# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 00:20:20 2021
#   Inital geometry file: a 128 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]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O)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
 8GT  8GT  '8-oxoguanosine 5'-(tetrahydrogen triphosphate)'  ligand  49  33  .  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_8GT
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
 8GT  PG    P  P     0   1.459  -30.6983  -15.9903   3.0854
 8GT  O1G   O  O     0  -0.674  -32.1417  -15.7518   3.1930
 8GT  O2G   O  OH1   0  -0.759  -29.8694  -15.6208   4.3593
 8GT  O3G   O  OH1   0  -0.733  -30.0883  -15.2842   1.7976
 8GT  O3B   O  O2    0  -0.716  -30.3279  -17.5790   2.8887
 8GT  PB    P  P     0   1.508  -29.9779  -18.4295   1.5790
 8GT  O1B   O  O     0  -0.661  -28.7990  -17.9985   0.8187
 8GT  O2B   O  OH1   0  -0.710  -31.3745  -18.4736   0.8444
 8GT  O3A   O  O2    0  -0.687  -29.7417  -19.8841   2.2228
 8GT  PA    P  P     0   1.497  -30.3511  -20.7049   3.4830
 8GT  O1A   O  O     0  -0.669  -29.8799  -22.0958   3.4543
 8GT  O2A   O  OH1   0  -0.724  -31.8894  -20.3889   3.3041
 8GT  O5'   O  O2    0  -0.584  -29.9542  -19.8586   4.7641
 8GT  C5'   C  CH2   0  -0.209  -28.7474  -20.0746   5.5108
 8GT  C4'   C  CH1   0  -0.001  -28.1824  -18.6986   5.8372
 8GT  O4'   O  O2    0  -0.490  -27.2517  -18.8143   6.9046
 8GT  C3'   C  CH1   0  -0.042  -27.4272  -18.0570   4.6788
 8GT  O3'   O  OH1   0  -0.701  -27.5542  -16.6484   4.7703
 8GT  C2'   C  CH1   0  -0.051  -25.9822  -18.4725   4.9592
 8GT  O2'   O  OH1   0  -0.653  -25.0302  -17.5724   4.4741
 8GT  C1'   C  CH1   0   0.216  -25.9532  -18.4820   6.4892
 8GT  N9    N  NR5   0  -0.623  -25.0056  -19.3926   7.0630
 8GT  C8    C  CR5   0   0.681  -24.9814  -20.7744   6.8448
 8GT  N7    N  NR15  0  -0.739  -23.9640  -21.2429   7.6102
 8GT  C5    C  CR56  0   0.071  -23.3616  -20.1996   8.2984
 8GT  C6    C  CR6   0   0.522  -22.2788  -20.1565   9.2009
 8GT  O6    O  O     0  -0.486  -21.5815  -21.0757   9.6058
 8GT  N1    N  NR16  0  -0.727  -22.0559  -18.8392   9.6280
 8GT  C2    C  CR6   0   0.708  -22.7714  -17.7467   9.2460
 8GT  N2    N  NH2   0  -0.830  -22.4376  -16.5702   9.7804
 8GT  N3    N  N     0  -0.516  -23.7741  -17.8168   8.3974
 8GT  C4    C  CR56  0   0.516  -24.0227  -19.0502   7.9589
 8GT  O8    O  O     0  -0.497  -25.7272  -21.4015   6.1140
 8GT  HOG2  H  HOH1  0   0.511  -28.9406  -15.9917   4.4882
 8GT  H3G   H  HOH1  0   0.498  -29.1267  -15.2767   1.6950
 8GT  HOB2  H  HOH1  0   0.515  -31.3340  -18.7056  -0.0949
 8GT  HOA2  H  HOH1  0   0.514  -32.4761  -20.8039   3.9526
 8GT  H5'1  H  HCH2  0   0.254  -28.0368  -20.6925   4.9603
 8GT  H5'2  H  HCH2  0   0.276  -29.0065  -20.5960   6.4323
 8GT  H4'   H  HCH1  0   0.273  -29.0108  -18.0611   6.1638
 8GT  H3'   H  HCH1  0   0.264  -27.7585  -18.4124   3.6998
 8GT  H2    H  HOH1  0   0.481  -26.7881  -16.2342   4.3455
 8GT  H1    H  HCH1  0   0.281  -25.8258  -19.4800   4.5661
 8GT  H2'   H  HOH1  0   0.474  -24.7735  -17.8345   3.5843
 8GT  H1'   H  HCH1  0   0.272  -25.6706  -17.4888   6.8543
 8GT  HN7   H  HNR5  0   0.423  -23.6971  -22.2134   7.6473
 8GT  HN1   H  HNR6  0   0.429  -21.2942  -18.7157  10.2834
 8GT  HN21  H  HNH2  0   0.420  -21.6089  -16.4503  10.3359
 8GT  HN22  H  HNH2  0   0.418  -22.9083  -15.7422   9.4590

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
 8GT  PG   O1G   double  1.467  0.020  1.467
 8GT  PG   O2G   single  1.564  0.020  1.564
 8GT  PG   O3G   single  1.590  0.020  1.590
 8GT  PG   O3B   single  1.643  0.020  1.643
 8GT  O2G  HOG2  single  0.850  0.020  0.980
 8GT  O3G  H3G   single  0.850  0.020  0.980
 8GT  O3B  PB    single  1.600  0.020  1.600
 8GT  PB   O1B   double  1.468  0.020  1.468
 8GT  PB   O2B   single  1.579  0.020  1.579
 8GT  PB   O3A   single  1.608  0.020  1.608
 8GT  O2B  HOB2  single  0.850  0.020  0.980
 8GT  O3A  PA    single  1.623  0.020  1.623
 8GT  PA   O1A   double  1.469  0.020  1.469
 8GT  PA   O2A   single  1.581  0.020  1.581
 8GT  PA   O5'   single  1.586  0.020  1.586
 8GT  O2A  HOA2  single  0.850  0.020  0.980
 8GT  O5'  C5'   single  1.435  0.020  1.435
 8GT  C5'  C4'   single  1.523  0.020  1.523
 8GT  C5'  H5'1  single  0.970  0.020  1.090
 8GT  C5'  H5'2  single  0.970  0.020  1.090
 8GT  C4'  O4'   single  1.421  0.020  1.421
 8GT  C4'  C3'   single  1.524  0.020  1.524
 8GT  C4'  H4'   single  0.970  0.020  1.090
 8GT  O4'  C1'   single  1.403  0.020  1.403
 8GT  C3'  O3'   single  1.417  0.020  1.417
 8GT  C3'  C2'   single  1.530  0.020  1.530
 8GT  C3'  H3'   single  0.970  0.020  1.090
 8GT  O3'  H2    single  0.850  0.020  0.980
 8GT  C2'  O2'   single  1.397  0.020  1.397
 8GT  C2'  C1'   single  1.530  0.020  1.530
 8GT  C2'  H1    single  0.970  0.020  1.090
 8GT  O2'  H2'   single  0.850  0.020  0.980
 8GT  C1'  N9    single  1.434  0.020  1.434
 8GT  C1'  H1'   single  0.970  0.020  1.090
 8GT  N9   C8    single  1.399  0.020  1.399
 8GT  N9   C4    single  1.373  0.020  1.373
 8GT  C8   N7    single  1.357  0.020  1.357
 8GT  C8   O8    double  1.218  0.020  1.218
 8GT  N7   C5    single  1.387  0.020  1.387
 8GT  N7   HN7   single  0.860  0.020  1.020
 8GT  C5   C6    single  1.410  0.020  1.410
 8GT  C5   C4    double  1.369  0.020  1.369
 8GT  C6   O6    double  1.223  0.020  1.223
 8GT  C6   N1    single  1.403  0.020  1.403
 8GT  N1   C2    single  1.361  0.020  1.361
 8GT  N1   HN1   single  0.860  0.020  1.020
 8GT  C2   N2    single  1.335  0.020  1.335
 8GT  C2   N3    double  1.316  0.020  1.316
 8GT  N2   HN21  single  0.860  0.020  1.020
 8GT  N2   HN22  single  0.860  0.020  1.020
 8GT  N3   C4    single  1.332  0.020  1.332

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
 8GT  O3B   PG   O3G   104.23  3.000
 8GT  O3B   PG   O2G   101.92  3.000
 8GT  O3G   PG   O2G   110.57  3.000
 8GT  O3B   PG   O1G   112.82  3.000
 8GT  O3G   PG   O1G   111.38  3.000
 8GT  O2G   PG   O1G   115.05  3.000
 8GT  HOG2  O2G  PG    120.35  3.000
 8GT  H3G   O3G  PG    118.09  3.000
 8GT  PB    O3B  PG    131.39  3.000
 8GT  O3A   PB   O2B   106.91  3.000
 8GT  O3A   PB   O1B   110.80  3.000
 8GT  O2B   PB   O1B   118.54  3.000
 8GT  O3A   PB   O3B   100.68  3.000
 8GT  O2B   PB   O3B   101.66  3.000
 8GT  O1B   PB   O3B   116.33  3.000
 8GT  HOB2  O2B  PB    114.90  3.000
 8GT  PA    O3A  PB    135.50  3.000
 8GT  O5'   PA   O2A   103.20  3.000
 8GT  O5'   PA   O1A   116.16  3.000
 8GT  O2A   PA   O1A   119.95  3.000
 8GT  O5'   PA   O3A   105.27  3.000
 8GT  O2A   PA   O3A   100.17  3.000
 8GT  O1A   PA   O3A   110.08  3.000
 8GT  HOA2  O2A  PA    115.37  3.000
 8GT  C5'   O5'  PA    123.39  3.000
 8GT  H5'2  C5'  H5'1  108.09  3.000
 8GT  H5'2  C5'  C4'   109.83  3.000
 8GT  H5'1  C5'  C4'   112.24  3.000
 8GT  H5'2  C5'  O5'   108.17  3.000
 8GT  H5'1  C5'  O5'   111.74  3.000
 8GT  C4'   C5'  O5'   106.71  3.000
 8GT  H4'   C4'  C3'   110.88  3.000
 8GT  H4'   C4'  O4'   108.59  3.000
 8GT  C3'   C4'  O4'   106.29  3.000
 8GT  H4'   C4'  C5'   108.02  3.000
 8GT  C3'   C4'  C5'   113.65  3.000
 8GT  O4'   C4'  C5'   109.30  3.000
 8GT  C1'   O4'  C4'   111.38  3.000
 8GT  H3'   C3'  C2'   111.24  3.000
 8GT  H3'   C3'  O3'   110.72  3.000
 8GT  C2'   C3'  O3'   110.05  3.000
 8GT  H3'   C3'  C4'   113.18  3.000
 8GT  C2'   C3'  C4'   102.38  3.000
 8GT  O3'   C3'  C4'   108.96  3.000
 8GT  H2    O3'  C3'   109.02  3.000
 8GT  H1    C2'  C1'   110.57  3.000
 8GT  H1    C2'  O2'   111.81  3.000
 8GT  C1'   C2'  O2'   109.77  3.000
 8GT  H1    C2'  C3'   108.64  3.000
 8GT  C1'   C2'  C3'   101.70  3.000
 8GT  O2'   C2'  C3'   113.90  3.000
 8GT  H2'   O2'  C2'   109.11  3.000
 8GT  H1'   C1'  N9    105.78  3.000
 8GT  H1'   C1'  C2'   109.42  3.000
 8GT  N9    C1'  C2'   114.61  3.000
 8GT  H1'   C1'  O4'   110.78  3.000
 8GT  N9    C1'  O4'   110.04  3.000
 8GT  C2'   C1'  O4'   106.26  3.000
 8GT  C4    N9   C8    109.62  3.000
 8GT  C4    N9   C1'   125.14  3.000
 8GT  C8    N9   C1'   125.18  3.000
 8GT  O8    C8   N7    128.31  3.000
 8GT  O8    C8   N9    126.26  3.000
 8GT  N7    C8   N9    105.43  3.000
 8GT  HN7   N7   C5    126.24  3.000
 8GT  HN7   N7   C8    123.52  3.000
 8GT  C5    N7   C8    110.23  3.000
 8GT  C4    C5   C6    120.26  3.000
 8GT  C4    C5   N7    107.38  3.000
 8GT  C6    C5   N7    132.36  3.000
 8GT  N1    C6   O6    120.97  3.000
 8GT  N1    C6   C5    110.22  3.000
 8GT  O6    C6   C5    128.81  3.000
 8GT  HN1   N1   C2    118.64  3.000
 8GT  HN1   N1   C6    115.55  3.000
 8GT  C2    N1   C6    125.81  3.000
 8GT  N3    C2   N2    119.73  3.000
 8GT  N3    C2   N1    122.62  3.000
 8GT  N2    C2   N1    117.64  3.000
 8GT  HN22  N2   HN21  117.68  3.000
 8GT  HN22  N2   C2    118.76  3.000
 8GT  HN21  N2   C2    122.20  3.000
 8GT  C4    N3   C2    113.82  3.000
 8GT  N3    C4   C5    127.27  3.000
 8GT  N3    C4   N9    125.39  3.000
 8GT  C5    C4   N9    107.34  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
 8GT  CONST_01  N7    C8   N9   C1'  180.00   0.0  0
 8GT  CONST_02  C5    C4   N9   C1'  180.00   0.0  0
 8GT  CONST_03  N3    C4   N9   C1'    0.00   0.0  0
 8GT  CONST_04  C5    N7   C8   N9     0.00   0.0  0
 8GT  CONST_05  N7    C5   C4   N9     0.00   0.0  0
 8GT  CONST_06  C2    N3   C4   N9   180.00   0.0  0
 8GT  CONST_07  C5    C4   N9   C8     0.00   0.0  0
 8GT  CONST_08  N3    C4   N9   C8   180.00   0.0  0
 8GT  CONST_09  C4    C5   N7   C8     0.00   0.0  0
 8GT  CONST_10  C4    N9   C8   N7     0.00   0.0  0
 8GT  CONST_11  C2    N1   C6   C5     0.00   0.0  0
 8GT  CONST_12  C2    N3   C4   C5     0.00   0.0  0
 8GT  CONST_13  N3    C2   N1   C6     0.00   0.0  0
 8GT  CONST_14  C4    N3   C2   N1     0.00   0.0  0
 8GT  CONST_15  O8    C8   N9   C1'    0.00   0.0  0
 8GT  CONST_16  O8    C8   N7   C5   180.00   0.0  0
 8GT  CONST_17  N2    C2   N1   C6   180.00   0.0  0
 8GT  CONST_18  C2    N1   C6   O6   180.00   0.0  0
 8GT  CONST_19  C4    N3   C2   N2   180.00   0.0  0
 8GT  CONST_20  O8    C8   N9   C4   180.00   0.0  0
 8GT  CONST_21  HN7   N7   C8   N9   180.00   0.0  0
 8GT  CONST_22  HN1   N1   C6   C5   180.00   0.0  0
 8GT  CONST_23  HN21  N2   C2   N1     0.00   0.0  0
 8GT  CONST_24  HN22  N2   C2   N1   180.00   0.0  0
 8GT  Var_01    C4'   C5'  O5'  PA   137.54  30.0  3
 8GT  Var_02    O1B   PB   O3B  PG    60.20  30.0  3
 8GT  Var_03    O1A   PA   O3A  PB   171.44  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
 8GT  chir_03  C4'  C5'  O4'  C3'  negativ
 8GT  chir_04  C3'  O3'  C4'  C2'  positiv
 8GT  chir_05  C2'  O2'  C3'  C1'  positiv
 8GT  chir_06  C1'  O4'  N9   C2'  negativ
 8GT  chir_07  PB   O1B  O2B  O3A  both
 8GT  chir_08  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
 8GT  plan-1  C1'   0.020
 8GT  plan-1  N9    0.020
 8GT  plan-1  C8    0.020
 8GT  plan-1  N7    0.020
 8GT  plan-1  C5    0.020
 8GT  plan-1  C6    0.020
 8GT  plan-1  O6    0.020
 8GT  plan-1  N1    0.020
 8GT  plan-1  C2    0.020
 8GT  plan-1  N2    0.020
 8GT  plan-1  N3    0.020
 8GT  plan-1  C4    0.020
 8GT  plan-1  O8    0.020
 8GT  plan-1  HN7   0.020
 8GT  plan-1  HN1   0.020
 8GT  plan-1  HN21  0.020
 8GT  plan-1  HN22  0.020

