# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jul  8 19:43:33 2020
#   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  62  34  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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  -0.010  -4.2703  -0.3162  -0.4386
 Y6W  C2    C  CH1    0   0.037  -4.9083   0.4456  -1.6084
 Y6W  O2    O  OH1    0  -0.678  -4.9215  -0.3995  -2.7337
 Y6W  C3    C  CH1    0   0.003  -4.1499   1.7413  -1.8784
 Y6W  O3    O  OH1    0  -0.674  -4.8140   2.4122  -2.9226
 Y6W  C4    C  CH1    0  -0.022  -4.0446   2.5803  -0.6035
 Y6W  O4    O  OH1    0  -0.672  -5.3282   3.0569  -0.2742
 Y6W  C5    C  CH1    0  -0.002  -3.4429   1.7033   0.4978
 Y6W  O5    O  O2     0  -0.496  -4.2153   0.5389   0.6871
 Y6W  C6    C  CH2    0  -0.171  -3.3467   2.4252   1.8240
 Y6W  O6    O  OH1    0  -0.658  -2.6311   1.6207   2.7338
 Y6W  C1'   C  CH1    0   0.212   3.1222  -0.4897  -0.5741
 Y6W  C2'   C  CH1    0  -0.034   4.1480  -0.6929   0.5346
 Y6W  O2'   O  OH1    0  -0.654   5.1913   0.2239   0.4005
 Y6W  C3'   C  CH1    0  -0.045   4.5301  -2.1568   0.2904
 Y6W  O3'   O  OH1    0  -0.668   5.3915  -2.2748  -0.8126
 Y6W  C4'   C  CH1    0  -0.022   3.1728  -2.7565  -0.0631
 Y6W  O4'   O  O2     0  -0.491   2.4037  -1.6885  -0.6323
 Y6W  C5'   C  CH2    0  -0.164   2.4908  -3.3257   1.1693
 Y6W  O5'   O  O2     0  -0.626   1.1818  -3.7512   0.8884
 Y6W  CAK   C  CH2    0  -0.467  -2.9215  -0.9606  -0.7630
 Y6W  CAL   C  CH2    0  -0.432  -2.2694  -1.6062   0.4538
 Y6W  CAM   C  CH2    0  -0.728  -0.9662  -2.3135   0.0936
 Y6W  PAN   P  P      0   1.299  -0.1570  -3.0260   1.5634
 Y6W  OAO   O  OP    -1  -0.794   0.3014  -1.9213   2.4878
 Y6W  NAZ   N  NR6    0  -0.569   2.2015   0.6138  -0.3542
 Y6W  CBA   C  CR6    0   0.733   2.2754   1.7175  -1.1822
 Y6W  CBB   C  CR16   0   0.084   1.2617   0.5358   0.6377
 Y6W  CBC   C  CR16   0  -0.541   0.3598   1.5036   0.8712
 Y6W  CBD   C  CR6    0   0.565   0.3537   2.6867   0.0491
 Y6W  OBE   O  O      0  -0.479   3.0897   1.8349  -2.0742
 Y6W  NBF   N  NR16   0  -0.732   1.3455   2.6883  -0.9206
 Y6W  OBG   O  O      0  -0.461  -0.4174   3.6254   0.1404
 Y6W  OBH   O  O      0  -0.798  -1.0074  -4.1421   2.1078
 Y6W  H1    H  HCH1   0   0.241  -4.9527  -1.1207  -0.1437
 Y6W  H2    H  HCH1   0   0.222  -5.9356   0.7038  -1.3115
 Y6W  HO2   H  HOH1   0   0.450  -5.3396   0.0773  -3.4579
 Y6W  H3    H  HCH1   0   0.218  -3.1248   1.4850  -2.1831
 Y6W  HO3   H  HOH1   0   0.454  -4.2271   3.0860  -3.2792
 Y6W  H4    H  HCH1   0   0.226  -3.3486   3.4117  -0.7885
 Y6W  HO4   H  HOH1   0   0.456  -5.2380   3.8146   0.3100
 Y6W  H5    H  HCH1   0   0.219  -2.4198   1.4455   0.1865
 Y6W  H6    H  HCH2   0   0.207  -2.8429   3.3836   1.6508
 Y6W  H6A   H  HCH2   0   0.200  -4.3536   2.6464   2.2012
 Y6W  HO6   H  HOH1   0   0.456  -2.5345   2.1130   3.5539
 Y6W  HO2'  H  HOH1   0   0.469   5.6712   0.2735   1.2334
 Y6W  H3'   H  HCH1   0   0.251   4.9588  -2.6228   1.1878
 Y6W  HO3'  H  HOH1   0   0.449   6.1136  -1.6471  -0.6920
 Y6W  H4'   H  HCH1   0   0.254   3.2794  -3.5401  -0.8198
 Y6W  H5'   H  HCH2   0   0.225   3.0813  -4.1873   1.5001
 Y6W  H5'A  H  HCH2   0   0.211   2.5064  -2.5950   1.9843
 Y6W  HAK   H  HCH2   0   0.239  -3.0874  -1.7195  -1.5311
 Y6W  HAKA  H  HCH2   0   0.217  -2.2201  -0.2445  -1.2038
 Y6W  HAL   H  HCH2   0   0.238  -2.0724  -0.8464   1.2137
 Y6W  HALA  H  HCH2   0   0.213  -2.9625  -2.3228   0.9057
 Y6W  HAM   H  HCH2   0   0.232  -1.1594  -3.1064  -0.6355
 Y6W  HAMA  H  HCH2   0   0.242  -0.2841  -1.6089  -0.3875
 Y6W  HBB   H  HCR6   0   0.338   1.2489  -0.3693   1.2355
 Y6W  HBC   H  HCR6   0   0.296  -0.3761   1.3918   1.6536
 Y6W  HNBF  H  HNR6   0   0.424   1.3926   3.5009  -1.5232
 Y6W  H1'   H  HCH1   0   0.267   3.6321  -0.2819  -1.5175
 Y6W  H2'   H  HCH1   0   0.246   3.6576  -0.6115   1.5138

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  1.415  0.020  1.415
 Y6W  C1   CAK   single  1.530  0.020  1.530
 Y6W  C1   H1    single  0.970  0.020  1.090
 Y6W  O2   C2    single  1.407  0.020  1.407
 Y6W  C2   C3    single  1.525  0.020  1.525
 Y6W  C2   H2    single  0.970  0.020  1.090
 Y6W  O2   HO2   single  0.850  0.020  0.980
 Y6W  O3   C3    single  1.408  0.020  1.408
 Y6W  C3   C4    single  1.530  0.020  1.530
 Y6W  C3   H3    single  0.970  0.020  1.090
 Y6W  O3   HO3   single  0.850  0.020  0.980
 Y6W  O4   C4    single  1.408  0.020  1.408
 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  1.410  0.020  1.410
 Y6W  C5   C6    single  1.513  0.020  1.513
 Y6W  C5   H5    single  0.970  0.020  1.090
 Y6W  O6   C6    single  1.410  0.020  1.410
 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  1.399  0.020  1.399
 Y6W  C1'  NAZ   single  1.454  0.020  1.454
 Y6W  C1'  H1'   single  0.970  0.020  1.090
 Y6W  C3'  C2'   single  1.533  0.020  1.533
 Y6W  C2'  O2'   single  1.395  0.020  1.395
 Y6W  C2'  H2'   single  0.970  0.020  1.090
 Y6W  O2'  HO2'  single  0.850  0.020  0.980
 Y6W  O3'  C3'   single  1.404  0.020  1.404
 Y6W  C3'  C4'   single  1.525  0.020  1.525
 Y6W  C3'  H3'   single  0.970  0.020  1.090
 Y6W  O3'  HO3'  single  0.850  0.020  0.980
 Y6W  C5'  C4'   single  1.519  0.020  1.519
 Y6W  C4'  O4'   single  1.434  0.020  1.434
 Y6W  C4'  H4'   single  0.970  0.020  1.090
 Y6W  O5'  C5'   single  1.405  0.020  1.405
 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  1.665  0.020  1.665
 Y6W  CAK  CAL   single  1.524  0.020  1.524
 Y6W  CAK  HAK   single  0.970  0.020  1.090
 Y6W  CAK  HAKA  single  0.970  0.020  1.090
 Y6W  CAL  CAM   single  1.526  0.020  1.526
 Y6W  CAL  HAL   single  0.970  0.020  1.090
 Y6W  CAL  HALA  single  0.970  0.020  1.090
 Y6W  CAM  PAN   single  1.823  0.020  1.823
 Y6W  CAM  HAM   single  0.970  0.020  1.090
 Y6W  CAM  HAMA  single  0.970  0.020  1.090
 Y6W  OBH  PAN   deloc   1.505  0.020  1.505
 Y6W  PAN  OAO   deloc   1.512  0.020  1.512
 Y6W  CBB  NAZ   single  1.369  0.020  1.369
 Y6W  NAZ  CBA   single  1.382  0.020  1.382
 Y6W  CBA  OBE   double  1.213  0.020  1.213
 Y6W  CBA  NBF   single  1.370  0.020  1.370
 Y6W  CBB  CBC   double  1.343  0.020  1.343
 Y6W  CBB  HBB   single  0.930  0.020  1.080
 Y6W  CBC  CBD   single  1.441  0.020  1.441
 Y6W  CBC  HBC   single  0.930  0.020  1.080
 Y6W  CBD  NBF   single  1.387  0.020  1.387
 Y6W  CBD  OBG   double  1.218  0.020  1.218
 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  107.28  3.000
 Y6W  H1    C1   O5   104.71  3.000
 Y6W  CAK   C1   O5   112.90  3.000
 Y6W  H1    C1   C2   108.10  3.000
 Y6W  CAK   C1   C2   114.46  3.000
 Y6W  O5    C1   C2   108.82  3.000
 Y6W  H2    C2   C3   108.22  3.000
 Y6W  H2    C2   O2   110.37  3.000
 Y6W  C3    C2   O2   111.92  3.000
 Y6W  H2    C2   C1   107.39  3.000
 Y6W  C3    C2   C1   110.47  3.000
 Y6W  O2    C2   C1   108.38  3.000
 Y6W  HO2   O2   C2   107.95  3.000
 Y6W  H3    C3   C4   107.13  3.000
 Y6W  H3    C3   O3   110.20  3.000
 Y6W  C4    C3   O3   112.91  3.000
 Y6W  H3    C3   C2   108.33  3.000
 Y6W  C4    C3   C2   110.65  3.000
 Y6W  O3    C3   C2   107.55  3.000
 Y6W  HO3   O3   C3   108.72  3.000
 Y6W  H4    C4   C5   107.77  3.000
 Y6W  H4    C4   O4   111.12  3.000
 Y6W  C5    C4   O4   112.57  3.000
 Y6W  H4    C4   C3   108.54  3.000
 Y6W  C5    C4   C3   108.20  3.000
 Y6W  O4    C4   C3   108.52  3.000
 Y6W  HO4   O4   C4   108.87  3.000
 Y6W  H5    C5   C6   107.50  3.000
 Y6W  H5    C5   O5   110.73  3.000
 Y6W  C6    C5   O5   108.12  3.000
 Y6W  H5    C5   C4   107.23  3.000
 Y6W  C6    C5   C4   112.47  3.000
 Y6W  O5    C5   C4   110.75  3.000
 Y6W  C5    O5   C1   114.43  3.000
 Y6W  H6A   C6   H6   107.43  3.000
 Y6W  H6A   C6   O6   111.03  3.000
 Y6W  H6    C6   O6   111.56  3.000
 Y6W  H6A   C6   C5   109.82  3.000
 Y6W  H6    C6   C5   107.92  3.000
 Y6W  O6    C6   C5   109.01  3.000
 Y6W  HO6   O6   C6   108.01  3.000
 Y6W  H1'   C1'  NAZ  106.38  3.000
 Y6W  H1'   C1'  O4'  111.52  3.000
 Y6W  NAZ   C1'  O4'  109.36  3.000
 Y6W  H1'   C1'  C2'  109.84  3.000
 Y6W  NAZ   C1'  C2'  114.67  3.000
 Y6W  O4'   C1'  C2'  105.17  3.000
 Y6W  H2'   C2'  C3'  108.92  3.000
 Y6W  H2'   C2'  O2'  111.77  3.000
 Y6W  C3'   C2'  O2'  115.21  3.000
 Y6W  H2'   C2'  C1'  109.76  3.000
 Y6W  O2'   C2'  C1'  110.23  3.000
 Y6W  C3'   C2'  C1'  100.33  3.000
 Y6W  HO2'  O2'  C2'  108.87  3.000
 Y6W  H3'   C3'  C4'  111.71  3.000
 Y6W  H3'   C3'  O3'  111.51  3.000
 Y6W  C4'   C3'  O3'  109.31  3.000
 Y6W  H3'   C3'  C2'  111.87  3.000
 Y6W  C4'   C3'  C2'  100.99  3.000
 Y6W  O3'   C3'  C2'  110.99  3.000
 Y6W  HO3'  O3'  C3'  107.84  3.000
 Y6W  H4'   C4'  C5'  109.65  3.000
 Y6W  H4'   C4'  O4'  108.12  3.000
 Y6W  C5'   C4'  O4'  111.12  3.000
 Y6W  H4'   C4'  C3'  110.80  3.000
 Y6W  O4'   C4'  C3'  106.05  3.000
 Y6W  C5'   C4'  C3'  111.02  3.000
 Y6W  C4'   O4'  C1'  110.26  3.000
 Y6W  H5'A  C5'  H5'  107.00  3.000
 Y6W  H5'A  C5'  O5'  111.37  3.000
 Y6W  H5'   C5'  O5'  108.93  3.000
 Y6W  H5'A  C5'  C4'  110.33  3.000
 Y6W  H5'   C5'  C4'  107.32  3.000
 Y6W  O5'   C5'  C4'  111.69  3.000
 Y6W  PAN   O5'  C5'  122.42  3.000
 Y6W  HAKA  CAK  HAK  105.57  3.000
 Y6W  HAKA  CAK  CAL  108.93  3.000
 Y6W  HAK   CAK  CAL  109.39  3.000
 Y6W  HAKA  CAK  C1   112.00  3.000
 Y6W  HAK   CAK  C1   107.94  3.000
 Y6W  CAL   CAK  C1   112.73  3.000
 Y6W  HALA  CAL  HAL  106.39  3.000
 Y6W  HALA  CAL  CAM  109.56  3.000
 Y6W  HAL   CAL  CAM  109.43  3.000
 Y6W  HALA  CAL  CAK  109.64  3.000
 Y6W  HAL   CAL  CAK  109.75  3.000
 Y6W  CAM   CAL  CAK  111.92  3.000
 Y6W  HAMA  CAM  HAM  106.51  3.000
 Y6W  HAMA  CAM  PAN  109.27  3.000
 Y6W  HAM   CAM  PAN  109.42  3.000
 Y6W  HAMA  CAM  CAL  109.77  3.000
 Y6W  HAM   CAM  CAL  110.02  3.000
 Y6W  PAN   CAM  CAL  111.71  3.000
 Y6W  OBH   PAN  OAO  119.48  3.000
 Y6W  OAO   PAN  CAM  110.01  3.000
 Y6W  OBH   PAN  CAM  109.31  3.000
 Y6W  OAO   PAN  O5'  108.80  3.000
 Y6W  OBH   PAN  O5'  106.13  3.000
 Y6W  CAM   PAN  O5'  101.55  3.000
 Y6W  CBB   NAZ  CBA  121.10  3.000
 Y6W  CBA   NAZ  C1'  118.80  3.000
 Y6W  CBB   NAZ  C1'  120.08  3.000
 Y6W  NBF   CBA  OBE  121.84  3.000
 Y6W  NBF   CBA  NAZ  114.54  3.000
 Y6W  OBE   CBA  NAZ  123.62  3.000
 Y6W  HBB   CBB  CBC  119.83  3.000
 Y6W  HBB   CBB  NAZ  117.06  3.000
 Y6W  CBC   CBB  NAZ  123.09  3.000
 Y6W  HBC   CBC  CBD  119.70  3.000
 Y6W  HBC   CBC  CBB  120.59  3.000
 Y6W  CBD   CBC  CBB  119.70  3.000
 Y6W  OBG   CBD  NBF  120.27  3.000
 Y6W  OBG   CBD  CBC  126.36  3.000
 Y6W  NBF   CBD  CBC  113.38  3.000
 Y6W  HNBF  NBF  CBD  116.76  3.000
 Y6W  HNBF  NBF  CBA  115.05  3.000
 Y6W  CBD   NBF  CBA  128.19  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   176.65  30.0  3
 Y6W  Var_02    CAM   PAN  O5'  C5'  114.97  30.0  3
 Y6W  Var_03    CAL   CAM  PAN  O5'  178.57  30.0  1
 Y6W  Var_04    PAN   CAM  CAL  CAK  177.71  30.0  3
 Y6W  Var_05    H5'   C5'  O5'  PAN  126.89  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

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

