# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jul  3 03:38:15 2020
#   Inital geometry file: a 143 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,3S,4S,5S,6R)-3,4,5-trihydroxy-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]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
 UFM  UFM  '[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)'  ligand  58  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_UFM
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
 UFM  N1    N  NR6    0  -0.578   0.0499  -1.6316   4.7380
 UFM  C2    C  CR6    0   0.747   1.1356  -0.8658   4.3483
 UFM  N3    N  NR16   0  -0.734   2.3461  -1.5037   4.4383
 UFM  C4    C  CR6    0   0.567   2.6095  -2.7943   4.8696
 UFM  C5    C  CR16   0  -0.510   1.4239  -3.5190   5.2527
 UFM  C6    C  CR16   0   0.098   0.2271  -2.9193   5.1650
 UFM  O2    O  O      0  -0.462   1.0444   0.2781   3.9624
 UFM  O4    O  O      0  -0.464   3.7497  -3.2185   4.8967
 UFM  C1D   C  CH1    0   0.240  -1.3035  -1.0975   4.6757
 UFM  C2D   C  CH1    0  -0.058  -1.5759   0.1534   5.5099
 UFM  O2D   O  OH1    0  -0.658  -1.7986  -0.2131   6.8419
 UFM  C3D   C  CH1    0  -0.040  -2.8117   0.7020   4.7881
 UFM  C4D   C  CH1    0  -0.028  -2.4990   0.3684   3.3329
 UFM  O4D   O  O2     0  -0.487  -1.6500  -0.7848   3.3628
 UFM  O3D   O  OH1    0  -0.670  -3.9677   0.0007   5.1715
 UFM  C5D   C  CH2    0  -0.144  -1.8363   1.5144   2.5969
 UFM  O5D   O  O2     0  -0.620  -1.5313   1.0861   1.2887
 UFM  PA    P  P      0   1.341  -1.2374   2.2525   0.1615
 UFM  O1A   O  O      0  -0.801  -2.5328   2.8650  -0.2727
 UFM  O2A   O  OP    -1  -0.795  -0.1123   3.1201   0.6310
 UFM  O3A   O  O2     0  -0.737  -0.7047   1.1833  -0.9595
 UFM  PB    P  P      0   1.357  -0.9236   1.3871  -2.5806
 UFM  O1B   O  O      0  -0.795  -2.2424   0.8196  -2.9971
 UFM  O2B   O  OP    -1  -0.776  -0.5010   2.7655  -2.9640
 UFM  O3B   O  O2     0  -0.637   0.2753   0.3155  -2.9793
 UFM  C1'   C  CH1    0   0.243   0.1259  -0.5449  -4.0681
 UFM  C2'   C  CH1    0  -0.025   1.3245  -1.4996  -4.0513
 UFM  C3'   C  CH1    0  -0.000   2.5870  -0.7130  -4.3855
 UFM  C4'   C  CH1    0   0.029   2.4181   0.0351  -5.7021
 UFM  C5'   C  CH1    0  -0.003   1.1613   0.9082  -5.6493
 UFM  C6'   C  CH2    0  -0.161   0.8683   1.5124  -7.0066
 UFM  O2'   O  OH1    0  -0.667   1.1629  -2.5137  -5.0102
 UFM  O3'   O  OH1    0  -0.674   3.7253  -1.5349  -4.5083
 UFM  O4'   O  OH1    0  -0.678   3.5199   0.8780  -5.9481
 UFM  O5'   O  O2     0  -0.495   0.0341   0.1315  -5.2831
 UFM  O6'   O  OH1    0  -0.663  -0.2247   2.3920  -6.9052
 UFM  HN3   H  HNR6   0   0.427   3.1435  -0.9444   4.1596
 UFM  H5    H  HCR6   0   0.294   1.5040  -4.5375   5.5989
 UFM  H6    H  HCR6   0   0.328  -0.6786  -3.4427   5.4357
 UFM  H1D   H  HCH1   0   0.249  -1.9352  -1.9070   5.0615
 UFM  H2D   H  HCH1   0   0.270  -0.7585   0.8705   5.4189
 UFM  HO2'  H  HOH1   0   0.470  -1.6126   0.5430   7.4067
 UFM  H3D   H  HCH1   0   0.247  -2.9276   1.7825   4.9454
 UFM  H4D   H  HCH1   0   0.253  -3.4198   0.1017   2.8037
 UFM  HO3'  H  HOH1   0   0.448  -3.9623  -0.0694   6.1335
 UFM  H5'1  H  HCH2   0   0.221  -0.9358   1.8460   3.1212
 UFM  H5'2  H  HCH2   0   0.210  -2.5454   2.3516   2.5940
 UFM  H1'   H  HCH1   0   0.232  -0.8081  -1.1142  -3.9887
 UFM  H2'   H  HCH1   0   0.225   1.4133  -1.9212  -3.0396
 UFM  H3'   H  HCH1   0   0.228   2.7328   0.0343  -3.5946
 UFM  H4'   H  HCH1   0   0.206   2.2997  -0.6982  -6.5142
 UFM  H5'   H  HCH1   0   0.228   1.3171   1.7166  -4.9226
 UFM  H6'1  H  HCH2   0   0.187   0.6723   0.6985  -7.7203
 UFM  H6'2  H  HCH2   0   0.207   1.7698   2.0291  -7.3536
 UFM  HO2A  H  HOH1   0   0.452   0.4161  -3.0611  -4.7490
 UFM  HO3A  H  HOH1   0   0.455   4.0721  -1.7154  -3.6300
 UFM  HO4'  H  HOH1   0   0.450   4.3151   0.3358  -5.9112
 UFM  HO6'  H  HOH1   0   0.451  -0.3278   2.8256  -7.7568

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
 UFM  N1   C2    single  1.385  0.020  1.385
 UFM  N1   C6    single  1.368  0.020  1.368
 UFM  N1   C1D   single  1.456  0.020  1.456
 UFM  C2   N3    single  1.371  0.020  1.371
 UFM  C2   O2    double  1.211  0.020  1.211
 UFM  N3   C4    single  1.386  0.020  1.386
 UFM  N3   HN3   single  0.860  0.020  1.020
 UFM  C4   C5    single  1.441  0.020  1.441
 UFM  C4   O4    double  1.217  0.020  1.217
 UFM  C5   C6    double  1.342  0.020  1.342
 UFM  C5   H5    single  0.930  0.020  1.080
 UFM  C6   H6    single  0.930  0.020  1.080
 UFM  C1D  C2D   single  1.528  0.020  1.528
 UFM  C1D  O4D   single  1.393  0.020  1.393
 UFM  C1D  H1D   single  0.970  0.020  1.090
 UFM  C2D  O2D   single  1.399  0.020  1.399
 UFM  C2D  C3D   single  1.533  0.020  1.533
 UFM  C2D  H2D   single  0.970  0.020  1.090
 UFM  O2D  HO2'  single  0.850  0.020  0.980
 UFM  C3D  C4D   single  1.525  0.020  1.525
 UFM  C3D  O3D   single  1.405  0.020  1.405
 UFM  C3D  H3D   single  0.970  0.020  1.090
 UFM  C4D  O4D   single  1.432  0.020  1.432
 UFM  C4D  C5D   single  1.515  0.020  1.515
 UFM  C4D  H4D   single  0.970  0.020  1.090
 UFM  O3D  HO3'  single  0.850  0.020  0.980
 UFM  C5D  O5D   single  1.410  0.020  1.410
 UFM  C5D  H5'1  single  0.970  0.020  1.090
 UFM  C5D  H5'2  single  0.970  0.020  1.090
 UFM  O5D  PA    single  1.648  0.020  1.648
 UFM  PA   O1A   deloc   1.497  0.020  1.497
 UFM  PA   O2A   deloc   1.496  0.020  1.496
 UFM  PA   O3A   single  1.638  0.020  1.638
 UFM  O3A  PB    single  1.648  0.020  1.648
 UFM  PB   O1B   deloc   1.495  0.020  1.495
 UFM  PB   O2B   deloc   1.492  0.020  1.492
 UFM  PB   O3B   single  1.657  0.020  1.657
 UFM  O3B  C1'   single  1.396  0.020  1.396
 UFM  C1'  C2'   single  1.532  0.020  1.532
 UFM  C1'  O5'   single  1.394  0.020  1.394
 UFM  C1'  H1'   single  0.970  0.020  1.090
 UFM  C2'  C3'   single  1.525  0.020  1.525
 UFM  C2'  O2'   single  1.405  0.020  1.405
 UFM  C2'  H2'   single  0.970  0.020  1.090
 UFM  C3'  C4'   single  1.524  0.020  1.524
 UFM  C3'  O3'   single  1.409  0.020  1.409
 UFM  C3'  H3'   single  0.970  0.020  1.090
 UFM  C4'  C5'   single  1.531  0.020  1.531
 UFM  C4'  O4'   single  1.409  0.020  1.409
 UFM  C4'  H4'   single  0.970  0.020  1.090
 UFM  C5'  C6'   single  1.514  0.020  1.514
 UFM  C5'  O5'   single  1.417  0.020  1.417
 UFM  C5'  H5'   single  0.970  0.020  1.090
 UFM  C6'  O6'   single  1.407  0.020  1.407
 UFM  C6'  H6'1  single  0.970  0.020  1.090
 UFM  C6'  H6'2  single  0.970  0.020  1.090
 UFM  O2'  HO2A  single  0.850  0.020  0.980
 UFM  O3'  HO3A  single  0.850  0.020  0.980
 UFM  O4'  HO4'  single  0.850  0.020  0.980
 UFM  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
 UFM  C1D   N1   C6    118.61  3.000
 UFM  C1D   N1   C2    120.92  3.000
 UFM  C6    N1   C2    120.45  3.000
 UFM  O2    C2   N3    121.80  3.000
 UFM  O2    C2   N1    123.59  3.000
 UFM  N3    C2   N1    114.61  3.000
 UFM  HN3   N3   C4    116.75  3.000
 UFM  HN3   N3   C2    114.84  3.000
 UFM  C4    N3   C2    128.41  3.000
 UFM  O4    C4   C5    126.12  3.000
 UFM  O4    C4   N3    120.64  3.000
 UFM  C5    C4   N3    113.24  3.000
 UFM  H5    C5   C6    120.62  3.000
 UFM  H5    C5   C4    119.93  3.000
 UFM  C6    C5   C4    119.45  3.000
 UFM  H6    C6   C5    120.99  3.000
 UFM  H6    C6   N1    115.19  3.000
 UFM  C5    C6   N1    123.83  3.000
 UFM  H1D   C1D  O4D   110.72  3.000
 UFM  H1D   C1D  C2D   108.02  3.000
 UFM  O4D   C1D  C2D   106.64  3.000
 UFM  H1D   C1D  N1    104.45  3.000
 UFM  O4D   C1D  N1    110.72  3.000
 UFM  C2D   C1D  N1    116.27  3.000
 UFM  H2D   C2D  C3D   109.24  3.000
 UFM  H2D   C2D  O2D   111.76  3.000
 UFM  C3D   C2D  O2D   114.44  3.000
 UFM  H2D   C2D  C1D   111.03  3.000
 UFM  C3D   C2D  C1D   100.35  3.000
 UFM  O2D   C2D  C1D   109.49  3.000
 UFM  HO2'  O2D  C2D   108.80  3.000
 UFM  H3D   C3D  O3D   111.42  3.000
 UFM  H3D   C3D  C4D   111.93  3.000
 UFM  O3D   C3D  C4D   108.65  3.000
 UFM  H3D   C3D  C2D   111.70  3.000
 UFM  O3D   C3D  C2D   110.86  3.000
 UFM  C4D   C3D  C2D   101.87  3.000
 UFM  H4D   C4D  C5D   108.50  3.000
 UFM  H4D   C4D  O4D   108.21  3.000
 UFM  C5D   C4D  O4D   111.10  3.000
 UFM  H4D   C4D  C3D   109.99  3.000
 UFM  C5D   C4D  C3D   112.82  3.000
 UFM  O4D   C4D  C3D   106.12  3.000
 UFM  C4D   O4D  C1D   110.35  3.000
 UFM  HO3'  O3D  C3D   107.69  3.000
 UFM  H5'2  C5D  H5'1  107.59  3.000
 UFM  H5'2  C5D  O5D   111.66  3.000
 UFM  H5'1  C5D  O5D   111.03  3.000
 UFM  H5'2  C5D  C4D   107.21  3.000
 UFM  H5'1  C5D  C4D   110.90  3.000
 UFM  O5D   C5D  C4D   108.40  3.000
 UFM  PA    O5D  C5D   117.26  3.000
 UFM  O3A   PA   O2A   110.40  3.000
 UFM  O3A   PA   O1A   110.48  3.000
 UFM  O2A   PA   O1A   120.29  3.000
 UFM  O3A   PA   O5D    93.67  3.000
 UFM  O2A   PA   O5D   109.26  3.000
 UFM  O1A   PA   O5D   109.48  3.000
 UFM  PB    O3A  PA    123.30  3.000
 UFM  O3B   PB   O2B   109.32  3.000
 UFM  O3B   PB   O1B   109.02  3.000
 UFM  O2B   PB   O1B   121.94  3.000
 UFM  O3B   PB   O3A    93.47  3.000
 UFM  O2B   PB   O3A   109.23  3.000
 UFM  O1B   PB   O3A   110.13  3.000
 UFM  C1'   O3B  PB    120.60  3.000
 UFM  H1'   C1'  O5'   105.01  3.000
 UFM  H1'   C1'  C2'   110.00  3.000
 UFM  O5'   C1'  C2'   111.31  3.000
 UFM  H1'   C1'  O3B   110.77  3.000
 UFM  O5'   C1'  O3B   112.83  3.000
 UFM  C2'   C1'  O3B   106.97  3.000
 UFM  H2'   C2'  O2'   111.13  3.000
 UFM  H2'   C2'  C3'   109.43  3.000
 UFM  O2'   C2'  C3'   108.55  3.000
 UFM  H2'   C2'  C1'   108.18  3.000
 UFM  O2'   C2'  C1'   110.62  3.000
 UFM  C3'   C2'  C1'   108.89  3.000
 UFM  H3'   C3'  O3'   110.64  3.000
 UFM  H3'   C3'  C4'   107.64  3.000
 UFM  O3'   C3'  C4'   107.49  3.000
 UFM  H3'   C3'  C2'   107.66  3.000
 UFM  O3'   C3'  C2'   112.77  3.000
 UFM  C4'   C3'  C2'   110.55  3.000
 UFM  H4'   C4'  O4'   110.73  3.000
 UFM  H4'   C4'  C5'   108.49  3.000
 UFM  O4'   C4'  C5'   107.86  3.000
 UFM  H4'   C4'  C3'   108.81  3.000
 UFM  O4'   C4'  C3'   110.97  3.000
 UFM  C5'   C4'  C3'   109.94  3.000
 UFM  H5'   C5'  O5'   110.21  3.000
 UFM  H5'   C5'  C6'   109.08  3.000
 UFM  O5'   C5'  C6'   107.24  3.000
 UFM  H5'   C5'  C4'   109.04  3.000
 UFM  O5'   C5'  C4'   110.44  3.000
 UFM  C6'   C5'  C4'   110.82  3.000
 UFM  H6'2  C6'  H6'1  106.86  3.000
 UFM  H6'2  C6'  O6'   111.56  3.000
 UFM  H6'1  C6'  O6'   111.77  3.000
 UFM  H6'2  C6'  C5'   108.23  3.000
 UFM  H6'1  C6'  C5'   108.71  3.000
 UFM  O6'   C6'  C5'   109.59  3.000
 UFM  HO2A  O2'  C2'   108.35  3.000
 UFM  HO3A  O3'  C3'   108.74  3.000
 UFM  HO4'  O4'  C4'   107.59  3.000
 UFM  C5'   O5'  C1'   116.04  3.000
 UFM  HO6'  O6'  C6'   107.55  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
 UFM  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 UFM  CONST_02  C5    C4   N3   C2     0.00   0.0  0
 UFM  CONST_03  C6    N1   C2   N3     0.00   0.0  0
 UFM  CONST_04  C1D   N1   C2   N3   180.00   0.0  0
 UFM  CONST_05  O4    C4   N3   C2   180.00   0.0  0
 UFM  CONST_06  O2    C2   N3   C4   180.00   0.0  0
 UFM  CONST_07  O2    C2   N1   C6   180.00   0.0  0
 UFM  CONST_08  C1D   N1   C2   O2     0.00   0.0  0
 UFM  CONST_09  HN3   N3   C2   N1   180.00   0.0  0
 UFM  Var_01    O1A   PA   O5D  C5D  -76.54  30.0  3
 UFM  Var_02    O1B   PB   O3A  PA   -87.26  30.0  3
 UFM  Var_03    H5'1  C5D  O5D  PA   -76.20  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
 UFM  chir_01  C1D  N1   C2D  O4D  negativ
 UFM  chir_02  C2D  O2D  C3D  C1D  positiv
 UFM  chir_03  C3D  O3D  C2D  C4D  negativ
 UFM  chir_04  C4D  O4D  C3D  C5D  negativ
 UFM  chir_07  C1'  O3B  C2'  O5'  positiv
 UFM  chir_08  C2'  O2'  C1'  C3'  positiv
 UFM  chir_09  C3'  O3'  C2'  C4'  positiv
 UFM  chir_10  C4'  O4'  C3'  C5'  negativ
 UFM  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
 UFM  plan-1  N1   0.020
 UFM  plan-1  C2   0.020
 UFM  plan-1  N3   0.020
 UFM  plan-1  C4   0.020
 UFM  plan-1  C5   0.020
 UFM  plan-1  C6   0.020
 UFM  plan-1  O2   0.020
 UFM  plan-1  O4   0.020
 UFM  plan-1  C1D  0.020
 UFM  plan-1  HN3  0.020
 UFM  plan-1  H5   0.020
 UFM  plan-1  H6   0.020

