# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jul  2 09:33:06 2020
#   Inital geometry file: a 158 line input string
#   Ligand name: (2R,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-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: CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1O[P@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O
#
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
 UD1  UD1  '(2R,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-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  64  39  .  2020-11-04  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UD1
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
 UD1  C1'   C  CH1    0   0.289  -0.3366  -0.7203  -4.4214
 UD1  C2'   C  CH1    0  -0.141  -0.5855   0.7759  -4.6671
 UD1  C3'   C  CH1    0   0.030  -1.9680   1.1770  -4.1767
 UD1  C4'   C  CH1    0  -0.007  -3.0135   0.2487  -4.7840
 UD1  C5'   C  CH1    0  -0.017  -2.6634  -1.2096  -4.4727
 UD1  C6'   C  CH2    0  -0.165  -3.6176  -2.1700  -5.1490
 UD1  C7'   C  C      0   0.531   1.6536   1.7678  -4.5653
 UD1  C8'   C  CH3    0  -0.789   2.6489   2.4169  -3.6401
 UD1  N2'   N  NH1    0  -0.620   0.4316   1.5732  -4.0325
 UD1  O1'   O  O2     0  -0.632  -0.1950  -0.9312  -3.0468
 UD1  O3'   O  OH1    0  -0.666  -2.1927   2.5163  -4.5345
 UD1  O4'   O  OH1    0  -0.674  -4.2606   0.6156  -4.2345
 UD1  O5'   O  O2     0  -0.490  -1.3609  -1.4991  -4.9512
 UD1  O6'   O  OH1    0  -0.667  -3.3102  -3.4843  -4.7518
 UD1  O7'   O  O      0  -0.509   1.9383   1.4416  -5.7100
 UD1  N1    N  NR6    0  -0.578  -0.0168   1.5924   4.6781
 UD1  C2    C  CR6    0   0.748  -1.0588   0.7195   4.4165
 UD1  N3    N  NR16   0  -0.735  -2.3090   1.2675   4.5473
 UD1  C4    C  CR6    0   0.567  -2.6480   2.5637   4.9033
 UD1  C5    C  CR16   0  -0.511  -1.5031   3.4050   5.1463
 UD1  C6    C  CR16   0   0.098  -0.2695   2.8930   5.0188
 UD1  O2    O  O      0  -0.463  -0.8986  -0.4389   4.1025
 UD1  O4    O  O      0  -0.463  -3.8146   2.9000   4.9822
 UD1  C1B   C  CH1    0   0.238   1.3674   1.1592   4.5564
 UD1  C2B   C  CH1    0  -0.058   1.7940  -0.0067   5.4470
 UD1  O2'   O  OH1    0  -0.658   2.0868   0.4696   6.7304
 UD1  C3B   C  CH1    0  -0.040   3.0131  -0.5176   4.6708
 UD1  C4B   C  CH1    0  -0.027   2.5786  -0.3041   3.2246
 UD1  O4B   O  O2     0  -0.486   1.6514   0.7866   3.2440
 UD1  O3B   O  OH1    0  -0.670   4.1396   0.2829   4.9241
 UD1  C5B   C  CH2    0  -0.146   1.9570  -1.5419   2.6131
 UD1  O5B   O  O2     0  -0.618   1.5280  -1.2318   1.3045
 UD1  PA    P  P      0   1.340   1.4190  -2.4873   0.2473
 UD1  O1A   O  O      0  -0.789   0.4237  -3.4829   0.7530
 UD1  O2A   O  OP    -1  -0.797   2.7916  -2.9242  -0.1576
 UD1  O3A   O  O2     0  -0.734   0.7333  -1.5894  -0.9445
 UD1  PB    P  P      0   1.343   1.1588  -1.7319  -2.5228
 UD1  O1B   O  O      0  -0.793   1.0921  -3.1590  -2.9631
 UD1  O2B   O  OP    -1  -0.771   2.3637  -0.8990  -2.8244
 UD1  H1'   H  HCH1   0   0.238   0.5638  -1.0166  -4.9701
 UD1  H2'   H  HCH1   0   0.267  -0.5375   0.9483  -5.7457
 UD1  H3'   H  HCH1   0   0.214  -2.0091   1.0552  -3.0815
 UD1  H4'   H  HCH1   0   0.224  -3.0087   0.3863  -5.8754
 UD1  H5'   H  HCH1   0   0.225  -2.7215  -1.3604  -3.3851
 UD1  H6'1  H  HCH2   0   0.203  -4.6399  -1.8959  -4.8644
 UD1  H6'2  H  HCH2   0   0.196  -3.5410  -2.0422  -6.2384
 UD1  H8'1  H  HCH3   0   0.254   3.3682   3.0036  -4.2068
 UD1  H8'2  H  HCH3   0   0.248   2.1778   3.0547  -2.8933
 UD1  H8'3  H  HCH3   0   0.274   3.1853   1.6268  -3.1136
 UD1  HN2'  H  HNH1   0   0.395   0.3245   1.7442  -3.0449
 UD1  HO3'  H  HOH1   0   0.450  -3.0759   2.7541  -4.2322
 UD1  HO4'  H  HOH1   0   0.463  -4.9517   0.4563  -4.8830
 UD1  HO6'  H  HOH1   0   0.456  -3.9786  -4.0679  -5.1211
 UD1  HN3   H  HNR6   0   0.427  -3.0746   0.6309   4.3612
 UD1  H5    H  HCR6   0   0.294  -1.6436   4.4393   5.4185
 UD1  H6    H  HCR6   0   0.329   0.6064   3.5042   5.1838
 UD1  H1B   H  HCH1   0   0.250   1.9555   2.0380   4.8468
 UD1  H2B   H  HCH1   0   0.269   1.0297  -0.7864   5.4721
 UD1  HO2'  H  HOH1   0   0.469   1.9861  -0.2514   7.3589
 UD1  H3B   H  HCH1   0   0.248   3.2149  -1.5753   4.8851
 UD1  H4B   H  HCH1   0   0.252   3.4394  -0.0104   2.6145
 UD1  HO3A  H  HOH1   0   0.448   4.1994   0.4112   5.8782
 UD1  H5'1  H  HCH2   0   0.224   1.1216  -1.9036   3.2183
 UD1  H5'2  H  HCH2   0   0.212   2.7286  -2.3214   2.6133

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
 UD1  C1'  C2'   single  1.536  0.020  1.536
 UD1  C1'  O1'   single  1.398  0.020  1.398
 UD1  C1'  O5'   single  1.392  0.020  1.392
 UD1  C1'  H1'   single  0.970  0.020  1.090
 UD1  C2'  C3'   single  1.521  0.020  1.521
 UD1  C2'  N2'   single  1.440  0.020  1.440
 UD1  C2'  H2'   single  0.970  0.020  1.090
 UD1  C3'  C4'   single  1.524  0.020  1.524
 UD1  C3'  O3'   single  1.404  0.020  1.404
 UD1  C3'  H3'   single  0.970  0.020  1.090
 UD1  C4'  C5'   single  1.532  0.020  1.532
 UD1  C4'  O4'   single  1.411  0.020  1.411
 UD1  C4'  H4'   single  0.970  0.020  1.090
 UD1  C5'  C6'   single  1.513  0.020  1.513
 UD1  C5'  O5'   single  1.418  0.020  1.418
 UD1  C5'  H5'   single  0.970  0.020  1.090
 UD1  C6'  O6'   single  1.407  0.020  1.407
 UD1  C6'  H6'1  single  0.970  0.020  1.090
 UD1  C6'  H6'2  single  0.970  0.020  1.090
 UD1  C7'  C8'   single  1.506  0.020  1.506
 UD1  C7'  N2'   single  1.347  0.020  1.347
 UD1  C7'  O7'   double  1.224  0.020  1.224
 UD1  C8'  H8'1  single  0.970  0.020  1.090
 UD1  C8'  H8'2  single  0.970  0.020  1.090
 UD1  C8'  H8'3  single  0.970  0.020  1.090
 UD1  N2'  HN2'  single  0.860  0.020  1.020
 UD1  O1'  PB    single  1.658  0.020  1.658
 UD1  O3'  HO3'  single  0.850  0.020  0.980
 UD1  O4'  HO4'  single  0.850  0.020  0.980
 UD1  O6'  HO6'  single  0.850  0.020  0.980
 UD1  N1   C2    single  1.384  0.020  1.384
 UD1  N1   C6    single  1.368  0.020  1.368
 UD1  N1   C1B   single  1.455  0.020  1.455
 UD1  C2   N3    single  1.371  0.020  1.371
 UD1  C2   O2    double  1.211  0.020  1.211
 UD1  N3   C4    single  1.386  0.020  1.386
 UD1  N3   HN3   single  0.860  0.020  1.020
 UD1  C4   C5    single  1.441  0.020  1.441
 UD1  C4   O4    double  1.217  0.020  1.217
 UD1  C5   C6    double  1.342  0.020  1.342
 UD1  C5   H5    single  0.930  0.020  1.080
 UD1  C6   H6    single  0.930  0.020  1.080
 UD1  C1B  C2B   single  1.528  0.020  1.528
 UD1  C1B  O4B   single  1.394  0.020  1.394
 UD1  C1B  H1B   single  0.970  0.020  1.090
 UD1  C2B  O2'   single  1.400  0.020  1.400
 UD1  C2B  C3B   single  1.533  0.020  1.533
 UD1  C2B  H2B   single  0.970  0.020  1.090
 UD1  O2'  HO2'  single  0.850  0.020  0.980
 UD1  C3B  C4B   single  1.525  0.020  1.525
 UD1  C3B  O3B   single  1.405  0.020  1.405
 UD1  C3B  H3B   single  0.970  0.020  1.090
 UD1  C4B  O4B   single  1.432  0.020  1.432
 UD1  C4B  C5B   single  1.514  0.020  1.514
 UD1  C4B  H4B   single  0.970  0.020  1.090
 UD1  O3B  HO3A  single  0.850  0.020  0.980
 UD1  C5B  O5B   single  1.412  0.020  1.412
 UD1  C5B  H5'1  single  0.970  0.020  1.090
 UD1  C5B  H5'2  single  0.970  0.020  1.090
 UD1  O5B  PA    single  1.645  0.020  1.645
 UD1  PA   O1A   deloc   1.496  0.020  1.496
 UD1  PA   O2A   deloc   1.496  0.020  1.496
 UD1  PA   O3A   single  1.642  0.020  1.642
 UD1  O3A  PB    single  1.641  0.020  1.641
 UD1  PB   O1B   deloc   1.495  0.020  1.495
 UD1  PB   O2B   deloc   1.495  0.020  1.495

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
 UD1  H1'   C1'  O5'   105.24  3.000
 UD1  H1'   C1'  O1'   111.63  3.000
 UD1  O5'   C1'  O1'   111.38  3.000
 UD1  H1'   C1'  C2'   108.45  3.000
 UD1  O5'   C1'  C2'   111.40  3.000
 UD1  O1'   C1'  C2'   108.70  3.000
 UD1  H2'   C2'  N2'   108.45  3.000
 UD1  H2'   C2'  C3'   108.45  3.000
 UD1  N2'   C2'  C3'   110.73  3.000
 UD1  H2'   C2'  C1'   107.71  3.000
 UD1  N2'   C2'  C1'   110.75  3.000
 UD1  C3'   C2'  C1'   110.64  3.000
 UD1  H3'   C3'  O3'   110.63  3.000
 UD1  H3'   C3'  C4'   107.63  3.000
 UD1  O3'   C3'  C4'   111.69  3.000
 UD1  H3'   C3'  C2'   108.97  3.000
 UD1  O3'   C3'  C2'   108.35  3.000
 UD1  C4'   C3'  C2'   109.54  3.000
 UD1  H4'   C4'  O4'   110.96  3.000
 UD1  H4'   C4'  C5'   108.64  3.000
 UD1  O4'   C4'  C5'   111.73  3.000
 UD1  H4'   C4'  C3'   108.43  3.000
 UD1  O4'   C4'  C3'   107.02  3.000
 UD1  C5'   C4'  C3'   110.00  3.000
 UD1  H5'   C5'  O5'   110.76  3.000
 UD1  H5'   C5'  C6'   108.77  3.000
 UD1  O5'   C5'  C6'   107.39  3.000
 UD1  H5'   C5'  C4'   108.63  3.000
 UD1  O5'   C5'  C4'   109.62  3.000
 UD1  C6'   C5'  C4'   111.67  3.000
 UD1  H6'2  C6'  H6'1  107.05  3.000
 UD1  H6'2  C6'  O6'   111.91  3.000
 UD1  H6'1  C6'  O6'   111.35  3.000
 UD1  H6'2  C6'  C5'   108.97  3.000
 UD1  H6'1  C6'  C5'   108.26  3.000
 UD1  O6'   C6'  C5'   109.20  3.000
 UD1  O7'   C7'  N2'   122.84  3.000
 UD1  O7'   C7'  C8'   122.40  3.000
 UD1  N2'   C7'  C8'   114.76  3.000
 UD1  H8'3  C8'  H8'2  107.82  3.000
 UD1  H8'3  C8'  H8'1  108.49  3.000
 UD1  H8'2  C8'  H8'1  109.11  3.000
 UD1  H8'3  C8'  C7'   108.03  3.000
 UD1  H8'2  C8'  C7'   112.81  3.000
 UD1  H8'1  C8'  C7'   110.45  3.000
 UD1  HN2'  N2'  C7'   117.34  3.000
 UD1  HN2'  N2'  C2'   116.79  3.000
 UD1  C7'   N2'  C2'   123.13  3.000
 UD1  PB    O1'  C1'   117.80  3.000
 UD1  HO3'  O3'  C3'   107.59  3.000
 UD1  HO4'  O4'  C4'   109.24  3.000
 UD1  C5'   O5'  C1'   115.69  3.000
 UD1  HO6'  O6'  C6'   107.87  3.000
 UD1  C1B   N1   C6    118.65  3.000
 UD1  C1B   N1   C2    120.82  3.000
 UD1  C6    N1   C2    120.50  3.000
 UD1  O2    C2   N3    121.85  3.000
 UD1  O2    C2   N1    123.55  3.000
 UD1  N3    C2   N1    114.60  3.000
 UD1  HN3   N3   C4    116.74  3.000
 UD1  HN3   N3   C2    114.86  3.000
 UD1  C4    N3   C2    128.40  3.000
 UD1  O4    C4   C5    126.11  3.000
 UD1  O4    C4   N3    120.63  3.000
 UD1  C5    C4   N3    113.25  3.000
 UD1  H5    C5   C6    120.64  3.000
 UD1  H5    C5   C4    119.91  3.000
 UD1  C6    C5   C4    119.45  3.000
 UD1  H6    C6   C5    120.99  3.000
 UD1  H6    C6   N1    115.21  3.000
 UD1  C5    C6   N1    123.80  3.000
 UD1  H1B   C1B  O4B   110.76  3.000
 UD1  H1B   C1B  C2B   107.91  3.000
 UD1  O4B   C1B  C2B   106.74  3.000
 UD1  H1B   C1B  N1    104.44  3.000
 UD1  O4B   C1B  N1    110.62  3.000
 UD1  C2B   C1B  N1    116.35  3.000
 UD1  H2B   C2B  C3B   109.28  3.000
 UD1  H2B   C2B  O2'   111.61  3.000
 UD1  C3B   C2B  O2'   114.28  3.000
 UD1  H2B   C2B  C1B   111.28  3.000
 UD1  C3B   C2B  C1B   100.44  3.000
 UD1  O2'   C2B  C1B   109.46  3.000
 UD1  HO2'  O2'  C2B   108.79  3.000
 UD1  H3B   C3B  O3B   111.49  3.000
 UD1  H3B   C3B  C4B   111.86  3.000
 UD1  O3B   C3B  C4B   108.64  3.000
 UD1  H3B   C3B  C2B   111.62  3.000
 UD1  O3B   C3B  C2B   110.89  3.000
 UD1  C4B   C3B  C2B   101.94  3.000
 UD1  H4B   C4B  C5B   108.48  3.000
 UD1  H4B   C4B  O4B   108.20  3.000
 UD1  C5B   C4B  O4B   111.25  3.000
 UD1  H4B   C4B  C3B   109.99  3.000
 UD1  C5B   C4B  C3B   112.67  3.000
 UD1  O4B   C4B  C3B   106.16  3.000
 UD1  C4B   O4B  C1B   110.39  3.000
 UD1  HO3A  O3B  C3B   107.69  3.000
 UD1  H5'2  C5B  H5'1  107.60  3.000
 UD1  H5'2  C5B  O5B   111.72  3.000
 UD1  H5'1  C5B  O5B   110.71  3.000
 UD1  H5'2  C5B  C4B   106.98  3.000
 UD1  H5'1  C5B  C4B   111.14  3.000
 UD1  O5B   C5B  C4B   108.64  3.000
 UD1  PA    O5B  C5B   116.63  3.000
 UD1  O3A   PA   O2A   110.26  3.000
 UD1  O3A   PA   O1A   109.36  3.000
 UD1  O2A   PA   O1A   120.50  3.000
 UD1  O3A   PA   O5B    94.40  3.000
 UD1  O2A   PA   O5B   109.63  3.000
 UD1  O1A   PA   O5B   109.56  3.000
 UD1  PB    O3A  PA    122.84  3.000
 UD1  O2B   PB   O1B   120.54  3.000
 UD1  O2B   PB   O3A   110.77  3.000
 UD1  O1B   PB   O3A   110.77  3.000
 UD1  O2B   PB   O1'   108.98  3.000
 UD1  O1B   PB   O1'   109.36  3.000
 UD1  O3A   PB   O1'    92.88  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
 UD1  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 UD1  CONST_02  C5    C4   N3   C2      0.00   0.0  0
 UD1  CONST_03  C6    N1   C2   N3      0.00   0.0  0
 UD1  CONST_04  C1B   N1   C2   N3    180.00   0.0  0
 UD1  CONST_05  O4    C4   N3   C2    180.00   0.0  0
 UD1  CONST_06  O2    C2   N3   C4    180.00   0.0  0
 UD1  CONST_07  O2    C2   N1   C6    180.00   0.0  0
 UD1  CONST_08  C1B   N1   C2   O2      0.00   0.0  0
 UD1  CONST_09  HN3   N3   C2   N1    180.00   0.0  0
 UD1  CONST_10  C8'   C7'  N2'  C2'   180.00   0.0  0
 UD1  CONST_11  O7'   C7'  N2'  C2'     0.00   0.0  0
 UD1  CONST_12  HN2'  N2'  C7'  C8'     0.00   0.0  0
 UD1  Var_01    O3A   PB   O1'  C1'   178.21  30.0  3
 UD1  Var_02    O1A   PA   O5B  C5B    61.06  30.0  3
 UD1  Var_03    H8'1  C8'  C7'  N2'  -150.10  30.0  3
 UD1  Var_04    H5'1  C5B  O5B  PA    -82.72  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
 UD1  chir_01  C1'  C2'  O1'  O5'  negativ
 UD1  chir_02  C2'  N2'  C3'  C1'  positiv
 UD1  chir_03  C3'  O3'  C2'  C4'  positiv
 UD1  chir_04  C4'  O4'  C5'  C3'  positiv
 UD1  chir_05  C5'  O5'  C4'  C6'  negativ
 UD1  chir_06  C1B  N1   C2B  O4B  negativ
 UD1  chir_07  C2B  O2'  C3B  C1B  positiv
 UD1  chir_08  C3B  O3B  C2B  C4B  negativ
 UD1  chir_09  C4B  O4B  C3B  C5B  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
 UD1  plan-1  C2'   0.020
 UD1  plan-1  C7'   0.020
 UD1  plan-1  C8'   0.020
 UD1  plan-1  N2'   0.020
 UD1  plan-1  O7'   0.020
 UD1  plan-1  HN2'  0.020
 UD1  plan-2  N1    0.020
 UD1  plan-2  C2    0.020
 UD1  plan-2  N3    0.020
 UD1  plan-2  C4    0.020
 UD1  plan-2  C5    0.020
 UD1  plan-2  C6    0.020
 UD1  plan-2  O2    0.020
 UD1  plan-2  O4    0.020
 UD1  plan-2  C1B   0.020
 UD1  plan-2  HN3   0.020
 UD1  plan-2  H5    0.020
 UD1  plan-2  H6    0.020

