# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 03:34:48 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: (2R,4S,6R)-4-amino-6-methyl-5-oxotetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-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](C[C@H](N)C1=O)O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=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
 DWN  DWN  '(2R,4S,6R)-4-amino-6-methyl-5-oxotetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  57  34  .  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_DWN
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
 DWN  O4   O  O      0  -0.391   3.3335  -4.3781  -0.2264
 DWN  C4   C  C      0   0.371   3.1730  -3.1811  -0.1602
 DWN  C5   C  CH1    0  -0.085   2.6571  -2.5241   1.1107
 DWN  C6   C  CH3    0  -0.696   3.8294  -2.1175   2.0059
 DWN  O5   O  O2     0  -0.483   1.7728  -1.4693   0.8144
 DWN  C3   C  CH1    0  -0.224   3.5386  -2.2493  -1.3083
 DWN  N3   N  NH2    0  -0.776   3.7567  -2.8946  -2.5803
 DWN  C2   C  CH2    0  -0.496   2.5292  -1.1077  -1.4329
 DWN  C1   C  CH1    0   0.334   2.2649  -0.4894  -0.0737
 DWN  O1   O  O2     0  -0.622   1.2973   0.4850  -0.1860
 DWN  P2   P  P      0   1.353   1.0448   1.5363   1.0777
 DWN  O3P  O  OP    -1  -0.751  -0.1869   1.1439   1.8210
 DWN  O4P  O  O      0  -0.804   2.3430   1.7414   1.7972
 DWN  OPP  O  O2     0  -0.742   0.7619   2.8098   0.0799
 DWN  P    P  P      0   1.354   0.2771   4.3187   0.5027
 DWN  O1P  O  OP    -1  -0.793   1.1183   5.2809  -0.2747
 DWN  O2P  O  O      0  -0.806   0.1395   4.4174   1.9893
 DWN  O5X  O  O2     0  -0.624  -1.1938   4.3789  -0.2140
 DWN  C5X  C  CH2    0  -0.183  -2.2771   3.6019   0.2655
 DWN  C4X  C  CH1    0   0.024  -2.9215   2.8629  -0.8843
 DWN  O4X  O  O2     0  -0.474  -2.0775   1.8060  -1.3092
 DWN  C3X  C  CH1    0   0.013  -4.2757   2.2458  -0.5301
 DWN  O3X  O  OH1    0  -0.672  -5.2932   3.1462  -0.9002
 DWN  C2X  C  CH2    0  -0.556  -4.2672   0.9383  -1.3215
 DWN  C1X  C  CH1    0   0.214  -2.7889   0.6356  -1.5726
 DWN  N11  N  NR6    0  -0.568  -2.2131  -0.4908  -0.8333
 DWN  C21  C  CR6    0   0.777  -2.3677  -0.5963   0.5306
 DWN  O21  O  O      0  -0.482  -3.0354   0.1668   1.1929
 DWN  N31  N  NR16   0  -0.734  -1.7581  -1.6909   1.0874
 DWN  C61  C  CR16   0   0.069  -1.5050  -1.4355  -1.5277
 DWN  C51  C  CR6    0  -0.182  -0.9479  -2.5282  -0.9796
 DWN  C5A  C  CH3    0  -0.730  -0.2525  -3.5779  -1.7812
 DWN  C41  C  CR6    0   0.581  -1.0620  -2.6976   0.4530
 DWN  O41  O  O      0  -0.472  -0.6214  -3.6444   1.0833
 DWN  H1   H  HCH1   0   0.271   2.0571  -3.2642   1.6433
 DWN  H2   H  HCH3   0   0.255   3.4551  -1.5947   2.8859
 DWN  H3   H  HCH3   0   0.248   4.3612  -3.0069   2.3438
 DWN  H4   H  HCH3   0   0.235   4.5511  -1.4678   1.5100
 DWN  H5   H  HCH1   0   0.275   4.4936  -1.8008  -0.9966
 DWN  H6   H  HNH2   0   0.354   4.4540  -3.6223  -2.4878
 DWN  H7   H  HNH2   0   0.339   2.9086  -3.3573  -2.8859
 DWN  H9   H  HCH2   0   0.254   2.9285  -0.3553  -2.1155
 DWN  H10  H  HCH2   0   0.249   1.5881  -1.4740  -1.8534
 DWN  H11  H  HCH1   0   0.191   3.2003  -0.0663   0.3222
 DWN  H14  H  HCH2   0   0.241  -1.9694   2.8775   1.0236
 DWN  H15  H  HCH2   0   0.210  -3.0214   4.2682   0.7160
 DWN  H16  H  HCH1   0   0.218  -3.0750   3.5612  -1.7200
 DWN  H17  H  HCH1   0   0.235  -4.3244   2.0356   0.5405
 DWN  H18  H  HOH1   0   0.455  -6.1083   2.8675  -0.4734
 DWN  H19  H  HCH2   0   0.270  -4.8040   0.1240  -0.8384
 DWN  H20  H  HCH2   0   0.261  -4.7411   1.1147  -2.2896
 DWN  H21  H  HCH1   0   0.243  -2.6502   0.3537  -2.6188
 DWN  H22  H  HNR6   0   0.413  -1.8494  -1.7638   2.0923
 DWN  H23  H  HCR6   0   0.306  -1.4382  -1.2590  -2.5932
 DWN  H24  H  HCH3   0   0.235   0.7286  -3.8137  -1.3694
 DWN  H25  H  HCH3   0   0.255  -0.8191  -4.5110  -1.7933
 DWN  H26  H  HCH3   0   0.245  -0.1203  -3.2583  -2.8141

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
 DWN  O41  C41  double  1.220  0.020  1.220
 DWN  C41  N31  single  1.379  0.020  1.379
 DWN  C41  C51  single  1.447  0.020  1.447
 DWN  C5A  C51  single  1.493  0.020  1.493
 DWN  N31  C21  single  1.371  0.020  1.371
 DWN  C51  C61  double  1.343  0.020  1.343
 DWN  C21  O21  double  1.211  0.020  1.211
 DWN  C21  N11  single  1.377  0.020  1.377
 DWN  C61  N11  single  1.370  0.020  1.370
 DWN  N11  C1X  single  1.465  0.020  1.465
 DWN  O2P  P    deloc   1.496  0.020  1.496
 DWN  O4X  C1X  single  1.395  0.020  1.395
 DWN  O4X  C4X  single  1.418  0.020  1.418
 DWN  C1X  C2X  single  1.530  0.020  1.530
 DWN  C5X  C4X  single  1.511  0.020  1.511
 DWN  C5X  O5X  single  1.417  0.020  1.417
 DWN  O1P  P    deloc   1.496  0.020  1.496
 DWN  P    O5X  single  1.637  0.020  1.637
 DWN  P    OPP  single  1.640  0.020  1.640
 DWN  C4X  C3X  single  1.530  0.020  1.530
 DWN  C2X  C3X  single  1.528  0.020  1.528
 DWN  O4P  P2   deloc   1.498  0.020  1.498
 DWN  OPP  P2   single  1.642  0.020  1.642
 DWN  C3X  O3X  single  1.408  0.020  1.408
 DWN  P2   O3P  deloc   1.491  0.020  1.491
 DWN  P2   O1   single  1.663  0.020  1.663
 DWN  C6   C5   single  1.530  0.020  1.530
 DWN  O1   C1   single  1.378  0.020  1.378
 DWN  C5   O5   single  1.408  0.020  1.408
 DWN  C5   C4   single  1.521  0.020  1.521
 DWN  O5   C1   single  1.411  0.020  1.411
 DWN  O4   C4   double  1.209  0.020  1.209
 DWN  C1   C2   single  1.516  0.020  1.516
 DWN  C4   C3   single  1.523  0.020  1.523
 DWN  C2   C3   single  1.529  0.020  1.529
 DWN  C3   N3   single  1.443  0.020  1.443
 DWN  C5   H1   single  0.970  0.020  1.090
 DWN  C6   H2   single  0.970  0.020  1.090
 DWN  C6   H3   single  0.970  0.020  1.090
 DWN  C6   H4   single  0.970  0.020  1.090
 DWN  C3   H5   single  0.970  0.020  1.090
 DWN  N3   H6   single  0.890  0.020  1.040
 DWN  N3   H7   single  0.890  0.020  1.040
 DWN  C2   H9   single  0.970  0.020  1.090
 DWN  C2   H10  single  0.970  0.020  1.090
 DWN  C1   H11  single  0.970  0.020  1.090
 DWN  C5X  H14  single  0.970  0.020  1.090
 DWN  C5X  H15  single  0.970  0.020  1.090
 DWN  C4X  H16  single  0.970  0.020  1.090
 DWN  C3X  H17  single  0.970  0.020  1.090
 DWN  O3X  H18  single  0.850  0.020  0.980
 DWN  C2X  H19  single  0.970  0.020  1.090
 DWN  C2X  H20  single  0.970  0.020  1.090
 DWN  C1X  H21  single  0.970  0.020  1.090
 DWN  N31  H22  single  0.860  0.020  1.020
 DWN  C61  H23  single  0.930  0.020  1.080
 DWN  C5A  H24  single  0.970  0.020  1.090
 DWN  C5A  H25  single  0.970  0.020  1.090
 DWN  C5A  H26  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
 DWN  C3   C4   C5   116.55  3.000
 DWN  C3   C4   O4   122.16  3.000
 DWN  C5   C4   O4   121.22  3.000
 DWN  H1   C5   O5   105.39  3.000
 DWN  H1   C5   C6   108.41  3.000
 DWN  O5   C5   C6   113.91  3.000
 DWN  H1   C5   C4   107.54  3.000
 DWN  O5   C5   C4   111.15  3.000
 DWN  C6   C5   C4   110.11  3.000
 DWN  H4   C6   H3   107.72  3.000
 DWN  H4   C6   H2   107.98  3.000
 DWN  H3   C6   H2   107.98  3.000
 DWN  H4   C6   C5   113.54  3.000
 DWN  H3   C6   C5   109.78  3.000
 DWN  H2   C6   C5   109.68  3.000
 DWN  C1   O5   C5   115.70  3.000
 DWN  H5   C3   C2   106.97  3.000
 DWN  H5   C3   N3   107.51  3.000
 DWN  C2   C3   N3   111.21  3.000
 DWN  H5   C3   C4   104.13  3.000
 DWN  N3   C3   C4   115.28  3.000
 DWN  C2   C3   C4   111.09  3.000
 DWN  H7   N3   H6   106.02  3.000
 DWN  H7   N3   C3   110.09  3.000
 DWN  H6   N3   C3   110.19  3.000
 DWN  H10  C2   H9   107.77  3.000
 DWN  H10  C2   C1   109.33  3.000
 DWN  H9   C2   C1   110.07  3.000
 DWN  H10  C2   C3   110.45  3.000
 DWN  H9   C2   C3   108.92  3.000
 DWN  C1   C2   C3   110.27  3.000
 DWN  H11  C1   O1   110.76  3.000
 DWN  H11  C1   C2   109.34  3.000
 DWN  O1   C1   C2   109.74  3.000
 DWN  H11  C1   O5   109.69  3.000
 DWN  C2   C1   O5   109.98  3.000
 DWN  O1   C1   O5   107.31  3.000
 DWN  P2   O1   C1   119.45  3.000
 DWN  OPP  P2   O4P  109.56  3.000
 DWN  OPP  P2   O3P  111.38  3.000
 DWN  O4P  P2   O3P  120.82  3.000
 DWN  O3P  P2   O1   109.74  3.000
 DWN  OPP  P2   O1    93.13  3.000
 DWN  O4P  P2   O1   108.66  3.000
 DWN  P    OPP  P2   127.42  3.000
 DWN  O5X  P    O2P  110.48  3.000
 DWN  O5X  P    O1P  104.72  3.000
 DWN  O2P  P    O1P  121.71  3.000
 DWN  O5X  P    OPP  100.75  3.000
 DWN  O1P  P    OPP  106.95  3.000
 DWN  O2P  P    OPP  110.12  3.000
 DWN  C5X  O5X  P    121.24  3.000
 DWN  H15  C5X  H14  108.00  3.000
 DWN  H15  C5X  C4X  108.69  3.000
 DWN  H14  C5X  C4X  108.89  3.000
 DWN  H15  C5X  O5X  108.97  3.000
 DWN  H14  C5X  O5X  112.52  3.000
 DWN  C4X  C5X  O5X  109.68  3.000
 DWN  H16  C4X  C3X  107.97  3.000
 DWN  H16  C4X  O4X  109.19  3.000
 DWN  C3X  C4X  O4X  107.20  3.000
 DWN  H16  C4X  C5X  109.10  3.000
 DWN  C3X  C4X  C5X  113.49  3.000
 DWN  O4X  C4X  C5X  109.80  3.000
 DWN  C1X  O4X  C4X  112.24  3.000
 DWN  H17  C3X  C2X  110.07  3.000
 DWN  H17  C3X  O3X  110.40  3.000
 DWN  C2X  C3X  O3X  114.51  3.000
 DWN  H17  C3X  C4X  110.13  3.000
 DWN  O3X  C3X  C4X  108.71  3.000
 DWN  C2X  C3X  C4X  102.73  3.000
 DWN  H18  O3X  C3X  108.09  3.000
 DWN  H20  C2X  H19  107.47  3.000
 DWN  H20  C2X  C1X  107.81  3.000
 DWN  H19  C2X  C1X  113.67  3.000
 DWN  H20  C2X  C3X  108.56  3.000
 DWN  H19  C2X  C3X  114.04  3.000
 DWN  C1X  C2X  C3X  105.05  3.000
 DWN  H21  C1X  N11  103.59  3.000
 DWN  H21  C1X  C2X  109.33  3.000
 DWN  N11  C1X  C2X  116.68  3.000
 DWN  H21  C1X  O4X  109.43  3.000
 DWN  C2X  C1X  O4X  107.21  3.000
 DWN  N11  C1X  O4X  110.45  3.000
 DWN  C61  N11  C21  120.49  3.000
 DWN  C61  N11  C1X  118.53  3.000
 DWN  C21  N11  C1X  120.98  3.000
 DWN  N31  C21  O21  121.74  3.000
 DWN  O21  C21  N11  123.74  3.000
 DWN  N31  C21  N11  114.43  3.000
 DWN  H22  N31  C41  116.75  3.000
 DWN  H22  N31  C21  114.89  3.000
 DWN  C41  N31  C21  128.36  3.000
 DWN  H23  C61  C51  120.59  3.000
 DWN  H23  C61  N11  114.74  3.000
 DWN  C51  C61  N11  124.65  3.000
 DWN  C41  C51  C5A  119.08  3.000
 DWN  C5A  C51  C61  123.10  3.000
 DWN  C41  C51  C61  117.81  3.000
 DWN  H26  C5A  H25  107.65  3.000
 DWN  H26  C5A  H24  108.21  3.000
 DWN  H25  C5A  H24  106.65  3.000
 DWN  H26  C5A  C51  111.07  3.000
 DWN  H25  C5A  C51  111.42  3.000
 DWN  H24  C5A  C51  111.63  3.000
 DWN  O41  C41  C51  125.03  3.000
 DWN  C51  C41  N31  114.19  3.000
 DWN  O41  C41  N31  120.76  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
 DWN  CONST_01  N31  C21  N11  C1X   180.00   0.0  0
 DWN  CONST_02  C41  N31  C21  N11     0.00   0.0  0
 DWN  CONST_03  C51  C41  N31  C21     0.00   0.0  0
 DWN  CONST_04  C61  N11  C21  N31     0.00   0.0  0
 DWN  CONST_05  O21  C21  N11  C1X     0.00   0.0  0
 DWN  CONST_06  O41  C41  N31  C21   180.00   0.0  0
 DWN  CONST_07  C41  N31  C21  O21   180.00   0.0  0
 DWN  CONST_08  C61  N11  C21  O21   180.00   0.0  0
 DWN  CONST_09  H22  N31  C21  N11   180.00   0.0  0
 DWN  Var_01    H24  C5A  C51  C61   130.15  30.0  3
 DWN  Var_02    O4P  P2   O1   C1     30.87  30.0  1
 DWN  Var_03    C4X  C5X  O5X  P    -130.56  30.0  2
 DWN  Var_04    O2P  P    OPP  P2      1.17  30.0  2

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
 DWN  chir_01  C5   C6   O5   C4   negativ
 DWN  chir_02  C3   N3   C2   C4   negativ
 DWN  chir_03  C1   O1   O5   C2   negativ
 DWN  chir_06  C4X  O4X  C5X  C3X  positiv
 DWN  chir_07  C3X  O3X  C4X  C2X  positiv
 DWN  chir_08  C1X  O4X  N11  C2X  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
 DWN  plan-1  O4   0.020
 DWN  plan-1  C4   0.020
 DWN  plan-1  C5   0.020
 DWN  plan-1  C3   0.020
 DWN  plan-2  C1X  0.020
 DWN  plan-2  N11  0.020
 DWN  plan-2  C21  0.020
 DWN  plan-2  O21  0.020
 DWN  plan-2  N31  0.020
 DWN  plan-2  C61  0.020
 DWN  plan-2  C51  0.020
 DWN  plan-2  C5A  0.020
 DWN  plan-2  C41  0.020
 DWN  plan-2  O41  0.020
 DWN  plan-2  H22  0.020
 DWN  plan-2  H23  0.020

