# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jul  4 19:29:44 2020
#   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,4S,5R,6R)-3-fluoro-4,5-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](F)[C@@H](O)[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
 UPF  UPF  '[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5R,6R)-3-fluoro-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)'  ligand  57  36  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UPF
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
 UPF  N1    N  NR6    0  -0.577   0.8029  -0.8463   3.9340
 UPF  C2    C  CR6    0   0.749   1.4128   0.3130   3.4851
 UPF  N3    N  NR16   0  -0.734   2.7752   0.2269   3.3520
 UPF  C4    C  CR6    0   0.567   3.6009  -0.8525   3.6235
 UPF  C5    C  CR16   0  -0.511   2.8841  -2.0125   4.0901
 UPF  C6    C  CR16   0   0.097   1.5489  -1.9583   4.2122
 UPF  O2    O  O      0  -0.460   0.8102   1.3313   3.2306
 UPF  O4    O  O      0  -0.464   4.8042  -0.7692   3.4616
 UPF  C1D   C  CR15   0   0.238  -0.6449  -0.9203   4.0745
 UPF  C2D   C  CR15   0  -0.059  -1.2840   0.0731   5.0437
 UPF  O2'   O  OH1    0  -0.659  -1.1684  -0.4152   6.3506
 UPF  C3D   C  CR15   0  -0.039  -2.7200   0.1029   4.5050
 UPF  C4D   C  CR15   0  -0.021  -2.4936  -0.0162   3.0020
 UPF  O4D   O  O      0  -0.485  -1.2662  -0.7350   2.8417
 UPF  O3D   O  OH1    0  -0.671  -3.4422  -1.0199   4.9436
 UPF  C5D   C  CH2    0  -0.153  -2.4367   1.3272   2.3032
 UPF  O5D   O  O2     0  -0.616  -2.1006   1.1263   0.9488
 UPF  PA    P  P      0   1.348  -2.9492   1.9534  -0.1894
 UPF  O1A   O  O      0  -0.794  -4.3734   1.4906  -0.1729
 UPF  O2A   O  OP    -1  -0.804  -2.6299   3.4133  -0.1082
 UPF  O3A   O  O2     0  -0.732  -2.2431   1.2618  -1.4919
 UPF  PB    P  P      0   1.353  -0.9158   1.8176  -2.2923
 UPF  O1B   O  O      0  -0.794  -1.3414   2.7720  -3.3613
 UPF  O2B   O  OP    -1  -0.773   0.1735   2.1427  -1.3278
 UPF  O3B   O  O2     0  -0.632  -0.5794   0.3446  -2.9793
 UPF  C1'   C  CH1    0   0.219  -0.2300   0.2417  -4.3201
 UPF  C2'   C  CH1    0   0.166  -0.1784  -1.2428  -4.6717
 UPF  C3'   C  CH1    0  -0.040   0.9422  -1.9436  -3.9257
 UPF  C4'   C  CH1    0  -0.015   2.2566  -1.2248  -4.2273
 UPF  C5'   C  CH1    0  -0.011   2.1112   0.2593  -3.9160
 UPF  C6'   C  CH2    0  -0.160   3.3522   1.0358  -4.3030
 UPF  F2'   F  F      0  -0.377  -1.3984  -1.8338  -4.3526
 UPF  O3'   O  OH1    0  -0.675   1.0923  -3.2859  -4.3231
 UPF  O4'   O  OH1    0  -0.672   2.6208  -1.3696  -5.5799
 UPF  O5'   O  O2     0  -0.502   1.0061   0.8234  -4.6073
 UPF  O6'   O  OH1    0  -0.666   3.2580   2.3386  -3.7792
 UPF  HN3   H  HNR6   0   0.426   3.2240   1.0730   3.0226
 UPF  H5    H  HCR6   0   0.294   3.4202  -2.9166   4.3326
 UPF  H6    H  HCR6   0   0.329   0.9891  -2.8183   4.5503
 UPF  H1D   H  HCR5   0   0.250  -0.8343  -1.9316   4.4534
 UPF  H2D   H  HCR5   0   0.269  -0.8425   1.0667   4.9448
 UPF  HO2'  H  HOH1   0   0.469  -1.2480   0.3211   6.9647
 UPF  H3D   H  HCR5   0   0.246  -3.2302   1.0385   4.7700
 UPF  H4D   H  HCR5   0   0.250  -3.2952  -0.6061   2.5453
 UPF  HO3'  H  HOH1   0   0.447  -3.2699  -1.1298   5.8865
 UPF  H5'1  H  HCH2   0   0.224  -1.7032   1.9851   2.7759
 UPF  H5'2  H  HCH2   0   0.212  -3.4210   1.7936   2.4267
 UPF  H1'   H  HCH1   0   0.241  -0.9520   0.7593  -4.9596
 UPF  H2'   H  HCH1   0   0.223  -0.0373  -1.3469  -5.7506
 UPF  H3'   H  HCH1   0   0.234   0.7550  -1.8728  -2.8461
 UPF  H4'   H  HCH1   0   0.237   3.0326  -1.6326  -3.5628
 UPF  H5'   H  HCH1   0   0.240   1.9695   0.3619  -2.8328
 UPF  H6'1  H  HCH2   0   0.205   3.4616   1.0442  -5.3932
 UPF  H6'2  H  HCH2   0   0.198   4.2211   0.4994  -3.8976
 UPF  HO3A  H  HOH1   0   0.460   0.3091  -3.7808  -4.0640
 UPF  HO4'  H  HOH1   0   0.454   2.6582  -2.3100  -5.7834
 UPF  HO6'  H  HOH1   0   0.454   4.0030   2.8441  -4.1153

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
 UPF  N1   C2    single  1.385  0.020  1.385
 UPF  N1   C6    single  1.368  0.020  1.368
 UPF  N1   C1D   single  1.456  0.020  1.456
 UPF  C2   N3    single  1.372  0.020  1.372
 UPF  C2   O2    double  1.210  0.020  1.210
 UPF  N3   C4    single  1.386  0.020  1.386
 UPF  N3   HN3   single  0.860  0.020  1.020
 UPF  C4   C5    single  1.441  0.020  1.441
 UPF  C4   O4    double  1.217  0.020  1.217
 UPF  C5   C6    double  1.342  0.020  1.342
 UPF  C5   H5    single  0.930  0.020  1.080
 UPF  C6   H6    single  0.930  0.020  1.080
 UPF  C1D  C2D   single  1.528  0.020  1.528
 UPF  C1D  O4D   single  1.393  0.020  1.393
 UPF  C1D  H1D   single  0.970  0.020  1.090
 UPF  C2D  O2'   single  1.400  0.020  1.400
 UPF  C2D  C3D   single  1.534  0.020  1.534
 UPF  C2D  H2D   single  0.970  0.020  1.090
 UPF  O2'  HO2'  single  0.850  0.020  0.980
 UPF  C3D  C4D   single  1.525  0.020  1.525
 UPF  C3D  O3D   single  1.405  0.020  1.405
 UPF  C3D  H3D   single  0.970  0.020  1.090
 UPF  C4D  O4D   single  1.431  0.020  1.431
 UPF  C4D  C5D   single  1.515  0.020  1.515
 UPF  C4D  H4D   single  0.970  0.020  1.090
 UPF  O3D  HO3'  single  0.850  0.020  0.980
 UPF  C5D  O5D   single  1.410  0.020  1.410
 UPF  C5D  H5'1  single  0.970  0.020  1.090
 UPF  C5D  H5'2  single  0.970  0.020  1.090
 UPF  O5D  PA    single  1.643  0.020  1.643
 UPF  PA   O1A   deloc   1.498  0.020  1.498
 UPF  PA   O2A   deloc   1.497  0.020  1.497
 UPF  PA   O3A   single  1.635  0.020  1.635
 UPF  O3A  PB    single  1.647  0.020  1.647
 UPF  PB   O1B   deloc   1.495  0.020  1.495
 UPF  PB   O2B   deloc   1.491  0.020  1.491
 UPF  PB   O3B   single  1.660  0.020  1.660
 UPF  O3B  C1'   single  1.389  0.020  1.389
 UPF  C1'  C2'   single  1.527  0.020  1.527
 UPF  C1'  O5'   single  1.396  0.020  1.396
 UPF  C1'  H1'   single  0.970  0.020  1.090
 UPF  C2'  C3'   single  1.518  0.020  1.518
 UPF  C2'  F2'   single  1.393  0.020  1.393
 UPF  C2'  H2'   single  0.970  0.020  1.090
 UPF  C3'  C4'   single  1.528  0.020  1.528
 UPF  C3'  O3'   single  1.408  0.020  1.408
 UPF  C3'  H3'   single  0.970  0.020  1.090
 UPF  C4'  C5'   single  1.523  0.020  1.523
 UPF  C4'  O4'   single  1.408  0.020  1.408
 UPF  C4'  H4'   single  0.970  0.020  1.090
 UPF  C5'  C6'   single  1.514  0.020  1.514
 UPF  C5'  O5'   single  1.420  0.020  1.420
 UPF  C5'  H5'   single  0.970  0.020  1.090
 UPF  C6'  O6'   single  1.407  0.020  1.407
 UPF  C6'  H6'1  single  0.970  0.020  1.090
 UPF  C6'  H6'2  single  0.970  0.020  1.090
 UPF  O3'  HO3A  single  0.850  0.020  0.980
 UPF  O4'  HO4'  single  0.850  0.020  0.980
 UPF  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
 UPF  C1D   N1   C6    118.77  3.000
 UPF  C1D   N1   C2    120.77  3.000
 UPF  C6    N1   C2    120.42  3.000
 UPF  O2    C2   N3    121.80  3.000
 UPF  O2    C2   N1    123.59  3.000
 UPF  N3    C2   N1    114.61  3.000
 UPF  HN3   N3   C4    116.77  3.000
 UPF  HN3   N3   C2    114.79  3.000
 UPF  C4    N3   C2    128.44  3.000
 UPF  O4    C4   C5    126.15  3.000
 UPF  O4    C4   N3    120.65  3.000
 UPF  C5    C4   N3    113.20  3.000
 UPF  H5    C5   C6    120.53  3.000
 UPF  H5    C5   C4    120.01  3.000
 UPF  C6    C5   C4    119.46  3.000
 UPF  H6    C6   C5    120.79  3.000
 UPF  H6    C6   N1    115.35  3.000
 UPF  C5    C6   N1    123.86  3.000
 UPF  H1D   C1D  O4D   110.58  3.000
 UPF  H1D   C1D  C2D   107.96  3.000
 UPF  O4D   C1D  C2D   106.76  3.000
 UPF  H1D   C1D  N1    104.59  3.000
 UPF  O4D   C1D  N1    110.56  3.000
 UPF  C2D   C1D  N1    116.36  3.000
 UPF  H2D   C2D  C3D   109.22  3.000
 UPF  H2D   C2D  O2'   111.63  3.000
 UPF  C3D   C2D  O2'   114.32  3.000
 UPF  H2D   C2D  C1D   111.41  3.000
 UPF  C3D   C2D  C1D   100.46  3.000
 UPF  O2'   C2D  C1D   109.32  3.000
 UPF  HO2'  O2'  C2D   108.79  3.000
 UPF  H3D   C3D  O3D   111.51  3.000
 UPF  H3D   C3D  C4D   111.93  3.000
 UPF  O3D   C3D  C4D   108.76  3.000
 UPF  H3D   C3D  C2D   111.52  3.000
 UPF  O3D   C3D  C2D   110.85  3.000
 UPF  C4D   C3D  C2D   101.87  3.000
 UPF  H4D   C4D  C5D   108.22  3.000
 UPF  H4D   C4D  O4D   108.09  3.000
 UPF  C5D   C4D  O4D   111.18  3.000
 UPF  H4D   C4D  C3D   110.15  3.000
 UPF  C5D   C4D  C3D   113.01  3.000
 UPF  O4D   C4D  C3D   106.08  3.000
 UPF  C4D   O4D  C1D   110.49  3.000
 UPF  HO3'  O3D  C3D   107.71  3.000
 UPF  H5'2  C5D  H5'1  107.32  3.000
 UPF  H5'2  C5D  O5D   112.52  3.000
 UPF  H5'1  C5D  O5D   109.96  3.000
 UPF  H5'2  C5D  C4D   106.95  3.000
 UPF  H5'1  C5D  C4D   111.06  3.000
 UPF  O5D   C5D  C4D   109.01  3.000
 UPF  PA    O5D  C5D   118.08  3.000
 UPF  O3A   PA   O2A   111.33  3.000
 UPF  O3A   PA   O1A   106.79  3.000
 UPF  O2A   PA   O1A   120.25  3.000
 UPF  O3A   PA   O5D    96.65  3.000
 UPF  O2A   PA   O5D   110.07  3.000
 UPF  O1A   PA   O5D   109.15  3.000
 UPF  PB    O3A  PA    126.34  3.000
 UPF  O3B   PB   O2B   108.26  3.000
 UPF  O3B   PB   O1B   109.16  3.000
 UPF  O2B   PB   O1B   122.10  3.000
 UPF  O3B   PB   O3A    93.73  3.000
 UPF  O2B   PB   O3A   110.37  3.000
 UPF  O1B   PB   O3A   109.49  3.000
 UPF  C1'   O3B  PB    121.07  3.000
 UPF  H1'   C1'  O5'   105.48  3.000
 UPF  H1'   C1'  C2'   110.34  3.000
 UPF  O5'   C1'  C2'   109.14  3.000
 UPF  H1'   C1'  O3B   111.28  3.000
 UPF  O5'   C1'  O3B   112.97  3.000
 UPF  C2'   C1'  O3B   107.63  3.000
 UPF  H2'   C2'  F2'   107.39  3.000
 UPF  H2'   C2'  C3'   110.24  3.000
 UPF  F2'   C2'  C3'   109.77  3.000
 UPF  H2'   C2'  C1'   108.93  3.000
 UPF  F2'   C2'  C1'   109.29  3.000
 UPF  C3'   C2'  C1'   111.15  3.000
 UPF  H3'   C3'  O3'   110.93  3.000
 UPF  H3'   C3'  C4'   108.09  3.000
 UPF  O3'   C3'  C4'   107.52  3.000
 UPF  H3'   C3'  C2'   109.13  3.000
 UPF  O3'   C3'  C2'   112.34  3.000
 UPF  C4'   C3'  C2'   108.71  3.000
 UPF  H4'   C4'  O4'   111.08  3.000
 UPF  H4'   C4'  C5'   107.76  3.000
 UPF  O4'   C4'  C5'   108.73  3.000
 UPF  H4'   C4'  C3'   108.25  3.000
 UPF  O4'   C4'  C3'   111.33  3.000
 UPF  C5'   C4'  C3'   109.62  3.000
 UPF  H5'   C5'  O5'   110.06  3.000
 UPF  H5'   C5'  C6'   108.07  3.000
 UPF  O5'   C5'  C6'   108.04  3.000
 UPF  H5'   C5'  C4'   107.76  3.000
 UPF  O5'   C5'  C4'   111.21  3.000
 UPF  C6'   C5'  C4'   111.66  3.000
 UPF  H6'2  C6'  H6'1  106.98  3.000
 UPF  H6'2  C6'  O6'   111.57  3.000
 UPF  H6'1  C6'  O6'   111.71  3.000
 UPF  H6'2  C6'  C5'   107.67  3.000
 UPF  H6'1  C6'  C5'   109.87  3.000
 UPF  O6'   C6'  C5'   108.95  3.000
 UPF  HO3A  O3'  C3'   109.12  3.000
 UPF  HO4'  O4'  C4'   108.26  3.000
 UPF  C5'   O5'  C1'   115.05  3.000
 UPF  HO6'  O6'  C6'   107.75  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
 UPF  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 UPF  CONST_02  C5    C4   N3   C2      0.00   0.0  0
 UPF  CONST_03  C6    N1   C2   N3      0.00   0.0  0
 UPF  CONST_04  C1D   N1   C2   N3    180.00   0.0  0
 UPF  CONST_05  O4    C4   N3   C2    180.00   0.0  0
 UPF  CONST_06  O2    C2   N3   C4    180.00   0.0  0
 UPF  CONST_07  O2    C2   N1   C6    180.00   0.0  0
 UPF  CONST_08  C1D   N1   C2   O2      0.00   0.0  0
 UPF  CONST_09  HN3   N3   C2   N1    180.00   0.0  0
 UPF  Var_01    O1A   PA   O5D  C5D   -65.35  30.0  3
 UPF  Var_02    O1B   PB   O3A  PA    -88.41  30.0  3
 UPF  Var_03    H5'1  C5D  O5D  PA   -102.72  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
 UPF  chir_01  C1D  N1   C2D  O4D  negativ
 UPF  chir_02  C2D  O2'  C3D  C1D  positiv
 UPF  chir_03  C3D  O3D  C2D  C4D  negativ
 UPF  chir_04  C4D  O4D  C3D  C5D  negativ
 UPF  chir_07  C1'  O3B  C2'  O5'  positiv
 UPF  chir_08  C2'  F2'  C3'  C1'  positiv
 UPF  chir_09  C3'  O3'  C2'  C4'  positiv
 UPF  chir_10  C4'  O4'  C3'  C5'  positiv
 UPF  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
 UPF  plan-1  N1   0.020
 UPF  plan-1  C2   0.020
 UPF  plan-1  N3   0.020
 UPF  plan-1  C4   0.020
 UPF  plan-1  C5   0.020
 UPF  plan-1  C6   0.020
 UPF  plan-1  O2   0.020
 UPF  plan-1  O4   0.020
 UPF  plan-1  C1D  0.020
 UPF  plan-1  HN3  0.020
 UPF  plan-1  H5   0.020
 UPF  plan-1  H6   0.020

