# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 06:35:03 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: (3~{S})-3-(benzotriazol-2-yl)piperidine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CC[C@H](n2nc3ccccc3n2)C(=O)N1
#
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
 7SE  7SE  "(3S)-3-(benzotriazol-2-yl)piperidine-2,6-dione"
  ligand  27  17  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7SE
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
 7SE  N1   N  NH1   0  -0.690  23.9681  15.8657   -7.7870
 7SE  N3   N  N     0  -0.284  26.2196  19.1145   -9.1343
 7SE  C4   C  C     0   0.581  25.1649  16.5222   -7.9213
 7SE  C5   C  CH1   0  -0.207  25.1978  17.9227   -7.3281
 7SE  C6   C  CR56  0   0.198  27.4118  19.6935   -9.3174
 7SE  C7   C  CR56  0   0.186  28.1597  19.5302   -8.1298
 7SE  C8   C  CR16  0  -0.290  29.4669  20.0437   -8.0122
 7SE  C10  C  CR16  0  -0.265  29.2141  20.8690  -10.2962
 7SE  C1   C  CH2   0  -0.471  23.8577  18.6221   -7.4852
 7SE  C2   C  CH2   0  -0.598  22.7944  17.7799   -6.8013
 7SE  C3   C  C     0   0.557  22.7804  16.3498   -7.2639
 7SE  N2   N  NR5   0  -0.084  26.2917  18.6598   -7.9140
 7SE  O1   O  O     0  -0.415  21.8162  15.6277   -7.1871
 7SE  O2   O  O     0  -0.400  26.1196  16.0081   -8.4468
 7SE  N4   N  N     0  -0.274  27.4011  18.8573   -7.2561
 7SE  C9   C  CR16  0  -0.264  29.9679  20.7034   -9.1002
 7SE  C11  C  CR16  0  -0.290  27.9452  20.3766  -10.4288
 7SE  H1   H  HNH1  0   0.422  23.9514  14.9069   -8.1193
 7SE  H2   H  HCH1  0   0.345  25.4335  17.8221   -6.2645
 7SE  H4   H  HCR6  0   0.265  29.6672  21.4028  -11.1213
 7SE  H5   H  HCH2  0   0.292  23.9029  19.6088   -7.0265
 7SE  H6   H  HCH2  0   0.276  23.6210  18.7573   -8.5415
 7SE  H7   H  HCH2  0   0.304  21.8005  18.1959   -6.9602
 7SE  H8   H  HCH2  0   0.299  22.9601  17.7685   -5.7186
 7SE  H9   H  HCR6  0   0.265  30.9666  21.1175   -9.0592
 7SE  H10  H  HCR6  0   0.272  27.3759  20.5044  -11.3394
 7SE  H3   H  HCR6  0   0.272  30.0422  19.9218   -7.1044

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
 7SE  C11  C10  aromatic  1.368  0.020  1.368
 7SE  C11  C6   aromatic  1.409  0.020  1.409
 7SE  C10  C9   aromatic  1.423  0.020  1.423
 7SE  C6   N3   aromatic  1.338  0.020  1.338
 7SE  C6   C7   aromatic  1.413  0.020  1.413
 7SE  N3   N2   aromatic  1.304  0.020  1.304
 7SE  C9   C8   aromatic  1.367  0.020  1.367
 7SE  O2   C4   double    1.205  0.020  1.205
 7SE  C7   C8   aromatic  1.409  0.020  1.409
 7SE  C7   N4   aromatic  1.338  0.020  1.338
 7SE  C4   N1   single    1.372  0.020  1.372
 7SE  C4   C5   single    1.521  0.020  1.521
 7SE  N1   C3   single    1.385  0.020  1.385
 7SE  N2   C5   single    1.443  0.020  1.443
 7SE  N2   N4   aromatic  1.305  0.020  1.305
 7SE  C3   O1   double    1.207  0.020  1.207
 7SE  C3   C2   single    1.503  0.020  1.503
 7SE  C1   C5   single    1.520  0.020  1.520
 7SE  C1   C2   single    1.519  0.020  1.519
 7SE  N1   H1   single    0.860  0.020  1.020
 7SE  C5   H2   single    0.970  0.020  1.090
 7SE  C8   H3   single    0.930  0.020  1.080
 7SE  C10  H4   single    0.930  0.020  1.080
 7SE  C1   H5   single    0.970  0.020  1.090
 7SE  C1   H6   single    0.970  0.020  1.090
 7SE  C2   H7   single    0.970  0.020  1.090
 7SE  C2   H8   single    0.970  0.020  1.090
 7SE  C9   H9   single    0.930  0.020  1.080
 7SE  C11  H10  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
 7SE  H1   N1   C3   116.09  3.000
 7SE  H1   N1   C4   115.75  3.000
 7SE  C3   N1   C4   128.16  3.000
 7SE  N2   N3   C6   103.28  3.000
 7SE  O2   C4   C5   123.07  3.000
 7SE  C5   C4   N1   114.92  3.000
 7SE  O2   C4   N1   121.99  3.000
 7SE  H2   C5   N2   106.16  3.000
 7SE  H2   C5   C1   109.44  3.000
 7SE  N2   C5   C1   113.03  3.000
 7SE  H2   C5   C4   107.41  3.000
 7SE  C1   C5   C4   111.36  3.000
 7SE  N2   C5   C4   109.16  3.000
 7SE  C11  C6   C7   121.23  3.000
 7SE  C7   C6   N3   107.86  3.000
 7SE  C11  C6   N3   130.91  3.000
 7SE  N4   C7   C8   130.87  3.000
 7SE  N4   C7   C6   107.86  3.000
 7SE  C8   C7   C6   121.26  3.000
 7SE  H3   C8   C9   121.82  3.000
 7SE  H3   C8   C7   121.49  3.000
 7SE  C9   C8   C7   116.69  3.000
 7SE  H4   C10  C11  119.49  3.000
 7SE  H4   C10  C9   118.45  3.000
 7SE  C11  C10  C9   122.06  3.000
 7SE  H6   C1   H5   107.74  3.000
 7SE  H6   C1   C2   110.65  3.000
 7SE  H5   C1   C2   109.98  3.000
 7SE  H6   C1   C5   110.40  3.000
 7SE  H5   C1   C5   109.68  3.000
 7SE  C2   C1   C5   108.39  3.000
 7SE  H8   C2   H7   106.63  3.000
 7SE  H8   C2   C3   107.20  3.000
 7SE  H7   C2   C3   108.06  3.000
 7SE  H8   C2   C1   110.18  3.000
 7SE  H7   C2   C1   111.18  3.000
 7SE  C3   C2   C1   113.29  3.000
 7SE  O1   C3   C2   123.85  3.000
 7SE  C2   C3   N1   116.15  3.000
 7SE  O1   C3   N1   119.99  3.000
 7SE  N4   N2   C5   121.13  3.000
 7SE  N4   N2   N3   117.77  3.000
 7SE  C5   N2   N3   121.06  3.000
 7SE  N2   N4   C7   103.23  3.000
 7SE  H9   C9   C10  118.43  3.000
 7SE  H9   C9   C8   119.52  3.000
 7SE  C10  C9   C8   122.05  3.000
 7SE  H10  C11  C10  121.83  3.000
 7SE  H10  C11  C6   121.47  3.000
 7SE  C10  C11  C6   116.70  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
 7SE  CONST_01  C10  C11  C6   N3    180.00   0.0  0
 7SE  CONST_02  C8   C7   C6   N3    180.00   0.0  0
 7SE  CONST_03  N4   C7   C6   N3      0.00   0.0  0
 7SE  CONST_04  C7   N4   N2   N3      0.00   0.0  0
 7SE  CONST_05  C9   C10  C11  C6      0.00   0.0  0
 7SE  CONST_06  N4   N2   N3   C6      0.00   0.0  0
 7SE  CONST_07  C9   C8   C7   C6      0.00   0.0  0
 7SE  CONST_08  N2   N4   C7   C6      0.00   0.0  0
 7SE  CONST_09  C10  C11  C6   C7      0.00   0.0  0
 7SE  CONST_10  N2   N3   C6   C7      0.00   0.0  0
 7SE  CONST_11  C10  C9   C8   C7      0.00   0.0  0
 7SE  CONST_12  C11  C10  C9   C8      0.00   0.0  0
 7SE  CONST_13  C11  C6   C7   C8      0.00   0.0  0
 7SE  CONST_14  N2   N4   C7   C8    180.00   0.0  0
 7SE  CONST_15  C11  C6   N3   N2    180.00   0.0  0
 7SE  CONST_16  C11  C6   C7   N4    180.00   0.0  0
 7SE  CONST_17  C9   C8   C7   N4    180.00   0.0  0
 7SE  CONST_18  C6   N3   N2   C5    180.00   0.0  0
 7SE  CONST_19  C7   N4   N2   C5    180.00   0.0  0
 7SE  CONST_20  C3   N1   C4   C5      0.00   0.0  0
 7SE  CONST_21  O2   C4   N1   C3    180.00   0.0  0
 7SE  CONST_22  H10  C11  C6   N3      0.00   0.0  0
 7SE  CONST_23  H4   C10  C11  C6    180.00   0.0  0
 7SE  CONST_24  H3   C8   C7   C6    180.00   0.0  0
 7SE  CONST_25  H10  C11  C6   C7    180.00   0.0  0
 7SE  CONST_26  H9   C9   C8   C7    180.00   0.0  0
 7SE  CONST_27  H4   C10  C9   C8    180.00   0.0  0
 7SE  CONST_28  H3   C8   C9   C10   180.00   0.0  0
 7SE  CONST_29  H3   C8   C7   N4      0.00   0.0  0
 7SE  CONST_30  H10  C11  C10  C9    180.00   0.0  0
 7SE  CONST_31  H9   C9   C10  C11   180.00   0.0  0
 7SE  CONST_32  H1   N1   C4   C5    180.00   0.0  0
 7SE  CONST_33  H1   N1   C4   O2      0.00   0.0  0
 7SE  Var_01    C1   C2   C3   N1     24.42  30.0  1
 7SE  Var_02    C2   C3   N1   C4      0.93  30.0  1
 7SE  Var_03    C3   C2   C1   C5    -53.16  30.0  1
 7SE  Var_04    O1   C3   N1   C4   -178.26  30.0  1
 7SE  Var_05    O1   C3   C2   C1   -156.43  30.0  1
 7SE  Var_06    H7   C2   C3   N1    148.07  30.0  1
 7SE  Var_07    H8   C2   C3   N1    -97.34  30.0  1
 7SE  Var_08    H7   C2   C1   C5   -175.08  30.0  1
 7SE  Var_09    H8   C2   C1   C5     66.92  30.0  1
 7SE  Var_10    H1   N1   C3   C2   -178.60  30.0  1
 7SE  Var_11    H5   C1   C2   C3   -173.07  30.0  1
 7SE  Var_12    H6   C1   C2   C3     68.02  30.0  1
 7SE  Var_13    H1   N1   C3   O1      2.21  30.0  1
 7SE  Var_14    H7   C2   C3   O1    -32.78  30.0  1
 7SE  Var_15    H8   C2   C3   O1     81.81  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 7SE  chir_01  C5  C4  N2  C1  negativ

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
 7SE  plan-1  N3   0.020
 7SE  plan-1  C5   0.020
 7SE  plan-1  C6   0.020
 7SE  plan-1  C7   0.020
 7SE  plan-1  C8   0.020
 7SE  plan-1  C10  0.020
 7SE  plan-1  N2   0.020
 7SE  plan-1  N4   0.020
 7SE  plan-1  C9   0.020
 7SE  plan-1  C11  0.020
 7SE  plan-1  H4   0.020
 7SE  plan-1  H9   0.020
 7SE  plan-1  H10  0.020
 7SE  plan-1  H3   0.020
 7SE  plan-2  N1   0.020
 7SE  plan-2  C4   0.020
 7SE  plan-2  C5   0.020
 7SE  plan-2  C3   0.020
 7SE  plan-2  O2   0.020
 7SE  plan-2  H1   0.020
 7SE  plan-3  N1   0.020
 7SE  plan-3  C2   0.020
 7SE  plan-3  C3   0.020
 7SE  plan-3  O1   0.020

