# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 20:42:30 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-hydroxy(phosphonoamino)phosphoryl]uridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@@H](O[C@@H]1CO[P@@](O)(=O)N[P](O)(O)=O)N2C=CC(=O)NC2=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
 DUN  DUN  2'-deoxy-5'-O-[(R)-hydroxy(phosphonoamino)phosphoryl]uridine  ligand  39  24  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DUN
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
 DUN  N1    N  NR6   0  -0.565   0.1889   0.2699   3.4139
 DUN  C2    C  CR6   0   0.749  -0.7771  -0.5732   2.9026
 DUN  N3    N  NR16  0  -0.732  -1.9966  -0.4928   3.5223
 DUN  C4    C  CR6   0   0.567  -2.3687   0.3221   4.5809
 DUN  C5    C  CR16  0  -0.512  -1.3031   1.1754   5.0438
 DUN  C6    C  CR16  0   0.100  -0.1018   1.1145   4.4474
 DUN  O2    O  OC    0  -0.467  -0.5740  -1.3333   1.9806
 DUN  O4    O  OC    0  -0.464  -3.4992   0.2774   5.0289
 DUN  C1'   C  CR15  0   0.213   1.5264   0.2955   2.8206
 DUN  C2'   C  CH2   0  -0.559   2.2816  -1.0356   2.8069
 DUN  C3'   C  CR15  0   0.019   2.3888  -1.4206   1.3311
 DUN  C4'   C  CR15  0   0.015   2.1831  -0.0790   0.6226
 DUN  O4'   O  O     0  -0.487   1.4398   0.7460   1.4991
 DUN  O3'   O  OH1   0  -0.666   3.6352  -1.9431   0.9484
 DUN  C5'   C  CH2   0  -0.185   1.4471  -0.2320  -0.6821
 DUN  O5'   O  O2    0  -0.588   1.3769   1.0504  -1.3167
 DUN  PA    P  P     0   1.468   0.7749   1.1894  -2.7890
 DUN  O1A   O  OH1   0  -0.723   0.8089   2.7664  -2.9892
 DUN  O2A   O  O     0  -0.698   1.4633   0.4751  -3.8787
 DUN  PB    P  P     0   1.433  -1.5634  -0.3338  -3.7565
 DUN  O1B   O  OH1   0  -0.734  -0.8155  -1.7133  -3.4556
 DUN  O2B   O  O     0  -0.700  -1.5883   0.0966  -5.1665
 DUN  O3B   O  OH1   0  -0.738  -3.0453  -0.4584  -3.1720
 DUN  N3A   N  NH1   0  -0.977  -0.8185   0.6941  -2.6581
 DUN  H3    H  HNR6  0   0.426  -2.7064  -1.1138   3.1533
 DUN  H5    H  HCR6  0   0.294  -1.4755   1.8588   5.8602
 DUN  H6    H  HCR6  0   0.329   0.7128   1.7464   4.7718
 DUN  H1'   H  HCR5  0   0.260   2.0716   1.0231   3.4252
 DUN  H2'1  H  HCH2  0   0.280   1.8130  -1.7997   3.4247
 DUN  H2'2  H  HCH2  0   0.271   3.2851  -0.8647   3.2005
 DUN  H3'   H  HCR5  0   0.239   1.5853  -2.1138   1.0684
 DUN  H4'   H  HCR5  0   0.243   3.1692   0.3700   0.4380
 DUN  HA    H  HOH1  0   0.459   3.6606  -2.8730   1.1915
 DUN  H5'1  H  HCH2  0   0.248   1.9882  -0.9409  -1.3142
 DUN  H5'2  H  HCH2  0   0.244   0.4407  -0.6190  -0.5034
 DUN  H1A   H  HOH1  0   0.500   0.4409   3.3104  -2.2803
 DUN  H1B   H  HOH1  0   0.498  -0.9017  -2.3630  -4.1668
 DUN  H3B   H  HOH1  0   0.497  -3.1384  -0.9440  -2.3418
 DUN  H3A   H  HNH1  0   0.443  -1.4154   1.1417  -1.9719

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
 DUN  N1   C2    aromatic  1.380  0.020  1.380
 DUN  N1   C6    aromatic  1.366  0.020  1.366
 DUN  N1   C1'   single    1.463  0.020  1.463
 DUN  C2   N3    aromatic  1.370  0.020  1.370
 DUN  C2   O2    double    1.212  0.020  1.212
 DUN  N3   C4    aromatic  1.387  0.020  1.387
 DUN  N3   H3    single    0.860  0.020  1.020
 DUN  C4   C5    aromatic  1.441  0.020  1.441
 DUN  C4   O4    double    1.217  0.020  1.217
 DUN  C5   C6    aromatic  1.343  0.020  1.343
 DUN  C5   H5    single    0.930  0.020  1.080
 DUN  C6   H6    single    0.930  0.020  1.080
 DUN  C1'  C2'   single    1.530  0.020  1.530
 DUN  C1'  O4'   single    1.399  0.020  1.399
 DUN  C1'  H1'   single    0.970  0.020  1.090
 DUN  C2'  C3'   single    1.529  0.020  1.529
 DUN  C2'  H2'1  single    0.970  0.020  1.090
 DUN  C2'  H2'2  single    0.970  0.020  1.090
 DUN  C3'  C4'   single    1.531  0.020  1.531
 DUN  C3'  O3'   single    1.405  0.020  1.405
 DUN  C3'  H3'   single    0.970  0.020  1.090
 DUN  C4'  O4'   single    1.415  0.020  1.415
 DUN  C4'  C5'   single    1.506  0.020  1.506
 DUN  C4'  H4'   single    0.970  0.020  1.090
 DUN  O3'  HA    single    0.850  0.020  0.980
 DUN  C5'  O5'   single    1.433  0.020  1.433
 DUN  C5'  H5'1  single    0.970  0.020  1.090
 DUN  C5'  H5'2  single    0.970  0.020  1.090
 DUN  O5'  PA    single    1.597  0.020  1.597
 DUN  PA   O1A   single    1.590  0.020  1.590
 DUN  PA   O2A   double    1.474  0.020  1.474
 DUN  PA   N3A   single    1.674  0.020  1.674
 DUN  O1A  H1A   single    0.850  0.020  0.980
 DUN  PB   O1B   single    1.598  0.020  1.598
 DUN  PB   O2B   double    1.474  0.020  1.474
 DUN  PB   O3B   single    1.598  0.020  1.598
 DUN  PB   N3A   single    1.679  0.020  1.679
 DUN  O1B  H1B   single    0.850  0.020  0.980
 DUN  O3B  H3B   single    0.850  0.020  0.980
 DUN  N3A  H3A   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
 DUN  C1'   N1   C6    119.37  3.000
 DUN  C1'   N1   C2    120.01  3.000
 DUN  C6    N1   C2    120.59  3.000
 DUN  O2    C2   N3    122.00  3.000
 DUN  O2    C2   N1    123.20  3.000
 DUN  N3    C2   N1    114.80  3.000
 DUN  H3    N3   C4    116.77  3.000
 DUN  H3    N3   C2    115.02  3.000
 DUN  C4    N3   C2    128.21  3.000
 DUN  O4    C4   C5    126.18  3.000
 DUN  O4    C4   N3    120.58  3.000
 DUN  C5    C4   N3    113.24  3.000
 DUN  H5    C5   C6    120.53  3.000
 DUN  H5    C5   C4    120.00  3.000
 DUN  C6    C5   C4    119.47  3.000
 DUN  H6    C6   C5    120.97  3.000
 DUN  H6    C6   N1    115.35  3.000
 DUN  C5    C6   N1    123.68  3.000
 DUN  H1'   C1'  O4'   109.84  3.000
 DUN  H1'   C1'  C2'   109.76  3.000
 DUN  O4'   C1'  C2'   107.59  3.000
 DUN  H1'   C1'  N1    104.09  3.000
 DUN  O4'   C1'  N1    109.39  3.000
 DUN  C2'   C1'  N1    116.07  3.000
 DUN  H2'2  C2'  H2'1  107.52  3.000
 DUN  H2'2  C2'  C3'   108.85  3.000
 DUN  H2'1  C2'  C3'   113.65  3.000
 DUN  H2'2  C2'  C1'   108.32  3.000
 DUN  H2'1  C2'  C1'   113.14  3.000
 DUN  C3'   C2'  C1'   105.20  3.000
 DUN  H3'   C3'  O3'   110.54  3.000
 DUN  H3'   C3'  C4'   110.23  3.000
 DUN  O3'   C3'  C4'   108.61  3.000
 DUN  H3'   C3'  C2'   109.88  3.000
 DUN  O3'   C3'  C2'   114.76  3.000
 DUN  C4'   C3'  C2'   102.51  3.000
 DUN  H4'   C4'  C5'   109.54  3.000
 DUN  H4'   C4'  O4'   109.71  3.000
 DUN  C5'   C4'  O4'   109.83  3.000
 DUN  H4'   C4'  C3'   108.37  3.000
 DUN  C5'   C4'  C3'   112.18  3.000
 DUN  O4'   C4'  C3'   107.15  3.000
 DUN  C4'   O4'  C1'   111.40  3.000
 DUN  HA    O3'  C3'   108.32  3.000
 DUN  H5'2  C5'  H5'1  108.71  3.000
 DUN  H5'2  C5'  O5'   110.14  3.000
 DUN  H5'1  C5'  O5'   110.40  3.000
 DUN  H5'2  C5'  C4'   110.15  3.000
 DUN  H5'1  C5'  C4'   108.96  3.000
 DUN  O5'   C5'  C4'   108.47  3.000
 DUN  PA    O5'  C5'   120.33  3.000
 DUN  N3A   PA   O2A   111.04  3.000
 DUN  N3A   PA   O1A   108.89  3.000
 DUN  O2A   PA   O1A   112.19  3.000
 DUN  N3A   PA   O5'   105.13  3.000
 DUN  O2A   PA   O5'   117.61  3.000
 DUN  O1A   PA   O5'   101.21  3.000
 DUN  H1A   O1A  PA    117.25  3.000
 DUN  N3A   PB   O3B   102.70  3.000
 DUN  N3A   PB   O2B   117.03  3.000
 DUN  O3B   PB   O2B   110.91  3.000
 DUN  N3A   PB   O1B   101.41  3.000
 DUN  O3B   PB   O1B   107.33  3.000
 DUN  O2B   PB   O1B   116.11  3.000
 DUN  H1B   O1B  PB    113.57  3.000
 DUN  H3B   O3B  PB    116.28  3.000
 DUN  H3A   N3A  PB    116.88  3.000
 DUN  H3A   N3A  PA    118.87  3.000
 DUN  PB    N3A  PA    123.54  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
 DUN  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 DUN  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 DUN  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 DUN  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 DUN  CONST_05  C6    N1   C2   N3      0.00   0.0  0
 DUN  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 DUN  CONST_07  C1'   N1   C2   N3    180.00   0.0  0
 DUN  CONST_08  C1'   N1   C6   C5    180.00   0.0  0
 DUN  CONST_09  O4    C4   N3   C2    180.00   0.0  0
 DUN  CONST_10  O2    C2   N3   C4    180.00   0.0  0
 DUN  CONST_11  O2    C2   N1   C6    180.00   0.0  0
 DUN  CONST_12  O4    C4   C5   C6    180.00   0.0  0
 DUN  CONST_13  C1'   N1   C2   O2      0.00   0.0  0
 DUN  CONST_14  H3    N3   C2   N1    180.00   0.0  0
 DUN  CONST_15  H5    C5   C6   N1    180.00   0.0  0
 DUN  CONST_16  H6    C6   N1   C2    180.00   0.0  0
 DUN  Var_01    O1A   PA   O5'  C5'   175.80  30.0  3
 DUN  Var_02    PB    N3A  PA   O5'  -135.42  30.0  3
 DUN  Var_03    O1B   PB   N3A  PA     69.62  30.0  1
 DUN  Var_04    H5'1  C5'  O5'  PA     54.82  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
 DUN  chir_01  C1'  N1   C2'  O4'  negativ
 DUN  chir_02  C3'  O3'  C4'  C2'  positiv
 DUN  chir_03  C4'  O4'  C3'  C5'  negativ
 DUN  chir_04  PA   O1A  O2A  N3A  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
 DUN  plan-1  N1   0.020
 DUN  plan-1  C2   0.020
 DUN  plan-1  N3   0.020
 DUN  plan-1  C4   0.020
 DUN  plan-1  C5   0.020
 DUN  plan-1  C6   0.020
 DUN  plan-1  O2   0.020
 DUN  plan-1  O4   0.020
 DUN  plan-1  C1'  0.020
 DUN  plan-1  H3   0.020
 DUN  plan-1  H5   0.020
 DUN  plan-1  H6   0.020

