# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 23:16:45 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 2-[(3S)-2,6-dioxopiperidin-3-yl]-1H-isoindole-1,3(2H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CC[C@H](N2C(=O)c3ccccc3C2=O)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
 EF2  EF2  2-[(3S)-2,6-dioxopiperidin-3-yl]-1H-isoindole-1,3(2H)-dione  ligand  29  19  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_EF2
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
 EF2  O01   O  O     0  -0.414   1.2638   0.3828   2.0246
 EF2  C02   C  C     0   0.587   1.8670   0.1148   1.0145
 EF2  N03   N  NH1   0  -0.690   3.2062   0.3874   0.8853
 EF2  C04   C  C     0   0.556   4.0363   0.1101  -0.1856
 EF2  O05   O  O     0  -0.427   5.2123   0.3832  -0.1243
 EF2  C06   C  CH2   0  -0.596   3.3899  -0.5539  -1.3675
 EF2  C07   C  CH2   0  -0.460   1.9098  -0.2345  -1.4867
 EF2  C08   C  CH1   0  -0.240   1.2213  -0.5801  -0.1736
 EF2  N09   N  NR5   0  -0.617  -0.1932  -0.3275  -0.1707
 EF2  C11   C  CR16  0  -0.239  -4.5411   1.1729  -0.0918
 EF2  C12   C  CR16  0  -0.294  -3.2408   1.6669  -0.1782
 EF2  C13   C  CR56  0  -0.022  -2.2159   0.7456  -0.1546
 EF2  C14   C  CR56  0  -0.036  -2.4617  -0.6139  -0.0511
 EF2  C19   C  CR16  0  -0.293  -3.7428  -1.1149   0.0358
 EF2  C20   C  CR16  0  -0.239  -4.7880  -0.1931   0.0140
 EF2  C3    C  CR5   0   0.591  -1.1602  -1.3186  -0.0490
 EF2  C4    C  CR5   0   0.598  -0.7513   0.9434  -0.2229
 EF2  H03   H  HNH1  0   0.420   3.6488   0.8151   1.6916
 EF2  H08   H  HCH1  0   0.337   1.3463  -1.6548   0.0046
 EF2  H061  H  HCH2  0   0.300   3.9323  -0.2567  -2.2640
 EF2  H062  H  HCH2  0   0.297   3.5370  -1.6332  -1.2527
 EF2  H071  H  HCH2  0   0.271   1.7700   0.8188  -1.7318
 EF2  H072  H  HCH2  0   0.284   1.4668  -0.8197  -2.2914
 EF2  H11   H  HCR6  0   0.281  -5.3740   1.8624  -0.1068
 EF2  H12   H  HCR6  0   0.277  -3.0511   2.7287  -0.2597
 EF2  H20   H  HCR6  0   0.281  -5.8093  -0.5431   0.0805
 EF2  H19   H  HCR6  0   0.278  -3.9338  -2.1764   0.1178
 EF2  O16   O  O     0  -0.396  -0.1274   1.9694  -0.3089
 EF2  O18   O  O     0  -0.394  -0.9403  -2.4987   0.0370

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
 EF2  O01  C02   double    1.207  0.020  1.207
 EF2  C02  N03   single    1.373  0.020  1.373
 EF2  C02  C08   single    1.520  0.020  1.520
 EF2  N03  C04   single    1.383  0.020  1.383
 EF2  C04  O05   double    1.209  0.020  1.209
 EF2  C04  C06   single    1.502  0.020  1.502
 EF2  C06  C07   single    1.519  0.020  1.519
 EF2  C07  C08   single    1.522  0.020  1.522
 EF2  C08  N09   single    1.437  0.020  1.437
 EF2  N09  C3    single    1.390  0.020  1.390
 EF2  N09  C4    single    1.389  0.020  1.389
 EF2  C11  C12   aromatic  1.394  0.020  1.394
 EF2  C11  C20   aromatic  1.392  0.020  1.392
 EF2  C12  C13   aromatic  1.378  0.020  1.378
 EF2  C13  C14   aromatic  1.385  0.020  1.385
 EF2  C13  C4    single    1.479  0.020  1.479
 EF2  C14  C19   aromatic  1.378  0.020  1.378
 EF2  C14  C3    single    1.480  0.020  1.480
 EF2  O16  C4    double    1.204  0.020  1.204
 EF2  O18  C3    double    1.204  0.020  1.204
 EF2  C19  C20   aromatic  1.394  0.020  1.394
 EF2  N03  H03   single    0.860  0.020  1.020
 EF2  C08  H08   single    0.970  0.020  1.090
 EF2  C06  H061  single    0.970  0.020  1.090
 EF2  C06  H062  single    0.970  0.020  1.090
 EF2  C07  H071  single    0.970  0.020  1.090
 EF2  C07  H072  single    0.970  0.020  1.090
 EF2  C11  H11   single    0.930  0.020  1.080
 EF2  C12  H12   single    0.930  0.020  1.080
 EF2  C20  H20   single    0.930  0.020  1.080
 EF2  C19  H19   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
 EF2  C08   C02  N03   115.57  3.000
 EF2  C08   C02  O01   122.91  3.000
 EF2  N03   C02  O01   121.49  3.000
 EF2  H03   N03  C04   115.98  3.000
 EF2  H03   N03  C02   115.76  3.000
 EF2  C04   N03  C02   128.21  3.000
 EF2  C06   C04  O05   123.95  3.000
 EF2  C06   C04  N03   116.08  3.000
 EF2  O05   C04  N03   119.95  3.000
 EF2  H062  C06  H061  106.76  3.000
 EF2  H062  C06  C07   110.26  3.000
 EF2  H061  C06  C07   111.30  3.000
 EF2  H062  C06  C04   107.18  3.000
 EF2  H061  C06  C04   108.23  3.000
 EF2  C07   C06  C04   112.84  3.000
 EF2  H072  C07  H071  107.50  3.000
 EF2  H072  C07  C08   109.35  3.000
 EF2  H071  C07  C08   110.81  3.000
 EF2  H072  C07  C06   109.96  3.000
 EF2  H071  C07  C06   110.23  3.000
 EF2  C08   C07  C06   108.98  3.000
 EF2  H08   C08  N09   106.51  3.000
 EF2  H08   C08  C07   108.13  3.000
 EF2  N09   C08  C07   114.02  3.000
 EF2  H08   C08  C02   105.82  3.000
 EF2  N09   C08  C02   109.65  3.000
 EF2  C07   C08  C02   112.22  3.000
 EF2  C4    N09  C3    112.10  3.000
 EF2  C4    N09  C08   123.80  3.000
 EF2  C3    N09  C08   124.03  3.000
 EF2  H11   C11  C20   119.34  3.000
 EF2  H11   C11  C12   119.45  3.000
 EF2  C20   C11  C12   121.20  3.000
 EF2  H12   C12  C13   121.80  3.000
 EF2  H12   C12  C11   121.08  3.000
 EF2  C13   C12  C11   117.12  3.000
 EF2  C4    C13  C14   108.07  3.000
 EF2  C4    C13  C12   130.24  3.000
 EF2  C14   C13  C12   121.68  3.000
 EF2  C3    C14  C19   130.10  3.000
 EF2  C3    C14  C13   108.14  3.000
 EF2  C19   C14  C13   121.76  3.000
 EF2  H19   C19  C20   121.18  3.000
 EF2  H19   C19  C14   121.71  3.000
 EF2  C20   C19  C14   117.11  3.000
 EF2  H20   C20  C19   119.55  3.000
 EF2  H20   C20  C11   119.32  3.000
 EF2  C19   C20  C11   121.14  3.000
 EF2  O18   C3   C14   128.88  3.000
 EF2  O18   C3   N09   125.33  3.000
 EF2  C14   C3   N09   105.79  3.000
 EF2  O16   C4   C13   129.07  3.000
 EF2  O16   C4   N09   125.05  3.000
 EF2  C13   C4   N09   105.88  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
 EF2  CONST_01  C14  C13  C12  C11    0.00   0.0  0
 EF2  CONST_02  C14  C19  C20  C11    0.00   0.0  0
 EF2  CONST_03  C19  C20  C11  C12    0.00   0.0  0
 EF2  CONST_04  C19  C14  C13  C12    0.00   0.0  0
 EF2  CONST_05  C20  C11  C12  C13    0.00   0.0  0
 EF2  CONST_06  C20  C19  C14  C13    0.00   0.0  0
 EF2  CONST_07  C08  C02  N03  C04    0.00   0.0  0
 EF2  CONST_08  C14  C3   N09  C08  180.00   0.0  0
 EF2  CONST_09  C4   N09  C3   C14    0.00   0.0  0
 EF2  CONST_10  C04  N03  C02  O01  180.00   0.0  0
 EF2  CONST_11  O18  C3   N09  C08    0.00   0.0  0
 EF2  CONST_12  C4   N09  C3   O18  180.00   0.0  0
 EF2  CONST_13  H19  C19  C20  C11  180.00   0.0  0
 EF2  CONST_14  H20  C20  C11  C12  180.00   0.0  0
 EF2  CONST_15  H11  C11  C12  C13  180.00   0.0  0
 EF2  CONST_16  H12  C12  C13  C14  180.00   0.0  0
 EF2  CONST_17  H03  N03  C02  C08  180.00   0.0  0
 EF2  Var_01    C06  C04  N03  C02    1.06  30.0  1
 EF2  Var_02    C07  C06  C04  N03   27.09  30.0  1
 EF2  Var_03    C08  C07  C06  C04  -54.18  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
 EF2  chir_01  C08  C02  C07  N09  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
 EF2  plan-1  C08  0.020
 EF2  plan-1  N09  0.020
 EF2  plan-1  C11  0.020
 EF2  plan-1  C12  0.020
 EF2  plan-1  C13  0.020
 EF2  plan-1  C14  0.020
 EF2  plan-1  C19  0.020
 EF2  plan-1  C20  0.020
 EF2  plan-1  C3   0.020
 EF2  plan-1  C4   0.020
 EF2  plan-1  H11  0.020
 EF2  plan-1  H12  0.020
 EF2  plan-1  H20  0.020
 EF2  plan-1  H19  0.020
 EF2  plan-1  O16  0.020
 EF2  plan-1  O18  0.020
 EF2  plan-2  O01  0.020
 EF2  plan-2  C02  0.020
 EF2  plan-2  N03  0.020
 EF2  plan-2  C04  0.020
 EF2  plan-2  C08  0.020
 EF2  plan-2  H03  0.020
 EF2  plan-3  N03  0.020
 EF2  plan-3  C04  0.020
 EF2  plan-3  O05  0.020
 EF2  plan-3  C06  0.020

