# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 23:40:20 2021
#   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  59  34  .  2021-08-08  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.387  21.4053  18.0920   1.8456
 DWN  C4   C  CR6   0   0.405  20.9308  16.9830   1.8652
 DWN  C5   C  CR16  0  -0.088  21.5268  15.8387   1.0589
 DWN  C6   C  CH3   0  -0.683  23.0393  15.7962   1.1096
 DWN  O5   O  O     0  -0.484  21.0344  14.6025   1.5549
 DWN  C3   C  CR16  0  -0.182  19.6824  16.6213   2.6357
 DWN  N3   N  NH2   0  -0.797  18.9163  17.8000   2.9638
 DWN  C2   C  C     0  -0.566  18.8730  15.6812   1.7404
 DWN  C1   C  CR16  0   0.296  19.6686  14.4106   1.4787
 DWN  O1   O  O2    0  -0.592  19.2832  13.9340   0.1779
 DWN  P2   P  P     0   1.496  19.9018  12.6505  -0.5261
 DWN  O3P  O  OH1   0  -0.729  20.3455  11.6360   0.6106
 DWN  O4P  O  O     0  -0.677  19.0474  12.1482  -1.6115
 DWN  OPP  O  O2    0  -0.683  21.3568  13.1777  -1.0013
 DWN  P    P  P     0   1.485  22.1931  12.7245  -2.3060
 DWN  O1P  O  OH1   0  -0.716  23.6603  13.1838  -1.9103
 DWN  O2P  O  O     0  -0.677  21.6774  13.2062  -3.5955
 DWN  O5X  O  O2    0  -0.588  22.2200  11.1552  -2.0669
 DWN  C5X  C  CH2   0  -0.197  22.7795  10.2710  -3.0441
 DWN  C4X  C  CH1   0  -0.009  23.0344   8.9509  -2.3358
 DWN  O4X  O  O2    0  -0.498  23.4214   7.9884  -3.3085
 DWN  C3X  C  CH1   0  -0.013  24.1730   9.0155  -1.3147
 DWN  O3X  O  OH1   0  -0.669  23.8826   8.0832  -0.3009
 DWN  C2X  C  CH2   0  -0.551  25.3651   8.5905  -2.1614
 DWN  C1X  C  CH1   0   0.207  24.7353   7.5373  -3.0594
 DWN  N11  N  NR6   0  -0.566  25.4070   7.3345  -4.3318
 DWN  C21  C  CR6   0   0.735  25.9427   6.0991  -4.6235
 DWN  O21  O  O     0  -0.481  25.9112   5.1529  -3.8637
 DWN  N31  N  NR16  0  -0.736  26.5350   6.0196  -5.8560
 DWN  C61  C  CR16  0   0.074  25.4649   8.3635  -5.2373
 DWN  C51  C  CR6   0  -0.186  26.0424   8.2748  -6.4457
 DWN  C5A  C  CH3   0  -0.708  26.0890   9.4069  -7.4179
 DWN  C41  C  CR6   0   0.563  26.6424   7.0075  -6.8178
 DWN  O41  O  O     0  -0.450  27.2034   6.7857  -7.8744
 DWN  H1   H  HCR6  0   0.277  21.2111  15.9936   0.0166
 DWN  H2   H  HCH3  0   0.247  23.4536  16.7358   0.7507
 DWN  H3   H  HCH3  0   0.242  23.3975  15.6268   2.1252
 DWN  H4   H  HCH3  0   0.248  23.4131  14.9980   0.4700
 DWN  H5   H  HCR6  0   0.269  20.0236  16.0536   3.5188
 DWN  H6   H  HNH2  0   0.357  18.1444  17.5354   3.5624
 DWN  H7   H  HNH2  0   0.355  19.4821  18.4426   3.5029
 DWN  H9   H  H     0   0.272  18.6388  16.1922   0.8033
 DWN  H10  H  H     0   0.290  17.9246  15.4275   2.2148
 DWN  H11  H  HCR6  0   0.270  19.4334  13.6388   2.2132
 DWN  H12  H  HOH1  0   0.510  19.6540  11.0173   0.8858
 DWN  H13  H  HOH1  0   0.510  23.9781  13.9633  -2.3873
 DWN  H14  H  HCH2  0   0.238  23.7047  10.6860  -3.4579
 DWN  H15  H  HCH2  0   0.278  22.0721  10.1327  -3.8634
 DWN  H16  H  HCH1  0   0.270  22.1057   8.6245  -1.8565
 DWN  H17  H  HCH1  0   0.256  24.2993  10.0243  -0.9062
 DWN  H18  H  HOH1  0   0.457  24.6297   8.0526   0.3052
 DWN  H19  H  HCH2  0   0.290  26.1936   8.1919  -1.5764
 DWN  H20  H  HCH2  0   0.267  25.7512   9.4366  -2.7347
 DWN  H21  H  HCH1  0   0.276  24.7158   6.5689  -2.5603
 DWN  H22  H  HNR6  0   0.427  26.9432   5.1201  -6.0798
 DWN  H23  H  HCR6  0   0.304  25.0021   9.2874  -4.9215
 DWN  H24  H  HCH3  0   0.248  25.5865  10.2861  -7.0181
 DWN  H25  H  HCH3  0   0.249  27.1164   9.6862  -7.6544
 DWN  H26  H  HCH3  0   0.249  25.6021   9.1410  -8.3570

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  1.217  0.020  1.217
 DWN  C41  N31  single  1.383  0.020  1.383
 DWN  C41  C51  single  1.451  0.020  1.451
 DWN  C5A  C51  single  1.493  0.020  1.493
 DWN  N31  C21  single  1.370  0.020  1.370
 DWN  C51  C61  double  1.342  0.020  1.342
 DWN  C21  O21  double  1.214  0.020  1.214
 DWN  C21  N11  single  1.378  0.020  1.378
 DWN  C61  N11  single  1.372  0.020  1.372
 DWN  N11  C1X  single  1.453  0.020  1.453
 DWN  O2P  P    double  1.470  0.020  1.470
 DWN  O4X  C1X  single  1.411  0.020  1.411
 DWN  O4X  C4X  single  1.422  0.020  1.422
 DWN  C1X  C2X  single  1.521  0.020  1.521
 DWN  C5X  C4X  single  1.520  0.020  1.520
 DWN  C5X  O5X  single  1.432  0.020  1.432
 DWN  O1P  P    single  1.588  0.020  1.588
 DWN  P    O5X  single  1.588  0.020  1.588
 DWN  P    OPP  single  1.615  0.020  1.615
 DWN  C4X  C3X  single  1.531  0.020  1.531
 DWN  C2X  C3X  single  1.523  0.020  1.523
 DWN  O4P  P2   double  1.470  0.020  1.470
 DWN  OPP  P2   single  1.619  0.020  1.619
 DWN  C3X  O3X  single  1.408  0.020  1.408
 DWN  P2   O3P  single  1.587  0.020  1.587
 DWN  P2   O1   single  1.589  0.020  1.589
 DWN  C6   C5   single  1.514  0.020  1.514
 DWN  O1   C1   single  1.438  0.020  1.438
 DWN  C5   O5   single  1.420  0.020  1.420
 DWN  C5   C4   single  1.521  0.020  1.521
 DWN  O5   C1   single  1.381  0.020  1.381
 DWN  O4   C4   double  1.206  0.020  1.206
 DWN  C1   C2   single  1.522  0.020  1.522
 DWN  C4   C3   single  1.511  0.020  1.511
 DWN  C2   C3   single  1.530  0.020  1.530
 DWN  C3   N3   single  1.444  0.020  1.444
 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  O3P  H12  single  0.850  0.020  0.980
 DWN  O1P  H13  single  0.850  0.020  0.980
 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   114.45  3.000
 DWN  C3   C4   O4   123.59  3.000
 DWN  C5   C4   O4   121.92  3.000
 DWN  H1   C5   O5   110.74  3.000
 DWN  H1   C5   C6   108.81  3.000
 DWN  O5   C5   C6   108.08  3.000
 DWN  H1   C5   C4   106.49  3.000
 DWN  O5   C5   C4   109.50  3.000
 DWN  C6   C5   C4   113.25  3.000
 DWN  H4   C6   H3   108.69  3.000
 DWN  H4   C6   H2   107.98  3.000
 DWN  H3   C6   H2   108.44  3.000
 DWN  H4   C6   C5   110.11  3.000
 DWN  H3   C6   C5   111.34  3.000
 DWN  H2   C6   C5   110.20  3.000
 DWN  C1   O5   C5   116.39  3.000
 DWN  H5   C3   C2   108.40  3.000
 DWN  H5   C3   N3   113.71  3.000
 DWN  C2   C3   N3   110.73  3.000
 DWN  H5   C3   C4   106.00  3.000
 DWN  N3   C3   C4   111.04  3.000
 DWN  C2   C3   C4   106.61  3.000
 DWN  H7   N3   H6   106.11  3.000
 DWN  H7   N3   C3   110.06  3.000
 DWN  H6   N3   C3   109.01  3.000
 DWN  H10  C2   H9   107.19  3.000
 DWN  H10  C2   C1   109.59  3.000
 DWN  H9   C2   C1   110.80  3.000
 DWN  H10  C2   C3   110.39  3.000
 DWN  H9   C2   C3   109.13  3.000
 DWN  C1   C2   C3   109.70  3.000
 DWN  H11  C1   O1   108.46  3.000
 DWN  H11  C1   C2   111.23  3.000
 DWN  O1   C1   C2   106.98  3.000
 DWN  H11  C1   O5   105.92  3.000
 DWN  C2   C1   O5   113.05  3.000
 DWN  O1   C1   O5   111.16  3.000
 DWN  P2   O1   C1   124.34  3.000
 DWN  OPP  P2   O4P  114.65  3.000
 DWN  OPP  P2   O3P   99.62  3.000
 DWN  O4P  P2   O3P  118.23  3.000
 DWN  O3P  P2   O1   107.93  3.000
 DWN  OPP  P2   O1   102.53  3.000
 DWN  O4P  P2   O1   112.14  3.000
 DWN  H12  O3P  P2   114.37  3.000
 DWN  P    OPP  P2   127.68  3.000
 DWN  O5X  P    O2P  117.51  3.000
 DWN  O5X  P    O1P  103.46  3.000
 DWN  O2P  P    O1P  116.62  3.000
 DWN  O5X  P    OPP   99.47  3.000
 DWN  O1P  P    OPP  101.31  3.000
 DWN  O2P  P    OPP  115.80  3.000
 DWN  H13  O1P  P    114.45  3.000
 DWN  C5X  O5X  P    120.95  3.000
 DWN  H15  C5X  H14  108.18  3.000
 DWN  H15  C5X  C4X  110.39  3.000
 DWN  H14  C5X  C4X  111.32  3.000
 DWN  H15  C5X  O5X  109.72  3.000
 DWN  H14  C5X  O5X  110.74  3.000
 DWN  C4X  C5X  O5X  106.49  3.000
 DWN  H16  C4X  C3X  110.58  3.000
 DWN  H16  C4X  O4X  109.18  3.000
 DWN  C3X  C4X  O4X  106.41  3.000
 DWN  H16  C4X  C5X  108.71  3.000
 DWN  C3X  C4X  C5X  113.51  3.000
 DWN  O4X  C4X  C5X  108.35  3.000
 DWN  C1X  O4X  C4X  110.42  3.000
 DWN  H17  C3X  C2X  111.97  3.000
 DWN  H17  C3X  O3X  111.41  3.000
 DWN  C2X  C3X  O3X  112.16  3.000
 DWN  H17  C3X  C4X  111.92  3.000
 DWN  O3X  C3X  C4X  107.40  3.000
 DWN  C2X  C3X  C4X  101.52  3.000
 DWN  H18  O3X  C3X  108.33  3.000
 DWN  H20  C2X  H19  107.23  3.000
 DWN  H20  C2X  C1X  111.89  3.000
 DWN  H19  C2X  C1X  112.24  3.000
 DWN  H20  C2X  C3X  110.63  3.000
 DWN  H19  C2X  C3X  113.50  3.000
 DWN  C1X  C2X  C3X  101.39  3.000
 DWN  H21  C1X  N11  106.58  3.000
 DWN  H21  C1X  C2X  110.64  3.000
 DWN  N11  C1X  C2X  114.98  3.000
 DWN  H21  C1X  O4X  110.38  3.000
 DWN  C2X  C1X  O4X  105.57  3.000
 DWN  N11  C1X  O4X  108.69  3.000
 DWN  C61  N11  C21  121.09  3.000
 DWN  C61  N11  C1X  119.52  3.000
 DWN  C21  N11  C1X  119.36  3.000
 DWN  N31  C21  O21  121.95  3.000
 DWN  O21  C21  N11  123.80  3.000
 DWN  N31  C21  N11  114.25  3.000
 DWN  H22  N31  C41  116.71  3.000
 DWN  H22  N31  C21  115.13  3.000
 DWN  C41  N31  C21  128.16  3.000
 DWN  H23  C61  C51  120.26  3.000
 DWN  H23  C61  N11  115.49  3.000
 DWN  C51  C61  N11  124.25  3.000
 DWN  C41  C51  C5A  118.85  3.000
 DWN  C5A  C51  C61  123.34  3.000
 DWN  C41  C51  C61  117.82  3.000
 DWN  H26  C5A  H25  107.23  3.000
 DWN  H26  C5A  H24  107.88  3.000
 DWN  H25  C5A  H24  107.92  3.000
 DWN  H26  C5A  C51  111.21  3.000
 DWN  H25  C5A  C51  111.39  3.000
 DWN  H24  C5A  C51  111.03  3.000
 DWN  O41  C41  C51  124.94  3.000
 DWN  C51  C41  N31  114.42  3.000
 DWN  O41  C41  N31  120.63  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   -0.80  30.0  3
 DWN  Var_02    O4P  P2   O1   C1   161.31  30.0  1
 DWN  Var_03    C4X  C5X  O5X  P    162.83  30.0  2
 DWN  Var_04    O2P  P    OPP  P2    72.25  30.0  1

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
 DWN  chir_09  P2   OPP  O3P  O1   both
 DWN  chir_10  P    O5X  O1P  O2P  both

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

