# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 09:39:06 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,5R,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
 GDU  GDU  '[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)'  ligand  58  36  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GDU
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
 GDU  N1    N  NR6    0  -0.575   1.0589  -1.0997   2.1773
 GDU  C2    C  CR6    0   0.745   1.6266   0.1625   2.1579
 GDU  N3    N  NR16   0  -0.738   2.9759   0.1785   1.9067
 GDU  C4    C  CR6    0   0.553   3.8255  -0.8960   1.6858
 GDU  C5    C  CR16   0  -0.507   3.1455  -2.1648   1.6941
 GDU  C6    C  CR16   0   0.110   1.8229  -2.2043   1.9211
 GDU  O2    O  O      0  -0.461   1.0050   1.1837   2.3496
 GDU  O4    O  O      0  -0.461   5.0147  -0.7154   1.4994
 GDU  C1D   C  CH1    0   0.243  -0.3715  -1.2777   2.3935
 GDU  C2D   C  CH1    0  -0.060  -0.9420  -0.6912   3.6850
 GDU  O2D   O  OH1    0  -0.660  -0.7080  -1.5759   4.7445
 GDU  C3D   C  CH1    0  -0.040  -2.4181  -0.5424   3.2955
 GDU  C4D   C  CH1    0  -0.013  -2.3149  -0.1433   1.8268
 GDU  O4D   O  O2     0  -0.470  -1.0996  -0.7191   1.3488
 GDU  O3D   O  OH1    0  -0.671  -3.0850  -1.7766   3.3813
 GDU  C5D   C  CH2    0  -0.149  -2.3266   1.3582   1.6256
 GDU  O5D   O  O2     0  -0.602  -2.1278   1.6387   0.2580
 GDU  PA    P  P      0   1.351  -2.8048   3.0118  -0.3227
 GDU  O1A   O  O      0  -0.795  -4.2892   2.8644  -0.4143
 GDU  O2A   O  OP    -1  -0.795  -2.2084   4.1999   0.3659
 GDU  O3A   O  O2     0  -0.727  -2.1317   2.9847  -1.8255
 GDU  PB    P  P      0   1.381  -2.1792   1.8565  -2.9924
 GDU  O1B   O  O      0  -0.792  -3.1184   0.7310  -2.6458
 GDU  O2B   O  OP    -1  -0.773  -2.3089   2.5521  -4.3074
 GDU  O3B   O  O2     0  -0.628  -0.6355   1.3274  -2.7913
 GDU  C1'   C  CH1    0   0.215  -0.0964   0.2726  -3.5531
 GDU  C2'   C  CH1    0   0.003  -0.3090  -1.0810  -2.8620
 GDU  C3'   C  CH1    0  -0.018   0.4113  -1.0655  -1.5156
 GDU  C4'   C  CH1    0  -0.007   1.8882  -0.7465  -1.7231
 GDU  C5'   C  CH1    0  -0.009   2.0259   0.5407  -2.5239
 GDU  C6'   C  CH2    0  -0.155   3.4637   0.8330  -2.8974
 GDU  O2'   O  OH1    0  -0.715  -1.6511  -1.4653  -2.7421
 GDU  O3'   O  OH1    0  -0.678   0.3364  -2.3215  -0.8783
 GDU  O4'   O  OH1    0  -0.675   2.5609  -1.7888  -2.3885
 GDU  O5'   O  O2     0  -0.495   1.2639   0.5107  -3.7238
 GDU  O6'   O  OH1    0  -0.671   3.5371   2.1468  -3.4003
 GDU  HN3   H  HNR6   0   0.425   3.3953   1.1006   1.9048
 GDU  H5    H  HCR6   0   0.291   3.6973  -3.0728   1.5078
 GDU  H6    H  HCR6   0   0.324   1.2891  -3.1432   1.9241
 GDU  H1D   H  HCH1   0   0.245  -0.5084  -2.3650   2.4282
 GDU  H2D   H  HCH1   0   0.269  -0.5254   0.2970   3.8856
 GDU  HO2'  H  HOH1   0   0.469  -0.7466  -1.0849   5.5710
 GDU  H3D   H  HCH1   0   0.246  -2.9202   0.2288   3.8949
 GDU  H4D   H  HCH1   0   0.248  -3.1446  -0.5736   1.2571
 GDU  HO3'  H  HOH1   0   0.447  -2.8573  -2.1739   4.2301
 GDU  H5'1  H  HCH2   0   0.220  -1.5553   1.8397   2.2335
 GDU  H5'2  H  HCH2   0   0.208  -3.2992   1.7202   1.9818
 GDU  H1'   H  HCH1   0   0.239  -0.5285   0.2567  -4.5617
 GDU  H2'   H  HCH1   0   0.213   0.1747  -1.8285  -3.5016
 GDU  H3'   H  HCH1   0   0.246  -0.0312  -0.2870  -0.8833
 GDU  H4'   H  HCH1   0   0.209   2.3444  -0.5587  -0.7394
 GDU  H5'   H  HCH1   0   0.231   1.6771   1.3552  -1.8758
 GDU  H6'1  H  HCH2   0   0.207   3.8179   0.0997  -3.6302
 GDU  H6'2  H  HCH2   0   0.197   4.0788   0.7107  -1.9954
 GDU  HO2A  H  HOH1   0   0.453  -2.2214  -0.6822  -2.5496
 GDU  HO3A  H  HOH1   0   0.449  -0.5934  -2.5020  -0.7071
 GDU  HO4'  H  HOH1   0   0.450   2.3479  -2.6107  -1.9332
 GDU  HO6'  H  HOH1   0   0.456   4.4398   2.3041  -3.6905

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
 GDU  N1   C2    single  1.384  0.020  1.384
 GDU  N1   C6    single  1.367  0.020  1.367
 GDU  N1   C1D   single  1.458  0.020  1.458
 GDU  C2   N3    single  1.373  0.020  1.373
 GDU  C2   O2    double  1.211  0.020  1.211
 GDU  N3   C4    single  1.388  0.020  1.388
 GDU  N3   HN3   single  0.860  0.020  1.020
 GDU  C4   C5    single  1.440  0.020  1.440
 GDU  C4   O4    double  1.217  0.020  1.217
 GDU  C5   C6    double  1.343  0.020  1.343
 GDU  C5   H5    single  0.930  0.020  1.080
 GDU  C6   H6    single  0.930  0.020  1.080
 GDU  C1D  C2D   single  1.529  0.020  1.529
 GDU  C1D  O4D   single  1.390  0.020  1.390
 GDU  C1D  H1D   single  0.970  0.020  1.090
 GDU  C2D  O2D   single  1.400  0.020  1.400
 GDU  C2D  C3D   single  1.534  0.020  1.534
 GDU  C2D  H2D   single  0.970  0.020  1.090
 GDU  O2D  HO2'  single  0.850  0.020  0.980
 GDU  C3D  C4D   single  1.526  0.020  1.526
 GDU  C3D  O3D   single  1.405  0.020  1.405
 GDU  C3D  H3D   single  0.970  0.020  1.090
 GDU  C4D  O4D   single  1.427  0.020  1.427
 GDU  C4D  C5D   single  1.515  0.020  1.515
 GDU  C4D  H4D   single  0.970  0.020  1.090
 GDU  O3D  HO3'  single  0.850  0.020  0.980
 GDU  C5D  O5D   single  1.410  0.020  1.410
 GDU  C5D  H5'1  single  0.970  0.020  1.090
 GDU  C5D  H5'2  single  0.970  0.020  1.090
 GDU  O5D  PA    single  1.637  0.020  1.637
 GDU  PA   O1A   deloc   1.495  0.020  1.495
 GDU  PA   O2A   deloc   1.497  0.020  1.497
 GDU  PA   O3A   single  1.647  0.020  1.647
 GDU  O3A  PB    single  1.624  0.020  1.624
 GDU  PB   O1B   deloc   1.506  0.020  1.506
 GDU  PB   O2B   deloc   1.493  0.020  1.493
 GDU  PB   O3B   single  1.644  0.020  1.644
 GDU  O3B  C1'   single  1.408  0.020  1.408
 GDU  C1'  C2'   single  1.535  0.020  1.535
 GDU  C1'  O5'   single  1.392  0.020  1.392
 GDU  C1'  H1'   single  0.970  0.020  1.090
 GDU  C2'  C3'   single  1.527  0.020  1.527
 GDU  C2'  O2'   single  1.401  0.020  1.401
 GDU  C2'  H2'   single  0.970  0.020  1.090
 GDU  C3'  C4'   single  1.525  0.020  1.525
 GDU  C3'  O3'   single  1.410  0.020  1.410
 GDU  C3'  H3'   single  0.970  0.020  1.090
 GDU  C4'  C5'   single  1.522  0.020  1.522
 GDU  C4'  O4'   single  1.408  0.020  1.408
 GDU  C4'  H4'   single  0.970  0.020  1.090
 GDU  C5'  C6'   single  1.514  0.020  1.514
 GDU  C5'  O5'   single  1.422  0.020  1.422
 GDU  C5'  H5'   single  0.970  0.020  1.090
 GDU  C6'  O6'   single  1.409  0.020  1.409
 GDU  C6'  H6'1  single  0.970  0.020  1.090
 GDU  C6'  H6'2  single  0.970  0.020  1.090
 GDU  O2'  HO2A  single  0.850  0.020  0.980
 GDU  O3'  HO3A  single  0.850  0.020  0.980
 GDU  O4'  HO4'  single  0.850  0.020  0.980
 GDU  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
 GDU  C1D   N1   C6    118.53  3.000
 GDU  C1D   N1   C2    121.06  3.000
 GDU  C6    N1   C2    120.32  3.000
 GDU  O2    C2   N3    121.58  3.000
 GDU  O2    C2   N1    123.80  3.000
 GDU  N3    C2   N1    114.61  3.000
 GDU  HN3   N3   C4    116.81  3.000
 GDU  HN3   N3   C2    114.71  3.000
 GDU  C4    N3   C2    128.46  3.000
 GDU  O4    C4   C5    126.38  3.000
 GDU  O4    C4   N3    120.52  3.000
 GDU  C5    C4   N3    113.11  3.000
 GDU  H5    C5   C6    120.56  3.000
 GDU  H5    C5   C4    119.96  3.000
 GDU  C6    C5   C4    119.48  3.000
 GDU  H6    C6   C5    120.86  3.000
 GDU  H6    C6   N1    115.19  3.000
 GDU  C5    C6   N1    123.95  3.000
 GDU  H1D   C1D  O4D   110.90  3.000
 GDU  H1D   C1D  C2D   107.88  3.000
 GDU  O4D   C1D  C2D   106.57  3.000
 GDU  H1D   C1D  N1    104.38  3.000
 GDU  O4D   C1D  N1    110.70  3.000
 GDU  C2D   C1D  N1    116.40  3.000
 GDU  H2D   C2D  C3D   109.04  3.000
 GDU  H2D   C2D  O2D   111.68  3.000
 GDU  C3D   C2D  O2D   114.48  3.000
 GDU  H2D   C2D  C1D   111.11  3.000
 GDU  C3D   C2D  C1D   100.47  3.000
 GDU  O2D   C2D  C1D   109.55  3.000
 GDU  HO2'  O2D  C2D   108.72  3.000
 GDU  H3D   C3D  O3D   111.49  3.000
 GDU  H3D   C3D  C4D   111.88  3.000
 GDU  O3D   C3D  C4D   108.70  3.000
 GDU  H3D   C3D  C2D   111.68  3.000
 GDU  O3D   C3D  C2D   110.85  3.000
 GDU  C4D   C3D  C2D   101.81  3.000
 GDU  H4D   C4D  C5D   108.34  3.000
 GDU  H4D   C4D  O4D   108.21  3.000
 GDU  C5D   C4D  O4D   111.22  3.000
 GDU  H4D   C4D  C3D   110.30  3.000
 GDU  C5D   C4D  C3D   112.75  3.000
 GDU  O4D   C4D  C3D   105.93  3.000
 GDU  C4D   O4D  C1D   110.88  3.000
 GDU  HO3'  O3D  C3D   107.66  3.000
 GDU  H5'2  C5D  H5'1  107.43  3.000
 GDU  H5'2  C5D  O5D   111.97  3.000
 GDU  H5'1  C5D  O5D   110.61  3.000
 GDU  H5'2  C5D  C4D   106.90  3.000
 GDU  H5'1  C5D  C4D   110.92  3.000
 GDU  O5D   C5D  C4D   108.96  3.000
 GDU  PA    O5D  C5D   116.91  3.000
 GDU  O3A   PA   O2A   105.66  3.000
 GDU  O3A   PA   O1A   110.39  3.000
 GDU  O2A   PA   O1A   120.14  3.000
 GDU  O3A   PA   O5D    98.10  3.000
 GDU  O2A   PA   O5D   109.74  3.000
 GDU  O1A   PA   O5D   110.47  3.000
 GDU  PB    O3A  PA    130.94  3.000
 GDU  O3B   PB   O2B   109.83  3.000
 GDU  O3B   PB   O1B   108.47  3.000
 GDU  O2B   PB   O1B   119.77  3.000
 GDU  O3B   PB   O3A    96.22  3.000
 GDU  O2B   PB   O3A   108.17  3.000
 GDU  O1B   PB   O3A   111.83  3.000
 GDU  C1'   O3B  PB    122.29  3.000
 GDU  H1'   C1'  O5'   105.94  3.000
 GDU  H1'   C1'  C2'   110.28  3.000
 GDU  O5'   C1'  C2'   109.97  3.000
 GDU  H1'   C1'  O3B   110.93  3.000
 GDU  O5'   C1'  O3B   108.20  3.000
 GDU  C2'   C1'  O3B   111.34  3.000
 GDU  H2'   C2'  O2'   106.59  3.000
 GDU  H2'   C2'  C3'   108.25  3.000
 GDU  O2'   C2'  C3'   112.28  3.000
 GDU  H2'   C2'  C1'   106.11  3.000
 GDU  O2'   C2'  C1'   114.40  3.000
 GDU  C3'   C2'  C1'   108.83  3.000
 GDU  H3'   C3'  O3'   110.51  3.000
 GDU  H3'   C3'  C4'   108.72  3.000
 GDU  O3'   C3'  C4'   107.41  3.000
 GDU  H3'   C3'  C2'   108.98  3.000
 GDU  O3'   C3'  C2'   111.36  3.000
 GDU  C4'   C3'  C2'   109.81  3.000
 GDU  H4'   C4'  O4'   110.54  3.000
 GDU  H4'   C4'  C5'   106.76  3.000
 GDU  O4'   C4'  C5'   109.53  3.000
 GDU  H4'   C4'  C3'   108.39  3.000
 GDU  O4'   C4'  C3'   111.85  3.000
 GDU  C5'   C4'  C3'   109.64  3.000
 GDU  H5'   C5'  O5'   110.10  3.000
 GDU  H5'   C5'  C6'   107.70  3.000
 GDU  O5'   C5'  C6'   107.75  3.000
 GDU  H5'   C5'  C4'   106.74  3.000
 GDU  O5'   C5'  C4'   112.19  3.000
 GDU  C6'   C5'  C4'   112.27  3.000
 GDU  H6'2  C6'  H6'1  107.07  3.000
 GDU  H6'2  C6'  O6'   111.58  3.000
 GDU  H6'1  C6'  O6'   111.63  3.000
 GDU  H6'2  C6'  C5'   107.93  3.000
 GDU  H6'1  C6'  C5'   110.05  3.000
 GDU  O6'   C6'  C5'   108.52  3.000
 GDU  HO2A  O2'  C2'   110.63  3.000
 GDU  HO3A  O3'  C3'   107.38  3.000
 GDU  HO4'  O4'  C4'   107.61  3.000
 GDU  C5'   O5'  C1'   115.09  3.000
 GDU  HO6'  O6'  C6'   108.03  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
 GDU  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 GDU  CONST_02  C5    C4   N3   C2     0.00   0.0  0
 GDU  CONST_03  C6    N1   C2   N3     0.00   0.0  0
 GDU  CONST_04  C1D   N1   C2   N3   180.00   0.0  0
 GDU  CONST_05  O4    C4   N3   C2   180.00   0.0  0
 GDU  CONST_06  O2    C2   N3   C4   180.00   0.0  0
 GDU  CONST_07  O2    C2   N1   C6   180.00   0.0  0
 GDU  CONST_08  C1D   N1   C2   O2     0.00   0.0  0
 GDU  CONST_09  HN3   N3   C2   N1   180.00   0.0  0
 GDU  Var_01    O1A   PA   O5D  C5D  -71.98  30.0  3
 GDU  Var_02    O1B   PB   O3A  PA     6.80  30.0  3
 GDU  Var_03    H5'1  C5D  O5D  PA   -87.27  30.0  2

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
 GDU  chir_01  C1D  N1   C2D  O4D  negativ
 GDU  chir_02  C2D  O2D  C3D  C1D  positiv
 GDU  chir_03  C3D  O3D  C2D  C4D  negativ
 GDU  chir_04  C4D  O4D  C3D  C5D  negativ
 GDU  chir_07  C1'  O3B  C2'  O5'  positiv
 GDU  chir_08  C2'  O2'  C1'  C3'  negativ
 GDU  chir_09  C3'  O3'  C2'  C4'  positiv
 GDU  chir_10  C4'  O4'  C3'  C5'  positiv
 GDU  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
 GDU  plan-1  N1   0.020
 GDU  plan-1  C2   0.020
 GDU  plan-1  N3   0.020
 GDU  plan-1  C4   0.020
 GDU  plan-1  C5   0.020
 GDU  plan-1  C6   0.020
 GDU  plan-1  O2   0.020
 GDU  plan-1  O4   0.020
 GDU  plan-1  C1D  0.020
 GDU  plan-1  HN3  0.020
 GDU  plan-1  H5   0.020
 GDU  plan-1  H6   0.020

