# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 25 03:13:27 2021
#   Inital geometry file: a 140 line input string
#   Ligand name: 5-{[4-{[(1S)-2-hydroxy-1-phenylethyl]amino}-5-(1,3,4-oxadiazol-2-yl)pyrimidin-2-yl]amino}-3,3-dimethyl-2-benzofuran-1(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)OC(=O)c2ccc(Nc3ncc(c(N[C@H](CO)c4ccccc4)n3)c5ocnn5)cc12
#
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
 W9D  W9D  5-{[4-{[(1S)-2-hydroxy-1-phenylethyl]amino}-5-(1,3,4-oxadiazol-2-yl)pyrimidin-2-yl]amino}-3,3-dimethyl-2-benzofuran-1(3H)-one  ligand  56  34  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_W9D
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
 W9D  C18  C  CR16  0  -0.281  29.9562  -83.7741  -5.0762
 W9D  C17  C  CR56  0  -0.172  28.9997  -82.7773  -5.2198
 W9D  C16  C  CR56  0   0.119  28.2448  -82.3596  -4.1456
 W9D  C15  C  CR16  0  -0.338  28.3986  -82.8963  -2.8825
 W9D  C19  C  CR16  0  -0.345  30.1339  -84.3194  -3.8249
 W9D  C20  C  CR16  0  -0.329  24.8389  -80.8205  -0.9661
 W9D  C21  C  CR16  0  -0.250  23.5681  -81.1750  -1.3977
 W9D  C22  C  CR16  0  -0.202  22.8794  -82.2023  -0.7648
 W9D  C23  C  CR16  0  -0.246  23.4720  -82.8639   0.3001
 W9D  C24  C  CR16  0  -0.281  24.7431  -82.5041   0.7321
 W9D  C11  C  CH2   0  -0.222  26.8187  -79.6333   1.1217
 W9D  C12  C  CR6   0   0.147  25.4419  -81.4790   0.1043
 W9D  C27  C  CR5   0   0.549  28.5941  -82.0081  -6.3930
 W9D  C1   C  CR6   0  -0.249  28.6311  -83.8550   2.3240
 W9D  C2   C  CR16  0  -0.038  29.4814  -84.8709   1.9082
 W9D  N3   N  N     0  -0.464  29.8287  -85.0809   0.6563
 W9D  C4   C  CR6   0   0.615  29.2811  -84.2469  -0.2372
 W9D  N5   N  N     0  -0.553  28.4656  -83.2434   0.0240
 W9D  C6   C  CR6   0   0.506  28.1458  -83.0002   1.2968
 W9D  C7   C  CR5   0   0.487  28.3038  -83.7605   3.7258
 W9D  N8   N  NH1   0  -0.575  27.3875  -81.9285   1.5508
 W9D  C10  C  CH1   0  -0.195  26.8272  -81.0474   0.5531
 W9D  C14  C  CR6   0   0.368  29.3707  -83.8892  -2.7178
 W9D  C25  C  CR5   0   0.165  27.3037  -81.2838  -4.6104
 W9D  O26  O  O     0  -0.450  27.6269  -81.1581  -6.0164
 W9D  C28  C  CH3   0  -0.646  25.8484  -81.7047  -4.4886
 W9D  C29  C  CH3   0  -0.659  27.5768  -79.9513  -3.9325
 W9D  O30  O  O     0  -0.285  28.9919  -82.0629  -7.5276
 W9D  O31  O  O     0  -0.467  27.1571  -83.1822   4.1292
 W9D  C32  C  CR15  0   0.166  27.1759  -83.3510   5.4620
 W9D  N33  N  N     0  -0.314  28.2219  -83.9751   5.8504
 W9D  N34  N  N     0  -0.357  28.9657  -84.2336   4.7285
 W9D  H43  H  HCR6  0   0.280  30.5557  -84.1118  -5.9114
 W9D  H42  H  HCR6  0   0.275  27.8005  -82.5662  -2.0483
 W9D  H44  H  HCR6  0   0.297  30.8805  -85.0907  -3.6812
 W9D  H45  H  HCR6  0   0.256  25.3619  -80.0154  -1.4722
 W9D  H46  H  HCR6  0   0.237  23.1217  -80.6514  -2.2333
 W9D  H47  H  HCR6  0   0.247  21.8900  -82.4843  -1.1000
 W9D  H48  H  HCR6  0   0.260  22.9433  -83.6641   0.8019
 W9D  H49  H  HCR6  0   0.243  25.1849  -83.0339   1.5660
 W9D  H39  H  HCH2  0   0.256  27.8529  -79.3376   1.3278
 W9D  H40  H  HCH2  0   0.233  26.4281  -78.9463   0.3615
 W9D  H35  H  HCR6  0   0.258  29.8893  -85.5555   2.6439
 W9D  H36  H  HNH1  0   0.433  27.1396  -81.7132   2.5031
 W9D  H38  H  HCH1  0   0.302  27.4934  -81.0403  -0.3122
 W9D  H41  H  HOH1  0   0.434  26.2736  -78.8722   2.8209
 W9D  H52  H  HCH3  0   0.189  25.5950  -81.8655  -3.4409
 W9D  H50  H  HCH3  0   0.283  25.1865  -80.9298  -4.8767
 W9D  H51  H  HCH3  0   0.241  25.6571  -82.6330  -5.0271
 W9D  H53  H  HCH3  0   0.230  27.4047  -80.0398  -2.8596
 W9D  H54  H  HCH3  0   0.257  28.6094  -79.6344  -4.0779
 W9D  H55  H  HCH3  0   0.241  26.9128  -79.1753  -4.3138
 W9D  H56  H  HCR5  0   0.315  26.3585  -82.9621   6.0474
 W9D  N9   N  NH1   0  -0.726  29.6573  -84.5131  -1.5188
 W9D  O13  O  OH1   0  -0.668  26.0308  -79.6346   2.2885
 W9D  H37  H  HNH1  0   0.420  30.3115  -85.2801  -1.5758

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
 W9D  O30  C27  double    1.204  0.020  1.204
 W9D  C27  O26  single    1.341  0.020  1.341
 W9D  C27  C17  single    1.460  0.020  1.460
 W9D  O26  C25  single    1.448  0.020  1.448
 W9D  C17  C18  aromatic  1.389  0.020  1.389
 W9D  C17  C16  aromatic  1.378  0.020  1.378
 W9D  C18  C19  aromatic  1.376  0.020  1.376
 W9D  C28  C25  single    1.520  0.020  1.520
 W9D  C25  C16  single    1.503  0.020  1.503
 W9D  C25  C29  single    1.520  0.020  1.520
 W9D  C16  C15  aromatic  1.381  0.020  1.381
 W9D  C19  C14  aromatic  1.412  0.020  1.412
 W9D  C15  C14  aromatic  1.399  0.020  1.399
 W9D  C14  N9   single    1.382  0.020  1.382
 W9D  N9   C4   single    1.362  0.020  1.362
 W9D  C21  C20  aromatic  1.388  0.020  1.388
 W9D  C21  C22  aromatic  1.389  0.020  1.389
 W9D  C20  C12  aromatic  1.394  0.020  1.394
 W9D  C22  C23  aromatic  1.387  0.020  1.387
 W9D  C4   N5   aromatic  1.319  0.020  1.319
 W9D  C4   N3   aromatic  1.339  0.020  1.339
 W9D  N5   C6   aromatic  1.335  0.020  1.335
 W9D  C12  C10  single    1.519  0.020  1.519
 W9D  C12  C24  aromatic  1.390  0.020  1.390
 W9D  C23  C24  aromatic  1.390  0.020  1.390
 W9D  C10  C11  single    1.524  0.020  1.524
 W9D  C10  N8   single    1.444  0.020  1.444
 W9D  N3   C2   aromatic  1.316  0.020  1.316
 W9D  C11  O13  single    1.408  0.020  1.408
 W9D  C6   N8   single    1.337  0.020  1.337
 W9D  C6   C1   aromatic  1.422  0.020  1.422
 W9D  C2   C1   aromatic  1.389  0.020  1.389
 W9D  C1   C7   single    1.443  0.020  1.443
 W9D  C7   O31  aromatic  1.346  0.020  1.346
 W9D  C7   N34  aromatic  1.291  0.020  1.291
 W9D  O31  C32  aromatic  1.344  0.020  1.344
 W9D  N34  N33  aromatic  1.371  0.020  1.371
 W9D  C32  N33  aromatic  1.279  0.020  1.279
 W9D  C18  H43  single    0.930  0.020  1.080
 W9D  C15  H42  single    0.930  0.020  1.080
 W9D  C19  H44  single    0.930  0.020  1.080
 W9D  C20  H45  single    0.930  0.020  1.080
 W9D  C21  H46  single    0.930  0.020  1.080
 W9D  C22  H47  single    0.930  0.020  1.080
 W9D  C23  H48  single    0.930  0.020  1.080
 W9D  C24  H49  single    0.930  0.020  1.080
 W9D  C11  H39  single    0.970  0.020  1.090
 W9D  C11  H40  single    0.970  0.020  1.090
 W9D  C2   H35  single    0.930  0.020  1.080
 W9D  N8   H36  single    0.860  0.020  1.020
 W9D  N9   H37  single    0.860  0.020  1.020
 W9D  C10  H38  single    0.970  0.020  1.090
 W9D  O13  H41  single    0.850  0.020  0.980
 W9D  C28  H52  single    0.970  0.020  1.090
 W9D  C28  H50  single    0.970  0.020  1.090
 W9D  C28  H51  single    0.970  0.020  1.090
 W9D  C29  H53  single    0.970  0.020  1.090
 W9D  C29  H54  single    0.970  0.020  1.090
 W9D  C29  H55  single    0.970  0.020  1.090
 W9D  C32  H56  single    0.930  0.020  1.080

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
 W9D  H43  C18  C19  120.43  3.000
 W9D  H43  C18  C17  121.72  3.000
 W9D  C19  C18  C17  117.85  3.000
 W9D  C27  C17  C16  108.32  3.000
 W9D  C16  C17  C18  120.96  3.000
 W9D  C27  C17  C18  130.72  3.000
 W9D  C25  C16  C15  129.11  3.000
 W9D  C15  C16  C17  122.29  3.000
 W9D  C25  C16  C17  108.60  3.000
 W9D  H42  C15  C14  120.76  3.000
 W9D  H42  C15  C16  121.79  3.000
 W9D  C14  C15  C16  117.44  3.000
 W9D  H44  C19  C14  119.05  3.000
 W9D  H44  C19  C18  119.46  3.000
 W9D  C14  C19  C18  121.49  3.000
 W9D  H45  C20  C12  120.01  3.000
 W9D  H45  C20  C21  119.05  3.000
 W9D  C12  C20  C21  120.94  3.000
 W9D  H46  C21  C22  120.32  3.000
 W9D  H46  C21  C20  119.61  3.000
 W9D  C22  C21  C20  120.07  3.000
 W9D  H47  C22  C23  120.29  3.000
 W9D  H47  C22  C21  120.32  3.000
 W9D  C23  C22  C21  119.39  3.000
 W9D  H48  C23  C24  119.60  3.000
 W9D  H48  C23  C22  120.00  3.000
 W9D  C24  C23  C22  120.40  3.000
 W9D  H49  C24  C12  120.25  3.000
 W9D  H49  C24  C23  119.08  3.000
 W9D  C12  C24  C23  120.67  3.000
 W9D  H40  C11  H39  107.31  3.000
 W9D  H40  C11  O13  112.07  3.000
 W9D  H39  C11  O13  111.88  3.000
 W9D  H40  C11  C10  108.95  3.000
 W9D  H39  C11  C10  108.38  3.000
 W9D  O13  C11  C10  108.15  3.000
 W9D  C10  C12  C24  122.30  3.000
 W9D  C24  C12  C20  118.54  3.000
 W9D  C10  C12  C20  119.16  3.000
 W9D  O30  C27  O26  122.13  3.000
 W9D  O26  C27  C17  107.97  3.000
 W9D  O30  C27  C17  129.90  3.000
 W9D  C7   C1   C6   125.82  3.000
 W9D  C7   C1   C2   118.55  3.000
 W9D  C6   C1   C2   115.63  3.000
 W9D  H35  C2   N3   116.45  3.000
 W9D  H35  C2   C1   119.27  3.000
 W9D  N3   C2   C1   124.28  3.000
 W9D  C4   N3   C2   115.30  3.000
 W9D  N9   C4   N5   120.38  3.000
 W9D  N5   C4   N3   126.46  3.000
 W9D  N9   C4   N3   113.15  3.000
 W9D  C6   N5   C4   118.39  3.000
 W9D  N8   C6   N5   117.58  3.000
 W9D  N8   C6   C1   122.56  3.000
 W9D  N5   C6   C1   119.84  3.000
 W9D  N34  C7   O31  111.18  3.000
 W9D  N34  C7   C1   127.90  3.000
 W9D  O31  C7   C1   120.84  3.000
 W9D  H36  N8   C10  115.29  3.000
 W9D  H36  N8   C6   119.37  3.000
 W9D  C10  N8   C6   125.30  3.000
 W9D  H38  C10  N8   108.34  3.000
 W9D  H38  C10  C12  108.91  3.000
 W9D  N8   C10  C12  112.62  3.000
 W9D  H38  C10  C11  107.03  3.000
 W9D  N8   C10  C11  108.09  3.000
 W9D  C12  C10  C11  111.64  3.000
 W9D  N9   C14  C19  115.52  3.000
 W9D  N9   C14  C15  124.52  3.000
 W9D  C19  C14  C15  119.96  3.000
 W9D  C29  C25  C28  112.28  3.000
 W9D  C29  C25  O26  108.48  3.000
 W9D  C28  C25  O26  108.39  3.000
 W9D  C29  C25  C16  112.16  3.000
 W9D  C28  C25  C16  112.12  3.000
 W9D  O26  C25  C16  102.86  3.000
 W9D  C25  O26  C27  112.24  3.000
 W9D  H51  C28  H50  108.83  3.000
 W9D  H51  C28  H52  107.96  3.000
 W9D  H50  C28  H52  107.81  3.000
 W9D  H51  C28  C25  111.36  3.000
 W9D  H50  C28  C25  110.85  3.000
 W9D  H52  C28  C25  109.91  3.000
 W9D  H55  C29  H54  108.87  3.000
 W9D  H55  C29  H53  107.81  3.000
 W9D  H54  C29  H53  107.73  3.000
 W9D  H55  C29  C25  111.02  3.000
 W9D  H54  C29  C25  111.45  3.000
 W9D  H53  C29  C25  109.84  3.000
 W9D  C32  O31  C7   103.38  3.000
 W9D  H56  C32  N33  129.16  3.000
 W9D  H56  C32  O31  118.87  3.000
 W9D  N33  C32  O31  111.97  3.000
 W9D  N34  N33  C32  106.70  3.000
 W9D  N33  N34  C7   106.76  3.000
 W9D  H37  N9   C14  115.37  3.000
 W9D  H37  N9   C4   112.37  3.000
 W9D  C14  N9   C4   132.15  3.000
 W9D  H41  O13  C11  108.48  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
 W9D  CONST_01  C15  C16  C17  C18     0.00   0.0  0
 W9D  CONST_02  C15  C14  C19  C18     0.00   0.0  0
 W9D  CONST_03  C14  C19  C18  C17     0.00   0.0  0
 W9D  CONST_04  C14  C15  C16  C17     0.00   0.0  0
 W9D  CONST_05  C19  C18  C17  C16     0.00   0.0  0
 W9D  CONST_06  C19  C14  C15  C16     0.00   0.0  0
 W9D  CONST_07  C23  C22  C21  C20     0.00   0.0  0
 W9D  CONST_08  C23  C24  C12  C20     0.00   0.0  0
 W9D  CONST_09  C24  C12  C20  C21     0.00   0.0  0
 W9D  CONST_10  C24  C23  C22  C21     0.00   0.0  0
 W9D  CONST_11  C12  C20  C21  C22     0.00   0.0  0
 W9D  CONST_12  C12  C24  C23  C22     0.00   0.0  0
 W9D  CONST_13  C4   N5   C6   C1      0.00   0.0  0
 W9D  CONST_14  C4   N3   C2   C1      0.00   0.0  0
 W9D  CONST_15  C32  O31  C7   C1    180.00   0.0  0
 W9D  CONST_16  N33  N34  C7   C1    180.00   0.0  0
 W9D  CONST_17  N5   C4   N3   C2      0.00   0.0  0
 W9D  CONST_18  N5   C6   C1   C2      0.00   0.0  0
 W9D  CONST_21  C6   N5   C4   N3      0.00   0.0  0
 W9D  CONST_22  C6   C1   C2   N3      0.00   0.0  0
 W9D  CONST_23  C7   C1   C2   N3    180.00   0.0  0
 W9D  CONST_24  C7   C1   C6   N5    180.00   0.0  0
 W9D  CONST_27  N33  C32  O31  C7      0.00   0.0  0
 W9D  CONST_28  C32  N33  N34  C7      0.00   0.0  0
 W9D  CONST_29  N33  N34  C7   O31     0.00   0.0  0
 W9D  CONST_30  N34  N33  C32  O31     0.00   0.0  0
 W9D  CONST_31  N34  C7   O31  C32     0.00   0.0  0
 W9D  CONST_32  N9   C14  C19  C18   180.00   0.0  0
 W9D  CONST_33  N9   C14  C15  C16   180.00   0.0  0
 W9D  CONST_34  C10  C12  C20  C21   180.00   0.0  0
 W9D  CONST_35  C10  C12  C24  C23   180.00   0.0  0
 W9D  CONST_36  N9   C4   N3   C2    180.00   0.0  0
 W9D  CONST_37  N8   C6   C1   C2    180.00   0.0  0
 W9D  CONST_38  N8   C6   N5   C4    180.00   0.0  0
 W9D  CONST_39  N9   C4   N5   C6    180.00   0.0  0
 W9D  CONST_40  N8   C6   C1   C7      0.00   0.0  0
 W9D  CONST_41  H44  C19  C18  C17   180.00   0.0  0
 W9D  CONST_42  H42  C15  C16  C17   180.00   0.0  0
 W9D  CONST_43  H43  C18  C17  C16   180.00   0.0  0
 W9D  CONST_44  H47  C22  C21  C20   180.00   0.0  0
 W9D  CONST_45  H49  C24  C12  C20   180.00   0.0  0
 W9D  CONST_46  H48  C23  C22  C21   180.00   0.0  0
 W9D  CONST_47  H45  C20  C21  C22   180.00   0.0  0
 W9D  CONST_48  H46  C21  C22  C23   180.00   0.0  0
 W9D  CONST_49  H35  C2   N3   C4    180.00   0.0  0
 W9D  CONST_50  H56  C32  O31  C7    180.00   0.0  0
 W9D  CONST_51  C10  N8   C6   C1    180.00   0.0  0
 W9D  CONST_52  C10  N8   C6   N5      0.00   0.0  0
 W9D  CONST_53  H36  N8   C6   C1      0.00   0.0  0
 W9D  Var_01    O26  C27  C17  C18  -179.86  30.0  1
 W9D  Var_02    O26  C25  C16  C17    -0.38  30.0  1
 W9D  Var_03    C4   N9   C14  C15   -10.79  30.0  2
 W9D  Var_04    C14  N9   C4   N3   -177.61  30.0  1
 W9D  Var_05    H52  C28  C25  C16    63.73  30.0  3
 W9D  Var_06    H53  C29  C25  C16   -63.29  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
 W9D  chir_01  C10  C12  C11  N8  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
 W9D  plan-1  C1   0.020
 W9D  plan-1  C7   0.020
 W9D  plan-1  O31  0.020
 W9D  plan-1  C32  0.020
 W9D  plan-1  N33  0.020
 W9D  plan-1  N34  0.020
 W9D  plan-1  H56  0.020
 W9D  plan-2  C20  0.020
 W9D  plan-2  C21  0.020
 W9D  plan-2  C22  0.020
 W9D  plan-2  C23  0.020
 W9D  plan-2  C24  0.020
 W9D  plan-2  C12  0.020
 W9D  plan-2  C10  0.020
 W9D  plan-2  H45  0.020
 W9D  plan-2  H46  0.020
 W9D  plan-2  H47  0.020
 W9D  plan-2  H48  0.020
 W9D  plan-2  H49  0.020
 W9D  plan-3  C18  0.020
 W9D  plan-3  C17  0.020
 W9D  plan-3  C16  0.020
 W9D  plan-3  C15  0.020
 W9D  plan-3  C19  0.020
 W9D  plan-3  C27  0.020
 W9D  plan-3  C14  0.020
 W9D  plan-3  C25  0.020
 W9D  plan-3  H43  0.020
 W9D  plan-3  H42  0.020
 W9D  plan-3  H44  0.020
 W9D  plan-3  N9   0.020
 W9D  plan-4  C1   0.020
 W9D  plan-4  C2   0.020
 W9D  plan-4  N3   0.020
 W9D  plan-4  C4   0.020
 W9D  plan-4  N5   0.020
 W9D  plan-4  C6   0.020
 W9D  plan-4  C7   0.020
 W9D  plan-4  N8   0.020
 W9D  plan-4  H35  0.020
 W9D  plan-4  N9   0.020
 W9D  plan-5  C6   0.020
 W9D  plan-5  N8   0.020
 W9D  plan-5  C10  0.020
 W9D  plan-5  H36  0.020
 W9D  plan-6  C17  0.020
 W9D  plan-6  C27  0.020
 W9D  plan-6  O26  0.020
 W9D  plan-6  O30  0.020

