# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 22:48:36 2021
#   Inital geometry file: a 166 line input string
#   Ligand name: 5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]-N-[3-(propanoylamino)propyl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)NCCCNC1=NC(=O)c2ncn([C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O)c2N1
#
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
 2UK  2UK  5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]-N-[3-(propanoylamino)propyl]guanosine  ligand  68  40  .  2021-08-04  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2UK
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
 2UK  OAB  O  O     0  -0.508  47.1745   0.8144  35.1142
 2UK  CBB  C  C     0   0.530  46.0599   0.3251  35.2509
 2UK  CAN  C  CH2   0  -0.558  45.3927  -0.4602  34.1418
 2UK  CAA  C  CH3   0  -0.662  46.1544  -1.7525  33.8573
 2UK  NAU  N  NH1   0  -0.633  45.3504   0.4258  36.3863
 2UK  CAP  C  CH2   0  -0.303  45.8748   0.9819  37.6115
 2UK  CAO  C  CH2   0  -0.487  46.6977  -0.0235  38.4198
 2UK  CAQ  C  CH2   0  -0.343  46.8519   0.4115  39.8846
 2UK  N2   N  NH1   0  -0.648  47.0667  -0.6883  40.8032
 2UK  C2   C  CR6   0   0.709  46.1628  -1.6330  41.0949
 2UK  N3   N  NR16  0  -0.751  44.9275  -1.4913  40.5245
 2UK  N1   N  N     0  -0.552  46.4814  -2.6297  41.8788
 2UK  C6   C  CR6   0   0.414  45.6090  -3.6454  42.1931
 2UK  O6   O  O     0  -0.492  45.9307  -4.5429  42.9625
 2UK  C5   C  CR56  0  -0.102  44.3214  -3.5765  41.5292
 2UK  C4   C  CR56  0   0.631  44.0528  -2.5071  40.7244
 2UK  N7   N  N     0  -0.439  43.2589  -4.4447  41.4949
 2UK  C8   C  CR15  0   0.087  42.3980  -3.9096  40.6847
 2UK  N9   N  NR5   0  -0.527  42.8289  -2.7000  40.1842
 2UK  C1'  C  CH1   0   0.203  42.2651  -1.9219  39.1065
 2UK  O4'  O  O2    0  -0.492  40.8800  -1.9339  39.1851
 2UK  C2'  C  CH1   0   0.015  42.6095  -2.4805  37.7286
 2UK  O2'  O  OH1   0  -0.650  43.9194  -2.1445  37.3992
 2UK  C3'  C  CH1   0  -0.059  41.5053  -1.8502  36.8812
 2UK  O3'  O  OH1   0  -0.660  41.9102  -0.5441  36.5686
 2UK  C4'  C  CH1   0  -0.007  40.3186  -1.8754  37.8670
 2UK  C5'  C  CH2   0  -0.216  39.3539  -3.0211  37.6810
 2UK  O5'  O  O2    0  -0.576  40.0545  -4.2708  37.7518
 2UK  PA   P  P     0   1.478  39.9178  -5.3472  36.5900
 2UK  O1A  O  OH1   0  -0.713  40.9374  -6.4576  37.0704
 2UK  O2A  O  O     0  -0.677  40.0181  -4.8493  35.2094
 2UK  O3A  O  O2    0  -0.692  38.4869  -6.0058  36.9633
 2UK  PB   P  P     0   1.471  37.5629  -6.9170  35.9752
 2UK  O1B  O  OH1   0  -0.713  36.5986  -7.5986  37.0347
 2UK  O2B  O  O     0  -0.684  38.3425  -7.7667  35.0613
 2UK  N3B  N  NH1   0  -0.957  36.5471  -5.8543  35.2160
 2UK  PG   P  P     0   1.437  36.3637  -5.7495  33.5450
 2UK  O1G  O  O     0  -0.688  37.6062  -5.5780  32.7728
 2UK  O2G  O  OH1   0  -0.733  35.5093  -7.0583  33.2281
 2UK  O3G  O  OH1   0  -0.735  35.2719  -4.5909  33.4123
 2UK  H1   H  HCH2  0   0.260  45.3796   0.1638  33.2459
 2UK  H2   H  HCH2  0   0.239  44.3527  -0.6864  34.3854
 2UK  H3   H  HCH3  0   0.241  45.6891  -2.2963  33.0361
 2UK  H4   H  HCH3  0   0.234  47.1887  -1.5502  33.5820
 2UK  H5   H  HCH3  0   0.224  46.1602  -2.4094  34.7284
 2UK  H6   H  HNH1  0   0.398  44.4939  -0.1033  36.4636
 2UK  H7   H  HCH2  0   0.258  46.4587   1.8741  37.3868
 2UK  H8   H  HCH2  0   0.243  45.0172   1.3168  38.1995
 2UK  H9   H  HCH2  0   0.244  46.1995  -0.9933  38.3669
 2UK  H10  H  HCH2  0   0.263  47.6790  -0.1650  37.9646
 2UK  H11  H  HCH2  0   0.294  47.6979   1.0854  39.9979
 2UK  H12  H  HCH2  0   0.249  45.9779   0.9904  40.2060
 2UK  H13  H  HNH1  0   0.412  47.9720  -0.8058  41.2272
 2UK  H14  H  HNR6  0   0.435  44.6709  -0.6676  40.0036
 2UK  H15  H  HCR5  0   0.295  41.4388  -4.3226  40.4142
 2UK  H16  H  HCH1  0   0.250  42.6605  -0.9017  39.2076
 2UK  H17  H  HCH1  0   0.260  42.4683  -3.5663  37.7484
 2UK  H18  H  HOH1  0   0.471  44.2778  -2.8100  36.8050
 2UK  H19  H  HCH1  0   0.259  41.2849  -2.4302  35.9779
 2UK  H20  H  HOH1  0   0.464  41.2835  -0.1646  35.9448
 2UK  H21  H  HCH1  0   0.277  39.7319  -0.9555  37.7721
 2UK  H22  H  HCH2  0   0.256  38.8446  -2.8946  36.7225
 2UK  H23  H  HCH2  0   0.279  38.5973  -3.0157  38.4662
 2UK  H24  H  HOH1  0   0.513  41.6900  -6.5919  36.4781
 2UK  H25  H  HOH1  0   0.509  37.0257  -8.2267  37.6353
 2UK  H26  H  HNH1  0   0.448  35.9122  -5.3055  35.7856
 2UK  H27  H  HOH1  0   0.500  35.5294  -7.3225  32.2981
 2UK  H28  H  HOH1  0   0.503  35.6475  -3.7024  33.3455

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
 2UK  O2A  PA   double    1.471  0.020  1.471
 2UK  O1G  PG   double    1.473  0.020  1.473
 2UK  CAA  CAN  single    1.527  0.020  1.527
 2UK  O3'  C3'  single    1.403  0.020  1.403
 2UK  O3G  PG   single    1.598  0.020  1.598
 2UK  CAN  CBB  single    1.514  0.020  1.514
 2UK  O2'  C2'  single    1.392  0.020  1.392
 2UK  C3'  C2'  single    1.528  0.020  1.528
 2UK  C3'  C4'  single    1.543  0.020  1.543
 2UK  PG   N3B  single    1.684  0.020  1.684
 2UK  PG   O2G  single    1.595  0.020  1.595
 2UK  PA   O1A  single    1.582  0.020  1.582
 2UK  PA   O5'  single    1.590  0.020  1.590
 2UK  PA   O3A  single    1.619  0.020  1.619
 2UK  C2'  C1'  single    1.526  0.020  1.526
 2UK  N3B  PB   single    1.655  0.020  1.655
 2UK  O2B  PB   double    1.471  0.020  1.471
 2UK  O5'  C5'  single    1.434  0.020  1.434
 2UK  C4'  C5'  single    1.509  0.020  1.509
 2UK  C4'  O4'  single    1.434  0.020  1.434
 2UK  CBB  NAU  single    1.343  0.020  1.343
 2UK  CBB  OAB  double    1.225  0.020  1.225
 2UK  PB   O3A  single    1.631  0.020  1.631
 2UK  PB   O1B  single    1.587  0.020  1.587
 2UK  NAU  CAP  single    1.444  0.020  1.444
 2UK  C1'  O4'  single    1.387  0.020  1.387
 2UK  C1'  N9   single    1.444  0.020  1.444
 2UK  N9   C8   aromatic  1.378  0.020  1.378
 2UK  N9   C4   aromatic  1.352  0.020  1.352
 2UK  CAP  CAO  single    1.530  0.020  1.530
 2UK  C8   N7   aromatic  1.298  0.020  1.298
 2UK  CAO  CAQ  single    1.536  0.020  1.536
 2UK  C4   N3   single    1.355  0.020  1.355
 2UK  C4   C5   aromatic  1.365  0.020  1.365
 2UK  N7   C5   aromatic  1.373  0.020  1.373
 2UK  N3   C2   single    1.368  0.020  1.368
 2UK  C5   C6   single    1.450  0.020  1.450
 2UK  CAQ  N2   single    1.449  0.020  1.449
 2UK  C2   N2   single    1.340  0.020  1.340
 2UK  C2   N1   double    1.307  0.020  1.307
 2UK  C6   N1   single    1.375  0.020  1.375
 2UK  C6   O6   double    1.225  0.020  1.225
 2UK  CAN  H1   single    0.970  0.020  1.090
 2UK  CAN  H2   single    0.970  0.020  1.090
 2UK  CAA  H3   single    0.970  0.020  1.090
 2UK  CAA  H4   single    0.970  0.020  1.090
 2UK  CAA  H5   single    0.970  0.020  1.090
 2UK  NAU  H6   single    0.860  0.020  1.020
 2UK  CAP  H7   single    0.970  0.020  1.090
 2UK  CAP  H8   single    0.970  0.020  1.090
 2UK  CAO  H9   single    0.970  0.020  1.090
 2UK  CAO  H10  single    0.970  0.020  1.090
 2UK  CAQ  H11  single    0.970  0.020  1.090
 2UK  CAQ  H12  single    0.970  0.020  1.090
 2UK  N2   H13  single    0.860  0.020  1.020
 2UK  N3   H14  single    0.860  0.020  1.020
 2UK  C8   H15  single    0.930  0.020  1.080
 2UK  C1'  H16  single    0.970  0.020  1.090
 2UK  C2'  H17  single    0.970  0.020  1.090
 2UK  O2'  H18  single    0.850  0.020  0.980
 2UK  C3'  H19  single    0.970  0.020  1.090
 2UK  O3'  H20  single    0.850  0.020  0.980
 2UK  C4'  H21  single    0.970  0.020  1.090
 2UK  C5'  H22  single    0.970  0.020  1.090
 2UK  C5'  H23  single    0.970  0.020  1.090
 2UK  O1A  H24  single    0.850  0.020  0.980
 2UK  O1B  H25  single    0.850  0.020  0.980
 2UK  N3B  H26  single    0.860  0.020  1.020
 2UK  O2G  H27  single    0.850  0.020  0.980
 2UK  O3G  H28  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
 2UK  NAU  CBB  CAN  115.18  3.000
 2UK  NAU  CBB  OAB  123.04  3.000
 2UK  CAN  CBB  OAB  121.77  3.000
 2UK  H2   CAN  H1   106.86  3.000
 2UK  H2   CAN  CAA  109.96  3.000
 2UK  H1   CAN  CAA  109.69  3.000
 2UK  H2   CAN  CBB  111.33  3.000
 2UK  H1   CAN  CBB  108.05  3.000
 2UK  CAA  CAN  CBB  110.84  3.000
 2UK  H5   CAA  H4   107.97  3.000
 2UK  H5   CAA  H3   107.67  3.000
 2UK  H4   CAA  H3   107.92  3.000
 2UK  H5   CAA  CAN  111.32  3.000
 2UK  H4   CAA  CAN  111.33  3.000
 2UK  H3   CAA  CAN  110.48  3.000
 2UK  H6   NAU  CAP  116.41  3.000
 2UK  H6   NAU  CBB  118.28  3.000
 2UK  CAP  NAU  CBB  123.68  3.000
 2UK  H8   CAP  H7   106.30  3.000
 2UK  H8   CAP  CAO  109.83  3.000
 2UK  H7   CAP  CAO  111.02  3.000
 2UK  H8   CAP  NAU  106.84  3.000
 2UK  H7   CAP  NAU  109.56  3.000
 2UK  CAO  CAP  NAU  112.98  3.000
 2UK  H10  CAO  H9   105.97  3.000
 2UK  H10  CAO  CAQ  110.14  3.000
 2UK  H9   CAO  CAQ  110.10  3.000
 2UK  H10  CAO  CAP  110.40  3.000
 2UK  H9   CAO  CAP  108.22  3.000
 2UK  CAQ  CAO  CAP  111.83  3.000
 2UK  H12  CAQ  H11  105.21  3.000
 2UK  H12  CAQ  N2   109.46  3.000
 2UK  H11  CAQ  N2   106.80  3.000
 2UK  H12  CAQ  CAO  110.43  3.000
 2UK  H11  CAQ  CAO  110.67  3.000
 2UK  N2   CAQ  CAO  113.86  3.000
 2UK  H13  N2   C2   115.65  3.000
 2UK  H13  N2   CAQ  119.27  3.000
 2UK  C2   N2   CAQ  124.98  3.000
 2UK  N1   C2   N3   123.29  3.000
 2UK  N1   C2   N2   120.25  3.000
 2UK  N3   C2   N2   116.46  3.000
 2UK  H14  N3   C4   121.63  3.000
 2UK  H14  N3   C2   122.01  3.000
 2UK  C4   N3   C2   116.34  3.000
 2UK  C6   N1   C2   123.06  3.000
 2UK  C5   C6   O6   123.74  3.000
 2UK  O6   C6   N1   121.20  3.000
 2UK  C5   C6   N1   115.05  3.000
 2UK  N7   C5   C4   109.18  3.000
 2UK  N7   C5   C6   131.96  3.000
 2UK  C4   C5   C6   118.81  3.000
 2UK  N9   C4   C5   107.57  3.000
 2UK  C5   C4   N3   123.17  3.000
 2UK  N9   C4   N3   129.23  3.000
 2UK  C8   N7   C5   105.56  3.000
 2UK  H15  C8   N9   121.53  3.000
 2UK  H15  C8   N7   126.05  3.000
 2UK  N9   C8   N7   112.41  3.000
 2UK  C1'  N9   C8   128.46  3.000
 2UK  C8   N9   C4   105.27  3.000
 2UK  C1'  N9   C4   125.10  3.000
 2UK  H16  C1'  C2'  109.98  3.000
 2UK  H16  C1'  O4'  111.23  3.000
 2UK  C2'  C1'  O4'  105.86  3.000
 2UK  H16  C1'  N9   106.93  3.000
 2UK  O4'  C1'  N9   110.05  3.000
 2UK  C2'  C1'  N9   112.86  3.000
 2UK  C4'  O4'  C1'  109.78  3.000
 2UK  H17  C2'  C3'  109.02  3.000
 2UK  H17  C2'  O2'  111.41  3.000
 2UK  C3'  C2'  O2'  116.69  3.000
 2UK  H17  C2'  C1'  108.51  3.000
 2UK  C3'  C2'  C1'  100.76  3.000
 2UK  O2'  C2'  C1'  109.74  3.000
 2UK  H18  O2'  C2'  109.27  3.000
 2UK  H19  C3'  C4'  111.30  3.000
 2UK  H19  C3'  O3'  111.55  3.000
 2UK  C4'  C3'  O3'  112.31  3.000
 2UK  H19  C3'  C2'  112.59  3.000
 2UK  C4'  C3'  C2'  101.23  3.000
 2UK  O3'  C3'  C2'  107.40  3.000
 2UK  H20  O3'  C3'  108.88  3.000
 2UK  H21  C4'  C5'  106.53  3.000
 2UK  H21  C4'  C3'  110.06  3.000
 2UK  C5'  C4'  C3'  115.17  3.000
 2UK  H21  C4'  O4'  108.89  3.000
 2UK  C5'  C4'  O4'  109.42  3.000
 2UK  C3'  C4'  O4'  106.67  3.000
 2UK  H23  C5'  H22  107.92  3.000
 2UK  H23  C5'  O5'  107.92  3.000
 2UK  H22  C5'  O5'  111.82  3.000
 2UK  H23  C5'  C4'  110.55  3.000
 2UK  H22  C5'  C4'  108.55  3.000
 2UK  O5'  C5'  C4'  110.07  3.000
 2UK  PA   O5'  C5'  120.79  3.000
 2UK  O3A  PA   O2A  114.47  3.000
 2UK  O3A  PA   O1A  102.36  3.000
 2UK  O2A  PA   O1A  118.60  3.000
 2UK  O3A  PA   O5'  100.54  3.000
 2UK  O1A  PA   O5'  101.42  3.000
 2UK  O2A  PA   O5'  116.80  3.000
 2UK  H24  O1A  PA   114.39  3.000
 2UK  PB   O3A  PA   126.04  3.000
 2UK  N3B  PB   O2B  114.28  3.000
 2UK  O2B  PB   O1B  119.26  3.000
 2UK  N3B  PB   O1B  102.07  3.000
 2UK  O1B  PB   O3A  100.36  3.000
 2UK  O2B  PB   O3A  113.50  3.000
 2UK  N3B  PB   O3A  105.49  3.000
 2UK  H25  O1B  PB   115.14  3.000
 2UK  H26  N3B  PG   117.09  3.000
 2UK  H26  N3B  PB   118.30  3.000
 2UK  PG   N3B  PB   124.20  3.000
 2UK  O3G  PG   O2G  102.27  3.000
 2UK  O2G  PG   O1G  116.31  3.000
 2UK  O3G  PG   O1G  116.65  3.000
 2UK  O2G  PG   N3B  101.79  3.000
 2UK  O3G  PG   N3B  101.65  3.000
 2UK  O1G  PG   N3B  115.82  3.000
 2UK  H27  O2G  PG   113.84  3.000
 2UK  H28  O3G  PG   114.00  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
 2UK  CONST_01  C8   N9   C4   C5      0.00   0.0  0
 2UK  CONST_02  N9   C8   N7   C5      0.00   0.0  0
 2UK  CONST_03  N7   C8   N9   C4      0.00   0.0  0
 2UK  CONST_04  C8   N7   C5   C4      0.00   0.0  0
 2UK  CONST_05  N9   C4   C5   N7      0.00   0.0  0
 2UK  CONST_06  C1'  N9   C4   N3      0.00   0.0  0
 2UK  CONST_07  C1'  N9   C4   C5    180.00   0.0  0
 2UK  CONST_08  C1'  N9   C8   N7    180.00   0.0  0
 2UK  CONST_09  C6   N1   C2   N3      0.00   0.0  0
 2UK  CONST_10  C4   N3   C2   N1      0.00   0.0  0
 2UK  CONST_11  C4   N3   C2   N2    180.00   0.0  0
 2UK  CONST_12  C6   N1   C2   N2    180.00   0.0  0
 2UK  CONST_13  H15  C8   N7   C5    180.00   0.0  0
 2UK  CONST_14  H14  N3   C2   N1    180.00   0.0  0
 2UK  CONST_15  N3   C2   N2   CAQ     0.00   0.0  0
 2UK  CONST_16  N1   C2   N2   CAQ   180.00   0.0  0
 2UK  CONST_17  H13  N2   C2   N3    180.00   0.0  0
 2UK  CONST_18  CAP  NAU  CBB  OAB     0.00   0.0  0
 2UK  CONST_19  CAP  NAU  CBB  CAN   180.00   0.0  0
 2UK  CONST_20  H6   NAU  CBB  OAB   180.00   0.0  0
 2UK  Var_01    C2   N2   CAQ  CAO   -67.09  30.0  3
 2UK  Var_02    CAA  CAN  CBB  OAB    65.94  30.0  1
 2UK  Var_03    CAO  CAP  NAU  CBB   -82.25  30.0  3
 2UK  Var_04    CAQ  CAO  CAP  NAU  -161.32  30.0  3
 2UK  Var_05    N2   CAQ  CAO  CAP   153.98  30.0  3
 2UK  Var_06    O2A  PA   O5'  C5'    45.37  30.0  1
 2UK  Var_07    N3B  PB   O3A  PA    -91.36  30.0  1
 2UK  Var_08    PG   N3B  PB   O3A   126.84  30.0  1
 2UK  Var_09    O1G  PG   N3B  PB    -53.07  30.0  2
 2UK  Var_10    H3   CAA  CAN  CBB  -178.09  30.0  3
 2UK  Var_11    H22  C5'  O5'  PA     -6.06  30.0  3

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
 2UK  chir_01  C1'  C2'  O4'  N9   negativ
 2UK  chir_02  C2'  O2'  C3'  C1'  positiv
 2UK  chir_03  C3'  O3'  C4'  C2'  positiv
 2UK  chir_04  C4'  O4'  C3'  C5'  negativ
 2UK  chir_05  PA   O1A  O5'  O3A  both
 2UK  chir_06  PB   O3A  O2B  N3B  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
 2UK  plan-1  CAQ  0.020
 2UK  plan-1  N2   0.020
 2UK  plan-1  C2   0.020
 2UK  plan-1  N3   0.020
 2UK  plan-1  N1   0.020
 2UK  plan-1  C6   0.020
 2UK  plan-1  O6   0.020
 2UK  plan-1  C5   0.020
 2UK  plan-1  C4   0.020
 2UK  plan-1  N7   0.020
 2UK  plan-1  C8   0.020
 2UK  plan-1  N9   0.020
 2UK  plan-1  C1'  0.020
 2UK  plan-1  H13  0.020
 2UK  plan-1  H14  0.020
 2UK  plan-1  H15  0.020
 2UK  plan-2  OAB  0.020
 2UK  plan-2  CBB  0.020
 2UK  plan-2  CAN  0.020
 2UK  plan-2  NAU  0.020
 2UK  plan-2  CAP  0.020
 2UK  plan-2  H6   0.020

