# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 00:05:57 2022
#   Inital geometry file: a 142 line input string
#   Ligand name: [(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[C@@H](O)[C@H]2O
#
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
 C5G  C5G  '[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)'  ligand  59  36  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_C5G
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
 C5G  N1    N  N      0  -0.562  23.0947  4.8756  28.9487
 C5G  C2    C  C      0   0.592  23.7094  4.1289  27.9225
 C5G  N3    N  N      0  -0.539  24.7701  3.3616  28.2489
 C5G  C4    C  C      0   0.513  25.2125  3.2973  29.4880
 C5G  C5    C  C1     0  -0.483  24.5990  4.0250  30.5542
 C5G  C6    C  C1     0   0.106  23.5611  4.8143  30.2207
 C5G  O2    O  OC     0  -0.507  23.2735  4.1954  26.7825
 C5G  N4    N  NH2    0  -0.808  26.2743  2.5332  29.7409
 C5G  C1D   C  CH1    0   0.195  21.9880  5.7552  28.6393
 C5G  C2D   C  CH1    0  -0.034  20.6957  5.4547  29.3932
 C5G  O2D   O  OH1    0  -0.654  20.0275  4.3893  28.7801
 C5G  C3D   C  CH1    0  -0.044  19.9818  6.8066  29.2938
 C5G  C4D   C  CH1    0   0.000  21.1498  7.7983  29.3522
 C5G  O4D   O  O2     0  -0.496  22.3271  7.0634  29.0065
 C5G  O3D   O  OH1    0  -0.667  19.3433  6.9471  28.0484
 C5G  C5D   C  CH2    0  -0.196  21.3427  8.4932  30.6777
 C5G  O5D   O  O2     0  -0.624  21.4246  7.5414  31.7182
 C5G  PA    P  P      0   1.378  21.7193  8.0235  33.2646
 C5G  O1A   O  O      0  -0.793  21.3145  9.4512  33.4486
 C5G  O2A   O  OP    -1  -0.768  21.2154  6.9208  34.1323
 C5G  O3A   O  O2     0  -0.753  23.3683  7.9147  33.3014
 C5G  PB    P  P      0   1.381  24.4812  9.1046  33.1590
 C5G  O1B   O  O      0  -0.761  24.6963  9.8015  34.4575
 C5G  O2B   O  OP    -1  -0.777  24.2212  9.9202  31.9198
 C5G  O1'   O  O2     0  -0.626  25.8048  8.1314  32.9633
 C5G  C1'   C  CH1    0   0.246  25.8383  7.1038  32.0155
 C5G  C2'   C  CH1    0  -0.015  27.2106  6.4193  32.0366
 C5G  O2'   O  OH1    0  -0.658  27.5880  6.0055  33.3212
 C5G  C3'   C  CH1    0  -0.012  28.2978  7.3349  31.4730
 C5G  O3'   O  OH1    0  -0.656  29.5472  6.6951  31.4137
 C5G  C4'   C  CH1    0   0.015  27.8689  7.8987  30.1101
 C5G  O4'   O  OH1    0  -0.655  28.8156  8.8035  29.5981
 C5G  C5'   C  CH1    0  -0.097  26.4866  8.5321  30.2573
 C5G  C6'   C  CH2    0  -0.116  25.8903  9.1121  28.9919
 C5G  O6'   O  OH1    0  -0.718  24.6981  9.8158  29.2390
 C5G  O5'   O  O2     0  -0.494  25.5699  7.5570  30.7292
 C5G  H5    H  H      0   0.290  24.9622  3.9711  31.5697
 C5G  H6    H  H      0   0.312  23.0644  5.4347  30.9549
 C5G  H41   H  HNH2   0   0.414  26.6487  2.4409  30.6690
 C5G  H42   H  HNH2   0   0.401  26.7125  2.0160  28.9976
 C5G  H1D   H  HCH1   0   0.262  21.8155  5.6666  27.5643
 C5G  H2D   H  HCH1   0   0.249  20.9088  5.2476  30.4479
 C5G  HO'2  H  HOH1   0   0.465  19.4309  3.9840  29.4168
 C5G  H3D   H  HCH1   0   0.243  19.2768  6.9578  30.1209
 C5G  H4D   H  HCH1   0   0.248  20.9826  8.5837  28.6057
 C5G  H3T   H  HOH1   0   0.444  18.8491  6.1366  27.8784
 C5G  H5'1  H  HCH2   0   0.213  20.4937  9.1685  30.8266
 C5G  H5'2  H  HCH2   0   0.236  22.2425  9.1101  30.6275
 C5G  H1'   H  HCH1   0   0.231  25.0618  6.3626  32.2354
 C5G  H2'   H  HCH1   0   0.216  27.1200  5.5566  31.3551
 C5G  HOD   H  HOH1   0   0.453  27.0127  5.2826  33.5914
 C5G  H3'   H  HCH1   0   0.232  28.4342  8.1787  32.1621
 C5G  HO'3  H  HOH1   0   0.441  29.4756  5.9311  30.8302
 C5G  H4'   H  HCH1   0   0.231  27.8109  7.0764  29.3851
 C5G  HO'4  H  HOH1   0   0.444  28.9101  9.5352  30.2192
 C5G  H5'   H  HCH1   0   0.222  26.5785  9.3542  30.9817
 C5G  H6'1  H  HCH2   0   0.184  25.7088  8.2992  28.2751
 C5G  H6'2  H  HCH2   0   0.189  26.6338  9.7745  28.5350
 C5G  HO'6  H  HOH1   0   0.466  24.5214  9.8342  30.2038

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
 C5G  N1   C2    aromatic  1.410  0.020  1.410
 C5G  N1   C6    aromatic  1.356  0.020  1.356
 C5G  N1   C1D   single    1.447  0.020  1.447
 C5G  C2   N3    aromatic  1.349  0.020  1.349
 C5G  C2   O2    double    1.222  0.020  1.222
 C5G  N3   C4    aromatic  1.317  0.020  1.317
 C5G  C4   C5    aromatic  1.429  0.020  1.429
 C5G  C4   N4    single    1.332  0.020  1.332
 C5G  C5   C6    aromatic  1.346  0.020  1.346
 C5G  C5   H5    single    0.930  0.020  1.080
 C5G  C6   H6    single    0.930  0.020  1.080
 C5G  N4   H41   single    0.860  0.020  1.020
 C5G  N4   H42   single    0.860  0.020  1.020
 C5G  C1D  C2D   single    1.526  0.020  1.526
 C5G  C1D  O4D   single    1.400  0.020  1.400
 C5G  C1D  H1D   single    0.970  0.020  1.090
 C5G  C2D  O2D   single    1.399  0.020  1.399
 C5G  C2D  C3D   single    1.532  0.020  1.532
 C5G  C2D  H2D   single    0.970  0.020  1.090
 C5G  O2D  HO'2  single    0.850  0.020  0.980
 C5G  C3D  C4D   single    1.533  0.020  1.533
 C5G  C3D  O3D   single    1.407  0.020  1.407
 C5G  C3D  H3D   single    0.970  0.020  1.090
 C5G  C4D  O4D   single    1.430  0.020  1.430
 C5G  C4D  C5D   single    1.509  0.020  1.509
 C5G  C4D  H4D   single    0.970  0.020  1.090
 C5G  O3D  H3T   single    0.850  0.020  0.980
 C5G  C5D  O5D   single    1.413  0.020  1.413
 C5G  C5D  H5'1  single    0.970  0.020  1.090
 C5G  C5D  H5'2  single    0.970  0.020  1.090
 C5G  O5D  PA    single    1.646  0.020  1.646
 C5G  PA   O1A   deloc     1.495  0.020  1.495
 C5G  PA   O2A   deloc     1.491  0.020  1.491
 C5G  PA   O3A   single    1.653  0.020  1.653
 C5G  O3A  PB    single    1.636  0.020  1.636
 C5G  PB   O1B   deloc     1.489  0.020  1.489
 C5G  PB   O2B   deloc     1.506  0.020  1.506
 C5G  PB   O1'   single    1.655  0.020  1.655
 C5G  O1'  C1'   single    1.398  0.020  1.398
 C5G  C1'  C2'   single    1.534  0.020  1.534
 C5G  C1'  O5'   single    1.390  0.020  1.390
 C5G  C1'  H1'   single    0.970  0.020  1.090
 C5G  C2'  O2'   single    1.401  0.020  1.401
 C5G  C2'  C3'   single    1.529  0.020  1.529
 C5G  C2'  H2'   single    0.970  0.020  1.090
 C5G  O2'  HOD   single    0.850  0.020  0.980
 C5G  C3'  O3'   single    1.405  0.020  1.405
 C5G  C3'  C4'   single    1.536  0.020  1.536
 C5G  C3'  H3'   single    0.970  0.020  1.090
 C5G  O3'  HO'3  single    0.850  0.020  0.980
 C5G  C4'  O4'   single    1.406  0.020  1.406
 C5G  C4'  C5'   single    1.528  0.020  1.528
 C5G  C4'  H4'   single    0.970  0.020  1.090
 C5G  O4'  HO'4  single    0.850  0.020  0.980
 C5G  C5'  C6'   single    1.514  0.020  1.514
 C5G  C5'  O5'   single    1.419  0.020  1.419
 C5G  C5'  H5'   single    0.970  0.020  1.090
 C5G  C6'  O6'   single    1.406  0.020  1.406
 C5G  C6'  H6'1  single    0.970  0.020  1.090
 C5G  C6'  H6'2  single    0.970  0.020  1.090
 C5G  O6'  HO'6  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
 C5G  C1D   N1   C6    119.41  3.000
 C5G  C1D   N1   C2    119.98  3.000
 C5G  C6    N1   C2    120.58  3.000
 C5G  O2    C2   N3    122.48  3.000
 C5G  O2    C2   N1    119.63  3.000
 C5G  N3    C2   N1    117.89  3.000
 C5G  C4    N3   C2    121.29  3.000
 C5G  N4    C4   C5    119.50  3.000
 C5G  N4    C4   N3    118.31  3.000
 C5G  C5    C4   N3    122.19  3.000
 C5G  H5    C5   C6    121.45  3.000
 C5G  H5    C5   C4    122.13  3.000
 C5G  C6    C5   C4    116.40  3.000
 C5G  H6    C6   C5    121.47  3.000
 C5G  H6    C6   N1    116.92  3.000
 C5G  C5    C6   N1    121.61  3.000
 C5G  H42   N4   H41   118.22  3.000
 C5G  H42   N4   C4    120.11  3.000
 C5G  H41   N4   C4    121.66  3.000
 C5G  H1D   C1D  O4D   111.84  3.000
 C5G  H1D   C1D  C2D   109.66  3.000
 C5G  O4D   C1D  C2D   105.04  3.000
 C5G  H1D   C1D  N1    106.37  3.000
 C5G  O4D   C1D  N1    109.06  3.000
 C5G  C2D   C1D  N1    114.98  3.000
 C5G  H2D   C2D  C3D   108.65  3.000
 C5G  H2D   C2D  O2D   111.76  3.000
 C5G  C3D   C2D  O2D   114.89  3.000
 C5G  H2D   C2D  C1D   110.37  3.000
 C5G  C3D   C2D  C1D   100.89  3.000
 C5G  O2D   C2D  C1D   109.75  3.000
 C5G  HO'2  O2D  C2D   109.09  3.000
 C5G  H3D   C3D  O3D   111.22  3.000
 C5G  H3D   C3D  C4D   111.81  3.000
 C5G  O3D   C3D  C4D   108.35  3.000
 C5G  H3D   C3D  C2D   111.85  3.000
 C5G  O3D   C3D  C2D   110.92  3.000
 C5G  C4D   C3D  C2D   102.31  3.000
 C5G  H4D   C4D  C5D   106.72  3.000
 C5G  H4D   C4D  O4D   109.21  3.000
 C5G  C5D   C4D  O4D   110.10  3.000
 C5G  H4D   C4D  C3D   108.74  3.000
 C5G  C5D   C4D  C3D   115.38  3.000
 C5G  O4D   C4D  C3D   106.59  3.000
 C5G  C4D   O4D  C1D   110.12  3.000
 C5G  H3T   O3D  C3D   107.74  3.000
 C5G  H5'2  C5D  H5'1  107.27  3.000
 C5G  H5'2  C5D  O5D   111.51  3.000
 C5G  H5'1  C5D  O5D   111.12  3.000
 C5G  H5'2  C5D  C4D   108.97  3.000
 C5G  H5'1  C5D  C4D   107.72  3.000
 C5G  O5D   C5D  C4D   110.13  3.000
 C5G  PA    O5D  C5D   120.33  3.000
 C5G  O3A   PA   O2A   105.99  3.000
 C5G  O3A   PA   O1A   109.28  3.000
 C5G  O2A   PA   O1A   122.90  3.000
 C5G  O3A   PA   O5D   100.38  3.000
 C5G  O2A   PA   O5D   105.64  3.000
 C5G  O1A   PA   O5D   110.28  3.000
 C5G  PB    O3A  PA    128.98  3.000
 C5G  O1'   PB   O2B   111.06  3.000
 C5G  O1'   PB   O1B   105.24  3.000
 C5G  O2B   PB   O1B   119.27  3.000
 C5G  O1'   PB   O3A    97.28  3.000
 C5G  O2B   PB   O3A   110.37  3.000
 C5G  O1B   PB   O3A   111.28  3.000
 C5G  C1'   O1'  PB    122.12  3.000
 C5G  H1'   C1'  O5'   105.63  3.000
 C5G  H1'   C1'  C2'   109.24  3.000
 C5G  O5'   C1'  C2'   109.33  3.000
 C5G  H1'   C1'  O1'   110.12  3.000
 C5G  O5'   C1'  O1'   112.52  3.000
 C5G  C2'   C1'  O1'   109.88  3.000
 C5G  H2'   C2'  C3'   107.40  3.000
 C5G  H2'   C2'  O2'   110.95  3.000
 C5G  C3'   C2'  O2'   108.86  3.000
 C5G  H2'   C2'  C1'   105.49  3.000
 C5G  C3'   C2'  C1'   111.34  3.000
 C5G  O2'   C2'  C1'   112.67  3.000
 C5G  HOD   O2'  C2'   108.55  3.000
 C5G  H3'   C3'  C4'   108.03  3.000
 C5G  H3'   C3'  O3'   105.42  3.000
 C5G  C4'   C3'  O3'   112.21  3.000
 C5G  H3'   C3'  C2'   108.49  3.000
 C5G  C4'   C3'  C2'   110.39  3.000
 C5G  O3'   C3'  C2'   112.03  3.000
 C5G  HO'3  O3'  C3'   108.69  3.000
 C5G  H4'   C4'  C5'   109.06  3.000
 C5G  H4'   C4'  O4'   106.09  3.000
 C5G  C5'   C4'  O4'   112.18  3.000
 C5G  H4'   C4'  C3'   109.01  3.000
 C5G  C5'   C4'  C3'   108.62  3.000
 C5G  O4'   C4'  C3'   111.79  3.000
 C5G  HO'4  O4'  C4'   108.64  3.000
 C5G  H5'   C5'  O5'   110.40  3.000
 C5G  H5'   C5'  C6'   107.28  3.000
 C5G  O5'   C5'  C6'   106.66  3.000
 C5G  H5'   C5'  C4'   107.33  3.000
 C5G  O5'   C5'  C4'   109.37  3.000
 C5G  C6'   C5'  C4'   115.76  3.000
 C5G  H6'2  C6'  H6'1  106.70  3.000
 C5G  H6'2  C6'  O6'   110.25  3.000
 C5G  H6'1  C6'  O6'   110.17  3.000
 C5G  H6'2  C6'  C5'   108.23  3.000
 C5G  H6'1  C6'  C5'   109.07  3.000
 C5G  O6'   C6'  C5'   112.25  3.000
 C5G  HO'6  O6'  C6'   109.56  3.000
 C5G  C5'   O5'  C1'   114.02  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
 C5G  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 C5G  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 C5G  CONST_03  C5    C6   N1   C2     0.00   0.0  0
 C5G  CONST_04  C5    C4   N3   C2     0.00   0.0  0
 C5G  CONST_05  C6    N1   C2   N3     0.00   0.0  0
 C5G  CONST_06  C6    C5   C4   N3     0.00   0.0  0
 C5G  CONST_07  C1D   N1   C2   N3   180.00   0.0  0
 C5G  CONST_08  C1D   N1   C6   C5   180.00   0.0  0
 C5G  CONST_09  N4    C4   N3   C2   180.00   0.0  0
 C5G  CONST_10  O2    C2   N3   C4   180.00   0.0  0
 C5G  CONST_11  O2    C2   N1   C6   180.00   0.0  0
 C5G  CONST_12  N4    C4   C5   C6   180.00   0.0  0
 C5G  CONST_13  C1D   N1   C2   O2     0.00   0.0  0
 C5G  CONST_14  H5    C5   C6   N1   180.00   0.0  0
 C5G  CONST_15  H6    C6   N1   C2   180.00   0.0  0
 C5G  CONST_16  H41   N4   C4   N3   180.00   0.0  0
 C5G  CONST_17  H42   N4   C4   N3     0.00   0.0  0
 C5G  Var_01    O1A   PA   O5D  C5D   23.32  30.0  3
 C5G  Var_02    O1B   PB   O3A  PA    82.42  30.0  3
 C5G  Var_03    H5'1  C5D  O5D  PA   -64.12  30.0  1

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
 C5G  chir_01  C1D  N1   C2D  O4D  negativ
 C5G  chir_02  C2D  O2D  C3D  C1D  positiv
 C5G  chir_03  C3D  O3D  C2D  C4D  negativ
 C5G  chir_04  C4D  O4D  C3D  C5D  negativ
 C5G  chir_07  C1'  O1'  C2'  O5'  positiv
 C5G  chir_08  C2'  O2'  C1'  C3'  negativ
 C5G  chir_09  C3'  O3'  C2'  C4'  positiv
 C5G  chir_10  C4'  O4'  C5'  C3'  positiv
 C5G  chir_11  C5'  O5'  C4'  C6'  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
 C5G  plan-1  N1   0.020
 C5G  plan-1  C2   0.020
 C5G  plan-1  N3   0.020
 C5G  plan-1  C4   0.020
 C5G  plan-1  C5   0.020
 C5G  plan-1  C6   0.020
 C5G  plan-1  O2   0.020
 C5G  plan-1  N4   0.020
 C5G  plan-1  C1D  0.020
 C5G  plan-1  H5   0.020
 C5G  plan-1  H6   0.020
 C5G  plan-2  C4   0.020
 C5G  plan-2  N4   0.020
 C5G  plan-2  H41  0.020
 C5G  plan-2  H42  0.020

