# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 03:07:38 2020
#   Inital geometry file: a 155 line input string
#   Ligand name: (2S)-2-[2-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)ethyl]-4-(4'-ethoxybiphenyl-4-yl)-4-oxobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1ccc(cc1)c2ccc(cc2)C(=O)C[C@H](CCN3C(=O)c4ccccc4C3=O)C(O)=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
 DEO  DEO  '(2S)-2-[2-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)ethyl]-4-(4'-ethoxybiphenyl-4-yl)-4-oxobutanoic acid'  ligand  59  35  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DEO
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
 DEO  N1    N  NR5    0  -0.596  -5.6489   0.1515   0.2461
 DEO  C1    C  CR5    0   0.575  -6.3153  -0.0266  -0.9545
 DEO  C2    C  CR56   0  -0.028  -7.1983  -1.2027  -0.7647
 DEO  C3    C  CR56   0  -0.029  -7.0092  -1.6726   0.5243
 DEO  C4    C  CR16   0  -0.297  -7.6933  -2.7680   1.0046
 DEO  C5    C  CR16   0  -0.242  -8.5890  -3.3896   0.1357
 DEO  C6    C  CR16   0  -0.242  -8.7793  -2.9176  -1.1597
 DEO  C7    C  CR16   0  -0.298  -8.0807  -1.8078  -1.6332
 DEO  C8    C  CR5    0   0.576  -6.0008  -0.8070   1.1812
 DEO  O1    O  O      0  -0.404  -5.5566  -0.8900   2.2991
 DEO  O2    O  O      0  -0.403  -6.1797   0.6582  -1.9375
 DEO  C9    C  CH2    0  -0.308  -4.6495   1.1782   0.4761
 DEO  C10   C  CH2    0  -0.435  -3.2508   0.6977   0.1078
 DEO  C11   C  CH1    0  -0.342  -2.1385   1.6703   0.5179
 DEO  C12   C  CH2    0  -0.572  -0.7942   0.9956   0.3081
 DEO  C13   C  C      0   0.382   0.3818   1.8217   0.7566
 DEO  O3    O  O      0  -0.402   0.2366   2.8893   1.3160
 DEO  C14   C  CR6    0  -0.027   1.7508   1.2748   0.5337
 DEO  C15   C  CR16   0  -0.249   2.8603   2.0158   0.9443
 DEO  C16   C  CR16   0  -0.305   4.1413   1.5266   0.7761
 DEO  C17   C  CR6    0   0.101   4.3656   0.2771   0.1884
 DEO  C18   C  CR16   0  -0.301   3.2537  -0.4578  -0.2283
 DEO  C19   C  CR16   0  -0.280   1.9700   0.0309  -0.0572
 DEO  C20   C  CR6    0   0.071   5.7312  -0.2492   0.0215
 DEO  C21   C  CR16   0  -0.294   5.9930  -1.6216   0.0962
 DEO  C22   C  CR16   0  -0.333   7.2717  -2.1196  -0.0479
 DEO  C23   C  CR6    0   0.383   8.3460  -1.2556  -0.2765
 DEO  C24   C  CR16   0  -0.370   8.1045   0.1144  -0.3596
 DEO  C25   C  CR16   0  -0.297   6.8123   0.5982  -0.2092
 DEO  O4    O  O2     0  -0.469   9.5540  -1.8279  -0.4009
 DEO  C26   C  CH2    0  -0.189  10.6981  -1.0056  -0.5938
 DEO  C27   C  CH3    0  -0.682  11.9097  -1.9049  -0.6573
 DEO  C28   C  C      0   0.430  -2.2671   2.9855  -0.2766
 DEO  O5    O  OC    -1  -0.617  -3.0540   3.8395   0.1814
 DEO  O6    O  O      0  -0.609  -1.6165   3.0735  -1.3370
 DEO  H4    H  HCR6   0   0.275  -7.5460  -3.1339   2.0120
 DEO  H5    H  HCR6   0   0.278  -9.1454  -4.2540   0.4722
 DEO  H6    H  HCR6   0   0.278  -9.4823  -3.4216  -1.8090
 DEO  H7    H  HCR6   0   0.275  -8.2295  -1.4431  -2.6407
 DEO  H91   H  HCH2   0   0.257  -4.6950   1.4557   1.5291
 DEO  H92   H  HCH2   0   0.267  -4.9365   2.0570  -0.0965
 DEO  H101  H  HCH2   0   0.229  -3.1993   0.5104  -0.9694
 DEO  H102  H  HCH2   0   0.235  -3.0739  -0.2650   0.5974
 DEO  H11   H  HCH1   0   0.219  -2.2678   1.8909   1.5827
 DEO  H121  H  HCH2   0   0.261  -0.6625   0.7341  -0.7453
 DEO  H122  H  HCH2   0   0.266  -0.7549   0.0468   0.8567
 DEO  H15   H  HCR6   0   0.259   2.7188   2.9807   1.4130
 DEO  H16   H  HCR6   0   0.257   4.9783   2.1157   1.1291
 DEO  H18   H  HCR6   0   0.259   3.3881  -1.4179  -0.7099
 DEO  H19   H  HCR6   0   0.264   1.1388  -0.5734  -0.3959
 DEO  H21   H  HCR6   0   0.257   5.1881  -2.3184   0.2937
 DEO  H22   H  HCR6   0   0.264   7.4512  -3.1849   0.0257
 DEO  H24   H  HCR6   0   0.281   8.9031   0.8197  -0.5441
 DEO  H25   H  HCR6   0   0.259   6.6548   1.6660  -0.2954
 DEO  H261  H  HCH2   0   0.226  10.7945  -0.2928   0.2317
 DEO  H262  H  HCH2   0   0.226  10.5996  -0.4297  -1.5199
 DEO  H271  H  HCH3   0   0.238  12.8045  -1.2985  -0.7936
 DEO  H272  H  HCH3   0   0.235  12.0289  -2.4746   0.2645
 DEO  H273  H  HCH3   0   0.236  11.8457  -2.6014  -1.4930

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
 DEO  N1   C1    single    1.385  0.020  1.385
 DEO  N1   C8    single    1.385  0.020  1.385
 DEO  N1   C9    single    1.451  0.020  1.451
 DEO  C1   C2    single    1.483  0.020  1.483
 DEO  C1   O2    double    1.206  0.020  1.206
 DEO  C2   C3    aromatic  1.385  0.020  1.385
 DEO  C2   C7    aromatic  1.378  0.020  1.378
 DEO  C3   C4    aromatic  1.378  0.020  1.378
 DEO  C3   C8    single    1.482  0.020  1.482
 DEO  C4   C5    aromatic  1.394  0.020  1.394
 DEO  C4   H4    single    0.930  0.020  1.080
 DEO  C5   C6    aromatic  1.392  0.020  1.392
 DEO  C5   H5    single    0.930  0.020  1.080
 DEO  C6   C7    aromatic  1.394  0.020  1.394
 DEO  C6   H6    single    0.930  0.020  1.080
 DEO  C7   H7    single    0.930  0.020  1.080
 DEO  C8   O1    double    1.206  0.020  1.206
 DEO  C9   C10   single    1.524  0.020  1.524
 DEO  C9   H91   single    0.970  0.020  1.090
 DEO  C9   H92   single    0.970  0.020  1.090
 DEO  C10  C11   single    1.533  0.020  1.533
 DEO  C10  H101  single    0.970  0.020  1.090
 DEO  C10  H102  single    0.970  0.020  1.090
 DEO  C11  C12   single    1.519  0.020  1.519
 DEO  C11  C28   single    1.542  0.020  1.542
 DEO  C11  H11   single    0.970  0.020  1.090
 DEO  C12  C13   single    1.505  0.020  1.505
 DEO  C12  H121  single    0.970  0.020  1.090
 DEO  C12  H122  single    0.970  0.020  1.090
 DEO  C13  O3    double    1.214  0.020  1.214
 DEO  C13  C14   single    1.491  0.020  1.491
 DEO  C14  C15   aromatic  1.396  0.020  1.396
 DEO  C14  C19   aromatic  1.394  0.020  1.394
 DEO  C15  C16   aromatic  1.381  0.020  1.381
 DEO  C15  H15   single    0.930  0.020  1.080
 DEO  C16  C17   aromatic  1.399  0.020  1.399
 DEO  C16  H16   single    0.930  0.020  1.080
 DEO  C17  C18   aromatic  1.396  0.020  1.396
 DEO  C17  C20   single    1.473  0.020  1.473
 DEO  C18  C19   aromatic  1.384  0.020  1.384
 DEO  C18  H18   single    0.930  0.020  1.080
 DEO  C19  H19   single    0.930  0.020  1.080
 DEO  C20  C21   aromatic  1.399  0.020  1.399
 DEO  C20  C25   aromatic  1.393  0.020  1.393
 DEO  C21  C22   aromatic  1.380  0.020  1.380
 DEO  C21  H21   single    0.930  0.020  1.080
 DEO  C22  C23   aromatic  1.397  0.020  1.397
 DEO  C22  H22   single    0.930  0.020  1.080
 DEO  C23  C24   aromatic  1.394  0.020  1.394
 DEO  C23  O4    single    1.342  0.020  1.342
 DEO  C24  C25   aromatic  1.388  0.020  1.388
 DEO  C24  H24   single    0.930  0.020  1.080
 DEO  C25  H25   single    0.930  0.020  1.080
 DEO  O4   C26   single    1.422  0.020  1.422
 DEO  C26  C27   single    1.510  0.020  1.510
 DEO  C26  H261  single    0.970  0.020  1.090
 DEO  C26  H262  single    0.970  0.020  1.090
 DEO  C27  H271  single    0.970  0.020  1.090
 DEO  C27  H272  single    0.970  0.020  1.090
 DEO  C27  H273  single    0.970  0.020  1.090
 DEO  C28  O5    deloc     1.248  0.020  1.248
 DEO  C28  O6    deloc     1.247  0.020  1.247

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
 DEO  C9    N1   C8    123.90  3.000
 DEO  C9    N1   C1    124.05  3.000
 DEO  C8    N1   C1    111.97  3.000
 DEO  O2    C1   C2    128.45  3.000
 DEO  O2    C1   N1    125.43  3.000
 DEO  C2    C1   N1    106.12  3.000
 DEO  C7    C2   C3    121.67  3.000
 DEO  C7    C2   C1    130.46  3.000
 DEO  C3    C2   C1    107.87  3.000
 DEO  C8    C3   C4    130.35  3.000
 DEO  C8    C3   C2    107.89  3.000
 DEO  C4    C3   C2    121.76  3.000
 DEO  H4    C4   C5    121.13  3.000
 DEO  H4    C4   C3    121.72  3.000
 DEO  C5    C4   C3    117.14  3.000
 DEO  H5    C5   C6    119.35  3.000
 DEO  H5    C5   C4    119.53  3.000
 DEO  C6    C5   C4    121.11  3.000
 DEO  H6    C6   C7    119.52  3.000
 DEO  H6    C6   C5    119.32  3.000
 DEO  C7    C6   C5    121.16  3.000
 DEO  H7    C7   C6    121.05  3.000
 DEO  H7    C7   C2    121.80  3.000
 DEO  C6    C7   C2    117.15  3.000
 DEO  O1    C8   C3    128.41  3.000
 DEO  O1    C8   N1    125.46  3.000
 DEO  C3    C8   N1    106.13  3.000
 DEO  H92   C9   H91   106.98  3.000
 DEO  H92   C9   C10   111.70  3.000
 DEO  H91   C9   C10   110.62  3.000
 DEO  H92   C9   N1    107.85  3.000
 DEO  H91   C9   N1    107.73  3.000
 DEO  C10   C9   N1    111.76  3.000
 DEO  H102  C10  H101  106.39  3.000
 DEO  H102  C10  C11   108.72  3.000
 DEO  H101  C10  C11   109.73  3.000
 DEO  H102  C10  C9    108.52  3.000
 DEO  H101  C10  C9    109.58  3.000
 DEO  C11   C10  C9    113.64  3.000
 DEO  H11   C11  C28   108.62  3.000
 DEO  H11   C11  C12   109.17  3.000
 DEO  C28   C11  C12   112.43  3.000
 DEO  H11   C11  C10   107.59  3.000
 DEO  C28   C11  C10   110.04  3.000
 DEO  C12   C11  C10   108.87  3.000
 DEO  H122  C12  H121  105.71  3.000
 DEO  H122  C12  C13   107.32  3.000
 DEO  H121  C12  C13   108.91  3.000
 DEO  H122  C12  C11   110.31  3.000
 DEO  H121  C12  C11   110.24  3.000
 DEO  C13   C12  C11   113.99  3.000
 DEO  C14   C13  O3    120.08  3.000
 DEO  C14   C13  C12   118.13  3.000
 DEO  O3    C13  C12   121.76  3.000
 DEO  C19   C14  C15   118.24  3.000
 DEO  C19   C14  C13   122.33  3.000
 DEO  C15   C14  C13   119.41  3.000
 DEO  H15   C15  C16   119.33  3.000
 DEO  H15   C15  C14   119.79  3.000
 DEO  C16   C15  C14   120.88  3.000
 DEO  H16   C16  C17   119.93  3.000
 DEO  H16   C16  C15   118.98  3.000
 DEO  C17   C16  C15   121.07  3.000
 DEO  C20   C17  C18   121.09  3.000
 DEO  C20   C17  C16   121.03  3.000
 DEO  C18   C17  C16   117.89  3.000
 DEO  H18   C18  C19   118.90  3.000
 DEO  H18   C18  C17   120.04  3.000
 DEO  C19   C18  C17   121.05  3.000
 DEO  H19   C19  C18   118.46  3.000
 DEO  H19   C19  C14   120.67  3.000
 DEO  C18   C19  C14   120.87  3.000
 DEO  C25   C20  C21   117.41  3.000
 DEO  C25   C20  C17   121.40  3.000
 DEO  C21   C20  C17   121.19  3.000
 DEO  H21   C21  C22   118.40  3.000
 DEO  H21   C21  C20   120.12  3.000
 DEO  C22   C21  C20   121.46  3.000
 DEO  H22   C22  C23   119.47  3.000
 DEO  H22   C22  C21   120.10  3.000
 DEO  C23   C22  C21   120.42  3.000
 DEO  O4    C23  C24   124.72  3.000
 DEO  O4    C23  C22   116.32  3.000
 DEO  C24   C23  C22   118.96  3.000
 DEO  H24   C24  C25   118.60  3.000
 DEO  H24   C24  C23   121.56  3.000
 DEO  C25   C24  C23   119.84  3.000
 DEO  H25   C25  C24   118.07  3.000
 DEO  H25   C25  C20   120.02  3.000
 DEO  C24   C25  C20   121.91  3.000
 DEO  C26   O4   C23   119.34  3.000
 DEO  H262  C26  H261  107.65  3.000
 DEO  H262  C26  C27   110.48  3.000
 DEO  H261  C26  C27   110.41  3.000
 DEO  H262  C26  O4    110.27  3.000
 DEO  H261  C26  O4    110.18  3.000
 DEO  C27   C26  O4    107.87  3.000
 DEO  H273  C27  H272  108.72  3.000
 DEO  H273  C27  H271  107.94  3.000
 DEO  H272  C27  H271  107.87  3.000
 DEO  H273  C27  C26   111.45  3.000
 DEO  H272  C27  C26   111.31  3.000
 DEO  H271  C27  C26   109.43  3.000
 DEO  O6    C28  O5    126.34  3.000
 DEO  O6    C28  C11   117.05  3.000
 DEO  O5    C28  C11   116.56  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
 DEO  CONST_01  C5    C4   C3   C2      0.00   0.0  0
 DEO  CONST_02  C5    C6   C7   C2      0.00   0.0  0
 DEO  CONST_03  C6    C7   C2   C3      0.00   0.0  0
 DEO  CONST_04  C6    C5   C4   C3      0.00   0.0  0
 DEO  CONST_05  C7    C2   C3   C4      0.00   0.0  0
 DEO  CONST_06  C7    C6   C5   C4      0.00   0.0  0
 DEO  CONST_07  C17   C16  C15  C14     0.00   0.0  0
 DEO  CONST_08  C17   C18  C19  C14     0.00   0.0  0
 DEO  CONST_09  C18   C19  C14  C15     0.00   0.0  0
 DEO  CONST_10  C18   C17  C16  C15     0.00   0.0  0
 DEO  CONST_11  C20   C17  C16  C15   180.00   0.0  0
 DEO  CONST_12  C19   C14  C15  C16     0.00   0.0  0
 DEO  CONST_13  C19   C18  C17  C16     0.00   0.0  0
 DEO  CONST_16  C22   C21  C20  C17   180.00   0.0  0
 DEO  CONST_17  C24   C25  C20  C17   180.00   0.0  0
 DEO  CONST_20  C20   C17  C18  C19   180.00   0.0  0
 DEO  CONST_21  C23   C22  C21  C20     0.00   0.0  0
 DEO  CONST_22  C23   C24  C25  C20     0.00   0.0  0
 DEO  CONST_23  C24   C25  C20  C21     0.00   0.0  0
 DEO  CONST_24  C24   C23  C22  C21     0.00   0.0  0
 DEO  CONST_25  C25   C20  C21  C22     0.00   0.0  0
 DEO  CONST_26  C25   C24  C23  C22     0.00   0.0  0
 DEO  CONST_27  C8    N1   C1   C2      0.00   0.0  0
 DEO  CONST_28  C16   C15  C14  C13   180.00   0.0  0
 DEO  CONST_29  C18   C19  C14  C13   180.00   0.0  0
 DEO  CONST_30  O4    C23  C22  C21   180.00   0.0  0
 DEO  CONST_31  O4    C23  C24  C25   180.00   0.0  0
 DEO  CONST_32  C9    N1   C1   C2    180.00   0.0  0
 DEO  CONST_33  O2    C1   N1   C8    180.00   0.0  0
 DEO  CONST_34  H7    C7   C2   C1      0.00   0.0  0
 DEO  CONST_35  H4    C4   C3   C2    180.00   0.0  0
 DEO  CONST_36  H6    C6   C7   C2    180.00   0.0  0
 DEO  CONST_37  H5    C5   C4   C3    180.00   0.0  0
 DEO  CONST_38  H16   C16  C15  C14   180.00   0.0  0
 DEO  CONST_39  H18   C18  C19  C14   180.00   0.0  0
 DEO  CONST_40  H19   C19  C14  C15   180.00   0.0  0
 DEO  CONST_41  H15   C15  C16  C17   180.00   0.0  0
 DEO  CONST_42  H21   C21  C20  C17     0.00   0.0  0
 DEO  CONST_43  H25   C25  C20  C17     0.00   0.0  0
 DEO  CONST_44  H22   C22  C21  C20   180.00   0.0  0
 DEO  CONST_45  H24   C24  C25  C20   180.00   0.0  0
 DEO  CONST_46  C9    N1   C1   O2      0.00   0.0  0
 DEO  Var_01    C10   C9   N1   C1    -88.81  30.0  3
 DEO  Var_02    C15   C14  C13  C12  -179.73  30.0  2
 DEO  Var_03    C11   C10  C9   N1   -171.78  30.0  3
 DEO  Var_04    C14   C13  C12  C11  -177.15  30.0  3
 DEO  Var_05    C27   C26  O4   C23   178.29  30.0  3
 DEO  Var_06    H271  C27  C26  O4   -179.36  30.0  3

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
 DEO  chir_01  C11  C10  C12  C28  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
 DEO  plan-1  C13  0.020
 DEO  plan-1  C14  0.020
 DEO  plan-1  C15  0.020
 DEO  plan-1  C16  0.020
 DEO  plan-1  C17  0.020
 DEO  plan-1  C18  0.020
 DEO  plan-1  C19  0.020
 DEO  plan-1  C20  0.020
 DEO  plan-1  H15  0.020
 DEO  plan-1  H16  0.020
 DEO  plan-1  H18  0.020
 DEO  plan-1  H19  0.020
 DEO  plan-2  C17  0.020
 DEO  plan-2  C20  0.020
 DEO  plan-2  C21  0.020
 DEO  plan-2  C22  0.020
 DEO  plan-2  C23  0.020
 DEO  plan-2  C24  0.020
 DEO  plan-2  C25  0.020
 DEO  plan-2  O4   0.020
 DEO  plan-2  H21  0.020
 DEO  plan-2  H22  0.020
 DEO  plan-2  H24  0.020
 DEO  plan-2  H25  0.020
 DEO  plan-3  N1   0.020
 DEO  plan-3  C1   0.020
 DEO  plan-3  C2   0.020
 DEO  plan-3  C3   0.020
 DEO  plan-3  C4   0.020
 DEO  plan-3  C5   0.020
 DEO  plan-3  C6   0.020
 DEO  plan-3  C7   0.020
 DEO  plan-3  C8   0.020
 DEO  plan-3  O1   0.020
 DEO  plan-3  O2   0.020
 DEO  plan-3  C9   0.020
 DEO  plan-3  H4   0.020
 DEO  plan-3  H5   0.020
 DEO  plan-3  H6   0.020
 DEO  plan-3  H7   0.020
 DEO  plan-4  C12  0.020
 DEO  plan-4  C13  0.020
 DEO  plan-4  O3   0.020
 DEO  plan-4  C14  0.020
 DEO  plan-5  C11  0.020
 DEO  plan-5  C28  0.020
 DEO  plan-5  O5   0.020
 DEO  plan-5  O6   0.020

