# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 01:35:45 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 2-{[4-(aminomethyl)benzyl]amino}-5-nitrobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(CNc2ccc(cc2C(N)=O)[N+]([O-])=O)cc1
#
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
 X96  X96  2-{[4-(aminomethyl)benzyl]amino}-5-nitrobenzamide  ligand  38  22  .  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_X96
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
 X96  C1    C  CR6    0   0.236  -3.9675  -0.5297   0.0169
 X96  N1    N  N      1   0.320  -5.3930  -0.6422   0.0746
 X96  O1    O  O      0  -0.405  -6.0503   0.3673   0.2282
 X96  C2    C  CR16   0  -0.317  -3.3693   0.7189   0.1123
 X96  N2    N  NH2    0  -0.806  -2.1422   3.2500  -0.2193
 X96  O2    O  O     -1  -0.402  -5.8881  -1.7454  -0.0325
 X96  C3    C  CR6    0  -0.121  -1.9951   0.8608   0.0754
 X96  N3    N  NH1    0  -0.675   0.1611  -0.2287  -0.0032
 X96  O3    O  O      0  -0.498  -0.2354   2.3773   0.5827
 X96  C4    C  CR6    0   0.414  -1.1725  -0.3051  -0.0189
 X96  N4    N  NH2    0  -0.792   7.4352  -0.1401  -0.6071
 X96  C5    C  CR16   0  -0.360  -1.8164  -1.5592  -0.1535
 X96  C6    C  CR16   0  -0.256  -3.1804  -1.6723  -0.1315
 X96  C7    C  C      0   0.534  -1.3815   2.2163   0.1664
 X96  C8    C  CH2    0  -0.350   1.0511  -1.3672  -0.1167
 X96  C9    C  CR6    0   0.051   2.4767  -0.9035  -0.0151
 X96  C10   C  CR16   0  -0.267   3.0418  -0.6330   1.2263
 X96  C11   C  CR16   0  -0.298   4.3485  -0.1751   1.3223
 X96  C12   C  CR6    0   0.088   5.1221   0.0290   0.1835
 X96  C13   C  CR16   0  -0.271   4.5548  -0.2481  -1.0584
 X96  C14   C  CR16   0  -0.280   3.2482  -0.7025  -1.1555
 X96  C15   C  CH2    0  -0.342   6.5310   0.5526   0.2949
 X96  H2    H  HCR6   0   0.292  -3.9954   1.5914   0.2352
 X96  HN2   H  HNH2   0   0.416  -2.9955   3.1364  -0.7374
 X96  HN2A  H  HNH2   0   0.410  -1.7565   4.1799  -0.1829
 X96  HN3   H  HNH1   0   0.414   0.5583   0.6795   0.1971
 X96  HN4   H  HNH2   0   0.353   8.3477   0.2952  -0.5665
 X96  HN4A  H  HNH2   0   0.343   7.5651  -1.0924  -0.2888
 X96  H5    H  HCR6   0   0.296  -1.2247  -2.4568  -0.2606
 X96  H6    H  HCR6   0   0.297  -3.6299  -2.6509  -0.2214
 X96  H8    H  HCH2   0   0.260   0.8387  -2.0949   0.6735
 X96  H8A   H  HCH2   0   0.261   0.8900  -1.8773  -1.0708
 X96  H10   H  HCR6   0   0.253   2.4636  -0.7913   2.1294
 X96  H11   H  HCR6   0   0.250   4.7730   0.0196   2.3003
 X96  H13   H  HCR6   0   0.248   5.1432  -0.1111  -1.9567
 X96  H14   H  HCR6   0   0.251   2.8255  -0.9094  -2.1317
 X96  H15   H  HCH2   0   0.215   6.8351   0.5165   1.3494
 X96  H15A  H  HCH2   0   0.240   6.5325   1.6117   0.0206

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
 X96  C1   N1    single    1.431  0.020  1.431
 X96  C1   C2    aromatic  1.388  0.020  1.388
 X96  C1   C6    aromatic  1.395  0.020  1.395
 X96  N1   O1    double    1.214  0.020  1.214
 X96  N1   O2    single    1.214  0.020  1.214
 X96  C2   C3    aromatic  1.382  0.020  1.382
 X96  C2   H2    single    0.930  0.020  1.080
 X96  N2   C7    single    1.340  0.020  1.340
 X96  N2   HN2   single    0.860  0.020  1.020
 X96  N2   HN2A  single    0.860  0.020  1.020
 X96  C3   C4    aromatic  1.430  0.020  1.430
 X96  C3   C7    single    1.491  0.020  1.491
 X96  N3   C4    single    1.336  0.020  1.336
 X96  N3   C8    single    1.450  0.020  1.450
 X96  N3   HN3   single    0.860  0.020  1.020
 X96  O3   C7    double    1.230  0.020  1.230
 X96  C4   C5    aromatic  1.416  0.020  1.416
 X96  N4   C15   single    1.453  0.020  1.453
 X96  N4   HN4   single    0.890  0.020  1.040
 X96  N4   HN4A  single    0.890  0.020  1.040
 X96  C5   C6    aromatic  1.369  0.020  1.369
 X96  C5   H5    single    0.930  0.020  1.080
 X96  C6   H6    single    0.930  0.020  1.080
 X96  C8   C9    single    1.503  0.020  1.503
 X96  C8   H8    single    0.970  0.020  1.090
 X96  C8   H8A   single    0.970  0.020  1.090
 X96  C9   C10   aromatic  1.391  0.020  1.391
 X96  C9   C14   aromatic  1.392  0.020  1.392
 X96  C10  C11   aromatic  1.388  0.020  1.388
 X96  C10  H10   single    0.930  0.020  1.080
 X96  C11  C12   aromatic  1.392  0.020  1.392
 X96  C11  H11   single    0.930  0.020  1.080
 X96  C12  C13   aromatic  1.393  0.020  1.393
 X96  C12  C15   single    1.507  0.020  1.507
 X96  C13  C14   aromatic  1.387  0.020  1.387
 X96  C13  H13   single    0.930  0.020  1.080
 X96  C14  H14   single    0.930  0.020  1.080
 X96  C15  H15   single    0.970  0.020  1.090
 X96  C15  H15A  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
 X96  C6    C1   C2   120.06  3.000
 X96  C6    C1   N1   120.12  3.000
 X96  C2    C1   N1   119.83  3.000
 X96  O2    N1   O1   123.08  3.000
 X96  O2    N1   C1   118.31  3.000
 X96  O1    N1   C1   118.61  3.000
 X96  H2    C2   C3   119.74  3.000
 X96  H2    C2   C1   118.97  3.000
 X96  C3    C2   C1   121.28  3.000
 X96  HN2A  N2   HN2  116.63  3.000
 X96  HN2A  N2   C7   118.97  3.000
 X96  HN2   N2   C7   122.90  3.000
 X96  C7    C3   C4   120.58  3.000
 X96  C7    C3   C2   120.07  3.000
 X96  C4    C3   C2   119.34  3.000
 X96  HN3   N3   C8   118.67  3.000
 X96  HN3   N3   C4   116.47  3.000
 X96  C8    N3   C4   124.55  3.000
 X96  C5    C4   N3   120.37  3.000
 X96  C5    C4   C3   117.83  3.000
 X96  N3    C4   C3   121.79  3.000
 X96  HN4A  N4   HN4  106.05  3.000
 X96  HN4A  N4   C15  109.45  3.000
 X96  HN4   N4   C15  109.34  3.000
 X96  H5    C5   C6   118.60  3.000
 X96  H5    C5   C4   119.75  3.000
 X96  C6    C5   C4   121.64  3.000
 X96  H6    C6   C5   119.20  3.000
 X96  H6    C6   C1   121.05  3.000
 X96  C5    C6   C1   119.75  3.000
 X96  O3    C7   C3   121.55  3.000
 X96  O3    C7   N2   121.69  3.000
 X96  C3    C7   N2   116.76  3.000
 X96  H8A   C8   H8   106.92  3.000
 X96  H8A   C8   C9   110.04  3.000
 X96  H8    C8   C9   109.90  3.000
 X96  H8A   C8   N3   110.13  3.000
 X96  H8    C8   N3   110.27  3.000
 X96  C9    C8   N3   109.56  3.000
 X96  C14   C9   C10  118.57  3.000
 X96  C14   C9   C8   121.01  3.000
 X96  C10   C9   C8   120.39  3.000
 X96  H10   C10  C11  119.52  3.000
 X96  H10   C10  C9   119.91  3.000
 X96  C11   C10  C9   120.56  3.000
 X96  H11   C11  C12  119.63  3.000
 X96  H11   C11  C10  119.36  3.000
 X96  C12   C11  C10  121.01  3.000
 X96  C15   C12  C13  121.04  3.000
 X96  C15   C12  C11  120.67  3.000
 X96  C13   C12  C11  118.29  3.000
 X96  H13   C13  C14  119.70  3.000
 X96  H13   C13  C12  119.55  3.000
 X96  C14   C13  C12  120.74  3.000
 X96  H14   C14  C13  119.55  3.000
 X96  H14   C14  C9   119.63  3.000
 X96  C13   C14  C9   120.82  3.000
 X96  H15A  C15  H15  105.79  3.000
 X96  H15A  C15  C12  108.60  3.000
 X96  H15   C15  C12  108.57  3.000
 X96  H15A  C15  N4   107.76  3.000
 X96  H15   C15  N4   114.09  3.000
 X96  C12   C15  N4   111.73  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
 X96  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 X96  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 X96  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 X96  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 X96  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 X96  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 X96  CONST_07  C12   C11  C10  C9      0.00   0.0  0
 X96  CONST_08  C12   C13  C14  C9      0.00   0.0  0
 X96  CONST_09  C13   C14  C9   C10     0.00   0.0  0
 X96  CONST_10  C13   C12  C11  C10     0.00   0.0  0
 X96  CONST_11  C14   C9   C10  C11     0.00   0.0  0
 X96  CONST_12  C14   C13  C12  C11     0.00   0.0  0
 X96  CONST_13  C7    C3   C2   C1    180.00   0.0  0
 X96  CONST_14  C3    C2   C1   N1    180.00   0.0  0
 X96  CONST_15  C5    C6   C1   N1    180.00   0.0  0
 X96  CONST_16  N3    C4   C3   C2    180.00   0.0  0
 X96  CONST_17  C6    C5   C4   N3    180.00   0.0  0
 X96  CONST_18  C7    C3   C4   C5    180.00   0.0  0
 X96  CONST_19  C11   C10  C9   C8    180.00   0.0  0
 X96  CONST_20  C13   C14  C9   C8    180.00   0.0  0
 X96  CONST_21  C15   C12  C11  C10   180.00   0.0  0
 X96  CONST_22  C15   C12  C13  C14   180.00   0.0  0
 X96  CONST_23  H5    C5   C6   C1    180.00   0.0  0
 X96  CONST_24  H6    C6   C1   C2    180.00   0.0  0
 X96  CONST_25  H2    C2   C3   C4    180.00   0.0  0
 X96  CONST_26  H11   C11  C10  C9    180.00   0.0  0
 X96  CONST_27  H13   C13  C14  C9    180.00   0.0  0
 X96  CONST_28  H14   C14  C9   C10   180.00   0.0  0
 X96  CONST_29  H10   C10  C11  C12   180.00   0.0  0
 X96  CONST_30  C2    C1   N1   O1      0.00   0.0  0
 X96  CONST_31  C6    C1   N1   O1    180.00   0.0  0
 X96  CONST_32  O2    N1   C1   C2    180.00   0.0  0
 X96  CONST_33  C6    C1   N1   O2      0.00   0.0  0
 X96  CONST_34  C8    N3   C4   C3    180.00   0.0  0
 X96  CONST_35  C8    N3   C4   C5      0.00   0.0  0
 X96  CONST_36  HN3   N3   C4   C3      0.00   0.0  0
 X96  CONST_37  HN2   N2   C7   C3      0.00   0.0  0
 X96  CONST_38  HN2A  N2   C7   C3    180.00   0.0  0
 X96  Var_01    N2    C7   C3   C2    -24.51  30.0  2
 X96  Var_02    C10   C9   C8   N3     79.90  30.0  2
 X96  Var_03    C9    C8   N3   C4   -178.19  30.0  3
 X96  Var_04    C11   C12  C15  N4    138.14  30.0  2
 X96  Var_05    HN4   N4   C15  C12   174.75  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
 X96  plan-1  C1    0.020
 X96  plan-1  N1    0.020
 X96  plan-1  C2    0.020
 X96  plan-1  C3    0.020
 X96  plan-1  N3    0.020
 X96  plan-1  C4    0.020
 X96  plan-1  C5    0.020
 X96  plan-1  C6    0.020
 X96  plan-1  C7    0.020
 X96  plan-1  H2    0.020
 X96  plan-1  H5    0.020
 X96  plan-1  H6    0.020
 X96  plan-2  C8    0.020
 X96  plan-2  C9    0.020
 X96  plan-2  C10   0.020
 X96  plan-2  C11   0.020
 X96  plan-2  C12   0.020
 X96  plan-2  C13   0.020
 X96  plan-2  C14   0.020
 X96  plan-2  C15   0.020
 X96  plan-2  H10   0.020
 X96  plan-2  H11   0.020
 X96  plan-2  H13   0.020
 X96  plan-2  H14   0.020
 X96  plan-3  N2    0.020
 X96  plan-3  C3    0.020
 X96  plan-3  O3    0.020
 X96  plan-3  C7    0.020
 X96  plan-3  HN2   0.020
 X96  plan-3  HN2A  0.020
 X96  plan-4  C1    0.020
 X96  plan-4  N1    0.020
 X96  plan-4  O1    0.020
 X96  plan-4  O2    0.020
 X96  plan-5  N3    0.020
 X96  plan-5  C4    0.020
 X96  plan-5  C8    0.020
 X96  plan-5  HN3   0.020

