# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun 22 14:33:17 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC=Nc34)[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
 R5I  R5I  '[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate'  ligand  56  36  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_R5I
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
 R5I  O1   O  O      0  -0.465   7.9604   1.0717   3.3913
 R5I  C6   C  CR6    0   0.512   7.5654   1.2012   2.2469
 R5I  N1   N  NR16   0  -0.664   8.3567   1.8077   1.2651
 R5I  C2   C  CR16   0   0.161   8.0108   2.0031  -0.0272
 R5I  N3   N  N      0  -0.450   6.8816   1.6485  -0.5480
 R5I  C4   C  CR56   0   0.483   6.0660   1.0526   0.3460
 R5I  C5   C  CR56   0  -0.053   6.3119   0.8023   1.6820
 R5I  N7   N  N      0  -0.442   5.2372   0.1919   2.2590
 R5I  C8   C  CR15   0   0.101   4.3666   0.0752   1.2967
 R5I  N9   N  NR5    0  -0.526   4.8166   0.5758   0.1076
 R5I  C1'  C  CH1    0   0.174   4.1263   0.6411  -1.1809
 R5I  O4'  O  O2     0  -0.494   2.7855   0.3163  -0.9948
 R5I  C4'  C  CH1    0   0.001   2.4661  -0.9387  -1.5991
 R5I  C5'  C  CH2    0  -0.149   1.5932  -1.7612  -0.6857
 R5I  O5'  O  O2     0  -0.619   0.3857  -1.0745  -0.4535
 R5I  PA   P  P      0   1.344  -0.8449  -1.9434   0.2233
 R5I  O2A  O  O      0  -0.790  -1.3540  -2.9270  -0.7818
 R5I  O1A  O  OP    -1  -0.799  -0.4454  -2.3904   1.5932
 R5I  O3A  O  O2     0  -0.736  -1.8448  -0.6455   0.3027
 R5I  PB   P  P      0   1.343  -3.0806  -0.5197   1.3768
 R5I  O2B  O  OP    -1  -0.792  -2.6398   0.2752   2.5654
 R5I  O1B  O  O      0  -0.800  -3.7631  -1.8389   1.5537
 R5I  O5D  O  O2     0  -0.616  -3.9785   0.4412   0.3848
 R5I  C5D  C  CH2    0  -0.142  -5.2596   0.8115   0.8422
 R5I  C4D  C  CH1    0  -0.048  -5.8403   1.8314  -0.1197
 R5I  O4D  O  O2     0  -0.503  -5.9157   1.3137  -1.4429
 R5I  C1D  C  CH1    0   0.280  -7.2477   1.0031  -1.7933
 R5I  O1D  O  OH1    0  -0.662  -7.3594  -0.2965  -2.2627
 R5I  C2D  C  CH1    0  -0.056  -8.0574   1.1626  -0.5058
 R5I  O2D  O  OH1    0  -0.667  -9.3844   1.5634  -0.6943
 R5I  C3D  C  CH1    0  -0.019  -7.2661   2.2215   0.2513
 R5I  O3D  O  OH1    0  -0.670  -7.5159   3.5140  -0.2430
 R5I  C3'  C  CH1    0  -0.041   3.8158  -1.5907  -1.8864
 R5I  O3'  O  OH1    0  -0.655   3.7085  -2.4767  -2.9636
 R5I  C2'  C  CH1    0  -0.043   4.6972  -0.3701  -2.1736
 R5I  O2'  O  OH1    0  -0.663   4.4653   0.1276  -3.4615
 R5I  H1   H  HNR6   0   0.436   9.2706   2.1321   1.5550
 R5I  H2   H  HCR6   0   0.305   8.7570   2.4933  -0.6381
 R5I  H3   H  HCR5   0   0.298   3.3839  -0.3541   1.4059
 R5I  H4   H  HCH1   0   0.288   4.2277   1.6661  -1.5471
 R5I  H5   H  HCH1   0   0.248   1.9348  -0.7570  -2.5410
 R5I  H6   H  HCH2   0   0.225   1.4241  -2.7279  -1.1762
 R5I  H7   H  HCH2   0   0.209   2.1210  -1.9664   0.2540
 R5I  H10  H  HCH2   0   0.209  -5.9151  -0.0643   0.9176
 R5I  H11  H  HCH2   0   0.213  -5.2125   1.2691   1.8379
 R5I  H12  H  HCH1   0   0.250  -5.1897   2.7123  -0.1276
 R5I  H13  H  HCH1   0   0.200  -7.5893   1.7177  -2.5548
 R5I  H14  H  HOH1   0   0.463  -7.1105  -0.3238  -3.1922
 R5I  H15  H  HCH1   0   0.231  -8.0027   0.2191   0.0555
 R5I  H16  H  HOH1   0   0.462  -9.8769   0.8360  -1.0867
 R5I  H17  H  HCH1   0   0.243  -7.4377   2.1661   1.3343
 R5I  H18  H  HOH1   0   0.452  -8.4647   3.6753  -0.2055
 R5I  H19  H  HCH1   0   0.246   4.1865  -2.0972  -0.9847
 R5I  H20  H  HOH1   0   0.470   4.4690  -3.0670  -2.9570
 R5I  H21  H  HCH1   0   0.262   5.7611  -0.5691  -1.9975
 R5I  H22  H  HOH1   0   0.453   4.3545  -0.6262  -4.0542

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
 R5I  O1D  C1D  single    1.386  0.020  1.386
 R5I  O1B  PB   deloc     1.496  0.020  1.496
 R5I  O2D  C2D  single    1.399  0.020  1.399
 R5I  C1D  C2D  single    1.529  0.020  1.529
 R5I  C1D  O4D  single    1.412  0.020  1.412
 R5I  C2D  C3D  single    1.523  0.020  1.523
 R5I  O4D  C4D  single    1.423  0.020  1.423
 R5I  O3A  PB   single    1.642  0.020  1.642
 R5I  O3A  PA   single    1.640  0.020  1.640
 R5I  PB   O5D  single    1.647  0.020  1.647
 R5I  PB   O2B  deloc     1.496  0.020  1.496
 R5I  O2A  PA   deloc     1.496  0.020  1.496
 R5I  C5D  O5D  single    1.410  0.020  1.410
 R5I  C5D  C4D  single    1.518  0.020  1.518
 R5I  C3D  C4D  single    1.524  0.020  1.524
 R5I  C3D  O3D  single    1.406  0.020  1.406
 R5I  PA   O1A  deloc     1.495  0.020  1.495
 R5I  PA   O5'  single    1.652  0.020  1.652
 R5I  O3'  C3'  single    1.399  0.020  1.399
 R5I  O5'  C5'  single    1.408  0.020  1.408
 R5I  C5'  C4'  single    1.508  0.020  1.508
 R5I  C3'  C4'  single    1.526  0.020  1.526
 R5I  C3'  C2'  single    1.533  0.020  1.533
 R5I  C4'  O4'  single    1.429  0.020  1.429
 R5I  C2'  O2'  single    1.400  0.020  1.400
 R5I  C2'  C1'  single    1.528  0.020  1.528
 R5I  O4'  C1'  single    1.392  0.020  1.392
 R5I  C8   N9   aromatic  1.366  0.020  1.366
 R5I  C8   N7   aromatic  1.303  0.020  1.303
 R5I  C1'  N9   single    1.463  0.020  1.463
 R5I  N9   C4   aromatic  1.358  0.020  1.358
 R5I  N7   C5   aromatic  1.364  0.020  1.364
 R5I  C4   C5   aromatic  1.381  0.020  1.381
 R5I  C4   N3   single    1.349  0.020  1.349
 R5I  C5   C6   single    1.432  0.020  1.432
 R5I  N3   C2   double    1.293  0.020  1.293
 R5I  C6   O1   double    1.218  0.020  1.218
 R5I  C6   N1   single    1.399  0.020  1.399
 R5I  C2   N1   single    1.352  0.020  1.352
 R5I  N1   H1   single    0.860  0.020  1.020
 R5I  C2   H2   single    0.930  0.020  1.080
 R5I  C8   H3   single    0.930  0.020  1.080
 R5I  C1'  H4   single    0.970  0.020  1.090
 R5I  C4'  H5   single    0.970  0.020  1.090
 R5I  C5'  H6   single    0.970  0.020  1.090
 R5I  C5'  H7   single    0.970  0.020  1.090
 R5I  C5D  H10  single    0.970  0.020  1.090
 R5I  C5D  H11  single    0.970  0.020  1.090
 R5I  C4D  H12  single    0.970  0.020  1.090
 R5I  C1D  H13  single    0.970  0.020  1.090
 R5I  O1D  H14  single    0.850  0.020  0.980
 R5I  C2D  H15  single    0.970  0.020  1.090
 R5I  O2D  H16  single    0.850  0.020  0.980
 R5I  C3D  H17  single    0.970  0.020  1.090
 R5I  O3D  H18  single    0.850  0.020  0.980
 R5I  C3'  H19  single    0.970  0.020  1.090
 R5I  O3'  H20  single    0.850  0.020  0.980
 R5I  C2'  H21  single    0.970  0.020  1.090
 R5I  O2'  H22  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
 R5I  C5   C6   N1   109.82  3.000
 R5I  N1   C6   O1   121.48  3.000
 R5I  C5   C6   O1   128.70  3.000
 R5I  H1   N1   C2   117.28  3.000
 R5I  H1   N1   C6   116.65  3.000
 R5I  C2   N1   C6   126.06  3.000
 R5I  H2   C2   N3   119.95  3.000
 R5I  H2   C2   N1   115.39  3.000
 R5I  N3   C2   N1   124.66  3.000
 R5I  C4   N3   C2   112.48  3.000
 R5I  N9   C4   C5   105.66  3.000
 R5I  C5   C4   N3   127.84  3.000
 R5I  N9   C4   N3   126.50  3.000
 R5I  N7   C5   C4   110.49  3.000
 R5I  C4   C5   C6   119.14  3.000
 R5I  N7   C5   C6   130.37  3.000
 R5I  C8   N7   C5   104.72  3.000
 R5I  H3   C8   N9   122.29  3.000
 R5I  H3   C8   N7   124.75  3.000
 R5I  N9   C8   N7   112.95  3.000
 R5I  C1'  N9   C8   128.85  3.000
 R5I  C1'  N9   C4   124.95  3.000
 R5I  C8   N9   C4   106.18  3.000
 R5I  H4   C1'  C2'  111.60  3.000
 R5I  H4   C1'  O4'  110.67  3.000
 R5I  C2'  C1'  O4'  107.00  3.000
 R5I  H4   C1'  N9   107.04  3.000
 R5I  O4'  C1'  N9   109.05  3.000
 R5I  C2'  C1'  N9   111.49  3.000
 R5I  C4'  O4'  C1'  111.33  3.000
 R5I  H5   C4'  C3'  109.73  3.000
 R5I  H5   C4'  C5'  109.29  3.000
 R5I  C3'  C4'  C5'  113.14  3.000
 R5I  H5   C4'  O4'  109.03  3.000
 R5I  C3'  C4'  O4'  104.90  3.000
 R5I  C5'  C4'  O4'  110.63  3.000
 R5I  H7   C5'  H6   106.99  3.000
 R5I  H7   C5'  O5'  111.25  3.000
 R5I  H6   C5'  O5'  111.79  3.000
 R5I  H7   C5'  C4'  110.03  3.000
 R5I  H6   C5'  C4'  107.41  3.000
 R5I  O5'  C5'  C4'  109.28  3.000
 R5I  PA   O5'  C5'  116.74  3.000
 R5I  O3A  PA   O1A  110.79  3.000
 R5I  O1A  PA   O2A  120.67  3.000
 R5I  O3A  PA   O2A  110.21  3.000
 R5I  O1A  PA   O5'  109.49  3.000
 R5I  O2A  PA   O5'  108.92  3.000
 R5I  O3A  PA   O5'   93.31  3.000
 R5I  PB   O3A  PA   123.44  3.000
 R5I  O5D  PB   O1B  109.69  3.000
 R5I  O5D  PB   O2B  109.21  3.000
 R5I  O1B  PB   O2B  120.60  3.000
 R5I  O2B  PB   O3A  109.79  3.000
 R5I  O5D  PB   O3A   93.50  3.000
 R5I  O1B  PB   O3A  110.68  3.000
 R5I  C5D  O5D  PB   116.95  3.000
 R5I  H11  C5D  H10  107.24  3.000
 R5I  H11  C5D  C4D  108.15  3.000
 R5I  H10  C5D  C4D  110.58  3.000
 R5I  H11  C5D  O5D  111.42  3.000
 R5I  H10  C5D  O5D  110.85  3.000
 R5I  C4D  C5D  O5D  108.58  3.000
 R5I  H12  C4D  C3D  110.59  3.000
 R5I  H12  C4D  O4D  108.51  3.000
 R5I  C3D  C4D  O4D  105.66  3.000
 R5I  H12  C4D  C5D  108.53  3.000
 R5I  C3D  C4D  C5D  112.07  3.000
 R5I  O4D  C4D  C5D  111.42  3.000
 R5I  C1D  O4D  C4D  111.15  3.000
 R5I  H13  C1D  C2D  110.55  3.000
 R5I  H13  C1D  O1D  110.48  3.000
 R5I  C2D  C1D  O1D  109.89  3.000
 R5I  H13  C1D  O4D  108.80  3.000
 R5I  C2D  C1D  O4D  105.52  3.000
 R5I  O1D  C1D  O4D  111.49  3.000
 R5I  H14  O1D  C1D  109.44  3.000
 R5I  H15  C2D  C3D  108.48  3.000
 R5I  H15  C2D  O2D  111.22  3.000
 R5I  C3D  C2D  O2D  111.13  3.000
 R5I  H15  C2D  C1D  108.30  3.000
 R5I  C3D  C2D  C1D  102.47  3.000
 R5I  O2D  C2D  C1D  114.75  3.000
 R5I  H16  O2D  C2D  108.90  3.000
 R5I  H17  C3D  O3D  111.43  3.000
 R5I  H17  C3D  C2D  111.97  3.000
 R5I  O3D  C3D  C2D  111.84  3.000
 R5I  H17  C3D  C4D  111.92  3.000
 R5I  O3D  C3D  C4D  108.42  3.000
 R5I  C2D  C3D  C4D  100.78  3.000
 R5I  H18  O3D  C3D  108.38  3.000
 R5I  H19  C3'  C2'  109.08  3.000
 R5I  H19  C3'  O3'  111.47  3.000
 R5I  C2'  C3'  O3'  113.84  3.000
 R5I  H19  C3'  C4'  109.94  3.000
 R5I  C2'  C3'  C4'  101.75  3.000
 R5I  O3'  C3'  C4'  110.35  3.000
 R5I  H20  O3'  C3'  108.81  3.000
 R5I  H21  C2'  O2'  111.90  3.000
 R5I  H21  C2'  C3'  112.54  3.000
 R5I  O2'  C2'  C3'  111.11  3.000
 R5I  H21  C2'  C1'  112.23  3.000
 R5I  O2'  C2'  C1'  107.49  3.000
 R5I  C3'  C2'  C1'  100.98  3.000
 R5I  H22  O2'  C2'  107.83  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
 R5I  CONST_01  N7   C8   N9   C4     0.00   0.0  0
 R5I  CONST_02  C8   N7   C5   C4     0.00   0.0  0
 R5I  CONST_03  N9   C8   N7   C5     0.00   0.0  0
 R5I  CONST_04  C8   N9   C4   C5     0.00   0.0  0
 R5I  CONST_05  N9   C4   C5   N7     0.00   0.0  0
 R5I  CONST_06  C1'  N9   C4   N3     0.00   0.0  0
 R5I  CONST_07  C1'  N9   C4   C5   180.00   0.0  0
 R5I  CONST_08  C1'  N9   C8   N7   180.00   0.0  0
 R5I  CONST_09  N3   C2   N1   C6     0.00   0.0  0
 R5I  CONST_10  C4   N3   C2   N1     0.00   0.0  0
 R5I  CONST_11  C5   C6   N1   C2     0.00   0.0  0
 R5I  CONST_12  C2   N1   C6   O1   180.00   0.0  0
 R5I  CONST_13  H3   C8   N9   C4   180.00   0.0  0
 R5I  CONST_14  H2   C2   N1   C6   180.00   0.0  0
 R5I  CONST_15  H1   N1   C2   N3   180.00   0.0  0
 R5I  Var_01    C4D  C5D  O5D  PB   172.63  30.0  2
 R5I  Var_02    O3A  PA   O5'  C5'  177.07  30.0  1
 R5I  Var_03    O1B  PB   O3A  PA   -38.78  30.0  3
 R5I  Var_04    H6   C5'  O5'  PA    47.31  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
 R5I  chir_01  C1'  C2'  O4'  N9   negativ
 R5I  chir_02  C4'  O4'  C3'  C5'  negativ
 R5I  chir_05  C4D  O4D  C5D  C3D  positiv
 R5I  chir_06  C1D  O1D  O4D  C2D  positiv
 R5I  chir_07  C2D  O2D  C1D  C3D  negativ
 R5I  chir_08  C3D  O3D  C2D  C4D  negativ
 R5I  chir_09  C3'  O3'  C4'  C2'  positiv
 R5I  chir_10  C2'  O2'  C3'  C1'  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
 R5I  plan-1  O1   0.020
 R5I  plan-1  C6   0.020
 R5I  plan-1  N1   0.020
 R5I  plan-1  C2   0.020
 R5I  plan-1  N3   0.020
 R5I  plan-1  C4   0.020
 R5I  plan-1  C5   0.020
 R5I  plan-1  N7   0.020
 R5I  plan-1  C8   0.020
 R5I  plan-1  N9   0.020
 R5I  plan-1  C1'  0.020
 R5I  plan-1  H1   0.020
 R5I  plan-1  H2   0.020
 R5I  plan-1  H3   0.020

