# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 02:26:23 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 4-amino-2-[(3S)-2,6-dioxopiperidin-3-yl]-1H-isoindole-1,3(2H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc2C(=O)N([C@H]3CCC(=O)NC3=O)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
 Y70  Y70  4-amino-2-[(3S)-2,6-dioxopiperidin-3-yl]-1H-isoindole-1,3(2H)-dione  ligand  31  20  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y70
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
 Y70  C1    C  CR16  0  -0.325  -4.1206  -1.0786  -0.1604
 Y70  C2    C  CR16  0  -0.243  -4.4719   0.2211   0.1298
 Y70  C3    C  CR16  0  -0.343  -3.5130   1.2321   0.3081
 Y70  C4    C  CR56  0  -0.053  -2.2062   0.8480   0.1719
 Y70  C5    C  CR56  0  -0.104  -1.8260  -0.4596  -0.1232
 Y70  C6    C  CR6   0   0.343  -2.7665  -1.4777  -0.2990
 Y70  C7    C  CR5   0   0.589  -0.9720   1.6593   0.2889
 Y70  N8    N  NR5   0  -0.619   0.0810   0.7865   0.0539
 Y70  C9    C  CR5   0   0.617  -0.3702  -0.5065  -0.1994
 Y70  N10   N  NH2   0  -0.859  -2.4400  -2.7527  -0.5651
 Y70  O11   O  O     0  -0.431   0.3594  -1.4442  -0.4382
 Y70  C12   C  CH1   0  -0.235   1.4654   1.2075   0.0777
 Y70  O13   O  O     0  -0.404  -0.8588   2.8338   0.5343
 Y70  C14   C  CH2   0  -0.451   2.1357   1.0729   1.4374
 Y70  C15   C  C     0   0.556   2.2381   0.5002  -1.0311
 Y70  N16   N  NH1   0  -0.674   3.2532  -0.3349  -0.6371
 Y70  C17   C  C     0   0.552   3.4598  -0.8802   0.6171
 Y70  C18   C  CH2   0  -0.598   2.5921  -0.3470   1.7191
 Y70  O19   O  O     0  -0.416   2.0117   0.7094  -2.1987
 Y70  O20   O  O     0  -0.429   4.2987  -1.7379   0.7690
 Y70  H1    H  HCR6  0   0.280  -4.8972  -1.8228  -0.2864
 Y70  H2    H  HCR6  0   0.276  -5.5222   0.4631   0.2238
 Y70  H3    H  HCR6  0   0.268  -3.7988   2.2489   0.5380
 Y70  H101  H  HNH2  0   0.406  -3.1539  -3.4284  -0.7728
 Y70  H102  H  HNH2  0   0.404  -1.4876  -3.0232  -0.7336
 Y70  H12   H  HCH1  0   0.331   1.4673   2.2626  -0.2052
 Y70  H141  H  HCH2  0   0.270   3.0015   1.7382   1.4471
 Y70  H142  H  HCH2  0   0.283   1.4632   1.4250   2.2185
 Y70  H181  H  HCH2  0   0.299   3.1581  -0.3976   2.6489
 Y70  H182  H  HCH2  0   0.292   1.7443  -1.0269   1.8378
 Y70  H16   H  HNH1  0   0.418   3.8119  -0.7288  -1.3865

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
 Y70  C1   C2    aromatic  1.377  0.020  1.377
 Y70  C1   C6    aromatic  1.419  0.020  1.419
 Y70  C2   C3    aromatic  1.405  0.020  1.405
 Y70  C3   C4    aromatic  1.369  0.020  1.369
 Y70  C4   C5    aromatic  1.393  0.020  1.393
 Y70  C4   C7    single    1.482  0.020  1.482
 Y70  C5   C6    aromatic  1.397  0.020  1.397
 Y70  C5   C9    single    1.459  0.020  1.459
 Y70  C6   N10   single    1.343  0.020  1.343
 Y70  C7   N8    single    1.388  0.020  1.388
 Y70  C7   O13   double    1.205  0.020  1.205
 Y70  N8   C9    single    1.393  0.020  1.393
 Y70  N8   C12   single    1.447  0.020  1.447
 Y70  C9   O11   double    1.212  0.020  1.212
 Y70  C12  C14   single    1.522  0.020  1.522
 Y70  C12  C15   single    1.525  0.020  1.525
 Y70  C14  C18   single    1.518  0.020  1.518
 Y70  C15  N16   single    1.372  0.020  1.372
 Y70  C15  O19   double    1.208  0.020  1.208
 Y70  N16  C17   single    1.383  0.020  1.383
 Y70  C17  C18   single    1.501  0.020  1.501
 Y70  C17  O20   double    1.209  0.020  1.209
 Y70  C1   H1    single    0.930  0.020  1.080
 Y70  C2   H2    single    0.930  0.020  1.080
 Y70  C3   H3    single    0.930  0.020  1.080
 Y70  N10  H101  single    0.860  0.020  1.020
 Y70  N10  H102  single    0.860  0.020  1.020
 Y70  C12  H12   single    0.970  0.020  1.090
 Y70  C14  H141  single    0.970  0.020  1.090
 Y70  C14  H142  single    0.970  0.020  1.090
 Y70  C18  H181  single    0.970  0.020  1.090
 Y70  C18  H182  single    0.970  0.020  1.090
 Y70  N16  H16   single    0.860  0.020  1.020

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
 Y70  H1    C1   C6    118.67  3.000
 Y70  H1    C1   C2    119.35  3.000
 Y70  C6    C1   C2    121.98  3.000
 Y70  H2    C2   C3    119.38  3.000
 Y70  H2    C2   C1    118.49  3.000
 Y70  C3    C2   C1    122.13  3.000
 Y70  H3    C3   C4    122.51  3.000
 Y70  H3    C3   C2    121.57  3.000
 Y70  C4    C3   C2    115.91  3.000
 Y70  C7    C4   C5    107.66  3.000
 Y70  C7    C4   C3    129.32  3.000
 Y70  C5    C4   C3    123.02  3.000
 Y70  C9    C5   C6    129.93  3.000
 Y70  C9    C5   C4    108.27  3.000
 Y70  C6    C5   C4    121.79  3.000
 Y70  N10   C6   C5    123.59  3.000
 Y70  N10   C6   C1    121.24  3.000
 Y70  C5    C6   C1    115.17  3.000
 Y70  O13   C7   N8    125.18  3.000
 Y70  O13   C7   C4    128.90  3.000
 Y70  N8    C7   C4    105.92  3.000
 Y70  C12   N8   C9    125.66  3.000
 Y70  C12   N8   C7    122.70  3.000
 Y70  C9    N8   C7    111.64  3.000
 Y70  O11   C9   N8    124.00  3.000
 Y70  O11   C9   C5    129.50  3.000
 Y70  N8    C9   C5    106.50  3.000
 Y70  H102  N10  H101  117.26  3.000
 Y70  H102  N10  C6    121.30  3.000
 Y70  H101  N10  C6    120.45  3.000
 Y70  H12   C12  C15   104.99  3.000
 Y70  H12   C12  C14   108.43  3.000
 Y70  C15   C12  C14   112.66  3.000
 Y70  H12   C12  N8    106.16  3.000
 Y70  C15   C12  N8    109.74  3.000
 Y70  C14   C12  N8    114.23  3.000
 Y70  H142  C14  H141  106.63  3.000
 Y70  H142  C14  C18   110.79  3.000
 Y70  H141  C14  C18   109.26  3.000
 Y70  H142  C14  C12   109.88  3.000
 Y70  H141  C14  C12   107.65  3.000
 Y70  C18   C14  C12   112.40  3.000
 Y70  O19   C15  N16   121.45  3.000
 Y70  O19   C15  C12   121.84  3.000
 Y70  N16   C15  C12   116.63  3.000
 Y70  H16   N16  C17   115.75  3.000
 Y70  H16   N16  C15   115.57  3.000
 Y70  C17   N16  C15   127.65  3.000
 Y70  O20   C17  C18   124.12  3.000
 Y70  O20   C17  N16   119.81  3.000
 Y70  C18   C17  N16   116.07  3.000
 Y70  H182  C18  H181  106.34  3.000
 Y70  H182  C18  C17   107.89  3.000
 Y70  H181  C18  C17   108.04  3.000
 Y70  H182  C18  C14   111.64  3.000
 Y70  H181  C18  C14   110.98  3.000
 Y70  C17   C18  C14   111.71  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
 Y70  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 Y70  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 Y70  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 Y70  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 Y70  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 Y70  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 Y70  CONST_07  C9    N8   C7   C4     0.00   0.0  0
 Y70  CONST_08  C12   N8   C7   C4   180.00   0.0  0
 Y70  CONST_10  N10   C6   C1   C2   180.00   0.0  0
 Y70  CONST_11  N10   C6   C5   C4   180.00   0.0  0
 Y70  CONST_12  N10   C6   C5   C9     0.00   0.0  0
 Y70  CONST_13  O13   C7   N8   C9   180.00   0.0  0
 Y70  CONST_14  O13   C7   N8   C12    0.00   0.0  0
 Y70  CONST_15  O19   C15  N16  C17  180.00   0.0  0
 Y70  CONST_16  H3    C3   C2   C1   180.00   0.0  0
 Y70  CONST_17  H1    C1   C2   C3   180.00   0.0  0
 Y70  CONST_18  H2    C2   C3   C4   180.00   0.0  0
 Y70  CONST_19  H16   N16  C15  C12  180.00   0.0  0
 Y70  CONST_20  H101  N10  C6   C1     0.00   0.0  0
 Y70  CONST_21  H102  N10  C6   C1   180.00   0.0  0
 Y70  Var_01    C17   C18  C14  C12   53.50  30.0  1
 Y70  Var_02    N16   C17  C18  C14  -26.84  30.0  1
 Y70  Var_03    C18   C17  N16  C15   -9.46  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
 Y70  chir_01  C12  N8  C14  C15  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
 Y70  plan-1  C1    0.020
 Y70  plan-1  C2    0.020
 Y70  plan-1  C3    0.020
 Y70  plan-1  C4    0.020
 Y70  plan-1  C5    0.020
 Y70  plan-1  C6    0.020
 Y70  plan-1  C7    0.020
 Y70  plan-1  N8    0.020
 Y70  plan-1  C9    0.020
 Y70  plan-1  N10   0.020
 Y70  plan-1  O11   0.020
 Y70  plan-1  C12   0.020
 Y70  plan-1  O13   0.020
 Y70  plan-1  H1    0.020
 Y70  plan-1  H2    0.020
 Y70  plan-1  H3    0.020
 Y70  plan-2  C6    0.020
 Y70  plan-2  N10   0.020
 Y70  plan-2  H101  0.020
 Y70  plan-2  H102  0.020
 Y70  plan-3  N16   0.020
 Y70  plan-3  C17   0.020
 Y70  plan-3  C18   0.020
 Y70  plan-3  O20   0.020
 Y70  plan-4  C12   0.020
 Y70  plan-4  C15   0.020
 Y70  plan-4  N16   0.020
 Y70  plan-4  C17   0.020
 Y70  plan-4  O19   0.020
 Y70  plan-4  H16   0.020

