# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 01:41:09 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 4-[(3-aminopropyl)amino]-5-nitro-2-[(pyridin-3-ylmethyl)amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCNc1cc(NCc2cccnc2)c(cc1[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
 X87  X87  4-[(3-aminopropyl)amino]-5-nitro-2-[(pyridin-3-ylmethyl)amino]benzamide  ligand  45  25  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X87
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
 X87  N01   N  NH1    0  -0.692   1.7687  -0.2320  -0.0105
 X87  N02   N  NH2    0  -0.809   1.0476  -4.3154   0.5234
 X87  N03   N  N      0  -0.401   5.6485   1.8474  -1.1957
 X87  N04   N  NH1    0  -0.683  -2.8896   0.6947  -0.0397
 X87  N05   N  NH2    0  -0.799  -5.1388   5.0160  -0.1785
 X87  N06   N  N      1   0.339  -3.4387  -2.1975  -0.1449
 X87  C07   C  CR16   0  -0.354  -1.0635  -2.5105  -0.0385
 X87  C08   C  CR6    0  -0.149   0.2441  -2.1007   0.0157
 X87  C09   C  CR6    0   0.453   0.5067  -0.6868  -0.0075
 X87  C10   C  CR16   0  -0.555  -0.5716   0.1971  -0.0002
 X87  C11   C  CR6    0   0.458  -1.9109  -0.2165  -0.0312
 X87  C12   C  CR6    0   0.176  -2.1461  -1.6301  -0.0706
 X87  C14   C  CH2    0  -0.344   2.1261   1.1661  -0.0745
 X87  C15   C  CR6    0  -0.023   3.6195   1.3078  -0.0364
 X87  C16   C  CR16   0  -0.091   4.3276   1.7196  -1.1585
 X87  C17   C  CR16   0  -0.064   6.3298   1.5583  -0.0945
 X87  C18   C  CR16   0  -0.319   5.7270   1.1367   1.0828
 X87  C19   C  CR16   0  -0.168   4.3486   1.0101   1.1101
 X87  C20   C  CH2    0  -0.262  -2.6848   2.1236   0.0265
 X87  C21   C  CH2    0  -0.478  -4.0147   2.8451  -0.1153
 X87  C22   C  CH2    0  -0.272  -3.8599   4.3514   0.0201
 X87  O23   O  O      0  -0.505   2.4858  -2.8154  -0.3235
 X87  O24   O  O      0  -0.420  -3.5589  -3.4078  -0.1992
 X87  O25   O  O     -1  -0.445  -4.4182  -1.4604  -0.1518
 X87  HN01  H  HNH1   0   0.410   2.4858  -0.9255  -0.1784
 X87  HN02  H  HNH2   0   0.414   0.2060  -4.5087   1.0373
 X87  HN0A  H  HNH2   0   0.407   1.7804  -5.0035   0.5856
 X87  HN04  H  HNH1   0   0.411  -3.8356   0.3505  -0.0616
 X87  HN05  H  HNH2   0   0.339  -5.7581   4.7851   0.5890
 X87  HN0B  H  HNH2   0   0.348  -5.0076   6.0180  -0.1265
 X87  H07   H  HCR6   0   0.289  -1.2834  -3.5674  -0.0816
 X87  H10   H  HCR6   0   0.302  -0.3729   1.2578   0.0062
 X87  H14   H  HCH2   0   0.259   1.7332   1.6337  -0.9850
 X87  H14A  H  HCH2   0   0.262   1.6854   1.7030   0.7715
 X87  H16   H  HCR6   0   0.263   3.7924   1.9601  -2.0722
 X87  H17   H  HCR6   0   0.267   7.4075   1.6654  -0.1476
 X87  H18   H  HCR6   0   0.275   6.3275   0.9144   1.9540
 X87  H19   H  HCR6   0   0.275   3.8456   0.6856   2.0130
 X87  H20   H  HCH2   0   0.237  -2.2069   2.3948   0.9749
 X87  H20A  H  HCH2   0   0.236  -2.0103   2.4479  -0.7729
 X87  H21   H  HCH2   0   0.237  -4.4543   2.6115  -1.0884
 X87  H21A  H  HCH2   0   0.233  -4.7100   2.4806   0.6481
 X87  H22   H  HCH2   0   0.218  -3.1656   4.7112  -0.7439
 X87  H22A  H  HCH2   0   0.195  -3.3938   4.5765   0.9901
 X87  C13   C  C      0   0.531   1.3475  -3.0923   0.0583

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
 X87  N01  C09   single    1.341  0.020  1.341
 X87  N01  C14   single    1.445  0.020  1.445
 X87  N01  HN01  single    0.860  0.020  1.020
 X87  N02  C13   single    1.343  0.020  1.343
 X87  N02  HN02  single    0.860  0.020  1.020
 X87  N02  HN0A  single    0.860  0.020  1.020
 X87  N03  C16   aromatic  1.328  0.020  1.328
 X87  N03  C17   aromatic  1.327  0.020  1.327
 X87  N04  C11   single    1.337  0.020  1.337
 X87  N04  C20   single    1.445  0.020  1.445
 X87  N04  HN04  single    0.860  0.020  1.020
 X87  N05  C22   single    1.455  0.020  1.455
 X87  N05  HN05  single    0.890  0.020  1.040
 X87  N05  HN0B  single    0.890  0.020  1.040
 X87  N06  C12   single    1.414  0.020  1.414
 X87  N06  O24   double    1.218  0.020  1.218
 X87  N06  O25   single    1.226  0.020  1.226
 X87  C07  C08   aromatic  1.371  0.020  1.371
 X87  C07  C12   aromatic  1.396  0.020  1.396
 X87  C07  H07   single    0.930  0.020  1.080
 X87  C08  C09   aromatic  1.438  0.020  1.438
 X87  C08  C13   single    1.484  0.020  1.484
 X87  C09  C10   aromatic  1.394  0.020  1.394
 X87  C10  C11   aromatic  1.402  0.020  1.402
 X87  C10  H10   single    0.930  0.020  1.080
 X87  C11  C12   aromatic  1.434  0.020  1.434
 X87  C13  O23   double    1.232  0.020  1.232
 X87  C14  C15   single    1.501  0.020  1.501
 X87  C14  H14   single    0.970  0.020  1.090
 X87  C14  H14A  single    0.970  0.020  1.090
 X87  C15  C16   aromatic  1.389  0.020  1.389
 X87  C15  C19   aromatic  1.391  0.020  1.391
 X87  C16  H16   single    0.930  0.020  1.080
 X87  C17  C18   aromatic  1.388  0.020  1.388
 X87  C17  H17   single    0.930  0.020  1.080
 X87  C18  C19   aromatic  1.384  0.020  1.384
 X87  C18  H18   single    0.930  0.020  1.080
 X87  C19  H19   single    0.930  0.020  1.080
 X87  C20  C21   single    1.520  0.020  1.520
 X87  C20  H20   single    0.970  0.020  1.090
 X87  C20  H20A  single    0.970  0.020  1.090
 X87  C21  C22   single    1.520  0.020  1.520
 X87  C21  H21   single    0.970  0.020  1.090
 X87  C21  H21A  single    0.970  0.020  1.090
 X87  C22  H22   single    0.970  0.020  1.090
 X87  C22  H22A  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
 X87  HN01  N01  C14   118.74  3.000
 X87  HN01  N01  C09   115.78  3.000
 X87  C14   N01  C09   124.13  3.000
 X87  HN0A  N02  HN02  116.52  3.000
 X87  HN0A  N02  C13   118.76  3.000
 X87  HN02  N02  C13   122.66  3.000
 X87  C17   N03  C16   117.82  3.000
 X87  HN04  N04  C20   118.18  3.000
 X87  HN04  N04  C11   117.05  3.000
 X87  C20   N04  C11   124.73  3.000
 X87  HN0B  N05  HN05  105.43  3.000
 X87  HN0B  N05  C22   109.35  3.000
 X87  HN05  N05  C22   109.26  3.000
 X87  O25   N06  O24   121.24  3.000
 X87  O25   N06  C12   119.31  3.000
 X87  O24   N06  C12   119.45  3.000
 X87  H07   C07  C12   117.27  3.000
 X87  H07   C07  C08   119.21  3.000
 X87  C12   C07  C08   123.50  3.000
 X87  C13   C08  C09   121.44  3.000
 X87  C13   C08  C07   120.69  3.000
 X87  C09   C08  C07   117.85  3.000
 X87  C10   C09  C08   118.81  3.000
 X87  C10   C09  N01   120.84  3.000
 X87  C08   C09  N01   120.33  3.000
 X87  H10   C10  C11   117.78  3.000
 X87  H10   C10  C09   118.73  3.000
 X87  C11   C10  C09   123.48  3.000
 X87  C12   C11  C10   116.63  3.000
 X87  C12   C11  N04   123.48  3.000
 X87  C10   C11  N04   119.88  3.000
 X87  C11   C12  C07   119.61  3.000
 X87  C11   C12  N06   123.18  3.000
 X87  C07   C12  N06   117.21  3.000
 X87  H14A  C14  H14   106.76  3.000
 X87  H14A  C14  C15   109.56  3.000
 X87  H14   C14  C15   109.72  3.000
 X87  H14A  C14  N01   109.93  3.000
 X87  H14   C14  N01   111.15  3.000
 X87  C15   C14  N01   109.66  3.000
 X87  C19   C15  C16   117.52  3.000
 X87  C19   C15  C14   121.50  3.000
 X87  C16   C15  C14   120.98  3.000
 X87  H16   C16  C15   119.61  3.000
 X87  H16   C16  N03   116.45  3.000
 X87  C15   C16  N03   123.94  3.000
 X87  H17   C17  C18   120.21  3.000
 X87  H17   C17  N03   116.63  3.000
 X87  C18   C17  N03   123.17  3.000
 X87  H18   C18  C19   121.22  3.000
 X87  H18   C18  C17   120.30  3.000
 X87  C19   C18  C17   118.48  3.000
 X87  H19   C19  C18   120.41  3.000
 X87  H19   C19  C15   120.51  3.000
 X87  C18   C19  C15   119.08  3.000
 X87  H20A  C20  H20   106.85  3.000
 X87  H20A  C20  C21   109.29  3.000
 X87  H20   C20  C21   110.17  3.000
 X87  H20A  C20  N04   110.28  3.000
 X87  H20   C20  N04   110.25  3.000
 X87  C21   C20  N04   109.95  3.000
 X87  H21A  C21  H21   107.11  3.000
 X87  H21A  C21  C22   109.41  3.000
 X87  H21   C21  C22   109.39  3.000
 X87  H21A  C21  C20   109.42  3.000
 X87  H21   C21  C20   109.49  3.000
 X87  C22   C21  C20   111.90  3.000
 X87  H22A  C22  H22   106.26  3.000
 X87  H22A  C22  C21   108.94  3.000
 X87  H22   C22  C21   109.18  3.000
 X87  H22A  C22  N05   113.56  3.000
 X87  H22   C22  N05   108.21  3.000
 X87  C21   C22  N05   110.55  3.000
 X87  O23   C13  C08   121.86  3.000
 X87  O23   C13  N02   121.23  3.000
 X87  C08   C13  N02   116.91  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
 X87  CONST_01  C19   C15  C16  N03    0.00   0.0  0
 X87  CONST_02  C19   C18  C17  N03    0.00   0.0  0
 X87  CONST_03  C10   C09  C08  C07    0.00   0.0  0
 X87  CONST_04  C10   C11  C12  C07    0.00   0.0  0
 X87  CONST_05  C11   C12  C07  C08    0.00   0.0  0
 X87  CONST_06  C11   C10  C09  C08    0.00   0.0  0
 X87  CONST_07  C12   C07  C08  C09    0.00   0.0  0
 X87  CONST_08  C12   C11  C10  C09    0.00   0.0  0
 X87  CONST_09  C17   N03  C16  C15    0.00   0.0  0
 X87  CONST_10  C17   C18  C19  C15    0.00   0.0  0
 X87  CONST_11  C18   C17  N03  C16    0.00   0.0  0
 X87  CONST_12  C18   C19  C15  C16    0.00   0.0  0
 X87  CONST_13  C07   C08  C09  N01  180.00   0.0  0
 X87  CONST_14  C11   C10  C09  N01  180.00   0.0  0
 X87  CONST_15  C14   C15  C16  N03  180.00   0.0  0
 X87  CONST_16  C09   C10  C11  N04  180.00   0.0  0
 X87  CONST_17  C07   C12  C11  N04  180.00   0.0  0
 X87  CONST_18  C08   C07  C12  N06  180.00   0.0  0
 X87  CONST_19  C10   C11  C12  N06  180.00   0.0  0
 X87  CONST_20  C13   C08  C09  C10  180.00   0.0  0
 X87  CONST_21  C13   C08  C07  C12  180.00   0.0  0
 X87  CONST_22  C18   C19  C15  C14  180.00   0.0  0
 X87  CONST_23  H18   C18  C17  N03  180.00   0.0  0
 X87  CONST_24  H10   C10  C09  C08  180.00   0.0  0
 X87  CONST_25  H07   C07  C08  C09  180.00   0.0  0
 X87  CONST_26  H17   C17  N03  C16  180.00   0.0  0
 X87  CONST_27  H19   C19  C15  C16  180.00   0.0  0
 X87  CONST_28  H16   C16  N03  C17  180.00   0.0  0
 X87  CONST_29  O24   N06  C12  C07    0.00   0.0  0
 X87  CONST_30  O25   N06  C12  C07  180.00   0.0  0
 X87  CONST_31  C14   N01  C09  C08  180.00   0.0  0
 X87  CONST_32  C14   N01  C09  C10    0.00   0.0  0
 X87  CONST_33  C20   N04  C11  C10    0.00   0.0  0
 X87  CONST_34  O24   N06  C12  C11  180.00   0.0  0
 X87  CONST_35  O25   N06  C12  C11    0.00   0.0  0
 X87  CONST_36  C20   N04  C11  C12  180.00   0.0  0
 X87  CONST_37  HN01  N01  C09  C08    0.00   0.0  0
 X87  CONST_38  HN04  N04  C11  C10  180.00   0.0  0
 X87  CONST_40  HN0A  N02  C13  C08  180.00   0.0  0
 X87  Var_01    C16   C15  C14  N01  109.96  30.0  2
 X87  Var_02    C07   C08  C13  N02  -23.63  30.0  2
 X87  Var_03    C15   C14  N01  C09  179.11  30.0  3
 X87  Var_04    C21   C20  N04  C11  175.60  30.0  3
 X87  Var_05    C22   C21  C20  N04  177.05  30.0  3
 X87  Var_06    C20   C21  C22  N05  177.51  30.0  1
 X87  Var_07    HN05  N05  C22  C21   67.63  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
 X87  plan-1  N03   0.020
 X87  plan-1  C14   0.020
 X87  plan-1  C15   0.020
 X87  plan-1  C16   0.020
 X87  plan-1  C17   0.020
 X87  plan-1  C18   0.020
 X87  plan-1  C19   0.020
 X87  plan-1  H16   0.020
 X87  plan-1  H17   0.020
 X87  plan-1  H18   0.020
 X87  plan-1  H19   0.020
 X87  plan-2  N01   0.020
 X87  plan-2  N04   0.020
 X87  plan-2  N06   0.020
 X87  plan-2  C07   0.020
 X87  plan-2  C08   0.020
 X87  plan-2  C09   0.020
 X87  plan-2  C10   0.020
 X87  plan-2  C11   0.020
 X87  plan-2  C12   0.020
 X87  plan-2  H07   0.020
 X87  plan-2  H10   0.020
 X87  plan-2  C13   0.020
 X87  plan-3  N02   0.020
 X87  plan-3  C08   0.020
 X87  plan-3  O23   0.020
 X87  plan-3  HN02  0.020
 X87  plan-3  HN0A  0.020
 X87  plan-3  C13   0.020
 X87  plan-4  N01   0.020
 X87  plan-4  C09   0.020
 X87  plan-4  C14   0.020
 X87  plan-4  HN01  0.020
 X87  plan-5  N04   0.020
 X87  plan-5  C11   0.020
 X87  plan-5  C20   0.020
 X87  plan-5  HN04  0.020
 X87  plan-6  N06   0.020
 X87  plan-6  C12   0.020
 X87  plan-6  O24   0.020
 X87  plan-6  O25   0.020

