# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jul 11 21:29:34 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: (2R,3R,4R,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-2,4-dihydroxytetrahydrofuran-3-yl acetate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)O[C@H]1[C@H](O)O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34)[C@H]1O
#
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
 ZOD  ZOD  '(2R,3R,4R,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-2,4-dihydroxytetrahydrofuran-3-yl acetate (non-preferred name)'  ligand  62  39  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ZOD
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
 ZOD  C01   C  CH3    0  -0.775   4.8668   3.3044   3.5833
 ZOD  C02   C  C      0   0.563   3.8540   2.3425   3.0406
 ZOD  O03   O  O      0  -0.439   3.1390   1.6372   3.7016
 ZOD  O04   O  O2     0  -0.471   3.8511   2.3642   1.7031
 ZOD  C05   C  CR15   0  -0.033   2.9567   1.5399   0.9788
 ZOD  C06   C  CR15   0   0.302   1.8296   2.3272   0.3288
 ZOD  O07   O  OH1    0  -0.687   0.8332   2.5986   1.2369
 ZOD  O08   O  O      0  -0.498   1.3829   1.4565  -0.6877
 ZOD  C09   C  CR15   0  -0.009   2.4497   0.6318  -1.1464
 ZOD  C10   C  CH2    0  -0.141   2.0377  -0.8248  -1.1532
 ZOD  O1B   O  O2     0  -0.606   1.0451  -1.0276  -2.1332
 ZOD  PB    P  P      0   1.380   0.7252  -2.5494  -2.6516
 ZOD  O2B   O  O      0  -0.790  -0.2628  -2.4246  -3.7627
 ZOD  O3B   O  OP    -1  -0.807   2.0144  -3.2908  -2.8425
 ZOD  O3A   O  O2     0  -0.742   0.0175  -3.1539  -1.3005
 ZOD  PA    P  P      0   1.369  -1.3263  -4.0693  -1.1559
 ZOD  O2A   O  OP    -1  -0.785  -2.5358  -3.3734  -1.7040
 ZOD  O1A   O  O      0  -0.793  -0.9988  -5.4682  -1.5728
 ZOD  O5'   O  O2     0  -0.615  -1.4053  -4.0946   0.4869
 ZOD  C5'   C  CH2    0  -0.166  -2.1932  -3.1866   1.2221
 ZOD  C4'   C  CH1    0  -0.020  -1.4014  -2.0011   1.7487
 ZOD  O4'   O  O2     0  -0.474  -0.9142  -1.1796   0.6853
 ZOD  C1'   C  CH1    0   0.228  -1.4876   0.0892   0.7378
 ZOD  N9    N  NR5    0  -0.539  -1.7686   0.5537  -0.6020
 ZOD  C8    C  CR15   0   0.092  -2.2109  -0.2043  -1.6532
 ZOD  N7    N  N      0  -0.472  -2.4961   0.5049  -2.7073
 ZOD  C5    C  CR56   0  -0.013  -2.2243   1.7948  -2.3380
 ZOD  C6    C  CR6    0   0.446  -2.3408   3.0191  -3.0175
 ZOD  N6    N  NH2    0  -0.818  -2.7803   3.1040  -4.2740
 ZOD  N1    N  N      0  -0.474  -1.9951   4.1395  -2.3700
 ZOD  C2    C  CR16   0   0.059  -1.5489   4.0464  -1.1240
 ZOD  N3    N  N      0  -0.536  -1.4033   2.9595  -0.3838
 ZOD  C4    C  CR56   0   0.555  -1.7605   1.8461  -1.0325
 ZOD  C2'   C  CH1    0  -0.044  -2.7453  -0.0722   1.5893
 ZOD  O2'   O  OH1    0  -0.654  -3.1356   1.1618   2.1159
 ZOD  C3'   C  CH1    0  -0.039  -2.2657  -1.0934   2.6211
 ZOD  O3'   O  OH1    0  -0.668  -1.4595  -0.4814   3.5954
 ZOD  C38   C  CR15   0  -0.058   3.6455   0.8962  -0.2190
 ZOD  O39   O  OH1    0  -0.665   4.5302   1.7747  -0.8675
 ZOD  H1    H  HCH3   0   0.263   4.8703   3.2789   4.6691
 ZOD  H10   H  HCH3   0   0.274   5.8631   3.0551   3.2171
 ZOD  H3    H  HCH3   0   0.275   4.6448   4.3186   3.2503
 ZOD  H4    H  HCR5   0   0.268   2.5201   0.7653   1.6149
 ZOD  H5    H  HCR5   0   0.188   2.2153   3.2563  -0.1253
 ZOD  H6    H  HOH1   0   0.475   0.0279   2.8980   0.7593
 ZOD  H7    H  HCR5   0   0.236   2.7279   0.9193  -2.1679
 ZOD  H11   H  HCH2   0   0.205   2.9299  -1.4210  -1.3726
 ZOD  H9    H  HCH2   0   0.217   1.6728  -1.1132  -0.1614
 ZOD  H5'1  H  HCH2   0   0.211  -3.0543  -2.8425   0.6401
 ZOD  H5'2  H  HCH2   0   0.228  -2.5846  -3.7278   2.0884
 ZOD  H4'   H  HCH1   0   0.247  -0.5430  -2.3724   2.3184
 ZOD  H1'   H  HCH1   0   0.252  -0.8111   0.8162   1.1944
 ZOD  H8    H  HCR5   0   0.330  -2.3008  -1.2819  -1.5880
 ZOD  HN61  H  HNH2   0   0.410  -3.0573   2.2828  -4.7823
 ZOD  HN62  H  HNH2   0   0.402  -2.8808   3.9996  -4.7191
 ZOD  H2    H  HCR6   0   0.255  -1.2666   4.9819  -0.6536
 ZOD  H2'   H  HCH1   0   0.244  -3.5387  -0.5257   0.9805
 ZOD  HO2'  H  HOH1   0   0.468  -4.0503   1.0990   2.4088
 ZOD  H3'   H  HCH1   0   0.243  -3.1027  -1.6389   3.0772
 ZOD  HO3'  H  HOH1   0   0.446  -1.8825   0.3480   3.8473
 ZOD  H24   H  HCR5   0   0.249   4.1516  -0.0344   0.0664
 ZOD  H25   H  HOH1   0   0.453   5.2636   1.9624  -0.2727

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
 ZOD  O2B  PB    deloc     1.492  0.020  1.492
 ZOD  O1B  PB    single    1.639  0.020  1.639
 ZOD  O1B  C10   single    1.410  0.020  1.410
 ZOD  O3B  PB    deloc     1.499  0.020  1.499
 ZOD  O3'  C3'   single    1.405  0.020  1.405
 ZOD  PB   O3A   single    1.641  0.020  1.641
 ZOD  C3'  C4'   single    1.527  0.020  1.527
 ZOD  C3'  C2'   single    1.529  0.020  1.529
 ZOD  C10  C09   single    1.514  0.020  1.514
 ZOD  C5'  O5'   single    1.409  0.020  1.409
 ZOD  C5'  C4'   single    1.520  0.020  1.520
 ZOD  C09  O08   single    1.424  0.020  1.424
 ZOD  C09  C38   single    1.536  0.020  1.536
 ZOD  O1A  PA    deloc     1.496  0.020  1.496
 ZOD  O3A  PA    single    1.632  0.020  1.632
 ZOD  O2'  C2'   single    1.397  0.020  1.397
 ZOD  O5'  PA    single    1.645  0.020  1.645
 ZOD  C4'  O4'   single    1.429  0.020  1.429
 ZOD  O08  C06   single    1.411  0.020  1.411
 ZOD  O39  C38   single    1.405  0.020  1.405
 ZOD  C2'  C1'   single    1.527  0.020  1.527
 ZOD  PA   O2A   deloc     1.499  0.020  1.499
 ZOD  C38  C05   single    1.524  0.020  1.524
 ZOD  C06  C05   single    1.521  0.020  1.521
 ZOD  C06  O07   single    1.375  0.020  1.375
 ZOD  O4'  C1'   single    1.393  0.020  1.393
 ZOD  C1'  N9    single    1.446  0.020  1.446
 ZOD  C05  O04   single    1.416  0.020  1.416
 ZOD  C01  C02   single    1.499  0.020  1.499
 ZOD  N9   C8    aromatic  1.369  0.020  1.369
 ZOD  N9   C4    aromatic  1.362  0.020  1.362
 ZOD  O04  C02   single    1.338  0.020  1.338
 ZOD  C02  O03   double    1.202  0.020  1.202
 ZOD  C8   N7    aromatic  1.302  0.020  1.302
 ZOD  C4   N3    aromatic  1.337  0.020  1.337
 ZOD  C4   C5    aromatic  1.386  0.020  1.386
 ZOD  N3   C2    aromatic  1.323  0.020  1.323
 ZOD  N7   C5    aromatic  1.369  0.020  1.369
 ZOD  C5   C6    aromatic  1.405  0.020  1.405
 ZOD  C2   N1    aromatic  1.327  0.020  1.327
 ZOD  N1   C6    aromatic  1.340  0.020  1.340
 ZOD  C6   N6    single    1.334  0.020  1.334
 ZOD  C01  H1    single    0.970  0.020  1.090
 ZOD  C01  H10   single    0.970  0.020  1.090
 ZOD  C01  H3    single    0.970  0.020  1.090
 ZOD  C05  H4    single    0.970  0.020  1.090
 ZOD  C06  H5    single    0.970  0.020  1.090
 ZOD  O07  H6    single    0.850  0.020  0.980
 ZOD  C09  H7    single    0.970  0.020  1.090
 ZOD  C10  H11   single    0.970  0.020  1.090
 ZOD  C10  H9    single    0.970  0.020  1.090
 ZOD  C5'  H5'1  single    0.970  0.020  1.090
 ZOD  C5'  H5'2  single    0.970  0.020  1.090
 ZOD  C4'  H4'   single    0.970  0.020  1.090
 ZOD  C1'  H1'   single    0.970  0.020  1.090
 ZOD  C8   H8    single    0.930  0.020  1.080
 ZOD  N6   HN61  single    0.860  0.020  1.020
 ZOD  N6   HN62  single    0.860  0.020  1.020
 ZOD  C2   H2    single    0.930  0.020  1.080
 ZOD  C2'  H2'   single    0.970  0.020  1.090
 ZOD  O2'  HO2'  single    0.850  0.020  0.980
 ZOD  C3'  H3'   single    0.970  0.020  1.090
 ZOD  O3'  HO3'  single    0.850  0.020  0.980
 ZOD  C38  H24   single    0.970  0.020  1.090
 ZOD  O39  H25   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
 ZOD  H3    C01  H10   107.23  3.000
 ZOD  H3    C01  H1    109.14  3.000
 ZOD  H10   C01  H1    109.11  3.000
 ZOD  H3    C01  C02   110.42  3.000
 ZOD  H10   C01  C02   110.44  3.000
 ZOD  H1    C01  C02   110.43  3.000
 ZOD  O04   C02  O03   123.91  3.000
 ZOD  O03   C02  C01   125.40  3.000
 ZOD  O04   C02  C01   110.68  3.000
 ZOD  C05   O04  C02   120.23  3.000
 ZOD  H4    C05  C38   109.79  3.000
 ZOD  H4    C05  C06   108.63  3.000
 ZOD  C38   C05  C06   102.57  3.000
 ZOD  H4    C05  O04   111.54  3.000
 ZOD  C06   C05  O04   112.67  3.000
 ZOD  C38   C05  O04   111.25  3.000
 ZOD  H5    C06  O08   109.49  3.000
 ZOD  H5    C06  O07   111.02  3.000
 ZOD  O08   C06  O07   111.60  3.000
 ZOD  H5    C06  C05   110.65  3.000
 ZOD  O07   C06  C05   110.91  3.000
 ZOD  O08   C06  C05   102.89  3.000
 ZOD  H6    O07  C06   109.45  3.000
 ZOD  C09   O08  C06   110.62  3.000
 ZOD  H7    C09  C38   108.64  3.000
 ZOD  H7    C09  C10   108.48  3.000
 ZOD  C38   C09  C10   112.34  3.000
 ZOD  H7    C09  O08   109.76  3.000
 ZOD  C38   C09  O08   106.80  3.000
 ZOD  C10   C09  O08   110.78  3.000
 ZOD  H9    C10  H11   108.02  3.000
 ZOD  H9    C10  O1B   110.92  3.000
 ZOD  H11   C10  O1B   110.86  3.000
 ZOD  H9    C10  C09   109.87  3.000
 ZOD  H11   C10  C09   107.64  3.000
 ZOD  O1B   C10  C09   109.47  3.000
 ZOD  PB    O1B  C10   119.40  3.000
 ZOD  O3A   PB   O3B   107.07  3.000
 ZOD  O3A   PB   O2B   111.01  3.000
 ZOD  O3B   PB   O2B   121.06  3.000
 ZOD  O3A   PB   O1B    99.55  3.000
 ZOD  O3B   PB   O1B   109.36  3.000
 ZOD  O2B   PB   O1B   106.68  3.000
 ZOD  PA    O3A  PB    129.40  3.000
 ZOD  O5'   PA   O1A   105.93  3.000
 ZOD  O5'   PA   O2A   109.48  3.000
 ZOD  O1A   PA   O2A   120.58  3.000
 ZOD  O2A   PA   O3A   111.81  3.000
 ZOD  O5'   PA   O3A    97.85  3.000
 ZOD  O1A   PA   O3A   108.63  3.000
 ZOD  C5'   O5'  PA    122.55  3.000
 ZOD  H5'2  C5'  H5'1  107.16  3.000
 ZOD  H5'2  C5'  C4'   107.33  3.000
 ZOD  H5'1  C5'  C4'   110.42  3.000
 ZOD  H5'2  C5'  O5'   107.13  3.000
 ZOD  H5'1  C5'  O5'   111.40  3.000
 ZOD  C4'   C5'  O5'   113.09  3.000
 ZOD  H4'   C4'  C3'   110.37  3.000
 ZOD  H4'   C4'  O4'   108.34  3.000
 ZOD  C3'   C4'  O4'   106.04  3.000
 ZOD  H4'   C4'  C5'   108.91  3.000
 ZOD  O4'   C4'  C5'   111.60  3.000
 ZOD  C3'   C4'  C5'   111.52  3.000
 ZOD  C1'   O4'  C4'   110.80  3.000
 ZOD  H1'   C1'  C2'   110.30  3.000
 ZOD  H1'   C1'  N9    107.08  3.000
 ZOD  C2'   C1'  N9    112.99  3.000
 ZOD  H1'   C1'  O4'   111.51  3.000
 ZOD  N9    C1'  O4'   109.74  3.000
 ZOD  C2'   C1'  O4'   105.29  3.000
 ZOD  C4    N9   C8    106.53  3.000
 ZOD  C4    N9   C1'   126.63  3.000
 ZOD  C8    N9   C1'   126.61  3.000
 ZOD  H8    C8   N7    124.91  3.000
 ZOD  H8    C8   N9    122.10  3.000
 ZOD  N7    C8   N9    112.99  3.000
 ZOD  C5    N7   C8    104.55  3.000
 ZOD  C4    C5   C6    116.80  3.000
 ZOD  C6    C5   N7    132.38  3.000
 ZOD  C4    C5   N7    110.81  3.000
 ZOD  N1    C6   N6    119.16  3.000
 ZOD  N6    C6   C5    122.58  3.000
 ZOD  N1    C6   C5    118.27  3.000
 ZOD  HN62  N6   HN61  118.47  3.000
 ZOD  HN62  N6   C6    120.45  3.000
 ZOD  HN61  N6   C6    121.02  3.000
 ZOD  C2    N1   C6    118.82  3.000
 ZOD  H2    C2   N3    115.93  3.000
 ZOD  H2    C2   N1    115.74  3.000
 ZOD  N3    C2   N1    128.32  3.000
 ZOD  C4    N3   C2    112.53  3.000
 ZOD  N3    C4   C5    125.24  3.000
 ZOD  C5    C4   N9    105.10  3.000
 ZOD  N3    C4   N9    129.66  3.000
 ZOD  H2'   C2'  C3'   108.96  3.000
 ZOD  H2'   C2'  O2'   111.83  3.000
 ZOD  C3'   C2'  O2'   115.04  3.000
 ZOD  H2'   C2'  C1'   109.24  3.000
 ZOD  O2'   C2'  C1'   110.29  3.000
 ZOD  C3'   C2'  C1'   100.87  3.000
 ZOD  HO2'  O2'  C2'   108.82  3.000
 ZOD  H3'   C3'  O3'   111.45  3.000
 ZOD  H3'   C3'  C2'   111.90  3.000
 ZOD  O3'   C3'  C2'   110.92  3.000
 ZOD  H3'   C3'  C4'   111.92  3.000
 ZOD  C2'   C3'  C4'   100.90  3.000
 ZOD  O3'   C3'  C4'   109.29  3.000
 ZOD  HO3'  O3'  C3'   107.70  3.000
 ZOD  H24   C38  O39   111.09  3.000
 ZOD  H24   C38  C09   111.73  3.000
 ZOD  O39   C38  C09   108.61  3.000
 ZOD  H24   C38  C05   111.24  3.000
 ZOD  O39   C38  C05   112.53  3.000
 ZOD  C09   C38  C05   101.26  3.000
 ZOD  H25   O39  C38   108.44  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
 ZOD  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 ZOD  CONST_02  C2    N3   C4   N9    180.00   0.0  0
 ZOD  CONST_03  N7    C5   C4   N9      0.00   0.0  0
 ZOD  CONST_04  C6    C5   C4   N9    180.00   0.0  0
 ZOD  CONST_05  N3    C4   N9   C8    180.00   0.0  0
 ZOD  CONST_06  C5    C4   N9   C8      0.00   0.0  0
 ZOD  CONST_07  C4    C5   N7   C8      0.00   0.0  0
 ZOD  CONST_08  C6    C5   N7   C8    180.00   0.0  0
 ZOD  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 ZOD  CONST_10  N3    C4   C5   N7    180.00   0.0  0
 ZOD  CONST_11  N1    C6   C5   N7    180.00   0.0  0
 ZOD  CONST_12  C2    N3   C4   C5      0.00   0.0  0
 ZOD  CONST_13  C2    N1   C6   C5      0.00   0.0  0
 ZOD  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 ZOD  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 ZOD  CONST_16  C4    N3   C2   N1      0.00   0.0  0
 ZOD  CONST_17  C4    C5   C6   N1      0.00   0.0  0
 ZOD  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 ZOD  CONST_19  N3    C4   N9   C1'     0.00   0.0  0
 ZOD  CONST_20  C5    C4   N9   C1'   180.00   0.0  0
 ZOD  CONST_21  N6    C6   C5   N7      0.00   0.0  0
 ZOD  CONST_22  C4    C5   C6   N6    180.00   0.0  0
 ZOD  CONST_23  C2    N1   C6   N6    180.00   0.0  0
 ZOD  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 ZOD  CONST_25  H2    C2   N1   C6    180.00   0.0  0
 ZOD  CONST_26  HN61  N6   C6   C5      0.00   0.0  0
 ZOD  CONST_27  HN62  N6   C6   C5    180.00   0.0  0
 ZOD  Var_01    C4'   C5'  O5'  PA    -97.27  30.0  2
 ZOD  Var_02    O2B   PB   O1B  C10  -174.78  30.0  3
 ZOD  Var_03    O1A   PA   O3A  PB     75.60  30.0  3
 ZOD  Var_04    H1    C01  C02  O03     0.07  30.0  3
 ZOD  Var_05    H11   C10  O1B  PB     44.11  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
 ZOD  chir_01  C05  C38  C06  O04  positiv
 ZOD  chir_02  C06  O08  O07  C05  negativ
 ZOD  chir_03  C09  O08  C38  C10  negativ
 ZOD  chir_06  C4'  C3'  C5'  O4'  negativ
 ZOD  chir_07  C1'  O4'  N9   C2'  negativ
 ZOD  chir_08  C2'  O2'  C1'  C3'  negativ
 ZOD  chir_09  C3'  O3'  C4'  C2'  positiv
 ZOD  chir_10  C38  C09  O39  C05  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
 ZOD  plan-1  C6    0.020
 ZOD  plan-1  N6    0.020
 ZOD  plan-1  HN61  0.020
 ZOD  plan-1  HN62  0.020
 ZOD  plan-2  C1'   0.020
 ZOD  plan-2  N9    0.020
 ZOD  plan-2  C8    0.020
 ZOD  plan-2  N7    0.020
 ZOD  plan-2  C5    0.020
 ZOD  plan-2  C6    0.020
 ZOD  plan-2  N6    0.020
 ZOD  plan-2  N1    0.020
 ZOD  plan-2  C2    0.020
 ZOD  plan-2  N3    0.020
 ZOD  plan-2  C4    0.020
 ZOD  plan-2  H8    0.020
 ZOD  plan-2  H2    0.020
 ZOD  plan-3  C01   0.020
 ZOD  plan-3  C02   0.020
 ZOD  plan-3  O03   0.020
 ZOD  plan-3  O04   0.020

