# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 16:22:28 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: N-(4-{[(3S)-3-(dimethylamino)pyrrolidin-1-yl]carbonyl}phenyl)-5-fluoro-4-[2-methyl-1-(1-methylethyl)-1H-imidazol-5-yl]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)n1c(C)ncc1c2nc(Nc3ccc(cc3)C(=O)N4CC[C@@H](C4)N(C)C)ncc2F
#
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
 I19  I19  N-(4-{[(3S)-3-(dimethylamino)pyrrolidin-1-yl]carbonyl}phenyl)-5-fluoro-4-[2-methyl-1-(1-methylethyl)-1H-imidazol-5-yl]pyrimidin-2-amine  ligand  63  33  .  2021-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_I19
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
 I19  C1    C  CH3   0  -0.646   0.4119  28.9584  12.1125
 I19  C2    C  CH1   0  -0.144   0.4633  28.4142  10.6907
 I19  C3    C  CH3   0  -0.678   1.1028  27.0370  10.5971
 I19  N1    N  NR5   0  -0.490  -0.8579  28.4620  10.0488
 I19  C4    C  CR5   0   0.441  -1.9621  27.7562  10.3958
 I19  C5    C  CH3   0  -0.768  -2.0053  26.6298  11.3661
 I19  N2    N  N     0  -0.452  -3.0267  28.1746   9.7433
 I19  C6    C  CR15  0  -0.228  -2.6117  29.1973   8.9638
 I19  C7    C  CR5   0   0.275  -1.2647  29.4046   9.1230
 I19  C8    C  CR6   0   0.079  -0.4090  30.3114   8.3734
 I19  N3    N  N     0  -0.467   0.8066  29.9157   7.9970
 I19  C9    C  CR6   0   0.582   1.5334  30.7345   7.2496
 I19  N4    N  NH1   0  -0.768   2.7653  30.3360   6.8167
 I19  C10   C  CR6   0   0.348   3.4031  29.1200   7.0496
 I19  C11   C  CR16  0  -0.273   3.4120  28.5118   8.3036
 I19  C12   C  CR16  0  -0.266   4.0562  27.3011   8.4817
 I19  C13   C  CR6   0  -0.057   4.7326  26.6849   7.4336
 I19  C14   C  CR16  0  -0.273   4.7811  27.3297   6.2011
 I19  C15   C  CR16  0  -0.314   4.1076  28.5219   6.0033
 I19  C16   C  C     0   0.513   5.4770  25.4064   7.6194
 I19  O1    O  O     0  -0.501   6.6192  25.2821   7.1872
 I19  N5    N  NT    0  -0.459   4.8503  24.4196   8.2789
 I19  C17   C  CH2   0  -0.265   3.4133  24.3133   8.5281
 I19  C18   C  CH2   0  -0.499   3.2090  22.8082   8.5863
 I19  C19   C  CH1   0  -0.125   4.4870  22.3084   9.2595
 I19  C20   C  CH2   0  -0.263   5.5264  23.1465   8.5121
 I19  N6    N  NT    0  -0.408   4.5220  22.5884  10.6913
 I19  C21   C  CH3   0  -0.526   3.3539  22.0994  11.3990
 I19  C22   C  CH3   0  -0.529   5.7157  22.0396  11.3070
 I19  N7    N  N     0  -0.444   1.1604  31.9460   6.8301
 I19  C23   C  CR16  0  -0.149  -0.0367  32.3548   7.2085
 I19  C24   C  CR6   0   0.394  -0.8584  31.5686   7.9861
 I19  F1    F  F     0  -0.294  -2.0601  32.0255   8.3596
 I19  H11C  H  HCH3  0   0.245   1.4275  29.0460  12.4987
 I19  H12C  H  HCH3  0   0.244  -0.0393  29.9503  12.1333
 I19  H13C  H  HCH3  0   0.231  -0.1417  28.3139  12.7951
 I19  H2    H  HCH1  0   0.283   1.0816  29.0887  10.1067
 I19  H31C  H  HCH3  0   0.246   1.1246  26.6834   9.5661
 I19  H32C  H  HCH3  0   0.244   2.1318  27.1050  10.9510
 I19  H33C  H  HCH3  0   0.248   0.6011  26.2918  11.2111
 I19  H51C  H  HCH3  0   0.264  -1.4981  25.7444  10.9819
 I19  H52C  H  HCH3  0   0.258  -1.5539  26.8764  12.3253
 I19  H53C  H  HCH3  0   0.274  -3.0456  26.3666  11.5417
 I19  H6    H  HCR5  0   0.265  -3.2843  29.7079   8.2921
 I19  H4    H  HNH1  0   0.408   3.1508  30.9154   6.0865
 I19  H11   H  HCR6  0   0.271   2.9379  28.9905   9.1461
 I19  H15   H  HCR6  0   0.272   4.1197  28.9911   5.0270
 I19  H12   H  HCR6  0   0.262   4.0555  26.8533   9.4669
 I19  H14   H  HCR6  0   0.262   5.3241  26.8849   5.3774
 I19  H171  H  HCH2  0   0.236   3.1330  24.7807   9.4754
 I19  H172  H  HCH2  0   0.258   2.8350  24.7845   7.7344
 I19  H201  H  HCH2  0   0.244   5.7835  22.6640   7.5647
 I19  H202  H  HCH2  0   0.253   6.4547  23.2962   9.0607
 I19  H181  H  HCH2  0   0.263   2.2794  22.5228   9.0728
 I19  H182  H  HCH2  0   0.259   3.1758  22.4020   7.5731
 I19  H19   H  HCH1  0   0.233   4.6434  21.2355   9.0625
 I19  H211  H  HCH3  0   0.237   3.4838  22.2758  12.4669
 I19  H212  H  HCH3  0   0.235   2.4507  22.6289  11.1000
 I19  H213  H  HCH3  0   0.196   3.1789  21.0212  11.2606
 I19  H221  H  HCH3  0   0.236   6.6221  22.4622  10.8762
 I19  H222  H  HCH3  0   0.237   5.7239  22.2799  12.3705
 I19  H223  H  HCH3  0   0.195   5.7827  20.9443  11.2126
 I19  H23   H  HCR6  0   0.297  -0.3585  33.3405   6.8898

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
 I19  C1   C2    single    1.523  0.020  1.523
 I19  C2   C3    single    1.521  0.020  1.521
 I19  C2   N1    single    1.470  0.020  1.470
 I19  N1   C4    aromatic  1.356  0.020  1.356
 I19  N1   C7    aromatic  1.382  0.020  1.382
 I19  C4   C5    single    1.487  0.020  1.487
 I19  C4   N2    aromatic  1.317  0.020  1.317
 I19  N2   C6    aromatic  1.351  0.020  1.351
 I19  C6   C7    aromatic  1.372  0.020  1.372
 I19  C7   C8    single    1.455  0.020  1.455
 I19  C8   N3    aromatic  1.333  0.020  1.333
 I19  C8   C24   aromatic  1.390  0.020  1.390
 I19  N3   C9    aromatic  1.326  0.020  1.326
 I19  C9   N4    single    1.365  0.020  1.365
 I19  C9   N7    aromatic  1.335  0.020  1.335
 I19  N4   C10   single    1.393  0.020  1.393
 I19  C10  C11   aromatic  1.394  0.020  1.394
 I19  C10  C15   aromatic  1.396  0.020  1.396
 I19  C11  C12   aromatic  1.383  0.020  1.383
 I19  C12  C13   aromatic  1.391  0.020  1.391
 I19  C13  C14   aromatic  1.392  0.020  1.392
 I19  C13  C16   single    1.491  0.020  1.491
 I19  C14  C15   aromatic  1.384  0.020  1.384
 I19  C16  O1    double    1.227  0.020  1.227
 I19  C16  N5    single    1.342  0.020  1.342
 I19  N5   C17   single    1.462  0.020  1.462
 I19  N5   C20   single    1.460  0.020  1.460
 I19  C17  C18   single    1.520  0.020  1.520
 I19  C18  C19   single    1.528  0.020  1.528
 I19  C19  C20   single    1.530  0.020  1.530
 I19  C19  N6    single    1.459  0.020  1.459
 I19  N6   C21   single    1.451  0.020  1.451
 I19  N6   C22   single    1.451  0.020  1.451
 I19  N7   C23   aromatic  1.320  0.020  1.320
 I19  C23  C24   aromatic  1.378  0.020  1.378
 I19  C24  F1    single    1.339  0.020  1.339
 I19  C1   H11C  single    0.970  0.020  1.090
 I19  C1   H12C  single    0.970  0.020  1.090
 I19  C1   H13C  single    0.970  0.020  1.090
 I19  C2   H2    single    0.970  0.020  1.090
 I19  C3   H31C  single    0.970  0.020  1.090
 I19  C3   H32C  single    0.970  0.020  1.090
 I19  C3   H33C  single    0.970  0.020  1.090
 I19  C5   H51C  single    0.970  0.020  1.090
 I19  C5   H52C  single    0.970  0.020  1.090
 I19  C5   H53C  single    0.970  0.020  1.090
 I19  C6   H6    single    0.930  0.020  1.080
 I19  N4   H4    single    0.860  0.020  1.020
 I19  C11  H11   single    0.930  0.020  1.080
 I19  C15  H15   single    0.930  0.020  1.080
 I19  C12  H12   single    0.930  0.020  1.080
 I19  C14  H14   single    0.930  0.020  1.080
 I19  C17  H171  single    0.970  0.020  1.090
 I19  C17  H172  single    0.970  0.020  1.090
 I19  C20  H201  single    0.970  0.020  1.090
 I19  C20  H202  single    0.970  0.020  1.090
 I19  C18  H181  single    0.970  0.020  1.090
 I19  C18  H182  single    0.970  0.020  1.090
 I19  C19  H19   single    0.970  0.020  1.090
 I19  C21  H211  single    0.970  0.020  1.090
 I19  C21  H212  single    0.970  0.020  1.090
 I19  C21  H213  single    0.970  0.020  1.090
 I19  C22  H221  single    0.970  0.020  1.090
 I19  C22  H222  single    0.970  0.020  1.090
 I19  C22  H223  single    0.970  0.020  1.090
 I19  C23  H23   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
 I19  H13C  C1   H12C  108.42  3.000
 I19  H13C  C1   H11C  107.38  3.000
 I19  H12C  C1   H11C  107.80  3.000
 I19  H13C  C1   C2    112.99  3.000
 I19  H12C  C1   C2    110.91  3.000
 I19  H11C  C1   C2    109.15  3.000
 I19  H2    C2   N1    104.88  3.000
 I19  H2    C2   C3    106.86  3.000
 I19  N1    C2   C3    112.36  3.000
 I19  H2    C2   C1    107.43  3.000
 I19  N1    C2   C1    111.45  3.000
 I19  C3    C2   C1    113.27  3.000
 I19  H33C  C3   H32C  107.14  3.000
 I19  H33C  C3   H31C  108.71  3.000
 I19  H32C  C3   H31C  107.96  3.000
 I19  H33C  C3   C2    113.04  3.000
 I19  H32C  C3   C2    108.68  3.000
 I19  H31C  C3   C2    111.12  3.000
 I19  C7    N1   C4    106.66  3.000
 I19  C7    N1   C2    125.40  3.000
 I19  C4    N1   C2    127.12  3.000
 I19  N2    C4   C5    122.71  3.000
 I19  N2    C4   N1    111.48  3.000
 I19  C5    C4   N1    125.80  3.000
 I19  H53C  C5   H52C  108.02  3.000
 I19  H53C  C5   H51C  107.79  3.000
 I19  H52C  C5   H51C  107.56  3.000
 I19  H53C  C5   C4    108.44  3.000
 I19  H52C  C5   C4    113.03  3.000
 I19  H51C  C5   C4    111.81  3.000
 I19  C6    N2   C4    106.14  3.000
 I19  H6    C6   C7    127.78  3.000
 I19  H6    C6   N2    121.73  3.000
 I19  C7    C6   N2    110.42  3.000
 I19  C8    C7   C6    127.72  3.000
 I19  C8    C7   N1    126.65  3.000
 I19  C6    C7   N1    105.28  3.000
 I19  C24   C8   N3    118.99  3.000
 I19  C24   C8   C7    121.14  3.000
 I19  N3    C8   C7    119.80  3.000
 I19  C9    N3   C8    118.42  3.000
 I19  N7    C9   N4    114.66  3.000
 I19  N7    C9   N3    125.76  3.000
 I19  N4    C9   N3    119.56  3.000
 I19  H4    N4   C10   116.59  3.000
 I19  H4    N4   C9    114.00  3.000
 I19  C10   N4   C9    127.95  3.000
 I19  C15   C10  C11   118.96  3.000
 I19  C15   C10  N4    118.67  3.000
 I19  C11   C10  N4    122.31  3.000
 I19  H11   C11  C12   119.51  3.000
 I19  H11   C11  C10   120.41  3.000
 I19  C12   C11  C10   120.06  3.000
 I19  H12   C12  C13   120.19  3.000
 I19  H12   C12  C11   118.64  3.000
 I19  C13   C12  C11   121.14  3.000
 I19  C16   C13  C14   119.35  3.000
 I19  C16   C13  C12   121.91  3.000
 I19  C14   C13  C12   118.61  3.000
 I19  H14   C14  C15   119.31  3.000
 I19  H14   C14  C13   120.07  3.000
 I19  C15   C14  C13   120.59  3.000
 I19  H15   C15  C14   119.78  3.000
 I19  H15   C15  C10   119.71  3.000
 I19  C14   C15  C10   120.51  3.000
 I19  N5    C16  O1    122.21  3.000
 I19  N5    C16  C13   117.29  3.000
 I19  O1    C16  C13   120.50  3.000
 I19  C20   N5   C17   111.37  3.000
 I19  C20   N5   C16   120.22  3.000
 I19  C17   N5   C16   126.59  3.000
 I19  H172  C17  H171  108.08  3.000
 I19  H172  C17  C18   112.63  3.000
 I19  H171  C17  C18   110.84  3.000
 I19  H172  C17  N5    111.48  3.000
 I19  H171  C17  N5    111.64  3.000
 I19  C18   C17  N5    102.16  3.000
 I19  H182  C18  H181  106.95  3.000
 I19  H182  C18  C19   108.21  3.000
 I19  H181  C18  C19   115.59  3.000
 I19  H182  C18  C17   109.69  3.000
 I19  H181  C18  C17   113.07  3.000
 I19  C19   C18  C17   103.19  3.000
 I19  H19   C19  N6    111.03  3.000
 I19  H19   C19  C20   110.45  3.000
 I19  N6    C19  C20   110.97  3.000
 I19  H19   C19  C18   110.99  3.000
 I19  N6    C19  C18   112.92  3.000
 I19  C20   C19  C18   100.00  3.000
 I19  H202  C20  H201  107.26  3.000
 I19  H202  C20  C19   114.10  3.000
 I19  H201  C20  C19   109.95  3.000
 I19  H202  C20  N5    110.81  3.000
 I19  H201  C20  N5    110.80  3.000
 I19  C19   C20  N5    103.95  3.000
 I19  C22   N6   C21   109.15  3.000
 I19  C22   N6   C19   111.32  3.000
 I19  C21   N6   C19   113.24  3.000
 I19  H213  C21  H212  108.05  3.000
 I19  H213  C21  H211  107.49  3.000
 I19  H212  C21  H211  106.81  3.000
 I19  H213  C21  N6    113.38  3.000
 I19  H212  C21  N6    111.72  3.000
 I19  H211  C21  N6    109.11  3.000
 I19  H223  C22  H222  107.59  3.000
 I19  H223  C22  H221  107.54  3.000
 I19  H222  C22  H221  107.10  3.000
 I19  H223  C22  N6    112.94  3.000
 I19  H222  C22  N6    109.68  3.000
 I19  H221  C22  N6    111.73  3.000
 I19  C23   N7   C9    116.37  3.000
 I19  H23   C23  C24   120.49  3.000
 I19  H23   C23  N7    117.78  3.000
 I19  C24   C23  N7    121.73  3.000
 I19  F1    C24  C23   119.87  3.000
 I19  F1    C24  C8    121.40  3.000
 I19  C23   C24  C8    118.72  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
 I19  CONST_01  C6    N2   C4   N1      0.00   0.0  0
 I19  CONST_02  N2    C6   C7   N1      0.00   0.0  0
 I19  CONST_05  C6    C7   N1   C4      0.00   0.0  0
 I19  CONST_06  C8    C7   N1   C4    180.00   0.0  0
 I19  CONST_07  C7    C6   N2   C4      0.00   0.0  0
 I19  CONST_08  C7    N1   C4   N2      0.00   0.0  0
 I19  CONST_09  C8    C7   C6   N2    180.00   0.0  0
 I19  CONST_12  C9    N3   C8   C7    180.00   0.0  0
 I19  CONST_13  C23   C24  C8   C7    180.00   0.0  0
 I19  CONST_14  N7    C9   N3   C8      0.00   0.0  0
 I19  CONST_15  N7    C23  C24  C8      0.00   0.0  0
 I19  CONST_16  C23   C24  C8   N3      0.00   0.0  0
 I19  CONST_17  C23   N7   C9   N3      0.00   0.0  0
 I19  CONST_18  C24   C8   N3   C9      0.00   0.0  0
 I19  CONST_19  C24   C23  N7   C9      0.00   0.0  0
 I19  CONST_20  C13   C12  C11  C10     0.00   0.0  0
 I19  CONST_21  C13   C14  C15  C10     0.00   0.0  0
 I19  CONST_22  C14   C15  C10  C11     0.00   0.0  0
 I19  CONST_23  C14   C13  C12  C11     0.00   0.0  0
 I19  CONST_24  C15   C10  C11  C12     0.00   0.0  0
 I19  CONST_25  C15   C14  C13  C12     0.00   0.0  0
 I19  CONST_26  N2    C4   N1   C2    180.00   0.0  0
 I19  CONST_27  C6    C7   N1   C2    180.00   0.0  0
 I19  CONST_29  C7    N1   C4   C5    180.00   0.0  0
 I19  CONST_30  C6    N2   C4   C5    180.00   0.0  0
 I19  CONST_31  F1    C24  C8   C7      0.00   0.0  0
 I19  CONST_32  N4    C9   N3   C8    180.00   0.0  0
 I19  CONST_33  F1    C24  C8   N3    180.00   0.0  0
 I19  CONST_34  C23   N7   C9   N4    180.00   0.0  0
 I19  CONST_35  C12   C11  C10  N4    180.00   0.0  0
 I19  CONST_36  C14   C15  C10  N4    180.00   0.0  0
 I19  CONST_37  C16   C13  C12  C11   180.00   0.0  0
 I19  CONST_38  C16   C13  C14  C15   180.00   0.0  0
 I19  CONST_39  F1    C24  C23  N7    180.00   0.0  0
 I19  CONST_41  C20   N5   C16  C13   180.00   0.0  0
 I19  CONST_42  H6    C6   C7   N1    180.00   0.0  0
 I19  CONST_43  H23   C23  C24  C8    180.00   0.0  0
 I19  CONST_44  H12   C12  C11  C10   180.00   0.0  0
 I19  CONST_45  H14   C14  C15  C10   180.00   0.0  0
 I19  CONST_46  H15   C15  C10  C11   180.00   0.0  0
 I19  CONST_47  H11   C11  C12  C13   180.00   0.0  0
 I19  CONST_49  C20   N5   C16  O1      0.00   0.0  0
 I19  Var_01    C19   C18  C17  N5     35.91  30.0  1
 I19  Var_02    C19   C20  N5   C17   -13.62  30.0  1
 I19  Var_03    C20   N5   C17  C18   -13.84  30.0  1
 I19  Var_04    C10   N4   C9   N3      0.61  30.0  2
 I19  Var_05    C11   C10  N4   C9    -43.82  30.0  2
 I19  Var_06    N5    C16  C13  C12    47.06  30.0  2
 I19  Var_07    C4    N1   C2   C1    -66.06  30.0  2
 I19  Var_08    H51C  C5   C4   N1    -69.51  30.0  2
 I19  Var_09    H11C  C1   C2   N1   -171.57  30.0  3
 I19  Var_10    H31C  C3   C2   N1     52.80  30.0  3
 I19  Var_11    H211  C21  N6   C19   175.76  30.0  3
 I19  Var_12    H221  C22  N6   C19    60.34  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
 I19  chir_01  C19  C18  C20  N6  negativ

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
 I19  plan-1  C2   0.020
 I19  plan-1  N1   0.020
 I19  plan-1  C4   0.020
 I19  plan-1  C5   0.020
 I19  plan-1  N2   0.020
 I19  plan-1  C6   0.020
 I19  plan-1  C7   0.020
 I19  plan-1  C8   0.020
 I19  plan-1  H6   0.020
 I19  plan-2  C7   0.020
 I19  plan-2  C8   0.020
 I19  plan-2  N3   0.020
 I19  plan-2  C9   0.020
 I19  plan-2  N4   0.020
 I19  plan-2  N7   0.020
 I19  plan-2  C23  0.020
 I19  plan-2  C24  0.020
 I19  plan-2  F1   0.020
 I19  plan-2  H23  0.020
 I19  plan-3  N4   0.020
 I19  plan-3  C10  0.020
 I19  plan-3  C11  0.020
 I19  plan-3  C12  0.020
 I19  plan-3  C13  0.020
 I19  plan-3  C14  0.020
 I19  plan-3  C15  0.020
 I19  plan-3  C16  0.020
 I19  plan-3  H11  0.020
 I19  plan-3  H15  0.020
 I19  plan-3  H12  0.020
 I19  plan-3  H14  0.020
 I19  plan-4  C13  0.020
 I19  plan-4  C16  0.020
 I19  plan-4  O1   0.020
 I19  plan-4  N5   0.020
 I19  plan-4  C17  0.020
 I19  plan-4  C20  0.020

