# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 04:23:38 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 2'-azido-2'-deoxyuridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](N=[N+]=[N-])[C@@H]1O)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
 UZ0  UZ0  '2'-azido-2'-deoxyuridine '  ligand  30  19  .  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_UZ0
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
 UZ0  N1   N  NR6    0  -0.574  -1.2106   0.0391   0.4244
 UZ0  C2   C  CR6    0   0.750  -1.5320   0.4325  -0.8611
 UZ0  O2   O  O      0  -0.466  -0.6971   0.6337  -1.7158
 UZ0  N3   N  NR16   0  -0.735  -2.8726   0.5681  -1.1004
 UZ0  C4   C  CR6    0   0.569  -3.9247   0.3663  -0.2184
 UZ0  O4   O  O      0  -0.460  -5.0745   0.5261  -0.5806
 UZ0  C5   C  CR16   0  -0.512  -3.4976  -0.0306   1.1009
 UZ0  C6   C  CR16   0   0.103  -2.1885  -0.1667   1.3590
 UZ0  C1'  C  CH1    0   0.242   0.1827  -0.0815   0.8155
 UZ0  C2'  C  CH1    0  -0.249   1.0500  -1.0240  -0.0422
 UZ0  C3'  C  CH1    0   0.053   2.1225  -0.0839  -0.6322
 UZ0  N3'  N  N      0  -0.372   1.6339  -1.9872   0.8889
 UZ0  O3'  O  OH1    0  -0.660   3.3899  -0.6603  -0.7337
 UZ0  C4'  C  CH1    0   0.003   2.1267   1.0667   0.3712
 UZ0  N4'  N  N      1   0.383   2.2644  -2.9069   0.3980
 UZ0  O4'  O  O2     0  -0.484   0.7783   1.1815   0.7942
 UZ0  C5'  C  CH2    0  -0.161   2.5964   2.3699  -0.2207
 UZ0  N5'  N  N     -1  -0.215   2.8459  -3.8050   0.0576
 UZ0  O5'  O  OH1    0  -0.670   2.6345   3.3503   0.7876
 UZ0  H1   H  HNR6   0   0.428  -3.1150   0.8500  -2.0428
 UZ0  H2   H  HCR6   0   0.296  -4.2316  -0.2084   1.8713
 UZ0  H3   H  HCR6   0   0.331  -1.8370  -0.4569   2.3389
 UZ0  H4   H  HCH1   0   0.268   0.1567  -0.4829   1.8325
 UZ0  H5   H  HCH1   0   0.305   0.4757  -1.5419  -0.8133
 UZ0  H6   H  HCH1   0   0.257   1.7635   0.2762  -1.5993
 UZ0  H7   H  HOH1   0   0.466   3.5488  -0.9102  -1.6478
 UZ0  H8   H  HCH1   0   0.236   2.7709   0.7944   1.2209
 UZ0  H9   H  HCH2   0   0.209   3.5878   2.1937  -0.6569
 UZ0  H10  H  HCH2   0   0.201   1.9261   2.6512  -1.0445
 UZ0  H12  H  HOH1   0   0.458   2.9830   4.1608   0.4055

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
 UZ0  O4   C4   double  1.216  0.020  1.216
 UZ0  N3   C4   single  1.388  0.020  1.388
 UZ0  N3   C2   single  1.369  0.020  1.369
 UZ0  C4   C5   single  1.442  0.020  1.442
 UZ0  O2   C2   double  1.212  0.020  1.212
 UZ0  C2   N1   single  1.382  0.020  1.382
 UZ0  C5   C6   double  1.341  0.020  1.341
 UZ0  N1   C6   single  1.368  0.020  1.368
 UZ0  N1   C1'  single  1.452  0.020  1.452
 UZ0  C1'  O4'  single  1.397  0.020  1.397
 UZ0  C1'  C2'  single  1.541  0.020  1.541
 UZ0  O4'  C4'  single  1.418  0.020  1.418
 UZ0  C4'  C5'  single  1.506  0.020  1.506
 UZ0  C4'  C3'  single  1.527  0.020  1.527
 UZ0  C2'  N3'  single  1.461  0.020  1.461
 UZ0  C2'  C3'  single  1.543  0.020  1.543
 UZ0  N3'  N4'  double  1.218  0.020  1.218
 UZ0  C5'  O5'  single  1.407  0.020  1.407
 UZ0  C3'  O3'  single  1.396  0.020  1.396
 UZ0  N4'  N5'  double  1.123  0.020  1.123
 UZ0  N3   H1   single  0.860  0.020  1.020
 UZ0  C5   H2   single  0.930  0.020  1.080
 UZ0  C6   H3   single  0.930  0.020  1.080
 UZ0  C1'  H4   single  0.970  0.020  1.090
 UZ0  C2'  H5   single  0.970  0.020  1.090
 UZ0  C3'  H6   single  0.970  0.020  1.090
 UZ0  O3'  H7   single  0.850  0.020  0.980
 UZ0  C4'  H8   single  0.970  0.020  1.090
 UZ0  C5'  H9   single  0.970  0.020  1.090
 UZ0  C5'  H10  single  0.970  0.020  1.090
 UZ0  O5'  H12  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
 UZ0  C1'  N1   C6   119.29  3.000
 UZ0  C1'  N1   C2   119.81  3.000
 UZ0  C6   N1   C2   120.79  3.000
 UZ0  N3   C2   O2   122.36  3.000
 UZ0  O2   C2   N1   122.90  3.000
 UZ0  N3   C2   N1   114.74  3.000
 UZ0  H1   N3   C4   116.77  3.000
 UZ0  H1   N3   C2   115.12  3.000
 UZ0  C4   N3   C2   128.11  3.000
 UZ0  C5   C4   O4   126.05  3.000
 UZ0  C5   C4   N3   113.39  3.000
 UZ0  O4   C4   N3   120.56  3.000
 UZ0  H2   C5   C6   120.66  3.000
 UZ0  H2   C5   C4   119.81  3.000
 UZ0  C6   C5   C4   119.53  3.000
 UZ0  H3   C6   C5   121.28  3.000
 UZ0  H3   C6   N1   115.30  3.000
 UZ0  C5   C6   N1   123.43  3.000
 UZ0  H4   C1'  O4'  110.87  3.000
 UZ0  H4   C1'  C2'  107.85  3.000
 UZ0  O4'  C1'  C2'  107.73  3.000
 UZ0  H4   C1'  N1   104.96  3.000
 UZ0  C2'  C1'  N1   116.15  3.000
 UZ0  O4'  C1'  N1   109.26  3.000
 UZ0  H5   C2'  N3'  110.33  3.000
 UZ0  H5   C2'  C3'  112.61  3.000
 UZ0  N3'  C2'  C3'  111.55  3.000
 UZ0  H5   C2'  C1'  112.77  3.000
 UZ0  C3'  C2'  C1'  103.37  3.000
 UZ0  N3'  C2'  C1'  105.86  3.000
 UZ0  H6   C3'  C4'  109.52  3.000
 UZ0  H6   C3'  O3'  111.72  3.000
 UZ0  C4'  C3'  O3'  110.88  3.000
 UZ0  H6   C3'  C2'  108.10  3.000
 UZ0  O3'  C3'  C2'  114.03  3.000
 UZ0  C4'  C3'  C2'  102.11  3.000
 UZ0  N4'  N3'  C2'  116.58  3.000
 UZ0  H7   O3'  C3'  109.07  3.000
 UZ0  H8   C4'  C5'  109.57  3.000
 UZ0  H8   C4'  O4'  110.26  3.000
 UZ0  C5'  C4'  O4'  110.10  3.000
 UZ0  H8   C4'  C3'  108.82  3.000
 UZ0  C5'  C4'  C3'  113.25  3.000
 UZ0  O4'  C4'  C3'  104.74  3.000
 UZ0  N5'  N4'  N3'  173.72  3.000
 UZ0  C4'  O4'  C1'  109.69  3.000
 UZ0  H10  C5'  H9   107.11  3.000
 UZ0  H10  C5'  O5'  112.06  3.000
 UZ0  H9   C5'  O5'  111.85  3.000
 UZ0  H10  C5'  C4'  109.02  3.000
 UZ0  H9   C5'  C4'  107.39  3.000
 UZ0  O5'  C5'  C4'  109.25  3.000
 UZ0  H12  O5'  C5'  108.20  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
 UZ0  CONST_01  C4   N3   C2   N1     0.00  0.0  0
 UZ0  CONST_02  C5   C4   N3   C2     0.00  0.0  0
 UZ0  CONST_03  C6   N1   C2   N3     0.00  0.0  0
 UZ0  CONST_04  C1'  N1   C2   N3   180.00  0.0  0
 UZ0  CONST_05  O4   C4   N3   C2   180.00  0.0  0
 UZ0  CONST_06  C4   N3   C2   O2   180.00  0.0  0
 UZ0  CONST_07  C6   N1   C2   O2   180.00  0.0  0
 UZ0  CONST_08  C1'  N1   C2   O2     0.00  0.0  0
 UZ0  CONST_09  H1   N3   C2   N1   180.00  0.0  0
 UZ0  CONST_10  N5'  N4'  N3'  C2'  180.00  0.0  0

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
 UZ0  chir_01  C1'  N1   O4'  C2'  positiv
 UZ0  chir_02  C2'  N3'  C3'  C1'  positiv
 UZ0  chir_03  C3'  O3'  C4'  C2'  positiv
 UZ0  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
 UZ0  plan-1  N1   0.020
 UZ0  plan-1  C2   0.020
 UZ0  plan-1  O2   0.020
 UZ0  plan-1  N3   0.020
 UZ0  plan-1  C4   0.020
 UZ0  plan-1  O4   0.020
 UZ0  plan-1  C5   0.020
 UZ0  plan-1  C6   0.020
 UZ0  plan-1  C1'  0.020
 UZ0  plan-1  H1   0.020
 UZ0  plan-1  H2   0.020
 UZ0  plan-1  H3   0.020
 UZ0  plan-2  C1'  0.020
 UZ0  plan-2  C2'  0.020
 UZ0  plan-2  C3'  0.020
 UZ0  plan-2  N3'  0.020
 UZ0  plan-2  N4'  0.020
 UZ0  plan-2  N5'  0.020
 UZ0  plan-2  H5   0.020

