# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jul  8 06:26:44 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,3R,4S,5S,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: CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)O2)C(=O)NC1=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
 DAU  DAU  '[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)'  ligand  60  36  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DAU
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
 DAU  O6    O  OH1    0  -0.671  -4.1973   3.6408   2.6370
 DAU  C6    C  CH2    0  -0.157  -4.1815   3.8357   1.2430
 DAU  C5    C  CH1    0  -0.011  -3.7179   2.5587   0.5722
 DAU  O5    O  O2     0  -0.495  -4.6941   1.5666   0.8570
 DAU  C4    C  CH1    0   0.021  -3.5612   2.7513  -0.9376
 DAU  O4    O  OH1    0  -0.673  -2.4947   3.6472  -1.1438
 DAU  C3    C  CH1    0  -0.005  -3.3210   1.4142  -1.6246
 DAU  O3    O  OH1    0  -0.678  -3.3047   1.6522  -3.0142
 DAU  C2    C  CH1    0  -0.032  -4.4239   0.4348  -1.2352
 DAU  O2    O  OH1    0  -0.705  -4.3207  -0.7867  -1.9110
 DAU  C1    C  CH1    0   0.231  -4.4773   0.3139   0.2948
 DAU  O1    O  O2     0  -0.626  -3.2834  -0.2047   0.8300
 DAU  P2    P  P      0   1.363  -2.9726  -1.8220   0.8622
 DAU  O3P   O  O      0  -0.770  -4.0660  -2.5336   1.5866
 DAU  O4P   O  OP    -1  -0.790  -2.5914  -2.2455  -0.5345
 DAU  OPP   O  O2     0  -0.724  -1.6536  -1.6671   1.8042
 DAU  P     P  P      0   1.360  -0.3764  -2.7033   1.8624
 DAU  O1P   O  O      0  -0.786   0.3309  -2.4371   3.1523
 DAU  O2P   O  OP    -1  -0.795  -0.8110  -4.0858   1.4966
 DAU  O5'   O  O2     0  -0.617   0.4668  -2.0273   0.6270
 DAU  C5'   C  CH2    0  -0.163   1.7449  -2.5548   0.3424
 DAU  C4'   C  CH1    0   0.014   2.2715  -1.9277  -0.9239
 DAU  O4'   O  O2     0  -0.490   2.4660  -0.5378  -0.7288
 DAU  C3'   C  CH1    0   0.023   3.6249  -2.4960  -1.3519
 DAU  O3'   O  OH1    0  -0.668   3.4080  -3.6064  -2.1857
 DAU  C2'   C  CH2    0  -0.562   4.2860  -1.2988  -2.0356
 DAU  C1'   C  CH1    0   0.220   3.5520  -0.0744  -1.4793
 DAU  N11   N  NR6    0  -0.567   4.3489   0.8351  -0.6585
 DAU  C61   C  CR16   0   0.058   4.4088   2.1621  -0.9977
 DAU  C51   C  CR6    0  -0.183   5.0830   3.0944  -0.3030
 DAU  C5A   C  CH3    0  -0.707   5.1379   4.5315  -0.7052
 DAU  C21   C  CR6    0   0.741   4.9805   0.3669   0.4703
 DAU  O21   O  O      0  -0.474   4.9526  -0.7931   0.8241
 DAU  N31   N  NR16   0  -0.733   5.6621   1.3239   1.1769
 DAU  C41   C  CR6    0   0.559   5.7845   2.6717   0.8918
 DAU  O41   O  O      0  -0.455   6.4361   3.4019   1.6164
 DAU  HO6   H  HOH1   0   0.456  -4.4776   4.4631   3.0480
 DAU  HC61  H  HCH2   0   0.195  -5.1760   4.0981   0.8560
 DAU  HC62  H  HCH2   0   0.211  -3.4999   4.6435   0.9555
 DAU  HC5   H  HCH1   0   0.228  -2.7441   2.2699   0.9917
 DAU  HC4   H  HCH1   0   0.206  -4.5035   3.1673  -1.3316
 DAU  HO4   H  HOH1   0   0.455  -2.4218   3.8124  -2.0892
 DAU  HC3   H  HCH1   0   0.207  -2.3496   1.0173  -1.2900
 DAU  HO3   H  HOH1   0   0.451  -3.1474   0.8114  -3.4562
 DAU  HC2   H  HCH1   0   0.227  -5.3847   0.8709  -1.5357
 DAU  HO2   H  HOH1   0   0.447  -3.5913  -1.3304  -1.5245
 DAU  HC1   H  HCH1   0   0.244  -5.3317  -0.3052   0.5939
 DAU  HC51  H  HCH2   0   0.211   2.4471  -2.3613   1.1619
 DAU  HC52  H  HCH2   0   0.213   1.7049  -3.6399   0.1882
 DAU  H4'C  H  HCH1   0   0.228   1.5516  -2.0909  -1.7400
 DAU  H3'C  H  HCH1   0   0.230   4.2025  -2.7853  -0.4686
 DAU  H3'O  H  HOH1   0   0.458   4.2383  -4.0832  -2.2742
 DAU  HC21  H  HCH2   0   0.276   5.3641  -1.2545  -1.8907
 DAU  HC22  H  HCH2   0   0.269   4.1003  -1.3557  -3.1095
 DAU  H1'C  H  HCH1   0   0.254   3.1987   0.5489  -2.3047
 DAU  H61C  H  HCR6   0   0.316   3.8683   2.4261  -1.8968
 DAU  H5A1  H  HCH3   0   0.248   4.7577   5.1800   0.0851
 DAU  H5A2  H  HCH3   0   0.248   6.1605   4.8466  -0.9174
 DAU  H5A3  H  HCH3   0   0.246   4.5416   4.7082  -1.5990
 DAU  H31N  H  HNR6   0   0.425   6.1308   0.9903   2.0103

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
 DAU  O6   C6    single  1.408  0.020  1.408
 DAU  O6   HO6   single  0.850  0.020  0.980
 DAU  C6   C5    single  1.515  0.020  1.515
 DAU  C6   HC61  single  0.970  0.020  1.090
 DAU  C6   HC62  single  0.970  0.020  1.090
 DAU  C5   O5    single  1.421  0.020  1.421
 DAU  C5   C4    single  1.530  0.020  1.530
 DAU  C5   HC5   single  0.970  0.020  1.090
 DAU  O5   C1    single  1.390  0.020  1.390
 DAU  C4   O4    single  1.408  0.020  1.408
 DAU  C4   C3    single  1.522  0.020  1.522
 DAU  C4   HC4   single  0.970  0.020  1.090
 DAU  O4   HO4   single  0.850  0.020  0.980
 DAU  C3   O3    single  1.410  0.020  1.410
 DAU  C3   C2    single  1.526  0.020  1.526
 DAU  C3   HC3   single  0.970  0.020  1.090
 DAU  O3   HO3   single  0.850  0.020  0.980
 DAU  C2   O2    single  1.400  0.020  1.400
 DAU  C2   C1    single  1.536  0.020  1.536
 DAU  C2   HC2   single  0.970  0.020  1.090
 DAU  O2   HO2   single  0.850  0.020  0.980
 DAU  C1   O1    single  1.407  0.020  1.407
 DAU  C1   HC1   single  0.970  0.020  1.090
 DAU  O1   P2    single  1.647  0.020  1.647
 DAU  P2   O3P   deloc   1.492  0.020  1.492
 DAU  P2   O4P   deloc   1.508  0.020  1.508
 DAU  P2   OPP   single  1.628  0.020  1.628
 DAU  OPP  P     single  1.646  0.020  1.646
 DAU  P    O1P   deloc   1.495  0.020  1.495
 DAU  P    O2P   deloc   1.495  0.020  1.495
 DAU  P    O5'   single  1.641  0.020  1.641
 DAU  O5'  C5'   single  1.412  0.020  1.412
 DAU  C5'  C4'   single  1.508  0.020  1.508
 DAU  C5'  HC51  single  0.970  0.020  1.090
 DAU  C5'  HC52  single  0.970  0.020  1.090
 DAU  C4'  O4'   single  1.417  0.020  1.417
 DAU  C4'  C3'   single  1.529  0.020  1.529
 DAU  C4'  H4'C  single  0.970  0.020  1.090
 DAU  O4'  C1'   single  1.399  0.020  1.399
 DAU  C3'  O3'   single  1.405  0.020  1.405
 DAU  C3'  C2'   single  1.529  0.020  1.529
 DAU  C3'  H3'C  single  0.970  0.020  1.090
 DAU  O3'  H3'O  single  0.850  0.020  0.980
 DAU  C2'  C1'   single  1.532  0.020  1.532
 DAU  C2'  HC21  single  0.970  0.020  1.090
 DAU  C2'  HC22  single  0.970  0.020  1.090
 DAU  C1'  N11   single  1.461  0.020  1.461
 DAU  C1'  H1'C  single  0.970  0.020  1.090
 DAU  N11  C61   single  1.371  0.020  1.371
 DAU  N11  C21   single  1.376  0.020  1.376
 DAU  C61  C51   double  1.344  0.020  1.344
 DAU  C61  H61C  single  0.930  0.020  1.080
 DAU  C51  C5A   single  1.493  0.020  1.493
 DAU  C51  C41   single  1.449  0.020  1.449
 DAU  C5A  H5A1  single  0.970  0.020  1.090
 DAU  C5A  H5A2  single  0.970  0.020  1.090
 DAU  C5A  H5A3  single  0.970  0.020  1.090
 DAU  C21  O21   double  1.213  0.020  1.213
 DAU  C21  N31   single  1.371  0.020  1.371
 DAU  N31  C41   single  1.383  0.020  1.383
 DAU  N31  H31N  single  0.860  0.020  1.020
 DAU  C41  O41   double  1.218  0.020  1.218

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
 DAU  HO6   O6   C6    107.96  3.000
 DAU  HC62  C6   HC61  107.13  3.000
 DAU  HC62  C6   C5    108.36  3.000
 DAU  HC61  C6   C5    108.80  3.000
 DAU  HC62  C6   O6    111.65  3.000
 DAU  HC61  C6   O6    111.82  3.000
 DAU  C5    C6   O6    108.98  3.000
 DAU  HC5   C5   C4    108.60  3.000
 DAU  HC5   C5   O5    110.42  3.000
 DAU  C4    C5   O5    110.86  3.000
 DAU  HC5   C5   C6    108.89  3.000
 DAU  C4    C5   C6    111.23  3.000
 DAU  O5    C5   C6    106.83  3.000
 DAU  C1    O5   C5    116.17  3.000
 DAU  HC4   C4   C3    107.76  3.000
 DAU  HC4   C4   O4    110.79  3.000
 DAU  C3    C4   O4    111.92  3.000
 DAU  HC4   C4   C5    108.21  3.000
 DAU  C3    C4   C5    110.54  3.000
 DAU  O4    C4   C5    107.58  3.000
 DAU  HO4   O4   C4    108.08  3.000
 DAU  HC3   C3   C2    109.19  3.000
 DAU  HC3   C3   O3    110.49  3.000
 DAU  C2    C3   O3    111.61  3.000
 DAU  HC3   C3   C4    108.58  3.000
 DAU  C2    C3   C4    109.55  3.000
 DAU  O3    C3   C4    107.35  3.000
 DAU  HO3   O3   C3    107.87  3.000
 DAU  HC2   C2   C1    105.89  3.000
 DAU  HC2   C2   O2    106.21  3.000
 DAU  C1    C2   O2    114.51  3.000
 DAU  HC2   C2   C3    107.94  3.000
 DAU  C1    C2   C3    109.27  3.000
 DAU  O2    C2   C3    112.56  3.000
 DAU  HO2   O2   C2    110.22  3.000
 DAU  HC1   C1   O1    110.44  3.000
 DAU  HC1   C1   C2    110.07  3.000
 DAU  O1    C1   C2    112.23  3.000
 DAU  HC1   C1   O5    106.08  3.000
 DAU  O1    C1   O5    108.10  3.000
 DAU  C2    C1   O5    109.72  3.000
 DAU  P2    O1   C1    121.96  3.000
 DAU  OPP   P2   O4P   110.96  3.000
 DAU  OPP   P2   O3P   110.98  3.000
 DAU  O4P   P2   O3P   120.05  3.000
 DAU  OPP   P2   O1     94.06  3.000
 DAU  O4P   P2   O1    107.78  3.000
 DAU  O3P   P2   O1    109.84  3.000
 DAU  P     OPP  P2    126.10  3.000
 DAU  O5'   P    O2P   110.25  3.000
 DAU  O5'   P    O1P   109.45  3.000
 DAU  O2P   P    O1P   120.89  3.000
 DAU  O5'   P    OPP    96.48  3.000
 DAU  O2P   P    OPP   110.37  3.000
 DAU  O1P   P    OPP   106.59  3.000
 DAU  C5'   O5'  P     117.58  3.000
 DAU  HC52  C5'  HC51  107.64  3.000
 DAU  HC52  C5'  C4'   107.82  3.000
 DAU  HC51  C5'  C4'   109.31  3.000
 DAU  HC52  C5'  O5'   111.41  3.000
 DAU  HC51  C5'  O5'   111.30  3.000
 DAU  C4'   C5'  O5'   109.27  3.000
 DAU  H4'C  C4'  C3'   108.44  3.000
 DAU  H4'C  C4'  O4'   109.72  3.000
 DAU  C3'   C4'  O4'   106.36  3.000
 DAU  H4'C  C4'  C5'   109.43  3.000
 DAU  C3'   C4'  C5'   112.93  3.000
 DAU  O4'   C4'  C5'   109.88  3.000
 DAU  C1'   O4'  C4'   110.95  3.000
 DAU  H3'C  C3'  C2'   109.86  3.000
 DAU  H3'C  C3'  O3'   110.57  3.000
 DAU  C2'   C3'  O3'   114.84  3.000
 DAU  H3'C  C3'  C4'   109.85  3.000
 DAU  C2'   C3'  C4'   102.52  3.000
 DAU  O3'   C3'  C4'   108.85  3.000
 DAU  H3'O  O3'  C3'   108.25  3.000
 DAU  HC22  C2'  HC21  107.55  3.000
 DAU  HC22  C2'  C1'   108.51  3.000
 DAU  HC21  C2'  C1'   113.17  3.000
 DAU  HC22  C2'  C3'   109.00  3.000
 DAU  HC21  C2'  C3'   113.61  3.000
 DAU  C1'   C2'  C3'   104.85  3.000
 DAU  H1'C  C1'  N11   104.22  3.000
 DAU  H1'C  C1'  C2'   109.65  3.000
 DAU  N11   C1'  C2'   116.11  3.000
 DAU  H1'C  C1'  O4'   110.06  3.000
 DAU  N11   C1'  O4'   109.16  3.000
 DAU  C2'   C1'  O4'   107.57  3.000
 DAU  C21   N11  C61   120.83  3.000
 DAU  C21   N11  C1'   119.96  3.000
 DAU  C61   N11  C1'   119.16  3.000
 DAU  H61C  C61  C51   120.73  3.000
 DAU  H61C  C61  N11   114.84  3.000
 DAU  C51   C61  N11   124.43  3.000
 DAU  C41   C51  C5A   119.03  3.000
 DAU  C41   C51  C61   117.83  3.000
 DAU  C5A   C51  C61   123.14  3.000
 DAU  H5A3  C5A  H5A2  107.87  3.000
 DAU  H5A3  C5A  H5A1  107.91  3.000
 DAU  H5A2  C5A  H5A1  107.21  3.000
 DAU  H5A3  C5A  C51   110.93  3.000
 DAU  H5A2  C5A  C51   111.40  3.000
 DAU  H5A1  C5A  C51   111.35  3.000
 DAU  N31   C21  O21   121.91  3.000
 DAU  N31   C21  N11   114.43  3.000
 DAU  O21   C21  N11   123.66  3.000
 DAU  H31N  N31  C41   116.73  3.000
 DAU  H31N  N31  C21   115.11  3.000
 DAU  C41   N31  C21   128.17  3.000
 DAU  O41   C41  N31   120.60  3.000
 DAU  O41   C41  C51   125.10  3.000
 DAU  N31   C41  C51   114.30  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
 DAU  CONST_01  N31   C21  N11  C1'   180.00   0.0  0
 DAU  CONST_02  C41   N31  C21  N11     0.00   0.0  0
 DAU  CONST_03  N31   C21  N11  C61     0.00   0.0  0
 DAU  CONST_04  C21   N31  C41  C51     0.00   0.0  0
 DAU  CONST_05  O21   C21  N11  C1'     0.00   0.0  0
 DAU  CONST_06  O21   C21  N11  C61   180.00   0.0  0
 DAU  CONST_07  O41   C41  N31  C21   180.00   0.0  0
 DAU  CONST_08  C41   N31  C21  O21   180.00   0.0  0
 DAU  CONST_09  H31N  N31  C21  N11   180.00   0.0  0
 DAU  Var_01    H5A1  C5A  C51  C61   121.98  30.0  3
 DAU  Var_02    O3P   P2   O1   C1    -56.46  30.0  3
 DAU  Var_03    C4'   C5'  O5'  P     172.66  30.0  3
 DAU  Var_04    O1P   P    OPP  P2   -160.77  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
 DAU  chir_01  C5   C6   O5   C4   negativ
 DAU  chir_02  C4   O4   C5   C3   positiv
 DAU  chir_03  C3   O3   C4   C2   negativ
 DAU  chir_04  C2   O2   C3   C1   positiv
 DAU  chir_05  C1   O5   O1   C2   positiv
 DAU  chir_08  C4'  C5'  O4'  C3'  negativ
 DAU  chir_09  C3'  O3'  C4'  C2'  positiv
 DAU  chir_10  C1'  O4'  N11  C2'  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
 DAU  plan-1  C1'   0.020
 DAU  plan-1  N11   0.020
 DAU  plan-1  C61   0.020
 DAU  plan-1  C51   0.020
 DAU  plan-1  C5A   0.020
 DAU  plan-1  C21   0.020
 DAU  plan-1  O21   0.020
 DAU  plan-1  N31   0.020
 DAU  plan-1  C41   0.020
 DAU  plan-1  O41   0.020
 DAU  plan-1  H61C  0.020
 DAU  plan-1  H31N  0.020

