# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 15:27:23 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 6-[5-chloranyl-2-(oxan-4-ylamino)pyrimidin-4-yl]-2-(2-morpholin-4-ylethyl)-3~{H}-isoindol-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cnc(NC2CCOCC2)nc1c3ccc4CN(CCN5CCOCC5)C(=O)c4c3
#
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
 ESQ  ESQ  6-[5-chloranyl-2-(oxan-4-ylamino)pyrimidin-4-yl]-2-(2-morpholin-4-ylethyl)-3~{H}-isoindol-1-one  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_ESQ
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
 ESQ  C2   C   CR6   0  -0.203   2.8641  -2.2616   0.8618
 ESQ  C3   C   CR16  0   0.032   4.1891  -2.0649   1.2153
 ESQ  N4   N   N     0  -0.455   4.8554  -0.9706   0.9089
 ESQ  C5   C   CR6   0   0.602   4.1762  -0.0251   0.2493
 ESQ  C7   C   CH1   0  -0.064   6.1926   1.4040   0.2334
 ESQ  C8   C   CH2   0  -0.469   6.4176   2.9060   0.3592
 ESQ  C11  C   CH2   0  -0.186   8.5596   1.2483  -0.5455
 ESQ  C12  C   CH2   0  -0.456   7.1238   0.8400  -0.8394
 ESQ  C14  C   CR6   0   0.323   2.2406  -1.2412   0.1391
 ESQ  C15  C   CR6   0   0.048   0.8331  -1.2985  -0.3097
 ESQ  C16  C   CR16  0  -0.266   0.3283  -2.4194  -0.9786
 ESQ  C19  C   CH2   0  -0.276  -3.2494  -1.1596  -1.4644
 ESQ  C22  C   CH2   0  -0.271  -5.5438   0.4924   0.3431
 ESQ  C24  C   CH2   0  -0.304  -7.4599   1.2283   1.6077
 ESQ  C25  C   CH2   0  -0.188  -8.8515   1.8180   1.4812
 ESQ  C27  C   CH2   0  -0.184  -9.1725   0.7321  -0.5484
 ESQ  C28  C   CH2   0  -0.311  -7.7871   0.1208  -0.4664
 ESQ  C31  C   CR56  0  -0.050  -1.3025  -0.2696  -0.5078
 ESQ  CL1  CL  CL    0  -0.117   2.0560  -3.6974   1.3774
 ESQ  N6   N   NH1   0  -0.667   4.7976   1.1313  -0.0319
 ESQ  C9   C   CH2   0  -0.184   7.8969   3.1905   0.5772
 ESQ  O10  O   O2    0  -0.483   8.6995   2.6495  -0.4484
 ESQ  N13  N   N     0  -0.476   2.9027  -0.1336  -0.1493
 ESQ  C17  C   CR16  0  -0.304  -0.9892  -2.4726  -1.4117
 ESQ  C18  C   CR56  0   0.080  -1.8054  -1.3862  -1.1537
 ESQ  N20  N   NR5   0  -0.506  -3.4758   0.1752  -0.9502
 ESQ  N23  N   NT    0  -0.431  -6.9017   0.9903   0.2882
 ESQ  O26  O   O2    0  -0.485  -9.7061   0.9818   0.7325
 ESQ  C29  C   CR5   0   0.551  -2.3851   0.7292  -0.3709
 ESQ  C32  C   CR16  0  -0.334   0.0118  -0.1968  -0.0869
 ESQ  H33  H   HCR6  0   0.289   4.7229  -2.8285   1.7711
 ESQ  H35  H   HCH1  0   0.246   6.4476   0.9375   1.1890
 ESQ  H37  H   HCH2  0   0.232   6.0754   3.4132  -0.5491
 ESQ  H36  H   HCH2  0   0.250   5.8442   3.3101   1.1968
 ESQ  H40  H   HCH2  0   0.200   8.8919   0.7662   0.3863
 ESQ  H41  H   HCH2  0   0.239   9.2268   0.9141  -1.3414
 ESQ  H42  H   HCH2  0   0.243   7.0548  -0.2497  -0.8694
 ESQ  H43  H   HCH2  0   0.227   6.8202   1.2157  -1.8212
 ESQ  H44  H   HCR6  0   0.268   0.9789  -3.2583  -1.1850
 ESQ  H46  H   HCH2  0   0.279  -3.4547  -1.2101  -2.5375
 ESQ  H47  H   HCH2  0   0.274  -3.8913  -1.8962  -0.9717
 ESQ  H48  H   HCH2  0   0.256  -5.3229   0.4085  -1.8214
 ESQ  H49  H   HCH2  0   0.259  -4.6793   1.8615  -1.0799
 ESQ  H50  H   HCH2  0   0.205  -5.5061  -0.5874   0.5648
 ESQ  H51  H   HCH2  0   0.244  -5.0222   0.9932   1.1619
 ESQ  H53  H   HCH2  0   0.199  -7.5010   0.3049   2.2102
 ESQ  H54  H   HCH2  0   0.237  -9.2992   1.9429   2.4684
 ESQ  H55  H   HCH2  0   0.200  -8.7796   2.8107   1.0145
 ESQ  H57  H   HCH2  0   0.200  -9.1272   1.6599  -1.1367
 ESQ  H56  H   HCH2  0   0.236  -9.8523   0.0471  -1.0572
 ESQ  H59  H   HCH2  0   0.201  -7.8543  -0.8816  -0.0094
 ESQ  H58  H   HCH2  0   0.244  -7.4109  -0.0173  -1.4820
 ESQ  H34  H   HNH1  0   0.392   4.2899   1.7768  -0.6165
 ESQ  H39  H   HCH2  0   0.241   8.0797   4.2658   0.5947
 ESQ  H38  H   HCH2  0   0.200   8.2036   2.7881   1.5542
 ESQ  H45  H   HCR6  0   0.266  -1.3569  -3.3462  -1.9334
 ESQ  H60  H   HCR6  0   0.262   0.3900   0.6848   0.4151
 ESQ  C21  C   CH2   0  -0.313  -4.7836   0.7841  -0.9506
 ESQ  O30  O   O     0  -0.482  -2.3227   1.8294   0.1531
 ESQ  H52  H   HCH2  0   0.244  -6.8264   1.9371   2.1462

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
 ESQ  O10  C9   single    1.410  0.020  1.410
 ESQ  O10  C11  single    1.411  0.020  1.411
 ESQ  C9   C8   single    1.522  0.020  1.522
 ESQ  C8   C7   single    1.524  0.020  1.524
 ESQ  C11  C12  single    1.521  0.020  1.521
 ESQ  C12  C7   single    1.528  0.020  1.528
 ESQ  C7   N6   single    1.446  0.020  1.446
 ESQ  C17  C16  aromatic  1.388  0.020  1.388
 ESQ  C17  C18  aromatic  1.383  0.020  1.383
 ESQ  C16  C15  aromatic  1.400  0.020  1.400
 ESQ  N6   C5   single    1.343  0.020  1.343
 ESQ  N13  C5   aromatic  1.339  0.020  1.339
 ESQ  N13  C14  aromatic  1.322  0.020  1.322
 ESQ  C18  C19  single    1.494  0.020  1.494
 ESQ  C18  C31  aromatic  1.384  0.020  1.384
 ESQ  C19  N20  single    1.448  0.020  1.448
 ESQ  C5   N4   aromatic  1.338  0.020  1.338
 ESQ  C15  C14  single    1.478  0.020  1.478
 ESQ  C15  C32  aromatic  1.392  0.020  1.392
 ESQ  C14  C2   aromatic  1.397  0.020  1.397
 ESQ  N4   C3   aromatic  1.317  0.020  1.317
 ESQ  C31  C32  aromatic  1.382  0.020  1.382
 ESQ  C31  C29  single    1.479  0.020  1.479
 ESQ  C3   C2   aromatic  1.385  0.020  1.385
 ESQ  C2   CL1  single    1.726  0.020  1.726
 ESQ  N20  C21  single    1.443  0.020  1.443
 ESQ  N20  C29  single    1.354  0.020  1.354
 ESQ  C22  C21  single    1.529  0.020  1.529
 ESQ  C22  N23  single    1.447  0.020  1.447
 ESQ  C29  O30  double    1.220  0.020  1.220
 ESQ  C24  N23  single    1.452  0.020  1.452
 ESQ  C24  C25  single    1.517  0.020  1.517
 ESQ  N23  C28  single    1.452  0.020  1.452
 ESQ  C25  O26  single    1.411  0.020  1.411
 ESQ  C28  C27  single    1.516  0.020  1.516
 ESQ  O26  C27  single    1.410  0.020  1.410
 ESQ  C3   H33  single    0.930  0.020  1.080
 ESQ  C7   H35  single    0.970  0.020  1.090
 ESQ  C8   H37  single    0.970  0.020  1.090
 ESQ  C8   H36  single    0.970  0.020  1.090
 ESQ  C11  H40  single    0.970  0.020  1.090
 ESQ  C11  H41  single    0.970  0.020  1.090
 ESQ  C12  H42  single    0.970  0.020  1.090
 ESQ  C12  H43  single    0.970  0.020  1.090
 ESQ  C16  H44  single    0.930  0.020  1.080
 ESQ  C19  H46  single    0.970  0.020  1.090
 ESQ  C19  H47  single    0.970  0.020  1.090
 ESQ  C21  H48  single    0.970  0.020  1.090
 ESQ  C21  H49  single    0.970  0.020  1.090
 ESQ  C22  H50  single    0.970  0.020  1.090
 ESQ  C22  H51  single    0.970  0.020  1.090
 ESQ  C24  H52  single    0.970  0.020  1.090
 ESQ  C24  H53  single    0.970  0.020  1.090
 ESQ  C25  H54  single    0.970  0.020  1.090
 ESQ  C25  H55  single    0.970  0.020  1.090
 ESQ  C27  H57  single    0.970  0.020  1.090
 ESQ  C27  H56  single    0.970  0.020  1.090
 ESQ  C28  H59  single    0.970  0.020  1.090
 ESQ  C28  H58  single    0.970  0.020  1.090
 ESQ  N6   H34  single    0.860  0.020  1.020
 ESQ  C9   H39  single    0.970  0.020  1.090
 ESQ  C9   H38  single    0.970  0.020  1.090
 ESQ  C17  H45  single    0.930  0.020  1.080
 ESQ  C32  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
 ESQ  CL1  C2   C14  123.57  3.000
 ESQ  CL1  C2   C3   119.32  3.000
 ESQ  C14  C2   C3   117.07  3.000
 ESQ  H33  C3   N4   117.06  3.000
 ESQ  H33  C3   C2   120.09  3.000
 ESQ  N4   C3   C2   122.85  3.000
 ESQ  C5   N4   C3   116.42  3.000
 ESQ  N13  C5   N6   116.60  3.000
 ESQ  N13  C5   N4   124.91  3.000
 ESQ  N6   C5   N4   118.49  3.000
 ESQ  H35  C7   N6   107.75  3.000
 ESQ  H35  C7   C12  108.30  3.000
 ESQ  N6   C7   C12  112.92  3.000
 ESQ  H35  C7   C8   108.30  3.000
 ESQ  N6   C7   C8   110.08  3.000
 ESQ  C12  C7   C8   109.37  3.000
 ESQ  H36  C8   H37  107.49  3.000
 ESQ  H36  C8   C9   109.34  3.000
 ESQ  H37  C8   C9   109.63  3.000
 ESQ  H36  C8   C7   110.51  3.000
 ESQ  H37  C8   C7   109.99  3.000
 ESQ  C9   C8   C7   109.84  3.000
 ESQ  H41  C11  H40  107.38  3.000
 ESQ  H41  C11  O10  107.08  3.000
 ESQ  H40  C11  O10  110.29  3.000
 ESQ  H41  C11  C12  110.73  3.000
 ESQ  H40  C11  C12  109.33  3.000
 ESQ  O10  C11  C12  111.91  3.000
 ESQ  H43  C12  H42  107.48  3.000
 ESQ  H43  C12  C11  110.06  3.000
 ESQ  H42  C12  C11  109.43  3.000
 ESQ  H43  C12  C7   109.52  3.000
 ESQ  H42  C12  C7   110.42  3.000
 ESQ  C11  C12  C7   109.90  3.000
 ESQ  N13  C14  C15  116.29  3.000
 ESQ  C15  C14  C2   123.61  3.000
 ESQ  N13  C14  C2   120.07  3.000
 ESQ  C32  C15  C16  119.84  3.000
 ESQ  C32  C15  C14  118.85  3.000
 ESQ  C16  C15  C14  121.30  3.000
 ESQ  H44  C16  C17  118.80  3.000
 ESQ  H44  C16  C15  119.70  3.000
 ESQ  C17  C16  C15  121.48  3.000
 ESQ  H47  C19  H46  107.50  3.000
 ESQ  H47  C19  N20  111.65  3.000
 ESQ  H46  C19  N20  111.19  3.000
 ESQ  H47  C19  C18  111.79  3.000
 ESQ  H46  C19  C18  112.23  3.000
 ESQ  N20  C19  C18  102.53  3.000
 ESQ  H51  C22  H50  106.37  3.000
 ESQ  H51  C22  N23  108.58  3.000
 ESQ  H50  C22  N23  112.12  3.000
 ESQ  H51  C22  C21  108.02  3.000
 ESQ  H50  C22  C21  109.87  3.000
 ESQ  N23  C22  C21  111.65  3.000
 ESQ  H53  C24  H52  107.18  3.000
 ESQ  H53  C24  N23  111.92  3.000
 ESQ  H52  C24  N23  109.35  3.000
 ESQ  H53  C24  C25  109.68  3.000
 ESQ  H52  C24  C25  108.71  3.000
 ESQ  N23  C24  C25  109.91  3.000
 ESQ  H55  C25  H54  107.91  3.000
 ESQ  H55  C25  O26  110.46  3.000
 ESQ  H54  C25  O26  107.42  3.000
 ESQ  H55  C25  C24  109.05  3.000
 ESQ  H54  C25  C24  110.22  3.000
 ESQ  O26  C25  C24  111.70  3.000
 ESQ  H56  C27  H57  107.82  3.000
 ESQ  H56  C27  O26  107.40  3.000
 ESQ  H57  C27  O26  110.62  3.000
 ESQ  H56  C27  C28  109.96  3.000
 ESQ  H57  C27  C28  109.36  3.000
 ESQ  O26  C27  C28  111.60  3.000
 ESQ  H58  C28  H59  106.94  3.000
 ESQ  H58  C28  N23  110.42  3.000
 ESQ  H59  C28  N23  111.45  3.000
 ESQ  H58  C28  C27  108.39  3.000
 ESQ  H59  C28  C27  109.45  3.000
 ESQ  N23  C28  C27  110.10  3.000
 ESQ  C32  C31  C29  129.21  3.000
 ESQ  C29  C31  C18  108.78  3.000
 ESQ  C32  C31  C18  122.01  3.000
 ESQ  H34  N6   C7   118.13  3.000
 ESQ  H34  N6   C5   116.10  3.000
 ESQ  C7   N6   C5   124.79  3.000
 ESQ  H38  C9   H39  107.43  3.000
 ESQ  H38  C9   O10  110.30  3.000
 ESQ  H39  C9   O10  107.13  3.000
 ESQ  H38  C9   C8   109.25  3.000
 ESQ  H39  C9   C8   110.45  3.000
 ESQ  O10  C9   C8   112.17  3.000
 ESQ  C9   O10  C11  111.99  3.000
 ESQ  C14  N13  C5   118.64  3.000
 ESQ  H45  C17  C18  121.57  3.000
 ESQ  H45  C17  C16  120.27  3.000
 ESQ  C18  C17  C16  118.16  3.000
 ESQ  C17  C18  C31  120.40  3.000
 ESQ  C31  C18  C19  109.01  3.000
 ESQ  C17  C18  C19  130.59  3.000
 ESQ  C29  N20  C21  123.91  3.000
 ESQ  C29  N20  C19  113.78  3.000
 ESQ  C21  N20  C19  122.05  3.000
 ESQ  C28  N23  C24  109.63  3.000
 ESQ  C28  N23  C22  112.68  3.000
 ESQ  C24  N23  C22  112.49  3.000
 ESQ  C27  O26  C25  110.97  3.000
 ESQ  N20  C29  C31  105.89  3.000
 ESQ  N20  C29  O30  126.44  3.000
 ESQ  C31  C29  O30  127.67  3.000
 ESQ  H60  C32  C31  121.09  3.000
 ESQ  H60  C32  C15  120.83  3.000
 ESQ  C31  C32  C15  118.08  3.000
 ESQ  H49  C21  H48  107.03  3.000
 ESQ  H49  C21  N20  109.30  3.000
 ESQ  H48  C21  N20  107.64  3.000
 ESQ  H49  C21  C22  109.67  3.000
 ESQ  H48  C21  C22  111.34  3.000
 ESQ  N20  C21  C22  111.72  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
 ESQ  CONST_01  C5   N13  C14  C2      0.00   0.0  0
 ESQ  CONST_04  C5   N4   C3   C2      0.00   0.0  0
 ESQ  CONST_05  N13  C5   N4   C3      0.00   0.0  0
 ESQ  CONST_06  N13  C14  C2   C3      0.00   0.0  0
 ESQ  CONST_07  C15  C14  C2   C3    180.00   0.0  0
 ESQ  CONST_08  C14  N13  C5   N4      0.00   0.0  0
 ESQ  CONST_09  C14  C2   C3   N4      0.00   0.0  0
 ESQ  CONST_10  C15  C14  N13  C5    180.00   0.0  0
 ESQ  CONST_11  C17  C16  C15  C14   180.00   0.0  0
 ESQ  CONST_12  C31  C32  C15  C14   180.00   0.0  0
 ESQ  CONST_13  C18  C17  C16  C15     0.00   0.0  0
 ESQ  CONST_14  C18  C31  C32  C15     0.00   0.0  0
 ESQ  CONST_15  C31  C18  C17  C16     0.00   0.0  0
 ESQ  CONST_17  C31  C32  C15  C16     0.00   0.0  0
 ESQ  CONST_19  C32  C15  C16  C17     0.00   0.0  0
 ESQ  CONST_20  C32  C31  C18  C17     0.00   0.0  0
 ESQ  CONST_21  C31  C29  N20  C19     0.00   0.0  0
 ESQ  CONST_22  N6   C5   N4   C3    180.00   0.0  0
 ESQ  CONST_23  CL1  C2   C3   N4    180.00   0.0  0
 ESQ  CONST_24  N6   C5   N13  C14   180.00   0.0  0
 ESQ  CONST_25  CL1  C2   C14  C15     0.00   0.0  0
 ESQ  CONST_26  N13  C14  C2   CL1   180.00   0.0  0
 ESQ  CONST_27  C7   N6   C5   N4      0.00   0.0  0
 ESQ  CONST_28  N13  C5   N6   C7    180.00   0.0  0
 ESQ  CONST_29  O30  C29  N20  C19   180.00   0.0  0
 ESQ  CONST_30  C31  C29  N20  C21   180.00   0.0  0
 ESQ  CONST_31  H33  C3   N4   C5    180.00   0.0  0
 ESQ  CONST_32  H44  C16  C15  C14     0.00   0.0  0
 ESQ  CONST_33  H60  C32  C15  C14     0.00   0.0  0
 ESQ  CONST_34  H45  C17  C16  C15   180.00   0.0  0
 ESQ  CONST_35  O30  C29  N20  C21     0.00   0.0  0
 ESQ  CONST_36  H34  N6   C5   N4    180.00   0.0  0
 ESQ  Var_01    O10  C9   C8   C7     56.39  30.0  1
 ESQ  Var_02    O10  C11  C12  C7    -56.52  30.0  1
 ESQ  Var_03    C27  C28  N23  C24    56.87  30.0  1
 ESQ  Var_04    C28  N23  C24  C25   -56.85  30.0  1
 ESQ  Var_05    C28  C27  O26  C25    56.84  30.0  1
 ESQ  Var_06    O26  C25  C24  N23    57.27  30.0  1
 ESQ  Var_07    O26  C27  C28  N23   -57.14  30.0  1
 ESQ  Var_08    H54  C25  O26  C27  -177.96  30.0  1
 ESQ  Var_09    H46  C19  C18  C31   120.18  30.0  1
 ESQ  Var_10    C22  C21  N20  C19    90.43  30.0  3
 ESQ  Var_11    C24  N23  C22  C21  -156.52  30.0  3
 ESQ  Var_12    N23  C22  C21  N20  -174.31  30.0  1

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
 ESQ  chir_01  C7  C8  C12  N6  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
 ESQ  plan-1  C2   0.020
 ESQ  plan-1  C3   0.020
 ESQ  plan-1  N4   0.020
 ESQ  plan-1  C5   0.020
 ESQ  plan-1  C14  0.020
 ESQ  plan-1  C15  0.020
 ESQ  plan-1  CL1  0.020
 ESQ  plan-1  N6   0.020
 ESQ  plan-1  N13  0.020
 ESQ  plan-1  H33  0.020
 ESQ  plan-2  C5   0.020
 ESQ  plan-2  C7   0.020
 ESQ  plan-2  N6   0.020
 ESQ  plan-2  H34  0.020
 ESQ  plan-3  C14  0.020
 ESQ  plan-3  C15  0.020
 ESQ  plan-3  C16  0.020
 ESQ  plan-3  C19  0.020
 ESQ  plan-3  C31  0.020
 ESQ  plan-3  C17  0.020
 ESQ  plan-3  C18  0.020
 ESQ  plan-3  N20  0.020
 ESQ  plan-3  C29  0.020
 ESQ  plan-3  C32  0.020
 ESQ  plan-3  H44  0.020
 ESQ  plan-3  H45  0.020
 ESQ  plan-3  H60  0.020
 ESQ  plan-3  C21  0.020
 ESQ  plan-3  O30  0.020

