# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 15:21:30 2021
#   Inital geometry file: a 131 line input string
#   Ligand name: 2-(4-chlorophenyl)-N-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)-2,2-difluoroacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(C(=O)NCc1ccc2c(CN([C@H]3CCC(=O)NC3=O)C2=O)c1)c4ccc(Cl)cc4
#
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
 V4M  V4M  2-(4-chlorophenyl)-N-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)-2,2-difluoroacetamide  ligand  50  32  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_V4M
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
 V4M  C1   C   CR16  0  -0.290  -15.5168  129.6399  26.4850
 V4M  C2   C   CR6   0   0.089  -16.1907  130.7257  25.9117
 V4M  C3   C   CR16  0  -0.358  -17.4703  131.0568  26.3422
 V4M  C4   C   CR16  0  -0.290  -16.0947  128.8822  27.4881
 V4M  C5   C   CR56  0  -0.097  -17.3697  129.2295  27.9066
 V4M  C6   C   CR56  0   0.119  -18.0483  130.2922  27.3408
 V4M  N1   N   NR5   0  -0.517  -19.3550  129.3677  28.9843
 V4M  N2   N   NH1   0  -0.686  -22.7472  128.1060  29.4613
 V4M  N3   N   NH1   0  -0.635  -16.2867  132.4618  24.1320
 V4M  C7   C   CH2   0  -0.287  -19.3894  130.4227  27.9898
 V4M  C8   C   CR5   0   0.564  -18.2210  128.6153  28.9412
 V4M  C9   C   CH1   0  -0.214  -20.4892  129.0121  29.7777
 V4M  C10  C   CH2   0  -0.480  -21.2032  130.2016  30.4056
 V4M  C11  C   CH2   0  -0.589  -22.3337  129.6910  31.2826
 V4M  C12  C   C     0   0.555  -23.2707  128.7673  30.5557
 V4M  C13  C   C     0   0.573  -21.4652  128.1702  28.9675
 V4M  C14  C   CH2   0  -0.328  -15.4624  131.5297  24.8603
 V4M  C15  C   C     0   0.426  -17.0870  132.0640  23.1413
 V4M  O2   O   O     0  -0.414  -21.1490  127.5718  27.9679
 V4M  C16  C   CT    0   0.707  -17.8608  133.1741  22.4099
 V4M  C17  C   CR6   0  -0.073  -17.2703  133.4400  21.0572
 V4M  C18  C   CR16  0  -0.285  -16.2886  134.4117  20.9016
 V4M  C19  C   CR16  0  -0.193  -15.7144  134.6329  19.6598
 V4M  C20  C   CR6   0  -0.041  -16.1279  133.8717  18.5782
 V4M  C21  C   CR16  0  -0.194  -17.1005  132.8940  18.7191
 V4M  C22  C   CR16  0  -0.282  -17.6688  132.6791  19.9641
 V4M  F1   F   F     0  -0.324  -19.1472  132.7650  22.3030
 V4M  F2   F   F     0  -0.327  -17.8753  134.3139  23.1525
 V4M  O3   O   O     0  -0.431  -24.4183  128.5772  30.8863
 V4M  O4   O   O     0  -0.453  -17.2083  130.9181  22.7558
 V4M  CL1  CL  CL    0  -0.115  -15.4155  134.1438  17.0260
 V4M  H1   H   HCR6  0   0.261  -14.5212  129.3946  26.1352
 V4M  H2   H   HCR6  0   0.248  -18.0059  131.8953  25.9152
 V4M  H3   H   HCR6  0   0.261  -15.5650  128.0475  27.9291
 V4M  H4   H   HNH1  0   0.418  -23.3846  127.4933  28.9642
 V4M  H5   H   HNH1  0   0.423  -16.2800  133.4260  24.4226
 V4M  H6   H   HCH2  0   0.281  -19.5231  131.4054  28.4488
 V4M  H7   H   HCH2  0   0.278  -20.2042  130.2774  27.2747
 V4M  H8   H   HCH1  0   0.320  -20.1311  128.3662  30.5885
 V4M  H9   H   HCH2  0   0.285  -20.4969  130.7780  31.0020
 V4M  H10  H   HCH2  0   0.268  -21.6031  130.8662  29.6362
 V4M  H11  H   HCH2  0   0.300  -22.9191  130.5120  31.6947
 V4M  H12  H   HCH2  0   0.295  -21.9295  129.1350  32.1354
 V4M  H13  H   HCH2  0   0.274  -14.9701  130.8545  24.1584
 V4M  H14  H   HCH2  0   0.294  -14.6715  132.1088  25.3379
 V4M  H15  H   HCR6  0   0.280  -15.9561  135.0125  21.7374
 V4M  H16  H   HCR6  0   0.290  -14.9539  135.3921  19.5423
 V4M  H17  H   HCR6  0   0.289  -17.4145  132.3027  17.8702
 V4M  H18  H   HCR6  0   0.280  -18.4241  131.9124  20.0642
 V4M  O1   O   O     0  -0.475  -17.9767  127.6442  29.6348

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
 V4M  CL1  C20  single    1.729  0.020  1.729
 V4M  C20  C21  aromatic  1.386  0.020  1.386
 V4M  C20  C19  aromatic  1.386  0.020  1.386
 V4M  C21  C22  aromatic  1.385  0.020  1.385
 V4M  C19  C18  aromatic  1.386  0.020  1.386
 V4M  C22  C17  aromatic  1.390  0.020  1.390
 V4M  C18  C17  aromatic  1.390  0.020  1.390
 V4M  C17  C16  single    1.500  0.020  1.500
 V4M  C16  F1   single    1.354  0.020  1.354
 V4M  C16  F2   single    1.360  0.020  1.360
 V4M  C16  C15  single    1.538  0.020  1.538
 V4M  O4   C15  double    1.215  0.020  1.215
 V4M  C15  N3   single    1.334  0.020  1.334
 V4M  N3   C14  single    1.442  0.020  1.442
 V4M  C14  C2   single    1.511  0.020  1.511
 V4M  C2   C1   aromatic  1.401  0.020  1.401
 V4M  C2   C3   aromatic  1.390  0.020  1.390
 V4M  C1   C4   aromatic  1.384  0.020  1.384
 V4M  C3   C6   aromatic  1.384  0.020  1.384
 V4M  C4   C5   aromatic  1.386  0.020  1.386
 V4M  C6   C5   aromatic  1.382  0.020  1.382
 V4M  C6   C7   single    1.496  0.020  1.496
 V4M  O2   C13  double    1.207  0.020  1.207
 V4M  C5   C8   single    1.474  0.020  1.474
 V4M  C7   N1   single    1.450  0.020  1.450
 V4M  C13  N2   single    1.375  0.020  1.375
 V4M  C13  C9   single    1.522  0.020  1.522
 V4M  C8   N1   single    1.362  0.020  1.362
 V4M  C8   O1   double    1.218  0.020  1.218
 V4M  N1   C9   single    1.429  0.020  1.429
 V4M  N2   C12  single    1.382  0.020  1.382
 V4M  C9   C10  single    1.523  0.020  1.523
 V4M  C12  O3   double    1.209  0.020  1.209
 V4M  C12  C11  single    1.503  0.020  1.503
 V4M  C10  C11  single    1.519  0.020  1.519
 V4M  C1   H1   single    0.930  0.020  1.080
 V4M  C3   H2   single    0.930  0.020  1.080
 V4M  C4   H3   single    0.930  0.020  1.080
 V4M  N2   H4   single    0.860  0.020  1.020
 V4M  N3   H5   single    0.860  0.020  1.020
 V4M  C7   H6   single    0.970  0.020  1.090
 V4M  C7   H7   single    0.970  0.020  1.090
 V4M  C9   H8   single    0.970  0.020  1.090
 V4M  C10  H9   single    0.970  0.020  1.090
 V4M  C10  H10  single    0.970  0.020  1.090
 V4M  C11  H11  single    0.970  0.020  1.090
 V4M  C11  H12  single    0.970  0.020  1.090
 V4M  C14  H13  single    0.970  0.020  1.090
 V4M  C14  H14  single    0.970  0.020  1.090
 V4M  C18  H15  single    0.930  0.020  1.080
 V4M  C19  H16  single    0.930  0.020  1.080
 V4M  C21  H17  single    0.930  0.020  1.080
 V4M  C22  H18  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
 V4M  H1   C1   C4   119.60  3.000
 V4M  H1   C1   C2   119.05  3.000
 V4M  C4   C1   C2   121.35  3.000
 V4M  C14  C2   C3   122.17  3.000
 V4M  C3   C2   C1   120.05  3.000
 V4M  C14  C2   C1   117.74  3.000
 V4M  H2   C3   C6   120.38  3.000
 V4M  H2   C3   C2   121.18  3.000
 V4M  C6   C3   C2   118.44  3.000
 V4M  H3   C4   C5   121.35  3.000
 V4M  H3   C4   C1   120.88  3.000
 V4M  C5   C4   C1   117.77  3.000
 V4M  C8   C5   C6   108.92  3.000
 V4M  C8   C5   C4   129.70  3.000
 V4M  C6   C5   C4   121.38  3.000
 V4M  C7   C6   C5   109.25  3.000
 V4M  C7   C6   C3   129.74  3.000
 V4M  C5   C6   C3   121.00  3.000
 V4M  C9   N1   C8   122.76  3.000
 V4M  C9   N1   C7   122.88  3.000
 V4M  C8   N1   C7   113.58  3.000
 V4M  H4   N2   C13  115.98  3.000
 V4M  H4   N2   C12  116.05  3.000
 V4M  C13  N2   C12  127.97  3.000
 V4M  H5   N3   C15  120.25  3.000
 V4M  H5   N3   C14  118.00  3.000
 V4M  C15  N3   C14  121.68  3.000
 V4M  H7   C7   H6   107.64  3.000
 V4M  H7   C7   N1   111.68  3.000
 V4M  H6   C7   N1   111.66  3.000
 V4M  H7   C7   C6   111.88  3.000
 V4M  H6   C7   C6   111.74  3.000
 V4M  N1   C7   C6   102.29  3.000
 V4M  O1   C8   N1   126.12  3.000
 V4M  O1   C8   C5   128.03  3.000
 V4M  N1   C8   C5   105.85  3.000
 V4M  H8   C9   C13  106.09  3.000
 V4M  H8   C9   C10  107.95  3.000
 V4M  C13  C9   C10  110.54  3.000
 V4M  H8   C9   N1   107.33  3.000
 V4M  C10  C9   N1   114.00  3.000
 V4M  C13  C9   N1   110.55  3.000
 V4M  H10  C10  H9   107.52  3.000
 V4M  H10  C10  C11  109.79  3.000
 V4M  H9   C10  C11  110.14  3.000
 V4M  H10  C10  C9   110.88  3.000
 V4M  H9   C10  C9   109.58  3.000
 V4M  C11  C10  C9   108.93  3.000
 V4M  H12  C11  H11  106.64  3.000
 V4M  H12  C11  C12  107.13  3.000
 V4M  H11  C11  C12  108.13  3.000
 V4M  H12  C11  C10  110.21  3.000
 V4M  H11  C11  C10  111.40  3.000
 V4M  C12  C11  C10  113.03  3.000
 V4M  O3   C12  C11  123.77  3.000
 V4M  C11  C12  N2   116.17  3.000
 V4M  O3   C12  N2   120.06  3.000
 V4M  O2   C13  C9   123.15  3.000
 V4M  C9   C13  N2   115.62  3.000
 V4M  O2   C13  N2   121.22  3.000
 V4M  H14  C14  H13  106.44  3.000
 V4M  H14  C14  N3   107.01  3.000
 V4M  H13  C14  N3   109.45  3.000
 V4M  H14  C14  C2   109.11  3.000
 V4M  H13  C14  C2   109.62  3.000
 V4M  N3   C14  C2   114.84  3.000
 V4M  O4   C15  C16  118.66  3.000
 V4M  O4   C15  N3   125.21  3.000
 V4M  C16  C15  N3   116.08  3.000
 V4M  F2   C16  F1   106.62  3.000
 V4M  F2   C16  C17  110.37  3.000
 V4M  F1   C16  C17  110.88  3.000
 V4M  F2   C16  C15  110.52  3.000
 V4M  F1   C16  C15  107.30  3.000
 V4M  C17  C16  C15  111.02  3.000
 V4M  C22  C17  C18  119.80  3.000
 V4M  C18  C17  C16  120.20  3.000
 V4M  C22  C17  C16  119.95  3.000
 V4M  H15  C18  C19  118.44  3.000
 V4M  H15  C18  C17  121.25  3.000
 V4M  C19  C18  C17  120.30  3.000
 V4M  H16  C19  C20  120.72  3.000
 V4M  H16  C19  C18  120.07  3.000
 V4M  C20  C19  C18  119.21  3.000
 V4M  CL1  C20  C21  119.42  3.000
 V4M  C21  C20  C19  121.16  3.000
 V4M  CL1  C20  C19  119.42  3.000
 V4M  H17  C21  C22  120.11  3.000
 V4M  H17  C21  C20  120.64  3.000
 V4M  C22  C21  C20  119.25  3.000
 V4M  H18  C22  C21  118.68  3.000
 V4M  H18  C22  C17  121.05  3.000
 V4M  C21  C22  C17  120.27  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
 V4M  CONST_01  C6   C3   C2   C1     0.00   0.0  0
 V4M  CONST_02  C6   C5   C4   C1     0.00   0.0  0
 V4M  CONST_03  C5   C4   C1   C2     0.00   0.0  0
 V4M  CONST_04  C5   C6   C3   C2     0.00   0.0  0
 V4M  CONST_05  C4   C1   C2   C3     0.00   0.0  0
 V4M  CONST_06  C4   C5   C6   C3     0.00   0.0  0
 V4M  CONST_07  C20  C21  C22  C17    0.00   0.0  0
 V4M  CONST_08  C20  C19  C18  C17    0.00   0.0  0
 V4M  CONST_09  C21  C20  C19  C18    0.00   0.0  0
 V4M  CONST_10  C21  C22  C17  C18    0.00   0.0  0
 V4M  CONST_11  C22  C21  C20  C19    0.00   0.0  0
 V4M  CONST_12  C22  C17  C18  C19    0.00   0.0  0
 V4M  CONST_13  C7   N1   C8   C5     0.00   0.0  0
 V4M  CONST_14  C9   N1   C8   C5   180.00   0.0  0
 V4M  CONST_15  C13  N2   C12  C11    0.00   0.0  0
 V4M  CONST_16  C14  C2   C1   C4   180.00   0.0  0
 V4M  CONST_17  C14  C2   C3   C6   180.00   0.0  0
 V4M  CONST_18  C21  C22  C17  C16  180.00   0.0  0
 V4M  CONST_19  C19  C18  C17  C16  180.00   0.0  0
 V4M  CONST_20  CL1  C20  C19  C18  180.00   0.0  0
 V4M  CONST_21  CL1  C20  C21  C22  180.00   0.0  0
 V4M  CONST_22  C7   N1   C8   O1   180.00   0.0  0
 V4M  CONST_23  C9   N1   C8   O1     0.00   0.0  0
 V4M  CONST_24  O3   C12  N2   C13  180.00   0.0  0
 V4M  CONST_25  H2   C3   C2   C1   180.00   0.0  0
 V4M  CONST_26  H3   C4   C1   C2   180.00   0.0  0
 V4M  CONST_27  H1   C1   C2   C3   180.00   0.0  0
 V4M  CONST_28  H17  C21  C22  C17  180.00   0.0  0
 V4M  CONST_29  H16  C19  C18  C17  180.00   0.0  0
 V4M  CONST_30  H18  C22  C17  C18  180.00   0.0  0
 V4M  CONST_31  H15  C18  C19  C20  180.00   0.0  0
 V4M  CONST_32  H4   N2   C12  C11  180.00   0.0  0
 V4M  CONST_33  C16  C15  N3   C14  180.00   0.0  0
 V4M  CONST_34  O4   C15  N3   C14    0.00   0.0  0
 V4M  CONST_35  H5   N3   C15  C16    0.00   0.0  0
 V4M  Var_01    C10  C11  C12  N2    24.63  30.0  1
 V4M  Var_02    C12  N2   C13  C9     3.84  30.0  1
 V4M  Var_03    C12  C11  C10  C9   -53.80  30.0  1
 V4M  Var_04    H6   C7   C6   C3   -57.91  30.0  1
 V4M  Var_05    N3   C14  C2   C1   168.65  30.0  1
 V4M  Var_06    C22  C17  C16  C15   86.03  30.0  2
 V4M  Var_07    C15  N3   C14  C2   -78.68  30.0  2
 V4M  Var_08    C17  C16  C15  N3   105.43  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
 V4M  chir_01  C9  C13  N1  C10  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
 V4M  plan-1  C16  0.020
 V4M  plan-1  C17  0.020
 V4M  plan-1  C18  0.020
 V4M  plan-1  C19  0.020
 V4M  plan-1  C20  0.020
 V4M  plan-1  C21  0.020
 V4M  plan-1  C22  0.020
 V4M  plan-1  CL1  0.020
 V4M  plan-1  H15  0.020
 V4M  plan-1  H16  0.020
 V4M  plan-1  H17  0.020
 V4M  plan-1  H18  0.020
 V4M  plan-2  N3   0.020
 V4M  plan-2  C14  0.020
 V4M  plan-2  C15  0.020
 V4M  plan-2  C16  0.020
 V4M  plan-2  O4   0.020
 V4M  plan-2  H5   0.020
 V4M  plan-3  N2   0.020
 V4M  plan-3  C9   0.020
 V4M  plan-3  C13  0.020
 V4M  plan-3  O2   0.020
 V4M  plan-4  C1   0.020
 V4M  plan-4  C2   0.020
 V4M  plan-4  C3   0.020
 V4M  plan-4  C4   0.020
 V4M  plan-4  C5   0.020
 V4M  plan-4  C6   0.020
 V4M  plan-4  N1   0.020
 V4M  plan-4  C7   0.020
 V4M  plan-4  C8   0.020
 V4M  plan-4  C9   0.020
 V4M  plan-4  C14  0.020
 V4M  plan-4  H1   0.020
 V4M  plan-4  H2   0.020
 V4M  plan-4  H3   0.020
 V4M  plan-4  O1   0.020
 V4M  plan-5  N2   0.020
 V4M  plan-5  C11  0.020
 V4M  plan-5  C12  0.020
 V4M  plan-5  C13  0.020
 V4M  plan-5  O3   0.020
 V4M  plan-5  H4   0.020

