# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 19 17:36:49 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)-~{N}-(piperidin-4-ylmethyl)oxolane-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@@H]([C@@H](O)[C@H]3O)C(=O)NCC4CCNCC4
#
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
 NX8  NX8  (2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)-~{N}-(piperidin-4-ylmethyl)oxolane-2-carboxamide  ligand  50  27  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NX8
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
 NX8  C4   C  CR56  0   0.485   3.6456  -0.2075  -0.3882
 NX8  C5   C  CR56  0  -0.002   3.9707   1.1316  -0.5320
 NX8  C6   C  CR6   0   0.456   5.3334   1.4571  -0.3970
 NX8  C8   C  CR15  0   0.089   1.8780   1.0125  -0.8028
 NX8  N1   N  N     0  -0.474   6.1933   0.4630  -0.1477
 NX8  N3   N  N     0  -0.460   4.4884  -1.2090  -0.1400
 NX8  C2   C  CR16  0   0.038   5.7346  -0.7809  -0.0369
 NX8  CAG  C  CH2   0  -0.292  -7.4702   1.0198   0.1967
 NX8  CAH  C  CH2   0  -0.290  -6.4243  -0.3836  -1.4503
 NX8  CAI  C  CH2   0  -0.418  -6.1195   1.4614   0.7420
 NX8  CAJ  C  CH2   0  -0.414  -5.0337   0.0070  -0.9715
 NX8  CAK  C  CH2   0  -0.269  -3.7027   0.8624   1.0173
 NX8  CAR  C  C     0   0.524  -1.6650  -0.0798  -0.0043
 NX8  CAV  C  CH1   0  -0.252  -5.0592   0.3864   0.5072
 NX8  CAW  C  CR15  0  -0.040   0.1134  -1.2868   1.3672
 NX8  CAX  C  CR15  0  -0.042   1.3668  -2.0333   0.8989
 NX8  CAY  C  CR15  0  -0.072  -0.7195  -1.2724   0.0790
 NX8  CAZ  C  CR15  0   0.169   1.5073  -1.4974  -0.5230
 NX8  N6   N  NH2   0  -0.817   5.7918   2.7050  -0.5027
 NX8  N7   N  N     0  -0.453   2.8515   1.8772  -0.7913
 NX8  N9   N  NR5   0  -0.540   2.2935  -0.2692  -0.5581
 NX8  NAO  N  NH1   0  -0.596  -7.3568   0.7049  -1.2162
 NX8  OAB  O  O     0  -0.481  -1.4961   0.8303  -0.8004
 NX8  OAC  O  OH1   0  -0.653  -0.5871  -1.9349   2.3883
 NX8  OAD  O  OH1   0  -0.661   1.1272  -3.4083   0.7967
 NX8  OAQ  O  O     0  -0.484   0.2134  -1.2363  -0.9794
 NX8  H1   H  HCR5  0   0.304   0.8420   1.2481  -0.9904
 NX8  H2   H  HCR6  0   0.252   6.4854  -1.5374   0.1646
 NX8  H4   H  HCH2  0   0.230  -8.2035   1.8191   0.3229
 NX8  H5   H  HCH2  0   0.230  -6.4034  -0.6066  -2.5191
 NX8  H6   H  HCH2  0   0.184  -6.7246  -1.3125  -0.9368
 NX8  H7   H  HCH2  0   0.214  -5.8145   2.3886   0.2445
 NX8  H8   H  HCH2  0   0.229  -6.2099   1.6837   1.8085
 NX8  H9   H  HCH2  0   0.228  -4.3447  -0.8228  -1.1446
 NX8  H10  H  HCH2  0   0.212  -4.6694   0.8555  -1.5606
 NX8  H11  H  HCH2  0   0.242  -3.3920   1.7548   0.4743
 NX8  H12  H  HCH2  0   0.251  -3.7839   1.1396   2.0710
 NX8  H13  H  HCH1  0   0.218  -5.3500  -0.5033   1.0828
 NX8  H14  H  HCR5  0   0.262   0.3883  -0.2649   1.6549
 NX8  H15  H  HCR5  0   0.268   2.2427  -1.8113   1.5196
 NX8  H16  H  HCR5  0   0.280  -1.3089  -2.1967   0.0226
 NX8  H17  H  HCR5  0   0.291   1.9987  -2.2189  -1.1805
 NX8  H18  H  HNH2  0   0.411   5.1769   3.4683  -0.7235
 NX8  H19  H  HNH2  0   0.404   6.7772   2.8909  -0.4299
 NX8  H20  H  HNH1  0   0.350  -8.2667   0.4520  -1.5787
 NX8  H23  H  HOH1  0   0.474  -0.2617  -1.6245   3.2394
 NX8  H24  H  HOH1  0   0.455   0.6833  -3.6970   1.6030
 NX8  NAP  N  NH1   0  -0.627  -2.6629  -0.1353   0.8867
 NX8  H3   H  HCH2  0   0.184  -7.8266   0.1629   0.7931
 NX8  H22  H  HNH1  0   0.400  -2.7080  -0.9314   1.5046

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
 NX8  CAG  CAI  single    1.522  0.020  1.522
 NX8  CAG  NAO  single    1.452  0.020  1.452
 NX8  CAI  CAV  single    1.528  0.020  1.528
 NX8  NAO  CAH  single    1.452  0.020  1.452
 NX8  CAV  CAK  single    1.525  0.020  1.525
 NX8  CAV  CAJ  single    1.527  0.020  1.527
 NX8  CAH  CAJ  single    1.522  0.020  1.522
 NX8  CAK  NAP  single    1.447  0.020  1.447
 NX8  OAB  CAR  double    1.221  0.020  1.221
 NX8  N7   C8   aromatic  1.302  0.020  1.302
 NX8  N7   C5   aromatic  1.370  0.020  1.370
 NX8  C8   N9   aromatic  1.369  0.020  1.369
 NX8  NAP  CAR  single    1.339  0.020  1.339
 NX8  CAR  CAY  single    1.524  0.020  1.524
 NX8  N6   C6   single    1.334  0.020  1.334
 NX8  C5   C6   aromatic  1.408  0.020  1.408
 NX8  C5   C4   aromatic  1.386  0.020  1.386
 NX8  N9   CAZ  single    1.459  0.020  1.459
 NX8  N9   C4   aromatic  1.364  0.020  1.364
 NX8  CAX  CAW  single    1.532  0.020  1.532
 NX8  CAX  OAD  single    1.399  0.020  1.399
 NX8  CAX  CAZ  single    1.526  0.020  1.526
 NX8  C6   N1   aromatic  1.338  0.020  1.338
 NX8  CAY  CAW  single    1.534  0.020  1.534
 NX8  CAY  OAQ  single    1.411  0.020  1.411
 NX8  CAW  OAC  single    1.398  0.020  1.398
 NX8  OAQ  CAZ  single    1.397  0.020  1.397
 NX8  C4   N3   aromatic  1.332  0.020  1.332
 NX8  N1   C2   aromatic  1.330  0.020  1.330
 NX8  N3   C2   aromatic  1.322  0.020  1.322
 NX8  C8   H1   single    0.930  0.020  1.080
 NX8  C2   H2   single    0.930  0.020  1.080
 NX8  CAG  H3   single    0.970  0.020  1.090
 NX8  CAG  H4   single    0.970  0.020  1.090
 NX8  CAH  H5   single    0.970  0.020  1.090
 NX8  CAH  H6   single    0.970  0.020  1.090
 NX8  CAI  H7   single    0.970  0.020  1.090
 NX8  CAI  H8   single    0.970  0.020  1.090
 NX8  CAJ  H9   single    0.970  0.020  1.090
 NX8  CAJ  H10  single    0.970  0.020  1.090
 NX8  CAK  H11  single    0.970  0.020  1.090
 NX8  CAK  H12  single    0.970  0.020  1.090
 NX8  CAV  H13  single    0.970  0.020  1.090
 NX8  CAW  H14  single    0.970  0.020  1.090
 NX8  CAX  H15  single    0.970  0.020  1.090
 NX8  CAY  H16  single    0.970  0.020  1.090
 NX8  CAZ  H17  single    0.970  0.020  1.090
 NX8  N6   H18  single    0.860  0.020  1.020
 NX8  N6   H19  single    0.860  0.020  1.020
 NX8  NAO  H20  single    0.890  0.020  1.040
 NX8  NAP  H22  single    0.860  0.020  1.020
 NX8  OAC  H23  single    0.850  0.020  0.980
 NX8  OAD  H24  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
 NX8  N9   C4   N3   128.04  3.000
 NX8  N3   C4   C5   126.69  3.000
 NX8  N9   C4   C5   105.27  3.000
 NX8  N7   C5   C6   133.11  3.000
 NX8  C6   C5   C4   116.15  3.000
 NX8  N7   C5   C4   110.74  3.000
 NX8  N6   C6   N1   119.29  3.000
 NX8  N1   C6   C5   117.92  3.000
 NX8  N6   C6   C5   122.79  3.000
 NX8  H1   C8   N9   121.79  3.000
 NX8  H1   C8   N7   125.06  3.000
 NX8  N9   C8   N7   113.15  3.000
 NX8  C2   N1   C6   119.25  3.000
 NX8  C2   N3   C4   111.56  3.000
 NX8  H2   C2   N3   116.18  3.000
 NX8  H2   C2   N1   115.40  3.000
 NX8  N3   C2   N1   128.42  3.000
 NX8  H4   CAG  H3   106.80  3.000
 NX8  H4   CAG  NAO  108.88  3.000
 NX8  H3   CAG  NAO  112.51  3.000
 NX8  H4   CAG  CAI  110.01  3.000
 NX8  H3   CAG  CAI  108.57  3.000
 NX8  NAO  CAG  CAI  110.01  3.000
 NX8  H6   CAH  H5   106.79  3.000
 NX8  H6   CAH  NAO  112.42  3.000
 NX8  H5   CAH  NAO  108.85  3.000
 NX8  H6   CAH  CAJ  108.58  3.000
 NX8  H5   CAH  CAJ  110.05  3.000
 NX8  NAO  CAH  CAJ  110.10  3.000
 NX8  H8   CAI  H7   107.10  3.000
 NX8  H8   CAI  CAV  110.50  3.000
 NX8  H7   CAI  CAV  109.41  3.000
 NX8  H8   CAI  CAG  109.58  3.000
 NX8  H7   CAI  CAG  109.26  3.000
 NX8  CAV  CAI  CAG  110.89  3.000
 NX8  H10  CAJ  H9   107.07  3.000
 NX8  H10  CAJ  CAV  109.51  3.000
 NX8  H9   CAJ  CAV  110.66  3.000
 NX8  H10  CAJ  CAH  109.49  3.000
 NX8  H9   CAJ  CAH  109.36  3.000
 NX8  CAV  CAJ  CAH  110.69  3.000
 NX8  H12  CAK  H11  107.10  3.000
 NX8  H12  CAK  NAP  108.38  3.000
 NX8  H11  CAK  NAP  108.35  3.000
 NX8  H12  CAK  CAV  109.60  3.000
 NX8  H11  CAK  CAV  110.02  3.000
 NX8  NAP  CAK  CAV  113.19  3.000
 NX8  OAB  CAR  NAP  124.60  3.000
 NX8  NAP  CAR  CAY  113.18  3.000
 NX8  OAB  CAR  CAY  122.21  3.000
 NX8  H13  CAV  CAK  108.23  3.000
 NX8  H13  CAV  CAJ  108.09  3.000
 NX8  CAK  CAV  CAJ  112.74  3.000
 NX8  H13  CAV  CAI  107.79  3.000
 NX8  CAJ  CAV  CAI  109.58  3.000
 NX8  CAK  CAV  CAI  110.25  3.000
 NX8  H14  CAW  OAC  111.48  3.000
 NX8  H14  CAW  CAY  110.34  3.000
 NX8  OAC  CAW  CAY  110.22  3.000
 NX8  H14  CAW  CAX  109.21  3.000
 NX8  OAC  CAW  CAX  114.05  3.000
 NX8  CAY  CAW  CAX  101.07  3.000
 NX8  H15  CAX  OAD  112.16  3.000
 NX8  H15  CAX  CAZ  112.52  3.000
 NX8  OAD  CAX  CAZ  107.02  3.000
 NX8  H15  CAX  CAW  112.45  3.000
 NX8  CAZ  CAX  CAW  100.90  3.000
 NX8  OAD  CAX  CAW  111.16  3.000
 NX8  H16  CAY  OAQ  109.75  3.000
 NX8  H16  CAY  CAW  109.07  3.000
 NX8  OAQ  CAY  CAW  105.73  3.000
 NX8  H16  CAY  CAR  108.84  3.000
 NX8  OAQ  CAY  CAR  110.43  3.000
 NX8  CAW  CAY  CAR  112.96  3.000
 NX8  H17  CAZ  OAQ  110.09  3.000
 NX8  H17  CAZ  N9   107.40  3.000
 NX8  OAQ  CAZ  N9   109.52  3.000
 NX8  H17  CAZ  CAX  111.72  3.000
 NX8  OAQ  CAZ  CAX  106.55  3.000
 NX8  N9   CAZ  CAX  111.57  3.000
 NX8  H19  N6   H18  118.38  3.000
 NX8  H19  N6   C6   120.28  3.000
 NX8  H18  N6   C6   121.19  3.000
 NX8  C8   N7   C5   104.54  3.000
 NX8  CAZ  N9   C8   128.96  3.000
 NX8  CAZ  N9   C4   124.70  3.000
 NX8  C8   N9   C4   106.30  3.000
 NX8  H20  NAO  CAH  109.42  3.000
 NX8  H20  NAO  CAG  109.43  3.000
 NX8  CAH  NAO  CAG  111.69  3.000
 NX8  H23  OAC  CAW  109.08  3.000
 NX8  H24  OAD  CAX  108.17  3.000
 NX8  CAZ  OAQ  CAY  111.26  3.000
 NX8  H22  NAP  CAR  118.27  3.000
 NX8  H22  NAP  CAK  117.18  3.000
 NX8  CAR  NAP  CAK  124.55  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
 NX8  CONST_01  C8   N7   C5   C4     0.00   0.0  0
 NX8  CONST_02  N1   C6   C5   C4     0.00   0.0  0
 NX8  CONST_03  N7   C8   N9   C4     0.00   0.0  0
 NX8  CONST_04  N1   C2   N3   C4     0.00   0.0  0
 NX8  CONST_05  N9   C8   N7   C5     0.00   0.0  0
 NX8  CONST_06  C2   N1   C6   C5     0.00   0.0  0
 NX8  CONST_07  C8   N9   C4   C5     0.00   0.0  0
 NX8  CONST_08  C2   N3   C4   C5     0.00   0.0  0
 NX8  CONST_09  C8   N7   C5   C6   180.00   0.0  0
 NX8  CONST_10  N9   C4   C5   C6   180.00   0.0  0
 NX8  CONST_11  N3   C4   C5   C6     0.00   0.0  0
 NX8  CONST_12  N3   C2   N1   C6     0.00   0.0  0
 NX8  CONST_13  N3   C4   N9   C8   180.00   0.0  0
 NX8  CONST_14  N7   C5   C6   N1   180.00   0.0  0
 NX8  CONST_15  N7   C5   C4   N3   180.00   0.0  0
 NX8  CONST_16  N9   C4   N3   C2   180.00   0.0  0
 NX8  CONST_17  N9   C4   C5   N7     0.00   0.0  0
 NX8  CONST_18  CAZ  N9   C4   C5   180.00   0.0  0
 NX8  CONST_19  CAZ  N9   C4   N3     0.00   0.0  0
 NX8  CONST_20  N7   C8   N9   CAZ  180.00   0.0  0
 NX8  CONST_21  N6   C6   C5   C4   180.00   0.0  0
 NX8  CONST_22  N6   C6   N1   C2   180.00   0.0  0
 NX8  CONST_23  N7   C5   C6   N6     0.00   0.0  0
 NX8  CONST_24  H1   C8   N9   C4   180.00   0.0  0
 NX8  CONST_25  H2   C2   N3   C4   180.00   0.0  0
 NX8  CONST_26  H18  N6   C6   C5     0.00   0.0  0
 NX8  CONST_27  H19  N6   C6   C5   180.00   0.0  0
 NX8  CONST_28  CAY  CAR  NAP  CAK  180.00   0.0  0
 NX8  CONST_29  H22  NAP  CAR  CAY    0.00   0.0  0
 NX8  CONST_30  OAB  CAR  NAP  CAK    0.00   0.0  0
 NX8  Var_01    CAJ  CAH  NAO  CAG  -61.42  30.0  1
 NX8  Var_02    CAI  CAG  NAO  CAH   61.17  30.0  1
 NX8  Var_03    NAO  CAG  CAI  CAV  -56.98  30.0  1
 NX8  Var_04    NAO  CAH  CAJ  CAV   57.31  30.0  1
 NX8  Var_05    CAV  CAK  NAP  CAR  107.68  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
 NX8  chir_01  CAV  CAI  CAK  CAJ  positiv
 NX8  chir_02  CAW  OAC  CAX  CAY  negativ
 NX8  chir_03  CAX  OAD  CAZ  CAW  negativ
 NX8  chir_04  CAY  OAQ  CAW  CAR  negativ
 NX8  chir_05  CAZ  OAQ  N9   CAX  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
 NX8  plan-1  CAK  0.020
 NX8  plan-1  CAR  0.020
 NX8  plan-1  CAY  0.020
 NX8  plan-1  OAB  0.020
 NX8  plan-1  NAP  0.020
 NX8  plan-1  H22  0.020
 NX8  plan-2  C6   0.020
 NX8  plan-2  N6   0.020
 NX8  plan-2  H18  0.020
 NX8  plan-2  H19  0.020
 NX8  plan-3  C4   0.020
 NX8  plan-3  C5   0.020
 NX8  plan-3  C6   0.020
 NX8  plan-3  C8   0.020
 NX8  plan-3  N1   0.020
 NX8  plan-3  N3   0.020
 NX8  plan-3  C2   0.020
 NX8  plan-3  CAZ  0.020
 NX8  plan-3  N6   0.020
 NX8  plan-3  N7   0.020
 NX8  plan-3  N9   0.020
 NX8  plan-3  H1   0.020
 NX8  plan-3  H2   0.020

