# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 07:53:43 2021
#   Inital geometry file: a 127 line input string
#   Ligand name: 4-[5-[2,6-bis(fluoranyl)phenyl]-2~{H}-pyrazolo[3,4-b]pyridin-3-yl]-2-(4-oxidanylpiperidin-1-yl)-1~{H}-pyrimidin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1CCN(CC1)C2=NC(=CC(=O)N2)c3[nH]nc4ncc(cc34)c5c(F)cccc5F
#
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
 SJS  SJS  4-[5-[2,6-bis(fluoranyl)phenyl]-2~{H}-pyrazolo[3,4-b]pyridin-3-yl]-2-(4-oxidanylpiperidin-1-yl)-1~{H}-pyrimidin-6-one  ligand  49  31  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SJS
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
 SJS  C4   C  CR6   0  -0.371  -31.5416  20.7743  -14.3080
 SJS  C5   C  CR6   0   0.544  -31.8435  21.6216  -13.2471
 SJS  C6   C  CR16  0  -0.418  -32.8591  21.3761  -12.3452
 SJS  C8   C  CR6   0   0.007  -30.4455  21.0521  -15.2545
 SJS  C10  C  CR56  0  -0.142  -28.1870  21.4930  -15.7947
 SJS  N12  N  NR15  0  -0.493  -26.5099  21.8328  -17.1252
 SJS  C15  C  CR56  0   0.354  -28.5737  21.5086  -17.1588
 SJS  C17  C  CR16  0  -0.080  -30.7223  21.1218  -16.6555
 SJS  C20  C  CR6   0   0.552  -23.6445  21.7173  -13.7777
 SJS  C24  C  CR6   0   0.794  -25.6608  22.1452  -12.4853
 SJS  C28  C  CH2   0  -0.470  -26.1560  20.7554   -9.5217
 SJS  C1   C  CR16  0  -0.232  -33.6183  20.2257  -12.5021
 SJS  C11  C  CR5   0   0.374  -26.8085  21.7138  -15.8234
 SJS  C18  C  CR6   0   0.287  -25.8514  21.8007  -14.7297
 SJS  C19  C  CR16  0  -0.511  -24.5094  21.6152  -14.9109
 SJS  C2   C  CR16  0  -0.418  -33.3607  19.3414  -13.5393
 SJS  C27  C  CH2   0  -0.366  -25.5878  22.0821  -10.0156
 SJS  C29  C  CH1   0   0.074  -27.6778  20.8257   -9.4102
 SJS  C3   C  CR6   0   0.551  -32.3324  19.6353  -14.4113
 SJS  C30  C  CH2   0  -0.474  -28.2866  21.2794  -10.7287
 SJS  C31  C  CH2   0  -0.344  -27.6461  22.5893  -11.1720
 SJS  C9   C  CR16  0  -0.240  -29.1606  21.2447  -14.8167
 SJS  F33  F  F     0  -0.299  -32.0634  18.7757  -15.4026
 SJS  F7   F  F     0  -0.299  -31.1118  22.7340  -13.1013
 SJS  N13  N  N     0  -0.271  -27.5283  21.7238  -17.9584
 SJS  N16  N  N     0  -0.416  -29.8377  21.3338  -17.5891
 SJS  N22  N  NR16  0  -0.736  -24.3157  21.9856  -12.5855
 SJS  N25  N  N     0  -0.549  -26.4335  22.0509  -13.5399
 SJS  N26  N  NT    0  -0.487  -26.1999  22.4440  -11.2880
 SJS  O32  O  OH1   0  -0.670  -28.2441  19.5825   -9.0634
 SJS  H1   H  HCR6  0   0.288  -33.0526  22.0735  -11.5413
 SJS  H2   H  HNR5  0   0.439  -25.5960  22.0317  -17.5088
 SJS  H3   H  HCR6  0   0.268  -31.7491  21.0007  -16.9858
 SJS  H4   H  HCH2  0   0.237  -25.8717  19.9563  -10.2136
 SJS  H5   H  HCH2  0   0.253  -25.7148  20.5199   -8.5494
 SJS  H6   H  HCR6  0   0.284  -34.4173  20.0149  -11.8050
 SJS  H7   H  HCR6  0   0.268  -24.0749  21.3716  -15.8698
 SJS  H8   H  HCR6  0   0.288  -33.9404  18.4369  -13.6630
 SJS  H9   H  HCH2  0   0.269  -24.5036  22.0340  -10.0788
 SJS  H10  H  HCH2  0   0.269  -25.8084  22.8810   -9.3038
 SJS  H11  H  HCH1  0   0.198  -27.9213  21.5867   -8.6515
 SJS  H12  H  HCH2  0   0.250  -29.3644  21.4220  -10.6194
 SJS  H13  H  HCH2  0   0.235  -28.1291  20.5147  -11.4971
 SJS  H14  H  HCH2  0   0.261  -27.8295  23.3672  -10.4262
 SJS  H15  H  HCH2  0   0.280  -28.0587  22.9383  -12.1130
 SJS  H16  H  HCR6  0   0.275  -28.8937  21.1847  -13.7712
 SJS  H17  H  HNR6  0   0.424  -23.7226  22.1104  -11.7768
 SJS  H18  H  HOH1  0   0.450  -27.9188  19.3353   -8.1919
 SJS  O21  O  O     0  -0.486  -22.4287  21.5933  -13.7708

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
 SJS  N13  C15  aromatic  1.334  0.020  1.334
 SJS  N13  N12  aromatic  1.320  0.020  1.320
 SJS  N16  C15  aromatic  1.347  0.020  1.347
 SJS  N16  C17  aromatic  1.303  0.020  1.303
 SJS  C15  C10  aromatic  1.418  0.020  1.418
 SJS  N12  C11  aromatic  1.341  0.020  1.341
 SJS  C17  C8   aromatic  1.430  0.020  1.430
 SJS  C10  C11  aromatic  1.396  0.020  1.396
 SJS  C10  C9   aromatic  1.402  0.020  1.402
 SJS  C11  C18  single    1.456  0.020  1.456
 SJS  F33  C3   single    1.339  0.020  1.339
 SJS  C8   C9   aromatic  1.371  0.020  1.371
 SJS  C8   C4   single    1.475  0.020  1.475
 SJS  C19  C18  double    1.367  0.020  1.367
 SJS  C19  C20  single    1.429  0.020  1.429
 SJS  C18  N25  single    1.348  0.020  1.348
 SJS  C3   C4   aromatic  1.390  0.020  1.390
 SJS  C3   C2   aromatic  1.380  0.020  1.380
 SJS  C4   C5   aromatic  1.391  0.020  1.391
 SJS  O21  C20  double    1.222  0.020  1.222
 SJS  C20  N22  single    1.394  0.020  1.394
 SJS  C2   C1   aromatic  1.387  0.020  1.387
 SJS  N25  C24  double    1.311  0.020  1.311
 SJS  C5   F7   single    1.339  0.020  1.339
 SJS  C5   C6   aromatic  1.380  0.020  1.380
 SJS  N22  C24  single    1.358  0.020  1.358
 SJS  C24  N26  single    1.347  0.020  1.347
 SJS  C1   C6   aromatic  1.387  0.020  1.387
 SJS  N26  C31  single    1.458  0.020  1.458
 SJS  N26  C27  single    1.458  0.020  1.458
 SJS  C31  C30  single    1.524  0.020  1.524
 SJS  C30  C29  single    1.521  0.020  1.521
 SJS  C27  C28  single    1.525  0.020  1.525
 SJS  C28  C29  single    1.528  0.020  1.528
 SJS  C29  O32  single    1.409  0.020  1.409
 SJS  C6   H1   single    0.930  0.020  1.080
 SJS  N12  H2   single    0.860  0.020  1.020
 SJS  C17  H3   single    0.930  0.020  1.080
 SJS  C28  H4   single    0.970  0.020  1.090
 SJS  C28  H5   single    0.970  0.020  1.090
 SJS  C1   H6   single    0.930  0.020  1.080
 SJS  C19  H7   single    0.930  0.020  1.080
 SJS  C2   H8   single    0.930  0.020  1.080
 SJS  C27  H9   single    0.970  0.020  1.090
 SJS  C27  H10  single    0.970  0.020  1.090
 SJS  C29  H11  single    0.970  0.020  1.090
 SJS  C30  H12  single    0.970  0.020  1.090
 SJS  C30  H13  single    0.970  0.020  1.090
 SJS  C31  H14  single    0.970  0.020  1.090
 SJS  C31  H15  single    0.970  0.020  1.090
 SJS  C9   H16  single    0.930  0.020  1.080
 SJS  N22  H17  single    0.860  0.020  1.020
 SJS  O32  H18  single    0.850  0.020  0.980

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
 SJS  C3   C4   C8   121.96  3.000
 SJS  C3   C4   C5   115.61  3.000
 SJS  C8   C4   C5   122.42  3.000
 SJS  F7   C5   C6   118.59  3.000
 SJS  C6   C5   C4   123.35  3.000
 SJS  F7   C5   C4   118.06  3.000
 SJS  H1   C6   C1   121.39  3.000
 SJS  H1   C6   C5   120.17  3.000
 SJS  C1   C6   C5   118.45  3.000
 SJS  C9   C8   C17  119.17  3.000
 SJS  C9   C8   C4   121.21  3.000
 SJS  C17  C8   C4   119.62  3.000
 SJS  C9   C10  C11  136.70  3.000
 SJS  C9   C10  C15  118.92  3.000
 SJS  C11  C10  C15  104.34  3.000
 SJS  H2   N12  N13  118.30  3.000
 SJS  H2   N12  C11  125.96  3.000
 SJS  N13  N12  C11  115.69  3.000
 SJS  N16  C15  N13  124.41  3.000
 SJS  N16  C15  C10  124.19  3.000
 SJS  N13  C15  C10  111.40  3.000
 SJS  H3   C17  N16  116.24  3.000
 SJS  H3   C17  C8   118.41  3.000
 SJS  N16  C17  C8   125.34  3.000
 SJS  O21  C20  N22  119.58  3.000
 SJS  N22  C20  C19  113.60  3.000
 SJS  O21  C20  C19  126.81  3.000
 SJS  N26  C24  N25  119.69  3.000
 SJS  N26  C24  N22  119.22  3.000
 SJS  N25  C24  N22  121.07  3.000
 SJS  H5   C28  H4   107.46  3.000
 SJS  H5   C28  C29  110.30  3.000
 SJS  H4   C28  C29  109.79  3.000
 SJS  H5   C28  C27  108.96  3.000
 SJS  H4   C28  C27  109.48  3.000
 SJS  C29  C28  C27  110.77  3.000
 SJS  H6   C1   C2   119.67  3.000
 SJS  H6   C1   C6   119.56  3.000
 SJS  C2   C1   C6   120.77  3.000
 SJS  C18  C11  N12  125.28  3.000
 SJS  C18  C11  C10  130.01  3.000
 SJS  N12  C11  C10  104.70  3.000
 SJS  N25  C18  C19  124.49  3.000
 SJS  N25  C18  C11  112.97  3.000
 SJS  C19  C18  C11  122.53  3.000
 SJS  H7   C19  C18  122.90  3.000
 SJS  H7   C19  C20  118.45  3.000
 SJS  C18  C19  C20  118.64  3.000
 SJS  H8   C2   C3   120.35  3.000
 SJS  H8   C2   C1   121.28  3.000
 SJS  C3   C2   C1   118.37  3.000
 SJS  H10  C27  H9   105.76  3.000
 SJS  H10  C27  N26  107.60  3.000
 SJS  H9   C27  N26  112.27  3.000
 SJS  H10  C27  C28  110.48  3.000
 SJS  H9   C27  C28  110.60  3.000
 SJS  N26  C27  C28  110.01  3.000
 SJS  H11  C29  O32  110.55  3.000
 SJS  H11  C29  C30  107.60  3.000
 SJS  O32  C29  C30  108.39  3.000
 SJS  H11  C29  C28  107.59  3.000
 SJS  O32  C29  C28  112.19  3.000
 SJS  C30  C29  C28  110.43  3.000
 SJS  F33  C3   C2   118.73  3.000
 SJS  C2   C3   C4   123.46  3.000
 SJS  F33  C3   C4   117.81  3.000
 SJS  H13  C30  H12  107.65  3.000
 SJS  H13  C30  C31  109.60  3.000
 SJS  H12  C30  C31  109.35  3.000
 SJS  H13  C30  C29  110.01  3.000
 SJS  H12  C30  C29  110.30  3.000
 SJS  C31  C30  C29  109.89  3.000
 SJS  H15  C31  H14  107.40  3.000
 SJS  H15  C31  N26  109.89  3.000
 SJS  H14  C31  N26  106.95  3.000
 SJS  H15  C31  C30  111.65  3.000
 SJS  H14  C31  C30  110.04  3.000
 SJS  N26  C31  C30  110.75  3.000
 SJS  H16  C9   C10  120.87  3.000
 SJS  H16  C9   C8   122.18  3.000
 SJS  C10  C9   C8   116.93  3.000
 SJS  C15  N13  N12  103.86  3.000
 SJS  C17  N16  C15  115.42  3.000
 SJS  H17  N22  C24  120.51  3.000
 SJS  H17  N22  C20  115.18  3.000
 SJS  C24  N22  C20  124.23  3.000
 SJS  C18  N25  C24  117.96  3.000
 SJS  C31  N26  C27  111.83  3.000
 SJS  C27  N26  C24  123.57  3.000
 SJS  C31  N26  C24  119.34  3.000
 SJS  H18  O32  C29  108.27  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
 SJS  CONST_01  N16  C17  C8   C4   180.00   0.0  0
 SJS  CONST_02  C10  C9   C8   C4   180.00   0.0  0
 SJS  CONST_03  C1   C2   C3   C4     0.00   0.0  0
 SJS  CONST_04  C1   C6   C5   C4     0.00   0.0  0
 SJS  CONST_07  C2   C3   C4   C5     0.00   0.0  0
 SJS  CONST_08  C2   C1   C6   C5     0.00   0.0  0
 SJS  CONST_09  C8   C4   C5   C6   180.00   0.0  0
 SJS  CONST_10  C3   C4   C5   C6     0.00   0.0  0
 SJS  CONST_11  C3   C2   C1   C6     0.00   0.0  0
 SJS  CONST_12  C15  N16  C17  C8     0.00   0.0  0
 SJS  CONST_13  C15  C10  C9   C8     0.00   0.0  0
 SJS  CONST_14  C11  C10  C9   C8   180.00   0.0  0
 SJS  CONST_15  C2   C3   C4   C8   180.00   0.0  0
 SJS  CONST_16  N12  N13  C15  C10    0.00   0.0  0
 SJS  CONST_17  C17  N16  C15  C10    0.00   0.0  0
 SJS  CONST_18  N13  N12  C11  C10    0.00   0.0  0
 SJS  CONST_19  C17  C8   C9   C10    0.00   0.0  0
 SJS  CONST_20  N16  C15  N13  N12  180.00   0.0  0
 SJS  CONST_21  C15  C10  C11  N12    0.00   0.0  0
 SJS  CONST_22  C9   C10  C11  N12  180.00   0.0  0
 SJS  CONST_23  C11  N12  N13  C15    0.00   0.0  0
 SJS  CONST_24  N13  C15  N16  C17  180.00   0.0  0
 SJS  CONST_26  N13  C15  C10  C11    0.00   0.0  0
 SJS  CONST_27  N16  C15  C10  C11  180.00   0.0  0
 SJS  CONST_29  N13  C15  C10  C9   180.00   0.0  0
 SJS  CONST_30  N16  C15  C10  C9     0.00   0.0  0
 SJS  CONST_31  N16  C17  C8   C9     0.00   0.0  0
 SJS  CONST_32  C18  C11  C10  C15  180.00   0.0  0
 SJS  CONST_33  N13  N12  C11  C18  180.00   0.0  0
 SJS  CONST_34  C9   C10  C11  C18    0.00   0.0  0
 SJS  CONST_35  N25  C24  N22  C20    0.00   0.0  0
 SJS  CONST_36  N26  C24  N22  C20  180.00   0.0  0
 SJS  CONST_37  C19  C20  N22  C24    0.00   0.0  0
 SJS  CONST_38  N22  C24  N25  C18    0.00   0.0  0
 SJS  CONST_39  N26  C24  N25  C18  180.00   0.0  0
 SJS  CONST_42  N25  C24  N26  C31    0.00   0.0  0
 SJS  CONST_43  N22  C24  N26  C31  180.00   0.0  0
 SJS  CONST_44  F33  C3   C4   C5   180.00   0.0  0
 SJS  CONST_45  F33  C3   C4   C8     0.00   0.0  0
 SJS  CONST_46  F7   C5   C4   C8     0.00   0.0  0
 SJS  CONST_47  F33  C3   C2   C1   180.00   0.0  0
 SJS  CONST_48  F7   C5   C6   C1   180.00   0.0  0
 SJS  CONST_49  F7   C5   C4   C3   180.00   0.0  0
 SJS  CONST_50  O21  C20  N22  C24  180.00   0.0  0
 SJS  CONST_51  H3   C17  C8   C4     0.00   0.0  0
 SJS  CONST_52  H16  C9   C8   C4     0.00   0.0  0
 SJS  CONST_53  H8   C2   C3   C4   180.00   0.0  0
 SJS  CONST_54  H1   C6   C5   C4   180.00   0.0  0
 SJS  CONST_55  H6   C1   C6   C5   180.00   0.0  0
 SJS  CONST_56  H2   N12  C11  C10  180.00   0.0  0
 SJS  CONST_57  H17  N22  C20  C19  180.00   0.0  0
 SJS  Var_01    C19  C18  C11  C10  159.49  30.0  2
 SJS  Var_02    C30  C31  N26  C24   94.40  30.0  1
 SJS  Var_03    C28  C27  N26  C24  -94.02  30.0  1
 SJS  Var_04    N26  C31  C30  C29   57.06  30.0  1
 SJS  Var_05    N26  C27  C28  C29  -56.30  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
 SJS  chir_01  C29  C30  C28  O32  positiv

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
 SJS  plan-1  C4   0.020
 SJS  plan-1  C5   0.020
 SJS  plan-1  C6   0.020
 SJS  plan-1  C8   0.020
 SJS  plan-1  C1   0.020
 SJS  plan-1  C2   0.020
 SJS  plan-1  C3   0.020
 SJS  plan-1  F33  0.020
 SJS  plan-1  F7   0.020
 SJS  plan-1  H1   0.020
 SJS  plan-1  H6   0.020
 SJS  plan-1  H8   0.020
 SJS  plan-2  C4   0.020
 SJS  plan-2  C8   0.020
 SJS  plan-2  C10  0.020
 SJS  plan-2  N12  0.020
 SJS  plan-2  C15  0.020
 SJS  plan-2  C17  0.020
 SJS  plan-2  C11  0.020
 SJS  plan-2  C18  0.020
 SJS  plan-2  C9   0.020
 SJS  plan-2  N13  0.020
 SJS  plan-2  N16  0.020
 SJS  plan-2  H2   0.020
 SJS  plan-2  H3   0.020
 SJS  plan-2  H16  0.020
 SJS  plan-3  C20  0.020
 SJS  plan-3  C24  0.020
 SJS  plan-3  C11  0.020
 SJS  plan-3  C18  0.020
 SJS  plan-3  C19  0.020
 SJS  plan-3  C27  0.020
 SJS  plan-3  C31  0.020
 SJS  plan-3  N22  0.020
 SJS  plan-3  N25  0.020
 SJS  plan-3  N26  0.020
 SJS  plan-3  H7   0.020
 SJS  plan-3  H17  0.020
 SJS  plan-3  O21  0.020

