# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jul  2 03:37:33 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 5'-O-[(R)-hydroxy{[(S)-hydroxy{[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]uridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[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
 U5F  U5F  5'-O-[(R)-hydroxy{[(S)-hydroxy{[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphoryl]uridine  ligand  48  37  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_U5F
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
 U5F  C1'  C  CH1    0   0.217   5.3134   1.4034  -1.0201
 U5F  C2   C  CR6    0   0.711   6.8905   2.6250   0.3670
 U5F  C4   C  CR6    0   0.554   7.3029   2.0142   2.7294
 U5F  C4'  C  CH1    0  -0.000   4.3501  -0.6542  -1.5425
 U5F  C5   C  CR16   0  -0.483   6.3266   0.9689   2.5604
 U5F  C5'  C  CH2    0  -0.161   3.7941  -1.7841  -0.7123
 U5F  C6   C  CR16   0   0.047   5.7164   0.8095   1.3730
 U5F  N1   N  NR6    0  -0.557   5.9801   1.5916   0.2896
 U5F  N3   N  NR16   0  -0.635   7.4933   2.7763   1.5859
 U5F  O01  O  OP    -1  -0.926  -3.3395   0.2911   2.9144
 U5F  O02  O  O      0  -0.844  -7.5386   0.2616  -2.2381
 U5F  O03  O  O      0  -0.932  -4.1581  -1.9642   1.9048
 U5F  O04  O  O      0  -0.866  -1.1227  -3.4986   1.7712
 U5F  O05  O  OP    -1  -0.728  -1.9783  -2.6717  -0.5462
 U5F  O06  O  O2     0  -0.652  -5.2434   0.9100  -1.3141
 U5F  O1A  O  O      0  -0.875   1.4691  -3.9500  -0.2975
 U5F  O1B  O  OP    -1  -0.800  -4.3176   2.5564   0.4201
 U5F  O1G  O  OP    -1  -1.021  -5.9874   1.8317  -3.5336
 U5F  O2A  O  OP    -1  -0.847   2.2203  -2.6302   1.8117
 U5F  O2B  O  O      0  -0.780  -6.0923   0.7957   1.1292
 U5F  O2G  O  O2     0  -0.644  -3.7460   0.0680   0.3845
 U5F  O3A  O  O2     0  -0.617   0.2277  -1.7973   0.4030
 U5F  O3B  O  O2     0  -0.760  -1.8078  -1.0411   1.4419
 U5F  O3G  O  OP    -1  -0.976  -7.1411   2.6543  -1.3924
 U5F  O4'  O  O2     0  -0.486   4.1936   0.5932  -0.8619
 U5F  O5'  O  O2     0  -0.624   2.4183  -1.5741  -0.5163
 U5F  P01  P  P      0   1.339  -3.3863  -0.6877   1.7820
 U5F  P02  P  P      0   1.379  -1.2676  -2.4217   0.7439
 U5F  PA   P  P      0   1.353   1.6148  -2.6577   0.4433
 U5F  PB   P  P      0   1.376  -4.9584   1.2101   0.2392
 U5F  PG   P  P      0   1.153  -6.6169   1.4719  -2.1937
 U5F  C2'  C  CH1    0  -0.015   6.2327   0.7032  -2.0213
 U5F  C3'  C  CH1    0  -0.018   5.8483  -0.7637  -1.7986
 U5F  O2'  O  OH1    0  -0.665   5.8642   1.1294  -3.3036
 U5F  O3'  O  OH1    0  -0.608   6.0990  -1.5875  -2.9012
 U5F  H1   H  HCH1   0   0.277   5.0170   2.3938  -1.3698
 U5F  H2   H  HCH1   0   0.224   3.8116  -0.6098  -2.4970
 U5F  H3   H  HCR6   0   0.304   6.0817   0.3245   3.3904
 U5F  H4   H  HCH2   0   0.222   3.9904  -2.7199  -1.2512
 U5F  H5   H  HCH2   0   0.237   4.3325  -1.8460   0.2415
 U5F  H6   H  HCR6   0   0.322   4.9650   0.0471   1.2409
 U5F  H7   H  HNR6   0   0.441   8.1662   3.5311   1.6448
 U5F  H14  H  HCH1   0   0.221   7.2930   0.8895  -1.8180
 U5F  H15  H  HCH1   0   0.229   6.3534  -1.1341  -0.8957
 U5F  H16  H  HOH1   0   0.459   6.0517   0.4085  -3.9175
 U5F  H17  H  HOH1   0   0.457   7.0173  -1.8767  -2.8704
 U5F  O2   O  O      0  -0.533   7.1383   3.3456  -0.5788
 U5F  O4   O  O      0  -0.468   7.9271   2.2580   3.7459

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
 U5F  O2   C2   double  1.215  0.020  1.215
 U5F  C2   N3   single  1.368  0.020  1.368
 U5F  C2   N1   single  1.379  0.020  1.379
 U5F  N3   C4   single  1.387  0.020  1.387
 U5F  C1'  O4'  single  1.391  0.020  1.391
 U5F  C1'  N1   single  1.482  0.020  1.482
 U5F  C1'  C2'  single  1.529  0.020  1.529
 U5F  O4'  C4'  single  1.430  0.020  1.430
 U5F  N1   C6   single  1.362  0.020  1.362
 U5F  C4   O4   double  1.217  0.020  1.217
 U5F  C4   C5   single  1.440  0.020  1.440
 U5F  C4'  C3'  single  1.524  0.020  1.524
 U5F  C4'  C5'  single  1.508  0.020  1.508
 U5F  O3'  C3'  single  1.399  0.020  1.399
 U5F  C6   C5   double  1.345  0.020  1.345
 U5F  O04  P02  deloc   1.495  0.020  1.495
 U5F  C2'  O2'  single  1.401  0.020  1.401
 U5F  C2'  C3'  single  1.533  0.020  1.533
 U5F  C5'  O5'  single  1.406  0.020  1.406
 U5F  O05  P02  deloc   1.494  0.020  1.494
 U5F  O3A  P02  single  1.656  0.020  1.656
 U5F  O3A  PA   single  1.633  0.020  1.633
 U5F  O02  PG   deloc   1.522  0.020  1.522
 U5F  P02  O3B  single  1.639  0.020  1.639
 U5F  O03  P01  deloc   1.497  0.020  1.497
 U5F  O5'  PA   single  1.655  0.020  1.655
 U5F  O3G  PG   deloc   1.521  0.020  1.521
 U5F  PA   O1A  deloc   1.497  0.020  1.497
 U5F  PA   O2A  deloc   1.497  0.020  1.497
 U5F  PG   O06  single  1.725  0.020  1.725
 U5F  PG   O1G  deloc   1.524  0.020  1.524
 U5F  P01  O3B  single  1.653  0.020  1.653
 U5F  P01  O01  deloc   1.498  0.020  1.498
 U5F  P01  O2G  single  1.629  0.020  1.629
 U5F  O06  PB   single  1.607  0.020  1.607
 U5F  O2B  PB   deloc   1.500  0.020  1.500
 U5F  PB   O2G  single  1.672  0.020  1.672
 U5F  PB   O1B  deloc   1.502  0.020  1.502
 U5F  C1'  H1   single  0.970  0.020  1.090
 U5F  C4'  H2   single  0.970  0.020  1.090
 U5F  C5   H3   single  0.930  0.020  1.080
 U5F  C5'  H4   single  0.970  0.020  1.090
 U5F  C5'  H5   single  0.970  0.020  1.090
 U5F  C6   H6   single  0.930  0.020  1.080
 U5F  N3   H7   single  0.860  0.020  1.020
 U5F  C2'  H14  single  0.970  0.020  1.090
 U5F  C3'  H15  single  0.970  0.020  1.090
 U5F  O2'  H16  single  0.850  0.020  0.980
 U5F  O3'  H17  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
 U5F  H1   C1'  C2'  111.66  3.000
 U5F  H1   C1'  O4'  110.27  3.000
 U5F  C2'  C1'  O4'  106.96  3.000
 U5F  H1   C1'  N1   106.87  3.000
 U5F  C2'  C1'  N1   111.49  3.000
 U5F  O4'  C1'  N1   109.62  3.000
 U5F  O2   C2   N3   122.56  3.000
 U5F  N3   C2   N1   115.06  3.000
 U5F  O2   C2   N1   122.38  3.000
 U5F  O4   C4   N3   120.52  3.000
 U5F  O4   C4   C5   126.22  3.000
 U5F  N3   C4   C5   113.26  3.000
 U5F  H2   C4'  C3'  109.84  3.000
 U5F  H2   C4'  O4'  108.98  3.000
 U5F  C3'  C4'  O4'  104.50  3.000
 U5F  H2   C4'  C5'  109.17  3.000
 U5F  C3'  C4'  C5'  113.64  3.000
 U5F  O4'  C4'  C5'  110.57  3.000
 U5F  H3   C5   C6   120.37  3.000
 U5F  H3   C5   C4   119.80  3.000
 U5F  C6   C5   C4   119.82  3.000
 U5F  H5   C5'  H4   106.92  3.000
 U5F  H5   C5'  O5'  111.57  3.000
 U5F  H4   C5'  O5'  111.77  3.000
 U5F  H5   C5'  C4'  109.87  3.000
 U5F  H4   C5'  C4'  107.61  3.000
 U5F  O5'  C5'  C4'  109.00  3.000
 U5F  H6   C6   N1   116.32  3.000
 U5F  H6   C6   C5   120.54  3.000
 U5F  N1   C6   C5   123.13  3.000
 U5F  C6   N1   C2   120.89  3.000
 U5F  C6   N1   C1'  122.89  3.000
 U5F  C2   N1   C1'  116.22  3.000
 U5F  H7   N3   C4   116.91  3.000
 U5F  H7   N3   C2   115.27  3.000
 U5F  C4   N3   C2   127.81  3.000
 U5F  PG   O06  PB   124.96  3.000
 U5F  PB   O2G  P01  123.48  3.000
 U5F  PA   O3A  P02  124.29  3.000
 U5F  P02  O3B  P01  125.64  3.000
 U5F  C4'  O4'  C1'  111.47  3.000
 U5F  PA   O5'  C5'  117.27  3.000
 U5F  O3B  P01  O2G   97.67  3.000
 U5F  O2G  P01  O03  110.62  3.000
 U5F  O3B  P01  O03  109.08  3.000
 U5F  O2G  P01  O01  110.63  3.000
 U5F  O3B  P01  O01  105.39  3.000
 U5F  O03  P01  O01  120.77  3.000
 U5F  O3B  P02  O3A   93.88  3.000
 U5F  O3B  P02  O05  110.61  3.000
 U5F  O3A  P02  O05  108.36  3.000
 U5F  O3B  P02  O04  110.25  3.000
 U5F  O3A  P02  O04  109.00  3.000
 U5F  O05  P02  O04  121.25  3.000
 U5F  O5'  PA   O3A   93.05  3.000
 U5F  O5'  PA   O2A  108.76  3.000
 U5F  O3A  PA   O2A  110.89  3.000
 U5F  O2A  PA   O1A  120.52  3.000
 U5F  O5'  PA   O1A  108.99  3.000
 U5F  O3A  PA   O1A  111.10  3.000
 U5F  O2G  PB   O2B  107.93  3.000
 U5F  O2G  PB   O1B  107.01  3.000
 U5F  O2B  PB   O1B  119.92  3.000
 U5F  O1B  PB   O06  111.06  3.000
 U5F  O2G  PB   O06   94.88  3.000
 U5F  O2B  PB   O06  112.81  3.000
 U5F  O3G  PG   O1G  114.96  3.000
 U5F  O1G  PG   O06  101.32  3.000
 U5F  O3G  PG   O06  105.01  3.000
 U5F  O1G  PG   O02  114.35  3.000
 U5F  O06  PG   O02  103.77  3.000
 U5F  O3G  PG   O02  115.14  3.000
 U5F  H14  C2'  O2'  111.89  3.000
 U5F  H14  C2'  C3'  112.24  3.000
 U5F  O2'  C2'  C3'  110.99  3.000
 U5F  H14  C2'  C1'  112.49  3.000
 U5F  C3'  C2'  C1'  101.09  3.000
 U5F  O2'  C2'  C1'  107.57  3.000
 U5F  H15  C3'  O3'  111.51  3.000
 U5F  H15  C3'  C2'  109.07  3.000
 U5F  O3'  C3'  C2'  113.83  3.000
 U5F  H15  C3'  C4'  109.76  3.000
 U5F  C2'  C3'  C4'  101.67  3.000
 U5F  O3'  C3'  C4'  110.55  3.000
 U5F  H16  O2'  C2'  107.69  3.000
 U5F  H17  O3'  C3'  108.81  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
 U5F  CONST_01  N3   C2   N1   C1'  180.00   0.0  0
 U5F  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 U5F  CONST_03  N1   C2   N3   C4     0.00   0.0  0
 U5F  CONST_04  N3   C2   N1   C6     0.00   0.0  0
 U5F  CONST_05  O2   C2   N1   C1'    0.00   0.0  0
 U5F  CONST_06  O4   C4   N3   C2   180.00   0.0  0
 U5F  CONST_07  O2   C2   N3   C4   180.00   0.0  0
 U5F  CONST_08  O2   C2   N1   C6   180.00   0.0  0
 U5F  CONST_09  H7   N3   C4   C5   180.00   0.0  0
 U5F  Var_01    O3A  PA   O5'  C5'  173.88  30.0  3
 U5F  Var_02    H4   C5'  O5'  PA    64.41  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
 U5F  chir_01  C1'  O4'  N1   C2'  negativ
 U5F  chir_02  C4'  O4'  C3'  C5'  negativ
 U5F  chir_07  C2'  C1'  O2'  C3'  positiv
 U5F  chir_08  C3'  O3'  C4'  C2'  positiv

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
 U5F  plan-1  C1'  0.020
 U5F  plan-1  C2   0.020
 U5F  plan-1  C4   0.020
 U5F  plan-1  C5   0.020
 U5F  plan-1  C6   0.020
 U5F  plan-1  N1   0.020
 U5F  plan-1  N3   0.020
 U5F  plan-1  H3   0.020
 U5F  plan-1  H6   0.020
 U5F  plan-1  H7   0.020
 U5F  plan-1  O2   0.020
 U5F  plan-1  O4   0.020

