# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 12:17:11 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: ~{N}-[5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]-2-methyl-phenyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1cc(Nc2cc(NC3CC3)n4ncc(C#N)c4n2)ccc1C
#
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
 5Y2  5Y2  ~{N}-[5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]-2-methyl-phenyl]ethanamide  ligand  46  27  .  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_5Y2
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
 5Y2  C1   C  CR6   0   0.043   4.0435  -1.1269   0.5988
 5Y2  C2   C  CR16  0  -0.298   2.9013  -1.8072   0.9982
 5Y2  C3   C  CR16  0  -0.298   1.6278  -1.2678   0.8937
 5Y2  N6   N  NH1   0  -0.673  -4.4387   1.3482  -0.4627
 5Y2  C7   C  C     0   0.511   5.2528   2.1778  -0.3541
 5Y2  C8   C  CH3   0  -0.786   6.6193   2.5834  -0.8441
 5Y2  C9   C  CR6   0   0.561  -0.9946   0.1626   0.0531
 5Y2  C10  C  CR16  0  -0.556  -2.0512   1.0881  -0.1209
 5Y2  C11  C  CR6   0   0.718  -3.3342   0.6187  -0.2989
 5Y2  C12  C  CR56  0   0.677  -2.4075  -1.5758  -0.1257
 5Y2  C13  C  CR5   0  -0.338  -2.9615  -2.8615  -0.1919
 5Y2  C14  C  CR15  0   0.031  -4.3411  -2.6555  -0.4056
 5Y2  C15  C  CSP   0  -0.008  -2.2635  -4.0711  -0.0696
 5Y2  C16  C  CH1   0  -0.109  -4.4023   2.7695  -0.5610
 5Y2  N5   N  NS    0  -0.271  -1.6885  -5.0682   0.0302
 5Y2  N4   N  N     0  -0.304  -4.6513  -1.3857  -0.4689
 5Y2  N2   N  N     0  -0.467  -3.4766  -0.7412  -0.2989
 5Y2  C18  C  CH2   0  -0.507  -5.5117   3.5333   0.0804
 5Y2  C17  C  CH2   0  -0.484  -4.1425   3.5676   0.6817
 5Y2  N3   N  N     0  -0.516  -1.1675  -1.1522   0.0530
 5Y2  C4   C  CR6   0   0.361   1.4774   0.0038   0.3476
 5Y2  C5   C  CR16  0  -0.402   2.6080   0.7067  -0.0701
 5Y2  C6   C  CR6   0   0.326   3.8772   0.1575   0.0598
 5Y2  C    C  CH3   0  -0.754   5.4025  -1.7463   0.7473
 5Y2  N    N  NH1   0  -0.741   5.0222   0.8387  -0.3802
 5Y2  O    O  O     0  -0.475   4.4401   2.9946   0.0413
 5Y2  H1   H  HCR6  0   0.252   3.0089  -2.7966   1.4265
 5Y2  H2   H  HCR6  0   0.273   0.7757  -1.8339   1.2321
 5Y2  H3   H  HNH1  0   0.418  -5.2906   0.8614  -0.7000
 5Y2  H4   H  HCH3  0   0.254   7.1967   1.7633  -1.2662
 5Y2  H5   H  HCH3  0   0.271   6.5156   3.3599  -1.6006
 5Y2  H6   H  HCH3  0   0.274   7.1845   3.0103  -0.0151
 5Y2  H7   H  HCR6  0   0.304  -1.8644   2.1516  -0.1181
 5Y2  H8   H  HCR5  0   0.294  -5.1029  -3.4122  -0.5137
 5Y2  H9   H  HCH1  0   0.282  -3.9996   3.1543  -1.4935
 5Y2  H10  H  HCH2  0   0.266  -5.8752   4.4104  -0.4377
 5Y2  H11  H  HCH2  0   0.265  -6.2754   2.9657   0.5966
 5Y2  H12  H  HCH2  0   0.265  -3.9812   3.0185   1.6005
 5Y2  H13  H  HCH2  0   0.264  -3.5510   4.4680   0.5817
 5Y2  H14  H  HNH1  0   0.418   0.3280   1.6659   0.1008
 5Y2  H15  H  HCR6  0   0.278   2.4831   1.6828  -0.5168
 5Y2  H16  H  HCH3  0   0.248   5.8701  -1.9568  -0.2185
 5Y2  H17  H  HCH3  0   0.250   6.0858  -1.1016   1.3038
 5Y2  H18  H  HCH3  0   0.261   5.3352  -2.6936   1.2797
 5Y2  H19  H  HNH1  0   0.416   5.7933   0.2594  -0.6734
 5Y2  N1   N  NH1   0  -0.792   0.2534   0.6671   0.2159

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
 5Y2  O    C7   double    1.218  0.020  1.218
 5Y2  N5   C15  triple    1.155  0.020  1.155
 5Y2  C15  C13  single    1.402  0.020  1.402
 5Y2  C7   C8   single    1.507  0.020  1.507
 5Y2  C7   N    single    1.359  0.020  1.359
 5Y2  N    C6   single    1.403  0.020  1.403
 5Y2  C13  C14  aromatic  1.411  0.020  1.411
 5Y2  C13  C12  aromatic  1.402  0.020  1.402
 5Y2  C14  N4   aromatic  1.309  0.020  1.309
 5Y2  C12  N3   aromatic  1.323  0.020  1.323
 5Y2  C12  N2   aromatic  1.367  0.020  1.367
 5Y2  C6   C5   aromatic  1.389  0.020  1.389
 5Y2  C6   C1   aromatic  1.403  0.020  1.403
 5Y2  N4   N2   aromatic  1.351  0.020  1.351
 5Y2  C    C1   single    1.501  0.020  1.501
 5Y2  N3   C9   aromatic  1.326  0.020  1.326
 5Y2  C5   C4   aromatic  1.395  0.020  1.395
 5Y2  N2   C11  aromatic  1.367  0.020  1.367
 5Y2  C1   C2   aromatic  1.388  0.020  1.388
 5Y2  C9   N1   single    1.356  0.020  1.356
 5Y2  C9   C10  aromatic  1.415  0.020  1.415
 5Y2  C4   N1   single    1.398  0.020  1.398
 5Y2  C4   C3   aromatic  1.392  0.020  1.392
 5Y2  C11  C10  aromatic  1.378  0.020  1.378
 5Y2  C11  N6   single    1.334  0.020  1.334
 5Y2  C2   C3   aromatic  1.387  0.020  1.387
 5Y2  N6   C16  single    1.425  0.020  1.425
 5Y2  C16  C18  single    1.492  0.020  1.492
 5Y2  C16  C17  single    1.500  0.020  1.500
 5Y2  C18  C17  single    1.496  0.020  1.496
 5Y2  C2   H1   single    0.930  0.020  1.080
 5Y2  C3   H2   single    0.930  0.020  1.080
 5Y2  N6   H3   single    0.860  0.020  1.020
 5Y2  C8   H4   single    0.970  0.020  1.090
 5Y2  C8   H5   single    0.970  0.020  1.090
 5Y2  C8   H6   single    0.970  0.020  1.090
 5Y2  C10  H7   single    0.930  0.020  1.080
 5Y2  C14  H8   single    0.930  0.020  1.080
 5Y2  C16  H9   single    0.970  0.020  1.090
 5Y2  C18  H10  single    0.970  0.020  1.090
 5Y2  C18  H11  single    0.970  0.020  1.090
 5Y2  C17  H12  single    0.970  0.020  1.090
 5Y2  C17  H13  single    0.970  0.020  1.090
 5Y2  N1   H14  single    0.860  0.020  1.020
 5Y2  C5   H15  single    0.930  0.020  1.080
 5Y2  C    H16  single    0.970  0.020  1.090
 5Y2  C    H17  single    0.970  0.020  1.090
 5Y2  C    H18  single    0.970  0.020  1.090
 5Y2  N    H19  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
 5Y2  C    C1   C6   121.55  3.000
 5Y2  C    C1   C2   120.95  3.000
 5Y2  C6   C1   C2   117.50  3.000
 5Y2  H1   C2   C3   118.44  3.000
 5Y2  H1   C2   C1   118.65  3.000
 5Y2  C3   C2   C1   122.90  3.000
 5Y2  H2   C3   C4   121.18  3.000
 5Y2  H2   C3   C2   119.87  3.000
 5Y2  C4   C3   C2   118.95  3.000
 5Y2  H3   N6   C16  119.09  3.000
 5Y2  H3   N6   C11  117.65  3.000
 5Y2  C16  N6   C11  122.19  3.000
 5Y2  O    C7   N    123.62  3.000
 5Y2  N    C7   C8   114.38  3.000
 5Y2  O    C7   C8   122.00  3.000
 5Y2  H6   C8   H5   107.36  3.000
 5Y2  H6   C8   H4   108.36  3.000
 5Y2  H5   C8   H4   108.57  3.000
 5Y2  H6   C8   C7   109.16  3.000
 5Y2  H5   C8   C7   109.35  3.000
 5Y2  H4   C8   C7   113.85  3.000
 5Y2  N1   C9   N3   119.27  3.000
 5Y2  N1   C9   C10  117.29  3.000
 5Y2  N3   C9   C10  123.44  3.000
 5Y2  H7   C10  C11  119.80  3.000
 5Y2  H7   C10  C9   120.97  3.000
 5Y2  C11  C10  C9   119.23  3.000
 5Y2  N2   C11  C10  115.84  3.000
 5Y2  C10  C11  N6   126.92  3.000
 5Y2  N2   C11  N6   117.24  3.000
 5Y2  N3   C12  N2   123.69  3.000
 5Y2  N2   C12  C13  104.17  3.000
 5Y2  N3   C12  C13  132.13  3.000
 5Y2  C15  C13  C14  128.75  3.000
 5Y2  C14  C13  C12  105.06  3.000
 5Y2  C15  C13  C12  126.20  3.000
 5Y2  H8   C14  N4   120.54  3.000
 5Y2  H8   C14  C13  127.09  3.000
 5Y2  N4   C14  C13  112.37  3.000
 5Y2  N5   C15  C13  180.00  3.000
 5Y2  H9   C16  C17  117.30  3.000
 5Y2  H9   C16  C18  117.61  3.000
 5Y2  C17  C16  C18   60.01  3.000
 5Y2  H9   C16  N6   114.96  3.000
 5Y2  C17  C16  N6   118.56  3.000
 5Y2  C18  C16  N6   117.52  3.000
 5Y2  N2   N4   C14  104.53  3.000
 5Y2  N4   N2   C12  113.87  3.000
 5Y2  N4   N2   C11  124.42  3.000
 5Y2  C12  N2   C11  121.71  3.000
 5Y2  H11  C18  H10  114.62  3.000
 5Y2  H11  C18  C17  117.78  3.000
 5Y2  H10  C18  C17  118.79  3.000
 5Y2  H11  C18  C16  117.46  3.000
 5Y2  H10  C18  C16  117.33  3.000
 5Y2  C17  C18  C16   60.25  3.000
 5Y2  H13  C17  H12  114.78  3.000
 5Y2  H13  C17  C18  118.84  3.000
 5Y2  H12  C17  C18  117.77  3.000
 5Y2  H13  C17  C16  117.46  3.000
 5Y2  H12  C17  C16  117.34  3.000
 5Y2  C18  C17  C16   59.74  3.000
 5Y2  C12  N3   C9   116.09  3.000
 5Y2  C5   C4   N1   116.23  3.000
 5Y2  N1   C4   C3   124.39  3.000
 5Y2  C5   C4   C3   119.34  3.000
 5Y2  H15  C5   C6   120.09  3.000
 5Y2  H15  C5   C4   119.02  3.000
 5Y2  C6   C5   C4   120.88  3.000
 5Y2  N    C6   C5   121.62  3.000
 5Y2  C5   C6   C1   120.42  3.000
 5Y2  N    C6   C1   117.92  3.000
 5Y2  H18  C    H17  107.66  3.000
 5Y2  H18  C    H16  106.90  3.000
 5Y2  H17  C    H16  107.23  3.000
 5Y2  H18  C    C1   110.58  3.000
 5Y2  H17  C    C1   111.93  3.000
 5Y2  H16  C    C1   112.29  3.000
 5Y2  H19  N    C6   115.88  3.000
 5Y2  H19  N    C7   116.23  3.000
 5Y2  C6   N    C7   127.65  3.000
 5Y2  H14  N1   C4   114.58  3.000
 5Y2  H14  N1   C9   115.02  3.000
 5Y2  C4   N1   C9   129.82  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
 5Y2  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 5Y2  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 5Y2  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 5Y2  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 5Y2  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 5Y2  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 5Y2  CONST_07  C13  C12  N3   C9    180.00   0.0  0
 5Y2  CONST_08  N2   C12  N3   C9      0.00   0.0  0
 5Y2  CONST_09  N2   C11  C10  C9      0.00   0.0  0
 5Y2  CONST_10  C12  N3   C9   C10     0.00   0.0  0
 5Y2  CONST_11  C12  N2   C11  C10     0.00   0.0  0
 5Y2  CONST_12  N4   N2   C11  C10   180.00   0.0  0
 5Y2  CONST_13  C13  C12  N2   C11   180.00   0.0  0
 5Y2  CONST_14  N3   C12  N2   C11     0.00   0.0  0
 5Y2  CONST_15  C14  N4   N2   C11   180.00   0.0  0
 5Y2  CONST_16  N3   C9   C10  C11     0.00   0.0  0
 5Y2  CONST_17  N4   C14  C13  C12     0.00   0.0  0
 5Y2  CONST_18  C14  N4   N2   C12     0.00   0.0  0
 5Y2  CONST_19  N2   N4   C14  C13     0.00   0.0  0
 5Y2  CONST_20  N4   N2   C12  C13     0.00   0.0  0
 5Y2  CONST_21  N3   C12  C13  C14   180.00   0.0  0
 5Y2  CONST_22  N2   C12  C13  C14     0.00   0.0  0
 5Y2  CONST_23  N3   C12  N2   N4    180.00   0.0  0
 5Y2  CONST_24  N    C6   C1   C2    180.00   0.0  0
 5Y2  CONST_25  N1   C4   C3   C2    180.00   0.0  0
 5Y2  CONST_26  C    C1   C2   C3    180.00   0.0  0
 5Y2  CONST_27  C12  N2   C11  N6    180.00   0.0  0
 5Y2  CONST_28  N4   N2   C11  N6      0.00   0.0  0
 5Y2  CONST_29  C9   C10  C11  N6    180.00   0.0  0
 5Y2  CONST_30  N1   C9   C10  C11   180.00   0.0  0
 5Y2  CONST_31  N1   C9   N3   C12   180.00   0.0  0
 5Y2  CONST_32  N4   C14  C13  C15   180.00   0.0  0
 5Y2  CONST_33  N3   C12  C13  C15     0.00   0.0  0
 5Y2  CONST_34  N2   C12  C13  C15   180.00   0.0  0
 5Y2  CONST_35  C6   C5   C4   N1    180.00   0.0  0
 5Y2  CONST_36  N    C6   C5   C4    180.00   0.0  0
 5Y2  CONST_37  C    C1   C6   C5    180.00   0.0  0
 5Y2  CONST_38  C16  N6   C11  C10     0.00   0.0  0
 5Y2  CONST_39  N2   C11  N6   C16   180.00   0.0  0
 5Y2  CONST_40  H15  C5   C6   C1    180.00   0.0  0
 5Y2  CONST_41  H2   C3   C2   C1    180.00   0.0  0
 5Y2  CONST_42  H8   C14  C13  C12   180.00   0.0  0
 5Y2  CONST_43  H7   C10  C11  N2    180.00   0.0  0
 5Y2  CONST_44  H1   C2   C3   C4    180.00   0.0  0
 5Y2  CONST_48  H3   N6   C11  C10   180.00   0.0  0
 5Y2  CONST_49  C6   N    C7   C8    180.00   0.0  0
 5Y2  CONST_50  O    C7   N    C6      0.00   0.0  0
 5Y2  Var_01    C9   N1   C4   C3    -28.86  30.0  2
 5Y2  Var_02    C17  C18  C16  N6    108.77  30.0  1
 5Y2  Var_03    C4   N1   C9   C10  -176.89  30.0  2
 5Y2  Var_04    C18  C16  N6   C11  -142.69  30.0  3
 5Y2  Var_05    H12  C17  C18  C16  -107.08  30.0  1
 5Y2  Var_06    H16  C    C1   C2    113.51  30.0  2
 5Y2  Var_07    H4   C8   C7   N       6.99  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
 5Y2  chir_01  C16  N6  C18  C17  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
 5Y2  plan-1  C1   0.020
 5Y2  plan-1  C2   0.020
 5Y2  plan-1  C3   0.020
 5Y2  plan-1  C4   0.020
 5Y2  plan-1  C5   0.020
 5Y2  plan-1  C6   0.020
 5Y2  plan-1  C    0.020
 5Y2  plan-1  N    0.020
 5Y2  plan-1  H1   0.020
 5Y2  plan-1  H2   0.020
 5Y2  plan-1  H15  0.020
 5Y2  plan-1  N1   0.020
 5Y2  plan-2  N6   0.020
 5Y2  plan-2  C9   0.020
 5Y2  plan-2  C10  0.020
 5Y2  plan-2  C11  0.020
 5Y2  plan-2  C12  0.020
 5Y2  plan-2  C13  0.020
 5Y2  plan-2  C14  0.020
 5Y2  plan-2  C15  0.020
 5Y2  plan-2  N5   0.020
 5Y2  plan-2  N4   0.020
 5Y2  plan-2  N2   0.020
 5Y2  plan-2  N3   0.020
 5Y2  plan-2  H7   0.020
 5Y2  plan-2  H8   0.020
 5Y2  plan-2  N1   0.020
 5Y2  plan-3  N6   0.020
 5Y2  plan-3  C11  0.020
 5Y2  plan-3  C16  0.020
 5Y2  plan-3  H3   0.020
 5Y2  plan-4  C7   0.020
 5Y2  plan-4  C8   0.020
 5Y2  plan-4  C6   0.020
 5Y2  plan-4  N    0.020
 5Y2  plan-4  O    0.020
 5Y2  plan-4  H19  0.020

