# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 22:43:33 2022
#   Inital geometry file: a 124 line input string
#   Ligand name: {3-[(2,3-dihydro-1,4-benzodioxin-6-yl)sulfanyl]-4-hydroxyphenyl}(1,3-dihydro-2H-isoindol-2-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1Sc2ccc3OCCOc3c2)C(=O)N4Cc5ccccc5C4
#
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
 ONG  ONG  {3-[(2,3-dihydro-1,4-benzodioxin-6-yl)sulfanyl]-4-hydroxyphenyl}(1,3-dihydro-2H-isoindol-2-yl)methanone  ligand  48  29  .  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_ONG
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
 ONG  C10  C  CR56  0   0.057  -32.3757   -8.2859  -26.0812
 ONG  C11  C  CH2   0  -0.282  -32.9997   -9.4281  -25.3447
 ONG  C12  C  CR16  0  -0.313  -32.6272   -7.0393  -28.1251
 ONG  C17  C  CR16  0  -0.326  -30.5987  -13.4576  -24.5254
 ONG  C16  C  CR6   0  -0.199  -31.2190  -12.8726  -23.4300
 ONG  C15  C  CR16  0  -0.312  -31.2665   -7.5357  -25.7235
 ONG  C14  C  CR16  0  -0.254  -30.8416   -6.5276  -26.5798
 ONG  C13  C  CR16  0  -0.253  -31.5178   -6.2807  -27.7716
 ONG  C18  C  CR6   0   0.321  -29.5718  -12.7940  -25.1851
 ONG  C19  C  CR6   0   0.321  -29.1787  -11.5215  -24.7550
 ONG  C20  C  CR16  0  -0.355  -29.7986  -10.9489  -23.6499
 ONG  C21  C  CR16  0  -0.217  -30.8030  -11.6227  -22.9784
 ONG  C22  C  CH2   0  -0.228  -27.7469  -12.8258  -26.6316
 ONG  C01  C  CR6   0  -0.047  -35.0992  -11.3348  -24.5932
 ONG  C02  C  CR16  0  -0.274  -36.2119  -11.3770  -23.7578
 ONG  C03  C  CR16  0  -0.366  -36.1859  -12.1195  -22.5904
 ONG  C04  C  CR6   0   0.369  -35.0497  -12.8433  -22.2406
 ONG  C05  C  CR6   0  -0.224  -33.9318  -12.8167  -23.0808
 ONG  C06  C  CR16  0  -0.227  -33.9771  -12.0823  -24.2548
 ONG  N01  N  NR5   0  -0.508  -34.1296   -9.7872  -26.2049
 ONG  O01  O  O     0  -0.486  -36.1849  -10.6215  -26.5648
 ONG  C08  C  CH2   0  -0.280  -34.1998   -8.9825  -27.4234
 ONG  C09  C  CR56  0   0.047  -33.0467   -8.0435  -27.2673
 ONG  S01  S  S2    0   0.092  -32.5064  -13.7438  -22.5815
 ONG  O02  O  OH1   0  -0.612  -34.9578  -13.5826  -21.1252
 ONG  O03  O  O2    0  -0.474  -28.9824  -13.4041  -26.2373
 ONG  C23  C  CH2   0  -0.227  -27.8670  -11.3217  -26.6701
 ONG  O04  O  O2    0  -0.471  -28.2081  -10.8261  -25.3834
 ONG  H1   H  HCH2  0   0.268  -33.3319   -9.1532  -24.3404
 ONG  H2   H  HCH2  0   0.262  -32.2820  -10.2442  -25.2363
 ONG  H3   H  HCR6  0   0.252  -33.1494   -6.8453  -29.0540
 ONG  H5   H  HCR6  0   0.252  -30.7396   -7.7296  -24.7970
 ONG  H6   H  HCR6  0   0.256  -29.9783   -5.9297  -26.3180
 ONG  H7   H  HCR6  0   0.255  -31.1753   -5.4916  -28.4285
 ONG  H8   H  HCR6  0   0.273  -29.4820   -9.9674  -23.3193
 ONG  H9   H  HCR6  0   0.272  -31.2753  -11.1672  -22.1183
 ONG  H10  H  HCH2  0   0.263  -27.5101  -13.2156  -27.6205
 ONG  H11  H  HCH2  0   0.246  -26.9528  -13.1288  -25.9409
 ONG  H12  H  HCR6  0   0.263  -37.1041  -10.8192  -24.0099
 ONG  H13  H  HCR6  0   0.279  -37.0530  -12.1326  -21.9399
 ONG  H14  H  HCR6  0   0.281  -33.1233  -12.1128  -24.9178
 ONG  H15  H  HCH2  0   0.260  -35.1540   -8.4535  -27.4916
 ONG  H16  H  HCH2  0   0.260  -34.1114   -9.6063  -28.3177
 ONG  H17  H  HOH1  0   0.483  -35.7691  -13.5284  -20.6054
 ONG  H18  H  HCH2  0   0.263  -26.9167  -10.8683  -26.9478
 ONG  H19  H  HCH2  0   0.247  -28.6239  -11.0169  -27.4004
 ONG  C07  C  C     0   0.516  -35.1819  -10.5577  -25.8640
 ONG  H4   H  HCR6  0   0.281  -30.9085  -14.4324  -24.8817

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
 ONG  C12  C09  aromatic  1.386  0.020  1.386
 ONG  C12  C13  aromatic  1.390  0.020  1.390
 ONG  C08  C09  single    1.495  0.020  1.495
 ONG  C08  N01  single    1.462  0.020  1.462
 ONG  O01  C07  double    1.225  0.020  1.225
 ONG  C09  C10  aromatic  1.384  0.020  1.384
 ONG  C13  C14  aromatic  1.392  0.020  1.392
 ONG  C23  C22  single    1.509  0.020  1.509
 ONG  C23  O04  single    1.420  0.020  1.420
 ONG  N01  C07  single    1.348  0.020  1.348
 ONG  N01  C11  single    1.465  0.020  1.465
 ONG  C07  C01  single    1.492  0.020  1.492
 ONG  C22  O03  single    1.420  0.020  1.420
 ONG  C14  C15  aromatic  1.389  0.020  1.389
 ONG  O04  C19  single    1.349  0.020  1.349
 ONG  C10  C11  single    1.495  0.020  1.495
 ONG  C10  C15  aromatic  1.386  0.020  1.386
 ONG  O03  C18  single    1.352  0.020  1.352
 ONG  C01  C06  aromatic  1.390  0.020  1.390
 ONG  C01  C02  aromatic  1.392  0.020  1.392
 ONG  C19  C18  aromatic  1.399  0.020  1.399
 ONG  C19  C20  aromatic  1.391  0.020  1.391
 ONG  C18  C17  aromatic  1.389  0.020  1.389
 ONG  C06  C05  aromatic  1.385  0.020  1.385
 ONG  C02  C03  aromatic  1.384  0.020  1.384
 ONG  C20  C21  aromatic  1.383  0.020  1.383
 ONG  C17  C16  aromatic  1.388  0.020  1.388
 ONG  C21  C16  aromatic  1.393  0.020  1.393
 ONG  C16  S01  single    1.771  0.020  1.771
 ONG  C05  C04  aromatic  1.399  0.020  1.399
 ONG  C05  S01  single    1.772  0.020  1.772
 ONG  C03  C04  aromatic  1.392  0.020  1.392
 ONG  C04  O02  single    1.341  0.020  1.341
 ONG  C11  H1   single    0.970  0.020  1.090
 ONG  C11  H2   single    0.970  0.020  1.090
 ONG  C12  H3   single    0.930  0.020  1.080
 ONG  C17  H4   single    0.930  0.020  1.080
 ONG  C15  H5   single    0.930  0.020  1.080
 ONG  C14  H6   single    0.930  0.020  1.080
 ONG  C13  H7   single    0.930  0.020  1.080
 ONG  C20  H8   single    0.930  0.020  1.080
 ONG  C21  H9   single    0.930  0.020  1.080
 ONG  C22  H10  single    0.970  0.020  1.090
 ONG  C22  H11  single    0.970  0.020  1.090
 ONG  C02  H12  single    0.930  0.020  1.080
 ONG  C03  H13  single    0.930  0.020  1.080
 ONG  C06  H14  single    0.930  0.020  1.080
 ONG  C08  H15  single    0.970  0.020  1.090
 ONG  C08  H16  single    0.970  0.020  1.090
 ONG  O02  H17  single    0.850  0.020  0.980
 ONG  C23  H18  single    0.970  0.020  1.090
 ONG  C23  H19  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
 ONG  C09  C10  C15  120.95  3.000
 ONG  C15  C10  C11  128.33  3.000
 ONG  C09  C10  C11  110.70  3.000
 ONG  H2   C11  H1   107.25  3.000
 ONG  H2   C11  N01  112.46  3.000
 ONG  H1   C11  N01  111.52  3.000
 ONG  H2   C11  C10  110.21  3.000
 ONG  H1   C11  C10  112.78  3.000
 ONG  N01  C11  C10  102.70  3.000
 ONG  H3   C12  C09  120.97  3.000
 ONG  H3   C12  C13  120.35  3.000
 ONG  C09  C12  C13  118.67  3.000
 ONG  H4   C17  C18  119.02  3.000
 ONG  H4   C17  C16  120.74  3.000
 ONG  C18  C17  C16  120.24  3.000
 ONG  S01  C16  C21  120.22  3.000
 ONG  S01  C16  C17  119.71  3.000
 ONG  C21  C16  C17  120.05  3.000
 ONG  H5   C15  C14  120.55  3.000
 ONG  H5   C15  C10  120.87  3.000
 ONG  C14  C15  C10  118.58  3.000
 ONG  H6   C14  C13  119.77  3.000
 ONG  H6   C14  C15  119.71  3.000
 ONG  C13  C14  C15  120.51  3.000
 ONG  H7   C13  C14  119.68  3.000
 ONG  H7   C13  C12  119.75  3.000
 ONG  C14  C13  C12  120.58  3.000
 ONG  O03  C18  C19  121.82  3.000
 ONG  C19  C18  C17  119.74  3.000
 ONG  O03  C18  C17  118.44  3.000
 ONG  O04  C19  C20  118.59  3.000
 ONG  C20  C19  C18  119.57  3.000
 ONG  O04  C19  C18  121.84  3.000
 ONG  H8   C20  C21  120.37  3.000
 ONG  H8   C20  C19  119.04  3.000
 ONG  C21  C20  C19  120.59  3.000
 ONG  H9   C21  C20  119.85  3.000
 ONG  H9   C21  C16  120.36  3.000
 ONG  C20  C21  C16  119.78  3.000
 ONG  H11  C22  H10  108.42  3.000
 ONG  H11  C22  C23  110.45  3.000
 ONG  H10  C22  C23  110.54  3.000
 ONG  H11  C22  O03  110.06  3.000
 ONG  H10  C22  O03  107.19  3.000
 ONG  C23  C22  O03  110.10  3.000
 ONG  C07  C01  C06  122.16  3.000
 ONG  C06  C01  C02  118.87  3.000
 ONG  C07  C01  C02  118.86  3.000
 ONG  H12  C02  C03  119.25  3.000
 ONG  H12  C02  C01  120.25  3.000
 ONG  C03  C02  C01  120.49  3.000
 ONG  H13  C03  C04  119.73  3.000
 ONG  H13  C03  C02  119.84  3.000
 ONG  C04  C03  C02  120.43  3.000
 ONG  O02  C04  C05  117.08  3.000
 ONG  O02  C04  C03  123.47  3.000
 ONG  C05  C04  C03  119.45  3.000
 ONG  S01  C05  C06  122.84  3.000
 ONG  S01  C05  C04  117.62  3.000
 ONG  C06  C05  C04  119.53  3.000
 ONG  H14  C06  C05  118.60  3.000
 ONG  H14  C06  C01  120.21  3.000
 ONG  C05  C06  C01  121.18  3.000
 ONG  C08  N01  C07  119.20  3.000
 ONG  C07  N01  C11  126.42  3.000
 ONG  C08  N01  C11  113.06  3.000
 ONG  H16  C08  H15  107.19  3.000
 ONG  H16  C08  C09  112.40  3.000
 ONG  H15  C08  C09  112.07  3.000
 ONG  H16  C08  N01  111.32  3.000
 ONG  H15  C08  N01  111.12  3.000
 ONG  C09  C08  N01  102.81  3.000
 ONG  C08  C09  C12  128.61  3.000
 ONG  C08  C09  C10  110.69  3.000
 ONG  C12  C09  C10  120.70  3.000
 ONG  C05  S01  C16  101.09  3.000
 ONG  H17  O02  C04  111.07  3.000
 ONG  C22  O03  C18  114.31  3.000
 ONG  H19  C23  H18  108.49  3.000
 ONG  H19  C23  O04  109.94  3.000
 ONG  H18  C23  O04  107.18  3.000
 ONG  H19  C23  C22  110.45  3.000
 ONG  H18  C23  C22  110.61  3.000
 ONG  O04  C23  C22  110.10  3.000
 ONG  C23  O04  C19  114.51  3.000
 ONG  O01  C07  N01  121.61  3.000
 ONG  N01  C07  C01  118.02  3.000
 ONG  O01  C07  C01  120.37  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
 ONG  CONST_01  C13  C12  C09  C10    0.00   0.0  0
 ONG  CONST_02  C13  C14  C15  C10    0.00   0.0  0
 ONG  CONST_03  C15  C10  C09  C12    0.00   0.0  0
 ONG  CONST_04  C15  C14  C13  C12    0.00   0.0  0
 ONG  CONST_05  C20  C19  C18  C17    0.00   0.0  0
 ONG  CONST_06  C20  C21  C16  C17    0.00   0.0  0
 ONG  CONST_07  C19  C18  C17  C16    0.00   0.0  0
 ONG  CONST_08  C19  C20  C21  C16    0.00   0.0  0
 ONG  CONST_09  C09  C12  C13  C14    0.00   0.0  0
 ONG  CONST_10  C09  C10  C15  C14    0.00   0.0  0
 ONG  CONST_11  C21  C20  C19  C18    0.00   0.0  0
 ONG  CONST_12  C21  C16  C17  C18    0.00   0.0  0
 ONG  CONST_13  C04  C05  C06  C01    0.00   0.0  0
 ONG  CONST_14  C04  C03  C02  C01    0.00   0.0  0
 ONG  CONST_15  C05  C06  C01  C02    0.00   0.0  0
 ONG  CONST_16  C05  C04  C03  C02    0.00   0.0  0
 ONG  CONST_17  C06  C01  C02  C03    0.00   0.0  0
 ONG  CONST_18  C06  C05  C04  C03    0.00   0.0  0
 ONG  CONST_19  S01  C16  C17  C18  180.00   0.0  0
 ONG  CONST_20  S01  C16  C21  C20  180.00   0.0  0
 ONG  CONST_21  S01  C05  C06  C01  180.00   0.0  0
 ONG  CONST_22  O02  C04  C03  C02  180.00   0.0  0
 ONG  CONST_23  C07  C01  C02  C03  180.00   0.0  0
 ONG  CONST_24  S01  C05  C04  C03  180.00   0.0  0
 ONG  CONST_25  C07  C01  C06  C05  180.00   0.0  0
 ONG  CONST_26  O02  C04  C05  C06  180.00   0.0  0
 ONG  CONST_27  C01  C07  N01  C11    0.00   0.0  0
 ONG  CONST_28  C08  N01  C07  C01  180.00   0.0  0
 ONG  CONST_29  H3   C12  C09  C10  180.00   0.0  0
 ONG  CONST_30  H6   C14  C15  C10  180.00   0.0  0
 ONG  CONST_31  H5   C15  C10  C11    0.00   0.0  0
 ONG  CONST_32  H9   C21  C16  C17  180.00   0.0  0
 ONG  CONST_33  H8   C20  C21  C16  180.00   0.0  0
 ONG  CONST_34  H7   C13  C14  C15  180.00   0.0  0
 ONG  CONST_35  H4   C17  C18  C19  180.00   0.0  0
 ONG  CONST_36  H13  C03  C02  C01  180.00   0.0  0
 ONG  CONST_37  H14  C06  C01  C02  180.00   0.0  0
 ONG  CONST_38  H12  C02  C03  C04  180.00   0.0  0
 ONG  CONST_39  O01  C07  N01  C11  180.00   0.0  0
 ONG  CONST_40  C08  N01  C07  O01    0.00   0.0  0
 ONG  Var_01    N01  C08  C09  C10    0.23  30.0  1
 ONG  Var_02    C08  N01  C11  C10    2.20  30.0  1
 ONG  Var_03    C09  C08  N01  C11   -1.58  30.0  1
 ONG  Var_04    N01  C11  C10  C15  179.38  30.0  1
 ONG  Var_05    C23  C22  O03  C18  -44.90  30.0  1
 ONG  Var_06    C22  C23  O04  C19  -44.37  30.0  1
 ONG  Var_07    O04  C23  C22  O03   60.33  30.0  1
 ONG  Var_08    C06  C05  S01  C16   25.00  30.0  2
 ONG  Var_09    N01  C07  C01  C02  137.09  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
 ONG  plan-1  C01  0.020
 ONG  plan-1  C02  0.020
 ONG  plan-1  C03  0.020
 ONG  plan-1  C04  0.020
 ONG  plan-1  C05  0.020
 ONG  plan-1  C06  0.020
 ONG  plan-1  S01  0.020
 ONG  plan-1  O02  0.020
 ONG  plan-1  H12  0.020
 ONG  plan-1  H13  0.020
 ONG  plan-1  H14  0.020
 ONG  plan-1  C07  0.020
 ONG  plan-2  C10  0.020
 ONG  plan-2  C11  0.020
 ONG  plan-2  C12  0.020
 ONG  plan-2  C15  0.020
 ONG  plan-2  C14  0.020
 ONG  plan-2  C13  0.020
 ONG  plan-2  C08  0.020
 ONG  plan-2  C09  0.020
 ONG  plan-2  H3   0.020
 ONG  plan-2  H5   0.020
 ONG  plan-2  H6   0.020
 ONG  plan-2  H7   0.020
 ONG  plan-3  C17  0.020
 ONG  plan-3  C16  0.020
 ONG  plan-3  C18  0.020
 ONG  plan-3  C19  0.020
 ONG  plan-3  C20  0.020
 ONG  plan-3  C21  0.020
 ONG  plan-3  S01  0.020
 ONG  plan-3  O03  0.020
 ONG  plan-3  O04  0.020
 ONG  plan-3  H8   0.020
 ONG  plan-3  H9   0.020
 ONG  plan-3  H4   0.020
 ONG  plan-4  C11  0.020
 ONG  plan-4  C01  0.020
 ONG  plan-4  N01  0.020
 ONG  plan-4  O01  0.020
 ONG  plan-4  C08  0.020
 ONG  plan-4  C07  0.020

