# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun May 24 14:30:26 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S)-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
#   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]4OCC[C@@H]4O)[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
 2RW  2RW  '[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S)-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  55  34  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2RW
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
 2RW  N1   N  N      0  -0.476   2.2890  -4.1544   1.1660
 2RW  C2   C  CR16   0   0.040   3.1743  -3.3179   1.7007
 2RW  N3   N  N      0  -0.458   3.2535  -2.0058   1.5623
 2RW  C4   C  CR56   0   0.479   2.3028  -1.5378   0.7565
 2RW  C5   C  CR56   0   0.011   1.3319  -2.2861   0.1086
 2RW  C6   C  CR6    0   0.443   1.3311  -3.6684   0.3663
 2RW  N6   N  NH2    0  -0.842   0.4299  -4.5067  -0.1559
 2RW  N7   N  N      0  -0.461   0.5168  -1.4765  -0.6374
 2RW  C8   C  CR15   0   0.087   0.9664  -0.2731  -0.4370
 2RW  N9   N  NR5    0  -0.544   2.0562  -0.2440   0.3955
 2RW  C1'  C  CH1    0   0.222   2.7786   0.9181   0.8483
 2RW  C2'  C  CH1    0  -0.051   3.6063   1.6074  -0.2369
 2RW  O2'  O  OH1    0  -0.654   4.8510   0.9861  -0.3536
 2RW  C3'  C  CH1    0  -0.033   3.6471   3.0443   0.2951
 2RW  O3'  O  OH1    0  -0.669   4.5750   3.1624   1.3419
 2RW  O4'  O  O2     0  -0.487   1.8686   1.8758   1.3028
 2RW  C4'  C  CH1    0  -0.042   2.2402   3.1825   0.8593
 2RW  C5'  C  CH2    0  -0.146   1.2650   3.6958  -0.1864
 2RW  O5'  O  O2     0  -0.617  -0.0452   3.5971   0.3145
 2RW  PA   P  P      0   1.358  -1.2764   3.2657  -0.7329
 2RW  O1A  O  OP    -1  -0.782  -0.8621   2.1641  -1.6611
 2RW  O2A  O  O      0  -0.791  -1.8018   4.5520  -1.2882
 2RW  O3A  O  O2     0  -0.733  -2.2738   2.7275   0.4505
 2RW  PB   P  P      0   1.357  -3.6458   1.8548   0.2306
 2RW  O1B  O  O      0  -0.808  -4.2128   2.0820  -1.1354
 2RW  O2B  O  OP    -1  -0.791  -4.4788   2.0895   1.4522
 2RW  O5D  O  O2     0  -0.610  -2.9698   0.3648   0.3204
 2RW  C5D  C  CH2    0  -0.143  -3.6195  -0.7267  -0.2912
 2RW  O4D  O  O2     0  -0.504  -2.6153  -2.2379   1.2928
 2RW  C1D  C  CH2    0  -0.160  -3.0065  -3.5704   1.5645
 2RW  C2D  C  CH2    0  -0.517  -3.9959  -3.9160   0.4668
 2RW  O3D  O  OH1    0  -0.671  -2.3415  -3.9538  -1.3373
 2RW  C3D  C  CH1    0  -0.012  -3.3834  -3.2050  -0.7341
 2RW  C4D  C  CH1    0  -0.033  -2.7627  -1.9587  -0.0959
 2RW  H1   H  HCR6   0   0.248   3.9222  -3.7768   2.3389
 2RW  H2   H  HNH2   0   0.393   0.4161  -5.4576   0.1728
 2RW  H3   H  HNH2   0   0.418  -0.4149  -4.1627  -0.5949
 2RW  H4   H  HCR5   0   0.324   0.5162   0.6248  -0.8453
 2RW  H5   H  HCH1   0   0.256   3.4346   0.5691   1.6538
 2RW  H6   H  HCH1   0   0.248   3.0567   1.5912  -1.1864
 2RW  H7   H  HOH1   0   0.469   5.2321   1.2105  -1.2083
 2RW  H8   H  HCH1   0   0.251   3.8392   3.7736  -0.5037
 2RW  H9   H  HOH1   0   0.449   5.3937   2.7375   1.0604
 2RW  H10  H  HCH1   0   0.259   2.2290   3.8516   1.7253
 2RW  H11  H  HCH2   0   0.224   1.5244   4.7380  -0.4081
 2RW  H12  H  HCH2   0   0.205   1.3771   3.1328  -1.1194
 2RW  H15  H  HCH2   0   0.195  -4.6210  -0.8906   0.1319
 2RW  H16  H  HCH2   0   0.205  -3.7441  -0.5582  -1.3659
 2RW  H19  H  HCH2   0   0.255  -4.1284  -4.9883   0.3142
 2RW  H20  H  HCH2   0   0.242  -4.9765  -3.4869   0.6859
 2RW  H21  H  HOH1   0   0.457  -2.7041  -4.7923  -1.6418
 2RW  H22  H  HCH1   0   0.237  -4.1403  -2.9474  -1.4846
 2RW  H23  H  HCH1   0   0.278  -1.7764  -1.7682  -0.5320
 2RW  H17  H  HCH2   0   0.196  -2.1431  -4.2478   1.5422
 2RW  H18  H  HCH2   0   0.228  -3.4389  -3.6163   2.5660

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
 2RW  C1D  C2D  single    1.518  0.020  1.518
 2RW  C1D  O4D  single    1.415  0.020  1.415
 2RW  C2D  C3D  single    1.524  0.020  1.524
 2RW  O3D  C3D  single    1.418  0.020  1.418
 2RW  O4D  C4D  single    1.424  0.020  1.424
 2RW  C3D  C4D  single    1.532  0.020  1.532
 2RW  C4D  C5D  single    1.513  0.020  1.513
 2RW  C5D  O5D  single    1.410  0.020  1.410
 2RW  O3'  C3'  single    1.404  0.020  1.404
 2RW  O5D  PB   single    1.639  0.020  1.639
 2RW  C4'  C5'  single    1.519  0.020  1.519
 2RW  C4'  O4'  single    1.429  0.020  1.429
 2RW  C4'  C3'  single    1.522  0.020  1.522
 2RW  C5'  O5'  single    1.406  0.020  1.406
 2RW  O4'  C1'  single    1.397  0.020  1.397
 2RW  C3'  C2'  single    1.533  0.020  1.533
 2RW  O5'  PA   single    1.650  0.020  1.650
 2RW  PB   O1B  deloc     1.496  0.020  1.496
 2RW  PB   O3A  single    1.641  0.020  1.641
 2RW  PB   O2B  deloc     1.497  0.020  1.497
 2RW  C1'  C2'  single    1.529  0.020  1.529
 2RW  C1'  N9   single    1.441  0.020  1.441
 2RW  O3A  PA   single    1.639  0.020  1.639
 2RW  C2'  O2'  single    1.396  0.020  1.396
 2RW  N3   C2   aromatic  1.322  0.020  1.322
 2RW  N3   C4   aromatic  1.331  0.020  1.331
 2RW  O2A  PA   deloc     1.496  0.020  1.496
 2RW  PA   O1A  deloc     1.499  0.020  1.499
 2RW  C2   N1   aromatic  1.330  0.020  1.330
 2RW  C4   N9   aromatic  1.366  0.020  1.366
 2RW  C4   C5   aromatic  1.386  0.020  1.386
 2RW  N9   C8   aromatic  1.372  0.020  1.372
 2RW  N1   C6   aromatic  1.339  0.020  1.339
 2RW  C8   N7   aromatic  1.300  0.020  1.300
 2RW  C5   C6   aromatic  1.406  0.020  1.406
 2RW  C5   N7   aromatic  1.370  0.020  1.370
 2RW  C6   N6   single    1.337  0.020  1.337
 2RW  C2   H1   single    0.930  0.020  1.080
 2RW  N6   H2   single    0.890  0.020  1.040
 2RW  N6   H3   single    0.890  0.020  1.040
 2RW  C8   H4   single    0.930  0.020  1.080
 2RW  C1'  H5   single    0.970  0.020  1.090
 2RW  C2'  H6   single    0.970  0.020  1.090
 2RW  O2'  H7   single    0.850  0.020  0.980
 2RW  C3'  H8   single    0.970  0.020  1.090
 2RW  O3'  H9   single    0.850  0.020  0.980
 2RW  C4'  H10  single    0.970  0.020  1.090
 2RW  C5'  H11  single    0.970  0.020  1.090
 2RW  C5'  H12  single    0.970  0.020  1.090
 2RW  C5D  H15  single    0.970  0.020  1.090
 2RW  C5D  H16  single    0.970  0.020  1.090
 2RW  C1D  H17  single    0.970  0.020  1.090
 2RW  C1D  H18  single    0.970  0.020  1.090
 2RW  C2D  H19  single    0.970  0.020  1.090
 2RW  C2D  H20  single    0.970  0.020  1.090
 2RW  O3D  H21  single    0.850  0.020  0.980
 2RW  C3D  H22  single    0.970  0.020  1.090
 2RW  C4D  H23  single    0.970  0.020  1.090

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
 2RW  C6   N1   C2   119.20  3.000
 2RW  H1   C2   N3   116.11  3.000
 2RW  H1   C2   N1   115.42  3.000
 2RW  N3   C2   N1   128.47  3.000
 2RW  C4   N3   C2   111.69  3.000
 2RW  N9   C4   C5   105.15  3.000
 2RW  C5   C4   N3   126.38  3.000
 2RW  N9   C4   N3   128.47  3.000
 2RW  N7   C5   C6   132.88  3.000
 2RW  N7   C5   C4   110.62  3.000
 2RW  C6   C5   C4   116.45  3.000
 2RW  N6   C6   C5   123.04  3.000
 2RW  N6   C6   N1   119.20  3.000
 2RW  C5   C6   N1   117.76  3.000
 2RW  H3   N6   H2   116.83  3.000
 2RW  H3   N6   C6   121.25  3.000
 2RW  H2   N6   C6   118.31  3.000
 2RW  C8   N7   C5   104.91  3.000
 2RW  H4   C8   N9   122.74  3.000
 2RW  H4   C8   N7   124.39  3.000
 2RW  N9   C8   N7   112.82  3.000
 2RW  C1'  N9   C8   127.30  3.000
 2RW  C8   N9   C4   106.49  3.000
 2RW  C1'  N9   C4   126.18  3.000
 2RW  H5   C1'  O4'  111.66  3.000
 2RW  H5   C1'  C2'  109.96  3.000
 2RW  O4'  C1'  C2'  105.93  3.000
 2RW  H5   C1'  N9   105.91  3.000
 2RW  C2'  C1'  N9   114.32  3.000
 2RW  O4'  C1'  N9   109.17  3.000
 2RW  H6   C2'  C3'  109.12  3.000
 2RW  H6   C2'  O2'  111.57  3.000
 2RW  C3'  C2'  O2'  114.99  3.000
 2RW  H6   C2'  C1'  109.66  3.000
 2RW  O2'  C2'  C1'  109.96  3.000
 2RW  C3'  C2'  C1'  101.00  3.000
 2RW  H7   O2'  C2'  108.88  3.000
 2RW  H8   C3'  C4'  111.77  3.000
 2RW  H8   C3'  O3'  111.76  3.000
 2RW  C4'  C3'  O3'  109.08  3.000
 2RW  H8   C3'  C2'  112.00  3.000
 2RW  C4'  C3'  C2'  100.90  3.000
 2RW  O3'  C3'  C2'  110.81  3.000
 2RW  H9   O3'  C3'  107.84  3.000
 2RW  C4'  O4'  C1'  110.88  3.000
 2RW  H10  C4'  C5'  109.36  3.000
 2RW  H10  C4'  O4'  108.11  3.000
 2RW  C5'  C4'  O4'  110.83  3.000
 2RW  H10  C4'  C3'  111.00  3.000
 2RW  O4'  C4'  C3'  105.80  3.000
 2RW  C5'  C4'  C3'  111.65  3.000
 2RW  H12  C5'  H11  106.98  3.000
 2RW  H12  C5'  O5'  111.26  3.000
 2RW  H11  C5'  O5'  111.04  3.000
 2RW  H12  C5'  C4'  110.30  3.000
 2RW  H11  C5'  C4'  107.96  3.000
 2RW  O5'  C5'  C4'  109.22  3.000
 2RW  PA   O5'  C5'  118.90  3.000
 2RW  O3A  PA   O2A  109.67  3.000
 2RW  O2A  PA   O1A  119.93  3.000
 2RW  O3A  PA   O1A  111.97  3.000
 2RW  O1A  PA   O5'  109.54  3.000
 2RW  O2A  PA   O5'  108.96  3.000
 2RW  O3A  PA   O5'   93.54  3.000
 2RW  PB   O3A  PA   125.94  3.000
 2RW  O5D  PB   O2B  109.11  3.000
 2RW  O2B  PB   O1B  120.68  3.000
 2RW  O5D  PB   O1B  110.14  3.000
 2RW  O2B  PB   O3A  105.81  3.000
 2RW  O1B  PB   O3A  111.00  3.000
 2RW  O5D  PB   O3A   97.55  3.000
 2RW  C5D  O5D  PB   119.34  3.000
 2RW  H16  C5D  H15  107.27  3.000
 2RW  H16  C5D  C4D  108.45  3.000
 2RW  H15  C5D  C4D  110.17  3.000
 2RW  H16  C5D  O5D  111.05  3.000
 2RW  H15  C5D  O5D  111.61  3.000
 2RW  C4D  C5D  O5D  108.26  3.000
 2RW  C4D  O4D  C1D  110.07  3.000
 2RW  H18  C1D  H17  107.71  3.000
 2RW  H18  C1D  C2D  113.31  3.000
 2RW  H17  C1D  C2D  110.95  3.000
 2RW  H18  C1D  O4D  108.98  3.000
 2RW  H17  C1D  O4D  111.09  3.000
 2RW  C2D  C1D  O4D  104.82  3.000
 2RW  H20  C2D  H19  107.76  3.000
 2RW  H20  C2D  C3D  109.60  3.000
 2RW  H19  C2D  C3D  113.40  3.000
 2RW  H20  C2D  C1D  110.53  3.000
 2RW  H19  C2D  C1D  113.84  3.000
 2RW  C3D  C2D  C1D  101.64  3.000
 2RW  H21  O3D  C3D  108.53  3.000
 2RW  H22  C3D  C4D  111.95  3.000
 2RW  H22  C3D  O3D  109.88  3.000
 2RW  C4D  C3D  O3D  108.01  3.000
 2RW  H22  C3D  C2D  111.81  3.000
 2RW  C4D  C3D  C2D  102.37  3.000
 2RW  O3D  C3D  C2D  112.59  3.000
 2RW  H23  C4D  C3D  109.91  3.000
 2RW  H23  C4D  O4D  109.23  3.000
 2RW  C3D  C4D  O4D  106.78  3.000
 2RW  H23  C4D  C5D  108.48  3.000
 2RW  C3D  C4D  C5D  112.28  3.000
 2RW  O4D  C4D  C5D  110.12  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
 2RW  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 2RW  CONST_02  C4   C5   C6   N1     0.00   0.0  0
 2RW  CONST_03  N7   C5   C6   N1   180.00   0.0  0
 2RW  CONST_04  N9   C4   N3   C2   180.00   0.0  0
 2RW  CONST_05  C5   C4   N3   C2     0.00   0.0  0
 2RW  CONST_06  C5   C6   N1   C2     0.00   0.0  0
 2RW  CONST_07  C6   N1   C2   N3     0.00   0.0  0
 2RW  CONST_08  C8   N9   C4   N3   180.00   0.0  0
 2RW  CONST_09  C6   C5   C4   N3     0.00   0.0  0
 2RW  CONST_10  N7   C5   C4   N3   180.00   0.0  0
 2RW  CONST_11  N7   C8   N9   C4     0.00   0.0  0
 2RW  CONST_12  C8   N7   C5   C4     0.00   0.0  0
 2RW  CONST_13  C8   N9   C4   C5     0.00   0.0  0
 2RW  CONST_14  N9   C8   N7   C5     0.00   0.0  0
 2RW  CONST_15  N9   C4   C5   C6   180.00   0.0  0
 2RW  CONST_16  C8   N7   C5   C6   180.00   0.0  0
 2RW  CONST_17  N9   C4   C5   N7     0.00   0.0  0
 2RW  CONST_18  C1'  N9   C4   N3     0.00   0.0  0
 2RW  CONST_19  C1'  N9   C4   C5   180.00   0.0  0
 2RW  CONST_20  C1'  N9   C8   N7   180.00   0.0  0
 2RW  CONST_21  N6   C6   N1   C2   180.00   0.0  0
 2RW  CONST_22  N6   C6   C5   C4   180.00   0.0  0
 2RW  CONST_23  N7   C5   C6   N6     0.00   0.0  0
 2RW  CONST_24  H1   C2   N3   C4   180.00   0.0  0
 2RW  CONST_25  H4   C8   N9   C4   180.00   0.0  0
 2RW  CONST_26  H2   N6   C6   N1     0.00   0.0  0
 2RW  CONST_27  H3   N6   C6   N1   180.00   0.0  0
 2RW  Var_01    C3D  C2D  C1D  O4D   37.29  30.0  1
 2RW  Var_02    C4D  C5D  O5D  PB   178.14  30.0  1
 2RW  Var_03    O3A  PA   O5'  C5'  159.34  30.0  3
 2RW  Var_04    O5D  PB   O3A  PA    90.71  30.0  2
 2RW  Var_05    H11  C5'  O5'  PA    94.60  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
 2RW  chir_01  C1'  O4'  C2'  N9   positiv
 2RW  chir_02  C2'  O2'  C1'  C3'  negativ
 2RW  chir_03  C3'  O3'  C4'  C2'  positiv
 2RW  chir_04  C4'  O4'  C3'  C5'  negativ
 2RW  chir_07  C3D  C2D  O3D  C4D  positiv
 2RW  chir_08  C4D  O4D  C3D  C5D  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
 2RW  plan-1  C6   0.020
 2RW  plan-1  N6   0.020
 2RW  plan-1  H2   0.020
 2RW  plan-1  H3   0.020
 2RW  plan-2  N1   0.020
 2RW  plan-2  C2   0.020
 2RW  plan-2  N3   0.020
 2RW  plan-2  C4   0.020
 2RW  plan-2  C5   0.020
 2RW  plan-2  C6   0.020
 2RW  plan-2  N6   0.020
 2RW  plan-2  N7   0.020
 2RW  plan-2  C8   0.020
 2RW  plan-2  N9   0.020
 2RW  plan-2  C1'  0.020
 2RW  plan-2  H1   0.020
 2RW  plan-2  H4   0.020

