# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 22:35:07 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  60  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  -0.600  -5.6362   0.1027   0.2325
 DEO  C1    C  CR5   0   0.578  -6.3113  -0.0653  -0.9666
 DEO  C2    C  CR56  0  -0.027  -7.2024  -1.2338  -0.7738
 DEO  C3    C  CR56  0  -0.029  -7.0101  -1.7095   0.5129
 DEO  C4    C  CR16  0  -0.296  -7.7012  -2.8006   0.9932
 DEO  C5    C  CR16  0  -0.241  -8.6070  -3.4114   0.1272
 DEO  C6    C  CR16  0  -0.241  -8.8003  -2.9335  -1.1657
 DEO  C7    C  CR16  0  -0.296  -8.0947  -1.8285  -1.6395
 DEO  C8    C  CR5   0   0.579  -5.9908  -0.8567   1.1683
 DEO  O1    O  O     0  -0.400  -5.5390  -0.9448   2.2818
 DEO  O2    O  O     0  -0.400  -6.1729   0.6236  -1.9455
 DEO  C9    C  CH2   0  -0.315  -4.6343   1.1219   0.4602
 DEO  C10   C  CH2   0  -0.440  -3.2449   0.6408   0.0562
 DEO  C11   C  CH1   0  -0.367  -2.1197   1.6122   0.4420
 DEO  C12   C  CH2   0  -0.582  -0.7725   0.9633   0.1577
 DEO  C13   C  C     0   0.385   0.3989   1.8386   0.5273
 DEO  O3    O  O     0  -0.398   0.2233   2.9696   0.9341
 DEO  C14   C  CR6   0  -0.026   1.7665   1.2799   0.3883
 DEO  C15   C  CR16  0  -0.245   2.8646   2.0430   0.7897
 DEO  C16   C  CR16  0  -0.305   4.1483   1.5469   0.6752
 DEO  C17   C  CR6   0   0.105   4.3864   0.2740   0.1451
 DEO  C18   C  CR16  0  -0.301   3.2845  -0.4826  -0.2608
 DEO  C19   C  CR16  0  -0.277   1.9971   0.0086  -0.1363
 DEO  C20   C  CR6   0   0.070   5.7562  -0.2514   0.0193
 DEO  C21   C  CR16  0  -0.293   6.0230  -1.6197   0.1406
 DEO  C22   C  CR16  0  -0.333   7.3053  -2.1158   0.0273
 DEO  C23   C  CR6   0   0.384   8.3784  -1.2543  -0.2165
 DEO  C24   C  CR16  0  -0.370   8.1323   0.1116  -0.3430
 DEO  C25   C  CR16  0  -0.296   6.8366   0.5937  -0.2233
 DEO  O4    O  O2    0  -0.468   9.5894  -1.8247  -0.3119
 DEO  C26   C  CH2   0  -0.190  10.7319  -1.0049  -0.5240
 DEO  C27   C  CH3   0  -0.682  11.9451  -1.9034  -0.5668
 DEO  C28   C  C     0   0.557  -2.2629   2.8993  -0.3370
 DEO  O5    O  OH1   0  -0.589  -2.8893   3.8481   0.3471
 DEO  O6    O  O     0  -0.445  -1.9019   3.0363  -1.4798
 DEO  H4    H  HCR6  0   0.276  -7.5516  -3.1713   1.9984
 DEO  H5    H  HCR6  0   0.279  -9.1690  -4.2720   0.4640
 DEO  H6    H  HCR6  0   0.279  -9.5112  -3.4294  -1.8126
 DEO  H7    H  HCR6  0   0.276  -8.2455  -1.4590  -2.6450
 DEO  H91   H  HCH2  0   0.274  -4.6564   1.3844   1.5178
 DEO  H92   H  HCH2  0   0.274  -4.9362   2.0086  -0.0963
 DEO  H101  H  HCH2  0   0.252  -3.2143   0.4458  -1.0188
 DEO  H102  H  HCH2  0   0.263  -3.0430  -0.3100   0.5549
 DEO  H11   H  HCH1  0   0.283  -2.2027   1.8282   1.5101
 DEO  H121  H  HCH2  0   0.287  -0.6922   0.6855  -0.8978
 DEO  H122  H  HCH2  0   0.295  -0.7007   0.0264   0.7174
 DEO  H15   H  HCR6  0   0.262   2.7116   3.0294   1.2074
 DEO  H16   H  HCR6  0   0.259   4.9767   2.1514   1.0217
 DEO  H18   H  HCR6  0   0.261   3.4302  -1.4612  -0.6994
 DEO  H19   H  HCR6  0   0.269   1.1740  -0.6112  -0.4671
 DEO  H21   H  HCR6  0   0.257   5.2191  -2.3141   0.3501
 DEO  H22   H  HCR6  0   0.265   7.4886  -3.1775   0.1354
 DEO  H24   H  HCR6  0   0.281   8.9302   0.8143  -0.5388
 DEO  H25   H  HCR6  0   0.260   6.6763   1.6577  -0.3447
 DEO  H261  H  HCH2  0   0.226  10.8268  -0.2728   0.2847
 DEO  H262  H  HCH2  0   0.226  10.6325  -0.4512  -1.4634
 DEO  H271  H  HCH3  0   0.238  12.8389  -1.2985  -0.7158
 DEO  H272  H  HCH3  0   0.235  12.0646  -2.4526   0.3672
 DEO  H273  H  HCH3  0   0.236  11.8823  -2.6180  -1.3872
 DEO  HO5   H  HOH1  0   0.479  -3.0026   4.6347  -0.2078

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    1.386  0.020  1.386
 DEO  N1   C8    single    1.386  0.020  1.386
 DEO  N1   C9    single    1.447  0.020  1.447
 DEO  C1   C2    single    1.482  0.020  1.482
 DEO  C1   O2    double    1.205  0.020  1.205
 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    1.205  0.020  1.205
 DEO  C9   C10   single    1.525  0.020  1.525
 DEO  C9   H91   single    0.970  0.020  1.090
 DEO  C9   H92   single    0.970  0.020  1.090
 DEO  C10  C11   single    1.536  0.020  1.536
 DEO  C10  H101  single    0.970  0.020  1.090
 DEO  C10  H102  single    0.970  0.020  1.090
 DEO  C11  C12   single    1.522  0.020  1.522
 DEO  C11  C28   single    1.511  0.020  1.511
 DEO  C11  H11   single    0.970  0.020  1.090
 DEO  C12  C13   single    1.508  0.020  1.508
 DEO  C12  H121  single    0.970  0.020  1.090
 DEO  C12  H122  single    0.970  0.020  1.090
 DEO  C13  O3    double    1.215  0.020  1.215
 DEO  C13  C14   single    1.484  0.020  1.484
 DEO  C14  C15   aromatic  1.396  0.020  1.396
 DEO  C14  C19   aromatic  1.395  0.020  1.395
 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  1.397  0.020  1.397
 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  1.398  0.020  1.398
 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    single    1.327  0.020  1.327
 DEO  C28  O6    double    1.206  0.020  1.206
 DEO  O5   HO5   single    0.850  0.020  0.980

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    123.93  3.000
 DEO  C9    N1   C1    123.96  3.000
 DEO  C8    N1   C1    112.05  3.000
 DEO  O2    C1   C2    128.72  3.000
 DEO  O2    C1   N1    125.27  3.000
 DEO  C2    C1   N1    106.01  3.000
 DEO  C7    C2   C3    121.68  3.000
 DEO  C7    C2   C1    130.38  3.000
 DEO  C3    C2   C1    107.94  3.000
 DEO  C8    C3   C4    130.28  3.000
 DEO  C8    C3   C2    107.98  3.000
 DEO  C4    C3   C2    121.74  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    119.36  3.000
 DEO  H5    C5   C4    119.52  3.000
 DEO  C6    C5   C4    121.12  3.000
 DEO  H6    C6   C7    119.53  3.000
 DEO  H6    C6   C5    119.30  3.000
 DEO  C7    C6   C5    121.16  3.000
 DEO  H7    C7   C6    121.06  3.000
 DEO  H7    C7   C2    121.79  3.000
 DEO  C6    C7   C2    117.15  3.000
 DEO  O1    C8   C3    128.65  3.000
 DEO  O1    C8   N1    125.35  3.000
 DEO  C3    C8   N1    106.00  3.000
 DEO  H92   C9   H91   107.10  3.000
 DEO  H92   C9   C10   111.96  3.000
 DEO  H91   C9   C10   110.58  3.000
 DEO  H92   C9   N1    107.51  3.000
 DEO  H91   C9   N1    107.95  3.000
 DEO  C10   C9   N1    111.52  3.000
 DEO  H102  C10  H101  106.77  3.000
 DEO  H102  C10  C11   107.48  3.000
 DEO  H101  C10  C11   109.84  3.000
 DEO  H102  C10  C9    108.79  3.000
 DEO  H101  C10  C9    110.02  3.000
 DEO  C11   C10  C9    113.67  3.000
 DEO  H11   C11  C28   109.16  3.000
 DEO  H11   C11  C12   109.51  3.000
 DEO  C28   C11  C12   110.53  3.000
 DEO  H11   C11  C10   108.35  3.000
 DEO  C28   C11  C10   109.86  3.000
 DEO  C12   C11  C10   109.39  3.000
 DEO  H122  C12  H121  105.74  3.000
 DEO  H122  C12  C13   108.71  3.000
 DEO  H121  C12  C13   109.06  3.000
 DEO  H122  C12  C11   109.13  3.000
 DEO  H121  C12  C11   110.69  3.000
 DEO  C13   C12  C11   113.22  3.000
 DEO  C14   C13  O3    121.01  3.000
 DEO  C14   C13  C12   118.32  3.000
 DEO  O3    C13  C12   120.67  3.000
 DEO  C19   C14  C15   118.45  3.000
 DEO  C19   C14  C13   122.07  3.000
 DEO  C15   C14  C13   119.49  3.000
 DEO  H15   C15  C16   119.40  3.000
 DEO  H15   C15  C14   119.87  3.000
 DEO  C16   C15  C14   120.72  3.000
 DEO  H16   C16  C17   119.94  3.000
 DEO  H16   C16  C15   118.96  3.000
 DEO  C17   C16  C15   121.09  3.000
 DEO  C20   C17  C18   121.05  3.000
 DEO  C20   C17  C16   121.01  3.000
 DEO  C18   C17  C16   117.94  3.000
 DEO  H18   C18  C19   118.86  3.000
 DEO  H18   C18  C17   120.09  3.000
 DEO  C19   C18  C17   121.04  3.000
 DEO  H19   C19  C18   118.49  3.000
 DEO  H19   C19  C14   120.75  3.000
 DEO  C18   C19  C14   120.76  3.000
 DEO  C25   C20  C21   117.42  3.000
 DEO  C25   C20  C17   121.33  3.000
 DEO  C21   C20  C17   121.25  3.000
 DEO  H21   C21  C22   118.38  3.000
 DEO  H21   C21  C20   120.16  3.000
 DEO  C22   C21  C20   121.45  3.000
 DEO  H22   C22  C23   119.46  3.000
 DEO  H22   C22  C21   120.12  3.000
 DEO  C23   C22  C21   120.42  3.000
 DEO  O4    C23  C24   124.72  3.000
 DEO  O4    C23  C22   116.31  3.000
 DEO  C24   C23  C22   118.97  3.000
 DEO  H24   C24  C25   118.61  3.000
 DEO  H24   C24  C23   121.55  3.000
 DEO  C25   C24  C23   119.84  3.000
 DEO  H25   C25  C24   118.03  3.000
 DEO  H25   C25  C20   120.06  3.000
 DEO  C24   C25  C20   121.90  3.000
 DEO  C26   O4   C23   119.38  3.000
 DEO  H262  C26  H261  107.66  3.000
 DEO  H262  C26  C27   110.45  3.000
 DEO  H261  C26  C27   110.43  3.000
 DEO  H262  C26  O4    110.28  3.000
 DEO  H261  C26  O4    110.18  3.000
 DEO  C27   C26  O4    107.86  3.000
 DEO  H273  C27  H272  108.72  3.000
 DEO  H273  C27  H271  107.96  3.000
 DEO  H272  C27  H271  107.87  3.000
 DEO  H273  C27  C26   111.42  3.000
 DEO  H272  C27  C26   111.32  3.000
 DEO  H271  C27  C26   109.43  3.000
 DEO  O6    C28  O5    123.27  3.000
 DEO  O6    C28  C11   123.83  3.000
 DEO  O5    C28  C11   112.83  3.000
 DEO  HO5   O5   C28   109.89  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  CONST_47  HO5   O5   C28  C11   180.00   0.0  0
 DEO  Var_01    C10   C9   N1   C1    -87.88  30.0  3
 DEO  Var_02    C15   C14  C13  C12  -176.65  30.0  2
 DEO  Var_03    C11   C10  C9   N1   -172.60  30.0  3
 DEO  Var_04    C14   C13  C12  C11   175.69  30.0  3
 DEO  Var_05    C27   C26  O4   C23   179.08  30.0  3
 DEO  Var_06    H271  C27  C26  O4   -179.27  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
 DEO  plan-5  HO5  0.020

