# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 20:24:03 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 2'-deoxyuridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](C[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
 DUR  DUR  '2'-deoxyuridine          '  ligand  28  16  .  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_DUR
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
 DUR  N1    N  NR6   0  -0.566  -0.2581   0.5857  -0.9805
 DUR  C2    C  CR6   0   0.745   0.0724  -0.7371  -1.1963
 DUR  N3    N  NR16  0  -0.732   0.3929  -1.0446  -2.4934
 DUR  C4    C  CR6   0   0.567   0.4359  -0.1980  -3.5911
 DUR  C5    C  CR16  0  -0.513   0.1159   1.1702  -3.2660
 DUR  C6    C  CR16  0   0.100  -0.2092   1.4896  -2.0033
 DUR  O2    O  O     0  -0.467   0.0757  -1.5740  -0.3199
 DUR  O4    O  O     0  -0.465   0.7241  -0.6281  -4.6930
 DUR  C1'   C  CH1   0   0.220  -0.6336   1.0442   0.3578
 DUR  C2'   C  CH2   0  -0.560  -1.8047   0.3107   1.0171
 DUR  C3'   C  CH1   0   0.023  -1.1856  -0.4243   2.2054
 DUR  C4'   C  CH1   0   0.021   0.0845   0.3868   2.4641
 DUR  O3'   O  OH1   0  -0.669  -1.9786  -0.4279   3.3657
 DUR  O4'   O  O2    0  -0.490   0.4677   0.9347   1.2129
 DUR  C5'   C  CH2   0  -0.163   1.2077  -0.4407   3.0357
 DUR  O5'   O  OH1   0  -0.672   2.2949   0.3975   3.3486
 DUR  HN3   H  HNR6  0   0.426   0.6183  -2.0181  -2.6592
 DUR  H5    H  HCR6  0   0.293   0.1338   1.9241  -4.0369
 DUR  H6    H  HCR6  0   0.328  -0.4587   2.5057  -1.7321
 DUR  H1'   H  HCH1  0   0.255  -0.8936   2.0953   0.2112
 DUR  H2'1  H  HCH2  0   0.267  -2.5080   1.0553   1.3934
 DUR  H2'2  H  HCH2  0   0.276  -2.3490  -0.3363   0.3314
 DUR  H3'   H  HCH1  0   0.235  -0.9203  -1.4442   1.9154
 DUR  H4'   H  HCH1  0   0.226  -0.1598   1.1991   3.1650
 DUR  HO3'  H  HOH1  0   0.458  -2.5488  -1.2009   3.3408
 DUR  H5'1  H  HCH2  0   0.199   1.4823  -1.2182   2.3104
 DUR  H5'2  H  HCH2  0   0.204   0.8189  -0.9509   3.9264
 DUR  HO5'  H  HOH1  0   0.457   2.9616  -0.1310   3.7961

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
 DUR  N1   C2    single  1.380  0.020  1.380
 DUR  N1   C6    single  1.366  0.020  1.366
 DUR  N1   C1'   single  1.464  0.020  1.464
 DUR  C2   N3    single  1.371  0.020  1.371
 DUR  C2   O2    double  1.212  0.020  1.212
 DUR  N3   C4    single  1.387  0.020  1.387
 DUR  N3   HN3   single  0.860  0.020  1.020
 DUR  C4   C5    single  1.442  0.020  1.442
 DUR  C4   O4    double  1.217  0.020  1.217
 DUR  C5   C6    double  1.342  0.020  1.342
 DUR  C5   H5    single  0.930  0.020  1.080
 DUR  C6   H6    single  0.930  0.020  1.080
 DUR  C1'  C2'   single  1.531  0.020  1.531
 DUR  C1'  O4'   single  1.399  0.020  1.399
 DUR  C1'  H1'   single  0.970  0.020  1.090
 DUR  C2'  C3'   single  1.528  0.020  1.528
 DUR  C2'  H2'1  single  0.970  0.020  1.090
 DUR  C2'  H2'2  single  0.970  0.020  1.090
 DUR  C3'  C4'   single  1.529  0.020  1.529
 DUR  C3'  O3'   single  1.405  0.020  1.405
 DUR  C3'  H3'   single  0.970  0.020  1.090
 DUR  C4'  O4'   single  1.419  0.020  1.419
 DUR  C4'  C5'   single  1.508  0.020  1.508
 DUR  C4'  H4'   single  0.970  0.020  1.090
 DUR  O3'  HO3'  single  0.850  0.020  0.980
 DUR  C5'  O5'   single  1.408  0.020  1.408
 DUR  C5'  H5'1  single  0.970  0.020  1.090
 DUR  C5'  H5'2  single  0.970  0.020  1.090
 DUR  O5'  HO5'  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
 DUR  C1'   N1   C6    119.12  3.000
 DUR  C1'   N1   C2    120.30  3.000
 DUR  C6    N1   C2    120.56  3.000
 DUR  O2    C2   N3    121.92  3.000
 DUR  O2    C2   N1    123.32  3.000
 DUR  N3    C2   N1    114.76  3.000
 DUR  HN3   N3   C4    116.76  3.000
 DUR  HN3   N3   C2    114.98  3.000
 DUR  C4    N3   C2    128.25  3.000
 DUR  O4    C4   C5    126.27  3.000
 DUR  O4    C4   N3    120.54  3.000
 DUR  C5    C4   N3    113.19  3.000
 DUR  H5    C5   C6    120.67  3.000
 DUR  H5    C5   C4    119.89  3.000
 DUR  C6    C5   C4    119.44  3.000
 DUR  H6    C6   C5    121.04  3.000
 DUR  H6    C6   N1    115.21  3.000
 DUR  C5    C6   N1    123.75  3.000
 DUR  H1'   C1'  O4'   110.16  3.000
 DUR  H1'   C1'  C2'   109.67  3.000
 DUR  O4'   C1'  C2'   107.55  3.000
 DUR  H1'   C1'  N1    103.87  3.000
 DUR  O4'   C1'  N1    109.42  3.000
 DUR  C2'   C1'  N1    116.10  3.000
 DUR  H2'2  C2'  H2'1  107.50  3.000
 DUR  H2'2  C2'  C3'   113.98  3.000
 DUR  H2'1  C2'  C3'   108.73  3.000
 DUR  H2'2  C2'  C1'   113.32  3.000
 DUR  H2'1  C2'  C1'   108.33  3.000
 DUR  C3'   C2'  C1'   104.80  3.000
 DUR  H3'   C3'  O3'   110.71  3.000
 DUR  H3'   C3'  C4'   109.77  3.000
 DUR  O3'   C3'  C4'   109.29  3.000
 DUR  H3'   C3'  C2'   109.93  3.000
 DUR  O3'   C3'  C2'   114.49  3.000
 DUR  C4'   C3'  C2'   102.29  3.000
 DUR  H4'   C4'  C5'   109.21  3.000
 DUR  H4'   C4'  O4'   109.68  3.000
 DUR  C5'   C4'  O4'   110.19  3.000
 DUR  H4'   C4'  C3'   108.36  3.000
 DUR  C5'   C4'  C3'   113.07  3.000
 DUR  O4'   C4'  C3'   106.26  3.000
 DUR  HO3'  O3'  C3'   108.39  3.000
 DUR  C4'   O4'  C1'   110.90  3.000
 DUR  H5'2  C5'  H5'1  107.18  3.000
 DUR  H5'2  C5'  O5'   111.71  3.000
 DUR  H5'1  C5'  O5'   112.03  3.000
 DUR  H5'2  C5'  C4'   107.39  3.000
 DUR  H5'1  C5'  C4'   108.93  3.000
 DUR  O5'   C5'  C4'   109.44  3.000
 DUR  HO5'  O5'  C5'   108.17  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
 DUR  CONST_01  C4   N3  C2  N1    0.00  0.0  0
 DUR  CONST_02  C5   C4  N3  C2    0.00  0.0  0
 DUR  CONST_03  C6   N1  C2  N3    0.00  0.0  0
 DUR  CONST_04  C1'  N1  C2  N3  180.00  0.0  0
 DUR  CONST_05  O4   C4  N3  C2  180.00  0.0  0
 DUR  CONST_06  O2   C2  N3  C4  180.00  0.0  0
 DUR  CONST_07  O2   C2  N1  C6  180.00  0.0  0
 DUR  CONST_08  C1'  N1  C2  O2    0.00  0.0  0
 DUR  CONST_09  HN3  N3  C2  N1  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
 DUR  chir_01  C1'  N1   C2'  O4'  negativ
 DUR  chir_02  C3'  O3'  C4'  C2'  positiv
 DUR  chir_03  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
 DUR  plan-1  N1   0.020
 DUR  plan-1  C2   0.020
 DUR  plan-1  N3   0.020
 DUR  plan-1  C4   0.020
 DUR  plan-1  C5   0.020
 DUR  plan-1  C6   0.020
 DUR  plan-1  O2   0.020
 DUR  plan-1  O4   0.020
 DUR  plan-1  C1'  0.020
 DUR  plan-1  HN3  0.020
 DUR  plan-1  H5   0.020
 DUR  plan-1  H6   0.020

