# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 15:43:18 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: ~{N}-[2-[2-azanylethyl(methyl)amino]-5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]phenyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCN)c1ccc(Nc2cc(NC3CC3)n4ncc(C#N)c4n2)cc1NC(C)=O
#
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
 5Y3  5Y3  ~{N}-[2-[2-azanylethyl(methyl)amino]-5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]phenyl]ethanamide  ligand  56  31  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5Y3
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
 5Y3  C1   C  C     0   0.511   3.6781  -3.3358   0.3957
 5Y3  C2   C  CR6   0   0.347   2.7508  -1.1207  -0.2574
 5Y3  C3   C  CR16  0  -0.472   1.3910  -1.3894  -0.1763
 5Y3  N6   N  N     0  -0.304  -5.4365   2.0369  -0.4927
 5Y3  C7   C  CR6   0   0.186   3.1886   0.1688  -0.6114
 5Y3  C8   C  CH3   0  -0.532   5.0274   0.8530  -1.9975
 5Y3  C9   C  CH2   0  -0.281   5.0948   1.2114   0.4177
 5Y3  C10  C  CH2   0  -0.296   6.5800   0.9996   0.6761
 5Y3  C11  C  CR6   0   0.579  -2.0398  -0.0829  -0.3956
 5Y3  C12  C  CR16  0  -0.566  -3.2457  -0.8192  -0.3047
 5Y3  C13  C  CR6   0   0.719  -4.4480  -0.1479  -0.3215
 5Y3  C14  C  CR56  0   0.686  -3.1673   1.8559  -0.5398
 5Y3  C15  C  CR5   0  -0.338  -3.5110   3.2084  -0.6624
 5Y3  C16  C  CR15  0   0.032  -4.9213   3.2330  -0.6248
 5Y3  C19  C  CH2   0  -0.507  -6.9679  -2.6191   0.6537
 5Y3  C20  C  CH2   0  -0.486  -5.5395  -2.8631   1.0243
 5Y3  N7   N  NS    0  -0.270  -1.8810   5.1630  -0.9120
 5Y3  C17  C  CSP   0  -0.007  -2.6176   4.2803  -0.7981
 5Y3  N4   N  N     0  -0.468  -4.3689   1.2119  -0.4414
 5Y3  N8   N  NH1   0  -0.673  -5.6664  -0.6829  -0.2293
 5Y3  C18  C  CH1   0  -0.108  -5.8772  -2.0924  -0.2168
 5Y3  N5   N  N     0  -0.526  -1.9983   1.2366  -0.5143
 5Y3  C4   C  CR6   0   0.397   0.4485  -0.3901  -0.4426
 5Y3  C5   C  CR16  0  -0.333   0.8769   0.8906  -0.7883
 5Y3  C6   C  CR16  0  -0.257   2.2398   1.1432  -0.8650
 5Y3  N1   N  NT    0  -0.513   4.5911   0.3997  -0.6859
 5Y3  N2   N  NH2   0  -0.801   6.9949   1.8193   1.8056
 5Y3  N    N  NH1   0  -0.729   3.7591  -2.0466  -0.0111
 5Y3  O    O  O     0  -0.477   2.6277  -3.9169   0.6149
 5Y3  C    C  CH3   0  -0.780   5.0114  -4.0231   0.5482
 5Y3  H1   H  HCR6  0   0.290   1.0522  -2.3773   0.0963
 5Y3  H2   H  HCH3  0   0.208   4.7317   1.8868  -2.2178
 5Y3  H3   H  HCH3  0   0.242   6.1124   0.7947  -2.0767
 5Y3  H4   H  HCH3  0   0.245   4.6068   0.2074  -2.7673
 5Y3  H5   H  HCH2  0   0.243   4.5532   0.9331   1.3237
 5Y3  H6   H  HCH2  0   0.206   4.8965   2.2821   0.2458
 5Y3  H7   H  HCH2  0   0.218   6.7401  -0.0514   0.9299
 5Y3  H8   H  HCH2  0   0.203   7.1605   1.1927  -0.2351
 5Y3  H9   H  HCR6  0   0.306  -3.2320  -1.8958  -0.2243
 5Y3  H10  H  HCR5  0   0.295  -5.5602   4.1000  -0.6926
 5Y3  H11  H  HCH2  0   0.266  -7.5543  -3.4434   0.2708
 5Y3  H12  H  HCH2  0   0.265  -7.5263  -1.9048   1.2450
 5Y3  H13  H  HCH2  0   0.266  -5.1329  -2.3097   1.8607
 5Y3  H14  H  HCH2  0   0.264  -5.1319  -3.8570   0.8949
 5Y3  H15  H  HNH1  0   0.418  -6.4578  -0.0731  -0.3743
 5Y3  H16  H  HCH1  0   0.282  -5.7118  -2.5891  -1.1686
 5Y3  H17  H  HNH1  0   0.422  -1.0074  -1.7826  -0.2158
 5Y3  H18  H  HCR6  0   0.286   0.1708   1.6779  -0.9896
 5Y3  H19  H  HCR6  0   0.257   2.5652   2.1403  -1.1365
 5Y3  H20  H  HNH2  0   0.351   7.9478   1.5893   2.0552
 5Y3  H21  H  HNH2  0   0.341   7.0173   2.7916   1.5229
 5Y3  H23  H  HNH1  0   0.404   4.6756  -1.6436  -0.1744
 5Y3  H24  H  HCH3  0   0.274   5.1223  -4.7703  -0.2386
 5Y3  H25  H  HCH3  0   0.250   5.8629  -3.3473   0.4969
 5Y3  H26  H  HCH3  0   0.269   5.0400  -4.5482   1.5020
 5Y3  N3   N  NH1   0  -0.801  -0.8842  -0.7917  -0.3561

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
 5Y3  C19  C20  single    1.496  0.020  1.496
 5Y3  C19  C18  single    1.492  0.020  1.492
 5Y3  C20  C18  single    1.499  0.020  1.499
 5Y3  C18  N8   single    1.425  0.020  1.425
 5Y3  N8   C13  single    1.334  0.020  1.334
 5Y3  C5   C6   aromatic  1.388  0.020  1.388
 5Y3  C5   C4   aromatic  1.394  0.020  1.394
 5Y3  C12  C13  aromatic  1.377  0.020  1.377
 5Y3  C12  C11  aromatic  1.416  0.020  1.416
 5Y3  N3   C4   single    1.394  0.020  1.394
 5Y3  N3   C11  single    1.356  0.020  1.356
 5Y3  C6   C7   aromatic  1.383  0.020  1.383
 5Y3  C13  N4   aromatic  1.367  0.020  1.367
 5Y3  C4   C3   aromatic  1.399  0.020  1.399
 5Y3  C11  N5   aromatic  1.326  0.020  1.326
 5Y3  C9   C10  single    1.522  0.020  1.522
 5Y3  C9   N1   single    1.460  0.020  1.460
 5Y3  C10  N2   single    1.456  0.020  1.456
 5Y3  C7   N1   single    1.423  0.020  1.423
 5Y3  C7   C2   aromatic  1.407  0.020  1.407
 5Y3  N4   C14  aromatic  1.367  0.020  1.367
 5Y3  N4   N6   aromatic  1.350  0.020  1.350
 5Y3  N1   C8   single    1.455  0.020  1.455
 5Y3  C3   C2   aromatic  1.388  0.020  1.388
 5Y3  N5   C14  aromatic  1.323  0.020  1.323
 5Y3  C2   N    single    1.391  0.020  1.391
 5Y3  C14  C15  aromatic  1.401  0.020  1.401
 5Y3  N6   C16  aromatic  1.309  0.020  1.309
 5Y3  N    C1   single    1.354  0.020  1.354
 5Y3  C16  C15  aromatic  1.411  0.020  1.411
 5Y3  C15  C17  single    1.402  0.020  1.402
 5Y3  C    C1   single    1.508  0.020  1.508
 5Y3  C1   O    double    1.220  0.020  1.220
 5Y3  C17  N7   triple    1.155  0.020  1.155
 5Y3  C3   H1   single    0.930  0.020  1.080
 5Y3  C8   H2   single    0.970  0.020  1.090
 5Y3  C8   H3   single    0.970  0.020  1.090
 5Y3  C8   H4   single    0.970  0.020  1.090
 5Y3  C9   H5   single    0.970  0.020  1.090
 5Y3  C9   H6   single    0.970  0.020  1.090
 5Y3  C10  H7   single    0.970  0.020  1.090
 5Y3  C10  H8   single    0.970  0.020  1.090
 5Y3  C12  H9   single    0.930  0.020  1.080
 5Y3  C16  H10  single    0.930  0.020  1.080
 5Y3  C19  H11  single    0.970  0.020  1.090
 5Y3  C19  H12  single    0.970  0.020  1.090
 5Y3  C20  H13  single    0.970  0.020  1.090
 5Y3  C20  H14  single    0.970  0.020  1.090
 5Y3  N8   H15  single    0.860  0.020  1.020
 5Y3  C18  H16  single    0.970  0.020  1.090
 5Y3  N3   H17  single    0.860  0.020  1.020
 5Y3  C5   H18  single    0.930  0.020  1.080
 5Y3  C6   H19  single    0.930  0.020  1.080
 5Y3  N2   H20  single    0.890  0.020  1.040
 5Y3  N2   H21  single    0.890  0.020  1.040
 5Y3  N    H23  single    0.860  0.020  1.020
 5Y3  C    H24  single    0.970  0.020  1.090
 5Y3  C    H25  single    0.970  0.020  1.090
 5Y3  C    H26  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
 5Y3  C    C1   O    121.74  3.000
 5Y3  O    C1   N    123.96  3.000
 5Y3  C    C1   N    114.29  3.000
 5Y3  N    C2   C7   115.41  3.000
 5Y3  N    C2   C3   124.81  3.000
 5Y3  C7   C2   C3   119.79  3.000
 5Y3  H1   C3   C4   119.36  3.000
 5Y3  H1   C3   C2   119.95  3.000
 5Y3  C4   C3   C2   120.69  3.000
 5Y3  N4   N6   C16  104.53  3.000
 5Y3  N1   C7   C6   123.50  3.000
 5Y3  N1   C7   C2   117.93  3.000
 5Y3  C6   C7   C2   118.57  3.000
 5Y3  H4   C8   H3   107.55  3.000
 5Y3  H4   C8   H2   108.20  3.000
 5Y3  H3   C8   H2   107.70  3.000
 5Y3  H4   C8   N1   109.68  3.000
 5Y3  H3   C8   N1   110.34  3.000
 5Y3  H2   C8   N1   113.18  3.000
 5Y3  H6   C9   H5   106.73  3.000
 5Y3  H6   C9   N1   111.11  3.000
 5Y3  H5   C9   N1   108.33  3.000
 5Y3  H6   C9   C10  109.70  3.000
 5Y3  H5   C9   C10  107.92  3.000
 5Y3  N1   C9   C10  112.81  3.000
 5Y3  H8   C10  H7   106.53  3.000
 5Y3  H8   C10  N2   113.22  3.000
 5Y3  H7   C10  N2   108.64  3.000
 5Y3  H8   C10  C9   110.52  3.000
 5Y3  H7   C10  C9   108.43  3.000
 5Y3  N2   C10  C9   109.35  3.000
 5Y3  N3   C11  N5   119.75  3.000
 5Y3  N5   C11  C12  123.37  3.000
 5Y3  N3   C11  C12  116.88  3.000
 5Y3  H9   C12  C13  119.87  3.000
 5Y3  H9   C12  C11  120.83  3.000
 5Y3  C13  C12  C11  119.30  3.000
 5Y3  N8   C13  N4   117.25  3.000
 5Y3  N4   C13  C12  115.80  3.000
 5Y3  N8   C13  C12  126.95  3.000
 5Y3  N5   C14  N4   123.70  3.000
 5Y3  N5   C14  C15  132.09  3.000
 5Y3  N4   C14  C15  104.21  3.000
 5Y3  C17  C15  C16  128.77  3.000
 5Y3  C17  C15  C14  126.18  3.000
 5Y3  C16  C15  C14  105.05  3.000
 5Y3  H10  C16  C15  127.16  3.000
 5Y3  H10  C16  N6   120.50  3.000
 5Y3  C15  C16  N6   112.34  3.000
 5Y3  H12  C19  H11  114.62  3.000
 5Y3  H12  C19  C18  117.58  3.000
 5Y3  H11  C19  C18  117.32  3.000
 5Y3  H12  C19  C20  117.70  3.000
 5Y3  H11  C19  C20  118.76  3.000
 5Y3  C18  C19  C20   60.25  3.000
 5Y3  H14  C20  H13  114.87  3.000
 5Y3  H14  C20  C18  117.26  3.000
 5Y3  H13  C20  C18  117.49  3.000
 5Y3  H14  C20  C19  118.68  3.000
 5Y3  H13  C20  C19  117.84  3.000
 5Y3  C18  C20  C19   59.74  3.000
 5Y3  N7   C17  C15  180.00  3.000
 5Y3  C14  N4   C13  121.72  3.000
 5Y3  C14  N4   N6   113.86  3.000
 5Y3  C13  N4   N6   124.42  3.000
 5Y3  H15  N8   C18  118.86  3.000
 5Y3  H15  N8   C13  117.63  3.000
 5Y3  C18  N8   C13  122.17  3.000
 5Y3  H16  C18  N8   114.96  3.000
 5Y3  H16  C18  C20  117.13  3.000
 5Y3  N8   C18  C20  118.83  3.000
 5Y3  H16  C18  C19  117.47  3.000
 5Y3  N8   C18  C19  117.55  3.000
 5Y3  C20  C18  C19   60.01  3.000
 5Y3  C14  N5   C11  116.10  3.000
 5Y3  C5   C4   N3   125.01  3.000
 5Y3  N3   C4   C3   115.23  3.000
 5Y3  C5   C4   C3   119.75  3.000
 5Y3  H18  C5   C6   120.04  3.000
 5Y3  H18  C5   C4   121.11  3.000
 5Y3  C6   C5   C4   118.85  3.000
 5Y3  H19  C6   C5   118.43  3.000
 5Y3  H19  C6   C7   119.22  3.000
 5Y3  C5   C6   C7   122.35  3.000
 5Y3  C9   N1   C8   113.88  3.000
 5Y3  C8   N1   C7   113.16  3.000
 5Y3  C9   N1   C7   113.00  3.000
 5Y3  H21  N2   H20  105.44  3.000
 5Y3  H21  N2   C10  109.29  3.000
 5Y3  H20  N2   C10  109.38  3.000
 5Y3  H23  N    C2   111.22  3.000
 5Y3  H23  N    C1   118.72  3.000
 5Y3  C2   N    C1   130.06  3.000
 5Y3  H26  C    H25  108.67  3.000
 5Y3  H26  C    H24  107.38  3.000
 5Y3  H25  C    H24  108.18  3.000
 5Y3  H26  C    C1   109.36  3.000
 5Y3  H25  C    C1   113.83  3.000
 5Y3  H24  C    C1   109.22  3.000
 5Y3  H17  N3   C4   114.11  3.000
 5Y3  H17  N3   C11  114.42  3.000
 5Y3  C4   N3   C11  131.45  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
 5Y3  CONST_01  C5   C6   C7   C2      0.00   0.0  0
 5Y3  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 5Y3  CONST_03  C6   C5   C4   C3      0.00   0.0  0
 5Y3  CONST_04  C6   C7   C2   C3      0.00   0.0  0
 5Y3  CONST_05  C12  C13  N4   N6    180.00   0.0  0
 5Y3  CONST_06  N5   C14  N4   N6    180.00   0.0  0
 5Y3  CONST_07  C15  C14  N4   N6      0.00   0.0  0
 5Y3  CONST_08  C14  C15  C16  N6      0.00   0.0  0
 5Y3  CONST_09  C4   C5   C6   C7      0.00   0.0  0
 5Y3  CONST_10  C4   C3   C2   C7      0.00   0.0  0
 5Y3  CONST_11  N4   C13  C12  C11     0.00   0.0  0
 5Y3  CONST_12  N4   C14  N5   C11     0.00   0.0  0
 5Y3  CONST_13  C15  C14  N5   C11   180.00   0.0  0
 5Y3  CONST_14  C14  N4   C13  C12     0.00   0.0  0
 5Y3  CONST_15  C14  N5   C11  C12     0.00   0.0  0
 5Y3  CONST_16  N5   C11  C12  C13     0.00   0.0  0
 5Y3  CONST_17  N5   C14  N4   C13     0.00   0.0  0
 5Y3  CONST_18  C15  C14  N4   C13   180.00   0.0  0
 5Y3  CONST_19  C16  N6   N4   C13   180.00   0.0  0
 5Y3  CONST_20  C16  N6   N4   C14     0.00   0.0  0
 5Y3  CONST_21  N4   N6   C16  C15     0.00   0.0  0
 5Y3  CONST_22  N4   C14  C15  C16     0.00   0.0  0
 5Y3  CONST_23  N5   C14  C15  C16   180.00   0.0  0
 5Y3  CONST_24  N3   C4   C3   C2    180.00   0.0  0
 5Y3  CONST_25  N1   C7   C2   C3    180.00   0.0  0
 5Y3  CONST_26  N8   C13  N4   N6      0.00   0.0  0
 5Y3  CONST_27  C17  C15  C16  N6    180.00   0.0  0
 5Y3  CONST_28  N8   C13  C12  C11   180.00   0.0  0
 5Y3  CONST_29  N3   C11  C12  C13   180.00   0.0  0
 5Y3  CONST_30  N8   C13  N4   C14   180.00   0.0  0
 5Y3  CONST_31  N3   C11  N5   C14   180.00   0.0  0
 5Y3  CONST_32  N4   C14  C15  C17   180.00   0.0  0
 5Y3  CONST_33  N5   C14  C15  C17     0.00   0.0  0
 5Y3  CONST_34  C6   C5   C4   N3    180.00   0.0  0
 5Y3  CONST_35  N    C2   C3   C4    180.00   0.0  0
 5Y3  CONST_36  N1   C7   C6   C5    180.00   0.0  0
 5Y3  CONST_37  N    C2   C7   C6    180.00   0.0  0
 5Y3  CONST_38  C18  N8   C13  C12     0.00   0.0  0
 5Y3  CONST_39  C18  N8   C13  N4    180.00   0.0  0
 5Y3  CONST_40  H19  C6   C7   C2    180.00   0.0  0
 5Y3  CONST_41  H18  C5   C4   C3    180.00   0.0  0
 5Y3  CONST_42  H1   C3   C2   C7    180.00   0.0  0
 5Y3  CONST_43  H10  C16  C15  C14   180.00   0.0  0
 5Y3  CONST_44  H9   C12  C13  N4    180.00   0.0  0
 5Y3  CONST_45  C7   C2   N    C1    180.00   0.0  0
 5Y3  CONST_46  C3   C2   N    C1      0.00   0.0  0
 5Y3  CONST_51  H23  N    C2   C3    180.00   0.0  0
 5Y3  CONST_52  H15  N8   C13  C12   180.00   0.0  0
 5Y3  CONST_53  C    C1   N    C2    180.00   0.0  0
 5Y3  CONST_54  O    C1   N    C2      0.00   0.0  0
 5Y3  Var_01    C11  N3   C4   C3    171.50  30.0  2
 5Y3  Var_02    C4   N3   C11  C12   178.75  30.0  2
 5Y3  Var_03    C19  C18  N8   C13   143.55  30.0  3
 5Y3  Var_04    N8   C18  C20  C19   106.97  30.0  1
 5Y3  Var_05    C10  C9   N1   C7    156.55  30.0  1
 5Y3  Var_06    H2   C8   N1   C7     72.30  30.0  3
 5Y3  Var_07    N2   C10  C9   N1   -178.75  30.0  3
 5Y3  Var_08    H20  N2   C10  C9    172.59  30.0  3
 5Y3  Var_09    H24  C    C1   N    -109.97  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
 5Y3  chir_01  C18  C19  C20  N8  both

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
 5Y3  plan-1  C2   0.020
 5Y3  plan-1  C3   0.020
 5Y3  plan-1  C7   0.020
 5Y3  plan-1  C4   0.020
 5Y3  plan-1  C5   0.020
 5Y3  plan-1  C6   0.020
 5Y3  plan-1  N1   0.020
 5Y3  plan-1  N    0.020
 5Y3  plan-1  H1   0.020
 5Y3  plan-1  H18  0.020
 5Y3  plan-1  H19  0.020
 5Y3  plan-1  N3   0.020
 5Y3  plan-2  N6   0.020
 5Y3  plan-2  C11  0.020
 5Y3  plan-2  C12  0.020
 5Y3  plan-2  C13  0.020
 5Y3  plan-2  C14  0.020
 5Y3  plan-2  C15  0.020
 5Y3  plan-2  C16  0.020
 5Y3  plan-2  N7   0.020
 5Y3  plan-2  C17  0.020
 5Y3  plan-2  N4   0.020
 5Y3  plan-2  N8   0.020
 5Y3  plan-2  N5   0.020
 5Y3  plan-2  H9   0.020
 5Y3  plan-2  H10  0.020
 5Y3  plan-2  N3   0.020
 5Y3  plan-3  C13  0.020
 5Y3  plan-3  N8   0.020
 5Y3  plan-3  C18  0.020
 5Y3  plan-3  H15  0.020
 5Y3  plan-4  C7   0.020
 5Y3  plan-4  C8   0.020
 5Y3  plan-4  C9   0.020
 5Y3  plan-4  N1   0.020
 5Y3  plan-5  C1   0.020
 5Y3  plan-5  C2   0.020
 5Y3  plan-5  N    0.020
 5Y3  plan-5  O    0.020
 5Y3  plan-5  C    0.020
 5Y3  plan-5  H23  0.020

