# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 17:17:25 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-[[3-(6-azanyl-9~{H}-purin-8-yl)prop-2-ynyl-methyl-amino]methyl]oxolane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CC#Cc1[nH]c2ncnc(N)c2n1)C[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45
#
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
 K2H  K2H  (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[3-(6-azanyl-9~{H}-purin-8-yl)prop-2-ynyl-methyl-amino]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_K2H
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
 K2H  C2   C  CR16  0   0.040   5.2961   2.4322  -0.9616
 K2H  C4   C  CR56  0   0.486   3.6993   1.0079  -0.4707
 K2H  C5   C  CR56  0  -0.010   2.8401   2.0189  -0.0669
 K2H  C6   C  CR6   0   0.453   3.3410   3.3311  -0.1476
 K2H  N9   N  NR5   0  -0.542   2.9896  -0.1459  -0.3124
 K2H  C8   C  CR15  0   0.095   1.7579   0.2186   0.1626
 K2H  CAK  C  CR15  0   0.225   3.4619  -1.4872  -0.5883
 K2H  CAM  C  CR15  0  -0.055   2.2651  -3.4655  -0.3295
 K2H  CAN  C  CH2   0  -0.302   1.1538  -3.3973   0.7173
 K2H  CAP  C  CH2   0  -0.455  -0.9909  -2.5814   1.3417
 K2H  CAQ  C  CSP   0   0.149  -2.0482  -1.6334   1.0099
 K2H  CAR  C  CSP   0   0.071  -2.9159  -0.8435   0.7420
 K2H  CAS  C  CR5   0   0.210  -3.9290   0.0878   0.4120
 K2H  CAU  C  CR56  0   0.471  -5.4596   1.0826  -0.8006
 K2H  CAW  C  CR16  0   0.042  -7.0324   2.4950  -1.3947
 K2H  CAY  C  CR6   0   0.445  -6.1662   2.7706   0.7188
 K2H  CAZ  C  CR56  0  -0.013  -5.3264   1.6711   0.4513
 K2H  CBC  C  CH3   0  -0.539  -0.6564  -3.4022  -0.8878
 K2H  CBD  C  CR15  0  -0.004   3.6188  -3.6707   0.3327
 K2H  CBF  C  CR15  0  -0.060   4.0021  -2.2191   0.6464
 K2H  N1   N  N     0  -0.474   4.5871   3.5001  -0.6035
 K2H  N3   N  N     0  -0.453   4.9412   1.1601  -0.9269
 K2H  N6   N  NH2   0  -0.817   2.6220   4.4007   0.1985
 K2H  N7   N  N     0  -0.454   1.6310   1.5041   0.3223
 K2H  NAO  N  NT    0  -0.413  -0.0477  -2.7382   0.2485
 K2H  NAT  N  NR15  0  -0.677  -4.5570   0.0692  -0.8046
 K2H  NAV  N  N     0  -0.452  -6.3003   1.4580  -1.7629
 K2H  NAX  N  N     0  -0.470  -7.0146   3.1564  -0.2396
 K2H  NBA  N  N     0  -0.438  -4.3697   1.0417   1.1928
 K2H  NBB  N  NH2   0  -0.814  -6.1412   3.4278   1.8771
 K2H  OAL  O  O     0  -0.484   2.3982  -2.2503  -1.0672
 K2H  OBE  O  OH1   0  -0.669   4.5053  -4.2288  -0.6000
 K2H  OBG  O  OH1   0  -0.652   5.3750  -1.9940   0.7704
 K2H  H1   H  HCR6  0   0.250   6.2961   2.6395  -1.3277
 K2H  H2   H  HCR5  0   0.305   0.9802  -0.5150   0.3323
 K2H  H3   H  HCR5  0   0.264   4.2506  -1.3861  -1.3418
 K2H  H4   H  HCR5  0   0.271   2.0563  -4.2614  -1.0487
 K2H  H5   H  HCH2  0   0.234   0.9667  -4.4319   1.0512
 K2H  H6   H  HCH2  0   0.247   1.5035  -2.8521   1.5991
 K2H  H7   H  HCH2  0   0.289  -0.4621  -2.1992   2.2189
 K2H  H8   H  HCH2  0   0.260  -1.4481  -3.5361   1.6498
 K2H  H9   H  HCR6  0   0.253  -7.7440   2.8601  -2.1279
 K2H  H10  H  HCH3  0   0.206  -0.9446  -4.4414  -0.6724
 K2H  H11  H  HCH3  0   0.248  -1.5511  -2.8622  -1.1964
 K2H  H12  H  HCH3  0   0.251   0.0206  -3.4064  -1.7402
 K2H  H13  H  HCR5  0   0.251   3.5425  -4.2829   1.2416
 K2H  H14  H  HCR5  0   0.253   3.4601  -1.8836   1.5383
 K2H  H15  H  HNH2  0   0.410   1.7075   4.3028   0.6032
 K2H  H16  H  HNH2  0   0.403   3.0345   5.3171   0.1702
 K2H  H18  H  HNR5  0   0.429  -4.3734  -0.5730  -1.5613
 K2H  H20  H  HNH2  0   0.405  -6.7564   4.2078   2.0330
 K2H  H21  H  HNH2  0   0.413  -5.5174   3.1563   2.6166
 K2H  H22  H  HOH1  0   0.449   5.4019  -3.9872  -0.3379
 K2H  H23  H  HOH1  0   0.469   5.6436  -2.2023   1.6710

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
 K2H  N6   C6   single    1.334  0.020  1.334
 K2H  N7   C5   aromatic  1.371  0.020  1.371
 K2H  N7   C8   aromatic  1.302  0.020  1.302
 K2H  C6   C5   aromatic  1.407  0.020  1.407
 K2H  C6   N1   aromatic  1.338  0.020  1.338
 K2H  C5   C4   aromatic  1.387  0.020  1.387
 K2H  C8   N9   aromatic  1.370  0.020  1.370
 K2H  CBF  OBG  single    1.397  0.020  1.397
 K2H  CBF  CBD  single    1.534  0.020  1.534
 K2H  CBF  CAK  single    1.534  0.020  1.534
 K2H  N1   C2   aromatic  1.331  0.020  1.331
 K2H  OBE  CBD  single    1.403  0.020  1.403
 K2H  C4   N9   aromatic  1.364  0.020  1.364
 K2H  C4   N3   aromatic  1.332  0.020  1.332
 K2H  N9   CAK  single    1.448  0.020  1.448
 K2H  CBD  CAM  single    1.521  0.020  1.521
 K2H  C2   N3   aromatic  1.321  0.020  1.321
 K2H  CAK  OAL  single    1.394  0.020  1.394
 K2H  OAL  CAM  single    1.428  0.020  1.428
 K2H  CAM  CAN  single    1.528  0.020  1.528
 K2H  CAN  NAO  single    1.448  0.020  1.448
 K2H  NBB  CAY  single    1.332  0.020  1.332
 K2H  CAY  NAX  aromatic  1.337  0.020  1.337
 K2H  CAY  CAZ  aromatic  1.409  0.020  1.409
 K2H  NAO  CBC  single    1.450  0.020  1.450
 K2H  NAO  CAP  single    1.452  0.020  1.452
 K2H  NBA  CAZ  aromatic  1.364  0.020  1.364
 K2H  NBA  CAS  aromatic  1.309  0.020  1.309
 K2H  NAX  CAW  aromatic  1.331  0.020  1.331
 K2H  CAZ  CAU  aromatic  1.390  0.020  1.390
 K2H  CAS  CAR  single    1.415  0.020  1.415
 K2H  CAS  NAT  aromatic  1.369  0.020  1.369
 K2H  CAR  CAQ  triple    1.204  0.020  1.204
 K2H  CAQ  CAP  single    1.458  0.020  1.458
 K2H  CAW  NAV  aromatic  1.322  0.020  1.322
 K2H  CAU  NAT  aromatic  1.357  0.020  1.357
 K2H  CAU  NAV  aromatic  1.332  0.020  1.332
 K2H  C2   H1   single    0.930  0.020  1.080
 K2H  C8   H2   single    0.930  0.020  1.080
 K2H  CAK  H3   single    0.970  0.020  1.090
 K2H  CAM  H4   single    0.970  0.020  1.090
 K2H  CAN  H5   single    0.970  0.020  1.090
 K2H  CAN  H6   single    0.970  0.020  1.090
 K2H  CAP  H7   single    0.970  0.020  1.090
 K2H  CAP  H8   single    0.970  0.020  1.090
 K2H  CAW  H9   single    0.930  0.020  1.080
 K2H  CBC  H10  single    0.970  0.020  1.090
 K2H  CBC  H11  single    0.970  0.020  1.090
 K2H  CBC  H12  single    0.970  0.020  1.090
 K2H  CBD  H13  single    0.970  0.020  1.090
 K2H  CBF  H14  single    0.970  0.020  1.090
 K2H  N6   H15  single    0.860  0.020  1.020
 K2H  N6   H16  single    0.860  0.020  1.020
 K2H  NAT  H18  single    0.860  0.020  1.020
 K2H  NBB  H20  single    0.860  0.020  1.020
 K2H  NBB  H21  single    0.860  0.020  1.020
 K2H  OBE  H22  single    0.850  0.020  0.980
 K2H  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
 K2H  H1   C2   N3   116.14  3.000
 K2H  H1   C2   N1   115.37  3.000
 K2H  N3   C2   N1   128.49  3.000
 K2H  N3   C4   N9   128.44  3.000
 K2H  N3   C4   C5   126.46  3.000
 K2H  N9   C4   C5   105.10  3.000
 K2H  N7   C5   C6   132.90  3.000
 K2H  C6   C5   C4   116.27  3.000
 K2H  N7   C5   C4   110.82  3.000
 K2H  N6   C6   N1   119.28  3.000
 K2H  N1   C6   C5   117.97  3.000
 K2H  N6   C6   C5   122.74  3.000
 K2H  CAK  N9   C8   127.28  3.000
 K2H  CAK  N9   C4   126.27  3.000
 K2H  C8   N9   C4   106.44  3.000
 K2H  H2   C8   N7   125.46  3.000
 K2H  H2   C8   N9   121.34  3.000
 K2H  N7   C8   N9   113.15  3.000
 K2H  H3   CAK  OAL  111.32  3.000
 K2H  H3   CAK  CBF  110.13  3.000
 K2H  OAL  CAK  CBF  106.51  3.000
 K2H  H3   CAK  N9   106.28  3.000
 K2H  OAL  CAK  N9   108.88  3.000
 K2H  CBF  CAK  N9   113.79  3.000
 K2H  H4   CAM  OAL  107.31  3.000
 K2H  H4   CAM  CBD  111.00  3.000
 K2H  OAL  CAM  CBD  104.88  3.000
 K2H  H4   CAM  CAN  110.14  3.000
 K2H  OAL  CAM  CAN  112.56  3.000
 K2H  CBD  CAM  CAN  110.80  3.000
 K2H  H6   CAN  H5   106.12  3.000
 K2H  H6   CAN  NAO  107.41  3.000
 K2H  H5   CAN  NAO  112.58  3.000
 K2H  H6   CAN  CAM  109.99  3.000
 K2H  H5   CAN  CAM  106.79  3.000
 K2H  NAO  CAN  CAM  113.69  3.000
 K2H  H8   CAP  H7   106.20  3.000
 K2H  H8   CAP  NAO  112.72  3.000
 K2H  H7   CAP  NAO  109.12  3.000
 K2H  H8   CAP  CAQ  109.02  3.000
 K2H  H7   CAP  CAQ  107.82  3.000
 K2H  NAO  CAP  CAQ  111.71  3.000
 K2H  CAR  CAQ  CAP  180.00  3.000
 K2H  CAS  CAR  CAQ  180.00  3.000
 K2H  NBA  CAS  NAT  112.67  3.000
 K2H  NAT  CAS  CAR  121.78  3.000
 K2H  NBA  CAS  CAR  125.55  3.000
 K2H  NAV  CAU  NAT  128.92  3.000
 K2H  NAV  CAU  CAZ  126.30  3.000
 K2H  NAT  CAU  CAZ  104.78  3.000
 K2H  H9   CAW  NAX  115.34  3.000
 K2H  H9   CAW  NAV  116.04  3.000
 K2H  NAX  CAW  NAV  128.62  3.000
 K2H  NBB  CAY  NAX  119.53  3.000
 K2H  NAX  CAY  CAZ  117.86  3.000
 K2H  NBB  CAY  CAZ  122.61  3.000
 K2H  NBA  CAZ  CAY  132.43  3.000
 K2H  NBA  CAZ  CAU  111.19  3.000
 K2H  CAY  CAZ  CAU  116.38  3.000
 K2H  H12  CBC  H11  106.90  3.000
 K2H  H12  CBC  H10  108.23  3.000
 K2H  H11  CBC  H10  107.97  3.000
 K2H  H12  CBC  NAO  110.75  3.000
 K2H  H11  CBC  NAO  109.86  3.000
 K2H  H10  CBC  NAO  112.91  3.000
 K2H  H13  CBD  OBE  111.86  3.000
 K2H  H13  CBD  CBF  112.06  3.000
 K2H  OBE  CBD  CBF  110.77  3.000
 K2H  H13  CBD  CAM  111.94  3.000
 K2H  OBE  CBD  CAM  109.07  3.000
 K2H  CBF  CBD  CAM  100.59  3.000
 K2H  H14  CBF  OBG  111.37  3.000
 K2H  H14  CBF  CBD  109.42  3.000
 K2H  OBG  CBF  CBD  114.60  3.000
 K2H  H14  CBF  CAK  109.56  3.000
 K2H  CBD  CBF  CAK  101.47  3.000
 K2H  OBG  CBF  CAK  109.92  3.000
 K2H  C6   N1   C2   119.12  3.000
 K2H  C4   N3   C2   111.69  3.000
 K2H  H16  N6   H15  118.27  3.000
 K2H  H16  N6   C6   120.15  3.000
 K2H  H15  N6   C6   121.11  3.000
 K2H  C8   N7   C5   104.49  3.000
 K2H  CBC  NAO  CAP  111.51  3.000
 K2H  CAP  NAO  CAN  110.14  3.000
 K2H  CBC  NAO  CAN  113.17  3.000
 K2H  H18  NAT  CAU  126.75  3.000
 K2H  H18  NAT  CAS  126.25  3.000
 K2H  CAU  NAT  CAS  106.99  3.000
 K2H  CAW  NAV  CAU  111.69  3.000
 K2H  CAY  NAX  CAW  119.15  3.000
 K2H  CAZ  NBA  CAS  104.36  3.000
 K2H  H21  NBB  H20  118.38  3.000
 K2H  H21  NBB  CAY  121.21  3.000
 K2H  H20  NBB  CAY  120.40  3.000
 K2H  CAM  OAL  CAK  111.07  3.000
 K2H  H22  OBE  CBD  107.88  3.000
 K2H  H23  OBG  CBF  108.81  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
 K2H  CONST_01  C5   C6   N1   C2      0.00   0.0  0
 K2H  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 K2H  CONST_03  N9   C4   N3   C2    180.00   0.0  0
 K2H  CONST_04  C8   N7   C5   C4      0.00   0.0  0
 K2H  CONST_05  N1   C6   C5   C4      0.00   0.0  0
 K2H  CONST_06  N7   C8   N9   C4      0.00   0.0  0
 K2H  CONST_07  N1   C2   N3   C4      0.00   0.0  0
 K2H  CONST_08  N9   C8   N7   C5      0.00   0.0  0
 K2H  CONST_09  C8   N9   C4   C5      0.00   0.0  0
 K2H  CONST_10  C8   N7   C5   C6    180.00   0.0  0
 K2H  CONST_11  N9   C4   C5   C6    180.00   0.0  0
 K2H  CONST_12  N3   C4   C5   C6      0.00   0.0  0
 K2H  CONST_13  N3   C2   N1   C6      0.00   0.0  0
 K2H  CONST_14  N7   C5   C4   N9      0.00   0.0  0
 K2H  CONST_15  N3   C4   N9   C8    180.00   0.0  0
 K2H  CONST_16  CAY  CAZ  NBA  CAS   180.00   0.0  0
 K2H  CONST_17  CAU  CAZ  NBA  CAS     0.00   0.0  0
 K2H  CONST_18  CAZ  CAU  NAT  CAS     0.00   0.0  0
 K2H  CONST_19  NAV  CAU  NAT  CAS   180.00   0.0  0
 K2H  CONST_20  NAX  CAY  CAZ  CAU     0.00   0.0  0
 K2H  CONST_21  NBA  CAS  NAT  CAU     0.00   0.0  0
 K2H  CONST_22  NAX  CAW  NAV  CAU     0.00   0.0  0
 K2H  CONST_23  CAZ  CAY  NAX  CAW     0.00   0.0  0
 K2H  CONST_24  CAZ  CAU  NAV  CAW     0.00   0.0  0
 K2H  CONST_25  NAT  CAU  NAV  CAW   180.00   0.0  0
 K2H  CONST_26  NAV  CAW  NAX  CAY     0.00   0.0  0
 K2H  CONST_27  NAT  CAU  CAZ  CAY   180.00   0.0  0
 K2H  CONST_28  NAV  CAU  CAZ  CAY     0.00   0.0  0
 K2H  CONST_29  NAT  CAS  NBA  CAZ     0.00   0.0  0
 K2H  CONST_30  N7   C5   C6   N1    180.00   0.0  0
 K2H  CONST_31  N7   C5   C4   N3    180.00   0.0  0
 K2H  CONST_32  NBA  CAZ  CAU  NAT     0.00   0.0  0
 K2H  CONST_33  NBA  CAZ  CAU  NAV   180.00   0.0  0
 K2H  CONST_34  NBA  CAZ  CAY  NAX   180.00   0.0  0
 K2H  CONST_35  CAK  N9   C4   C5    180.00   0.0  0
 K2H  CONST_36  N7   C8   N9   CAK   180.00   0.0  0
 K2H  CONST_37  N3   C4   N9   CAK     0.00   0.0  0
 K2H  CONST_38  N6   C6   N1   C2    180.00   0.0  0
 K2H  CONST_39  N6   C6   C5   C4    180.00   0.0  0
 K2H  CONST_40  CAZ  NBA  CAS  CAR   180.00   0.0  0
 K2H  CONST_41  CAU  NAT  CAS  CAR   180.00   0.0  0
 K2H  CONST_42  NBB  CAY  CAZ  CAU   180.00   0.0  0
 K2H  CONST_43  NBB  CAY  NAX  CAW   180.00   0.0  0
 K2H  CONST_44  N7   C5   C6   N6      0.00   0.0  0
 K2H  CONST_45  NBB  CAY  CAZ  NBA     0.00   0.0  0
 K2H  CONST_46  H2   C8   N9   C4    180.00   0.0  0
 K2H  CONST_47  H1   C2   N3   C4    180.00   0.0  0
 K2H  CONST_48  H9   CAW  NAV  CAU   180.00   0.0  0
 K2H  CONST_49  H18  NAT  CAU  CAZ   180.00   0.0  0
 K2H  CONST_50  H15  N6   C6   C5      0.00   0.0  0
 K2H  CONST_51  H16  N6   C6   C5    180.00   0.0  0
 K2H  CONST_52  H20  NBB  CAY  CAZ   180.00   0.0  0
 K2H  CONST_53  H21  NBB  CAY  CAZ     0.00   0.0  0
 K2H  Var_01    CBC  NAO  CAN  CAM    60.85  30.0  3
 K2H  Var_02    CAQ  CAP  NAO  CAN   165.25  30.0  3
 K2H  Var_03    NAO  CAP  CAQ  CAR  -101.99  30.0  3
 K2H  Var_04    H10  CBC  NAO  CAN    59.55  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
 K2H  chir_01  CAK  CBF  N9   OAL  positiv
 K2H  chir_02  CAM  OAL  CAN  CBD  positiv
 K2H  chir_03  CBD  OBE  CAM  CBF  positiv
 K2H  chir_04  CBF  OBG  CBD  CAK  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
 K2H  plan-1  C2   0.020
 K2H  plan-1  C4   0.020
 K2H  plan-1  C5   0.020
 K2H  plan-1  C6   0.020
 K2H  plan-1  N9   0.020
 K2H  plan-1  C8   0.020
 K2H  plan-1  CAK  0.020
 K2H  plan-1  N1   0.020
 K2H  plan-1  N3   0.020
 K2H  plan-1  N6   0.020
 K2H  plan-1  N7   0.020
 K2H  plan-1  H1   0.020
 K2H  plan-1  H2   0.020
 K2H  plan-2  CAQ  0.020
 K2H  plan-2  CAR  0.020
 K2H  plan-2  CAS  0.020
 K2H  plan-2  CAU  0.020
 K2H  plan-2  CAW  0.020
 K2H  plan-2  CAY  0.020
 K2H  plan-2  CAZ  0.020
 K2H  plan-2  NAT  0.020
 K2H  plan-2  NAV  0.020
 K2H  plan-2  NAX  0.020
 K2H  plan-2  NBA  0.020
 K2H  plan-2  NBB  0.020
 K2H  plan-2  H9   0.020
 K2H  plan-2  H18  0.020
 K2H  plan-3  C6   0.020
 K2H  plan-3  N6   0.020
 K2H  plan-3  H15  0.020
 K2H  plan-3  H16  0.020
 K2H  plan-4  CAY  0.020
 K2H  plan-4  NBB  0.020
 K2H  plan-4  H20  0.020
 K2H  plan-4  H21  0.020

