# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 21:07:43 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 4-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(azidomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]sulfanylbutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n([C@@H]3O[C@H](CN=[N+]=[N-])[C@@H](O)[C@H]3O)c(SCCCC(O)=O)nc12
#
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
 E2K  E2K  '4-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(azidomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]sulfanylbutanoic acid'  ligand  46  28  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E2K
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
 E2K  C4   C  CR56   0   0.492   2.5340   1.5155  -0.3418
 E2K  C5   C  CR56   0   0.005   1.7380   2.6296  -0.5317
 E2K  C6   C  CR6    0   0.447   2.4068   3.8430  -0.7641
 E2K  C8   C  CR5    0   0.326   0.3992   1.0205  -0.2213
 E2K  N1   N  N      0  -0.471   3.7451   3.8256  -0.7876
 E2K  N3   N  N      0  -0.458   3.8616   1.4796  -0.3634
 E2K  C2   C  CR16   0   0.042   4.3808   2.6748  -0.5941
 E2K  CAH  C  CR15   0   0.205   2.0612  -0.8700   0.1768
 E2K  CAJ  C  CR15   0  -0.002   1.1895  -3.0091   0.0862
 E2K  CAK  C  CH2    0  -0.339  -0.2781  -3.3877   0.2136
 E2K  CAO  C  CR15   0  -0.055   1.8637  -2.8268   1.4575
 E2K  CAQ  C  CR15   0   0.004   1.8048  -1.3051   1.6162
 E2K  CAU  C  CH2    0  -0.549  -2.2953   1.3396   0.0251
 E2K  CAV  C  CH2    0  -0.437  -3.6464   0.6610   0.2027
 E2K  CAW  C  CH2    0  -0.574  -4.7522   1.7037   0.2364
 E2K  CAX  C  C      0   0.553  -6.1234   1.1088   0.4022
 E2K  N6   N  NH2    0  -0.819   1.7631   4.9943  -0.9715
 E2K  N7   N  N      0  -0.457   0.4089   2.2995  -0.4583
 E2K  N9   N  NR5    0  -0.585   1.6627   0.4769  -0.1358
 E2K  NAL  N  N      0  -0.348  -0.9682  -3.4016  -1.0760
 E2K  NAM  N  N      1   0.356  -0.7879  -4.3807  -1.7763
 E2K  NAN  N  N     -1  -0.223  -0.6901  -5.2368  -2.4991
 E2K  OAI  O  O      0  -0.492   1.3318  -1.7680  -0.6099
 E2K  OAP  O  OH1    0  -0.664   3.2126  -3.2082   1.4497
 E2K  OAR  O  OH1    0  -0.651   2.7490  -0.7293   2.4580
 E2K  OAY  O  O      0  -0.443  -6.3633  -0.0689   0.4942
 E2K  OAZ  O  OH1    0  -0.596  -7.0642   2.0470   0.4351
 E2K  SAT  S  S2     0   0.067  -1.0291   0.0407  -0.0664
 E2K  H1   H  HCR6   0   0.252   5.4637   2.7266  -0.6289
 E2K  H2   H  HCR5   0   0.265   3.1362  -0.9148  -0.0349
 E2K  H3   H  HCR5   0   0.261   1.7080  -3.7884  -0.4849
 E2K  H4   H  HCH2   0   0.277  -0.3420  -4.3617   0.7073
 E2K  H5   H  HCH2   0   0.264  -0.8164  -2.6714   0.8314
 E2K  H6   H  HCR5   0   0.256   1.3035  -3.3452   2.2457
 E2K  H7   H  HCR5   0   0.242   0.7802  -1.0286   1.9007
 E2K  H8   H  HCH2   0   0.282  -2.2661   1.9245  -0.8941
 E2K  H9   H  HCH2   0   0.281  -2.0732   2.0024   0.8615
 E2K  H10  H  HCH2   0   0.251  -3.8198  -0.0385  -0.6178
 E2K  H11  H  HCH2   0   0.253  -3.6514   0.0797   1.1269
 E2K  H12  H  HCH2   0   0.285  -4.5881   2.4160   1.0506
 E2K  H13  H  HCH2   0   0.285  -4.7474   2.2992  -0.6818
 E2K  H14  H  HNH2   0   0.410   0.7629   5.0489  -0.8932
 E2K  H15  H  HNH2   0   0.403   2.2789   5.8512  -1.0718
 E2K  H17  H  HOH1   0   0.458   3.2594  -4.1617   1.3277
 E2K  H18  H  HOH1   0   0.464   2.4827  -0.8776   3.3705
 E2K  H19  H  HOH1   0   0.480  -7.9373   1.6388   0.5346

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
 E2K  OAY  CAX  double    1.205  0.020  1.205
 E2K  N6   C6   single    1.335  0.020  1.335
 E2K  CAX  OAZ  single    1.329  0.020  1.329
 E2K  CAX  CAW  single    1.504  0.020  1.504
 E2K  N7   C5   aromatic  1.371  0.020  1.371
 E2K  N7   C8   aromatic  1.301  0.020  1.301
 E2K  C6   C5   aromatic  1.405  0.020  1.405
 E2K  C6   N1   aromatic  1.339  0.020  1.339
 E2K  C5   C4   aromatic  1.382  0.020  1.382
 E2K  SAT  C8   single    1.739  0.020  1.739
 E2K  SAT  CAU  single    1.816  0.020  1.816
 E2K  N1   C2   aromatic  1.329  0.020  1.329
 E2K  C8   N9   aromatic  1.378  0.020  1.378
 E2K  CAK  NAL  single    1.463  0.020  1.463
 E2K  CAK  CAJ  single    1.521  0.020  1.521
 E2K  OAI  CAJ  single    1.430  0.020  1.430
 E2K  OAI  CAH  single    1.399  0.020  1.399
 E2K  C4   N9   aromatic  1.371  0.020  1.371
 E2K  C4   N3   aromatic  1.328  0.020  1.328
 E2K  CAW  CAV  single    1.520  0.020  1.520
 E2K  C2   N3   aromatic  1.323  0.020  1.323
 E2K  N9   CAH  single    1.439  0.020  1.439
 E2K  NAL  NAM  double    1.217  0.020  1.217
 E2K  CAJ  CAO  single    1.539  0.020  1.539
 E2K  CAH  CAQ  single    1.525  0.020  1.525
 E2K  CAU  CAV  single    1.522  0.020  1.522
 E2K  NAM  NAN  double    1.125  0.020  1.125
 E2K  CAQ  CAO  single    1.531  0.020  1.531
 E2K  CAQ  OAR  single    1.390  0.020  1.390
 E2K  CAO  OAP  single    1.402  0.020  1.402
 E2K  C2   H1   single    0.930  0.020  1.080
 E2K  CAH  H2   single    0.970  0.020  1.090
 E2K  CAJ  H3   single    0.970  0.020  1.090
 E2K  CAK  H4   single    0.970  0.020  1.090
 E2K  CAK  H5   single    0.970  0.020  1.090
 E2K  CAO  H6   single    0.970  0.020  1.090
 E2K  CAQ  H7   single    0.970  0.020  1.090
 E2K  CAU  H8   single    0.970  0.020  1.090
 E2K  CAU  H9   single    0.970  0.020  1.090
 E2K  CAV  H10  single    0.970  0.020  1.090
 E2K  CAV  H11  single    0.970  0.020  1.090
 E2K  CAW  H12  single    0.970  0.020  1.090
 E2K  CAW  H13  single    0.970  0.020  1.090
 E2K  N6   H14  single    0.860  0.020  1.020
 E2K  N6   H15  single    0.860  0.020  1.020
 E2K  OAP  H17  single    0.850  0.020  0.980
 E2K  OAR  H18  single    0.850  0.020  0.980
 E2K  OAZ  H19  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
 E2K  N9   C4   N3   128.10  3.000
 E2K  N3   C4   C5   126.52  3.000
 E2K  N9   C4   C5   105.37  3.000
 E2K  N7   C5   C6   132.69  3.000
 E2K  C6   C5   C4   116.40  3.000
 E2K  N7   C5   C4   110.91  3.000
 E2K  N6   C6   N1   119.37  3.000
 E2K  N1   C6   C5   117.88  3.000
 E2K  N6   C6   C5   122.75  3.000
 E2K  SAT  C8   N9   121.69  3.000
 E2K  N9   C8   N7   113.10  3.000
 E2K  SAT  C8   N7   125.19  3.000
 E2K  C2   N1   C6   119.14  3.000
 E2K  C2   N3   C4   111.75  3.000
 E2K  H1   C2   N3   116.13  3.000
 E2K  H1   C2   N1   115.57  3.000
 E2K  N3   C2   N1   128.31  3.000
 E2K  H2   CAH  OAI  112.10  3.000
 E2K  H2   CAH  N9   105.53  3.000
 E2K  OAI  CAH  N9   109.53  3.000
 E2K  H2   CAH  CAQ  109.59  3.000
 E2K  N9   CAH  CAQ  115.18  3.000
 E2K  OAI  CAH  CAQ  105.07  3.000
 E2K  H3   CAJ  OAI  108.44  3.000
 E2K  H3   CAJ  CAO  109.94  3.000
 E2K  OAI  CAJ  CAO  106.70  3.000
 E2K  H3   CAJ  CAK  108.85  3.000
 E2K  CAO  CAJ  CAK  112.18  3.000
 E2K  OAI  CAJ  CAK  110.66  3.000
 E2K  H5   CAK  H4   107.51  3.000
 E2K  H5   CAK  NAL  105.87  3.000
 E2K  H4   CAK  NAL  111.22  3.000
 E2K  H5   CAK  CAJ  111.16  3.000
 E2K  H4   CAK  CAJ  108.41  3.000
 E2K  NAL  CAK  CAJ  112.56  3.000
 E2K  H6   CAO  OAP  111.51  3.000
 E2K  H6   CAO  CAQ  112.05  3.000
 E2K  OAP  CAO  CAQ  107.93  3.000
 E2K  H6   CAO  CAJ  111.14  3.000
 E2K  OAP  CAO  CAJ  112.61  3.000
 E2K  CAQ  CAO  CAJ  101.14  3.000
 E2K  H7   CAQ  OAR  111.86  3.000
 E2K  H7   CAQ  CAO  108.23  3.000
 E2K  OAR  CAQ  CAO  116.64  3.000
 E2K  H7   CAQ  CAH  109.23  3.000
 E2K  OAR  CAQ  CAH  109.83  3.000
 E2K  CAO  CAQ  CAH  100.32  3.000
 E2K  H9   CAU  H8   108.38  3.000
 E2K  H9   CAU  SAT  109.36  3.000
 E2K  H8   CAU  SAT  108.82  3.000
 E2K  H9   CAU  CAV  111.24  3.000
 E2K  H8   CAU  CAV  111.18  3.000
 E2K  SAT  CAU  CAV  107.81  3.000
 E2K  H11  CAV  H10  107.11  3.000
 E2K  H11  CAV  CAW  110.06  3.000
 E2K  H10  CAV  CAW  109.91  3.000
 E2K  H11  CAV  CAU  109.88  3.000
 E2K  H10  CAV  CAU  109.80  3.000
 E2K  CAW  CAV  CAU  110.02  3.000
 E2K  H13  CAW  H12  105.63  3.000
 E2K  H13  CAW  CAX  108.16  3.000
 E2K  H12  CAW  CAX  108.19  3.000
 E2K  H13  CAW  CAV  110.58  3.000
 E2K  H12  CAW  CAV  110.73  3.000
 E2K  CAX  CAW  CAV  113.23  3.000
 E2K  OAZ  CAX  OAY  123.15  3.000
 E2K  OAZ  CAX  CAW  111.65  3.000
 E2K  OAY  CAX  CAW  125.19  3.000
 E2K  H15  N6   H14  118.18  3.000
 E2K  H15  N6   C6   120.21  3.000
 E2K  H14  N6   C6   120.97  3.000
 E2K  C8   N7   C5   104.69  3.000
 E2K  CAH  N9   C8   129.53  3.000
 E2K  CAH  N9   C4   124.45  3.000
 E2K  C8   N9   C4   105.93  3.000
 E2K  NAM  NAL  CAK  116.43  3.000
 E2K  NAN  NAM  NAL  174.23  3.000
 E2K  CAJ  OAI  CAH  109.59  3.000
 E2K  H17  OAP  CAO  108.48  3.000
 E2K  H18  OAR  CAQ  108.83  3.000
 E2K  H19  OAZ  CAX  110.06  3.000
 E2K  CAU  SAT  C8   100.03  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
 E2K  CONST_01  C8   N7   C5   C4      0.00   0.0  0
 E2K  CONST_02  N1   C6   C5   C4      0.00   0.0  0
 E2K  CONST_03  N7   C8   N9   C4      0.00   0.0  0
 E2K  CONST_04  N1   C2   N3   C4      0.00   0.0  0
 E2K  CONST_05  N9   C8   N7   C5      0.00   0.0  0
 E2K  CONST_06  C2   N1   C6   C5      0.00   0.0  0
 E2K  CONST_07  C8   N9   C4   C5      0.00   0.0  0
 E2K  CONST_08  C2   N3   C4   C5      0.00   0.0  0
 E2K  CONST_09  C8   N7   C5   C6    180.00   0.0  0
 E2K  CONST_10  N9   C4   C5   C6    180.00   0.0  0
 E2K  CONST_11  N3   C4   C5   C6      0.00   0.0  0
 E2K  CONST_12  N3   C2   N1   C6      0.00   0.0  0
 E2K  CONST_13  N3   C4   N9   C8    180.00   0.0  0
 E2K  CONST_14  N7   C5   C6   N1    180.00   0.0  0
 E2K  CONST_15  N7   C5   C4   N3    180.00   0.0  0
 E2K  CONST_16  N9   C4   N3   C2    180.00   0.0  0
 E2K  CONST_17  N9   C4   C5   N7      0.00   0.0  0
 E2K  CONST_18  CAH  N9   C4   C5    180.00   0.0  0
 E2K  CONST_19  CAH  N9   C4   N3      0.00   0.0  0
 E2K  CONST_20  N7   C8   N9   CAH   180.00   0.0  0
 E2K  CONST_21  N6   C6   C5   C4    180.00   0.0  0
 E2K  CONST_22  SAT  C8   N9   C4    180.00   0.0  0
 E2K  CONST_23  SAT  C8   N7   C5    180.00   0.0  0
 E2K  CONST_24  N6   C6   N1   C2    180.00   0.0  0
 E2K  CONST_25  SAT  C8   N9   CAH     0.00   0.0  0
 E2K  CONST_26  N7   C5   C6   N6      0.00   0.0  0
 E2K  CONST_27  H1   C2   N3   C4    180.00   0.0  0
 E2K  CONST_28  H14  N6   C6   C5      0.00   0.0  0
 E2K  CONST_29  H15  N6   C6   C5    180.00   0.0  0
 E2K  CONST_30  H19  OAZ  CAX  CAW   180.00   0.0  0
 E2K  Var_01    N7   C8   SAT  CAU   -11.28  30.0  2
 E2K  Var_02    CAV  CAU  SAT  C8   -178.57  30.0  3
 E2K  Var_03    CAX  CAW  CAV  CAU   179.67  30.0  1
 E2K  Var_04    OAY  CAX  CAW  CAV    -0.43  30.0  3
 E2K  Var_05    SAT  CAU  CAV  CAW  -178.02  30.0  1
 E2K  Var_06    H4   CAK  NAL  NAM   -43.16  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
 E2K  chir_01  CAH  OAI  N9   CAQ  negativ
 E2K  chir_02  CAJ  OAI  CAK  CAO  positiv
 E2K  chir_03  CAO  OAP  CAJ  CAQ  positiv
 E2K  chir_04  CAQ  OAR  CAO  CAH  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
 E2K  plan-1  C4   0.020
 E2K  plan-1  C5   0.020
 E2K  plan-1  C6   0.020
 E2K  plan-1  C8   0.020
 E2K  plan-1  N1   0.020
 E2K  plan-1  N3   0.020
 E2K  plan-1  C2   0.020
 E2K  plan-1  CAH  0.020
 E2K  plan-1  N6   0.020
 E2K  plan-1  N7   0.020
 E2K  plan-1  N9   0.020
 E2K  plan-1  SAT  0.020
 E2K  plan-1  H1   0.020
 E2K  plan-2  C6   0.020
 E2K  plan-2  N6   0.020
 E2K  plan-2  H14  0.020
 E2K  plan-2  H15  0.020
 E2K  plan-3  CAW  0.020
 E2K  plan-3  CAX  0.020
 E2K  plan-3  OAY  0.020
 E2K  plan-3  OAZ  0.020
 E2K  plan-3  H19  0.020
 E2K  plan-4  CAK  0.020
 E2K  plan-4  NAL  0.020
 E2K  plan-4  NAM  0.020
 E2K  plan-4  NAN  0.020

