# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 17:45:11 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 6-[5-chloranyl-2-(oxan-4-ylamino)pyrimidin-4-yl]-2,3-dihydroisoindol-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cnc(NC2CCOCC2)nc1c3ccc4CNC(=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
 EU2  EU2  6-[5-chloranyl-2-(oxan-4-ylamino)pyrimidin-4-yl]-2,3-dihydroisoindol-1-one  ligand  41  24  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_EU2
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
 EU2  C2   C   CR6   0  -0.202  -0.0869  -2.2489   0.3211
 EU2  C3   C   CR16  0   0.031   1.2734  -2.4964   0.4090
 EU2  N4   N   N     0  -0.454   2.1846  -1.5907   0.1178
 EU2  C5   C   CR6   0   0.602   1.7308  -0.3911  -0.2644
 EU2  C7   C   CH1   0  -0.064   4.0530   0.4391  -0.3847
 EU2  C8   C   CH2   0  -0.471   4.7840   1.4514  -1.2586
 EU2  C11  C   CH2   0  -0.186   5.9841   0.6111   1.1913
 EU2  C12  C   CH2   0  -0.457   4.4680   0.6392   1.0728
 EU2  C14  C   CR6   0   0.321  -0.4754  -0.9752  -0.0998
 EU2  C15  C   CR6   0   0.047  -1.8846  -0.5473  -0.2298
 EU2  C16  C   CR16  0  -0.267  -2.8157  -1.3154  -0.9377
 EU2  C19  C   CH2   0  -0.272  -5.8389   0.9877  -0.4834
 EU2  C21  C   CR5   0   0.527  -4.2593   2.2793   0.6947
 EU2  C23  C   CR56  0  -0.061  -3.5880   1.0594   0.1871
 EU2  C24  C   CR16  0  -0.328  -2.2707   0.6676   0.3289
 EU2  CL1  CL  CL    0  -0.116  -1.2048  -3.4728   0.8032
 EU2  N6   N   NH1   0  -0.666   2.6251   0.5590  -0.5821
 EU2  C9   C   CH2   0  -0.184   6.2817   1.3823  -0.9959
 EU2  O10  O   O2    0  -0.483   6.5931   1.5796   0.3651
 EU2  N13  N   N     0  -0.475   0.4385  -0.0609  -0.3774
 EU2  C17  C   CR16  0  -0.299  -4.1313  -0.9003  -1.0904
 EU2  C18  C   CR56  0   0.082  -4.5112   0.2956  -0.5076
 EU2  N20  N   NR15  0  -0.665  -5.5393   2.1797   0.2769
 EU2  O22  O   O     0  -0.476  -3.7647   3.1821   1.3489
 EU2  H25  H   HCR6  0   0.290   1.6293  -3.4665   0.7394
 EU2  H27  H   HCH1  0   0.245   4.3511  -0.5664  -0.6971
 EU2  H28  H   HCH2  0   0.251   4.5925   1.2566  -2.3163
 EU2  H29  H   HCH2  0   0.232   4.4209   2.4612  -1.0385
 EU2  H33  H   HCH2  0   0.239   6.2945   0.8233   2.2155
 EU2  H32  H   HCH2  0   0.199   6.3548  -0.3937   0.9373
 EU2  H34  H   HCH2  0   0.227   4.0845   1.5998   1.4313
 EU2  H35  H   HCH2  0   0.244   4.0400  -0.1431   1.7038
 EU2  H36  H   HCR6  0   0.269  -2.5053  -2.2432  -1.3990
 EU2  H39  H   HCH2  0   0.275  -6.1938   1.2277  -1.4889
 EU2  H38  H   HCH2  0   0.275  -6.6064   0.3808   0.0037
 EU2  H41  H   HCR6  0   0.265  -1.5604   1.2792   0.8708
 EU2  H26  H   HNH1  0   0.392   2.2477   1.4732  -0.7780
 EU2  H30  H   HCH2  0   0.200   6.6683   0.4111  -1.3389
 EU2  H31  H   HCH2  0   0.241   6.8013   2.1583  -1.5597
 EU2  H37  H   HCR6  0   0.267  -4.8307  -1.5031  -1.6546
 EU2  H40  H   HNR5  0   0.408  -6.2388   2.8714   0.4943

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
 EU2  O10  C11  single    1.411  0.020  1.411
 EU2  O10  C9   single    1.410  0.020  1.410
 EU2  C11  C12  single    1.521  0.020  1.521
 EU2  C12  C7   single    1.529  0.020  1.529
 EU2  C9   C8   single    1.522  0.020  1.522
 EU2  C8   C7   single    1.524  0.020  1.524
 EU2  C7   N6   single    1.446  0.020  1.446
 EU2  N6   C5   single    1.343  0.020  1.343
 EU2  C5   N13  aromatic  1.339  0.020  1.339
 EU2  C5   N4   aromatic  1.338  0.020  1.338
 EU2  N13  C14  aromatic  1.322  0.020  1.322
 EU2  N4   C3   aromatic  1.317  0.020  1.317
 EU2  C16  C17  aromatic  1.388  0.020  1.388
 EU2  C16  C15  aromatic  1.399  0.020  1.399
 EU2  C17  C18  aromatic  1.384  0.020  1.384
 EU2  C14  C15  single    1.478  0.020  1.478
 EU2  C14  C2   aromatic  1.397  0.020  1.397
 EU2  C15  C24  aromatic  1.392  0.020  1.392
 EU2  C18  C19  single    1.497  0.020  1.497
 EU2  C18  C23  aromatic  1.385  0.020  1.385
 EU2  C19  N20  single    1.445  0.020  1.445
 EU2  C24  C23  aromatic  1.382  0.020  1.382
 EU2  C23  C21  single    1.482  0.020  1.482
 EU2  C3   C2   aromatic  1.385  0.020  1.385
 EU2  N20  C21  single    1.350  0.020  1.350
 EU2  C2   CL1  single    1.726  0.020  1.726
 EU2  C21  O22  double    1.220  0.020  1.220
 EU2  C3   H25  single    0.930  0.020  1.080
 EU2  C7   H27  single    0.970  0.020  1.090
 EU2  C8   H28  single    0.970  0.020  1.090
 EU2  C8   H29  single    0.970  0.020  1.090
 EU2  C11  H33  single    0.970  0.020  1.090
 EU2  C11  H32  single    0.970  0.020  1.090
 EU2  C12  H34  single    0.970  0.020  1.090
 EU2  C12  H35  single    0.970  0.020  1.090
 EU2  C16  H36  single    0.930  0.020  1.080
 EU2  C19  H39  single    0.970  0.020  1.090
 EU2  C19  H38  single    0.970  0.020  1.090
 EU2  C24  H41  single    0.930  0.020  1.080
 EU2  N6   H26  single    0.860  0.020  1.020
 EU2  C9   H30  single    0.970  0.020  1.090
 EU2  C9   H31  single    0.970  0.020  1.090
 EU2  C17  H37  single    0.930  0.020  1.080
 EU2  N20  H40  single    0.860  0.020  1.020

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
 EU2  CL1  C2   C14  123.41  3.000
 EU2  CL1  C2   C3   119.44  3.000
 EU2  C14  C2   C3   117.08  3.000
 EU2  H25  C3   N4   117.08  3.000
 EU2  H25  C3   C2   120.07  3.000
 EU2  N4   C3   C2   122.84  3.000
 EU2  C5   N4   C3   116.42  3.000
 EU2  N13  C5   N6   116.64  3.000
 EU2  N13  C5   N4   124.93  3.000
 EU2  N6   C5   N4   118.42  3.000
 EU2  H27  C7   N6   107.83  3.000
 EU2  H27  C7   C12  108.57  3.000
 EU2  N6   C7   C12  112.78  3.000
 EU2  H27  C7   C8   108.42  3.000
 EU2  N6   C7   C8   109.89  3.000
 EU2  C12  C7   C8   109.24  3.000
 EU2  H29  C8   H28  107.51  3.000
 EU2  H29  C8   C9   109.47  3.000
 EU2  H28  C8   C9   109.36  3.000
 EU2  H29  C8   C7   109.76  3.000
 EU2  H28  C8   C7   110.65  3.000
 EU2  C9   C8   C7   110.04  3.000
 EU2  H32  C11  H33  107.36  3.000
 EU2  H32  C11  O10  110.25  3.000
 EU2  H33  C11  O10  107.06  3.000
 EU2  H32  C11  C12  109.54  3.000
 EU2  H33  C11  C12  110.68  3.000
 EU2  O10  C11  C12  111.83  3.000
 EU2  H35  C12  H34  107.57  3.000
 EU2  H35  C12  C11  109.41  3.000
 EU2  H34  C12  C11  109.86  3.000
 EU2  H35  C12  C7   110.53  3.000
 EU2  H34  C12  C7   109.40  3.000
 EU2  C11  C12  C7   110.03  3.000
 EU2  N13  C14  C15  116.11  3.000
 EU2  C15  C14  C2   123.76  3.000
 EU2  N13  C14  C2   120.11  3.000
 EU2  C24  C15  C16  119.85  3.000
 EU2  C24  C15  C14  118.80  3.000
 EU2  C16  C15  C14  121.32  3.000
 EU2  H36  C16  C17  118.79  3.000
 EU2  H36  C16  C15  119.72  3.000
 EU2  C17  C16  C15  121.47  3.000
 EU2  H38  C19  H39  107.69  3.000
 EU2  H38  C19  N20  111.65  3.000
 EU2  H39  C19  N20  111.73  3.000
 EU2  H38  C19  C18  111.92  3.000
 EU2  H39  C19  C18  111.99  3.000
 EU2  N20  C19  C18  101.88  3.000
 EU2  O22  C21  N20  127.23  3.000
 EU2  O22  C21  C23  127.54  3.000
 EU2  N20  C21  C23  105.23  3.000
 EU2  C18  C23  C24  122.05  3.000
 EU2  C24  C23  C21  129.06  3.000
 EU2  C18  C23  C21  108.89  3.000
 EU2  H41  C24  C23  121.11  3.000
 EU2  H41  C24  C15  120.80  3.000
 EU2  C23  C24  C15  118.09  3.000
 EU2  H26  N6   C7   118.11  3.000
 EU2  H26  N6   C5   115.99  3.000
 EU2  C7   N6   C5   124.50  3.000
 EU2  H31  C9   H30  107.42  3.000
 EU2  H31  C9   O10  107.10  3.000
 EU2  H30  C9   O10  110.30  3.000
 EU2  H31  C9   C8   110.31  3.000
 EU2  H30  C9   C8   109.40  3.000
 EU2  O10  C9   C8   112.18  3.000
 EU2  C9   O10  C11  111.95  3.000
 EU2  C14  N13  C5   118.62  3.000
 EU2  H37  C17  C18  121.58  3.000
 EU2  H37  C17  C16  120.22  3.000
 EU2  C18  C17  C16  118.20  3.000
 EU2  C17  C18  C23  120.32  3.000
 EU2  C23  C18  C19  109.15  3.000
 EU2  C17  C18  C19  130.53  3.000
 EU2  H40  N20  C21  122.74  3.000
 EU2  H40  N20  C19  122.41  3.000
 EU2  C21  N20  C19  114.84  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
 EU2  CONST_01  C5   N13  C14  C2      0.00   0.0  0
 EU2  CONST_04  C5   N4   C3   C2      0.00   0.0  0
 EU2  CONST_05  N13  C5   N4   C3      0.00   0.0  0
 EU2  CONST_06  N13  C14  C2   C3      0.00   0.0  0
 EU2  CONST_07  C15  C14  C2   C3    180.00   0.0  0
 EU2  CONST_08  C14  N13  C5   N4      0.00   0.0  0
 EU2  CONST_09  C14  C2   C3   N4      0.00   0.0  0
 EU2  CONST_10  C15  C14  N13  C5    180.00   0.0  0
 EU2  CONST_11  C17  C16  C15  C14   180.00   0.0  0
 EU2  CONST_12  C23  C24  C15  C14   180.00   0.0  0
 EU2  CONST_13  C18  C17  C16  C15     0.00   0.0  0
 EU2  CONST_14  C18  C23  C24  C15     0.00   0.0  0
 EU2  CONST_15  C23  C18  C17  C16     0.00   0.0  0
 EU2  CONST_17  C23  C24  C15  C16     0.00   0.0  0
 EU2  CONST_18  C17  C16  C15  C24     0.00   0.0  0
 EU2  CONST_20  C17  C18  C23  C24     0.00   0.0  0
 EU2  CONST_21  C23  C21  N20  C19     0.00   0.0  0
 EU2  CONST_22  N6   C5   N4   C3    180.00   0.0  0
 EU2  CONST_23  CL1  C2   C3   N4    180.00   0.0  0
 EU2  CONST_24  N6   C5   N13  C14   180.00   0.0  0
 EU2  CONST_25  CL1  C2   C14  C15     0.00   0.0  0
 EU2  CONST_26  N13  C14  C2   CL1   180.00   0.0  0
 EU2  CONST_27  C7   N6   C5   N4      0.00   0.0  0
 EU2  CONST_28  N13  C5   N6   C7    180.00   0.0  0
 EU2  CONST_29  O22  C21  N20  C19   180.00   0.0  0
 EU2  CONST_30  H25  C3   N4   C5    180.00   0.0  0
 EU2  CONST_31  H36  C16  C15  C14     0.00   0.0  0
 EU2  CONST_32  H41  C24  C15  C14     0.00   0.0  0
 EU2  CONST_33  H37  C17  C16  C15   180.00   0.0  0
 EU2  CONST_34  H40  N20  C21  C23   180.00   0.0  0
 EU2  CONST_35  H26  N6   C5   N4    180.00   0.0  0
 EU2  Var_01    O10  C11  C12  C7     56.72  30.0  1
 EU2  Var_02    O10  C9   C8   C7    -56.20  30.0  1
 EU2  Var_03    H39  C19  N20  C21  -119.94  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
 EU2  chir_01  C7  C12  C8  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
 EU2  plan-1  C2   0.020
 EU2  plan-1  C3   0.020
 EU2  plan-1  N4   0.020
 EU2  plan-1  C5   0.020
 EU2  plan-1  C14  0.020
 EU2  plan-1  C15  0.020
 EU2  plan-1  CL1  0.020
 EU2  plan-1  N6   0.020
 EU2  plan-1  N13  0.020
 EU2  plan-1  H25  0.020
 EU2  plan-2  C5   0.020
 EU2  plan-2  C7   0.020
 EU2  plan-2  N6   0.020
 EU2  plan-2  H26  0.020
 EU2  plan-3  C14  0.020
 EU2  plan-3  C15  0.020
 EU2  plan-3  C16  0.020
 EU2  plan-3  C19  0.020
 EU2  plan-3  C21  0.020
 EU2  plan-3  C23  0.020
 EU2  plan-3  C24  0.020
 EU2  plan-3  C17  0.020
 EU2  plan-3  C18  0.020
 EU2  plan-3  N20  0.020
 EU2  plan-3  O22  0.020
 EU2  plan-3  H36  0.020
 EU2  plan-3  H41  0.020
 EU2  plan-3  H37  0.020
 EU2  plan-3  H40  0.020

