# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 12:14:55 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 1-[(3~{R})-3-[4-azanyl-3-(1~{H}-pyrrolo[2,3-b]pyridin-5-yl)pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl]propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N1CCC[C@H](C1)n2nc(c3cnc4[nH]ccc4c3)c5c(N)ncnc25
#
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
 J3N  J3N  1-[(3~{R})-3-[4-azanyl-3-(1~{H}-pyrrolo[2,3-b]pyridin-5-yl)pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl]propan-1-one  ligand  51  29  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_J3N
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
 J3N  C11  C  C     0   0.566   5.1219   0.7626  -0.7858
 J3N  C13  C  CH3   0  -0.650   7.6062   0.5875  -1.2367
 J3N  C16  C  CR56  0   0.469  -4.7233   1.9727  -0.2383
 J3N  C17  C  CR16  0  -0.099  -2.5579   1.6956  -0.7199
 J3N  C18  C  CR15  0  -0.447  -6.1625   0.6597   0.9514
 J3N  C19  C  CR15  0   0.004  -6.8077   1.7756   0.5028
 J3N  N    N  N     0  -0.477  -0.9503  -3.9711  -0.5717
 J3N  C    C  CR16  0   0.058   0.3513  -3.9449  -0.2890
 J3N  O    O  O     0  -0.500   4.9478   0.0895  -1.7924
 J3N  C1   C  CR56  0   0.586   0.3943  -1.7770   0.0865
 J3N  C10  C  CH2   0  -0.309   2.7239   0.8461  -0.3746
 J3N  C12  C  CH2   0  -0.595   6.5202   1.1222  -0.3196
 J3N  C14  C  CR16  0  -0.294  -3.6593  -0.0020   0.5910
 J3N  C15  C  CR56  0   0.027  -4.8174   0.7602   0.4863
 J3N  C2   C  CR56  0  -0.274  -0.9785  -1.6465  -0.1392
 J3N  C3   C  CR6   0   0.433  -1.6452  -2.8319  -0.5278
 J3N  C4   C  CR5   0   0.274  -1.2427  -0.2624   0.0526
 J3N  C5   C  CR6   0  -0.077  -2.5093   0.4693  -0.0310
 J3N  C6   C  CH1   0  -0.096   2.2171  -0.1520   0.6714
 J3N  C7   C  CH2   0  -0.443   2.3318   0.4276   2.0798
 J3N  C8   C  CH2   0  -0.438   3.7484   0.9290   2.3422
 J3N  C9   C  CH2   0  -0.328   4.1975   1.8824   1.2418
 J3N  N1   N  N     0  -0.465   1.1005  -2.9095   0.0281
 J3N  N2   N  NR5   0  -0.383   0.8581  -0.5450   0.3667
 J3N  N3   N  N     0  -0.279  -0.1280   0.3643   0.3489
 J3N  N5   N  NT    0  -0.459   4.0814   1.2355  -0.0551
 J3N  N6   N  N     0  -0.419  -3.6384   2.4476  -0.8291
 J3N  N7   N  NR15  0  -0.661  -5.9457   2.5633  -0.2103
 J3N  H1   H  HCH3  0   0.231   8.5834   0.8939  -0.8649
 J3N  H2   H  HCH3  0   0.227   7.5954  -0.5005  -1.2832
 J3N  H3   H  HCH3  0   0.227   7.5038   0.9678  -2.2521
 J3N  H5   H  HCR5  0   0.257  -6.5965  -0.1338   1.5374
 J3N  H7   H  HCR5  0   0.292  -7.8336   2.0764   0.6384
 J3N  H8   H  HCR6  0   0.255   0.8553  -4.9047  -0.3386
 J3N  H9   H  HCH2  0   0.275   2.6840   0.4132  -1.3704
 J3N  H10  H  HCH2  0   0.254   2.0888   1.7369  -0.3670
 J3N  H11  H  HCH2  0   0.267   6.6043   2.2092  -0.2375
 J3N  H12  H  HCH2  0   0.264   6.6737   0.7387   0.6933
 J3N  H13  H  HCR6  0   0.276  -3.6477  -0.9214   1.1651
 J3N  H14  H  HCH1  0   0.273   2.8144  -1.0638   0.6018
 J3N  H15  H  HCH2  0   0.237   1.6258   1.2568   2.1810
 J3N  H16  H  HCH2  0   0.254   2.0496  -0.3288   2.8148
 J3N  H17  H  HCH2  0   0.249   3.7902   1.4368   3.3074
 J3N  H18  H  HCH2  0   0.233   4.4443   0.0864   2.3909
 J3N  H19  H  HCH2  0   0.249   3.5598   2.7721   1.2378
 J3N  H20  H  HCH2  0   0.278   5.2123   2.2278   1.4145
 J3N  H21  H  HNH2  0   0.406  -3.3249  -3.7386  -1.1999
 J3N  H22  H  HNH2  0   0.414  -3.4724  -2.0391  -1.0037
 J3N  H6   H  HNR5  0   0.414  -6.1796   3.4427  -0.6416
 J3N  N4   N  NH2   0  -0.815  -2.9393  -2.8771  -0.8504
 J3N  H4   H  HCR6  0   0.257  -1.6615   2.0634  -1.2065

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
 J3N  C    N    aromatic  1.332  0.020  1.332
 J3N  C    N1   aromatic  1.317  0.020  1.317
 J3N  N    C3   aromatic  1.335  0.020  1.335
 J3N  N1   C1   aromatic  1.336  0.020  1.336
 J3N  C3   N4   single    1.334  0.020  1.334
 J3N  C3   C2   aromatic  1.414  0.020  1.414
 J3N  C1   C2   aromatic  1.397  0.020  1.397
 J3N  C1   N2   aromatic  1.346  0.020  1.346
 J3N  C2   C4   aromatic  1.422  0.020  1.422
 J3N  C7   C6   single    1.527  0.020  1.527
 J3N  C7   C8   single    1.525  0.020  1.525
 J3N  O    C11  double    1.223  0.020  1.223
 J3N  C6   N2   single    1.447  0.020  1.447
 J3N  C6   C10  single    1.532  0.020  1.532
 J3N  N2   N3   aromatic  1.341  0.020  1.341
 J3N  C8   C9   single    1.524  0.020  1.524
 J3N  C11  N5   single    1.356  0.020  1.356
 J3N  C11  C12  single    1.517  0.020  1.517
 J3N  C4   N3   aromatic  1.313  0.020  1.313
 J3N  C4   C5   single    1.465  0.020  1.465
 J3N  N5   C10  single    1.448  0.020  1.448
 J3N  N5   C9   single    1.454  0.020  1.454
 J3N  C12  C13  single    1.519  0.020  1.519
 J3N  C14  C5   aromatic  1.390  0.020  1.390
 J3N  C14  C15  aromatic  1.390  0.020  1.390
 J3N  C5   C17  aromatic  1.407  0.020  1.407
 J3N  C18  C15  aromatic  1.427  0.020  1.427
 J3N  C18  C19  aromatic  1.365  0.020  1.365
 J3N  C15  C16  aromatic  1.416  0.020  1.416
 J3N  C17  N6   aromatic  1.321  0.020  1.321
 J3N  C19  N7   aromatic  1.368  0.020  1.368
 J3N  C16  N6   aromatic  1.324  0.020  1.324
 J3N  C16  N7   aromatic  1.358  0.020  1.358
 J3N  C13  H1   single    0.970  0.020  1.090
 J3N  C13  H2   single    0.970  0.020  1.090
 J3N  C13  H3   single    0.970  0.020  1.090
 J3N  C17  H4   single    0.930  0.020  1.080
 J3N  C18  H5   single    0.930  0.020  1.080
 J3N  C19  H7   single    0.930  0.020  1.080
 J3N  C    H8   single    0.930  0.020  1.080
 J3N  C10  H9   single    0.970  0.020  1.090
 J3N  C10  H10  single    0.970  0.020  1.090
 J3N  C12  H11  single    0.970  0.020  1.090
 J3N  C12  H12  single    0.970  0.020  1.090
 J3N  C14  H13  single    0.930  0.020  1.080
 J3N  C6   H14  single    0.970  0.020  1.090
 J3N  C7   H15  single    0.970  0.020  1.090
 J3N  C7   H16  single    0.970  0.020  1.090
 J3N  C8   H17  single    0.970  0.020  1.090
 J3N  C8   H18  single    0.970  0.020  1.090
 J3N  C9   H19  single    0.970  0.020  1.090
 J3N  C9   H20  single    0.970  0.020  1.090
 J3N  N4   H21  single    0.860  0.020  1.020
 J3N  N4   H22  single    0.860  0.020  1.020
 J3N  N7   H6   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
 J3N  N5   C11  C12  117.31  3.000
 J3N  C12  C11  O    120.96  3.000
 J3N  N5   C11  O    121.72  3.000
 J3N  H3   C13  H2   107.95  3.000
 J3N  H3   C13  H1   107.72  3.000
 J3N  H2   C13  H1   107.72  3.000
 J3N  H3   C13  C12  111.88  3.000
 J3N  H2   C13  C12  111.74  3.000
 J3N  H1   C13  C12  109.65  3.000
 J3N  N7   C16  N6   126.23  3.000
 J3N  N7   C16  C15  107.58  3.000
 J3N  N6   C16  C15  126.18  3.000
 J3N  H4   C17  N6   116.49  3.000
 J3N  H4   C17  C5   119.12  3.000
 J3N  N6   C17  C5   124.39  3.000
 J3N  H5   C18  C15  127.50  3.000
 J3N  H5   C18  C19  126.19  3.000
 J3N  C15  C18  C19  106.31  3.000
 J3N  H7   C19  N7   120.31  3.000
 J3N  H7   C19  C18  129.56  3.000
 J3N  N7   C19  C18  110.14  3.000
 J3N  C3   N    C    119.00  3.000
 J3N  H8   C    N1   116.24  3.000
 J3N  H8   C    N    115.26  3.000
 J3N  N1   C    N    128.50  3.000
 J3N  N2   C1   N1   127.08  3.000
 J3N  N2   C1   C2   106.66  3.000
 J3N  N1   C1   C2   126.26  3.000
 J3N  H10  C10  H9   108.03  3.000
 J3N  H10  C10  N5   108.89  3.000
 J3N  H9   C10  N5   110.11  3.000
 J3N  H10  C10  C6   109.49  3.000
 J3N  H9   C10  C6   110.73  3.000
 J3N  N5   C10  C6   109.55  3.000
 J3N  H12  C12  H11  105.56  3.000
 J3N  H12  C12  C13  109.59  3.000
 J3N  H11  C12  C13  109.90  3.000
 J3N  H12  C12  C11  109.31  3.000
 J3N  H11  C12  C11  109.25  3.000
 J3N  C13  C12  C11  112.96  3.000
 J3N  H13  C14  C5   121.05  3.000
 J3N  H13  C14  C15  120.91  3.000
 J3N  C5   C14  C15  118.01  3.000
 J3N  C14  C15  C18  136.23  3.000
 J3N  C18  C15  C16  106.85  3.000
 J3N  C14  C15  C16  116.92  3.000
 J3N  C4   C2   C3   139.92  3.000
 J3N  C4   C2   C1   104.57  3.000
 J3N  C3   C2   C1   115.42  3.000
 J3N  N4   C3   C2   123.50  3.000
 J3N  C2   C3   N    118.61  3.000
 J3N  N4   C3   N    117.90  3.000
 J3N  N3   C4   C5   120.57  3.000
 J3N  C5   C4   C2   129.72  3.000
 J3N  N3   C4   C2   109.71  3.000
 J3N  C4   C5   C14  121.36  3.000
 J3N  C14  C5   C17  119.08  3.000
 J3N  C4   C5   C17  119.54  3.000
 J3N  H14  C6   N2   105.87  3.000
 J3N  H14  C6   C7   109.54  3.000
 J3N  N2   C6   C7   111.57  3.000
 J3N  H14  C6   C10  108.63  3.000
 J3N  N2   C6   C10  110.11  3.000
 J3N  C7   C6   C10  110.95  3.000
 J3N  H16  C7   H15  107.23  3.000
 J3N  H16  C7   C8   110.60  3.000
 J3N  H15  C7   C8   109.53  3.000
 J3N  H16  C7   C6   109.78  3.000
 J3N  H15  C7   C6   108.94  3.000
 J3N  C8   C7   C6   110.67  3.000
 J3N  H18  C8   H17  107.13  3.000
 J3N  H18  C8   C9   109.07  3.000
 J3N  H17  C8   C9   109.65  3.000
 J3N  H18  C8   C7   110.20  3.000
 J3N  H17  C8   C7   109.91  3.000
 J3N  C9   C8   C7   110.80  3.000
 J3N  H20  C9   H19  106.65  3.000
 J3N  H20  C9   N5   110.98  3.000
 J3N  H19  C9   N5   108.17  3.000
 J3N  H20  C9   C8   111.08  3.000
 J3N  H19  C9   C8   109.84  3.000
 J3N  N5   C9   C8   110.02  3.000
 J3N  C1   N1   C    112.11  3.000
 J3N  N3   N2   C6   120.60  3.000
 J3N  N3   N2   C1   111.37  3.000
 J3N  C6   N2   C1   128.03  3.000
 J3N  N2   N3   C4   107.68  3.000
 J3N  C9   N5   C10  113.04  3.000
 J3N  C9   N5   C11  125.05  3.000
 J3N  C10  N5   C11  120.43  3.000
 J3N  C17  N6   C16  115.42  3.000
 J3N  H6   N7   C19  125.43  3.000
 J3N  H6   N7   C16  125.46  3.000
 J3N  C19  N7   C16  109.11  3.000
 J3N  H22  N4   H21  117.23  3.000
 J3N  H22  N4   C3   121.54  3.000
 J3N  H21  N4   C3   118.98  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
 J3N  CONST_01  C5   C14  C15  C16     0.00   0.0  0
 J3N  CONST_02  C19  C18  C15  C16     0.00   0.0  0
 J3N  CONST_03  C5   C17  N6   C16     0.00   0.0  0
 J3N  CONST_04  C18  C19  N7   C16     0.00   0.0  0
 J3N  CONST_07  C15  C14  C5   C17     0.00   0.0  0
 J3N  CONST_08  C15  C16  N6   C17     0.00   0.0  0
 J3N  CONST_09  N7   C16  N6   C17   180.00   0.0  0
 J3N  CONST_10  C5   C14  C15  C18   180.00   0.0  0
 J3N  CONST_11  N6   C16  C15  C18   180.00   0.0  0
 J3N  CONST_12  N7   C16  C15  C18     0.00   0.0  0
 J3N  CONST_13  C14  C15  C18  C19   180.00   0.0  0
 J3N  CONST_14  C15  C16  N7   C19     0.00   0.0  0
 J3N  CONST_15  N6   C16  N7   C19   180.00   0.0  0
 J3N  CONST_16  C1   N1   C    N       0.00   0.0  0
 J3N  CONST_17  C1   C2   C3   N       0.00   0.0  0
 J3N  CONST_18  C4   C2   C3   N     180.00   0.0  0
 J3N  CONST_19  C2   C3   N    C       0.00   0.0  0
 J3N  CONST_20  C2   C1   N1   C       0.00   0.0  0
 J3N  CONST_21  N2   C1   N1   C     180.00   0.0  0
 J3N  CONST_22  N3   C4   C2   C1      0.00   0.0  0
 J3N  CONST_23  C5   C4   C2   C1    180.00   0.0  0
 J3N  CONST_24  C4   N3   N2   C1      0.00   0.0  0
 J3N  CONST_27  N6   C17  C5   C14     0.00   0.0  0
 J3N  CONST_28  N6   C16  C15  C14     0.00   0.0  0
 J3N  CONST_29  N7   C16  C15  C14   180.00   0.0  0
 J3N  CONST_30  C4   C5   C14  C15   180.00   0.0  0
 J3N  CONST_31  N7   C19  C18  C15     0.00   0.0  0
 J3N  CONST_32  N3   N2   C1   C2      0.00   0.0  0
 J3N  CONST_33  N2   N3   C4   C2      0.00   0.0  0
 J3N  CONST_34  N1   C    N    C3      0.00   0.0  0
 J3N  CONST_35  N1   C1   C2   C3      0.00   0.0  0
 J3N  CONST_36  N2   C1   C2   C3    180.00   0.0  0
 J3N  CONST_37  N3   C4   C2   C3    180.00   0.0  0
 J3N  CONST_38  C5   C4   C2   C3      0.00   0.0  0
 J3N  CONST_39  N1   C1   C2   C4    180.00   0.0  0
 J3N  CONST_40  N2   C1   C2   C4      0.00   0.0  0
 J3N  CONST_41  N6   C17  C5   C4    180.00   0.0  0
 J3N  CONST_42  N2   N3   C4   C5    180.00   0.0  0
 J3N  CONST_43  N3   N2   C1   N1    180.00   0.0  0
 J3N  CONST_44  C6   N2   C1   C2    180.00   0.0  0
 J3N  CONST_45  C6   N2   N3   C4    180.00   0.0  0
 J3N  CONST_46  N1   C1   N2   C6      0.00   0.0  0
 J3N  CONST_47  N4   C3   N    C     180.00   0.0  0
 J3N  CONST_48  N4   C3   C2   C1    180.00   0.0  0
 J3N  CONST_49  N4   C3   C2   C4      0.00   0.0  0
 J3N  CONST_50  H13  C14  C15  C16   180.00   0.0  0
 J3N  CONST_51  H5   C18  C15  C16   180.00   0.0  0
 J3N  CONST_52  H4   C17  N6   C16   180.00   0.0  0
 J3N  CONST_53  H7   C19  N7   C16   180.00   0.0  0
 J3N  CONST_54  H6   N7   C19  C18   180.00   0.0  0
 J3N  CONST_55  H8   C    N1   C1    180.00   0.0  0
 J3N  CONST_56  C10  N5   C11  O       0.00   0.0  0
 J3N  CONST_57  C9   N5   C11  O     180.00   0.0  0
 J3N  CONST_58  C12  C11  N5   C10   180.00   0.0  0
 J3N  CONST_59  C9   N5   C11  C12     0.00   0.0  0
 J3N  CONST_60  H21  N4   C3   N       0.00   0.0  0
 J3N  CONST_61  H22  N4   C3   N     180.00   0.0  0
 J3N  Var_01    C8   C9   N5   C10    61.00  30.0  1
 J3N  Var_02    C9   C8   C7   C6     52.55  30.0  1
 J3N  Var_03    C9   N5   C10  C6    -60.75  30.0  1
 J3N  Var_04    N5   C9   C8   C7    -55.67  30.0  1
 J3N  Var_05    N5   C11  C12  C13  -177.80  30.0  1
 J3N  Var_06    H1   C13  C12  C11   178.79  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
 J3N  chir_01  C6  C7  N2  C10  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
 J3N  plan-1  C16  0.020
 J3N  plan-1  C17  0.020
 J3N  plan-1  C18  0.020
 J3N  plan-1  C19  0.020
 J3N  plan-1  C14  0.020
 J3N  plan-1  C15  0.020
 J3N  plan-1  C4   0.020
 J3N  plan-1  C5   0.020
 J3N  plan-1  N6   0.020
 J3N  plan-1  N7   0.020
 J3N  plan-1  H5   0.020
 J3N  plan-1  H7   0.020
 J3N  plan-1  H13  0.020
 J3N  plan-1  H6   0.020
 J3N  plan-1  H4   0.020
 J3N  plan-2  N    0.020
 J3N  plan-2  C    0.020
 J3N  plan-2  C1   0.020
 J3N  plan-2  C2   0.020
 J3N  plan-2  C3   0.020
 J3N  plan-2  C4   0.020
 J3N  plan-2  C5   0.020
 J3N  plan-2  C6   0.020
 J3N  plan-2  N1   0.020
 J3N  plan-2  N2   0.020
 J3N  plan-2  N3   0.020
 J3N  plan-2  H8   0.020
 J3N  plan-2  N4   0.020
 J3N  plan-3  C3   0.020
 J3N  plan-3  H21  0.020
 J3N  plan-3  H22  0.020
 J3N  plan-3  N4   0.020
 J3N  plan-4  C11  0.020
 J3N  plan-4  O    0.020
 J3N  plan-4  C10  0.020
 J3N  plan-4  C12  0.020
 J3N  plan-4  C9   0.020
 J3N  plan-4  N5   0.020

