# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:03:15 2022
#   Inital geometry file: a 145 line input string
#   Ligand name: 4-[4-(1-amino-1-methylethyl)phenyl]-5-chloro-N-[4-(2-morpholin-4-ylethyl)phenyl]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(N)c1ccc(cc1)c2nc(Nc3ccc(CCN4CCOCC4)cc3)ncc2Cl
#
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
 AA2  AA2  4-[4-(1-amino-1-methylethyl)phenyl]-5-chloro-N-[4-(2-morpholin-4-ylethyl)phenyl]pyrimidin-2-amine  ligand  62  32  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AA2
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
 AA2  N1    N   N     0  -0.506   2.0073   0.1810    0.5297
 AA2  C2    C   CR6   0   0.604   0.7599  -0.1801    0.8172
 AA2  N3    N   N     0  -0.500   0.2295  -0.2070    2.0445
 AA2  C4    C   CR6   0   0.261   0.9779   0.1571    3.0733
 AA2  C5    C   CR6   0  -0.176   2.2949   0.5783    2.8561
 AA2  C6    C   CR16  0   0.046   2.7537   0.5624    1.5492
 AA2  C7    C   CR6   0   0.120   0.3357   0.1285    4.4005
 AA2  C8    C   CR16  0  -0.335  -0.9392   0.6591    4.5517
 AA2  C9    C   CR16  0  -0.305  -1.5678   0.6484    5.7877
 AA2  C10   C   CR6   0   0.073  -0.9596   0.0866    6.9048
 AA2  C11   C   CR16  0  -0.234   0.3075  -0.4729    6.7324
 AA2  C12   C   CR16  0  -0.292   0.9519  -0.4466    5.5096
 AA2  C13   C   CR6   0   0.457   0.0647  -0.6558   -1.5521
 AA2  C14   C   CR16  0  -0.402  -1.0310  -1.1460   -2.2671
 AA2  C15   C   CR16  0  -0.262  -0.9868  -1.2642   -3.6428
 AA2  C16   C   CR6   0   0.011   0.1480  -0.9027   -4.3624
 AA2  C17   C   CR16  0  -0.266   1.2304  -0.4169   -3.6405
 AA2  C18   C   CR16  0  -0.249   1.2077  -0.2902   -2.2601
 AA2  N19   N   NH1   0  -0.697  -0.0869  -0.5692   -0.1670
 AA2  CL20  CL  CL    0  -0.124   3.3198   1.1689    4.1062
 AA2  C21   C   CT    0  -0.057  -1.6381   0.0620    8.2791
 AA2  C22   C   CH3   0  -0.654  -0.7181   0.7275    9.3076
 AA2  C23   C   CH3   0  -0.601  -1.9045  -1.3928    8.6773
 AA2  N24   N   NH2   0  -0.732  -2.9130   0.7584    8.3355
 AA2  C25   C   CH2   0  -0.486   0.1851  -0.9826   -5.8613
 AA2  C26   C   CH2   0  -0.261  -0.3221   0.3134   -6.4948
 AA2  N27   N   NT    0  -0.384  -0.2151   0.3186   -7.9388
 AA2  C28   C   CH2   0  -0.312  -0.3210   1.6582   -8.4857
 AA2  C29   C   CH2   0  -0.220  -0.1260   1.6215   -9.9897
 AA2  O30   O   O2    0  -0.465  -1.0620   0.7756  -10.6124
 AA2  C31   C   CH2   0  -0.197  -0.9867  -0.5267  -10.0869
 AA2  C32   C   CH2   0  -0.326  -1.1882  -0.5432   -8.5825
 AA2  H6    H   HCR6  0   0.294   3.7655   0.8824    1.3259
 AA2  H8    H   HCR6  0   0.254  -1.4399   1.1001    3.6995
 AA2  H9    H   HCR6  0   0.255  -2.5519   1.0917    5.8680
 AA2  H11   H   HCR6  0   0.243   0.8131  -0.9396    7.5686
 AA2  H12   H   HCR6  0   0.257   1.9297  -0.9005    5.4196
 AA2  H14   H   HCR6  0   0.255  -1.9288  -1.4440   -1.7370
 AA2  H15   H   HCR6  0   0.256  -1.8543  -1.6529   -4.1631
 AA2  H17   H   HCR6  0   0.244   2.1320  -0.1262   -4.1670
 AA2  H18   H   HCR6  0   0.270   2.0753   0.0864   -1.7458
 AA2  H19   H   HNH1  0   0.403  -0.9905  -0.8454    0.1841
 AA2  H221  H   HCH3  0   0.245  -1.1996   0.7304   10.2855
 AA2  H222  H   HCH3  0   0.259   0.2349   0.2083    9.4014
 AA2  H223  H   HCH3  0   0.226  -0.5037   1.7613    9.0298
 AA2  H231  H   HCH3  0   0.219  -0.9929  -1.9895    8.6789
 AA2  H232  H   HCH3  0   0.223  -2.3408  -1.4304    9.6758
 AA2  H233  H   HCH3  0   0.214  -2.6036  -1.8643    7.9833
 AA2  H241  H   HNH2  0   0.344  -2.8129   1.7289    8.0643
 AA2  H242  H   HNH2  0   0.352  -3.5868   0.3396    7.7063
 AA2  H251  H   HCH2  0   0.181   1.2068  -1.1614   -6.2041
 AA2  H252  H   HCH2  0   0.302  -0.4131  -1.8337   -6.1962
 AA2  H261  H   HCH2  0   0.168  -1.3553   0.5076   -6.1565
 AA2  H262  H   HCH2  0   0.254   0.2830   1.1385   -6.1092
 AA2  H281  H   HCH2  0   0.211  -1.2954   2.1223   -8.2512
 AA2  H282  H   HCH2  0   0.255   0.4518   2.2916   -8.0422
 AA2  H291  H   HCH2  0   0.230  -0.2573   2.6192  -10.4122
 AA2  H292  H   HCH2  0   0.200   0.8997   1.2913  -10.2094
 AA2  H311  H   HCH2  0   0.201  -1.7625  -1.1194  -10.5747
 AA2  H312  H   HCH2  0   0.232  -0.0140  -0.9824  -10.3234
 AA2  H321  H   HCH2  0   0.267  -1.0684  -1.5709   -8.2328
 AA2  H322  H   HCH2  0   0.158  -2.2221  -0.2360   -8.3428

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
 AA2  N1   C2    aromatic  1.330  0.020  1.330
 AA2  N1   C6    aromatic  1.320  0.020  1.320
 AA2  C2   N3    aromatic  1.337  0.020  1.337
 AA2  C2   N19   single    1.355  0.020  1.355
 AA2  N3   C4    aromatic  1.323  0.020  1.323
 AA2  C4   C5    aromatic  1.400  0.020  1.400
 AA2  C4   C7    single    1.475  0.020  1.475
 AA2  C5   C6    aromatic  1.385  0.020  1.385
 AA2  C5   CL20  single    1.721  0.020  1.721
 AA2  C6   H6    single    0.930  0.020  1.080
 AA2  C7   C8    aromatic  1.389  0.020  1.389
 AA2  C7   C12   aromatic  1.393  0.020  1.393
 AA2  C8   C9    aromatic  1.387  0.020  1.387
 AA2  C8   H8    single    0.930  0.020  1.080
 AA2  C9   C10   aromatic  1.391  0.020  1.391
 AA2  C9   H9    single    0.930  0.020  1.080
 AA2  C10  C11   aromatic  1.396  0.020  1.396
 AA2  C10  C21   single    1.533  0.020  1.533
 AA2  C11  C12   aromatic  1.382  0.020  1.382
 AA2  C11  H11   single    0.930  0.020  1.080
 AA2  C12  H12   single    0.930  0.020  1.080
 AA2  C13  C14   aromatic  1.397  0.020  1.397
 AA2  C13  C18   aromatic  1.393  0.020  1.393
 AA2  C13  N19   single    1.396  0.020  1.396
 AA2  C14  C15   aromatic  1.381  0.020  1.381
 AA2  C14  H14   single    0.930  0.020  1.080
 AA2  C15  C16   aromatic  1.391  0.020  1.391
 AA2  C15  H15   single    0.930  0.020  1.080
 AA2  C16  C17   aromatic  1.389  0.020  1.389
 AA2  C16  C25   single    1.502  0.020  1.502
 AA2  C17  C18   aromatic  1.386  0.020  1.386
 AA2  C17  H17   single    0.930  0.020  1.080
 AA2  C18  H18   single    0.930  0.020  1.080
 AA2  N19  H19   single    0.860  0.020  1.020
 AA2  C21  C22   single    1.532  0.020  1.532
 AA2  C21  C23   single    1.532  0.020  1.532
 AA2  C21  N24   single    1.454  0.020  1.454
 AA2  C22  H221  single    0.970  0.020  1.090
 AA2  C22  H222  single    0.970  0.020  1.090
 AA2  C22  H223  single    0.970  0.020  1.090
 AA2  C23  H231  single    0.970  0.020  1.090
 AA2  C23  H232  single    0.970  0.020  1.090
 AA2  C23  H233  single    0.970  0.020  1.090
 AA2  N24  H241  single    0.890  0.020  1.040
 AA2  N24  H242  single    0.890  0.020  1.040
 AA2  C25  C26   single    1.529  0.020  1.529
 AA2  C25  H251  single    0.970  0.020  1.090
 AA2  C25  H252  single    0.970  0.020  1.090
 AA2  C26  N27   single    1.448  0.020  1.448
 AA2  C26  H261  single    0.970  0.020  1.090
 AA2  C26  H262  single    0.970  0.020  1.090
 AA2  N27  C28   single    1.451  0.020  1.451
 AA2  N27  C32   single    1.450  0.020  1.450
 AA2  C28  C29   single    1.517  0.020  1.517
 AA2  C28  H281  single    0.970  0.020  1.090
 AA2  C28  H282  single    0.970  0.020  1.090
 AA2  C29  O30   single    1.407  0.020  1.407
 AA2  C29  H291  single    0.970  0.020  1.090
 AA2  C29  H292  single    0.970  0.020  1.090
 AA2  O30  C31   single    1.406  0.020  1.406
 AA2  C31  C32   single    1.518  0.020  1.518
 AA2  C31  H311  single    0.970  0.020  1.090
 AA2  C31  H312  single    0.970  0.020  1.090
 AA2  C32  H321  single    0.970  0.020  1.090
 AA2  C32  H322  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
 AA2  C6    N1   C2    116.22  3.000
 AA2  N19   C2   N3    114.38  3.000
 AA2  N19   C2   N1    120.46  3.000
 AA2  N3    C2   N1    125.16  3.000
 AA2  C4    N3   C2    118.92  3.000
 AA2  C7    C4   C5    123.73  3.000
 AA2  C7    C4   N3    116.62  3.000
 AA2  C5    C4   N3    119.63  3.000
 AA2  CL20  C5   C6    119.47  3.000
 AA2  CL20  C5   C4    123.43  3.000
 AA2  C6    C5   C4    117.04  3.000
 AA2  H6    C6   C5    119.99  3.000
 AA2  H6    C6   N1    116.99  3.000
 AA2  C5    C6   N1    123.01  3.000
 AA2  C12   C7   C8    118.48  3.000
 AA2  C12   C7   C4    122.14  3.000
 AA2  C8    C7   C4    119.36  3.000
 AA2  H8    C8   C9    119.69  3.000
 AA2  H8    C8   C7    119.63  3.000
 AA2  C9    C8   C7    120.67  3.000
 AA2  H9    C9   C10   120.23  3.000
 AA2  H9    C9   C8    118.37  3.000
 AA2  C10   C9   C8    121.40  3.000
 AA2  C21   C10  C11   120.40  3.000
 AA2  C21   C10  C9    122.22  3.000
 AA2  C11   C10  C9    117.37  3.000
 AA2  H11   C11  C12   118.27  3.000
 AA2  H11   C11  C10   120.08  3.000
 AA2  C12   C11  C10   121.65  3.000
 AA2  H12   C12  C11   119.14  3.000
 AA2  H12   C12  C7    120.45  3.000
 AA2  C11   C12  C7    120.40  3.000
 AA2  N19   C13  C18   125.24  3.000
 AA2  N19   C13  C14   116.38  3.000
 AA2  C18   C13  C14   118.38  3.000
 AA2  H14   C14  C15   119.32  3.000
 AA2  H14   C14  C13   119.71  3.000
 AA2  C15   C14  C13   120.97  3.000
 AA2  H15   C15  C16   119.86  3.000
 AA2  H15   C15  C14   118.89  3.000
 AA2  C16   C15  C14   121.25  3.000
 AA2  C25   C16  C17   121.21  3.000
 AA2  C25   C16  C15   121.50  3.000
 AA2  C17   C16  C15   117.24  3.000
 AA2  H17   C17  C18   118.22  3.000
 AA2  H17   C17  C16   119.32  3.000
 AA2  C18   C17  C16   122.46  3.000
 AA2  H18   C18  C17   119.63  3.000
 AA2  H18   C18  C13   120.67  3.000
 AA2  C17   C18  C13   119.70  3.000
 AA2  H19   N19  C13   115.21  3.000
 AA2  H19   N19  C2    112.70  3.000
 AA2  C13   N19  C2    132.10  3.000
 AA2  N24   C21  C23   107.00  3.000
 AA2  N24   C21  C22   107.01  3.000
 AA2  C23   C21  C22   110.03  3.000
 AA2  N24   C21  C10   114.54  3.000
 AA2  C23   C21  C10   108.99  3.000
 AA2  C22   C21  C10   109.22  3.000
 AA2  H223  C22  H222  107.54  3.000
 AA2  H223  C22  H221  108.21  3.000
 AA2  H222  C22  H221  108.09  3.000
 AA2  H223  C22  C21   111.01  3.000
 AA2  H222  C22  C21   112.09  3.000
 AA2  H221  C22  C21   109.77  3.000
 AA2  H233  C23  H232  108.12  3.000
 AA2  H233  C23  H231  107.47  3.000
 AA2  H232  C23  H231  108.33  3.000
 AA2  H233  C23  C21   110.87  3.000
 AA2  H232  C23  C21   109.90  3.000
 AA2  H231  C23  C21   112.02  3.000
 AA2  H242  N24  H241  107.20  3.000
 AA2  H242  N24  C21   111.18  3.000
 AA2  H241  N24  C21   111.22  3.000
 AA2  H252  C25  H251  106.76  3.000
 AA2  H252  C25  C26   110.58  3.000
 AA2  H251  C25  C26   108.60  3.000
 AA2  H252  C25  C16   109.50  3.000
 AA2  H251  C25  C16   110.19  3.000
 AA2  C26   C25  C16   111.12  3.000
 AA2  H262  C26  H261  106.08  3.000
 AA2  H262  C26  N27   107.95  3.000
 AA2  H261  C26  N27   111.96  3.000
 AA2  H262  C26  C25   108.05  3.000
 AA2  H261  C26  C25   109.42  3.000
 AA2  N27   C26  C25   113.06  3.000
 AA2  C32   N27  C28   109.41  3.000
 AA2  C32   N27  C26   113.01  3.000
 AA2  C28   N27  C26   111.95  3.000
 AA2  H282  C28  H281  107.10  3.000
 AA2  H282  C28  C29   108.98  3.000
 AA2  H281  C28  C29   109.52  3.000
 AA2  H282  C28  N27   109.30  3.000
 AA2  H281  C28  N27   111.86  3.000
 AA2  C29   C28  N27   110.00  3.000
 AA2  H292  C29  H291  108.02  3.000
 AA2  H292  C29  O30   110.59  3.000
 AA2  H291  C29  O30   107.35  3.000
 AA2  H292  C29  C28   108.98  3.000
 AA2  H291  C29  C28   110.26  3.000
 AA2  O30   C29  C28   111.58  3.000
 AA2  C31   O30  C29   110.84  3.000
 AA2  H312  C31  H311  107.91  3.000
 AA2  H312  C31  C32   109.02  3.000
 AA2  H311  C31  C32   110.05  3.000
 AA2  H312  C31  O30   110.53  3.000
 AA2  H311  C31  O30   107.33  3.000
 AA2  C32   C31  O30   111.92  3.000
 AA2  H322  C32  H321  107.15  3.000
 AA2  H322  C32  C31   109.64  3.000
 AA2  H321  C32  C31   108.24  3.000
 AA2  H322  C32  N27   111.49  3.000
 AA2  H321  C32  N27   110.09  3.000
 AA2  C31   C32  N27   110.14  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
 AA2  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 AA2  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 AA2  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 AA2  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 AA2  CONST_05  C7    C4   N3   C2    180.00   0.0  0
 AA2  CONST_06  C6    N1   C2   N3      0.00   0.0  0
 AA2  CONST_07  C6    C5   C4   N3      0.00   0.0  0
 AA2  CONST_10  C9    C8   C7   C4    180.00   0.0  0
 AA2  CONST_11  C11   C12  C7   C4    180.00   0.0  0
 AA2  CONST_14  C7    C4   C5   C6    180.00   0.0  0
 AA2  CONST_15  C10   C9   C8   C7      0.00   0.0  0
 AA2  CONST_16  C10   C11  C12  C7      0.00   0.0  0
 AA2  CONST_17  C11   C12  C7   C8      0.00   0.0  0
 AA2  CONST_18  C11   C10  C9   C8      0.00   0.0  0
 AA2  CONST_19  C12   C7   C8   C9      0.00   0.0  0
 AA2  CONST_20  C12   C11  C10  C9      0.00   0.0  0
 AA2  CONST_21  C16   C15  C14  C13     0.00   0.0  0
 AA2  CONST_22  C16   C17  C18  C13     0.00   0.0  0
 AA2  CONST_23  C17   C18  C13  C14     0.00   0.0  0
 AA2  CONST_24  C17   C16  C15  C14     0.00   0.0  0
 AA2  CONST_25  C18   C13  C14  C15     0.00   0.0  0
 AA2  CONST_26  C18   C17  C16  C15     0.00   0.0  0
 AA2  CONST_27  CL20  C5   C6   N1    180.00   0.0  0
 AA2  CONST_28  CL20  C5   C4   N3    180.00   0.0  0
 AA2  CONST_29  N19   C2   N3   C4    180.00   0.0  0
 AA2  CONST_30  N19   C2   N1   C6    180.00   0.0  0
 AA2  CONST_31  CL20  C5   C4   C7      0.00   0.0  0
 AA2  CONST_32  C21   C10  C9   C8    180.00   0.0  0
 AA2  CONST_33  C21   C10  C11  C12   180.00   0.0  0
 AA2  CONST_34  C25   C16  C15  C14   180.00   0.0  0
 AA2  CONST_35  N19   C13  C14  C15   180.00   0.0  0
 AA2  CONST_36  N19   C13  C18  C17   180.00   0.0  0
 AA2  CONST_37  C25   C16  C17  C18   180.00   0.0  0
 AA2  CONST_38  H6    C6   N1   C2    180.00   0.0  0
 AA2  CONST_39  H8    C8   C7   C4      0.00   0.0  0
 AA2  CONST_40  H12   C12  C7   C4      0.00   0.0  0
 AA2  CONST_41  H9    C9   C8   C7    180.00   0.0  0
 AA2  CONST_42  H11   C11  C12  C7    180.00   0.0  0
 AA2  CONST_43  H15   C15  C14  C13   180.00   0.0  0
 AA2  CONST_44  H17   C17  C18  C13   180.00   0.0  0
 AA2  CONST_45  H18   C18  C13  C14   180.00   0.0  0
 AA2  CONST_46  H14   C14  C15  C16   180.00   0.0  0
 AA2  Var_01    O30   C29  C28  N27    57.81  30.0  1
 AA2  Var_02    O30   C31  C32  N27   -56.79  30.0  1
 AA2  Var_03    C31   C32  N27  C28    56.53  30.0  1
 AA2  Var_04    C32   N27  C28  C29   -57.07  30.0  1
 AA2  Var_05    C32   C31  O30  C29    56.65  30.0  1
 AA2  Var_06    C13   N19  C2   N1     -1.80  30.0  2
 AA2  Var_07    C14   C13  N19  C2    178.16  30.0  3
 AA2  Var_08    C22   C21  C10  C9   -124.37  30.0  2
 AA2  Var_09    C26   C25  C16  C15    88.24  30.0  2
 AA2  Var_10    N27   C26  C25  C16   175.85  30.0  3
 AA2  Var_11    C28   N27  C26  C25  -163.10  30.0  3
 AA2  Var_12    H221  C22  C21  C10   179.02  30.0  3
 AA2  Var_13    H231  C23  C21  C10    56.63  30.0  3
 AA2  Var_14    H241  N24  C21  C10   -57.98  30.0  3

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
 AA2  plan-1  N1    0.020
 AA2  plan-1  C2    0.020
 AA2  plan-1  N3    0.020
 AA2  plan-1  C4    0.020
 AA2  plan-1  C5    0.020
 AA2  plan-1  C6    0.020
 AA2  plan-1  C7    0.020
 AA2  plan-1  N19   0.020
 AA2  plan-1  CL20  0.020
 AA2  plan-1  H6    0.020
 AA2  plan-2  C4    0.020
 AA2  plan-2  C7    0.020
 AA2  plan-2  C8    0.020
 AA2  plan-2  C9    0.020
 AA2  plan-2  C10   0.020
 AA2  plan-2  C11   0.020
 AA2  plan-2  C12   0.020
 AA2  plan-2  C21   0.020
 AA2  plan-2  H8    0.020
 AA2  plan-2  H9    0.020
 AA2  plan-2  H11   0.020
 AA2  plan-2  H12   0.020
 AA2  plan-3  C13   0.020
 AA2  plan-3  C14   0.020
 AA2  plan-3  C15   0.020
 AA2  plan-3  C16   0.020
 AA2  plan-3  C17   0.020
 AA2  plan-3  C18   0.020
 AA2  plan-3  N19   0.020
 AA2  plan-3  C25   0.020
 AA2  plan-3  H14   0.020
 AA2  plan-3  H15   0.020
 AA2  plan-3  H17   0.020
 AA2  plan-3  H18   0.020

