# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 14:54:21 2022
#   Inital geometry file: a 141 line input string
#   Ligand name: [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4R,5S,6R)-5-fluoro-3,4-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](O)[C@@H](O)[C@@H]1F
#
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
 UFG  UFG  '[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4R,5S,6R)-5-fluoro-3,4-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)'  ligand  57  36  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UFG
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
 UFG  N1    N  NR6    0  -0.566  15.8216  15.2241  39.7620
 UFG  C2    C  CR6    0   0.730  15.4237  16.5030  40.1019
 UFG  N3    N  NR16   0  -0.735  16.4480  17.3393  40.4626
 UFG  C4    C  CR6    0   0.566  17.8043  17.0553  40.5335
 UFG  C5    C  CR16   0  -0.518  18.1240  15.7013  40.1539
 UFG  C6    C  CR16   0   0.090  17.1401  14.8619  39.7967
 UFG  O2    O  O      0  -0.470  14.2695  16.8736  40.0874
 UFG  O4    O  O      0  -0.455  18.5972  17.9061  40.8884
 UFG  C1D   C  CH1    0   0.188  14.8162  14.2320  39.4105
 UFG  C2D   C  CH1    0  -0.005  14.9206  13.7187  37.9759
 UFG  O2D   O  OH1    0  -0.654  14.3153  14.6323  37.1145
 UFG  C3D   C  CH1    0  -0.065  14.2535  12.3498  38.1098
 UFG  C4D   C  CH1    0  -0.026  14.7341  11.9088  39.5006
 UFG  O4'   O  O2     0  -0.493  14.9766  13.1141  40.2341
 UFG  O3D   O  OH1    0  -0.669  12.8614  12.5533  38.0766
 UFG  C5D   C  CH2    0  -0.176  15.9550  11.0150  39.5194
 UFG  O5D   O  O2     0  -0.634  17.0220  11.6269  38.8265
 UFG  PA    P  P      0   1.380  18.4642  10.8438  38.6556
 UFG  O1A   O  O      0  -0.778  19.4050  11.8621  38.1052
 UFG  O2A   O  OP    -1  -0.784  18.7708  10.0628  39.8919
 UFG  O3A   O  O2     0  -0.743  18.0817   9.7198  37.5144
 UFG  PB    P  P      0   1.346  17.1941   9.8641  36.1422
 UFG  O1B   O  O      0  -0.773  15.7589   9.5370  36.4249
 UFG  O2B   O  OP    -1  -0.773  17.5693  11.1013  35.3948
 UFG  O3B   O  O2     0  -0.622  17.8952   8.5569  35.4007
 UFG  C1'   C  CH1    0   0.251  17.1333   7.5705  34.7845
 UFG  C2'   C  CH1    0   0.007  17.9297   6.2682  34.7640
 UFG  C3'   C  CH1    0  -0.054  19.1603   6.4107  33.8743
 UFG  C4'   C  CH1    0   0.184  18.7183   6.8953  32.5053
 UFG  C5'   C  CH1    0  -0.051  17.8791   8.1653  32.6100
 UFG  C6'   C  CH2    0  -0.188  17.3344   8.6403  31.2803
 UFG  O2'   O  OH1    0  -0.663  18.2586   5.9267  36.0817
 UFG  O3'   O  OH1    0  -0.669  19.7803   5.1463  33.8137
 UFG  O5'   O  O2     0  -0.501  16.7827   7.9289  33.4768
 UFG  O6'   O  OH1    0  -0.667  16.5850   7.6140  30.6778
 UFG  F4'   F  F      0  -0.379  19.8467   7.1755  31.7315
 UFG  HN3   H  HNR6   0   0.423  16.1649  18.2789  40.7136
 UFG  H5    H  HCR6   0   0.287  19.1508  15.3698  40.1661
 UFG  H6    H  HCR6   0   0.335  17.3536  13.8394  39.5186
 UFG  H1D   H  HCH1   0   0.267  13.8447  14.7069  39.5638
 UFG  H2D   H  HCH1   0   0.247  15.9727  13.5551  37.7151
 UFG  HO2'  H  HOH1   0   0.459  14.5358  14.3945  36.2088
 UFG  H3D   H  HCH1   0   0.258  14.5778  11.6452  37.3360
 UFG  H4D   H  HCH1   0   0.252  13.9371  11.3501  40.0058
 UFG  HO3'  H  HOH1   0   0.452  12.4292  11.7002  38.1820
 UFG  H5'1  H  HCH2   0   0.226  16.2294  10.8094  40.5588
 UFG  H5'2  H  HCH2   0   0.219  15.6724  10.0637  39.0586
 UFG  H1'   H  HCH1   0   0.245  16.1852   7.4177  35.3076
 UFG  H2'   H  HCH1   0   0.219  17.2724   5.5092  34.3116
 UFG  H3'   H  HCH1   0   0.231  19.8342   7.1578  34.3158
 UFG  H4'   H  HCH1   0   0.219  18.1594   6.1038  31.9978
 UFG  H5'   H  HCH1   0   0.238  18.5112   8.9745  32.9997
 UFG  H6'1  H  HCH2   0   0.218  16.7294   9.5384  31.4612
 UFG  H6'2  H  HCH2   0   0.211  18.1818   8.9527  30.6590
 UFG  HO2A  H  HOH1   0   0.450  18.7121   5.0777  36.0651
 UFG  HO3A  H  HOH1   0   0.457  20.6983   5.2591  33.5506
 UFG  HO6'  H  HOH1   0   0.457  16.3179   7.9085  29.8028

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
 UFG  N1   C2    single  1.382  0.020  1.382
 UFG  N1   C6    single  1.368  0.020  1.368
 UFG  N1   C1D   single  1.456  0.020  1.456
 UFG  C2   N3    single  1.371  0.020  1.371
 UFG  C2   O2    double  1.212  0.020  1.212
 UFG  N3   C4    single  1.387  0.020  1.387
 UFG  N3   HN3   single  0.860  0.020  1.020
 UFG  C4   C5    single  1.442  0.020  1.442
 UFG  C4   O4    double  1.216  0.020  1.216
 UFG  C5   C6    double  1.342  0.020  1.342
 UFG  C5   H5    single  0.930  0.020  1.080
 UFG  C6   H6    single  0.930  0.020  1.080
 UFG  C1D  C2D   single  1.527  0.020  1.527
 UFG  C1D  O4'   single  1.398  0.020  1.398
 UFG  C1D  H1D   single  0.970  0.020  1.090
 UFG  C2D  O2D   single  1.394  0.020  1.394
 UFG  C2D  C3D   single  1.529  0.020  1.529
 UFG  C2D  H2D   single  0.970  0.020  1.090
 UFG  O2D  HO2'  single  0.850  0.020  0.980
 UFG  C3D  C4D   single  1.536  0.020  1.536
 UFG  C3D  O3D   single  1.407  0.020  1.407
 UFG  C3D  H3D   single  0.970  0.020  1.090
 UFG  C4D  O4'   single  1.432  0.020  1.432
 UFG  C4D  C5D   single  1.513  0.020  1.513
 UFG  C4D  H4D   single  0.970  0.020  1.090
 UFG  O3D  HO3'  single  0.850  0.020  0.980
 UFG  C5D  O5D   single  1.412  0.020  1.412
 UFG  C5D  H5'1  single  0.970  0.020  1.090
 UFG  C5D  H5'2  single  0.970  0.020  1.090
 UFG  O5D  PA    single  1.650  0.020  1.650
 UFG  PA   O1A   deloc   1.492  0.020  1.492
 UFG  PA   O2A   deloc   1.494  0.020  1.494
 UFG  PA   O3A   single  1.647  0.020  1.647
 UFG  O3A  PB    single  1.641  0.020  1.641
 UFG  PB   O1B   deloc   1.499  0.020  1.499
 UFG  PB   O2B   deloc   1.493  0.020  1.493
 UFG  PB   O3B   single  1.658  0.020  1.658
 UFG  O3B  C1'   single  1.390  0.020  1.390
 UFG  C1'  C2'   single  1.527  0.020  1.527
 UFG  C1'  O5'   single  1.400  0.020  1.400
 UFG  C1'  H1'   single  0.970  0.020  1.090
 UFG  C2'  C3'   single  1.525  0.020  1.525
 UFG  C2'  O2'   single  1.400  0.020  1.400
 UFG  C2'  H2'   single  0.970  0.020  1.090
 UFG  C3'  C4'   single  1.518  0.020  1.518
 UFG  C3'  O3'   single  1.410  0.020  1.410
 UFG  C3'  H3'   single  0.970  0.020  1.090
 UFG  C4'  C5'   single  1.526  0.020  1.526
 UFG  C4'  F4'   single  1.397  0.020  1.397
 UFG  C4'  H4'   single  0.970  0.020  1.090
 UFG  C5'  C6'   single  1.513  0.020  1.513
 UFG  C5'  O5'   single  1.417  0.020  1.417
 UFG  C5'  H5'   single  0.970  0.020  1.090
 UFG  C6'  O6'   single  1.406  0.020  1.406
 UFG  C6'  H6'1  single  0.970  0.020  1.090
 UFG  C6'  H6'2  single  0.970  0.020  1.090
 UFG  O2'  HO2A  single  0.850  0.020  0.980
 UFG  O3'  HO3A  single  0.850  0.020  0.980
 UFG  O6'  HO6'  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
 UFG  C1D   N1   C6    119.44  3.000
 UFG  C1D   N1   C2    119.43  3.000
 UFG  C6    N1   C2    121.09  3.000
 UFG  O2    C2   N3    121.88  3.000
 UFG  O2    C2   N1    123.65  3.000
 UFG  N3    C2   N1    114.47  3.000
 UFG  HN3   N3   C4    116.77  3.000
 UFG  HN3   N3   C2    114.98  3.000
 UFG  C4    N3   C2    128.25  3.000
 UFG  O4    C4   C5    126.10  3.000
 UFG  O4    C4   N3    120.60  3.000
 UFG  C5    C4   N3    113.30  3.000
 UFG  H5    C5   C6    120.57  3.000
 UFG  H5    C5   C4    119.77  3.000
 UFG  C6    C5   C4    119.66  3.000
 UFG  H6    C6   C5    121.03  3.000
 UFG  H6    C6   N1    115.74  3.000
 UFG  C5    C6   N1    123.23  3.000
 UFG  H1D   C1D  O4'   111.54  3.000
 UFG  H1D   C1D  C2D   109.81  3.000
 UFG  O4'   C1D  C2D   106.07  3.000
 UFG  H1D   C1D  N1    106.51  3.000
 UFG  O4'   C1D  N1    108.88  3.000
 UFG  C2D   C1D  N1    114.12  3.000
 UFG  H2D   C2D  C3D   107.82  3.000
 UFG  H2D   C2D  O2D   111.57  3.000
 UFG  C3D   C2D  O2D   116.84  3.000
 UFG  H2D   C2D  C1D   109.83  3.000
 UFG  C3D   C2D  C1D   100.89  3.000
 UFG  O2D   C2D  C1D   109.30  3.000
 UFG  HO2'  O2D  C2D   108.67  3.000
 UFG  H3D   C3D  O3D   111.66  3.000
 UFG  H3D   C3D  C4D   111.24  3.000
 UFG  O3D   C3D  C4D   111.86  3.000
 UFG  H3D   C3D  C2D   112.64  3.000
 UFG  O3D   C3D  C2D   107.47  3.000
 UFG  C4D   C3D  C2D   101.53  3.000
 UFG  H4D   C4D  C5D   106.24  3.000
 UFG  H4D   C4D  O4'   108.42  3.000
 UFG  C5D   C4D  O4'   110.75  3.000
 UFG  H4D   C4D  C3D   109.63  3.000
 UFG  C5D   C4D  C3D   115.67  3.000
 UFG  O4'   C4D  C3D   105.97  3.000
 UFG  C4D   O4'  C1D   110.61  3.000
 UFG  HO3'  O3D  C3D   108.27  3.000
 UFG  H5'2  C5D  H5'1  107.54  3.000
 UFG  H5'2  C5D  O5D   111.43  3.000
 UFG  H5'1  C5D  O5D   110.98  3.000
 UFG  H5'2  C5D  C4D   107.45  3.000
 UFG  H5'1  C5D  C4D   108.97  3.000
 UFG  O5D   C5D  C4D   110.34  3.000
 UFG  PA    O5D  C5D   120.38  3.000
 UFG  O3A   PA   O2A   105.32  3.000
 UFG  O3A   PA   O1A   110.90  3.000
 UFG  O2A   PA   O1A   122.19  3.000
 UFG  O3A   PA   O5D   101.11  3.000
 UFG  O2A   PA   O5D   109.98  3.000
 UFG  O1A   PA   O5D   105.40  3.000
 UFG  PB    O3A  PA    130.18  3.000
 UFG  O3B   PB   O2B   108.85  3.000
 UFG  O3B   PB   O1B   108.49  3.000
 UFG  O2B   PB   O1B   121.05  3.000
 UFG  O3B   PB   O3A    94.35  3.000
 UFG  O2B   PB   O3A   110.83  3.000
 UFG  O1B   PB   O3A   109.94  3.000
 UFG  C1'   O3B  PB    121.72  3.000
 UFG  H1'   C1'  O5'   105.39  3.000
 UFG  H1'   C1'  C2'   109.85  3.000
 UFG  O5'   C1'  C2'   109.65  3.000
 UFG  H1'   C1'  O3B   111.23  3.000
 UFG  O5'   C1'  O3B   111.68  3.000
 UFG  C2'   C1'  O3B   108.98  3.000
 UFG  H2'   C2'  O2'   111.01  3.000
 UFG  H2'   C2'  C3'   107.84  3.000
 UFG  O2'   C2'  C3'   112.47  3.000
 UFG  H2'   C2'  C1'   106.38  3.000
 UFG  O2'   C2'  C1'   108.54  3.000
 UFG  C3'   C2'  C1'   110.43  3.000
 UFG  H3'   C3'  O3'   110.95  3.000
 UFG  H3'   C3'  C4'   108.90  3.000
 UFG  O3'   C3'  C4'   112.06  3.000
 UFG  H3'   C3'  C2'   108.90  3.000
 UFG  O3'   C3'  C2'   107.23  3.000
 UFG  C4'   C3'  C2'   108.72  3.000
 UFG  H4'   C4'  F4'   107.51  3.000
 UFG  H4'   C4'  C5'   110.68  3.000
 UFG  F4'   C4'  C5'   108.38  3.000
 UFG  H4'   C4'  C3'   109.65  3.000
 UFG  F4'   C4'  C3'   109.17  3.000
 UFG  C5'   C4'  C3'   111.34  3.000
 UFG  H5'   C5'  O5'   110.55  3.000
 UFG  H5'   C5'  C6'   106.71  3.000
 UFG  O5'   C5'  C6'   108.13  3.000
 UFG  H5'   C5'  C4'   108.73  3.000
 UFG  O5'   C5'  C4'   109.18  3.000
 UFG  C6'   C5'  C4'   113.51  3.000
 UFG  H6'2  C6'  H6'1  106.64  3.000
 UFG  H6'2  C6'  O6'   112.15  3.000
 UFG  H6'1  C6'  O6'   111.95  3.000
 UFG  H6'2  C6'  C5'   108.01  3.000
 UFG  H6'1  C6'  C5'   108.08  3.000
 UFG  O6'   C6'  C5'   109.82  3.000
 UFG  HO2A  O2'  C2'   108.03  3.000
 UFG  HO3A  O3'  C3'   109.05  3.000
 UFG  C5'   O5'  C1'   114.84  3.000
 UFG  HO6'  O6'  C6'   108.33  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
 UFG  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 UFG  CONST_02  C5    C4   N3   C2      0.00   0.0  0
 UFG  CONST_03  C6    N1   C2   N3      0.00   0.0  0
 UFG  CONST_04  C1D   N1   C2   N3    180.00   0.0  0
 UFG  CONST_05  O4    C4   N3   C2    180.00   0.0  0
 UFG  CONST_06  O2    C2   N3   C4    180.00   0.0  0
 UFG  CONST_07  O2    C2   N1   C6    180.00   0.0  0
 UFG  CONST_08  C1D   N1   C2   O2      0.00   0.0  0
 UFG  CONST_09  HN3   N3   C2   N1    180.00   0.0  0
 UFG  Var_01    O1A   PA   O5D  C5D  -170.13  30.0  3
 UFG  Var_02    O1B   PB   O3A  PA    -91.64  30.0  3
 UFG  Var_03    H5'1  C5D  O5D  PA     60.96  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
 UFG  chir_01  C1D  N1   C2D  O4'  negativ
 UFG  chir_02  C2D  O2D  C3D  C1D  positiv
 UFG  chir_03  C3D  O3D  C2D  C4D  negativ
 UFG  chir_04  C4D  O4'  C3D  C5D  negativ
 UFG  chir_07  C1'  O3B  C2'  O5'  positiv
 UFG  chir_08  C2'  O2'  C1'  C3'  negativ
 UFG  chir_09  C3'  O3'  C2'  C4'  positiv
 UFG  chir_10  C4'  F4'  C3'  C5'  negativ
 UFG  chir_11  C5'  O5'  C4'  C6'  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
 UFG  plan-1  N1   0.020
 UFG  plan-1  C2   0.020
 UFG  plan-1  N3   0.020
 UFG  plan-1  C4   0.020
 UFG  plan-1  C5   0.020
 UFG  plan-1  C6   0.020
 UFG  plan-1  O2   0.020
 UFG  plan-1  O4   0.020
 UFG  plan-1  C1D  0.020
 UFG  plan-1  HN3  0.020
 UFG  plan-1  H5   0.020
 UFG  plan-1  H6   0.020

