# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 22:39:20 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: (2R,3R,3aS,6S,6aR)-6-[(2-amino-3-bromoquinolin-7-yl)oxy]-2-(4-methyl-7H-pyrrolo[2,3-d]pyrimidin-7-yl)hexahydro-3aH-cyclopenta[b]furan-3,3a-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncnc2n(ccc12)[C@@H]3O[C@@H]4[C@H](CC[C@]4(O)[C@H]3O)Oc5ccc6cc(Br)c(N)nc6c5
#
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
 WFS  WFS  (2R,3R,3aS,6S,6aR)-6-[(2-amino-3-bromoquinolin-7-yl)oxy]-2-(4-methyl-7H-pyrrolo[2,3-d]pyrimidin-7-yl)hexahydro-3aH-cyclopenta[b]furan-3,3a-diol  ligand  55  33  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WFS
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
 WFS  N1   N   NH2   0  -0.828  18.6259  -44.5393  -11.2111
 WFS  N3   N   N     0  -0.438  13.4010  -34.5592   -3.1316
 WFS  C4   C   CR15  0  -0.034  19.1399  -39.9394   -5.6150
 WFS  C5   C   CR6   0   0.397  20.7563  -40.8687   -7.1115
 WFS  C6   C   CR16  0  -0.355  22.1338  -40.9781   -7.4259
 WFS  C7   C   CR16  0  -0.293  22.5393  -41.7822   -8.4513
 WFS  C8   C   CR66  0   0.041  21.6000  -42.5110   -9.2103
 WFS  C10  C   CR16  0  -0.444  19.8194  -41.5714   -7.8350
 WFS  C13  C   CR16  0  -0.151  21.9590  -43.3611  -10.2767
 WFS  C15  C   CR15  0  -0.037  17.6678  -39.0277   -2.7642
 WFS  C17  C   CR56  0  -0.014  13.8364  -36.7332   -3.9123
 WFS  C20  C   CR6   0   0.232  12.9509  -35.6789   -3.6887
 WFS  C21  C   CR16  0   0.032  14.6913  -34.4776   -2.8006
 WFS  C22  C   CH3   0  -0.739  11.5085  -35.7726   -4.0593
 WFS  C12  C   CR6   0  -0.241  20.9914  -44.0317  -10.9579
 WFS  C11  C   CR6   0   0.460  19.6165  -43.8623  -10.5870
 WFS  N    N   N     0  -0.503  19.2797  -43.0703   -9.5939
 WFS  C9   C   CR66  0   0.251  20.2257  -42.4038   -8.9008
 WFS  O    O   O2    0  -0.484  20.4759  -40.0366   -6.0941
 WFS  C    C   CH2   0  -0.508  18.7850  -41.1420   -4.7370
 WFS  C3   C   C     0   0.054  19.1134  -38.7383   -4.6631
 WFS  O1   O   O     0  -0.490  17.9119  -38.0014   -4.8321
 WFS  C14  C   CR15  0   0.204  17.2929  -37.8013   -3.5893
 WFS  O2   O   OH1   0  -0.653  17.5547  -38.7467   -1.3992
 WFS  C2   C   C     0   0.168  19.1158  -39.3056   -3.2256
 WFS  O3   O   OH1   0  -0.673  20.0232  -38.6083   -2.4214
 WFS  C1   C   CH2   0  -0.476  19.4049  -40.8004   -3.3842
 WFS  N2   N   NR5   0  -0.559  15.8861  -37.6330   -3.8005
 WFS  C19  C   CR15  0   0.011  15.0383  -38.5519   -4.3880
 WFS  C18  C   CR15  0  -0.464  13.7792  -38.0463   -4.4704
 WFS  N4   N   N     0  -0.430  15.6207  -35.4019   -2.9569
 WFS  C16  C   CR56  0   0.531  15.1659  -36.5142   -3.5137
 WFS  H1   H   HNH2  0   0.394  17.6855  -44.2475  -11.0004
 WFS  H2   H   HNH2  0   0.400  18.7596  -44.9140  -12.1345
 WFS  H3   H   HCR5  0   0.269  18.4461  -39.7871   -6.4472
 WFS  H5   H   HCR6  0   0.263  23.5925  -41.8673   -8.6900
 WFS  H6   H   HCR6  0   0.276  18.7607  -41.5200   -7.6209
 WFS  H7   H   HCR6  0   0.288  23.0047  -43.4722  -10.5378
 WFS  H8   H   HCR5  0   0.259  17.0226  -39.8674   -3.0471
 WFS  H9   H   HCR6  0   0.251  15.0101  -33.5433   -2.3518
 WFS  H10  H   HCH3  0   0.256  10.9833  -34.8511   -3.8195
 WFS  H11  H   HCH3  0   0.257  11.3965  -35.9734   -5.1260
 WFS  H12  H   HCH3  0   0.258  11.0278  -36.5970   -3.5298
 WFS  H13  H   HCH2  0   0.255  17.6968  -41.2169   -4.6636
 WFS  H14  H   HCH2  0   0.272  19.1301  -42.0914   -5.1474
 WFS  H15  H   H     0   0.260  19.9773  -38.0871   -4.8333
 WFS  H16  H   HCR5  0   0.259  17.6478  -36.8894   -3.0937
 WFS  H17  H   HOH1  0   0.470  17.3729  -39.5627   -0.9219
 WFS  H18  H   HOH1  0   0.443  19.6696  -38.5929   -1.5224
 WFS  H19  H   HCH2  0   0.252  18.9999  -41.3963   -2.5637
 WFS  H20  H   HCH2  0   0.251  20.4847  -40.9640   -3.4059
 WFS  H21  H   HCR5  0   0.305  15.4081  -39.5113   -4.7149
 WFS  H22  H   HCR5  0   0.260  12.9208  -38.5507   -4.8836
 WFS  H4   H   HCR6  0   0.265  22.8532  -40.4180   -6.8427
 WFS  BR   BR  BR    0  -0.030  21.4684  -45.1909  -12.3680

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
 WFS  BR   C12  single    1.887  0.020  1.887
 WFS  N1   C11  single    1.352  0.020  1.352
 WFS  C12  C11  aromatic  1.434  0.020  1.434
 WFS  C12  C13  aromatic  1.360  0.020  1.360
 WFS  C11  N    aromatic  1.314  0.020  1.314
 WFS  C13  C8   aromatic  1.410  0.020  1.410
 WFS  N    C9   aromatic  1.349  0.020  1.349
 WFS  C8   C9   aromatic  1.413  0.020  1.413
 WFS  C8   C7   aromatic  1.411  0.020  1.411
 WFS  C9   C10  aromatic  1.412  0.020  1.412
 WFS  C7   C6   aromatic  1.365  0.020  1.365
 WFS  C10  C5   aromatic  1.377  0.020  1.377
 WFS  C6   C5   aromatic  1.417  0.020  1.417
 WFS  C5   O    single    1.344  0.020  1.344
 WFS  O    C4   single    1.423  0.020  1.423
 WFS  C4   C    single    1.531  0.020  1.531
 WFS  C4   C3   single    1.533  0.020  1.533
 WFS  C    C1   single    1.527  0.020  1.527
 WFS  O1   C3   single    1.420  0.020  1.420
 WFS  O1   C14  single    1.403  0.020  1.403
 WFS  C3   C2   single    1.545  0.020  1.545
 WFS  C19  C18  aromatic  1.359  0.020  1.359
 WFS  C19  N2   aromatic  1.381  0.020  1.381
 WFS  C18  C17  aromatic  1.428  0.020  1.428
 WFS  C1   C2   single    1.531  0.020  1.531
 WFS  N2   C14  single    1.432  0.020  1.432
 WFS  N2   C16  aromatic  1.361  0.020  1.361
 WFS  C17  C20  aromatic  1.395  0.020  1.395
 WFS  C17  C16  aromatic  1.405  0.020  1.405
 WFS  C14  C15  single    1.525  0.020  1.525
 WFS  C22  C20  single    1.492  0.020  1.492
 WFS  C2   C15  single    1.545  0.020  1.545
 WFS  C2   O3   single    1.399  0.020  1.399
 WFS  C20  N3   aromatic  1.329  0.020  1.329
 WFS  C16  N4   aromatic  1.324  0.020  1.324
 WFS  C15  O2   single    1.398  0.020  1.398
 WFS  N3   C21  aromatic  1.335  0.020  1.335
 WFS  N4   C21  aromatic  1.320  0.020  1.320
 WFS  N1   H1   single    0.890  0.020  1.040
 WFS  N1   H2   single    0.890  0.020  1.040
 WFS  C4   H3   single    0.970  0.020  1.090
 WFS  C6   H4   single    0.930  0.020  1.080
 WFS  C7   H5   single    0.930  0.020  1.080
 WFS  C10  H6   single    0.930  0.020  1.080
 WFS  C13  H7   single    0.930  0.020  1.080
 WFS  C15  H8   single    0.970  0.020  1.090
 WFS  C21  H9   single    0.930  0.020  1.080
 WFS  C22  H10  single    0.970  0.020  1.090
 WFS  C22  H11  single    0.970  0.020  1.090
 WFS  C22  H12  single    0.970  0.020  1.090
 WFS  C    H13  single    0.970  0.020  1.090
 WFS  C    H14  single    0.970  0.020  1.090
 WFS  C3   H15  single    0.970  0.020  1.090
 WFS  C14  H16  single    0.970  0.020  1.090
 WFS  O2   H17  single    0.850  0.020  0.980
 WFS  O3   H18  single    0.850  0.020  0.980
 WFS  C1   H19  single    0.970  0.020  1.090
 WFS  C1   H20  single    0.970  0.020  1.090
 WFS  C19  H21  single    0.930  0.020  1.080
 WFS  C18  H22  single    0.930  0.020  1.080

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
 WFS  H2   N1   H1   115.11  3.000
 WFS  H2   N1   C11  120.86  3.000
 WFS  H1   N1   C11  116.26  3.000
 WFS  C21  N3   C20  118.87  3.000
 WFS  H3   C4   C3   110.63  3.000
 WFS  H3   C4   C    113.49  3.000
 WFS  C3   C4   C    104.80  3.000
 WFS  H3   C4   O    110.42  3.000
 WFS  C3   C4   O    106.19  3.000
 WFS  C    C4   O    110.93  3.000
 WFS  O    C5   C10  124.88  3.000
 WFS  O    C5   C6   114.74  3.000
 WFS  C10  C5   C6   120.37  3.000
 WFS  H4   C6   C7   120.82  3.000
 WFS  H4   C6   C5   119.12  3.000
 WFS  C7   C6   C5   120.07  3.000
 WFS  H5   C7   C8   119.22  3.000
 WFS  H5   C7   C6   120.05  3.000
 WFS  C8   C7   C6   120.72  3.000
 WFS  C9   C8   C13  117.33  3.000
 WFS  C9   C8   C7   119.39  3.000
 WFS  C13  C8   C7   123.29  3.000
 WFS  H6   C10  C9   117.33  3.000
 WFS  H6   C10  C5   122.55  3.000
 WFS  C9   C10  C5   120.12  3.000
 WFS  H7   C13  C12  121.01  3.000
 WFS  H7   C13  C8   119.33  3.000
 WFS  C12  C13  C8   119.66  3.000
 WFS  H8   C15  C2   109.68  3.000
 WFS  H8   C15  O2   111.00  3.000
 WFS  C2   C15  O2   113.80  3.000
 WFS  H8   C15  C14  109.38  3.000
 WFS  O2   C15  C14  110.29  3.000
 WFS  C2   C15  C14  102.33  3.000
 WFS  C16  C17  C18  106.98  3.000
 WFS  C16  C17  C20  115.94  3.000
 WFS  C18  C17  C20  137.08  3.000
 WFS  C22  C20  C17  121.76  3.000
 WFS  C22  C20  N3   118.96  3.000
 WFS  C17  C20  N3   119.27  3.000
 WFS  H9   C21  N4   116.45  3.000
 WFS  H9   C21  N3   116.08  3.000
 WFS  N4   C21  N3   127.48  3.000
 WFS  H12  C22  H11  106.86  3.000
 WFS  H12  C22  H10  108.68  3.000
 WFS  H11  C22  H10  108.78  3.000
 WFS  H12  C22  C20  110.65  3.000
 WFS  H11  C22  C20  110.70  3.000
 WFS  H10  C22  C20  111.04  3.000
 WFS  C11  C12  BR   120.54  3.000
 WFS  C11  C12  C13  119.62  3.000
 WFS  BR   C12  C13  119.83  3.000
 WFS  N    C11  C12  120.82  3.000
 WFS  N    C11  N1   117.56  3.000
 WFS  C12  C11  N1   121.58  3.000
 WFS  C9   N    C11  120.42  3.000
 WFS  N    C9   C10  118.51  3.000
 WFS  C10  C9   C8   119.34  3.000
 WFS  N    C9   C8   122.15  3.000
 WFS  C5   O    C4   119.55  3.000
 WFS  H14  C    H13  106.30  3.000
 WFS  H14  C    C1   113.56  3.000
 WFS  H13  C    C1   111.10  3.000
 WFS  H14  C    C4   113.25  3.000
 WFS  H13  C    C4   108.86  3.000
 WFS  C1   C    C4   103.79  3.000
 WFS  H15  C3   C2   111.20  3.000
 WFS  H15  C3   O1   109.90  3.000
 WFS  C2   C3   O1   107.61  3.000
 WFS  H15  C3   C4   110.85  3.000
 WFS  C2   C3   C4   106.86  3.000
 WFS  O1   C3   C4   110.33  3.000
 WFS  C14  O1   C3   110.01  3.000
 WFS  H16  C14  N2   106.66  3.000
 WFS  H16  C14  O1   112.09  3.000
 WFS  N2   C14  O1   108.63  3.000
 WFS  H16  C14  C15  110.16  3.000
 WFS  N2   C14  C15  114.56  3.000
 WFS  O1   C14  C15  104.84  3.000
 WFS  H17  O2   C15  109.21  3.000
 WFS  C1   C2   O3   115.08  3.000
 WFS  O3   C2   C3   110.66  3.000
 WFS  C1   C2   C3   105.21  3.000
 WFS  O3   C2   C15  110.28  3.000
 WFS  C1   C2   C15  112.56  3.000
 WFS  C3   C2   C15  102.15  3.000
 WFS  H18  O3   C2   107.79  3.000
 WFS  H20  C1   H19  107.45  3.000
 WFS  H20  C1   C2   109.57  3.000
 WFS  H19  C1   C2   112.64  3.000
 WFS  H20  C1   C    110.51  3.000
 WFS  H19  C1   C    113.15  3.000
 WFS  C2   C1   C    103.51  3.000
 WFS  C16  N2   C19  108.16  3.000
 WFS  C16  N2   C14  125.81  3.000
 WFS  C19  N2   C14  125.96  3.000
 WFS  H21  C19  C18  129.04  3.000
 WFS  H21  C19  N2   120.67  3.000
 WFS  C18  C19  N2   110.29  3.000
 WFS  H22  C18  C19  125.93  3.000
 WFS  H22  C18  C17  127.73  3.000
 WFS  C19  C18  C17  106.33  3.000
 WFS  C16  N4   C21  113.34  3.000
 WFS  N4   C16  N2   126.67  3.000
 WFS  N4   C16  C17  125.10  3.000
 WFS  N2   C16  C17  108.23  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
 WFS  CONST_01  C18  C17  C20  N3   180.00   0.0  0
 WFS  CONST_02  C16  C17  C20  N3     0.00   0.0  0
 WFS  CONST_03  C16  N4   C21  N3     0.00   0.0  0
 WFS  CONST_04  N    C9   C10  C5   180.00   0.0  0
 WFS  CONST_05  C8   C9   C10  C5     0.00   0.0  0
 WFS  CONST_06  C8   C7   C6   C5     0.00   0.0  0
 WFS  CONST_07  C13  C8   C7   C6   180.00   0.0  0
 WFS  CONST_08  C9   C8   C7   C6     0.00   0.0  0
 WFS  CONST_09  C9   C10  C5   C6     0.00   0.0  0
 WFS  CONST_10  C12  C13  C8   C7   180.00   0.0  0
 WFS  CONST_11  N    C9   C8   C7   180.00   0.0  0
 WFS  CONST_12  C10  C9   C8   C7     0.00   0.0  0
 WFS  CONST_13  C10  C5   C6   C7     0.00   0.0  0
 WFS  CONST_14  C11  C12  C13  C8     0.00   0.0  0
 WFS  CONST_15  C11  N    C9   C8     0.00   0.0  0
 WFS  CONST_16  C11  N    C9   C10  180.00   0.0  0
 WFS  CONST_17  C13  C8   C9   C10  180.00   0.0  0
 WFS  CONST_18  N    C11  C12  C13    0.00   0.0  0
 WFS  CONST_19  N    C9   C8   C13    0.00   0.0  0
 WFS  CONST_20  N2   C19  C18  C17    0.00   0.0  0
 WFS  CONST_21  C21  N3   C20  C17    0.00   0.0  0
 WFS  CONST_22  C19  N2   C16  C17    0.00   0.0  0
 WFS  CONST_23  C21  N4   C16  C17    0.00   0.0  0
 WFS  CONST_24  C19  C18  C17  C20  180.00   0.0  0
 WFS  CONST_25  N2   C16  C17  C20  180.00   0.0  0
 WFS  CONST_26  N4   C16  C17  C20    0.00   0.0  0
 WFS  CONST_27  N4   C21  N3   C20    0.00   0.0  0
 WFS  CONST_28  N2   C16  N4   C21  180.00   0.0  0
 WFS  CONST_29  C9   N    C11  C12    0.00   0.0  0
 WFS  CONST_30  C9   C8   C13  C12    0.00   0.0  0
 WFS  CONST_31  C18  C17  C16  N2     0.00   0.0  0
 WFS  CONST_32  C16  C17  C18  C19    0.00   0.0  0
 WFS  CONST_33  N4   C16  N2   C19  180.00   0.0  0
 WFS  CONST_34  C16  N2   C19  C18    0.00   0.0  0
 WFS  CONST_35  N4   C16  C17  C18  180.00   0.0  0
 WFS  CONST_36  C14  N2   C16  C17  180.00   0.0  0
 WFS  CONST_37  C18  C19  N2   C14  180.00   0.0  0
 WFS  CONST_38  N4   C16  N2   C14    0.00   0.0  0
 WFS  CONST_39  C13  C12  C11  N1   180.00   0.0  0
 WFS  CONST_40  C9   N    C11  N1   180.00   0.0  0
 WFS  CONST_41  O    C5   C6   C7   180.00   0.0  0
 WFS  CONST_42  BR   C12  C13  C8   180.00   0.0  0
 WFS  CONST_43  C22  C20  N3   C21  180.00   0.0  0
 WFS  CONST_44  C18  C17  C20  C22    0.00   0.0  0
 WFS  CONST_45  C16  C17  C20  C22  180.00   0.0  0
 WFS  CONST_46  N    C11  C12  BR   180.00   0.0  0
 WFS  CONST_47  O    C5   C10  C9   180.00   0.0  0
 WFS  CONST_48  H5   C7   C6   C5   180.00   0.0  0
 WFS  CONST_49  H6   C10  C5   C6   180.00   0.0  0
 WFS  CONST_50  H7   C13  C8   C7     0.00   0.0  0
 WFS  CONST_51  H4   C6   C7   C8   180.00   0.0  0
 WFS  CONST_52  H21  C19  C18  C17  180.00   0.0  0
 WFS  CONST_53  H22  C18  C17  C20    0.00   0.0  0
 WFS  CONST_54  H9   C21  N3   C20  180.00   0.0  0
 WFS  CONST_55  H1   N1   C11  C12  180.00   0.0  0
 WFS  Var_01    C2   C1   C    C4    40.35  30.0  1
 WFS  Var_02    C10  C5   O    C4     6.26  30.0  1
 WFS  Var_03    H10  C22  C20  N3     0.62  30.0  2

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
 WFS  chir_01  C4   O    C   C3   negativ
 WFS  chir_02  C15  O2   C2  C14  positiv
 WFS  chir_03  C3   O1   C4  C2   positiv
 WFS  chir_04  C14  O1   N2  C15  negativ
 WFS  chir_05  C2   C15  C1  C3   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
 WFS  plan-1  N3   0.020
 WFS  plan-1  C17  0.020
 WFS  plan-1  C20  0.020
 WFS  plan-1  C21  0.020
 WFS  plan-1  C22  0.020
 WFS  plan-1  C14  0.020
 WFS  plan-1  N2   0.020
 WFS  plan-1  C19  0.020
 WFS  plan-1  C18  0.020
 WFS  plan-1  N4   0.020
 WFS  plan-1  C16  0.020
 WFS  plan-1  H9   0.020
 WFS  plan-1  H21  0.020
 WFS  plan-1  H22  0.020
 WFS  plan-2  N1   0.020
 WFS  plan-2  C5   0.020
 WFS  plan-2  C6   0.020
 WFS  plan-2  C7   0.020
 WFS  plan-2  C8   0.020
 WFS  plan-2  C10  0.020
 WFS  plan-2  C13  0.020
 WFS  plan-2  C12  0.020
 WFS  plan-2  C11  0.020
 WFS  plan-2  N    0.020
 WFS  plan-2  C9   0.020
 WFS  plan-2  O    0.020
 WFS  plan-2  H5   0.020
 WFS  plan-2  H6   0.020
 WFS  plan-2  H7   0.020
 WFS  plan-2  H4   0.020
 WFS  plan-2  BR   0.020
 WFS  plan-3  N1   0.020
 WFS  plan-3  C11  0.020
 WFS  plan-3  H1   0.020
 WFS  plan-3  H2   0.020

