# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  4 06:38:55 2021
#   Inital geometry file: a 146 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 hydrogen (S)-{3-[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]propyl}phosphonate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](CCC[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](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
 Y6W  Y6W  '[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl hydrogen (S)-{3-[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]propyl}phosphonate (non-preferred name)'  ligand  63  34  .  2022-07-22  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Y6W
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
 Y6W  C1    C  CH1   0  -0.011  23.9156  -25.4474   6.7323
 Y6W  C2    C  CH1   0   0.037  23.1602  -26.7688   6.5345
 Y6W  O2    O  OH1   0  -0.677  21.7797  -26.4988   6.5749
 Y6W  C3    C  CH1   0   0.000  23.5747  -27.7900   7.5897
 Y6W  O3    O  OH1   0  -0.676  22.8817  -28.9852   7.3130
 Y6W  C4    C  CH1   0   0.015  25.0927  -27.9704   7.5822
 Y6W  O4    O  OH1   0  -0.692  25.4658  -28.6001   6.3812
 Y6W  C5    C  CH1   0  -0.048  25.7275  -26.5898   7.7697
 Y6W  O5    O  O2    0  -0.495  25.3090  -25.7067   6.7503
 Y6W  C6    C  CH2   0  -0.183  27.2421  -26.5973   7.8054
 Y6W  O6    O  OH1   0  -0.672  27.7665  -27.1263   6.6021
 Y6W  C1'   C  CH1   0   0.184  28.0518  -25.0771  13.3453
 Y6W  C2'   C  CH1   0   0.009  28.2379  -25.9050  12.0791
 Y6W  O2'   O  OH1   0  -0.648  28.8802  -27.0974  12.3887
 Y6W  C3'   C  CH1   0  -0.065  29.0221  -24.9070  11.2136
 Y6W  O3'   O  OH1   0  -0.659  30.3888  -25.0817  11.4696
 Y6W  C4'   C  CH1   0   0.015  28.4934  -23.5392  11.7185
 Y6W  O4'   O  O2    0  -0.512  27.6704  -23.8116  12.8561
 Y6W  C5'   C  CH2   0  -0.246  27.7168  -22.7417  10.6999
 Y6W  O5'   O  O2    0  -0.592  26.6436  -23.4984  10.1565
 Y6W  CAK   C  CH2   0  -0.485  23.4592  -24.6418   7.9496
 Y6W  CAL   C  CH2   0  -0.458  24.2487  -23.3434   8.1073
 Y6W  CAM   C  CH2   0  -0.725  24.1367  -22.7168   9.5016
 Y6W  PAN   P  P     0   1.394  25.1384  -23.5686  10.7320
 Y6W  OAO   O  OH1   0  -0.747  25.0714  -22.5671  11.9854
 Y6W  NAZ   N  NR6   0  -0.584  27.0768  -25.5548  14.2918
 Y6W  CBA   C  CR6   0   0.744  27.4296  -25.6116  15.6329
 Y6W  CBB   C  CR16  0   0.076  25.8121  -25.8892  13.8847
 Y6W  CBC   C  CR16  0  -0.516  24.8622  -26.3273  14.7236
 Y6W  CBD   C  CR6   0   0.571  25.1536  -26.4583  16.1300
 Y6W  OBE   O  O     0  -0.472  28.5186  -25.2817  16.0493
 Y6W  NBF   N  NR16  0  -0.736  26.4464  -26.0796  16.4607
 Y6W  OBG   O  O     0  -0.458  24.3858  -26.8505  16.9873
 Y6W  OBH   O  O     0  -0.689  24.7568  -24.9802  11.0158
 Y6W  H1    H  HCH1  0   0.244  23.7594  -24.8301   5.8415
 Y6W  H2    H  HCH1  0   0.223  23.4445  -27.1649   5.5491
 Y6W  HO2   H  HOH1  0   0.450  21.3131  -27.3282   6.4290
 Y6W  H3    H  HCH1  0   0.216  23.2936  -27.4078   8.5816
 Y6W  HO3   H  HOH1  0   0.454  22.9102  -29.5461   8.0941
 Y6W  H4    H  HCH1  0   0.208  25.3776  -28.5819   8.4548
 Y6W  HO4   H  HOH1  0   0.448  26.3907  -28.3702   6.2113
 Y6W  H5    H  HCH1  0   0.235  25.4244  -26.2239   8.7616
 Y6W  H6    H  HCH2  0   0.224  27.5971  -25.5726   7.9736
 Y6W  H6A   H  HCH2  0   0.214  27.5501  -27.1943   8.6717
 Y6W  HO6   H  HOH1  0   0.470  28.6826  -27.3795   6.7491
 Y6W  H2'   H  HCH1  0   0.240  27.2654  -26.0731  11.5977
 Y6W  HO2'  H  HOH1  0   0.462  28.9271  -27.6461  11.5998
 Y6W  H3'   H  HCH1  0   0.253  28.8024  -25.0437  10.1481
 Y6W  HO3'  H  HOH1  0   0.459  30.8833  -24.4843  10.8996
 Y6W  H4'   H  HCH1  0   0.266  29.3478  -22.9236  12.0275
 Y6W  H5'   H  HCH2  0   0.262  27.3698  -21.7987  11.1295
 Y6W  H5'A  H  HCH2  0   0.270  28.3833  -22.4942   9.8729
 Y6W  HAK   H  HCH2  0   0.251  22.4014  -24.4022   7.8301
 Y6W  HAKA  H  HCH2  0   0.241  23.5216  -25.2402   8.8603
 Y6W  HAL   H  HCH2  0   0.246  25.3007  -23.4996   7.8639
 Y6W  HALA  H  HCH2  0   0.255  23.8832  -22.6130   7.3823
 Y6W  HAM   H  HCH2  0   0.291  24.4644  -21.6752   9.4723
 Y6W  HAMA  H  HCH2  0   0.284  23.0998  -22.7142   9.8473
 Y6W  HOAO  H  HOH1  0   0.488  25.6066  -22.8380  12.7467
 Y6W  HBB   H  HCR6  0   0.343  25.5990  -25.7698  12.8307
 Y6W  HBC   H  HCR6  0   0.293  23.8802  -26.5807  14.3552
 Y6W  HNBF  H  HNR6  0   0.429  26.7014  -26.1336  17.4397
 Y6W  H1'   H  HCH1  0   0.284  29.0041  -25.0210  13.8787

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
 Y6W  C2   C1    single  1.535  0.020  1.535
 Y6W  C1   O5    single  1.417  0.020  1.417
 Y6W  C1   CAK   single  1.529  0.020  1.529
 Y6W  C1   H1    single  0.970  0.020  1.090
 Y6W  O2   C2    single  1.407  0.020  1.407
 Y6W  C2   C3    single  1.526  0.020  1.526
 Y6W  C2   H2    single  0.970  0.020  1.090
 Y6W  O2   HO2   single  0.850  0.020  0.980
 Y6W  O3   C3    single  1.409  0.020  1.409
 Y6W  C3   C4    single  1.529  0.020  1.529
 Y6W  C3   H3    single  0.970  0.020  1.090
 Y6W  O3   HO3   single  0.850  0.020  0.980
 Y6W  O4   C4    single  1.406  0.020  1.406
 Y6W  C4   C5    single  1.531  0.020  1.531
 Y6W  C4   H4    single  0.970  0.020  1.090
 Y6W  O4   HO4   single  0.850  0.020  0.980
 Y6W  O5   C5    single  1.412  0.020  1.412
 Y6W  C5   C6    single  1.515  0.020  1.515
 Y6W  C5   H5    single  0.970  0.020  1.090
 Y6W  O6   C6    single  1.415  0.020  1.415
 Y6W  C6   H6    single  0.970  0.020  1.090
 Y6W  C6   H6A   single  0.970  0.020  1.090
 Y6W  O6   HO6   single  0.850  0.020  0.980
 Y6W  C2'  C1'   single  1.524  0.020  1.524
 Y6W  O4'  C1'   single  1.409  0.020  1.409
 Y6W  C1'  NAZ   single  1.440  0.020  1.440
 Y6W  C1'  H1'   single  0.970  0.020  1.090
 Y6W  C3'  C2'   single  1.536  0.020  1.536
 Y6W  C2'  O2'   single  1.389  0.020  1.389
 Y6W  C2'  H2'   single  0.970  0.020  1.090
 Y6W  O2'  HO2'  single  0.850  0.020  0.980
 Y6W  O3'  C3'   single  1.401  0.020  1.401
 Y6W  C3'  C4'   single  1.551  0.020  1.551
 Y6W  C3'  H3'   single  0.970  0.020  1.090
 Y6W  O3'  HO3'  single  0.850  0.020  0.980
 Y6W  C5'  C4'   single  1.509  0.020  1.509
 Y6W  C4'  O4'   single  1.430  0.020  1.430
 Y6W  C4'  H4'   single  0.970  0.020  1.090
 Y6W  O5'  C5'   single  1.421  0.020  1.421
 Y6W  C5'  H5'   single  0.970  0.020  1.090
 Y6W  C5'  H5'A  single  0.970  0.020  1.090
 Y6W  O5'  PAN   single  1.613  0.020  1.613
 Y6W  CAK  CAL   single  1.528  0.020  1.528
 Y6W  CAK  HAK   single  0.970  0.020  1.090
 Y6W  CAK  HAKA  single  0.970  0.020  1.090
 Y6W  CAL  CAM   single  1.533  0.020  1.533
 Y6W  CAL  HAL   single  0.970  0.020  1.090
 Y6W  CAL  HALA  single  0.970  0.020  1.090
 Y6W  CAM  PAN   single  1.801  0.020  1.801
 Y6W  CAM  HAM   single  0.970  0.020  1.090
 Y6W  CAM  HAMA  single  0.970  0.020  1.090
 Y6W  OBH  PAN   double  1.490  0.020  1.490
 Y6W  PAN  OAO   single  1.606  0.020  1.606
 Y6W  OAO  HOAO  single  0.850  0.020  0.980
 Y6W  CBB  NAZ   single  1.370  0.020  1.370
 Y6W  NAZ  CBA   single  1.388  0.020  1.388
 Y6W  CBA  OBE   double  1.212  0.020  1.212
 Y6W  CBA  NBF   single  1.368  0.020  1.368
 Y6W  CBB  CBC   double  1.341  0.020  1.341
 Y6W  CBB  HBB   single  0.930  0.020  1.080
 Y6W  CBC  CBD   single  1.442  0.020  1.442
 Y6W  CBC  HBC   single  0.930  0.020  1.080
 Y6W  CBD  NBF   single  1.387  0.020  1.387
 Y6W  CBD  OBG   double  1.216  0.020  1.216
 Y6W  NBF  HNBF  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
 Y6W  H1    C1   CAK  107.94  3.000
 Y6W  H1    C1   O5   104.69  3.000
 Y6W  CAK   C1   O5   112.31  3.000
 Y6W  H1    C1   C2   108.08  3.000
 Y6W  CAK   C1   C2   114.16  3.000
 Y6W  O5    C1   C2   109.15  3.000
 Y6W  H2    C2   C3   107.97  3.000
 Y6W  H2    C2   O2   110.40  3.000
 Y6W  C3    C2   O2   112.02  3.000
 Y6W  H2    C2   C1   107.36  3.000
 Y6W  C3    C2   C1   110.69  3.000
 Y6W  O2    C2   C1   108.30  3.000
 Y6W  HO2   O2   C2   107.81  3.000
 Y6W  H3    C3   C4   107.42  3.000
 Y6W  H3    C3   O3   110.26  3.000
 Y6W  C4    C3   O3   112.78  3.000
 Y6W  H3    C3   C2   108.77  3.000
 Y6W  C4    C3   C2   110.20  3.000
 Y6W  O3    C3   C2   107.36  3.000
 Y6W  HO3   O3   C3   108.69  3.000
 Y6W  H4    C4   C5   107.21  3.000
 Y6W  H4    C4   O4   111.03  3.000
 Y6W  C5    C4   O4   113.47  3.000
 Y6W  H4    C4   C3   108.55  3.000
 Y6W  C5    C4   C3   107.74  3.000
 Y6W  O4    C4   C3   108.69  3.000
 Y6W  HO4   O4   C4   107.27  3.000
 Y6W  H5    C5   C6   104.83  3.000
 Y6W  H5    C5   O5   111.18  3.000
 Y6W  C6    C5   O5   108.44  3.000
 Y6W  H5    C5   C4   107.23  3.000
 Y6W  C6    C5   C4   114.39  3.000
 Y6W  O5    C5   C4   110.65  3.000
 Y6W  C5    O5   C1   114.51  3.000
 Y6W  H6A   C6   H6   107.25  3.000
 Y6W  H6A   C6   O6   111.36  3.000
 Y6W  H6    C6   O6   111.07  3.000
 Y6W  H6A   C6   C5   107.59  3.000
 Y6W  H6    C6   C5   108.80  3.000
 Y6W  O6    C6   C5   110.63  3.000
 Y6W  HO6   O6   C6   108.75  3.000
 Y6W  H1'   C1'  NAZ  106.63  3.000
 Y6W  H1'   C1'  O4'  111.04  3.000
 Y6W  NAZ   C1'  O4'  110.04  3.000
 Y6W  H1'   C1'  C2'  109.08  3.000
 Y6W  NAZ   C1'  C2'  116.64  3.000
 Y6W  O4'   C1'  C2'  103.44  3.000
 Y6W  H2'   C2'  C3'  107.73  3.000
 Y6W  H2'   C2'  O2'  112.07  3.000
 Y6W  C3'   C2'  O2'  116.55  3.000
 Y6W  H2'   C2'  C1'  109.83  3.000
 Y6W  O2'   C2'  C1'  109.72  3.000
 Y6W  C3'   C2'  C1'  100.23  3.000
 Y6W  HO2'  O2'  C2'  109.23  3.000
 Y6W  H3'   C3'  C4'  110.97  3.000
 Y6W  H3'   C3'  O3'  110.95  3.000
 Y6W  C4'   C3'  O3'  112.51  3.000
 Y6W  H3'   C3'  C2'  111.36  3.000
 Y6W  C4'   C3'  C2'  102.44  3.000
 Y6W  O3'   C3'  C2'  108.30  3.000
 Y6W  HO3'  O3'  C3'  108.39  3.000
 Y6W  H4'   C4'  C5'  107.12  3.000
 Y6W  H4'   C4'  O4'  109.32  3.000
 Y6W  C5'   C4'  O4'  109.96  3.000
 Y6W  H4'   C4'  C3'  108.72  3.000
 Y6W  O4'   C4'  C3'  106.68  3.000
 Y6W  C5'   C4'  C3'  114.95  3.000
 Y6W  C4'   O4'  C1'  106.94  3.000
 Y6W  H5'A  C5'  H5'  107.24  3.000
 Y6W  H5'A  C5'  O5'  107.00  3.000
 Y6W  H5'   C5'  O5'  111.72  3.000
 Y6W  H5'A  C5'  C4'  108.50  3.000
 Y6W  H5'   C5'  C4'  110.74  3.000
 Y6W  O5'   C5'  C4'  111.43  3.000
 Y6W  PAN   O5'  C5'  126.26  3.000
 Y6W  HAKA  CAK  HAK  105.50  3.000
 Y6W  HAKA  CAK  CAL  110.51  3.000
 Y6W  HAK   CAK  CAL  109.01  3.000
 Y6W  HAKA  CAK  C1   110.99  3.000
 Y6W  HAK   CAK  C1   108.53  3.000
 Y6W  CAL   CAK  C1   112.06  3.000
 Y6W  HALA  CAL  HAL  105.68  3.000
 Y6W  HALA  CAL  CAM  107.82  3.000
 Y6W  HAL   CAL  CAM  109.38  3.000
 Y6W  HALA  CAL  CAK  109.09  3.000
 Y6W  HAL   CAL  CAK  110.71  3.000
 Y6W  CAM   CAL  CAK  113.80  3.000
 Y6W  HAMA  CAM  HAM  106.91  3.000
 Y6W  HAMA  CAM  PAN  108.23  3.000
 Y6W  HAM   CAM  PAN  107.61  3.000
 Y6W  HAMA  CAM  CAL  110.98  3.000
 Y6W  HAM   CAM  CAL  110.09  3.000
 Y6W  PAN   CAM  CAL  112.80  3.000
 Y6W  OBH   PAN  OAO  115.57  3.000
 Y6W  OAO   PAN  CAM  102.42  3.000
 Y6W  OBH   PAN  CAM  115.84  3.000
 Y6W  OAO   PAN  O5'  106.88  3.000
 Y6W  OBH   PAN  O5'  110.38  3.000
 Y6W  CAM   PAN  O5'  104.76  3.000
 Y6W  HOAO  OAO  PAN  114.56  3.000
 Y6W  CBB   NAZ  CBA  120.78  3.000
 Y6W  CBA   NAZ  C1'  118.46  3.000
 Y6W  CBB   NAZ  C1'  120.70  3.000
 Y6W  NBF   CBA  OBE  122.09  3.000
 Y6W  NBF   CBA  NAZ  114.59  3.000
 Y6W  OBE   CBA  NAZ  123.33  3.000
 Y6W  HBB   CBB  CBC  120.39  3.000
 Y6W  HBB   CBB  NAZ  116.39  3.000
 Y6W  CBC   CBB  NAZ  123.21  3.000
 Y6W  HBC   CBC  CBD  119.70  3.000
 Y6W  HBC   CBC  CBB  120.52  3.000
 Y6W  CBD   CBC  CBB  119.78  3.000
 Y6W  OBG   CBD  NBF  120.57  3.000
 Y6W  OBG   CBD  CBC  126.11  3.000
 Y6W  NBF   CBD  CBC  113.33  3.000
 Y6W  HNBF  NBF  CBD  116.77  3.000
 Y6W  HNBF  NBF  CBA  114.97  3.000
 Y6W  CBD   NBF  CBA  128.25  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
 Y6W  CONST_01  NBF   CBA  NAZ  C1'   180.00   0.0  0
 Y6W  CONST_02  CBD   NBF  CBA  NAZ     0.00   0.0  0
 Y6W  CONST_03  CBC   CBD  NBF  CBA     0.00   0.0  0
 Y6W  CONST_04  NBF   CBA  NAZ  CBB     0.00   0.0  0
 Y6W  CONST_05  OBE   CBA  NAZ  C1'     0.00   0.0  0
 Y6W  CONST_06  OBG   CBD  NBF  CBA   180.00   0.0  0
 Y6W  CONST_07  OBE   CBA  NAZ  CBB   180.00   0.0  0
 Y6W  CONST_08  OBE   CBA  NBF  CBD   180.00   0.0  0
 Y6W  CONST_09  HNBF  NBF  CBA  NAZ   180.00   0.0  0
 Y6W  Var_01    CAM   CAL  CAK  C1   -162.70  30.0  3
 Y6W  Var_02    CAM   PAN  O5'  C5'   110.95  30.0  3
 Y6W  Var_03    CAL   CAM  PAN  O5'    57.90  30.0  1
 Y6W  Var_04    PAN   CAM  CAL  CAK    76.25  30.0  3
 Y6W  Var_05    H5'   C5'  O5'  PAN   -34.43  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
 Y6W  chir_01  C1   C2   O5   CAK  positiv
 Y6W  chir_02  C2   O2   C1   C3   negativ
 Y6W  chir_03  C3   O3   C2   C4   positiv
 Y6W  chir_04  C4   O4   C5   C3   negativ
 Y6W  chir_05  C5   O5   C4   C6   negativ
 Y6W  chir_06  C1'  C2'  O4'  NAZ  negativ
 Y6W  chir_07  C2'  O2'  C3'  C1'  positiv
 Y6W  chir_08  C3'  O3'  C4'  C2'  positiv
 Y6W  chir_09  C4'  O4'  C3'  C5'  negativ
 Y6W  chir_10  PAN  CAM  OBH  OAO  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
 Y6W  plan-1  C1'   0.020
 Y6W  plan-1  NAZ   0.020
 Y6W  plan-1  CBA   0.020
 Y6W  plan-1  CBB   0.020
 Y6W  plan-1  CBC   0.020
 Y6W  plan-1  CBD   0.020
 Y6W  plan-1  OBE   0.020
 Y6W  plan-1  NBF   0.020
 Y6W  plan-1  OBG   0.020
 Y6W  plan-1  HBB   0.020
 Y6W  plan-1  HBC   0.020
 Y6W  plan-1  HNBF  0.020

