# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 14:34:46 2021
#   Inital geometry file: a 133 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~{S},4~{R})-4-oxidanylpyrrolidin-2-yl]methyl hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@@H]4C[C@@H](O)CN4)[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
 A3R  A3R  '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{S},4~{R})-4-oxidanylpyrrolidin-2-yl]methyl hydrogen phosphate'  ligand  58  34  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_A3R
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
 A3R  C3N  C  CH2   0  -0.520  -16.9777   3.2525  24.4661
 A3R  C2N  C  CH1   0   0.028  -18.4889   3.2143  24.2328
 A3R  O2N  O  OH1   0  -0.673  -19.2187   3.8271  25.2738
 A3R  C1N  C  CH2   0  -0.294  -18.6195   4.0698  22.9862
 A3R  N4N  N  NH1   0  -0.622  -17.7027   5.1672  23.2545
 A3R  C4N  C  CH1   0  -0.073  -16.5308   4.6324  23.9459
 A3R  C5N  C  CH2   0  -0.210  -15.3438   4.5311  23.0030
 A3R  O5N  O  O2    0  -0.568  -14.2207   4.0183  23.7435
 A3R  PB   P  P     0   1.476  -13.1075   3.1523  23.0283
 A3R  O2B  O  OH1   0  -0.711  -12.1375   2.8213  24.2325
 A3R  O1B  O  O     0  -0.687  -12.5271   3.6665  21.7779
 A3R  O3A  O  O2    0  -0.704  -13.9099   1.7490  22.8273
 A3R  PA   P  P     0   1.507  -13.4825   0.5557  21.8125
 A3R  O1A  O  O     0  -0.668  -12.0574   0.2083  21.8604
 A3R  O2A  O  OH1   0  -0.730  -14.5626  -0.5507  22.1676
 A3R  O5'  O  O2    0  -0.581  -13.9494   1.0363  20.3800
 A3R  C5'  C  CH2   0  -0.240  -15.2712   1.4862  20.0608
 A3R  C4'  C  CH1   0   0.022  -15.8417   0.6946  18.9124
 A3R  O4'  O  O2    0  -0.495  -15.0912   0.9296  17.7249
 A3R  C3'  C  CH1   0  -0.015  -15.8485  -0.8286  19.0640
 A3R  O3'  O  OH1   0  -0.661  -16.9083  -1.3178  19.8293
 A3R  C2'  C  CH1   0  -0.053  -15.9534  -1.2602  17.6035
 A3R  O2'  O  OH1   0  -0.661  -17.2439  -1.0730  17.0904
 A3R  C1'  C  CH1   0   0.181  -15.0504  -0.2212  16.9330
 A3R  N9   N  NR5   0  -0.537  -13.6719  -0.6830  16.8382
 A3R  C8   C  CR15  0   0.096  -12.5788  -0.2915  17.5634
 A3R  N7   N  N     0  -0.452  -11.4826  -0.8962  17.2063
 A3R  C5   C  CR56  0  -0.001  -11.8667  -1.7308  16.1906
 A3R  C4   C  CR56  0   0.486  -13.2249  -1.6110  15.9444
 A3R  N3   N  N     0  -0.459  -13.9288  -2.2723  15.0272
 A3R  C2   C  CR16  0   0.039  -13.1668  -3.1008  14.3343
 A3R  N1   N  N     0  -0.473  -11.8608  -3.3224  14.4586
 A3R  C6   C  CR6   0   0.456  -11.1686  -2.6488  15.3844
 A3R  N6   N  NH2   0  -0.816   -9.8564  -2.8599  15.5010
 A3R  H1   H  HCH2  0   0.234  -16.5133   2.4496  23.8873
 A3R  H2   H  HCH2  0   0.260  -16.7058   3.0818  25.5084
 A3R  H3   H  HCH1  0   0.222  -18.8378   2.1906  24.0532
 A3R  H4   H  HOH1  0   0.448  -19.0571   3.3326  26.0827
 A3R  H5   H  HCH2  0   0.238  -19.6383   4.4312  22.8292
 A3R  H6   H  HCH2  0   0.205  -18.3506   3.4631  22.1096
 A3R  H7   H  HNH1  0   0.356  -17.4672   5.6919  22.4227
 A3R  H9   H  HCH1  0   0.241  -16.2524   5.2918  24.7752
 A3R  H10  H  HCH2  0   0.227  -15.6011   3.8762  22.1631
 A3R  H11  H  HCH2  0   0.268  -15.0724   5.5086  22.5994
 A3R  H12  H  HOH1  0   0.514  -11.2331   3.1429  24.1136
 A3R  H13  H  HOH1  0   0.515  -14.4446  -1.0078  23.0128
 A3R  H14  H  HCH2  0   0.285  -15.2052   2.5439  19.8012
 A3R  H15  H  HCH2  0   0.253  -15.9544   1.3954  20.9094
 A3R  H16  H  HCH1  0   0.258  -16.8718   1.0487  18.7786
 A3R  H17  H  HCH1  0   0.244  -14.8808  -1.1748  19.4460
 A3R  H18  H  HOH1  0   0.463  -16.6317  -1.3761  20.7487
 A3R  H19  H  HCH1  0   0.269  -15.5923  -2.2819  17.4406
 A3R  H20  H  HOH1  0   0.461  -17.8579  -1.6120  17.6008
 A3R  H21  H  HCH1  0   0.286  -15.3893  -0.0028  15.9164
 A3R  H22  H  HCR5  0   0.299  -12.6452   0.4502  18.3417
 A3R  H23  H  HCR6  0   0.252  -13.6661  -3.6780  13.5636
 A3R  H24  H  HNH2  0   0.403   -9.4108  -3.5789  14.9574
 A3R  H25  H  HNH2  0   0.411   -9.3270  -2.4263  16.2367

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
 A3R  N1   C2   aromatic  1.330  0.020  1.330
 A3R  N1   C6   aromatic  1.338  0.020  1.338
 A3R  C2   N3   aromatic  1.322  0.020  1.322
 A3R  N6   C6   single    1.334  0.020  1.334
 A3R  C6   C5   aromatic  1.407  0.020  1.407
 A3R  N3   C4   aromatic  1.332  0.020  1.332
 A3R  C5   C4   aromatic  1.385  0.020  1.385
 A3R  C5   N7   aromatic  1.370  0.020  1.370
 A3R  C4   N9   aromatic  1.364  0.020  1.364
 A3R  N7   C8   aromatic  1.302  0.020  1.302
 A3R  N9   C1'  single    1.457  0.020  1.457
 A3R  N9   C8   aromatic  1.369  0.020  1.369
 A3R  O2'  C2'  single    1.401  0.020  1.401
 A3R  C1'  C2'  single    1.531  0.020  1.531
 A3R  C1'  O4'  single    1.398  0.020  1.398
 A3R  C2'  C3'  single    1.527  0.020  1.527
 A3R  O4'  C4'  single    1.424  0.020  1.424
 A3R  C4'  C3'  single    1.531  0.020  1.531
 A3R  C4'  C5'  single    1.507  0.020  1.507
 A3R  C3'  O3'  single    1.396  0.020  1.396
 A3R  C5'  O5'  single    1.432  0.020  1.432
 A3R  O5'  PA   single    1.582  0.020  1.582
 A3R  O1B  PB   double    1.471  0.020  1.471
 A3R  PA   O1A  double    1.468  0.020  1.468
 A3R  PA   O2A  single    1.586  0.020  1.586
 A3R  PA   O3A  single    1.624  0.020  1.624
 A3R  N4N  C1N  single    1.455  0.020  1.455
 A3R  N4N  C4N  single    1.462  0.020  1.462
 A3R  C5N  C4N  single    1.519  0.020  1.519
 A3R  C5N  O5N  single    1.440  0.020  1.440
 A3R  O3A  PB   single    1.629  0.020  1.629
 A3R  PB   O5N  single    1.581  0.020  1.581
 A3R  PB   O2B  single    1.581  0.020  1.581
 A3R  C1N  C2N  single    1.518  0.020  1.518
 A3R  C4N  C3N  single    1.541  0.020  1.541
 A3R  C3N  C2N  single    1.529  0.020  1.529
 A3R  C2N  O2N  single    1.411  0.020  1.411
 A3R  C3N  H1   single    0.970  0.020  1.090
 A3R  C3N  H2   single    0.970  0.020  1.090
 A3R  C2N  H3   single    0.970  0.020  1.090
 A3R  O2N  H4   single    0.850  0.020  0.980
 A3R  C1N  H5   single    0.970  0.020  1.090
 A3R  C1N  H6   single    0.970  0.020  1.090
 A3R  N4N  H7   single    0.890  0.020  1.040
 A3R  C4N  H9   single    0.970  0.020  1.090
 A3R  C5N  H10  single    0.970  0.020  1.090
 A3R  C5N  H11  single    0.970  0.020  1.090
 A3R  O2B  H12  single    0.850  0.020  0.980
 A3R  O2A  H13  single    0.850  0.020  0.980
 A3R  C5'  H14  single    0.970  0.020  1.090
 A3R  C5'  H15  single    0.970  0.020  1.090
 A3R  C4'  H16  single    0.970  0.020  1.090
 A3R  C3'  H17  single    0.970  0.020  1.090
 A3R  O3'  H18  single    0.850  0.020  0.980
 A3R  C2'  H19  single    0.970  0.020  1.090
 A3R  O2'  H20  single    0.850  0.020  0.980
 A3R  C1'  H21  single    0.970  0.020  1.090
 A3R  C8   H22  single    0.930  0.020  1.080
 A3R  C2   H23  single    0.930  0.020  1.080
 A3R  N6   H24  single    0.860  0.020  1.020
 A3R  N6   H25  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
 A3R  H2   C3N  H1   106.56  3.000
 A3R  H2   C3N  C4N  112.98  3.000
 A3R  H1   C3N  C4N  110.84  3.000
 A3R  H2   C3N  C2N  112.84  3.000
 A3R  H1   C3N  C2N  108.70  3.000
 A3R  C4N  C3N  C2N  104.92  3.000
 A3R  H3   C2N  C1N  111.37  3.000
 A3R  H3   C2N  O2N  111.20  3.000
 A3R  C1N  C2N  O2N  108.46  3.000
 A3R  H3   C2N  C3N  111.27  3.000
 A3R  O2N  C2N  C3N  112.81  3.000
 A3R  C1N  C2N  C3N  101.32  3.000
 A3R  H4   O2N  C2N  108.08  3.000
 A3R  H6   C1N  H5   107.22  3.000
 A3R  H6   C1N  N4N  114.15  3.000
 A3R  H5   C1N  N4N  111.39  3.000
 A3R  H6   C1N  C2N  108.83  3.000
 A3R  H5   C1N  C2N  112.63  3.000
 A3R  N4N  C1N  C2N  102.68  3.000
 A3R  H7   N4N  C4N  113.10  3.000
 A3R  H7   N4N  C1N  112.73  3.000
 A3R  C4N  N4N  C1N  108.44  3.000
 A3R  H9   C4N  C5N  108.14  3.000
 A3R  H9   C4N  N4N  109.97  3.000
 A3R  C5N  C4N  N4N  110.92  3.000
 A3R  H9   C4N  C3N  110.93  3.000
 A3R  C5N  C4N  C3N  112.11  3.000
 A3R  N4N  C4N  C3N  104.76  3.000
 A3R  H11  C5N  H10  108.06  3.000
 A3R  H11  C5N  O5N  108.37  3.000
 A3R  H10  C5N  O5N  111.38  3.000
 A3R  H11  C5N  C4N  111.34  3.000
 A3R  H10  C5N  C4N  109.39  3.000
 A3R  O5N  C5N  C4N  108.31  3.000
 A3R  PB   O5N  C5N  120.77  3.000
 A3R  O3A  PB   O1B  112.98  3.000
 A3R  O3A  PB   O2B  102.46  3.000
 A3R  O1B  PB   O2B  118.58  3.000
 A3R  O2B  PB   O5N  101.66  3.000
 A3R  O3A  PB   O5N  100.42  3.000
 A3R  O1B  PB   O5N  118.07  3.000
 A3R  H12  O2B  PB   114.22  3.000
 A3R  PA   O3A  PB   125.49  3.000
 A3R  O5'  PA   O2A  102.34  3.000
 A3R  O2A  PA   O1A  119.26  3.000
 A3R  O5'  PA   O1A  112.84  3.000
 A3R  O2A  PA   O3A  101.15  3.000
 A3R  O1A  PA   O3A  114.15  3.000
 A3R  O5'  PA   O3A  105.37  3.000
 A3R  H13  O2A  PA   116.21  3.000
 A3R  C5'  O5'  PA   124.73  3.000
 A3R  H15  C5'  H14  107.64  3.000
 A3R  H15  C5'  C4'  108.14  3.000
 A3R  H14  C5'  C4'  110.54  3.000
 A3R  H15  C5'  O5'  112.19  3.000
 A3R  H14  C5'  O5'  107.56  3.000
 A3R  C4'  C5'  O5'  110.74  3.000
 A3R  H16  C4'  C3'  109.20  3.000
 A3R  H16  C4'  O4'  109.86  3.000
 A3R  C3'  C4'  O4'  104.42  3.000
 A3R  H16  C4'  C5'  106.19  3.000
 A3R  C3'  C4'  C5'  116.68  3.000
 A3R  O4'  C4'  C5'  110.44  3.000
 A3R  C1'  O4'  C4'  110.61  3.000
 A3R  H17  C3'  C2'  107.74  3.000
 A3R  H17  C3'  O3'  111.62  3.000
 A3R  C2'  C3'  O3'  111.92  3.000
 A3R  H17  C3'  C4'  110.16  3.000
 A3R  O3'  C3'  C4'  113.98  3.000
 A3R  C2'  C3'  C4'  100.77  3.000
 A3R  H18  O3'  C3'  109.09  3.000
 A3R  H19  C2'  C1'  111.91  3.000
 A3R  H19  C2'  O2'  111.94  3.000
 A3R  C1'  C2'  O2'  106.99  3.000
 A3R  H19  C2'  C3'  112.53  3.000
 A3R  C1'  C2'  C3'  100.76  3.000
 A3R  O2'  C2'  C3'  112.07  3.000
 A3R  H20  O2'  C2'  108.56  3.000
 A3R  H21  C1'  N9   107.22  3.000
 A3R  H21  C1'  C2'  111.09  3.000
 A3R  N9   C1'  C2'  111.80  3.000
 A3R  H21  C1'  O4'  110.68  3.000
 A3R  C2'  C1'  O4'  107.06  3.000
 A3R  N9   C1'  O4'  108.99  3.000
 A3R  C4   N9   C8   106.26  3.000
 A3R  C8   N9   C1'  129.09  3.000
 A3R  C4   N9   C1'  124.64  3.000
 A3R  H22  C8   N7   124.75  3.000
 A3R  H22  C8   N9   122.03  3.000
 A3R  N7   C8   N9   113.22  3.000
 A3R  C5   N7   C8   104.50  3.000
 A3R  C6   C5   C4   116.17  3.000
 A3R  C4   C5   N7   110.73  3.000
 A3R  C6   C5   N7   133.10  3.000
 A3R  N3   C4   C5   126.69  3.000
 A3R  C5   C4   N9   105.29  3.000
 A3R  N3   C4   N9   128.02  3.000
 A3R  C2   N3   C4   111.56  3.000
 A3R  H23  C2   N1   115.45  3.000
 A3R  H23  C2   N3   116.15  3.000
 A3R  N1   C2   N3   128.41  3.000
 A3R  C6   N1   C2   119.25  3.000
 A3R  N6   C6   N1   119.32  3.000
 A3R  N6   C6   C5   122.76  3.000
 A3R  N1   C6   C5   117.92  3.000
 A3R  H25  N6   H24  118.10  3.000
 A3R  H25  N6   C6   120.92  3.000
 A3R  H24  N6   C6   120.12  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
 A3R  CONST_01  C2   N3   C4   N9    180.00   0.0  0
 A3R  CONST_02  C6   C5   C4   N9    180.00   0.0  0
 A3R  CONST_03  N7   C5   C4   N9      0.00   0.0  0
 A3R  CONST_04  C5   N7   C8   N9      0.00   0.0  0
 A3R  CONST_05  C6   C5   N7   C8    180.00   0.0  0
 A3R  CONST_06  C4   C5   N7   C8      0.00   0.0  0
 A3R  CONST_07  N3   C4   N9   C8    180.00   0.0  0
 A3R  CONST_08  C5   C4   N9   C8      0.00   0.0  0
 A3R  CONST_09  N1   C6   C5   N7    180.00   0.0  0
 A3R  CONST_10  N3   C4   C5   N7    180.00   0.0  0
 A3R  CONST_11  C4   N9   C8   N7      0.00   0.0  0
 A3R  CONST_12  C2   N1   C6   C5      0.00   0.0  0
 A3R  CONST_13  C2   N3   C4   C5      0.00   0.0  0
 A3R  CONST_14  N1   C2   N3   C4      0.00   0.0  0
 A3R  CONST_15  N1   C6   C5   C4      0.00   0.0  0
 A3R  CONST_16  C6   N1   C2   N3      0.00   0.0  0
 A3R  CONST_17  C6   C5   C4   N3      0.00   0.0  0
 A3R  CONST_18  N3   C4   N9   C1'     0.00   0.0  0
 A3R  CONST_19  C5   C4   N9   C1'   180.00   0.0  0
 A3R  CONST_20  N7   C8   N9   C1'   180.00   0.0  0
 A3R  CONST_21  N6   C6   C5   N7      0.00   0.0  0
 A3R  CONST_22  N6   C6   C5   C4    180.00   0.0  0
 A3R  CONST_23  N6   C6   N1   C2    180.00   0.0  0
 A3R  CONST_24  H22  C8   N9   C1'     0.00   0.0  0
 A3R  CONST_25  H23  C2   N3   C4    180.00   0.0  0
 A3R  CONST_26  H24  N6   C6   C5    180.00   0.0  0
 A3R  CONST_27  H25  N6   C6   C5      0.00   0.0  0
 A3R  Var_01    C4N  N4N  C1N  C2N    37.61  30.0  1
 A3R  Var_02    C4'  C5'  O5'  PA   -124.98  30.0  1
 A3R  Var_03    O1B  PB   O5N  C5N    49.27  30.0  1
 A3R  Var_04    O5'  PA   O3A  PB    -78.36  30.0  2
 A3R  Var_05    H10  C5N  O5N  PB     29.66  30.0  2

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
 A3R  chir_01  C2N  C1N  C3N  O2N  negativ
 A3R  chir_02  C4N  N4N  C5N  C3N  positiv
 A3R  chir_05  C4'  O4'  C3'  C5'  negativ
 A3R  chir_06  C3'  O3'  C4'  C2'  positiv
 A3R  chir_07  C2'  O2'  C3'  C1'  positiv
 A3R  chir_08  C1'  O4'  N9   C2'  negativ
 A3R  chir_09  PB   O3A  O5N  O2B  both
 A3R  chir_10  PA   O2A  O1A  O5'  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
 A3R  plan-1  C6   0.020
 A3R  plan-1  N6   0.020
 A3R  plan-1  H24  0.020
 A3R  plan-1  H25  0.020
 A3R  plan-2  C1'  0.020
 A3R  plan-2  N9   0.020
 A3R  plan-2  C8   0.020
 A3R  plan-2  N7   0.020
 A3R  plan-2  C5   0.020
 A3R  plan-2  C4   0.020
 A3R  plan-2  N3   0.020
 A3R  plan-2  C2   0.020
 A3R  plan-2  N1   0.020
 A3R  plan-2  C6   0.020
 A3R  plan-2  N6   0.020
 A3R  plan-2  H22  0.020
 A3R  plan-2  H23  0.020

