# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 01:14:44 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: [4-({(1S)-1-[(2,4-dichlorophenyl)carbamoyl]-1,3-dihydro-2H-isoindol-2-yl}methyl)-2-methylphenoxy]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(CN2Cc3ccccc3[C@H]2C(=O)Nc4ccc(Cl)cc4Cl)ccc1OCC(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
 3OZ  3OZ  '[4-({(1S)-1-[(2,4-dichlorophenyl)carbamoyl]-1,3-dihydro-2H-isoindol-2-yl}methyl)-2-methylphenoxy]acetic acid'  ligand  54  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3OZ
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
 3OZ  C1    C   CR6    0   0.440  -3.9837   0.6798  -0.3828
 3OZ  C2    C   CR6    0  -0.118  -4.4897   1.4797  -1.4073
 3OZ  C3    C   CR16   0  -0.294  -4.5639   0.7870   0.8783
 3OZ  C4    C   CR16   0  -0.172  -5.5408   2.3568  -1.1943
 3OZ  C5    C   CR16   0  -0.206  -5.6016   1.6702   1.1162
 3OZ  C6    C   CR6    0  -0.054  -6.0830   2.4490   0.0756
 3OZ  CL7   CL  CL     0  -0.113  -7.3856   3.5497   0.3594
 3OZ  CL8   CL  CL     0  -0.093  -3.7953   1.3856  -2.9869
 3OZ  N9    N   NH1    0  -0.745  -2.9384  -0.2144  -0.6322
 3OZ  C10   C   C      0   0.572  -1.8326  -0.3454   0.1507
 3OZ  C11   C   CR15   0  -0.328  -0.8868  -1.4523  -0.3041
 3OZ  O12   O   O      0  -0.441  -1.6381   0.3088   1.1525
 3OZ  C13   C   CR56   0   0.122  -1.2290  -2.7045   0.4706
 3OZ  C14   C   CR56   0   0.068  -0.2518  -2.9038   1.4333
 3OZ  C15   C   CH2    0  -0.333   0.7755  -1.8112   1.3335
 3OZ  N16   N   NR5    0  -0.414   0.4878  -1.1430   0.0592
 3OZ  C17   C   CH2    0  -0.352   1.4464  -1.4894  -0.9796
 3OZ  C18   C   CR16   0  -0.315  -2.3123  -3.5581   0.3539
 3OZ  C19   C   CR16   0  -0.258  -2.3952  -4.6418   1.2224
 3OZ  C20   C   CR16   0  -0.254  -1.4149  -4.8488   2.1883
 3OZ  C21   C   CR16   0  -0.321  -0.3356  -3.9780   2.3038
 3OZ  C22   C   CR6    0   0.007   5.2140  -1.0321  -0.5780
 3OZ  C23   C   CR6    0   0.340   5.2927   0.3477  -0.3352
 3OZ  C24   C   CR16   0  -0.348   3.9603  -1.5977  -0.7683
 3OZ  C25   C   CR16   0  -0.371   4.1265   1.1104  -0.2848
 3OZ  C26   C   CR6    0   0.089   2.7867  -0.8496  -0.7323
 3OZ  C27   C   CR16   0  -0.289   2.8896   0.5105  -0.4796
 3OZ  C30   C   CH2    0  -0.331   6.6834   2.2287   0.0704
 3OZ  C31   C   C      0   0.381   8.1656   2.5974   0.2456
 3OZ  O32   O   OC    -1  -0.625   8.3549   3.8182   0.4165
 3OZ  O33   O   O      0  -0.589   9.0097   1.6914   0.2089
 3OZ  H3    H   HCR6   0   0.287  -4.2139   0.1604   1.6856
 3OZ  H4    H   HCR6   0   0.305  -5.9162   2.9639  -2.0060
 3OZ  H5    H   HCR6   0   0.290  -6.0371   1.7374   2.1032
 3OZ  HN9   H   HNH1   0   0.411  -2.9483  -0.7022  -1.5154
 3OZ  H11   H   HCR5   0   0.294  -0.9808  -1.6030  -1.3840
 3OZ  H15   H   HCH2   0   0.256   0.6844  -1.1169   2.1730
 3OZ  H15A  H   HCH2   0   0.251   1.7982  -2.1934   1.3512
 3OZ  H17   H   HCH2   0   0.221   1.5779  -2.5778  -1.0916
 3OZ  H17A  H   HCH2   0   0.255   1.0494  -1.1276  -1.9319
 3OZ  H18   H   HCR6   0   0.252  -3.0760  -3.3981  -0.3973
 3OZ  H19   H   HCR6   0   0.257  -3.2262  -5.3307   1.1450
 3OZ  H20   H   HCR6   0   0.257  -1.4909  -5.6989   2.8539
 3OZ  H21   H   HCR6   0   0.253   0.4244  -4.1451   3.0574
 3OZ  H24   H   HCR6   0   0.239   3.8965  -2.6665  -0.9468
 3OZ  H25   H   HCR6   0   0.271   4.1642   2.1740  -0.0926
 3OZ  H27   H   HCR6   0   0.244   1.9941   1.1173  -0.4258
 3OZ  H28   H   HCH3   0   0.240   7.0377  -1.7893   0.2963
 3OZ  H28A  H   HCH3   0   0.237   6.2122  -2.9168  -0.7773
 3OZ  H28B  H   HCH3   0   0.240   7.1207  -1.5607  -1.4377
 3OZ  H30   H   HCH2   0   0.224   6.2684   2.8064  -0.7652
 3OZ  H30A  H   HCH2   0   0.224   6.1350   2.5358   0.9703
 3OZ  C28   C   CH3    0  -0.710   6.4589  -1.8669  -0.6255
 3OZ  O29   O   O2     0  -0.451   6.5306   0.8429  -0.1583

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
 3OZ  N9   C1    single    1.398  0.020  1.398
 3OZ  C3   C1    aromatic  1.392  0.020  1.392
 3OZ  C1   C2    aromatic  1.395  0.020  1.395
 3OZ  C2   CL8   single    1.728  0.020  1.728
 3OZ  C2   C4    aromatic  1.386  0.020  1.386
 3OZ  C3   C5    aromatic  1.383  0.020  1.383
 3OZ  C3   H3    single    0.930  0.020  1.080
 3OZ  C6   C4    aromatic  1.384  0.020  1.384
 3OZ  C4   H4    single    0.930  0.020  1.080
 3OZ  C5   C6    aromatic  1.386  0.020  1.386
 3OZ  C5   H5    single    0.930  0.020  1.080
 3OZ  C6   CL7   single    1.729  0.020  1.729
 3OZ  C10  N9    single    1.361  0.020  1.361
 3OZ  N9   HN9   single    0.860  0.020  1.020
 3OZ  C11  C10   single    1.525  0.020  1.525
 3OZ  O12  C10   double    1.212  0.020  1.212
 3OZ  C13  C11   single    1.512  0.020  1.512
 3OZ  C11  N16   single    1.455  0.020  1.455
 3OZ  C11  H11   single    0.970  0.020  1.090
 3OZ  C18  C13   aromatic  1.384  0.020  1.384
 3OZ  C14  C13   aromatic  1.386  0.020  1.386
 3OZ  C21  C14   aromatic  1.385  0.020  1.385
 3OZ  C14  C15   single    1.503  0.020  1.503
 3OZ  C15  N16   single    1.467  0.020  1.467
 3OZ  C15  H15   single    0.970  0.020  1.090
 3OZ  C15  H15A  single    0.970  0.020  1.090
 3OZ  N16  C17   single    1.455  0.020  1.455
 3OZ  C17  C26   single    1.506  0.020  1.506
 3OZ  C17  H17   single    0.970  0.020  1.090
 3OZ  C17  H17A  single    0.970  0.020  1.090
 3OZ  C19  C18   aromatic  1.391  0.020  1.391
 3OZ  C18  H18   single    0.930  0.020  1.080
 3OZ  C20  C19   aromatic  1.392  0.020  1.392
 3OZ  C19  H19   single    0.930  0.020  1.080
 3OZ  C20  C21   aromatic  1.392  0.020  1.392
 3OZ  C20  H20   single    0.930  0.020  1.080
 3OZ  C21  H21   single    0.930  0.020  1.080
 3OZ  C24  C22   aromatic  1.388  0.020  1.388
 3OZ  C23  C22   aromatic  1.403  0.020  1.403
 3OZ  C22  C28   single    1.500  0.020  1.500
 3OZ  C25  C23   aromatic  1.394  0.020  1.394
 3OZ  C23  O29   single    1.345  0.020  1.345
 3OZ  C26  C24   aromatic  1.392  0.020  1.392
 3OZ  C24  H24   single    0.930  0.020  1.080
 3OZ  C27  C25   aromatic  1.388  0.020  1.388
 3OZ  C25  H25   single    0.930  0.020  1.080
 3OZ  C27  C26   aromatic  1.387  0.020  1.387
 3OZ  C27  H27   single    0.930  0.020  1.080
 3OZ  C28  H28   single    0.970  0.020  1.090
 3OZ  C28  H28A  single    0.970  0.020  1.090
 3OZ  C28  H28B  single    0.970  0.020  1.090
 3OZ  O29  C30   single    1.413  0.020  1.413
 3OZ  C31  C30   single    1.537  0.020  1.537
 3OZ  C30  H30   single    0.970  0.020  1.090
 3OZ  C30  H30A  single    0.970  0.020  1.090
 3OZ  O33  C31   deloc     1.239  0.020  1.239
 3OZ  O32  C31   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
 3OZ  N9    C1   C3    121.49  3.000
 3OZ  C3    C1   C2    118.03  3.000
 3OZ  N9    C1   C2    120.47  3.000
 3OZ  CL8   C2   C4    118.68  3.000
 3OZ  C4    C2   C1    121.69  3.000
 3OZ  CL8   C2   C1    119.63  3.000
 3OZ  H3    C3   C5    119.01  3.000
 3OZ  H3    C3   C1    119.82  3.000
 3OZ  C5    C3   C1    121.17  3.000
 3OZ  H4    C4   C6    121.04  3.000
 3OZ  H4    C4   C2    120.24  3.000
 3OZ  C6    C4   C2    118.72  3.000
 3OZ  H5    C5   C6    120.71  3.000
 3OZ  H5    C5   C3    119.93  3.000
 3OZ  C6    C5   C3    119.35  3.000
 3OZ  CL7   C6   C5    119.75  3.000
 3OZ  CL7   C6   C4    119.22  3.000
 3OZ  C5    C6   C4    121.03  3.000
 3OZ  HN9   N9   C10   117.70  3.000
 3OZ  HN9   N9   C1    117.26  3.000
 3OZ  C10   N9   C1    124.50  3.000
 3OZ  O12   C10  C11   122.59  3.000
 3OZ  O12   C10  N9    123.62  3.000
 3OZ  C11   C10  N9    113.71  3.000
 3OZ  H11   C11  N16   110.90  3.000
 3OZ  H11   C11  C13   111.85  3.000
 3OZ  N16   C11  C13   105.19  3.000
 3OZ  H11   C11  C10   109.93  3.000
 3OZ  N16   C11  C10   110.92  3.000
 3OZ  C13   C11  C10   107.93  3.000
 3OZ  C18   C13  C14   121.44  3.000
 3OZ  C14   C13  C11   108.39  3.000
 3OZ  C18   C13  C11   130.15  3.000
 3OZ  C21   C14  C15   130.30  3.000
 3OZ  C15   C14  C13   109.34  3.000
 3OZ  C21   C14  C13   120.36  3.000
 3OZ  H15A  C15  H15   106.73  3.000
 3OZ  H15A  C15  N16   110.92  3.000
 3OZ  H15   C15  N16   111.18  3.000
 3OZ  H15A  C15  C14   112.62  3.000
 3OZ  H15   C15  C14   110.72  3.000
 3OZ  N16   C15  C14   104.76  3.000
 3OZ  C17   N16  C15   112.48  3.000
 3OZ  C17   N16  C11   113.17  3.000
 3OZ  C15   N16  C11   107.77  3.000
 3OZ  H17A  C17  H17   106.36  3.000
 3OZ  H17A  C17  C26   109.00  3.000
 3OZ  H17   C17  C26   109.28  3.000
 3OZ  H17A  C17  N16   107.69  3.000
 3OZ  H17   C17  N16   112.72  3.000
 3OZ  C26   C17  N16   111.59  3.000
 3OZ  H18   C18  C19   120.40  3.000
 3OZ  H18   C18  C13   121.28  3.000
 3OZ  C19   C18  C13   118.32  3.000
 3OZ  H19   C19  C20   119.73  3.000
 3OZ  H19   C19  C18   119.80  3.000
 3OZ  C20   C19  C18   120.47  3.000
 3OZ  H20   C20  C21   119.66  3.000
 3OZ  H20   C20  C19   119.61  3.000
 3OZ  C21   C20  C19   120.72  3.000
 3OZ  H21   C21  C20   120.36  3.000
 3OZ  H21   C21  C14   120.96  3.000
 3OZ  C20   C21  C14   118.68  3.000
 3OZ  C28   C22  C24   121.22  3.000
 3OZ  C28   C22  C23   120.42  3.000
 3OZ  C24   C22  C23   118.36  3.000
 3OZ  O29   C23  C25   124.30  3.000
 3OZ  O29   C23  C22   115.88  3.000
 3OZ  C25   C23  C22   119.82  3.000
 3OZ  H24   C24  C26   118.93  3.000
 3OZ  H24   C24  C22   118.48  3.000
 3OZ  C26   C24  C22   122.59  3.000
 3OZ  H25   C25  C27   118.75  3.000
 3OZ  H25   C25  C23   121.01  3.000
 3OZ  C27   C25  C23   120.24  3.000
 3OZ  C27   C26  C24   117.97  3.000
 3OZ  C27   C26  C17   120.84  3.000
 3OZ  C24   C26  C17   121.18  3.000
 3OZ  H27   C27  C26   119.80  3.000
 3OZ  H27   C27  C25   119.18  3.000
 3OZ  C26   C27  C25   121.02  3.000
 3OZ  H30A  C30  H30   106.74  3.000
 3OZ  H30A  C30  C31   108.73  3.000
 3OZ  H30   C30  C31   108.97  3.000
 3OZ  H30A  C30  O29   110.68  3.000
 3OZ  H30   C30  O29   110.62  3.000
 3OZ  C31   C30  O29   110.98  3.000
 3OZ  O33   C31  O32   128.07  3.000
 3OZ  O32   C31  C30   113.37  3.000
 3OZ  O33   C31  C30   118.56  3.000
 3OZ  H28B  C28  H28A  107.70  3.000
 3OZ  H28B  C28  H28   106.68  3.000
 3OZ  H28A  C28  H28   107.84  3.000
 3OZ  H28B  C28  C22   111.76  3.000
 3OZ  H28A  C28  C22   110.67  3.000
 3OZ  H28   C28  C22   111.96  3.000
 3OZ  C30   O29  C23   118.82  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
 3OZ  CONST_01  C6   C5   C3   C1      0.00   0.0  0
 3OZ  CONST_02  C6   C4   C2   C1      0.00   0.0  0
 3OZ  CONST_03  C5   C3   C1   C2      0.00   0.0  0
 3OZ  CONST_04  C5   C6   C4   C2      0.00   0.0  0
 3OZ  CONST_05  C4   C2   C1   C3      0.00   0.0  0
 3OZ  CONST_06  C4   C6   C5   C3      0.00   0.0  0
 3OZ  CONST_07  C20  C19  C18  C13     0.00   0.0  0
 3OZ  CONST_08  C20  C21  C14  C13     0.00   0.0  0
 3OZ  CONST_09  C19  C18  C13  C14     0.00   0.0  0
 3OZ  CONST_10  C19  C20  C21  C14     0.00   0.0  0
 3OZ  CONST_11  C21  C14  C13  C18     0.00   0.0  0
 3OZ  CONST_12  C21  C20  C19  C18     0.00   0.0  0
 3OZ  CONST_13  C27  C26  C24  C22     0.00   0.0  0
 3OZ  CONST_14  C27  C25  C23  C22     0.00   0.0  0
 3OZ  CONST_15  C26  C24  C22  C23     0.00   0.0  0
 3OZ  CONST_16  C26  C27  C25  C23     0.00   0.0  0
 3OZ  CONST_17  C25  C23  C22  C24     0.00   0.0  0
 3OZ  CONST_18  C25  C27  C26  C24     0.00   0.0  0
 3OZ  CONST_19  CL7  C6   C4   C2    180.00   0.0  0
 3OZ  CONST_20  CL8  C2   C1   C3    180.00   0.0  0
 3OZ  CONST_21  CL7  C6   C5   C3    180.00   0.0  0
 3OZ  CONST_22  N9   C1   C2   C4    180.00   0.0  0
 3OZ  CONST_23  N9   C1   C3   C5    180.00   0.0  0
 3OZ  CONST_24  CL8  C2   C4   C6    180.00   0.0  0
 3OZ  CONST_25  C22  C24  C26  C17   180.00   0.0  0
 3OZ  CONST_26  C25  C27  C26  C17   180.00   0.0  0
 3OZ  CONST_27  O29  C23  C22  C24   180.00   0.0  0
 3OZ  CONST_28  C28  C22  C23  C25   180.00   0.0  0
 3OZ  CONST_29  C28  C22  C24  C26   180.00   0.0  0
 3OZ  CONST_30  O29  C23  C25  C27   180.00   0.0  0
 3OZ  CONST_31  H5   C5   C3   C1    180.00   0.0  0
 3OZ  CONST_32  H4   C4   C2   C1    180.00   0.0  0
 3OZ  CONST_33  H3   C3   C1   C2    180.00   0.0  0
 3OZ  CONST_34  H18  C18  C13  C11     0.00   0.0  0
 3OZ  CONST_35  H19  C19  C18  C13   180.00   0.0  0
 3OZ  CONST_36  H21  C21  C14  C13   180.00   0.0  0
 3OZ  CONST_37  H20  C20  C21  C14   180.00   0.0  0
 3OZ  CONST_38  H25  C25  C23  C22   180.00   0.0  0
 3OZ  CONST_39  H24  C24  C22  C23   180.00   0.0  0
 3OZ  CONST_40  H27  C27  C25  C23   180.00   0.0  0
 3OZ  CONST_41  C11  C10  N9   C1    180.00   0.0  0
 3OZ  CONST_45  O12  C10  N9   C1      0.00   0.0  0
 3OZ  Var_01    C14  C15  N16  C11    20.71  30.0  1
 3OZ  Var_02    N16  C15  C14  C13   -12.39  30.0  1
 3OZ  Var_03    C26  C17  N16  C11   165.48  30.0  3
 3OZ  Var_04    C24  C26  C17  N16   129.98  30.0  2
 3OZ  Var_05    H28  C28  C22  C23    57.03  30.0  2
 3OZ  Var_06    C31  C30  O29  C23  -179.94  30.0  3
 3OZ  Var_07    O33  C31  C30  O29    -1.97  30.0  2

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
 3OZ  chir_01  C11  C10  C13  N16  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
 3OZ  plan-1  C1   0.020
 3OZ  plan-1  C2   0.020
 3OZ  plan-1  C3   0.020
 3OZ  plan-1  C4   0.020
 3OZ  plan-1  C5   0.020
 3OZ  plan-1  C6   0.020
 3OZ  plan-1  CL7  0.020
 3OZ  plan-1  CL8  0.020
 3OZ  plan-1  N9   0.020
 3OZ  plan-1  H3   0.020
 3OZ  plan-1  H4   0.020
 3OZ  plan-1  H5   0.020
 3OZ  plan-2  C17  0.020
 3OZ  plan-2  C22  0.020
 3OZ  plan-2  C23  0.020
 3OZ  plan-2  C24  0.020
 3OZ  plan-2  C25  0.020
 3OZ  plan-2  C26  0.020
 3OZ  plan-2  C27  0.020
 3OZ  plan-2  H24  0.020
 3OZ  plan-2  H25  0.020
 3OZ  plan-2  H27  0.020
 3OZ  plan-2  C28  0.020
 3OZ  plan-2  O29  0.020
 3OZ  plan-3  C11  0.020
 3OZ  plan-3  C13  0.020
 3OZ  plan-3  C14  0.020
 3OZ  plan-3  C15  0.020
 3OZ  plan-3  C18  0.020
 3OZ  plan-3  C19  0.020
 3OZ  plan-3  C20  0.020
 3OZ  plan-3  C21  0.020
 3OZ  plan-3  H18  0.020
 3OZ  plan-3  H19  0.020
 3OZ  plan-3  H20  0.020
 3OZ  plan-3  H21  0.020
 3OZ  plan-4  C1   0.020
 3OZ  plan-4  N9   0.020
 3OZ  plan-4  C10  0.020
 3OZ  plan-4  C11  0.020
 3OZ  plan-4  O12  0.020
 3OZ  plan-4  HN9  0.020
 3OZ  plan-5  C30  0.020
 3OZ  plan-5  C31  0.020
 3OZ  plan-5  O32  0.020
 3OZ  plan-5  O33  0.020

