# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 20:09:27 2020
#   Inital geometry file: a 115 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]methoxy-oxidanyl-phosphoryl] 2-methyl-2-oxidanyl-propanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(O)C(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 8LE  8LE  '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 2-methyl-2-oxidanyl-propanoate'  ligand  49  29  .  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_8LE
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
 8LE  C2   C  CR16  0   0.027   3.2053   2.4081  -1.7658
 8LE  CAA  C  CH3   0  -0.740  -1.4742   1.9740  -1.1784
 8LE  CAZ  C  CT    0   0.106  -2.9579   1.8143  -0.8476
 8LE  CAB  C  CH3   0  -0.624  -3.6155   3.1708  -0.6355
 8LE  OAF  O  OH1   0  -0.722  -3.5436   1.1114  -1.9153
 8LE  CAS  C  C     0   0.680  -3.0554   0.9877   0.4375
 8LE  OAD  O  O     0  -0.434  -3.3080   1.4109   1.5270
 8LE  OAQ  O  O2    0  -0.571  -2.7894  -0.3197   0.2098
 8LE  PBC  P  P     0   1.492  -2.6956  -1.4078   1.4288
 8LE  OAI  O  OH1   0  -0.679  -4.1869  -1.5855   1.9331
 8LE  OAE  O  O     0  -0.747  -1.7666  -1.0801   2.5202
 8LE  O5'  O  O2    0  -0.592  -2.3854  -2.7150   0.5855
 8LE  C5'  C  CH2   0  -0.186  -1.1288  -3.3942   0.6661
 8LE  C4'  C  CH1   0   0.053  -0.2354  -3.0053  -0.4935
 8LE  O4'  O  O2    0  -0.491  -0.0876  -1.5842  -0.5444
 8LE  C3'  C  CH1   0  -0.018   1.1686  -3.5863  -0.3331
 8LE  O3'  O  OH1   0  -0.647   1.6656  -3.9006  -1.6049
 8LE  C2'  C  CH1   0  -0.004   1.9208  -2.3960   0.2751
 8LE  O2'  O  OH1   0  -0.662   3.3003  -2.4060   0.0723
 8LE  C1'  C  CH1   0   0.146   1.2699  -1.2439  -0.4816
 8LE  N9   N  NR5   0  -0.454   1.4105   0.0465   0.1341
 8LE  C8   C  CR15  0   0.092   0.9067   0.4662   1.3384
 8LE  N7   N  N     0  -0.494   1.1906   1.7058   1.6087
 8LE  C5   C  CR56  0   0.037   1.9224   2.1332   0.5304
 8LE  C4   C  CR56  0   0.418   2.0658   1.1188  -0.4018
 8LE  N3   N  N     0  -0.446   2.6988   1.2041  -1.5682
 8LE  N1   N  N     0  -0.440   3.1502   3.4683  -0.9653
 8LE  C6   C  CR6   0   0.412   2.5090   3.3662   0.2011
 8LE  N6   N  NH2   0  -0.796   2.4655   4.4240   1.0217
 8LE  H1   H  HCR6  0   0.271   3.7366   2.5570  -2.6992
 8LE  H2   H  HCH3  0   0.298  -1.3637   2.6281  -2.0433
 8LE  H3   H  HCH3  0   0.313  -0.9357   2.4267  -0.3463
 8LE  H4   H  HCH3  0   0.209  -1.0145   1.0135  -1.4082
 8LE  H5   H  HCH3  0   0.288  -3.5399   3.7541  -1.5530
 8LE  H6   H  HCH3  0   0.247  -4.6725   3.0739  -0.3803
 8LE  H7   H  HCH3  0   0.205  -3.1332   3.7370   0.1589
 8LE  H8   H  HOH1  0   0.461  -4.5019   1.1483  -1.8277
 8LE  H9   H  HOH1  0   0.524  -4.8546  -1.8357   1.2824
 8LE  H10  H  HCH2  0   0.235  -0.6523  -3.2008   1.6293
 8LE  H11  H  HCH2  0   0.227  -1.3478  -4.4600   0.6108
 8LE  H12  H  HCH1  0   0.196  -0.6871  -3.3500  -1.4284
 8LE  H13  H  HCH1  0   0.239   1.1801  -4.4585   0.3339
 8LE  H14  H  HOH1  0   0.458   2.6098  -4.0697  -1.5226
 8LE  H15  H  HCH1  0   0.301   1.6684  -2.3164   1.3407
 8LE  H16  H  HOH1  0   0.447   3.7170  -2.8576   0.8110
 8LE  H17  H  HCH1  0   0.314   1.7137  -1.1479  -1.4790
 8LE  H18  H  HCR5  0   0.263   0.3073  -0.1776   1.9643
 8LE  H19  H  HNH2  0   0.403   1.8796   4.4049   1.8373
 8LE  H20  H  HNH2  0   0.389   2.7695   5.3220   0.6887

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
 8LE  OAE  PBC  double    1.470  0.020  1.470
 8LE  OAI  PBC  single    1.584  0.020  1.584
 8LE  PBC  O5'  single    1.586  0.020  1.586
 8LE  PBC  OAQ  single    1.637  0.020  1.637
 8LE  O5'  C5'  single    1.431  0.020  1.431
 8LE  OAQ  CAS  single    1.353  0.020  1.353
 8LE  CAA  CAZ  single    1.528  0.020  1.528
 8LE  C5'  C4'  single    1.515  0.020  1.515
 8LE  CAS  OAD  double    1.196  0.020  1.196
 8LE  CAS  CAZ  single    1.531  0.020  1.531
 8LE  C4'  C3'  single    1.528  0.020  1.528
 8LE  C4'  O4'  single    1.430  0.020  1.430
 8LE  O3'  C3'  single    1.401  0.020  1.401
 8LE  CAZ  OAF  single    1.406  0.020  1.406
 8LE  CAZ  CAB  single    1.522  0.020  1.522
 8LE  C3'  C2'  single    1.534  0.020  1.534
 8LE  O4'  C1'  single    1.401  0.020  1.401
 8LE  O2'  C2'  single    1.394  0.020  1.394
 8LE  C2'  C1'  single    1.524  0.020  1.524
 8LE  C1'  N9   single    1.437  0.020  1.437
 8LE  C8   N9   aromatic  1.371  0.020  1.371
 8LE  C8   N7   aromatic  1.300  0.020  1.300
 8LE  N9   C4   aromatic  1.366  0.020  1.366
 8LE  N7   C5   aromatic  1.371  0.020  1.371
 8LE  C4   C5   aromatic  1.385  0.020  1.385
 8LE  C4   N3   aromatic  1.330  0.020  1.330
 8LE  C5   C6   aromatic  1.405  0.020  1.405
 8LE  N3   C2   aromatic  1.321  0.020  1.321
 8LE  C6   N6   single    1.339  0.020  1.339
 8LE  C6   N1   aromatic  1.335  0.020  1.335
 8LE  C2   N1   aromatic  1.330  0.020  1.330
 8LE  C2   H1   single    0.930  0.020  1.080
 8LE  CAA  H2   single    0.970  0.020  1.090
 8LE  CAA  H3   single    0.970  0.020  1.090
 8LE  CAA  H4   single    0.970  0.020  1.090
 8LE  CAB  H5   single    0.970  0.020  1.090
 8LE  CAB  H6   single    0.970  0.020  1.090
 8LE  CAB  H7   single    0.970  0.020  1.090
 8LE  OAF  H8   single    0.850  0.020  0.980
 8LE  OAI  H9   single    0.850  0.020  0.980
 8LE  C5'  H10  single    0.970  0.020  1.090
 8LE  C5'  H11  single    0.970  0.020  1.090
 8LE  C4'  H12  single    0.970  0.020  1.090
 8LE  C3'  H13  single    0.970  0.020  1.090
 8LE  O3'  H14  single    0.850  0.020  0.980
 8LE  C2'  H15  single    0.970  0.020  1.090
 8LE  O2'  H16  single    0.850  0.020  0.980
 8LE  C1'  H17  single    0.970  0.020  1.090
 8LE  C8   H18  single    0.930  0.020  1.080
 8LE  N6   H19  single    0.860  0.020  1.020
 8LE  N6   H20  single    0.860  0.020  1.020

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
 8LE  H1   C2   N1   115.41  3.000
 8LE  H1   C2   N3   116.21  3.000
 8LE  N1   C2   N3   128.37  3.000
 8LE  H4   CAA  H3   108.59  3.000
 8LE  H4   CAA  H2   108.60  3.000
 8LE  H3   CAA  H2   107.85  3.000
 8LE  H4   CAA  CAZ  111.29  3.000
 8LE  H3   CAA  CAZ  110.97  3.000
 8LE  H2   CAA  CAZ  109.44  3.000
 8LE  CAS  CAZ  OAF  109.93  3.000
 8LE  OAF  CAZ  CAB  111.79  3.000
 8LE  CAS  CAZ  CAB  109.67  3.000
 8LE  CAB  CAZ  CAA  110.88  3.000
 8LE  OAF  CAZ  CAA  107.00  3.000
 8LE  CAS  CAZ  CAA  107.45  3.000
 8LE  H7   CAB  H6   107.73  3.000
 8LE  H7   CAB  H5   107.78  3.000
 8LE  H6   CAB  H5   108.15  3.000
 8LE  H7   CAB  CAZ  111.95  3.000
 8LE  H6   CAB  CAZ  111.82  3.000
 8LE  H5   CAB  CAZ  109.25  3.000
 8LE  H8   OAF  CAZ  109.04  3.000
 8LE  OAQ  CAS  OAD  122.46  3.000
 8LE  OAD  CAS  CAZ  125.95  3.000
 8LE  OAQ  CAS  CAZ  111.58  3.000
 8LE  PBC  OAQ  CAS  121.88  3.000
 8LE  O5'  PBC  OAE  117.05  3.000
 8LE  O5'  PBC  OAI  105.12  3.000
 8LE  OAE  PBC  OAI  112.55  3.000
 8LE  O5'  PBC  OAQ   99.39  3.000
 8LE  OAI  PBC  OAQ  104.94  3.000
 8LE  OAE  PBC  OAQ  116.16  3.000
 8LE  H9   OAI  PBC  117.75  3.000
 8LE  C5'  O5'  PBC  122.21  3.000
 8LE  H11  C5'  H10  107.80  3.000
 8LE  H11  C5'  C4'  109.32  3.000
 8LE  H10  C5'  C4'  111.87  3.000
 8LE  H11  C5'  O5'  106.56  3.000
 8LE  H10  C5'  O5'  110.42  3.000
 8LE  C4'  C5'  O5'  110.67  3.000
 8LE  H12  C4'  C3'  110.44  3.000
 8LE  H12  C4'  O4'  108.99  3.000
 8LE  C3'  C4'  O4'  106.66  3.000
 8LE  H12  C4'  C5'  109.25  3.000
 8LE  O4'  C4'  C5'  110.09  3.000
 8LE  C3'  C4'  C5'  111.35  3.000
 8LE  C1'  O4'  C4'  109.88  3.000
 8LE  H13  C3'  C2'  111.74  3.000
 8LE  H13  C3'  O3'  111.68  3.000
 8LE  C2'  C3'  O3'  111.10  3.000
 8LE  H13  C3'  C4'  112.05  3.000
 8LE  C2'  C3'  C4'  101.37  3.000
 8LE  O3'  C3'  C4'  108.42  3.000
 8LE  H14  O3'  C3'  108.04  3.000
 8LE  H15  C2'  C1'  109.19  3.000
 8LE  H15  C2'  O2'  111.66  3.000
 8LE  C1'  C2'  O2'  110.84  3.000
 8LE  H15  C2'  C3'  109.17  3.000
 8LE  C1'  C2'  C3'  100.39  3.000
 8LE  O2'  C2'  C3'  114.96  3.000
 8LE  H16  O2'  C2'  108.70  3.000
 8LE  H17  C1'  N9   105.77  3.000
 8LE  H17  C1'  C2'  110.18  3.000
 8LE  N9   C1'  C2'  115.11  3.000
 8LE  H17  C1'  O4'  111.89  3.000
 8LE  N9   C1'  O4'  109.41  3.000
 8LE  C2'  C1'  O4'  104.62  3.000
 8LE  C4   N9   C8   106.29  3.000
 8LE  C4   N9   C1'  125.72  3.000
 8LE  C8   N9   C1'  127.98  3.000
 8LE  H18  C8   N7   124.70  3.000
 8LE  H18  C8   N9   122.04  3.000
 8LE  N7   C8   N9   113.22  3.000
 8LE  C5   N7   C8   104.49  3.000
 8LE  C6   C5   C4   116.22  3.000
 8LE  C6   C5   N7   132.90  3.000
 8LE  C4   C5   N7   110.86  3.000
 8LE  N3   C4   C5   126.34  3.000
 8LE  N3   C4   N9   128.51  3.000
 8LE  C5   C4   N9   105.14  3.000
 8LE  C4   N3   C2   111.85  3.000
 8LE  C6   N1   C2   119.01  3.000
 8LE  N6   C6   N1   119.37  3.000
 8LE  N1   C6   C5   118.20  3.000
 8LE  N6   C6   C5   122.42  3.000
 8LE  H20  N6   H19  117.55  3.000
 8LE  H20  N6   C6   119.53  3.000
 8LE  H19  N6   C6   120.09  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
 8LE  CONST_01  N9   C4   N3   C2   180.00   0.0  0
 8LE  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 8LE  CONST_03  C5   C6   N1   C2     0.00   0.0  0
 8LE  CONST_04  C5   N7   C8   N9     0.00   0.0  0
 8LE  CONST_05  N7   C5   C4   N9     0.00   0.0  0
 8LE  CONST_06  C6   C5   C4   N9   180.00   0.0  0
 8LE  CONST_07  C5   C4   N9   C8     0.00   0.0  0
 8LE  CONST_08  N3   C4   N9   C8   180.00   0.0  0
 8LE  CONST_09  C4   C5   N7   C8     0.00   0.0  0
 8LE  CONST_10  C6   C5   N7   C8   180.00   0.0  0
 8LE  CONST_11  C4   N9   C8   N7     0.00   0.0  0
 8LE  CONST_12  N3   C4   C5   N7   180.00   0.0  0
 8LE  CONST_13  N1   C6   C5   N7   180.00   0.0  0
 8LE  CONST_14  N1   C6   C5   C4     0.00   0.0  0
 8LE  CONST_15  N1   C2   N3   C4     0.00   0.0  0
 8LE  CONST_16  C6   C5   C4   N3     0.00   0.0  0
 8LE  CONST_17  C6   N1   C2   N3     0.00   0.0  0
 8LE  CONST_18  N7   C8   N9   C1'  180.00   0.0  0
 8LE  CONST_19  C5   C4   N9   C1'  180.00   0.0  0
 8LE  CONST_20  N3   C4   N9   C1'    0.00   0.0  0
 8LE  CONST_21  N6   C6   N1   C2   180.00   0.0  0
 8LE  CONST_22  N6   C6   C5   N7     0.00   0.0  0
 8LE  CONST_23  N6   C6   C5   C4   180.00   0.0  0
 8LE  CONST_24  H18  C8   N9   C1'    0.00   0.0  0
 8LE  CONST_25  H1   C2   N3   C4   180.00   0.0  0
 8LE  CONST_26  H19  N6   C6   C5     0.00   0.0  0
 8LE  CONST_27  H20  N6   C6   C5   180.00   0.0  0
 8LE  Var_01    C4'  C5'  O5'  PBC  -98.91  30.0  3
 8LE  Var_02    OAQ  CAS  CAZ  CAA  -74.54  30.0  2
 8LE  Var_03    OAE  PBC  OAQ  CAS  -53.92  30.0  2
 8LE  Var_04    H5   CAB  CAZ  CAA   61.35  30.0  3
 8LE  Var_05    H2   CAA  CAZ  CAB  -55.51  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
 8LE  chir_02  C4'  C5'  C3'  O4'  positiv
 8LE  chir_03  C3'  O3'  C2'  C4'  negativ
 8LE  chir_04  C2'  O2'  C1'  C3'  negativ
 8LE  chir_05  C1'  O4'  N9   C2'  negativ
 8LE  chir_06  PBC  OAI  O5'  OAQ  both

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
 8LE  plan-1  C2   0.020
 8LE  plan-1  C1'  0.020
 8LE  plan-1  N9   0.020
 8LE  plan-1  C8   0.020
 8LE  plan-1  N7   0.020
 8LE  plan-1  C5   0.020
 8LE  plan-1  C4   0.020
 8LE  plan-1  N3   0.020
 8LE  plan-1  N1   0.020
 8LE  plan-1  C6   0.020
 8LE  plan-1  N6   0.020
 8LE  plan-1  H1   0.020
 8LE  plan-1  H18  0.020
 8LE  plan-2  C6   0.020
 8LE  plan-2  N6   0.020
 8LE  plan-2  H19  0.020
 8LE  plan-2  H20  0.020
 8LE  plan-3  CAZ  0.020
 8LE  plan-3  CAS  0.020
 8LE  plan-3  OAD  0.020
 8LE  plan-3  OAQ  0.020

