# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 10:42:08 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  55  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   0.439  -3.9832   0.6542  -0.4049
 3OZ  C2    C   CR6   0  -0.117  -4.4861   1.4477  -1.4355
 3OZ  C3    C   CR16  0  -0.293  -4.5634   0.7717   0.8551
 3OZ  C4    C   CR16  0  -0.172  -5.5360   2.3281  -1.2297
 3OZ  C5    C   CR16  0  -0.206  -5.5996   1.6586   1.0860
 3OZ  C6    C   CR6   0  -0.054  -6.0788   2.4303   0.0391
 3OZ  CL7   CL  CL    0  -0.113  -7.3801   3.5348   0.3137
 3OZ  CL8   CL  CL    0  -0.093  -3.7892   1.3412  -3.0129
 3OZ  N9    N   NH1   0  -0.745  -2.9394  -0.2446  -0.6461
 3OZ  C10   C   C     0   0.573  -1.8280  -0.3591   0.1309
 3OZ  C11   C   CR15  0  -0.329  -0.8847  -1.4748  -0.3074
 3OZ  O12   O   O     0  -0.441  -1.6267   0.3153   1.1179
 3OZ  C13   C   CR56  0   0.122  -1.2197  -2.7088   0.4991
 3OZ  C14   C   CR56  0   0.068  -0.2354  -2.8846   1.4591
 3OZ  C15   C   CH2   0  -0.332   0.7910  -1.7951   1.3256
 3OZ  N16   N   NR5   0  -0.415   0.4922  -1.1556   0.0392
 3OZ  C17   C   CH2   0  -0.350   1.4441  -1.5195  -0.9982
 3OZ  C18   C   CR16  0  -0.315  -2.3046  -3.5642   0.4127
 3OZ  C19   C   CR16  0  -0.258  -2.3816  -4.6252   1.3093
 3OZ  C20   C   CR16  0  -0.254  -1.3940  -4.8084   2.2726
 3OZ  C21   C   CR16  0  -0.321  -0.3131  -3.9361   2.3573
 3OZ  C22   C   CR6   0   0.015   5.2144  -1.0363  -0.6654
 3OZ  C23   C   CR6   0   0.339   5.2795   0.3406  -0.4192
 3OZ  C24   C   CR16  0  -0.348   3.9607  -1.6096  -0.8336
 3OZ  C25   C   CR16  0  -0.364   4.1151   1.0985  -0.3426
 3OZ  C26   C   CR6   0   0.092   2.7835  -0.8693  -0.7720
 3OZ  C27   C   CR16  0  -0.289   2.8790   0.4906  -0.5158
 3OZ  O29   O   O2    0  -0.456   6.5245   0.8474  -0.2623
 3OZ  C30   C   CH2   0  -0.293   6.6603   2.2177  -0.0205
 3OZ  C31   C   C     0   0.510   8.1324   2.5138   0.1306
 3OZ  O32   O   OH1   0  -0.592   8.3175   3.8092   0.3391
 3OZ  O33   O   O     0  -0.422   9.0110   1.6977   0.0744
 3OZ  H3    H   HCR6  0   0.287  -4.2146   0.1498   1.6666
 3OZ  H4    H   HCR6  0   0.305  -5.9099   2.9300  -2.0460
 3OZ  H5    H   HCR6  0   0.290  -6.0357   1.7342   2.0722
 3OZ  HN9   H   HNH1  0   0.411  -2.9568  -0.7508  -1.5187
 3OZ  H11   H   HCR5  0   0.294  -0.9866  -1.6502  -1.3831
 3OZ  H15   H   HCH2  0   0.256   0.7076  -1.0816   2.1497
 3OZ  H15A  H   HCH2  0   0.251   1.8136  -2.1778   1.3431
 3OZ  H17   H   HCH2  0   0.222   1.5798  -2.6090  -1.0904
 3OZ  H17A  H   HCH2  0   0.257   1.0420  -1.1770  -1.9554
 3OZ  H18   H   HCR6  0   0.253  -3.0740  -3.4215  -0.3362
 3OZ  H19   H   HCR6  0   0.257  -3.2141  -5.3145   1.2561
 3OZ  H20   H   HCR6  0   0.257  -1.4660  -5.6408   2.9605
 3OZ  H21   H   HCR6  0   0.253   0.4520  -4.0845   3.1096
 3OZ  H24   H   HCR6  0   0.243   3.9008  -2.6781  -1.0139
 3OZ  H25   H   HCR6  0   0.278   4.1479   2.1620  -0.1474
 3OZ  H27   H   HCR6  0   0.249   1.9799   1.0893  -0.4422
 3OZ  H28   H   HCH3  0   0.243   7.0603  -1.7816   0.1709
 3OZ  H28A  H   HCH3  0   0.241   6.2223  -2.9119  -0.8894
 3OZ  H28B  H   HCH3  0   0.243   7.1065  -1.5477  -1.5652
 3OZ  H30   H   HCH2  0   0.272   6.2574   2.8242  -0.8413
 3OZ  H30A  H   HCH2  0   0.273   6.1426   2.5301   0.8951
 3OZ  HO32  H   HOH1  0   0.490   9.2617   4.0026   0.4419
 3OZ  C28   C   CH3   0  -0.711   6.4647  -1.8608  -0.7398

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    1.454  0.020  1.454
 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  1.389  0.020  1.389
 3OZ  C23  C22   aromatic  1.400  0.020  1.400
 3OZ  C22  C28   single    1.500  0.020  1.500
 3OZ  C25  C23   aromatic  1.391  0.020  1.391
 3OZ  C23  O29   single    1.353  0.020  1.353
 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    1.398  0.020  1.398
 3OZ  C31  C30   single    1.509  0.020  1.509
 3OZ  C30  H30   single    0.970  0.020  1.090
 3OZ  C30  H30A  single    0.970  0.020  1.090
 3OZ  O33  C31   double    1.200  0.020  1.200
 3OZ  O32  C31   single    1.325  0.020  1.325
 3OZ  O32  HO32  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
 3OZ  N9    C1   C3    121.43  3.000
 3OZ  C3    C1   C2    118.07  3.000
 3OZ  N9    C1   C2    120.49  3.000
 3OZ  CL8   C2   C4    118.71  3.000
 3OZ  C4    C2   C1    121.67  3.000
 3OZ  CL8   C2   C1    119.62  3.000
 3OZ  H3    C3   C5    119.05  3.000
 3OZ  H3    C3   C1    119.78  3.000
 3OZ  C5    C3   C1    121.16  3.000
 3OZ  H4    C4   C6    121.04  3.000
 3OZ  H4    C4   C2    120.25  3.000
 3OZ  C6    C4   C2    118.71  3.000
 3OZ  H5    C5   C6    120.71  3.000
 3OZ  H5    C5   C3    119.96  3.000
 3OZ  C6    C5   C3    119.33  3.000
 3OZ  CL7   C6   C5    119.73  3.000
 3OZ  CL7   C6   C4    119.21  3.000
 3OZ  C5    C6   C4    121.05  3.000
 3OZ  HN9   N9   C10   117.75  3.000
 3OZ  HN9   N9   C1    117.31  3.000
 3OZ  C10   N9   C1    124.41  3.000
 3OZ  O12   C10  C11   122.56  3.000
 3OZ  O12   C10  N9    123.62  3.000
 3OZ  C11   C10  N9    113.73  3.000
 3OZ  H11   C11  N16   110.94  3.000
 3OZ  H11   C11  C13   111.89  3.000
 3OZ  N16   C11  C13   105.17  3.000
 3OZ  H11   C11  C10   110.00  3.000
 3OZ  N16   C11  C10   110.87  3.000
 3OZ  C13   C11  C10   107.86  3.000
 3OZ  C18   C13  C14   121.43  3.000
 3OZ  C14   C13  C11   108.40  3.000
 3OZ  C18   C13  C11   130.15  3.000
 3OZ  C21   C14  C15   130.26  3.000
 3OZ  C15   C14  C13   109.37  3.000
 3OZ  C21   C14  C13   120.37  3.000
 3OZ  H15A  C15  H15   106.75  3.000
 3OZ  H15A  C15  N16   110.94  3.000
 3OZ  H15   C15  N16   111.16  3.000
 3OZ  H15A  C15  C14   112.59  3.000
 3OZ  H15   C15  C14   110.74  3.000
 3OZ  N16   C15  C14   104.76  3.000
 3OZ  C17   N16  C15   112.52  3.000
 3OZ  C17   N16  C11   113.24  3.000
 3OZ  C15   N16  C11   107.81  3.000
 3OZ  H17A  C17  H17   106.37  3.000
 3OZ  H17A  C17  C26   108.87  3.000
 3OZ  H17   C17  C26   109.27  3.000
 3OZ  H17A  C17  N16   107.78  3.000
 3OZ  H17   C17  N16   112.82  3.000
 3OZ  C26   C17  N16   111.53  3.000
 3OZ  H18   C18  C19   120.44  3.000
 3OZ  H18   C18  C13   121.23  3.000
 3OZ  C19   C18  C13   118.32  3.000
 3OZ  H19   C19  C20   119.74  3.000
 3OZ  H19   C19  C18   119.78  3.000
 3OZ  C20   C19  C18   120.47  3.000
 3OZ  H20   C20  C21   119.68  3.000
 3OZ  H20   C20  C19   119.60  3.000
 3OZ  C21   C20  C19   120.72  3.000
 3OZ  H21   C21  C20   120.34  3.000
 3OZ  H21   C21  C14   120.98  3.000
 3OZ  C20   C21  C14   118.68  3.000
 3OZ  C28   C22  C24   121.31  3.000
 3OZ  C28   C22  C23   120.70  3.000
 3OZ  C24   C22  C23   117.99  3.000
 3OZ  O29   C23  C25   124.02  3.000
 3OZ  O29   C23  C22   115.56  3.000
 3OZ  C25   C23  C22   120.42  3.000
 3OZ  H24   C24  C26   118.96  3.000
 3OZ  H24   C24  C22   118.45  3.000
 3OZ  C26   C24  C22   122.58  3.000
 3OZ  H25   C25  C27   118.69  3.000
 3OZ  H25   C25  C23   121.34  3.000
 3OZ  C27   C25  C23   119.98  3.000
 3OZ  C27   C26  C24   118.13  3.000
 3OZ  C27   C26  C17   120.81  3.000
 3OZ  C24   C26  C17   121.06  3.000
 3OZ  H27   C27  C26   119.84  3.000
 3OZ  H27   C27  C25   119.25  3.000
 3OZ  C26   C27  C25   120.90  3.000
 3OZ  C30   O29  C23   118.46  3.000
 3OZ  H30A  C30  H30   107.07  3.000
 3OZ  H30A  C30  C31   108.71  3.000
 3OZ  H30   C30  C31   108.94  3.000
 3OZ  H30A  C30  O29   112.18  3.000
 3OZ  H30   C30  O29   112.13  3.000
 3OZ  C31   C30  O29   107.72  3.000
 3OZ  O33   C31  O32   124.73  3.000
 3OZ  O32   C31  C30   110.11  3.000
 3OZ  O33   C31  C30   125.16  3.000
 3OZ  HO32  O32  C31   110.36  3.000
 3OZ  H28B  C28  H28A  107.69  3.000
 3OZ  H28B  C28  H28   106.82  3.000
 3OZ  H28A  C28  H28   107.83  3.000
 3OZ  H28B  C28  C22   111.72  3.000
 3OZ  H28A  C28  C22   110.60  3.000
 3OZ  H28   C28  C22   111.95  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  CONST_46  HO32  O32  C31  C30  180.00   0.0  0
 3OZ  Var_01    C14   C15  N16  C11   20.56  30.0  1
 3OZ  Var_02    N16   C15  C14  C13  -12.26  30.0  1
 3OZ  Var_03    C26   C17  N16  C11  165.40  30.0  3
 3OZ  Var_04    C24   C26  C17  N16  131.59  30.0  2
 3OZ  Var_05    H28   C28  C22  C23   56.99  30.0  2
 3OZ  Var_06    C31   C30  O29  C23  179.32  30.0  3
 3OZ  Var_07    O33   C31  C30  O29   -1.27  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  O29   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-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
 3OZ  plan-5  HO32  0.020

