# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 00:17:44 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: (2~{S},3~{S})-3-[[5-fluoranyl-2-(5-fluoranyl-1~{H}-pyrazolo[3,4-b]pyridin-3-yl)pyrimidin-4-yl]amino]bicyclo[2.2.2]octane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H]1C2CCC(CC2)[C@@H]1Nc3nc(ncc3F)c4n[nH]c5ncc(F)cc45
#
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
 BYB  BYB  '(2~{S},3~{S})-3-[[5-fluoranyl-2-(5-fluoranyl-1~{H}-pyrazolo[3,4-b]pyridin-3-yl)pyrimidin-4-yl]amino]bicyclo[2.2.2]octane-2-carboxylic acid'  ligand  47  29  .  2022-07-24  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_BYB
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
 BYB  C1   C  CR6   0   0.446   5.8618  -0.1067  -0.6182
 BYB  C2   C  CR16  0  -0.202   6.0591   1.1429  -1.2257
 BYB  C4   C  CR16  0  -0.389   4.6153  -0.5872  -0.3117
 BYB  C5   C  CR56  0  -0.089   3.5520   0.2541  -0.6474
 BYB  C6   C  CR56  0   0.523   3.8582   1.4842  -1.2527
 BYB  N3   N  N     0  -0.408   5.0665   1.9460  -1.5473
 BYB  N7   N  NR15  0  -0.504   2.6729   2.1012  -1.4695
 BYB  N8   N  N     0  -0.222   1.6476   1.3745  -1.0546
 BYB  C9   C  CR5   0   0.150   2.1305   0.2579  -0.5541
 BYB  C10  C  CR6   0   0.355   1.2625  -0.7797   0.0053
 BYB  N11  N  N     0  -0.470  -0.0405  -0.5302   0.0445
 BYB  C12  C  CR6   0   0.446  -0.8455  -1.4514   0.5611
 BYB  C13  C  CR6   0   0.349  -0.2728  -2.6562   1.0239
 BYB  C14  C  CR16  0  -0.176   1.0740  -2.8253   0.9378
 BYB  N15  N  N     0  -0.459   1.8683  -1.8774   0.4239
 BYB  N16  N  NH1   0  -0.683  -2.1622  -1.2301   0.6400
 BYB  C17  C  CH1   0  -0.048  -2.8016   0.0025   0.2397
 BYB  C18  C  CH1   0  -0.253  -3.4572  -0.0789  -1.1467
 BYB  C19  C  CH2   0  -0.450  -4.7555  -0.8808  -1.0655
 BYB  C20  C  CH2   0  -0.436  -5.7841  -0.0883  -0.2307
 BYB  C21  C  CH1   0  -0.248  -5.0689   1.0360   0.5228
 BYB  C22  C  CH1   0  -0.398  -3.8837   0.4156   1.2691
 BYB  F23  F  F     0  -0.308   6.9504  -0.8379  -0.3371
 BYB  F24  F  F     0  -0.301  -1.0684  -3.6038   1.5424
 BYB  C25  C  C     0   0.567  -3.3218   1.2949   2.3592
 BYB  O26  O  O     0  -0.437  -3.8028   2.3361   2.7328
 BYB  O27  O  OH1   0  -0.586  -2.2217   0.7775   2.8952
 BYB  C28  C  CH2   0  -0.444  -3.7750   1.3478  -1.5991
 BYB  C29  C  CH2   0  -0.445  -4.5683   2.0687  -0.4897
 BYB  H1   H  HCR6  0   0.289   7.0674   1.4761  -1.4452
 BYB  H2   H  HCR6  0   0.292   4.4672  -1.5495   0.1574
 BYB  H3   H  HNR5  0   0.425   2.5168   3.0031  -1.8925
 BYB  H4   H  HCR6  0   0.290   1.5390  -3.7394   1.2906
 BYB  H5   H  HNH1  0   0.403  -2.7358  -1.9444   1.0592
 BYB  H6   H  HCH1  0   0.279  -2.0157   0.7592   0.1868
 BYB  H7   H  HCH1  0   0.241  -2.7548  -0.5498  -1.8385
 BYB  H8   H  HCH2  0   0.242  -5.1352  -1.0739  -2.0704
 BYB  H9   H  HCH2  0   0.227  -4.5671  -1.8630  -0.6231
 BYB  H10  H  HCH2  0   0.234  -6.5517   0.3490  -0.8739
 BYB  H11  H  HCH2  0   0.238  -6.3021  -0.7461   0.4706
 BYB  H12  H  HCH1  0   0.241  -5.7525   1.5047   1.2322
 BYB  H13  H  HCH1  0   0.297  -4.2414  -0.4904   1.7776
 BYB  H14  H  HOH1  0   0.480  -1.8878   1.3624   3.5921
 BYB  H15  H  HCH2  0   0.237  -2.8524   1.8851  -1.8305
 BYB  H16  H  HCH2  0   0.234  -4.3494   1.3075  -2.5278
 BYB  H17  H  HCH2  0   0.238  -5.4194   2.6091  -0.9085
 BYB  H18  H  HCH2  0   0.234  -3.9477   2.8145   0.0112

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
 BYB  N8   N7   aromatic  1.323  0.020  1.323
 BYB  N8   C9   aromatic  1.315  0.020  1.315
 BYB  N15  C14  aromatic  1.339  0.020  1.339
 BYB  N15  C10  aromatic  1.322  0.020  1.322
 BYB  C14  C13  aromatic  1.360  0.020  1.360
 BYB  N7   C6   aromatic  1.354  0.020  1.354
 BYB  C9   C10  single    1.464  0.020  1.464
 BYB  C9   C5   aromatic  1.424  0.020  1.424
 BYB  C10  N11  aromatic  1.327  0.020  1.327
 BYB  C13  F24  single    1.342  0.020  1.342
 BYB  C13  C12  aromatic  1.412  0.020  1.412
 BYB  C6   C5   aromatic  1.405  0.020  1.405
 BYB  C6   N3   aromatic  1.327  0.020  1.327
 BYB  C5   C4   aromatic  1.397  0.020  1.397
 BYB  N3   C2   aromatic  1.317  0.020  1.317
 BYB  N11  C12  aromatic  1.328  0.020  1.328
 BYB  C12  N16  single    1.337  0.020  1.337
 BYB  C2   C1   aromatic  1.403  0.020  1.403
 BYB  C4   C1   aromatic  1.371  0.020  1.371
 BYB  N16  C17  single    1.445  0.020  1.445
 BYB  C1   F23  single    1.341  0.020  1.341
 BYB  C17  C18  single    1.536  0.020  1.536
 BYB  C17  C22  single    1.550  0.020  1.550
 BYB  O26  C25  double    1.206  0.020  1.206
 BYB  C25  C22  single    1.509  0.020  1.509
 BYB  C25  O27  single    1.329  0.020  1.329
 BYB  C18  C19  single    1.528  0.020  1.528
 BYB  C18  C28  single    1.530  0.020  1.530
 BYB  C22  C21  single    1.532  0.020  1.532
 BYB  C19  C20  single    1.544  0.020  1.544
 BYB  C28  C29  single    1.543  0.020  1.543
 BYB  C21  C20  single    1.531  0.020  1.531
 BYB  C21  C29  single    1.530  0.020  1.530
 BYB  C2   H1   single    0.930  0.020  1.080
 BYB  C4   H2   single    0.930  0.020  1.080
 BYB  N7   H3   single    0.860  0.020  1.020
 BYB  C14  H4   single    0.930  0.020  1.080
 BYB  N16  H5   single    0.860  0.020  1.020
 BYB  C17  H6   single    0.970  0.020  1.090
 BYB  C18  H7   single    0.970  0.020  1.090
 BYB  C19  H8   single    0.970  0.020  1.090
 BYB  C19  H9   single    0.970  0.020  1.090
 BYB  C20  H10  single    0.970  0.020  1.090
 BYB  C20  H11  single    0.970  0.020  1.090
 BYB  C21  H12  single    0.970  0.020  1.090
 BYB  C22  H13  single    0.970  0.020  1.090
 BYB  O27  H14  single    0.850  0.020  0.980
 BYB  C28  H15  single    0.970  0.020  1.090
 BYB  C28  H16  single    0.970  0.020  1.090
 BYB  C29  H17  single    0.970  0.020  1.090
 BYB  C29  H18  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
 BYB  F23  C1   C4   120.01  3.000
 BYB  F23  C1   C2   117.52  3.000
 BYB  C4   C1   C2   122.47  3.000
 BYB  H1   C2   N3   117.65  3.000
 BYB  H1   C2   C1   119.47  3.000
 BYB  N3   C2   C1   122.88  3.000
 BYB  H2   C4   C5   122.43  3.000
 BYB  H2   C4   C1   122.27  3.000
 BYB  C5   C4   C1   115.30  3.000
 BYB  C9   C5   C6   104.09  3.000
 BYB  C6   C5   C4   117.71  3.000
 BYB  C9   C5   C4   138.20  3.000
 BYB  N7   C6   N3   127.10  3.000
 BYB  N3   C6   C5   126.80  3.000
 BYB  N7   C6   C5   106.10  3.000
 BYB  C6   N3   C2   114.84  3.000
 BYB  H3   N7   N8   120.19  3.000
 BYB  H3   N7   C6   127.62  3.000
 BYB  N8   N7   C6   112.20  3.000
 BYB  C9   N8   N7   107.52  3.000
 BYB  C10  C9   N8   121.96  3.000
 BYB  C10  C9   C5   127.94  3.000
 BYB  N8   C9   C5   110.10  3.000
 BYB  N15  C10  N11  126.63  3.000
 BYB  N11  C10  C9   117.40  3.000
 BYB  N15  C10  C9   115.97  3.000
 BYB  C12  N11  C10  118.44  3.000
 BYB  N16  C12  C13  121.41  3.000
 BYB  N16  C12  N11  120.33  3.000
 BYB  C13  C12  N11  118.26  3.000
 BYB  F24  C13  C14  121.59  3.000
 BYB  F24  C13  C12  119.26  3.000
 BYB  C14  C13  C12  119.14  3.000
 BYB  H4   C14  N15  117.84  3.000
 BYB  H4   C14  C13  120.58  3.000
 BYB  N15  C14  C13  121.57  3.000
 BYB  C14  N15  C10  115.94  3.000
 BYB  H5   N16  C17  117.91  3.000
 BYB  H5   N16  C12  117.88  3.000
 BYB  C17  N16  C12  124.08  3.000
 BYB  H6   C17  C22  110.48  3.000
 BYB  H6   C17  C18  107.47  3.000
 BYB  C22  C17  C18  108.40  3.000
 BYB  H6   C17  N16  106.62  3.000
 BYB  C22  C17  N16  110.63  3.000
 BYB  C18  C17  N16  113.19  3.000
 BYB  H7   C18  C28  110.38  3.000
 BYB  H7   C18  C19  110.71  3.000
 BYB  C28  C18  C19  109.19  3.000
 BYB  H7   C18  C17  108.66  3.000
 BYB  C28  C18  C17  107.83  3.000
 BYB  C19  C18  C17  110.03  3.000
 BYB  H9   C19  H8   105.88  3.000
 BYB  H9   C19  C20  110.92  3.000
 BYB  H8   C19  C20  110.91  3.000
 BYB  H9   C19  C18  110.27  3.000
 BYB  H8   C19  C18  109.84  3.000
 BYB  C20  C19  C18  108.99  3.000
 BYB  H11  C20  H10  106.61  3.000
 BYB  H11  C20  C21  110.36  3.000
 BYB  H10  C20  C21  108.91  3.000
 BYB  H11  C20  C19  110.73  3.000
 BYB  H10  C20  C19  110.80  3.000
 BYB  C21  C20  C19  109.38  3.000
 BYB  H12  C21  C29  110.20  3.000
 BYB  H12  C21  C22  110.00  3.000
 BYB  C29  C21  C22  110.03  3.000
 BYB  H12  C21  C20  110.05  3.000
 BYB  C29  C21  C20  108.83  3.000
 BYB  C22  C21  C20  107.69  3.000
 BYB  H13  C22  C25  105.50  3.000
 BYB  H13  C22  C21  107.91  3.000
 BYB  C25  C22  C21  113.83  3.000
 BYB  H13  C22  C17  108.36  3.000
 BYB  C21  C22  C17  108.94  3.000
 BYB  C25  C22  C17  112.04  3.000
 BYB  O27  C25  O26  122.78  3.000
 BYB  O27  C25  C22  111.89  3.000
 BYB  O26  C25  C22  125.32  3.000
 BYB  H14  O27  C25  109.90  3.000
 BYB  H16  C28  H15  106.38  3.000
 BYB  H16  C28  C29  110.98  3.000
 BYB  H15  C28  C29  110.90  3.000
 BYB  H16  C28  C18  109.03  3.000
 BYB  H15  C28  C18  110.24  3.000
 BYB  C29  C28  C18  109.27  3.000
 BYB  H18  C29  H17  106.32  3.000
 BYB  H18  C29  C28  110.90  3.000
 BYB  H17  C29  C28  110.88  3.000
 BYB  H18  C29  C21  110.07  3.000
 BYB  H17  C29  C21  109.44  3.000
 BYB  C28  C29  C21  109.18  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
 BYB  CONST_01  C6   N3   C2   C1     0.00   0.0  0
 BYB  CONST_02  C9   C5   C4   C1   180.00   0.0  0
 BYB  CONST_03  C6   C5   C4   C1     0.00   0.0  0
 BYB  CONST_04  N7   C6   N3   C2   180.00   0.0  0
 BYB  CONST_05  C5   C6   N3   C2     0.00   0.0  0
 BYB  CONST_06  C5   C4   C1   C2     0.00   0.0  0
 BYB  CONST_07  N8   C9   C5   C4   180.00   0.0  0
 BYB  CONST_08  C10  C9   C5   C4     0.00   0.0  0
 BYB  CONST_09  N7   C6   C5   C4   180.00   0.0  0
 BYB  CONST_10  N3   C6   C5   C4     0.00   0.0  0
 BYB  CONST_11  N3   C2   C1   C4     0.00   0.0  0
 BYB  CONST_12  N7   N8   C9   C5     0.00   0.0  0
 BYB  CONST_13  N15  C10  C9   C5     0.00   0.0  0
 BYB  CONST_14  N11  C10  C9   C5   180.00   0.0  0
 BYB  CONST_15  N8   N7   C6   C5     0.00   0.0  0
 BYB  CONST_16  C9   N8   N7   C6     0.00   0.0  0
 BYB  CONST_17  N8   C9   C5   C6     0.00   0.0  0
 BYB  CONST_18  C10  C9   C5   C6   180.00   0.0  0
 BYB  CONST_19  N8   N7   C6   N3   180.00   0.0  0
 BYB  CONST_20  C9   C5   C6   N3   180.00   0.0  0
 BYB  CONST_21  C10  C9   N8   N7   180.00   0.0  0
 BYB  CONST_22  C9   C5   C6   N7     0.00   0.0  0
 BYB  CONST_23  N15  C10  C9   N8   180.00   0.0  0
 BYB  CONST_24  N11  C10  C9   N8     0.00   0.0  0
 BYB  CONST_25  C14  N15  C10  C9   180.00   0.0  0
 BYB  CONST_26  C12  N11  C10  C9   180.00   0.0  0
 BYB  CONST_27  C13  C14  N15  C10    0.00   0.0  0
 BYB  CONST_28  C13  C12  N11  C10    0.00   0.0  0
 BYB  CONST_29  C14  N15  C10  N11    0.00   0.0  0
 BYB  CONST_30  C14  C13  C12  N11    0.00   0.0  0
 BYB  CONST_31  N15  C14  C13  C12    0.00   0.0  0
 BYB  CONST_32  N15  C10  N11  C12    0.00   0.0  0
 BYB  CONST_33  F23  C1   C4   C5   180.00   0.0  0
 BYB  CONST_34  F23  C1   C2   N3   180.00   0.0  0
 BYB  CONST_35  N16  C12  N11  C10  180.00   0.0  0
 BYB  CONST_36  F24  C13  C12  N11  180.00   0.0  0
 BYB  CONST_37  N16  C12  C13  C14  180.00   0.0  0
 BYB  CONST_38  F24  C13  C14  N15  180.00   0.0  0
 BYB  CONST_39  C17  N16  C12  N11    0.00   0.0  0
 BYB  CONST_40  C17  N16  C12  C13  180.00   0.0  0
 BYB  CONST_41  H2   C4   C1   C2   180.00   0.0  0
 BYB  CONST_42  H1   C2   C1   C4   180.00   0.0  0
 BYB  CONST_43  H3   N7   C6   C5   180.00   0.0  0
 BYB  CONST_44  H4   C14  N15  C10  180.00   0.0  0
 BYB  CONST_45  H5   N16  C12  N11  180.00   0.0  0
 BYB  CONST_46  H14  O27  C25  C22  180.00   0.0  0
 BYB  Var_01    C21  C20  C19  C18  -14.33  30.0  1
 BYB  Var_02    C21  C29  C28  C18  -13.94  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
 BYB  chir_01  C17  N16  C18  C22  negativ
 BYB  chir_02  C18  C28  C19  C17  positiv
 BYB  chir_03  C21  C22  C20  C29  positiv
 BYB  chir_04  C22  C21  C25  C17  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
 BYB  plan-1  C9   0.020
 BYB  plan-1  C10  0.020
 BYB  plan-1  N11  0.020
 BYB  plan-1  C12  0.020
 BYB  plan-1  C13  0.020
 BYB  plan-1  C14  0.020
 BYB  plan-1  N15  0.020
 BYB  plan-1  N16  0.020
 BYB  plan-1  F24  0.020
 BYB  plan-1  H4   0.020
 BYB  plan-2  C1   0.020
 BYB  plan-2  C2   0.020
 BYB  plan-2  C4   0.020
 BYB  plan-2  C5   0.020
 BYB  plan-2  C6   0.020
 BYB  plan-2  N3   0.020
 BYB  plan-2  N7   0.020
 BYB  plan-2  N8   0.020
 BYB  plan-2  C9   0.020
 BYB  plan-2  C10  0.020
 BYB  plan-2  F23  0.020
 BYB  plan-2  H1   0.020
 BYB  plan-2  H2   0.020
 BYB  plan-2  H3   0.020
 BYB  plan-3  C12  0.020
 BYB  plan-3  N16  0.020
 BYB  plan-3  C17  0.020
 BYB  plan-3  H5   0.020
 BYB  plan-4  C22  0.020
 BYB  plan-4  C25  0.020
 BYB  plan-4  O26  0.020
 BYB  plan-4  O27  0.020
 BYB  plan-4  H14  0.020

