# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 08:47:46 2022
#   Inital geometry file: a 149 line input string
#   Ligand name: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2S,3R,4S,5S,6R)-6-[(1S)-1,2-dihydroxyethyl]-3-fluoro-4,5-dihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)O[C@@H]4O[C@H]([C@@H](O)CO)[C@@H](O)[C@H](O)[C@H]4F)[C@@H](O)[C@H]3O
#
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
 AFH  AFH  '[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2S,3R,4S,5S,6R)-6-[(1S)-1,2-dihydroxyethyl]-3-fluoro-4,5-dihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)'  ligand  64  40  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AFH
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
 AFH  N9    N  NR5    0  -0.539  47.3432  11.4228   5.3041
 AFH  C8    C  CR15   0   0.109  47.9893  10.7513   4.3000
 AFH  N7    N  N      0  -0.447  49.0830  10.1682   4.6894
 AFH  C5    C  CR56   0  -0.011  49.1701  10.4641   6.0261
 AFH  C6    C  CR6    0   0.459  50.1084  10.1320   7.0208
 AFH  N6    N  NH2    0  -0.816  51.1917   9.3941   6.7749
 AFH  N1    N  N      0  -0.472  49.8917  10.5826   8.2620
 AFH  C2    C  CR16   0   0.045  48.8099  11.3180   8.5039
 AFH  N3    N  N      0  -0.455  47.8664  11.6959   7.6591
 AFH  C4    C  CR56   0   0.488  48.0949  11.2394   6.4301
 AFH  C1D   C  CH1    0   0.182  46.0963  12.1353   5.2125
 AFH  C2D   C  CH1    0  -0.033  46.1066  13.3077   4.2223
 AFH  O2'   O  OH1    0  -0.647  46.7017  14.4645   4.7094
 AFH  C3D   C  CH1    0  -0.043  44.6166  13.4129   3.8768
 AFH  C4D   C  CH1    0  -0.038  44.2064  11.9425   3.8581
 AFH  O4D   O  O2     0  -0.492  45.0987  11.2661   4.7550
 AFH  O3D   O  OH1    0  -0.666  43.9280  14.2048   4.8173
 AFH  C5D   C  CH2    0  -0.221  44.3285  11.3049   2.4798
 AFH  O5D   O  O2     0  -0.613  43.3442  11.8266   1.6116
 AFH  PA    P  P      0   1.365  41.9543  10.9815   1.3589
 AFH  O1A   O  O      0  -0.770  41.1047  11.8582   0.5024
 AFH  O2A   O  OP    -1  -0.791  41.4690  10.4018   2.6486
 AFH  O3A   O  O2     0  -0.739  42.5376   9.7908   0.3700
 AFH  PB    P  P      0   1.340  42.8483   8.2046   0.5673
 AFH  O1B   O  O      0  -0.773  43.3197   7.6904  -0.7547
 AFH  O2B   O  OP    -1  -0.777  43.6279   7.9206   1.8124
 AFH  O3B   O  O2     0  -0.635  41.2668   7.7255   0.8158
 AFH  C1'   C  CH1    0   0.258  40.9914   6.3765   0.8703
 AFH  C2'   C  CH1    0   0.148  39.9020   6.1092   1.8988
 AFH  C3'   C  CH1    0  -0.037  39.4675   4.6503   1.8838
 AFH  C4'   C  CH1    0   0.008  39.1076   4.2250   0.4639
 AFH  C5'   C  CH1    0   0.015  40.2657   4.5977  -0.4715
 AFH  C6'   C  CH1    0  -0.037  40.0128   4.2550  -1.9372
 AFH  C7'   C  CH2    0  -0.164  41.1576   4.7017  -2.8400
 AFH  F     F  F      0  -0.376  40.3934   6.4147   3.1670
 AFH  O3'   O  OH1    0  -0.662  38.3510   4.4347   2.7073
 AFH  O4'   O  OH1    0  -0.665  38.8809   2.8367   0.4708
 AFH  O5'   O  O2     0  -0.497  40.5054   5.9850  -0.3817
 AFH  O6'   O  OH1    0  -0.671  38.8481   4.8774  -2.4354
 AFH  O7'   O  OH1    0  -0.669  42.3575   4.1313  -2.3733
 AFH  H8    H  HCR5   0   0.301  47.5966  10.7235   3.2937
 AFH  HN61  H  HNH2   0   0.411  51.3802   9.0365   5.8550
 AFH  HN62  H  HNH2   0   0.402  51.8344   9.1722   7.5156
 AFH  H2    H  HCR6   0   0.249  48.6923  11.6487   9.5305
 AFH  H1D   H  HCH1   0   0.257  45.8841  12.4963   6.2273
 AFH  H2D   H  HCH1   0   0.266  46.6583  13.0134   3.3235
 AFH  HO2'  H  HOH1   0   0.445  46.0786  14.8905   5.3115
 AFH  H3D   H  HCH1   0   0.271  44.4585  13.8841   2.9050
 AFH  H4D   H  HCH1   0   0.258  43.1809  11.8099   4.2165
 AFH  HO3A  H  HOH1   0   0.459  43.7320  13.6963   5.6120
 AFH  H5'1  H  HCH2   0   0.242  44.2662  10.2184   2.5811
 AFH  H5'2  H  HCH2   0   0.225  45.3091  11.5287   2.0467
 AFH  H1'   H  HCH1   0   0.192  41.8835   5.7785   1.1336
 AFH  H2'   H  HCH1   0   0.222  39.0445   6.7631   1.7064
 AFH  H3'   H  HCH1   0   0.223  40.3251   4.0389   2.2088
 AFH  H4'   H  HCH1   0   0.228  38.2093   4.7788   0.1568
 AFH  H5'   H  HCH1   0   0.225  41.1547   4.0359  -0.1456
 AFH  H6'   H  HCH1   0   0.228  39.9360   3.1621  -2.0053
 AFH  H7'1  H  HCH2   0   0.204  41.2051   5.7963  -2.8531
 AFH  H7'2  H  HCH2   0   0.206  40.9283   4.3766  -3.8631
 AFH  HO3'  H  HOH1   0   0.454  38.6281   4.4882   3.6271
 AFH  HO4'  H  HOH1   0   0.458  38.2407   2.6182  -0.2122
 AFH  HO6'  H  HOH1   0   0.457  38.0937   4.3017  -2.2851
 AFH  HO7'  H  HOH1   0   0.456  43.0906   4.5591  -2.8237

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
 AFH  N9   C8    aromatic  1.370  0.020  1.370
 AFH  N9   C4    aromatic  1.366  0.020  1.366
 AFH  N9   C1D   single    1.439  0.020  1.439
 AFH  C8   N7    aromatic  1.299  0.020  1.299
 AFH  C8   H8    single    0.930  0.020  1.080
 AFH  N7   C5    aromatic  1.372  0.020  1.372
 AFH  C5   C6    aromatic  1.407  0.020  1.407
 AFH  C5   C4    aromatic  1.386  0.020  1.386
 AFH  C6   N6    single    1.334  0.020  1.334
 AFH  C6   N1    aromatic  1.338  0.020  1.338
 AFH  N6   HN61  single    0.860  0.020  1.020
 AFH  N6   HN62  single    0.860  0.020  1.020
 AFH  N1   C2    aromatic  1.330  0.020  1.330
 AFH  C2   N3    aromatic  1.322  0.020  1.322
 AFH  C2   H2    single    0.930  0.020  1.080
 AFH  N3   C4    aromatic  1.331  0.020  1.331
 AFH  C1D  C2D   single    1.535  0.020  1.535
 AFH  C1D  O4D   single    1.400  0.020  1.400
 AFH  C1D  H1D   single    0.970  0.020  1.090
 AFH  C2D  O2'   single    1.389  0.020  1.389
 AFH  C2D  C3D   single    1.533  0.020  1.533
 AFH  C2D  H2D   single    0.970  0.020  1.090
 AFH  O2'  HO2'  single    0.850  0.020  0.980
 AFH  C3D  C4D   single    1.527  0.020  1.527
 AFH  C3D  O3D   single    1.409  0.020  1.409
 AFH  C3D  H3D   single    0.970  0.020  1.090
 AFH  C4D  O4D   single    1.435  0.020  1.435
 AFH  C4D  C5D   single    1.524  0.020  1.524
 AFH  C4D  H4D   single    0.970  0.020  1.090
 AFH  O3D  HO3A  single    0.850  0.020  0.980
 AFH  C5D  O5D   single    1.412  0.020  1.412
 AFH  C5D  H5'1  single    0.970  0.020  1.090
 AFH  C5D  H5'2  single    0.970  0.020  1.090
 AFH  O5D  PA    single    1.646  0.020  1.646
 AFH  PA   O1A   deloc     1.491  0.020  1.491
 AFH  PA   O2A   deloc     1.495  0.020  1.495
 AFH  PA   O3A   single    1.654  0.020  1.654
 AFH  O3A  PB    single    1.628  0.020  1.628
 AFH  PB   O1B   deloc     1.495  0.020  1.495
 AFH  PB   O2B   deloc     1.496  0.020  1.496
 AFH  PB   O3B   single    1.671  0.020  1.671
 AFH  O3B  C1'   single    1.378  0.020  1.378
 AFH  C1'  C2'   single    1.522  0.020  1.522
 AFH  C1'  O5'   single    1.399  0.020  1.399
 AFH  C1'  H1'   single    0.970  0.020  1.090
 AFH  C2'  C3'   single    1.522  0.020  1.522
 AFH  C2'  F     single    1.394  0.020  1.394
 AFH  C2'  H2'   single    0.970  0.020  1.090
 AFH  C3'  C4'   single    1.525  0.020  1.525
 AFH  C3'  O3'   single    1.404  0.020  1.404
 AFH  C3'  H3'   single    0.970  0.020  1.090
 AFH  C4'  C5'   single    1.535  0.020  1.535
 AFH  C4'  O4'   single    1.407  0.020  1.407
 AFH  C4'  H4'   single    0.970  0.020  1.090
 AFH  C5'  C6'   single    1.526  0.020  1.526
 AFH  C5'  O5'   single    1.411  0.020  1.411
 AFH  C5'  H5'   single    0.970  0.020  1.090
 AFH  C6'  C7'   single    1.525  0.020  1.525
 AFH  C6'  O6'   single    1.411  0.020  1.411
 AFH  C6'  H6'   single    0.970  0.020  1.090
 AFH  C7'  O7'   single    1.408  0.020  1.408
 AFH  C7'  H7'1  single    0.970  0.020  1.090
 AFH  C7'  H7'2  single    0.970  0.020  1.090
 AFH  O3'  HO3'  single    0.850  0.020  0.980
 AFH  O4'  HO4'  single    0.850  0.020  0.980
 AFH  O6'  HO6'  single    0.850  0.020  0.980
 AFH  O7'  HO7'  single    0.850  0.020  0.980

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
 AFH  C1D   N9   C4    126.56  3.000
 AFH  C1D   N9   C8    127.21  3.000
 AFH  C4    N9   C8    106.19  3.000
 AFH  H8    C8   N7    125.00  3.000
 AFH  H8    C8   N9    121.58  3.000
 AFH  N7    C8   N9    113.42  3.000
 AFH  C5    N7   C8    104.40  3.000
 AFH  C4    C5   C6    116.31  3.000
 AFH  C4    C5   N7    110.82  3.000
 AFH  C6    C5   N7    132.86  3.000
 AFH  N1    C6   N6    119.27  3.000
 AFH  N1    C6   C5    117.92  3.000
 AFH  N6    C6   C5    122.81  3.000
 AFH  HN62  N6   HN61  118.43  3.000
 AFH  HN62  N6   C6    120.36  3.000
 AFH  HN61  N6   C6    121.20  3.000
 AFH  C2    N1   C6    119.11  3.000
 AFH  H2    C2   N3    116.12  3.000
 AFH  H2    C2   N1    115.39  3.000
 AFH  N3    C2   N1    128.49  3.000
 AFH  C4    N3   C2    111.70  3.000
 AFH  N3    C4   C5    126.47  3.000
 AFH  N3    C4   N9    128.36  3.000
 AFH  C5    C4   N9    105.17  3.000
 AFH  H1D   C1D  O4D   111.62  3.000
 AFH  H1D   C1D  C2D   110.28  3.000
 AFH  O4D   C1D  C2D   105.56  3.000
 AFH  H1D   C1D  N9    105.75  3.000
 AFH  O4D   C1D  N9    109.32  3.000
 AFH  C2D   C1D  N9    114.43  3.000
 AFH  H2D   C2D  C3D   108.86  3.000
 AFH  H2D   C2D  O2'   107.20  3.000
 AFH  C3D   C2D  O2'   115.99  3.000
 AFH  H2D   C2D  C1D   109.13  3.000
 AFH  C3D   C2D  C1D   101.03  3.000
 AFH  O2'   C2D  C1D   114.38  3.000
 AFH  HO2'  O2'  C2D   108.03  3.000
 AFH  H3D   C3D  O3D   106.31  3.000
 AFH  H3D   C3D  C4D   111.47  3.000
 AFH  O3D   C3D  C4D   114.72  3.000
 AFH  H3D   C3D  C2D   111.78  3.000
 AFH  O3D   C3D  C2D   111.29  3.000
 AFH  C4D   C3D  C2D   101.41  3.000
 AFH  H4D   C4D  C5D   108.71  3.000
 AFH  H4D   C4D  O4D   108.72  3.000
 AFH  C5D   C4D  O4D   108.57  3.000
 AFH  H4D   C4D  C3D   111.37  3.000
 AFH  C5D   C4D  C3D   113.12  3.000
 AFH  O4D   C4D  C3D   106.22  3.000
 AFH  C4D   O4D  C1D   110.78  3.000
 AFH  HO3A  O3D  C3D   110.69  3.000
 AFH  H5'2  C5D  H5'1  106.91  3.000
 AFH  H5'2  C5D  O5D   107.78  3.000
 AFH  H5'1  C5D  O5D   112.61  3.000
 AFH  H5'2  C5D  C4D   110.12  3.000
 AFH  H5'1  C5D  C4D   109.12  3.000
 AFH  O5D   C5D  C4D   110.22  3.000
 AFH  PA    O5D  C5D   119.55  3.000
 AFH  O3A   PA   O2A   110.55  3.000
 AFH  O3A   PA   O1A   106.30  3.000
 AFH  O2A   PA   O1A   122.59  3.000
 AFH  O3A   PA   O5D    99.42  3.000
 AFH  O2A   PA   O5D   109.92  3.000
 AFH  O1A   PA   O5D   105.51  3.000
 AFH  PB    O3A  PA    134.12  3.000
 AFH  O3B   PB   O2B   108.36  3.000
 AFH  O3B   PB   O1B   109.35  3.000
 AFH  O2B   PB   O1B   120.42  3.000
 AFH  O3B   PB   O3A    96.70  3.000
 AFH  O2B   PB   O3A   112.65  3.000
 AFH  O1B   PB   O3A   106.75  3.000
 AFH  C1'   O3B  PB    118.41  3.000
 AFH  H1'   C1'  O5'   110.00  3.000
 AFH  H1'   C1'  C2'   108.76  3.000
 AFH  O5'   C1'  C2'   107.88  3.000
 AFH  H1'   C1'  O3B   112.18  3.000
 AFH  O5'   C1'  O3B   107.94  3.000
 AFH  C2'   C1'  O3B   109.98  3.000
 AFH  H2'   C2'  F     107.76  3.000
 AFH  H2'   C2'  C3'   110.30  3.000
 AFH  F     C2'  C3'   108.64  3.000
 AFH  H2'   C2'  C1'   109.68  3.000
 AFH  F     C2'  C1'   108.91  3.000
 AFH  C3'   C2'  C1'   111.46  3.000
 AFH  H3'   C3'  O3'   111.13  3.000
 AFH  H3'   C3'  C4'   107.66  3.000
 AFH  O3'   C3'  C4'   108.39  3.000
 AFH  H3'   C3'  C2'   107.86  3.000
 AFH  O3'   C3'  C2'   111.62  3.000
 AFH  C4'   C3'  C2'   110.11  3.000
 AFH  H4'   C4'  O4'   111.53  3.000
 AFH  H4'   C4'  C5'   108.91  3.000
 AFH  O4'   C4'  C5'   111.37  3.000
 AFH  H4'   C4'  C3'   108.20  3.000
 AFH  O4'   C4'  C3'   107.98  3.000
 AFH  C5'   C4'  C3'   108.76  3.000
 AFH  H5'   C5'  O5'   110.23  3.000
 AFH  H5'   C5'  C6'   107.66  3.000
 AFH  O5'   C5'  C6'   108.06  3.000
 AFH  H5'   C5'  C4'   107.76  3.000
 AFH  O5'   C5'  C4'   109.17  3.000
 AFH  C6'   C5'  C4'   113.94  3.000
 AFH  H6'   C6'  O6'   111.06  3.000
 AFH  H6'   C6'  C7'   107.91  3.000
 AFH  O6'   C6'  C7'   106.34  3.000
 AFH  H6'   C6'  C5'   107.14  3.000
 AFH  O6'   C6'  C5'   112.12  3.000
 AFH  C7'   C6'  C5'   112.23  3.000
 AFH  H7'2  C7'  H7'1  107.09  3.000
 AFH  H7'2  C7'  O7'   111.53  3.000
 AFH  H7'1  C7'  O7'   111.82  3.000
 AFH  H7'2  C7'  C6'   107.95  3.000
 AFH  H7'1  C7'  C6'   109.41  3.000
 AFH  O7'   C7'  C6'   108.96  3.000
 AFH  HO3'  O3'  C3'   108.85  3.000
 AFH  HO4'  O4'  C4'   109.16  3.000
 AFH  C5'   O5'  C1'   113.03  3.000
 AFH  HO6'  O6'  C6'   109.18  3.000
 AFH  HO7'  O7'  C7'   108.32  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
 AFH  CONST_01  C5    N7   C8   N9     0.00   0.0  0
 AFH  CONST_02  N7    C5   C4   N9     0.00   0.0  0
 AFH  CONST_03  C6    C5   C4   N9   180.00   0.0  0
 AFH  CONST_04  C2    N3   C4   N9   180.00   0.0  0
 AFH  CONST_05  C5    C4   N9   C8     0.00   0.0  0
 AFH  CONST_06  N3    C4   N9   C8   180.00   0.0  0
 AFH  CONST_07  C6    C5   N7   C8   180.00   0.0  0
 AFH  CONST_08  C4    C5   N7   C8     0.00   0.0  0
 AFH  CONST_09  C4    N9   C8   N7     0.00   0.0  0
 AFH  CONST_10  N1    C6   C5   N7   180.00   0.0  0
 AFH  CONST_11  N3    C4   C5   N7   180.00   0.0  0
 AFH  CONST_12  C2    N1   C6   C5     0.00   0.0  0
 AFH  CONST_13  C2    N3   C4   C5     0.00   0.0  0
 AFH  CONST_14  N3    C4   C5   C6     0.00   0.0  0
 AFH  CONST_15  N3    C2   N1   C6     0.00   0.0  0
 AFH  CONST_16  C4    C5   C6   N1     0.00   0.0  0
 AFH  CONST_17  C4    N3   C2   N1     0.00   0.0  0
 AFH  CONST_18  C1D   N9   C8   N7   180.00   0.0  0
 AFH  CONST_19  C1D   N9   C4   C5   180.00   0.0  0
 AFH  CONST_20  C1D   N9   C4   N3     0.00   0.0  0
 AFH  CONST_21  N6    C6   C5   N7     0.00   0.0  0
 AFH  CONST_22  C4    C5   C6   N6   180.00   0.0  0
 AFH  CONST_23  C2    N1   C6   N6   180.00   0.0  0
 AFH  CONST_24  H8    C8   N7   C5   180.00   0.0  0
 AFH  CONST_25  H2    C2   N1   C6   180.00   0.0  0
 AFH  CONST_26  HN61  N6   C6   C5     0.00   0.0  0
 AFH  CONST_27  HN62  N6   C6   C5   180.00   0.0  0
 AFH  Var_01    O1A   PA   O5D  C5D  175.24  30.0  3
 AFH  Var_02    O1B   PB   O3A  PA   177.91  30.0  3
 AFH  Var_03    H5'1  C5D  O5D  PA    23.97  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
 AFH  chir_01  C1D  N9   C2D  O4D  negativ
 AFH  chir_02  C2D  O2'  C3D  C1D  positiv
 AFH  chir_03  C3D  O3D  C4D  C2D  positiv
 AFH  chir_04  C4D  O4D  C3D  C5D  negativ
 AFH  chir_07  C1'  O3B  C2'  O5'  negativ
 AFH  chir_08  C2'  F    C3'  C1'  positiv
 AFH  chir_09  C3'  O3'  C2'  C4'  positiv
 AFH  chir_10  C4'  O4'  C5'  C3'  positiv
 AFH  chir_11  C5'  O5'  C6'  C4'  positiv
 AFH  chir_12  C6'  O6'  C5'  C7'  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
 AFH  plan-1  C6    0.020
 AFH  plan-1  N6    0.020
 AFH  plan-1  HN61  0.020
 AFH  plan-1  HN62  0.020
 AFH  plan-2  N9    0.020
 AFH  plan-2  C8    0.020
 AFH  plan-2  N7    0.020
 AFH  plan-2  C5    0.020
 AFH  plan-2  C6    0.020
 AFH  plan-2  N6    0.020
 AFH  plan-2  N1    0.020
 AFH  plan-2  C2    0.020
 AFH  plan-2  N3    0.020
 AFH  plan-2  C4    0.020
 AFH  plan-2  C1D   0.020
 AFH  plan-2  H8    0.020
 AFH  plan-2  H2    0.020

