# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 11:20:31 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CC[C@H](N2Cc3c(OCc4ccc(CN5CCOCC5)cc4)cccc3C2=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
 8W7  8W7  (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione  ligand  60  33  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8W7
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
 8W7  C1   C  CR16  0  -0.247  -3.0409  -4.3419   0.3151
 8W7  C2   C  CR16  0  -0.383  -1.7783  -3.7478   0.2552
 8W7  C3   C  CR6   0   0.356  -1.6463  -2.3650   0.1361
 8W7  C4   C  CR16  0  -0.335  -4.2006  -3.5879   0.2582
 8W7  C5   C  CR56  0  -0.069  -4.0484  -2.2147   0.1379
 8W7  C6   C  CR56  0  -0.000  -2.8116  -1.6089   0.0784
 8W7  N1   N  NR5   0  -0.527  -4.4161   0.0161  -0.0773
 8W7  N2   N  NH1   0  -0.673  -3.5756   3.1552  -0.3646
 8W7  N3   N  NT    0  -0.419   6.3151   0.9150   0.0689
 8W7  C7   C  CH2   0  -0.294  -2.9698  -0.1308  -0.0643
 8W7  C8   C  CR5   0   0.581  -5.0824  -1.1660   0.0342
 8W7  C9   C  CH1   0  -0.221  -5.1381   1.2620  -0.2371
 8W7  C10  C  CH2   0  -0.457  -5.5620   1.8968   1.0802
 8W7  C11  C  CH2   0  -0.601  -4.3724   2.4473   1.8453
 8W7  C12  C  C     0   0.553  -3.5135   3.3480   1.0062
 8W7  C13  C  C     0   0.537  -4.2983   2.2214  -1.0656
 8W7  C14  C  CH2   0  -0.272   0.7288  -2.4369   0.0473
 8W7  C15  C  CR6   0   0.083   1.8562  -1.4617  -0.0923
 8W7  O2   O  O     0  -0.406  -4.2448   2.1670  -2.2715
 8W7  C22  C  CH2   0  -0.300   6.8624  -0.2208  -0.6509
 8W7  C23  C  CH2   0  -0.186   8.1429  -0.6902   0.0121
 8W7  O5   O  O2    0  -0.485   9.0958   0.3464   0.0994
 8W7  C24  C  CH2   0  -0.188   8.5702   1.4529   0.7989
 8W7  C25  C  CH2   0  -0.303   7.3037   1.9741   0.1477
 8W7  C20  C  CR6   0   0.078   3.9583   0.3780  -0.3657
 8W7  C19  C  CR16  0  -0.266   3.7228  -0.2551   0.8517
 8W7  C17  C  CR16  0  -0.288   2.6817  -1.1615   0.9865
 8W7  C18  C  CR16  0  -0.299   3.1313   0.0768  -1.4431
 8W7  C16  C  CR16  0  -0.270   2.0905  -0.8303  -1.3095
 8W7  O4   O  O2    0  -0.459  -0.4862  -1.6926   0.0689
 8W7  O3   O  O     0  -0.424  -2.7846   4.1999   1.4576
 8W7  H1   H  HCR6  0   0.269  -3.1004  -5.4183   0.4057
 8W7  H2   H  HCR6  0   0.294  -0.9078  -4.3877   0.3038
 8W7  H3   H  HCR6  0   0.258  -5.1787  -4.0478   0.3025
 8W7  H4   H  HNH1  0   0.421  -3.0032   3.7809  -0.9224
 8W7  H6   H  HCH2  0   0.276  -2.5056   0.4097   0.7654
 8W7  H7   H  HCH2  0   0.282  -2.5162   0.2323  -0.9913
 8W7  H8   H  HCH1  0   0.315  -6.0295   1.0475  -0.8298
 8W7  H9   H  HCH2  0   0.267  -6.2685   2.7016   0.8631
 8W7  H10  H  HCH2  0   0.282  -6.0984   1.1661   1.6843
 8W7  H11  H  HCH2  0   0.306  -4.6907   3.0101   2.7226
 8W7  H12  H  HCH2  0   0.292  -3.7406   1.6373   2.2233
 8W7  H13  H  HCH2  0   0.246   0.7194  -3.1374  -0.7943
 8W7  H14  H  HCH2  0   0.248   0.8336  -3.0207   0.9672
 8W7  H15  H  HCH2  0   0.246   6.1435  -1.0431  -0.6439
 8W7  H16  H  HCH2  0   0.198   7.0622   0.0287  -1.7078
 8W7  H17  H  HCH2  0   0.200   7.9105  -1.0844   1.0116
 8W7  H18  H  HCH2  0   0.236   8.5899  -1.4967  -0.5712
 8W7  H19  H  HCH2  0   0.200   8.3560   1.1811   1.8424
 8W7  H20  H  HCH2  0   0.237   9.3358   2.2298   0.8052
 8W7  H21  H  HCH2  0   0.197   7.5454   2.3868  -0.8473
 8W7  H22  H  HCH2  0   0.242   6.9094   2.7969   0.7498
 8W7  H23  H  HCH2  0   0.254   4.7861   2.3007   0.0168
 8W7  H24  H  HCH2  0   0.214   5.1836   1.6563  -1.5689
 8W7  H25  H  HCR6  0   0.247   4.3666  -0.0437   1.6963
 8W7  H26  H  HCR6  0   0.252   2.5141  -1.6447   1.9419
 8W7  H27  H  HCR6  0   0.251   3.3086   0.5495  -2.4020
 8W7  H28  H  HCR6  0   0.252   1.4666  -1.0588  -2.1658
 8W7  O1   O  O     0  -0.474  -6.2921  -1.3023   0.0384
 8W7  C21  C  CH2   0  -0.322   5.0722   1.3823  -0.5062

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
 8W7  C11  C10  single    1.518  0.020  1.518
 8W7  C11  C12  single    1.501  0.020  1.501
 8W7  C10  C9   single    1.522  0.020  1.522
 8W7  O3   C12  double    1.209  0.020  1.209
 8W7  C12  N2   single    1.386  0.020  1.386
 8W7  C9   N1   single    1.449  0.020  1.449
 8W7  C9   C13  single    1.521  0.020  1.521
 8W7  C7   N1   single    1.454  0.020  1.454
 8W7  C7   C6   single    1.493  0.020  1.493
 8W7  N1   C8   single    1.361  0.020  1.361
 8W7  O4   C3   single    1.343  0.020  1.343
 8W7  O4   C14  single    1.425  0.020  1.425
 8W7  C6   C3   aromatic  1.390  0.020  1.390
 8W7  C6   C5   aromatic  1.379  0.020  1.379
 8W7  C8   O1   double    1.217  0.020  1.217
 8W7  C8   C5   single    1.476  0.020  1.476
 8W7  C3   C2   aromatic  1.394  0.020  1.394
 8W7  C5   C4   aromatic  1.387  0.020  1.387
 8W7  C2   C1   aromatic  1.397  0.020  1.397
 8W7  C14  C15  single    1.497  0.020  1.497
 8W7  N2   C13  single    1.373  0.020  1.373
 8W7  C4   C1   aromatic  1.384  0.020  1.384
 8W7  C13  O2   double    1.208  0.020  1.208
 8W7  C15  C17  aromatic  1.391  0.020  1.391
 8W7  C15  C16  aromatic  1.391  0.020  1.391
 8W7  C17  C19  aromatic  1.387  0.020  1.387
 8W7  C16  C18  aromatic  1.387  0.020  1.387
 8W7  C19  C20  aromatic  1.392  0.020  1.392
 8W7  C18  C20  aromatic  1.391  0.020  1.391
 8W7  C20  C21  single    1.506  0.020  1.506
 8W7  C21  N3   single    1.447  0.020  1.447
 8W7  N3   C25  single    1.451  0.020  1.451
 8W7  N3   C22  single    1.452  0.020  1.452
 8W7  C25  C24  single    1.517  0.020  1.517
 8W7  C24  O5   single    1.411  0.020  1.411
 8W7  C22  C23  single    1.516  0.020  1.516
 8W7  C23  O5   single    1.411  0.020  1.411
 8W7  C1   H1   single    0.930  0.020  1.080
 8W7  C2   H2   single    0.930  0.020  1.080
 8W7  C4   H3   single    0.930  0.020  1.080
 8W7  N2   H4   single    0.860  0.020  1.020
 8W7  C7   H6   single    0.970  0.020  1.090
 8W7  C7   H7   single    0.970  0.020  1.090
 8W7  C9   H8   single    0.970  0.020  1.090
 8W7  C10  H9   single    0.970  0.020  1.090
 8W7  C10  H10  single    0.970  0.020  1.090
 8W7  C11  H11  single    0.970  0.020  1.090
 8W7  C11  H12  single    0.970  0.020  1.090
 8W7  C14  H13  single    0.970  0.020  1.090
 8W7  C14  H14  single    0.970  0.020  1.090
 8W7  C22  H15  single    0.970  0.020  1.090
 8W7  C22  H16  single    0.970  0.020  1.090
 8W7  C23  H17  single    0.970  0.020  1.090
 8W7  C23  H18  single    0.970  0.020  1.090
 8W7  C24  H19  single    0.970  0.020  1.090
 8W7  C24  H20  single    0.970  0.020  1.090
 8W7  C25  H21  single    0.970  0.020  1.090
 8W7  C25  H22  single    0.970  0.020  1.090
 8W7  C21  H23  single    0.970  0.020  1.090
 8W7  C21  H24  single    0.970  0.020  1.090
 8W7  C19  H25  single    0.930  0.020  1.080
 8W7  C17  H26  single    0.930  0.020  1.080
 8W7  C18  H27  single    0.930  0.020  1.080
 8W7  C16  H28  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
 8W7  H1   C1   C4   119.95  3.000
 8W7  H1   C1   C2   118.46  3.000
 8W7  C4   C1   C2   121.59  3.000
 8W7  H2   C2   C3   120.96  3.000
 8W7  H2   C2   C1   118.29  3.000
 8W7  C3   C2   C1   120.74  3.000
 8W7  O4   C3   C6   116.73  3.000
 8W7  C6   C3   C2   117.62  3.000
 8W7  O4   C3   C2   125.65  3.000
 8W7  H3   C4   C5   121.58  3.000
 8W7  H3   C4   C1   121.62  3.000
 8W7  C5   C4   C1   116.80  3.000
 8W7  C8   C5   C6   108.25  3.000
 8W7  C8   C5   C4   129.24  3.000
 8W7  C6   C5   C4   122.51  3.000
 8W7  C7   C6   C5   110.12  3.000
 8W7  C5   C6   C3   120.74  3.000
 8W7  C7   C6   C3   129.13  3.000
 8W7  C9   N1   C8   120.78  3.000
 8W7  C8   N1   C7   113.48  3.000
 8W7  C9   N1   C7   125.70  3.000
 8W7  H4   N2   C13  115.81  3.000
 8W7  H4   N2   C12  115.64  3.000
 8W7  C13  N2   C12  128.55  3.000
 8W7  C21  N3   C25  111.78  3.000
 8W7  C25  N3   C22  109.95  3.000
 8W7  C21  N3   C22  112.30  3.000
 8W7  H7   C7   H6   107.63  3.000
 8W7  H7   C7   N1   111.80  3.000
 8W7  H6   C7   N1   112.28  3.000
 8W7  H7   C7   C6   111.44  3.000
 8W7  H6   C7   C6   111.82  3.000
 8W7  N1   C7   C6   101.90  3.000
 8W7  O1   C8   N1   125.72  3.000
 8W7  O1   C8   C5   128.04  3.000
 8W7  N1   C8   C5   106.24  3.000
 8W7  H8   C9   C13  106.21  3.000
 8W7  H8   C9   C10  108.93  3.000
 8W7  C13  C9   C10  111.23  3.000
 8W7  H8   C9   N1   107.32  3.000
 8W7  C13  C9   N1   109.12  3.000
 8W7  C10  C9   N1   113.69  3.000
 8W7  H10  C10  H9   106.61  3.000
 8W7  H10  C10  C11  110.47  3.000
 8W7  H9   C10  C11  109.86  3.000
 8W7  H10  C10  C9   109.71  3.000
 8W7  H9   C10  C9   108.37  3.000
 8W7  C11  C10  C9   111.67  3.000
 8W7  H12  C11  H11  105.83  3.000
 8W7  H12  C11  C12  107.86  3.000
 8W7  H11  C11  C12  107.89  3.000
 8W7  H12  C11  C10  110.98  3.000
 8W7  H11  C11  C10  111.36  3.000
 8W7  C12  C11  C10  112.60  3.000
 8W7  O3   C12  C11  124.00  3.000
 8W7  O3   C12  N2   119.65  3.000
 8W7  C11  C12  N2   116.35  3.000
 8W7  O2   C13  C9   122.68  3.000
 8W7  O2   C13  N2   121.11  3.000
 8W7  C9   C13  N2   116.21  3.000
 8W7  H14  C14  H13  107.79  3.000
 8W7  H14  C14  O4   110.33  3.000
 8W7  H13  C14  O4   109.78  3.000
 8W7  H14  C14  C15  110.72  3.000
 8W7  H13  C14  C15  110.58  3.000
 8W7  O4   C14  C15  107.66  3.000
 8W7  C16  C15  C17  118.73  3.000
 8W7  C16  C15  C14  120.27  3.000
 8W7  C17  C15  C14  121.00  3.000
 8W7  H16  C22  H15  107.17  3.000
 8W7  H16  C22  C23  109.61  3.000
 8W7  H15  C22  C23  108.66  3.000
 8W7  H16  C22  N3   111.47  3.000
 8W7  H15  C22  N3   109.73  3.000
 8W7  C23  C22  N3   110.11  3.000
 8W7  H18  C23  H17  107.91  3.000
 8W7  H18  C23  O5   107.43  3.000
 8W7  H17  C23  O5   110.49  3.000
 8W7  H18  C23  C22  109.94  3.000
 8W7  H17  C23  C22  109.26  3.000
 8W7  O5   C23  C22  111.72  3.000
 8W7  C24  O5   C23  110.82  3.000
 8W7  H20  C24  H19  107.90  3.000
 8W7  H20  C24  C25  110.11  3.000
 8W7  H19  C24  C25  109.26  3.000
 8W7  H20  C24  O5   107.46  3.000
 8W7  H19  C24  O5   110.45  3.000
 8W7  C25  C24  O5   111.58  3.000
 8W7  H22  C25  H21  107.10  3.000
 8W7  H22  C25  C24  108.87  3.000
 8W7  H21  C25  C24  109.43  3.000
 8W7  H22  C25  N3   109.49  3.000
 8W7  H21  C25  N3   111.91  3.000
 8W7  C24  C25  N3   109.96  3.000
 8W7  C18  C20  C19  118.57  3.000
 8W7  C18  C20  C21  120.78  3.000
 8W7  C19  C20  C21  120.65  3.000
 8W7  H25  C19  C17  119.87  3.000
 8W7  H25  C19  C20  119.52  3.000
 8W7  C17  C19  C20  120.61  3.000
 8W7  H26  C17  C19  119.55  3.000
 8W7  H26  C17  C15  119.71  3.000
 8W7  C19  C17  C15  120.73  3.000
 8W7  H27  C18  C16  119.55  3.000
 8W7  H27  C18  C20  119.58  3.000
 8W7  C16  C18  C20  120.87  3.000
 8W7  H28  C16  C18  119.58  3.000
 8W7  H28  C16  C15  119.91  3.000
 8W7  C18  C16  C15  120.50  3.000
 8W7  C14  O4   C3   118.42  3.000
 8W7  H24  C21  H23  106.16  3.000
 8W7  H24  C21  C20  109.28  3.000
 8W7  H23  C21  C20  108.74  3.000
 8W7  H24  C21  N3   112.11  3.000
 8W7  H23  C21  N3   107.79  3.000
 8W7  C20  C21  N3   112.51  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
 8W7  CONST_01  C6   C3   C2   C1     0.00   0.0  0
 8W7  CONST_02  C6   C5   C4   C1     0.00   0.0  0
 8W7  CONST_03  C5   C6   C3   C2     0.00   0.0  0
 8W7  CONST_04  C5   C4   C1   C2     0.00   0.0  0
 8W7  CONST_05  C4   C5   C6   C3     0.00   0.0  0
 8W7  CONST_06  C4   C1   C2   C3     0.00   0.0  0
 8W7  CONST_07  C20  C19  C17  C15    0.00   0.0  0
 8W7  CONST_08  C20  C18  C16  C15    0.00   0.0  0
 8W7  CONST_09  C16  C15  C17  C19    0.00   0.0  0
 8W7  CONST_10  C16  C18  C20  C19    0.00   0.0  0
 8W7  CONST_11  C18  C16  C15  C17    0.00   0.0  0
 8W7  CONST_12  C18  C20  C19  C17    0.00   0.0  0
 8W7  CONST_13  C9   N1   C8   C5   180.00   0.0  0
 8W7  CONST_14  C7   N1   C8   C5     0.00   0.0  0
 8W7  CONST_15  C13  N2   C12  C11    0.00   0.0  0
 8W7  CONST_16  O4   C3   C2   C1   180.00   0.0  0
 8W7  CONST_17  O4   C3   C6   C5   180.00   0.0  0
 8W7  CONST_18  O4   C3   C6   C7     0.00   0.0  0
 8W7  CONST_19  C19  C17  C15  C14  180.00   0.0  0
 8W7  CONST_20  C18  C16  C15  C14  180.00   0.0  0
 8W7  CONST_21  C17  C19  C20  C21  180.00   0.0  0
 8W7  CONST_22  C16  C18  C20  C21  180.00   0.0  0
 8W7  CONST_23  C9   N1   C8   O1     0.00   0.0  0
 8W7  CONST_24  C7   N1   C8   O1   180.00   0.0  0
 8W7  CONST_25  O3   C12  N2   C13  180.00   0.0  0
 8W7  CONST_26  H3   C4   C1   C2   180.00   0.0  0
 8W7  CONST_27  H1   C1   C2   C3   180.00   0.0  0
 8W7  CONST_28  H2   C2   C1   C4   180.00   0.0  0
 8W7  CONST_29  H25  C19  C17  C15  180.00   0.0  0
 8W7  CONST_30  H27  C18  C16  C15  180.00   0.0  0
 8W7  CONST_31  H26  C17  C19  C20  180.00   0.0  0
 8W7  CONST_32  H28  C16  C18  C20  180.00   0.0  0
 8W7  CONST_33  H4   N2   C12  C11  180.00   0.0  0
 8W7  Var_01    C10  C11  C12  N2   -24.14  30.0  1
 8W7  Var_02    O5   C24  C25  N3    57.37  30.0  1
 8W7  Var_03    O5   C23  C22  N3   -56.77  30.0  1
 8W7  Var_04    C12  C11  C10  C9    51.45  30.0  1
 8W7  Var_05    C12  N2   C13  C9    -0.41  30.0  1
 8W7  Var_06    C24  C25  N3   C22  -56.52  30.0  1
 8W7  Var_07    C25  N3   C22  C23   56.25  30.0  1
 8W7  Var_08    C25  C24  O5   C23  -57.36  30.0  1
 8W7  Var_09    C19  C20  C21  N3    46.78  30.0  1
 8W7  Var_10    C20  C21  N3   C22   66.43  30.0  1
 8W7  Var_11    H6   C7   C6   C3   -60.65  30.0  1
 8W7  Var_12    C15  C14  O4   C3   177.45  30.0  3
 8W7  Var_13    O4   C14  C15  C17  106.01  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
 8W7  chir_01  C9  C10  N1  C13  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
 8W7  plan-1  C14  0.020
 8W7  plan-1  C15  0.020
 8W7  plan-1  C20  0.020
 8W7  plan-1  C19  0.020
 8W7  plan-1  C17  0.020
 8W7  plan-1  C18  0.020
 8W7  plan-1  C16  0.020
 8W7  plan-1  H25  0.020
 8W7  plan-1  H26  0.020
 8W7  plan-1  H27  0.020
 8W7  plan-1  H28  0.020
 8W7  plan-1  C21  0.020
 8W7  plan-2  C1   0.020
 8W7  plan-2  C2   0.020
 8W7  plan-2  C3   0.020
 8W7  plan-2  C4   0.020
 8W7  plan-2  C5   0.020
 8W7  plan-2  C6   0.020
 8W7  plan-2  N1   0.020
 8W7  plan-2  C7   0.020
 8W7  plan-2  C8   0.020
 8W7  plan-2  C9   0.020
 8W7  plan-2  O4   0.020
 8W7  plan-2  H1   0.020
 8W7  plan-2  H2   0.020
 8W7  plan-2  H3   0.020
 8W7  plan-2  O1   0.020
 8W7  plan-3  N2   0.020
 8W7  plan-3  C11  0.020
 8W7  plan-3  C12  0.020
 8W7  plan-3  C13  0.020
 8W7  plan-3  O3   0.020
 8W7  plan-3  H4   0.020
 8W7  plan-4  N2   0.020
 8W7  plan-4  C9   0.020
 8W7  plan-4  C13  0.020
 8W7  plan-4  O2   0.020

