# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 06:50:37 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 2-[(4-tert-butyl-3-nitrophenyl)carbonyl]-N-(naphthalen-1-yl)hydrazinecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)c1ccc(cc1[N+]([O-])=O)C(=O)NNC(=O)Nc2cccc3ccccc23
#
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
 AGY  AGY  2-[(4-tert-butyl-3-nitrophenyl)carbonyl]-N-(naphthalen-1-yl)hydrazinecarboxamide  ligand  52  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AGY
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
 AGY  C1    C  CR66   0   0.084   4.1688  -0.5067   0.4970
 AGY  N1    N  NH1    0  -0.765   2.8846   1.0816  -0.8320
 AGY  O1    O  O      0  -0.499   3.4867   3.2362  -0.3998
 AGY  C2    C  CR6    0   0.306   4.1227   0.4880  -0.5193
 AGY  N2    N  NH1    0  -0.495   1.3803   2.8147  -1.0883
 AGY  O2    O  O      0  -0.434   0.0560   1.9245   1.0944
 AGY  C3    C  CR66   0   0.096   5.4057  -1.1556   0.7580
 AGY  N3    N  NH1    0  -0.545   0.3519   1.9194  -1.1445
 AGY  O3    O  O      0  -0.358  -5.0268   0.8380   1.9865
 AGY  C4    C  CR16   0  -0.300   3.0341  -0.8733   1.2596
 AGY  N4    N  N      1   0.321  -4.4265  -0.1904   1.7973
 AGY  O4    O  O     -1  -0.357  -4.4741  -1.1594   2.5147
 AGY  C5    C  CR16   0  -0.287   5.2597   0.8374  -1.1989
 AGY  C6    C  CR16   0  -0.318   6.5605  -0.7680   0.0404
 AGY  C7    C  CR16   0  -0.310   5.4560  -2.1692   1.7442
 AGY  C8    C  CR16   0  -0.252   3.1175  -1.8531   2.2113
 AGY  C9    C  CR16   0  -0.267   6.4882   0.2158  -0.9066
 AGY  C10   C  C      0   0.661   2.6523   2.4147  -0.7327
 AGY  C11   C  CR16   0  -0.255   4.3382  -2.5160   2.4514
 AGY  C12   C  C      0   0.526  -0.3003   1.5517  -0.0044
 AGY  C13   C  CR6    0  -0.058  -1.4607   0.6406  -0.2007
 AGY  C14   C  CR16   0  -0.252  -2.4397   0.6139   0.7793
 AGY  C15   C  CR16   0  -0.244  -1.5979  -0.2088  -1.2906
 AGY  C16   C  CR6    0   0.174  -3.5209  -0.2386   0.6500
 AGY  C17   C  CR16   0  -0.317  -2.7043  -1.0319  -1.4026
 AGY  C18   C  CR6    0   0.218  -3.7264  -1.0782  -0.4504
 AGY  C19   C  CT     0  -0.171  -4.9302  -2.0021  -0.6740
 AGY  C20   C  CH3    0  -0.676  -6.2507  -1.4050  -0.1605
 AGY  C21   C  CH3    0  -0.663  -5.1339  -2.2643  -2.1744
 AGY  C22   C  CH3    0  -0.631  -4.6549  -3.3500   0.0081
 AGY  HN1   H  HNH1   0   0.409   2.1281   0.4740  -1.1080
 AGY  HN2   H  HNH1   0   0.410   1.1360   3.7569  -0.8126
 AGY  HN3   H  HNH1   0   0.428  -0.0786   1.8010  -2.0496
 AGY  H4    H  HCR6   0   0.237   2.0928  -0.3624   1.1061
 AGY  H5    H  HCR6   0   0.267   5.2128   1.5827  -1.9810
 AGY  H6    H  HCR6   0   0.258   7.5016  -1.2614   0.2502
 AGY  H7    H  HCR6   0   0.258   6.3997  -2.6674   1.9317
 AGY  H8    H  HCR6   0   0.262   2.2419  -2.1175   2.7898
 AGY  H9    H  HCR6   0   0.262   7.3726   0.5103  -1.4560
 AGY  H11   H  HCR6   0   0.261   4.3876  -3.2929   3.2027
 AGY  H14   H  HCR6   0   0.297  -2.3524   1.2500   1.6507
 AGY  H15   H  HCR6   0   0.279  -0.8432  -0.2620  -2.0644
 AGY  H17   H  HCR6   0   0.277  -2.7602  -1.6600  -2.2782
 AGY  H120  H  HCH3   0   0.243  -6.3848  -0.3724  -0.4858
 AGY  H220  H  HCH3   0   0.249  -7.0787  -1.9810  -0.5743
 AGY  H320  H  HCH3   0   0.236  -6.3701  -1.4569   0.9190
 AGY  H121  H  HCH3   0   0.239  -4.3163  -2.8245  -2.6256
 AGY  H221  H  HCH3   0   0.245  -6.0326  -2.8673  -2.3055
 AGY  H321  H  HCH3   0   0.242  -5.2682  -1.3379  -2.7350
 AGY  H122  H  HCH3   0   0.240  -4.5068  -3.2454   1.0810
 AGY  H222  H  HCH3   0   0.236  -5.5004  -4.0219  -0.1504
 AGY  H322  H  HCH3   0   0.235  -3.7659  -3.8255  -0.4099

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
 AGY  O1   C10   double    1.217  0.020  1.217
 AGY  C10  N2    single    1.380  0.020  1.380
 AGY  C10  N1    single    1.357  0.020  1.357
 AGY  C9   C6    aromatic  1.367  0.020  1.367
 AGY  C9   C5    aromatic  1.407  0.020  1.407
 AGY  C6   C3    aromatic  1.414  0.020  1.414
 AGY  C5   C2    aromatic  1.370  0.020  1.370
 AGY  N2   N3    single    1.365  0.020  1.365
 AGY  C3   C7    aromatic  1.415  0.020  1.415
 AGY  C3   C1    aromatic  1.421  0.020  1.421
 AGY  C7   C11   aromatic  1.367  0.020  1.367
 AGY  C2   C1    aromatic  1.423  0.020  1.423
 AGY  C2   N1    single    1.408  0.020  1.408
 AGY  C1   C4    aromatic  1.415  0.020  1.415
 AGY  C11  C8    aromatic  1.410  0.020  1.410
 AGY  C4   C8    aromatic  1.368  0.020  1.368
 AGY  N3   C12   single    1.364  0.020  1.364
 AGY  O2   C12   double    1.214  0.020  1.214
 AGY  C12  C13   single    1.488  0.020  1.488
 AGY  C13  C14   aromatic  1.385  0.020  1.385
 AGY  C13  C15   aromatic  1.389  0.020  1.389
 AGY  C14  C16   aromatic  1.383  0.020  1.383
 AGY  O4   N4    single    1.207  0.020  1.207
 AGY  C15  C17   aromatic  1.384  0.020  1.384
 AGY  C16  N4    single    1.462  0.020  1.462
 AGY  C16  C18   aromatic  1.399  0.020  1.399
 AGY  N4   O3    double    1.206  0.020  1.206
 AGY  C17  C18   aromatic  1.398  0.020  1.398
 AGY  C18  C19   single    1.534  0.020  1.534
 AGY  C19  C21   single    1.537  0.020  1.537
 AGY  C19  C22   single    1.536  0.020  1.536
 AGY  C19  C20   single    1.537  0.020  1.537
 AGY  N1   HN1   single    0.860  0.020  1.020
 AGY  N2   HN2   single    0.890  0.020  1.040
 AGY  N3   HN3   single    0.890  0.020  1.040
 AGY  C4   H4    single    0.930  0.020  1.080
 AGY  C5   H5    single    0.930  0.020  1.080
 AGY  C6   H6    single    0.930  0.020  1.080
 AGY  C7   H7    single    0.930  0.020  1.080
 AGY  C8   H8    single    0.930  0.020  1.080
 AGY  C9   H9    single    0.930  0.020  1.080
 AGY  C11  H11   single    0.930  0.020  1.080
 AGY  C14  H14   single    0.930  0.020  1.080
 AGY  C15  H15   single    0.930  0.020  1.080
 AGY  C17  H17   single    0.930  0.020  1.080
 AGY  C20  H120  single    0.970  0.020  1.090
 AGY  C20  H220  single    0.970  0.020  1.090
 AGY  C20  H320  single    0.970  0.020  1.090
 AGY  C21  H121  single    0.970  0.020  1.090
 AGY  C21  H221  single    0.970  0.020  1.090
 AGY  C21  H321  single    0.970  0.020  1.090
 AGY  C22  H122  single    0.970  0.020  1.090
 AGY  C22  H222  single    0.970  0.020  1.090
 AGY  C22  H322  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
 AGY  C4    C1   C3    118.72  3.000
 AGY  C4    C1   C2    122.68  3.000
 AGY  C3    C1   C2    118.60  3.000
 AGY  HN1   N1   C10   118.91  3.000
 AGY  HN1   N1   C2    117.79  3.000
 AGY  C10   N1   C2    123.26  3.000
 AGY  C5    C2   N1    120.80  3.000
 AGY  N1    C2   C1    118.80  3.000
 AGY  C5    C2   C1    120.38  3.000
 AGY  HN2   N2   C10   114.98  3.000
 AGY  HN2   N2   N3    116.12  3.000
 AGY  C10   N2   N3    121.00  3.000
 AGY  C7    C3   C6    121.40  3.000
 AGY  C7    C3   C1    119.08  3.000
 AGY  C6    C3   C1    119.51  3.000
 AGY  HN3   N3   C12   120.93  3.000
 AGY  HN3   N3   N2    115.81  3.000
 AGY  C12   N3   N2    120.19  3.000
 AGY  H4    C4   C8    119.32  3.000
 AGY  H4    C4   C1    119.92  3.000
 AGY  C8    C4   C1    120.75  3.000
 AGY  C16   N4   O4    117.67  3.000
 AGY  C16   N4   O3    117.35  3.000
 AGY  O4    N4   O3    124.89  3.000
 AGY  H5    C5   C9    119.50  3.000
 AGY  H5    C5   C2    119.91  3.000
 AGY  C9    C5   C2    120.58  3.000
 AGY  H6    C6   C9    120.52  3.000
 AGY  H6    C6   C3    119.11  3.000
 AGY  C9    C6   C3    120.37  3.000
 AGY  H7    C7   C11   120.39  3.000
 AGY  H7    C7   C3    118.75  3.000
 AGY  C11   C7   C3    120.86  3.000
 AGY  H8    C8   C11   119.65  3.000
 AGY  H8    C8   C4    119.83  3.000
 AGY  C11   C8   C4    120.52  3.000
 AGY  H9    C9   C6    120.28  3.000
 AGY  H9    C9   C5    119.19  3.000
 AGY  C6    C9   C5    120.51  3.000
 AGY  N2    C10  O1    120.45  3.000
 AGY  N2    C10  N1    115.07  3.000
 AGY  O1    C10  N1    124.45  3.000
 AGY  H11   C11  C8    119.70  3.000
 AGY  H11   C11  C7    120.26  3.000
 AGY  C8    C11  C7    120.04  3.000
 AGY  C13   C12  N3    115.32  3.000
 AGY  C13   C12  O2    122.43  3.000
 AGY  N3    C12  O2    122.24  3.000
 AGY  C15   C13  C14   118.27  3.000
 AGY  C15   C13  C12   123.71  3.000
 AGY  C14   C13  C12   118.00  3.000
 AGY  H14   C14  C16   120.04  3.000
 AGY  H14   C14  C13   120.08  3.000
 AGY  C16   C14  C13   119.88  3.000
 AGY  H15   C15  C17   118.07  3.000
 AGY  H15   C15  C13   121.49  3.000
 AGY  C17   C15  C13   120.43  3.000
 AGY  C18   C16  C14   123.93  3.000
 AGY  C18   C16  N4    123.08  3.000
 AGY  C14   C16  N4    112.98  3.000
 AGY  H17   C17  C18   119.72  3.000
 AGY  H17   C17  C15   116.96  3.000
 AGY  C18   C17  C15   123.32  3.000
 AGY  C19   C18  C17   119.64  3.000
 AGY  C19   C18  C16   126.25  3.000
 AGY  C17   C18  C16   114.11  3.000
 AGY  C22   C19  C21   107.92  3.000
 AGY  C22   C19  C20   110.27  3.000
 AGY  C21   C19  C20   106.18  3.000
 AGY  C20   C19  C18   113.04  3.000
 AGY  C22   C19  C18   108.86  3.000
 AGY  C21   C19  C18   110.43  3.000
 AGY  H320  C20  H220  105.55  3.000
 AGY  H320  C20  H120  109.13  3.000
 AGY  H220  C20  H120  107.06  3.000
 AGY  H320  C20  C19   114.04  3.000
 AGY  H220  C20  C19   108.68  3.000
 AGY  H120  C20  C19   111.94  3.000
 AGY  H321  C21  H221  107.84  3.000
 AGY  H321  C21  H121  108.44  3.000
 AGY  H221  C21  H121  106.54  3.000
 AGY  H321  C21  C19   111.91  3.000
 AGY  H221  C21  C19   108.73  3.000
 AGY  H121  C21  C19   113.13  3.000
 AGY  H322  C22  H222  107.89  3.000
 AGY  H322  C22  H122  107.97  3.000
 AGY  H222  C22  H122  107.93  3.000
 AGY  H322  C22  C19   111.00  3.000
 AGY  H222  C22  C19   109.69  3.000
 AGY  H122  C22  C19   112.21  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
 AGY  CONST_01  C9    C6   C3   C1     0.00   0.0  0
 AGY  CONST_02  C11   C7   C3   C1     0.00   0.0  0
 AGY  CONST_03  C9    C5   C2   C1     0.00   0.0  0
 AGY  CONST_04  C11   C8   C4   C1     0.00   0.0  0
 AGY  CONST_05  C6    C9   C5   C2     0.00   0.0  0
 AGY  CONST_06  C6    C3   C1   C2     0.00   0.0  0
 AGY  CONST_07  C7    C3   C1   C2   180.00   0.0  0
 AGY  CONST_08  C8    C4   C1   C2   180.00   0.0  0
 AGY  CONST_09  C5    C9   C6   C3     0.00   0.0  0
 AGY  CONST_10  C8    C11  C7   C3     0.00   0.0  0
 AGY  CONST_11  C5    C2   C1   C3     0.00   0.0  0
 AGY  CONST_12  C8    C4   C1   C3     0.00   0.0  0
 AGY  CONST_13  C6    C3   C1   C4   180.00   0.0  0
 AGY  CONST_14  C7    C3   C1   C4     0.00   0.0  0
 AGY  CONST_15  C5    C2   C1   C4   180.00   0.0  0
 AGY  CONST_16  C7    C11  C8   C4     0.00   0.0  0
 AGY  CONST_17  C11   C7   C3   C6   180.00   0.0  0
 AGY  CONST_18  C9    C6   C3   C7   180.00   0.0  0
 AGY  CONST_19  C18   C16  C14  C13    0.00   0.0  0
 AGY  CONST_20  C18   C17  C15  C13    0.00   0.0  0
 AGY  CONST_21  C17   C15  C13  C14    0.00   0.0  0
 AGY  CONST_22  C17   C18  C16  C14    0.00   0.0  0
 AGY  CONST_23  C16   C14  C13  C15    0.00   0.0  0
 AGY  CONST_24  C16   C18  C17  C15    0.00   0.0  0
 AGY  CONST_25  C9    C5   C2   N1   180.00   0.0  0
 AGY  CONST_26  C3    C1   C2   N1   180.00   0.0  0
 AGY  CONST_27  C4    C1   C2   N1     0.00   0.0  0
 AGY  CONST_28  C13   C14  C16  N4   180.00   0.0  0
 AGY  CONST_29  C17   C18  C16  N4   180.00   0.0  0
 AGY  CONST_30  C16   C14  C13  C12  180.00   0.0  0
 AGY  CONST_31  C17   C15  C13  C12  180.00   0.0  0
 AGY  CONST_32  C19   C18  C16  C14  180.00   0.0  0
 AGY  CONST_33  C19   C18  C17  C15  180.00   0.0  0
 AGY  CONST_34  H6    C6   C3   C1   180.00   0.0  0
 AGY  CONST_35  H7    C7   C3   C1   180.00   0.0  0
 AGY  CONST_36  H5    C5   C2   C1   180.00   0.0  0
 AGY  CONST_37  H8    C8   C4   C1   180.00   0.0  0
 AGY  CONST_38  H9    C9   C5   C2   180.00   0.0  0
 AGY  CONST_39  H4    C4   C1   C2     0.00   0.0  0
 AGY  CONST_40  H11   C11  C7   C3   180.00   0.0  0
 AGY  CONST_41  H17   C17  C15  C13  180.00   0.0  0
 AGY  CONST_42  H15   C15  C13  C14  180.00   0.0  0
 AGY  CONST_43  H14   C14  C13  C15  180.00   0.0  0
 AGY  CONST_51  C2    N1   C10  O1     0.00   0.0  0
 AGY  CONST_52  C13   C12  N3   N2   180.00   0.0  0
 AGY  CONST_53  N2    C10  N1   C2   180.00   0.0  0
 AGY  CONST_56  O2    C12  N3   N2     0.00   0.0  0
 AGY  Var_01    C14   C13  C12  O2    24.40  30.0  2
 AGY  Var_02    C21   C19  C18  C16  154.70  30.0  2
 AGY  Var_03    H121  C21  C19  C18   65.59  30.0  3
 AGY  Var_04    H122  C22  C19  C18   60.55  30.0  3
 AGY  Var_05    H120  C20  C19  C18   47.53  30.0  3
 AGY  Var_06    C12   N3   N2   C10   81.33  30.0  2

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
 AGY  plan-1  N4   0.020
 AGY  plan-1  C12  0.020
 AGY  plan-1  C13  0.020
 AGY  plan-1  C14  0.020
 AGY  plan-1  C15  0.020
 AGY  plan-1  C16  0.020
 AGY  plan-1  C17  0.020
 AGY  plan-1  C18  0.020
 AGY  plan-1  C19  0.020
 AGY  plan-1  H14  0.020
 AGY  plan-1  H15  0.020
 AGY  plan-1  H17  0.020
 AGY  plan-2  C1   0.020
 AGY  plan-2  N1   0.020
 AGY  plan-2  C2   0.020
 AGY  plan-2  C3   0.020
 AGY  plan-2  C4   0.020
 AGY  plan-2  C5   0.020
 AGY  plan-2  C6   0.020
 AGY  plan-2  C7   0.020
 AGY  plan-2  C8   0.020
 AGY  plan-2  C9   0.020
 AGY  plan-2  C11  0.020
 AGY  plan-2  H4   0.020
 AGY  plan-2  H5   0.020
 AGY  plan-2  H6   0.020
 AGY  plan-2  H7   0.020
 AGY  plan-2  H8   0.020
 AGY  plan-2  H9   0.020
 AGY  plan-2  H11  0.020
 AGY  plan-3  N1   0.020
 AGY  plan-3  O1   0.020
 AGY  plan-3  C2   0.020
 AGY  plan-3  N2   0.020
 AGY  plan-3  N3   0.020
 AGY  plan-3  C10  0.020
 AGY  plan-3  HN1  0.020
 AGY  plan-3  HN2  0.020
 AGY  plan-4  N2   0.020
 AGY  plan-4  O2   0.020
 AGY  plan-4  N3   0.020
 AGY  plan-4  C12  0.020
 AGY  plan-4  C13  0.020
 AGY  plan-4  HN3  0.020
 AGY  plan-5  O3   0.020
 AGY  plan-5  N4   0.020
 AGY  plan-5  O4   0.020
 AGY  plan-5  C16  0.020

