# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 09:11:06 2021
#   Inital geometry file: a 112 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@@H](O[C@@H]1CO[P@](O)(=O)O[P@@](O)(=O)O[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
 DUT  DUT  '2'-deoxyuridine 5'-(tetrahydrogen triphosphate)'  ligand  43  28  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DUT
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
 DUT  N1    N  NR6   0  -0.565  10.1345  -3.4814  28.7165
 DUT  C2    C  CR6   0   0.740  10.9464  -3.4796  29.8306
 DUT  N3    N  NR16  0  -0.731  11.6472  -4.6359  30.0398
 DUT  C4    C  CR6   0   0.565  11.6273  -5.7931  29.2740
 DUT  C5    C  CR16  0  -0.512  10.7313  -5.7139  28.1500
 DUT  C6    C  CR16  0   0.085  10.0340  -4.5858  27.9261
 DUT  O2    O  O     0  -0.482  11.0348  -2.5193  30.5693
 DUT  O4    O  O     0  -0.467  12.3172  -6.7486  29.5793
 DUT  C1'   C  CH1   0   0.213   9.3828  -2.2292  28.4589
 DUT  C2'   C  CH2   0  -0.539  10.2669  -1.1323  27.8790
 DUT  C3'   C  CH1   0   0.015  10.0910  -1.3158  26.3807
 DUT  C4'   C  CH1   0  -0.009   8.6148  -1.7195  26.3172
 DUT  O4'   O  O2    0  -0.514   8.3884  -2.4769  27.5056
 DUT  O3'   O  OH1   0  -0.653  10.3903  -0.1407  25.6868
 DUT  C5'   C  CH2   0  -0.207   8.2548  -2.5448  25.1080
 DUT  O5'   O  O2    0  -0.592   6.8632  -2.8780  25.1032
 DUT  PA    P  P     0   1.482   6.2766  -4.1069  25.9290
 DUT  O1A   O  O     0  -0.666   7.1946  -5.2337  26.1576
 DUT  O2A   O  OH1   0  -0.708   5.5069  -3.5192  27.1830
 DUT  O3A   O  O2    0  -0.667   4.9782  -4.4519  25.0256
 DUT  PB    P  P     0   1.497   4.7611  -4.2467  23.4418
 DUT  O1B   O  O     0  -0.664   4.4394  -2.8832  23.0116
 DUT  O2B   O  OH1   0  -0.702   3.7271  -5.3955  23.1225
 DUT  O3B   O  O2    0  -0.698   6.1436  -4.8706  22.9002
 DUT  PG    P  P     0   1.486   6.9316  -4.6185  21.5030
 DUT  O1G   O  O     0  -0.669   7.9614  -5.6447  21.2933
 DUT  O2G   O  OH1   0  -0.735   5.6837  -4.5592  20.5280
 DUT  O3G   O  OH1   0  -0.727   7.4416  -3.1175  21.6066
 DUT  HN3   H  HNR6  0   0.427  12.2528  -4.6325  30.8518
 DUT  H5    H  HCR6  0   0.290  10.6137  -6.5660  27.4988
 DUT  H6    H  HCR6  0   0.322   9.3340  -4.5303  27.1084
 DUT  H1'   H  HCH1  0   0.289   8.9202  -1.9414  29.4027
 DUT  H2'1  H  HCH2  0   0.274   9.8678  -0.1593  28.1749
 DUT  H2'2  H  HCH2  0   0.289  11.3023  -1.1892  28.2070
 DUT  H3'   H  HCH1  0   0.235  10.7140  -2.1531  26.0336
 DUT  H4'   H  HCH1  0   0.264   7.9920  -0.8171  26.3412
 DUT  HO3'  H  HOH1  0   0.461  10.5044  -0.3452  24.7540
 DUT  H5'1  H  HCH2  0   0.274   8.4249  -1.9551  24.2079
 DUT  H5'2  H  HCH2  0   0.252   8.8669  -3.4478  25.0433
 DUT  HOA2  H  HOH1  0   0.506   6.0105  -3.5573  28.0083
 DUT  HOB2  H  HOH1  0   0.517   2.8517  -5.0840  22.8513
 DUT  HOG2  H  HOH1  0   0.514   5.8836  -4.3486  19.6046
 DUT  HOG3  H  HOH1  0   0.509   8.4037  -3.0229  21.5818

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
 DUT  N1   C2    single  1.379  0.020  1.379
 DUT  N1   C6    single  1.362  0.020  1.362
 DUT  N1   C1'   single  1.483  0.020  1.483
 DUT  C2   N3    single  1.368  0.020  1.368
 DUT  C2   O2    double  1.215  0.020  1.215
 DUT  N3   C4    single  1.388  0.020  1.388
 DUT  N3   HN3   single  0.860  0.020  1.020
 DUT  C4   C5    single  1.440  0.020  1.440
 DUT  C4   O4    double  1.217  0.020  1.217
 DUT  C5   C6    double  1.345  0.020  1.345
 DUT  C5   H5    single  0.930  0.020  1.080
 DUT  C6   H6    single  0.930  0.020  1.080
 DUT  C1'  C2'   single  1.523  0.020  1.523
 DUT  C1'  O4'   single  1.400  0.020  1.400
 DUT  C1'  H1'   single  0.970  0.020  1.090
 DUT  C2'  C3'   single  1.520  0.020  1.520
 DUT  C2'  H2'1  single  0.970  0.020  1.090
 DUT  C2'  H2'2  single  0.970  0.020  1.090
 DUT  C3'  C4'   single  1.532  0.020  1.532
 DUT  C3'  O3'   single  1.397  0.020  1.397
 DUT  C3'  H3'   single  0.970  0.020  1.090
 DUT  C4'  O4'   single  1.427  0.020  1.427
 DUT  C4'  C5'   single  1.508  0.020  1.508
 DUT  C4'  H4'   single  0.970  0.020  1.090
 DUT  O3'  HO3'  single  0.850  0.020  0.980
 DUT  C5'  O5'   single  1.431  0.020  1.431
 DUT  C5'  H5'1  single  0.970  0.020  1.090
 DUT  C5'  H5'2  single  0.970  0.020  1.090
 DUT  O5'  PA    single  1.593  0.020  1.593
 DUT  PA   O1A   double  1.471  0.020  1.471
 DUT  PA   O2A   single  1.584  0.020  1.584
 DUT  PA   O3A   single  1.619  0.020  1.619
 DUT  O2A  HOA2  single  0.850  0.020  0.980
 DUT  O3A  PB    single  1.612  0.020  1.612
 DUT  PB   O1B   double  1.466  0.020  1.466
 DUT  PB   O2B   single  1.578  0.020  1.578
 DUT  PB   O3B   single  1.611  0.020  1.611
 DUT  O2B  HOB2  single  0.850  0.020  0.980
 DUT  O3B  PG    single  1.624  0.020  1.624
 DUT  PG   O1G   double  1.469  0.020  1.469
 DUT  PG   O2G   single  1.585  0.020  1.585
 DUT  PG   O3G   single  1.589  0.020  1.589
 DUT  O2G  HOG2  single  0.850  0.020  0.980
 DUT  O3G  HOG3  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
 DUT  C1'   N1   C6    123.13  3.000
 DUT  C1'   N1   C2    115.96  3.000
 DUT  C6    N1   C2    120.90  3.000
 DUT  O2    C2   N3    122.53  3.000
 DUT  O2    C2   N1    122.37  3.000
 DUT  N3    C2   N1    115.10  3.000
 DUT  HN3   N3   C4    116.99  3.000
 DUT  HN3   N3   C2    115.21  3.000
 DUT  C4    N3   C2    127.80  3.000
 DUT  O4    C4   C5    126.27  3.000
 DUT  O4    C4   N3    120.52  3.000
 DUT  C5    C4   N3    113.20  3.000
 DUT  H5    C5   C6    120.36  3.000
 DUT  H5    C5   C4    119.71  3.000
 DUT  C6    C5   C4    119.92  3.000
 DUT  H6    C6   C5    120.41  3.000
 DUT  H6    C6   N1    116.52  3.000
 DUT  C5    C6   N1    123.05  3.000
 DUT  H1'   C1'  O4'   109.58  3.000
 DUT  H1'   C1'  C2'   112.70  3.000
 DUT  O4'   C1'  C2'   106.29  3.000
 DUT  H1'   C1'  N1    106.72  3.000
 DUT  O4'   C1'  N1    109.21  3.000
 DUT  C2'   C1'  N1    112.33  3.000
 DUT  H2'2  C2'  H2'1  108.22  3.000
 DUT  H2'2  C2'  C3'   113.65  3.000
 DUT  H2'1  C2'  C3'   109.40  3.000
 DUT  H2'2  C2'  C1'   113.58  3.000
 DUT  H2'1  C2'  C1'   109.04  3.000
 DUT  C3'   C2'  C1'   102.78  3.000
 DUT  H3'   C3'  O3'   111.24  3.000
 DUT  H3'   C3'  C4'   109.40  3.000
 DUT  O3'   C3'  C4'   114.05  3.000
 DUT  H3'   C3'  C2'   109.72  3.000
 DUT  O3'   C3'  C2'   111.31  3.000
 DUT  C4'   C3'  C2'   100.62  3.000
 DUT  H4'   C4'  C5'   109.41  3.000
 DUT  H4'   C4'  O4'   109.17  3.000
 DUT  C5'   C4'  O4'   109.84  3.000
 DUT  H4'   C4'  C3'   109.24  3.000
 DUT  C5'   C4'  C3'   114.06  3.000
 DUT  O4'   C4'  C3'   104.96  3.000
 DUT  C4'   O4'  C1'   111.13  3.000
 DUT  HO3'  O3'  C3'   109.16  3.000
 DUT  H5'2  C5'  H5'1  108.12  3.000
 DUT  H5'2  C5'  O5'   110.62  3.000
 DUT  H5'1  C5'  O5'   105.97  3.000
 DUT  H5'2  C5'  C4'   111.48  3.000
 DUT  H5'1  C5'  C4'   109.21  3.000
 DUT  O5'   C5'  C4'   111.25  3.000
 DUT  PA    O5'  C5'   122.42  3.000
 DUT  O3A   PA   O2A    97.53  3.000
 DUT  O3A   PA   O1A   115.09  3.000
 DUT  O2A   PA   O1A   117.66  3.000
 DUT  O3A   PA   O5'    99.82  3.000
 DUT  O2A   PA   O5'   107.64  3.000
 DUT  O1A   PA   O5'   116.21  3.000
 DUT  HOA2  O2A  PA    114.06  3.000
 DUT  PB    O3A  PA    129.00  3.000
 DUT  O3B   PB   O2B   102.26  3.000
 DUT  O3B   PB   O1B   116.75  3.000
 DUT  O2B   PB   O1B   118.30  3.000
 DUT  O3B   PB   O3A    99.52  3.000
 DUT  O2B   PB   O3A   101.21  3.000
 DUT  O1B   PB   O3A   115.88  3.000
 DUT  HOB2  O2B  PB    114.52  3.000
 DUT  PG    O3B  PB    130.22  3.000
 DUT  O3G   PG   O2G   104.92  3.000
 DUT  O3G   PG   O1G   116.38  3.000
 DUT  O2G   PG   O1G   119.37  3.000
 DUT  O3G   PG   O3B   104.26  3.000
 DUT  O2G   PG   O3B    98.80  3.000
 DUT  O1G   PG   O3B   110.77  3.000
 DUT  HOG2  O2G  PG    115.62  3.000
 DUT  HOG3  O3G  PG    114.21  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
 DUT  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 DUT  CONST_02  C5    C4   N3   C2      0.00   0.0  0
 DUT  CONST_03  C6    N1   C2   N3      0.00   0.0  0
 DUT  CONST_04  C1'   N1   C2   N3    180.00   0.0  0
 DUT  CONST_05  O4    C4   N3   C2    180.00   0.0  0
 DUT  CONST_06  O2    C2   N3   C4    180.00   0.0  0
 DUT  CONST_07  O2    C2   N1   C6    180.00   0.0  0
 DUT  CONST_08  C1'   N1   C2   O2      0.00   0.0  0
 DUT  CONST_09  HN3   N3   C2   N1    180.00   0.0  0
 DUT  Var_01    O1A   PA   O5'  C5'   -28.45  30.0  3
 DUT  Var_02    O1B   PB   O3A  PA    -79.03  30.0  3
 DUT  Var_03    O1G   PG   O3B  PB   -165.60  30.0  3
 DUT  Var_04    H5'1  C5'  O5'  PA    158.70  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
 DUT  chir_01  C1'  N1   C2'  O4'  negativ
 DUT  chir_02  C3'  O3'  C4'  C2'  positiv
 DUT  chir_03  C4'  O4'  C3'  C5'  negativ
 DUT  chir_04  PA   O1A  O2A  O3A  both
 DUT  chir_05  PB   O2B  O1B  O3A  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
 DUT  plan-1  N1   0.020
 DUT  plan-1  C2   0.020
 DUT  plan-1  N3   0.020
 DUT  plan-1  C4   0.020
 DUT  plan-1  C5   0.020
 DUT  plan-1  C6   0.020
 DUT  plan-1  O2   0.020
 DUT  plan-1  O4   0.020
 DUT  plan-1  C1'  0.020
 DUT  plan-1  HN3  0.020
 DUT  plan-1  H5   0.020
 DUT  plan-1  H6   0.020

