# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 12:53:44 2020
#   Inital geometry file: a 143 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]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)NC(=O)CN1Cc2ccc(cc2C1=O)c3nc(NC4CCOCC4)ncc3Cl
#
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
 ER8  ER8  ~{N}-~{tert}-butyl-2-[5-[5-chloranyl-2-(oxan-4-ylamino)pyrimidin-4-yl]-3-oxidanylidene-1~{H}-isoindol-2-yl]ethanamide  ligand  60  32  .  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_ER8
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
 ER8  C1   C   CH3   0  -0.643   7.3770   2.0685  -2.1969
 ER8  C2   C   CT    0   0.099   7.8403   1.2158  -1.0157
 ER8  C3   C   CH3   0  -0.641   8.1115  -0.2231  -1.4566
 ER8  C6   C   C     0   0.552   5.5771   0.8323   0.0078
 ER8  C8   C   CH2   0  -0.444   4.7952   1.0623   1.3052
 ER8  C10  C   CH2   0  -0.272   3.4435  -1.0366   1.5811
 ER8  C11  C   CR56  0   0.081   2.0222  -1.3373   1.2321
 ER8  C12  C   CR16  0  -0.305   1.3015  -2.5133   1.3353
 ER8  C13  C   CR16  0  -0.264  -0.0199  -2.5108   0.9113
 ER8  C14  C   CR6   0   0.048  -0.6229  -1.3534   0.4058
 ER8  C15  C   CR16  0  -0.331   0.1035  -0.1685   0.3323
 ER8  C16  C   CR56  0  -0.057   1.4237  -0.1898   0.7406
 ER8  C19  C   CR6   0   0.320  -2.0412  -1.3485  -0.0119
 ER8  C21  C   CR6   0   0.601  -4.0720  -0.2991   0.0957
 ER8  C23  C   CH1   0  -0.067  -6.1620   1.0077   0.2501
 ER8  C24  C   CH2   0  -0.469  -6.8458   1.7713   1.3769
 ER8  C25  C   CH2   0  -0.183  -8.2591   2.1558   0.9635
 ER8  C27  C   CH2   0  -0.185  -7.7191   2.1835  -1.3127
 ER8  C28  C   CH2   0  -0.456  -6.2695   1.8064  -1.0479
 ER8  C31  C   CR6   0  -0.201  -2.5997  -2.3001  -0.8684
 ER8  C4   C   CH3   0  -0.680   9.1221   1.8090  -0.4342
 ER8  N5   N   NH1   0  -0.650   6.8477   1.2479   0.0674
 ER8  O7   O   O     0  -0.486   5.0411   0.3296  -0.9665
 ER8  N9   N   NR5   0  -0.493   3.5426   0.3789   1.2917
 ER8  C17  C   CR5   0   0.554   2.4184   0.9035   0.7424
 ER8  O18  O   O     0  -0.476   2.2709   2.0479   0.3513
 ER8  N20  N   N     0  -0.476  -2.7821  -0.3554   0.4497
 ER8  N22  N   NH1   0  -0.665  -4.7941   0.7090   0.6109
 ER8  O26  O   O2    0  -0.483  -8.2823   2.8985  -0.2347
 ER8  N29  N   N     0  -0.454  -4.6847  -1.1773  -0.7066
 ER8  C30  C   CR16  0   0.032  -3.9423  -2.1575  -1.1790
 ER8  CL3  CL  CL    0  -0.117  -1.6912  -3.5699  -1.6045
 ER8  H34  H   HCH3  0   0.227   8.1524   2.0973  -2.9639
 ER8  H33  H   HCH3  0   0.239   6.4713   1.6722  -2.6533
 ER8  H35  H   HCH3  0   0.228   7.1812   3.0939  -1.8796
 ER8  H38  H   HCH3  0   0.226   8.8933  -0.2384  -2.2173
 ER8  H37  H   HCH3  0   0.227   8.4528  -0.8261  -0.6135
 ER8  H36  H   HCH3  0   0.239   7.2252  -0.6917  -1.8792
 ER8  H43  H   HCH2  0   0.291   5.3804   0.7373   2.1680
 ER8  H44  H   HCH2  0   0.302   4.6239   2.1339   1.4275
 ER8  H45  H   HCH2  0   0.278   3.6665  -1.2437   2.6311
 ER8  H46  H   HCH2  0   0.274   4.1404  -1.6201   0.9722
 ER8  H47  H   HCR6  0   0.266   1.7451  -3.4163   1.7335
 ER8  H48  H   HCR6  0   0.268  -0.5975  -3.4211   0.9969
 ER8  H49  H   HCR6  0   0.263  -0.3505   0.7390  -0.0448
 ER8  H51  H   HCH1  0   0.247  -6.6828   0.0560   0.1141
 ER8  H52  H   HCH2  0   0.250  -6.8895   1.1603   2.2815
 ER8  H53  H   HCH2  0   0.232  -6.2756   2.6742   1.6205
 ER8  H54  H   HCH2  0   0.200  -8.8704   1.2468   0.8615
 ER8  H55  H   HCH2  0   0.240  -8.7246   2.7742   1.7323
 ER8  H57  H   HCH2  0   0.239  -7.7957   2.8213  -2.1948
 ER8  H56  H   HCH2  0   0.199  -8.3032   1.2728  -1.5143
 ER8  H58  H   HCH2  0   0.227  -5.6547   2.7089  -0.9749
 ER8  H59  H   HCH2  0   0.243  -5.8875   1.2214  -1.8877
 ER8  H39  H   HCH3  0   0.239   8.9711   2.8373  -0.1000
 ER8  H41  H   HCH3  0   0.239   9.4788   1.2215   0.4142
 ER8  H40  H   HCH3  0   0.243   9.9084   1.8156  -1.1884
 ER8  H42  H   HNH1  0   0.403   7.1610   1.6251   0.9486
 ER8  H50  H   HNH1  0   0.391  -4.2779   1.4027   1.1294
 ER8  H60  H   HCR6  0   0.289  -4.4247  -2.8638  -1.8464

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
 ER8  O26  C27  single    1.411  0.020  1.411
 ER8  O26  C25  single    1.410  0.020  1.410
 ER8  C27  C28  single    1.521  0.020  1.521
 ER8  C28  C23  single    1.528  0.020  1.528
 ER8  C25  C24  single    1.522  0.020  1.522
 ER8  C24  C23  single    1.523  0.020  1.523
 ER8  C23  N22  single    1.446  0.020  1.446
 ER8  N22  C21  single    1.343  0.020  1.343
 ER8  C21  N20  aromatic  1.339  0.020  1.339
 ER8  C21  N29  aromatic  1.338  0.020  1.338
 ER8  N20  C19  aromatic  1.322  0.020  1.322
 ER8  N29  C30  aromatic  1.317  0.020  1.317
 ER8  C19  C14  single    1.479  0.020  1.479
 ER8  C19  C31  aromatic  1.397  0.020  1.397
 ER8  C30  C31  aromatic  1.385  0.020  1.385
 ER8  C14  C13  aromatic  1.400  0.020  1.400
 ER8  C14  C15  aromatic  1.392  0.020  1.392
 ER8  C13  C12  aromatic  1.388  0.020  1.388
 ER8  C15  C16  aromatic  1.382  0.020  1.382
 ER8  C31  CL3  single    1.726  0.020  1.726
 ER8  C12  C11  aromatic  1.383  0.020  1.383
 ER8  C16  C11  aromatic  1.384  0.020  1.384
 ER8  C16  C17  single    1.478  0.020  1.478
 ER8  C11  C10  single    1.494  0.020  1.494
 ER8  O18  C17  double    1.218  0.020  1.218
 ER8  C17  N9   single    1.357  0.020  1.357
 ER8  C10  N9   single    1.448  0.020  1.448
 ER8  N9   C8   single    1.427  0.020  1.427
 ER8  C8   C6   single    1.532  0.020  1.532
 ER8  C6   N5   single    1.338  0.020  1.338
 ER8  C6   O7   double    1.220  0.020  1.220
 ER8  N5   C2   single    1.470  0.020  1.470
 ER8  C1   C2   single    1.529  0.020  1.529
 ER8  C2   C4   single    1.527  0.020  1.527
 ER8  C2   C3   single    1.529  0.020  1.529
 ER8  C1   H34  single    0.970  0.020  1.090
 ER8  C1   H33  single    0.970  0.020  1.090
 ER8  C1   H35  single    0.970  0.020  1.090
 ER8  C3   H38  single    0.970  0.020  1.090
 ER8  C3   H37  single    0.970  0.020  1.090
 ER8  C3   H36  single    0.970  0.020  1.090
 ER8  C8   H43  single    0.970  0.020  1.090
 ER8  C8   H44  single    0.970  0.020  1.090
 ER8  C10  H45  single    0.970  0.020  1.090
 ER8  C10  H46  single    0.970  0.020  1.090
 ER8  C12  H47  single    0.930  0.020  1.080
 ER8  C13  H48  single    0.930  0.020  1.080
 ER8  C15  H49  single    0.930  0.020  1.080
 ER8  C23  H51  single    0.970  0.020  1.090
 ER8  C24  H52  single    0.970  0.020  1.090
 ER8  C24  H53  single    0.970  0.020  1.090
 ER8  C25  H54  single    0.970  0.020  1.090
 ER8  C25  H55  single    0.970  0.020  1.090
 ER8  C27  H57  single    0.970  0.020  1.090
 ER8  C27  H56  single    0.970  0.020  1.090
 ER8  C28  H58  single    0.970  0.020  1.090
 ER8  C28  H59  single    0.970  0.020  1.090
 ER8  C4   H39  single    0.970  0.020  1.090
 ER8  C4   H41  single    0.970  0.020  1.090
 ER8  C4   H40  single    0.970  0.020  1.090
 ER8  N5   H42  single    0.860  0.020  1.020
 ER8  N22  H50  single    0.860  0.020  1.020
 ER8  C30  H60  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
 ER8  H35  C1   H33  108.34  3.000
 ER8  H35  C1   H34  107.89  3.000
 ER8  H33  C1   H34  107.82  3.000
 ER8  H35  C1   C2   110.73  3.000
 ER8  H33  C1   C2   111.90  3.000
 ER8  H34  C1   C2   110.03  3.000
 ER8  N5   C2   C4   106.13  3.000
 ER8  C4   C2   C3   109.05  3.000
 ER8  N5   C2   C3   110.66  3.000
 ER8  C3   C2   C1   110.84  3.000
 ER8  C4   C2   C1   109.38  3.000
 ER8  N5   C2   C1   110.65  3.000
 ER8  H36  C3   H37  108.47  3.000
 ER8  H36  C3   H38  107.88  3.000
 ER8  H37  C3   H38  107.87  3.000
 ER8  H36  C3   C2   111.89  3.000
 ER8  H37  C3   C2   110.65  3.000
 ER8  H38  C3   C2   109.96  3.000
 ER8  O7   C6   N5   125.49  3.000
 ER8  O7   C6   C8   120.91  3.000
 ER8  N5   C6   C8   113.59  3.000
 ER8  H44  C8   H43  106.72  3.000
 ER8  H44  C8   N9   109.47  3.000
 ER8  H43  C8   N9   109.59  3.000
 ER8  H44  C8   C6   108.79  3.000
 ER8  H43  C8   C6   110.54  3.000
 ER8  N9   C8   C6   111.59  3.000
 ER8  H46  C10  H45  107.68  3.000
 ER8  H46  C10  N9   111.50  3.000
 ER8  H45  C10  N9   111.29  3.000
 ER8  H46  C10  C11  111.63  3.000
 ER8  H45  C10  C11  112.35  3.000
 ER8  N9   C10  C11  102.42  3.000
 ER8  C16  C11  C12  120.40  3.000
 ER8  C16  C11  C10  109.11  3.000
 ER8  C12  C11  C10  130.49  3.000
 ER8  H47  C12  C13  120.29  3.000
 ER8  H47  C12  C11  121.56  3.000
 ER8  C13  C12  C11  118.15  3.000
 ER8  H48  C13  C14  119.64  3.000
 ER8  H48  C13  C12  118.87  3.000
 ER8  C14  C13  C12  121.47  3.000
 ER8  C19  C14  C15  118.88  3.000
 ER8  C15  C14  C13  119.88  3.000
 ER8  C19  C14  C13  121.20  3.000
 ER8  H49  C15  C16  121.09  3.000
 ER8  H49  C15  C14  120.88  3.000
 ER8  C16  C15  C14  118.03  3.000
 ER8  C17  C16  C15  129.19  3.000
 ER8  C17  C16  C11  108.77  3.000
 ER8  C15  C16  C11  122.04  3.000
 ER8  N20  C19  C31  120.11  3.000
 ER8  C31  C19  C14  123.68  3.000
 ER8  N20  C19  C14  116.19  3.000
 ER8  N29  C21  N22  118.46  3.000
 ER8  N29  C21  N20  124.90  3.000
 ER8  N22  C21  N20  116.63  3.000
 ER8  H51  C23  N22  107.57  3.000
 ER8  H51  C23  C28  108.41  3.000
 ER8  N22  C23  C28  112.74  3.000
 ER8  H51  C23  C24  108.34  3.000
 ER8  N22  C23  C24  110.10  3.000
 ER8  C28  C23  C24  109.56  3.000
 ER8  H53  C24  H52  107.32  3.000
 ER8  H53  C24  C25  109.61  3.000
 ER8  H52  C24  C25  109.21  3.000
 ER8  H53  C24  C23  110.13  3.000
 ER8  H52  C24  C23  110.49  3.000
 ER8  C25  C24  C23  110.03  3.000
 ER8  H55  C25  H54  107.25  3.000
 ER8  H55  C25  O26  107.05  3.000
 ER8  H54  C25  O26  110.32  3.000
 ER8  H55  C25  C24  110.36  3.000
 ER8  H54  C25  C24  109.42  3.000
 ER8  O26  C25  C24  112.29  3.000
 ER8  H56  C27  H57  107.36  3.000
 ER8  H56  C27  O26  110.33  3.000
 ER8  H57  C27  O26  107.07  3.000
 ER8  H56  C27  C28  109.42  3.000
 ER8  H57  C27  C28  110.65  3.000
 ER8  O26  C27  C28  111.91  3.000
 ER8  H59  C28  H58  107.25  3.000
 ER8  H59  C28  C27  109.40  3.000
 ER8  H58  C28  C27  110.03  3.000
 ER8  H59  C28  C23  110.40  3.000
 ER8  H58  C28  C23  109.56  3.000
 ER8  C27  C28  C23  110.15  3.000
 ER8  CL3  C31  C30  119.36  3.000
 ER8  CL3  C31  C19  123.52  3.000
 ER8  C30  C31  C19  117.05  3.000
 ER8  H40  C4   H41  107.78  3.000
 ER8  H40  C4   H39  107.82  3.000
 ER8  H41  C4   H39  108.30  3.000
 ER8  H40  C4   C2   110.15  3.000
 ER8  H41  C4   C2   111.16  3.000
 ER8  H39  C4   C2   111.48  3.000
 ER8  H42  N5   C6   116.75  3.000
 ER8  H42  N5   C2   116.25  3.000
 ER8  C6   N5   C2   126.99  3.000
 ER8  C17  N9   C10  113.71  3.000
 ER8  C10  N9   C8   121.75  3.000
 ER8  C17  N9   C8   123.09  3.000
 ER8  O18  C17  N9   126.40  3.000
 ER8  N9   C17  C16  105.79  3.000
 ER8  O18  C17  C16  127.80  3.000
 ER8  C21  N20  C19  118.63  3.000
 ER8  H50  N22  C23  118.08  3.000
 ER8  H50  N22  C21  116.01  3.000
 ER8  C23  N22  C21  124.62  3.000
 ER8  C27  O26  C25  112.08  3.000
 ER8  C30  N29  C21  116.45  3.000
 ER8  H60  C30  N29  117.03  3.000
 ER8  H60  C30  C31  120.12  3.000
 ER8  N29  C30  C31  122.85  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
 ER8  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 ER8  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 ER8  CONST_03  C19  C14  C13  C12   180.00   0.0  0
 ER8  CONST_04  C15  C14  C13  C12     0.00   0.0  0
 ER8  CONST_05  C15  C16  C11  C12     0.00   0.0  0
 ER8  CONST_08  C16  C15  C14  C13     0.00   0.0  0
 ER8  CONST_09  C16  C11  C12  C13     0.00   0.0  0
 ER8  CONST_10  C21  N20  C19  C14   180.00   0.0  0
 ER8  CONST_11  C30  C31  C19  C14   180.00   0.0  0
 ER8  CONST_14  C19  C14  C15  C16   180.00   0.0  0
 ER8  CONST_15  N29  C21  N20  C19     0.00   0.0  0
 ER8  CONST_16  N29  C30  C31  C19     0.00   0.0  0
 ER8  CONST_17  C31  C19  N20  C21     0.00   0.0  0
 ER8  CONST_18  C31  C30  N29  C21     0.00   0.0  0
 ER8  CONST_19  C30  N29  C21  N20     0.00   0.0  0
 ER8  CONST_20  C30  C31  C19  N20     0.00   0.0  0
 ER8  CONST_21  C16  C17  N9   C10     0.00   0.0  0
 ER8  CONST_22  CL3  C31  C19  C14     0.00   0.0  0
 ER8  CONST_23  N22  C21  N20  C19   180.00   0.0  0
 ER8  CONST_24  CL3  C31  C19  N20   180.00   0.0  0
 ER8  CONST_25  C30  N29  C21  N22   180.00   0.0  0
 ER8  CONST_26  CL3  C31  C30  N29   180.00   0.0  0
 ER8  CONST_27  N20  C21  N22  C23   180.00   0.0  0
 ER8  CONST_28  N29  C21  N22  C23     0.00   0.0  0
 ER8  CONST_29  C16  C17  N9   C8    180.00   0.0  0
 ER8  CONST_30  O18  C17  N9   C10   180.00   0.0  0
 ER8  CONST_31  H47  C12  C11  C10     0.00   0.0  0
 ER8  CONST_32  H48  C13  C12  C11   180.00   0.0  0
 ER8  CONST_33  H49  C15  C16  C11   180.00   0.0  0
 ER8  CONST_34  H60  C30  C31  C19   180.00   0.0  0
 ER8  CONST_35  O18  C17  N9   C8      0.00   0.0  0
 ER8  CONST_36  H50  N22  C21  N20     0.00   0.0  0
 ER8  CONST_37  C8   C6   N5   C2    180.00   0.0  0
 ER8  CONST_38  O7   C6   N5   C2      0.00   0.0  0
 ER8  CONST_39  H42  N5   C6   C8      0.00   0.0  0
 ER8  Var_01    O26  C27  C28  C23    56.19  30.0  1
 ER8  Var_02    O26  C25  C24  C23   -55.92  30.0  1
 ER8  Var_03    C28  C27  O26  C25   -59.64  30.0  1
 ER8  Var_04    H45  C10  C11  C12   -57.94  30.0  1
 ER8  Var_05    C17  N9   C8   C6    -85.37  30.0  2
 ER8  Var_06    N9   C8   C6   N5   -168.62  30.0  1
 ER8  Var_07    C6   N5   C2   C1     61.10  30.0  3
 ER8  Var_08    H39  C4   C2   C1     58.99  30.0  3
 ER8  Var_09    H38  C3   C2   C1     60.30  30.0  3
 ER8  Var_10    H34  C1   C2   C3    -60.99  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
 ER8  chir_01  C23  C28  C24  N22  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
 ER8  plan-1  C14  0.020
 ER8  plan-1  C19  0.020
 ER8  plan-1  C21  0.020
 ER8  plan-1  C31  0.020
 ER8  plan-1  N20  0.020
 ER8  plan-1  N22  0.020
 ER8  plan-1  N29  0.020
 ER8  plan-1  C30  0.020
 ER8  plan-1  CL3  0.020
 ER8  plan-1  H60  0.020
 ER8  plan-2  C2   0.020
 ER8  plan-2  C6   0.020
 ER8  plan-2  C8   0.020
 ER8  plan-2  N5   0.020
 ER8  plan-2  O7   0.020
 ER8  plan-2  H42  0.020
 ER8  plan-3  C21  0.020
 ER8  plan-3  C23  0.020
 ER8  plan-3  N22  0.020
 ER8  plan-3  H50  0.020
 ER8  plan-4  C8   0.020
 ER8  plan-4  C10  0.020
 ER8  plan-4  C11  0.020
 ER8  plan-4  C12  0.020
 ER8  plan-4  C13  0.020
 ER8  plan-4  C14  0.020
 ER8  plan-4  C15  0.020
 ER8  plan-4  C16  0.020
 ER8  plan-4  C19  0.020
 ER8  plan-4  N9   0.020
 ER8  plan-4  C17  0.020
 ER8  plan-4  O18  0.020
 ER8  plan-4  H47  0.020
 ER8  plan-4  H48  0.020
 ER8  plan-4  H49  0.020

