# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jul  3 15:28:03 2020
#   Inital geometry file: a 158 line input string
#   Ligand name: (2R,3R,4R,5R,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
 UD2  UD2  '(2R,3R,4R,5R,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  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UD2
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
 UD2  C1'   C  CH1    0   0.274   2.9947   0.6956  -0.3467
 UD2  C2'   C  CH1    0  -0.115   2.4085   0.5272   1.0677
 UD2  C3'   C  CH1    0   0.015   1.2860   1.5336   1.2695
 UD2  C4'   C  CH1    0  -0.034   1.8101   2.9455   1.0065
 UD2  C5'   C  CH1    0   0.000   2.4135   2.9950  -0.3993
 UD2  C6'   C  CH2    0  -0.168   3.0387   4.3398  -0.6990
 UD2  C8'   C  CH3    0  -0.782   2.1470  -3.2166   1.3439
 UD2  N2'   N  NH1    0  -0.648   1.9331  -0.8182   1.2635
 UD2  O1'   O  O2     0  -0.627   2.0421   0.3586  -1.3173
 UD2  O3'   O  OH1    0  -0.670   0.7552   1.3766   2.5566
 UD2  O4'   O  OH1    0  -0.668   2.7427   3.2721   2.0071
 UD2  O5'   O  O2     0  -0.491   3.4145   2.0059  -0.5587
 UD2  O6'   O  OH1    0  -0.666   3.4010   4.3855  -2.0571
 UD2  O7'   O  O      0  -0.514   3.9569  -1.7011   1.7368
 UD2  N1    N  NR6    0  -0.564  -2.0472   0.9734   0.2038
 UD2  C2    C  CR6    0   0.729  -1.9282   2.2952   0.5746
 UD2  N3    N  NR16   0  -0.735  -1.7408   3.1667  -0.4619
 UD2  C4    C  CR6    0   0.562  -1.6328   2.8769  -1.8185
 UD2  C5    C  CR16   0  -0.509  -1.7289   1.4704  -2.1057
 UD2  C6    C  CR16   0   0.097  -1.9335   0.5965  -1.1082
 UD2  O2    O  O      0  -0.490  -1.9680   2.6774   1.7307
 UD2  O4    O  O      0  -0.460  -1.4673   3.7725  -2.6244
 UD2  C1B   C  CH1    0   0.216  -2.2419  -0.0376   1.2349
 UD2  C2B   C  CH1    0  -0.034  -3.6294  -0.6717   1.2227
 UD2  O2'   O  OH1    0  -0.651  -4.5373   0.1520   1.8877
 UD2  C3B   C  CH1    0  -0.036  -3.3344  -2.0074   1.9107
 UD2  C4B   C  CH1    0  -0.028  -1.9761  -2.3496   1.3111
 UD2  O4B   O  O2     0  -0.495  -1.3485  -1.0923   1.0266
 UD2  O3B   O  OH1    0  -0.667  -3.1886  -1.8364   3.2970
 UD2  C5B   C  CH2    0  -0.167  -2.1150  -3.1970   0.0586
 UD2  O5B   O  O2     0  -0.610  -0.8682  -3.4903  -0.5195
 UD2  PA    P  P      0   1.393  -0.3555  -2.8210  -1.9349
 UD2  O1A   O  OP    -1  -0.788   0.4395  -3.8740  -2.6342
 UD2  O2A   O  O      0  -0.781  -1.5195  -2.1504  -2.6047
 UD2  O3A   O  O2     0  -0.735   0.6513  -1.6870  -1.3182
 UD2  PB    P  P      0   1.382   1.9712  -1.0967  -2.0939
 UD2  O1B   O  OP    -1  -0.789   3.1802  -1.9037  -1.7335
 UD2  O2B   O  O      0  -0.786   1.6233  -0.8079  -3.5170
 UD2  H1'   H  HCH1   0   0.239   3.8852   0.0700  -0.4435
 UD2  H2'   H  HCH1   0   0.259   3.2061   0.7237   1.7882
 UD2  H3'   H  HCH1   0   0.214   0.5290   1.3323   0.4991
 UD2  H4'   H  HCH1   0   0.227   0.9555   3.6395   1.0251
 UD2  H5'   H  HCH1   0   0.214   1.5961   2.8344  -1.1179
 UD2  H6'1  H  HCH2   0   0.199   2.3015   5.1170  -0.4514
 UD2  H6'2  H  HCH2   0   0.202   3.9050   4.4944  -0.0446
 UD2  H8'1  H  HCH3   0   0.246   2.6371  -3.9212   2.0126
 UD2  H8'2  H  HCH3   0   0.243   1.0764  -3.2245   1.5351
 UD2  H8'3  H  HCH3   0   0.273   2.2921  -3.5514   0.3157
 UD2  HN2'  H  HNH1   0   0.419   0.9934  -1.0250   0.9548
 UD2  HO3'  H  HOH1   0   0.446  -0.0164   1.9482   2.6424
 UD2  HO4'  H  HOH1   0   0.457   2.7547   4.2251   2.1276
 UD2  HO6'  H  HOH1   0   0.455   3.8758   5.2073  -2.2086
 UD2  HN3   H  HNR6   0   0.428  -1.6901   4.1437  -0.1982
 UD2  H5    H  HCR6   0   0.284  -1.6191   1.1167  -3.1189
 UD2  H6    H  HCR6   0   0.334  -1.9855  -0.4620  -1.3278
 UD2  H1B   H  HCH1   0   0.270  -2.0641   0.4529   2.1935
 UD2  H2B   H  HCH1   0   0.245  -3.9401  -0.8640   0.1863
 UD2  HO2'  H  HOH1   0   0.469  -5.4307  -0.1023   1.6354
 UD2  H3B   H  HCH1   0   0.254  -4.0907  -2.7682   1.6749
 UD2  H4B   H  HCH1   0   0.258  -1.3550  -2.8821   2.0381
 UD2  HO3A  H  HOH1   0   0.450  -3.9462  -1.3326   3.6167
 UD2  H5'1  H  HCH2   0   0.231  -2.5849  -4.1400   0.3561
 UD2  H5'2  H  HCH2   0   0.211  -2.7869  -2.7172  -0.6605
 UD2  C7'   C  C      0   0.511   2.7700  -1.8517   1.4725

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
 UD2  O4   C4    double  1.216  0.020  1.216
 UD2  C4   N3    single  1.391  0.020  1.391
 UD2  C4   C5    single  1.439  0.020  1.439
 UD2  N3   C2    single  1.367  0.020  1.367
 UD2  C5   C6    double  1.342  0.020  1.342
 UD2  C2   O2    double  1.218  0.020  1.218
 UD2  C2   N1    single  1.378  0.020  1.378
 UD2  C6   N1    single  1.370  0.020  1.370
 UD2  N1   C1B   single  1.457  0.020  1.457
 UD2  O2'  C2B   single  1.395  0.020  1.395
 UD2  C1B  C2B   single  1.526  0.020  1.526
 UD2  C1B  O4B   single  1.398  0.020  1.398
 UD2  C2B  C3B   single  1.531  0.020  1.531
 UD2  O2A  PA    deloc   1.501  0.020  1.501
 UD2  O4B  C4B   single  1.434  0.020  1.434
 UD2  O6'  C6'   single  1.406  0.020  1.406
 UD2  O5B  PA    single  1.648  0.020  1.648
 UD2  O5B  C5B   single  1.405  0.020  1.405
 UD2  C3B  C4B   single  1.524  0.020  1.524
 UD2  C3B  O3B   single  1.404  0.020  1.404
 UD2  PA   O3A   single  1.637  0.020  1.637
 UD2  PA   O1A   deloc   1.493  0.020  1.493
 UD2  C4B  C5B   single  1.519  0.020  1.519
 UD2  O3A  PB    single  1.641  0.020  1.641
 UD2  C6'  C5'   single  1.513  0.020  1.513
 UD2  O2B  PB    deloc   1.493  0.020  1.493
 UD2  C5'  O5'   single  1.416  0.020  1.416
 UD2  C5'  C4'   single  1.531  0.020  1.531
 UD2  PB   O1B   deloc   1.498  0.020  1.498
 UD2  PB   O1'   single  1.651  0.020  1.651
 UD2  O5'  C1'   single  1.392  0.020  1.392
 UD2  C4'  O4'   single  1.406  0.020  1.406
 UD2  C4'  C3'   single  1.529  0.020  1.529
 UD2  O1'  C1'   single  1.401  0.020  1.401
 UD2  C1'  C2'   single  1.540  0.020  1.540
 UD2  C3'  C2'   single  1.521  0.020  1.521
 UD2  C3'  O3'   single  1.401  0.020  1.401
 UD2  C2'  N2'   single  1.440  0.020  1.440
 UD2  N2'  C7'   single  1.346  0.020  1.346
 UD2  C7'  O7'   double  1.225  0.020  1.225
 UD2  C7'  C8'   single  1.506  0.020  1.506
 UD2  C1'  H1'   single  0.970  0.020  1.090
 UD2  C2'  H2'   single  0.970  0.020  1.090
 UD2  C3'  H3'   single  0.970  0.020  1.090
 UD2  C4'  H4'   single  0.970  0.020  1.090
 UD2  C5'  H5'   single  0.970  0.020  1.090
 UD2  C6'  H6'1  single  0.970  0.020  1.090
 UD2  C6'  H6'2  single  0.970  0.020  1.090
 UD2  C8'  H8'1  single  0.970  0.020  1.090
 UD2  C8'  H8'2  single  0.970  0.020  1.090
 UD2  C8'  H8'3  single  0.970  0.020  1.090
 UD2  N2'  HN2'  single  0.860  0.020  1.020
 UD2  O3'  HO3'  single  0.850  0.020  0.980
 UD2  O4'  HO4'  single  0.850  0.020  0.980
 UD2  O6'  HO6'  single  0.850  0.020  0.980
 UD2  N3   HN3   single  0.860  0.020  1.020
 UD2  C5   H5    single  0.930  0.020  1.080
 UD2  C6   H6    single  0.930  0.020  1.080
 UD2  C1B  H1B   single  0.970  0.020  1.090
 UD2  C2B  H2B   single  0.970  0.020  1.090
 UD2  O2'  HO2'  single  0.850  0.020  0.980
 UD2  C3B  H3B   single  0.970  0.020  1.090
 UD2  C4B  H4B   single  0.970  0.020  1.090
 UD2  O3B  HO3A  single  0.850  0.020  0.980
 UD2  C5B  H5'1  single  0.970  0.020  1.090
 UD2  C5B  H5'2  single  0.970  0.020  1.090

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
 UD2  H1'   C1'  O5'   106.24  3.000
 UD2  H1'   C1'  O1'   110.80  3.000
 UD2  O5'   C1'  O1'   109.02  3.000
 UD2  H1'   C1'  C2'   109.20  3.000
 UD2  O1'   C1'  C2'   110.55  3.000
 UD2  O5'   C1'  C2'   110.95  3.000
 UD2  H2'   C2'  N2'   108.61  3.000
 UD2  H2'   C2'  C3'   109.40  3.000
 UD2  N2'   C2'  C3'   110.88  3.000
 UD2  H2'   C2'  C1'   107.94  3.000
 UD2  N2'   C2'  C1'   110.65  3.000
 UD2  C3'   C2'  C1'   109.29  3.000
 UD2  H3'   C3'  O3'   111.26  3.000
 UD2  H3'   C3'  C4'   106.55  3.000
 UD2  O3'   C3'  C4'   113.04  3.000
 UD2  H3'   C3'  C2'   107.10  3.000
 UD2  O3'   C3'  C2'   109.11  3.000
 UD2  C4'   C3'  C2'   109.59  3.000
 UD2  H4'   C4'  O4'   110.88  3.000
 UD2  H4'   C4'  C5'   107.52  3.000
 UD2  O4'   C4'  C5'   112.61  3.000
 UD2  H4'   C4'  C3'   108.25  3.000
 UD2  O4'   C4'  C3'   108.63  3.000
 UD2  C5'   C4'  C3'   108.84  3.000
 UD2  H5'   C5'  O5'   110.46  3.000
 UD2  H5'   C5'  C6'   107.90  3.000
 UD2  O5'   C5'  C6'   107.84  3.000
 UD2  H5'   C5'  C4'   107.60  3.000
 UD2  O5'   C5'  C4'   111.07  3.000
 UD2  C6'   C5'  C4'   111.94  3.000
 UD2  H6'2  C6'  H6'1  107.20  3.000
 UD2  H6'2  C6'  O6'   111.60  3.000
 UD2  H6'1  C6'  O6'   111.54  3.000
 UD2  H6'2  C6'  C5'   109.48  3.000
 UD2  H6'1  C6'  C5'   107.86  3.000
 UD2  O6'   C6'  C5'   109.07  3.000
 UD2  H8'3  C8'  H8'2  107.13  3.000
 UD2  H8'3  C8'  H8'1  108.70  3.000
 UD2  H8'2  C8'  H8'1  109.31  3.000
 UD2  H8'3  C8'  C7'   107.67  3.000
 UD2  H8'2  C8'  C7'   113.50  3.000
 UD2  H8'1  C8'  C7'   110.37  3.000
 UD2  HN2'  N2'  C7'   117.93  3.000
 UD2  HN2'  N2'  C2'   117.16  3.000
 UD2  C7'   N2'  C2'   122.22  3.000
 UD2  PB    O1'  C1'   124.54  3.000
 UD2  HO3'  O3'  C3'   108.58  3.000
 UD2  HO4'  O4'  C4'   109.14  3.000
 UD2  C5'   O5'  C1'   115.28  3.000
 UD2  HO6'  O6'  C6'   107.90  3.000
 UD2  C1B   N1   C6    119.86  3.000
 UD2  C1B   N1   C2    119.12  3.000
 UD2  C6    N1   C2    120.97  3.000
 UD2  O2    C2   N3    121.60  3.000
 UD2  O2    C2   N1    123.60  3.000
 UD2  N3    C2   N1    114.79  3.000
 UD2  HN3   N3   C4    116.79  3.000
 UD2  HN3   N3   C2    115.10  3.000
 UD2  C4    N3   C2    128.10  3.000
 UD2  O4    C4   C5    126.64  3.000
 UD2  C5    C4   N3    113.14  3.000
 UD2  O4    C4   N3    120.22  3.000
 UD2  H5    C5   C6    120.01  3.000
 UD2  H5    C5   C4    120.08  3.000
 UD2  C6    C5   C4    119.90  3.000
 UD2  H6    C6   C5    119.57  3.000
 UD2  H6    C6   N1    117.35  3.000
 UD2  C5    C6   N1    123.06  3.000
 UD2  H1B   C1B  O4B   111.46  3.000
 UD2  H1B   C1B  C2B   110.00  3.000
 UD2  O4B   C1B  C2B   105.46  3.000
 UD2  H1B   C1B  N1    106.74  3.000
 UD2  O4B   C1B  N1    109.43  3.000
 UD2  C2B   C1B  N1    113.84  3.000
 UD2  H2B   C2B  C3B   109.00  3.000
 UD2  H2B   C2B  O2'   111.65  3.000
 UD2  C3B   C2B  O2'   115.24  3.000
 UD2  H2B   C2B  C1B   109.72  3.000
 UD2  C3B   C2B  C1B   100.59  3.000
 UD2  O2'   C2B  C1B   110.05  3.000
 UD2  HO2'  O2'  C2B   108.85  3.000
 UD2  H3B   C3B  O3B   111.58  3.000
 UD2  H3B   C3B  C4B   111.95  3.000
 UD2  O3B   C3B  C4B   108.86  3.000
 UD2  H3B   C3B  C2B   112.03  3.000
 UD2  O3B   C3B  C2B   110.93  3.000
 UD2  C4B   C3B  C2B   101.00  3.000
 UD2  H4B   C4B  C5B   109.17  3.000
 UD2  H4B   C4B  O4B   108.06  3.000
 UD2  C5B   C4B  O4B   111.45  3.000
 UD2  H4B   C4B  C3B   110.72  3.000
 UD2  C5B   C4B  C3B   111.61  3.000
 UD2  O4B   C4B  C3B   105.74  3.000
 UD2  C4B   O4B  C1B   110.63  3.000
 UD2  HO3A  O3B  C3B   108.02  3.000
 UD2  H5'2  C5B  H5'1  107.01  3.000
 UD2  H5'2  C5B  O5B   111.46  3.000
 UD2  H5'1  C5B  O5B   108.23  3.000
 UD2  H5'2  C5B  C4B   110.69  3.000
 UD2  H5'1  C5B  C4B   107.20  3.000
 UD2  O5B   C5B  C4B   112.00  3.000
 UD2  PA    O5B  C5B   123.01  3.000
 UD2  O3A   PA   O2A   109.61  3.000
 UD2  O3A   PA   O1A   109.72  3.000
 UD2  O2A   PA   O1A   121.26  3.000
 UD2  O1A   PA   O5B   106.35  3.000
 UD2  O3A   PA   O5B    98.58  3.000
 UD2  O2A   PA   O5B   108.87  3.000
 UD2  PB    O3A  PA    124.46  3.000
 UD2  O2B   PB   O1B   121.45  3.000
 UD2  O1B   PB   O3A   109.98  3.000
 UD2  O2B   PB   O3A   109.43  3.000
 UD2  O1B   PB   O1'   109.09  3.000
 UD2  O2B   PB   O1'   106.73  3.000
 UD2  O3A   PB   O1'    97.43  3.000
 UD2  O7'   C7'  N2'   122.77  3.000
 UD2  O7'   C7'  C8'   122.05  3.000
 UD2  N2'   C7'  C8'   115.18  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
 UD2  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 UD2  CONST_02  C5    C4   N3   C2      0.00   0.0  0
 UD2  CONST_03  C6    N1   C2   N3      0.00   0.0  0
 UD2  CONST_04  C1B   N1   C2   N3    180.00   0.0  0
 UD2  CONST_05  O4    C4   N3   C2    180.00   0.0  0
 UD2  CONST_06  O2    C2   N3   C4    180.00   0.0  0
 UD2  CONST_07  O2    C2   N1   C6    180.00   0.0  0
 UD2  CONST_08  C1B   N1   C2   O2      0.00   0.0  0
 UD2  CONST_09  HN3   N3   C2   N1    180.00   0.0  0
 UD2  CONST_10  O7'   C7'  N2'  C2'     0.00   0.0  0
 UD2  CONST_11  C8'   C7'  N2'  C2'   180.00   0.0  0
 UD2  CONST_12  HN2'  N2'  C7'  C8'     0.00   0.0  0
 UD2  Var_01    O3A   PB   O1'  C1'   106.55  30.0  1
 UD2  Var_02    O2A   PA   O5B  C5B   -12.75  30.0  3
 UD2  Var_03    H8'1  C8'  C7'  N2'  -148.65  30.0  3
 UD2  Var_04    H5'1  C5B  O5B  PA    133.33  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
 UD2  chir_01  C1'  O5'  O1'  C2'  positiv
 UD2  chir_02  C2'  N2'  C3'  C1'  positiv
 UD2  chir_03  C3'  O3'  C2'  C4'  positiv
 UD2  chir_04  C4'  O4'  C5'  C3'  negativ
 UD2  chir_05  C5'  O5'  C4'  C6'  negativ
 UD2  chir_06  C1B  N1   C2B  O4B  negativ
 UD2  chir_07  C2B  O2'  C3B  C1B  positiv
 UD2  chir_08  C3B  O3B  C4B  C2B  positiv
 UD2  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
 UD2  plan-1  C2'   0.020
 UD2  plan-1  C8'   0.020
 UD2  plan-1  N2'   0.020
 UD2  plan-1  O7'   0.020
 UD2  plan-1  HN2'  0.020
 UD2  plan-1  C7'   0.020
 UD2  plan-2  N1    0.020
 UD2  plan-2  C2    0.020
 UD2  plan-2  N3    0.020
 UD2  plan-2  C4    0.020
 UD2  plan-2  C5    0.020
 UD2  plan-2  C6    0.020
 UD2  plan-2  O2    0.020
 UD2  plan-2  O4    0.020
 UD2  plan-2  C1B   0.020
 UD2  plan-2  HN3   0.020
 UD2  plan-2  H5    0.020
 UD2  plan-2  H6    0.020

