# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri May 29 04:16:10 2020
#   Inital geometry file: a 139 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,5S,6R)-3,3,4,4-tetrafluoro-5-hydroxy-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(F)(F)C(F)(F)[C@H]1O
#
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
 3UC  3UC  '[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,5S,6R)-3,3,4,4-tetrafluoro-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)'  ligand  56  38  .  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_3UC
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
 3UC  F2''  F  F      0  -0.333  -5.1199   1.1807  -1.9807
 3UC  C2'   C  CT     0   0.674  -3.8863   0.9237  -1.4825
 3UC  F2'   F  F      0  -0.331  -3.1451   0.4347  -2.5010
 3UC  C3'   C  CT     0   0.665  -3.2866   2.2426  -0.9816
 3UC  F3''  F  F      0  -0.339  -3.3924   3.1840  -1.9538
 3UC  F3'   F  F      0  -0.328  -1.9620   2.0547  -0.7651
 3UC  C4'   C  CH1    0  -0.118  -3.9460   2.7323   0.3105
 3UC  O4'   O  OH1    0  -0.655  -5.2410   3.1928   0.0656
 3UC  C5'   C  CH1    0  -0.039  -4.0069   1.5720   1.3016
 3UC  C6'   C  CH2    0  -0.156  -4.7512   1.9588   2.5627
 3UC  O6'   O  OH1    0  -0.665  -4.5524   0.9493   3.5219
 3UC  O5'   O  O2     0  -0.490  -4.6687   0.4575   0.7207
 3UC  C1'   C  CH1    0   0.158  -4.0178  -0.1206  -0.3639
 3UC  O3B   O  O2     0  -0.620  -2.7533  -0.5747  -0.0549
 3UC  PB    P  P      0   1.343  -2.4940  -2.2060   0.1751
 3UC  O1B   O  O      0  -0.778  -2.8796  -2.5858   1.5646
 3UC  O2B   O  OP    -1  -0.781  -3.0545  -2.9334  -1.0048
 3UC  O3A   O  O2     0  -0.730  -0.8750  -2.0689   0.0289
 3UC  PA    P  P      0   1.346   0.2178  -2.8711   0.9654
 3UC  O1A   O  OP    -1  -0.794   0.3964  -2.1862   2.2819
 3UC  O2A   O  O      0  -0.793  -0.0461  -4.3413   0.8908
 3UC  O5D   O  O2     0  -0.621   1.4797  -2.4869  -0.0214
 3UC  C5D   C  CH2    0  -0.151   2.7781  -2.4595   0.5291
 3UC  C4D   C  CH1    0   0.011   3.7654  -2.0876  -0.5486
 3UC  C3D   C  CH1    0  -0.032   5.2087  -2.0935  -0.0479
 3UC  O3D   O  OH1    0  -0.663   5.7766  -3.3647  -0.2384
 3UC  C2D   C  CH1    0  -0.048   5.8787  -1.0099  -0.9148
 3UC  O2D   O  OH1    0  -0.674   6.4283  -1.5781  -2.0747
 3UC  O4D   O  O2     0  -0.488   3.5148  -0.7638  -0.9906
 3UC  C1D   C  CH1    0   0.204   4.7009  -0.1205  -1.3510
 3UC  N1    N  NT     0  -0.568   4.6873   1.2409  -0.8281
 3UC  C6    C  C1     0   0.103   4.5927   2.2907  -1.6981
 3UC  C5    C  C1     0  -0.513   4.5220   3.5734  -1.3099
 3UC  C4    C  C      0   0.568   4.5301   3.8911   0.0961
 3UC  O4    O  O      0  -0.463   4.4700   5.0055   0.5808
 3UC  N3    N  NH1    0  -0.734   4.6138   2.7712   0.9103
 3UC  C2    C  C      0   0.748   4.6906   1.4563   0.5354
 3UC  O2    O  O      0  -0.468   4.7626   0.5586   1.3465
 3UC  H1    H  HCH1   0   0.277  -3.2989   3.5139   0.7318
 3UC  H2    H  HOH1   0   0.466  -5.1988   4.0465  -0.3768
 3UC  H3    H  HCH1   0   0.258  -2.9810   1.3084   1.5836
 3UC  H4    H  HCH2   0   0.206  -4.3571   2.9257   2.9027
 3UC  H5    H  HCH2   0   0.212  -5.8136   2.1048   2.3394
 3UC  H6    H  HOH1   0   0.457  -5.0748   1.1735   4.2970
 3UC  H7    H  HCH1   0   0.269  -4.6764  -0.9208  -0.7243
 3UC  H10   H  HCH2   0   0.215   2.8484  -1.7352   1.3471
 3UC  H11   H  HCH2   0   0.213   3.0701  -3.4395   0.9269
 3UC  H12   H  HCH1   0   0.236   3.6771  -2.7873  -1.3921
 3UC  H13   H  HCH1   0   0.259   5.2486  -1.7995   1.0022
 3UC  H14   H  HOH1   0   0.470   6.4662  -3.4982   0.4190
 3UC  H15   H  HCH1   0   0.250   6.6360  -0.4461  -0.3590
 3UC  H16   H  HOH1   0   0.449   6.6592  -2.4918  -1.8570
 3UC  H17   H  HCH1   0   0.261   4.7610   0.0027  -2.4362
 3UC  H18   H  H      0   0.329   4.5823   2.0249  -2.7455
 3UC  H19   H  H      0   0.295   4.4540   4.3649  -2.0394
 3UC  H20   H  HNH1   0   0.427   4.6213   2.9320   1.9103

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
 3UC  O6'   C6'  single  1.407  0.020  1.407
 3UC  C6'   C5'  single  1.515  0.020  1.515
 3UC  O4    C4   double  1.217  0.020  1.217
 3UC  C4'   O4'  single  1.396  0.020  1.396
 3UC  C4'   C5'  single  1.527  0.020  1.527
 3UC  C4'   C3'  single  1.531  0.020  1.531
 3UC  C5'   O5'  single  1.420  0.020  1.420
 3UC  F3''  C3'  single  1.357  0.020  1.357
 3UC  C3'   F3'  single  1.355  0.020  1.355
 3UC  C3'   C2'  single  1.533  0.020  1.533
 3UC  C4    C5   single  1.441  0.020  1.441
 3UC  C4    N3   single  1.387  0.020  1.387
 3UC  C5    C6   double  1.342  0.020  1.342
 3UC  O5'   C1'  single  1.391  0.020  1.391
 3UC  O2A   PA   deloc   1.496  0.020  1.496
 3UC  N3    C2   single  1.370  0.020  1.370
 3UC  F2''  C2'  single  1.355  0.020  1.355
 3UC  C2'   C1'  single  1.536  0.020  1.536
 3UC  C2'   F2'  single  1.351  0.020  1.351
 3UC  C6    N1   single  1.367  0.020  1.367
 3UC  C1'   O3B  single  1.379  0.020  1.379
 3UC  C2    N1   single  1.380  0.020  1.380
 3UC  C2    O2   double  1.212  0.020  1.212
 3UC  O3B   PB   single  1.668  0.020  1.668
 3UC  PA    O1A  deloc   1.495  0.020  1.495
 3UC  PA    O5D  single  1.647  0.020  1.647
 3UC  PA    O3A  single  1.648  0.020  1.648
 3UC  N1    C1D  single  1.458  0.020  1.458
 3UC  O5D   C5D  single  1.411  0.020  1.411
 3UC  O3A   PB   single  1.631  0.020  1.631
 3UC  O4D   C1D  single  1.397  0.020  1.397
 3UC  O4D   C4D  single  1.418  0.020  1.418
 3UC  PB    O1B  deloc   1.491  0.020  1.491
 3UC  PB    O2B  deloc   1.495  0.020  1.495
 3UC  C1D   C2D  single  1.539  0.020  1.539
 3UC  C5D   C4D  single  1.508  0.020  1.508
 3UC  C4D   C3D  single  1.528  0.020  1.528
 3UC  C2D   C3D  single  1.541  0.020  1.541
 3UC  C2D   O2D  single  1.404  0.020  1.404
 3UC  C3D   O3D  single  1.405  0.020  1.405
 3UC  C4'   H1   single  0.970  0.020  1.090
 3UC  O4'   H2   single  0.850  0.020  0.980
 3UC  C5'   H3   single  0.970  0.020  1.090
 3UC  C6'   H4   single  0.970  0.020  1.090
 3UC  C6'   H5   single  0.970  0.020  1.090
 3UC  O6'   H6   single  0.850  0.020  0.980
 3UC  C1'   H7   single  0.970  0.020  1.090
 3UC  C5D   H10  single  0.970  0.020  1.090
 3UC  C5D   H11  single  0.970  0.020  1.090
 3UC  C4D   H12  single  0.970  0.020  1.090
 3UC  C3D   H13  single  0.970  0.020  1.090
 3UC  O3D   H14  single  0.850  0.020  0.980
 3UC  C2D   H15  single  0.970  0.020  1.090
 3UC  O2D   H16  single  0.850  0.020  0.980
 3UC  C1D   H17  single  0.970  0.020  1.090
 3UC  C6    H18  single  0.930  0.020  1.080
 3UC  C5    H19  single  0.930  0.020  1.080
 3UC  N3    H20  single  0.860  0.020  1.020

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
 3UC  C1'   C2'  C3'   112.36  3.000
 3UC  C1'   C2'  F2'   110.48  3.000
 3UC  C3'   C2'  F2'   110.06  3.000
 3UC  F2'   C2'  F2''  106.91  3.000
 3UC  C1'   C2'  F2''  108.59  3.000
 3UC  C3'   C2'  F2''  108.25  3.000
 3UC  C4'   C3'  F3'   109.29  3.000
 3UC  F3'   C3'  F3''  106.66  3.000
 3UC  C4'   C3'  F3''  110.43  3.000
 3UC  F3'   C3'  C2'   108.38  3.000
 3UC  F3''  C3'  C2'   109.40  3.000
 3UC  C4'   C3'  C2'   112.48  3.000
 3UC  H1    C4'  C5'   108.37  3.000
 3UC  H1    C4'  O4'   112.26  3.000
 3UC  C5'   C4'  O4'   109.12  3.000
 3UC  H1    C4'  C3'   107.30  3.000
 3UC  C5'   C4'  C3'   108.78  3.000
 3UC  O4'   C4'  C3'   110.91  3.000
 3UC  H2    O4'  C4'   109.42  3.000
 3UC  H3    C5'  O5'   110.64  3.000
 3UC  H3    C5'  C6'   107.89  3.000
 3UC  O5'   C5'  C6'   108.17  3.000
 3UC  H3    C5'  C4'   108.20  3.000
 3UC  O5'   C5'  C4'   110.44  3.000
 3UC  C6'   C5'  C4'   111.47  3.000
 3UC  H5    C6'  H4    107.09  3.000
 3UC  H5    C6'  O6'   111.82  3.000
 3UC  H4    C6'  O6'   111.72  3.000
 3UC  H5    C6'  C5'   109.94  3.000
 3UC  H4    C6'  C5'   107.83  3.000
 3UC  O6'   C6'  C5'   108.36  3.000
 3UC  H6    O6'  C6'   107.80  3.000
 3UC  C1'   O5'  C5'   115.28  3.000
 3UC  H7    C1'  O3B   112.58  3.000
 3UC  H7    C1'  O5'   106.16  3.000
 3UC  O3B   C1'  O5'   113.04  3.000
 3UC  H7    C1'  C2'   107.94  3.000
 3UC  O3B   C1'  C2'   107.97  3.000
 3UC  O5'   C1'  C2'   108.99  3.000
 3UC  PB    O3B  C1'   119.71  3.000
 3UC  O3A   PB   O2B   110.01  3.000
 3UC  O2B   PB   O1B   120.96  3.000
 3UC  O3A   PB   O1B   111.20  3.000
 3UC  O2B   PB   O3B   107.98  3.000
 3UC  O1B   PB   O3B   109.72  3.000
 3UC  O3A   PB   O3B    93.42  3.000
 3UC  PA    O3A  PB    124.50  3.000
 3UC  O5D   PA   O2A   109.54  3.000
 3UC  O5D   PA   O1A   109.22  3.000
 3UC  O2A   PA   O1A   121.03  3.000
 3UC  O5D   PA   O3A    93.10  3.000
 3UC  O1A   PA   O3A   110.90  3.000
 3UC  O2A   PA   O3A   109.46  3.000
 3UC  C5D   O5D  PA    118.42  3.000
 3UC  H11   C5D  H10   107.63  3.000
 3UC  H11   C5D  C4D   107.77  3.000
 3UC  H10   C5D  C4D   109.20  3.000
 3UC  H11   C5D  O5D   111.66  3.000
 3UC  H10   C5D  O5D   111.31  3.000
 3UC  C4D   C5D  O5D   109.18  3.000
 3UC  H12   C4D  O4D   109.93  3.000
 3UC  H12   C4D  C3D   108.96  3.000
 3UC  O4D   C4D  C3D   105.83  3.000
 3UC  H12   C4D  C5D   109.80  3.000
 3UC  C3D   C4D  C5D   112.54  3.000
 3UC  O4D   C4D  C5D   109.71  3.000
 3UC  H13   C3D  C2D   109.64  3.000
 3UC  H13   C3D  O3D   111.06  3.000
 3UC  C2D   C3D  O3D   112.59  3.000
 3UC  H13   C3D  C4D   110.42  3.000
 3UC  O3D   C3D  C4D   109.93  3.000
 3UC  C2D   C3D  C4D   102.93  3.000
 3UC  H14   O3D  C3D   108.82  3.000
 3UC  H15   C2D  C1D   112.05  3.000
 3UC  H15   C2D  O2D   110.91  3.000
 3UC  C1D   C2D  O2D   107.42  3.000
 3UC  H15   C2D  C3D   112.15  3.000
 3UC  O2D   C2D  C3D   110.52  3.000
 3UC  C1D   C2D  C3D   103.48  3.000
 3UC  H16   O2D  C2D   106.85  3.000
 3UC  C1D   O4D  C4D   111.13  3.000
 3UC  H17   C1D  N1    104.54  3.000
 3UC  H17   C1D  O4D   110.77  3.000
 3UC  N1    C1D  O4D   109.24  3.000
 3UC  H17   C1D  C2D   107.71  3.000
 3UC  O4D   C1D  C2D   108.09  3.000
 3UC  N1    C1D  C2D   116.42  3.000
 3UC  C2    N1   C6    120.60  3.000
 3UC  C2    N1   C1D   119.99  3.000
 3UC  C6    N1   C1D   119.30  3.000
 3UC  H18   C6   C5    120.99  3.000
 3UC  H18   C6   N1    115.38  3.000
 3UC  C5    C6   N1    123.62  3.000
 3UC  H19   C5   C4    119.89  3.000
 3UC  H19   C5   C6    120.60  3.000
 3UC  C4    C5   C6    119.50  3.000
 3UC  N3    C4   O4    120.57  3.000
 3UC  N3    C4   C5    113.26  3.000
 3UC  O4    C4   C5    126.17  3.000
 3UC  H20   N3   C2    114.98  3.000
 3UC  H20   N3   C4    116.86  3.000
 3UC  C2    N3   C4    128.16  3.000
 3UC  O2    C2   N3    122.09  3.000
 3UC  O2    C2   N1    123.07  3.000
 3UC  N3    C2   N1    114.84  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
 3UC  CONST_01  N3   C2   N1   C1D  180.00   0.0  0
 3UC  CONST_02  C4   N3   C2   N1     0.00   0.0  0
 3UC  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 3UC  CONST_04  C2   N3   C4   C5     0.00   0.0  0
 3UC  CONST_05  O2   C2   N1   C1D    0.00   0.0  0
 3UC  CONST_06  O2   C2   N1   C6   180.00   0.0  0
 3UC  CONST_07  O2   C2   N3   C4   180.00   0.0  0
 3UC  CONST_08  C2   N3   C4   O4   180.00   0.0  0
 3UC  CONST_09  H20  N3   C2   N1   180.00   0.0  0
 3UC  Var_01    C1'  C2'  C3'  C4'  -47.29  30.0  1
 3UC  Var_02    O3A  PB   O3B  C1'  163.89  30.0  3
 3UC  Var_03    C4D  C5D  O5D  PA   179.98  30.0  3
 3UC  Var_04    O2A  PA   O3A  PB    55.33  30.0  2

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
 3UC  chir_01  C4'  O4'  C5'  C3'  negativ
 3UC  chir_02  C5'  O5'  C4'  C6'  negativ
 3UC  chir_03  C1'  O5'  O3B  C2'  positiv
 3UC  chir_06  C4D  O4D  C5D  C3D  positiv
 3UC  chir_07  C3D  O3D  C4D  C2D  positiv
 3UC  chir_08  C2D  O2D  C3D  C1D  positiv
 3UC  chir_09  C1D  O4D  N1   C2D  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
 3UC  plan-1  C1D  0.020
 3UC  plan-1  N1   0.020
 3UC  plan-1  C6   0.020
 3UC  plan-1  C5   0.020
 3UC  plan-1  C4   0.020
 3UC  plan-1  O4   0.020
 3UC  plan-1  N3   0.020
 3UC  plan-1  C2   0.020
 3UC  plan-1  O2   0.020
 3UC  plan-1  H18  0.020
 3UC  plan-1  H19  0.020
 3UC  plan-1  H20  0.020

