# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue May 19 23:49:21 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},6~{R})-6-methyl-3,4-bis(oxidanyl)-5-oxidanylidene-oxan-2-yl] hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC(=Nc34)N)[C@@H](O)[C@@H](O)C1=O
#
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
 F7E  F7E  '[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},6~{R})-6-methyl-3,4-bis(oxidanyl)-5-oxidanylidene-oxan-2-yl] hydrogen phosphate'  ligand  59  38  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_F7E
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
 F7E  O3   O  O2     0  -0.618   0.1538  -2.9261   0.1341
 F7E  C3   C  CR15   0   0.226   3.6116  -1.2870  -0.7541
 F7E  C4   C  CR15   0  -0.053   4.3096  -2.3582   0.0875
 F7E  O4   O  OP    -1  -0.787  -1.4588  -3.7574   1.9454
 F7E  C7   C  CH2    0  -0.151   1.4201  -3.4891   0.3738
 F7E  C9   C  CH1    0   0.003  -5.3125   0.1632  -1.4689
 F7E  O7   O  OH1    0  -0.660  -5.4938  -1.2131  -1.2957
 F7E  O8   O  O2     0  -0.498  -4.0520   2.0261  -0.7080
 F7E  C8   C  CH1    0   0.315  -4.2733   0.6530  -0.4661
 F7E  O6   O  O2     0  -0.629  -3.0778   0.0109  -0.6993
 F7E  C6   C  CR15   0  -0.049   2.3199  -3.2219  -0.8193
 F7E  C5   C  CR15   0  -0.026   3.7544  -3.6412  -0.5371
 F7E  O5   O  O2     0  -0.735  -1.8900  -1.6574   0.6254
 F7E  C1   C  CR5    0  -0.098   3.6447   1.9616   0.7683
 F7E  O1   O  OH1    0  -0.653   5.6958  -2.2129  -0.0001
 F7E  C2   C  CR15   0   0.084   2.4201   0.2359   0.8798
 F7E  O2   O  OH1    0  -0.669   4.3962  -3.9280  -1.7524
 F7E  O13  O  O      0  -0.794   0.0198  -1.6659   2.3711
 F7E  P    P  P      0   1.371  -0.7719  -2.5292   1.4361
 F7E  P1   P  P      0   1.337  -1.8827  -0.0153   0.4586
 F7E  O11  O  OP    -1  -0.755  -0.6304   0.4302  -0.2150
 F7E  O12  O  O      0  -0.787  -2.3981   0.6138   1.7115
 F7E  C10  C  CH1    0  -0.088  -5.1303   2.8983  -0.4514
 F7E  C11  C  CH3    0  -0.686  -5.4178   3.1058   1.0337
 F7E  C12  C  C      0   0.380  -6.3681   2.4457  -1.2094
 F7E  O10  O  O      0  -0.381  -7.1528   3.2362  -1.6761
 F7E  C13  C  CH1    0  -0.145  -6.6145   0.9403  -1.2759
 F7E  O9   O  OH1    0  -0.650  -7.1821   0.5660  -0.0400
 F7E  O14  O  O      0  -0.482   2.3790  -1.8263  -1.1224
 F7E  N1   N  NR5    0  -0.544   3.3985  -0.0440  -0.0469
 F7E  N    N  N      0  -0.460   2.5419   1.4261   1.3839
 F7E  C14  C  CR5    0   0.500   4.1874   1.0609  -0.1292
 F7E  N2   N  N      0  -0.510   5.2519   1.2226  -0.9288
 F7E  C15  C  C      0   0.684   5.8158   2.3971  -0.8053
 F7E  N3   N  NH2    0  -0.834   6.9151   2.6914  -1.5167
 F7E  N4   N  NH1    0  -0.726   5.3606   3.3548   0.0552
 F7E  C    C  C      0   0.496   4.2544   3.2400   0.9074
 F7E  O    O  O      0  -0.480   3.9351   4.1676   1.6341
 F7E  H1   H  HCR5   0   0.254   4.2216  -1.0400  -1.6304
 F7E  H2   H  HCR5   0   0.250   3.9624  -2.2846   1.1255
 F7E  H4   H  HCH2   0   0.207   1.8696  -3.0789   1.2859
 F7E  H5   H  HCH2   0   0.225   1.3527  -4.5754   0.5110
 F7E  H7   H  HOH1   0   0.456  -6.1065  -1.5285  -1.9677
 F7E  H8   H  HCH1   0   0.204  -4.6208   0.4908   0.5618
 F7E  H9   H  HCR5   0   0.259   1.9218  -3.7399  -1.6971
 F7E  H10  H  HCR5   0   0.249   3.8043  -4.4893   0.1591
 F7E  H11  H  HOH1   0   0.468   6.1030  -2.6693   0.7430
 F7E  H12  H  HCR5   0   0.320   1.6292  -0.4618   1.1143
 F7E  H13  H  HOH1   0   0.448   5.3461  -3.8322  -1.6158
 F7E  H15  H  HCH1   0   0.278  -4.8313   3.8609  -0.8745
 F7E  H16  H  HCH3   0   0.250  -4.5117   3.4458   1.5344
 F7E  H17  H  HCH3   0   0.243  -6.1792   3.8762   1.1567
 F7E  H18  H  HCH3   0   0.242  -5.7702   2.2053   1.5323
 F7E  H19  H  HCH1   0   0.262  -7.2964   0.7341  -2.1116
 F7E  H20  H  HOH1   0   0.466  -8.0914   0.8814  -0.0098
 F7E  H21  H  HNH2   0   0.411   7.1717   2.0625  -2.2585
 F7E  H22  H  HNH2   0   0.413   7.2443   3.6381  -1.5976
 F7E  H23  H  HNH1   0   0.423   5.8522   4.2387   0.0922
 F7E  H6   H  HCH1   0   0.227  -4.9376   0.4037  -2.4755

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
 F7E  O2   C5   single    1.404  0.020  1.404
 F7E  C6   C5   single    1.521  0.020  1.521
 F7E  C6   O14  single    1.429  0.020  1.429
 F7E  C6   C7   single    1.518  0.020  1.518
 F7E  C5   C4   single    1.531  0.020  1.531
 F7E  O14  C3   single    1.395  0.020  1.395
 F7E  C3   C4   single    1.531  0.020  1.531
 F7E  C3   N1   single    1.446  0.020  1.446
 F7E  C7   O3   single    1.406  0.020  1.406
 F7E  O12  P1   deloc     1.494  0.020  1.494
 F7E  C11  C10  single    1.527  0.020  1.527
 F7E  C2   N1   aromatic  1.376  0.020  1.376
 F7E  C2   N    aromatic  1.298  0.020  1.298
 F7E  O1   C4   single    1.397  0.020  1.397
 F7E  N1   C14  aromatic  1.360  0.020  1.360
 F7E  O3   P    single    1.646  0.020  1.646
 F7E  C10  O8   single    1.410  0.020  1.410
 F7E  C10  C12  single    1.520  0.020  1.520
 F7E  N    C1   aromatic  1.372  0.020  1.372
 F7E  O8   C8   single    1.412  0.020  1.412
 F7E  P1   O5   single    1.651  0.020  1.651
 F7E  P1   O11  deloc     1.490  0.020  1.490
 F7E  P1   O6   single    1.664  0.020  1.664
 F7E  O5   P    single    1.633  0.020  1.633
 F7E  C14  C1   aromatic  1.383  0.020  1.383
 F7E  C14  N2   single    1.341  0.020  1.341
 F7E  O13  P    deloc     1.499  0.020  1.499
 F7E  O6   C8   single    1.377  0.020  1.377
 F7E  P    O4   deloc     1.497  0.020  1.497
 F7E  C8   C9   single    1.525  0.020  1.525
 F7E  C1   C    single    1.423  0.020  1.423
 F7E  C12  O10  double    1.208  0.020  1.208
 F7E  C12  C13  single    1.527  0.020  1.527
 F7E  N2   C15  double    1.309  0.020  1.309
 F7E  C    O    double    1.221  0.020  1.221
 F7E  C    N4   single    1.401  0.020  1.401
 F7E  C9   C13  single    1.528  0.020  1.528
 F7E  C9   O7   single    1.399  0.020  1.399
 F7E  C13  O9   single    1.411  0.020  1.411
 F7E  C15  N4   single    1.366  0.020  1.366
 F7E  C15  N3   single    1.342  0.020  1.342
 F7E  C3   H1   single    0.970  0.020  1.090
 F7E  C4   H2   single    0.970  0.020  1.090
 F7E  C7   H4   single    0.970  0.020  1.090
 F7E  C7   H5   single    0.970  0.020  1.090
 F7E  C9   H6   single    0.970  0.020  1.090
 F7E  O7   H7   single    0.850  0.020  0.980
 F7E  C8   H8   single    0.970  0.020  1.090
 F7E  C6   H9   single    0.970  0.020  1.090
 F7E  C5   H10  single    0.970  0.020  1.090
 F7E  O1   H11  single    0.850  0.020  0.980
 F7E  C2   H12  single    0.930  0.020  1.080
 F7E  O2   H13  single    0.850  0.020  0.980
 F7E  C10  H15  single    0.970  0.020  1.090
 F7E  C11  H16  single    0.970  0.020  1.090
 F7E  C11  H17  single    0.970  0.020  1.090
 F7E  C11  H18  single    0.970  0.020  1.090
 F7E  C13  H19  single    0.970  0.020  1.090
 F7E  O9   H20  single    0.850  0.020  0.980
 F7E  N3   H21  single    0.890  0.020  1.040
 F7E  N3   H22  single    0.890  0.020  1.040
 F7E  N4   H23  single    0.860  0.020  1.020

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
 F7E  P    O3   C7   117.91  3.000
 F7E  H1   C3   N1   106.22  3.000
 F7E  H1   C3   O14  111.59  3.000
 F7E  N1   C3   O14  109.35  3.000
 F7E  H1   C3   C4   110.09  3.000
 F7E  N1   C3   C4   113.57  3.000
 F7E  O14  C3   C4   106.11  3.000
 F7E  H2   C4   O1   111.50  3.000
 F7E  H2   C4   C5   109.11  3.000
 F7E  O1   C4   C5   114.93  3.000
 F7E  H2   C4   C3   109.21  3.000
 F7E  O1   C4   C3   110.21  3.000
 F7E  C5   C4   C3   101.35  3.000
 F7E  H5   C7   H4   106.96  3.000
 F7E  H5   C7   C6   108.00  3.000
 F7E  H4   C7   C6   110.18  3.000
 F7E  H5   C7   O3   111.25  3.000
 F7E  H4   C7   O3   111.17  3.000
 F7E  C6   C7   O3   109.22  3.000
 F7E  H6   C9   C13  107.13  3.000
 F7E  H6   C9   C8   107.40  3.000
 F7E  C13  C9   C8   109.52  3.000
 F7E  H6   C9   O7   111.86  3.000
 F7E  C13  C9   O7   111.97  3.000
 F7E  C8   C9   O7   108.84  3.000
 F7E  H7   O7   C9   108.57  3.000
 F7E  C10  O8   C8   116.78  3.000
 F7E  H8   C8   O6   111.39  3.000
 F7E  H8   C8   O8   110.73  3.000
 F7E  O6   C8   O8   106.77  3.000
 F7E  H8   C8   C9   110.65  3.000
 F7E  O6   C8   C9   109.30  3.000
 F7E  O8   C8   C9   107.85  3.000
 F7E  P1   O6   C8   120.86  3.000
 F7E  H9   C6   O14  107.89  3.000
 F7E  H9   C6   C5   111.19  3.000
 F7E  O14  C6   C5   105.63  3.000
 F7E  H9   C6   C7   109.36  3.000
 F7E  O14  C6   C7   111.29  3.000
 F7E  C5   C6   C7   111.39  3.000
 F7E  H10  C5   O2   111.73  3.000
 F7E  H10  C5   C6   111.92  3.000
 F7E  O2   C5   C6   109.08  3.000
 F7E  H10  C5   C4   111.84  3.000
 F7E  C6   C5   C4   100.76  3.000
 F7E  O2   C5   C4   111.01  3.000
 F7E  P1   O5   P    125.33  3.000
 F7E  C    C1   C14  118.72  3.000
 F7E  C    C1   N    130.64  3.000
 F7E  C14  C1   N    110.64  3.000
 F7E  H11  O1   C4   108.79  3.000
 F7E  H12  C2   N    125.20  3.000
 F7E  H12  C2   N1   122.36  3.000
 F7E  N    C2   N1   112.40  3.000
 F7E  H13  O2   C5   107.89  3.000
 F7E  O13  P    O5   111.33  3.000
 F7E  O13  P    O4   120.19  3.000
 F7E  O5   P    O4   107.02  3.000
 F7E  O4   P    O3   109.23  3.000
 F7E  O13  P    O3   109.59  3.000
 F7E  O5   P    O3    96.95  3.000
 F7E  O12  P1   O11  122.91  3.000
 F7E  O11  P1   O5   110.29  3.000
 F7E  O12  P1   O5   109.43  3.000
 F7E  O11  P1   O6   106.51  3.000
 F7E  O5   P1   O6    94.75  3.000
 F7E  O12  P1   O6   109.22  3.000
 F7E  H15  C10  C12  106.97  3.000
 F7E  H15  C10  C11  107.96  3.000
 F7E  C12  C10  C11  111.84  3.000
 F7E  H15  C10  O8   105.37  3.000
 F7E  C12  C10  O8   110.34  3.000
 F7E  C11  C10  O8   113.89  3.000
 F7E  H18  C11  H17  107.88  3.000
 F7E  H18  C11  H16  108.49  3.000
 F7E  H17  C11  H16  107.97  3.000
 F7E  H18  C11  C10  113.22  3.000
 F7E  H17  C11  C10  109.71  3.000
 F7E  H16  C11  C10  109.43  3.000
 F7E  C13  C12  O10  121.58  3.000
 F7E  C13  C12  C10  116.52  3.000
 F7E  O10  C12  C10  121.79  3.000
 F7E  H19  C13  O9   111.53  3.000
 F7E  H19  C13  C12  108.57  3.000
 F7E  O9   C13  C12  106.76  3.000
 F7E  H19  C13  C9   109.72  3.000
 F7E  O9   C13  C9   108.57  3.000
 F7E  C12  C13  C9   111.67  3.000
 F7E  H20  O9   C13  108.69  3.000
 F7E  C6   O14  C3   110.98  3.000
 F7E  C14  N1   C2   106.73  3.000
 F7E  C14  N1   C3   125.68  3.000
 F7E  C2   N1   C3   127.51  3.000
 F7E  C2   N    C1   105.02  3.000
 F7E  N2   C14  N1   126.47  3.000
 F7E  N2   C14  C1   128.32  3.000
 F7E  N1   C14  C1   105.20  3.000
 F7E  C15  N2   C14  113.20  3.000
 F7E  N4   C15  N3   116.96  3.000
 F7E  N3   C15  N2   119.98  3.000
 F7E  N4   C15  N2   123.04  3.000
 F7E  H22  N3   H21  116.47  3.000
 F7E  H22  N3   C15  121.15  3.000
 F7E  H21  N3   C15  117.57  3.000
 F7E  H23  N4   C    115.64  3.000
 F7E  H23  N4   C15  118.27  3.000
 F7E  C    N4   C15  126.09  3.000
 F7E  O    C    N4   120.42  3.000
 F7E  N4   C    C1   110.63  3.000
 F7E  O    C    C1   128.95  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
 F7E  CONST_01  N1   C2   N    C1     0.00   0.0  0
 F7E  CONST_02  C2   N1   C14  C1     0.00   0.0  0
 F7E  CONST_03  C14  C1   N    C2     0.00   0.0  0
 F7E  CONST_04  N    C1   C14  N1     0.00   0.0  0
 F7E  CONST_05  C14  N1   C2   N      0.00   0.0  0
 F7E  CONST_06  N    C2   N1   C3   180.00   0.0  0
 F7E  CONST_07  C1   C14  N1   C3   180.00   0.0  0
 F7E  CONST_08  N2   C14  N1   C3     0.00   0.0  0
 F7E  CONST_09  C15  N4   C    C1     0.00   0.0  0
 F7E  CONST_10  N4   C15  N2   C14    0.00   0.0  0
 F7E  CONST_11  C    N4   C15  N2     0.00   0.0  0
 F7E  CONST_12  N3   C15  N2   C14  180.00   0.0  0
 F7E  CONST_13  O    C    N4   C15  180.00   0.0  0
 F7E  CONST_14  C    N4   C15  N3   180.00   0.0  0
 F7E  CONST_15  H12  C2   N1   C3     0.00   0.0  0
 F7E  CONST_16  H23  N4   C    C1   180.00   0.0  0
 F7E  CONST_17  H21  N3   C15  N2     0.00   0.0  0
 F7E  CONST_18  H22  N3   C15  N2   180.00   0.0  0
 F7E  Var_01    O12  P1   O6   C8     5.43  30.0  2
 F7E  Var_02    O5   P    O3   C7   168.00  30.0  3
 F7E  Var_03    H4   C7   O3   P    -33.57  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
 F7E  chir_01  C3   O14  C4   N1   positiv
 F7E  chir_02  C4   O1   C3   C5   negativ
 F7E  chir_03  C9   C8   C13  O7   positiv
 F7E  chir_04  C8   O6   O8   C9   negativ
 F7E  chir_05  C6   C5   O14  C7   positiv
 F7E  chir_06  C5   O2   C4   C6   negativ
 F7E  chir_09  C10  C11  O8   C12  negativ
 F7E  chir_10  C13  O9   C9   C12  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
 F7E  plan-1  C10  0.020
 F7E  plan-1  C12  0.020
 F7E  plan-1  O10  0.020
 F7E  plan-1  C13  0.020
 F7E  plan-2  C3   0.020
 F7E  plan-2  C1   0.020
 F7E  plan-2  C2   0.020
 F7E  plan-2  N1   0.020
 F7E  plan-2  N    0.020
 F7E  plan-2  C14  0.020
 F7E  plan-2  N2   0.020
 F7E  plan-2  C15  0.020
 F7E  plan-2  N3   0.020
 F7E  plan-2  N4   0.020
 F7E  plan-2  C    0.020
 F7E  plan-2  O    0.020
 F7E  plan-2  H12  0.020
 F7E  plan-2  H21  0.020
 F7E  plan-2  H22  0.020
 F7E  plan-2  H23  0.020

