# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun 28 17:55:33 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: (2R,3R,4S,6S)-3,4-dihydroxy-6-methyl-5-oxotetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@H](O[P@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@H](O)C1=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
 TDO  TDO  '(2R,3R,4S,6S)-3,4-dihydroxy-6-methyl-5-oxotetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  57  35  .  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_TDO
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
 TDO  O4P   O  O      0  -0.783  -3.0168  -0.5782   2.9271
 TDO  P2    P  P      0   1.333  -2.7585  -1.1389   1.5680
 TDO  O3P   O  OP    -1  -0.785  -3.2430  -2.5016   1.1899
 TDO  O1    O  O2     0  -0.625  -3.2778  -0.0636   0.4052
 TDO  C1    C  CH1    0   0.299  -4.6321   0.0604   0.1861
 TDO  C2    C  CH1    0  -0.032  -4.8960   0.2962  -1.2963
 TDO  O2    O  OH1    0  -0.660  -4.2209   1.4561  -1.6922
 TDO  C3    C  CH1    0  -0.073  -6.4053   0.4594  -1.4964
 TDO  O3    O  OH1    0  -0.664  -6.6864   0.7488  -2.8315
 TDO  C4    C  C      0   0.359  -6.9088   1.5298  -0.5525
 TDO  O4    O  O      0  -0.382  -7.6060   2.4350  -0.9413
 TDO  C5    C  CH1    0  -0.066  -6.4861   1.3409   0.8965
 TDO  O5    O  O2     0  -0.481  -5.0850   1.1595   0.9385
 TDO  C6    C  CH3    0  -0.685  -6.8557   2.5028   1.7885
 TDO  OPP   O  O2     0  -0.733  -1.1879  -0.9482   1.1487
 TDO  P     P  P      0   1.345   0.0630  -1.2832   2.1632
 TDO  O1P   O  O      0  -0.799  -0.2512  -2.4776   3.0071
 TDO  O2P   O  OP    -1  -0.788   0.5551  -0.0165   2.7873
 TDO  O5'   O  O2     0  -0.620   1.0723  -1.7207   0.9391
 TDO  C5'   C  CH2    0  -0.156   2.3480  -2.2054   1.3021
 TDO  C4'   C  CH1    0   0.015   3.1956  -2.3592   0.0642
 TDO  O4'   O  O2     0  -0.489   3.4793  -1.0866  -0.4919
 TDO  C3'   C  CH1    0   0.021   4.5434  -3.0243   0.3448
 TDO  O3'   O  OH1    0  -0.669   4.4010  -4.4151   0.1964
 TDO  C2'   C  CH2    0  -0.561   5.4603  -2.3627  -0.6838
 TDO  C1'   C  CH1    0   0.217   4.7616  -1.0501  -1.0482
 TDO  N11   N  NR6    0  -0.567   5.4360   0.1796  -0.6310
 TDO  C21   C  CR6    0   0.743   5.7336   0.3874   0.6957
 TDO  O21   O  OC     0  -0.471   5.5027  -0.4196   1.5712
 TDO  N31   N  NR16   0  -0.733   6.3271   1.5943   0.9623
 TDO  C41   C  CR6    0   0.558   6.6419   2.6068   0.0746
 TDO  O41   O  OC     0  -0.456   7.1731   3.6306   0.4651
 TDO  C51   C  CR6    0  -0.185   6.2808   2.3271  -1.3000
 TDO  C5A   C  CH3    0  -0.706   6.5614   3.3553  -2.3458
 TDO  C61   C  CR16   0   0.059   5.6999   1.1450  -1.5681
 TDO  H1    H  HCH1   0   0.201  -5.1847  -0.8462   0.4890
 TDO  H2    H  HCH1   0   0.244  -4.5597  -0.5906  -1.8525
 TDO  HA    H  HOH1   0   0.453  -4.4705   1.6459  -2.6035
 TDO  H3    H  HCH1   0   0.259  -6.8958  -0.4768  -1.1806
 TDO  HB    H  HOH1   0   0.455  -7.3122   1.4847  -2.8583
 TDO  H5    H  HCH1   0   0.255  -6.9952   0.4295   1.2552
 TDO  H6C1  H  HCH3   0   0.239  -6.3979   3.4316   1.4490
 TDO  H6C2  H  HCH3   0   0.243  -7.9352   2.6395   1.8086
 TDO  H6C3  H  HCH3   0   0.252  -6.5271   2.3062   2.8082
 TDO  H5'1  H  HCH2   0   0.213   2.8546  -1.5282   1.9996
 TDO  H5'2  H  HCH2   0   0.214   2.2722  -3.1861   1.7866
 TDO  H4'   H  HCH1   0   0.227   2.6560  -2.9719  -0.6728
 TDO  H3'   H  HCH1   0   0.234   4.8795  -2.7774   1.3556
 TDO  HC    H  HOH1   0   0.457   5.1769  -4.8393   0.5739
 TDO  H2'1  H  HCH2   0   0.267   5.4983  -2.9899  -1.5764
 TDO  H2'2  H  HCH2   0   0.275   6.4830  -2.2235  -0.3371
 TDO  H1'   H  HCH1   0   0.253   4.6957  -0.9585  -2.1347
 TDO  H31   H  HNR6   0   0.425   6.5516   1.7567   1.9364
 TDO  H5A1  H  HCH3   0   0.247   6.0680   4.3004  -2.1149
 TDO  H5A2  H  HCH3   0   0.247   7.6297   3.5610  -2.4259
 TDO  H5A3  H  HCH3   0   0.247   6.2110   3.0231  -3.3215
 TDO  H61   H  HCR6   0   0.316   5.4085   0.8892  -2.5780

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
 TDO  O4P  P2    deloc     1.493  0.020  1.493
 TDO  P2   O3P   deloc     1.495  0.020  1.495
 TDO  P2   O1    single    1.667  0.020  1.667
 TDO  P2   OPP   single    1.637  0.020  1.637
 TDO  O1   C1    single    1.377  0.020  1.377
 TDO  C1   C2    single    1.524  0.020  1.524
 TDO  C1   O5    single    1.407  0.020  1.407
 TDO  C1   H1    single    0.970  0.020  1.090
 TDO  C2   O2    single    1.399  0.020  1.399
 TDO  C2   C3    single    1.531  0.020  1.531
 TDO  C2   H2    single    0.970  0.020  1.090
 TDO  O2   HA    single    0.850  0.020  0.980
 TDO  C3   O3    single    1.395  0.020  1.395
 TDO  C3   C4    single    1.513  0.020  1.513
 TDO  C3   H3    single    0.970  0.020  1.090
 TDO  O3   HB    single    0.850  0.020  0.980
 TDO  C4   O4    double    1.207  0.020  1.207
 TDO  C4   C5    single    1.521  0.020  1.521
 TDO  C5   O5    single    1.413  0.020  1.413
 TDO  C5   C6    single    1.511  0.020  1.511
 TDO  C5   H5    single    0.970  0.020  1.090
 TDO  C6   H6C1  single    0.970  0.020  1.090
 TDO  C6   H6C2  single    0.970  0.020  1.090
 TDO  C6   H6C3  single    0.970  0.020  1.090
 TDO  OPP  P     single    1.645  0.020  1.645
 TDO  P    O1P   deloc     1.496  0.020  1.496
 TDO  P    O2P   deloc     1.495  0.020  1.495
 TDO  P    O5'   single    1.646  0.020  1.646
 TDO  O5'  C5'   single    1.412  0.020  1.412
 TDO  C5'  C4'   single    1.508  0.020  1.508
 TDO  C5'  H5'1  single    0.970  0.020  1.090
 TDO  C5'  H5'2  single    0.970  0.020  1.090
 TDO  C4'  O4'   single    1.417  0.020  1.417
 TDO  C4'  C3'   single    1.529  0.020  1.529
 TDO  C4'  H4'   single    0.970  0.020  1.090
 TDO  O4'  C1'   single    1.398  0.020  1.398
 TDO  C3'  O3'   single    1.406  0.020  1.406
 TDO  C3'  C2'   single    1.529  0.020  1.529
 TDO  C3'  H3'   single    0.970  0.020  1.090
 TDO  O3'  HC    single    0.850  0.020  0.980
 TDO  C2'  C1'   single    1.531  0.020  1.531
 TDO  C2'  H2'1  single    0.970  0.020  1.090
 TDO  C2'  H2'2  single    0.970  0.020  1.090
 TDO  C1'  N11   single    1.463  0.020  1.463
 TDO  C1'  H1'   single    0.970  0.020  1.090
 TDO  N11  C21   aromatic  1.375  0.020  1.375
 TDO  N11  C61   aromatic  1.371  0.020  1.371
 TDO  C21  O21   double    1.213  0.020  1.213
 TDO  C21  N31   aromatic  1.371  0.020  1.371
 TDO  N31  C41   aromatic  1.383  0.020  1.383
 TDO  N31  H31   single    0.860  0.020  1.020
 TDO  C41  O41   double    1.218  0.020  1.218
 TDO  C41  C51   aromatic  1.449  0.020  1.449
 TDO  C51  C5A   single    1.493  0.020  1.493
 TDO  C51  C61   aromatic  1.344  0.020  1.344
 TDO  C5A  H5A1  single    0.970  0.020  1.090
 TDO  C5A  H5A2  single    0.970  0.020  1.090
 TDO  C5A  H5A3  single    0.970  0.020  1.090
 TDO  C61  H61   single    0.930  0.020  1.080

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
 TDO  OPP   P2   O1     92.58  3.000
 TDO  OPP   P2   O3P   110.63  3.000
 TDO  O1    P2   O3P   108.10  3.000
 TDO  OPP   P2   O4P   110.83  3.000
 TDO  O1    P2   O4P   109.81  3.000
 TDO  O3P   P2   O4P   121.11  3.000
 TDO  C1    O1   P2    118.38  3.000
 TDO  H1    C1   O5    109.49  3.000
 TDO  H1    C1   C2    107.89  3.000
 TDO  O5    C1   C2    110.09  3.000
 TDO  H1    C1   O1    112.00  3.000
 TDO  O5    C1   O1    107.56  3.000
 TDO  C2    C1   O1    109.81  3.000
 TDO  H2    C2   C3    108.74  3.000
 TDO  H2    C2   O2    112.20  3.000
 TDO  C3    C2   O2    110.51  3.000
 TDO  H2    C2   C1    108.31  3.000
 TDO  C3    C2   C1    108.32  3.000
 TDO  O2    C2   C1    108.66  3.000
 TDO  HA    O2   C2    107.81  3.000
 TDO  H3    C3   C4    105.89  3.000
 TDO  H3    C3   O3    111.14  3.000
 TDO  C4    C3   O3    112.53  3.000
 TDO  H3    C3   C2    108.08  3.000
 TDO  C4    C3   C2    108.77  3.000
 TDO  O3    C3   C2    110.24  3.000
 TDO  HB    O3   C3    108.37  3.000
 TDO  C5    C4   O4    124.09  3.000
 TDO  C5    C4   C3    114.45  3.000
 TDO  O4    C4   C3    121.45  3.000
 TDO  H5    C5   C6    109.29  3.000
 TDO  H5    C5   O5    109.97  3.000
 TDO  C6    C5   O5    108.89  3.000
 TDO  H5    C5   C4    106.49  3.000
 TDO  C6    C5   C4    113.51  3.000
 TDO  O5    C5   C4    108.65  3.000
 TDO  C5    O5   C1    113.80  3.000
 TDO  H6C3  C6   H6C2  107.74  3.000
 TDO  H6C3  C6   H6C1  108.59  3.000
 TDO  H6C2  C6   H6C1  108.38  3.000
 TDO  H6C3  C6   C5    109.89  3.000
 TDO  H6C2  C6   C5    110.50  3.000
 TDO  H6C1  C6   C5    111.64  3.000
 TDO  P     OPP  P2    123.22  3.000
 TDO  O5'   P    O2P   109.50  3.000
 TDO  O5'   P    O1P   109.64  3.000
 TDO  O2P   P    O1P   120.67  3.000
 TDO  O5'   P    OPP    93.54  3.000
 TDO  O2P   P    OPP   109.58  3.000
 TDO  O1P   P    OPP   110.54  3.000
 TDO  C5'   O5'  P     117.01  3.000
 TDO  H5'2  C5'  H5'1  107.66  3.000
 TDO  H5'2  C5'  C4'   108.08  3.000
 TDO  H5'1  C5'  C4'   109.00  3.000
 TDO  H5'2  C5'  O5'   110.99  3.000
 TDO  H5'1  C5'  O5'   111.65  3.000
 TDO  C4'   C5'  O5'   109.37  3.000
 TDO  H4'   C4'  C3'   108.24  3.000
 TDO  H4'   C4'  O4'   109.60  3.000
 TDO  C3'   C4'  O4'   106.63  3.000
 TDO  H4'   C4'  C5'   109.34  3.000
 TDO  C3'   C4'  C5'   112.90  3.000
 TDO  O4'   C4'  C5'   110.06  3.000
 TDO  C1'   O4'  C4'   111.29  3.000
 TDO  H3'   C3'  C2'   109.87  3.000
 TDO  H3'   C3'  O3'   110.61  3.000
 TDO  C2'   C3'  O3'   114.70  3.000
 TDO  H3'   C3'  C4'   110.01  3.000
 TDO  C2'   C3'  C4'   102.54  3.000
 TDO  O3'   C3'  C4'   108.77  3.000
 TDO  HC    O3'  C3'   108.25  3.000
 TDO  H2'2  C2'  H2'1  107.53  3.000
 TDO  H2'2  C2'  C1'   113.25  3.000
 TDO  H2'1  C2'  C1'   108.30  3.000
 TDO  H2'2  C2'  C3'   113.86  3.000
 TDO  H2'1  C2'  C3'   108.81  3.000
 TDO  C1'   C2'  C3'   104.92  3.000
 TDO  H1'   C1'  N11   103.95  3.000
 TDO  H1'   C1'  C2'   109.64  3.000
 TDO  N11   C1'  C2'   116.25  3.000
 TDO  H1'   C1'  O4'   110.03  3.000
 TDO  N11   C1'  O4'   109.34  3.000
 TDO  C2'   C1'  O4'   107.54  3.000
 TDO  C61   N11  C21   120.74  3.000
 TDO  C61   N11  C1'   119.05  3.000
 TDO  C21   N11  C1'   120.12  3.000
 TDO  N31   C21  O21   121.86  3.000
 TDO  N31   C21  N11   114.47  3.000
 TDO  O21   C21  N11   123.67  3.000
 TDO  H31   N31  C41   116.72  3.000
 TDO  H31   N31  C21   115.09  3.000
 TDO  C41   N31  C21   128.19  3.000
 TDO  C51   C41  O41   125.13  3.000
 TDO  C51   C41  N31   114.27  3.000
 TDO  O41   C41  N31   120.60  3.000
 TDO  C61   C51  C5A   123.17  3.000
 TDO  C61   C51  C41   117.83  3.000
 TDO  C5A   C51  C41   119.00  3.000
 TDO  H5A3  C5A  H5A2  107.88  3.000
 TDO  H5A3  C5A  H5A1  107.97  3.000
 TDO  H5A2  C5A  H5A1  107.17  3.000
 TDO  H5A3  C5A  C51   110.92  3.000
 TDO  H5A2  C5A  C51   111.42  3.000
 TDO  H5A1  C5A  C51   111.31  3.000
 TDO  H61   C61  C51   120.70  3.000
 TDO  H61   C61  N11   114.82  3.000
 TDO  C51   C61  N11   124.48  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
 TDO  CONST_01  C41   N31  C21  N11     0.00   0.0  0
 TDO  CONST_02  C41   C51  C61  N11     0.00   0.0  0
 TDO  CONST_03  C51   C61  N11  C21     0.00   0.0  0
 TDO  CONST_04  C51   C41  N31  C21     0.00   0.0  0
 TDO  CONST_05  C61   N11  C21  N31     0.00   0.0  0
 TDO  CONST_06  C61   C51  C41  N31     0.00   0.0  0
 TDO  CONST_07  N31   C21  N11  C1'   180.00   0.0  0
 TDO  CONST_08  C51   C61  N11  C1'   180.00   0.0  0
 TDO  CONST_09  O21   C21  N11  C1'     0.00   0.0  0
 TDO  CONST_10  C5A   C51  C61  N11   180.00   0.0  0
 TDO  CONST_11  O41   C41  N31  C21   180.00   0.0  0
 TDO  CONST_12  C61   N11  C21  O21   180.00   0.0  0
 TDO  CONST_13  C41   N31  C21  O21   180.00   0.0  0
 TDO  CONST_14  C5A   C51  C41  N31   180.00   0.0  0
 TDO  CONST_15  C61   C51  C41  O41   180.00   0.0  0
 TDO  CONST_16  H61   C61  N11  C1'     0.00   0.0  0
 TDO  CONST_17  H31   N31  C21  N11   180.00   0.0  0
 TDO  Var_01    H5A1  C5A  C51  C41   -58.02  30.0  2
 TDO  Var_02    OPP   P2   O1   C1    172.19  30.0  2
 TDO  Var_03    C4'   C5'  O5'  P    -171.68  30.0  3
 TDO  Var_04    O1P   P    OPP  P2     36.30  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
 TDO  chir_02  C1   O1   C2   O5   positiv
 TDO  chir_03  C2   O2   C1   C3   negativ
 TDO  chir_04  C3   O3   C2   C4   negativ
 TDO  chir_05  C5   O5   C4   C6   positiv
 TDO  chir_07  C4'  C5'  O4'  C3'  negativ
 TDO  chir_08  C3'  O3'  C4'  C2'  positiv
 TDO  chir_09  C1'  O4'  N11  C2'  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
 TDO  plan-1  C1'  0.020
 TDO  plan-1  N11  0.020
 TDO  plan-1  C21  0.020
 TDO  plan-1  O21  0.020
 TDO  plan-1  N31  0.020
 TDO  plan-1  C41  0.020
 TDO  plan-1  O41  0.020
 TDO  plan-1  C51  0.020
 TDO  plan-1  C5A  0.020
 TDO  plan-1  C61  0.020
 TDO  plan-1  H31  0.020
 TDO  plan-1  H61  0.020
 TDO  plan-2  C3   0.020
 TDO  plan-2  C4   0.020
 TDO  plan-2  O4   0.020
 TDO  plan-2  C5   0.020

