# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 09:22:52 2022
#   Inital geometry file: a 155 line input string
#   Ligand name: (2R,3R,4R,6R)-3-(acetylamino)-4-hydroxy-6-methyl-5-oxotetrahydro-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: C[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](NC(C)=O)[C@@H](O)C1=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
 UD7  UD7  '(2R,3R,4R,6R)-3-(acetylamino)-4-hydroxy-6-methyl-5-oxotetrahydro-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  61  38  .  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_UD7
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
 UD7  N1   N  NR6    0  -0.573  -58.5374   -8.9196  12.8877
 UD7  C2   C  CR6    0   0.733  -59.2243   -8.1318  13.7874
 UD7  O2   O  O      0  -0.476  -58.6724   -7.5451  14.6964
 UD7  N3   N  NR16   0  -0.732  -60.5760   -8.0622  13.5803
 UD7  C4   C  CR6    0   0.560  -61.3136   -8.6446  12.5563
 UD7  O4   O  O      0  -0.460  -62.5201   -8.4941  12.5034
 UD7  C5   C  CR16   0  -0.517  -60.5014   -9.3827  11.6255
 UD7  C6   C  CR16   0   0.081  -59.1737   -9.4772  11.8202
 UD7  PA   P  P      0   1.379  -58.3702  -12.5141   9.8686
 UD7  PB   P  P      0   1.374  -56.6476  -13.7492   7.7682
 UD7  C1'  C  CH1    0   0.267  -57.7465  -13.3314   5.3421
 UD7  O1'  O  O2     0  -0.636  -57.8401  -13.2557   6.7322
 UD7  O1A  O  OP    -1  -0.760  -59.7049  -13.0486  10.2631
 UD7  C1B  C  CH1    0   0.203  -57.0693   -9.0194  13.0757
 UD7  O1B  O  O      0  -0.760  -56.2851  -15.1654   7.4725
 UD7  C2'  C  CH1    0  -0.168  -57.3926  -11.9582   4.7569
 UD7  O2'  O  OH1    0  -0.663  -55.4721   -9.3535  14.7848
 UD7  O2A  O  O      0  -0.785  -58.2245  -11.2397   9.0956
 UD7  C2B  C  CH1    0  -0.046  -56.6993   -9.8411  14.3137
 UD7  O2B  O  OP    -1  -0.774  -55.5857  -12.6854   7.8146
 UD7  C3'  C  CH1    0  -0.046  -58.5084  -10.9497   5.0992
 UD7  O3'  O  OH1    0  -0.640  -58.2783   -9.6725   4.5973
 UD7  O3A  O  O2     0  -0.731  -57.5522  -13.7417   9.1205
 UD7  C3B  C  CH1    0  -0.039  -56.5460  -11.2389  13.7110
 UD7  O3B  O  OH1    0  -0.657  -55.6917  -12.0780  14.4382
 UD7  C4'  C  C      0   0.349  -59.8377  -11.5362   4.6566
 UD7  O4'  O  O      0  -0.371  -60.6210  -10.9173   3.9811
 UD7  C4B  C  CH1    0   0.030  -55.9406  -10.9301  12.3474
 UD7  O4B  O  O2     0  -0.499  -56.5047   -9.6680  11.9823
 UD7  C5'  C  CH1    0  -0.073  -60.0963  -12.9613   5.1311
 UD7  O5'  O  O2     0  -0.485  -58.9627  -13.7693   4.8271
 UD7  C5B  C  CH2    0  -0.200  -56.1684  -11.9759  11.2781
 UD7  O5B  O  O2     0  -0.617  -57.5066  -12.4212  11.2614
 UD7  C6'  C  CH3    0  -0.684  -61.3073  -13.5991   4.4916
 UD7  C7'  C  C      0   0.512  -55.1935  -10.9470   4.4072
 UD7  O7'  O  O      0  -0.501  -55.3818  -10.7301   3.2174
 UD7  C8'  C  CH3    0  -0.778  -53.8941  -10.5751   5.0789
 UD7  N2'  N  NH1    0  -0.661  -56.1046  -11.5194   5.2151
 UD7  H1   H  HNR6   0   0.422  -61.0866   -7.5001  14.2507
 UD7  H2   H  HCR6   0   0.282  -60.9570   -9.8482  10.7651
 UD7  H3   H  HCR6   0   0.320  -58.5505   -9.9879  11.1046
 UD7  H4   H  HCH1   0   0.253  -57.0021  -14.0698   5.0246
 UD7  H6   H  HCH1   0   0.279  -56.6857   -7.9987  13.1461
 UD7  H7   H  HCH1   0   0.274  -57.3432  -12.0711   3.6698
 UD7  H8   H  HOH1   0   0.448  -55.0022  -10.0923  15.1913
 UD7  H9   H  HCH1   0   0.256  -57.4701   -9.8113  15.0904
 UD7  H11  H  HCH1   0   0.273  -58.5534  -10.8523   6.1912
 UD7  H12  H  HOH1   0   0.446  -58.2424   -9.7103   3.6349
 UD7  H13  H  HCH1   0   0.252  -57.5411  -11.6806  13.5884
 UD7  H14  H  HOH1   0   0.465  -56.1978  -12.5109  15.1330
 UD7  H15  H  HCH1   0   0.241  -54.8543  -10.8120  12.4496
 UD7  H16  H  HCH1   0   0.262  -60.2471  -12.9145   6.2192
 UD7  H17  H  HCH2   0   0.226  -55.5089  -12.8187  11.5094
 UD7  H18  H  HCH2   0   0.237  -55.8478  -11.5798  10.3106
 UD7  H19  H  HCH3   0   0.241  -62.2075  -13.0408   4.7422
 UD7  H20  H  HCH3   0   0.235  -61.2189  -13.6385   3.4061
 UD7  H21  H  HCH3   0   0.248  -61.4347  -14.6140   4.8666
 UD7  H22  H  HCH3   0   0.259  -53.0599  -10.9767   4.5048
 UD7  H23  H  HCH3   0   0.263  -53.7891   -9.4896   5.0846
 UD7  H24  H  HCH3   0   0.244  -53.8148  -10.9313   6.1043
 UD7  H25  H  HNH1   0   0.420  -55.8587  -11.6987   6.1895

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
 UD7  O7'  C7'  double  1.224  0.020  1.224
 UD7  O3'  C3'  single  1.391  0.020  1.391
 UD7  C7'  N2'  single  1.346  0.020  1.346
 UD7  C7'  C8'  single  1.509  0.020  1.509
 UD7  O4'  C4'  double  1.205  0.020  1.205
 UD7  C2'  N2'  single  1.436  0.020  1.436
 UD7  C2'  C3'  single  1.542  0.020  1.542
 UD7  C2'  C1'  single  1.534  0.020  1.534
 UD7  O5'  C1'  single  1.391  0.020  1.391
 UD7  O5'  C5'  single  1.425  0.020  1.425
 UD7  C4'  C3'  single  1.519  0.020  1.519
 UD7  C4'  C5'  single  1.524  0.020  1.524
 UD7  C1'  O1'  single  1.395  0.020  1.395
 UD7  C6'  C5'  single  1.511  0.020  1.511
 UD7  O1'  PB   single  1.655  0.020  1.655
 UD7  O1B  PB   deloc   1.491  0.020  1.491
 UD7  PB   O2B  deloc   1.504  0.020  1.504
 UD7  PB   O3A  single  1.627  0.020  1.627
 UD7  O2A  PA   deloc   1.498  0.020  1.498
 UD7  O3A  PA   single  1.654  0.020  1.654
 UD7  PA   O1A  deloc   1.491  0.020  1.491
 UD7  PA   O5B  single  1.641  0.020  1.641
 UD7  C5B  O5B  single  1.410  0.020  1.410
 UD7  C5B  C4B  single  1.513  0.020  1.513
 UD7  O4B  C4B  single  1.430  0.020  1.430
 UD7  O4B  C1B  single  1.391  0.020  1.391
 UD7  C6   C5   double  1.345  0.020  1.345
 UD7  C6   N1   single  1.362  0.020  1.362
 UD7  C4B  C3B  single  1.524  0.020  1.524
 UD7  C5   C4   single  1.439  0.020  1.439
 UD7  N1   C1B  single  1.483  0.020  1.483
 UD7  N1   C2   single  1.379  0.020  1.379
 UD7  C1B  C2B  single  1.531  0.020  1.531
 UD7  C4   O4   double  1.217  0.020  1.217
 UD7  C4   N3   single  1.390  0.020  1.390
 UD7  C3B  C2B  single  1.530  0.020  1.530
 UD7  C3B  O3B  single  1.401  0.020  1.401
 UD7  C2   N3   single  1.369  0.020  1.369
 UD7  C2   O2   double  1.214  0.020  1.214
 UD7  C2B  O2'  single  1.402  0.020  1.402
 UD7  N3   H1   single  0.860  0.020  1.020
 UD7  C5   H2   single  0.930  0.020  1.080
 UD7  C6   H3   single  0.930  0.020  1.080
 UD7  C1'  H4   single  0.970  0.020  1.090
 UD7  C1B  H6   single  0.970  0.020  1.090
 UD7  C2'  H7   single  0.970  0.020  1.090
 UD7  O2'  H8   single  0.850  0.020  0.980
 UD7  C2B  H9   single  0.970  0.020  1.090
 UD7  C3'  H11  single  0.970  0.020  1.090
 UD7  O3'  H12  single  0.850  0.020  0.980
 UD7  C3B  H13  single  0.970  0.020  1.090
 UD7  O3B  H14  single  0.850  0.020  0.980
 UD7  C4B  H15  single  0.970  0.020  1.090
 UD7  C5'  H16  single  0.970  0.020  1.090
 UD7  C5B  H17  single  0.970  0.020  1.090
 UD7  C5B  H18  single  0.970  0.020  1.090
 UD7  C6'  H19  single  0.970  0.020  1.090
 UD7  C6'  H20  single  0.970  0.020  1.090
 UD7  C6'  H21  single  0.970  0.020  1.090
 UD7  C8'  H22  single  0.970  0.020  1.090
 UD7  C8'  H23  single  0.970  0.020  1.090
 UD7  C8'  H24  single  0.970  0.020  1.090
 UD7  N2'  H25  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
 UD7  C1B  N1   C6   122.28  3.000
 UD7  C1B  N1   C2   116.65  3.000
 UD7  C6   N1   C2   120.83  3.000
 UD7  N3   C2   O2   122.49  3.000
 UD7  O2   C2   N1   122.55  3.000
 UD7  N3   C2   N1   114.96  3.000
 UD7  H1   N3   C4   116.91  3.000
 UD7  H1   N3   C2   115.20  3.000
 UD7  C4   N3   C2   127.88  3.000
 UD7  C5   C4   O4   126.50  3.000
 UD7  O4   C4   N3   120.42  3.000
 UD7  C5   C4   N3   113.07  3.000
 UD7  H2   C5   C6   120.12  3.000
 UD7  H2   C5   C4   119.91  3.000
 UD7  C6   C5   C4   119.97  3.000
 UD7  H3   C6   C5   120.53  3.000
 UD7  H3   C6   N1   116.37  3.000
 UD7  C5   C6   N1   123.07  3.000
 UD7  O5B  PA   O3A   99.54  3.000
 UD7  O5B  PA   O2A  109.79  3.000
 UD7  O3A  PA   O2A  110.49  3.000
 UD7  O5B  PA   O1A  105.47  3.000
 UD7  O3A  PA   O1A  107.24  3.000
 UD7  O2A  PA   O1A  121.92  3.000
 UD7  O3A  PB   O2B  111.33  3.000
 UD7  O3A  PB   O1B  107.72  3.000
 UD7  O2B  PB   O1B  120.41  3.000
 UD7  O3A  PB   O1'   96.80  3.000
 UD7  O2B  PB   O1'  108.50  3.000
 UD7  O1B  PB   O1'  109.52  3.000
 UD7  H4   C1'  O5'  105.93  3.000
 UD7  H4   C1'  C2'  109.64  3.000
 UD7  O5'  C1'  C2'  110.01  3.000
 UD7  H4   C1'  O1'  111.77  3.000
 UD7  O5'  C1'  O1'  109.09  3.000
 UD7  C2'  C1'  O1'  110.30  3.000
 UD7  C1'  O1'  PB   124.00  3.000
 UD7  H6   C1B  O4B  110.10  3.000
 UD7  H6   C1B  C2B  111.37  3.000
 UD7  O4B  C1B  C2B  106.69  3.000
 UD7  H6   C1B  N1   107.02  3.000
 UD7  C2B  C1B  N1   112.19  3.000
 UD7  O4B  C1B  N1   109.48  3.000
 UD7  H7   C2'  N2'  107.94  3.000
 UD7  H7   C2'  C3'  108.70  3.000
 UD7  N2'  C2'  C3'  112.23  3.000
 UD7  H7   C2'  C1'  107.28  3.000
 UD7  C3'  C2'  C1'  109.50  3.000
 UD7  N2'  C2'  C1'  111.02  3.000
 UD7  H8   O2'  C2B  107.54  3.000
 UD7  H9   C2B  C3B  112.02  3.000
 UD7  H9   C2B  O2'  111.62  3.000
 UD7  C3B  C2B  O2'  111.25  3.000
 UD7  H9   C2B  C1B  112.89  3.000
 UD7  O2'  C2B  C1B  107.25  3.000
 UD7  C3B  C2B  C1B  101.30  3.000
 UD7  H11  C3'  C4'  106.76  3.000
 UD7  H11  C3'  O3'  106.52  3.000
 UD7  C4'  C3'  O3'  113.21  3.000
 UD7  H11  C3'  C2'  107.97  3.000
 UD7  C4'  C3'  C2'  108.42  3.000
 UD7  O3'  C3'  C2'  113.61  3.000
 UD7  H12  O3'  C3'  109.29  3.000
 UD7  PB   O3A  PA   130.87  3.000
 UD7  H13  C3B  C4B  110.03  3.000
 UD7  H13  C3B  O3B  111.74  3.000
 UD7  C4B  C3B  O3B  110.10  3.000
 UD7  H13  C3B  C2B  108.75  3.000
 UD7  O3B  C3B  C2B  113.82  3.000
 UD7  C4B  C3B  C2B  101.96  3.000
 UD7  H14  O3B  C3B  108.87  3.000
 UD7  C5'  C4'  O4'  122.98  3.000
 UD7  C5'  C4'  C3'  114.76  3.000
 UD7  O4'  C4'  C3'  122.26  3.000
 UD7  H15  C4B  C5B  106.81  3.000
 UD7  H15  C4B  O4B  108.62  3.000
 UD7  C5B  C4B  O4B  111.73  3.000
 UD7  H15  C4B  C3B  109.38  3.000
 UD7  O4B  C4B  C3B  104.52  3.000
 UD7  C5B  C4B  C3B  115.64  3.000
 UD7  C4B  O4B  C1B  111.77  3.000
 UD7  H16  C5'  C6'  109.09  3.000
 UD7  H16  C5'  O5'  110.14  3.000
 UD7  C6'  C5'  O5'  107.94  3.000
 UD7  H16  C5'  C4'  106.95  3.000
 UD7  C6'  C5'  C4'  113.51  3.000
 UD7  O5'  C5'  C4'  109.20  3.000
 UD7  C5'  O5'  C1'  115.98  3.000
 UD7  H18  C5B  H17  106.81  3.000
 UD7  H18  C5B  O5B  112.46  3.000
 UD7  H17  C5B  O5B  109.33  3.000
 UD7  H18  C5B  C4B  109.32  3.000
 UD7  H17  C5B  C4B  106.98  3.000
 UD7  O5B  C5B  C4B  111.67  3.000
 UD7  C5B  O5B  PA   121.81  3.000
 UD7  H21  C6'  H20  108.58  3.000
 UD7  H21  C6'  H19  107.57  3.000
 UD7  H20  C6'  H19  108.36  3.000
 UD7  H21  C6'  C5'  109.95  3.000
 UD7  H20  C6'  C5'  111.83  3.000
 UD7  H19  C6'  C5'  110.42  3.000
 UD7  N2'  C7'  C8'  114.87  3.000
 UD7  C8'  C7'  O7'  121.43  3.000
 UD7  N2'  C7'  O7'  123.70  3.000
 UD7  H24  C8'  H23  108.29  3.000
 UD7  H24  C8'  H22  108.67  3.000
 UD7  H23  C8'  H22  107.21  3.000
 UD7  H24  C8'  C7'  113.67  3.000
 UD7  H23  C8'  C7'  109.30  3.000
 UD7  H22  C8'  C7'  109.50  3.000
 UD7  H25  N2'  C7'  118.99  3.000
 UD7  H25  N2'  C2'  117.85  3.000
 UD7  C7'  N2'  C2'  123.08  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
 UD7  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 UD7  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 UD7  CONST_03  C6   N1   C2   N3     0.00   0.0  0
 UD7  CONST_04  C1B  N1   C2   N3   180.00   0.0  0
 UD7  CONST_05  O4   C4   N3   C2   180.00   0.0  0
 UD7  CONST_06  C6   N1   C2   O2   180.00   0.0  0
 UD7  CONST_07  C1B  N1   C2   O2     0.00   0.0  0
 UD7  CONST_08  C4   N3   C2   O2   180.00   0.0  0
 UD7  CONST_09  H1   N3   C2   N1   180.00   0.0  0
 UD7  CONST_10  O7'  C7'  N2'  C2'    0.00   0.0  0
 UD7  CONST_11  C8'  C7'  N2'  C2'  180.00   0.0  0
 UD7  CONST_12  H25  N2'  C7'  O7'  180.00   0.0  0
 UD7  Var_01    C4B  C5B  O5B  PA   131.51  30.0  1
 UD7  Var_02    O1B  PB   O1'  C1'  -54.65  30.0  3
 UD7  Var_03    O1'  PB   O3A  PA   -60.31  30.0  1
 UD7  Var_04    O2A  PA   O3A  PB     1.31  30.0  3
 UD7  Var_05    H22  C8'  C7'  O7'  -51.27  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
 UD7  chir_03  C1'  C2'  O5'  O1'  positiv
 UD7  chir_04  C1B  O4B  N1   C2B  negativ
 UD7  chir_05  C2'  N2'  C3'  C1'  positiv
 UD7  chir_06  C2B  O2'  C1B  C3B  negativ
 UD7  chir_07  C3'  O3'  C2'  C4'  positiv
 UD7  chir_08  C3B  O3B  C4B  C2B  positiv
 UD7  chir_09  C4B  O4B  C3B  C5B  negativ
 UD7  chir_10  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
 UD7  plan-1  N1   0.020
 UD7  plan-1  C2   0.020
 UD7  plan-1  O2   0.020
 UD7  plan-1  N3   0.020
 UD7  plan-1  C4   0.020
 UD7  plan-1  O4   0.020
 UD7  plan-1  C5   0.020
 UD7  plan-1  C6   0.020
 UD7  plan-1  C1B  0.020
 UD7  plan-1  H1   0.020
 UD7  plan-1  H2   0.020
 UD7  plan-1  H3   0.020
 UD7  plan-2  C3'  0.020
 UD7  plan-2  C4'  0.020
 UD7  plan-2  O4'  0.020
 UD7  plan-2  C5'  0.020
 UD7  plan-3  C2'  0.020
 UD7  plan-3  C7'  0.020
 UD7  plan-3  O7'  0.020
 UD7  plan-3  C8'  0.020
 UD7  plan-3  N2'  0.020
 UD7  plan-3  H25  0.020

