# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 11:56:58 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)N2CCC(=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
 THU  THU  '2'-deoxyuridine          '  ligand  30  16  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_THU
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
 THU  N1    N  NT    0  -0.509  -0.9130  -0.3405  -0.0991
 THU  C2    C  C     0   0.729  -1.8554  -0.8965  -0.8927
 THU  O2    O  O     0  -0.495  -1.6653  -1.8083  -1.6763
 THU  N3    N  NH1   0  -0.719  -3.1365  -0.3634  -0.7574
 THU  C4    C  C     0   0.540  -3.4772   0.8519  -0.2212
 THU  O4    O  O     0  -0.438  -4.6126   1.2700  -0.2758
 THU  C5    C  CH2   0  -0.595  -2.3225   1.5878   0.3899
 THU  C6    C  CH2   0  -0.320  -1.2936   0.6162   0.9270
 THU  C1'   C  CH1   0   0.225   0.4679  -0.7327  -0.2211
 THU  C2'   C  CH2   0  -0.559   1.0919  -1.2750   1.0626
 THU  C3'   C  CH1   0  -0.011   2.5553  -0.8999   0.8854
 THU  O3'   O  OH1   0  -0.672   3.2208  -1.7643  -0.0066
 THU  C4'   C  CH1   0   0.012   2.4134   0.4732   0.2362
 THU  O4'   O  O2    0  -0.506   1.2430   0.3975  -0.5738
 THU  C5'   C  CH2   0  -0.155   3.5980   0.9188  -0.5891
 THU  O5'   O  OH1   0  -0.673   3.3838   2.2561  -0.9823
 THU  HN3   H  HNH1  0   0.417  -3.8562  -0.8557  -1.2715
 THU  H51   H  HCH2  0   0.293  -2.6876   2.2405   1.1810
 THU  H52   H  HCH2  0   0.296  -1.8765   2.2219  -0.3825
 THU  H61   H  HCH2  0   0.266  -1.6849   0.0965   1.8060
 THU  H62   H  HCH2  0   0.282  -0.4098   1.1671   1.2410
 THU  H1'   H  HCH1  0   0.256   0.5198  -1.4784  -1.0149
 THU  H2'1  H  HCH2  0   0.265   0.6898  -0.7744   1.9466
 THU  H2'2  H  HCH2  0   0.276   0.9236  -2.3456   1.1849
 THU  H3'   H  HCH1  0   0.246   3.0844  -0.8244   1.8424
 THU  HO3'  H  HOH1  0   0.456   3.2266  -2.6467   0.3770
 THU  H4'   H  HCH1  0   0.229   2.2578   1.2076   1.0390
 THU  H5'1  H  HCH2  0   0.205   3.7195   0.2574  -1.4529
 THU  H5'2  H  HCH2  0   0.200   4.5009   0.8203   0.0283
 THU  HO5'  H  HOH1  0   0.456   4.0991   2.5098  -1.5718

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
 THU  N1   C2    single  1.352  0.020  1.352
 THU  N1   C6    single  1.454  0.020  1.454
 THU  N1   C1'   single  1.441  0.020  1.441
 THU  C2   O2    double  1.217  0.020  1.217
 THU  C2   N3    single  1.394  0.020  1.394
 THU  N3   C4    single  1.371  0.020  1.371
 THU  N3   HN3   single  0.860  0.020  1.020
 THU  C4   O4    double  1.211  0.020  1.211
 THU  C4   C5    single  1.499  0.020  1.499
 THU  C5   C6    single  1.514  0.020  1.514
 THU  C5   H51   single  0.970  0.020  1.090
 THU  C5   H52   single  0.970  0.020  1.090
 THU  C6   H61   single  0.970  0.020  1.090
 THU  C6   H62   single  0.970  0.020  1.090
 THU  C1'  C2'   single  1.527  0.020  1.527
 THU  C1'  O4'   single  1.415  0.020  1.415
 THU  C1'  H1'   single  0.970  0.020  1.090
 THU  C2'  C3'   single  1.521  0.020  1.521
 THU  C2'  H2'1  single  0.970  0.020  1.090
 THU  C2'  H2'2  single  0.970  0.020  1.090
 THU  C3'  O3'   single  1.409  0.020  1.409
 THU  C3'  C4'   single  1.525  0.020  1.525
 THU  C3'  H3'   single  0.970  0.020  1.090
 THU  O3'  HO3'  single  0.850  0.020  0.980
 THU  C4'  O4'   single  1.425  0.020  1.425
 THU  C4'  C5'   single  1.511  0.020  1.511
 THU  C4'  H4'   single  0.970  0.020  1.090
 THU  C5'  O5'   single  1.410  0.020  1.410
 THU  C5'  H5'1  single  0.970  0.020  1.090
 THU  C5'  H5'2  single  0.970  0.020  1.090
 THU  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
 THU  C1'   N1   C6    119.33  3.000
 THU  C1'   N1   C2    120.44  3.000
 THU  C6    N1   C2    120.18  3.000
 THU  N3    C2   O2    119.50  3.000
 THU  N3    C2   N1    115.24  3.000
 THU  O2    C2   N1    125.25  3.000
 THU  HN3   N3   C4    116.94  3.000
 THU  HN3   N3   C2    114.71  3.000
 THU  C4    N3   C2    127.23  3.000
 THU  C5    C4   O4    124.81  3.000
 THU  C5    C4   N3    113.77  3.000
 THU  O4    C4   N3    121.41  3.000
 THU  H52   C5   H51   107.59  3.000
 THU  H52   C5   C6    110.20  3.000
 THU  H51   C5   C6    110.79  3.000
 THU  H52   C5   C4    108.09  3.000
 THU  H51   C5   C4    109.40  3.000
 THU  C6    C5   C4    110.67  3.000
 THU  H62   C6   H61   107.42  3.000
 THU  H62   C6   C5    109.25  3.000
 THU  H61   C6   C5    110.30  3.000
 THU  H62   C6   N1    108.93  3.000
 THU  H61   C6   N1    110.39  3.000
 THU  C5    C6   N1    110.48  3.000
 THU  H1'   C1'  O4'   109.80  3.000
 THU  H1'   C1'  C2'   110.47  3.000
 THU  O4'   C1'  C2'   105.63  3.000
 THU  H1'   C1'  N1    107.07  3.000
 THU  O4'   C1'  N1    109.19  3.000
 THU  C2'   C1'  N1    114.66  3.000
 THU  H2'2  C2'  H2'1  107.60  3.000
 THU  H2'2  C2'  C3'   113.80  3.000
 THU  H2'1  C2'  C3'   109.59  3.000
 THU  H2'2  C2'  C1'   112.32  3.000
 THU  H2'1  C2'  C1'   111.54  3.000
 THU  C3'   C2'  C1'   101.98  3.000
 THU  H3'   C3'  C4'   110.76  3.000
 THU  H3'   C3'  O3'   111.53  3.000
 THU  C4'   C3'  O3'   109.07  3.000
 THU  H3'   C3'  C2'   112.31  3.000
 THU  C4'   C3'  C2'   100.49  3.000
 THU  O3'   C3'  C2'   112.14  3.000
 THU  HO3'  O3'  C3'   108.24  3.000
 THU  H4'   C4'  C5'   108.24  3.000
 THU  H4'   C4'  O4'   109.54  3.000
 THU  C5'   C4'  O4'   110.43  3.000
 THU  H4'   C4'  C3'   107.68  3.000
 THU  C5'   C4'  C3'   115.15  3.000
 THU  O4'   C4'  C3'   105.69  3.000
 THU  C4'   O4'  C1'   110.52  3.000
 THU  H5'2  C5'  H5'1  107.36  3.000
 THU  H5'2  C5'  O5'   111.51  3.000
 THU  H5'1  C5'  O5'   111.70  3.000
 THU  H5'2  C5'  C4'   108.12  3.000
 THU  H5'1  C5'  C4'   109.87  3.000
 THU  O5'   C5'  C4'   108.23  3.000
 THU  HO5'  O5'  C5'   107.95  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
 THU  CONST_02  C5   C4  N3  C2    0.00   0.0  0
 THU  CONST_03  C6   N1  C2  N3    0.00   0.0  0
 THU  CONST_04  C1'  N1  C2  N3  180.00   0.0  0
 THU  CONST_05  O4   C4  N3  C2  180.00   0.0  0
 THU  CONST_06  C6   N1  C2  O2  180.00   0.0  0
 THU  CONST_07  C1'  N1  C2  O2    0.00   0.0  0
 THU  CONST_09  HN3  N3  C2  N1  180.00   0.0  0
 THU  Var_01    H51  C5  C6  N1  174.11  30.0  1
 THU  Var_02    H61  C6  N1  C2   79.47  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
 THU  chir_01  C1'  N1   C2'  O4'  positiv
 THU  chir_02  C3'  O3'  C4'  C2'  negativ
 THU  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
 THU  plan-1  N1   0.020
 THU  plan-1  C2   0.020
 THU  plan-1  O2   0.020
 THU  plan-1  N3   0.020
 THU  plan-1  C4   0.020
 THU  plan-1  O4   0.020
 THU  plan-1  C5   0.020
 THU  plan-1  C6   0.020
 THU  plan-1  C1'  0.020
 THU  plan-1  HN3  0.020

