# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 00:39:38 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  46  29  .  2022-07-24  2022-07-26
;
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   5.7496  -0.3340  -0.9096
 BYB  C2   C  CR16   0  -0.202   5.9600   0.9210  -1.5008
 BYB  C4   C  CR16   0  -0.390   4.5149  -0.7482  -0.4822
 BYB  C5   C  CR56   0  -0.089   3.4774   0.1665  -0.6769
 BYB  C6   C  CR56   0   0.522   3.7949   1.3956  -1.2783
 BYB  N3   N  N      0  -0.408   4.9918   1.7932  -1.6902
 BYB  N7   N  NR15   0  -0.505   2.6341   2.0882  -1.3509
 BYB  N8   N  N      0  -0.221   1.6137   1.4085  -0.8507
 BYB  C9   C  CR5    0   0.149   2.0759   0.2496  -0.4345
 BYB  C10  C  CR6    0   0.346   1.2093  -0.7588   0.1796
 BYB  N11  N  N      0  -0.464  -0.0758  -0.4584   0.3168
 BYB  C12  C  CR6    0   0.429  -0.8791  -1.3604   0.8751
 BYB  C13  C  CR6    0   0.355  -0.3165  -2.5910   1.2855
 BYB  C14  C  CR16   0  -0.179   1.0120  -2.8091   1.1002
 BYB  N15  N  N      0  -0.463   1.8028  -1.8844   0.5381
 BYB  N16  N  NH1    0  -0.687  -2.1750  -1.0942   1.0426
 BYB  C17  C  CH1    0   0.002  -2.8174   0.1340   0.6072
 BYB  C18  C  CH1    0  -0.260  -3.0931   0.1462  -0.9021
 BYB  C19  C  CH2    0  -0.436  -4.1991  -0.8477  -1.2489
 BYB  C20  C  CH2    0  -0.430  -5.5072  -0.4204  -0.5487
 BYB  C21  C  CH1    0  -0.239  -5.2292   0.7549   0.3900
 BYB  C22  C  CH1    0  -0.422  -4.1306   0.3510   1.3801
 BYB  F23  F  F      0  -0.308   6.8131  -1.1390  -0.7678
 BYB  F24  F  F      0  -0.303  -1.1080  -3.5189   1.8462
 BYB  C25  C  C      0   0.434  -3.9963   1.3135   2.5849
 BYB  O26  O  O      0  -0.613  -5.0653   1.7274   3.0779
 BYB  O27  O  OC    -1  -0.595  -2.8494   1.5728   2.9972
 BYB  C28  C  CH2    0  -0.441  -3.5363   1.5608  -1.2758
 BYB  C29  C  CH2    0  -0.436  -4.7721   1.9564  -0.4372
 BYB  H1   H  HCR6   0   0.288   6.9580   1.1995  -1.8207
 BYB  H2   H  HCR6   0   0.292   4.3565  -1.7154  -0.0265
 BYB  H3   H  HNR5   0   0.424   2.4905   3.0114  -1.7297
 BYB  H4   H  HCR6   0   0.286   1.4659  -3.7457   1.4056
 BYB  H5   H  HNH1   0   0.397  -2.7488  -1.8011   1.4729
 BYB  H6   H  HCH1   0   0.246  -2.1273   0.9494   0.8290
 BYB  H7   H  HCH1   0   0.229  -2.1729  -0.1054  -1.4352
 BYB  H8   H  HCH2   0   0.227  -4.3284  -0.8876  -2.3330
 BYB  H9   H  HCH2   0   0.221  -3.9043  -1.8553  -0.9435
 BYB  H10  H  HCH2   0   0.221  -6.2673  -0.1366  -1.2816
 BYB  H11  H  HCH2   0   0.223  -5.9279  -1.2517   0.0228
 BYB  H12  H  HCH1   0   0.217  -6.1326   1.0049   0.9467
 BYB  H13  H  HCH1   0   0.237  -4.4468  -0.6102   1.8137
 BYB  H15  H  HCH2   0   0.227  -2.7133   2.2602  -1.1084
 BYB  H16  H  HCH2   0   0.225  -3.7619   1.6006  -2.3445
 BYB  H17  H  HCH2   0   0.223  -5.5885   2.2901  -1.0822
 BYB  H18  H  HCH2   0   0.225  -4.5463   2.7984   0.2223

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  1.324  0.020  1.324
 BYB  N8   C9   aromatic  1.315  0.020  1.315
 BYB  N15  C14  aromatic  1.340  0.020  1.340
 BYB  N15  C10  aromatic  1.322  0.020  1.322
 BYB  C14  C13  aromatic  1.359  0.020  1.359
 BYB  N7   C6   aromatic  1.354  0.020  1.354
 BYB  C9   C10  single    1.465  0.020  1.465
 BYB  C9   C5   aromatic  1.425  0.020  1.425
 BYB  C10  N11  aromatic  1.327  0.020  1.327
 BYB  C13  F24  single    1.342  0.020  1.342
 BYB  C13  C12  aromatic  1.414  0.020  1.414
 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  1.331  0.020  1.331
 BYB  C12  N16  single    1.333  0.020  1.333
 BYB  C2   C1   aromatic  1.403  0.020  1.403
 BYB  C4   C1   aromatic  1.371  0.020  1.371
 BYB  N16  C17  single    1.453  0.020  1.453
 BYB  C1   F23  single    1.341  0.020  1.341
 BYB  C17  C18  single    1.534  0.020  1.534
 BYB  C17  C22  single    1.539  0.020  1.539
 BYB  O26  C25  deloc     1.248  0.020  1.248
 BYB  C25  C22  single    1.548  0.020  1.548
 BYB  C25  O27  deloc     1.246  0.020  1.246
 BYB  C18  C19  single    1.527  0.020  1.527
 BYB  C18  C28  single    1.529  0.020  1.529
 BYB  C22  C21  single    1.533  0.020  1.533
 BYB  C19  C20  single    1.544  0.020  1.544
 BYB  C28  C29  single    1.545  0.020  1.545
 BYB  C21  C20  single    1.530  0.020  1.530
 BYB  C21  C29  single    1.529  0.020  1.529
 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  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   119.99  3.000
 BYB  F23  C1   C2   117.54  3.000
 BYB  C4   C1   C2   122.46  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   122.41  3.000
 BYB  H2   C4   C1   122.27  3.000
 BYB  C5   C4   C1   115.32  3.000
 BYB  C9   C5   C6   104.13  3.000
 BYB  C6   C5   C4   117.70  3.000
 BYB  C9   C5   C4   138.17  3.000
 BYB  N7   C6   N3   127.13  3.000
 BYB  N3   C6   C5   126.80  3.000
 BYB  N7   C6   C5   106.07  3.000
 BYB  C6   N3   C2   114.84  3.000
 BYB  H3   N7   N8   120.15  3.000
 BYB  H3   N7   C6   127.65  3.000
 BYB  N8   N7   C6   112.21  3.000
 BYB  C9   N8   N7   107.52  3.000
 BYB  C10  C9   N8   122.10  3.000
 BYB  C10  C9   C5   127.82  3.000
 BYB  N8   C9   C5   110.07  3.000
 BYB  N15  C10  N11  126.84  3.000
 BYB  N11  C10  C9   117.42  3.000
 BYB  N15  C10  C9   115.74  3.000
 BYB  C12  N11  C10  118.34  3.000
 BYB  N16  C12  C13  121.60  3.000
 BYB  N16  C12  N11  120.27  3.000
 BYB  C13  C12  N11  118.13  3.000
 BYB  F24  C13  C14  121.50  3.000
 BYB  F24  C13  C12  119.22  3.000
 BYB  C14  C13  C12  119.28  3.000
 BYB  H4   C14  N15  117.83  3.000
 BYB  H4   C14  C13  120.62  3.000
 BYB  N15  C14  C13  121.55  3.000
 BYB  C14  N15  C10  115.86  3.000
 BYB  H5   N16  C17  118.01  3.000
 BYB  H5   N16  C12  117.86  3.000
 BYB  C17  N16  C12  124.11  3.000
 BYB  H6   C17  C22  109.40  3.000
 BYB  H6   C17  C18  107.92  3.000
 BYB  C22  C17  C18  109.85  3.000
 BYB  H6   C17  N16  106.93  3.000
 BYB  C22  C17  N16  110.24  3.000
 BYB  C18  C17  N16  112.39  3.000
 BYB  H7   C18  C28  109.75  3.000
 BYB  H7   C18  C19  110.45  3.000
 BYB  C28  C18  C19  109.68  3.000
 BYB  H7   C18  C17  109.07  3.000
 BYB  C28  C18  C17  107.45  3.000
 BYB  C19  C18  C17  110.39  3.000
 BYB  H9   C19  H8   105.99  3.000
 BYB  H9   C19  C20  110.91  3.000
 BYB  H8   C19  C20  111.09  3.000
 BYB  H9   C19  C18  109.95  3.000
 BYB  H8   C19  C18  109.56  3.000
 BYB  C20  C19  C18  109.30  3.000
 BYB  H11  C20  H10  106.28  3.000
 BYB  H11  C20  C21  109.47  3.000
 BYB  H10  C20  C21  109.77  3.000
 BYB  H11  C20  C19  110.65  3.000
 BYB  H10  C20  C19  110.91  3.000
 BYB  C21  C20  C19  109.69  3.000
 BYB  H12  C21  C29  110.11  3.000
 BYB  H12  C21  C22  108.93  3.000
 BYB  C29  C21  C22  110.01  3.000
 BYB  H12  C21  C20  109.82  3.000
 BYB  C29  C21  C20  109.04  3.000
 BYB  C22  C21  C20  108.91  3.000
 BYB  H13  C22  C25  105.14  3.000
 BYB  H13  C22  C21  106.18  3.000
 BYB  C25  C22  C21  113.64  3.000
 BYB  H13  C22  C17  108.65  3.000
 BYB  C21  C22  C17  108.92  3.000
 BYB  C25  C22  C17  113.86  3.000
 BYB  O27  C25  O26  126.07  3.000
 BYB  O27  C25  C22  117.83  3.000
 BYB  O26  C25  C22  116.07  3.000
 BYB  H16  C28  H15  106.37  3.000
 BYB  H16  C28  C29  110.88  3.000
 BYB  H15  C28  C29  110.81  3.000
 BYB  H16  C28  C18  109.42  3.000
 BYB  H15  C28  C18  109.66  3.000
 BYB  C29  C28  C18  109.65  3.000
 BYB  H18  C29  H17  105.98  3.000
 BYB  H18  C29  C28  111.07  3.000
 BYB  H17  C29  C28  110.82  3.000
 BYB  H18  C29  C21  109.92  3.000
 BYB  H17  C29  C21  109.64  3.000
 BYB  C28  C29  C21  109.37  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  Var_01    C21  C20  C19  C18   -6.69  30.0  1
 BYB  Var_02    C21  C29  C28  C18   -5.55  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

