# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 16:11:09 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: ~{N}-~{tert}-butyl-2-[5-[5-chloranyl-2-(oxan-4-ylamino)pyrimidin-4-yl]-3-oxidanylidene-1~{H}-isoindol-2-yl]-~{N}-methyl-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C(=O)CN1Cc2ccc(cc2C1=O)c3nc(NC4CCOCC4)ncc3Cl)C(C)(C)C
#
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
 ERW  ERW  ~{N}-~{tert}-butyl-2-[5-[5-chloranyl-2-(oxan-4-ylamino)pyrimidin-4-yl]-3-oxidanylidene-1~{H}-isoindol-2-yl]-~{N}-methyl-ethanamide  ligand  63  33  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ERW
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
 ERW  C1   C   CH3   0  -0.547  -7.2677  -1.7773   1.2178
 ERW  C3   C   C     0   0.574  -5.3916  -0.6894   0.1095
 ERW  C5   C   CH2   0  -0.457  -4.6492  -0.7966   1.4536
 ERW  C7   C   CH2   0  -0.273  -3.2534   1.2875   1.6254
 ERW  C8   C   CR56  0   0.080  -1.8274   1.5412   1.2589
 ERW  C10  C   CR16  0  -0.266   0.2439   2.6501   0.8962
 ERW  C11  C   CR6   0   0.050   0.8134   1.4644   0.4176
 ERW  C12  C   CR16  0  -0.332   0.0546   0.2977   0.3823
 ERW  C13  C   CR56  0  -0.056  -1.2613   0.3643   0.7986
 ERW  C14  C   CR5   0   0.554  -2.2826  -0.7035   0.8467
 ERW  C16  C   CR6   0   0.324   2.2283   1.4083  -0.0074
 ERW  C21  C   CH2   0  -0.470   6.8782  -1.9977   1.2792
 ERW  C22  C   CH2   0  -0.184   8.2750  -2.4231   0.8498
 ERW  C24  C   CH2   0  -0.186   7.7649  -2.2521  -1.4244
 ERW  C25  C   CH2   0  -0.457   6.3326  -1.8222  -1.1463
 ERW  C27  C   CR16  0   0.032   4.1626   2.1563  -1.1620
 ERW  C28  C   CR6   0  -0.203   2.8234   2.3422  -0.8592
 ERW  C31  C   CH3   0  -0.646  -6.7200  -1.7279  -2.4074
 ERW  N2   N   NT    0  -0.474  -6.6245  -1.2324   0.0323
 ERW  O4   O   O     0  -0.490  -4.8275  -0.1294  -0.8180
 ERW  N6   N   NR5   0  -0.494  -3.3858  -0.1345   1.3904
 ERW  C9   C   CR16  0  -0.305  -1.0751   2.6997   1.3251
 ERW  N17  N   N     0  -0.477   2.9316   0.3836   0.4453
 ERW  C18  C   CR6   0   0.602   4.2170   0.2785   0.0883
 ERW  N19  N   NH1   0  -0.666   4.8960  -0.7710   0.5789
 ERW  C20  C   CH1   0  -0.063   6.2504  -1.1154   0.2068
 ERW  O23  O   O2    0  -0.483   8.2724  -3.0783  -0.3990
 ERW  N26  N   N     0  -0.454   4.8676   1.1462  -0.6961
 ERW  CL2  CL  CL    0  -0.117   1.9664   3.6455  -1.5996
 ERW  C30  C   CT    0   0.093  -7.4349  -1.0853  -1.2147
 ERW  C32  C   CH3   0  -0.643  -7.7330   0.3940  -1.4774
 ERW  C33  C   CH3   0  -0.690  -8.7776  -1.8084  -1.0650
 ERW  H36  H   HCH3  0   0.244  -8.0111  -1.0927   1.6315
 ERW  H35  H   HCH3  0   0.258  -7.7555  -2.7223   0.9971
 ERW  H34  H   HCH3  0   0.279  -6.5458  -1.9864   1.9979
 ERW  H37  H   HCH2  0   0.298  -5.2343  -0.3520   2.2603
 ERW  H38  H   HCH2  0   0.299  -4.4923  -1.8443   1.7174
 ERW  H39  H   HCH2  0   0.277  -3.4648   1.5401   2.6679
 ERW  H40  H   HCH2  0   0.275  -3.9400   1.8628   0.9977
 ERW  H42  H   HCR6  0   0.268   0.8452   3.5467   0.9584
 ERW  H43  H   HCR6  0   0.262   0.4824  -0.6321   0.0295
 ERW  H47  H   HCH2  0   0.250   6.9408  -1.4617   2.2291
 ERW  H48  H   HCH2  0   0.200   8.9291  -1.5396   0.8137
 ERW  H49  H   HCH2  0   0.241   8.7025  -3.1164   1.5755
 ERW  H51  H   HCH2  0   0.239   7.8227  -2.8213  -2.3535
 ERW  H50  H   HCH2  0   0.199   8.3992  -1.3608  -1.5435
 ERW  H52  H   HCH2  0   0.243   5.9905  -1.1593  -1.9441
 ERW  H53  H   HCH2  0   0.227   5.6745  -2.6964  -1.1401
 ERW  H54  H   HCR6  0   0.290   4.6734   2.8539  -1.8174
 ERW  H57  H   HCH3  0   0.227  -6.4541  -2.7623  -2.1824
 ERW  H56  H   HCH3  0   0.224  -7.3939  -1.7408  -3.2658
 ERW  H55  H   HCH3  0   0.245  -5.8199  -1.1948  -2.6970
 ERW  H41  H   HCR6  0   0.266  -1.4920   3.6251   1.7002
 ERW  H44  H   HNH1  0   0.392   4.3525  -1.4542   1.0829
 ERW  H45  H   HCH1  0   0.245   6.8244  -0.1864   0.1474
 ERW  H59  H   HCH3  0   0.242  -6.8339   0.9637  -1.6975
 ERW  H58  H   HCH3  0   0.225  -8.4061   0.4880  -2.3312
 ERW  H60  H   HCH3  0   0.226  -8.2281   0.8466  -0.6161
 ERW  H61  H   HCH3  0   0.241  -9.3868  -1.4145  -0.2516
 ERW  H63  H   HCH3  0   0.250  -9.3412  -1.6634  -1.9864
 ERW  H62  H   HCH3  0   0.240  -8.6617  -2.8839  -0.9261
 ERW  O15  O   O     0  -0.477  -2.1695  -1.8646   0.4940
 ERW  H46  H   HCH2  0   0.232   6.2584  -2.8853   1.4451

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
 ERW  O23  C24  single    1.411  0.020  1.411
 ERW  O23  C22  single    1.410  0.020  1.410
 ERW  C24  C25  single    1.521  0.020  1.521
 ERW  C25  C20  single    1.529  0.020  1.529
 ERW  C22  C21  single    1.522  0.020  1.522
 ERW  C21  C20  single    1.524  0.020  1.524
 ERW  C20  N19  single    1.446  0.020  1.446
 ERW  N19  C18  single    1.343  0.020  1.343
 ERW  C18  N17  aromatic  1.338  0.020  1.338
 ERW  C18  N26  aromatic  1.338  0.020  1.338
 ERW  N17  C16  aromatic  1.323  0.020  1.323
 ERW  N26  C27  aromatic  1.317  0.020  1.317
 ERW  C16  C11  single    1.478  0.020  1.478
 ERW  C16  C28  aromatic  1.397  0.020  1.397
 ERW  C11  C10  aromatic  1.400  0.020  1.400
 ERW  C11  C12  aromatic  1.392  0.020  1.392
 ERW  C27  C28  aromatic  1.386  0.020  1.386
 ERW  C10  C9   aromatic  1.388  0.020  1.388
 ERW  C12  C13  aromatic  1.382  0.020  1.382
 ERW  C9   C8   aromatic  1.383  0.020  1.383
 ERW  C13  C8   aromatic  1.385  0.020  1.385
 ERW  C13  C14  single    1.478  0.020  1.478
 ERW  C28  CL2  single    1.727  0.020  1.727
 ERW  C8   C7   single    1.494  0.020  1.494
 ERW  C14  O15  double    1.219  0.020  1.219
 ERW  C14  N6   single    1.355  0.020  1.355
 ERW  C7   N6   single    1.447  0.020  1.447
 ERW  N6   C5   single    1.428  0.020  1.428
 ERW  C5   C3   single    1.539  0.020  1.539
 ERW  C1   N2   single    1.455  0.020  1.455
 ERW  C3   N2   single    1.349  0.020  1.349
 ERW  C3   O4   double    1.222  0.020  1.222
 ERW  N2   C30  single    1.494  0.020  1.494
 ERW  C30  C33  single    1.532  0.020  1.532
 ERW  C30  C31  single    1.532  0.020  1.532
 ERW  C30  C32  single    1.532  0.020  1.532
 ERW  C1   H36  single    0.970  0.020  1.090
 ERW  C1   H35  single    0.970  0.020  1.090
 ERW  C1   H34  single    0.970  0.020  1.090
 ERW  C5   H37  single    0.970  0.020  1.090
 ERW  C5   H38  single    0.970  0.020  1.090
 ERW  C7   H39  single    0.970  0.020  1.090
 ERW  C7   H40  single    0.970  0.020  1.090
 ERW  C10  H42  single    0.930  0.020  1.080
 ERW  C12  H43  single    0.930  0.020  1.080
 ERW  C21  H46  single    0.970  0.020  1.090
 ERW  C21  H47  single    0.970  0.020  1.090
 ERW  C22  H48  single    0.970  0.020  1.090
 ERW  C22  H49  single    0.970  0.020  1.090
 ERW  C24  H51  single    0.970  0.020  1.090
 ERW  C24  H50  single    0.970  0.020  1.090
 ERW  C25  H52  single    0.970  0.020  1.090
 ERW  C25  H53  single    0.970  0.020  1.090
 ERW  C27  H54  single    0.930  0.020  1.080
 ERW  C31  H57  single    0.970  0.020  1.090
 ERW  C31  H56  single    0.970  0.020  1.090
 ERW  C31  H55  single    0.970  0.020  1.090
 ERW  C9   H41  single    0.930  0.020  1.080
 ERW  N19  H44  single    0.860  0.020  1.020
 ERW  C20  H45  single    0.970  0.020  1.090
 ERW  C32  H59  single    0.970  0.020  1.090
 ERW  C32  H58  single    0.970  0.020  1.090
 ERW  C32  H60  single    0.970  0.020  1.090
 ERW  C33  H61  single    0.970  0.020  1.090
 ERW  C33  H63  single    0.970  0.020  1.090
 ERW  C33  H62  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
 ERW  H34  C1   H35  106.12  3.000
 ERW  H34  C1   H36  107.57  3.000
 ERW  H35  C1   H36  108.47  3.000
 ERW  H34  C1   N2   111.37  3.000
 ERW  H35  C1   N2   111.04  3.000
 ERW  H36  C1   N2   112.02  3.000
 ERW  O4   C3   N2   124.26  3.000
 ERW  O4   C3   C5   118.18  3.000
 ERW  N2   C3   C5   117.56  3.000
 ERW  H38  C5   H37  106.82  3.000
 ERW  H38  C5   N6   109.18  3.000
 ERW  H37  C5   N6   108.56  3.000
 ERW  H38  C5   C3   110.31  3.000
 ERW  H37  C5   C3   111.01  3.000
 ERW  N6   C5   C3   110.85  3.000
 ERW  H40  C7   H39  107.72  3.000
 ERW  H40  C7   N6   111.48  3.000
 ERW  H39  C7   N6   111.35  3.000
 ERW  H40  C7   C8   111.66  3.000
 ERW  H39  C7   C8   112.28  3.000
 ERW  N6   C7   C8   102.37  3.000
 ERW  C9   C8   C13  120.37  3.000
 ERW  C13  C8   C7   109.11  3.000
 ERW  C9   C8   C7   130.52  3.000
 ERW  H42  C10  C9   118.76  3.000
 ERW  H42  C10  C11  119.72  3.000
 ERW  C9   C10  C11  121.51  3.000
 ERW  C16  C11  C12  118.85  3.000
 ERW  C12  C11  C10  119.79  3.000
 ERW  C16  C11  C10  121.32  3.000
 ERW  H43  C12  C13  121.05  3.000
 ERW  H43  C12  C11  120.85  3.000
 ERW  C13  C12  C11  118.10  3.000
 ERW  C14  C13  C12  129.26  3.000
 ERW  C14  C13  C8   108.70  3.000
 ERW  C12  C13  C8   122.04  3.000
 ERW  O15  C14  N6   126.28  3.000
 ERW  N6   C14  C13  105.79  3.000
 ERW  O15  C14  C13  127.92  3.000
 ERW  N17  C16  C28  120.00  3.000
 ERW  C28  C16  C11  123.89  3.000
 ERW  N17  C16  C11  116.10  3.000
 ERW  H47  C21  H46  107.36  3.000
 ERW  H47  C21  C20  110.57  3.000
 ERW  H46  C21  C20  110.04  3.000
 ERW  H47  C21  C22  109.26  3.000
 ERW  H46  C21  C22  109.61  3.000
 ERW  C20  C21  C22  109.96  3.000
 ERW  H49  C22  H48  107.41  3.000
 ERW  H49  C22  O23  107.13  3.000
 ERW  H48  C22  O23  110.20  3.000
 ERW  H49  C22  C21  110.46  3.000
 ERW  H48  C22  C21  109.30  3.000
 ERW  O23  C22  C21  112.21  3.000
 ERW  H50  C24  H51  107.45  3.000
 ERW  H50  C24  O23  110.21  3.000
 ERW  H51  C24  O23  107.11  3.000
 ERW  H50  C24  C25  109.49  3.000
 ERW  H51  C24  C25  110.67  3.000
 ERW  O23  C24  C25  111.79  3.000
 ERW  H53  C25  H52  107.49  3.000
 ERW  H53  C25  C20  109.39  3.000
 ERW  H52  C25  C20  110.43  3.000
 ERW  H53  C25  C24  109.97  3.000
 ERW  H52  C25  C24  109.45  3.000
 ERW  C20  C25  C24  110.07  3.000
 ERW  H54  C27  N26  117.06  3.000
 ERW  H54  C27  C28  120.05  3.000
 ERW  N26  C27  C28  122.89  3.000
 ERW  CL2  C28  C27  119.17  3.000
 ERW  CL2  C28  C16  123.68  3.000
 ERW  C27  C28  C16  117.08  3.000
 ERW  H55  C31  H56  107.94  3.000
 ERW  H55  C31  H57  108.57  3.000
 ERW  H56  C31  H57  107.54  3.000
 ERW  H55  C31  C30  112.87  3.000
 ERW  H56  C31  C30  109.22  3.000
 ERW  H57  C31  C30  110.54  3.000
 ERW  C30  N2   C3   120.24  3.000
 ERW  C30  N2   C1   118.50  3.000
 ERW  C3   N2   C1   120.54  3.000
 ERW  C14  N6   C7   113.78  3.000
 ERW  C7   N6   C5   121.96  3.000
 ERW  C14  N6   C5   122.91  3.000
 ERW  H41  C9   C10  120.25  3.000
 ERW  H41  C9   C8   121.56  3.000
 ERW  C10  C9   C8   118.18  3.000
 ERW  C18  N17  C16  118.70  3.000
 ERW  N26  C18  N19  118.36  3.000
 ERW  N26  C18  N17  124.92  3.000
 ERW  N19  C18  N17  116.72  3.000
 ERW  H44  N19  C20  118.18  3.000
 ERW  H44  N19  C18  116.08  3.000
 ERW  C20  N19  C18  124.45  3.000
 ERW  H45  C20  N19  107.65  3.000
 ERW  H45  C20  C25  108.45  3.000
 ERW  N19  C20  C25  112.84  3.000
 ERW  H45  C20  C21  108.29  3.000
 ERW  N19  C20  C21  110.04  3.000
 ERW  C25  C20  C21  109.45  3.000
 ERW  C24  O23  C22  111.84  3.000
 ERW  C18  N26  C27  116.38  3.000
 ERW  C33  C30  C32  107.58  3.000
 ERW  C32  C30  N2   110.10  3.000
 ERW  C33  C30  N2   110.31  3.000
 ERW  C32  C30  C31  111.25  3.000
 ERW  C33  C30  C31  106.68  3.000
 ERW  N2   C30  C31  110.81  3.000
 ERW  H60  C32  H58  107.57  3.000
 ERW  H60  C32  H59  108.52  3.000
 ERW  H58  C32  H59  107.85  3.000
 ERW  H60  C32  C30  110.70  3.000
 ERW  H58  C32  C30  109.72  3.000
 ERW  H59  C32  C30  112.33  3.000
 ERW  H62  C33  H63  107.09  3.000
 ERW  H62  C33  H61  108.71  3.000
 ERW  H63  C33  H61  107.08  3.000
 ERW  H62  C33  C30  112.63  3.000
 ERW  H63  C33  C30  107.92  3.000
 ERW  H61  C33  C30  113.09  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
 ERW  CONST_01  C11  C10  C9   C8      0.00   0.0  0
 ERW  CONST_02  C11  C12  C13  C8      0.00   0.0  0
 ERW  CONST_05  C13  C12  C11  C10     0.00   0.0  0
 ERW  CONST_06  C13  C8   C9   C10     0.00   0.0  0
 ERW  CONST_07  C18  N17  C16  C11   180.00   0.0  0
 ERW  CONST_08  C27  C28  C16  C11   180.00   0.0  0
 ERW  CONST_11  C9   C10  C11  C12     0.00   0.0  0
 ERW  CONST_12  C9   C8   C13  C12     0.00   0.0  0
 ERW  CONST_13  C16  C11  C12  C13   180.00   0.0  0
 ERW  CONST_14  N26  C18  N17  C16     0.00   0.0  0
 ERW  CONST_15  C9   C10  C11  C16   180.00   0.0  0
 ERW  CONST_16  N26  C27  C28  C16     0.00   0.0  0
 ERW  CONST_17  N17  C18  N26  C27     0.00   0.0  0
 ERW  CONST_18  N17  C16  C28  C27     0.00   0.0  0
 ERW  CONST_19  C18  N17  C16  C28     0.00   0.0  0
 ERW  CONST_20  C18  N26  C27  C28     0.00   0.0  0
 ERW  CONST_21  C13  C14  N6   C7      0.00   0.0  0
 ERW  CONST_22  CL2  C28  C16  C11     0.00   0.0  0
 ERW  CONST_23  N19  C18  N17  C16   180.00   0.0  0
 ERW  CONST_24  N19  C18  N26  C27   180.00   0.0  0
 ERW  CONST_25  CL2  C28  C16  N17   180.00   0.0  0
 ERW  CONST_26  CL2  C28  C27  N26   180.00   0.0  0
 ERW  CONST_27  C20  N19  C18  N17   180.00   0.0  0
 ERW  CONST_28  N26  C18  N19  C20     0.00   0.0  0
 ERW  CONST_29  C13  C14  N6   C5    180.00   0.0  0
 ERW  CONST_30  O15  C14  N6   C7    180.00   0.0  0
 ERW  CONST_31  H41  C9   C8   C7      0.00   0.0  0
 ERW  CONST_32  H42  C10  C9   C8    180.00   0.0  0
 ERW  CONST_33  H43  C12  C13  C8    180.00   0.0  0
 ERW  CONST_34  H54  C27  C28  C16   180.00   0.0  0
 ERW  CONST_35  O15  C14  N6   C5      0.00   0.0  0
 ERW  CONST_36  H44  N19  C18  N17     0.00   0.0  0
 ERW  CONST_37  C5   C3   N2   C1      0.00   0.0  0
 ERW  CONST_38  O4   C3   N2   C1    180.00   0.0  0
 ERW  CONST_39  C30  N2   C3   C5    180.00   0.0  0
 ERW  CONST_40  C30  N2   C3   O4      0.00   0.0  0
 ERW  Var_01    C25  C24  O23  C22   -60.10  30.0  1
 ERW  Var_02    O23  C24  C25  C20    56.57  30.0  1
 ERW  Var_03    O23  C22  C21  C20   -56.21  30.0  1
 ERW  Var_04    H39  C7   C8   C13   122.38  30.0  1
 ERW  Var_05    H48  C22  O23  C24   -62.02  30.0  1
 ERW  Var_06    C14  N6   C5   C3    -81.07  30.0  2
 ERW  Var_07    N6   C5   C3   N2   -177.83  30.0  1
 ERW  Var_08    C33  C30  N2   C1    -10.84  30.0  3
 ERW  Var_09    H36  C1   N2   C3    101.38  30.0  3
 ERW  Var_10    H61  C33  C30  C31  -178.72  30.0  3
 ERW  Var_11    H59  C32  C30  C31   -57.63  30.0  3
 ERW  Var_12    H57  C31  C30  N2     53.39  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
 ERW  chir_01  C20  C25  C21  N19  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
 ERW  plan-1  C11  0.020
 ERW  plan-1  C16  0.020
 ERW  plan-1  C27  0.020
 ERW  plan-1  C28  0.020
 ERW  plan-1  N17  0.020
 ERW  plan-1  C18  0.020
 ERW  plan-1  N19  0.020
 ERW  plan-1  N26  0.020
 ERW  plan-1  CL2  0.020
 ERW  plan-1  H54  0.020
 ERW  plan-2  C1   0.020
 ERW  plan-2  C3   0.020
 ERW  plan-2  C5   0.020
 ERW  plan-2  N2   0.020
 ERW  plan-2  O4   0.020
 ERW  plan-2  C30  0.020
 ERW  plan-3  C18  0.020
 ERW  plan-3  N19  0.020
 ERW  plan-3  C20  0.020
 ERW  plan-3  H44  0.020
 ERW  plan-4  C5   0.020
 ERW  plan-4  C7   0.020
 ERW  plan-4  C8   0.020
 ERW  plan-4  C10  0.020
 ERW  plan-4  C11  0.020
 ERW  plan-4  C12  0.020
 ERW  plan-4  C13  0.020
 ERW  plan-4  C14  0.020
 ERW  plan-4  C16  0.020
 ERW  plan-4  N6   0.020
 ERW  plan-4  C9   0.020
 ERW  plan-4  H42  0.020
 ERW  plan-4  H43  0.020
 ERW  plan-4  H41  0.020
 ERW  plan-4  O15  0.020

