# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 04:02:57 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 4-{[3-(morpholin-4-yl)propyl]amino}-5-nitro-2-[(pyridin-3-ylmethyl)amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(c(NCCCN2CCOCC2)cc1NCc3cccnc3)[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
 X85  X85  4-{[3-(morpholin-4-yl)propyl]amino}-5-nitro-2-[(pyridin-3-ylmethyl)amino]benzamide  ligand  56  30  .  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_X85
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
 X85  C1    C  CR16   0  -0.565  -0.8754  -0.4977  -0.0269
 X85  C2    C  CR6    0   0.458   0.0073  -1.5857  -0.0473
 X85  C3    C  CR6    0   0.179  -0.5846  -2.8883  -0.1343
 X85  C4    C  CR16   0  -0.357  -1.9742  -3.0144  -0.1675
 X85  C5    C  CR6    0  -0.147  -2.8356  -1.9478  -0.1202
 X85  C6    C  CR6    0   0.454  -2.2638  -0.6286  -0.0770
 X85  C7    C  C      0   0.533  -4.3049  -2.1541  -0.1521
 X85  N8    N  NH2    0  -0.812  -4.7620  -3.3641   0.2066
 X85  O9    O  O      0  -0.506  -5.0779  -1.2601  -0.5016
 X85  N10   N  N      1   0.339   0.1741  -4.0788  -0.2029
 X85  O11   O  O      0  -0.445   1.3968  -4.0143  -0.1498
 X85  O12   O  O     -1  -0.420  -0.3980  -5.1483  -0.3110
 X85  N13   N  NH1    0  -0.690  -3.0502   0.4562  -0.0589
 X85  C14   C  CH2    0  -0.349  -2.5559   1.8139  -0.0121
 X85  N15   N  NH1    0  -0.685   1.3271  -1.3711   0.0038
 X85  C16   C  CH2    0  -0.259   1.9334  -0.0597   0.0284
 X85  C17   C  CH2    0  -0.497   3.4462  -0.1756   0.1113
 X85  C18   C  CH2    0  -0.251   4.0918   1.1984  -0.0099
 X85  C19   C  CH2    0  -0.189   7.4961   2.5347   0.7452
 X85  C20   C  CH2    0  -0.302   6.0209   2.5517   0.3963
 X85  N21   N  NT     0  -0.427   5.5112   1.1971   0.2818
 X85  C22   C  CH2    0  -0.309   6.2914   0.4615  -0.6972
 X85  C23   C  CH2    0  -0.185   7.7621   0.4949  -0.3269
 X85  O24   O  O2     0  -0.485   8.2445   1.8148  -0.2092
 X85  C25   C  CR16   0  -0.064  -5.8238   4.4791   0.1609
 X85  N26   N  N      0  -0.401  -5.1546   4.2039   1.2739
 X85  C27   C  CR16   0  -0.086  -4.1267   3.3691   1.1878
 X85  C28   C  CR6    0  -0.024  -3.7091   2.7725   0.0039
 X85  C29   C  CR16   0  -0.168  -4.4191   3.0736  -1.1528
 X85  C30   C  CR16   0  -0.320  -5.4961   3.9410  -1.0754
 X85  H1    H  HCR6   0   0.310  -0.4566   0.4958   0.0170
 X85  H4    H  HCR6   0   0.287  -2.3729  -4.0145  -0.2542
 X85  H1N8  H  HNH2   0   0.414  -4.1955  -4.0470   0.6774
 X85  H2N8  H  HNH2   0   0.407  -5.7557  -3.5277   0.2040
 X85  HN13  H  HNH1   0   0.412  -4.0384   0.2956  -0.2021
 X85  H114  H  HCH2   0   0.262  -1.9395   1.9590   0.8804
 X85  H214  H  HCH2   0   0.261  -1.9128   2.0183  -0.8755
 X85  HN15  H  HNH1   0   0.410   1.9296  -2.1758  -0.0457
 X85  H116  H  HCH2   0   0.239   1.6486   0.5013  -0.8692
 X85  H216  H  HCH2   0   0.240   1.5637   0.5087   0.8877
 X85  H117  H  HCH2   0   0.241   3.7308  -0.6281   1.0646
 X85  H217  H  HCH2   0   0.243   3.7983  -0.8402  -0.6821
 X85  H118  H  HCH2   0   0.195   3.8829   1.6093  -1.0128
 X85  H218  H  HCH2   0   0.232   3.6118   1.8741   0.7045
 X85  H219  H  HCH2   0   0.199   7.6309   2.1008   1.7463
 X85  H120  H  HCH2   0   0.241   5.4774   3.0774   1.1859
 X85  H220  H  HCH2   0   0.195   5.8753   3.1271  -0.5347
 X85  H122  H  HCH2   0   0.245   5.9750  -0.5829  -0.7241
 X85  H222  H  HCH2   0   0.195   6.1538   0.8675  -1.7150
 X85  H123  H  HCH2   0   0.199   7.9098  -0.0534   0.6146
 X85  H223  H  HCH2   0   0.236   8.3520  -0.0010  -1.0991
 X85  H25   H  HCR6   0   0.267  -6.6614   5.1613   0.2536
 X85  H27   H  HCR6   0   0.263  -3.5954   3.1586   2.1111
 X85  H29   H  HCR6   0   0.276  -4.1313   2.6382  -2.1023
 X85  H30   H  HCR6   0   0.275  -6.0717   4.1998  -1.9533
 X85  H119  H  HCH2   0   0.236   7.8859   3.5536   0.7670

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
 X85  C1   C2    aromatic  1.401  0.020  1.401
 X85  C1   H1    single    0.930  0.020  1.080
 X85  C2   N15   single    1.338  0.020  1.338
 X85  C3   N10   single    1.413  0.020  1.413
 X85  C3   C2    aromatic  1.433  0.020  1.433
 X85  C4   C3    aromatic  1.396  0.020  1.396
 X85  C4   H4    single    0.930  0.020  1.080
 X85  C5   C4    aromatic  1.372  0.020  1.372
 X85  C5   C6    aromatic  1.438  0.020  1.438
 X85  C6   C1    aromatic  1.395  0.020  1.395
 X85  C7   C5    single    1.484  0.020  1.484
 X85  N8   C7    single    1.342  0.020  1.342
 X85  N8   H1N8  single    0.860  0.020  1.020
 X85  N8   H2N8  single    0.860  0.020  1.020
 X85  O9   C7    double    1.232  0.020  1.232
 X85  N10  O12   single    1.218  0.020  1.218
 X85  O11  N10   double    1.226  0.020  1.226
 X85  N13  C6    single    1.340  0.020  1.340
 X85  N13  C14   single    1.446  0.020  1.446
 X85  N13  HN13  single    0.860  0.020  1.020
 X85  C14  C28   single    1.500  0.020  1.500
 X85  C14  H114  single    0.970  0.020  1.090
 X85  C14  H214  single    0.970  0.020  1.090
 X85  N15  C16   single    1.445  0.020  1.445
 X85  N15  HN15  single    0.860  0.020  1.020
 X85  C16  C17   single    1.519  0.020  1.519
 X85  C16  H116  single    0.970  0.020  1.090
 X85  C16  H216  single    0.970  0.020  1.090
 X85  C17  C18   single    1.523  0.020  1.523
 X85  C17  H117  single    0.970  0.020  1.090
 X85  C17  H217  single    0.970  0.020  1.090
 X85  C18  N21   single    1.449  0.020  1.449
 X85  C18  H118  single    0.970  0.020  1.090
 X85  C18  H218  single    0.970  0.020  1.090
 X85  C19  H119  single    0.970  0.020  1.090
 X85  C19  H219  single    0.970  0.020  1.090
 X85  C20  C19   single    1.516  0.020  1.516
 X85  C20  H120  single    0.970  0.020  1.090
 X85  C20  H220  single    0.970  0.020  1.090
 X85  N21  C20   single    1.452  0.020  1.452
 X85  N21  C22   single    1.452  0.020  1.452
 X85  C22  C23   single    1.517  0.020  1.517
 X85  C22  H122  single    0.970  0.020  1.090
 X85  C22  H222  single    0.970  0.020  1.090
 X85  C23  H123  single    0.970  0.020  1.090
 X85  C23  H223  single    0.970  0.020  1.090
 X85  O24  C19   single    1.410  0.020  1.410
 X85  O24  C23   single    1.410  0.020  1.410
 X85  C25  C30   aromatic  1.388  0.020  1.388
 X85  C25  H25   single    0.930  0.020  1.080
 X85  N26  C25   aromatic  1.327  0.020  1.327
 X85  C27  C28   aromatic  1.390  0.020  1.390
 X85  C27  N26   aromatic  1.327  0.020  1.327
 X85  C27  H27   single    0.930  0.020  1.080
 X85  C28  C29   aromatic  1.390  0.020  1.390
 X85  C29  C30   aromatic  1.385  0.020  1.385
 X85  C29  H29   single    0.930  0.020  1.080
 X85  C30  H30   single    0.930  0.020  1.080

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
 X85  H1    C1   C6    118.29  3.000
 X85  C6    C1   C2    123.60  3.000
 X85  H1    C1   C2    118.10  3.000
 X85  N15   C2   C3    123.73  3.000
 X85  C3    C2   C1    116.52  3.000
 X85  N15   C2   C1    119.75  3.000
 X85  N10   C3   C4    117.21  3.000
 X85  C4    C3   C2    119.64  3.000
 X85  N10   C3   C2    123.15  3.000
 X85  H4    C4   C5    119.39  3.000
 X85  C5    C4   C3    123.65  3.000
 X85  H4    C4   C3    116.94  3.000
 X85  C7    C5   C6    121.45  3.000
 X85  C7    C5   C4    120.85  3.000
 X85  C6    C5   C4    117.68  3.000
 X85  N13   C6   C5    120.64  3.000
 X85  N13   C6   C1    120.50  3.000
 X85  C5    C6   C1    118.85  3.000
 X85  O9    C7   N8    121.07  3.000
 X85  O9    C7   C5    121.75  3.000
 X85  N8    C7   C5    117.18  3.000
 X85  H2N8  N8   H1N8  116.57  3.000
 X85  H2N8  N8   C7    118.80  3.000
 X85  H1N8  N8   C7    123.10  3.000
 X85  O12   N10  O11   121.25  3.000
 X85  O11   N10  C3    119.28  3.000
 X85  O12   N10  C3    119.47  3.000
 X85  HN13  N13  C14   119.20  3.000
 X85  HN13  N13  C6    116.29  3.000
 X85  C14   N13  C6    124.06  3.000
 X85  H214  C14  H114  106.70  3.000
 X85  H214  C14  C28   109.91  3.000
 X85  H114  C14  C28   109.86  3.000
 X85  H214  C14  N13   110.50  3.000
 X85  H114  C14  N13   110.09  3.000
 X85  C28   C14  N13   109.74  3.000
 X85  HN15  N15  C16   118.38  3.000
 X85  HN15  N15  C2    117.40  3.000
 X85  C16   N15  C2    124.06  3.000
 X85  H216  C16  H116  106.82  3.000
 X85  H216  C16  C17   109.45  3.000
 X85  H116  C16  C17   110.03  3.000
 X85  H216  C16  N15   110.05  3.000
 X85  H116  C16  N15   109.97  3.000
 X85  C17   C16  N15   110.45  3.000
 X85  H217  C17  H117  107.30  3.000
 X85  H217  C17  C18   110.74  3.000
 X85  H117  C17  C18   109.43  3.000
 X85  H217  C17  C16   109.11  3.000
 X85  H117  C17  C16   109.78  3.000
 X85  C18   C17  C16   110.42  3.000
 X85  H218  C18  H118  106.28  3.000
 X85  H218  C18  N21   107.39  3.000
 X85  H118  C18  N21   111.63  3.000
 X85  H218  C18  C17   108.61  3.000
 X85  H118  C18  C17   109.15  3.000
 X85  N21   C18  C17   113.48  3.000
 X85  H219  C19  H119  107.85  3.000
 X85  H219  C19  O24   110.47  3.000
 X85  H119  C19  O24   107.49  3.000
 X85  O24   C19  C20   111.49  3.000
 X85  H219  C19  C20   109.47  3.000
 X85  H119  C19  C20   109.98  3.000
 X85  H220  C20  H120  107.03  3.000
 X85  H220  C20  N21   111.93  3.000
 X85  H120  C20  N21   109.34  3.000
 X85  N21   C20  C19   110.45  3.000
 X85  H220  C20  C19   109.16  3.000
 X85  H120  C20  C19   108.84  3.000
 X85  C22   N21  C20   109.71  3.000
 X85  C22   N21  C18   113.02  3.000
 X85  C20   N21  C18   111.03  3.000
 X85  H222  C22  H122  107.03  3.000
 X85  H222  C22  C23   109.73  3.000
 X85  H122  C22  C23   107.94  3.000
 X85  H222  C22  N21   111.61  3.000
 X85  H122  C22  N21   110.22  3.000
 X85  C23   C22  N21   110.19  3.000
 X85  H223  C23  H123  107.87  3.000
 X85  H223  C23  O24   107.43  3.000
 X85  H123  C23  O24   110.45  3.000
 X85  O24   C23  C22   111.88  3.000
 X85  H223  C23  C22   109.96  3.000
 X85  H123  C23  C22   109.16  3.000
 X85  C23   O24  C19   110.65  3.000
 X85  H25   C25  C30   120.17  3.000
 X85  H25   C25  N26   116.63  3.000
 X85  C30   C25  N26   123.20  3.000
 X85  C27   N26  C25   117.81  3.000
 X85  H27   C27  C28   119.60  3.000
 X85  H27   C27  N26   116.48  3.000
 X85  C28   C27  N26   123.92  3.000
 X85  C29   C28  C27   117.54  3.000
 X85  C29   C28  C14   121.49  3.000
 X85  C27   C28  C14   120.96  3.000
 X85  H29   C29  C30   120.47  3.000
 X85  H29   C29  C28   120.43  3.000
 X85  C30   C29  C28   119.10  3.000
 X85  H30   C30  C29   121.23  3.000
 X85  H30   C30  C25   120.33  3.000
 X85  C29   C30  C25   118.44  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
 X85  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 X85  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 X85  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 X85  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 X85  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 X85  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 X85  CONST_07  C28   C29  C30  C25     0.00   0.0  0
 X85  CONST_08  C28   C27  N26  C25     0.00   0.0  0
 X85  CONST_09  C29   C30  C25  N26     0.00   0.0  0
 X85  CONST_10  C29   C28  C27  N26     0.00   0.0  0
 X85  CONST_11  C30   C29  C28  C27     0.00   0.0  0
 X85  CONST_12  C30   C25  N26  C27     0.00   0.0  0
 X85  CONST_13  N10   C3   C2   C1    180.00   0.0  0
 X85  CONST_14  C7    C5   C6   C1    180.00   0.0  0
 X85  CONST_15  N13   C6   C1   C2    180.00   0.0  0
 X85  CONST_16  C7    C5   C4   C3    180.00   0.0  0
 X85  CONST_17  N15   C2   C3   C4    180.00   0.0  0
 X85  CONST_18  N13   C6   C5   C4    180.00   0.0  0
 X85  CONST_19  N10   C3   C4   C5    180.00   0.0  0
 X85  CONST_20  N15   C2   C1   C6    180.00   0.0  0
 X85  CONST_21  N26   C27  C28  C14   180.00   0.0  0
 X85  CONST_22  C30   C29  C28  C14   180.00   0.0  0
 X85  CONST_23  H4    C4   C3   C2    180.00   0.0  0
 X85  CONST_24  H1    C1   C2   C3    180.00   0.0  0
 X85  CONST_25  H29   C29  C30  C25   180.00   0.0  0
 X85  CONST_26  H27   C27  N26  C25   180.00   0.0  0
 X85  CONST_27  H30   C30  C25  N26   180.00   0.0  0
 X85  CONST_28  H25   C25  N26  C27   180.00   0.0  0
 X85  CONST_29  C16   N15  C2   C1      0.00   0.0  0
 X85  CONST_30  C14   N13  C6   C1      0.00   0.0  0
 X85  CONST_31  O12   N10  C3   C2    180.00   0.0  0
 X85  CONST_32  O11   N10  C3   C2      0.00   0.0  0
 X85  CONST_33  C16   N15  C2   C3    180.00   0.0  0
 X85  CONST_34  O12   N10  C3   C4      0.00   0.0  0
 X85  CONST_35  O11   N10  C3   C4    180.00   0.0  0
 X85  CONST_36  C14   N13  C6   C5    180.00   0.0  0
 X85  CONST_37  HN15  N15  C2   C1    180.00   0.0  0
 X85  CONST_38  HN13  N13  C6   C1    180.00   0.0  0
 X85  CONST_39  H1N8  N8   C7   C5      0.00   0.0  0
 X85  CONST_40  H2N8  N8   C7   C5    180.00   0.0  0
 X85  Var_01    C22   N21  C20  C19   -56.17  30.0  1
 X85  Var_02    C22   C23  O24  C19    57.27  30.0  1
 X85  Var_03    C23   C22  N21  C20    55.81  30.0  1
 X85  Var_04    O24   C19  C20  N21    57.28  30.0  1
 X85  Var_05    O24   C23  C22  N21   -56.93  30.0  1
 X85  Var_06    N8    C7   C5   C4     21.19  30.0  2
 X85  Var_07    C28   C14  N13  C6   -179.70  30.0  3
 X85  Var_08    C27   C28  C14  N13   101.01  30.0  2
 X85  Var_09    C20   N21  C18  C17  -169.34  30.0  3
 X85  Var_10    C17   C16  N15  C2    179.00  30.0  3
 X85  Var_11    N21   C18  C17  C16   170.29  30.0  3
 X85  Var_12    C18   C17  C16  N15   174.07  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
 X85  plan-1  C1    0.020
 X85  plan-1  C2    0.020
 X85  plan-1  C3    0.020
 X85  plan-1  C4    0.020
 X85  plan-1  C5    0.020
 X85  plan-1  C6    0.020
 X85  plan-1  C7    0.020
 X85  plan-1  N10   0.020
 X85  plan-1  N13   0.020
 X85  plan-1  N15   0.020
 X85  plan-1  H1    0.020
 X85  plan-1  H4    0.020
 X85  plan-2  C14   0.020
 X85  plan-2  C25   0.020
 X85  plan-2  N26   0.020
 X85  plan-2  C27   0.020
 X85  plan-2  C28   0.020
 X85  plan-2  C29   0.020
 X85  plan-2  C30   0.020
 X85  plan-2  H25   0.020
 X85  plan-2  H27   0.020
 X85  plan-2  H29   0.020
 X85  plan-2  H30   0.020
 X85  plan-3  C3    0.020
 X85  plan-3  N10   0.020
 X85  plan-3  O11   0.020
 X85  plan-3  O12   0.020
 X85  plan-4  C6    0.020
 X85  plan-4  N13   0.020
 X85  plan-4  C14   0.020
 X85  plan-4  HN13  0.020
 X85  plan-5  C2    0.020
 X85  plan-5  N15   0.020
 X85  plan-5  C16   0.020
 X85  plan-5  HN15  0.020
 X85  plan-6  C5    0.020
 X85  plan-6  C7    0.020
 X85  plan-6  N8    0.020
 X85  plan-6  O9    0.020
 X85  plan-6  H1N8  0.020
 X85  plan-6  H2N8  0.020

