# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri May 29 22:20:19 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: (2R,5S)-5-[(1R)-1,2-dihydroxyethyl]-3,3,4,4-tetrafluorotetrahydrofuran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[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)C1(F)F
#
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
 3UA  3UA  '(2R,5S)-5-[(1R)-1,2-dihydroxyethyl]-3,3,4,4-tetrafluorotetrahydrofuran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl 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_3UA
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
 3UA  F58  F  F      0  -0.318   1.1844  -3.2201   0.7441
 3UA  C11  C  CT     0   0.612   1.8072  -2.8799  -0.3946
 3UA  F6   F  F      0  -0.329   1.1440  -3.4809  -1.4045
 3UA  C12  C  CT     0   0.727   3.2856  -3.3321  -0.3459
 3UA  F7   F  F      0  -0.318   3.4930  -4.2795   0.5865
 3UA  F57  F  F      0  -0.332   3.6105  -3.8814  -1.5416
 3UA  C1   C  CH1    0   0.217   1.8726  -1.3511  -0.6058
 3UA  O    O  O2     0  -0.499   3.2383  -1.0397  -0.6600
 3UA  C    C  CH1    0  -0.182   4.0845  -2.0492  -0.1290
 3UA  C13  C  CH1    0  -0.008   4.5355  -1.7744   1.3075
 3UA  O15  O  OH1    0  -0.702   3.4755  -1.6303   2.2005
 3UA  C14  C  CH2    0  -0.177   5.4975  -0.5910   1.3139
 3UA  O16  O  OH1    0  -0.672   6.0382  -0.4721   2.6087
 3UA  O1   O  O2     0  -0.619   1.1880  -0.7396   0.4210
 3UA  P    P  P      0   1.394   1.4674   0.8577   0.7845
 3UA  O3   O  OP    -1  -0.774   1.6598   1.6334  -0.4716
 3UA  O2   O  O      0  -0.780   2.4986   0.8662   1.8835
 3UA  O4   O  O2     0  -0.732  -0.0124   1.0871   1.4314
 3UA  P1   P  P      0   1.363  -0.4449   2.4737   2.2298
 3UA  O6   O  O      0  -0.780   0.6148   3.5048   2.0300
 3UA  O5   O  OP    -1  -0.784  -0.9318   2.0653   3.5820
 3UA  O7   O  O2     0  -0.617  -1.7139   2.9299   1.2984
 3UA  C2   C  CH2    0  -0.146  -3.0241   2.5227   1.6169
 3UA  C3   C  CH1    0  -0.052  -3.9101   2.7961   0.4182
 3UA  O8   O  O2     0  -0.492  -3.4726   2.0477  -0.7262
 3UA  C6   C  CH1    0  -0.031  -5.3509   2.3708   0.6612
 3UA  O10  O  OH1    0  -0.667  -6.1958   3.1442  -0.1506
 3UA  C5   C  CH1    0  -0.040  -5.3062   0.9202   0.1810
 3UA  O9   O  OH1    0  -0.652  -6.5363   0.3786  -0.1929
 3UA  C4   C  CH1    0   0.209  -4.3904   1.0432  -1.0379
 3UA  N    N  NR6    0  -0.567  -3.6775  -0.1973  -1.3375
 3UA  C10  C  CR6    0   0.735  -4.1767  -1.0191  -2.3292
 3UA  O12  O  O      0  -0.478  -5.1087  -0.7141  -3.0434
 3UA  C7   C  CR16   0   0.088  -2.6121  -0.5834  -0.5737
 3UA  C8   C  CR16   0  -0.516  -2.0069  -1.7741  -0.7033
 3UA  C9   C  CR6    0   0.569  -2.4815  -2.7131  -1.6895
 3UA  N1   N  NR16   0  -0.733  -3.5343  -2.2227  -2.4485
 3UA  O11  O  O      0  -0.457  -2.0441  -3.8297  -1.8893
 3UA  H1   H  HCH1   0   0.256   1.4443  -1.0814  -1.5769
 3UA  H2   H  HCH1   0   0.285   4.9768  -2.0895  -0.7614
 3UA  H3   H  HCH1   0   0.233   5.1154  -2.6532   1.6171
 3UA  H4   H  HOH1   0   0.463   3.1251  -0.7102   2.1402
 3UA  H5   H  HCH2   0   0.195   6.2817  -0.7735   0.5670
 3UA  H6   H  HCH2   0   0.213   4.9683   0.3204   1.0141
 3UA  H7   H  HOH1   0   0.455   6.5378   0.3479   2.6484
 3UA  H10  H  HCH2   0   0.206  -3.0737   1.4622   1.8928
 3UA  H11  H  HCH2   0   0.236  -3.4145   3.0882   2.4696
 3UA  H12  H  HCH1   0   0.265  -3.8536   3.8595   0.1679
 3UA  H13  H  HCH1   0   0.253  -5.6268   2.4446   1.7216
 3UA  H14  H  HOH1   0   0.450  -7.0291   2.6687  -0.2485
 3UA  H15  H  HCH1   0   0.250  -4.8113   0.3073   0.9472
 3UA  H16  H  HOH1   0   0.469  -6.9826   0.0499   0.5941
 3UA  H17  H  HCH1   0   0.272  -4.9673   1.2956  -1.9298
 3UA  H18  H  HCR6   0   0.330  -2.2476   0.1405   0.1405
 3UA  H19  H  HCR6   0   0.284  -1.1688  -2.0283  -0.0764
 3UA  H20  H  HNR6   0   0.425  -3.9059  -2.8359  -3.1635

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
 3UA  O15  C13  single  1.393  0.020  1.393
 3UA  C13  C14  single  1.525  0.020  1.525
 3UA  C13  C    single  1.530  0.020  1.530
 3UA  C14  O16  single  1.408  0.020  1.408
 3UA  F7   C12  single  1.345  0.020  1.345
 3UA  O11  C9   double  1.216  0.020  1.216
 3UA  C    C12  single  1.527  0.020  1.527
 3UA  C    O    single  1.420  0.020  1.420
 3UA  C12  F57  single  1.355  0.020  1.355
 3UA  C12  C11  single  1.547  0.020  1.547
 3UA  C9   C8   single  1.442  0.020  1.442
 3UA  C9   N1   single  1.387  0.020  1.387
 3UA  F58  C11  single  1.342  0.020  1.342
 3UA  C8   C7   double  1.342  0.020  1.342
 3UA  O    C1   single  1.402  0.020  1.402
 3UA  C11  F6   single  1.349  0.020  1.349
 3UA  C11  C1   single  1.545  0.020  1.545
 3UA  N1   C10  single  1.370  0.020  1.370
 3UA  O6   P1   deloc   1.492  0.020  1.492
 3UA  C1   O1   single  1.377  0.020  1.377
 3UA  C7   N    single  1.367  0.020  1.367
 3UA  C10  N    single  1.381  0.020  1.381
 3UA  C10  O12  double  1.213  0.020  1.213
 3UA  O1   P    single  1.662  0.020  1.662
 3UA  P1   O5   deloc   1.494  0.020  1.494
 3UA  P1   O7   single  1.639  0.020  1.639
 3UA  P1   O4   single  1.657  0.020  1.657
 3UA  N    C4   single  1.462  0.020  1.462
 3UA  O7   C2   single  1.408  0.020  1.408
 3UA  O4   P    single  1.631  0.020  1.631
 3UA  P    O2   deloc   1.507  0.020  1.507
 3UA  P    O3   deloc   1.489  0.020  1.489
 3UA  C4   O8   single  1.396  0.020  1.396
 3UA  C4   C5   single  1.530  0.020  1.530
 3UA  O8   C3   single  1.436  0.020  1.436
 3UA  C2   C3   single  1.515  0.020  1.515
 3UA  C3   C6   single  1.522  0.020  1.522
 3UA  C5   C6   single  1.529  0.020  1.529
 3UA  C5   O9   single  1.395  0.020  1.395
 3UA  C6   O10  single  1.404  0.020  1.404
 3UA  C1   H1   single  0.970  0.020  1.090
 3UA  C    H2   single  0.970  0.020  1.090
 3UA  C13  H3   single  0.970  0.020  1.090
 3UA  O15  H4   single  0.850  0.020  0.980
 3UA  C14  H5   single  0.970  0.020  1.090
 3UA  C14  H6   single  0.970  0.020  1.090
 3UA  O16  H7   single  0.850  0.020  0.980
 3UA  C2   H10  single  0.970  0.020  1.090
 3UA  C2   H11  single  0.970  0.020  1.090
 3UA  C3   H12  single  0.970  0.020  1.090
 3UA  C6   H13  single  0.970  0.020  1.090
 3UA  O10  H14  single  0.850  0.020  0.980
 3UA  C5   H15  single  0.970  0.020  1.090
 3UA  O9   H16  single  0.850  0.020  0.980
 3UA  C4   H17  single  0.970  0.020  1.090
 3UA  C7   H18  single  0.930  0.020  1.080
 3UA  C8   H19  single  0.930  0.020  1.080
 3UA  N1   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
 3UA  C1   C11  C12  104.67  3.000
 3UA  C1   C11  F6   111.06  3.000
 3UA  C12  C11  F6   111.29  3.000
 3UA  C1   C11  F58  112.75  3.000
 3UA  F6   C11  F58  107.10  3.000
 3UA  C12  C11  F58  110.05  3.000
 3UA  C    C12  F57  109.90  3.000
 3UA  F57  C12  F7   106.80  3.000
 3UA  C    C12  F7   114.37  3.000
 3UA  F57  C12  C11  108.66  3.000
 3UA  C    C12  C11  105.01  3.000
 3UA  F7   C12  C11  112.03  3.000
 3UA  H1   C1   O1   110.94  3.000
 3UA  H1   C1   O    106.97  3.000
 3UA  O1   C1   O    114.49  3.000
 3UA  H1   C1   C11  110.39  3.000
 3UA  O1   C1   C11  108.45  3.000
 3UA  O    C1   C11  105.45  3.000
 3UA  C    O    C1   114.09  3.000
 3UA  H2   C    C13  107.98  3.000
 3UA  H2   C    O    107.21  3.000
 3UA  C13  C    O    113.51  3.000
 3UA  H2   C    C12  108.28  3.000
 3UA  O    C    C12  103.43  3.000
 3UA  C13  C    C12  116.00  3.000
 3UA  H3   C13  C14  106.67  3.000
 3UA  H3   C13  O15  107.70  3.000
 3UA  C14  C13  O15  113.38  3.000
 3UA  H3   C13  C    106.06  3.000
 3UA  C14  C13  C    109.22  3.000
 3UA  O15  C13  C    113.33  3.000
 3UA  H4   O15  C13  109.11  3.000
 3UA  H6   C14  H5   107.28  3.000
 3UA  H6   C14  O16  111.52  3.000
 3UA  H5   C14  O16  111.42  3.000
 3UA  H6   C14  C13  109.85  3.000
 3UA  H5   C14  C13  108.58  3.000
 3UA  O16  C14  C13  108.15  3.000
 3UA  H7   O16  C14  108.03  3.000
 3UA  P    O1   C1   120.41  3.000
 3UA  O4   P    O2   109.31  3.000
 3UA  O2   P    O3   121.59  3.000
 3UA  O4   P    O3   112.25  3.000
 3UA  O3   P    O1   109.76  3.000
 3UA  O2   P    O1   106.26  3.000
 3UA  O4   P    O1    93.98  3.000
 3UA  P1   O4   P    123.05  3.000
 3UA  O7   P1   O5   109.76  3.000
 3UA  O7   P1   O6   106.35  3.000
 3UA  O5   P1   O6   122.79  3.000
 3UA  O7   P1   O4    99.27  3.000
 3UA  O5   P1   O4   106.99  3.000
 3UA  O6   P1   O4   109.17  3.000
 3UA  C2   O7   P1   120.75  3.000
 3UA  H11  C2   H10  106.69  3.000
 3UA  H11  C2   C3   108.32  3.000
 3UA  H10  C2   C3   110.30  3.000
 3UA  H11  C2   O7   111.00  3.000
 3UA  H10  C2   O7   112.24  3.000
 3UA  C3   C2   O7   108.23  3.000
 3UA  H12  C3   C6   110.92  3.000
 3UA  H12  C3   O8   107.98  3.000
 3UA  C6   C3   O8   105.67  3.000
 3UA  H12  C3   C2   109.03  3.000
 3UA  C6   C3   C2   112.13  3.000
 3UA  O8   C3   C2   111.00  3.000
 3UA  C4   O8   C3   110.65  3.000
 3UA  H13  C6   C5   111.99  3.000
 3UA  H13  C6   O10  111.72  3.000
 3UA  C5   C6   O10  111.02  3.000
 3UA  H13  C6   C3   111.92  3.000
 3UA  O10  C6   C3   108.87  3.000
 3UA  C5   C6   C3   100.80  3.000
 3UA  H14  O10  C6   107.88  3.000
 3UA  H15  C5   C4   109.32  3.000
 3UA  H15  C5   O9   111.56  3.000
 3UA  C4   C5   O9   110.21  3.000
 3UA  H15  C5   C6   108.87  3.000
 3UA  O9   C5   C6   115.26  3.000
 3UA  C4   C5   C6   101.04  3.000
 3UA  H16  O9   C5   108.80  3.000
 3UA  H17  C4   N    106.64  3.000
 3UA  H17  C4   C5   110.69  3.000
 3UA  N    C4   C5   112.77  3.000
 3UA  H17  C4   O8   111.31  3.000
 3UA  C5   C4   O8   105.88  3.000
 3UA  N    C4   O8   109.62  3.000
 3UA  C7   N    C10  121.00  3.000
 3UA  C10  N    C4   118.41  3.000
 3UA  C7   N    C4   120.36  3.000
 3UA  N1   C10  O12  122.00  3.000
 3UA  O12  C10  N    123.42  3.000
 3UA  N1   C10  N    114.57  3.000
 3UA  H18  C7   C8   120.41  3.000
 3UA  H18  C7   N    116.31  3.000
 3UA  C8   C7   N    123.25  3.000
 3UA  H19  C8   C9   120.03  3.000
 3UA  H19  C8   C7   120.28  3.000
 3UA  C9   C8   C7   119.69  3.000
 3UA  O11  C9   N1   120.51  3.000
 3UA  N1   C9   C8   113.19  3.000
 3UA  O11  C9   C8   126.30  3.000
 3UA  H20  N1   C9   116.79  3.000
 3UA  H20  N1   C10  114.94  3.000
 3UA  C9   N1   C10  128.23  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
 3UA  CONST_01  N1   C10  N    C4    180.00   0.0  0
 3UA  CONST_02  C9   N1   C10  N       0.00   0.0  0
 3UA  CONST_03  C8   C9   N1   C10     0.00   0.0  0
 3UA  CONST_04  N1   C10  N    C7      0.00   0.0  0
 3UA  CONST_05  O12  C10  N    C4      0.00   0.0  0
 3UA  CONST_06  O11  C9   N1   C10   180.00   0.0  0
 3UA  CONST_07  C9   N1   C10  O12   180.00   0.0  0
 3UA  CONST_08  C7   N    C10  O12   180.00   0.0  0
 3UA  CONST_09  H20  N1   C10  N     180.00   0.0  0
 3UA  Var_01    C    C12  C11  C1     15.63  30.0  1
 3UA  Var_02    O4   P    O1   C1    154.10  30.0  3
 3UA  Var_03    C3   C2   O7   P1   -166.13  30.0  3
 3UA  Var_04    O6   P1   O4   P      10.16  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
 3UA  chir_01  C1   O    C11  O1   negativ
 3UA  chir_02  C    O    C12  C13  positiv
 3UA  chir_03  C13  O15  C    C14  negativ
 3UA  chir_06  C3   O8   C2   C6   positiv
 3UA  chir_07  C6   O10  C3   C5   positiv
 3UA  chir_08  C5   O9   C6   C4   positiv
 3UA  chir_09  C4   O8   N    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
 3UA  plan-1  C4   0.020
 3UA  plan-1  N    0.020
 3UA  plan-1  C10  0.020
 3UA  plan-1  O12  0.020
 3UA  plan-1  C7   0.020
 3UA  plan-1  C8   0.020
 3UA  plan-1  C9   0.020
 3UA  plan-1  N1   0.020
 3UA  plan-1  O11  0.020
 3UA  plan-1  H18  0.020
 3UA  plan-1  H19  0.020
 3UA  plan-1  H20  0.020

