# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 16:42:37 2022
#   Inital geometry file: a 124 line input string
#   Ligand name: (1,3-dihydro-2H-isoindol-2-yl){3-[(3,4-dimethylphenyl)sulfanyl]-4-hydroxyphenyl}methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(Sc2cc(ccc2O)C(=O)N3Cc4ccccc4C3)cc1C
#
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
 ONJ  ONJ  (1,3-dihydro-2H-isoindol-2-yl){3-[(3,4-dimethylphenyl)sulfanyl]-4-hydroxyphenyl}methanone  ligand  48  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ONJ
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
 ONJ  C01  C  CR6   0  -0.051  -34.4128  -11.4974  -24.8439
 ONJ  C02  C  CR16  0  -0.280  -35.6249  -11.8941  -24.2922
 ONJ  C03  C  CR16  0  -0.365  -35.6564  -12.5314  -23.0628
 ONJ  C04  C  CR6   0   0.369  -34.4750  -12.8150  -22.3866
 ONJ  C05  C  CR6   0  -0.215  -33.2478  -12.4586  -22.9582
 ONJ  C06  C  CR16  0  -0.234  -33.2306  -11.7888  -24.1710
 ONJ  C07  C  C     0   0.509  -34.3976  -10.8515  -26.1895
 ONJ  N01  N  NR5   0  -0.503  -33.7508   -9.6769  -26.3009
 ONJ  O01  O  O     0  -0.483  -34.9544  -11.3811  -27.1428
 ONJ  C08  C  CH2   0  -0.279  -33.7043   -8.9884  -27.5889
 ONJ  C09  C  CR56  0   0.046  -33.1822   -7.6363  -27.2199
 ONJ  C10  C  CR56  0   0.054  -32.9649   -7.5523  -25.8549
 ONJ  C11  C  CH2   0  -0.275  -33.2961   -8.8475  -25.1838
 ONJ  C12  C  CR16  0  -0.312  -32.9272   -6.5521  -28.0448
 ONJ  C13  C  CR16  0  -0.253  -32.4516   -5.3774  -27.4752
 ONJ  C14  C  CR16  0  -0.255  -32.2355   -5.2935  -26.1023
 ONJ  C15  C  CR16  0  -0.310  -32.4905   -6.3841  -25.2803
 ONJ  S01  S  S2    0   0.088  -31.7884  -12.8843  -22.0492
 ONJ  C16  C  CR6   0  -0.188  -30.5399  -12.7720  -23.2999
 ONJ  O02  O  OH1   0  -0.615  -34.4306  -13.4287  -21.1928
 ONJ  C17  C  CR16  0  -0.249  -30.4416  -13.7634  -24.2729
 ONJ  C18  C  CR6   0   0.082  -29.4642  -13.7106  -25.2569
 ONJ  C19  C  CR6   0   0.069  -28.5449  -12.6482  -25.2524
 ONJ  C20  C  CR16  0  -0.289  -28.6439  -11.6738  -24.2662
 ONJ  C21  C  CR16  0  -0.233  -29.6352  -11.7218  -23.2940
 ONJ  C22  C  CH3   0  -0.735  -27.4736  -12.5698  -26.2975
 ONJ  C23  C  CH3   0  -0.735  -29.3900  -14.7801  -26.3053
 ONJ  H1   H  HCR6  0   0.263  -36.5539  -11.6951  -24.8103
 ONJ  H2   H  HCR6  0   0.278  -36.6067  -12.8210  -22.6286
 ONJ  H3   H  HCR6  0   0.280  -32.2795  -11.5142  -24.6091
 ONJ  H4   H  HCH2  0   0.260  -34.6966   -8.9334  -28.0451
 ONJ  H5   H  HCH2  0   0.267  -34.0765   -8.7340  -24.4264
 ONJ  H6   H  HCR6  0   0.253  -33.0946   -6.6147  -29.1130
 ONJ  H7   H  HCR6  0   0.256  -32.2470   -4.5205  -28.1039
 ONJ  H8   H  HCR6  0   0.256  -31.8651   -4.3719  -25.6722
 ONJ  H9   H  HCR6  0   0.252  -32.3194   -6.3188  -24.2128
 ONJ  H10  H  HOH1  0   0.482  -35.3172  -13.6445  -20.8785
 ONJ  H11  H  HCR6  0   0.262  -31.1469  -14.5863  -24.2688
 ONJ  H12  H  HCR6  0   0.252  -27.9374  -10.8525  -24.2578
 ONJ  H13  H  HCR6  0   0.265  -29.7029  -10.9450  -22.5436
 ONJ  H14  H  HCH3  0   0.247  -27.9000  -12.5155  -27.3014
 ONJ  H15  H  HCH3  0   0.253  -26.8405  -11.6953  -26.1551
 ONJ  H16  H  HCH3  0   0.247  -26.8326  -13.4535  -26.2766
 ONJ  H17  H  HCH3  0   0.246  -28.4334  -15.3060  -26.2762
 ONJ  H18  H  HCH3  0   0.252  -30.1799  -15.5172  -26.1720
 ONJ  H19  H  HCH3  0   0.246  -29.4888  -14.3622  -27.3091
 ONJ  H20  H  HCH2  0   0.260  -33.0524   -9.5111  -28.2949
 ONJ  H21  H  HCH2  0   0.264  -32.4182   -9.2664  -24.6871

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
 ONJ  C12  C09  aromatic  1.386  0.020  1.386
 ONJ  C12  C13  aromatic  1.390  0.020  1.390
 ONJ  C08  C09  single    1.496  0.020  1.496
 ONJ  C08  N01  single    1.461  0.020  1.461
 ONJ  O01  C07  double    1.224  0.020  1.224
 ONJ  C09  C10  aromatic  1.385  0.020  1.385
 ONJ  C13  C14  aromatic  1.392  0.020  1.392
 ONJ  N01  C07  single    1.346  0.020  1.346
 ONJ  N01  C11  single    1.464  0.020  1.464
 ONJ  C07  C01  single    1.493  0.020  1.493
 ONJ  C22  C19  single    1.499  0.020  1.499
 ONJ  C14  C15  aromatic  1.389  0.020  1.389
 ONJ  C10  C11  single    1.496  0.020  1.496
 ONJ  C10  C15  aromatic  1.386  0.020  1.386
 ONJ  C23  C18  single    1.499  0.020  1.499
 ONJ  C19  C18  aromatic  1.405  0.020  1.405
 ONJ  C19  C20  aromatic  1.390  0.020  1.390
 ONJ  C01  C06  aromatic  1.391  0.020  1.391
 ONJ  C01  C02  aromatic  1.390  0.020  1.390
 ONJ  C18  C17  aromatic  1.388  0.020  1.388
 ONJ  C20  C21  aromatic  1.389  0.020  1.389
 ONJ  C06  C05  aromatic  1.386  0.020  1.386
 ONJ  C02  C03  aromatic  1.385  0.020  1.385
 ONJ  C17  C16  aromatic  1.393  0.020  1.393
 ONJ  C21  C16  aromatic  1.386  0.020  1.386
 ONJ  C16  S01  single    1.771  0.020  1.771
 ONJ  C05  C04  aromatic  1.400  0.020  1.400
 ONJ  C05  S01  single    1.771  0.020  1.771
 ONJ  C03  C04  aromatic  1.390  0.020  1.390
 ONJ  C04  O02  single    1.343  0.020  1.343
 ONJ  C02  H1   single    0.930  0.020  1.080
 ONJ  C03  H2   single    0.930  0.020  1.080
 ONJ  C06  H3   single    0.930  0.020  1.080
 ONJ  C08  H4   single    0.970  0.020  1.090
 ONJ  C11  H5   single    0.970  0.020  1.090
 ONJ  C12  H6   single    0.930  0.020  1.080
 ONJ  C13  H7   single    0.930  0.020  1.080
 ONJ  C14  H8   single    0.930  0.020  1.080
 ONJ  C15  H9   single    0.930  0.020  1.080
 ONJ  O02  H10  single    0.850  0.020  0.980
 ONJ  C17  H11  single    0.930  0.020  1.080
 ONJ  C20  H12  single    0.930  0.020  1.080
 ONJ  C21  H13  single    0.930  0.020  1.080
 ONJ  C22  H14  single    0.970  0.020  1.090
 ONJ  C22  H15  single    0.970  0.020  1.090
 ONJ  C22  H16  single    0.970  0.020  1.090
 ONJ  C23  H17  single    0.970  0.020  1.090
 ONJ  C23  H18  single    0.970  0.020  1.090
 ONJ  C23  H19  single    0.970  0.020  1.090
 ONJ  C08  H20  single    0.970  0.020  1.090
 ONJ  C11  H21  single    0.970  0.020  1.090

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
 ONJ  C07  C01  C06  121.20  3.000
 ONJ  C06  C01  C02  119.30  3.000
 ONJ  C07  C01  C02  119.36  3.000
 ONJ  H1   C02  C03  119.34  3.000
 ONJ  H1   C02  C01  120.41  3.000
 ONJ  C03  C02  C01  120.24  3.000
 ONJ  H2   C03  C04  119.70  3.000
 ONJ  H2   C03  C02  119.89  3.000
 ONJ  C04  C03  C02  120.41  3.000
 ONJ  O02  C04  C05  116.77  3.000
 ONJ  O02  C04  C03  123.61  3.000
 ONJ  C05  C04  C03  119.62  3.000
 ONJ  S01  C05  C06  123.72  3.000
 ONJ  S01  C05  C04  116.84  3.000
 ONJ  C06  C05  C04  119.43  3.000
 ONJ  H3   C06  C05  119.19  3.000
 ONJ  H3   C06  C01  119.85  3.000
 ONJ  C05  C06  C01  120.94  3.000
 ONJ  O01  C07  N01  122.12  3.000
 ONJ  N01  C07  C01  117.21  3.000
 ONJ  O01  C07  C01  120.67  3.000
 ONJ  C11  N01  C08  113.32  3.000
 ONJ  C11  N01  C07  125.51  3.000
 ONJ  C08  N01  C07  119.97  3.000
 ONJ  H20  C08  H4   107.20  3.000
 ONJ  H20  C08  C09  112.53  3.000
 ONJ  H4   C08  C09  111.98  3.000
 ONJ  H20  C08  N01  111.26  3.000
 ONJ  H4   C08  N01  111.26  3.000
 ONJ  C09  C08  N01  102.68  3.000
 ONJ  C12  C09  C10  120.69  3.000
 ONJ  C10  C09  C08  110.66  3.000
 ONJ  C12  C09  C08  128.65  3.000
 ONJ  C15  C10  C11  128.30  3.000
 ONJ  C15  C10  C09  120.91  3.000
 ONJ  C11  C10  C09  110.79  3.000
 ONJ  H21  C11  H5   107.37  3.000
 ONJ  H21  C11  C10  110.98  3.000
 ONJ  H5   C11  C10  112.26  3.000
 ONJ  H21  C11  N01  112.30  3.000
 ONJ  H5   C11  N01  111.46  3.000
 ONJ  C10  C11  N01  102.53  3.000
 ONJ  H6   C12  C13  120.40  3.000
 ONJ  H6   C12  C09  120.90  3.000
 ONJ  C13  C12  C09  118.70  3.000
 ONJ  H7   C13  C14  119.72  3.000
 ONJ  H7   C13  C12  119.73  3.000
 ONJ  C14  C13  C12  120.55  3.000
 ONJ  H8   C14  C15  119.74  3.000
 ONJ  H8   C14  C13  119.75  3.000
 ONJ  C15  C14  C13  120.50  3.000
 ONJ  H9   C15  C14  120.45  3.000
 ONJ  H9   C15  C10  120.90  3.000
 ONJ  C14  C15  C10  118.64  3.000
 ONJ  C16  S01  C05  101.72  3.000
 ONJ  C21  C16  C17  119.75  3.000
 ONJ  C21  C16  S01  120.35  3.000
 ONJ  C17  C16  S01  119.88  3.000
 ONJ  H10  O02  C04  111.18  3.000
 ONJ  H11  C17  C18  119.33  3.000
 ONJ  H11  C17  C16  119.47  3.000
 ONJ  C18  C17  C16  121.20  3.000
 ONJ  C23  C18  C19  120.61  3.000
 ONJ  C19  C18  C17  119.16  3.000
 ONJ  C23  C18  C17  120.22  3.000
 ONJ  C22  C19  C20  120.60  3.000
 ONJ  C20  C19  C18  119.07  3.000
 ONJ  C22  C19  C18  120.34  3.000
 ONJ  H12  C20  C21  119.08  3.000
 ONJ  H12  C20  C19  119.38  3.000
 ONJ  C21  C20  C19  121.54  3.000
 ONJ  H13  C21  C20  120.33  3.000
 ONJ  H13  C21  C16  120.40  3.000
 ONJ  C20  C21  C16  119.27  3.000
 ONJ  H16  C22  H15  107.83  3.000
 ONJ  H16  C22  H14  106.67  3.000
 ONJ  H15  C22  H14  107.90  3.000
 ONJ  H16  C22  C19  111.34  3.000
 ONJ  H15  C22  C19  111.50  3.000
 ONJ  H14  C22  C19  111.38  3.000
 ONJ  H19  C23  H18  107.82  3.000
 ONJ  H19  C23  H17  106.74  3.000
 ONJ  H18  C23  H17  107.84  3.000
 ONJ  H19  C23  C18  111.43  3.000
 ONJ  H18  C23  C18  111.19  3.000
 ONJ  H17  C23  C18  111.61  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
 ONJ  CONST_01  C04  C05  C06  C01     0.00   0.0  0
 ONJ  CONST_02  C04  C03  C02  C01     0.00   0.0  0
 ONJ  CONST_03  C05  C06  C01  C02     0.00   0.0  0
 ONJ  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 ONJ  CONST_05  C06  C01  C02  C03     0.00   0.0  0
 ONJ  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 ONJ  CONST_07  C14  C13  C12  C09     0.00   0.0  0
 ONJ  CONST_08  C14  C15  C10  C09     0.00   0.0  0
 ONJ  CONST_09  C13  C12  C09  C10     0.00   0.0  0
 ONJ  CONST_10  C13  C14  C15  C10     0.00   0.0  0
 ONJ  CONST_11  C15  C10  C09  C12     0.00   0.0  0
 ONJ  CONST_12  C15  C14  C13  C12     0.00   0.0  0
 ONJ  CONST_13  C19  C18  C17  C16     0.00   0.0  0
 ONJ  CONST_14  C19  C20  C21  C16     0.00   0.0  0
 ONJ  CONST_15  C20  C19  C18  C17     0.00   0.0  0
 ONJ  CONST_16  C20  C21  C16  C17     0.00   0.0  0
 ONJ  CONST_17  C21  C20  C19  C18     0.00   0.0  0
 ONJ  CONST_18  C21  C16  C17  C18     0.00   0.0  0
 ONJ  CONST_19  S01  C05  C06  C01   180.00   0.0  0
 ONJ  CONST_20  O02  C04  C03  C02   180.00   0.0  0
 ONJ  CONST_21  C07  C01  C02  C03   180.00   0.0  0
 ONJ  CONST_22  S01  C05  C04  C03   180.00   0.0  0
 ONJ  CONST_23  C07  C01  C06  C05   180.00   0.0  0
 ONJ  CONST_24  O02  C04  C05  C06   180.00   0.0  0
 ONJ  CONST_25  C18  C17  C16  S01   180.00   0.0  0
 ONJ  CONST_26  C20  C21  C16  S01   180.00   0.0  0
 ONJ  CONST_27  C23  C18  C17  C16   180.00   0.0  0
 ONJ  CONST_28  C22  C19  C18  C17   180.00   0.0  0
 ONJ  CONST_29  C23  C18  C19  C20   180.00   0.0  0
 ONJ  CONST_30  C22  C19  C20  C21   180.00   0.0  0
 ONJ  CONST_31  C08  N01  C07  C01   180.00   0.0  0
 ONJ  CONST_32  C11  N01  C07  C01     0.00   0.0  0
 ONJ  CONST_33  H2   C03  C02  C01   180.00   0.0  0
 ONJ  CONST_34  H3   C06  C01  C02   180.00   0.0  0
 ONJ  CONST_35  H1   C02  C03  C04   180.00   0.0  0
 ONJ  CONST_36  H6   C12  C09  C08     0.00   0.0  0
 ONJ  CONST_37  H7   C13  C12  C09   180.00   0.0  0
 ONJ  CONST_38  H9   C15  C10  C09   180.00   0.0  0
 ONJ  CONST_39  H8   C14  C15  C10   180.00   0.0  0
 ONJ  CONST_40  H12  C20  C21  C16   180.00   0.0  0
 ONJ  CONST_41  H13  C21  C16  C17   180.00   0.0  0
 ONJ  CONST_42  H11  C17  C18  C19   180.00   0.0  0
 ONJ  CONST_43  C08  N01  C07  O01     0.00   0.0  0
 ONJ  CONST_44  C11  N01  C07  O01   180.00   0.0  0
 ONJ  Var_01    C12  C09  C08  N01   179.86  30.0  1
 ONJ  Var_02    C09  C10  C11  N01    -1.04  30.0  1
 ONJ  Var_03    C10  C11  N01  C08     0.66  30.0  1
 ONJ  Var_04    C11  N01  C08  C09    -0.08  30.0  1
 ONJ  Var_05    N01  C07  C01  C02   128.00  30.0  2
 ONJ  Var_06    C17  C16  S01  C05   -74.25  30.0  1
 ONJ  Var_07    H17  C23  C18  C17  -119.40  30.0  2
 ONJ  Var_08    H14  C22  C19  C18    59.74  30.0  2

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
 ONJ  plan-1  C01  0.020
 ONJ  plan-1  C02  0.020
 ONJ  plan-1  C03  0.020
 ONJ  plan-1  C04  0.020
 ONJ  plan-1  C05  0.020
 ONJ  plan-1  C06  0.020
 ONJ  plan-1  C07  0.020
 ONJ  plan-1  S01  0.020
 ONJ  plan-1  O02  0.020
 ONJ  plan-1  H1   0.020
 ONJ  plan-1  H2   0.020
 ONJ  plan-1  H3   0.020
 ONJ  plan-2  S01  0.020
 ONJ  plan-2  C16  0.020
 ONJ  plan-2  C17  0.020
 ONJ  plan-2  C18  0.020
 ONJ  plan-2  C19  0.020
 ONJ  plan-2  C20  0.020
 ONJ  plan-2  C21  0.020
 ONJ  plan-2  C22  0.020
 ONJ  plan-2  C23  0.020
 ONJ  plan-2  H11  0.020
 ONJ  plan-2  H12  0.020
 ONJ  plan-2  H13  0.020
 ONJ  plan-3  C08  0.020
 ONJ  plan-3  C09  0.020
 ONJ  plan-3  C10  0.020
 ONJ  plan-3  C11  0.020
 ONJ  plan-3  C12  0.020
 ONJ  plan-3  C13  0.020
 ONJ  plan-3  C14  0.020
 ONJ  plan-3  C15  0.020
 ONJ  plan-3  H6   0.020
 ONJ  plan-3  H7   0.020
 ONJ  plan-3  H8   0.020
 ONJ  plan-3  H9   0.020
 ONJ  plan-4  C01  0.020
 ONJ  plan-4  C07  0.020
 ONJ  plan-4  N01  0.020
 ONJ  plan-4  O01  0.020
 ONJ  plan-4  C08  0.020
 ONJ  plan-4  C11  0.020

