# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jul  2 21:55:51 2020
#   Inital geometry file: a 135 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 (2S,3R,4S,5S)-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CO[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]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
 UAD  UAD  '[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2S,3R,4S,5S)-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)'  ligand  54  34  .  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_UAD
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
 UAD  N1    N  NR6    0  -0.547   2.9332  -0.6517   0.2484
 UAD  C2    C  CR6    0   0.707   2.7174  -1.9422   0.6941
 UAD  O2    O  O      0  -0.506   2.9035  -2.2933   1.8419
 UAD  N3    N  NR16   0  -0.709   2.3142  -2.8210  -0.2719
 UAD  C4    C  CR6    0   0.576   1.9410  -2.5386  -1.5749
 UAD  O4    O  O      0  -0.486   1.5182  -3.4219  -2.3003
 UAD  C5    C  CR16   0  -0.480   2.1324  -1.1603  -1.9387
 UAD  C6    C  CR16   0   0.145   2.5945  -0.2947  -1.0282
 UAD  PA    P  P      0   1.353   0.1620   2.5736  -0.9922
 UAD  PB    P  P      0   1.305  -0.9387  -0.1294  -0.6872
 UAD  O01   O  O      0  -0.821  -1.1419   3.2652  -1.2124
 UAD  O02   O  O2     0  -0.616  -0.1079   1.1615  -0.1823
 UAD  C1A   C  CH1    0   0.262  -3.5279  -0.4778  -0.1990
 UAD  O1A   O  OP    -1  -0.799   1.1284   2.3425  -2.1121
 UAD  O1B   O  OP    -1  -0.880  -0.3957  -1.3240   0.0610
 UAD  C1C   C  CH1    0   0.160   3.3659   0.3586   1.1955
 UAD  C2A   C  CH1    0   0.008  -3.6077  -1.7081   0.7260
 UAD  O2A   O  OH1    0  -0.691  -2.6730  -2.6841   0.3574
 UAD  O2B   O  O      0  -0.821  -1.1197  -0.1589  -2.1669
 UAD  C2C   C  CH1    0   0.019   4.5410   1.2155   0.7266
 UAD  O2C   O  OH1    0  -0.641   5.7448   0.5549   0.9861
 UAD  C3A   C  CH1    0   0.030  -4.9922  -2.3355   0.6163
 UAD  O3A   O  OH1    0  -0.695  -5.0664  -3.3995   1.5304
 UAD  O3B   O  O2     0  -0.649  -2.3761   0.2661   0.0367
 UAD  C3C   C  CH1    0  -0.082   4.3185   2.4911   1.5483
 UAD  O3C   O  OH1    0  -0.693   4.7493   2.3171   2.8736
 UAD  C4A   C  CH1    0  -0.037  -6.0862  -1.2930   0.8247
 UAD  O4A   O  OH1    0  -0.696  -6.0584  -0.8723   2.1673
 UAD  C4C   C  CH1    0   0.015   2.7982   2.5939   1.5289
 UAD  O4C   O  O2     0  -0.525   2.3189   1.2539   1.4459
 UAD  O5A   O  O2     0  -0.551  -4.5687   0.4233   0.0442
 UAD  C5C   C  CH2    0  -0.156   2.3108   3.4293   0.3553
 UAD  O5C   O  O2     0  -0.662   0.9075   3.3852   0.2267
 UAD  C5M   C  CH2    0  -0.239  -5.8439  -0.1453  -0.1433
 UAD  H5    H  HCR6   0   0.276   1.8450  -0.8192  -2.9197
 UAD  H6    H  HCR6   0   0.345   2.6880   0.7490  -1.2838
 UAD  H1A   H  HCH1   0   0.270  -3.5705  -0.8301  -1.2468
 UAD  H1C   H  HCH1   0   0.288   3.6528  -0.1749   2.1034
 UAD  H2A   H  HCH1   0   0.242  -3.4508  -1.3565   1.7583
 UAD  HO2A  H  HOH1   0   0.450  -1.7729  -2.2809   0.3345
 UAD  H2C   H  HCH1   0   0.258   4.4459   1.4623  -0.3379
 UAD  HO2C  H  HOH1   0   0.458   6.4356   0.9457   0.4416
 UAD  H3A   H  HCH1   0   0.248  -5.1079  -2.6986  -0.4180
 UAD  HO3A  H  HOH1   0   0.460  -5.9281  -3.8180   1.4376
 UAD  H3C   H  HCH1   0   0.252   4.7958   3.3625   1.0807
 UAD  HO3C  H  HOH1   0   0.441   5.6184   1.8994   2.8496
 UAD  H4A   H  HCH1   0   0.255  -7.0579  -1.7430   0.5687
 UAD  HO4A  H  HOH1   0   0.449  -6.7746  -0.2438   2.3027
 UAD  H4C   H  HCH1   0   0.262   2.4276   3.0330   2.4607
 UAD  H5C   H  HCH2   0   0.251   2.6053   4.4663   0.5433
 UAD  H5CA  H  HCH2   0   0.263   2.8024   3.1261  -0.5733
 UAD  H5M   H  HCH2   0   0.233  -5.9729  -0.5035  -1.1749
 UAD  H5MA  H  HCH2   0   0.281  -6.5732   0.6518   0.0133
 UAD  HN3   H  HNR6   0   0.419   2.1639  -3.7694   0.0490

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
 UAD  C1C  N1    single  1.451  0.020  1.451
 UAD  C6   N1    single  1.368  0.020  1.368
 UAD  N1   C2    single  1.382  0.020  1.382
 UAD  C2   O2    double  1.215  0.020  1.215
 UAD  C2   N3    single  1.367  0.020  1.367
 UAD  C4   N3    single  1.385  0.020  1.385
 UAD  C5   C4    single  1.438  0.020  1.438
 UAD  C4   O4    double  1.219  0.020  1.219
 UAD  C6   C5    double  1.339  0.020  1.339
 UAD  C5   H5    single  0.930  0.020  1.080
 UAD  C6   H6    single  0.930  0.020  1.080
 UAD  O01  PA    deloc   1.492  0.020  1.492
 UAD  O02  PA    single  1.650  0.020  1.650
 UAD  O1A  PA    deloc   1.497  0.020  1.497
 UAD  PA   O5C   single  1.643  0.020  1.643
 UAD  O2B  PB    deloc   1.491  0.020  1.491
 UAD  O02  PB    single  1.616  0.020  1.616
 UAD  PB   O3B   single  1.657  0.020  1.657
 UAD  PB   O1B   deloc   1.511  0.020  1.511
 UAD  O5A  C1A   single  1.398  0.020  1.398
 UAD  C1A  O3B   single  1.391  0.020  1.391
 UAD  C1A  C2A   single  1.541  0.020  1.541
 UAD  C1A  H1A   single  0.970  0.020  1.090
 UAD  C2C  C1C   single  1.528  0.020  1.528
 UAD  O4C  C1C   single  1.400  0.020  1.400
 UAD  C1C  H1C   single  0.970  0.020  1.090
 UAD  C3A  C2A   single  1.524  0.020  1.524
 UAD  C2A  O2A   single  1.401  0.020  1.401
 UAD  C2A  H2A   single  0.970  0.020  1.090
 UAD  O2A  HO2A  single  0.850  0.020  0.980
 UAD  C3C  C2C   single  1.534  0.020  1.534
 UAD  C2C  O2C   single  1.397  0.020  1.397
 UAD  C2C  H2C   single  0.970  0.020  1.090
 UAD  O2C  HO2C  single  0.850  0.020  0.980
 UAD  C4A  C3A   single  1.526  0.020  1.526
 UAD  C3A  O3A   single  1.405  0.020  1.405
 UAD  C3A  H3A   single  0.970  0.020  1.090
 UAD  O3A  HO3A  single  0.850  0.020  0.980
 UAD  C3C  O3C   single  1.404  0.020  1.404
 UAD  C3C  C4C   single  1.524  0.020  1.524
 UAD  C3C  H3C   single  0.970  0.020  1.090
 UAD  O3C  HO3C  single  0.850  0.020  0.980
 UAD  C5M  C4A   single  1.521  0.020  1.521
 UAD  C4A  O4A   single  1.407  0.020  1.407
 UAD  C4A  H4A   single  0.970  0.020  1.090
 UAD  O4A  HO4A  single  0.850  0.020  0.980
 UAD  C5C  C4C   single  1.521  0.020  1.521
 UAD  C4C  O4C   single  1.426  0.020  1.426
 UAD  C4C  H4C   single  0.970  0.020  1.090
 UAD  C5M  O5A   single  1.409  0.020  1.409
 UAD  O5C  C5C   single  1.410  0.020  1.410
 UAD  C5C  H5C   single  0.970  0.020  1.090
 UAD  C5C  H5CA  single  0.970  0.020  1.090
 UAD  C5M  H5M   single  0.970  0.020  1.090
 UAD  C5M  H5MA  single  0.970  0.020  1.090
 UAD  N3   HN3   single  0.860  0.020  1.020

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
 UAD  C1C   N1   C6   120.08  3.000
 UAD  C6    N1   C2   120.39  3.000
 UAD  C1C   N1   C2   119.09  3.000
 UAD  N3    C2   O2   121.81  3.000
 UAD  N3    C2   N1   114.74  3.000
 UAD  O2    C2   N1   123.41  3.000
 UAD  HN3   N3   C4   116.70  3.000
 UAD  HN3   N3   C2   114.97  3.000
 UAD  C4    N3   C2   127.84  3.000
 UAD  C5    C4   O4   126.17  3.000
 UAD  O4    C4   N3   120.39  3.000
 UAD  C5    C4   N3   113.43  3.000
 UAD  H5    C5   C6   120.43  3.000
 UAD  H5    C5   C4   119.88  3.000
 UAD  C6    C5   C4   119.57  3.000
 UAD  H6    C6   C5   119.63  3.000
 UAD  H6    C6   N1   116.88  3.000
 UAD  C5    C6   N1   123.46  3.000
 UAD  O5C   PA   O1A  109.77  3.000
 UAD  O5C   PA   O02   97.63  3.000
 UAD  O1A   PA   O02  109.92  3.000
 UAD  O5C   PA   O01  106.07  3.000
 UAD  O1A   PA   O01  121.68  3.000
 UAD  O02   PA   O01  109.04  3.000
 UAD  O3B   PB   O2B  109.45  3.000
 UAD  O3B   PB   O1B  106.51  3.000
 UAD  O2B   PB   O1B  121.30  3.000
 UAD  O1B   PB   O02  106.99  3.000
 UAD  O3B   PB   O02   96.83  3.000
 UAD  O2B   PB   O02  112.84  3.000
 UAD  PB    O02  PA   127.90  3.000
 UAD  H1A   C1A  O5A  109.96  3.000
 UAD  H1A   C1A  O3B  111.26  3.000
 UAD  O5A   C1A  O3B  104.02  3.000
 UAD  H1A   C1A  C2A  108.19  3.000
 UAD  O3B   C1A  C2A  111.59  3.000
 UAD  O5A   C1A  C2A  111.81  3.000
 UAD  H1C   C1C  O4C  111.12  3.000
 UAD  H1C   C1C  C2C  109.10  3.000
 UAD  O4C   C1C  C2C  105.74  3.000
 UAD  H1C   C1C  N1   106.33  3.000
 UAD  O4C   C1C  N1   109.82  3.000
 UAD  C2C   C1C  N1   114.80  3.000
 UAD  H2A   C2A  C3A  109.16  3.000
 UAD  H2A   C2A  O2A  111.96  3.000
 UAD  C3A   C2A  O2A  107.49  3.000
 UAD  H2A   C2A  C1A  107.47  3.000
 UAD  O2A   C2A  C1A  111.32  3.000
 UAD  C3A   C2A  C1A  109.42  3.000
 UAD  HO2A  O2A  C2A  109.28  3.000
 UAD  H2C   C2C  C3C  108.68  3.000
 UAD  H2C   C2C  O2C  111.18  3.000
 UAD  C3C   C2C  O2C  114.75  3.000
 UAD  H2C   C2C  C1C  110.93  3.000
 UAD  O2C   C2C  C1C  109.90  3.000
 UAD  C3C   C2C  C1C  100.98  3.000
 UAD  HO2C  O2C  C2C  108.74  3.000
 UAD  H3A   C3A  C4A  106.14  3.000
 UAD  H3A   C3A  O3A  110.83  3.000
 UAD  C4A   C3A  O3A  113.01  3.000
 UAD  H3A   C3A  C2A  107.37  3.000
 UAD  O3A   C3A  C2A  108.24  3.000
 UAD  C4A   C3A  C2A  111.12  3.000
 UAD  HO3A  O3A  C3A  108.30  3.000
 UAD  C1A   O3B  PB   121.10  3.000
 UAD  H3C   C3C  C4C  112.00  3.000
 UAD  H3C   C3C  O3C  111.52  3.000
 UAD  C4C   C3C  O3C  109.05  3.000
 UAD  H3C   C3C  C2C  111.64  3.000
 UAD  C4C   C3C  C2C  101.19  3.000
 UAD  O3C   C3C  C2C  110.98  3.000
 UAD  HO3C  O3C  C3C  107.85  3.000
 UAD  H4A   C4A  C5M  107.53  3.000
 UAD  H4A   C4A  O4A  111.19  3.000
 UAD  C5M   C4A  O4A  112.24  3.000
 UAD  H4A   C4A  C3A  108.77  3.000
 UAD  O4A   C4A  C3A  108.69  3.000
 UAD  C5M   C4A  C3A  108.33  3.000
 UAD  HO4A  O4A  C4A  108.34  3.000
 UAD  H4C   C4C  C5C  109.15  3.000
 UAD  H4C   C4C  O4C  108.23  3.000
 UAD  C5C   C4C  O4C  111.32  3.000
 UAD  H4C   C4C  C3C  110.73  3.000
 UAD  O4C   C4C  C3C  105.83  3.000
 UAD  C5C   C4C  C3C  111.51  3.000
 UAD  C4C   O4C  C1C  111.10  3.000
 UAD  C5M   O5A  C1A  112.99  3.000
 UAD  H5CA  C5C  H5C  106.72  3.000
 UAD  H5CA  C5C  O5C  111.18  3.000
 UAD  H5C   C5C  O5C  108.25  3.000
 UAD  H5CA  C5C  C4C  111.03  3.000
 UAD  H5C   C5C  C4C  107.56  3.000
 UAD  O5C   C5C  C4C  111.85  3.000
 UAD  C5C   O5C  PA   122.32  3.000
 UAD  H5MA  C5M  H5M  107.10  3.000
 UAD  H5MA  C5M  O5A  106.91  3.000
 UAD  H5M   C5M  O5A  111.25  3.000
 UAD  H5MA  C5M  C4A  110.69  3.000
 UAD  H5M   C5M  C4A  109.42  3.000
 UAD  O5A   C5M  C4A  111.36  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
 UAD  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 UAD  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 UAD  CONST_03  C1C  N1   C2   N3    180.00   0.0  0
 UAD  CONST_04  C6   N1   C2   N3      0.00   0.0  0
 UAD  CONST_05  O4   C4   N3   C2    180.00   0.0  0
 UAD  CONST_06  C1C  N1   C2   O2      0.00   0.0  0
 UAD  CONST_07  C6   N1   C2   O2    180.00   0.0  0
 UAD  CONST_08  C4   N3   C2   O2    180.00   0.0  0
 UAD  CONST_09  HN3  N3   C2   N1    180.00   0.0  0
 UAD  Var_01    C4A  C5M  O5A  C1A    62.24  30.0  1
 UAD  Var_02    C4C  C5C  O5C  PA   -108.40  30.0  3
 UAD  Var_03    O2B  PB   O3B  C1A    56.03  30.0  1
 UAD  Var_04    O01  PA   O02  PB     64.13  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
 UAD  chir_03  C1A  O5A  O3B  C2A  negativ
 UAD  chir_04  C1C  N1   C2C  O4C  negativ
 UAD  chir_05  C2A  O2A  C1A  C3A  negativ
 UAD  chir_06  C2C  C1C  C3C  O2C  negativ
 UAD  chir_07  C3A  O3A  C2A  C4A  positiv
 UAD  chir_08  C3C  O3C  C4C  C2C  positiv
 UAD  chir_09  C4A  O4A  C3A  C5M  positiv
 UAD  chir_10  C4C  C3C  C5C  O4C  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
 UAD  plan-1  N1   0.020
 UAD  plan-1  C2   0.020
 UAD  plan-1  O2   0.020
 UAD  plan-1  N3   0.020
 UAD  plan-1  C4   0.020
 UAD  plan-1  O4   0.020
 UAD  plan-1  C5   0.020
 UAD  plan-1  C6   0.020
 UAD  plan-1  C1C  0.020
 UAD  plan-1  H5   0.020
 UAD  plan-1  H6   0.020
 UAD  plan-1  HN3  0.020

