# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 11:59:05 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: (3~{S})-3-(5-azanyl-2-methyl-4-oxidanylidene-quinazolin-3-yl)piperidine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=Nc2cccc(N)c2C(=O)N1[C@H]3CCC(=O)NC3=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
 835  835  "(3S)-3-(5-azanyl-2-methyl-4-oxidanylidene-quinazolin-3-yl)piperidine-2,6-dione"
  ligand  35  21  .  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_835
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
 835  O2   O  O     0  -0.416  23.0543  -15.3530   0.6032
 835  C3   C  C     0   0.598  23.8633  -14.9664  -0.2042
 835  N1   N  NH1   0  -0.690  23.7421  -15.2733  -1.5381
 835  C4   C  C     0   0.548  24.4849  -14.7895  -2.5989
 835  O1   O  O     0  -0.420  24.2356  -15.1468  -3.7261
 835  C5   C  CH2   0  -0.599  25.5469  -13.7882  -2.2463
 835  C1   C  CH2   0  -0.446  26.1367  -14.0242  -0.8656
 835  C2   C  CH1   0  -0.262  25.0137  -14.0402   0.1607
 835  N2   N  NR6   0  -0.564  25.4564  -14.3180   1.5176
 835  C9   C  CR6   0   0.638  25.8282  -15.6316   1.7898
 835  O3   O  O     0  -0.486  25.7726  -16.4592   0.8870
 835  C8   C  CR66  0  -0.183  26.2442  -15.9011   3.1441
 835  C13  C  CR6   0   0.346  26.6404  -17.2033   3.5623
 835  N4   N  NH2   0  -0.864  26.7169  -18.2504   2.7121
 835  C12  C  CR16  0  -0.359  26.9880  -17.3760   4.9100
 835  C11  C  CR16  0  -0.231  26.9581  -16.3155   5.7973
 835  C10  C  CR16  0  -0.366  26.5886  -15.0423   5.3966
 835  C7   C  CR66  0   0.249  26.2311  -14.8351   4.0679
 835  N3   N  N     0  -0.484  25.8702  -13.5647   3.6890
 835  C6   C  CR6   0   0.476  25.5080  -13.3351   2.4802
 835  C14  C  CH3   0  -0.793  25.1370  -11.9362   2.1060
 835  H1   H  HNH1  0   0.416  22.9689  -15.8846  -1.7784
 835  H2   H  HCH2  0   0.296  26.3171  -13.8149  -3.0155
 835  H3   H  HCH2  0   0.293  25.0834  -12.7964  -2.2944
 835  H4   H  HCH2  0   0.272  26.6973  -14.9576  -0.8510
 835  H5   H  HCH2  0   0.277  26.8312  -13.2202  -0.6221
 835  H6   H  HCH1  0   0.352  24.5590  -13.0476   0.1564
 835  H7   H  HNH2  0   0.392  26.8303  -19.1739   3.0930
 835  H8   H  HNH2  0   0.404  26.3166  -18.1728   1.7933
 835  H9   H  HCR6  0   0.261  27.2857  -18.3595   5.2524
 835  H10  H  HCR6  0   0.260  27.2327  -16.4915   6.8299
 835  H11  H  HCR6  0   0.250  26.5709  -14.2115   6.0883
 835  H12  H  HCH3  0   0.286  25.3058  -11.2957   2.9664
 835  H13  H  HCH3  0   0.275  25.7359  -11.5627   1.2740
 835  H14  H  HCH3  0   0.276  24.0856  -11.8558   1.8238

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
 835  O1   C4   double    1.208  0.020  1.208
 835  C4   C5   single    1.502  0.020  1.502
 835  C4   N1   single    1.382  0.020  1.382
 835  C5   C1   single    1.520  0.020  1.520
 835  N1   C3   single    1.374  0.020  1.374
 835  C1   C2   single    1.521  0.020  1.521
 835  C3   C2   single    1.521  0.020  1.521
 835  C3   O2   double    1.206  0.020  1.206
 835  C2   N2   single    1.454  0.020  1.454
 835  O3   C9   double    1.226  0.020  1.226
 835  N2   C9   single    1.392  0.020  1.392
 835  N2   C6   single    1.377  0.020  1.377
 835  C9   C8   single    1.442  0.020  1.442
 835  C14  C6   single    1.495  0.020  1.495
 835  C6   N3   double    1.283  0.020  1.283
 835  N4   C13  single    1.351  0.020  1.351
 835  C8   C13  aromatic  1.424  0.020  1.424
 835  C8   C7   aromatic  1.411  0.020  1.411
 835  C13  C12  aromatic  1.403  0.020  1.403
 835  N3   C7   single    1.374  0.020  1.374
 835  C7   C10  aromatic  1.391  0.020  1.391
 835  C12  C11  aromatic  1.383  0.020  1.383
 835  C10  C11  aromatic  1.385  0.020  1.385
 835  N1   H1   single    0.860  0.020  1.020
 835  C5   H2   single    0.970  0.020  1.090
 835  C5   H3   single    0.970  0.020  1.090
 835  C1   H4   single    0.970  0.020  1.090
 835  C1   H5   single    0.970  0.020  1.090
 835  C2   H6   single    0.970  0.020  1.090
 835  N4   H7   single    0.890  0.020  1.040
 835  N4   H8   single    0.890  0.020  1.040
 835  C12  H9   single    0.930  0.020  1.080
 835  C11  H10  single    0.930  0.020  1.080
 835  C10  H11  single    0.930  0.020  1.080
 835  C14  H12  single    0.970  0.020  1.090
 835  C14  H13  single    0.970  0.020  1.090
 835  C14  H14  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
 835  C2   C3   N1   115.82  3.000
 835  C2   C3   O2   122.80  3.000
 835  N1   C3   O2   121.26  3.000
 835  H1   N1   C4   116.02  3.000
 835  H1   N1   C3   115.58  3.000
 835  C4   N1   C3   128.26  3.000
 835  C5   C4   O1   124.20  3.000
 835  C5   C4   N1   115.67  3.000
 835  O1   C4   N1   120.09  3.000
 835  H3   C5   H2   106.88  3.000
 835  H3   C5   C1   110.15  3.000
 835  H2   C5   C1   111.31  3.000
 835  H3   C5   C4   107.11  3.000
 835  H2   C5   C4   108.55  3.000
 835  C1   C5   C4   112.60  3.000
 835  H5   C1   H4   107.53  3.000
 835  H5   C1   C2   109.11  3.000
 835  H4   C1   C2   111.22  3.000
 835  H5   C1   C5   109.61  3.000
 835  H4   C1   C5   110.19  3.000
 835  C2   C1   C5   109.14  3.000
 835  H6   C2   N2   107.71  3.000
 835  H6   C2   C1   107.17  3.000
 835  N2   C2   C1   114.00  3.000
 835  H6   C2   C3   103.75  3.000
 835  N2   C2   C3   109.74  3.000
 835  C1   C2   C3   113.75  3.000
 835  C6   N2   C9   121.80  3.000
 835  C6   N2   C2   121.83  3.000
 835  C9   N2   C2   116.36  3.000
 835  C8   C9   O3   125.34  3.000
 835  C8   C9   N2   115.91  3.000
 835  O3   C9   N2   118.74  3.000
 835  C7   C8   C13  120.09  3.000
 835  C7   C8   C9   118.11  3.000
 835  C13  C8   C9   121.80  3.000
 835  C12  C13  N4   119.69  3.000
 835  C12  C13  C8   117.63  3.000
 835  N4   C13  C8   122.67  3.000
 835  H8   N4   H7   117.52  3.000
 835  H8   N4   C13  119.53  3.000
 835  H7   N4   C13  118.68  3.000
 835  H9   C12  C11  119.96  3.000
 835  H9   C12  C13  118.93  3.000
 835  C11  C12  C13  121.11  3.000
 835  H10  C11  C10  119.54  3.000
 835  H10  C11  C12  118.79  3.000
 835  C10  C11  C12  121.68  3.000
 835  H11  C10  C7   119.49  3.000
 835  H11  C10  C11  121.71  3.000
 835  C7   C10  C11  118.80  3.000
 835  N3   C7   C10  117.94  3.000
 835  C10  C7   C8   120.69  3.000
 835  N3   C7   C8   121.37  3.000
 835  C6   N3   C7   119.98  3.000
 835  C14  C6   N3   118.26  3.000
 835  N3   C6   N2   122.80  3.000
 835  C14  C6   N2   118.94  3.000
 835  H14  C14  H13  107.84  3.000
 835  H14  C14  H12  108.12  3.000
 835  H13  C14  H12  108.48  3.000
 835  H14  C14  C6   111.89  3.000
 835  H13  C14  C6   112.03  3.000
 835  H12  C14  C6   108.37  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
 835  CONST_01  C11  C12  C13  C8      0.00   0.0  0
 835  CONST_02  C11  C10  C7   C8      0.00   0.0  0
 835  CONST_03  C10  C7   C8   C13     0.00   0.0  0
 835  CONST_04  C10  C11  C12  C13     0.00   0.0  0
 835  CONST_05  C7   C8   C13  C12     0.00   0.0  0
 835  CONST_06  C7   C10  C11  C12     0.00   0.0  0
 835  CONST_07  C2   C3   N1   C4      0.00   0.0  0
 835  CONST_08  C8   C9   N2   C2    180.00   0.0  0
 835  CONST_09  N3   C6   N2   C2    180.00   0.0  0
 835  CONST_10  C7   N3   C6   N2      0.00   0.0  0
 835  CONST_11  N3   C6   N2   C9      0.00   0.0  0
 835  CONST_12  C6   N2   C9   C8      0.00   0.0  0
 835  CONST_13  N4   C13  C8   C9      0.00   0.0  0
 835  CONST_14  C7   C8   C13  N4    180.00   0.0  0
 835  CONST_15  C11  C12  C13  N4    180.00   0.0  0
 835  CONST_16  C4   N1   C3   O2    180.00   0.0  0
 835  CONST_17  O3   C9   N2   C2      0.00   0.0  0
 835  CONST_18  C14  C6   N2   C2      0.00   0.0  0
 835  CONST_19  C14  C6   N2   C9    180.00   0.0  0
 835  CONST_20  C6   N2   C9   O3    180.00   0.0  0
 835  CONST_21  C14  C6   N3   C7    180.00   0.0  0
 835  CONST_22  H9   C12  C13  C8    180.00   0.0  0
 835  CONST_23  H11  C10  C7   C8    180.00   0.0  0
 835  CONST_24  H10  C11  C12  C13   180.00   0.0  0
 835  CONST_25  H11  C10  C11  C12   180.00   0.0  0
 835  CONST_26  H9   C12  C11  C10   180.00   0.0  0
 835  CONST_27  H10  C11  C10  C7    180.00   0.0  0
 835  CONST_28  H11  C10  C7   N3      0.00   0.0  0
 835  CONST_29  H1   N1   C3   C2    180.00   0.0  0
 835  CONST_30  H7   N4   C13  C8    180.00   0.0  0
 835  CONST_31  H8   N4   C13  C8      0.00   0.0  0
 835  CONST_32  H7   N4   C13  C12     0.00   0.0  0
 835  CONST_33  H8   N4   C13  C12   180.00   0.0  0
 835  CONST_34  H1   N1   C3   O2      0.00   0.0  0
 835  Var_01    C5   C4   N1   C3     -0.85  30.0  1
 835  Var_02    C1   C5   C4   N1     31.52  30.0  1
 835  Var_03    C2   C1   C5   C4    -55.29  30.0  1
 835  Var_04    O1   C4   N1   C3   -178.79  30.0  1
 835  Var_05    C1   C5   C4   O1   -150.64  30.0  1
 835  Var_06    H2   C5   C4   N1    155.22  30.0  1
 835  Var_07    H3   C5   C4   N1    -89.72  30.0  1
 835  Var_08    H4   C1   C5   C4     67.12  30.0  1
 835  Var_09    H5   C1   C5   C4   -174.73  30.0  1
 835  Var_10    H1   N1   C4   C5    174.63  30.0  1
 835  Var_11    H2   C5   C1   C2   -177.44  30.0  1
 835  Var_12    H3   C5   C1   C2     64.19  30.0  1
 835  Var_13    H2   C5   C4   O1    -26.94  30.0  1
 835  Var_14    H3   C5   C4   O1     88.12  30.0  1
 835  Var_15    H1   N1   C4   O1     -3.31  30.0  1
 835  Var_16    H12  C14  C6   N2   -175.99  30.0  3
 835  Var_17    H13  C14  C6   N2    -56.35  30.0  3
 835  Var_18    H14  C14  C6   N2     64.89  30.0  3
 835  Var_19    H12  C14  C6   N3      3.58  30.0  3
 835  Var_20    H13  C14  C6   N3    123.23  30.0  3
 835  Var_21    H14  C14  C6   N3   -115.53  30.0  3

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
 835  chir_01  C2  C1  C3  N2  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
 835  plan-1  C13  0.020
 835  plan-1  N4   0.020
 835  plan-1  H7   0.020
 835  plan-1  H8   0.020
 835  plan-2  N1   0.020
 835  plan-2  C4   0.020
 835  plan-2  O1   0.020
 835  plan-2  C5   0.020
 835  plan-3  C2   0.020
 835  plan-3  N2   0.020
 835  plan-3  C9   0.020
 835  plan-3  O3   0.020
 835  plan-3  C8   0.020
 835  plan-3  C13  0.020
 835  plan-3  N4   0.020
 835  plan-3  C12  0.020
 835  plan-3  C11  0.020
 835  plan-3  C10  0.020
 835  plan-3  C7   0.020
 835  plan-3  N3   0.020
 835  plan-3  C6   0.020
 835  plan-3  C14  0.020
 835  plan-3  H9   0.020
 835  plan-3  H10  0.020
 835  plan-3  H11  0.020
 835  plan-4  O2   0.020
 835  plan-4  C3   0.020
 835  plan-4  N1   0.020
 835  plan-4  C4   0.020
 835  plan-4  C2   0.020
 835  plan-4  H1   0.020

