# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 00:38:35 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 3-oxo-2-piperidin-4-yl-1H-isoindole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cccc2CN(C3CCNCC3)C(=O)c12
#
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
 L3L  L3L  3-oxo-2-piperidin-4-yl-1H-isoindole-4-carboxamide  ligand  36  19  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_L3L
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
 L3L  C1    C  CR16  0  -0.235  -3.6901   1.9505  -0.0055
 L3L  C2    C  CR16  0  -0.273  -3.8450   0.5723  -0.1473
 L3L  C3    C  CR16  0  -0.330  -2.4299   2.5308   0.0411
 L3L  C4    C  CR56  0  -0.060  -1.4816   0.3283  -0.1970
 L3L  C5    C  CR6   0  -0.081  -2.7375  -0.2609  -0.2540
 L3L  C6    C  CR56  0   0.084  -1.3298   1.6958  -0.0489
 L3L  C7    C  CR5   0   0.556  -0.1388  -0.3014  -0.2073
 L3L  C8    C  C     0   0.440  -2.9208  -1.7270  -0.5191
 L3L  C9    C  CH2   0  -0.281   0.1272   2.0172  -0.0077
 L3L  C10   C  CH2   0  -0.443   2.8154  -0.1560  -1.2420
 L3L  C11   C  CH2   0  -0.441   2.6709  -0.0024   1.2619
 L3L  C12   C  CH2   0  -0.323   4.3383  -0.1543  -1.0999
 L3L  C13   C  CH2   0  -0.322   4.1999  -0.0206   1.3007
 L3L  C14   C  CH1   0  -0.052   2.1969   0.5912  -0.0634
 L3L  N15   N  NH1   0  -0.574   4.8133  -0.6897   0.1654
 L3L  N16   N  NR5   0  -0.531   0.7507   0.7169  -0.1446
 L3L  N17   N  NH2   0  -0.784  -3.4221  -2.4190   0.5097
 L3L  O18   O  O     0  -0.485   0.1088  -1.4958  -0.2444
 L3L  O19   O  O     0  -0.469  -2.6700  -2.2040  -1.6131
 L3L  H1    H  HCR6  0   0.270  -4.5700   2.5757   0.0684
 L3L  H2    H  HCR6  0   0.271  -4.8427   0.1533  -0.1870
 L3L  H3    H  HCR6  0   0.265  -2.3179   3.6019   0.1491
 L3L  H10A  H  HCH2  0   0.233   2.4574  -1.1868  -1.2702
 L3L  H11   H  HCH2  0   0.229   2.2890  -1.0205   1.3754
 L3L  H11A  H  HCH2  0   0.233   2.2821   0.5848   2.0987
 L3L  H12   H  HCH2  0   0.240   4.7885  -0.7249  -1.9144
 L3L  H12A  H  HCH2  0   0.217   4.7093   0.8721  -1.1987
 L3L  H13   H  HCH2  0   0.217   4.5686   1.0108   1.3286
 L3L  H13A  H  HCH2  0   0.240   4.5449  -0.4978   2.2197
 L3L  H14   H  HCH1  0   0.245   2.5664   1.6213  -0.1110
 L3L  HN15  H  HNH1  0   0.340   4.5889  -1.6777   0.2070
 L3L  HN17  H  HNH2  0   0.414  -3.5740  -1.9948   1.4084
 L3L  HN1A  H  HNH2  0   0.406  -3.6016  -3.4071   0.4249
 L3L  H9    H  HCH2  0   0.276   0.4239   2.6884  -0.8187
 L3L  H17   H  HCH2  0   0.273   0.4153   2.4925   0.9349
 L3L  H10   H  HCH2  0   0.234   2.5231   0.3186  -2.1824

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
 L3L  C1   C2    aromatic  1.394  0.020  1.394
 L3L  C1   C3    aromatic  1.388  0.020  1.388
 L3L  C1   H1    single    0.930  0.020  1.080
 L3L  C2   C5    aromatic  1.390  0.020  1.390
 L3L  C2   H2    single    0.930  0.020  1.080
 L3L  C3   C6    aromatic  1.384  0.020  1.384
 L3L  C3   H3    single    0.930  0.020  1.080
 L3L  C4   C5    aromatic  1.388  0.020  1.388
 L3L  C4   C6    aromatic  1.384  0.020  1.384
 L3L  C4   C7    single    1.483  0.020  1.483
 L3L  C5   C8    single    1.501  0.020  1.501
 L3L  C6   C9    single    1.493  0.020  1.493
 L3L  C7   N16   single    1.354  0.020  1.354
 L3L  C7   O18   double    1.220  0.020  1.220
 L3L  C8   N17   single    1.337  0.020  1.337
 L3L  C8   O19   double    1.220  0.020  1.220
 L3L  C9   N16   single    1.449  0.020  1.449
 L3L  C10  C12   single    1.529  0.020  1.529
 L3L  C10  C14   single    1.526  0.020  1.526
 L3L  C10  H10   single    0.970  0.020  1.090
 L3L  C10  H10A  single    0.970  0.020  1.090
 L3L  C11  C13   single    1.530  0.020  1.530
 L3L  C11  C14   single    1.528  0.020  1.528
 L3L  C11  H11   single    0.970  0.020  1.090
 L3L  C11  H11A  single    0.970  0.020  1.090
 L3L  C12  N15   single    1.454  0.020  1.454
 L3L  C12  H12   single    0.970  0.020  1.090
 L3L  C12  H12A  single    0.970  0.020  1.090
 L3L  C13  N15   single    1.454  0.020  1.454
 L3L  C13  H13   single    0.970  0.020  1.090
 L3L  C13  H13A  single    0.970  0.020  1.090
 L3L  C14  N16   single    1.454  0.020  1.454
 L3L  C14  H14   single    0.970  0.020  1.090
 L3L  N15  HN15  single    0.890  0.020  1.040
 L3L  N17  HN17  single    0.860  0.020  1.020
 L3L  N17  HN1A  single    0.860  0.020  1.020
 L3L  C9   H9    single    0.970  0.020  1.090
 L3L  C9   H17   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
 L3L  H1    C1   C3    119.63  3.000
 L3L  H1    C1   C2    119.20  3.000
 L3L  C3    C1   C2    121.17  3.000
 L3L  H2    C2   C5    119.96  3.000
 L3L  H2    C2   C1    119.25  3.000
 L3L  C5    C2   C1    120.79  3.000
 L3L  H3    C3   C6    121.42  3.000
 L3L  H3    C3   C1    120.73  3.000
 L3L  C6    C3   C1    117.85  3.000
 L3L  C7    C4   C6    108.72  3.000
 L3L  C7    C4   C5    129.68  3.000
 L3L  C6    C4   C5    121.53  3.000
 L3L  C8    C5   C4    122.15  3.000
 L3L  C8    C5   C2    120.11  3.000
 L3L  C4    C5   C2    117.59  3.000
 L3L  C9    C6   C4    108.84  3.000
 L3L  C9    C6   C3    130.10  3.000
 L3L  C4    C6   C3    121.06  3.000
 L3L  O18   C7   N16   127.18  3.000
 L3L  O18   C7   C4    126.83  3.000
 L3L  N16   C7   C4    105.98  3.000
 L3L  O19   C8   N17   124.39  3.000
 L3L  O19   C8   C5    121.02  3.000
 L3L  N17   C8   C5    114.54  3.000
 L3L  H17   C9   H9    107.50  3.000
 L3L  H17   C9   N16   110.97  3.000
 L3L  H9    C9   N16   111.35  3.000
 L3L  H17   C9   C6    111.98  3.000
 L3L  H9    C9   C6    112.12  3.000
 L3L  N16   C9   C6    102.96  3.000
 L3L  H10A  C10  H10   107.47  3.000
 L3L  H10A  C10  C14   110.44  3.000
 L3L  H10   C10  C14   110.09  3.000
 L3L  H10A  C10  C12   109.27  3.000
 L3L  H10   C10  C12   110.22  3.000
 L3L  C14   C10  C12   109.34  3.000
 L3L  H11A  C11  H11   107.24  3.000
 L3L  H11A  C11  C14   110.18  3.000
 L3L  H11   C11  C14   110.09  3.000
 L3L  H11A  C11  C13   110.02  3.000
 L3L  H11   C11  C13   109.60  3.000
 L3L  C14   C11  C13   109.68  3.000
 L3L  H12A  C12  H12   106.42  3.000
 L3L  H12A  C12  N15   108.23  3.000
 L3L  H12   C12  N15   108.79  3.000
 L3L  H12A  C12  C10   109.25  3.000
 L3L  H12   C12  C10   109.92  3.000
 L3L  N15   C12  C10   113.94  3.000
 L3L  H13A  C13  H13   106.48  3.000
 L3L  H13A  C13  N15   108.84  3.000
 L3L  H13   C13  N15   108.13  3.000
 L3L  H13A  C13  C11   110.03  3.000
 L3L  H13   C13  C11   109.01  3.000
 L3L  N15   C13  C11   114.05  3.000
 L3L  H14   C14  N16   104.58  3.000
 L3L  H14   C14  C11   107.36  3.000
 L3L  N16   C14  C11   113.00  3.000
 L3L  H14   C14  C10   106.87  3.000
 L3L  N16   C14  C10   113.72  3.000
 L3L  C11   C14  C10   110.74  3.000
 L3L  HN15  N15  C13   108.85  3.000
 L3L  HN15  N15  C12   108.80  3.000
 L3L  C13   N15  C12   111.86  3.000
 L3L  C14   N16  C9    120.03  3.000
 L3L  C14   N16  C7    126.25  3.000
 L3L  C9    N16  C7    113.38  3.000
 L3L  HN1A  N17  HN17  117.52  3.000
 L3L  HN1A  N17  C8    120.62  3.000
 L3L  HN17  N17  C8    121.73  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
 L3L  CONST_01  C4    C5   C2   C1     0.00   0.0  0
 L3L  CONST_02  C4    C6   C3   C1     0.00   0.0  0
 L3L  CONST_03  C6    C3   C1   C2     0.00   0.0  0
 L3L  CONST_04  C6    C4   C5   C2     0.00   0.0  0
 L3L  CONST_05  C5    C2   C1   C3     0.00   0.0  0
 L3L  CONST_06  C5    C4   C6   C3     0.00   0.0  0
 L3L  CONST_07  C9    N16  C7   C4     0.00   0.0  0
 L3L  CONST_08  C14   N16  C7   C4   180.00   0.0  0
 L3L  CONST_09  C8    C5   C2   C1   180.00   0.0  0
 L3L  CONST_10  C8    C5   C4   C6   180.00   0.0  0
 L3L  CONST_11  C8    C5   C4   C7     0.00   0.0  0
 L3L  CONST_12  O18   C7   N16  C9   180.00   0.0  0
 L3L  CONST_13  O18   C7   N16  C14    0.00   0.0  0
 L3L  CONST_14  H3    C3   C1   C2   180.00   0.0  0
 L3L  CONST_15  H2    C2   C1   C3   180.00   0.0  0
 L3L  CONST_16  H1    C1   C2   C5   180.00   0.0  0
 L3L  CONST_17  HN17  N17  C8   C5     0.00   0.0  0
 L3L  CONST_18  HN1A  N17  C8   C5   180.00   0.0  0
 L3L  Var_01    C13   N15  C12  C10  -54.03  30.0  1
 L3L  Var_02    C12   N15  C13  C11   53.44  30.0  1
 L3L  Var_03    N15   C12  C10  C14   55.07  30.0  1
 L3L  Var_04    N15   C13  C11  C14  -54.03  30.0  1
 L3L  Var_05    H9    C9   C6   C3   -60.50  30.0  1
 L3L  Var_06    N17   C8   C5   C2   -71.03  30.0  2

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
 L3L  chir_01  C14  C10  C11  N16  positiv

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
 L3L  plan-1  C5    0.020
 L3L  plan-1  C8    0.020
 L3L  plan-1  N17   0.020
 L3L  plan-1  O19   0.020
 L3L  plan-1  HN17  0.020
 L3L  plan-1  HN1A  0.020
 L3L  plan-2  C1    0.020
 L3L  plan-2  C2    0.020
 L3L  plan-2  C3    0.020
 L3L  plan-2  C4    0.020
 L3L  plan-2  C5    0.020
 L3L  plan-2  C6    0.020
 L3L  plan-2  C7    0.020
 L3L  plan-2  C8    0.020
 L3L  plan-2  C9    0.020
 L3L  plan-2  C14   0.020
 L3L  plan-2  N16   0.020
 L3L  plan-2  O18   0.020
 L3L  plan-2  H1    0.020
 L3L  plan-2  H2    0.020
 L3L  plan-2  H3    0.020

