# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 06:04:38 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 2'-deoxy-2'-triaza-1,2-dien-2-ium-1-yluridine 5'-(dihydrogen phosphate)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1[C@@H](CO[P](O)(O)=O)O[C@H]([C@@H]1N=[N+]=N)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
 UZR  UZR  '2'-deoxy-2'-triaza-1,2-dien-2-ium-1-yluridine 5'-(dihydrogen phosphate)'  ligand  36  23  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UZR
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
 UZR  P     P  P     0   1.464   3.5078  -1.3962   0.4989
 UZR  N1    N  NR6   0  -0.579  -1.5937  -0.5187  -0.2483
 UZR  C2    C  CR6   0   0.766  -2.8926  -0.5918   0.2045
 UZR  O2    O  O     0  -0.482  -3.5753   0.4072   0.3282
 UZR  N3    N  NR16  0  -0.733  -3.3348  -1.8446   0.5055
 UZR  C4    C  CR6   0   0.572  -2.6272  -3.0367   0.4049
 UZR  O4    O  O     0  -0.453  -3.1474  -4.0903   0.7133
 UZR  C5    C  CR16  0  -0.500  -1.2809  -2.8657  -0.0865
 UZR  C6    C  CR16  0   0.093  -0.8256  -1.6412  -0.3934
 UZR  C1'   C  CH1   0   0.269  -1.1271   0.8234  -0.6078
 UZR  C2'   C  CH1   0  -0.274  -0.9696   1.7351   0.6381
 UZR  C3'   C  CH1   0   0.019   0.2764   2.5752   0.2872
 UZR  N3'   N  N     0  -0.075  -2.1058   2.5849   0.9153
 UZR  O3'   O  OH1   0  -0.658  -0.1215   3.5890  -0.5792
 UZR  C4'   C  CH1   0  -0.073   1.0951   1.5114  -0.4397
 UZR  N4'   N  N     1   0.488  -2.5603   3.3573   0.1812
 UZR  O4'   O  O2    0  -0.475   0.1350   0.7539  -1.1722
 UZR  C5'   C  CH2   0  -0.189   1.8865   0.6487   0.5234
 UZR  N5'   N  N     0  -0.321  -3.2565   4.0211  -0.4833
 UZR  O5'   O  O2    0  -0.590   2.4803  -0.4022  -0.2299
 UZR  H3    H  HNR6  0   0.433  -4.2867  -1.9005   0.8483
 UZR  H5    H  HCR6  0   0.299  -0.6494  -3.7307  -0.2156
 UZR  H6    H  HCR6  0   0.328   0.1707  -1.4925  -0.7787
 UZR  H1'   H  HCH1  0   0.307  -1.8350   1.2418  -1.3298
 UZR  H2'   H  HCH1  0   0.377  -0.8129   1.1523   1.5430
 UZR  H3'   H  HCH1  0   0.321   0.7685   2.9497   1.1871
 UZR  HO3'  H  HOH1  0   0.491   0.2794   4.4236  -0.3149
 UZR  H4'   H  HCH1  0   0.312   1.7724   1.9711  -1.1616
 UZR  H5'   H  HCH2  0   0.277   2.6458   1.2768   0.9985
 UZR  H5''  H  HCH2  0   0.254   1.2571   0.2325   1.3158
 UZR  HN5'  H  H     0   0.493  -2.9780   5.0032  -0.5852
 UZR  OP1   O  O     0  -0.704   3.1176  -1.8393   1.8488
 UZR  OP2   O  OH1   0  -0.728   3.5720  -2.4764  -0.6667
 UZR  OP3   O  OH1   0  -0.735   4.9113  -0.6413   0.5568
 UZR  HOP2  H  HOH1  0   0.507   4.1139  -3.2509  -0.4624
 UZR  HOP3  H  HOH1  0   0.499   5.2764  -0.3629  -0.2944

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
 UZR  P    O5'   single  1.605  0.020  1.605
 UZR  N1   C2    single  1.377  0.020  1.377
 UZR  N1   C6    single  1.368  0.020  1.368
 UZR  N1   C1'   single  1.466  0.020  1.466
 UZR  C2   O2    double  1.216  0.020  1.216
 UZR  C2   N3    single  1.362  0.020  1.362
 UZR  N3   C4    single  1.390  0.020  1.390
 UZR  N3   H3    single  0.860  0.020  1.020
 UZR  C4   O4    double  1.215  0.020  1.215
 UZR  C4   C5    single  1.443  0.020  1.443
 UZR  C5   C6    double  1.342  0.020  1.342
 UZR  C5   H5    single  0.930  0.020  1.080
 UZR  C6   H6    single  0.930  0.020  1.080
 UZR  C1'  C2'   single  1.552  0.020  1.552
 UZR  C1'  O4'   single  1.384  0.020  1.384
 UZR  C1'  H1'   single  0.970  0.020  1.090
 UZR  C2'  C3'   single  1.543  0.020  1.543
 UZR  C2'  N3'   single  1.446  0.020  1.446
 UZR  C2'  H2'   single  0.970  0.020  1.090
 UZR  C3'  O3'   single  1.392  0.020  1.392
 UZR  C3'  C4'   single  1.527  0.020  1.527
 UZR  C3'  H3'   single  0.970  0.020  1.090
 UZR  N3'  N4'   double  1.159  0.020  1.159
 UZR  O3'  HO3'  single  0.850  0.020  0.980
 UZR  C4'  O4'   single  1.426  0.020  1.426
 UZR  C4'  C5'   single  1.516  0.020  1.516
 UZR  C4'  H4'   single  0.970  0.020  1.090
 UZR  N4'  N5'   double  1.169  0.020  1.169
 UZR  C5'  O5'   single  1.423  0.020  1.423
 UZR  C5'  H5'   single  0.970  0.020  1.090
 UZR  C5'  H5''  single  0.970  0.020  1.090
 UZR  N5'  HN5'  single  0.890  0.020  1.040
 UZR  P    OP1   double  1.473  0.020  1.473
 UZR  P    OP2   single  1.591  0.020  1.591
 UZR  P    OP3   single  1.595  0.020  1.595
 UZR  OP2  HOP2  single  0.850  0.020  0.980
 UZR  OP3  HOP3  single  0.850  0.020  0.980

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
 UZR  OP3   P    OP2  108.21  3.000
 UZR  OP3   P    OP1  110.01  3.000
 UZR  OP2   P    OP1  118.55  3.000
 UZR  OP3   P    O5'  106.67  3.000
 UZR  OP2   P    O5'   96.53  3.000
 UZR  OP1   P    O5'  115.65  3.000
 UZR  C1'   N1   C6   123.14  3.000
 UZR  C1'   N1   C2   115.43  3.000
 UZR  C6    N1   C2   121.39  3.000
 UZR  N3    C2   O2   123.41  3.000
 UZR  N3    C2   N1   115.31  3.000
 UZR  O2    C2   N1   121.27  3.000
 UZR  H3    N3   C4   117.09  3.000
 UZR  H3    N3   C2   115.50  3.000
 UZR  C4    N3   C2   127.41  3.000
 UZR  C5    C4   O4   126.06  3.000
 UZR  C5    C4   N3   113.44  3.000
 UZR  O4    C4   N3   120.50  3.000
 UZR  H5    C5   C6   120.38  3.000
 UZR  H5    C5   C4   119.46  3.000
 UZR  C6    C5   C4   120.16  3.000
 UZR  H6    C6   C5   121.39  3.000
 UZR  H6    C6   N1   116.33  3.000
 UZR  C5    C6   N1   122.28  3.000
 UZR  H1'   C1'  O4'  109.88  3.000
 UZR  H1'   C1'  C2'  111.76  3.000
 UZR  O4'   C1'  C2'  105.33  3.000
 UZR  H1'   C1'  N1   107.82  3.000
 UZR  O4'   C1'  N1   110.14  3.000
 UZR  C2'   C1'  N1   111.92  3.000
 UZR  H2'   C2'  N3'  105.58  3.000
 UZR  H2'   C2'  C3'  111.38  3.000
 UZR  N3'   C2'  C3'  110.99  3.000
 UZR  H2'   C2'  C1'  111.58  3.000
 UZR  N3'   C2'  C1'  114.80  3.000
 UZR  C3'   C2'  C1'  102.67  3.000
 UZR  H3'   C3'  C4'  112.94  3.000
 UZR  H3'   C3'  O3'  113.08  3.000
 UZR  C4'   C3'  O3'  111.38  3.000
 UZR  H3'   C3'  C2'  111.30  3.000
 UZR  C4'   C3'  C2'   99.32  3.000
 UZR  O3'   C3'  C2'  107.90  3.000
 UZR  N4'   N3'  C2'  125.37  3.000
 UZR  HO3'  O3'  C3'  109.97  3.000
 UZR  H4'   C4'  C5'  109.63  3.000
 UZR  H4'   C4'  O4'  107.57  3.000
 UZR  C5'   C4'  O4'  112.06  3.000
 UZR  H4'   C4'  C3'  110.75  3.000
 UZR  C5'   C4'  C3'  111.97  3.000
 UZR  O4'   C4'  C3'  104.70  3.000
 UZR  N5'   N4'  N3'  166.49  3.000
 UZR  C4'   O4'  C1'  112.20  3.000
 UZR  H5''  C5'  H5'  107.65  3.000
 UZR  H5''  C5'  O5'  110.03  3.000
 UZR  H5'   C5'  O5'  111.37  3.000
 UZR  H5''  C5'  C4'  112.10  3.000
 UZR  H5'   C5'  C4'  108.15  3.000
 UZR  O5'   C5'  C4'  107.57  3.000
 UZR  HN5'  N5'  N4'  115.99  3.000
 UZR  C5'   O5'  P    118.97  3.000
 UZR  HOP2  OP2  P    114.31  3.000
 UZR  HOP3  OP3  P    115.88  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
 UZR  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 UZR  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 UZR  CONST_03  C6   N1   C2   N3     0.00   0.0  0
 UZR  CONST_04  C1'  N1   C2   N3   180.00   0.0  0
 UZR  CONST_05  O4   C4   N3   C2   180.00   0.0  0
 UZR  CONST_06  C6   N1   C2   O2   180.00   0.0  0
 UZR  CONST_07  C1'  N1   C2   O2     0.00   0.0  0
 UZR  CONST_08  C4   N3   C2   O2   180.00   0.0  0
 UZR  CONST_09  H3   N3   C2   N1   180.00   0.0  0
 UZR  Var_01    C4'  C5'  O5'  P    173.76  30.0  1
 UZR  Var_02    OP1  P    O5'  C5'   42.34  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
 UZR  chir_01  C1'  N1   C2'  O4'  negativ
 UZR  chir_02  C2'  N3'  C3'  C1'  positiv
 UZR  chir_03  C3'  O3'  C2'  C4'  negativ
 UZR  chir_04  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
 UZR  plan-1  N1    0.020
 UZR  plan-1  C2    0.020
 UZR  plan-1  O2    0.020
 UZR  plan-1  N3    0.020
 UZR  plan-1  C4    0.020
 UZR  plan-1  O4    0.020
 UZR  plan-1  C5    0.020
 UZR  plan-1  C6    0.020
 UZR  plan-1  C1'   0.020
 UZR  plan-1  H3    0.020
 UZR  plan-1  H5    0.020
 UZR  plan-1  H6    0.020
 UZR  plan-2  C1'   0.020
 UZR  plan-2  C2'   0.020
 UZR  plan-2  C3'   0.020
 UZR  plan-2  N3'   0.020
 UZR  plan-2  N4'   0.020
 UZR  plan-2  N5'   0.020
 UZR  plan-2  H2'   0.020
 UZR  plan-2  HN5'  0.020

