# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 00:10:48 2022
#   Inital geometry file: a 127 line input string
#   Ligand name: (2R,3R,3aS,6S,6aR)-6-[(2-amino-3-bromoquinolin-7-yl)oxy]-2-(4-amino-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: Nc1nc2cc(O[C@H]3CC[C@]4(O)[C@@H](O)[C@@H](O[C@H]34)n5ccc6c(N)ncnc56)ccc2cc1Br
#
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
 WFM  WFM  (2R,3R,3aS,6S,6aR)-6-[(2-amino-3-bromoquinolin-7-yl)oxy]-2-(4-amino-7H-pyrrolo[2,3-d]pyrimidin-7-yl)hexahydro-3aH-cyclopenta[b]furan-3,3a-diol  ligand  54  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_WFM
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
 WFM  N1   N   N     0  -0.503  19.3785  -43.2462   -9.6299
 WFM  N3   N   N     0  -0.462  15.7228  -35.4428   -3.2033
 WFM  C4   C   CR6   0   0.397  20.8581  -40.9991   -7.1901
 WFM  C5   C   CR16  0  -0.355  22.2344  -41.1082   -7.5096
 WFM  C6   C   CR16  0  -0.293  22.6382  -41.9276   -8.5235
 WFM  C7   C   CR66  0   0.041  21.6982  -42.6720   -9.2664
 WFM  C8   C   CR16  0  -0.151  22.0554  -43.5350  -10.3230
 WFM  C10  C   CR6   0   0.461  19.7134  -44.0497  -10.6144
 WFM  C13  C   CH1   0   0.054  19.2097  -38.8193   -4.7886
 WFM  C15  C   CR56  0   0.514  15.2525  -36.5815   -3.7145
 WFM  C17  C   CR6   0   0.441  13.0422  -35.7463   -3.9125
 WFM  C20  C   CR15  0  -0.010  15.1311  -38.6612   -4.5006
 WFM  C21  C   CH1   0  -0.039  17.7646  -39.0651   -2.8824
 WFM  C9   C   CR6   0  -0.241  21.0870  -44.2176  -10.9910
 WFM  N    N   NH2   0  -0.828  18.7223  -44.7392  -11.2237
 WFM  C11  C   CR66  0   0.252  20.3251  -42.5655   -8.9515
 WFM  C12  C   CR16  0  -0.444  19.9207  -41.7186   -7.8965
 WFM  O1   O   O2    0  -0.484  20.5789  -40.1505   -6.1860
 WFM  C3   C   CH1   0  -0.034  19.2423  -40.0427   -5.7111
 WFM  C2   C   CH2   0  -0.507  18.8877  -41.2247   -4.8052
 WFM  C1   C   CH2   0  -0.476  19.5049  -40.8493   -3.4603
 WFM  O2   O   O2    0  -0.490  18.0051  -38.0936   -4.9775
 WFM  C14  C   CH1   0   0.205  17.3812  -37.8640   -3.7408
 WFM  O3   O   OH1   0  -0.653  17.6528  -38.7452   -1.5252
 WFM  C    C   CT    0   0.170  19.2127  -39.3515   -3.3371
 WFM  O    O   OH1   0  -0.674  20.1196  -38.6354   -2.5488
 WFM  N2   N   NR5   0  -0.557  15.9744  -37.7119   -3.9556
 WFM  C19  C   CR15  0  -0.434  13.8717  -38.1584   -4.5987
 WFM  C18  C   CR56  0  -0.085  13.9321  -36.8228   -4.0974
 WFM  N4   N   N     0  -0.475  13.5019  -34.6002   -3.4025
 WFM  C16  C   CR16  0   0.043  14.7918  -34.5172   -3.0845
 WFM  H1   H   HCR6  0   0.265  22.9544  -40.5350   -6.9398
 WFM  H2   H   HCR6  0   0.263  23.6906  -42.0123   -8.7660
 WFM  H3   H   HCR6  0   0.288  23.1002  -43.6454  -10.5878
 WFM  H4   H   HCH1  0   0.258  20.0710  -38.1680   -4.9721
 WFM  H5   H   HCR5  0   0.299  15.5016  -39.6330   -4.7860
 WFM  H6   H   HCH1  0   0.258  17.1223  -39.9156   -3.1387
 WFM  H7   H   HNH2  0   0.394  17.7820  -44.4489  -11.0110
 WFM  H8   H   HNH2  0   0.400  18.8521  -45.1260  -12.1427
 WFM  H9   H   HCR6  0   0.276  18.8630  -41.6698   -7.6771
 WFM  H10  H   HCH1  0   0.269  18.5497  -39.9118   -6.5481
 WFM  H11  H   HCH2  0   0.254  17.7995  -41.3000   -4.7322
 WFM  H12  H   HCH2  0   0.271  19.2365  -42.1827   -5.1917
 WFM  H13  H   HCH2  0   0.252  19.1013  -41.4259   -2.6255
 WFM  H14  H   HCH2  0   0.251  20.5852  -41.0103   -3.4776
 WFM  H15  H   HCH1  0   0.257  17.7300  -36.9368   -3.2703
 WFM  H16  H   HOH1  0   0.470  17.4887  -39.5501   -1.0231
 WFM  H17  H   HOH1  0   0.443  19.7543  -38.5799   -1.6559
 WFM  H18  H   HCR5  0   0.257  13.0126  -38.6823   -4.9862
 WFM  H19  H   HNH2  0   0.397  11.1691  -35.0029   -4.1721
 WFM  H20  H   HNH2  0   0.408  11.3746  -36.6170   -4.7211
 WFM  H21  H   HCR6  0   0.244  15.1119  -33.5637   -2.6769
 WFM  BR   BR  BR    0  -0.030  21.5616  -45.3901  -12.3911
 WFM  N5   N   NH2   0  -0.822  11.7384  -35.8313   -4.2110

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
 WFM  BR   C9   single    1.887  0.020  1.887
 WFM  N    C10  single    1.352  0.020  1.352
 WFM  C9   C10  aromatic  1.434  0.020  1.434
 WFM  C9   C8   aromatic  1.360  0.020  1.360
 WFM  C10  N1   aromatic  1.314  0.020  1.314
 WFM  C8   C7   aromatic  1.410  0.020  1.410
 WFM  N1   C11  aromatic  1.349  0.020  1.349
 WFM  C7   C11  aromatic  1.413  0.020  1.413
 WFM  C7   C6   aromatic  1.411  0.020  1.411
 WFM  C11  C12  aromatic  1.412  0.020  1.412
 WFM  C6   C5   aromatic  1.365  0.020  1.365
 WFM  C12  C4   aromatic  1.377  0.020  1.377
 WFM  C5   C4   aromatic  1.417  0.020  1.417
 WFM  C4   O1   single    1.344  0.020  1.344
 WFM  O1   C3   single    1.423  0.020  1.423
 WFM  C3   C2   single    1.531  0.020  1.531
 WFM  C3   C13  single    1.533  0.020  1.533
 WFM  C2   C1   single    1.527  0.020  1.527
 WFM  C13  O2   single    1.419  0.020  1.419
 WFM  C13  C    single    1.546  0.020  1.546
 WFM  O2   C14  single    1.404  0.020  1.404
 WFM  C20  C19  aromatic  1.360  0.020  1.360
 WFM  C20  N2   aromatic  1.382  0.020  1.382
 WFM  C19  C18  aromatic  1.428  0.020  1.428
 WFM  C1   C    single    1.531  0.020  1.531
 WFM  N2   C14  single    1.431  0.020  1.431
 WFM  N2   C15  aromatic  1.363  0.020  1.363
 WFM  N5   C17  single    1.340  0.020  1.340
 WFM  C18  C17  aromatic  1.409  0.020  1.409
 WFM  C18  C15  aromatic  1.396  0.020  1.396
 WFM  C14  C21  single    1.525  0.020  1.525
 WFM  C    C21  single    1.545  0.020  1.545
 WFM  C    O    single    1.399  0.020  1.399
 WFM  C17  N4   aromatic  1.336  0.020  1.336
 WFM  C15  N3   aromatic  1.334  0.020  1.334
 WFM  C21  O3   single    1.399  0.020  1.399
 WFM  N4   C16  aromatic  1.331  0.020  1.331
 WFM  N3   C16  aromatic  1.318  0.020  1.318
 WFM  C5   H1   single    0.930  0.020  1.080
 WFM  C6   H2   single    0.930  0.020  1.080
 WFM  C8   H3   single    0.930  0.020  1.080
 WFM  C13  H4   single    0.970  0.020  1.090
 WFM  C20  H5   single    0.930  0.020  1.080
 WFM  C21  H6   single    0.970  0.020  1.090
 WFM  N    H7   single    0.890  0.020  1.040
 WFM  N    H8   single    0.890  0.020  1.040
 WFM  C12  H9   single    0.930  0.020  1.080
 WFM  C3   H10  single    0.970  0.020  1.090
 WFM  C2   H11  single    0.970  0.020  1.090
 WFM  C2   H12  single    0.970  0.020  1.090
 WFM  C1   H13  single    0.970  0.020  1.090
 WFM  C1   H14  single    0.970  0.020  1.090
 WFM  C14  H15  single    0.970  0.020  1.090
 WFM  O3   H16  single    0.850  0.020  0.980
 WFM  O    H17  single    0.850  0.020  0.980
 WFM  C19  H18  single    0.930  0.020  1.080
 WFM  N5   H19  single    0.860  0.020  1.020
 WFM  N5   H20  single    0.860  0.020  1.020
 WFM  C16  H21  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
 WFM  C11  N1   C10  120.43  3.000
 WFM  C16  N3   C15  112.64  3.000
 WFM  O1   C4   C12  124.89  3.000
 WFM  O1   C4   C5   114.76  3.000
 WFM  C12  C4   C5   120.35  3.000
 WFM  H1   C5   C6   120.82  3.000
 WFM  H1   C5   C4   119.11  3.000
 WFM  C6   C5   C4   120.07  3.000
 WFM  H2   C6   C7   119.23  3.000
 WFM  H2   C6   C5   120.05  3.000
 WFM  C7   C6   C5   120.73  3.000
 WFM  C11  C7   C8   117.34  3.000
 WFM  C11  C7   C6   119.38  3.000
 WFM  C8   C7   C6   123.28  3.000
 WFM  H3   C8   C9   121.02  3.000
 WFM  H3   C8   C7   119.32  3.000
 WFM  C9   C8   C7   119.66  3.000
 WFM  N    C10  C9   121.59  3.000
 WFM  C9   C10  N1   120.82  3.000
 WFM  N    C10  N1   117.55  3.000
 WFM  H4   C13  C    111.13  3.000
 WFM  H4   C13  O2   109.95  3.000
 WFM  C    C13  O2   107.62  3.000
 WFM  H4   C13  C3   110.92  3.000
 WFM  C    C13  C3   106.87  3.000
 WFM  O2   C13  C3   110.25  3.000
 WFM  C18  C15  N2   108.01  3.000
 WFM  C18  C15  N3   125.89  3.000
 WFM  N2   C15  N3   126.10  3.000
 WFM  N4   C17  N5   118.30  3.000
 WFM  N4   C17  C18  119.23  3.000
 WFM  N5   C17  C18  122.47  3.000
 WFM  H5   C20  C19  129.22  3.000
 WFM  H5   C20  N2   120.91  3.000
 WFM  C19  C20  N2   109.86  3.000
 WFM  H6   C21  C    109.67  3.000
 WFM  H6   C21  O3   110.95  3.000
 WFM  C    C21  O3   113.76  3.000
 WFM  H6   C21  C14  109.40  3.000
 WFM  O3   C21  C14  110.24  3.000
 WFM  C    C21  C14  102.47  3.000
 WFM  BR   C9   C10  120.56  3.000
 WFM  C10  C9   C8   119.62  3.000
 WFM  BR   C9   C8   119.82  3.000
 WFM  H8   N    H7   115.13  3.000
 WFM  H8   N    C10  120.88  3.000
 WFM  H7   N    C10  116.24  3.000
 WFM  C12  C11  C7   119.34  3.000
 WFM  C12  C11  N1   118.52  3.000
 WFM  C7   C11  N1   122.14  3.000
 WFM  H9   C12  C11  117.31  3.000
 WFM  H9   C12  C4   122.57  3.000
 WFM  C11  C12  C4   120.12  3.000
 WFM  C3   O1   C4   119.50  3.000
 WFM  H10  C3   C2   113.48  3.000
 WFM  H10  C3   O1   110.39  3.000
 WFM  C2   C3   O1   110.90  3.000
 WFM  H10  C3   C13  110.58  3.000
 WFM  C2   C3   C13  104.78  3.000
 WFM  O1   C3   C13  106.34  3.000
 WFM  H12  C2   H11  106.35  3.000
 WFM  H12  C2   C1   113.52  3.000
 WFM  H11  C2   C1   111.14  3.000
 WFM  H12  C2   C3   113.23  3.000
 WFM  H11  C2   C3   108.86  3.000
 WFM  C1   C2   C3   103.76  3.000
 WFM  H14  C1   H13  107.44  3.000
 WFM  H14  C1   C    109.53  3.000
 WFM  H13  C1   C    112.62  3.000
 WFM  H14  C1   C2   110.46  3.000
 WFM  H13  C1   C2   113.22  3.000
 WFM  C    C1   C2   103.55  3.000
 WFM  C14  O2   C13  110.09  3.000
 WFM  H15  C14  N2   106.69  3.000
 WFM  H15  C14  O2   112.01  3.000
 WFM  N2   C14  O2   108.78  3.000
 WFM  H15  C14  C21  110.14  3.000
 WFM  N2   C14  C21  114.53  3.000
 WFM  O2   C14  C21  104.79  3.000
 WFM  H16  O3   C21  109.17  3.000
 WFM  O    C    C1   114.99  3.000
 WFM  O    C    C21  110.30  3.000
 WFM  C1   C    C21  112.58  3.000
 WFM  O    C    C13  110.74  3.000
 WFM  C21  C    C13  102.17  3.000
 WFM  C1   C    C13  105.17  3.000
 WFM  H17  O    C    107.76  3.000
 WFM  C14  N2   C20  125.88  3.000
 WFM  C14  N2   C15  125.61  3.000
 WFM  C20  N2   C15  108.44  3.000
 WFM  H18  C19  C18  127.90  3.000
 WFM  H18  C19  C20  125.75  3.000
 WFM  C18  C19  C20  106.34  3.000
 WFM  C19  C18  C17  137.23  3.000
 WFM  C17  C18  C15  115.43  3.000
 WFM  C19  C18  C15  107.33  3.000
 WFM  C16  N4   C17  118.56  3.000
 WFM  H21  C16  N4   115.49  3.000
 WFM  H21  C16  N3   116.26  3.000
 WFM  N4   C16  N3   128.25  3.000
 WFM  H20  N5   H19  117.30  3.000
 WFM  H20  N5   C17  120.98  3.000
 WFM  H19  N5   C17  119.33  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
 WFM  CONST_01  C8   C9   C10  N1     0.00   0.0  0
 WFM  CONST_02  C8   C7   C11  N1     0.00   0.0  0
 WFM  CONST_03  C6   C7   C11  N1   180.00   0.0  0
 WFM  CONST_04  C4   C12  C11  N1   180.00   0.0  0
 WFM  CONST_05  C20  N2   C15  N3   180.00   0.0  0
 WFM  CONST_06  C19  C18  C15  N3   180.00   0.0  0
 WFM  CONST_07  C17  C18  C15  N3     0.00   0.0  0
 WFM  CONST_08  C17  N4   C16  N3     0.00   0.0  0
 WFM  CONST_09  C7   C11  C12  C4     0.00   0.0  0
 WFM  CONST_10  C7   C6   C5   C4     0.00   0.0  0
 WFM  CONST_11  C8   C7   C6   C5   180.00   0.0  0
 WFM  CONST_12  C11  C7   C6   C5     0.00   0.0  0
 WFM  CONST_13  C11  C12  C4   C5     0.00   0.0  0
 WFM  CONST_14  C9   C8   C7   C6   180.00   0.0  0
 WFM  CONST_15  C12  C11  C7   C6     0.00   0.0  0
 WFM  CONST_16  C12  C4   C5   C6     0.00   0.0  0
 WFM  CONST_17  C10  C9   C8   C7     0.00   0.0  0
 WFM  CONST_18  C10  N1   C11  C7     0.00   0.0  0
 WFM  CONST_19  C12  C11  C7   C8   180.00   0.0  0
 WFM  CONST_20  C12  C11  N1   C10  180.00   0.0  0
 WFM  CONST_21  C19  C20  N2   C15    0.00   0.0  0
 WFM  CONST_22  C20  C19  C18  C15    0.00   0.0  0
 WFM  CONST_23  N4   C17  C18  C15    0.00   0.0  0
 WFM  CONST_24  N4   C16  N3   C15    0.00   0.0  0
 WFM  CONST_25  C20  C19  C18  C17  180.00   0.0  0
 WFM  CONST_26  N2   C15  C18  C17  180.00   0.0  0
 WFM  CONST_27  C18  C15  N2   C20    0.00   0.0  0
 WFM  CONST_28  C11  N1   C10  C9     0.00   0.0  0
 WFM  CONST_29  C11  C7   C8   C9     0.00   0.0  0
 WFM  CONST_30  C18  C19  C20  N2     0.00   0.0  0
 WFM  CONST_31  C19  C18  C15  N2     0.00   0.0  0
 WFM  CONST_32  C16  N3   C15  N2   180.00   0.0  0
 WFM  CONST_33  N4   C17  C18  C19  180.00   0.0  0
 WFM  CONST_34  C16  N4   C17  C18    0.00   0.0  0
 WFM  CONST_35  C16  N3   C15  C18    0.00   0.0  0
 WFM  CONST_36  C14  N2   C15  N3     0.00   0.0  0
 WFM  CONST_37  C19  C20  N2   C14  180.00   0.0  0
 WFM  CONST_38  C18  C15  N2   C14  180.00   0.0  0
 WFM  CONST_39  BR   C9   C10  N1   180.00   0.0  0
 WFM  CONST_40  O1   C4   C5   C6   180.00   0.0  0
 WFM  CONST_41  BR   C9   C8   C7   180.00   0.0  0
 WFM  CONST_42  N    C10  C9   C8   180.00   0.0  0
 WFM  CONST_43  N5   C17  C18  C15  180.00   0.0  0
 WFM  CONST_44  C11  N1   C10  N    180.00   0.0  0
 WFM  CONST_45  O1   C4   C12  C11  180.00   0.0  0
 WFM  CONST_46  N5   C17  C18  C19    0.00   0.0  0
 WFM  CONST_47  C16  N4   C17  N5   180.00   0.0  0
 WFM  CONST_48  H9   C12  C11  N1     0.00   0.0  0
 WFM  CONST_49  H2   C6   C5   C4   180.00   0.0  0
 WFM  CONST_50  H3   C8   C7   C6     0.00   0.0  0
 WFM  CONST_51  H1   C5   C6   C7   180.00   0.0  0
 WFM  CONST_52  H5   C20  N2   C15  180.00   0.0  0
 WFM  CONST_53  H18  C19  C18  C15  180.00   0.0  0
 WFM  CONST_54  H21  C16  N3   C15  180.00   0.0  0
 WFM  CONST_55  H7   N    C10  N1     0.00   0.0  0
 WFM  CONST_57  H19  N5   C17  C18  180.00   0.0  0
 WFM  CONST_58  H20  N5   C17  C18    0.00   0.0  0
 WFM  Var_01    C    C1   C2   C3    40.38  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
 WFM  chir_01  C13  C3   O2  C    negativ
 WFM  chir_02  C21  O3   C   C14  positiv
 WFM  chir_03  C3   O1   C2  C13  negativ
 WFM  chir_04  C14  O2   N2  C21  negativ
 WFM  chir_05  C    C21  C1  C13  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
 WFM  plan-1  N3   0.020
 WFM  plan-1  C15  0.020
 WFM  plan-1  C17  0.020
 WFM  plan-1  C20  0.020
 WFM  plan-1  C14  0.020
 WFM  plan-1  N2   0.020
 WFM  plan-1  C19  0.020
 WFM  plan-1  C18  0.020
 WFM  plan-1  N4   0.020
 WFM  plan-1  C16  0.020
 WFM  plan-1  H5   0.020
 WFM  plan-1  H18  0.020
 WFM  plan-1  H21  0.020
 WFM  plan-1  N5   0.020
 WFM  plan-2  N1   0.020
 WFM  plan-2  C4   0.020
 WFM  plan-2  C5   0.020
 WFM  plan-2  C6   0.020
 WFM  plan-2  C7   0.020
 WFM  plan-2  C8   0.020
 WFM  plan-2  C10  0.020
 WFM  plan-2  C9   0.020
 WFM  plan-2  N    0.020
 WFM  plan-2  C11  0.020
 WFM  plan-2  C12  0.020
 WFM  plan-2  O1   0.020
 WFM  plan-2  H1   0.020
 WFM  plan-2  H2   0.020
 WFM  plan-2  H3   0.020
 WFM  plan-2  H9   0.020
 WFM  plan-2  BR   0.020
 WFM  plan-3  C10  0.020
 WFM  plan-3  N    0.020
 WFM  plan-3  H7   0.020
 WFM  plan-3  H8   0.020
 WFM  plan-4  C17  0.020
 WFM  plan-4  H19  0.020
 WFM  plan-4  H20  0.020
 WFM  plan-4  N5   0.020

