# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 16:55:02 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 1-[4-(2-nitrophenyl)piperazin-1-yl]ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCN(CC1)c2ccccc2[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
 T2J  T2J  1-[4-(2-nitrophenyl)piperazin-1-yl]ethan-1-one  ligand  33  18  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_T2J
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
 T2J  N1   N  NT     0  -0.508  -0.0304   0.1452   0.1054
 T2J  C4   C  CR16   0  -0.291  -1.6067   2.0056   0.3607
 T2J  C5   C  CR6    0   0.322  -1.3355   0.6697   0.0665
 T2J  C6   C  CH2    0  -0.302   0.7675   0.5389   1.2568
 T2J  C7   C  CH2    0  -0.304   2.0060  -0.3394   1.3266
 T2J  C8   C  CH2    0  -0.315   1.9680  -0.5587  -1.0847
 T2J  C    C  CR6    0   0.197  -2.4359  -0.1477  -0.2165
 T2J  O    O  O     -1  -0.383  -3.0139  -2.3260   0.0860
 T2J  C1   C  CR16   0  -0.268  -3.7382   0.3306  -0.2094
 T2J  C11  C  CH3    0  -0.806   4.7486   0.2135  -1.2571
 T2J  C2   C  CR16   0  -0.264  -3.9700   1.6672   0.0602
 T2J  C3   C  CR16   0  -0.230  -2.9004   2.5018   0.3537
 T2J  C9   C  CH2    0  -0.288   0.7211   0.3075  -1.1325
 T2J  N2   N  NT     0  -0.449   2.7581  -0.2429   0.0898
 T2J  O1   O  O      0  -0.362  -1.3912  -1.9119  -1.2386
 T2J  O2   O  O      0  -0.508   4.6742   0.3514   1.1197
 T2J  H3   H  HCR6   0   0.275  -0.7843   2.6686   0.5967
 T2J  H5   H  HCH2   0   0.217   1.0846   1.5917   1.2164
 T2J  H4   H  HCH2   0   0.260   0.1798   0.4037   2.1657
 T2J  H7   H  HCH2   0   0.267   2.6318  -0.0325   2.1595
 T2J  H6   H  HCH2   0   0.243   1.7070  -1.3795   1.4908
 T2J  H9   H  HCH2   0   0.247   1.6705  -1.6113  -1.0478
 T2J  H8   H  HCH2   0   0.276   2.5438  -0.4126  -1.9939
 T2J  H    H  HCR6   0   0.292  -4.5657  -0.3322  -0.4223
 T2J  H15  H  HCH3   0   0.264   4.2729   0.9521  -1.9031
 T2J  H13  H  HCH3   0   0.269   5.7825   0.5109  -1.1028
 T2J  H12  H  HCH3   0   0.266   4.7424  -0.7392  -1.7882
 T2J  H1   H  HCR6   0   0.276  -4.9812   2.0497   0.0520
 T2J  H2   H  HCR6   0   0.275  -3.0729   3.5468   0.5740
 T2J  H11  H  HCH2   0   0.261   0.1095   0.0051  -1.9800
 T2J  H10  H  HCH2   0   0.221   1.0089   1.3586  -1.2894
 T2J  C10  C  C      0   0.518   4.0620   0.1148   0.0850
 T2J  N    N  N      1   0.335  -2.2593  -1.5650  -0.4764

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
 T2J  N    O    single    1.210  0.020  1.210
 T2J  N    O1   double    1.206  0.020  1.206
 T2J  C    N    single    1.452  0.020  1.452
 T2J  C    C1   aromatic  1.387  0.020  1.387
 T2J  C2   C1   aromatic  1.383  0.020  1.383
 T2J  C3   C2   aromatic  1.388  0.020  1.388
 T2J  C4   C3   aromatic  1.386  0.020  1.386
 T2J  C5   C4   aromatic  1.395  0.020  1.395
 T2J  C5   C    aromatic  1.400  0.020  1.400
 T2J  N1   C5   single    1.407  0.020  1.407
 T2J  C6   N1   single    1.455  0.020  1.455
 T2J  C7   C6   single    1.520  0.020  1.520
 T2J  N2   C7   single    1.451  0.020  1.451
 T2J  N2   C8   single    1.450  0.020  1.450
 T2J  C8   C9   single    1.519  0.020  1.519
 T2J  C9   N1   single    1.457  0.020  1.457
 T2J  C10  N2   single    1.352  0.020  1.352
 T2J  C10  O2   double    1.225  0.020  1.225
 T2J  C11  C10  single    1.511  0.020  1.511
 T2J  C4   H3   single    0.930  0.020  1.080
 T2J  C6   H5   single    0.970  0.020  1.090
 T2J  C6   H4   single    0.970  0.020  1.090
 T2J  C7   H7   single    0.970  0.020  1.090
 T2J  C7   H6   single    0.970  0.020  1.090
 T2J  C8   H9   single    0.970  0.020  1.090
 T2J  C8   H8   single    0.970  0.020  1.090
 T2J  C1   H    single    0.930  0.020  1.080
 T2J  C11  H15  single    0.970  0.020  1.090
 T2J  C11  H13  single    0.970  0.020  1.090
 T2J  C11  H12  single    0.970  0.020  1.090
 T2J  C2   H1   single    0.930  0.020  1.080
 T2J  C3   H2   single    0.930  0.020  1.080
 T2J  C9   H11  single    0.970  0.020  1.090
 T2J  C9   H10  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
 T2J  C9   N1   C6   111.06  3.000
 T2J  C9   N1   C5   114.41  3.000
 T2J  C6   N1   C5   115.45  3.000
 T2J  H3   C4   C3   119.41  3.000
 T2J  H3   C4   C5   119.02  3.000
 T2J  C3   C4   C5   121.57  3.000
 T2J  C    C5   C4   116.69  3.000
 T2J  C    C5   N1   121.14  3.000
 T2J  C4   C5   N1   122.11  3.000
 T2J  H4   C6   H5   107.73  3.000
 T2J  H4   C6   C7   109.22  3.000
 T2J  H5   C6   C7   108.65  3.000
 T2J  H4   C6   N1   109.29  3.000
 T2J  H5   C6   N1   112.82  3.000
 T2J  C7   C6   N1   109.08  3.000
 T2J  H6   C7   H7   108.11  3.000
 T2J  H6   C7   N2   109.43  3.000
 T2J  H7   C7   N2   109.65  3.000
 T2J  H6   C7   C6   109.48  3.000
 T2J  H7   C7   C6   109.96  3.000
 T2J  N2   C7   C6   110.17  3.000
 T2J  H8   C8   H9   107.56  3.000
 T2J  H8   C8   N2   111.10  3.000
 T2J  H9   C8   N2   109.28  3.000
 T2J  H8   C8   C9   109.40  3.000
 T2J  H9   C8   C9   109.05  3.000
 T2J  N2   C8   C9   110.40  3.000
 T2J  C1   C    N    116.85  3.000
 T2J  C1   C    C5   122.38  3.000
 T2J  N    C    C5   120.71  3.000
 T2J  H    C1   C2   120.16  3.000
 T2J  H    C1   C    120.40  3.000
 T2J  C2   C1   C    119.44  3.000
 T2J  H12  C11  H13  108.28  3.000
 T2J  H12  C11  H15  107.50  3.000
 T2J  H13  C11  H15  108.28  3.000
 T2J  H12  C11  C10  111.90  3.000
 T2J  H13  C11  C10  108.92  3.000
 T2J  H15  C11  C10  111.85  3.000
 T2J  H1   C2   C3   120.64  3.000
 T2J  H1   C2   C1   119.82  3.000
 T2J  C3   C2   C1   119.54  3.000
 T2J  H2   C3   C2   120.06  3.000
 T2J  H2   C3   C4   119.59  3.000
 T2J  C2   C3   C4   120.35  3.000
 T2J  H10  C9   H11  107.54  3.000
 T2J  H10  C9   C8   109.53  3.000
 T2J  H11  C9   C8   109.12  3.000
 T2J  H10  C9   N1   111.23  3.000
 T2J  H11  C9   N1   109.93  3.000
 T2J  C8   C9   N1   109.46  3.000
 T2J  C10  N2   C8   125.45  3.000
 T2J  C10  N2   C7   121.37  3.000
 T2J  C8   N2   C7   113.18  3.000
 T2J  O2   C10  N2   122.00  3.000
 T2J  O2   C10  C11  120.69  3.000
 T2J  N2   C10  C11  117.31  3.000
 T2J  O1   N    O    124.16  3.000
 T2J  O1   N    C    118.78  3.000
 T2J  O    N    C    117.05  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
 T2J  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 T2J  CONST_02  C1   C    C5   C4     0.00   0.0  0
 T2J  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 T2J  CONST_04  C2   C1   C    C5     0.00   0.0  0
 T2J  CONST_05  C3   C2   C1   C      0.00   0.0  0
 T2J  CONST_06  C3   C4   C5   C      0.00   0.0  0
 T2J  CONST_07  C3   C4   C5   N1   180.00   0.0  0
 T2J  CONST_08  C1   C    C5   N1   180.00   0.0  0
 T2J  CONST_09  N    C    C5   N1     0.00   0.0  0
 T2J  CONST_10  N    C    C5   C4   180.00   0.0  0
 T2J  CONST_11  C2   C1   C    N    180.00   0.0  0
 T2J  CONST_12  H3   C4   C5   N1     0.00   0.0  0
 T2J  CONST_13  H1   C2   C3   C4   180.00   0.0  0
 T2J  CONST_14  H2   C3   C4   C5   180.00   0.0  0
 T2J  CONST_15  H    C1   C    C5   180.00   0.0  0
 T2J  CONST_16  O2   C10  N2   C7     0.00   0.0  0
 T2J  CONST_17  C11  C10  N2   C7   180.00   0.0  0
 T2J  CONST_18  O2   C10  N2   C8   180.00   0.0  0
 T2J  CONST_19  C11  C10  N2   C8     0.00   0.0  0
 T2J  Var_01    N2   C7   C6   N1    56.86  30.0  1
 T2J  Var_02    N2   C8   C9   N1   -55.63  30.0  1
 T2J  Var_03    C6   N1   C5   C4    44.25  30.0  2
 T2J  Var_04    C7   C6   N1   C5   167.15  30.0  1
 T2J  Var_05    C8   C9   N1   C5  -167.16  30.0  1
 T2J  Var_06    C8   N2   C7   C6   -55.32  30.0  1
 T2J  Var_07    C9   C8   N2   C7    54.70  30.0  1
 T2J  Var_08    H15  C11  C10  N2    60.18  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
 T2J  plan-1  N1   0.020
 T2J  plan-1  C4   0.020
 T2J  plan-1  C5   0.020
 T2J  plan-1  C    0.020
 T2J  plan-1  C1   0.020
 T2J  plan-1  C2   0.020
 T2J  plan-1  C3   0.020
 T2J  plan-1  H3   0.020
 T2J  plan-1  H    0.020
 T2J  plan-1  H1   0.020
 T2J  plan-1  H2   0.020
 T2J  plan-1  N    0.020
 T2J  plan-2  C    0.020
 T2J  plan-2  O    0.020
 T2J  plan-2  O1   0.020
 T2J  plan-2  N    0.020
 T2J  plan-3  C7   0.020
 T2J  plan-3  C8   0.020
 T2J  plan-3  C11  0.020
 T2J  plan-3  N2   0.020
 T2J  plan-3  O2   0.020
 T2J  plan-3  C10  0.020

