# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 08:56:18 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: 1-cyclopentyl-6-({(2R)-1-[(3S)-3-fluoropyrrolidin-1-yl]-1-oxopropan-2-yl}amino)-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC1=Nc2n(ncc2C(=O)N1)C3CCCC3)C(=O)N4CC[C@H](F)C4
#
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
 9Q9  9Q9  1-cyclopentyl-6-({(2R)-1-[(3S)-3-fluoropyrrolidin-1-yl]-1-oxopropan-2-yl}amino)-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one  ligand  49  26  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9Q9
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
 9Q9  C4   C  CR6   0   0.779  -0.4423  -1.7775  -0.0473
 9Q9  C6   C  CR56  0   0.613  -2.3348  -0.6365   0.1570
 9Q9  C7   C  CR56  0  -0.366  -3.1148  -1.7539   0.4467
 9Q9  C8   C  CR6   0   0.514  -2.4880  -3.0343   0.4960
 9Q9  C12  C  CR15  0  -0.071  -4.4201  -1.2457   0.6008
 9Q9  N3   N  NH1   0  -0.684   0.8723  -1.8995  -0.2620
 9Q9  C13  C  CR15  0  -0.079  -2.8346   1.7959  -0.1402
 9Q9  C1   C  C     0   0.572   3.1468  -1.1749  -0.3453
 9Q9  C2   C  CH1   0  -0.205   1.7038  -0.7829  -0.6454
 9Q9  N5   N  N     0  -0.524  -1.0150  -0.6028  -0.0910
 9Q9  N9   N  NR16  0  -0.750  -1.1212  -2.9362   0.2279
 9Q9  N10  N  NR5   0  -0.388  -3.1630   0.4192   0.1597
 9Q9  N11  N  N     0  -0.271  -4.4341   0.0519   0.4236
 9Q9  O14  O  O     0  -0.499   3.4941  -2.3487  -0.4008
 9Q9  O15  O  O     0  -0.465  -2.9983  -4.1167   0.7281
 9Q9  C16  C  CH2   0  -0.450  -3.2462   2.7735   0.9661
 9Q9  C17  C  CH2   0  -0.452  -3.4238   4.0910   0.2214
 9Q9  C18  C  CH2   0  -0.446  -4.1406   3.6658  -1.0608
 9Q9  C19  C  CH2   0  -0.454  -3.4981   2.3225  -1.4369
 9Q9  C20  C  CH3   0  -0.657   1.5662  -0.4486  -2.1330
 9Q9  N21  N  NR5   0  -0.485   4.0051  -0.1871  -0.0752
 9Q9  C22  C  CH2   0  -0.273   5.4229  -0.4672   0.1632
 9Q9  C23  C  CH2   0  -0.549   5.9648   0.8566   0.6852
 9Q9  C24  C  CR15  0   0.187   5.0674   1.8724   0.0100
 9Q9  C25  C  CH2   0  -0.334   3.6883   1.2267   0.0586
 9Q9  F26  F  F     0  -0.366   5.0654   3.0967   0.6568
 9Q9  H1   H  HCR5  0   0.270  -5.3300  -1.7786   0.8318
 9Q9  H2   H  HNH1  0   0.406   1.2860  -2.8174  -0.3322
 9Q9  H3   H  HCR5  0   0.273  -1.7503   1.8129  -0.2513
 9Q9  H4   H  HCH1  0   0.288   1.4010   0.0802  -0.0509
 9Q9  H5   H  HNR6  0   0.424  -0.6039  -3.8059   0.2387
 9Q9  H6   H  HCH2  0   0.236  -4.2006   2.4624   1.3978
 9Q9  H7   H  HCH2  0   0.244  -2.5131   2.8158   1.7724
 9Q9  H8   H  HCH2  0   0.238  -3.9830   4.8296   0.7968
 9Q9  H9   H  HCH2  0   0.223  -2.4495   4.5286  -0.0142
 9Q9  H10  H  HCH2  0   0.226  -5.2039   3.5280  -0.8513
 9Q9  H11  H  HCH2  0   0.235  -4.0629   4.4052  -1.8580
 9Q9  H12  H  HCH2  0   0.241  -2.7411   2.4505  -2.2114
 9Q9  H13  H  HCH2  0   0.245  -4.2309   1.6155  -1.8255
 9Q9  H14  H  HCH3  0   0.242   2.1936   0.3968  -2.4160
 9Q9  H15  H  HCH3  0   0.240   1.8542  -1.3032  -2.7451
 9Q9  H16  H  HCH3  0   0.257   0.5338  -0.1878  -2.3585
 9Q9  H17  H  HCH2  0   0.263   5.5488  -1.2774   0.8800
 9Q9  H18  H  HCH2  0   0.253   5.9093  -0.7649  -0.7685
 9Q9  H19  H  HCH2  0   0.259   5.8336   0.9210   1.7679
 9Q9  H20  H  HCH2  0   0.273   7.0206   0.9920   0.4568
 9Q9  H21  H  HCR5  0   0.230   5.3756   2.0444  -1.0236
 9Q9  H22  H  HCH2  0   0.272   3.0409   1.5853  -0.7408
 9Q9  H23  H  HCH2  0   0.264   3.2098   1.4441   1.0185

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
 9Q9  C23  C24  single    1.514  0.020  1.514
 9Q9  C23  C22  single    1.523  0.020  1.523
 9Q9  C24  F26  single    1.385  0.020  1.385
 9Q9  C24  C25  single    1.524  0.020  1.524
 9Q9  C22  N21  single    1.465  0.020  1.465
 9Q9  C25  N21  single    1.455  0.020  1.455
 9Q9  N21  C1   single    1.336  0.020  1.336
 9Q9  C17  C18  single    1.529  0.020  1.529
 9Q9  C17  C16  single    1.524  0.020  1.524
 9Q9  C18  C19  single    1.536  0.020  1.536
 9Q9  C1   O14  double    1.225  0.020  1.225
 9Q9  C1   C2   single    1.525  0.020  1.525
 9Q9  C16  C13  single    1.533  0.020  1.533
 9Q9  C20  C2   single    1.531  0.020  1.531
 9Q9  C2   N3   single    1.444  0.020  1.444
 9Q9  C13  C19  single    1.549  0.020  1.549
 9Q9  C13  N10  single    1.447  0.020  1.447
 9Q9  N5   C4   double    1.308  0.020  1.308
 9Q9  N5   C6   single    1.343  0.020  1.343
 9Q9  N3   C4   single    1.338  0.020  1.338
 9Q9  N10  C6   aromatic  1.342  0.020  1.342
 9Q9  N10  N11  aromatic  1.349  0.020  1.349
 9Q9  C4   N9   single    1.371  0.020  1.371
 9Q9  C6   C7   aromatic  1.393  0.020  1.393
 9Q9  N11  C12  aromatic  1.310  0.020  1.310
 9Q9  N9   C8   single    1.396  0.020  1.396
 9Q9  C7   C12  aromatic  1.409  0.020  1.409
 9Q9  C7   C8   single    1.426  0.020  1.426
 9Q9  C8   O15  double    1.219  0.020  1.219
 9Q9  C12  H1   single    0.930  0.020  1.080
 9Q9  N3   H2   single    0.860  0.020  1.020
 9Q9  C13  H3   single    0.970  0.020  1.090
 9Q9  C2   H4   single    0.970  0.020  1.090
 9Q9  N9   H5   single    0.860  0.020  1.020
 9Q9  C16  H6   single    0.970  0.020  1.090
 9Q9  C16  H7   single    0.970  0.020  1.090
 9Q9  C17  H8   single    0.970  0.020  1.090
 9Q9  C17  H9   single    0.970  0.020  1.090
 9Q9  C18  H10  single    0.970  0.020  1.090
 9Q9  C18  H11  single    0.970  0.020  1.090
 9Q9  C19  H12  single    0.970  0.020  1.090
 9Q9  C19  H13  single    0.970  0.020  1.090
 9Q9  C20  H14  single    0.970  0.020  1.090
 9Q9  C20  H15  single    0.970  0.020  1.090
 9Q9  C20  H16  single    0.970  0.020  1.090
 9Q9  C22  H17  single    0.970  0.020  1.090
 9Q9  C22  H18  single    0.970  0.020  1.090
 9Q9  C23  H19  single    0.970  0.020  1.090
 9Q9  C23  H20  single    0.970  0.020  1.090
 9Q9  C24  H21  single    0.970  0.020  1.090
 9Q9  C25  H22  single    0.970  0.020  1.090
 9Q9  C25  H23  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
 9Q9  N9   C4   N5   123.30  3.000
 9Q9  N9   C4   N3   116.22  3.000
 9Q9  N5   C4   N3   120.47  3.000
 9Q9  N10  C6   N5   125.95  3.000
 9Q9  N10  C6   C7   106.56  3.000
 9Q9  N5   C6   C7   127.49  3.000
 9Q9  C12  C7   C8   136.63  3.000
 9Q9  C8   C7   C6   118.76  3.000
 9Q9  C12  C7   C6   104.60  3.000
 9Q9  O15  C8   N9   120.58  3.000
 9Q9  O15  C8   C7   128.29  3.000
 9Q9  N9   C8   C7   111.13  3.000
 9Q9  H1   C12  N11  120.60  3.000
 9Q9  H1   C12  C7   128.76  3.000
 9Q9  N11  C12  C7   110.63  3.000
 9Q9  H2   N3   C2   116.66  3.000
 9Q9  H2   N3   C4   119.80  3.000
 9Q9  C2   N3   C4   122.55  3.000
 9Q9  H3   C13  C19  109.60  3.000
 9Q9  H3   C13  C16  109.31  3.000
 9Q9  C19  C13  C16  105.81  3.000
 9Q9  H3   C13  N10  105.18  3.000
 9Q9  C19  C13  N10  113.57  3.000
 9Q9  C16  C13  N10  113.35  3.000
 9Q9  N21  C1   O14  122.36  3.000
 9Q9  O14  C1   C2   120.36  3.000
 9Q9  N21  C1   C2   117.23  3.000
 9Q9  H4   C2   C20  109.39  3.000
 9Q9  H4   C2   C1   111.02  3.000
 9Q9  C20  C2   C1   109.41  3.000
 9Q9  H4   C2   N3   107.90  3.000
 9Q9  C20  C2   N3   112.03  3.000
 9Q9  C1   C2   N3   107.09  3.000
 9Q9  C6   N5   C4   113.68  3.000
 9Q9  H5   N9   C8   115.98  3.000
 9Q9  H5   N9   C4   118.38  3.000
 9Q9  C8   N9   C4   125.64  3.000
 9Q9  N11  N10  C13  120.90  3.000
 9Q9  N11  N10  C6   111.58  3.000
 9Q9  C13  N10  C6   127.46  3.000
 9Q9  N10  N11  C12  106.63  3.000
 9Q9  H7   C16  H6   107.82  3.000
 9Q9  H7   C16  C17  113.96  3.000
 9Q9  H6   C16  C17  109.72  3.000
 9Q9  H7   C16  C13  112.20  3.000
 9Q9  H6   C16  C13  109.76  3.000
 9Q9  C17  C16  C13  103.30  3.000
 9Q9  H9   C17  H8   107.42  3.000
 9Q9  H9   C17  C18  110.37  3.000
 9Q9  H8   C17  C18  112.97  3.000
 9Q9  H9   C17  C16  110.33  3.000
 9Q9  H8   C17  C16  112.80  3.000
 9Q9  C18  C17  C16  102.95  3.000
 9Q9  H11  C18  H10  107.17  3.000
 9Q9  H11  C18  C19  112.61  3.000
 9Q9  H10  C18  C19  110.11  3.000
 9Q9  H11  C18  C17  113.03  3.000
 9Q9  H10  C18  C17  109.29  3.000
 9Q9  C19  C18  C17  104.62  3.000
 9Q9  H13  C19  H12  106.84  3.000
 9Q9  H13  C19  C18  111.92  3.000
 9Q9  H12  C19  C18  111.20  3.000
 9Q9  H13  C19  C13  111.47  3.000
 9Q9  H12  C19  C13  109.70  3.000
 9Q9  C18  C19  C13  105.76  3.000
 9Q9  H16  C20  H15  108.79  3.000
 9Q9  H16  C20  H14  107.83  3.000
 9Q9  H15  C20  H14  108.07  3.000
 9Q9  H16  C20  C2   109.81  3.000
 9Q9  H15  C20  C2   110.54  3.000
 9Q9  H14  C20  C2   111.71  3.000
 9Q9  C25  N21  C22  112.43  3.000
 9Q9  C25  N21  C1   126.66  3.000
 9Q9  C22  N21  C1   120.88  3.000
 9Q9  H18  C22  H17  107.89  3.000
 9Q9  H18  C22  C23  111.77  3.000
 9Q9  H17  C22  C23  112.33  3.000
 9Q9  H18  C22  N21  110.13  3.000
 9Q9  H17  C22  N21  111.18  3.000
 9Q9  C23  C22  N21  103.53  3.000
 9Q9  H20  C23  H19  108.49  3.000
 9Q9  H20  C23  C24  113.44  3.000
 9Q9  H19  C23  C24  109.34  3.000
 9Q9  H20  C23  C22  112.41  3.000
 9Q9  H19  C23  C22  110.37  3.000
 9Q9  C24  C23  C22  102.68  3.000
 9Q9  H21  C24  F26  107.65  3.000
 9Q9  H21  C24  C25  110.63  3.000
 9Q9  F26  C24  C25  111.01  3.000
 9Q9  H21  C24  C23  111.12  3.000
 9Q9  C25  C24  C23  103.77  3.000
 9Q9  F26  C24  C23  112.69  3.000
 9Q9  H23  C25  H22  108.57  3.000
 9Q9  H23  C25  C24  109.85  3.000
 9Q9  H22  C25  C24  112.03  3.000
 9Q9  H23  C25  N21  111.64  3.000
 9Q9  H22  C25  N21  112.44  3.000
 9Q9  C24  C25  N21  102.23  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
 9Q9  CONST_01  C12  N11  N10  C6     0.00   0.0  0
 9Q9  CONST_02  N11  C12  C7   C6     0.00   0.0  0
 9Q9  CONST_03  N11  N10  C6   C7     0.00   0.0  0
 9Q9  CONST_04  N10  N11  C12  C7     0.00   0.0  0
 9Q9  CONST_05  N10  C6   C7   C12    0.00   0.0  0
 9Q9  CONST_06  C13  N10  C6   C7   180.00   0.0  0
 9Q9  CONST_07  C13  N10  N11  C12  180.00   0.0  0
 9Q9  CONST_08  N5   C6   N10  C13    0.00   0.0  0
 9Q9  CONST_09  C7   C8   N9   C4     0.00   0.0  0
 9Q9  CONST_10  N9   C4   N5   C6     0.00   0.0  0
 9Q9  CONST_11  N5   C4   N9   C8     0.00   0.0  0
 9Q9  CONST_12  O15  C8   N9   C4   180.00   0.0  0
 9Q9  CONST_13  N3   C4   N5   C6   180.00   0.0  0
 9Q9  CONST_14  N3   C4   N9   C8   180.00   0.0  0
 9Q9  CONST_15  H1   C12  C7   C6   180.00   0.0  0
 9Q9  CONST_16  H5   N9   C8   C7   180.00   0.0  0
 9Q9  CONST_17  C22  N21  C1   C2   180.00   0.0  0
 9Q9  CONST_18  C25  N21  C1   C2     0.00   0.0  0
 9Q9  CONST_19  C22  N21  C1   O14    0.00   0.0  0
 9Q9  CONST_20  C25  N21  C1   O14  180.00   0.0  0
 9Q9  CONST_21  N5   C4   N3   C2     0.00   0.0  0
 9Q9  CONST_22  N9   C4   N3   C2   180.00   0.0  0
 9Q9  CONST_23  H2   N3   C4   N5   180.00   0.0  0
 9Q9  Var_01    C18  C17  C16  C13   41.69  30.0  1
 9Q9  Var_02    C17  C18  C19  C13   19.70  30.0  1
 9Q9  Var_03    C19  C18  C17  C16  -38.12  30.0  1
 9Q9  Var_04    C24  C23  C22  N21  -29.47  30.0  1
 9Q9  Var_05    C24  C25  N21  C22   15.43  30.0  1
 9Q9  Var_06    C25  N21  C22  C23    8.80  30.0  1

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
 9Q9  chir_01  C13  C16  C19  N10  positiv
 9Q9  chir_02  C2   N3   C1   C20  negativ
 9Q9  chir_03  C24  F26  C23  C25  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
 9Q9  plan-1  C1   0.020
 9Q9  plan-1  C2   0.020
 9Q9  plan-1  O14  0.020
 9Q9  plan-1  N21  0.020
 9Q9  plan-1  C22  0.020
 9Q9  plan-1  C25  0.020
 9Q9  plan-2  C4   0.020
 9Q9  plan-2  C6   0.020
 9Q9  plan-2  C7   0.020
 9Q9  plan-2  C8   0.020
 9Q9  plan-2  C12  0.020
 9Q9  plan-2  N3   0.020
 9Q9  plan-2  C13  0.020
 9Q9  plan-2  C2   0.020
 9Q9  plan-2  N5   0.020
 9Q9  plan-2  N9   0.020
 9Q9  plan-2  N10  0.020
 9Q9  plan-2  N11  0.020
 9Q9  plan-2  O15  0.020
 9Q9  plan-2  H1   0.020
 9Q9  plan-2  H2   0.020
 9Q9  plan-2  H5   0.020

