# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jul  2 10:00:29 2020
#   Inital geometry file: a 162 line input string
#   Ligand name: [(2~{S},3~{R},4~{R},5~{R},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]methyl-[[(3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-phosphinic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@@H](O)[C@@H](CO)O[C@@H]1C[P](O)(=O)O[P](O)(=O)OC[C@@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=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
 UDN  UDN  '[(2~{S},3~{R},4~{R},5~{R},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]methyl-[[(3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-phosphinic acid'  ligand  66  39  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UDN
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
 UDN  C1'  C  CH1    0   0.030   4.4370   0.0543  -0.2619
 UDN  C2'  C  CH1    0  -0.116   4.9517  -1.3932  -0.1353
 UDN  C3'  C  CH1    0   0.052   4.8843  -1.8499   1.3202
 UDN  C4'  C  CH1    0  -0.036   5.6517  -0.8665   2.2028
 UDN  C5'  C  CH1    0   0.017   5.1172   0.5511   1.9694
 UDN  C6'  C  CH2    0  -0.175   5.9332   1.5655   2.7449
 UDN  C8'  C  CH3    0  -0.783   3.8398  -3.9895  -2.6605
 UDN  N2'  N  NH1    0  -0.632   4.2223  -2.2903  -0.9965
 UDN  CB   C  CH2    0  -0.801   2.9229   0.1677  -0.0887
 UDN  O3'  O  OH1    0  -0.663   5.3866  -3.1568   1.3951
 UDN  O4'  O  OH1    0  -0.675   7.0221  -0.9841   1.8943
 UDN  O5'  O  O2     0  -0.492   5.1733   0.8929   0.6019
 UDN  O6'  O  OH1    0  -0.656   5.3214   2.8291   2.6852
 UDN  O7'  O  O      0  -0.505   5.9587  -2.9519  -2.2904
 UDN  N1   N  NT     0  -0.571  -5.3783  -1.3253  -0.0356
 UDN  C2   C  C      0   0.746  -4.9069  -1.6318   1.2271
 UDN  N3   N  NH1    0  -0.734  -5.0147  -2.9534   1.5725
 UDN  C4   C  C      0   0.567  -5.5367  -3.9971   0.8232
 UDN  C5   C  C1     0  -0.512  -5.9980  -3.5882  -0.4797
 UDN  C6   C  C1     0   0.101  -5.8939  -2.2999  -0.8421
 UDN  O2   O  O      0  -0.469  -4.4386  -0.8064   1.9815
 UDN  O4   O  O      0  -0.464  -5.5708  -5.1265   1.2753
 UDN  C1D  C  CH1    0   0.227  -5.3072   0.0488  -0.5314
 UDN  C2D  C  CH1    0  -0.066  -6.1444   1.0612   0.2622
 UDN  O2'  O  OH1    0  -0.657  -7.4364   1.1113  -0.2748
 UDN  C3D  C  CH1    0  -0.026  -5.3257   2.3413   0.0700
 UDN  C4D  C  CH1    0  -0.010  -3.9159   1.7772   0.1208
 UDN  O4D  O  O2     0  -0.489  -3.9968   0.5116  -0.5431
 UDN  O3D  O  OH1    0  -0.672  -5.5739   2.9097  -1.1896
 UDN  C5D  C  CH2    0  -0.142  -2.8565   2.6304  -0.5332
 UDN  O5D  O  O2     0  -0.623  -1.6001   2.0325  -0.2981
 UDN  PA   P  P      0   1.338  -0.3076   2.6312  -1.1350
 UDN  O1A  O  OP    -1  -0.801  -0.5126   2.3758  -2.5975
 UDN  O2A  O  O      0  -0.811  -0.0076   4.0197  -0.6575
 UDN  O3A  O  O2     0  -0.752   0.7453   1.5492  -0.5260
 UDN  PB   P  P      0   1.315   2.3260   1.9011  -0.0977
 UDN  O1B  O  O      0  -0.784   2.3133   2.4682   1.2906
 UDN  O2B  O  OP    -1  -0.813   2.9687   2.6462  -1.2358
 UDN  H1   H  HCH1   0   0.245   4.6767   0.4062  -1.2682
 UDN  H2   H  HCH1   0   0.270   5.9925  -1.4097  -0.4626
 UDN  H3   H  HCH1   0   0.213   3.8339  -1.8201   1.6480
 UDN  H4   H  HCH1   0   0.234   5.4638  -1.1275   3.2552
 UDN  H5   H  HCH1   0   0.221   4.0814   0.5927   2.3345
 UDN  H6   H  HCH2   0   0.195   6.0132   1.2054   3.7812
 UDN  H7   H  HCH2   0   0.194   6.9522   1.5967   2.3376
 UDN  H8   H  HCH3   0   0.268   4.1080  -5.0110  -2.3878
 UDN  H9   H  HCH3   0   0.248   2.7930  -3.8349  -2.4050
 UDN  H10  H  HCH3   0   0.263   3.9524  -3.9008  -3.7400
 UDN  H11  H  HNH1   0   0.398   3.2566  -2.4682  -0.7689
 UDN  H12  H  HCH2   0   0.258   2.4582  -0.3538  -0.9289
 UDN  H13  H  HCH2   0   0.250   2.5703  -0.3297   0.8186
 UDN  H14  H  HOH1   0   0.450   5.2591  -3.4797   2.2928
 UDN  H15  H  HOH1   0   0.457   7.5366  -0.6528   2.6352
 UDN  H16  H  HOH1   0   0.450   5.8999   3.4500   3.1370
 UDN  H17  H  HNH1   0   0.426  -4.6710  -3.1837   2.4971
 UDN  H18  H  H      0   0.293  -6.4146  -4.3177  -1.1567
 UDN  H19  H  H      0   0.329  -6.2250  -1.9663  -1.8154
 UDN  H20  H  HCH1   0   0.259  -5.6956  -0.0073  -1.5535
 UDN  H21  H  HCH1   0   0.269  -6.1611   0.8074   1.3248
 UDN  H22  H  HOH1   0   0.470  -8.0370   1.4515   0.3956
 UDN  H23  H  HCH1   0   0.246  -5.4910   3.0612   0.8816
 UDN  H24  H  HCH1   0   0.238  -3.6471   1.6184   1.1723
 UDN  H25  H  HOH1   0   0.450  -6.5231   2.8577  -1.3545
 UDN  H26  H  HCH2   0   0.213  -3.0584   2.7264  -1.6044
 UDN  H27  H  HCH2   0   0.213  -2.9041   3.6350  -0.0953
 UDN  C7'  C  C      0   0.522   4.7801  -3.0314  -1.9717

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
 UDN  O4   C4   double  1.217  0.020  1.217
 UDN  N3   C4   single  1.387  0.020  1.387
 UDN  N3   C2   single  1.370  0.020  1.370
 UDN  C4   C5   single  1.441  0.020  1.441
 UDN  O2   C2   double  1.212  0.020  1.212
 UDN  C2   N1   single  1.382  0.020  1.382
 UDN  O2'  C2D  single  1.400  0.020  1.400
 UDN  C5   C6   double  1.342  0.020  1.342
 UDN  N1   C6   single  1.366  0.020  1.366
 UDN  N1   C1D  single  1.463  0.020  1.463
 UDN  C2D  C1D  single  1.535  0.020  1.535
 UDN  C2D  C3D  single  1.532  0.020  1.532
 UDN  C1D  O4D  single  1.390  0.020  1.390
 UDN  C3D  O3D  single  1.404  0.020  1.404
 UDN  C3D  C4D  single  1.519  0.020  1.519
 UDN  O4D  C4D  single  1.431  0.020  1.431
 UDN  C4D  C5D  single  1.509  0.020  1.509
 UDN  C5D  O5D  single  1.411  0.020  1.411
 UDN  O5D  PA   single  1.652  0.020  1.652
 UDN  O2A  PA   deloc   1.499  0.020  1.499
 UDN  PA   O1A  deloc   1.499  0.020  1.499
 UDN  PA   O3A  single  1.628  0.020  1.628
 UDN  O3A  PB   single  1.675  0.020  1.675
 UDN  PB   O1B  deloc   1.500  0.020  1.500
 UDN  PB   O2B  deloc   1.505  0.020  1.505
 UDN  PB   CB   single  1.833  0.020  1.833
 UDN  C6'  C5'  single  1.515  0.020  1.515
 UDN  C6'  O6'  single  1.405  0.020  1.405
 UDN  CB   C1'  single  1.528  0.020  1.528
 UDN  C5'  O5'  single  1.411  0.020  1.411
 UDN  C5'  C4'  single  1.533  0.020  1.533
 UDN  O5'  C1'  single  1.411  0.020  1.411
 UDN  C1'  C2'  single  1.542  0.020  1.542
 UDN  C4'  C3'  single  1.528  0.020  1.528
 UDN  C4'  O4'  single  1.410  0.020  1.410
 UDN  C3'  C2'  single  1.527  0.020  1.527
 UDN  C3'  O3'  single  1.402  0.020  1.402
 UDN  C2'  N2'  single  1.442  0.020  1.442
 UDN  N2'  C7'  single  1.346  0.020  1.346
 UDN  C7'  C8'  single  1.509  0.020  1.509
 UDN  C7'  O7'  double  1.223  0.020  1.223
 UDN  C1'  H1   single  0.970  0.020  1.090
 UDN  C2'  H2   single  0.970  0.020  1.090
 UDN  C3'  H3   single  0.970  0.020  1.090
 UDN  C4'  H4   single  0.970  0.020  1.090
 UDN  C5'  H5   single  0.970  0.020  1.090
 UDN  C6'  H6   single  0.970  0.020  1.090
 UDN  C6'  H7   single  0.970  0.020  1.090
 UDN  C8'  H8   single  0.970  0.020  1.090
 UDN  C8'  H9   single  0.970  0.020  1.090
 UDN  C8'  H10  single  0.970  0.020  1.090
 UDN  N2'  H11  single  0.860  0.020  1.020
 UDN  CB   H12  single  0.970  0.020  1.090
 UDN  CB   H13  single  0.970  0.020  1.090
 UDN  O3'  H14  single  0.850  0.020  0.980
 UDN  O4'  H15  single  0.850  0.020  0.980
 UDN  O6'  H16  single  0.850  0.020  0.980
 UDN  N3   H17  single  0.860  0.020  1.020
 UDN  C5   H18  single  0.930  0.020  1.080
 UDN  C6   H19  single  0.930  0.020  1.080
 UDN  C1D  H20  single  0.970  0.020  1.090
 UDN  C2D  H21  single  0.970  0.020  1.090
 UDN  O2'  H22  single  0.850  0.020  0.980
 UDN  C3D  H23  single  0.970  0.020  1.090
 UDN  C4D  H24  single  0.970  0.020  1.090
 UDN  O3D  H25  single  0.850  0.020  0.980
 UDN  C5D  H26  single  0.970  0.020  1.090
 UDN  C5D  H27  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
 UDN  H1   C1'  O5'  104.95  3.000
 UDN  H1   C1'  CB   107.33  3.000
 UDN  O5'  C1'  CB   113.80  3.000
 UDN  H1   C1'  C2'  107.75  3.000
 UDN  O5'  C1'  C2'  109.48  3.000
 UDN  CB   C1'  C2'  113.03  3.000
 UDN  H2   C2'  N2'  107.09  3.000
 UDN  H2   C2'  C3'  108.87  3.000
 UDN  N2'  C2'  C3'  111.16  3.000
 UDN  H2   C2'  C1'  107.94  3.000
 UDN  N2'  C2'  C1'  111.49  3.000
 UDN  C3'  C2'  C1'  110.15  3.000
 UDN  H3   C3'  O3'  110.56  3.000
 UDN  H3   C3'  C4'  106.85  3.000
 UDN  O3'  C3'  C4'  112.90  3.000
 UDN  H3   C3'  C2'  108.53  3.000
 UDN  O3'  C3'  C2'  108.30  3.000
 UDN  C4'  C3'  C2'  109.63  3.000
 UDN  H4   C4'  O4'  110.83  3.000
 UDN  H4   C4'  C5'  107.78  3.000
 UDN  O4'  C4'  C5'  112.51  3.000
 UDN  H4   C4'  C3'  108.30  3.000
 UDN  O4'  C4'  C3'  107.95  3.000
 UDN  C5'  C4'  C3'  109.40  3.000
 UDN  H5   C5'  O5'  110.50  3.000
 UDN  H5   C5'  C6'  108.19  3.000
 UDN  O5'  C5'  C6'  108.21  3.000
 UDN  H5   C5'  C4'  108.24  3.000
 UDN  O5'  C5'  C4'  110.97  3.000
 UDN  C6'  C5'  C4'  110.70  3.000
 UDN  H7   C6'  H6   106.93  3.000
 UDN  H7   C6'  O6'  111.28  3.000
 UDN  H6   C6'  O6'  111.48  3.000
 UDN  H7   C6'  C5'  109.20  3.000
 UDN  H6   C6'  C5'  107.58  3.000
 UDN  O6'  C6'  C5'  110.23  3.000
 UDN  H10  C8'  H9   108.70  3.000
 UDN  H10  C8'  H8   107.38  3.000
 UDN  H9   C8'  H8   108.11  3.000
 UDN  H10  C8'  C7'  109.65  3.000
 UDN  H9   C8'  C7'  113.70  3.000
 UDN  H8   C8'  C7'  109.10  3.000
 UDN  H11  N2'  C7'  117.62  3.000
 UDN  H11  N2'  C2'  117.36  3.000
 UDN  C7'  N2'  C2'  124.45  3.000
 UDN  H13  CB   H12  106.49  3.000
 UDN  H13  CB   PB   109.22  3.000
 UDN  H12  CB   PB   108.00  3.000
 UDN  H13  CB   C1'  112.33  3.000
 UDN  H12  CB   C1'  107.39  3.000
 UDN  PB   CB   C1'  113.09  3.000
 UDN  H14  O3'  C3'  108.36  3.000
 UDN  H15  O4'  C4'  108.84  3.000
 UDN  C5'  O5'  C1'  115.38  3.000
 UDN  H16  O6'  C6'  107.38  3.000
 UDN  C1D  N1   C6   119.24  3.000
 UDN  C1D  N1   C2   120.09  3.000
 UDN  C6   N1   C2   120.66  3.000
 UDN  O2   C2   N3   122.02  3.000
 UDN  O2   C2   N1   123.32  3.000
 UDN  N3   C2   N1   114.66  3.000
 UDN  H17  N3   C4   116.73  3.000
 UDN  H17  N3   C2   115.01  3.000
 UDN  C4   N3   C2   128.26  3.000
 UDN  O4   C4   C5   126.16  3.000
 UDN  C5   C4   N3   113.29  3.000
 UDN  O4   C4   N3   120.55  3.000
 UDN  H18  C5   C6   120.63  3.000
 UDN  H18  C5   C4   119.93  3.000
 UDN  C6   C5   C4   119.44  3.000
 UDN  H19  C6   C5   121.03  3.000
 UDN  H19  C6   N1   115.29  3.000
 UDN  C5   C6   N1   123.68  3.000
 UDN  H20  C1D  O4D  110.10  3.000
 UDN  H20  C1D  C2D  108.84  3.000
 UDN  O4D  C1D  C2D  107.40  3.000
 UDN  H20  C1D  N1   104.54  3.000
 UDN  O4D  C1D  N1   111.19  3.000
 UDN  C2D  C1D  N1   114.70  3.000
 UDN  H21  C2D  C3D  108.93  3.000
 UDN  H21  C2D  O2'  111.54  3.000
 UDN  C3D  C2D  O2'  114.54  3.000
 UDN  H21  C2D  C1D  110.98  3.000
 UDN  C3D  C2D  C1D  101.23  3.000
 UDN  O2'  C2D  C1D  109.19  3.000
 UDN  H22  O2'  C2D  108.75  3.000
 UDN  H23  C3D  O3D  111.80  3.000
 UDN  H23  C3D  C4D  111.02  3.000
 UDN  O3D  C3D  C4D  110.14  3.000
 UDN  H23  C3D  C2D  112.02  3.000
 UDN  C4D  C3D  C2D  100.46  3.000
 UDN  O3D  C3D  C2D  110.88  3.000
 UDN  H24  C4D  C5D  108.98  3.000
 UDN  H24  C4D  O4D  109.30  3.000
 UDN  C5D  C4D  O4D  109.79  3.000
 UDN  H24  C4D  C3D  108.25  3.000
 UDN  C5D  C4D  C3D  115.27  3.000
 UDN  O4D  C4D  C3D  105.09  3.000
 UDN  C4D  O4D  C1D  110.11  3.000
 UDN  H25  O3D  C3D  107.78  3.000
 UDN  H27  C5D  H26  107.60  3.000
 UDN  H27  C5D  O5D  111.11  3.000
 UDN  H26  C5D  O5D  111.38  3.000
 UDN  H27  C5D  C4D  108.32  3.000
 UDN  H26  C5D  C4D  110.14  3.000
 UDN  O5D  C5D  C4D  108.25  3.000
 UDN  PA   O5D  C5D  117.30  3.000
 UDN  O3A  PA   O2A  111.54  3.000
 UDN  O3A  PA   O1A  109.89  3.000
 UDN  O2A  PA   O1A  119.75  3.000
 UDN  O3A  PA   O5D   94.34  3.000
 UDN  O1A  PA   O5D  108.99  3.000
 UDN  O2A  PA   O5D  109.33  3.000
 UDN  PB   O3A  PA   124.50  3.000
 UDN  O2B  PB   O1B  121.10  3.000
 UDN  O2B  PB   O3A  108.29  3.000
 UDN  O1B  PB   O3A  107.95  3.000
 UDN  O2B  PB   CB   109.44  3.000
 UDN  O1B  PB   CB   110.84  3.000
 UDN  O3A  PB   CB    96.31  3.000
 UDN  O7'  C7'  N2'  123.52  3.000
 UDN  O7'  C7'  C8'  121.51  3.000
 UDN  N2'  C7'  C8'  114.97  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
 UDN  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 UDN  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 UDN  CONST_03  C6   N1   C2   N3      0.00   0.0  0
 UDN  CONST_04  C1D  N1   C2   N3    180.00   0.0  0
 UDN  CONST_05  O4   C4   N3   C2    180.00   0.0  0
 UDN  CONST_06  O2   C2   N3   C4    180.00   0.0  0
 UDN  CONST_07  O2   C2   N1   C6    180.00   0.0  0
 UDN  CONST_08  C1D  N1   C2   O2      0.00   0.0  0
 UDN  CONST_09  H17  N3   C2   N1    180.00   0.0  0
 UDN  CONST_10  C8'  C7'  N2'  C2'   180.00   0.0  0
 UDN  CONST_11  O7'  C7'  N2'  C2'     0.00   0.0  0
 UDN  CONST_12  H11  N2'  C7'  C8'     0.00   0.0  0
 UDN  Var_01    O3A  PB   CB   C1'   157.93  30.0  1
 UDN  Var_02    O2A  PA   O5D  C5D    68.07  30.0  3
 UDN  Var_03    H8   C8'  C7'  N2'  -110.39  30.0  3
 UDN  Var_04    H26  C5D  O5D  PA     48.30  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
 UDN  chir_01  C1'  CB   O5'  C2'  negativ
 UDN  chir_02  C2'  N2'  C3'  C1'  positiv
 UDN  chir_03  C3'  O3'  C2'  C4'  positiv
 UDN  chir_04  C4'  O4'  C5'  C3'  negativ
 UDN  chir_05  C5'  O5'  C6'  C4'  positiv
 UDN  chir_06  C1D  N1   C2D  O4D  negativ
 UDN  chir_07  C2D  O2'  C3D  C1D  positiv
 UDN  chir_08  C3D  O3D  C4D  C2D  positiv
 UDN  chir_09  C4D  O4D  C3D  C5D  positiv

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
 UDN  plan-1  C2'  0.020
 UDN  plan-1  C8'  0.020
 UDN  plan-1  N2'  0.020
 UDN  plan-1  O7'  0.020
 UDN  plan-1  H11  0.020
 UDN  plan-1  C7'  0.020
 UDN  plan-2  N1   0.020
 UDN  plan-2  C2   0.020
 UDN  plan-2  N3   0.020
 UDN  plan-2  C4   0.020
 UDN  plan-2  C5   0.020
 UDN  plan-2  C6   0.020
 UDN  plan-2  O2   0.020
 UDN  plan-2  O4   0.020
 UDN  plan-2  C1D  0.020
 UDN  plan-2  H17  0.020
 UDN  plan-2  H18  0.020
 UDN  plan-2  H19  0.020

