# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 22:13:22 2021
#   Inital geometry file: a 137 line input string
#   Ligand name: (2R,3R,4S,5S)-5-amino-3,4-dihydroxytetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CO[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](O)[C@H]1O
#
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
 G3N  G3N  '(2R,3R,4S,5S)-5-amino-3,4-dihydroxytetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  57  34  .  2021-08-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_G3N
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
 G3N  O2B  O  OH1   0  -0.727  31.1030  39.6625  -27.3861
 G3N  PB   P  P     0   1.497  29.5938  40.0405  -27.6863
 G3N  O1B  O  O     0  -0.663  29.2737  41.3812  -28.1900
 G3N  O3B  O  O2    0  -0.599  29.0924  38.8084  -28.5527
 G3N  C1'  C  CH1   0   0.313  27.8942  38.8166  -29.3202
 G3N  O5'  O  O2    0  -0.483  28.2637  38.2091  -30.5091
 G3N  C5'  C  CH2   0  -0.186  27.1941  38.1099  -31.4363
 G3N  C4'  C  CH1   0  -0.126  26.0222  37.3151  -30.8669
 G3N  N4'  N  NH2   0  -0.797  24.9745  37.2457  -31.8673
 G3N  C3'  C  CH1   0  -0.019  25.5935  37.9086  -29.5206
 G3N  O3'  O  OH1   0  -0.671  25.0333  39.1780  -29.7741
 G3N  C2'  C  CH1   0  -0.064  26.8045  38.0336  -28.5878
 G3N  O2'  O  OH1   0  -0.697  27.2281  36.7471  -28.2425
 G3N  O3A  O  O2    0  -0.697  28.9454  39.8156  -26.2189
 G3N  PA   P  P     0   1.521  28.8621  38.5371  -25.2392
 G3N  O1A  O  O     0  -0.678  28.6312  37.2384  -25.8987
 G3N  O2A  O  OH1   0  -0.716  27.7323  39.1093  -24.2912
 G3N  O5D  O  O2    0  -0.567  30.2272  38.5155  -24.4400
 G3N  C5D  C  CH2   0  -0.216  30.7935  39.6680  -23.8067
 G3N  C4D  C  CH1   0  -0.048  31.7222  39.1942  -22.7063
 G3N  C3D  C  CH1   0  -0.042  32.6104  40.3368  -22.2041
 G3N  O3D  O  OH1   0  -0.662  33.0736  40.1192  -20.9017
 G3N  C2D  C  CH1   0  -0.003  33.8008  40.1991  -23.1577
 G3N  O2D  O  OH1   0  -0.649  35.0068  40.7408  -22.7323
 G3N  O4D  O  O2    0  -0.489  32.6140  38.1875  -23.1837
 G3N  C1D  C  CH1   0   0.197  33.9221  38.6786  -23.2565
 G3N  N1   N  NR6   0  -0.566  34.5353  38.2130  -24.4962
 G3N  C6   C  CR16  0   0.103  33.8224  38.2183  -25.6613
 G3N  C5   C  CR16  0  -0.511  34.3318  37.8322  -26.8407
 G3N  C4   C  CR6   0   0.572  35.6993  37.3774  -26.9101
 G3N  O4   O  O     0  -0.460  36.2782  37.0015  -27.9114
 G3N  N3   N  NR16  0  -0.734  36.3457  37.3938  -25.6839
 G3N  C2   C  CR6   0   0.740  35.8503  37.7880  -24.4689
 G3N  O2   O  O     0  -0.474  36.5211  37.7599  -23.4597
 G3N  H1   H  HOH1  0   0.517  31.7321  39.9378  -28.0695
 G3N  H2   H  HCH1  0   0.218  27.5592  39.8498  -29.4894
 G3N  H3   H  HCH2  0   0.252  27.5926  37.6040  -32.3150
 G3N  H4   H  HCH2  0   0.213  26.8652  39.1099  -31.7497
 G3N  H5   H  HCH1  0   0.251  26.3689  36.2958  -30.6788
 G3N  H6   H  HNH2  0   0.351  24.2717  36.5770  -31.5789
 G3N  H7   H  HNH2  0   0.342  24.4991  38.1380  -31.9290
 G3N  H9   H  HCH1  0   0.238  24.8606  37.2403  -29.0486
 G3N  H10  H  HOH1  0   0.459  24.6137  39.4991  -28.9700
 G3N  H11  H  HCH1  0   0.230  26.5016  38.6125  -27.7003
 G3N  H12  H  HOH1  0   0.463  27.7654  36.8102  -27.4354
 G3N  H13  H  HOH1  0   0.516  27.3989  38.4813  -23.6335
 G3N  H14  H  HCH2  0   0.246  31.3240  40.2581  -24.5580
 G3N  H15  H  HCH2  0   0.282  30.0230  40.3029  -23.3627
 G3N  H16  H  HCH1  0   0.280  31.1249  38.7628  -21.8983
 G3N  H17  H  HCH1  0   0.264  32.1138  41.3106  -22.3043
 G3N  H18  H  HOH1  0   0.461  32.3300  40.1949  -20.2950
 G3N  H19  H  HCH1  0   0.242  33.5019  40.6047  -24.1364
 G3N  H20  H  HOH1  0   0.465  34.9642  41.6985  -22.8161
 G3N  H21  H  HCH1  0   0.279  34.5353  38.2933  -22.4398
 G3N  H22  H  HCR6  0   0.315  32.7926  38.5310  -25.5847
 G3N  H23  H  HCR6  0   0.289  33.7255  37.8437  -27.7329
 G3N  H24  H  HNR6  0   0.428  37.3085  37.0794  -25.6720

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
 G3N  C5'  C4'  single  1.526  0.020  1.526
 G3N  C5'  O5'  single  1.419  0.020  1.419
 G3N  N4'  C4'  single  1.450  0.020  1.450
 G3N  C4'  C3'  single  1.532  0.020  1.532
 G3N  O5'  C1'  single  1.385  0.020  1.385
 G3N  C1'  O3B  single  1.423  0.020  1.423
 G3N  C1'  C2'  single  1.529  0.020  1.529
 G3N  O3'  C3'  single  1.410  0.020  1.410
 G3N  C3'  C2'  single  1.534  0.020  1.534
 G3N  O3B  PB   single  1.587  0.020  1.587
 G3N  C2'  O2'  single  1.398  0.020  1.398
 G3N  O1B  PB   double  1.468  0.020  1.468
 G3N  PB   O2B  single  1.585  0.020  1.585
 G3N  PB   O3A  single  1.620  0.020  1.620
 G3N  O4   C4   double  1.216  0.020  1.216
 G3N  C5   C4   single  1.443  0.020  1.443
 G3N  C5   C6   double  1.341  0.020  1.341
 G3N  O3A  PA   single  1.613  0.020  1.613
 G3N  C4   N3   single  1.386  0.020  1.386
 G3N  O1A  PA   double  1.475  0.020  1.475
 G3N  C6   N1   single  1.366  0.020  1.366
 G3N  PA   O5D  single  1.582  0.020  1.582
 G3N  PA   O2A  single  1.582  0.020  1.582
 G3N  N3   C2   single  1.370  0.020  1.370
 G3N  O5D  C5D  single  1.432  0.020  1.432
 G3N  C5D  C4D  single  1.516  0.020  1.516
 G3N  N1   C2   single  1.382  0.020  1.382
 G3N  N1   C1D  single  1.459  0.020  1.459
 G3N  C2   O2   double  1.212  0.020  1.212
 G3N  O4D  C1D  single  1.399  0.020  1.399
 G3N  O4D  C4D  single  1.427  0.020  1.427
 G3N  C2D  C1D  single  1.529  0.020  1.529
 G3N  C2D  O2D  single  1.389  0.020  1.389
 G3N  C2D  C3D  single  1.531  0.020  1.531
 G3N  C4D  C3D  single  1.532  0.020  1.532
 G3N  C3D  O3D  single  1.399  0.020  1.399
 G3N  O2B  H1   single  0.850  0.020  0.980
 G3N  C1'  H2   single  0.970  0.020  1.090
 G3N  C5'  H3   single  0.970  0.020  1.090
 G3N  C5'  H4   single  0.970  0.020  1.090
 G3N  C4'  H5   single  0.970  0.020  1.090
 G3N  N4'  H6   single  0.890  0.020  1.040
 G3N  N4'  H7   single  0.890  0.020  1.040
 G3N  C3'  H9   single  0.970  0.020  1.090
 G3N  O3'  H10  single  0.850  0.020  0.980
 G3N  C2'  H11  single  0.970  0.020  1.090
 G3N  O2'  H12  single  0.850  0.020  0.980
 G3N  O2A  H13  single  0.850  0.020  0.980
 G3N  C5D  H14  single  0.970  0.020  1.090
 G3N  C5D  H15  single  0.970  0.020  1.090
 G3N  C4D  H16  single  0.970  0.020  1.090
 G3N  C3D  H17  single  0.970  0.020  1.090
 G3N  O3D  H18  single  0.850  0.020  0.980
 G3N  C2D  H19  single  0.970  0.020  1.090
 G3N  O2D  H20  single  0.850  0.020  0.980
 G3N  C1D  H21  single  0.970  0.020  1.090
 G3N  C6   H22  single  0.930  0.020  1.080
 G3N  C5   H23  single  0.930  0.020  1.080
 G3N  N3   H24  single  0.860  0.020  1.020

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
 G3N  H1   O2B  PB   114.65  3.000
 G3N  O3A  PB   O3B  105.08  3.000
 G3N  O3A  PB   O1B  110.51  3.000
 G3N  O3B  PB   O1B  116.93  3.000
 G3N  O3A  PB   O2B  100.16  3.000
 G3N  O1B  PB   O2B  119.39  3.000
 G3N  O3B  PB   O2B  102.66  3.000
 G3N  C1'  O3B  PB   123.77  3.000
 G3N  H2   C1'  C2'  109.75  3.000
 G3N  H2   C1'  O5'  111.18  3.000
 G3N  C2'  C1'  O5'  112.13  3.000
 G3N  H2   C1'  O3B  110.18  3.000
 G3N  C2'  C1'  O3B  109.81  3.000
 G3N  O5'  C1'  O3B  103.64  3.000
 G3N  C5'  O5'  C1'  112.98  3.000
 G3N  H4   C5'  H3   107.59  3.000
 G3N  H4   C5'  C4'  110.53  3.000
 G3N  H3   C5'  C4'  109.87  3.000
 G3N  H4   C5'  O5'  110.39  3.000
 G3N  H3   C5'  O5'  106.48  3.000
 G3N  C4'  C5'  O5'  111.80  3.000
 G3N  H5   C4'  C3'  107.38  3.000
 G3N  H5   C4'  N4'  107.65  3.000
 G3N  C3'  C4'  N4'  114.99  3.000
 G3N  H5   C4'  C5'  107.84  3.000
 G3N  C3'  C4'  C5'  109.93  3.000
 G3N  N4'  C4'  C5'  108.80  3.000
 G3N  H7   N4'  H6   105.87  3.000
 G3N  H7   N4'  C4'  109.82  3.000
 G3N  H6   N4'  C4'  109.67  3.000
 G3N  H9   C3'  C2'  108.36  3.000
 G3N  H9   C3'  O3'  111.09  3.000
 G3N  C2'  C3'  O3'  110.46  3.000
 G3N  H9   C3'  C4'  109.18  3.000
 G3N  C2'  C3'  C4'  110.18  3.000
 G3N  O3'  C3'  C4'  107.57  3.000
 G3N  H10  O3'  C3'  108.87  3.000
 G3N  H11  C2'  O2'  111.58  3.000
 G3N  H11  C2'  C3'  108.40  3.000
 G3N  O2'  C2'  C3'  108.33  3.000
 G3N  H11  C2'  C1'  108.22  3.000
 G3N  O2'  C2'  C1'  111.94  3.000
 G3N  C3'  C2'  C1'  108.25  3.000
 G3N  H12  O2'  C2'  108.24  3.000
 G3N  PA   O3A  PB   132.92  3.000
 G3N  O5D  PA   O2A  108.57  3.000
 G3N  O2A  PA   O1A  118.34  3.000
 G3N  O5D  PA   O1A  110.43  3.000
 G3N  O2A  PA   O3A   96.56  3.000
 G3N  O5D  PA   O3A  105.85  3.000
 G3N  O1A  PA   O3A  115.75  3.000
 G3N  H13  O2A  PA   114.73  3.000
 G3N  C5D  O5D  PA   123.63  3.000
 G3N  H15  C5D  H14  107.93  3.000
 G3N  H15  C5D  C4D  108.58  3.000
 G3N  H14  C5D  C4D  111.75  3.000
 G3N  H15  C5D  O5D  111.62  3.000
 G3N  H14  C5D  O5D  108.82  3.000
 G3N  C4D  C5D  O5D  108.17  3.000
 G3N  H16  C4D  O4D  108.07  3.000
 G3N  H16  C4D  C3D  111.64  3.000
 G3N  O4D  C4D  C3D  105.87  3.000
 G3N  H16  C4D  C5D  108.97  3.000
 G3N  C3D  C4D  C5D  111.10  3.000
 G3N  O4D  C4D  C5D  111.13  3.000
 G3N  H17  C3D  C2D  112.00  3.000
 G3N  H17  C3D  O3D  111.88  3.000
 G3N  C2D  C3D  O3D  107.95  3.000
 G3N  H17  C3D  C4D  111.68  3.000
 G3N  O3D  C3D  C4D  112.39  3.000
 G3N  C2D  C3D  C4D  100.34  3.000
 G3N  H18  O3D  C3D  108.58  3.000
 G3N  H19  C2D  C1D  109.31  3.000
 G3N  H19  C2D  O2D  111.37  3.000
 G3N  C1D  C2D  O2D  109.81  3.000
 G3N  H19  C2D  C3D  108.02  3.000
 G3N  O2D  C2D  C3D  116.69  3.000
 G3N  C1D  C2D  C3D  101.03  3.000
 G3N  H20  O2D  C2D  108.85  3.000
 G3N  C1D  O4D  C4D  110.74  3.000
 G3N  H21  C1D  N1   106.67  3.000
 G3N  H21  C1D  O4D  111.25  3.000
 G3N  N1   C1D  O4D  108.97  3.000
 G3N  H21  C1D  C2D  110.32  3.000
 G3N  O4D  C1D  C2D  105.76  3.000
 G3N  N1   C1D  C2D  113.93  3.000
 G3N  C2   N1   C6   120.97  3.000
 G3N  C2   N1   C1D  118.76  3.000
 G3N  C6   N1   C1D  120.27  3.000
 G3N  H22  C6   C5   120.55  3.000
 G3N  H22  C6   N1   116.02  3.000
 G3N  C5   C6   N1   123.41  3.000
 G3N  H23  C5   C4   119.75  3.000
 G3N  H23  C5   C6   120.70  3.000
 G3N  C4   C5   C6   119.53  3.000
 G3N  N3   C4   O4   120.66  3.000
 G3N  N3   C4   C5   113.31  3.000
 G3N  O4   C4   C5   126.03  3.000
 G3N  H24  N3   C2   115.00  3.000
 G3N  H24  N3   C4   116.74  3.000
 G3N  C2   N3   C4   128.26  3.000
 G3N  O2   C2   N3   122.11  3.000
 G3N  O2   C2   N1   123.37  3.000
 G3N  N3   C2   N1   114.52  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
 G3N  CONST_01  N3   C2   N1   C1D  180.00   0.0  0
 G3N  CONST_02  C4   N3   C2   N1     0.00   0.0  0
 G3N  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 G3N  CONST_04  C2   N3   C4   C5     0.00   0.0  0
 G3N  CONST_05  O2   C2   N1   C1D    0.00   0.0  0
 G3N  CONST_06  O2   C2   N1   C6   180.00   0.0  0
 G3N  CONST_07  O2   C2   N3   C4   180.00   0.0  0
 G3N  CONST_08  C2   N3   C4   O4   180.00   0.0  0
 G3N  CONST_09  H24  N3   C2   N1   180.00   0.0  0
 G3N  Var_01    C4'  C5'  O5'  C1'  -58.89  30.0  1
 G3N  Var_02    O3A  PB   O3B  C1'   90.55  30.0  3
 G3N  Var_03    C4D  C5D  O5D  PA   156.76  30.0  3
 G3N  Var_04    O1A  PA   O3A  PB   -38.52  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
 G3N  chir_02  C1'  O5'  O3B  C2'  positiv
 G3N  chir_03  C4'  N4'  C3'  C5'  positiv
 G3N  chir_04  C3'  O3'  C2'  C4'  positiv
 G3N  chir_05  C2'  O2'  C1'  C3'  negativ
 G3N  chir_07  C4D  C5D  O4D  C3D  negativ
 G3N  chir_08  C3D  O3D  C4D  C2D  positiv
 G3N  chir_09  C2D  O2D  C3D  C1D  positiv
 G3N  chir_10  C1D  O4D  N1   C2D  negativ
 G3N  chir_11  PB   O1B  O2B  O3A  both
 G3N  chir_12  PA   O1A  O5D  O2A  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
 G3N  plan-1  C1D  0.020
 G3N  plan-1  N1   0.020
 G3N  plan-1  C6   0.020
 G3N  plan-1  C5   0.020
 G3N  plan-1  C4   0.020
 G3N  plan-1  O4   0.020
 G3N  plan-1  N3   0.020
 G3N  plan-1  C2   0.020
 G3N  plan-1  O2   0.020
 G3N  plan-1  H22  0.020
 G3N  plan-1  H23  0.020
 G3N  plan-1  H24  0.020

