  C17  N03   110.10  3.000
 18Z  H17   C17  N03   110.49  3.000
 18Z  C18   C17  N03   110.22  3.000
 18Z  C21   C18  C19   114.70  3.000
 18Z  C21   C18  C17   122.64  3.000
 18Z  C19   C18  C17   122.65  3.000
 18Z  H19   C19  C18   120.15  3.000
 18Z  H19   C19  N04   116.34  3.000
 18Z  C18   C19  N04   123.51  3.000
 18Z  N06   C20  N05   117.39  3.000
 18Z  N06   C20  N04   117.36  3.000
 18Z  N05   C20  N04   125.24  3.000
 18Z  H21   C21  C18   120.15  3.000
 18Z  H21   C21  N05   116.33  3.000
 18Z  C18   C21  N05   123.52  3.000
 18Z  H22A  C22  H22   107.17  3.000
 18Z  H22A  C22  C23   110.71  3.000
 18Z  H22   C22  C23   109.02  3.000
 18Z  H22A  C22  N02   110.01  3.000
 18Z  H22   C22  N02   110.76  3.000
 18Z  C23   C22  N02   109.15  3.000
 18Z  H23A  C23  H23   106.71  3.000
 18Z  H23A  C23  C22   109.52  3.000
 18Z  H23   C23  C22   108.09  3.000
 18Z  H23A  C23  N07   112.16  3.000
 18Z  H23   C23  N07   108.00  3.000
 18Z  C22   C23  N07   112.12  3.000
 18Z  H24A  C24  H24   106.89  3.000
 18Z  H24A  C24  C25   109.76  3.000
 18Z  H24   C24  C25   109.17  3.000
 18Z  H24A  C24  N07   108.95  3.000
 18Z  H24   C24  N07   111.41  3.000
 18Z  C25   C24  N07   110.58  3.000
 18Z  H25A  C25  H25   107.11  3.000
 18Z  H25A  C25  C24   109.63  3.000
 18Z  H25   C25  C24   108.97  3.000
 18Z  H25A  C25  N08   109.30  3.000
 18Z  H25   C25  N08   108.24  3.000
 18Z  C24   C25  N08   113.39  3.000
 18Z  H26A  C26  H26   107.05  3.000
 18Z  H26A  C26  C27   108.78  3.000
 18Z  H26   C26  C27   109.58  3.000
 18Z  H26A  C26  N08   108.19  3.000
 18Z  H26   C26  N08   109.32  3.000
 18Z  C27   C26  N08   113.69  3.000
 18Z  H27A  C27  H27   106.75  3.000
 18Z  H27A  C27  C26   109.59  3.000
 18Z  H27   C27  C26   108.88  3.000
 18Z  H27A  C27  N07   111.10  3.000
 18Z  H27   C27  N07   109.96  3.000
 18Z  C26   C27  N07   110.47  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
 18Z  CONST_01  C21   C18  C19  N04     0.00   0.0  0
 18Z  CONST_02  C21   N05  C20  N04     0.00   0.0  0
 18Z  CONST_03  C19   N04  C20  N05     0.00   0.0  0
 18Z  CONST_04  C19   C18  C21  N05     0.00   0.0  0
 18Z  CONST_05  C13   C12  C11  C10     0.00   0.0  0
 18Z  CONST_06  C13   C14  C15  C10     0.00   0.0  0
 18Z  CONST_07  C14   C15  C10  C11     0.00   0.0  0
 18Z  CONST_08  C14   C13  C12  C11     0.00   0.0  0
 18Z  CONST_09  C15   C10  C11  C12     0.00   0.0  0
 18Z  CONST_10  C15   C14  C13  C12     0.00   0.0  0
 18Z  CONST_11  C20   N04  C19  C18     0.00   0.0  0
 18Z  CONST_12  C20   N05  C21  C18     0.00   0.0  0
 18Z  CONST_13  C12   C13  C14  N02   180.00   0.0  0
 18Z  CONST_14  C10   C15  C14  N02   180.00   0.0  0
 18Z  CONST_15  C10   C11  C12  N03   180.00   0.0  0
 18Z  CONST_16  C14   C13  C12  N03   180.00   0.0  0
 18Z  CONST_17  C17   C18  C19  N04   180.00   0.0  0
 18Z  CONST_18  C17   C18  C21  N05   180.00   0.0  0
 18Z  CONST_19  C19   N04  C20  N06   180.00   0.0  0
 18Z  CONST_20  C21   N05  C20  N06   180.00   0.0  0
 18Z  CONST_21  C11   C10  C15  N09   180.00   0.0  0
 18Z  CONST_22  C13   C14  C15  N09   180.00   0.0  0
 18Z  CONST_23  C16   C11  C12  C13   180.00   0.0  0
 18Z  CONST_24  C16   C11  C10  C15   180.00   0.0  0
 18Z  CONST_25  H13   C13  C12  C11   180.00   0.0  0
 18Z  CONST_26  H10   C10  C11  C12   180.00   0.0  0
 18Z  CONST_27  H21   C21  C18  C19   180.00   0.0  0
 18Z  CONST_28  H19   C19  N04  C20   180.00   0.0  0
 18Z  CONST_29  O29   N09  C15  C10     0.00   0.0  0
 18Z  CONST_30  O30   N09  C15  C10   180.00   0.0  0
 18Z  CONST_31  C17   N03  C12  C11   180.00   0.0  0
 18Z  CONST_32  C17   N03  C12  C13     0.00   0.0  0
 18Z  CONST_33  C22   N02  C14  C13     0.00   0.0  0
 18Z  CONST_34  O29   N09  C15  C14   180.00   0.0  0
 18Z  CONST_35  O30   N09  C15  C14     0.00   0.0  0
 18Z  CONST_36  C22   N02  C14  C15   180.00   0.0  0
 18Z  CONST_37  HN06  N06  C20  N04     0.00   0.0  0
 18Z  CONST_38  HN0B  N06  C20  N04   180.00   0.0  0
 18Z  CONST_39  HN03  N03  C12  C11     0.00   0.0  0
 18Z  CONST_40  HN02  N02  C14  C13   180.00   0.0  0
 18Z  CONST_41  HN01  N01  C16  C11     0.00   0.0  0
 18Z  CONST_42  HN0A  N01  C16  C11   180.00   0.0  0
 18Z  Var_01    N08   C25  C24  N07    55.60  30.0  1
 18Z  Var_02    N08   C26  C27  N07   -55.16  30.0  1
 18Z  Var_03    C26   C27  N07  C24    57.33  30.0  1
 18Z  Var_04    C26   N08  C25  C24   -51.41  30.0  1
 18Z  Var_05    C27   C26  N08  C25    51.30  30.0  1
 18Z  Var_06    C27   N07  C24  C25   -57.68  30.0  1
 18Z  Var_07    C10   C11  C16  N01   -21.15  30.0  2
 18Z  Var_08    C19   C18  C17  N03    90.98  30.0  2
 18Z  Var_09    C18   C17  N03  C12  -178.46  30.0  3
 18Z  Var_10    C24   N07  C23  C22  -162.61  30.0  3
 18Z  Var_11    N07   C23  C22  N02   175.61  30.0  3
 18Z  Var_12    C23   C22  N02  C14  -178.66  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
 18Z  plan-1  N04   0.020
 18Z  plan-1  N05   0.020
 18Z  plan-1  N06   0.020
 18Z  plan-1  C17   0.020
 18Z  plan-1  C18   0.020
 18Z  plan-1  C19   0.020
 18Z  plan-1  C20   0.020
 18Z  plan-1  C21   0.020
 18Z  plan-1  H19   0.020
 18Z  plan-1  H21   0.020
 18Z  plan-2  N01   0.020
 18Z  plan-2  C11   0.020
 18Z  plan-2  C16   0.020
 18Z  plan-2  O28   0.020
 18Z  plan-2  HN01  0.020
 18Z  plan-2  HN0A  0.020
 18Z  plan-3  N02   0.020
 18Z  plan-3  N03   0.020
 18Z  plan-3  N09   0.020
 18Z  plan-3  C10   0.020
 18Z  plan-3  C11   0.020
 18Z  plan-3  C12   0.020
 18Z  plan-3  C13   0.020
 18Z  plan-3  C14   0.020
 18Z  plan-3  C15   0.020
 18Z  plan-3  C16   0.020
 18Z  plan-3  H10   0.020
 18Z  plan-3  H13   0.020
 18Z  plan-4  N02   0.020
 18Z  plan-4  C14   0.020
 18Z  plan-4  C22   0.020
 18Z  plan-4  HN02  0.020
 18Z  plan-5  N03   0.020
 18Z  plan-5  C12   0.020
 18Z  plan-5  C17   0.020
 18Z  plan-5  HN03  0.020
 18Z  plan-6  N06   0.020
 18Z  plan-6  C20   0.020
 18Z  plan-6  HN06  0.020
 18Z  plan-6  HN0B  0.020
 18Z  plan-7  N09   0.020
 18Z  plan-7  C15   0.020
 18Z  plan-7  O29   0.020
 18Z  plan-7  O30   0.020

