# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun 28 09:31:58 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{S},3~{S},4~{S},5~{R},6~{R})-6-methyl-3,4,5-tris(oxidanyl)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)[C@H]1O
#
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
 C06  C06  '[[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{S},3~{S},4~{S},5~{R},6~{R})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate'  ligand  61  38  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_C06
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
 C06  O3   O  O      0  -0.790  -4.0628   2.5979   1.5655
 C06  C4   C  CH1    0  -0.043  -6.4194   0.1044  -0.6448
 C06  C5   C  CH1    0   0.295  -5.2975  -0.1699   0.3596
 C06  O4   O  O2     0  -0.733  -2.0922   1.7072   0.1614
 C06  C6   C  CH2    0  -0.147   1.4363   2.7899  -0.4994
 C06  N1   N  N      0  -0.451   4.3990  -2.8756  -0.5076
 C06  C7   C  CR15   0   0.006   2.4753   1.8403  -1.0407
 C06  C8   C  CR15   0  -0.044   3.7804   2.5421  -1.4108
 C06  N2   N  N      0  -0.514   6.4030  -0.7072   1.4967
 C06  C9   C  CR15   0  -0.041   4.7996   1.4097  -1.2579
 C06  C10  C  CR15   0   0.193   4.2342   0.6985  -0.0280
 C06  C11  C  CR15   0   0.108   3.8765  -1.7045  -0.7024
 C06  C12  C  CR56   0  -0.094   5.4421  -2.6536   0.3555
 C06  N3   N  NR16   0  -0.726   7.2797  -2.8725   1.7582
 C06  C13  C  CR56   0   0.505   5.5271  -1.3136   0.6833
 C06  C14  C  CR6    0   0.688   7.2722  -1.5334   2.0233
 C06  O8   O  O      0  -0.500   2.8429   0.8872  -0.0494
 C06  C15  C  CR6    0   0.503   6.3872  -3.5556   0.9213
 C06  N4   N  NH2    0  -0.832   8.2336  -1.0681   2.8353
 C06  N    N  NR5    0  -0.527   4.5147  -0.7139   0.0020
 C06  C    C  CH3    0  -0.703  -5.4023  -3.7844   0.8470
 C06  O    O  O2     0  -0.486  -4.9216  -1.5171   0.3447
 C06  P    P  P      0   1.333  -3.3240   1.3560   1.1834
 C06  P1   P  P      0   1.346  -1.0039   2.9083   0.4294
 C06  C1   C  CH1    0   0.014  -5.9690  -2.3848   0.7326
 C06  O1   O  O2     0  -0.636  -4.1833   0.5697  -0.0028
 C06  C2   C  CH1    0   0.008  -7.1464  -2.2951  -0.2460
 C06  O2   O  OP    -1  -0.781  -2.8945   0.3667   2.2158
 C06  C3   C  CH1    0   0.034  -7.5813  -0.8380  -0.3391
 C06  O9   O  O      0  -0.475   6.4884  -4.7607   0.7600
 C06  O10  O  OH1    0  -0.659   4.7647   0.5440  -2.3554
 C06  O11  O  OH1    0  -0.655   3.7022   3.0650  -2.7059
 C06  O13  O  OH1    0  -0.666  -8.6376  -0.7291  -1.2558
 C06  O14  O  OH1    0  -0.662  -6.8302  -2.7886  -1.5227
 C06  H1   H  HCH1   0   0.217  -6.7632   1.1368  -0.4645
 C06  H2   H  HCH1   0   0.181  -5.6694   0.1005   1.3650
 C06  H3   H  HCH2   0   0.209   1.8162   3.2580   0.4178
 C06  H4   H  HCH2   0   0.221   1.2867   3.5861  -1.2373
 C06  H5   H  HCR5   0   0.237   2.0724   1.3234  -1.9216
 C06  H6   H  HCR5   0   0.249   4.0007   3.3215  -0.6690
 C06  H7   H  HCR5   0   0.251   5.8127   1.7801  -1.0600
 C06  H8   H  HCR5   0   0.272   4.6693   1.1262   0.8808
 C06  H10  H  HCR5   0   0.288   3.0219  -1.4996  -1.3266
 C06  H11  H  HNR6   0   0.425   7.9955  -3.4425   2.1906
 C06  H12  H  HNH2   0   0.414   8.7550  -1.6937   3.4261
 C06  H13  H  HNH2   0   0.412   8.1420  -0.1219   3.1646
 C06  H14  H  HCH3   0   0.248  -4.6346  -3.8317   1.6188
 C06  H15  H  HCH3   0   0.235  -6.1907  -4.4871   1.1193
 C06  H16  H  HCH3   0   0.230  -4.9559  -4.1175  -0.0908
 C06  H17  H  HCH1   0   0.207  -6.3498  -2.0831   1.7223
 C06  H18  H  HCH1   0   0.224  -7.9774  -2.8631   0.1985
 C06  H20  H  HCH1   0   0.216  -7.9177  -0.5712   0.6756
 C06  H21  H  HOH1   0   0.454   4.6655   1.0815  -3.1513
 C06  H22  H  HOH1   0   0.468   4.3822   3.7378  -2.8135
 C06  H23  H  HOH1   0   0.446  -5.2836   0.5674  -2.1265
 C06  H24  H  HOH1   0   0.450  -8.9689   0.1742  -1.2297
 C06  H25  H  HOH1   0   0.451  -6.8289  -3.7490  -1.4781
 C06  O5   O  O      0  -0.794  -0.7596   3.0651   1.8962
 C06  O6   O  OP    -1  -0.792  -1.3353   4.0949  -0.4191
 C06  O7   O  O2     0  -0.619   0.2405   2.0804  -0.2627
 C06  O12  O  OH1    0  -0.661  -5.9958  -0.0609  -1.9687

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
 C06  C    C1   single    1.514  0.020  1.514
 C06  C1   O    single    1.414  0.020  1.414
 C06  C1   C2   single    1.534  0.020  1.534
 C06  O3   P    deloc     1.495  0.020  1.495
 C06  O14  C2   single    1.405  0.020  1.405
 C06  N4   C14  single    1.342  0.020  1.342
 C06  O11  C8   single    1.399  0.020  1.399
 C06  O    C5   single    1.399  0.020  1.399
 C06  O10  C9   single    1.398  0.020  1.398
 C06  C2   C3   single    1.524  0.020  1.524
 C06  C14  N3   single    1.365  0.020  1.365
 C06  C14  N2   double    1.310  0.020  1.310
 C06  N3   C15  single    1.401  0.020  1.401
 C06  O4   P    single    1.639  0.020  1.639
 C06  O4   P1   single    1.643  0.020  1.643
 C06  P    O2   deloc     1.493  0.020  1.493
 C06  P    O1   single    1.662  0.020  1.662
 C06  N2   C13  single    1.340  0.020  1.340
 C06  C8   C9   single    1.531  0.020  1.531
 C06  C8   C7   single    1.527  0.020  1.527
 C06  C9   C10  single    1.529  0.020  1.529
 C06  C5   O1   single    1.386  0.020  1.386
 C06  C5   C4   single    1.531  0.020  1.531
 C06  C15  O9   double    1.220  0.020  1.220
 C06  C15  C12  single    1.424  0.020  1.424
 C06  C3   O13  single    1.403  0.020  1.403
 C06  C3   C4   single    1.527  0.020  1.527
 C06  O7   P1   single    1.647  0.020  1.647
 C06  O7   C6   single    1.410  0.020  1.410
 C06  C13  C12  aromatic  1.382  0.020  1.382
 C06  C13  N    aromatic  1.360  0.020  1.360
 C06  C7   C6   single    1.508  0.020  1.508
 C06  C7   O8   single    1.423  0.020  1.423
 C06  C12  N1   aromatic  1.372  0.020  1.372
 C06  C4   O12  single    1.400  0.020  1.400
 C06  P1   O5   deloc     1.495  0.020  1.495
 C06  P1   O6   deloc     1.496  0.020  1.496
 C06  C10  N    single    1.440  0.020  1.440
 C06  C10  O8   single    1.404  0.020  1.404
 C06  N    C11  aromatic  1.373  0.020  1.373
 C06  N1   C11  aromatic  1.297  0.020  1.297
 C06  C4   H1   single    0.970  0.020  1.090
 C06  C5   H2   single    0.970  0.020  1.090
 C06  C6   H3   single    0.970  0.020  1.090
 C06  C6   H4   single    0.970  0.020  1.090
 C06  C7   H5   single    0.970  0.020  1.090
 C06  C8   H6   single    0.970  0.020  1.090
 C06  C9   H7   single    0.970  0.020  1.090
 C06  C10  H8   single    0.970  0.020  1.090
 C06  C11  H10  single    0.930  0.020  1.080
 C06  N3   H11  single    0.860  0.020  1.020
 C06  N4   H12  single    0.890  0.020  1.040
 C06  N4   H13  single    0.890  0.020  1.040
 C06  C    H14  single    0.970  0.020  1.090
 C06  C    H15  single    0.970  0.020  1.090
 C06  C    H16  single    0.970  0.020  1.090
 C06  C1   H17  single    0.970  0.020  1.090
 C06  C2   H18  single    0.970  0.020  1.090
 C06  C3   H20  single    0.970  0.020  1.090
 C06  O10  H21  single    0.850  0.020  0.980
 C06  O11  H22  single    0.850  0.020  0.980
 C06  O12  H23  single    0.850  0.020  0.980
 C06  O13  H24  single    0.850  0.020  0.980
 C06  O14  H25  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
 C06  H1   C4   O12  111.07  3.000
 C06  H1   C4   C3   107.93  3.000
 C06  O12  C4   C3   110.28  3.000
 C06  H1   C4   C5   106.80  3.000
 C06  O12  C4   C5   112.19  3.000
 C06  C3   C4   C5   108.41  3.000
 C06  H2   C5   O1   112.20  3.000
 C06  H2   C5   O    109.61  3.000
 C06  O1   C5   O    107.17  3.000
 C06  H2   C5   C4   107.84  3.000
 C06  O1   C5   C4   108.79  3.000
 C06  O    C5   C4   111.26  3.000
 C06  P1   O4   P    123.57  3.000
 C06  H4   C6   H3   107.47  3.000
 C06  H4   C6   O7   111.27  3.000
 C06  H3   C6   O7   111.58  3.000
 C06  H4   C6   C7   108.05  3.000
 C06  H3   C6   C7   109.27  3.000
 C06  O7   C6   C7   109.12  3.000
 C06  C12  N1   C11  104.75  3.000
 C06  H5   C7   O8   109.77  3.000
 C06  H5   C7   C8   109.60  3.000
 C06  O8   C7   C8   104.82  3.000
 C06  H5   C7   C6   109.36  3.000
 C06  O8   C7   C6   110.46  3.000
 C06  C8   C7   C6   112.73  3.000
 C06  H6   C8   O11  111.79  3.000
 C06  H6   C8   C9   108.90  3.000
 C06  O11  C8   C9   113.97  3.000
 C06  H6   C8   C7   109.50  3.000
 C06  C9   C8   C7   101.82  3.000
 C06  O11  C8   C7   110.39  3.000
 C06  C14  N2   C13  113.10  3.000
 C06  H7   C9   O10  111.95  3.000
 C06  H7   C9   C10  110.70  3.000
 C06  O10  C9   C10  109.52  3.000
 C06  H7   C9   C8   112.53  3.000
 C06  C10  C9   C8   100.26  3.000
 C06  O10  C9   C8   111.27  3.000
 C06  H8   C10  N    106.77  3.000
 C06  H8   C10  O8   110.74  3.000
 C06  N    C10  O8   108.97  3.000
 C06  H8   C10  C9   109.82  3.000
 C06  O8   C10  C9   106.95  3.000
 C06  N    C10  C9   113.63  3.000
 C06  H10  C11  N    121.91  3.000
 C06  H10  C11  N1   125.30  3.000
 C06  N    C11  N1   112.78  3.000
 C06  C15  C12  C13  118.63  3.000
 C06  C13  C12  N1   110.66  3.000
 C06  C15  C12  N1   130.71  3.000
 C06  H11  N3   C15  115.54  3.000
 C06  H11  N3   C14  118.26  3.000
 C06  C15  N3   C14  126.21  3.000
 C06  N    C13  C12  105.24  3.000
 C06  N    C13  N2   126.24  3.000
 C06  C12  C13  N2   128.51  3.000
 C06  N4   C14  N3   116.99  3.000
 C06  N3   C14  N2   122.98  3.000
 C06  N4   C14  N2   120.01  3.000
 C06  C10  O8   C7   110.88  3.000
 C06  O9   C15  N3   120.50  3.000
 C06  O9   C15  C12  128.93  3.000
 C06  N3   C15  C12  110.57  3.000
 C06  H13  N4   H12  116.09  3.000
 C06  H13  N4   C14  117.32  3.000
 C06  H12  N4   C14  120.73  3.000
 C06  C13  N    C11  106.56  3.000
 C06  C11  N    C10  127.33  3.000
 C06  C13  N    C10  126.01  3.000
 C06  H16  C    H15  108.28  3.000
 C06  H16  C    H14  107.91  3.000
 C06  H15  C    H14  107.73  3.000
 C06  H16  C    C1   111.74  3.000
 C06  H15  C    C1   110.11  3.000
 C06  H14  C    C1   110.94  3.000
 C06  C1   O    C5   112.89  3.000
 C06  O2   P    O1   109.19  3.000
 C06  O1   P    O4    92.58  3.000
 C06  O2   P    O4   110.92  3.000
 C06  O1   P    O3   108.65  3.000
 C06  O2   P    O3   121.06  3.000
 C06  O4   P    O3   110.66  3.000
 C06  O7   P1   O6   109.13  3.000
 C06  O6   P1   O5   120.62  3.000
 C06  O7   P1   O5   109.97  3.000
 C06  O6   P1   O4   109.92  3.000
 C06  O5   P1   O4   110.18  3.000
 C06  O7   P1   O4    93.70  3.000
 C06  H17  C1   C2   106.96  3.000
 C06  H17  C1   O    109.52  3.000
 C06  C2   C1   O    110.95  3.000
 C06  H17  C1   C    108.33  3.000
 C06  C2   C1   C    112.93  3.000
 C06  O    C1   C    108.09  3.000
 C06  P    O1   C5   118.79  3.000
 C06  H18  C2   O14  110.84  3.000
 C06  H18  C2   C3   107.63  3.000
 C06  O14  C2   C3   110.16  3.000
 C06  H18  C2   C1   106.96  3.000
 C06  C3   C2   C1   108.31  3.000
 C06  O14  C2   C1   112.74  3.000
 C06  H20  C3   O13  110.68  3.000
 C06  H20  C3   C2   105.21  3.000
 C06  O13  C3   C2   109.21  3.000
 C06  H20  C3   C4   105.50  3.000
 C06  O13  C3   C4   113.22  3.000
 C06  C2   C3   C4   112.66  3.000
 C06  H21  O10  C9   107.76  3.000
 C06  H22  O11  C8   108.98  3.000
 C06  H24  O13  C3   108.32  3.000
 C06  H25  O14  C2   108.00  3.000
 C06  P1   O7   C6   117.27  3.000
 C06  H23  O12  C4   107.57  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
 C06  CONST_01  N    C13  C12  N1     0.00   0.0  0
 C06  CONST_02  C13  N    C11  N1     0.00   0.0  0
 C06  CONST_03  C12  C13  N    C11    0.00   0.0  0
 C06  CONST_04  C13  C12  N1   C11    0.00   0.0  0
 C06  CONST_05  N    C11  N1   C12    0.00   0.0  0
 C06  CONST_06  C10  N    C11  N1   180.00   0.0  0
 C06  CONST_07  C10  N    C13  N2     0.00   0.0  0
 C06  CONST_08  C12  C13  N    C10  180.00   0.0  0
 C06  CONST_09  C15  N3   C14  N2     0.00   0.0  0
 C06  CONST_10  C14  N3   C15  C12    0.00   0.0  0
 C06  CONST_11  C13  N2   C14  N3     0.00   0.0  0
 C06  CONST_12  N4   C14  N2   C13  180.00   0.0  0
 C06  CONST_13  O9   C15  N3   C14  180.00   0.0  0
 C06  CONST_14  N4   C14  N3   C15  180.00   0.0  0
 C06  CONST_15  H10  C11  N    C10    0.00   0.0  0
 C06  CONST_16  H11  N3   C14  N2   180.00   0.0  0
 C06  CONST_18  H13  N4   C14  N2     0.00   0.0  0
 C06  Var_01    O4   P    O1   C5   169.32  30.0  1
 C06  Var_02    O5   P1   O7   C6   -77.34  30.0  3
 C06  Var_03    H3   C6   O7   P1    55.14  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
 C06  chir_01  C4   C5   C3   O12  positiv
 C06  chir_02  C5   O    O1   C4   negativ
 C06  chir_03  C7   C8   C6   O8   positiv
 C06  chir_04  C8   O11  C9   C7   positiv
 C06  chir_05  C9   O10  C10  C8   positiv
 C06  chir_06  C10  O8   N    C9   negativ
 C06  chir_09  C1   C    O    C2   negativ
 C06  chir_10  C2   O14  C1   C3   negativ
 C06  chir_11  C3   O13  C2   C4   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
 C06  plan-1  N1   0.020
 C06  plan-1  N2   0.020
 C06  plan-1  C10  0.020
 C06  plan-1  C11  0.020
 C06  plan-1  C12  0.020
 C06  plan-1  N3   0.020
 C06  plan-1  C13  0.020
 C06  plan-1  C14  0.020
 C06  plan-1  C15  0.020
 C06  plan-1  N4   0.020
 C06  plan-1  N    0.020
 C06  plan-1  O9   0.020
 C06  plan-1  H10  0.020
 C06  plan-1  H11  0.020
 C06  plan-1  H12  0.020
 C06  plan-1  H13  0.020

