# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 20:15:45 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[4-(6-azanyl-9~{H}-purin-8-yl)but-3-ynylamino]methyl]oxolane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CNCCC#Cc4[nH]c5ncnc(N)c5n4)[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
 K2K  K2K  (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[4-(6-azanyl-9~{H}-purin-8-yl)but-3-ynylamino]methyl]oxolane-3,4-diol  ligand  54  33  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_K2K
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
 K2K  C2   C  CR16  0   0.038    8.0276  -0.9630   0.0304
 K2K  C4   C  CR56  0   0.486    5.8522  -0.6956   0.1501
 K2K  C5   C  CR56  0  -0.002    5.6057  -1.9535  -0.3769
 K2K  C6   C  CR6   0   0.458    6.7380  -2.7213  -0.7077
 K2K  N9   N  NR5   0  -0.538    4.6217  -0.1547   0.3813
 K2K  C8   C  CR15  0   0.101    3.7112  -1.1021   0.0013
 K2K  CAK  C  CH1   0   0.177    4.3825   1.1641   0.9647
 K2K  CAL  C  CH1   0  -0.042    4.7448   2.2771  -0.0155
 K2K  CAM  C  CH1   0  -0.035    3.4204   2.4401  -0.7681
 K2K  CAN  C  CH1   0   0.023    2.3986   2.2246   0.3445
 K2K  CAP  C  CH2   0  -0.273    1.0763   1.6739  -0.1396
 K2K  CAR  C  CH2   0  -0.259   -1.1727   1.0792   0.4806
 K2K  CAS  C  CH2   0  -0.629   -2.1754   1.0991   1.6352
 K2K  CAT  C  CSP   0   0.138   -3.4888   0.6322   1.2276
 K2K  CAU  C  CSP   0   0.059   -4.5727   0.2496   0.8672
 K2K  CAV  C  CR5   0   0.219   -5.8502  -0.1981   0.4560
 K2K  CAX  C  CR56  0   0.469   -7.7324  -1.3193   0.5288
 K2K  CAZ  C  CR16  0   0.041   -9.7282  -2.0481  -0.0249
 K2K  CBB  C  CR6   0   0.442   -8.7758  -0.5152  -1.4517
 K2K  CBC  C  CR56  0  -0.013   -7.6612  -0.4978  -0.5903
 K2K  N1   N  N     0  -0.474    7.9440  -2.1861  -0.4869
 K2K  N3   N  N     0  -0.459    7.0458  -0.1490   0.3771
 K2K  N6   N  NH2   0  -0.817    6.6535  -3.9446  -1.2316
 K2K  N7   N  N     0  -0.451    4.2593  -2.1886  -0.4610
 K2K  NAQ  N  NH1   0  -0.609    0.1154   1.5579   0.9369
 K2K  NAW  N  NR15  0  -0.676   -6.5624  -1.1131   1.1842
 K2K  NAY  N  N     0  -0.451   -8.7463  -2.1180   0.8570
 K2K  NBA  N  N     0  -0.470   -9.8009  -1.3109  -1.1309
 K2K  NBD  N  N     0  -0.440   -6.4846   0.1929  -0.6207
 K2K  NBE  N  NH2   0  -0.814   -8.8370   0.2167  -2.5647
 K2K  OAO  O  O2    0  -0.501    3.0251   1.3039   1.2450
 K2K  OBF  O  OH1   0  -0.657    3.2465   3.7029  -1.3460
 K2K  OBG  O  OH1   0  -0.665    5.0385   3.4212   0.7379
 K2K  H1   H  HCR6  0   0.252    9.0345  -0.5908   0.1857
 K2K  H2   H  HCR5  0   0.295    2.6485  -0.9455   0.0959
 K2K  H3   H  HCH1  0   0.286    4.9722   1.2247   1.8836
 K2K  H4   H  HCH1  0   0.261    5.5762   1.9981  -0.6733
 K2K  H5   H  HCH1  0   0.243    3.3295   1.6429  -1.5177
 K2K  H6   H  HCH1  0   0.244    2.2192   3.1683   0.8735
 K2K  H7   H  HCH2  0   0.247    0.6835   2.3763  -0.8809
 K2K  H8   H  HCH2  0   0.198    1.2449   0.7252  -0.6751
 K2K  H9   H  HCH2  0   0.214   -1.1307   0.0678   0.0516
 K2K  H10  H  HCH2  0   0.238   -1.5283   1.7405  -0.3130
 K2K  H11  H  HCH2  0   0.280   -1.8157   0.4696   2.4545
 K2K  H12  H  HCH2  0   0.281   -2.2561   2.1145   2.0318
 K2K  H13  H  HCR6  0   0.253  -10.5936  -2.6709   0.1749
 K2K  H14  H  HNH2  0   0.412    5.7640  -4.3869  -1.3816
 K2K  H15  H  HNH2  0   0.404    7.4876  -4.4711  -1.4267
 K2K  H16  H  HNH1  0   0.348    0.4731   0.9156   1.6350
 K2K  H18  H  HNR5  0   0.430   -6.2677  -1.5440   2.0479
 K2K  H20  H  HNH2  0   0.404   -9.6853   0.2430  -3.1041
 K2K  H21  H  HNH2  0   0.412   -8.1141   0.8780  -2.7883
 K2K  H22  H  HOH1  0   0.469    3.6780   3.7105  -2.2065
 K2K  H23  H  HOH1  0   0.452    4.8165   4.1910   0.1997

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
 K2K  N6   C6   single    1.333  0.020  1.333
 K2K  N7   C8   aromatic  1.302  0.020  1.302
 K2K  N7   C5   aromatic  1.369  0.020  1.369
 K2K  C6   C5   aromatic  1.408  0.020  1.408
 K2K  C6   N1   aromatic  1.338  0.020  1.338
 K2K  OBF  CAM  single    1.400  0.020  1.400
 K2K  C8   N9   aromatic  1.368  0.020  1.368
 K2K  C5   C4   aromatic  1.386  0.020  1.386
 K2K  CAM  CAL  single    1.532  0.020  1.532
 K2K  CAM  CAN  single    1.526  0.020  1.526
 K2K  CAL  OBG  single    1.401  0.020  1.401
 K2K  CAL  CAK  single    1.527  0.020  1.527
 K2K  N1   C2   aromatic  1.331  0.020  1.331
 K2K  N9   C4   aromatic  1.364  0.020  1.364
 K2K  N9   CAK  single    1.462  0.020  1.462
 K2K  C4   N3   aromatic  1.332  0.020  1.332
 K2K  C2   N3   aromatic  1.322  0.020  1.322
 K2K  CAK  OAO  single    1.393  0.020  1.393
 K2K  CAN  OAO  single    1.432  0.020  1.432
 K2K  CAN  CAP  single    1.512  0.020  1.512
 K2K  CAP  NAQ  single    1.448  0.020  1.448
 K2K  NBE  CBB  single    1.334  0.020  1.334
 K2K  NAQ  CAR  single    1.448  0.020  1.448
 K2K  CBB  NBA  aromatic  1.337  0.020  1.337
 K2K  CBB  CBC  aromatic  1.409  0.020  1.409
 K2K  NBA  CAZ  aromatic  1.331  0.020  1.331
 K2K  NBD  CBC  aromatic  1.365  0.020  1.365
 K2K  NBD  CAV  aromatic  1.309  0.020  1.309
 K2K  CBC  CAX  aromatic  1.390  0.020  1.390
 K2K  CAR  CAS  single    1.529  0.020  1.529
 K2K  CAZ  NAY  aromatic  1.322  0.020  1.322
 K2K  CAV  CAU  single    1.415  0.020  1.415
 K2K  CAV  NAW  aromatic  1.369  0.020  1.369
 K2K  CAX  NAY  aromatic  1.332  0.020  1.332
 K2K  CAX  NAW  aromatic  1.357  0.020  1.357
 K2K  CAU  CAT  triple    1.205  0.020  1.205
 K2K  CAT  CAS  single    1.452  0.020  1.452
 K2K  C2   H1   single    0.930  0.020  1.080
 K2K  C8   H2   single    0.930  0.020  1.080
 K2K  CAK  H3   single    0.970  0.020  1.090
 K2K  CAL  H4   single    0.970  0.020  1.090
 K2K  CAM  H5   single    0.970  0.020  1.090
 K2K  CAN  H6   single    0.970  0.020  1.090
 K2K  CAP  H7   single    0.970  0.020  1.090
 K2K  CAP  H8   single    0.970  0.020  1.090
 K2K  CAR  H9   single    0.970  0.020  1.090
 K2K  CAR  H10  single    0.970  0.020  1.090
 K2K  CAS  H11  single    0.970  0.020  1.090
 K2K  CAS  H12  single    0.970  0.020  1.090
 K2K  CAZ  H13  single    0.930  0.020  1.080
 K2K  N6   H14  single    0.860  0.020  1.020
 K2K  N6   H15  single    0.860  0.020  1.020
 K2K  NAQ  H16  single    0.890  0.020  1.040
 K2K  NAW  H18  single    0.860  0.020  1.020
 K2K  NBE  H20  single    0.860  0.020  1.020
 K2K  NBE  H21  single    0.860  0.020  1.020
 K2K  OBF  H22  single    0.850  0.020  0.980
 K2K  OBG  H23  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
 K2K  H1   C2   N3   116.14  3.000
 K2K  H1   C2   N1   115.43  3.000
 K2K  N3   C2   N1   128.43  3.000
 K2K  N3   C4   N9   128.07  3.000
 K2K  N3   C4   C5   126.62  3.000
 K2K  N9   C4   C5   105.31  3.000
 K2K  N7   C5   C6   133.07  3.000
 K2K  C6   C5   C4   116.19  3.000
 K2K  N7   C5   C4   110.74  3.000
 K2K  N6   C6   N1   119.28  3.000
 K2K  N1   C6   C5   117.91  3.000
 K2K  N6   C6   C5   122.81  3.000
 K2K  CAK  N9   C8   128.81  3.000
 K2K  CAK  N9   C4   124.97  3.000
 K2K  C8   N9   C4   106.19  3.000
 K2K  H2   C8   N7   124.56  3.000
 K2K  H2   C8   N9   122.08  3.000
 K2K  N7   C8   N9   113.35  3.000
 K2K  H3   CAK  OAO  110.54  3.000
 K2K  H3   CAK  CAL  111.78  3.000
 K2K  OAO  CAK  CAL  106.69  3.000
 K2K  H3   CAK  N9   107.29  3.000
 K2K  OAO  CAK  N9   109.29  3.000
 K2K  CAL  CAK  N9   111.26  3.000
 K2K  H4   CAL  OBG  111.81  3.000
 K2K  H4   CAL  CAM  112.83  3.000
 K2K  OBG  CAL  CAM  111.00  3.000
 K2K  H4   CAL  CAK  112.32  3.000
 K2K  OBG  CAL  CAK  107.44  3.000
 K2K  CAM  CAL  CAK  100.83  3.000
 K2K  H5   CAM  OBF  111.28  3.000
 K2K  H5   CAM  CAN  109.86  3.000
 K2K  OBF  CAM  CAN  110.20  3.000
 K2K  H5   CAM  CAL  109.24  3.000
 K2K  CAN  CAM  CAL  101.87  3.000
 K2K  OBF  CAM  CAL  113.97  3.000
 K2K  H6   CAN  OAO  108.75  3.000
 K2K  H6   CAN  CAP  108.96  3.000
 K2K  OAO  CAN  CAP  110.47  3.000
 K2K  H6   CAN  CAM  109.85  3.000
 K2K  CAP  CAN  CAM  113.81  3.000
 K2K  OAO  CAN  CAM  104.85  3.000
 K2K  H8   CAP  H7   106.16  3.000
 K2K  H8   CAP  NAQ  113.19  3.000
 K2K  H7   CAP  NAQ  108.47  3.000
 K2K  H8   CAP  CAN  109.59  3.000
 K2K  H7   CAP  CAN  107.28  3.000
 K2K  NAQ  CAP  CAN  111.82  3.000
 K2K  H10  CAR  H9   106.61  3.000
 K2K  H10  CAR  NAQ  108.56  3.000
 K2K  H9   CAR  NAQ  113.15  3.000
 K2K  H10  CAR  CAS  109.09  3.000
 K2K  H9   CAR  CAS  109.37  3.000
 K2K  NAQ  CAR  CAS  109.94  3.000
 K2K  H12  CAS  H11  106.69  3.000
 K2K  H12  CAS  CAT  109.49  3.000
 K2K  H11  CAS  CAT  108.81  3.000
 K2K  H12  CAS  CAR  109.54  3.000
 K2K  H11  CAS  CAR  110.02  3.000
 K2K  CAT  CAS  CAR  112.14  3.000
 K2K  CAU  CAT  CAS  180.00  3.000
 K2K  CAV  CAU  CAT  180.00  3.000
 K2K  NBD  CAV  NAW  112.64  3.000
 K2K  NAW  CAV  CAU  121.78  3.000
 K2K  NBD  CAV  CAU  125.59  3.000
 K2K  NAY  CAX  NAW  128.94  3.000
 K2K  NAW  CAX  CBC  104.77  3.000
 K2K  NAY  CAX  CBC  126.28  3.000
 K2K  H13  CAZ  NBA  115.30  3.000
 K2K  H13  CAZ  NAY  116.07  3.000
 K2K  NBA  CAZ  NAY  128.63  3.000
 K2K  NBE  CBB  NBA  119.46  3.000
 K2K  NBA  CBB  CBC  117.87  3.000
 K2K  NBE  CBB  CBC  122.67  3.000
 K2K  NBD  CBC  CBB  132.44  3.000
 K2K  NBD  CBC  CAX  111.17  3.000
 K2K  CBB  CBC  CAX  116.39  3.000
 K2K  C6   N1   C2   119.24  3.000
 K2K  C4   N3   C2   111.59  3.000
 K2K  H15  N6   H14  118.35  3.000
 K2K  H15  N6   C6   120.27  3.000
 K2K  H14  N6   C6   121.24  3.000
 K2K  C8   N7   C5   104.41  3.000
 K2K  H16  NAQ  CAR  108.74  3.000
 K2K  H16  NAQ  CAP  109.18  3.000
 K2K  CAR  NAQ  CAP  112.50  3.000
 K2K  H18  NAW  CAX  126.89  3.000
 K2K  H18  NAW  CAV  126.06  3.000
 K2K  CAX  NAW  CAV  107.05  3.000
 K2K  CAZ  NAY  CAX  111.68  3.000
 K2K  CBB  NBA  CAZ  119.15  3.000
 K2K  CBC  NBD  CAV  104.37  3.000
 K2K  H21  NBE  H20  118.05  3.000
 K2K  H21  NBE  CBB  120.92  3.000
 K2K  H20  NBE  CBB  120.05  3.000
 K2K  CAN  OAO  CAK  111.36  3.000
 K2K  H22  OBF  CAM  108.69  3.000
 K2K  H23  OBG  CAL  107.65  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
 K2K  CONST_01  C5   C6   N1   C2      0.00   0.0  0
 K2K  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 K2K  CONST_03  N9   C4   N3   C2    180.00   0.0  0
 K2K  CONST_04  C8   N7   C5   C4      0.00   0.0  0
 K2K  CONST_05  N1   C6   C5   C4      0.00   0.0  0
 K2K  CONST_06  N7   C8   N9   C4      0.00   0.0  0
 K2K  CONST_07  N1   C2   N3   C4      0.00   0.0  0
 K2K  CONST_08  N9   C8   N7   C5      0.00   0.0  0
 K2K  CONST_09  C8   N9   C4   C5      0.00   0.0  0
 K2K  CONST_10  C8   N7   C5   C6    180.00   0.0  0
 K2K  CONST_11  N9   C4   C5   C6    180.00   0.0  0
 K2K  CONST_12  N3   C4   C5   C6      0.00   0.0  0
 K2K  CONST_13  N3   C2   N1   C6      0.00   0.0  0
 K2K  CONST_14  N7   C5   C4   N9      0.00   0.0  0
 K2K  CONST_15  N3   C4   N9   C8    180.00   0.0  0
 K2K  CONST_16  CBB  CBC  NBD  CAV   180.00   0.0  0
 K2K  CONST_17  CAX  CBC  NBD  CAV     0.00   0.0  0
 K2K  CONST_18  CBC  CAX  NAW  CAV     0.00   0.0  0
 K2K  CONST_19  NAY  CAX  NAW  CAV   180.00   0.0  0
 K2K  CONST_20  NBA  CBB  CBC  CAX     0.00   0.0  0
 K2K  CONST_21  NBA  CAZ  NAY  CAX     0.00   0.0  0
 K2K  CONST_22  NBD  CAV  NAW  CAX     0.00   0.0  0
 K2K  CONST_23  CBC  CBB  NBA  CAZ     0.00   0.0  0
 K2K  CONST_24  CBC  CAX  NAY  CAZ     0.00   0.0  0
 K2K  CONST_25  NAW  CAX  NAY  CAZ   180.00   0.0  0
 K2K  CONST_26  NAY  CAZ  NBA  CBB     0.00   0.0  0
 K2K  CONST_27  NAY  CAX  CBC  CBB     0.00   0.0  0
 K2K  CONST_28  NAW  CAX  CBC  CBB   180.00   0.0  0
 K2K  CONST_29  NAW  CAV  NBD  CBC     0.00   0.0  0
 K2K  CONST_30  N7   C5   C6   N1    180.00   0.0  0
 K2K  CONST_31  N7   C5   C4   N3    180.00   0.0  0
 K2K  CONST_32  NBD  CBC  CAX  NAW     0.00   0.0  0
 K2K  CONST_33  NBD  CBC  CAX  NAY   180.00   0.0  0
 K2K  CONST_34  NBD  CBC  CBB  NBA   180.00   0.0  0
 K2K  CONST_35  CAK  N9   C4   C5    180.00   0.0  0
 K2K  CONST_36  N7   C8   N9   CAK   180.00   0.0  0
 K2K  CONST_37  N3   C4   N9   CAK     0.00   0.0  0
 K2K  CONST_38  N6   C6   N1   C2    180.00   0.0  0
 K2K  CONST_39  N6   C6   C5   C4    180.00   0.0  0
 K2K  CONST_40  CBC  NBD  CAV  CAU   180.00   0.0  0
 K2K  CONST_41  CAX  NAW  CAV  CAU   180.00   0.0  0
 K2K  CONST_42  NBE  CBB  CBC  CAX   180.00   0.0  0
 K2K  CONST_43  NBE  CBB  NBA  CAZ   180.00   0.0  0
 K2K  CONST_44  N7   C5   C6   N6      0.00   0.0  0
 K2K  CONST_45  NBE  CBB  CBC  NBD     0.00   0.0  0
 K2K  CONST_46  H2   C8   N9   C4    180.00   0.0  0
 K2K  CONST_47  H1   C2   N3   C4    180.00   0.0  0
 K2K  CONST_48  H13  CAZ  NAY  CAX   180.00   0.0  0
 K2K  CONST_49  H18  NAW  CAX  CBC   180.00   0.0  0
 K2K  CONST_50  H14  N6   C6   C5      0.00   0.0  0
 K2K  CONST_51  H15  N6   C6   C5    180.00   0.0  0
 K2K  CONST_52  H20  NBE  CBB  CBC   180.00   0.0  0
 K2K  CONST_53  H21  NBE  CBB  CBC     0.00   0.0  0
 K2K  Var_01    CAR  NAQ  CAP  CAN   177.82  30.0  3
 K2K  Var_02    CAS  CAR  NAQ  CAP  -174.90  30.0  3
 K2K  Var_03    NAQ  CAR  CAS  CAT   179.75  30.0  1
 K2K  Var_04    H11  CAS  CAT  CAU  -142.77  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
 K2K  chir_01  CAK  CAL  N9   OAO  positiv
 K2K  chir_02  CAL  OBG  CAK  CAM  negativ
 K2K  chir_03  CAM  OBF  CAL  CAN  negativ
 K2K  chir_04  CAN  OAO  CAM  CAP  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
 K2K  plan-1  C2   0.020
 K2K  plan-1  C4   0.020
 K2K  plan-1  C5   0.020
 K2K  plan-1  C6   0.020
 K2K  plan-1  N9   0.020
 K2K  plan-1  C8   0.020
 K2K  plan-1  CAK  0.020
 K2K  plan-1  N1   0.020
 K2K  plan-1  N3   0.020
 K2K  plan-1  N6   0.020
 K2K  plan-1  N7   0.020
 K2K  plan-1  H1   0.020
 K2K  plan-1  H2   0.020
 K2K  plan-2  CAT  0.020
 K2K  plan-2  CAU  0.020
 K2K  plan-2  CAV  0.020
 K2K  plan-2  CAX  0.020
 K2K  plan-2  CAZ  0.020
 K2K  plan-2  CBB  0.020
 K2K  plan-2  CBC  0.020
 K2K  plan-2  NAW  0.020
 K2K  plan-2  NAY  0.020
 K2K  plan-2  NBA  0.020
 K2K  plan-2  NBD  0.020
 K2K  plan-2  NBE  0.020
 K2K  plan-2  H13  0.020
 K2K  plan-2  H18  0.020
 K2K  plan-3  C6   0.020
 K2K  plan-3  N6   0.020
 K2K  plan-3  H14  0.020
 K2K  plan-3  H15  0.020
 K2K  plan-4  CBB  0.020
 K2K  plan-4  NBE  0.020
 K2K  plan-4  H20  0.020
 K2K  plan-4  H21  0.020

