# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 10:15:17 2021
#   Inital geometry file: a 123 line input string
#   Ligand name: 3'-amino-2',3'-dideoxyguanosine 5'-(tetrahydrogen triphosphate)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1C[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2cnc3C(=O)N=C(N)Nc23
#
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
 NG3  NG3  '3'-amino-2',3'-dideoxyguanosine 5'-(tetrahydrogen triphosphate)'  ligand  48  31  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NG3
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
 NG3  C2   C  CR6   0   0.670  -16.4408  -13.5684  -11.7754
 NG3  C4   C  CR56  0   0.635  -18.5038  -14.5657  -12.0986
 NG3  C5   C  CR56  0  -0.109  -18.6518  -13.9135  -13.2923
 NG3  C6   C  CR6   0   0.415  -17.6043  -13.0274  -13.7491
 NG3  C8   C  CR15  0   0.083  -20.3929  -15.0966  -13.0205
 NG3  C1'  C  CR15  0   0.170  -19.8990  -16.1538  -10.7454
 NG3  C2'  C  CH2   0  -0.510  -20.6067  -15.3859   -9.6320
 NG3  C3'  C  CR15  0  -0.134  -22.0768  -15.6986   -9.8796
 NG3  C4'  C  CR15  0   0.048  -21.9609  -17.1390  -10.3740
 NG3  C5'  C  CH2   0  -0.232  -23.1030  -17.6806  -11.1956
 NG3  N1   N  N     0  -0.538  -16.5246  -12.9186  -12.9047
 NG3  O6   O  O     0  -0.494  -17.6495  -12.4046  -14.8035
 NG3  O4'  O  O     0  -0.492  -20.7565  -17.1823  -11.1341
 NG3  N2   N  NH2   0  -0.827  -15.3459  -13.4504  -11.0131
 NG3  N3   N  NR16  0  -0.739  -17.4106  -14.4120  -11.3071
 NG3  N3'  N  NH2   0  -0.811  -22.8674  -15.6074   -8.6703
 NG3  N7   N  N     0  -0.442  -19.8496  -14.2651  -13.8565
 NG3  N9   N  NR5   0  -0.520  -19.6051  -15.3263  -11.9152
 NG3  O1A  O  OH1   0  -0.741  -25.7399  -17.5551  -12.7037
 NG3  O1B  O  OH1   0  -0.697  -26.2469  -13.8452  -10.2628
 NG3  O1G  O  OH1   0  -0.723  -28.4812  -17.9020  -10.9729
 NG3  O2A  O  O     0  -0.652  -24.5531  -15.7926  -14.2648
 NG3  O2B  O  O     0  -0.666  -26.0876  -16.3721   -9.5998
 NG3  O2G  O  OH1   0  -0.734  -29.3363  -15.8975   -9.7779
 NG3  O3A  O  O2    0  -0.688  -25.1932  -15.3303  -11.8216
 NG3  O3B  O  O2    0  -0.683  -27.6472  -15.5347  -11.5059
 NG3  O3G  O  O     0  -0.671  -29.9450  -16.2233  -12.3232
 NG3  O5'  O  O2    0  -0.575  -23.2846  -16.8885  -12.3777
 NG3  PA   P  P     0   1.521  -24.6816  -16.3967  -12.9355
 NG3  PB   P  P     0   1.490  -26.2935  -15.3716  -10.6573
 NG3  PG   P  P     0   1.482  -28.9836  -16.4204  -11.2305
 NG3  H1   H  HCR5  0   0.291  -21.3436  -15.5855  -13.1514
 NG3  H2   H  HCR5  0   0.274  -18.9427  -16.5671  -10.4117
 NG3  H3   H  HCH2  0   0.268  -20.3119  -15.7998   -8.6654
 NG3  H4   H  HCH2  0   0.285  -20.3700  -14.3222   -9.6335
 NG3  H5   H  HCR5  0   0.236  -22.4475  -15.0612  -10.6955
 NG3  H6   H  HCR5  0   0.252  -21.8777  -17.7976   -9.4988
 NG3  H7   H  HCH2  0   0.252  -23.9992  -17.7014  -10.5713
 NG3  H8   H  HCH2  0   0.283  -22.8981  -18.7051  -11.5083
 NG3  H9   H  HNH2  0   0.412  -14.6684  -12.7526  -11.2673
 NG3  H10  H  HNH2  0   0.414  -15.3245  -13.7849  -10.0650
 NG3  H11  H  HNR6  0   0.437  -17.2913  -14.9064  -10.4351
 NG3  H12  H  HNH2  0   0.359  -22.9000  -14.6449   -8.3587
 NG3  H13  H  HNH2  0   0.347  -23.8288  -15.8717   -8.8484
 NG3  H15  H  HOH1  0   0.518  -25.7565  -18.2470  -13.3814
 NG3  H16  H  HOH1  0   0.518  -26.5342  -13.6460   -9.3600
 NG3  H17  H  HOH1  0   0.506  -28.4941  -18.4736  -11.7529
 NG3  H18  H  HOH1  0   0.513  -30.1581  -16.2447   -9.4016

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
 NG3  O6   C6   double    1.225  0.020  1.225
 NG3  O2A  PA   double    1.466  0.020  1.466
 NG3  C6   C5   single    1.446  0.020  1.446
 NG3  C6   N1   single    1.375  0.020  1.375
 NG3  N7   C5   aromatic  1.370  0.020  1.370
 NG3  N7   C8   aromatic  1.298  0.020  1.298
 NG3  C5   C4   aromatic  1.368  0.020  1.368
 NG3  O3G  PG   double    1.469  0.020  1.469
 NG3  N1   C2   double    1.306  0.020  1.306
 NG3  C8   N9   aromatic  1.377  0.020  1.377
 NG3  PA   O1A  single    1.586  0.020  1.586
 NG3  PA   O5'  single    1.583  0.020  1.583
 NG3  PA   O3A  single    1.625  0.020  1.625
 NG3  C4   N9   aromatic  1.351  0.020  1.351
 NG3  C4   N3   single    1.358  0.020  1.358
 NG3  O5'  C5'  single    1.434  0.020  1.434
 NG3  C2   N2   single    1.339  0.020  1.339
 NG3  C2   N3   single    1.368  0.020  1.368
 NG3  N9   C1'  single    1.463  0.020  1.463
 NG3  PG   O1G  single    1.586  0.020  1.586
 NG3  PG   O3B  single    1.627  0.020  1.627
 NG3  PG   O2G  single    1.584  0.020  1.584
 NG3  O3B  PB   single    1.606  0.020  1.606
 NG3  O3A  PB   single    1.602  0.020  1.602
 NG3  O4'  C1'  single    1.394  0.020  1.394
 NG3  O4'  C4'  single    1.425  0.020  1.425
 NG3  C1'  C2'  single    1.527  0.020  1.527
 NG3  C5'  C4'  single    1.508  0.020  1.508
 NG3  PB   O2B  double    1.470  0.020  1.470
 NG3  PB   O1B  single    1.577  0.020  1.577
 NG3  C4'  C3'  single    1.527  0.020  1.527
 NG3  C2'  C3'  single    1.523  0.020  1.523
 NG3  C3'  N3'  single    1.448  0.020  1.448
 NG3  C8   H1   single    0.930  0.020  1.080
 NG3  C1'  H2   single    0.970  0.020  1.090
 NG3  C2'  H3   single    0.970  0.020  1.090
 NG3  C2'  H4   single    0.970  0.020  1.090
 NG3  C3'  H5   single    0.970  0.020  1.090
 NG3  C4'  H6   single    0.970  0.020  1.090
 NG3  C5'  H7   single    0.970  0.020  1.090
 NG3  C5'  H8   single    0.970  0.020  1.090
 NG3  N2   H9   single    0.890  0.020  1.040
 NG3  N2   H10  single    0.890  0.020  1.040
 NG3  N3   H11  single    0.860  0.020  1.020
 NG3  N3'  H12  single    0.890  0.020  1.040
 NG3  N3'  H13  single    0.890  0.020  1.040
 NG3  O1A  H15  single    0.850  0.020  0.980
 NG3  O1B  H16  single    0.850  0.020  0.980
 NG3  O1G  H17  single    0.850  0.020  0.980
 NG3  O2G  H18  single    0.850  0.020  0.980

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
 NG3  N3   C2   N2   116.04  3.000
 NG3  N3   C2   N1   123.89  3.000
 NG3  N2   C2   N1   120.06  3.000
 NG3  N9   C4   N3   129.84  3.000
 NG3  N3   C4   C5   122.78  3.000
 NG3  N9   C4   C5   107.37  3.000
 NG3  N7   C5   C6   131.34  3.000
 NG3  N7   C5   C4   109.36  3.000
 NG3  C6   C5   C4   119.29  3.000
 NG3  O6   C6   N1   121.14  3.000
 NG3  N1   C6   C5   115.04  3.000
 NG3  O6   C6   C5   123.81  3.000
 NG3  H1   C8   N9   121.80  3.000
 NG3  H1   C8   N7   125.58  3.000
 NG3  N9   C8   N7   112.61  3.000
 NG3  H2   C1'  N9   106.39  3.000
 NG3  H2   C1'  O4'  110.12  3.000
 NG3  N9   C1'  O4'  108.54  3.000
 NG3  H2   C1'  C2'  111.89  3.000
 NG3  O4'  C1'  C2'  106.81  3.000
 NG3  N9   C1'  C2'  113.07  3.000
 NG3  H4   C2'  H3   108.21  3.000
 NG3  H4   C2'  C3'  114.19  3.000
 NG3  H3   C2'  C3'  109.06  3.000
 NG3  H4   C2'  C1'  112.92  3.000
 NG3  H3   C2'  C1'  109.26  3.000
 NG3  C3'  C2'  C1'  103.04  3.000
 NG3  H5   C3'  N3'  113.53  3.000
 NG3  H5   C3'  C4'  109.39  3.000
 NG3  N3'  C3'  C4'  111.80  3.000
 NG3  H5   C3'  C2'  109.08  3.000
 NG3  N3'  C3'  C2'  112.23  3.000
 NG3  C4'  C3'  C2'   99.96  3.000
 NG3  H6   C4'  O4'  110.04  3.000
 NG3  H6   C4'  C5'  106.03  3.000
 NG3  O4'  C4'  C5'  109.80  3.000
 NG3  H6   C4'  C3'  108.26  3.000
 NG3  C5'  C4'  C3'  117.24  3.000
 NG3  O4'  C4'  C3'  105.40  3.000
 NG3  H8   C5'  H7   107.47  3.000
 NG3  H8   C5'  O5'  107.83  3.000
 NG3  H7   C5'  O5'  112.18  3.000
 NG3  H8   C5'  C4'  110.58  3.000
 NG3  H7   C5'  C4'  108.48  3.000
 NG3  O5'  C5'  C4'  110.28  3.000
 NG3  C6   N1   C2   122.83  3.000
 NG3  C4'  O4'  C1'  110.41  3.000
 NG3  H10  N2   H9   117.07  3.000
 NG3  H10  N2   C2   121.64  3.000
 NG3  H9   N2   C2   117.91  3.000
 NG3  H11  N3   C4   122.89  3.000
 NG3  H11  N3   C2   120.93  3.000
 NG3  C4   N3   C2   116.15  3.000
 NG3  H13  N3'  H12  105.76  3.000
 NG3  H13  N3'  C3'  110.80  3.000
 NG3  H12  N3'  C3'  109.55  3.000
 NG3  C8   N7   C5   105.37  3.000
 NG3  C1'  N9   C8   128.43  3.000
 NG3  C1'  N9   C4   126.22  3.000
 NG3  C8   N9   C4   105.28  3.000
 NG3  H15  O1A  PA   115.52  3.000
 NG3  H16  O1B  PB   115.06  3.000
 NG3  H17  O1G  PG   114.65  3.000
 NG3  H18  O2G  PG   115.29  3.000
 NG3  PB   O3A  PA   134.22  3.000
 NG3  PG   O3B  PB   131.17  3.000
 NG3  PA   O5'  C5'  125.02  3.000
 NG3  O5'  PA   O3A  103.90  3.000
 NG3  O3A  PA   O2A  112.26  3.000
 NG3  O5'  PA   O2A  111.74  3.000
 NG3  O3A  PA   O1A   99.73  3.000
 NG3  O5'  PA   O1A  108.09  3.000
 NG3  O2A  PA   O1A  119.48  3.000
 NG3  O3B  PB   O3A  101.39  3.000
 NG3  O3A  PB   O2B  116.36  3.000
 NG3  O3B  PB   O2B  115.40  3.000
 NG3  O2B  PB   O1B  118.33  3.000
 NG3  O3A  PB   O1B   97.84  3.000
 NG3  O3B  PB   O1B  104.80  3.000
 NG3  O3G  PG   O3B  109.80  3.000
 NG3  O3B  PG   O2G   99.12  3.000
 NG3  O3G  PG   O2G  119.49  3.000
 NG3  O2G  PG   O1G  103.30  3.000
 NG3  O3B  PG   O1G  106.02  3.000
 NG3  O3G  PG   O1G  116.98  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
 NG3  CONST_01  C8   N7   C5   C4      0.00   0.0  0
 NG3  CONST_02  N7   C8   N9   C4      0.00   0.0  0
 NG3  CONST_03  N9   C8   N7   C5      0.00   0.0  0
 NG3  CONST_04  C8   N9   C4   C5      0.00   0.0  0
 NG3  CONST_05  N9   C4   C5   N7      0.00   0.0  0
 NG3  CONST_06  C1'  N9   C4   C5    180.00   0.0  0
 NG3  CONST_07  N7   C8   N9   C1'   180.00   0.0  0
 NG3  CONST_08  N3   C4   N9   C1'     0.00   0.0  0
 NG3  CONST_09  N1   C2   N3   C4      0.00   0.0  0
 NG3  CONST_10  N3   C2   N1   C6      0.00   0.0  0
 NG3  CONST_11  N2   C2   N3   C4    180.00   0.0  0
 NG3  CONST_12  N2   C2   N1   C6    180.00   0.0  0
 NG3  CONST_13  H1   C8   N9   C4    180.00   0.0  0
 NG3  CONST_14  H11  N3   C2   N1    180.00   0.0  0
 NG3  CONST_15  H9   N2   C2   N1      0.00   0.0  0
 NG3  CONST_16  H10  N2   C2   N1    180.00   0.0  0
 NG3  Var_01    O2A  PA   O5'  C5'  -170.96  30.0  1
 NG3  Var_02    H7   C5'  O5'  PA    -14.72  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
 NG3  chir_01  C1'  N9   O4'  C2'  positiv
 NG3  chir_02  C3'  N3'  C4'  C2'  positiv
 NG3  chir_03  C4'  O4'  C3'  C5'  negativ
 NG3  chir_04  PA   O1A  O5'  O3A  both
 NG3  chir_05  PB   O3A  O2B  O1B  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
 NG3  plan-1  C2   0.020
 NG3  plan-1  C4   0.020
 NG3  plan-1  C5   0.020
 NG3  plan-1  C6   0.020
 NG3  plan-1  C8   0.020
 NG3  plan-1  C1'  0.020
 NG3  plan-1  N1   0.020
 NG3  plan-1  O6   0.020
 NG3  plan-1  N2   0.020
 NG3  plan-1  N3   0.020
 NG3  plan-1  N7   0.020
 NG3  plan-1  N9   0.020
 NG3  plan-1  H1   0.020
 NG3  plan-1  H9   0.020
 NG3  plan-1  H10  0.020
 NG3  plan-1  H11  0.020

