# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 16 18:04:02 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl 4-ethyl-3-fluorosulfonyl-benzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1ccc(cc1[S](F)(=O)=O)C(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34
#
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
 9K8  9K8  '[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl 4-ethyl-3-fluorosulfonyl-benzoate'  ligand  53  33  .  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_9K8
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
 9K8  C1   C  CH2   0  -0.539   5.8617   1.6549   1.8775
 9K8  C2   C  CR6   0   0.212   4.8253   0.8406   1.1529
 9K8  C3   C  CR16  0  -0.281   3.5635   0.7376   1.7342
 9K8  O4   O  O2    0  -0.491  -2.0251  -0.8133   0.9103
 9K8  O5   O  OH1   0  -0.663  -3.9568  -2.7858   2.0584
 9K8  C7   C  CR6   0  -0.315   4.9793   0.2319  -0.1001
 9K8  C9   C  CH2   0  -0.178  -0.6310  -1.9399  -0.7025
 9K8  C10  C  CH1   0  -0.004  -1.6737  -2.0850   0.3748
 9K8  C11  C  CH1   0  -0.037  -2.9828  -2.6689  -0.1532
 9K8  C12  C  CH1   0  -0.046  -3.9953  -2.0925   0.8426
 9K8  C13  C  CH1   0   0.176  -3.4057  -0.7046   1.0876
 9K8  C14  C  CR15  0   0.101  -3.2925   0.8902  -0.8996
 9K8  C15  C  CR56  0  -0.002  -5.2356   1.7150  -0.8566
 9K8  C16  C  CR56  0   0.487  -5.1847   0.8080   0.1896
 9K8  O2   O  O     0  -0.435   1.7029  -1.6158  -1.9849
 9K8  C5   C  CR6   0  -0.090   2.6966  -0.5072  -0.1318
 9K8  C4   C  CR16  0  -0.223   2.5178   0.0753   1.1198
 9K8  C6   C  CR16  0  -0.223   3.9385  -0.4247  -0.7427
 9K8  S    S  S     0   1.566   6.5374   0.1758  -0.9216
 9K8  O1   O  OS    0  -0.597   7.5859  -0.2756  -0.0469
 9K8  O    O  OS    0  -0.595   6.3993  -0.3755  -2.2422
 9K8  C    C  CH3   0  -0.655   5.6258   3.1532   1.6751
 9K8  O3   O  O2    0  -0.461   0.5197  -1.3368  -0.1114
 9K8  O6   O  OH1   0  -0.654  -2.9208  -4.0650  -0.1624
 9K8  N    N  NR5   0  -0.536  -3.9287   0.2784   0.1457
 9K8  N2   N  N     0  -0.459  -6.1639   0.5271   1.0480
 9K8  C17  C  CR16  0   0.039  -7.2505   1.2352   0.7933
 9K8  N3   N  N     0  -0.474  -7.4456   2.1341  -0.1681
 9K8  C18  C  CR6   0   0.459  -6.4514   2.4052  -1.0214
 9K8  N4   N  NH2   0  -0.817  -6.6451   3.3049  -1.9858
 9K8  N1   N  N     0  -0.450  -4.0410   1.7517  -1.5252
 9K8  F    F  F     0  -0.410   6.7966   1.7410  -1.1339
 9K8  H1   H  HCH2  0   0.271   5.7850   1.4227   2.9410
 9K8  H2   H  HCH2  0   0.261   6.8765   1.3962   1.5878
 9K8  H3   H  HCR6  0   0.282   3.3993   1.1917   2.7031
 9K8  H5   H  HCH2  0   0.266  -0.3894  -2.9295  -1.0966
 9K8  H6   H  HCH2  0   0.245  -0.9921  -1.3227  -1.5302
 9K8  H7   H  HCH1  0   0.260  -1.2813  -2.7212   1.1774
 9K8  H8   H  HCH1  0   0.251  -3.1945  -2.2672  -1.1531
 9K8  H9   H  HCH1  0   0.265  -5.0098  -2.0427   0.4303
 9K8  H10  H  HCH1  0   0.288  -3.6353  -0.3443   2.0942
 9K8  H11  H  HCR5  0   0.294  -2.2666   0.6738  -1.1514
 9K8  H12  H  HCR6  0   0.283   1.5619   0.0272   1.6224
 9K8  H13  H  HCR6  0   0.298   4.0869  -0.8794  -1.7124
 9K8  H15  H  HCH3  0   0.236   4.6424   3.4507   2.0386
 9K8  H16  H  HCH3  0   0.246   6.3733   3.7246   2.2242
 9K8  H17  H  HCH3  0   0.233   5.6937   3.4336   0.6247
 9K8  H18  H  HOH1  0   0.471  -3.5990  -4.4028  -0.7563
 9K8  H19  H  HCR6  0   0.253  -8.0968   1.0648   1.4500
 9K8  H20  H  HNH2  0   0.412  -5.9089   3.5490  -2.6244
 9K8  H21  H  HNH2  0   0.404  -7.5215   3.7923  -2.0581
 9K8  C8   C  C     0   0.622   1.6062  -1.2108  -0.8537
 9K8  H4   H  HOH1  0   0.454  -3.8692  -3.7267   1.8616

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
 9K8  C1   C2   single    1.504  0.020  1.504
 9K8  C1   C    single    1.530  0.020  1.530
 9K8  C2   C3   aromatic  1.393  0.020  1.393
 9K8  C2   C7   aromatic  1.402  0.020  1.402
 9K8  C3   C4   aromatic  1.382  0.020  1.382
 9K8  O4   C10  single    1.424  0.020  1.424
 9K8  O4   C13  single    1.396  0.020  1.396
 9K8  O5   C12  single    1.400  0.020  1.400
 9K8  C7   C6   aromatic  1.388  0.020  1.388
 9K8  C7   S    single    1.762  0.020  1.762
 9K8  C8   O2   double    1.205  0.020  1.205
 9K8  C8   C5   single    1.485  0.020  1.485
 9K8  C8   O3   single    1.322  0.020  1.322
 9K8  C9   C10  single    1.506  0.020  1.506
 9K8  C9   O3   single    1.427  0.020  1.427
 9K8  C10  C11  single    1.528  0.020  1.528
 9K8  C11  C12  single    1.533  0.020  1.533
 9K8  C11  O6   single    1.397  0.020  1.397
 9K8  C12  C13  single    1.528  0.020  1.528
 9K8  C13  N    single    1.458  0.020  1.458
 9K8  C14  N    aromatic  1.368  0.020  1.368
 9K8  C14  N1   aromatic  1.301  0.020  1.301
 9K8  C15  C16  aromatic  1.386  0.020  1.386
 9K8  C15  C18  aromatic  1.408  0.020  1.408
 9K8  C15  N1   aromatic  1.369  0.020  1.369
 9K8  C16  N    aromatic  1.364  0.020  1.364
 9K8  C16  N2   aromatic  1.332  0.020  1.332
 9K8  C5   C4   aromatic  1.392  0.020  1.392
 9K8  C5   C6   aromatic  1.387  0.020  1.387
 9K8  S    O1   double    1.438  0.020  1.438
 9K8  S    O    double    1.438  0.020  1.438
 9K8  S    F    single    1.601  0.020  1.601
 9K8  N2   C17  aromatic  1.322  0.020  1.322
 9K8  C17  N3   aromatic  1.331  0.020  1.331
 9K8  N3   C18  aromatic  1.338  0.020  1.338
 9K8  C18  N4   single    1.333  0.020  1.333
 9K8  C1   H1   single    0.970  0.020  1.090
 9K8  C1   H2   single    0.970  0.020  1.090
 9K8  C3   H3   single    0.930  0.020  1.080
 9K8  O5   H4   single    0.850  0.020  0.980
 9K8  C9   H5   single    0.970  0.020  1.090
 9K8  C9   H6   single    0.970  0.020  1.090
 9K8  C10  H7   single    0.970  0.020  1.090
 9K8  C11  H8   single    0.970  0.020  1.090
 9K8  C12  H9   single    0.970  0.020  1.090
 9K8  C13  H10  single    0.970  0.020  1.090
 9K8  C14  H11  single    0.930  0.020  1.080
 9K8  C4   H12  single    0.930  0.020  1.080
 9K8  C6   H13  single    0.930  0.020  1.080
 9K8  C    H15  single    0.970  0.020  1.090
 9K8  C    H16  single    0.970  0.020  1.090
 9K8  C    H17  single    0.970  0.020  1.090
 9K8  O6   H18  single    0.850  0.020  0.980
 9K8  C17  H19  single    0.930  0.020  1.080
 9K8  N4   H20  single    0.860  0.020  1.020
 9K8  N4   H21  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
 9K8  H2   C1   H1   105.95  3.000
 9K8  H2   C1   C    109.99  3.000
 9K8  H1   C1   C    109.05  3.000
 9K8  H2   C1   C2   112.72  3.000
 9K8  H1   C1   C2   107.81  3.000
 9K8  C    C1   C2   111.11  3.000
 9K8  C7   C2   C3   116.14  3.000
 9K8  C7   C2   C1   126.16  3.000
 9K8  C3   C2   C1   117.59  3.000
 9K8  H3   C3   C4   118.96  3.000
 9K8  H3   C3   C2   118.67  3.000
 9K8  C4   C3   C2   122.37  3.000
 9K8  C13  O4   C10  111.18  3.000
 9K8  H4   O5   C12  107.95  3.000
 9K8  S    C7   C6   115.60  3.000
 9K8  S    C7   C2   121.86  3.000
 9K8  C6   C7   C2   122.47  3.000
 9K8  H6   C9   H5   108.13  3.000
 9K8  H6   C9   O3   109.95  3.000
 9K8  H5   C9   O3   110.73  3.000
 9K8  H6   C9   C10  111.53  3.000
 9K8  H5   C9   C10  108.90  3.000
 9K8  O3   C9   C10  107.61  3.000
 9K8  H7   C10  C11  109.74  3.000
 9K8  H7   C10  C9   109.36  3.000
 9K8  C11  C10  C9   112.51  3.000
 9K8  H7   C10  O4   109.34  3.000
 9K8  C11  C10  O4   105.07  3.000
 9K8  C9   C10  O4   110.72  3.000
 9K8  H8   C11  O6   111.59  3.000
 9K8  H8   C11  C12  109.06  3.000
 9K8  O6   C11  C12  114.16  3.000
 9K8  H8   C11  C10  109.89  3.000
 9K8  O6   C11  C10  110.25  3.000
 9K8  C12  C11  C10  101.41  3.000
 9K8  H9   C12  C13  112.10  3.000
 9K8  H9   C12  C11  112.59  3.000
 9K8  C13  C12  C11  101.00  3.000
 9K8  H9   C12  O5   112.00  3.000
 9K8  C13  C12  O5   107.45  3.000
 9K8  C11  C12  O5   111.09  3.000
 9K8  H10  C13  N    107.28  3.000
 9K8  H10  C13  C12  111.46  3.000
 9K8  N    C13  C12  111.74  3.000
 9K8  H10  C13  O4   110.50  3.000
 9K8  N    C13  O4   108.97  3.000
 9K8  C12  C13  O4   106.89  3.000
 9K8  H11  C14  N1   124.59  3.000
 9K8  H11  C14  N    122.08  3.000
 9K8  N1   C14  N    113.32  3.000
 9K8  N1   C15  C18  133.08  3.000
 9K8  N1   C15  C16  110.74  3.000
 9K8  C18  C15  C16  116.17  3.000
 9K8  N2   C16  N    128.02  3.000
 9K8  N2   C16  C15  126.69  3.000
 9K8  N    C16  C15  105.29  3.000
 9K8  C6   C5   C4   119.10  3.000
 9K8  C6   C5   C8   118.15  3.000
 9K8  C4   C5   C8   122.75  3.000
 9K8  H12  C4   C5   120.86  3.000
 9K8  H12  C4   C3   118.93  3.000
 9K8  C5   C4   C3   120.20  3.000
 9K8  H13  C6   C5   119.54  3.000
 9K8  H13  C6   C7   120.74  3.000
 9K8  C5   C6   C7   119.72  3.000
 9K8  F    S    O    105.58  3.000
 9K8  F    S    O1   105.64  3.000
 9K8  O    S    O1   120.55  3.000
 9K8  F    S    C7   100.01  3.000
 9K8  O    S    C7   110.82  3.000
 9K8  O1   S    C7   111.79  3.000
 9K8  H17  C    H16  107.95  3.000
 9K8  H17  C    H15  107.92  3.000
 9K8  H16  C    H15  107.93  3.000
 9K8  H17  C    C1   111.72  3.000
 9K8  H16  C    C1   109.94  3.000
 9K8  H15  C    C1   111.24  3.000
 9K8  C9   O3   C8   118.06  3.000
 9K8  H18  O6   C11  108.86  3.000
 9K8  C16  N    C14  106.22  3.000
 9K8  C16  N    C13  124.84  3.000
 9K8  C14  N    C13  128.91  3.000
 9K8  C17  N2   C16  111.54  3.000
 9K8  H19  C17  N3   115.42  3.000
 9K8  H19  C17  N2   116.14  3.000
 9K8  N3   C17  N2   128.44  3.000
 9K8  C18  N3   C17  119.26  3.000
 9K8  N4   C18  N3   119.35  3.000
 9K8  N4   C18  C15  122.75  3.000
 9K8  N3   C18  C15  117.89  3.000
 9K8  H21  N4   H20  118.38  3.000
 9K8  H21  N4   C18  120.39  3.000
 9K8  H20  N4   C18  121.16  3.000
 9K8  C15  N1   C14  104.43  3.000
 9K8  O3   C8   C5   112.07  3.000
 9K8  O3   C8   O2   124.12  3.000
 9K8  C5   C8   O2   123.81  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
 9K8  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 9K8  CONST_02  C5   C6   C7   C2     0.00   0.0  0
 9K8  CONST_03  C6   C7   C2   C3     0.00   0.0  0
 9K8  CONST_04  C6   C5   C4   C3     0.00   0.0  0
 9K8  CONST_05  C4   C3   C2   C7     0.00   0.0  0
 9K8  CONST_06  C4   C5   C6   C7     0.00   0.0  0
 9K8  CONST_07  C15  C16  N    C14    0.00   0.0  0
 9K8  CONST_08  N2   C16  N    C14  180.00   0.0  0
 9K8  CONST_09  C16  C15  N1   C14    0.00   0.0  0
 9K8  CONST_10  C18  C15  N1   C14  180.00   0.0  0
 9K8  CONST_11  C17  N2   C16  C15    0.00   0.0  0
 9K8  CONST_12  C17  N3   C18  C15    0.00   0.0  0
 9K8  CONST_13  N    C14  N1   C15    0.00   0.0  0
 9K8  CONST_14  N3   C18  C15  C16    0.00   0.0  0
 9K8  CONST_15  N1   C14  N    C16    0.00   0.0  0
 9K8  CONST_16  N3   C17  N2   C16    0.00   0.0  0
 9K8  CONST_17  C18  C15  C16  N    180.00   0.0  0
 9K8  CONST_18  N1   C15  C16  N      0.00   0.0  0
 9K8  CONST_19  C17  N2   C16  N    180.00   0.0  0
 9K8  CONST_20  C18  C15  C16  N2     0.00   0.0  0
 9K8  CONST_21  N1   C15  C16  N2   180.00   0.0  0
 9K8  CONST_22  C18  N3   C17  N2     0.00   0.0  0
 9K8  CONST_23  N1   C15  C18  N3   180.00   0.0  0
 9K8  CONST_24  N1   C14  N    C13  180.00   0.0  0
 9K8  CONST_25  C15  C16  N    C13  180.00   0.0  0
 9K8  CONST_26  N2   C16  N    C13    0.00   0.0  0
 9K8  CONST_27  C4   C3   C2   C1   180.00   0.0  0
 9K8  CONST_28  C6   C7   C2   C1   180.00   0.0  0
 9K8  CONST_29  S    C7   C2   C3   180.00   0.0  0
 9K8  CONST_30  C8   C5   C4   C3   180.00   0.0  0
 9K8  CONST_31  C8   C5   C6   C7   180.00   0.0  0
 9K8  CONST_32  N4   C18  C15  C16  180.00   0.0  0
 9K8  CONST_33  S    C7   C6   C5   180.00   0.0  0
 9K8  CONST_34  N4   C18  N3   C17  180.00   0.0  0
 9K8  CONST_35  N1   C15  C18  N4     0.00   0.0  0
 9K8  CONST_36  H12  C4   C3   C2   180.00   0.0  0
 9K8  CONST_37  H13  C6   C7   C2   180.00   0.0  0
 9K8  CONST_38  H3   C3   C2   C7   180.00   0.0  0
 9K8  CONST_39  H11  C14  N    C13    0.00   0.0  0
 9K8  CONST_40  H19  C17  N2   C16  180.00   0.0  0
 9K8  CONST_41  H20  N4   C18  C15    0.00   0.0  0
 9K8  CONST_42  H21  N4   C18  C15  180.00   0.0  0
 9K8  Var_01    O1   S    C7   C2    48.45  30.0  2
 9K8  Var_02    C    C1   C2   C3   -77.50  30.0  3
 9K8  Var_03    C4   C5   C8   O2   173.03  30.0  2
 9K8  Var_04    C10  C9   O3   C8   174.66  30.0  1
 9K8  Var_05    C5   C8   O3   C9   177.12  30.0  1
 9K8  Var_06    H15  C    C1   C2    59.31  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
 9K8  chir_01  C10  O4  C9   C11  positiv
 9K8  chir_02  C11  O6  C10  C12  positiv
 9K8  chir_03  C12  O5  C11  C13  positiv
 9K8  chir_04  C13  O4  N    C12  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
 9K8  plan-1  C1   0.020
 9K8  plan-1  C2   0.020
 9K8  plan-1  C3   0.020
 9K8  plan-1  C7   0.020
 9K8  plan-1  C5   0.020
 9K8  plan-1  C4   0.020
 9K8  plan-1  C6   0.020
 9K8  plan-1  S    0.020
 9K8  plan-1  H3   0.020
 9K8  plan-1  H12  0.020
 9K8  plan-1  H13  0.020
 9K8  plan-1  C8   0.020
 9K8  plan-2  C13  0.020
 9K8  plan-2  C14  0.020
 9K8  plan-2  C15  0.020
 9K8  plan-2  C16  0.020
 9K8  plan-2  N    0.020
 9K8  plan-2  N2   0.020
 9K8  plan-2  C17  0.020
 9K8  plan-2  N3   0.020
 9K8  plan-2  C18  0.020
 9K8  plan-2  N4   0.020
 9K8  plan-2  N1   0.020
 9K8  plan-2  H11  0.020
 9K8  plan-2  H19  0.020
 9K8  plan-3  C18  0.020
 9K8  plan-3  N4   0.020
 9K8  plan-3  H20  0.020
 9K8  plan-3  H21  0.020
 9K8  plan-4  O2   0.020
 9K8  plan-4  C5   0.020
 9K8  plan-4  O3   0.020
 9K8  plan-4  C8   0.020

