# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon May 25 06:06:49 2020
#   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  64  40  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.509  11.7683   2.3392   0.8436
 2UK  CBB  C  C      0   0.556  11.4172   2.2360  -0.3252
 2UK  CAN  C  CH2    0  -0.569  12.2974   2.6779  -1.4757
 2UK  CAA  C  CH3    0  -0.659  13.7686   2.3729  -1.2360
 2UK  NAU  N  NH1    0  -0.644  10.2167   1.7477  -0.6717
 2UK  CAP  C  CH2    0  -0.238   9.2377   1.3014   0.2960
 2UK  CAO  C  CH2    0  -0.512   7.9147   1.0079  -0.3919
 2UK  CAQ  C  CH2    0  -0.244   6.8739   0.5295   0.6078
 2UK  N2   N  NH1    0  -0.681   5.6452   0.1948  -0.0773
 2UK  C2   C  CR6    0   0.738   4.4432   0.1973   0.5178
 2UK  N3   N  NR16   0  -0.753   3.4044  -0.2643  -0.2474
 2UK  N1   N  N      0  -0.549   4.3037   0.6357   1.7386
 2UK  C6   C  CR6    0   0.414   3.0915   0.6693   2.3886
 2UK  O6   O  O      0  -0.495   3.0038   1.0875   3.5377
 2UK  C5   C  CR56   0  -0.118   1.9706   0.1779   1.6203
 2UK  C4   C  CR56   0   0.624   2.1809  -0.2594   0.3407
 2UK  N7   N  N      0  -0.450   0.6416   0.0501   1.9317
 2UK  C8   C  CR15   0   0.049   0.0788  -0.4453   0.8705
 2UK  N9   N  NR5    0  -0.534   0.9830  -0.6438  -0.1520
 2UK  C1'  C  CH1    0   0.214   0.7373  -1.2014  -1.4704
 2UK  O4'  O  O2     0  -0.489  -0.5799  -0.9644  -1.8355
 2UK  C2'  C  CH1    0  -0.046   0.9457  -2.7151  -1.5219
 2UK  O2'  O  OH1    0  -0.657   2.2925  -2.9877  -1.7801
 2UK  C3'  C  CH1    0  -0.030  -0.0273  -3.1128  -2.6340
 2UK  O3'  O  OH1    0  -0.667   0.5130  -2.8287  -3.8981
 2UK  C4'  C  CH1    0  -0.051  -1.1802  -2.1547  -2.3693
 2UK  C5'  C  CH2    0  -0.140  -2.2068  -2.7081  -1.4015
 2UK  O5'  O  O2     0  -0.623  -3.1995  -1.7335  -1.2085
 2UK  PA   P  P      0   1.344  -3.9897  -1.7136   0.2492
 2UK  O1A  O  OP    -1  -0.792  -2.9798  -1.4236   1.3261
 2UK  O2A  O  O      0  -0.809  -4.8371  -2.9446   0.3557
 2UK  O3A  O  O2     0  -0.754  -4.8454  -0.3901  -0.1039
 2UK  PB   P  P      0   1.299  -6.3559  -0.0144   0.5626
 2UK  O1B  O  OP    -1  -0.827  -6.3344  -0.4544   1.9971
 2UK  O2B  O  O      0  -0.828  -7.3658  -0.5968  -0.3909
 2UK  N3B  N  NH1    0  -0.973  -6.2409   1.6550   0.4533
 2UK  PG   P  P      0   1.190  -7.1806   2.7232   1.5252
 2UK  O1G  O  O      0  -0.909  -6.3461   2.8675   2.7945
 2UK  O2G  O  OP    -1  -0.917  -7.2610   3.9991   0.6823
 2UK  O3G  O  OP    -1  -0.910  -8.5302   2.0384   1.7447
 2UK  H1   H  HCH2   0   0.248  11.9619   2.2257  -2.4110
 2UK  H2   H  HCH2   0   0.267  12.1591   3.7570  -1.5953
 2UK  H3   H  HCH3   0   0.234  14.3700   2.7285  -2.0719
 2UK  H4   H  HCH3   0   0.229  14.1328   2.8596  -0.3328
 2UK  H5   H  HCH3   0   0.228  13.9416   1.3011  -1.1346
 2UK  H6   H  HNH1   0   0.400   9.9992   1.6409  -1.6490
 2UK  H7   H  HCH2   0   0.233   9.5951   0.4044   0.8114
 2UK  H8   H  HCH2   0   0.238   9.0983   2.0710   1.0587
 2UK  H9   H  HCH2   0   0.250   7.5506   1.9073  -0.8948
 2UK  H10  H  HCH2   0   0.244   8.0670   0.2441  -1.1615
 2UK  H11  H  HCH2   0   0.235   7.2547  -0.3352   1.1622
 2UK  H12  H  HCH2   0   0.254   6.6642   1.3103   1.3370
 2UK  H13  H  HNH1   0   0.405   5.7355  -0.2821  -0.9608
 2UK  H14  H  HNR6   0   0.431   3.5662  -0.6873  -1.1504
 2UK  H15  H  HCR5   0   0.325  -0.9718  -0.6912   0.7727
 2UK  H16  H  HCH1   0   0.260   1.4323  -0.7031  -2.1594
 2UK  H17  H  HCH1   0   0.261   0.6165  -3.1616  -0.5759
 2UK  H18  H  HOH1   0   0.473   2.5106  -3.8623  -1.4432
 2UK  H19  H  HCH1   0   0.254  -0.3404  -4.1616  -2.5485
 2UK  H20  H  HOH1   0   0.450   1.4083  -3.1858  -3.9257
 2UK  H21  H  HCH1   0   0.265  -1.6806  -1.8846  -3.3039
 2UK  H22  H  HCH2   0   0.223  -2.6290  -3.6244  -1.8323
 2UK  H23  H  HCH2   0   0.203  -1.7209  -2.9920  -0.4587
 2UK  H26  H  HNH1   0   0.340  -6.3099   1.9796  -0.5037

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   deloc     1.498  0.020  1.498
 2UK  O1G  PG   deloc     1.526  0.020  1.526
 2UK  CAA  CAN  single    1.521  0.020  1.521
 2UK  O3'  C3'  single    1.404  0.020  1.404
 2UK  O3G  PG   deloc     1.529  0.020  1.529
 2UK  CAN  CBB  single    1.514  0.020  1.514
 2UK  O2'  C2'  single    1.398  0.020  1.398
 2UK  C3'  C2'  single    1.530  0.020  1.530
 2UK  C3'  C4'  single    1.522  0.020  1.522
 2UK  PG   N3B  single    1.781  0.020  1.781
 2UK  PG   O2G  deloc     1.531  0.020  1.531
 2UK  PA   O1A  deloc     1.505  0.020  1.505
 2UK  PA   O5'  single    1.658  0.020  1.658
 2UK  PA   O3A  single    1.615  0.020  1.615
 2UK  C2'  C1'  single    1.529  0.020  1.529
 2UK  N3B  PB   single    1.677  0.020  1.677
 2UK  O2B  PB   deloc     1.506  0.020  1.506
 2UK  O5'  C5'  single    1.405  0.020  1.405
 2UK  C4'  C5'  single    1.515  0.020  1.515
 2UK  C4'  O4'  single    1.436  0.020  1.436
 2UK  CBB  NAU  single    1.342  0.020  1.342
 2UK  CBB  OAB  double    1.225  0.020  1.225
 2UK  PB   O3A  single    1.693  0.020  1.693
 2UK  PB   O1B  deloc     1.501  0.020  1.501
 2UK  NAU  CAP  single    1.447  0.020  1.447
 2UK  C1'  O4'  single    1.387  0.020  1.387
 2UK  C1'  N9   single    1.452  0.020  1.452
 2UK  N9   C8   aromatic  1.379  0.020  1.379
 2UK  N9   C4   aromatic  1.351  0.020  1.351
 2UK  CAP  CAO  single    1.520  0.020  1.520
 2UK  C8   N7   aromatic  1.299  0.020  1.299
 2UK  CAO  CAQ  single    1.520  0.020  1.520
 2UK  C4   N3   single    1.358  0.020  1.358
 2UK  C4   C5   aromatic  1.368  0.020  1.368
 2UK  N7   C5   aromatic  1.371  0.020  1.371
 2UK  N3   C2   single    1.370  0.020  1.370
 2UK  C5   C6   single    1.445  0.020  1.445
 2UK  CAQ  N2   single    1.446  0.020  1.446
 2UK  C2   N2   single    1.341  0.020  1.341
 2UK  C2   N1   double    1.305  0.020  1.305
 2UK  C6   N1   single    1.376  0.020  1.376
 2UK  C6   O6   double    1.226  0.020  1.226
 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  N3B  H26  single    0.890  0.020  1.040

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  115.47  3.000
 2UK  NAU  CBB  OAB  122.25  3.000
 2UK  CAN  CBB  OAB  122.26  3.000
 2UK  H2   CAN  H1   106.02  3.000
 2UK  H2   CAN  CAA  109.70  3.000
 2UK  H1   CAN  CAA  110.43  3.000
 2UK  H2   CAN  CBB  107.29  3.000
 2UK  H1   CAN  CBB  110.57  3.000
 2UK  CAA  CAN  CBB  112.57  3.000
 2UK  H5   CAA  H4   108.01  3.000
 2UK  H5   CAA  H3   107.74  3.000
 2UK  H4   CAA  H3   107.81  3.000
 2UK  H5   CAA  CAN  111.41  3.000
 2UK  H4   CAA  CAN  111.38  3.000
 2UK  H3   CAA  CAN  110.34  3.000
 2UK  H6   NAU  CAP  118.05  3.000
 2UK  H6   NAU  CBB  118.85  3.000
 2UK  CAP  NAU  CBB  123.02  3.000
 2UK  H8   CAP  H7   106.87  3.000
 2UK  H8   CAP  CAO  109.94  3.000
 2UK  H7   CAP  CAO  109.83  3.000
 2UK  H8   CAP  NAU  109.63  3.000
 2UK  H7   CAP  NAU  110.29  3.000
 2UK  CAO  CAP  NAU  110.23  3.000
 2UK  H10  CAO  H9   107.28  3.000
 2UK  H10  CAO  CAQ  109.75  3.000
 2UK  H9   CAO  CAQ  109.48  3.000
 2UK  H10  CAO  CAP  109.38  3.000
 2UK  H9   CAO  CAP  109.84  3.000
 2UK  CAQ  CAO  CAP  111.04  3.000
 2UK  H12  CAQ  H11  107.10  3.000
 2UK  H12  CAQ  N2   108.64  3.000
 2UK  H11  CAQ  N2   110.64  3.000
 2UK  H12  CAQ  CAO  110.28  3.000
 2UK  H11  CAQ  CAO  110.07  3.000
 2UK  N2   CAQ  CAO  110.06  3.000
 2UK  H13  N2   C2   118.04  3.000
 2UK  H13  N2   CAQ  116.65  3.000
 2UK  C2   N2   CAQ  123.42  3.000
 2UK  N1   C2   N3   123.69  3.000
 2UK  N1   C2   N2   120.77  3.000
 2UK  N3   C2   N2   115.53  3.000
 2UK  H14  N3   C4   122.21  3.000
 2UK  H14  N3   C2   121.25  3.000
 2UK  C4   N3   C2   116.11  3.000
 2UK  C6   N1   C2   122.99  3.000
 2UK  C5   C6   O6   123.98  3.000
 2UK  O6   C6   N1   120.94  3.000
 2UK  C5   C6   N1   115.08  3.000
 2UK  N7   C5   C4   109.37  3.000
 2UK  N7   C5   C6   131.51  3.000
 2UK  C4   C5   C6   119.12  3.000
 2UK  N9   C4   C5   107.20  3.000
 2UK  C5   C4   N3   123.00  3.000
 2UK  N9   C4   N3   129.80  3.000
 2UK  C8   N7   C5   105.65  3.000
 2UK  H15  C8   N9   122.42  3.000
 2UK  H15  C8   N7   125.47  3.000
 2UK  N9   C8   N7   112.11  3.000
 2UK  C1'  N9   C8   128.12  3.000
 2UK  C8   N9   C4   105.66  3.000
 2UK  C1'  N9   C4   126.17  3.000
 2UK  H16  C1'  C2'  109.99  3.000
 2UK  H16  C1'  O4'  110.99  3.000
 2UK  C2'  C1'  O4'  106.84  3.000
 2UK  H16  C1'  N9   106.75  3.000
 2UK  O4'  C1'  N9   109.51  3.000
 2UK  C2'  C1'  N9   112.81  3.000
 2UK  C4'  O4'  C1'  110.68  3.000
 2UK  H17  C2'  C3'  109.28  3.000
 2UK  H17  C2'  O2'  111.66  3.000
 2UK  C3'  C2'  O2'  115.32  3.000
 2UK  H17  C2'  C1'  109.46  3.000
 2UK  C3'  C2'  C1'  101.25  3.000
 2UK  O2'  C2'  C1'  109.31  3.000
 2UK  H18  O2'  C2'  109.33  3.000
 2UK  H19  C3'  C4'  111.82  3.000
 2UK  H19  C3'  O3'  111.92  3.000
 2UK  C4'  C3'  O3'  108.71  3.000
 2UK  H19  C3'  C2'  111.90  3.000
 2UK  C4'  C3'  C2'  101.04  3.000
 2UK  O3'  C3'  C2'  110.92  3.000
 2UK  H20  O3'  C3'  107.95  3.000
 2UK  H21  C4'  C5'  109.02  3.000
 2UK  H21  C4'  C3'  110.68  3.000
 2UK  C5'  C4'  C3'  113.22  3.000
 2UK  H21  C4'  O4'  107.71  3.000
 2UK  C5'  C4'  O4'  110.40  3.000
 2UK  C3'  C4'  O4'  105.65  3.000
 2UK  H23  C5'  H22  106.96  3.000
 2UK  H23  C5'  O5'  111.97  3.000
 2UK  H22  C5'  O5'  111.20  3.000
 2UK  H23  C5'  C4'  110.06  3.000
 2UK  H22  C5'  C4'  108.36  3.000
 2UK  O5'  C5'  C4'  108.25  3.000
 2UK  PA   O5'  C5'  117.77  3.000
 2UK  O3A  PA   O2A  112.90  3.000
 2UK  O3A  PA   O1A  110.74  3.000
 2UK  O2A  PA   O1A  119.15  3.000
 2UK  O3A  PA   O5'   94.02  3.000
 2UK  O1A  PA   O5'  108.16  3.000
 2UK  O2A  PA   O5'  108.79  3.000
 2UK  PB   O3A  PA   124.64  3.000
 2UK  N3B  PB   O2B  112.94  3.000
 2UK  O2B  PB   O1B  120.09  3.000
 2UK  N3B  PB   O1B  110.68  3.000
 2UK  O1B  PB   O3A  107.37  3.000
 2UK  O2B  PB   O3A  105.26  3.000
 2UK  N3B  PB   O3A   97.70  3.000
 2UK  H26  N3B  PG   109.91  3.000
 2UK  H26  N3B  PB   112.08  3.000
 2UK  PG   N3B  PB   121.44  3.000
 2UK  O3G  PG   O2G  113.94  3.000
 2UK  O2G  PG   O1G  114.07  3.000
 2UK  O3G  PG   O1G  113.93  3.000
 2UK  O2G  PG   N3B  101.31  3.000
 2UK  O3G  PG   N3B  106.47  3.000
 2UK  O1G  PG   N3B  105.59  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   180.00   0.0  0
 2UK  CONST_16  N1   C2   N2   CAQ     0.00   0.0  0
 2UK  CONST_17  H13  N2   C2   N3      0.00   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  -155.91  30.0  3
 2UK  Var_02    CAA  CAN  CBB  OAB    37.98  30.0  2
 2UK  Var_03    CAO  CAP  NAU  CBB   171.34  30.0  3
 2UK  Var_04    CAQ  CAO  CAP  NAU   179.67  30.0  3
 2UK  Var_05    N2   CAQ  CAO  CAP  -177.23  30.0  3
 2UK  Var_06    O2A  PA   O5'  C5'   -68.22  30.0  2
 2UK  Var_07    N3B  PB   O3A  PA    151.64  30.0  1
 2UK  Var_08    PG   N3B  PB   O3A  -155.71  30.0  2
 2UK  Var_09    O1G  PG   N3B  PB     85.62  30.0  2
 2UK  Var_10    H3   CAA  CAN  CBB  -178.51  30.0  3
 2UK  Var_11    H22  C5'  O5'  PA     90.23  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

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

