# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 18:10:12 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 5-[4-(dimethylamino)phenyl]-6-[(6-morpholin-4-ylpyridin-3-yl)ethynyl]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1ccc(cc1)c2c(N)ncnc2C#Cc3ccc(nc3)N4CCOCC4
#
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
 89I  89I  5-[4-(dimethylamino)phenyl]-6-[(6-morpholin-4-ylpyridin-3-yl)ethynyl]pyrimidin-4-amine  ligand  54  30  .  2021-08-06  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_89I
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
 89I  C1    C  CR16  0   0.040   7.5871  -2.4113   7.3602
 89I  N2    N  N     0  -0.454   6.5086  -2.4624   6.6076
 89I  C3    C  CR6   0   0.090   6.6086  -1.8540   5.4107
 89I  C4    C  CR6   0  -0.079   7.7599  -1.2129   4.9751
 89I  C5    C  CR6   0   0.465   8.8500  -1.2452   5.8808
 89I  N6    N  N     0  -0.454   8.7455  -1.8453   7.0697
 89I  C8    C  CR6   0  -0.029   7.8498  -0.5492   3.6626
 89I  C9    C  CR16  0  -0.283   8.0913   0.8206   3.5583
 89I  C10   C  CR16  0  -0.346   8.1422   1.4610   2.3340
 89I  C11   C  CR6   0   0.387   7.9539   0.7488   1.1329
 89I  C12   C  CR16  0  -0.344   7.7094  -0.6352   1.2413
 89I  C13   C  CR16  0  -0.263   7.6638  -1.2558   2.4750
 89I  C18   C  CR16  0  -0.082   2.1582  -2.4974   3.3296
 89I  N19   N  N     0  -0.469   1.1158  -2.5640   2.5270
 89I  C20   C  CR6   0   0.557   1.2020  -2.0827   1.2813
 89I  C21   C  CR16  0  -0.396   2.4127  -1.5212   0.8108
 89I  C22   C  CR16  0  -0.192   3.4892  -1.4581   1.6575
 89I  C23   C  CR6   0  -0.239   3.3886  -1.9524   2.9674
 89I  C27   C  CH2   0  -0.320   0.1023  -1.8706  -0.9067
 89I  C28   C  CH2   0  -0.184  -1.2606  -1.3924  -1.3763
 89I  O29   O  O2    0  -0.481  -2.2872  -2.2880  -1.0257
 89I  C30   C  CH2   0  -0.194  -2.3405  -2.4358   0.3746
 89I  C31   C  CH2   0  -0.315  -1.0414  -2.9799   0.9342
 89I  N32   N  NT    0  -0.508   0.0786  -2.1489   0.5180
 89I  C41   C  CSP   0   0.122   5.4518  -1.8879   4.5809
 89I  C42   C  CSP   0   0.101   4.4829  -1.9209   3.8603
 89I  N43   N  NT    0  -0.504   8.0080   1.3693  -0.0798
 89I  C44   C  CH3   0  -0.537   8.2376   2.7922  -0.1536
 89I  C48   C  CH3   0  -0.536   7.7302   0.6241  -1.2844
 89I  N52   N  NH2   0  -0.819  10.0246  -0.6656   5.5878
 89I  H1    H  HCR6  0   0.253   7.5218  -2.8932   8.3306
 89I  H9    H  HCR6  0   0.253   8.2239   1.4141   4.4556
 89I  H10   H  HCR6  0   0.267   8.3209   2.5268   2.3209
 89I  H12   H  HCR6  0   0.266   7.5607  -1.2409   0.3586
 89I  H13   H  HCR6  0   0.246   7.4798  -2.3227   2.5104
 89I  H21   H  HCR6  0   0.278   2.5167  -1.1473  -0.1961
 89I  H22   H  HCR6  0   0.263   4.4232  -1.0335   1.3108
 89I  H311  H  HCH2  0   0.272  -1.1024  -2.9969   2.0185
 89I  H312  H  HCH2  0   0.234  -0.8889  -4.0131   0.5966
 89I  H301  H  HCH2  0   0.245  -3.1514  -3.1277   0.6052
 89I  H302  H  HCH2  0   0.209  -2.5690  -1.4723   0.8516
 89I  H281  H  HCH2  0   0.210  -1.4586  -0.3980  -0.9525
 89I  H282  H  HCH2  0   0.247  -1.2535  -1.3003  -2.4630
 89I  H271  H  HCH2  0   0.241   0.4076  -2.7636  -1.4666
 89I  H272  H  HCH2  0   0.265   0.8142  -1.0809  -1.1356
 89I  H441  H  HCH3  0   0.257   8.2959   3.0933  -1.1957
 89I  H442  H  HCH3  0   0.236   9.1791   3.0771   0.3232
 89I  H443  H  HCH3  0   0.231   7.4365   3.3723   0.3161
 89I  H481  H  HCH3  0   0.234   8.4524  -0.1810  -1.4463
 89I  H482  H  HCH3  0   0.257   7.7849   1.2901  -2.1408
 89I  H483  H  HCH3  0   0.231   6.7309   0.1785  -1.2746
 89I  H521  H  HNH2  0   0.398  10.8126  -0.8526   6.1847
 89I  H522  H  HNH2  0   0.406  10.2249  -0.3651   4.6495
 89I  H18   H  HCR6  0   0.263   2.0234  -2.9040   4.3268

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
 89I  C1   N2    aromatic  1.316  0.020  1.316
 89I  C1   N6    aromatic  1.322  0.020  1.322
 89I  C1   H1    single    0.930  0.020  1.080
 89I  N2   C3    aromatic  1.346  0.020  1.346
 89I  C3   C41   single    1.424  0.020  1.424
 89I  C3   C4    aromatic  1.388  0.020  1.388
 89I  C4   C8    single    1.474  0.020  1.474
 89I  C4   C5    aromatic  1.418  0.020  1.418
 89I  C5   N52   single    1.342  0.020  1.342
 89I  C5   N6    aromatic  1.336  0.020  1.336
 89I  C8   C13   aromatic  1.394  0.020  1.394
 89I  C8   C9    aromatic  1.395  0.020  1.395
 89I  C9   C10   aromatic  1.383  0.020  1.383
 89I  C9   H9    single    0.930  0.020  1.080
 89I  C10  C11   aromatic  1.409  0.020  1.409
 89I  C10  H10   single    0.930  0.020  1.080
 89I  C11  N43   single    1.363  0.020  1.363
 89I  C11  C12   aromatic  1.410  0.020  1.410
 89I  C12  C13   aromatic  1.382  0.020  1.382
 89I  C12  H12   single    0.930  0.020  1.080
 89I  C13  H13   single    0.930  0.020  1.080
 89I  C18  N19   aromatic  1.317  0.020  1.317
 89I  C18  C23   aromatic  1.394  0.020  1.394
 89I  C18  H18   single    0.930  0.020  1.080
 89I  N19  C20   aromatic  1.338  0.020  1.338
 89I  C20  N32   single    1.360  0.020  1.360
 89I  C20  C21   aromatic  1.415  0.020  1.415
 89I  C21  C22   aromatic  1.371  0.020  1.371
 89I  C21  H21   single    0.930  0.020  1.080
 89I  C22  C23   aromatic  1.404  0.020  1.404
 89I  C22  H22   single    0.930  0.020  1.080
 89I  C23  C42   single    1.413  0.020  1.413
 89I  C27  C28   single    1.519  0.020  1.519
 89I  C27  N32   single    1.452  0.020  1.452
 89I  C27  H271  single    0.970  0.020  1.090
 89I  C27  H272  single    0.970  0.020  1.090
 89I  C28  O29   single    1.407  0.020  1.407
 89I  C28  H281  single    0.970  0.020  1.090
 89I  C28  H282  single    0.970  0.020  1.090
 89I  O29  C30   single    1.409  0.020  1.409
 89I  C30  C31   single    1.516  0.020  1.516
 89I  C30  H301  single    0.970  0.020  1.090
 89I  C30  H302  single    0.970  0.020  1.090
 89I  C31  N32   single    1.455  0.020  1.455
 89I  C31  H311  single    0.970  0.020  1.090
 89I  C31  H312  single    0.970  0.020  1.090
 89I  C41  C42   triple    1.208  0.020  1.208
 89I  N43  C44   single    1.443  0.020  1.443
 89I  N43  C48   single    1.443  0.020  1.443
 89I  C44  H441  single    0.970  0.020  1.090
 89I  C44  H442  single    0.970  0.020  1.090
 89I  C44  H443  single    0.970  0.020  1.090
 89I  C48  H481  single    0.970  0.020  1.090
 89I  C48  H482  single    0.970  0.020  1.090
 89I  C48  H483  single    0.970  0.020  1.090
 89I  N52  H521  single    0.890  0.020  1.040
 89I  N52  H522  single    0.890  0.020  1.040

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
 89I  H1    C1   N6    116.07  3.000
 89I  H1    C1   N2    116.40  3.000
 89I  N6    C1   N2    127.53  3.000
 89I  C3    N2   C1    115.47  3.000
 89I  C41   C3   C4    120.13  3.000
 89I  C4    C3   N2    123.32  3.000
 89I  C41   C3   N2    116.55  3.000
 89I  C8    C4   C5    122.18  3.000
 89I  C5    C4   C3    115.27  3.000
 89I  C8    C4   C3    122.56  3.000
 89I  N52   C5   N6    117.17  3.000
 89I  N6    C5   C4    121.25  3.000
 89I  N52   C5   C4    121.57  3.000
 89I  C5    N6   C1    117.16  3.000
 89I  C13   C8   C9    117.20  3.000
 89I  C9    C8   C4    121.29  3.000
 89I  C13   C8   C4    121.48  3.000
 89I  H9    C9   C10   118.36  3.000
 89I  H9    C9   C8    119.80  3.000
 89I  C10   C9   C8    121.83  3.000
 89I  H10   C10  C11   120.68  3.000
 89I  H10   C10  C9    118.26  3.000
 89I  C11   C10  C9    121.05  3.000
 89I  N43   C11  C12   121.48  3.000
 89I  C12   C11  C10   116.99  3.000
 89I  N43   C11  C10   121.52  3.000
 89I  H12   C12  C13   118.23  3.000
 89I  H12   C12  C11   120.75  3.000
 89I  C13   C12  C11   121.03  3.000
 89I  H13   C13  C12   118.50  3.000
 89I  H13   C13  C8    119.61  3.000
 89I  C12   C13  C8    121.90  3.000
 89I  H18   C18  C23   119.67  3.000
 89I  H18   C18  N19   116.27  3.000
 89I  C23   C18  N19   124.07  3.000
 89I  C20   N19  C18   119.86  3.000
 89I  N32   C20  C21   122.65  3.000
 89I  C21   C20  N19   120.49  3.000
 89I  N32   C20  N19   116.85  3.000
 89I  H21   C21  C22   118.99  3.000
 89I  H21   C21  C20   122.02  3.000
 89I  C22   C21  C20   118.99  3.000
 89I  H22   C22  C23   119.91  3.000
 89I  H22   C22  C21   119.84  3.000
 89I  C23   C22  C21   120.25  3.000
 89I  C42   C23  C22   121.77  3.000
 89I  C42   C23  C18   121.89  3.000
 89I  C22   C23  C18   116.33  3.000
 89I  H272  C27  H271  107.54  3.000
 89I  H272  C27  N32   110.88  3.000
 89I  H271  C27  N32   110.44  3.000
 89I  H272  C27  C28   107.08  3.000
 89I  H271  C27  C28   110.37  3.000
 89I  N32   C27  C28   110.43  3.000
 89I  H282  C28  H281  108.00  3.000
 89I  H282  C28  O29   107.87  3.000
 89I  H281  C28  O29   110.39  3.000
 89I  H282  C28  C27   109.20  3.000
 89I  H281  C28  C27   109.11  3.000
 89I  O29   C28  C27   112.17  3.000
 89I  C30   O29  C28   110.00  3.000
 89I  H302  C30  H301  108.04  3.000
 89I  H302  C30  C31   109.44  3.000
 89I  H301  C30  C31   109.36  3.000
 89I  H302  C30  O29   110.32  3.000
 89I  H301  C30  O29   107.74  3.000
 89I  C31   C30  O29   111.85  3.000
 89I  H312  C31  H311  107.47  3.000
 89I  H312  C31  N32   110.04  3.000
 89I  H311  C31  N32   109.73  3.000
 89I  H312  C31  C30   110.09  3.000
 89I  H311  C31  C30   109.03  3.000
 89I  N32   C31  C30   110.43  3.000
 89I  C31   N32  C27   113.74  3.000
 89I  C31   N32  C20   120.20  3.000
 89I  C27   N32  C20   121.87  3.000
 89I  C42   C41  C3    180.00  3.000
 89I  C41   C42  C23   180.00  3.000
 89I  C48   N43  C44   119.80  3.000
 89I  C48   N43  C11   119.97  3.000
 89I  C44   N43  C11   120.04  3.000
 89I  H443  C44  H442  107.76  3.000
 89I  H443  C44  H441  107.69  3.000
 89I  H442  C44  H441  107.46  3.000
 89I  H443  C44  N43   112.58  3.000
 89I  H442  C44  N43   111.82  3.000
 89I  H441  C44  N43   109.32  3.000
 89I  H483  C48  H482  107.62  3.000
 89I  H483  C48  H481  107.74  3.000
 89I  H482  C48  H481  107.54  3.000
 89I  H483  C48  N43   112.25  3.000
 89I  H482  C48  N43   109.37  3.000
 89I  H481  C48  N43   112.12  3.000
 89I  H522  N52  H521  116.95  3.000
 89I  H522  N52  C5    120.47  3.000
 89I  H521  N52  C5    118.40  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
 89I  CONST_01  C4    C3   N2   C1      0.00   0.0  0
 89I  CONST_02  C4    C5   N6   C1      0.00   0.0  0
 89I  CONST_03  C5    N6   C1   N2      0.00   0.0  0
 89I  CONST_04  C8    C4   C3   N2    180.00   0.0  0
 89I  CONST_05  C5    C4   C3   N2      0.00   0.0  0
 89I  CONST_06  N6    C1   N2   C3      0.00   0.0  0
 89I  CONST_09  N6    C5   C4   C3      0.00   0.0  0
 89I  CONST_10  C12   C13  C8   C4    180.00   0.0  0
 89I  CONST_11  C10   C9   C8   C4    180.00   0.0  0
 89I  CONST_14  C8    C4   C5   N6    180.00   0.0  0
 89I  CONST_15  C11   C12  C13  C8      0.00   0.0  0
 89I  CONST_16  C11   C10  C9   C8      0.00   0.0  0
 89I  CONST_17  C12   C13  C8   C9      0.00   0.0  0
 89I  CONST_18  C12   C11  C10  C9      0.00   0.0  0
 89I  CONST_19  C13   C8   C9   C10     0.00   0.0  0
 89I  CONST_20  C13   C12  C11  C10     0.00   0.0  0
 89I  CONST_21  C21   C20  N19  C18     0.00   0.0  0
 89I  CONST_22  C21   C22  C23  C18     0.00   0.0  0
 89I  CONST_23  C22   C23  C18  N19     0.00   0.0  0
 89I  CONST_24  C22   C21  C20  N19     0.00   0.0  0
 89I  CONST_25  C23   C18  N19  C20     0.00   0.0  0
 89I  CONST_26  C23   C22  C21  C20     0.00   0.0  0
 89I  CONST_27  N32   C20  N19  C18   180.00   0.0  0
 89I  CONST_28  N32   C20  C21  C22   180.00   0.0  0
 89I  CONST_29  C41   C3   N2   C1    180.00   0.0  0
 89I  CONST_30  N52   C5   N6   C1    180.00   0.0  0
 89I  CONST_31  N52   C5   C4   C3    180.00   0.0  0
 89I  CONST_32  C41   C3   C4   C5    180.00   0.0  0
 89I  CONST_33  C41   C3   C4   C8      0.00   0.0  0
 89I  CONST_34  N52   C5   C4   C8      0.00   0.0  0
 89I  CONST_35  N43   C11  C10  C9    180.00   0.0  0
 89I  CONST_36  N43   C11  C12  C13   180.00   0.0  0
 89I  CONST_37  C42   C23  C18  N19   180.00   0.0  0
 89I  CONST_38  C42   C23  C22  C21   180.00   0.0  0
 89I  CONST_39  H1    C1   N2   C3    180.00   0.0  0
 89I  CONST_40  H13   C13  C8   C4      0.00   0.0  0
 89I  CONST_41  H9    C9   C8   C4      0.00   0.0  0
 89I  CONST_42  H12   C12  C13  C8    180.00   0.0  0
 89I  CONST_43  H10   C10  C9   C8    180.00   0.0  0
 89I  CONST_44  H22   C22  C23  C18   180.00   0.0  0
 89I  CONST_45  H21   C21  C20  N19   180.00   0.0  0
 89I  CONST_46  H18   C18  N19  C20   180.00   0.0  0
 89I  CONST_47  C44   N43  C11  C10     0.00   0.0  0
 89I  CONST_48  C48   N43  C11  C10   180.00   0.0  0
 89I  CONST_49  C44   N43  C11  C12   180.00   0.0  0
 89I  CONST_50  C48   N43  C11  C12     0.00   0.0  0
 89I  CONST_51  H521  N52  C5   C4    180.00   0.0  0
 89I  CONST_52  H522  N52  C5   C4      0.00   0.0  0
 89I  Var_01    C27   N32  C20  N19  -169.49  30.0  2
 89I  Var_02    C28   C27  N32  C20  -154.00  30.0  1
 89I  Var_03    C30   C31  N32  C20   153.11  30.0  1
 89I  Var_04    C31   C30  O29  C28   -60.29  30.0  1
 89I  Var_05    N32   C27  C28  O29   -53.98  30.0  1
 89I  Var_06    N32   C31  C30  O29    54.67  30.0  1
 89I  Var_07    H281  C28  O29  C30   -61.93  30.0  1
 89I  Var_08    H441  C44  N43  C11   177.26  30.0  3
 89I  Var_09    H481  C48  N43  C11   -62.92  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
 89I  plan-1  C1    0.020
 89I  plan-1  N2    0.020
 89I  plan-1  C3    0.020
 89I  plan-1  C4    0.020
 89I  plan-1  C5    0.020
 89I  plan-1  N6    0.020
 89I  plan-1  C8    0.020
 89I  plan-1  C41   0.020
 89I  plan-1  C42   0.020
 89I  plan-1  N52   0.020
 89I  plan-1  H1    0.020
 89I  plan-2  C4    0.020
 89I  plan-2  C8    0.020
 89I  plan-2  C9    0.020
 89I  plan-2  C10   0.020
 89I  plan-2  C11   0.020
 89I  plan-2  C12   0.020
 89I  plan-2  C13   0.020
 89I  plan-2  N43   0.020
 89I  plan-2  H9    0.020
 89I  plan-2  H10   0.020
 89I  plan-2  H12   0.020
 89I  plan-2  H13   0.020
 89I  plan-3  C18   0.020
 89I  plan-3  N19   0.020
 89I  plan-3  C20   0.020
 89I  plan-3  C21   0.020
 89I  plan-3  C22   0.020
 89I  plan-3  C23   0.020
 89I  plan-3  N32   0.020
 89I  plan-3  C41   0.020
 89I  plan-3  C42   0.020
 89I  plan-3  H21   0.020
 89I  plan-3  H22   0.020
 89I  plan-3  H18   0.020
 89I  plan-4  C11   0.020
 89I  plan-4  N43   0.020
 89I  plan-4  C44   0.020
 89I  plan-4  C48   0.020
 89I  plan-5  C5    0.020
 89I  plan-5  N52   0.020
 89I  plan-5  H521  0.020
 89I  plan-5  H522  0.020

