# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 23 03:19:16 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~{S})-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
 R7I  R7I  '[[(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~{S})-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 PERFECT
;

data_comp_R7I
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
 R7I  O1B  O  OP    -1  -0.775  -0.0448  -1.2305   0.6266
 R7I  PB   P  P      0   1.376   0.7618   0.0137   0.8230
 R7I  O2B  O  O      0  -0.809   0.9478   0.6158   2.1798
 R7I  O5D  O  O2     0  -0.620   2.2493  -0.2121   0.1308
 R7I  C5D  C  CH2    0  -0.148   3.1047  -1.1442   0.7504
 R7I  C4D  C  CH1    0   0.008   4.2906  -1.4146  -0.1445
 R7I  C3D  C  CH1    0   0.003   5.2204  -2.4892   0.4174
 R7I  O3D  O  OH1    0  -0.661   4.7251  -3.7639   0.1359
 R7I  C2D  C  CH1    0  -0.089   6.5462  -2.1243  -0.2412
 R7I  O2D  O  OH1    0  -0.668   6.5321  -2.6047  -1.5580
 R7I  C1D  C  CH1    0   0.277   6.4810  -0.5968  -0.1814
 R7I  O1D  O  OH1    0  -0.666   7.1888  -0.0463  -1.2353
 R7I  O4D  O  O2     0  -0.512   5.1070  -0.2601  -0.2610
 R7I  O3A  O  O2     0  -0.727   0.2387   1.1211  -0.2535
 R7I  PA   P  P      0   1.367   0.2935   2.7537  -0.1341
 R7I  O2A  O  O      0  -0.791   1.7148   3.2131  -0.1133
 R7I  O1A  O  OP    -1  -0.789  -0.6930   3.2394   0.8849
 R7I  O5'  O  O2     0  -0.616  -0.2648   3.1062  -1.6448
 R7I  C5'  C  CH2    0  -0.168  -1.6253   3.3636  -1.9013
 R7I  C4'  C  CH1    0  -0.030  -2.2917   2.2137  -2.6407
 R7I  O4'  O  O2     0  -0.474  -2.1416   0.9851  -1.9317
 R7I  C3'  C  CH1    0  -0.031  -3.7934   2.4285  -2.7831
 R7I  O3'  O  OH1    0  -0.669  -4.2456   1.7514  -3.9275
 R7I  C2'  C  CH1    0  -0.059  -4.3060   1.7510  -1.5081
 R7I  O2'  O  OH1    0  -0.655  -5.6304   1.3108  -1.5626
 R7I  C1'  C  CH1    0   0.219  -3.3627   0.5519  -1.4146
 R7I  N9   N  NR5    0  -0.529  -3.1881   0.0469  -0.0763
 R7I  C4   C  CR56   0   0.491  -3.4043  -1.2331   0.3270
 R7I  N3   N  N      0  -0.453  -3.7976  -2.2661  -0.4445
 R7I  C2   C  CR16   0   0.159  -3.9043  -3.3706   0.2183
 R7I  N1   N  NR16   0  -0.664  -3.6598  -3.4974   1.5420
 R7I  C8   C  CR15   0   0.106  -2.7694   0.7292   1.0339
 R7I  N7   N  N      0  -0.452  -2.7431  -0.0101   2.1025
 R7I  C5   C  CR56   0  -0.038  -3.1347  -1.2469   1.6801
 R7I  C6   C  CR6    0   0.499  -3.2558  -2.4713   2.4037
 R7I  O1   O  O      0  -0.477  -3.0551  -2.6830   3.5886
 R7I  H2   H  HCH2   0   0.200   3.4586  -0.7764   1.7223
 R7I  H3   H  HCH2   0   0.204   2.5949  -2.0994   0.9299
 R7I  H4   H  HCH1   0   0.218   3.9283  -1.7267  -1.1344
 R7I  H5   H  HCH1   0   0.227   5.3301  -2.3310   1.5006
 R7I  H6   H  HOH1   0   0.458   5.1797  -4.4003   0.6953
 R7I  H7   H  HCH1   0   0.237   7.4135  -2.4993   0.3179
 R7I  H8   H  HOH1   0   0.451   7.2396  -2.1682  -2.0443
 R7I  H9   H  HCH1   0   0.208   6.8725  -0.2369   0.7785
 R7I  H10  H  HOH1   0   0.470   7.4779   0.8419  -1.0050
 R7I  H12  H  HCH2   0   0.212  -2.1618   3.6015  -0.9778
 R7I  H13  H  HCH2   0   0.227  -1.6895   4.2483  -2.5430
 R7I  H14  H  HCH1   0   0.253  -1.8226   2.0981  -3.6229
 R7I  H15  H  HCH1   0   0.248  -4.0561   3.4946  -2.8133
 R7I  H16  H  HOH1   0   0.448  -5.1909   1.5916  -3.8231
 R7I  H17  H  HCH1   0   0.249  -4.1431   2.4254  -0.6586
 R7I  H18  H  HOH1   0   0.469  -6.2116   2.0431  -1.3336
 R7I  H19  H  HCH1   0   0.254  -3.7687  -0.2829  -1.9970
 R7I  H20  H  HCR6   0   0.300  -4.2071  -4.2776  -0.2874
 R7I  H21  H  HNR6   0   0.432  -3.7739  -4.4165   1.9496
 R7I  H22  H  HCR5   0   0.297  -2.4606   1.7637   0.9910

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
 R7I  O2B  PB   deloc     1.496  0.020  1.496
 R7I  O2D  C2D  single    1.402  0.020  1.402
 R7I  C2D  C1D  single    1.530  0.020  1.530
 R7I  C2D  C3D  single    1.525  0.020  1.525
 R7I  C1D  O4D  single    1.417  0.020  1.417
 R7I  C1D  O1D  single    1.384  0.020  1.384
 R7I  O4D  C4D  single    1.419  0.020  1.419
 R7I  O3A  PB   single    1.631  0.020  1.631
 R7I  O3A  PA   single    1.638  0.020  1.638
 R7I  PB   O5D  single    1.656  0.020  1.656
 R7I  PB   O1B  deloc     1.496  0.020  1.496
 R7I  O2A  PA   deloc     1.494  0.020  1.494
 R7I  C5D  O5D  single    1.409  0.020  1.409
 R7I  C5D  C4D  single    1.510  0.020  1.510
 R7I  C3D  C4D  single    1.528  0.020  1.528
 R7I  C3D  O3D  single    1.396  0.020  1.396
 R7I  PA   O1A  deloc     1.499  0.020  1.499
 R7I  PA   O5'  single    1.649  0.020  1.649
 R7I  O3'  C3'  single    1.405  0.020  1.405
 R7I  O5'  C5'  single    1.408  0.020  1.408
 R7I  C5'  C4'  single    1.521  0.020  1.521
 R7I  C3'  C4'  single    1.524  0.020  1.524
 R7I  C3'  C2'  single    1.532  0.020  1.532
 R7I  C4'  O4'  single    1.426  0.020  1.426
 R7I  C2'  O2'  single    1.397  0.020  1.397
 R7I  C2'  C1'  single    1.529  0.020  1.529
 R7I  O4'  C1'  single    1.395  0.020  1.395
 R7I  C8   N9   aromatic  1.369  0.020  1.369
 R7I  C8   N7   aromatic  1.300  0.020  1.300
 R7I  C1'  N9   single    1.441  0.020  1.441
 R7I  N9   C4   aromatic  1.359  0.020  1.359
 R7I  N7   C5   aromatic  1.364  0.020  1.364
 R7I  C4   C5   aromatic  1.380  0.020  1.380
 R7I  C4   N3   single    1.348  0.020  1.348
 R7I  C5   C6   single    1.427  0.020  1.427
 R7I  N3   C2   double    1.292  0.020  1.292
 R7I  C6   O1   double    1.220  0.020  1.220
 R7I  C6   N1   single    1.399  0.020  1.399
 R7I  C2   N1   single    1.352  0.020  1.352
 R7I  C5D  H2   single    0.970  0.020  1.090
 R7I  C5D  H3   single    0.970  0.020  1.090
 R7I  C4D  H4   single    0.970  0.020  1.090
 R7I  C3D  H5   single    0.970  0.020  1.090
 R7I  O3D  H6   single    0.850  0.020  0.980
 R7I  C2D  H7   single    0.970  0.020  1.090
 R7I  O2D  H8   single    0.850  0.020  0.980
 R7I  C1D  H9   single    0.970  0.020  1.090
 R7I  O1D  H10  single    0.850  0.020  0.980
 R7I  C5'  H12  single    0.970  0.020  1.090
 R7I  C5'  H13  single    0.970  0.020  1.090
 R7I  C4'  H14  single    0.970  0.020  1.090
 R7I  C3'  H15  single    0.970  0.020  1.090
 R7I  O3'  H16  single    0.850  0.020  0.980
 R7I  C2'  H17  single    0.970  0.020  1.090
 R7I  O2'  H18  single    0.850  0.020  0.980
 R7I  C1'  H19  single    0.970  0.020  1.090
 R7I  C2   H20  single    0.930  0.020  1.080
 R7I  N1   H21  single    0.860  0.020  1.020
 R7I  C8   H22  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
 R7I  O3A  PB   O5D   96.02  3.000
 R7I  O5D  PB   O2B  108.80  3.000
 R7I  O3A  PB   O2B  111.43  3.000
 R7I  O5D  PB   O1B  108.42  3.000
 R7I  O3A  PB   O1B  107.77  3.000
 R7I  O2B  PB   O1B  121.40  3.000
 R7I  C5D  O5D  PB   116.86  3.000
 R7I  H3   C5D  H2   107.25  3.000
 R7I  H3   C5D  C4D  107.81  3.000
 R7I  H2   C5D  C4D  109.36  3.000
 R7I  H3   C5D  O5D  111.45  3.000
 R7I  H2   C5D  O5D  111.31  3.000
 R7I  C4D  C5D  O5D  109.56  3.000
 R7I  H4   C4D  O4D  110.29  3.000
 R7I  H4   C4D  C3D  109.39  3.000
 R7I  O4D  C4D  C3D  104.61  3.000
 R7I  H4   C4D  C5D  109.01  3.000
 R7I  C3D  C4D  C5D  112.70  3.000
 R7I  O4D  C4D  C5D  110.78  3.000
 R7I  H5   C3D  C2D  107.71  3.000
 R7I  H5   C3D  O3D  111.42  3.000
 R7I  C2D  C3D  O3D  116.10  3.000
 R7I  H5   C3D  C4D  108.76  3.000
 R7I  O3D  C3D  C4D  110.61  3.000
 R7I  C2D  C3D  C4D  101.65  3.000
 R7I  H6   O3D  C3D  108.61  3.000
 R7I  H7   C2D  C1D  110.78  3.000
 R7I  H7   C2D  O2D  111.67  3.000
 R7I  C1D  C2D  O2D  112.23  3.000
 R7I  H7   C2D  C3D  112.66  3.000
 R7I  C1D  C2D  C3D  100.66  3.000
 R7I  O2D  C2D  C3D  108.36  3.000
 R7I  H8   O2D  C2D  108.16  3.000
 R7I  H9   C1D  O4D  108.49  3.000
 R7I  H9   C1D  O1D  110.69  3.000
 R7I  O4D  C1D  O1D  111.02  3.000
 R7I  H9   C1D  C2D  110.27  3.000
 R7I  O1D  C1D  C2D  110.22  3.000
 R7I  O4D  C1D  C2D  106.04  3.000
 R7I  H10  O1D  C1D  109.80  3.000
 R7I  C1D  O4D  C4D  111.10  3.000
 R7I  PA   O3A  PB   128.18  3.000
 R7I  O5'  PA   O1A  109.31  3.000
 R7I  O5'  PA   O2A  105.62  3.000
 R7I  O1A  PA   O2A  121.13  3.000
 R7I  O5'  PA   O3A   97.76  3.000
 R7I  O1A  PA   O3A  110.52  3.000
 R7I  O2A  PA   O3A  109.84  3.000
 R7I  C5'  O5'  PA   122.22  3.000
 R7I  H13  C5'  H12  106.87  3.000
 R7I  H13  C5'  C4'  107.48  3.000
 R7I  H12  C5'  C4'  111.09  3.000
 R7I  H13  C5'  O5'  108.13  3.000
 R7I  H12  C5'  O5'  111.08  3.000
 R7I  C4'  C5'  O5'  111.94  3.000
 R7I  H14  C4'  C3'  110.70  3.000
 R7I  H14  C4'  O4'  108.05  3.000
 R7I  C3'  C4'  O4'  105.76  3.000
 R7I  H14  C4'  C5'  109.17  3.000
 R7I  O4'  C4'  C5'  111.31  3.000
 R7I  C3'  C4'  C5'  111.76  3.000
 R7I  C1'  O4'  C4'  111.07  3.000
 R7I  H15  C3'  C2'  111.84  3.000
 R7I  H15  C3'  O3'  111.63  3.000
 R7I  C2'  C3'  O3'  110.93  3.000
 R7I  H15  C3'  C4'  112.03  3.000
 R7I  C2'  C3'  C4'  100.93  3.000
 R7I  O3'  C3'  C4'  108.99  3.000
 R7I  H16  O3'  C3'  107.89  3.000
 R7I  H17  C2'  C1'  110.08  3.000
 R7I  H17  C2'  O2'  111.40  3.000
 R7I  C1'  C2'  O2'  109.90  3.000
 R7I  H17  C2'  C3'  108.84  3.000
 R7I  C1'  C2'  C3'  101.03  3.000
 R7I  O2'  C2'  C3'  115.09  3.000
 R7I  H18  O2'  C2'  108.87  3.000
 R7I  H19  C1'  N9   105.75  3.000
 R7I  H19  C1'  C2'  109.66  3.000
 R7I  N9   C1'  C2'  113.98  3.000
 R7I  H19  C1'  O4'  111.34  3.000
 R7I  N9   C1'  O4'  110.31  3.000
 R7I  C2'  C1'  O4'  105.90  3.000
 R7I  C8   N9   C4   106.10  3.000
 R7I  C4   N9   C1'  125.90  3.000
 R7I  C8   N9   C1'  128.00  3.000
 R7I  C5   C4   N3   127.64  3.000
 R7I  N3   C4   N9   126.74  3.000
 R7I  C5   C4   N9   105.62  3.000
 R7I  C2   N3   C4   112.67  3.000
 R7I  H20  C2   N1   115.44  3.000
 R7I  H20  C2   N3   120.00  3.000
 R7I  N1   C2   N3   124.56  3.000
 R7I  H21  N1   C6   116.78  3.000
 R7I  H21  N1   C2   117.33  3.000
 R7I  C6   N1   C2   125.89  3.000
 R7I  H22  C8   N7   124.86  3.000
 R7I  H22  C8   N9   122.17  3.000
 R7I  N7   C8   N9   112.92  3.000
 R7I  C5   N7   C8   104.79  3.000
 R7I  C6   C5   N7   130.16  3.000
 R7I  C6   C5   C4   119.28  3.000
 R7I  N7   C5   C4   110.53  3.000
 R7I  O1   C6   C5   128.84  3.000
 R7I  O1   C6   N1   121.21  3.000
 R7I  C5   C6   N1   109.95  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
 R7I  CONST_01  C5   N7   C8   N9      0.00   0.0  0
 R7I  CONST_02  N7   C5   C4   N9      0.00   0.0  0
 R7I  CONST_03  N7   C8   N9   C4      0.00   0.0  0
 R7I  CONST_04  C8   N7   C5   C4      0.00   0.0  0
 R7I  CONST_05  C5   C4   N9   C8      0.00   0.0  0
 R7I  CONST_06  N7   C8   N9   C1'   180.00   0.0  0
 R7I  CONST_07  C5   C4   N9   C1'   180.00   0.0  0
 R7I  CONST_08  N3   C4   N9   C1'     0.00   0.0  0
 R7I  CONST_09  N1   C2   N3   C4      0.00   0.0  0
 R7I  CONST_10  C6   N1   C2   N3      0.00   0.0  0
 R7I  CONST_11  C5   C6   N1   C2      0.00   0.0  0
 R7I  CONST_12  O1   C6   N1   C2    180.00   0.0  0
 R7I  CONST_13  H22  C8   N9   C1'     0.00   0.0  0
 R7I  CONST_14  H20  C2   N3   C4    180.00   0.0  0
 R7I  CONST_15  H21  N1   C2   N3    180.00   0.0  0
 R7I  Var_01    C4D  C5D  O5D  PB    169.37  30.0  1
 R7I  Var_02    C4'  C5'  O5'  PA   -107.27  30.0  3
 R7I  Var_03    O2A  PA   O3A  PB     64.76  30.0  3
 R7I  Var_04    O3A  PB   O5D  C5D  -179.68  30.0  2

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
 R7I  chir_02  C4D  O4D  C5D  C3D  positiv
 R7I  chir_03  C3D  O3D  C4D  C2D  positiv
 R7I  chir_04  C2D  O2D  C3D  C1D  positiv
 R7I  chir_05  C1D  O4D  O1D  C2D  positiv
 R7I  chir_07  C4'  C5'  C3'  O4'  positiv
 R7I  chir_08  C3'  O3'  C2'  C4'  negativ
 R7I  chir_09  C2'  O2'  C1'  C3'  negativ
 R7I  chir_10  C1'  O4'  N9   C2'  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
 R7I  plan-1  C1'  0.020
 R7I  plan-1  N9   0.020
 R7I  plan-1  C4   0.020
 R7I  plan-1  N3   0.020
 R7I  plan-1  C2   0.020
 R7I  plan-1  N1   0.020
 R7I  plan-1  C8   0.020
 R7I  plan-1  N7   0.020
 R7I  plan-1  C5   0.020
 R7I  plan-1  C6   0.020
 R7I  plan-1  O1   0.020
 R7I  plan-1  H20  0.020
 R7I  plan-1  H21  0.020
 R7I  plan-1  H22  0.020

