# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 16 17:22:50 2020
#   Inital geometry file: a 118 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 3-fluorosulfonylbenzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](COC(=O)c4cccc(c4)[S](F)(=O)=O)[C@@H](O)[C@H]3O
#
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
 9K5  9K5  '[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl 3-fluorosulfonylbenzoate'  ligand  47  31  .  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_9K5
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
 9K5  C1   C  CR16  0  -0.237  -2.8609  -0.0954   1.5317
 9K5  C2   C  CR6   0  -0.073  -3.0962   0.1436   0.1798
 9K5  C3   C  CR16  0  -0.231  -4.3264  -0.1859  -0.3768
 9K5  O4   O  O2    0  -0.493   1.6796   0.8167   0.8175
 9K5  O5   O  OH1   0  -0.662   3.4990   3.0824   1.5954
 9K5  C7   C  CH2   0  -0.180   0.1099   1.6327  -0.8161
 9K5  C8   C  CH1   0  -0.002   1.2006   1.9849   0.1602
 9K5  C9   C  CH1   0  -0.035   2.4281   2.5889  -0.5165
 9K5  C10  C  CH1   0  -0.049   3.5313   2.2299   0.4853
 9K5  C11  C  CH1   0   0.178   3.0695   0.8501   0.9535
 9K5  C12  C  CR15  0   0.102   3.0605  -0.9891  -0.8143
 9K5  C13  C  CR56  0  -0.002   5.0431  -1.6978  -0.6523
 9K5  C14  C  CR56  0   0.487   4.9305  -0.6702   0.2700
 9K5  C15  C  CR16  0   0.040   7.0061  -0.9064   0.9395
 9K5  C16  C  CR6   0   0.459   6.2952  -2.3382  -0.7179
 9K5  O2   O  O     0  -0.433  -2.2331   0.9012  -1.9012
 9K5  C6   C  C     0   0.627  -2.0697   0.7389  -0.7184
 9K5  C4   C  CR6   0  -0.233  -5.2937  -0.7510   0.4356
 9K5  S    S  S     0   1.581  -6.8508  -1.1606  -0.2599
 9K5  O1   O  OS    0  -0.597  -6.8032  -1.1151  -1.6954
 9K5  O    O  OS    0  -0.598  -7.4570  -2.2591   0.4409
 9K5  C5   C  CR16  0  -0.207  -5.0727  -1.0028   1.7851
 9K5  C    C  CR16  0  -0.228  -3.8446  -0.6659   2.3265
 9K5  O3   O  O2    0  -0.460  -0.9672   1.0647  -0.0695
 9K5  O6   O  OH1   0  -0.654   2.2518   3.9626  -0.7038
 9K5  N    N  NR5   0  -0.536   3.6490  -0.2194   0.1515
 9K5  N2   N  N     0  -0.458   5.8810  -0.2299   1.0927
 9K5  N3   N  N     0  -0.474   7.2612  -1.9085   0.1023
 9K5  N4   N  NH2   0  -0.816   6.5476  -3.3451  -1.5540
 9K5  N1   N  N     0  -0.450   3.8616  -1.8813  -1.3202
 9K5  H1   H  HCR6  0   0.287  -1.9080   0.1550   1.9761
 9K5  H2   H  HCR6  0   0.300  -4.5112  -0.0030  -1.4265
 9K5  H4   H  HCH2  0   0.266  -0.2163   2.5414  -1.3276
 9K5  H5   H  HCH2  0   0.246   0.4598   0.9244  -1.5717
 9K5  H6   H  HCH1  0   0.260   0.8059   2.6874   0.9042
 9K5  H7   H  HCH1  0   0.250   2.6262   2.0744  -1.4664
 9K5  H8   H  HCH1  0   0.265   4.5246   2.1948   0.0223
 9K5  H9   H  HCH1  0   0.286   3.3610   0.6676   1.9915
 9K5  H10  H  HCR5  0   0.294   2.0284  -0.8633  -1.1005
 9K5  H11  H  HCR6  0   0.253   7.8329  -0.6104   1.5762
 9K5  H14  H  HCR6  0   0.306  -5.8342  -1.4540   2.4066
 9K5  H15  H  HCR6  0   0.292  -3.6517  -0.8529   3.3731
 9K5  H16  H  HOH1  0   0.471   2.8580   4.2643  -1.3881
 9K5  H17  H  HNH2  0   0.412   5.8452  -3.6830  -2.1877
 9K5  H18  H  HNH2  0   0.404   7.4567  -3.7740  -1.5755
 9K5  F1   F  F     0  -0.414  -7.6756   0.1346   0.1880
 9K5  H3   H  HOH1  0   0.454   3.3608   3.9823   1.2752

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
 9K5  C15  N2   aromatic  1.322  0.020  1.322
 9K5  C15  N3   aromatic  1.330  0.020  1.330
 9K5  N2   C14  aromatic  1.332  0.020  1.332
 9K5  O6   C9   single    1.398  0.020  1.398
 9K5  O4   C8   single    1.423  0.020  1.423
 9K5  O4   C11  single    1.397  0.020  1.397
 9K5  C8   C7   single    1.506  0.020  1.506
 9K5  C8   C9   single    1.526  0.020  1.526
 9K5  N3   C16  aromatic  1.338  0.020  1.338
 9K5  C11  N    single    1.457  0.020  1.457
 9K5  C11  C10  single    1.528  0.020  1.528
 9K5  C14  N    aromatic  1.364  0.020  1.364
 9K5  C14  C13  aromatic  1.385  0.020  1.385
 9K5  C7   O3   single    1.428  0.020  1.428
 9K5  C9   C10  single    1.533  0.020  1.533
 9K5  N    C12  aromatic  1.368  0.020  1.368
 9K5  C16  C13  aromatic  1.408  0.020  1.408
 9K5  C16  N4   single    1.333  0.020  1.333
 9K5  C10  O5   single    1.400  0.020  1.400
 9K5  C13  N1   aromatic  1.370  0.020  1.370
 9K5  O3   C6   single    1.320  0.020  1.320
 9K5  C12  N1   aromatic  1.301  0.020  1.301
 9K5  O2   C6   double    1.205  0.020  1.205
 9K5  C6   C2   single    1.488  0.020  1.488
 9K5  C2   C1   aromatic  1.393  0.020  1.393
 9K5  C2   C3   aromatic  1.390  0.020  1.390
 9K5  C1   C    aromatic  1.387  0.020  1.387
 9K5  C3   C4   aromatic  1.384  0.020  1.384
 9K5  C    C5   aromatic  1.384  0.020  1.384
 9K5  C4   C5   aromatic  1.390  0.020  1.390
 9K5  C4   S    single    1.754  0.020  1.754
 9K5  O    S    double    1.437  0.020  1.437
 9K5  S    O1   double    1.437  0.020  1.437
 9K5  C1   H1   single    0.930  0.020  1.080
 9K5  C3   H2   single    0.930  0.020  1.080
 9K5  O5   H3   single    0.850  0.020  0.980
 9K5  C7   H4   single    0.970  0.020  1.090
 9K5  C7   H5   single    0.970  0.020  1.090
 9K5  C8   H6   single    0.970  0.020  1.090
 9K5  C9   H7   single    0.970  0.020  1.090
 9K5  C10  H8   single    0.970  0.020  1.090
 9K5  C11  H9   single    0.970  0.020  1.090
 9K5  C12  H10  single    0.930  0.020  1.080
 9K5  C15  H11  single    0.930  0.020  1.080
 9K5  C5   H14  single    0.930  0.020  1.080
 9K5  C    H15  single    0.930  0.020  1.080
 9K5  O6   H16  single    0.850  0.020  0.980
 9K5  N4   H17  single    0.860  0.020  1.020
 9K5  N4   H18  single    0.860  0.020  1.020
 9K5  S    F1   single    1.600  0.020  1.600

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
 9K5  H1   C1   C    119.00  3.000
 9K5  H1   C1   C2   120.55  3.000
 9K5  C    C1   C2   120.45  3.000
 9K5  C6   C2   C3   117.62  3.000
 9K5  C3   C2   C1   119.84  3.000
 9K5  C6   C2   C1   122.54  3.000
 9K5  H2   C3   C4   121.29  3.000
 9K5  H2   C3   C2   120.00  3.000
 9K5  C4   C3   C2   118.71  3.000
 9K5  C11  O4   C8   111.11  3.000
 9K5  H3   O5   C10  107.94  3.000
 9K5  H5   C7   H4   108.11  3.000
 9K5  H5   C7   O3   110.19  3.000
 9K5  H4   C7   O3   110.51  3.000
 9K5  H5   C7   C8   111.58  3.000
 9K5  H4   C7   C8   108.98  3.000
 9K5  O3   C7   C8   107.48  3.000
 9K5  H6   C8   C9   109.68  3.000
 9K5  H6   C8   C7   109.21  3.000
 9K5  C9   C8   C7   112.81  3.000
 9K5  H6   C8   O4   109.48  3.000
 9K5  C9   C8   O4   105.00  3.000
 9K5  C7   C8   O4   110.56  3.000
 9K5  H7   C9   O6   111.55  3.000
 9K5  H7   C9   C10  109.01  3.000
 9K5  O6   C9   C10  114.12  3.000
 9K5  H7   C9   C8   110.07  3.000
 9K5  C10  C9   C8   101.32  3.000
 9K5  O6   C9   C8   110.30  3.000
 9K5  H8   C10  C11  111.98  3.000
 9K5  H8   C10  C9   112.55  3.000
 9K5  C11  C10  C9   101.20  3.000
 9K5  H8   C10  O5   112.04  3.000
 9K5  C9   C10  O5   111.04  3.000
 9K5  C11  C10  O5   107.45  3.000
 9K5  H9   C11  N    107.09  3.000
 9K5  H9   C11  C10  111.16  3.000
 9K5  N    C11  C10  111.95  3.000
 9K5  H9   C11  O4   110.71  3.000
 9K5  C10  C11  O4   107.00  3.000
 9K5  N    C11  O4   108.94  3.000
 9K5  H10  C12  N1   124.47  3.000
 9K5  H10  C12  N    122.24  3.000
 9K5  N1   C12  N    113.29  3.000
 9K5  N1   C13  C16  133.12  3.000
 9K5  N1   C13  C14  110.73  3.000
 9K5  C16  C13  C14  116.15  3.000
 9K5  N2   C14  N    127.95  3.000
 9K5  N    C14  C13  105.29  3.000
 9K5  N2   C14  C13  126.76  3.000
 9K5  H11  C15  N3   115.39  3.000
 9K5  H11  C15  N2   116.18  3.000
 9K5  N3   C15  N2   128.44  3.000
 9K5  N4   C16  N3   119.37  3.000
 9K5  N4   C16  C13  122.77  3.000
 9K5  N3   C16  C13  117.87  3.000
 9K5  O3   C6   O2   124.23  3.000
 9K5  O2   C6   C2   123.56  3.000
 9K5  O3   C6   C2   112.21  3.000
 9K5  C5   C4   S    118.93  3.000
 9K5  S    C4   C3   118.89  3.000
 9K5  C5   C4   C3   122.18  3.000
 9K5  F1   S    O    105.36  3.000
 9K5  F1   S    O1   105.74  3.000
 9K5  O    S    O1   121.69  3.000
 9K5  F1   S    C4    99.07  3.000
 9K5  O1   S    C4   111.06  3.000
 9K5  O    S    C4   111.08  3.000
 9K5  H14  C5   C    120.11  3.000
 9K5  H14  C5   C4   121.42  3.000
 9K5  C    C5   C4   118.47  3.000
 9K5  H15  C    C5   119.69  3.000
 9K5  H15  C    C1   119.96  3.000
 9K5  C5   C    C1   120.35  3.000
 9K5  C6   O3   C7   118.10  3.000
 9K5  H16  O6   C9   108.90  3.000
 9K5  C14  N    C12  106.24  3.000
 9K5  C12  N    C11  129.08  3.000
 9K5  C14  N    C11  124.65  3.000
 9K5  C15  N2   C14  111.51  3.000
 9K5  C16  N3   C15  119.28  3.000
 9K5  H18  N4   H17  118.38  3.000
 9K5  H18  N4   C16  120.46  3.000
 9K5  H17  N4   C16  121.16  3.000
 9K5  C13  N1   C12  104.45  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
 9K5  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 9K5  CONST_02  C4   C5   C    C1     0.00   0.0  0
 9K5  CONST_03  C5   C    C1   C2     0.00   0.0  0
 9K5  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 9K5  CONST_05  C    C1   C2   C3     0.00   0.0  0
 9K5  CONST_06  C    C5   C4   C3     0.00   0.0  0
 9K5  CONST_07  N2   C14  N    C12  180.00   0.0  0
 9K5  CONST_08  C13  C14  N    C12    0.00   0.0  0
 9K5  CONST_09  C14  C13  N1   C12    0.00   0.0  0
 9K5  CONST_10  C16  C13  N1   C12  180.00   0.0  0
 9K5  CONST_11  C15  N2   C14  C13    0.00   0.0  0
 9K5  CONST_12  C15  N3   C16  C13    0.00   0.0  0
 9K5  CONST_13  N    C12  N1   C13    0.00   0.0  0
 9K5  CONST_14  N3   C15  N2   C14    0.00   0.0  0
 9K5  CONST_15  N1   C12  N    C14    0.00   0.0  0
 9K5  CONST_16  N3   C16  C13  C14    0.00   0.0  0
 9K5  CONST_17  N    C14  N2   C15  180.00   0.0  0
 9K5  CONST_18  N2   C15  N3   C16    0.00   0.0  0
 9K5  CONST_19  N2   C14  C13  C16    0.00   0.0  0
 9K5  CONST_20  N    C14  C13  C16  180.00   0.0  0
 9K5  CONST_21  N1   C13  C14  N      0.00   0.0  0
 9K5  CONST_22  N1   C13  C14  N2   180.00   0.0  0
 9K5  CONST_23  N1   C13  C16  N3   180.00   0.0  0
 9K5  CONST_24  N2   C14  N    C11    0.00   0.0  0
 9K5  CONST_25  C13  C14  N    C11  180.00   0.0  0
 9K5  CONST_26  N1   C12  N    C11  180.00   0.0  0
 9K5  CONST_27  S    C4   C3   C2   180.00   0.0  0
 9K5  CONST_28  N4   C16  C13  C14  180.00   0.0  0
 9K5  CONST_29  N4   C16  N3   C15  180.00   0.0  0
 9K5  CONST_30  C    C1   C2   C6   180.00   0.0  0
 9K5  CONST_31  C4   C3   C2   C6   180.00   0.0  0
 9K5  CONST_32  C    C5   C4   S    180.00   0.0  0
 9K5  CONST_33  N1   C13  C16  N4     0.00   0.0  0
 9K5  CONST_34  H2   C3   C2   C1   180.00   0.0  0
 9K5  CONST_35  H14  C5   C    C1   180.00   0.0  0
 9K5  CONST_36  H15  C    C1   C2   180.00   0.0  0
 9K5  CONST_37  H1   C1   C2   C3   180.00   0.0  0
 9K5  CONST_38  H10  C12  N    C11    0.00   0.0  0
 9K5  CONST_39  H11  C15  N2   C14  180.00   0.0  0
 9K5  CONST_40  H17  N4   C16  C13    0.00   0.0  0
 9K5  CONST_41  H18  N4   C16  C13  180.00   0.0  0
 9K5  Var_01    O3   C6   C2   C1    -3.23  30.0  2
 9K5  Var_02    O    S    C4   C3   151.73  30.0  2
 9K5  Var_03    H4   C7   O3   C6    57.89  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
 9K5  chir_01  C8   O4  C7  C9   positiv
 9K5  chir_02  C9   O6  C8  C10  positiv
 9K5  chir_03  C10  O5  C9  C11  positiv
 9K5  chir_04  C11  O4  N   C10  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
 9K5  plan-1  C1   0.020
 9K5  plan-1  C2   0.020
 9K5  plan-1  C3   0.020
 9K5  plan-1  C6   0.020
 9K5  plan-1  C4   0.020
 9K5  plan-1  S    0.020
 9K5  plan-1  C5   0.020
 9K5  plan-1  C    0.020
 9K5  plan-1  H1   0.020
 9K5  plan-1  H2   0.020
 9K5  plan-1  H14  0.020
 9K5  plan-1  H15  0.020
 9K5  plan-2  C11  0.020
 9K5  plan-2  C12  0.020
 9K5  plan-2  C13  0.020
 9K5  plan-2  C14  0.020
 9K5  plan-2  C15  0.020
 9K5  plan-2  C16  0.020
 9K5  plan-2  N    0.020
 9K5  plan-2  N2   0.020
 9K5  plan-2  N3   0.020
 9K5  plan-2  N4   0.020
 9K5  plan-2  N1   0.020
 9K5  plan-2  H10  0.020
 9K5  plan-2  H11  0.020
 9K5  plan-3  C16  0.020
 9K5  plan-3  N4   0.020
 9K5  plan-3  H17  0.020
 9K5  plan-3  H18  0.020
 9K5  plan-4  C2   0.020
 9K5  plan-4  O2   0.020
 9K5  plan-4  C6   0.020
 9K5  plan-4  O3   0.020

