# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 17:32:18 2021
#   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  57  34  .  2021-08-04  2022-11-17
;
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  -0.472  -4.9153  -0.2667  41.4383
 2RW  C2   C  CR16  0   0.044  -3.8076  -0.6067  40.7853
 2RW  N3   N  N     0  -0.458  -3.0195  -1.6486  40.9921
 2RW  C4   C  CR56  0   0.493  -3.4531  -2.4005  41.9995
 2RW  C5   C  CR56  0  -0.002  -4.5780  -2.1731  42.7723
 2RW  C6   C  CR6   0   0.458  -5.3385  -1.0353  42.4485
 2RW  N6   N  NH2   0  -0.816  -6.4497  -0.6999  43.1043
 2RW  N7   N  N     0  -0.440  -4.7395  -3.1660  43.7045
 2RW  C8   C  CR15  0   0.115  -3.7408  -3.9686  43.5003
 2RW  N9   N  NR5   0  -0.553  -2.9096  -3.5587  42.4867
 2RW  C1'  C  CR15  0   0.228  -1.7720  -4.2370  41.9341
 2RW  C2'  C  CR15  0  -0.059  -0.8411  -4.8697  42.9685
 2RW  O2'  O  OH1   0  -0.653   0.0691  -3.9136  43.4241
 2RW  C3'  C  CR15  0  -0.031  -0.2126  -6.0060  42.1537
 2RW  O3'  O  OH1   0  -0.667   0.8102  -5.5122  41.3282
 2RW  O4'  O  O     0  -0.510  -2.2046  -5.2925  41.1107
 2RW  C4'  C  CR15  0  -0.015  -1.3657  -6.4398  41.2518
 2RW  C5'  C  CH2   0  -0.197  -2.1711  -7.6253  41.7241
 2RW  O5'  O  O2    0  -0.586  -2.6514  -7.3818  43.0554
 2RW  PA   P  P     0   1.496  -3.8022  -8.2750  43.6847
 2RW  O1A  O  OH1   0  -0.709  -3.2873  -8.3778  45.1771
 2RW  O2A  O  O     0  -0.676  -4.1617  -9.5084  42.9686
 2RW  O3A  O  O2    0  -0.710  -4.9928  -7.1745  43.7544
 2RW  PB   P  P     0   1.508  -6.5944  -7.1868  43.9738
 2RW  O1B  O  O     0  -0.662  -7.0449  -6.2142  44.9758
 2RW  O2B  O  OH1   0  -0.740  -6.8181  -8.7331  44.2654
 2RW  O5D  O  O2    0  -0.573  -7.1841  -6.8569  42.5415
 2RW  C5D  C  CH2   0  -0.242  -6.9467  -7.6523  41.3694
 2RW  O4D  O  O2    0  -0.503  -7.7403  -5.9672  39.8731
 2RW  C1D  C  CH2   0  -0.167  -7.3198  -4.6433  39.5938
 2RW  C2D  C  CH2   0  -0.496  -6.1272  -4.4267  40.5062
 2RW  O3D  O  OH1   0  -0.687  -4.5250  -5.9048  39.3864
 2RW  C3D  C  CH1   0  -0.042  -5.4358  -5.7883  40.4557
 2RW  C4D  C  CH1   0   0.042  -6.6117  -6.7546  40.2020
 2RW  H1   H  HCR6  0   0.254  -3.5186   0.0584  39.9784
 2RW  H2   H  HNH2  0   0.404  -6.9974   0.0870  42.8016
 2RW  H3   H  HNH2  0   0.412  -6.8218  -1.2879  43.8292
 2RW  H4   H  HCR5  0   0.291  -3.5531  -4.8676  44.0636
 2RW  H5   H  HCR5  0   0.268  -1.2279  -3.4909  41.3464
 2RW  H6   H  HCR5  0   0.261  -1.4163  -5.2997  43.7933
 2RW  H7   H  HOH1  0   0.472   0.3964  -4.1821  44.2885
 2RW  H8   H  HCR5  0   0.260   0.1425  -6.8245  42.7925
 2RW  H9   H  HOH1  0   0.451   1.3676  -4.9312  41.8599
 2RW  H10  H  HCR5  0   0.283  -0.9738  -6.7206  40.2687
 2RW  H11  H  HCH2  0   0.260  -3.0007  -7.7915  41.0333
 2RW  H12  H  HCH2  0   0.271  -1.5375  -8.5135  41.7167
 2RW  H13  H  HOH1  0   0.512  -3.7166  -9.0581  45.7149
 2RW  H14  H  HOH1  0   0.511  -7.7022  -8.9671  44.5829
 2RW  H15  H  HCH2  0   0.273  -7.8502  -8.2293  41.1669
 2RW  H16  H  HCH2  0   0.241  -6.1306  -8.3638  41.5151
 2RW  H18  H  HCH2  0   0.206  -7.0322  -4.5335  38.5406
 2RW  H19  H  HCH2  0   0.247  -5.4775  -3.6138  40.1802
 2RW  H20  H  HCH2  0   0.241  -6.4585  -4.2094  41.5234
 2RW  H21  H  HOH1  0   0.453  -3.7112  -5.4659  39.6618
 2RW  H22  H  HCH1  0   0.228  -4.9333  -6.0052  41.4029
 2RW  H23  H  HCH1  0   0.245  -6.3512  -7.4206  39.3675
 2RW  H17  H  HCH2  0   0.237  -8.1519  -3.9659  39.7893

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    1.517  0.020  1.517
 2RW  C1D  O4D  single    1.417  0.020  1.417
 2RW  C2D  C3D  single    1.528  0.020  1.528
 2RW  O3D  C3D  single    1.409  0.020  1.409
 2RW  O4D  C4D  single    1.415  0.020  1.415
 2RW  C3D  C4D  single    1.543  0.020  1.543
 2RW  C4D  C5D  single    1.510  0.020  1.510
 2RW  C5D  O5D  single    1.436  0.020  1.436
 2RW  O3'  C3'  single    1.404  0.020  1.404
 2RW  O5D  PB   single    1.584  0.020  1.584
 2RW  C4'  C5'  single    1.509  0.020  1.509
 2RW  C4'  O4'  single    1.428  0.020  1.428
 2RW  C4'  C3'  single    1.527  0.020  1.527
 2RW  C5'  O5'  single    1.436  0.020  1.436
 2RW  O4'  C1'  single    1.407  0.020  1.407
 2RW  C3'  C2'  single    1.533  0.020  1.533
 2RW  O5'  PA   single    1.587  0.020  1.587
 2RW  PB   O1B  double    1.467  0.020  1.467
 2RW  PB   O3A  single    1.617  0.020  1.617
 2RW  PB   O2B  single    1.589  0.020  1.589
 2RW  C1'  C2'  single    1.529  0.020  1.529
 2RW  C1'  N9   single    1.435  0.020  1.435
 2RW  O3A  PA   single    1.623  0.020  1.623
 2RW  C2'  O2'  single    1.396  0.020  1.396
 2RW  N3   C2   aromatic  1.323  0.020  1.323
 2RW  N3   C4   aromatic  1.330  0.020  1.330
 2RW  O2A  PA   double    1.471  0.020  1.471
 2RW  PA   O1A  single    1.582  0.020  1.582
 2RW  C2   N1   aromatic  1.330  0.020  1.330
 2RW  C4   N9   aromatic  1.369  0.020  1.369
 2RW  C4   C5   aromatic  1.384  0.020  1.384
 2RW  N9   C8   aromatic  1.373  0.020  1.373
 2RW  N1   C6   aromatic  1.338  0.020  1.338
 2RW  C8   N7   aromatic  1.297  0.020  1.297
 2RW  C5   C6   aromatic  1.406  0.020  1.406
 2RW  C5   N7   aromatic  1.371  0.020  1.371
 2RW  C6   N6   single    1.333  0.020  1.333
 2RW  C2   H1   single    0.930  0.020  1.080
 2RW  N6   H2   single    0.860  0.020  1.020
 2RW  N6   H3   single    0.860  0.020  1.020
 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  O1A  H13  single    0.850  0.020  0.980
 2RW  O2B  H14  single    0.850  0.020  0.980
 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   119.16  3.000
 2RW  H1   C2   N3   116.13  3.000
 2RW  H1   C2   N1   115.48  3.000
 2RW  N3   C2   N1   128.38  3.000
 2RW  C4   N3   C2   111.68  3.000
 2RW  N9   C4   C5   105.25  3.000
 2RW  C5   C4   N3   126.54  3.000
 2RW  N9   C4   N3   128.21  3.000
 2RW  N7   C5   C6   132.73  3.000
 2RW  N7   C5   C4   110.87  3.000
 2RW  C6   C5   C4   116.36  3.000
 2RW  N6   C6   C5   122.75  3.000
 2RW  N6   C6   N1   119.37  3.000
 2RW  C5   C6   N1   117.87  3.000
 2RW  H3   N6   H2   118.26  3.000
 2RW  H3   N6   C6   121.08  3.000
 2RW  H2   N6   C6   120.19  3.000
 2RW  C8   N7   C5   104.50  3.000
 2RW  H4   C8   N9   121.97  3.000
 2RW  H4   C8   N7   124.61  3.000
 2RW  N9   C8   N7   113.41  3.000
 2RW  C1'  N9   C8   128.53  3.000
 2RW  C8   N9   C4   105.95  3.000
 2RW  C1'  N9   C4   125.28  3.000
 2RW  H5   C1'  O4'  110.49  3.000
 2RW  H5   C1'  C2'  110.04  3.000
 2RW  O4'  C1'  C2'  105.83  3.000
 2RW  H5   C1'  N9   106.18  3.000
 2RW  C2'  C1'  N9   114.69  3.000
 2RW  O4'  C1'  N9   109.65  3.000
 2RW  H6   C2'  C3'  108.97  3.000
 2RW  H6   C2'  O2'  111.46  3.000
 2RW  C3'  C2'  O2'  114.44  3.000
 2RW  H6   C2'  C1'  110.66  3.000
 2RW  O2'  C2'  C1'  109.53  3.000
 2RW  C3'  C2'  C1'  101.35  3.000
 2RW  H7   O2'  C2'  108.89  3.000
 2RW  H8   C3'  C4'  112.11  3.000
 2RW  H8   C3'  O3'  111.65  3.000
 2RW  C4'  C3'  O3'  107.63  3.000
 2RW  H8   C3'  C2'  112.09  3.000
 2RW  C4'  C3'  C2'  102.41  3.000
 2RW  O3'  C3'  C2'  110.52  3.000
 2RW  H9   O3'  C3'  107.98  3.000
 2RW  C4'  O4'  C1'  111.36  3.000
 2RW  H10  C4'  C5'  105.70  3.000
 2RW  H10  C4'  O4'  109.12  3.000
 2RW  C5'  C4'  O4'  110.39  3.000
 2RW  H10  C4'  C3'  109.44  3.000
 2RW  O4'  C4'  C3'  105.88  3.000
 2RW  C5'  C4'  C3'  116.19  3.000
 2RW  H12  C5'  H11  108.23  3.000
 2RW  H12  C5'  O5'  109.78  3.000
 2RW  H11  C5'  O5'  110.98  3.000
 2RW  H12  C5'  C4'  109.12  3.000
 2RW  H11  C5'  C4'  109.09  3.000
 2RW  O5'  C5'  C4'  109.60  3.000
 2RW  PA   O5'  C5'  120.98  3.000
 2RW  O3A  PA   O2A  114.22  3.000
 2RW  O2A  PA   O1A  118.97  3.000
 2RW  O3A  PA   O1A  104.02  3.000
 2RW  O1A  PA   O5'  100.06  3.000
 2RW  O2A  PA   O5'  117.14  3.000
 2RW  O3A  PA   O5'   99.63  3.000
 2RW  H13  O1A  PA   115.18  3.000
 2RW  PB   O3A  PA   136.68  3.000
 2RW  O5D  PB   O2B  108.43  3.000
 2RW  O2B  PB   O1B  118.45  3.000
 2RW  O5D  PB   O1B  111.42  3.000
 2RW  O2B  PB   O3A   99.89  3.000
 2RW  O1B  PB   O3A  113.07  3.000
 2RW  O5D  PB   O3A  104.16  3.000
 2RW  H14  O2B  PB   115.08  3.000
 2RW  C5D  O5D  PB   124.14  3.000
 2RW  H16  C5D  H15  107.40  3.000
 2RW  H16  C5D  C4D  108.94  3.000
 2RW  H15  C5D  C4D  110.76  3.000
 2RW  H16  C5D  O5D  112.04  3.000
 2RW  H15  C5D  O5D  107.91  3.000
 2RW  C4D  C5D  O5D  109.77  3.000
 2RW  C4D  O4D  C1D  109.21  3.000
 2RW  H18  C1D  H17  108.05  3.000
 2RW  H18  C1D  C2D  110.91  3.000
 2RW  H17  C1D  C2D  113.78  3.000
 2RW  H18  C1D  O4D  111.13  3.000
 2RW  H17  C1D  O4D  108.58  3.000
 2RW  C2D  C1D  O4D  104.37  3.000
 2RW  H20  C2D  H19  108.13  3.000
 2RW  H20  C2D  C3D  110.21  3.000
 2RW  H19  C2D  C3D  112.64  3.000
 2RW  H20  C2D  C1D  110.50  3.000
 2RW  H19  C2D  C1D  113.26  3.000
 2RW  C3D  C2D  C1D  102.04  3.000
 2RW  H21  O3D  C3D  106.92  3.000
 2RW  H22  C3D  C4D  111.61  3.000
 2RW  H22  C3D  O3D  110.10  3.000
 2RW  C4D  C3D  O3D  108.42  3.000
 2RW  H22  C3D  C2D  110.85  3.000
 2RW  C4D  C3D  C2D  102.63  3.000
 2RW  O3D  C3D  C2D  113.02  3.000
 2RW  H23  C4D  C3D  108.89  3.000
 2RW  H23  C4D  O4D  110.47  3.000
 2RW  C3D  C4D  O4D  107.32  3.000
 2RW  H23  C4D  C5D  106.22  3.000
 2RW  C3D  C4D  C5D  114.46  3.000
 2RW  O4D  C4D  C5D  109.48  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    38.29  30.0  1
 2RW  Var_02    C4D  C5D  O5D  PB   -134.97  30.0  2
 2RW  Var_03    O3A  PA   O5'  C5'  -111.81  30.0  3
 2RW  Var_04    O5D  PB   O3A  PA   -107.28  30.0  2
 2RW  Var_05    H11  C5'  O5'  PA     44.60  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
 2RW  chir_09  PA   O3A  O2A  O1A  both
 2RW  chir_10  PB   O1B  O3A  O2B  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
 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

