# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 03:58:00 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: (3S)-3-(4-amino-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc2C(=O)N(Cc12)[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
 LVY  LVY  (3S)-3-(4-amino-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione  ligand  32  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 PERFECT
;

data_comp_LVY
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
 LVY  C1    C  CH1   0  -0.222   1.5200   1.1777  -0.0298
 LVY  C2    C  CH2   0  -0.456   2.2023   1.1066   1.3296
 LVY  C3    C  CH2   0  -0.602   2.5018  -0.3224   1.7430
 LVY  C4    C  C     0   0.552   3.2240  -1.0929   0.6761
 LVY  N5    N  NH1   0  -0.673   3.0652  -0.6408  -0.6238
 LVY  C6    C  C     0   0.537   2.2965   0.4012  -1.0816
 LVY  C7    C  CR56  0  -0.082  -2.1134   0.7656   0.1962
 LVY  C8    C  CR56  0   0.053  -1.7739  -0.5267  -0.1550
 LVY  C9    C  CH2   0  -0.301  -0.2915  -0.6337  -0.3176
 LVY  N10   N  NR5   0  -0.525   0.1471   0.7188  -0.0219
 LVY  C11   C  CR5   0   0.573  -0.8759   1.5654   0.2793
 LVY  C12   C  CR16  0  -0.258  -4.3977   0.1880   0.2742
 LVY  C13   C  CR16  0  -0.320  -4.0728  -1.1162  -0.0828
 LVY  C14   C  CR6   0   0.251  -2.7475  -1.5137  -0.3079
 LVY  C15   C  CR16  0  -0.344  -3.4204   1.1631   0.4220
 LVY  O16   O  O     0  -0.476  -0.7613   2.7454   0.5585
 LVY  N17   N  NH2   0  -0.860  -2.4181  -2.8152  -0.6036
 LVY  O18   O  O     0  -0.407   2.2377   0.6615  -2.2601
 LVY  O19   O  O     0  -0.425   3.9079  -2.0661   0.8916
 LVY  H1    H  HCH1  0   0.316   1.5123   2.2168  -0.3645
 LVY  H21C  H  HCH2  0   0.266   3.1317   1.6784   1.2748
 LVY  H22C  H  HCH2  0   0.281   1.5793   1.5960   2.0770
 LVY  H31C  H  HCH2  0   0.306   3.1121  -0.3502   2.6456
 LVY  H32C  H  HCH2  0   0.292   1.5833  -0.8651   1.9879
 LVY  H5    H  HNH1  0   0.421   3.5693  -1.1621  -1.3338
 LVY  H15   H  HCR6  0   0.253  -3.6675   2.1795   0.6971
 LVY  H91   H  HCH2  0   0.273   0.1406  -1.3681   0.3690
 LVY  H92   H  HCH2  0   0.279  -0.0134  -0.9322  -1.3342
 LVY  H12   H  HCR6  0   0.261  -5.4383   0.4388   0.4340
 LVY  H13   H  HCR6  0   0.266  -4.8655  -1.8470  -0.1908
 LVY  H171  H  HNH2  0   0.385  -1.5740  -2.9563  -1.1355
 LVY  H172  H  HNH2  0   0.386  -3.1714  -3.3888  -0.9483

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
 LVY  C1   C2    single    1.523  0.020  1.523
 LVY  C1   C6    single    1.520  0.020  1.520
 LVY  C1   N10   single    1.448  0.020  1.448
 LVY  C2   C3    single    1.517  0.020  1.517
 LVY  C3   C4    single    1.501  0.020  1.501
 LVY  C4   N5    single    1.385  0.020  1.385
 LVY  C4   O19   double    1.209  0.020  1.209
 LVY  N5   C6    single    1.373  0.020  1.373
 LVY  C6   O18   double    1.208  0.020  1.208
 LVY  C7   C8    aromatic  1.382  0.020  1.382
 LVY  C7   C11   single    1.476  0.020  1.476
 LVY  C7   C15   aromatic  1.385  0.020  1.385
 LVY  C8   C9    single    1.495  0.020  1.495
 LVY  C8   C14   aromatic  1.395  0.020  1.395
 LVY  C9   N10   single    1.452  0.020  1.452
 LVY  N10  C11   single    1.362  0.020  1.362
 LVY  C11  O16   double    1.218  0.020  1.218
 LVY  C12  C13   aromatic  1.391  0.020  1.391
 LVY  C12  C15   aromatic  1.388  0.020  1.388
 LVY  C13  C14   aromatic  1.402  0.020  1.402
 LVY  C14  N17   single    1.375  0.020  1.375
 LVY  C1   H1    single    0.970  0.020  1.090
 LVY  C2   H21C  single    0.970  0.020  1.090
 LVY  C2   H22C  single    0.970  0.020  1.090
 LVY  C3   H31C  single    0.970  0.020  1.090
 LVY  C3   H32C  single    0.970  0.020  1.090
 LVY  N5   H5    single    0.860  0.020  1.020
 LVY  C15  H15   single    0.930  0.020  1.080
 LVY  C9   H91   single    0.970  0.020  1.090
 LVY  C9   H92   single    0.970  0.020  1.090
 LVY  C12  H12   single    0.930  0.020  1.080
 LVY  C13  H13   single    0.930  0.020  1.080
 LVY  N17  H171  single    0.890  0.020  1.040
 LVY  N17  H172  single    0.890  0.020  1.040

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
 LVY  H1    C1   N10   107.26  3.000
 LVY  H1    C1   C6    106.12  3.000
 LVY  N10   C1   C6    109.04  3.000
 LVY  H1    C1   C2    108.74  3.000
 LVY  N10   C1   C2    113.91  3.000
 LVY  C6    C1   C2    111.40  3.000
 LVY  H22C  C2   H21C  106.61  3.000
 LVY  H22C  C2   C3    110.43  3.000
 LVY  H21C  C2   C3    109.79  3.000
 LVY  H22C  C2   C1    109.59  3.000
 LVY  H21C  C2   C1    108.17  3.000
 LVY  C3    C2   C1    112.07  3.000
 LVY  H32C  C3   H31C  105.78  3.000
 LVY  H32C  C3   C4    107.95  3.000
 LVY  H31C  C3   C4    107.83  3.000
 LVY  H32C  C3   C2    111.23  3.000
 LVY  H31C  C3   C2    111.11  3.000
 LVY  C4    C3   C2    112.62  3.000
 LVY  O19   C4   N5    119.66  3.000
 LVY  O19   C4   C3    123.96  3.000
 LVY  N5    C4   C3    116.37  3.000
 LVY  H5    N5   C6    115.76  3.000
 LVY  H5    N5   C4    115.59  3.000
 LVY  C6    N5   C4    128.64  3.000
 LVY  O18   C6   N5    121.05  3.000
 LVY  O18   C6   C1    122.67  3.000
 LVY  N5    C6   C1    116.28  3.000
 LVY  C15   C7   C11   128.81  3.000
 LVY  C15   C7   C8    122.81  3.000
 LVY  C11   C7   C8    108.37  3.000
 LVY  C14   C8   C9    129.01  3.000
 LVY  C14   C8   C7    121.22  3.000
 LVY  C9    C8   C7    109.77  3.000
 LVY  H92   C9   H91   107.40  3.000
 LVY  H92   C9   N10   111.47  3.000
 LVY  H91   C9   N10   112.21  3.000
 LVY  H92   C9   C8    111.85  3.000
 LVY  H91   C9   C8    111.80  3.000
 LVY  N10   C9   C8    102.16  3.000
 LVY  C11   N10  C9    113.40  3.000
 LVY  C11   N10  C1    121.11  3.000
 LVY  C9    N10  C1    125.49  3.000
 LVY  O16   C11  N10   125.62  3.000
 LVY  O16   C11  C7    128.09  3.000
 LVY  N10   C11  C7    106.29  3.000
 LVY  H12   C12  C15   119.89  3.000
 LVY  H12   C12  C13   118.68  3.000
 LVY  C15   C12  C13   121.43  3.000
 LVY  H13   C13  C14   118.97  3.000
 LVY  H13   C13  C12   119.16  3.000
 LVY  C14   C13  C12   121.87  3.000
 LVY  N17   C14  C13   121.97  3.000
 LVY  N17   C14  C8    121.76  3.000
 LVY  C13   C14  C8    116.21  3.000
 LVY  H15   C15  C12   121.75  3.000
 LVY  H15   C15  C7    121.80  3.000
 LVY  C12   C15  C7    116.45  3.000
 LVY  H172  N17  H171  111.47  3.000
 LVY  H172  N17  C14   115.68  3.000
 LVY  H171  N17  C14   116.54  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
 LVY  CONST_01  C13  C14  C8   C7     0.00   0.0  0
 LVY  CONST_02  C13  C12  C15  C7     0.00   0.0  0
 LVY  CONST_03  C12  C15  C7   C8     0.00   0.0  0
 LVY  CONST_04  C12  C13  C14  C8     0.00   0.0  0
 LVY  CONST_05  C15  C7   C8   C14    0.00   0.0  0
 LVY  CONST_06  C15  C12  C13  C14    0.00   0.0  0
 LVY  CONST_07  C7   C11  N10  C1   180.00   0.0  0
 LVY  CONST_08  C6   N5   C4   C3     0.00   0.0  0
 LVY  CONST_09  C9   N10  C11  C7     0.00   0.0  0
 LVY  CONST_10  N17  C14  C8   C7   180.00   0.0  0
 LVY  CONST_11  N17  C14  C8   C9     0.00   0.0  0
 LVY  CONST_12  N17  C14  C13  C12  180.00   0.0  0
 LVY  CONST_13  O16  C11  N10  C1     0.00   0.0  0
 LVY  CONST_14  O19  C4   N5   C6   180.00   0.0  0
 LVY  CONST_15  O16  C11  N10  C9   180.00   0.0  0
 LVY  CONST_16  H12  C12  C15  C7   180.00   0.0  0
 LVY  CONST_17  H15  C15  C7   C8   180.00   0.0  0
 LVY  CONST_18  H13  C13  C14  C8   180.00   0.0  0
 LVY  CONST_19  H5   N5   C4   C3   180.00   0.0  0
 LVY  Var_01    C4   C3   C2   C1    50.90  30.0  1
 LVY  Var_02    C4   N5   C6   C1     0.56  30.0  1
 LVY  Var_03    N5   C4   C3   C2   -23.84  30.0  1
 LVY  Var_04    H91  C9   N10  C1    59.92  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
 LVY  chir_01  C1  C2  C6  N10  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
 LVY  plan-1  C14   0.020
 LVY  plan-1  N17   0.020
 LVY  plan-1  H171  0.020
 LVY  plan-1  H172  0.020
 LVY  plan-2  C1    0.020
 LVY  plan-2  N5    0.020
 LVY  plan-2  C6    0.020
 LVY  plan-2  O18   0.020
 LVY  plan-3  C3    0.020
 LVY  plan-3  C4    0.020
 LVY  plan-3  N5    0.020
 LVY  plan-3  C6    0.020
 LVY  plan-3  O19   0.020
 LVY  plan-3  H5    0.020
 LVY  plan-4  C1    0.020
 LVY  plan-4  C7    0.020
 LVY  plan-4  C8    0.020
 LVY  plan-4  C9    0.020
 LVY  plan-4  N10   0.020
 LVY  plan-4  C11   0.020
 LVY  plan-4  C12   0.020
 LVY  plan-4  C13   0.020
 LVY  plan-4  C14   0.020
 LVY  plan-4  C15   0.020
 LVY  plan-4  O16   0.020
 LVY  plan-4  N17   0.020
 LVY  plan-4  H15   0.020
 LVY  plan-4  H12   0.020
 LVY  plan-4  H13   0.020

