# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 23:17:41 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 4-(hexylamino)-5-nitro-2-[(pyridin-3-ylmethyl)amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCNc1cc(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
 22Z  22Z  4-(hexylamino)-5-nitro-2-[(pyridin-3-ylmethyl)amino]benzamide  ligand  52  27  .  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_22Z
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
 22Z  N01   N  NH1    0  -0.689   2.3271   0.2606   0.0194
 22Z  N02   N  NH2    0  -0.812   3.4290  -3.7650  -0.3617
 22Z  N03   N  N      0  -0.401   5.0690   3.5990  -1.1408
 22Z  N04   N  NH1    0  -0.684  -2.2742  -0.8982   0.1074
 22Z  N05   N  N      1   0.339  -1.5297  -3.7416   0.3040
 22Z  C06   C  CR16   0  -0.357   0.7497  -3.0100   0.1677
 22Z  C07   C  CR6    0  -0.146   1.7567  -2.0834   0.0756
 22Z  C08   C  CR6    0   0.454   1.3867  -0.6929   0.0541
 22Z  C09   C  CR16   0  -0.559   0.0329  -0.3561   0.0451
 22Z  C10   C  CR6    0   0.457  -0.9996  -1.3013   0.1128
 22Z  C11   C  CR6    0   0.176  -0.6056  -2.6776   0.1962
 22Z  C13   C  CH2    0  -0.347   2.0449   1.6774  -0.0099
 22Z  C14   C  CR6    0  -0.027   3.3302   2.4492   0.0450
 22Z  C15   C  CR16   0  -0.083   3.9232   2.9305  -1.1166
 22Z  C16   C  CR16   0  -0.064   5.6843   3.8153   0.0156
 22Z  C17   C  CR16   0  -0.320   5.1857   3.3788   1.2347
 22Z  C18   C  CR16   0  -0.168   3.9878   2.6837   1.2468
 22Z  C19   C  CH2    0  -0.257  -2.7013   0.4796   0.0191
 22Z  C20   C  CH2    0  -0.468  -4.2191   0.5573   0.0459
 22Z  C21   C  CH2    0  -0.416  -4.7266   1.9871  -0.0815
 22Z  C22   C  CH2    0  -0.407  -6.2471   2.0748  -0.0372
 22Z  C23   C  CH2    0  -0.420  -6.7726   3.4967  -0.1898
 22Z  C24   C  CH3    0  -0.661  -8.2926   3.5723  -0.1414
 22Z  O25   O  O      0  -0.507   4.0948  -1.7401   0.3338
 22Z  O26   O  O     -1  -0.420  -1.1189  -4.8844   0.3940
 22Z  O27   O  O      0  -0.445  -2.7310  -3.4964   0.3039
 22Z  HN01  H  HNH1   0   0.412   3.2842  -0.0526   0.1157
 22Z  HN02  H  HNH2   0   0.415   2.7343  -4.3623  -0.7735
 22Z  HN0A  H  HNH2   0   0.408   4.3832  -4.0848  -0.4000
 22Z  HN04  H  HNH1   0   0.411  -2.9800  -1.6141   0.1518
 22Z  H06   H  HCR6   0   0.287   0.9995  -4.0587   0.2403
 22Z  H09   H  HCR6   0   0.303  -0.2381   0.6875  -0.0049
 22Z  H13   H  HCH2   0   0.260   1.4953   1.9387  -0.9201
 22Z  H13A  H  HCH2   0   0.260   1.4088   1.9598   0.8361
 22Z  H15   H  HCR6   0   0.263   3.4377   2.7670  -2.0742
 22Z  H16   H  HCR6   0   0.267   6.6182   4.3645  -0.0265
 22Z  H17   H  HCR6   0   0.275   5.7238   3.5832   2.1500
 22Z  H18   H  HCR6   0   0.275   3.5654   2.3335   2.1810
 22Z  H19   H  HCH2   0   0.235  -2.2880   1.0581   0.8526
 22Z  H19A  H  HCH2   0   0.235  -2.3227   0.9359  -0.9027
 22Z  H20   H  HCH2   0   0.232  -4.6258  -0.0479  -0.7707
 22Z  H20A  H  HCH2   0   0.232  -4.5861   0.1184   0.9792
 22Z  H21   H  HCH2   0   0.216  -4.3034   2.5990   0.7221
 22Z  H21A  H  HCH2   0   0.216  -4.3649   2.4206  -1.0200
 22Z  H22   H  HCH2   0   0.209  -6.6697   1.4472  -0.8296
 22Z  H22A  H  HCH2   0   0.209  -6.6074   1.6537   0.9080
 22Z  H23   H  HCH2   0   0.211  -6.3496   4.1263   0.5991
 22Z  H23A  H  HCH2   0   0.211  -6.4159   3.9147  -1.1364
 22Z  H24   H  HCH3   0   0.216  -8.6765   3.2006   0.8105
 22Z  H24A  H  HCH3   0   0.226  -8.6467   4.5967  -0.2626
 22Z  H24B  H  HCH3   0   0.216  -8.7424   2.9715  -0.9341
 22Z  C12   C  C      0   0.534   3.1785  -2.5061   0.0282

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
 22Z  N01  C08   single    1.340  0.020  1.340
 22Z  N01  C13   single    1.445  0.020  1.445
 22Z  N01  HN01  single    0.860  0.020  1.020
 22Z  N02  C12   single    1.342  0.020  1.342
 22Z  N02  HN02  single    0.860  0.020  1.020
 22Z  N02  HN0A  single    0.860  0.020  1.020
 22Z  N03  C15   aromatic  1.327  0.020  1.327
 22Z  N03  C16   aromatic  1.328  0.020  1.328
 22Z  N04  C10   single    1.337  0.020  1.337
 22Z  N04  C19   single    1.445  0.020  1.445
 22Z  N04  HN04  single    0.860  0.020  1.020
 22Z  N05  C11   single    1.413  0.020  1.413
 22Z  N05  O26   single    1.218  0.020  1.218
 22Z  N05  O27   double    1.226  0.020  1.226
 22Z  C06  C07   aromatic  1.372  0.020  1.372
 22Z  C06  C11   aromatic  1.396  0.020  1.396
 22Z  C06  H06   single    0.930  0.020  1.080
 22Z  C07  C08   aromatic  1.439  0.020  1.439
 22Z  C07  C12   single    1.484  0.020  1.484
 22Z  C08  C09   aromatic  1.395  0.020  1.395
 22Z  C09  C10   aromatic  1.401  0.020  1.401
 22Z  C09  H09   single    0.930  0.020  1.080
 22Z  C10  C11   aromatic  1.434  0.020  1.434
 22Z  C12  O25   double    1.233  0.020  1.233
 22Z  C13  C14   single    1.500  0.020  1.500
 22Z  C13  H13   single    0.970  0.020  1.090
 22Z  C13  H13A  single    0.970  0.020  1.090
 22Z  C14  C15   aromatic  1.390  0.020  1.390
 22Z  C14  C18   aromatic  1.390  0.020  1.390
 22Z  C15  H15   single    0.930  0.020  1.080
 22Z  C16  C17   aromatic  1.388  0.020  1.388
 22Z  C16  H16   single    0.930  0.020  1.080
 22Z  C17  C18   aromatic  1.385  0.020  1.385
 22Z  C17  H17   single    0.930  0.020  1.080
 22Z  C18  H18   single    0.930  0.020  1.080
 22Z  C19  C20   single    1.520  0.020  1.520
 22Z  C19  H19   single    0.970  0.020  1.090
 22Z  C19  H19A  single    0.970  0.020  1.090
 22Z  C20  C21   single    1.522  0.020  1.522
 22Z  C20  H20   single    0.970  0.020  1.090
 22Z  C20  H20A  single    0.970  0.020  1.090
 22Z  C21  C22   single    1.524  0.020  1.524
 22Z  C21  H21   single    0.970  0.020  1.090
 22Z  C21  H21A  single    0.970  0.020  1.090
 22Z  C22  C23   single    1.524  0.020  1.524
 22Z  C22  H22   single    0.970  0.020  1.090
 22Z  C22  H22A  single    0.970  0.020  1.090
 22Z  C23  C24   single    1.523  0.020  1.523
 22Z  C23  H23   single    0.970  0.020  1.090
 22Z  C23  H23A  single    0.970  0.020  1.090
 22Z  C24  H24   single    0.970  0.020  1.090
 22Z  C24  H24A  single    0.970  0.020  1.090
 22Z  C24  H24B  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
 22Z  HN01  N01  C13   119.36  3.000
 22Z  HN01  N01  C08   116.18  3.000
 22Z  C13   N01  C08   124.15  3.000
 22Z  HN0A  N02  HN02  116.80  3.000
 22Z  HN0A  N02  C12   119.07  3.000
 22Z  HN02  N02  C12   123.23  3.000
 22Z  C16   N03  C15   117.81  3.000
 22Z  HN04  N04  C19   118.27  3.000
 22Z  HN04  N04  C10   117.00  3.000
 22Z  C19   N04  C10   124.72  3.000
 22Z  O27   N05  O26   121.21  3.000
 22Z  O27   N05  C11   119.34  3.000
 22Z  O26   N05  C11   119.44  3.000
 22Z  H06   C06  C11   117.02  3.000
 22Z  H06   C06  C07   119.37  3.000
 22Z  C11   C06  C07   123.60  3.000
 22Z  C12   C07  C08   121.41  3.000
 22Z  C12   C07  C06   120.87  3.000
 22Z  C08   C07  C06   117.71  3.000
 22Z  C09   C08  C07   118.87  3.000
 22Z  C09   C08  N01   120.61  3.000
 22Z  C07   C08  N01   120.51  3.000
 22Z  H09   C09  C10   117.99  3.000
 22Z  H09   C09  C08   118.52  3.000
 22Z  C10   C09  C08   123.49  3.000
 22Z  C11   C10  C09   116.60  3.000
 22Z  C11   C10  N04   123.48  3.000
 22Z  C09   C10  N04   119.92  3.000
 22Z  C10   C11  C06   119.61  3.000
 22Z  C10   C11  N05   123.18  3.000
 22Z  C06   C11  N05   117.20  3.000
 22Z  H13A  C13  H13   106.80  3.000
 22Z  H13A  C13  C14   109.67  3.000
 22Z  H13   C13  C14   109.74  3.000
 22Z  H13A  C13  N01   110.52  3.000
 22Z  H13   C13  N01   110.42  3.000
 22Z  C14   C13  N01   109.65  3.000
 22Z  C18   C14  C15   117.54  3.000
 22Z  C18   C14  C13   121.59  3.000
 22Z  C15   C14  C13   120.86  3.000
 22Z  H15   C15  C14   119.61  3.000
 22Z  H15   C15  N03   116.47  3.000
 22Z  C14   C15  N03   123.92  3.000
 22Z  H16   C16  C17   120.19  3.000
 22Z  H16   C16  N03   116.61  3.000
 22Z  C17   C16  N03   123.20  3.000
 22Z  H17   C17  C18   121.19  3.000
 22Z  H17   C17  C16   120.36  3.000
 22Z  C18   C17  C16   118.44  3.000
 22Z  H18   C18  C17   120.46  3.000
 22Z  H18   C18  C14   120.44  3.000
 22Z  C17   C18  C14   119.10  3.000
 22Z  H19A  C19  H19   106.84  3.000
 22Z  H19A  C19  C20   109.78  3.000
 22Z  H19   C19  C20   109.65  3.000
 22Z  H19A  C19  N04   110.26  3.000
 22Z  H19   C19  N04   110.21  3.000
 22Z  C20   C19  N04   110.05  3.000
 22Z  H20A  C20  H20   106.85  3.000
 22Z  H20A  C20  C21   109.64  3.000
 22Z  H20   C20  C21   109.45  3.000
 22Z  H20A  C20  C19   109.22  3.000
 22Z  H20   C20  C19   109.24  3.000
 22Z  C21   C20  C19   112.29  3.000
 22Z  H21A  C21  H21   106.26  3.000
 22Z  H21A  C21  C22   109.37  3.000
 22Z  H21   C21  C22   109.39  3.000
 22Z  H21A  C21  C20   109.48  3.000
 22Z  H21   C21  C20   109.54  3.000
 22Z  C22   C21  C20   112.60  3.000
 22Z  H22A  C22  H22   106.08  3.000
 22Z  H22A  C22  C23   109.37  3.000
 22Z  H22   C22  C23   109.22  3.000
 22Z  H22A  C22  C21   109.33  3.000
 22Z  H22   C22  C21   109.32  3.000
 22Z  C23   C22  C21   113.27  3.000
 22Z  H23A  C23  H23   106.12  3.000
 22Z  H23A  C23  C24   109.51  3.000
 22Z  H23   C23  C24   109.54  3.000
 22Z  H23A  C23  C22   109.31  3.000
 22Z  H23   C23  C22   109.35  3.000
 22Z  C24   C23  C22   112.80  3.000
 22Z  H24B  C24  H24A  107.60  3.000
 22Z  H24B  C24  H24   107.51  3.000
 22Z  H24A  C24  H24   107.61  3.000
 22Z  H24B  C24  C23   111.16  3.000
 22Z  H24A  C24  C23   111.54  3.000
 22Z  H24   C24  C23   111.22  3.000
 22Z  O25   C12  C07   121.82  3.000
 22Z  O25   C12  N02   121.09  3.000
 22Z  C07   C12  N02   117.09  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
 22Z  CONST_01  C18   C14  C15  N03     0.00   0.0  0
 22Z  CONST_02  C18   C17  C16  N03     0.00   0.0  0
 22Z  CONST_03  C09   C08  C07  C06     0.00   0.0  0
 22Z  CONST_04  C09   C10  C11  C06     0.00   0.0  0
 22Z  CONST_05  C10   C11  C06  C07     0.00   0.0  0
 22Z  CONST_06  C10   C09  C08  C07     0.00   0.0  0
 22Z  CONST_07  C11   C06  C07  C08     0.00   0.0  0
 22Z  CONST_08  C11   C10  C09  C08     0.00   0.0  0
 22Z  CONST_09  C16   N03  C15  C14     0.00   0.0  0
 22Z  CONST_10  C16   C17  C18  C14     0.00   0.0  0
 22Z  CONST_11  C17   C16  N03  C15     0.00   0.0  0
 22Z  CONST_12  C17   C18  C14  C15     0.00   0.0  0
 22Z  CONST_13  C06   C07  C08  N01   180.00   0.0  0
 22Z  CONST_14  C10   C09  C08  N01   180.00   0.0  0
 22Z  CONST_15  C13   C14  C15  N03   180.00   0.0  0
 22Z  CONST_16  C08   C09  C10  N04   180.00   0.0  0
 22Z  CONST_17  C06   C11  C10  N04   180.00   0.0  0
 22Z  CONST_18  C07   C06  C11  N05   180.00   0.0  0
 22Z  CONST_19  C09   C10  C11  N05   180.00   0.0  0
 22Z  CONST_20  C12   C07  C08  C09   180.00   0.0  0
 22Z  CONST_21  C12   C07  C06  C11   180.00   0.0  0
 22Z  CONST_22  C17   C18  C14  C13   180.00   0.0  0
 22Z  CONST_23  H17   C17  C16  N03   180.00   0.0  0
 22Z  CONST_24  H09   C09  C08  C07   180.00   0.0  0
 22Z  CONST_25  H06   C06  C07  C08   180.00   0.0  0
 22Z  CONST_26  H16   C16  N03  C15   180.00   0.0  0
 22Z  CONST_27  H18   C18  C14  C15   180.00   0.0  0
 22Z  CONST_28  H15   C15  N03  C16   180.00   0.0  0
 22Z  CONST_29  O26   N05  C11  C06     0.00   0.0  0
 22Z  CONST_30  O27   N05  C11  C06   180.00   0.0  0
 22Z  CONST_31  C13   N01  C08  C07   180.00   0.0  0
 22Z  CONST_32  C13   N01  C08  C09     0.00   0.0  0
 22Z  CONST_33  C19   N04  C10  C09     0.00   0.0  0
 22Z  CONST_34  O26   N05  C11  C10   180.00   0.0  0
 22Z  CONST_35  O27   N05  C11  C10     0.00   0.0  0
 22Z  CONST_36  C19   N04  C10  C11   180.00   0.0  0
 22Z  CONST_37  HN01  N01  C08  C07     0.00   0.0  0
 22Z  CONST_38  HN04  N04  C10  C09   180.00   0.0  0
 22Z  CONST_39  HN02  N02  C12  C07     0.00   0.0  0
 22Z  CONST_40  HN0A  N02  C12  C07   180.00   0.0  0
 22Z  Var_01    C15   C14  C13  N01    97.15  30.0  2
 22Z  Var_02    C06   C07  C12  N02    21.47  30.0  2
 22Z  Var_03    C14   C13  N01  C08   176.35  30.0  3
 22Z  Var_04    C20   C19  N04  C10  -179.79  30.0  3
 22Z  Var_05    C21   C20  C19  N04  -178.49  30.0  3
 22Z  Var_06    C22   C21  C20  C19  -179.25  30.0  3
 22Z  Var_07    C23   C22  C21  C20  -178.92  30.0  3
 22Z  Var_08    C24   C23  C22  C21  -179.89  30.0  3
 22Z  Var_09    H24   C24  C23  C22    60.43  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
 22Z  plan-1  N03   0.020
 22Z  plan-1  C13   0.020
 22Z  plan-1  C14   0.020
 22Z  plan-1  C15   0.020
 22Z  plan-1  C16   0.020
 22Z  plan-1  C17   0.020
 22Z  plan-1  C18   0.020
 22Z  plan-1  H15   0.020
 22Z  plan-1  H16   0.020
 22Z  plan-1  H17   0.020
 22Z  plan-1  H18   0.020
 22Z  plan-2  N01   0.020
 22Z  plan-2  N04   0.020
 22Z  plan-2  N05   0.020
 22Z  plan-2  C06   0.020
 22Z  plan-2  C07   0.020
 22Z  plan-2  C08   0.020
 22Z  plan-2  C09   0.020
 22Z  plan-2  C10   0.020
 22Z  plan-2  C11   0.020
 22Z  plan-2  H06   0.020
 22Z  plan-2  H09   0.020
 22Z  plan-2  C12   0.020
 22Z  plan-3  N02   0.020
 22Z  plan-3  C07   0.020
 22Z  plan-3  O25   0.020
 22Z  plan-3  HN02  0.020
 22Z  plan-3  HN0A  0.020
 22Z  plan-3  C12   0.020
 22Z  plan-4  N01   0.020
 22Z  plan-4  C08   0.020
 22Z  plan-4  C13   0.020
 22Z  plan-4  HN01  0.020
 22Z  plan-5  N04   0.020
 22Z  plan-5  C10   0.020
 22Z  plan-5  C19   0.020
 22Z  plan-5  HN04  0.020
 22Z  plan-6  N05   0.020
 22Z  plan-6  C11   0.020
 22Z  plan-6  O26   0.020
 22Z  plan-6  O27   0.020

