# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun 28 23:50:30 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,3R,4S,5R)-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[C@H]3OC[C@@H](O)[C@H](O)[C@H]3O)O2)C(=O)NC1=O
#
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
 TDX  TDX  '[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,3R,4S,5R)-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)'  ligand  56  34  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TDX
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
 TDX  O4    O  O      0  -0.456   3.9235   0.4979  -6.2930
 TDX  C4    C  CR6    0   0.559   2.8008   0.7181  -5.8762
 TDX  N3    N  NR16   0  -0.733   1.9357  -0.3244  -5.5982
 TDX  C2    C  CR6    0   0.741   0.6492  -0.2555  -5.1293
 TDX  O2    O  O      0  -0.472  -0.0111  -1.2521  -4.9232
 TDX  C5    C  CR6    0  -0.185   2.2487   2.0333  -5.6247
 TDX  C5M   C  CH3    0  -0.706   3.0977   3.2353  -5.8792
 TDX  C6    C  CR16   0   0.059   0.9894   2.1076  -5.1611
 TDX  N1    N  NR6    0  -0.567   0.1851   1.0229  -4.9234
 TDX  C1B   C  CH1    0   0.218  -1.1543   1.2358  -4.3758
 TDX  C2B   C  CH2    0  -0.560  -2.3135   0.6194  -5.1647
 TDX  C3B   C  CH1    0   0.021  -2.8796  -0.4649  -4.2472
 TDX  O3B   O  OH1    0  -0.669  -4.2825  -0.5511  -4.2324
 TDX  O4B   O  O2     0  -0.490  -1.2063   0.7201  -3.0768
 TDX  C4B   C  CH1    0   0.017  -2.4009  -0.0130  -2.8669
 TDX  C5B   C  CH2    0  -0.157  -2.1401  -1.1641  -1.9268
 TDX  O5B   O  O2     0  -0.621  -1.7943  -0.6602  -0.6541
 TDX  PA    P  P      0   1.341  -1.9283  -1.6898   0.6251
 TDX  O1A   O  O      0  -0.795  -1.0605  -2.8849   0.3869
 TDX  O2A   O  OP    -1  -0.799  -3.3712  -1.8582   0.9844
 TDX  O3A   O  O2     0  -0.735  -1.2009  -0.6448   1.6626
 TDX  PB    P  P      0   1.351  -1.4234  -0.6848   3.2899
 TDX  O1B   O  O      0  -0.783  -1.4839  -2.1048   3.7520
 TDX  O2B   O  OP    -1  -0.790  -2.4626   0.3115   3.6938
 TDX  O1'   O  O2     0  -0.626   0.0749  -0.0603   3.6201
 TDX  C1'   C  CH1    0   0.242   0.2611   0.7350   4.7489
 TDX  O5'   O  O2     0  -0.496   0.0072   0.0397   5.9354
 TDX  C5'   C  CH2    0  -0.224   0.8628  -1.0686   6.1501
 TDX  C2'   C  CH1    0  -0.001   1.7010   1.2668   4.7292
 TDX  O2'   O  OH1    0  -0.664   1.9978   1.9320   3.5311
 TDX  C3'   C  CH1    0   0.010   2.6866   0.1238   4.9161
 TDX  O3'   O  OH1    0  -0.671   3.9840   0.6641   4.9853
 TDX  C4'   C  CH1    0  -0.008   2.3232  -0.6321   6.1889
 TDX  O4'   O  OH1    0  -0.673   3.1842  -1.7450   6.2863
 TDX  H3    H  HNR6   0   0.425   2.2857  -1.2615  -5.7562
 TDX  H5M1  H  HCH3   0   0.246   3.4358   3.2707  -6.9155
 TDX  H5M2  H  HCH3   0   0.247   2.5457   4.1515  -5.6757
 TDX  H5M3  H  HCH3   0   0.247   3.9882   3.2343  -5.2490
 TDX  H6    H  HCR6   0   0.317   0.5345   3.0661  -4.9501
 TDX  H1B   H  HCH1   0   0.254  -1.2634   2.3230  -4.3536
 TDX  H2'1  H  HCH2   0   0.266  -3.0749   1.3868  -5.3151
 TDX  H2'2  H  HCH2   0   0.275  -2.0165   0.2539  -6.1461
 TDX  H3B   H  HCH1   0   0.233  -2.4366  -1.4328  -4.4968
 TDX  HO3'  H  HOH1   0   0.457  -4.5634  -1.0294  -5.0177
 TDX  H4B   H  HCH1   0   0.226  -3.1677   0.6438  -2.4306
 TDX  H5'1  H  HCH2   0   0.211  -3.0526  -1.7723  -1.8897
 TDX  H5'2  H  HCH2   0   0.214  -1.3405  -1.7913  -2.3352
 TDX  H1'   H  HCH1   0   0.237  -0.4441   1.5740   4.7529
 TDX  H5B   H  HCH2   0   0.239   0.5716  -1.4981   7.1105
 TDX  H5D   H  HCH2   0   0.221   0.7172  -1.8382   5.3852
 TDX  H2'   H  HCH1   0   0.219   1.7966   1.9428   5.5922
 TDX  HO2'  H  HOH1   0   0.454   1.4740   2.7383   3.4932
 TDX  H3'   H  HCH1   0   0.211   2.5964  -0.5674   4.0639
 TDX  HO3A  H  HOH1   0   0.448   4.5943  -0.0608   5.1569
 TDX  H4'   H  HCH1   0   0.216   2.4659   0.0495   7.0400
 TDX  HO4'  H  HOH1   0   0.459   3.1841  -2.0561   7.1963

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
 TDX  O4   C4    double  1.218  0.020  1.218
 TDX  C4   N3    single  1.383  0.020  1.383
 TDX  C4   C5    single  1.448  0.020  1.448
 TDX  N3   C2    single  1.371  0.020  1.371
 TDX  N3   H3    single  0.860  0.020  1.020
 TDX  C2   O2    double  1.213  0.020  1.213
 TDX  C2   N1    single  1.376  0.020  1.376
 TDX  C5   C5M   single  1.493  0.020  1.493
 TDX  C5   C6    double  1.344  0.020  1.344
 TDX  C5M  H5M1  single  0.970  0.020  1.090
 TDX  C5M  H5M2  single  0.970  0.020  1.090
 TDX  C5M  H5M3  single  0.970  0.020  1.090
 TDX  C6   N1    single  1.371  0.020  1.371
 TDX  C6   H6    single  0.930  0.020  1.080
 TDX  N1   C1B   single  1.463  0.020  1.463
 TDX  C1B  C2B   single  1.532  0.020  1.532
 TDX  C1B  O4B   single  1.399  0.020  1.399
 TDX  C1B  H1B   single  0.970  0.020  1.090
 TDX  C2B  C3B   single  1.529  0.020  1.529
 TDX  C2B  H2'1  single  0.970  0.020  1.090
 TDX  C2B  H2'2  single  0.970  0.020  1.090
 TDX  C3B  O3B   single  1.406  0.020  1.406
 TDX  C3B  C4B   single  1.529  0.020  1.529
 TDX  C3B  H3B   single  0.970  0.020  1.090
 TDX  O3B  HO3'  single  0.850  0.020  0.980
 TDX  O4B  C4B   single  1.417  0.020  1.417
 TDX  C4B  C5B   single  1.509  0.020  1.509
 TDX  C4B  H4B   single  0.970  0.020  1.090
 TDX  C5B  O5B   single  1.412  0.020  1.412
 TDX  C5B  H5'1  single  0.970  0.020  1.090
 TDX  C5B  H5'2  single  0.970  0.020  1.090
 TDX  O5B  PA    single  1.648  0.020  1.648
 TDX  PA   O1A   deloc   1.496  0.020  1.496
 TDX  PA   O2A   deloc   1.496  0.020  1.496
 TDX  PA   O3A   single  1.642  0.020  1.642
 TDX  O3A  PB    single  1.643  0.020  1.643
 TDX  PB   O1B   deloc   1.495  0.020  1.495
 TDX  PB   O2B   deloc   1.495  0.020  1.495
 TDX  PB   O1'   single  1.656  0.020  1.656
 TDX  O1'  C1'   single  1.393  0.020  1.393
 TDX  C1'  O5'   single  1.398  0.020  1.398
 TDX  C1'  C2'   single  1.535  0.020  1.535
 TDX  C1'  H1'   single  0.970  0.020  1.090
 TDX  O5'  C5'   single  1.416  0.020  1.416
 TDX  C5'  C4'   single  1.525  0.020  1.525
 TDX  C5'  H5B   single  0.970  0.020  1.090
 TDX  C5'  H5D   single  0.970  0.020  1.090
 TDX  C2'  O2'   single  1.402  0.020  1.402
 TDX  C2'  C3'   single  1.521  0.020  1.521
 TDX  C2'  H2'   single  0.970  0.020  1.090
 TDX  O2'  HO2'  single  0.850  0.020  0.980
 TDX  C3'  O3'   single  1.407  0.020  1.407
 TDX  C3'  C4'   single  1.524  0.020  1.524
 TDX  C3'  H3'   single  0.970  0.020  1.090
 TDX  O3'  HO3A  single  0.850  0.020  0.980
 TDX  C4'  O4'   single  1.410  0.020  1.410
 TDX  C4'  H4'   single  0.970  0.020  1.090
 TDX  O4'  HO4'  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
 TDX  C5    C4   N3    114.28  3.000
 TDX  C5    C4   O4    125.10  3.000
 TDX  N3    C4   O4    120.61  3.000
 TDX  H3    N3   C2    115.09  3.000
 TDX  H3    N3   C4    116.75  3.000
 TDX  C2    N3   C4    128.16  3.000
 TDX  N1    C2   O2    123.67  3.000
 TDX  N1    C2   N3    114.48  3.000
 TDX  O2    C2   N3    121.84  3.000
 TDX  C6    C5   C5M   123.16  3.000
 TDX  C6    C5   C4    117.85  3.000
 TDX  C5M   C5   C4    118.99  3.000
 TDX  H5M3  C5M  H5M2  107.86  3.000
 TDX  H5M3  C5M  H5M1  107.21  3.000
 TDX  H5M2  C5M  H5M1  107.91  3.000
 TDX  H5M3  C5M  C5    111.40  3.000
 TDX  H5M2  C5M  C5    110.93  3.000
 TDX  H5M1  C5M  C5    111.36  3.000
 TDX  H6    C6   N1    114.86  3.000
 TDX  H6    C6   C5    120.69  3.000
 TDX  N1    C6   C5    124.45  3.000
 TDX  C1B   N1   C6    119.14  3.000
 TDX  C1B   N1   C2    120.02  3.000
 TDX  C6    N1   C2    120.76  3.000
 TDX  H1B   C1B  O4B   110.14  3.000
 TDX  H1B   C1B  C2B   109.58  3.000
 TDX  O4B   C1B  C2B   107.57  3.000
 TDX  H1B   C1B  N1    104.12  3.000
 TDX  O4B   C1B  N1    109.16  3.000
 TDX  C2B   C1B  N1    116.20  3.000
 TDX  H2'2  C2B  H2'1  107.59  3.000
 TDX  H2'2  C2B  C3B   113.82  3.000
 TDX  H2'1  C2B  C3B   108.84  3.000
 TDX  H2'2  C2B  C1B   113.14  3.000
 TDX  H2'1  C2B  C1B   108.42  3.000
 TDX  C3B   C2B  C1B   104.86  3.000
 TDX  H3B   C3B  C4B   109.93  3.000
 TDX  H3B   C3B  O3B   110.64  3.000
 TDX  C4B   C3B  O3B   108.73  3.000
 TDX  H3B   C3B  C2B   109.92  3.000
 TDX  C4B   C3B  C2B   102.48  3.000
 TDX  O3B   C3B  C2B   114.79  3.000
 TDX  HO3'  O3B  C3B   108.28  3.000
 TDX  C4B   O4B  C1B   111.08  3.000
 TDX  H4B   C4B  C5B   109.20  3.000
 TDX  H4B   C4B  O4B   109.72  3.000
 TDX  C5B   C4B  O4B   109.95  3.000
 TDX  H4B   C4B  C3B   108.43  3.000
 TDX  C5B   C4B  C3B   113.02  3.000
 TDX  O4B   C4B  C3B   106.44  3.000
 TDX  H5'2  C5B  H5'1  107.60  3.000
 TDX  H5'2  C5B  O5B   111.20  3.000
 TDX  H5'1  C5B  O5B   111.78  3.000
 TDX  H5'2  C5B  C4B   109.31  3.000
 TDX  H5'1  C5B  C4B   107.47  3.000
 TDX  O5B   C5B  C4B   109.37  3.000
 TDX  PA    O5B  C5B   117.19  3.000
 TDX  O3A   PA   O2A   110.30  3.000
 TDX  O3A   PA   O1A   110.61  3.000
 TDX  O2A   PA   O1A   120.51  3.000
 TDX  O3A   PA   O5B    93.26  3.000
 TDX  O2A   PA   O5B   109.58  3.000
 TDX  O1A   PA   O5B   109.17  3.000
 TDX  PB    O3A  PA    123.38  3.000
 TDX  O1'   PB   O2B   108.89  3.000
 TDX  O1'   PB   O1B   109.46  3.000
 TDX  O2B   PB   O1B   121.43  3.000
 TDX  O1'   PB   O3A    93.77  3.000
 TDX  O2B   PB   O3A   110.21  3.000
 TDX  O1B   PB   O3A   109.56  3.000
 TDX  C1'   O1'  PB    119.84  3.000
 TDX  H1'   C1'  C2'   109.78  3.000
 TDX  H1'   C1'  O5'   105.11  3.000
 TDX  C2'   C1'  O5'   110.69  3.000
 TDX  H1'   C1'  O1'   110.73  3.000
 TDX  C2'   C1'  O1'   108.22  3.000
 TDX  O5'   C1'  O1'   112.29  3.000
 TDX  C5'   O5'  C1'   114.07  3.000
 TDX  H5D   C5'  H5B   107.61  3.000
 TDX  H5D   C5'  C4'   110.27  3.000
 TDX  H5B   C5'  C4'   110.22  3.000
 TDX  H5D   C5'  O5'   111.34  3.000
 TDX  H5B   C5'  O5'   106.27  3.000
 TDX  C4'   C5'  O5'   111.00  3.000
 TDX  H2'   C2'  C3'   108.00  3.000
 TDX  H2'   C2'  O2'   111.12  3.000
 TDX  C3'   C2'  O2'   108.93  3.000
 TDX  H2'   C2'  C1'   106.51  3.000
 TDX  C3'   C2'  C1'   110.24  3.000
 TDX  O2'   C2'  C1'   111.95  3.000
 TDX  HO2'  O2'  C2'   108.43  3.000
 TDX  H3'   C3'  C4'   108.39  3.000
 TDX  H3'   C3'  O3'   110.77  3.000
 TDX  C4'   C3'  O3'   111.67  3.000
 TDX  H3'   C3'  C2'   108.88  3.000
 TDX  C4'   C3'  C2'   108.71  3.000
 TDX  O3'   C3'  C2'   108.36  3.000
 TDX  HO3A  O3'  C3'   107.70  3.000
 TDX  H4'   C4'  O4'   110.88  3.000
 TDX  H4'   C4'  C3'   107.93  3.000
 TDX  O4'   C4'  C3'   107.66  3.000
 TDX  H4'   C4'  C5'   108.75  3.000
 TDX  O4'   C4'  C5'   111.14  3.000
 TDX  C3'   C4'  C5'   110.43  3.000
 TDX  HO4'  O4'  C4'   108.69  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
 TDX  CONST_01  N1    C2   N3   C4     0.00   0.0  0
 TDX  CONST_02  C6    N1   C2   N3     0.00   0.0  0
 TDX  CONST_03  C1B   N1   C2   N3   180.00   0.0  0
 TDX  CONST_04  C5    C4   N3   C2     0.00   0.0  0
 TDX  CONST_05  C2    N3   C4   O4   180.00   0.0  0
 TDX  CONST_06  O2    C2   N3   C4   180.00   0.0  0
 TDX  CONST_07  C6    N1   C2   O2   180.00   0.0  0
 TDX  CONST_08  C1B   N1   C2   O2     0.00   0.0  0
 TDX  CONST_09  H3    N3   C4   C5   180.00   0.0  0
 TDX  Var_01    C4'   C5'  O5'  C1'   58.86  30.0  1
 TDX  Var_02    H5M1  C5M  C5   C4    58.12  30.0  3
 TDX  Var_03    O1A   PA   O5B  C5B   58.68  30.0  3
 TDX  Var_04    O1B   PB   O3A  PA    39.01  30.0  3
 TDX  Var_05    H5'1  C5B  O5B  PA    42.42  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
 TDX  chir_01  C1B  N1   C2B  O4B  negativ
 TDX  chir_02  C3B  O3B  C4B  C2B  positiv
 TDX  chir_03  C4B  O4B  C3B  C5B  negativ
 TDX  chir_06  C1'  O1'  O5'  C2'  negativ
 TDX  chir_07  C2'  O2'  C1'  C3'  negativ
 TDX  chir_08  C3'  O3'  C2'  C4'  positiv
 TDX  chir_09  C4'  O4'  C3'  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
 TDX  plan-1  O4   0.020
 TDX  plan-1  C4   0.020
 TDX  plan-1  N3   0.020
 TDX  plan-1  C2   0.020
 TDX  plan-1  O2   0.020
 TDX  plan-1  C5   0.020
 TDX  plan-1  C5M  0.020
 TDX  plan-1  C6   0.020
 TDX  plan-1  N1   0.020
 TDX  plan-1  C1B  0.020
 TDX  plan-1  H3   0.020
 TDX  plan-1  H6   0.020

