# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 11:07:26 2021
#   Inital geometry file: a 126 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC2=C(NC(=O)N2[C@H]3C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3)C(=O)N1
#
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
 8DG  8DG  '2'-deoxy-8-oxoguanosine 5'-(tetrahydrogen triphosphate)'  ligand  48  32  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8DG
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
 8DG  PG    P  P     0   1.458  -30.7952  -16.0182   3.0374
 8DG  O1G   O  O     0  -0.673  -32.2415  -15.8219   3.1842
 8DG  O2G   O  OH1   0  -0.758  -29.9476  -15.6642   4.3043
 8DG  O3G   O  OH1   0  -0.733  -30.2332  -15.2565   1.7595
 8DG  O3B   O  O2    0  -0.716  -30.3908  -17.5895   2.7831
 8DG  PB    P  P     0   1.508  -29.9645  -18.3760   1.4561
 8DG  O1B   O  O     0  -0.662  -28.7919  -17.8537   0.7441
 8DG  O2B   O  OH1   0  -0.710  -31.3376  -18.4665   0.6825
 8DG  O3A   O  O2    0  -0.687  -29.6722  -19.8384   2.0568
 8DG  PA    P  P     0   1.498  -30.2556  -20.7040   3.3009
 8DG  O1A   O  O     0  -0.669  -29.7330  -22.0758   3.2507
 8DG  O2A   O  OH1   0  -0.725  -31.8040  -20.4447   3.1162
 8DG  O5'   O  O2    0  -0.584  -29.8990  -19.8643   4.5969
 8DG  C5'   C  CH2   0  -0.209  -28.6851  -20.0376   5.3452
 8DG  C4'   C  CH1   0   0.008  -28.1542  -18.6443   5.6576
 8DG  O4'   O  O2    0  -0.494  -27.2415  -18.7141   6.7380
 8DG  C3'   C  CH1   0  -0.020  -27.3871  -18.0126   4.4948
 8DG  O3'   O  OH1   0  -0.699  -27.5668  -16.6003   4.5708
 8DG  C2'   C  CH2   0  -0.557  -25.9572  -18.4169   4.7971
 8DG  C1'   C  CH1   0   0.229  -25.9291  -18.4081   6.3216
 8DG  N9    N  NR5   0  -0.620  -25.0002  -19.3267   6.9206
 8DG  C8    C  CR5   0   0.679  -24.9828  -20.7110   6.7196
 8DG  N7    N  NR15  0  -0.739  -23.9886  -21.1796   7.5164
 8DG  C5    C  CR56  0   0.072  -23.3969  -20.1346   8.2100
 8DG  C6    C  CR6   0   0.521  -22.3390  -20.0910   9.1415
 8DG  O6    O  O     0  -0.486  -21.6618  -21.0120   9.5758
 8DG  N1    N  NR16  0  -0.726  -22.1168  -18.7715   9.5614
 8DG  C2    C  CR6   0   0.705  -22.8115  -17.6774   9.1476
 8DG  N2    N  NH2   0  -0.830  -22.4854  -16.4980   9.6842
 8DG  N3    N  N     0  -0.516  -23.7906  -17.7479   8.2728
 8DG  C4    C  CR56  0   0.514  -24.0402  -18.9841   7.8408
 8DG  O8    O  O     0  -0.497  -25.7144  -21.3446   5.9805
 8DG  HOG2  H  HOH1  0   0.508  -29.0034  -16.0077   4.3923
 8DG  H3G   H  HOH1  0   0.498  -29.2760  -15.2314   1.6240
 8DG  HOB2  H  HOH1  0   0.515  -31.2611  -18.6556  -0.2642
 8DG  HOA2  H  HOH1  0   0.514  -32.3783  -20.8871   3.7577
 8DG  H5'1  H  HCH2  0   0.255  -27.9593  -20.6432   4.8015
 8DG  H5'2  H  HCH2  0   0.274  -28.9320  -20.5555   6.2720
 8DG  H4'   H  HCH1  0   0.266  -29.0013  -18.0192   5.9599
 8DG  H3'   H  HCH1  0   0.263  -27.7061  -18.3847   3.5189
 8DG  H1    H  HOH1  0   0.487  -26.9151  -16.1572   4.0133
 8DG  H2'1  H  HCH2  0   0.293  -25.2158  -17.7436   4.3669
 8DG  H2'2  H  HCH2  0   0.289  -25.7703  -19.4118   4.3959
 8DG  H1'   H  HCH1  0   0.270  -25.6431  -17.4212   6.6931
 8DG  HN7   H  HNR5  0   0.422  -23.7325  -22.1520   7.5720
 8DG  HN1   H  HNR6  0   0.429  -21.3739  -18.6477  10.2379
 8DG  HN21  H  HNH2  0   0.419  -21.6486  -16.3769  10.2277
 8DG  HN22  H  HNH2  0   0.416  -22.9203  -15.6690   9.3173

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
 8DG  PG   O1G   double  1.467  0.020  1.467
 8DG  PG   O2G   single  1.565  0.020  1.565
 8DG  PG   O3G   single  1.590  0.020  1.590
 8DG  PG   O3B   single  1.642  0.020  1.642
 8DG  O2G  HOG2  single  0.850  0.020  0.980
 8DG  O3G  H3G   single  0.850  0.020  0.980
 8DG  O3B  PB    single  1.600  0.020  1.600
 8DG  PB   O1B   double  1.468  0.020  1.468
 8DG  PB   O2B   single  1.579  0.020  1.579
 8DG  PB   O3A   single  1.608  0.020  1.608
 8DG  O2B  HOB2  single  0.850  0.020  0.980
 8DG  O3A  PA    single  1.624  0.020  1.624
 8DG  PA   O1A   double  1.469  0.020  1.469
 8DG  PA   O2A   single  1.581  0.020  1.581
 8DG  PA   O5'   single  1.585  0.020  1.585
 8DG  O2A  HOA2  single  0.850  0.020  0.980
 8DG  O5'  C5'   single  1.436  0.020  1.436
 8DG  C5'  C4'   single  1.523  0.020  1.523
 8DG  C5'  H5'1  single  0.970  0.020  1.090
 8DG  C5'  H5'2  single  0.970  0.020  1.090
 8DG  C4'  O4'   single  1.416  0.020  1.416
 8DG  C4'  C3'   single  1.530  0.020  1.530
 8DG  C4'  H4'   single  0.970  0.020  1.090
 8DG  O4'  C1'   single  1.411  0.020  1.411
 8DG  C3'  O3'   single  1.426  0.020  1.426
 8DG  C3'  C2'   single  1.516  0.020  1.516
 8DG  C3'  H3'   single  0.970  0.020  1.090
 8DG  O3'  H1    single  0.850  0.020  0.980
 8DG  C2'  C1'   single  1.525  0.020  1.525
 8DG  C2'  H2'1  single  0.970  0.020  1.090
 8DG  C2'  H2'2  single  0.970  0.020  1.090
 8DG  C1'  N9    single  1.437  0.020  1.437
 8DG  C1'  H1'   single  0.970  0.020  1.090
 8DG  N9   C8    single  1.399  0.020  1.399
 8DG  N9   C4    single  1.373  0.020  1.373
 8DG  C8   N7    single  1.358  0.020  1.358
 8DG  C8   O8    double  1.218  0.020  1.218
 8DG  N7   C5    single  1.387  0.020  1.387
 8DG  N7   HN7   single  0.860  0.020  1.020
 8DG  C5   C6    single  1.410  0.020  1.410
 8DG  C5   C4    double  1.369  0.020  1.369
 8DG  C6   O6    double  1.223  0.020  1.223
 8DG  C6   N1    single  1.403  0.020  1.403
 8DG  N1   C2    single  1.360  0.020  1.360
 8DG  N1   HN1   single  0.860  0.020  1.020
 8DG  C2   N2    single  1.336  0.020  1.336
 8DG  C2   N3    double  1.315  0.020  1.315
 8DG  N2   HN21  single  0.860  0.020  1.020
 8DG  N2   HN22  single  0.860  0.020  1.020
 8DG  N3   C4    single  1.333  0.020  1.333

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
 8DG  O3B   PG   O3G   104.29  3.000
 8DG  O3B   PG   O2G   102.03  3.000
 8DG  O3G   PG   O2G   110.53  3.000
 8DG  O3B   PG   O1G   112.72  3.000
 8DG  O3G   PG   O1G   111.39  3.000
 8DG  O2G   PG   O1G   115.01  3.000
 8DG  HOG2  O2G  PG    120.04  3.000
 8DG  H3G   O3G  PG    118.35  3.000
 8DG  PB    O3B  PG    131.62  3.000
 8DG  O3A   PB   O2B   106.80  3.000
 8DG  O3A   PB   O1B   111.08  3.000
 8DG  O2B   PB   O1B   118.52  3.000
 8DG  O3A   PB   O3B   100.70  3.000
 8DG  O2B   PB   O3B   101.70  3.000
 8DG  O1B   PB   O3B   116.11  3.000
 8DG  HOB2  O2B  PB    114.94  3.000
 8DG  PA    O3A  PB    134.89  3.000
 8DG  O5'   PA   O2A   103.24  3.000
 8DG  O5'   PA   O1A   116.28  3.000
 8DG  O2A   PA   O1A   119.85  3.000
 8DG  O5'   PA   O3A   105.26  3.000
 8DG  O2A   PA   O3A   100.07  3.000
 8DG  O1A   PA   O3A   110.11  3.000
 8DG  HOA2  O2A  PA    115.38  3.000
 8DG  C5'   O5'  PA    123.52  3.000
 8DG  H5'2  C5'  H5'1  108.11  3.000
 8DG  H5'2  C5'  C4'   109.83  3.000
 8DG  H5'1  C5'  C4'   112.22  3.000
 8DG  H5'2  C5'  O5'   107.99  3.000
 8DG  H5'1  C5'  O5'   111.70  3.000
 8DG  C4'   C5'  O5'   106.92  3.000
 8DG  H4'   C4'  C3'   111.22  3.000
 8DG  H4'   C4'  O4'   108.42  3.000
 8DG  C3'   C4'  O4'   106.09  3.000
 8DG  H4'   C4'  C5'   108.00  3.000
 8DG  C3'   C4'  C5'   113.37  3.000
 8DG  O4'   C4'  C5'   109.63  3.000
 8DG  C1'   O4'  C4'   111.33  3.000
 8DG  H3'   C3'  C2'   111.27  3.000
 8DG  H3'   C3'  O3'   110.39  3.000
 8DG  C2'   C3'  O3'   111.86  3.000
 8DG  H3'   C3'  C4'   113.09  3.000
 8DG  C2'   C3'  C4'   102.19  3.000
 8DG  O3'   C3'  C4'   107.78  3.000
 8DG  H1    O3'  C3'   109.80  3.000
 8DG  H2'2  C2'  H2'1  107.59  3.000
 8DG  H2'2  C2'  C1'   111.75  3.000
 8DG  H2'1  C2'  C1'   112.24  3.000
 8DG  H2'2  C2'  C3'   109.39  3.000
 8DG  H2'1  C2'  C3'   113.46  3.000
 8DG  C1'   C2'  C3'   102.43  3.000
 8DG  H1'   C1'  N9    105.45  3.000
 8DG  H1'   C1'  C2'   110.49  3.000
 8DG  N9    C1'  C2'   115.15  3.000
 8DG  H1'   C1'  O4'   109.83  3.000
 8DG  N9    C1'  O4'   109.85  3.000
 8DG  C2'   C1'  O4'   106.07  3.000
 8DG  C4    N9   C8    109.54  3.000
 8DG  C4    N9   C1'   124.87  3.000
 8DG  C8    N9   C1'   125.49  3.000
 8DG  O8    C8   N7    128.07  3.000
 8DG  O8    C8   N9    126.49  3.000
 8DG  N7    C8   N9    105.45  3.000
 8DG  HN7   N7   C5    126.26  3.000
 8DG  HN7   N7   C8    123.50  3.000
 8DG  C5    N7   C8    110.24  3.000
 8DG  C4    C5   C6    120.31  3.000
 8DG  C4    C5   N7    107.33  3.000
 8DG  C6    C5   N7    132.36  3.000
 8DG  N1    C6   O6    120.96  3.000
 8DG  N1    C6   C5    110.22  3.000
 8DG  O6    C6   C5    128.81  3.000
 8DG  HN1   N1   C2    118.66  3.000
 8DG  HN1   N1   C6    115.56  3.000
 8DG  C2    N1   C6    125.78  3.000
 8DG  N3    C2   N2    119.75  3.000
 8DG  N3    C2   N1    122.65  3.000
 8DG  N2    C2   N1    117.59  3.000
 8DG  HN22  N2   HN21  117.27  3.000
 8DG  HN22  N2   C2    118.40  3.000
 8DG  HN21  N2   C2    121.78  3.000
 8DG  C4    N3   C2    113.87  3.000
 8DG  N3    C4   C5    127.16  3.000
 8DG  N3    C4   N9    125.41  3.000
 8DG  C5    C4   N9    107.43  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
 8DG  CONST_01  N7    C8   N9   C1'  180.00   0.0  0
 8DG  CONST_02  C5    C4   N9   C1'  180.00   0.0  0
 8DG  CONST_03  N3    C4   N9   C1'    0.00   0.0  0
 8DG  CONST_04  C5    N7   C8   N9     0.00   0.0  0
 8DG  CONST_05  N7    C5   C4   N9     0.00   0.0  0
 8DG  CONST_06  C2    N3   C4   N9   180.00   0.0  0
 8DG  CONST_07  C5    C4   N9   C8     0.00   0.0  0
 8DG  CONST_08  N3    C4   N9   C8   180.00   0.0  0
 8DG  CONST_09  C4    C5   N7   C8     0.00   0.0  0
 8DG  CONST_10  C4    N9   C8   N7     0.00   0.0  0
 8DG  CONST_11  C2    N1   C6   C5     0.00   0.0  0
 8DG  CONST_12  C2    N3   C4   C5     0.00   0.0  0
 8DG  CONST_13  N3    C2   N1   C6     0.00   0.0  0
 8DG  CONST_14  C4    N3   C2   N1     0.00   0.0  0
 8DG  CONST_15  O8    C8   N9   C1'    0.00   0.0  0
 8DG  CONST_16  O8    C8   N7   C5   180.00   0.0  0
 8DG  CONST_17  N2    C2   N1   C6   180.00   0.0  0
 8DG  CONST_18  C2    N1   C6   O6   180.00   0.0  0
 8DG  CONST_19  C4    N3   C2   N2   180.00   0.0  0
 8DG  CONST_20  O8    C8   N9   C4   180.00   0.0  0
 8DG  CONST_21  HN7   N7   C8   N9   180.00   0.0  0
 8DG  CONST_22  HN1   N1   C6   C5   180.00   0.0  0
 8DG  CONST_23  HN21  N2   C2   N1     0.00   0.0  0
 8DG  CONST_24  HN22  N2   C2   N1   180.00   0.0  0
 8DG  Var_01    C4'   C5'  O5'  PA   135.61  30.0  3
 8DG  Var_02    O1B   PB   O3B  PG    57.47  30.0  3
 8DG  Var_03    O1A   PA   O3A  PB   171.98  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
 8DG  chir_03  C4'  C5'  O4'  C3'  negativ
 8DG  chir_04  C3'  O3'  C4'  C2'  positiv
 8DG  chir_05  C1'  O4'  N9   C2'  negativ
 8DG  chir_06  PB   O1B  O2B  O3A  both
 8DG  chir_07  PA   O1A  O2A  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
 8DG  plan-1  C1'   0.020
 8DG  plan-1  N9    0.020
 8DG  plan-1  C8    0.020
 8DG  plan-1  N7    0.020
 8DG  plan-1  C5    0.020
 8DG  plan-1  C6    0.020
 8DG  plan-1  O6    0.020
 8DG  plan-1  N1    0.020
 8DG  plan-1  C2    0.020
 8DG  plan-1  N2    0.020
 8DG  plan-1  N3    0.020
 8DG  plan-1  C4    0.020
 8DG  plan-1  O8    0.020
 8DG  plan-1  HN7   0.020
 8DG  plan-1  HN1   0.020
 8DG  plan-1  HN21  0.020
 8DG  plan-1  HN22  0.020

