# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 08:21:06 2021
#   Inital geometry file: a 123 line input string
#   Ligand name: 3-[(2-fluorophenyl)methyl]-5-(1-piperidin-4-ylpyrazol-4-yl)-1~{H}-pyrrolo[2,3-b]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccccc1Cc2c[nH]c3ncc(cc23)c4cnn(c4)C5CCNCC5
#
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
 SWK  SWK  3-[(2-fluorophenyl)methyl]-5-(1-piperidin-4-ylpyrazol-4-yl)-1~{H}-pyrrolo[2,3-b]pyridine  ligand  50  28  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SWK
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
 SWK  C1   C  CR16  0  -0.406  194.6006  -32.0741  80.0215
 SWK  C2   C  CR16  0  -0.253  193.4022  -31.9329  80.7089
 SWK  C3   C  CR16  0  -0.257  193.3725  -32.0804  82.0883
 SWK  C7   C  CR5   0  -0.056  197.8784  -31.5861  83.0519
 SWK  C8   C  CR15  0  -0.033  197.5359  -30.2803  82.8422
 SWK  C9   C  CR56  0   0.460  199.6288  -30.2113  83.5833
 SWK  C10  C  CR16  0  -0.146  201.6762  -30.7038  84.3337
 SWK  C11  C  CR6   0  -0.013  201.4117  -32.0873  84.3392
 SWK  C12  C  CR16  0  -0.320  200.1553  -32.5200  83.9274
 SWK  C13  C  CR56  0   0.019  199.2266  -31.5649  83.5301
 SWK  C14  C  CR5   0  -0.167  202.4462  -33.0317  84.7543
 SWK  C15  C  CR15  0  -0.090  202.5842  -34.3879  84.3972
 SWK  C16  C  CR15  0   0.024  203.5314  -32.8067  85.5808
 SWK  C19  C  CH2   0  -0.323  206.7286  -35.5712  88.0182
 SWK  C20  C  CH2   0  -0.323  207.9220  -34.5900  86.1742
 SWK  C21  C  CH2   0  -0.438  206.6264  -34.3482  85.3999
 SWK  C    C  CR6   0   0.521  195.7456  -32.3601  80.7381
 SWK  C5   C  CR6   0  -0.102  195.7582  -32.5202  82.1161
 SWK  C4   C  CR16  0  -0.282  194.5428  -32.3715  82.7771
 SWK  C6   C  CH2   0  -0.562  197.0310  -32.8059  82.8608
 SWK  N    N  NR15  0  -0.673  198.5824  -29.4548  83.1608
 SWK  N1   N  N     0  -0.417  200.8134  -29.7695  83.9718
 SWK  N3   N  NR5   0  -0.286  204.2108  -33.9624  85.6665
 SWK  N2   N  N     0  -0.282  203.6527  -34.9302  84.9497
 SWK  C17  C  CH1   0  -0.066  205.4627  -34.1847  86.3717
 SWK  N4   N  NH1   0  -0.574  207.8538  -35.6997  87.1084
 SWK  C18  C  CH2   0  -0.442  205.3804  -35.3721  87.3229
 SWK  H1   H  HCR6  0   0.277  194.6455  -31.9661  78.9456
 SWK  H2   H  HCR6  0   0.266  192.4964  -31.7075  80.1620
 SWK  H3   H  HCR6  0   0.260  192.4417  -31.9705  82.6286
 SWK  H4   H  HCR5  0   0.285  196.6082  -29.8648  82.4820
 SWK  H5   H  HCR6  0   0.249  202.6565  -30.3508  84.6371
 SWK  H6   H  HCR6  0   0.253  199.9050  -33.5746  83.9262
 SWK  H7   H  HCR5  0   0.257  201.9501  -34.9746  83.7488
 SWK  H8   H  HCR5  0   0.290  203.8513  -31.9241  86.1120
 SWK  H10  H  HCH2  0   0.220  206.9206  -34.7204  88.6813
 SWK  H11  H  HCH2  0   0.243  208.7426  -34.7642  85.4760
 SWK  H12  H  HCH2  0   0.220  208.1806  -33.6849  86.7347
 SWK  H13  H  HCH2  0   0.230  206.4317  -35.1938  84.7335
 SWK  H14  H  HCH2  0   0.240  206.7214  -33.4570  84.7741
 SWK  H15  H  HCR6  0   0.261  194.5181  -32.4871  83.8540
 SWK  H16  H  HCH2  0   0.264  196.7770  -33.2339  83.8350
 SWK  H17  H  HCH2  0   0.260  197.6112  -33.5751  82.3434
 SWK  H18  H  HNR5  0   0.409  198.5780  -28.4512  83.0838
 SWK  H19  H  HCH1  0   0.254  205.6247  -33.2784  86.9626
 SWK  H20  H  HNH1  0   0.341  207.7605  -36.5644  86.5874
 SWK  H22  H  HCH2  0   0.240  204.5955  -35.2061  88.0652
 SWK  H23  H  HCH2  0   0.232  205.1162  -36.2747  86.7660
 SWK  F    F  F     0  -0.310  196.9047  -32.4913  80.0686
 SWK  H9   H  HCH2  0   0.244  206.6874  -36.4556  88.6560

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
 SWK  F    C    single    1.345  0.020  1.345
 SWK  C1   C    aromatic  1.381  0.020  1.381
 SWK  C1   C2   aromatic  1.389  0.020  1.389
 SWK  C    C5   aromatic  1.387  0.020  1.387
 SWK  C2   C3   aromatic  1.388  0.020  1.388
 SWK  C5   C4   aromatic  1.392  0.020  1.392
 SWK  C5   C6   single    1.502  0.020  1.502
 SWK  C3   C4   aromatic  1.389  0.020  1.389
 SWK  C6   C7   single    1.498  0.020  1.498
 SWK  C8   C7   aromatic  1.366  0.020  1.366
 SWK  C8   N    aromatic  1.370  0.020  1.370
 SWK  C7   C13  aromatic  1.431  0.020  1.431
 SWK  N    C9   aromatic  1.359  0.020  1.359
 SWK  C13  C9   aromatic  1.413  0.020  1.413
 SWK  C13  C12  aromatic  1.390  0.020  1.390
 SWK  C9   N1   aromatic  1.323  0.020  1.323
 SWK  C12  C11  aromatic  1.391  0.020  1.391
 SWK  C15  C14  aromatic  1.409  0.020  1.409
 SWK  C15  N2   aromatic  1.319  0.020  1.319
 SWK  N1   C10  aromatic  1.322  0.020  1.322
 SWK  C11  C10  aromatic  1.409  0.020  1.409
 SWK  C11  C14  single    1.461  0.020  1.461
 SWK  C14  C16  aromatic  1.383  0.020  1.383
 SWK  N2   N3   aromatic  1.327  0.020  1.327
 SWK  C21  C17  single    1.525  0.020  1.525
 SWK  C21  C20  single    1.529  0.020  1.529
 SWK  C16  N3   aromatic  1.343  0.020  1.343
 SWK  N3   C17  single    1.454  0.020  1.454
 SWK  C17  C18  single    1.524  0.020  1.524
 SWK  C20  N4   single    1.452  0.020  1.452
 SWK  N4   C19  single    1.453  0.020  1.453
 SWK  C18  C19  single    1.530  0.020  1.530
 SWK  C1   H1   single    0.930  0.020  1.080
 SWK  C2   H2   single    0.930  0.020  1.080
 SWK  C3   H3   single    0.930  0.020  1.080
 SWK  C8   H4   single    0.930  0.020  1.080
 SWK  C10  H5   single    0.930  0.020  1.080
 SWK  C12  H6   single    0.930  0.020  1.080
 SWK  C15  H7   single    0.930  0.020  1.080
 SWK  C16  H8   single    0.930  0.020  1.080
 SWK  C19  H9   single    0.970  0.020  1.090
 SWK  C19  H10  single    0.970  0.020  1.090
 SWK  C20  H11  single    0.970  0.020  1.090
 SWK  C20  H12  single    0.970  0.020  1.090
 SWK  C21  H13  single    0.970  0.020  1.090
 SWK  C21  H14  single    0.970  0.020  1.090
 SWK  C4   H15  single    0.930  0.020  1.080
 SWK  C6   H16  single    0.970  0.020  1.090
 SWK  C6   H17  single    0.970  0.020  1.090
 SWK  N    H18  single    0.860  0.020  1.020
 SWK  C17  H19  single    0.970  0.020  1.090
 SWK  N4   H20  single    0.890  0.020  1.040
 SWK  C18  H22  single    0.970  0.020  1.090
 SWK  C18  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
 SWK  H1   C1   C    120.15  3.000
 SWK  H1   C1   C2   121.18  3.000
 SWK  C    C1   C2   118.67  3.000
 SWK  H2   C2   C3   120.45  3.000
 SWK  H2   C2   C1   119.57  3.000
 SWK  C3   C2   C1   119.98  3.000
 SWK  H3   C3   C4   119.91  3.000
 SWK  H3   C3   C2   120.27  3.000
 SWK  C4   C3   C2   119.82  3.000
 SWK  C6   C7   C13  126.02  3.000
 SWK  C13  C7   C8   105.86  3.000
 SWK  C6   C7   C8   128.11  3.000
 SWK  H4   C8   N    120.16  3.000
 SWK  H4   C8   C7   129.43  3.000
 SWK  N    C8   C7   110.41  3.000
 SWK  N1   C9   N    126.52  3.000
 SWK  N1   C9   C13  125.87  3.000
 SWK  N    C9   C13  107.61  3.000
 SWK  H5   C10  N1   115.86  3.000
 SWK  H5   C10  C11  119.21  3.000
 SWK  N1   C10  C11  124.93  3.000
 SWK  C14  C11  C12  121.51  3.000
 SWK  C14  C11  C10  120.20  3.000
 SWK  C12  C11  C10  118.29  3.000
 SWK  H6   C12  C13  120.92  3.000
 SWK  H6   C12  C11  120.77  3.000
 SWK  C13  C12  C11  118.31  3.000
 SWK  C12  C13  C9   117.20  3.000
 SWK  C12  C13  C7   135.64  3.000
 SWK  C9   C13  C7   107.16  3.000
 SWK  C16  C14  C15  103.37  3.000
 SWK  C16  C14  C11  128.35  3.000
 SWK  C15  C14  C11  128.27  3.000
 SWK  H7   C15  N2   120.24  3.000
 SWK  H7   C15  C14  128.12  3.000
 SWK  N2   C15  C14  111.63  3.000
 SWK  H8   C16  N3   121.51  3.000
 SWK  H8   C16  C14  131.33  3.000
 SWK  N3   C16  C14  107.16  3.000
 SWK  H10  C19  H9   106.39  3.000
 SWK  H10  C19  C18  109.17  3.000
 SWK  H9   C19  C18  109.75  3.000
 SWK  H10  C19  N4   108.18  3.000
 SWK  H9   C19  N4   108.88  3.000
 SWK  C18  C19  N4   114.17  3.000
 SWK  H12  C20  H11  106.36  3.000
 SWK  H12  C20  N4   108.25  3.000
 SWK  H11  C20  N4   108.95  3.000
 SWK  H12  C20  C21  109.18  3.000
 SWK  H11  C20  C21  109.78  3.000
 SWK  N4   C20  C21  114.01  3.000
 SWK  H14  C21  H13  107.28  3.000
 SWK  H14  C21  C17  110.10  3.000
 SWK  H13  C21  C17  109.58  3.000
 SWK  H14  C21  C20  110.20  3.000
 SWK  H13  C21  C20  109.70  3.000
 SWK  C17  C21  C20  109.93  3.000
 SWK  C5   C    F    118.38  3.000
 SWK  C5   C    C1   123.16  3.000
 SWK  F    C    C1   118.46  3.000
 SWK  C6   C5   C4   121.67  3.000
 SWK  C6   C5   C    121.47  3.000
 SWK  C4   C5   C    116.84  3.000
 SWK  H15  C4   C5   118.73  3.000
 SWK  H15  C4   C3   119.75  3.000
 SWK  C5   C4   C3   121.52  3.000
 SWK  H17  C6   H16  105.62  3.000
 SWK  H17  C6   C5   110.42  3.000
 SWK  H16  C6   C5   108.61  3.000
 SWK  H17  C6   C7   109.45  3.000
 SWK  H16  C6   C7   109.66  3.000
 SWK  C5   C6   C7   112.82  3.000
 SWK  H18  N    C9   125.62  3.000
 SWK  H18  N    C8   125.41  3.000
 SWK  C9   N    C8   108.96  3.000
 SWK  C10  N1   C9   115.39  3.000
 SWK  C17  N3   N2   120.83  3.000
 SWK  C17  N3   C16  126.72  3.000
 SWK  N2   N3   C16  112.35  3.000
 SWK  N3   N2   C15  105.48  3.000
 SWK  H19  C17  C18  108.45  3.000
 SWK  H19  C17  N3   105.24  3.000
 SWK  C18  C17  N3   112.05  3.000
 SWK  H19  C17  C21  108.67  3.000
 SWK  C18  C17  C21  110.82  3.000
 SWK  N3   C17  C21  111.37  3.000
 SWK  H20  N4   C20  108.99  3.000
 SWK  H20  N4   C19  109.02  3.000
 SWK  C20  N4   C19  111.82  3.000
 SWK  H23  C18  H22  107.33  3.000
 SWK  H23  C18  C17  109.79  3.000
 SWK  H22  C18  C17  110.15  3.000
 SWK  H23  C18  C19  109.70  3.000
 SWK  H22  C18  C19  110.12  3.000
 SWK  C17  C18  C19  109.73  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
 SWK  CONST_01  C4   C5   C    C1     0.00   0.0  0
 SWK  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 SWK  CONST_03  C5   C    C1   C2     0.00   0.0  0
 SWK  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 SWK  CONST_05  C    C1   C2   C3     0.00   0.0  0
 SWK  CONST_06  C    C5   C4   C3     0.00   0.0  0
 SWK  CONST_07  C9   N    C8   C7     0.00   0.0  0
 SWK  CONST_08  N    C9   C13  C7     0.00   0.0  0
 SWK  CONST_09  N1   C9   C13  C7   180.00   0.0  0
 SWK  CONST_10  C11  C12  C13  C7   180.00   0.0  0
 SWK  CONST_11  C9   C13  C7   C8     0.00   0.0  0
 SWK  CONST_12  C12  C13  C7   C8   180.00   0.0  0
 SWK  CONST_13  C13  C9   N    C8     0.00   0.0  0
 SWK  CONST_14  N1   C9   N    C8   180.00   0.0  0
 SWK  CONST_15  C11  C12  C13  C9     0.00   0.0  0
 SWK  CONST_16  C11  C10  N1   C9     0.00   0.0  0
 SWK  CONST_17  N    C9   N1   C10  180.00   0.0  0
 SWK  CONST_18  C13  C9   N1   C10    0.00   0.0  0
 SWK  CONST_19  C13  C12  C11  C10    0.00   0.0  0
 SWK  CONST_22  N2   C15  C14  C11  180.00   0.0  0
 SWK  CONST_23  N3   C16  C14  C11  180.00   0.0  0
 SWK  CONST_24  N    C9   C13  C12  180.00   0.0  0
 SWK  CONST_25  N1   C9   C13  C12    0.00   0.0  0
 SWK  CONST_26  N1   C10  C11  C12    0.00   0.0  0
 SWK  CONST_29  N    C8   C7   C13    0.00   0.0  0
 SWK  CONST_30  C14  C11  C12  C13  180.00   0.0  0
 SWK  CONST_31  N3   N2   C15  C14    0.00   0.0  0
 SWK  CONST_32  N1   C10  C11  C14  180.00   0.0  0
 SWK  CONST_33  N2   N3   C16  C14    0.00   0.0  0
 SWK  CONST_34  N3   C16  C14  C15    0.00   0.0  0
 SWK  CONST_35  C16  N3   N2   C15    0.00   0.0  0
 SWK  CONST_36  N2   C15  C14  C16    0.00   0.0  0
 SWK  CONST_37  C17  N3   C16  C14  180.00   0.0  0
 SWK  CONST_38  C17  N3   N2   C15  180.00   0.0  0
 SWK  CONST_39  C6   C5   C    C1   180.00   0.0  0
 SWK  CONST_40  F    C    C1   C2   180.00   0.0  0
 SWK  CONST_41  C6   C5   C4   C3   180.00   0.0  0
 SWK  CONST_42  C6   C7   C13  C9   180.00   0.0  0
 SWK  CONST_43  C6   C7   C13  C12    0.00   0.0  0
 SWK  CONST_44  C4   C5   C    F    180.00   0.0  0
 SWK  CONST_45  N    C8   C7   C6   180.00   0.0  0
 SWK  CONST_46  H3   C3   C2   C1   180.00   0.0  0
 SWK  CONST_47  H15  C4   C3   C2   180.00   0.0  0
 SWK  CONST_48  H1   C1   C2   C3   180.00   0.0  0
 SWK  CONST_49  H18  N    C8   C7   180.00   0.0  0
 SWK  CONST_50  H6   C12  C13  C7     0.00   0.0  0
 SWK  CONST_51  H4   C8   N    C9   180.00   0.0  0
 SWK  CONST_52  H5   C10  N1   C9   180.00   0.0  0
 SWK  CONST_53  H7   C15  C14  C11    0.00   0.0  0
 SWK  CONST_54  H8   C16  C14  C11    0.00   0.0  0
 SWK  CONST_55  H2   C2   C1   C    180.00   0.0  0
 SWK  Var_01    C21  C20  N4   C19  -53.49  30.0  1
 SWK  Var_02    C18  C19  N4   C20   53.60  30.0  1
 SWK  Var_03    N4   C20  C21  C17   54.18  30.0  1
 SWK  Var_04    N4   C19  C18  C17  -54.22  30.0  1
 SWK  Var_05    C    C5   C6   C7    77.91  30.0  2
 SWK  Var_06    C5   C6   C7   C8    11.91  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
 SWK  chir_01  C17  C21  N3  C18  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
 SWK  plan-1  C11  0.020
 SWK  plan-1  C14  0.020
 SWK  plan-1  C15  0.020
 SWK  plan-1  C16  0.020
 SWK  plan-1  N3   0.020
 SWK  plan-1  N2   0.020
 SWK  plan-1  C17  0.020
 SWK  plan-1  H7   0.020
 SWK  plan-1  H8   0.020
 SWK  plan-2  C1   0.020
 SWK  plan-2  C2   0.020
 SWK  plan-2  C3   0.020
 SWK  plan-2  C    0.020
 SWK  plan-2  C5   0.020
 SWK  plan-2  C4   0.020
 SWK  plan-2  C6   0.020
 SWK  plan-2  H1   0.020
 SWK  plan-2  H2   0.020
 SWK  plan-2  H3   0.020
 SWK  plan-2  H15  0.020
 SWK  plan-2  F    0.020
 SWK  plan-3  C7   0.020
 SWK  plan-3  C8   0.020
 SWK  plan-3  C9   0.020
 SWK  plan-3  C10  0.020
 SWK  plan-3  C11  0.020
 SWK  plan-3  C12  0.020
 SWK  plan-3  C13  0.020
 SWK  plan-3  C14  0.020
 SWK  plan-3  C6   0.020
 SWK  plan-3  N    0.020
 SWK  plan-3  N1   0.020
 SWK  plan-3  H4   0.020
 SWK  plan-3  H5   0.020
 SWK  plan-3  H6   0.020
 SWK  plan-3  H18  0.020

