# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jul  1 13:02:59 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,5S,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
 U2F  U2F  '[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5S,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 PERFECT
;

data_comp_U2F
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
 U2F  C1    C  CH1    0   0.189   7.0726   2.6922  -4.8946
 U2F  O1    O  O2     0  -0.632   6.1739   2.0688  -5.7541
 U2F  PB    P  P      0   1.374   5.8907   0.4411  -5.6520
 U2F  O1B   O  O      0  -0.778   5.0585   0.1333  -6.8508
 U2F  O2B   O  OP    -1  -0.791   7.1555  -0.2895  -5.3414
 U2F  O3A   O  O2     0  -0.747   4.8962   0.4040  -4.3473
 U2F  PA    P  P      0   1.365   5.2489  -0.0927  -2.8171
 U2F  O1A   O  O      0  -0.788   6.4218   0.6670  -2.2796
 U2F  O2A   O  OP    -1  -0.783   5.1730  -1.5817  -2.7420
 U2F  O5'   O  O2     0  -0.617   3.8726   0.4556  -2.1070
 U2F  C5'   C  CH2    0  -0.177   3.6632   1.8442  -1.9643
 U2F  C4'   C  CH1    0  -0.017   2.1725   2.0974  -2.1329
 U2F  O4'   O  O2     0  -0.499   1.8883   3.4559  -1.7740
 U2F  C1'   C  CH1    0   0.182   1.3214   4.1317  -2.8623
 U2F  C2'   C  CH1    0  -0.027   1.7702   3.3474  -4.0991
 U2F  C3'   C  CH1    0  -0.047   1.6851   1.9180  -3.5689
 U2F  O3'   O  OH1    0  -0.670   0.3553   1.4621  -3.5359
 U2F  O2'   O  OH1    0  -0.657   0.9529   3.5385  -5.2129
 U2F  N1    N  NR6    0  -0.568   1.7563   5.5186  -2.8341
 U2F  C6'   C  CR6    0   0.736   0.8134   6.5287  -2.8938
 U2F  O6'   O  O      0  -0.473  -0.3801   6.3262  -2.9599
 U2F  N3    N  NR16   0  -0.734   1.3362   7.7946  -2.8786
 U2F  C7'   C  CR6    0   0.570   2.6682   8.1734  -2.8056
 U2F  O7'   O  O      0  -0.461   2.9779   9.3497  -2.8062
 U2F  C8'   C  CR16   0  -0.510   3.5773   7.0562  -2.7295
 U2F  C9'   C  CR16   0   0.110   3.0895   5.8072  -2.7398
 U2F  C2    C  CH1    0   0.165   6.6976   4.1671  -4.7932
 U2F  F1    F  F      0  -0.363   5.3688   4.2725  -4.3960
 U2F  C3    C  CH1    0  -0.053   6.9009   4.9097  -6.1045
 U2F  O3    O  OH1    0  -0.654   6.5812   6.2713  -5.9954
 U2F  C4    C  CH1    0  -0.007   8.3355   4.6747  -6.5997
 U2F  O4    O  OH1    0  -0.655   8.5704   5.2839  -7.8424
 U2F  C5    C  CH1    0  -0.058   8.6203   3.1724  -6.6336
 U2F  C6    C  CH2    0  -0.152  10.0539   2.8208  -6.9828
 U2F  O6    O  OH1    0  -0.669  10.2324   1.4291  -7.1014
 U2F  O5    O  O2     0  -0.505   8.3889   2.6119  -5.3513
 U2F  H1    H  HCH1   0   0.268   7.0690   2.2339  -3.9012
 U2F  H5'1  H  HCH2   0   0.237   3.9797   2.1792  -0.9713
 U2F  H5'2  H  HCH2   0   0.207   4.2326   2.4266  -2.6980
 U2F  H4'   H  HCH1   0   0.258   1.6212   1.4328  -1.4601
 U2F  H1'   H  HCH1   0   0.273   0.2308   4.1417  -2.8089
 U2F  H2'   H  HCH1   0   0.239   2.8206   3.5730  -4.3277
 U2F  H3'   H  HCH1   0   0.266   2.3322   1.2386  -4.1337
 U2F  HB    H  HOH1   0   0.455   0.0183   1.4444  -4.4380
 U2F  HA    H  HOH1   0   0.467   1.2862   4.2771  -5.7298
 U2F  H3    H  HNR6   0   0.427   0.6527   8.5402  -2.9290
 U2F  H8'   H  HCR6   0   0.291   4.6392   7.2309  -2.6566
 U2F  H9'   H  HCR6   0   0.313   3.7512   4.9590  -2.6626
 U2F  H2    H  HCH1   0   0.227   7.3080   4.6254  -4.0076
 U2F  HC    H  HCH1   0   0.247   6.2088   4.5011  -6.8505
 U2F  HD    H  HOH1   0   0.446   7.1620   6.6812  -5.3447
 U2F  H4    H  HCH1   0   0.239   9.0332   5.1481  -5.8965
 U2F  HE    H  HOH1   0   0.448   7.9710   4.9025  -8.4938
 U2F  H5    H  HCH1   0   0.228   7.9631   2.7057  -7.3824
 U2F  H6C1  H  HCH2   0   0.196  10.7271   3.2570  -6.2310
 U2F  H6C2  H  HCH2   0   0.227  10.3101   3.2644  -7.9449
 U2F  H6    H  HOH1   0   0.444   9.8479   1.0135  -6.3214

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
 U2F  C1   O1    single  1.391  0.020  1.391
 U2F  C1   C2    single  1.525  0.020  1.525
 U2F  C1   O5    single  1.396  0.020  1.396
 U2F  C1   H1    single  0.970  0.020  1.090
 U2F  O1   PB    single  1.655  0.020  1.655
 U2F  PB   O1B   deloc   1.492  0.020  1.492
 U2F  PB   O2B   deloc   1.493  0.020  1.493
 U2F  PB   O3A   single  1.641  0.020  1.641
 U2F  O3A  PA    single  1.647  0.020  1.647
 U2F  PA   O1A   deloc   1.497  0.020  1.497
 U2F  PA   O2A   deloc   1.493  0.020  1.493
 U2F  PA   O5'   single  1.643  0.020  1.643
 U2F  O5'  C5'   single  1.411  0.020  1.411
 U2F  C5'  C4'   single  1.521  0.020  1.521
 U2F  C5'  H5'1  single  0.970  0.020  1.090
 U2F  C5'  H5'2  single  0.970  0.020  1.090
 U2F  C4'  O4'   single  1.434  0.020  1.434
 U2F  C4'  C3'   single  1.527  0.020  1.527
 U2F  C4'  H4'   single  0.970  0.020  1.090
 U2F  O4'  C1'   single  1.401  0.020  1.401
 U2F  C1'  C2'   single  1.532  0.020  1.532
 U2F  C1'  N1    single  1.454  0.020  1.454
 U2F  C1'  H1'   single  0.970  0.020  1.090
 U2F  C2'  C3'   single  1.527  0.020  1.527
 U2F  C2'  O2'   single  1.395  0.020  1.395
 U2F  C2'  H2'   single  0.970  0.020  1.090
 U2F  C3'  O3'   single  1.406  0.020  1.406
 U2F  C3'  H3'   single  0.970  0.020  1.090
 U2F  O3'  HB    single  0.850  0.020  0.980
 U2F  O2'  HA    single  0.850  0.020  0.980
 U2F  N1   C6'   single  1.383  0.020  1.383
 U2F  N1   C9'   single  1.367  0.020  1.367
 U2F  C6'  O6'   double  1.212  0.020  1.212
 U2F  C6'  N3    single  1.370  0.020  1.370
 U2F  N3   C7'   single  1.387  0.020  1.387
 U2F  N3   H3    single  0.860  0.020  1.020
 U2F  C7'  O7'   double  1.216  0.020  1.216
 U2F  C7'  C8'   single  1.442  0.020  1.442
 U2F  C8'  C9'   double  1.341  0.020  1.341
 U2F  C8'  H8'   single  0.930  0.020  1.080
 U2F  C9'  H9'   single  0.930  0.020  1.080
 U2F  C2   F1    single  1.391  0.020  1.391
 U2F  C2   C3    single  1.521  0.020  1.521
 U2F  C2   H2    single  0.970  0.020  1.090
 U2F  C3   O3    single  1.403  0.020  1.403
 U2F  C3   C4    single  1.536  0.020  1.536
 U2F  C3   HC    single  0.970  0.020  1.090
 U2F  O3   HD    single  0.850  0.020  0.980
 U2F  C4   O4    single  1.404  0.020  1.404
 U2F  C4   C5    single  1.529  0.020  1.529
 U2F  C4   H4    single  0.970  0.020  1.090
 U2F  O4   HE    single  0.850  0.020  0.980
 U2F  C5   C6    single  1.517  0.020  1.517
 U2F  C5   O5    single  1.418  0.020  1.418
 U2F  C5   H5    single  0.970  0.020  1.090
 U2F  C6   O6    single  1.408  0.020  1.408
 U2F  C6   H6C1  single  0.970  0.020  1.090
 U2F  C6   H6C2  single  0.970  0.020  1.090
 U2F  O6   H6    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
 U2F  H1    C1   O5    106.03  3.000
 U2F  H1    C1   C2    110.11  3.000
 U2F  O5    C1   C2    108.01  3.000
 U2F  H1    C1   O1    111.79  3.000
 U2F  O5    C1   O1    112.42  3.000
 U2F  C2    C1   O1    108.40  3.000
 U2F  PB    O1   C1    120.87  3.000
 U2F  O3A   PB   O2B   109.69  3.000
 U2F  O3A   PB   O1B   107.23  3.000
 U2F  O2B   PB   O1B   122.60  3.000
 U2F  O3A   PB   O1    100.08  3.000
 U2F  O2B   PB   O1    110.43  3.000
 U2F  O1B   PB   O1    104.41  3.000
 U2F  PA    O3A  PB    128.01  3.000
 U2F  O5'   PA   O2A   105.58  3.000
 U2F  O5'   PA   O1A   109.38  3.000
 U2F  O2A   PA   O1A   121.86  3.000
 U2F  O5'   PA   O3A    96.98  3.000
 U2F  O2A   PA   O3A   109.67  3.000
 U2F  O1A   PA   O3A   110.38  3.000
 U2F  C5'   O5'  PA    119.76  3.000
 U2F  H5'2  C5'  H5'1  107.11  3.000
 U2F  H5'2  C5'  C4'   110.26  3.000
 U2F  H5'1  C5'  C4'   109.44  3.000
 U2F  H5'2  C5'  O5'   112.21  3.000
 U2F  H5'1  C5'  O5'   110.48  3.000
 U2F  C4'   C5'  O5'   107.33  3.000
 U2F  H4'   C4'  C3'   110.24  3.000
 U2F  H4'   C4'  O4'   108.76  3.000
 U2F  C3'   C4'  O4'   106.47  3.000
 U2F  H4'   C4'  C5'   108.92  3.000
 U2F  C3'   C4'  C5'   113.42  3.000
 U2F  O4'   C4'  C5'   108.92  3.000
 U2F  C1'   O4'  C4'   110.05  3.000
 U2F  H1'   C1'  N1    106.80  3.000
 U2F  H1'   C1'  C2'   109.68  3.000
 U2F  N1    C1'  C2'   114.61  3.000
 U2F  H1'   C1'  O4'   111.75  3.000
 U2F  N1    C1'  O4'   108.91  3.000
 U2F  C2'   C1'  O4'   105.17  3.000
 U2F  H2'   C2'  O2'   111.47  3.000
 U2F  H2'   C2'  C3'   108.53  3.000
 U2F  O2'   C2'  C3'   111.90  3.000
 U2F  H2'   C2'  C1'   110.07  3.000
 U2F  O2'   C2'  C1'   113.77  3.000
 U2F  C3'   C2'  C1'   100.52  3.000
 U2F  H3'   C3'  O3'   111.70  3.000
 U2F  H3'   C3'  C2'   111.64  3.000
 U2F  O3'   C3'  C2'   111.37  3.000
 U2F  H3'   C3'  C4'   111.67  3.000
 U2F  O3'   C3'  C4'   108.54  3.000
 U2F  C2'   C3'  C4'   101.46  3.000
 U2F  HB    O3'  C3'   108.35  3.000
 U2F  HA    O2'  C2'   109.37  3.000
 U2F  C9'   N1   C6'   120.90  3.000
 U2F  C9'   N1   C1'   119.63  3.000
 U2F  C6'   N1   C1'   119.47  3.000
 U2F  N3    C6'  O6'   122.05  3.000
 U2F  N3    C6'  N1    114.47  3.000
 U2F  O6'   C6'  N1    123.48  3.000
 U2F  H3    N3   C7'   116.73  3.000
 U2F  H3    N3   C6'   114.98  3.000
 U2F  C7'   N3   C6'   128.29  3.000
 U2F  C8'   C7'  O7'   126.06  3.000
 U2F  C8'   C7'  N3    113.36  3.000
 U2F  O7'   C7'  N3    120.57  3.000
 U2F  H8'   C8'  C9'   120.63  3.000
 U2F  H8'   C8'  C7'   119.90  3.000
 U2F  C9'   C8'  C7'   119.46  3.000
 U2F  H9'   C9'  C8'   120.58  3.000
 U2F  H9'   C9'  N1    115.93  3.000
 U2F  C8'   C9'  N1    123.49  3.000
 U2F  H2    C2   C3    109.86  3.000
 U2F  H2    C2   F1    107.21  3.000
 U2F  C3    C2   F1    109.69  3.000
 U2F  H2    C2   C1    108.38  3.000
 U2F  C3    C2   C1    112.46  3.000
 U2F  F1    C2   C1    109.10  3.000
 U2F  HC    C3   C4    108.25  3.000
 U2F  HC    C3   O3    105.70  3.000
 U2F  C4    C3   O3    112.74  3.000
 U2F  HC    C3   C2    108.68  3.000
 U2F  C4    C3   C2    109.16  3.000
 U2F  O3    C3   C2    112.11  3.000
 U2F  HD    O3   C3    109.14  3.000
 U2F  H4    C4   C5    108.63  3.000
 U2F  H4    C4   O4    105.87  3.000
 U2F  C5    C4   O4    112.05  3.000
 U2F  H4    C4   C3    108.73  3.000
 U2F  C5    C4   C3    109.35  3.000
 U2F  O4    C4   C3    112.05  3.000
 U2F  HE    O4   C4    108.81  3.000
 U2F  H5    C5   O5    110.50  3.000
 U2F  H5    C5   C6    108.03  3.000
 U2F  O5    C5   C6    105.71  3.000
 U2F  H5    C5   C4    108.70  3.000
 U2F  O5    C5   C4    109.74  3.000
 U2F  C6    C5   C4    114.13  3.000
 U2F  H6C2  C6   H6C1  107.36  3.000
 U2F  H6C2  C6   O6    107.34  3.000
 U2F  H6C1  C6   O6    111.85  3.000
 U2F  H6C2  C6   C5    109.33  3.000
 U2F  H6C1  C6   C5    109.23  3.000
 U2F  O6    C6   C5    111.61  3.000
 U2F  H6    O6   C6    107.91  3.000
 U2F  C5    O5   C1    115.27  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
 U2F  CONST_01  N3   C6'  N1   C1'   180.00   0.0  0
 U2F  CONST_02  C7'  N3   C6'  N1      0.00   0.0  0
 U2F  CONST_03  C8'  C7'  N3   C6'     0.00   0.0  0
 U2F  CONST_04  C9'  N1   C6'  N3      0.00   0.0  0
 U2F  CONST_05  O6'  C6'  N1   C1'     0.00   0.0  0
 U2F  CONST_06  O7'  C7'  N3   C6'   180.00   0.0  0
 U2F  CONST_07  C9'  N1   C6'  O6'   180.00   0.0  0
 U2F  CONST_08  C7'  N3   C6'  O6'   180.00   0.0  0
 U2F  CONST_09  H3   N3   C6'  N1    180.00   0.0  0
 U2F  Var_01    O1B  PB   O1   C1   -171.38  30.0  3
 U2F  Var_02    C4'  C5'  O5'  PA    145.21  30.0  3
 U2F  Var_03    O1A  PA   O3A  PB     55.79  30.0  3

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
 U2F  chir_01  C1   O1   C2   O5   positiv
 U2F  chir_04  C4'  C5'  O4'  C3'  negativ
 U2F  chir_05  C1'  O4'  N1   C2'  negativ
 U2F  chir_06  C2'  O2'  C1'  C3'  negativ
 U2F  chir_07  C3'  O3'  C4'  C2'  positiv
 U2F  chir_08  C2   C1   F1   C3   positiv
 U2F  chir_09  C3   O3   C2   C4   positiv
 U2F  chir_10  C4   O4   C5   C3   positiv
 U2F  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
 U2F  plan-1  C1'  0.020
 U2F  plan-1  N1   0.020
 U2F  plan-1  C6'  0.020
 U2F  plan-1  O6'  0.020
 U2F  plan-1  N3   0.020
 U2F  plan-1  C7'  0.020
 U2F  plan-1  O7'  0.020
 U2F  plan-1  C8'  0.020
 U2F  plan-1  C9'  0.020
 U2F  plan-1  H3   0.020
 U2F  plan-1  H8'  0.020
 U2F  plan-1  H9'  0.020

