# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 15:30:34 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: [[(2S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@H]3CC[C@@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)O3
#
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
 DG3  DG3  '[[(2S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate'  ligand  42  30  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DG3
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
 DG3  PG    P  P      0   1.222  -1.5675  -1.5095   5.5048
 DG3  O1G   O  O      0  -0.894  -2.8683  -1.8231   4.7823
 DG3  O2G   O  OP    -1  -0.896  -0.7992  -2.7322   5.9872
 DG3  O3G   O  OP    -1  -0.896  -1.6391  -0.3595   6.4987
 DG3  O3B   O  O2     0  -0.777  -0.5350  -0.9287   4.2447
 DG3  PB    P  P      0   1.337  -0.1792   0.6191   4.0136
 DG3  O1B   O  O      0  -0.833  -1.3929   1.4622   3.7525
 DG3  O2B   O  OP    -1  -0.824   0.8707   1.0957   4.9733
 DG3  O3A   O  O2     0  -0.746   0.5841   0.3609   2.5437
 DG3  PA    P  P      0   1.337   0.6261   1.4519   1.3441
 DG3  O1A   O  O      0  -0.810   1.0228   2.8109   1.8362
 DG3  O2A   O  OP    -1  -0.789  -0.5736   1.3163   0.4487
 DG3  O5'   O  O2     0  -0.621   1.9243   0.7444   0.6059
 DG3  C5'   C  CH2    0  -0.148   2.3229   1.2548  -0.6443
 DG3  C4'   C  CH1    0   0.017   2.7528   0.1259  -1.5511
 DG3  O4'   O  O2     0  -0.494   1.6735  -0.7998  -1.7582
 DG3  C3'   C  CH2    0  -0.507   3.1644   0.6018  -2.9394
 DG3  C2'   C  CH2    0  -0.506   2.7162  -0.5508  -3.8262
 DG3  C1'   C  CH1    0   0.197   1.4587  -1.0271  -3.1103
 DG3  N9    N  NR5    0  -0.533   0.2640  -0.2835  -3.5372
 DG3  C8    C  CR15   0   0.048  -0.5860   0.4664  -2.7605
 DG3  N7    N  N      0  -0.454  -1.5942   0.9392  -3.4341
 DG3  C5    C  CR56   0  -0.089  -1.4138   0.4728  -4.7087
 DG3  C6    C  CR6    0   0.496  -2.2023   0.6484  -5.8814
 DG3  O6    O  O      0  -0.478  -3.2363   1.2814  -6.0235
 DG3  N1    N  NR16   0  -0.726  -1.6346  -0.0345  -6.9647
 DG3  C2    C  CR6    0   0.679  -0.4922  -0.7819  -6.9362
 DG3  N2    N  NH2    0  -0.833  -0.0955  -1.3298  -8.0957
 DG3  N3    N  N      0  -0.514   0.2263  -0.9461  -5.8549
 DG3  C4    C  CR56   0   0.499  -0.2675  -0.2980  -4.7869
 DG3  H5'1  H  HCH2   0   0.219   3.1716   1.9401  -0.5286
 DG3  H5'2  H  HCH2   0   0.203   1.5233   1.8214  -1.1354
 DG3  H4'   H  HCH1   0   0.235   3.5713  -0.4293  -1.0785
 DG3  H3'1  H  HCH2   0   0.267   4.2336   0.7957  -3.0053
 DG3  H3'2  H  HCH2   0   0.245   2.6424   1.5240  -3.2091
 DG3  H2'1  H  HCH2   0   0.259   3.4493  -1.3598  -3.8109
 DG3  H2'2  H  HCH2   0   0.273   2.5449  -0.2759  -4.8644
 DG3  H1'   H  HCH1   0   0.272   1.2537  -2.0874  -3.2767
 DG3  H8    H  HCR5   0   0.317  -0.4239   0.6238  -1.7020
 DG3  HN1   H  HNR6   0   0.423  -2.1293   0.0522  -7.8432
 DG3  HN21  H  HNH2   0   0.410   0.6567  -1.9963  -8.0598
 DG3  HN22  H  HNH2   0   0.413  -0.7266  -1.4096  -8.8748

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
 DG3  PG   O1G   deloc     1.521  0.020  1.521
 DG3  PG   O2G   deloc     1.523  0.020  1.523
 DG3  PG   O3G   deloc     1.522  0.020  1.522
 DG3  PG   O3B   single    1.730  0.020  1.730
 DG3  O3B  PB    single    1.605  0.020  1.605
 DG3  PB   O1B   deloc     1.501  0.020  1.501
 DG3  PB   O2B   deloc     1.500  0.020  1.500
 DG3  PB   O3A   single    1.676  0.020  1.676
 DG3  O3A  PA    single    1.622  0.020  1.622
 DG3  PA   O1A   deloc     1.499  0.020  1.499
 DG3  PA   O2A   deloc     1.503  0.020  1.503
 DG3  PA   O5'   single    1.653  0.020  1.653
 DG3  O5'  C5'   single    1.408  0.020  1.408
 DG3  C5'  C4'   single    1.510  0.020  1.510
 DG3  C5'  H5'1  single    0.970  0.020  1.090
 DG3  C5'  H5'2  single    0.970  0.020  1.090
 DG3  C4'  O4'   single    1.437  0.020  1.437
 DG3  C4'  C3'   single    1.524  0.020  1.524
 DG3  C4'  H4'   single    0.970  0.020  1.090
 DG3  O4'  C1'   single    1.388  0.020  1.388
 DG3  C3'  C2'   single    1.522  0.020  1.522
 DG3  C3'  H3'1  single    0.970  0.020  1.090
 DG3  C3'  H3'2  single    0.970  0.020  1.090
 DG3  C2'  C1'   single    1.523  0.020  1.523
 DG3  C2'  H2'1  single    0.970  0.020  1.090
 DG3  C2'  H2'2  single    0.970  0.020  1.090
 DG3  C1'  N9    single    1.470  0.020  1.470
 DG3  C1'  H1'   single    0.970  0.020  1.090
 DG3  N9   C8    aromatic  1.374  0.020  1.374
 DG3  N9   C4    aromatic  1.358  0.020  1.358
 DG3  C8   N7    aromatic  1.301  0.020  1.301
 DG3  C8   H8    single    0.930  0.020  1.080
 DG3  N7   C5    aromatic  1.369  0.020  1.369
 DG3  C5   C6    single    1.424  0.020  1.424
 DG3  C5   C4    aromatic  1.384  0.020  1.384
 DG3  C6   O6    double    1.221  0.020  1.221
 DG3  C6   N1    single    1.401  0.020  1.401
 DG3  N1   C2    single    1.365  0.020  1.365
 DG3  N1   HN1   single    0.860  0.020  1.020
 DG3  C2   N2    single    1.342  0.020  1.342
 DG3  C2   N3    double    1.309  0.020  1.309
 DG3  N2   HN21  single    0.890  0.020  1.040
 DG3  N2   HN22  single    0.890  0.020  1.040
 DG3  N3   C4    single    1.343  0.020  1.343

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
 DG3  O3B   PG   O3G   104.49  3.000
 DG3  O3B   PG   O2G   101.49  3.000
 DG3  O3G   PG   O2G   115.07  3.000
 DG3  O3B   PG   O1G   103.52  3.000
 DG3  O3G   PG   O1G   115.21  3.000
 DG3  O2G   PG   O1G   114.62  3.000
 DG3  PB    O3B  PG    124.13  3.000
 DG3  O3A   PB   O2B   106.93  3.000
 DG3  O3A   PB   O1B   107.59  3.000
 DG3  O2B   PB   O1B   119.92  3.000
 DG3  O3A   PB   O3B    94.51  3.000
 DG3  O2B   PB   O3B   111.68  3.000
 DG3  O1B   PB   O3B   112.81  3.000
 DG3  PA    O3A  PB    123.83  3.000
 DG3  O5'   PA   O2A   108.80  3.000
 DG3  O5'   PA   O1A   109.08  3.000
 DG3  O2A   PA   O1A   119.25  3.000
 DG3  O5'   PA   O3A    93.60  3.000
 DG3  O2A   PA   O3A   111.05  3.000
 DG3  O1A   PA   O3A   111.95  3.000
 DG3  C5'   O5'  PA    117.63  3.000
 DG3  H5'2  C5'  H5'1  106.78  3.000
 DG3  H5'2  C5'  C4'   108.96  3.000
 DG3  H5'1  C5'  C4'   108.06  3.000
 DG3  H5'2  C5'  O5'   112.26  3.000
 DG3  H5'1  C5'  O5'   110.60  3.000
 DG3  C4'   C5'  O5'   110.04  3.000
 DG3  H4'   C4'  C3'   110.43  3.000
 DG3  H4'   C4'  O4'   107.26  3.000
 DG3  C3'   C4'  O4'   105.82  3.000
 DG3  H4'   C4'  C5'   109.41  3.000
 DG3  C3'   C4'  C5'   112.97  3.000
 DG3  O4'   C4'  C5'   110.75  3.000
 DG3  C1'   O4'  C4'   111.24  3.000
 DG3  H3'2  C3'  H3'1  107.68  3.000
 DG3  H3'2  C3'  C2'   110.76  3.000
 DG3  H3'1  C3'  C2'   112.89  3.000
 DG3  H3'2  C3'  C4'   111.04  3.000
 DG3  H3'1  C3'  C4'   112.09  3.000
 DG3  C2'   C3'  C4'   102.40  3.000
 DG3  H2'2  C2'  H2'1  107.85  3.000
 DG3  H2'2  C2'  C1'   113.43  3.000
 DG3  H2'1  C2'  C1'   108.42  3.000
 DG3  H2'2  C2'  C3'   114.28  3.000
 DG3  H2'1  C2'  C3'   110.81  3.000
 DG3  C1'   C2'  C3'   101.89  3.000
 DG3  H1'   C1'  N9    107.10  3.000
 DG3  H1'   C1'  C2'   112.75  3.000
 DG3  N9    C1'  C2'   112.09  3.000
 DG3  H1'   C1'  O4'   109.65  3.000
 DG3  N9    C1'  O4'   109.01  3.000
 DG3  C2'   C1'  O4'   106.19  3.000
 DG3  C4    N9   C8    106.49  3.000
 DG3  C4    N9   C1'   125.43  3.000
 DG3  C8    N9   C1'   127.91  3.000
 DG3  H8    C8   N7    124.71  3.000
 DG3  H8    C8   N9    122.65  3.000
 DG3  N7    C8   N9    112.64  3.000
 DG3  C5    N7   C8    104.83  3.000
 DG3  C4    C5   C6    118.74  3.000
 DG3  C4    C5   N7    110.58  3.000
 DG3  C6    C5   N7    130.67  3.000
 DG3  N1    C6   O6    120.40  3.000
 DG3  N1    C6   C5    110.63  3.000
 DG3  O6    C6   C5    128.97  3.000
 DG3  HN1   N1   C2    118.30  3.000
 DG3  HN1   N1   C6    115.56  3.000
 DG3  C2    N1   C6    126.14  3.000
 DG3  N3    C2   N2    120.02  3.000
 DG3  N3    C2   N1    123.04  3.000
 DG3  N2    C2   N1    116.91  3.000
 DG3  HN22  N2   HN21  116.38  3.000
 DG3  HN22  N2   C2    121.07  3.000
 DG3  HN21  N2   C2    117.44  3.000
 DG3  C4    N3   C2    113.24  3.000
 DG3  N3    C4   C5    128.19  3.000
 DG3  N3    C4   N9    126.36  3.000
 DG3  C5    C4   N9    105.44  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
 DG3  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 DG3  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 DG3  CONST_03  C5    C4   N9   C8      0.00   0.0  0
 DG3  CONST_04  C4    C5   N7   C8      0.00   0.0  0
 DG3  CONST_05  C4    N9   C8   N7      0.00   0.0  0
 DG3  CONST_06  N7    C8   N9   C1'   180.00   0.0  0
 DG3  CONST_07  C5    C4   N9   C1'   180.00   0.0  0
 DG3  CONST_08  N3    C4   N9   C1'     0.00   0.0  0
 DG3  CONST_09  C2    N1   C6   C5      0.00   0.0  0
 DG3  CONST_10  N3    C2   N1   C6      0.00   0.0  0
 DG3  CONST_11  C4    N3   C2   N1      0.00   0.0  0
 DG3  CONST_12  N2    C2   N1   C6    180.00   0.0  0
 DG3  CONST_13  C2    N1   C6   O6    180.00   0.0  0
 DG3  CONST_14  C4    N3   C2   N2    180.00   0.0  0
 DG3  CONST_15  H8    C8   N9   C1'     0.00   0.0  0
 DG3  CONST_16  HN1   N1   C6   C5    180.00   0.0  0
 DG3  CONST_17  HN21  N2   C2   N1    180.00   0.0  0
 DG3  Var_01    C1'   C2'  C3'  C4'    33.95  30.0  1
 DG3  Var_02    C4'   C5'  O5'  PA   -141.66  30.0  3
 DG3  Var_03    O1B   PB   O3B  PG    -59.71  30.0  3
 DG3  Var_04    O1A   PA   O3A  PB     48.03  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
 DG3  chir_03  C4'  C5'  O4'  C3'  negativ
 DG3  chir_04  C1'  O4'  N9   C2'  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
 DG3  plan-1  C1'   0.020
 DG3  plan-1  N9    0.020
 DG3  plan-1  C8    0.020
 DG3  plan-1  N7    0.020
 DG3  plan-1  C5    0.020
 DG3  plan-1  C6    0.020
 DG3  plan-1  O6    0.020
 DG3  plan-1  N1    0.020
 DG3  plan-1  C2    0.020
 DG3  plan-1  N2    0.020
 DG3  plan-1  N3    0.020
 DG3  plan-1  C4    0.020
 DG3  plan-1  H8    0.020
 DG3  plan-1  HN1   0.020
 DG3  plan-1  HN21  0.020
 DG3  plan-1  HN22  0.020

