# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun 18 21:42:40 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: ~{O}-[(2~{S},3~{R},4~{R},5~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2,4-bis(oxidanyl)oxolan-3-yl] ethanethioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=S)O[C@H]1[C@@H](O)O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34)[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
 9X8  9X8  '~{O}-[(2~{S},3~{R},4~{R},5~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2,4-bis(oxidanyl)oxolan-3-yl] ethanethioate'  ligand  62  39  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9X8
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
 9X8  C1   C  CR56   0   0.486   3.6469  -1.9426   0.2358
 9X8  C2   C  CR56   0  -0.012   3.0769  -2.3308  -0.9663
 9X8  C3   C  CR6    0   0.452   3.0322  -3.7140  -1.2170
 9X8  C4   C  CR15   0   0.072   2.9651  -0.2183  -0.9335
 9X8  N1   N  N      0  -0.476   3.5306  -4.5371  -0.2874
 9X8  N2   N  N      0  -0.456   4.1469  -2.7484   1.1704
 9X8  C7   C  CR15   0  -0.137  -5.4054  -1.7300   0.1560
 9X8  C8   C  CR15   0   0.025  -5.1254  -0.7317  -0.9655
 9X8  O2   O  OH1    0  -0.653  -5.1418  -1.2498  -2.2574
 9X8  C9   C  CR15   0   0.296  -4.7355  -1.0643   1.3650
 9X8  O3   O  OH1    0  -0.643  -4.1405  -2.0131   2.1686
 9X8  O4   O  O      0  -0.510  -3.7850  -0.1585   0.8319
 9X8  C10  C  CR15   0  -0.006  -3.7373  -0.2275  -0.5828
 9X8  C11  C  CH2    0  -0.148  -3.4207   1.1306  -1.1582
 9X8  O5   O  O2     0  -0.618  -2.1076   1.4904  -0.7906
 9X8  P1   P  P      0   1.345  -1.5913   2.9961  -1.2181
 9X8  O6   O  O      0  -0.800  -1.4299   3.0694  -2.7034
 9X8  O7   O  OP    -1  -0.794  -2.4035   4.0192  -0.4884
 9X8  O8   O  O2     0  -0.731  -0.1348   2.8098  -0.4848
 9X8  P2   P  P      0   1.361   1.2238   3.5931  -0.9592
 9X8  O9   O  O      0  -0.790   0.8989   5.0086  -1.3149
 9X8  O10  O  OP    -1  -0.777   2.0164   2.7401  -1.9052
 9X8  O11  O  O2     0  -0.615   1.9196   3.5474   0.5316
 9X8  C13  C  CH1    0  -0.038   3.6836   2.5332   1.7830
 9X8  O12  O  O2     0  -0.489   3.0826   1.2507   1.5763
 9X8  C14  C  CH1    0  -0.035   5.1844   2.2849   1.8414
 9X8  O13  O  OH1    0  -0.669   5.5434   1.9501   3.1567
 9X8  C15  C  CH1    0  -0.051   5.3136   1.0720   0.9144
 9X8  O14  O  OH1    0  -0.653   6.4476   0.2862   1.1281
 9X8  C16  C  CH1    0   0.225   4.0547   0.2902   1.2854
 9X8  N3   N  NR5    0  -0.543   3.5710  -0.5798   0.2420
 9X8  N4   N  N      0  -0.459   2.6550  -1.2390  -1.6799
 9X8  C17  C  CR16   0   0.042   4.0438  -4.0200   0.8262
 9X8  N5   N  NH2    0  -0.818   2.5248  -4.2272  -2.3396
 9X8  H1   H  HCR5   0   0.324   2.7528   0.8157  -1.1824
 9X8  H2   H  HCH3   0   0.262  -4.5112  -6.1511   0.1679
 9X8  H3   H  HCH3   0   0.274  -4.1640  -5.2045  -1.2898
 9X8  H4   H  HCH3   0   0.272  -3.1867  -4.9710   0.1506
 9X8  H9   H  HOH1   0   0.463  -6.0557  -1.3520  -2.5401
 9X8  H10  H  HCR5   0   0.229  -5.4744  -0.4780   1.9223
 9X8  H11  H  HOH1   0   0.469  -4.0538  -1.6621   3.0606
 9X8  H12  H  HCR5   0   0.229  -2.9756  -0.9478  -0.9162
 9X8  H13  H  HCH2   0   0.216  -3.5279   1.0766  -2.2482
 9X8  H14  H  HCH2   0   0.207  -4.1548   1.8586  -0.7906
 9X8  H19  H  HCH1   0   0.259   3.3152   2.9309   2.7334
 9X8  H20  H  HCH1   0   0.251   5.7564   3.1464   1.4707
 9X8  H21  H  HOH1   0   0.449   6.3732   1.4593   3.1229
 9X8  H22  H  HCH1   0   0.250   5.2441   1.4058  -0.1292
 9X8  H23  H  HOH1   0   0.469   7.1811   0.6579   0.6280
 9X8  H24  H  HCH1   0   0.256   4.2568  -0.3584   2.1456
 9X8  H25  H  HCR6   0   0.250   4.4261  -4.7412   1.5409
 9X8  H26  H  HNH2   0   0.410   2.0940  -3.6381  -3.0300
 9X8  H27  H  HNH2   0   0.402   2.4700  -5.2233  -2.4625
 9X8  H7   H  HCR5   0   0.291  -6.4653  -1.9273   0.3220
 9X8  O1   O  O2     0  -0.390  -4.7251  -2.9330  -0.1707
 9X8  C6   C  C      0   0.254  -5.1332  -4.1054   0.2566
 9X8  C12  C  CH2    0  -0.149   3.3197   3.4879   0.6600
 9X8  H8   H  HCR5   0   0.243  -5.8413   0.0944  -0.8449
 9X8  H17  H  HCH2   0   0.212   3.7928   3.1707  -0.2746
 9X8  H18  H  HCH2   0   0.225   3.7245   4.4755   0.9084
 9X8  C5   C  CH3    0  -0.721  -4.1997  -5.1793  -0.1987
 9X8  S1   S  S1     0  -0.287  -6.4840  -4.3911   1.1349

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
 9X8  C17  N1   aromatic  1.331  0.020  1.331
 9X8  C17  N2   aromatic  1.321  0.020  1.321
 9X8  N1   C3   aromatic  1.338  0.020  1.338
 9X8  N2   C1   aromatic  1.331  0.020  1.331
 9X8  C3   N5   single    1.335  0.020  1.335
 9X8  C3   C2   aromatic  1.406  0.020  1.406
 9X8  C1   C2   aromatic  1.386  0.020  1.386
 9X8  C1   N3   aromatic  1.365  0.020  1.365
 9X8  C2   N4   aromatic  1.371  0.020  1.371
 9X8  O12  C16  single    1.397  0.020  1.397
 9X8  O12  C13  single    1.431  0.020  1.431
 9X8  C16  N3   single    1.442  0.020  1.442
 9X8  C16  C15  single    1.528  0.020  1.528
 9X8  O6   P1   deloc     1.496  0.020  1.496
 9X8  N3   C4   aromatic  1.371  0.020  1.371
 9X8  C13  C14  single    1.522  0.020  1.522
 9X8  C13  C12  single    1.518  0.020  1.518
 9X8  O13  C14  single    1.404  0.020  1.404
 9X8  O7   P1   deloc     1.496  0.020  1.496
 9X8  N4   C4   aromatic  1.302  0.020  1.302
 9X8  O14  C15  single    1.396  0.020  1.396
 9X8  P1   O5   single    1.648  0.020  1.648
 9X8  P1   O8   single    1.641  0.020  1.641
 9X8  C14  C15  single    1.532  0.020  1.532
 9X8  C12  O11  single    1.407  0.020  1.407
 9X8  C11  O5   single    1.410  0.020  1.410
 9X8  C11  C10  single    1.509  0.020  1.509
 9X8  O11  P2   single    1.646  0.020  1.646
 9X8  O2   C8   single    1.392  0.020  1.392
 9X8  O8   P2   single    1.638  0.020  1.638
 9X8  C10  C8   single    1.526  0.020  1.526
 9X8  C10  O4   single    1.417  0.020  1.417
 9X8  P2   O9   deloc     1.495  0.020  1.495
 9X8  P2   O10  deloc     1.500  0.020  1.500
 9X8  C8   C7   single    1.527  0.020  1.527
 9X8  C5   C6   single    1.494  0.020  1.494
 9X8  O4   C9   single    1.417  0.020  1.417
 9X8  C6   S1   double    1.636  0.020  1.636
 9X8  C6   O1   single    1.313  0.020  1.313
 9X8  O1   C7   single    1.420  0.020  1.420
 9X8  C7   C9   single    1.534  0.020  1.534
 9X8  C9   O3   single    1.378  0.020  1.378
 9X8  C4   H1   single    0.930  0.020  1.080
 9X8  C5   H2   single    0.970  0.020  1.090
 9X8  C5   H3   single    0.970  0.020  1.090
 9X8  C5   H4   single    0.970  0.020  1.090
 9X8  C7   H7   single    0.970  0.020  1.090
 9X8  C8   H8   single    0.970  0.020  1.090
 9X8  O2   H9   single    0.850  0.020  0.980
 9X8  C9   H10  single    0.970  0.020  1.090
 9X8  O3   H11  single    0.850  0.020  0.980
 9X8  C10  H12  single    0.970  0.020  1.090
 9X8  C11  H13  single    0.970  0.020  1.090
 9X8  C11  H14  single    0.970  0.020  1.090
 9X8  C12  H17  single    0.970  0.020  1.090
 9X8  C12  H18  single    0.970  0.020  1.090
 9X8  C13  H19  single    0.970  0.020  1.090
 9X8  C14  H20  single    0.970  0.020  1.090
 9X8  O13  H21  single    0.850  0.020  0.980
 9X8  C15  H22  single    0.970  0.020  1.090
 9X8  O14  H23  single    0.850  0.020  0.980
 9X8  C16  H24  single    0.970  0.020  1.090
 9X8  C17  H25  single    0.930  0.020  1.080
 9X8  N5   H26  single    0.860  0.020  1.020
 9X8  N5   H27  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
 9X8  N3   C1   N2   128.46  3.000
 9X8  N3   C1   C2   105.11  3.000
 9X8  N2   C1   C2   126.42  3.000
 9X8  N4   C2   C3   132.90  3.000
 9X8  N4   C2   C1   110.79  3.000
 9X8  C3   C2   C1   116.30  3.000
 9X8  N5   C3   N1   119.31  3.000
 9X8  N5   C3   C2   122.70  3.000
 9X8  N1   C3   C2   118.00  3.000
 9X8  H1   C4   N4   124.70  3.000
 9X8  H1   C4   N3   122.32  3.000
 9X8  N4   C4   N3   112.96  3.000
 9X8  C17  N1   C3   119.08  3.000
 9X8  C17  N2   C1   111.73  3.000
 9X8  H7   C7   C9   112.51  3.000
 9X8  H7   C7   C8   114.09  3.000
 9X8  C9   C7   C8   102.41  3.000
 9X8  H7   C7   O1   110.32  3.000
 9X8  C9   C7   O1   109.86  3.000
 9X8  C8   C7   O1   107.28  3.000
 9X8  H8   C8   C10  108.46  3.000
 9X8  H8   C8   O2   111.94  3.000
 9X8  C10  C8   O2   111.50  3.000
 9X8  H8   C8   C7   106.92  3.000
 9X8  C10  C8   C7   101.46  3.000
 9X8  O2   C8   C7   115.85  3.000
 9X8  H9   O2   C8   108.87  3.000
 9X8  H10  C9   O4   107.56  3.000
 9X8  H10  C9   O3   111.28  3.000
 9X8  O4   C9   O3   111.70  3.000
 9X8  H10  C9   C7   109.79  3.000
 9X8  O3   C9   C7   110.44  3.000
 9X8  O4   C9   C7   105.89  3.000
 9X8  H11  O3   C9   109.16  3.000
 9X8  C10  O4   C9   111.53  3.000
 9X8  H12  C10  C11  109.18  3.000
 9X8  H12  C10  O4   110.96  3.000
 9X8  C11  C10  O4   110.12  3.000
 9X8  H12  C10  C8   109.73  3.000
 9X8  O4   C10  C8   103.64  3.000
 9X8  C11  C10  C8   113.13  3.000
 9X8  H14  C11  H13  107.47  3.000
 9X8  H14  C11  O5   111.49  3.000
 9X8  H13  C11  O5   111.27  3.000
 9X8  H14  C11  C10  109.21  3.000
 9X8  H13  C11  C10  108.32  3.000
 9X8  O5   C11  C10  109.01  3.000
 9X8  P1   O5   C11  117.21  3.000
 9X8  O8   P1   O7   109.97  3.000
 9X8  O8   P1   O6   110.70  3.000
 9X8  O7   P1   O6   120.62  3.000
 9X8  O8   P1   O5    93.35  3.000
 9X8  O7   P1   O5   109.15  3.000
 9X8  O6   P1   O5   109.64  3.000
 9X8  P2   O8   P1   123.52  3.000
 9X8  O11  P2   O10  109.40  3.000
 9X8  O10  P2   O9   120.20  3.000
 9X8  O11  P2   O9   109.49  3.000
 9X8  O10  P2   O8   110.42  3.000
 9X8  O9   P2   O8   109.95  3.000
 9X8  O11  P2   O8    94.30  3.000
 9X8  C12  O11  P2   120.29  3.000
 9X8  H19  C13  C14  110.97  3.000
 9X8  H19  C13  O12  108.05  3.000
 9X8  C14  C13  O12  105.86  3.000
 9X8  H19  C13  C12  109.46  3.000
 9X8  C14  C13  C12  111.54  3.000
 9X8  O12  C13  C12  110.85  3.000
 9X8  C16  O12  C13  110.73  3.000
 9X8  H20  C14  C15  111.89  3.000
 9X8  H20  C14  O13  111.72  3.000
 9X8  C15  C14  O13  110.89  3.000
 9X8  H20  C14  C13  111.87  3.000
 9X8  C15  C14  C13  100.89  3.000
 9X8  O13  C14  C13  109.08  3.000
 9X8  H21  O13  C14  107.97  3.000
 9X8  H22  C15  C16  109.53  3.000
 9X8  H22  C15  O14  111.59  3.000
 9X8  C16  C15  O14  110.12  3.000
 9X8  H22  C15  C14  109.22  3.000
 9X8  O14  C15  C14  114.93  3.000
 9X8  C16  C15  C14  100.88  3.000
 9X8  H23  O14  C15  108.79  3.000
 9X8  H24  C16  N3   105.83  3.000
 9X8  H24  C16  C15  109.97  3.000
 9X8  N3   C16  C15  114.17  3.000
 9X8  H24  C16  O12  111.82  3.000
 9X8  C15  C16  O12  105.78  3.000
 9X8  N3   C16  O12  109.39  3.000
 9X8  C16  N3   C4   127.56  3.000
 9X8  C4   N3   C1   106.49  3.000
 9X8  C16  N3   C1   125.94  3.000
 9X8  C4   N4   C2   104.63  3.000
 9X8  H25  C17  N2   116.14  3.000
 9X8  H25  C17  N1   115.39  3.000
 9X8  N2   C17  N1   128.46  3.000
 9X8  H27  N5   H26  118.27  3.000
 9X8  H27  N5   C3   120.31  3.000
 9X8  H26  N5   C3   121.04  3.000
 9X8  C7   O1   C6   122.19  3.000
 9X8  O1   C6   S1   125.95  3.000
 9X8  O1   C6   C5   110.39  3.000
 9X8  S1   C6   C5   123.64  3.000
 9X8  H18  C12  H17  107.16  3.000
 9X8  H18  C12  C13  108.09  3.000
 9X8  H17  C12  C13  110.23  3.000
 9X8  H18  C12  O11  110.50  3.000
 9X8  H17  C12  O11  111.37  3.000
 9X8  C13  C12  O11  109.42  3.000
 9X8  H4   C5   H3   107.09  3.000
 9X8  H4   C5   H2   109.23  3.000
 9X8  H3   C5   H2   109.06  3.000
 9X8  H4   C5   C6   110.19  3.000
 9X8  H3   C5   C6   109.97  3.000
 9X8  H2   C5   C6   111.20  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
 9X8  CONST_01  N1   C17  N2   C1      0.00   0.0  0
 9X8  CONST_02  N1   C3   C2   C1      0.00   0.0  0
 9X8  CONST_03  C4   N4   C2   C1      0.00   0.0  0
 9X8  CONST_04  N4   C4   N3   C1      0.00   0.0  0
 9X8  CONST_05  C17  N1   C3   C2      0.00   0.0  0
 9X8  CONST_06  C17  N2   C1   C2      0.00   0.0  0
 9X8  CONST_07  C4   N3   C1   C2      0.00   0.0  0
 9X8  CONST_08  N3   C4   N4   C2      0.00   0.0  0
 9X8  CONST_09  N2   C17  N1   C3      0.00   0.0  0
 9X8  CONST_10  N2   C1   C2   C3      0.00   0.0  0
 9X8  CONST_11  N3   C1   C2   C3    180.00   0.0  0
 9X8  CONST_12  C4   N4   C2   C3    180.00   0.0  0
 9X8  CONST_13  N2   C1   N3   C4    180.00   0.0  0
 9X8  CONST_14  N4   C2   C3   N1    180.00   0.0  0
 9X8  CONST_15  N4   C2   C1   N2    180.00   0.0  0
 9X8  CONST_16  C17  N2   C1   N3    180.00   0.0  0
 9X8  CONST_17  N4   C2   C1   N3      0.00   0.0  0
 9X8  CONST_18  C16  N3   C1   C2    180.00   0.0  0
 9X8  CONST_19  C16  N3   C1   N2      0.00   0.0  0
 9X8  CONST_20  N4   C4   N3   C16   180.00   0.0  0
 9X8  CONST_21  N5   C3   C2   C1    180.00   0.0  0
 9X8  CONST_22  N5   C3   C2   N4      0.00   0.0  0
 9X8  CONST_23  N5   C3   N1   C17   180.00   0.0  0
 9X8  CONST_24  H25  C17  N2   C1    180.00   0.0  0
 9X8  CONST_25  H1   C4   N3   C1    180.00   0.0  0
 9X8  CONST_26  H26  N5   C3   C2      0.00   0.0  0
 9X8  CONST_27  H27  N5   C3   C2    180.00   0.0  0
 9X8  Var_01    C13  C12  O11  P2   -139.70  30.0  1
 9X8  Var_02    O6   P1   O5   C11   -69.05  30.0  2
 9X8  Var_03    O11  P2   O8   P1    153.13  30.0  3
 9X8  Var_04    H2   C5   C6   S1     -2.68  30.0  3
 9X8  Var_05    H13  C11  O5   P1     65.17  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
 9X8  chir_01  C7   C8   O1   C9   negativ
 9X8  chir_02  C8   O2   C7   C10  negativ
 9X8  chir_03  C9   O3   O4   C7   negativ
 9X8  chir_04  C10  O4   C8   C11  negativ
 9X8  chir_07  C13  O12  C14  C12  negativ
 9X8  chir_08  C14  O13  C13  C15  positiv
 9X8  chir_09  C15  O14  C14  C16  positiv
 9X8  chir_10  C16  O12  N3   C15  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
 9X8  plan-1  C3   0.020
 9X8  plan-1  N5   0.020
 9X8  plan-1  H26  0.020
 9X8  plan-1  H27  0.020
 9X8  plan-2  C1   0.020
 9X8  plan-2  C2   0.020
 9X8  plan-2  C3   0.020
 9X8  plan-2  C4   0.020
 9X8  plan-2  N1   0.020
 9X8  plan-2  N2   0.020
 9X8  plan-2  C16  0.020
 9X8  plan-2  N3   0.020
 9X8  plan-2  N4   0.020
 9X8  plan-2  C17  0.020
 9X8  plan-2  N5   0.020
 9X8  plan-2  H1   0.020
 9X8  plan-2  H25  0.020
 9X8  plan-3  O1   0.020
 9X8  plan-3  C6   0.020
 9X8  plan-3  C5   0.020
 9X8  plan-3  S1   0.020

