# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 02:27:49 2022
#   Inital geometry file: a 143 line input string
#   Ligand name: [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-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: OC[C@H]1O[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](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
 UPG  UPG  '[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-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  58  36  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UPG
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
 UPG  N1    N  NR6    0  -0.568  25.2187   6.8322  43.2381
 UPG  C2    C  CR6    0   0.728  24.0122   6.2896  43.6384
 UPG  N3    N  NR16   0  -0.735  23.2274   7.1337  44.3816
 UPG  C4    C  CR6    0   0.566  23.4971   8.4382  44.7728
 UPG  C5    C  CR16   0  -0.521  24.7719   8.9191  44.3036
 UPG  C6    C  CR16   0   0.077  25.5606   8.1123  43.5770
 UPG  O2    O  O      0  -0.471  23.6582   5.1630  43.3628
 UPG  O4    O  O      0  -0.456  22.6969   9.0612  45.4440
 UPG  C1C   C  CH1    0   0.189  26.1597   6.0117  42.4861
 UPG  C2C   C  CH1    0  -0.014  26.4602   6.5323  41.0803
 UPG  O2C   O  OH1    0  -0.655  25.4583   6.1033  40.2093
 UPG  C3C   C  CH1    0  -0.052  27.8599   5.9580  40.8471
 UPG  C4C   C  CH1    0  -0.028  28.4778   6.0592  42.2493
 UPG  O4C   O  O2     0  -0.492  27.3820   5.9759  43.1661
 UPG  O3C   O  OH1    0  -0.668  27.7080   4.6195  40.4418
 UPG  C5C   C  CH2    0  -0.168  29.2971   7.3054  42.5124
 UPG  O5C   O  O2     0  -0.633  28.4915   8.4392  42.3063
 UPG  PA    P  P      0   1.381  29.0569   9.9786  42.4675
 UPG  O1A   O  O      0  -0.780  30.1382  10.0204  43.4975
 UPG  O2A   O  OP    -1  -0.781  27.8380  10.8360  42.5653
 UPG  O3A   O  O2     0  -0.751  29.7999  10.1899  41.0152
 UPG  PB    P  P      0   1.361  29.3044   9.6741  39.5302
 UPG  O1B   O  O      0  -0.773  27.8160   9.6927  39.4179
 UPG  O2B   O  OP    -1  -0.781  30.1168   8.4677  39.1711
 UPG  O3B   O  O2     0  -0.621  29.8271  10.9743  38.6555
 UPG  C1'   C  CH1    0   0.255  31.1114  11.0385  38.1148
 UPG  C2'   C  CH1    0   0.014  31.5914  12.4874  38.1459
 UPG  C3'   C  CH1    0  -0.003  30.7566  13.3380  37.1999
 UPG  C4'   C  CH1    0  -0.005  30.7946  12.7317  35.8024
 UPG  C5'   C  CH1    0  -0.016  30.3531  11.2648  35.8638
 UPG  C6'   C  CH2    0  -0.161  30.5194  10.5691  34.5296
 UPG  O2'   O  OH1    0  -0.665  31.5431  12.9428  39.4711
 UPG  O3'   O  OH1    0  -0.671  31.2900  14.6409  37.2216
 UPG  O4'   O  OH1    0  -0.669  29.9437  13.5036  34.9834
 UPG  O5'   O  O2     0  -0.496  31.1439  10.5565  36.8052
 UPG  O6'   O  OH1    0  -0.664  29.9946   9.2663  34.6205
 UPG  HN3   H  HNR6   0   0.422  22.3415   6.7427  44.6790
 UPG  H5    H  HCR6   0   0.284  25.0887   9.9230  44.5414
 UPG  H6    H  HCR6   0   0.350  26.5236   8.4524  43.2254
 UPG  H1C   H  HCH1   0   0.267  25.7150   5.0166  42.4202
 UPG  H2C   H  HCH1   0   0.250  26.5411   7.6239  41.0872
 UPG  HO2C  H  HOH1   0   0.459  25.5172   6.6150  39.3969
 UPG  H3C   H  HCH1   0   0.248  28.4331   6.5399  40.1159
 UPG  H4C   H  HCH1   0   0.252  29.1426   5.2046  42.4222
 UPG  HO3C  H  HOH1   0   0.452  28.5838   4.2422  40.3128
 UPG  H5C1  H  HCH2   0   0.227  29.6832   7.2750  43.5363
 UPG  H5C2  H  HCH2   0   0.214  30.1603   7.2916  41.8379
 UPG  H1'   H  HCH1   0   0.237  31.8117  10.4075  38.6713
 UPG  H2'   H  HCH1   0   0.213  32.6267  12.4822  37.7702
 UPG  H3'   H  HCH1   0   0.212  29.7127  13.3406  37.5484
 UPG  H4'   H  HCH1   0   0.218  31.8328  12.7710  35.4401
 UPG  H5'   H  HCH1   0   0.221  29.2910  11.2311  36.1456
 UPG  H6'1  H  HCH2   0   0.199  29.9967  11.1567  33.7653
 UPG  H6'2  H  HCH2   0   0.195  31.5848  10.5651  34.2589
 UPG  HO2'  H  HOH1   0   0.450  31.9016  13.8356  39.4905
 UPG  HO3'  H  HOH1   0   0.450  30.7143  15.2093  36.7001
 UPG  HO4'  H  HOH1   0   0.458  30.2763  13.4935  34.0818
 UPG  HO6'  H  HOH1   0   0.453  30.0667   8.8544  33.7551

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
 UPG  N1   C2    single  1.382  0.020  1.382
 UPG  N1   C6    single  1.368  0.020  1.368
 UPG  N1   C1C   single  1.458  0.020  1.458
 UPG  C2   N3    single  1.371  0.020  1.371
 UPG  C2   O2    double  1.213  0.020  1.213
 UPG  N3   C4    single  1.388  0.020  1.388
 UPG  N3   HN3   single  0.860  0.020  1.020
 UPG  C4   C5    single  1.441  0.020  1.441
 UPG  C4   O4    double  1.216  0.020  1.216
 UPG  C5   C6    double  1.342  0.020  1.342
 UPG  C5   H5    single  0.930  0.020  1.080
 UPG  C6   H6    single  0.930  0.020  1.080
 UPG  C1C  C2C   single  1.529  0.020  1.529
 UPG  C1C  O4C   single  1.399  0.020  1.399
 UPG  C1C  H1C   single  0.970  0.020  1.090
 UPG  C2C  O2C   single  1.395  0.020  1.395
 UPG  C2C  C3C   single  1.531  0.020  1.531
 UPG  C2C  H2C   single  0.970  0.020  1.090
 UPG  O2C  HO2C  single  0.850  0.020  0.980
 UPG  C3C  C4C   single  1.536  0.020  1.536
 UPG  C3C  O3C   single  1.407  0.020  1.407
 UPG  C3C  H3C   single  0.970  0.020  1.090
 UPG  C4C  O4C   single  1.431  0.020  1.431
 UPG  C4C  C5C   single  1.514  0.020  1.514
 UPG  C4C  H4C   single  0.970  0.020  1.090
 UPG  O3C  HO3C  single  0.850  0.020  0.980
 UPG  C5C  O5C   single  1.406  0.020  1.406
 UPG  C5C  H5C1  single  0.970  0.020  1.090
 UPG  C5C  H5C2  single  0.970  0.020  1.090
 UPG  O5C  PA    single  1.648  0.020  1.648
 UPG  PA   O1A   deloc   1.494  0.020  1.494
 UPG  PA   O2A   deloc   1.493  0.020  1.493
 UPG  PA   O3A   single  1.645  0.020  1.645
 UPG  O3A  PB    single  1.648  0.020  1.648
 UPG  PB   O1B   deloc   1.493  0.020  1.493
 UPG  PB   O2B   deloc   1.498  0.020  1.498
 UPG  PB   O3B   single  1.652  0.020  1.652
 UPG  O3B  C1'   single  1.395  0.020  1.395
 UPG  C1'  C2'   single  1.527  0.020  1.527
 UPG  C1'  O5'   single  1.396  0.020  1.396
 UPG  C1'  H1'   single  0.970  0.020  1.090
 UPG  C2'  C3'   single  1.522  0.020  1.522
 UPG  C2'  O2'   single  1.402  0.020  1.402
 UPG  C2'  H2'   single  0.970  0.020  1.090
 UPG  C3'  C4'   single  1.524  0.020  1.524
 UPG  C3'  O3'   single  1.408  0.020  1.408
 UPG  C3'  H3'   single  0.970  0.020  1.090
 UPG  C4'  C5'   single  1.533  0.020  1.533
 UPG  C4'  O4'   single  1.411  0.020  1.411
 UPG  C4'  H4'   single  0.970  0.020  1.090
 UPG  C5'  C6'   single  1.514  0.020  1.514
 UPG  C5'  O5'   single  1.419  0.020  1.419
 UPG  C5'  H5'   single  0.970  0.020  1.090
 UPG  C6'  O6'   single  1.407  0.020  1.407
 UPG  C6'  H6'1  single  0.970  0.020  1.090
 UPG  C6'  H6'2  single  0.970  0.020  1.090
 UPG  O2'  HO2'  single  0.850  0.020  0.980
 UPG  O3'  HO3'  single  0.850  0.020  0.980
 UPG  O4'  HO4'  single  0.850  0.020  0.980
 UPG  O6'  HO6'  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
 UPG  C1C   N1   C6    119.56  3.000
 UPG  C1C   N1   C2    119.48  3.000
 UPG  C6    N1   C2    120.93  3.000
 UPG  O2    C2   N3    121.87  3.000
 UPG  O2    C2   N1    123.62  3.000
 UPG  N3    C2   N1    114.51  3.000
 UPG  HN3   N3   C4    116.73  3.000
 UPG  HN3   N3   C2    114.96  3.000
 UPG  C4    N3   C2    128.30  3.000
 UPG  O4    C4   C5    126.21  3.000
 UPG  O4    C4   N3    120.60  3.000
 UPG  C5    C4   N3    113.18  3.000
 UPG  H5    C5   C6    120.40  3.000
 UPG  H5    C5   C4    119.89  3.000
 UPG  C6    C5   C4    119.71  3.000
 UPG  H6    C6   C5    120.73  3.000
 UPG  H6    C6   N1    115.91  3.000
 UPG  C5    C6   N1    123.36  3.000
 UPG  H1C   C1C  O4C   111.21  3.000
 UPG  H1C   C1C  C2C   109.56  3.000
 UPG  O4C   C1C  C2C   106.49  3.000
 UPG  H1C   C1C  N1    106.33  3.000
 UPG  O4C   C1C  N1    109.13  3.000
 UPG  C2C   C1C  N1    114.18  3.000
 UPG  H2C   C2C  C3C   107.91  3.000
 UPG  H2C   C2C  O2C   111.32  3.000
 UPG  C3C   C2C  O2C   116.50  3.000
 UPG  H2C   C2C  C1C   110.38  3.000
 UPG  C3C   C2C  C1C   101.07  3.000
 UPG  O2C   C2C  C1C   109.16  3.000
 UPG  HO2C  O2C  C2C   108.65  3.000
 UPG  H3C   C3C  O3C   111.67  3.000
 UPG  H3C   C3C  C4C   111.33  3.000
 UPG  O3C   C3C  C4C   111.67  3.000
 UPG  H3C   C3C  C2C   112.37  3.000
 UPG  O3C   C3C  C2C   107.58  3.000
 UPG  C4C   C3C  C2C   101.78  3.000
 UPG  H4C   C4C  C5C   106.62  3.000
 UPG  H4C   C4C  O4C   108.54  3.000
 UPG  C5C   C4C  O4C   110.54  3.000
 UPG  H4C   C4C  C3C   109.67  3.000
 UPG  C5C   C4C  C3C   115.50  3.000
 UPG  O4C   C4C  C3C   105.84  3.000
 UPG  C4C   O4C  C1C   110.86  3.000
 UPG  HO3C  O3C  C3C   108.26  3.000
 UPG  H5C2  C5C  H5C1  107.31  3.000
 UPG  H5C2  C5C  O5C   111.80  3.000
 UPG  H5C1  C5C  O5C   111.20  3.000
 UPG  H5C2  C5C  C4C   107.99  3.000
 UPG  H5C1  C5C  C4C   109.29  3.000
 UPG  O5C   C5C  C4C   109.16  3.000
 UPG  PA    O5C  C5C   122.85  3.000
 UPG  O3A   PA   O2A   110.65  3.000
 UPG  O3A   PA   O1A   106.15  3.000
 UPG  O2A   PA   O1A   121.98  3.000
 UPG  O3A   PA   O5C   100.87  3.000
 UPG  O2A   PA   O5C   105.23  3.000
 UPG  O1A   PA   O5C   109.99  3.000
 UPG  PB    O3A  PA    128.28  3.000
 UPG  O3B   PB   O2B   109.59  3.000
 UPG  O3B   PB   O1B   105.41  3.000
 UPG  O2B   PB   O1B   122.19  3.000
 UPG  O3B   PB   O3A    97.80  3.000
 UPG  O2B   PB   O3A   107.76  3.000
 UPG  O1B   PB   O3A   111.32  3.000
 UPG  C1'   O3B  PB    122.19  3.000
 UPG  H1'   C1'  O5'   105.25  3.000
 UPG  H1'   C1'  C2'   109.61  3.000
 UPG  O5'   C1'  C2'   109.85  3.000
 UPG  H1'   C1'  O3B   111.44  3.000
 UPG  O5'   C1'  O3B   111.66  3.000
 UPG  C2'   C1'  O3B   108.98  3.000
 UPG  H2'   C2'  O2'   110.87  3.000
 UPG  H2'   C2'  C3'   107.83  3.000
 UPG  O2'   C2'  C3'   112.78  3.000
 UPG  H2'   C2'  C1'   106.50  3.000
 UPG  O2'   C2'  C1'   108.46  3.000
 UPG  C3'   C2'  C1'   110.20  3.000
 UPG  H3'   C3'  O3'   110.63  3.000
 UPG  H3'   C3'  C4'   108.36  3.000
 UPG  O3'   C3'  C4'   111.89  3.000
 UPG  H3'   C3'  C2'   108.96  3.000
 UPG  O3'   C3'  C2'   107.45  3.000
 UPG  C4'   C3'  C2'   109.52  3.000
 UPG  H4'   C4'  O4'   111.00  3.000
 UPG  H4'   C4'  C5'   108.60  3.000
 UPG  O4'   C4'  C5'   111.90  3.000
 UPG  H4'   C4'  C3'   108.14  3.000
 UPG  O4'   C4'  C3'   107.44  3.000
 UPG  C5'   C4'  C3'   109.68  3.000
 UPG  H5'   C5'  O5'   110.68  3.000
 UPG  H5'   C5'  C6'   108.54  3.000
 UPG  O5'   C5'  C6'   107.10  3.000
 UPG  H5'   C5'  C4'   108.53  3.000
 UPG  O5'   C5'  C4'   110.10  3.000
 UPG  C6'   C5'  C4'   111.89  3.000
 UPG  H6'2  C6'  H6'1  106.99  3.000
 UPG  H6'2  C6'  O6'   111.96  3.000
 UPG  H6'1  C6'  O6'   111.31  3.000
 UPG  H6'2  C6'  C5'   108.97  3.000
 UPG  H6'1  C6'  C5'   108.40  3.000
 UPG  O6'   C6'  C5'   109.11  3.000
 UPG  HO2'  O2'  C2'   107.91  3.000
 UPG  HO3'  O3'  C3'   108.15  3.000
 UPG  HO4'  O4'  C4'   109.28  3.000
 UPG  C5'   O5'  C1'   115.92  3.000
 UPG  HO6'  O6'  C6'   108.09  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
 UPG  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 UPG  CONST_02  C5    C4   N3   C2     0.00   0.0  0
 UPG  CONST_03  C6    N1   C2   N3     0.00   0.0  0
 UPG  CONST_04  C1C   N1   C2   N3   180.00   0.0  0
 UPG  CONST_05  O4    C4   N3   C2   180.00   0.0  0
 UPG  CONST_06  O2    C2   N3   C4   180.00   0.0  0
 UPG  CONST_07  O2    C2   N1   C6   180.00   0.0  0
 UPG  CONST_08  C1C   N1   C2   O2     0.00   0.0  0
 UPG  CONST_09  HN3   N3   C2   N1   180.00   0.0  0
 UPG  Var_01    O1A   PA   O5C  C5C  -30.72  30.0  3
 UPG  Var_02    O1B   PB   O3A  PA    33.82  30.0  3
 UPG  Var_03    H5C1  C5C  O5C  PA    60.75  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
 UPG  chir_01  C1C  N1   C2C  O4C  negativ
 UPG  chir_02  C2C  O2C  C3C  C1C  positiv
 UPG  chir_03  C3C  O3C  C2C  C4C  negativ
 UPG  chir_04  C4C  O4C  C3C  C5C  negativ
 UPG  chir_07  C1'  O3B  C2'  O5'  positiv
 UPG  chir_08  C2'  O2'  C1'  C3'  negativ
 UPG  chir_09  C3'  O3'  C2'  C4'  positiv
 UPG  chir_10  C4'  O4'  C3'  C5'  negativ
 UPG  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
 UPG  plan-1  N1   0.020
 UPG  plan-1  C2   0.020
 UPG  plan-1  N3   0.020
 UPG  plan-1  C4   0.020
 UPG  plan-1  C5   0.020
 UPG  plan-1  C6   0.020
 UPG  plan-1  O2   0.020
 UPG  plan-1  O4   0.020
 UPG  plan-1  C1C  0.020
 UPG  plan-1  HN3  0.020
 UPG  plan-1  H5   0.020
 UPG  plan-1  H6   0.020

