# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 27 05:02:57 2022
#   Inital geometry file: a 194 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1[C@H](O[C@H](CO)[C@@H](O)[C@@H]1O[C@@](CF)(O[P](O)(O)=O)C(O)=O)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
#
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
 TET  TET  '(2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(R)-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}-3-fluoro-2-(phosphonooxy)propanoic acid (non-preferred name)'  ligand  76  50  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TET
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
 TET  C1    C  CR6    0   0.562  47.9457  22.8884  36.1083
 TET  N1    N  NR16   0  -0.734  47.9666  24.0686  36.8395
 TET  C3    C  CR6    0   0.723  47.7075  24.2476  38.1748
 TET  N2    N  NR6    0  -0.562  47.3936  23.0888  38.8552
 TET  C5    C  CR16   0   0.092  47.3433  21.8861  38.2115
 TET  C6    C  CR16   0  -0.531  47.6000  21.7376  36.9012
 TET  O1    O  O      0  -0.462  48.2033  22.8961  34.9185
 TET  O2    O  O      0  -0.474  47.7566  25.3433  38.6936
 TET  C9    C  CH1    0  -0.017  45.6315  22.9037  40.6236
 TET  C2    C  CH1    0   0.192  47.1019  23.1480  40.2855
 TET  O3    O  O2     0  -0.499  47.8326  22.1469  40.9313
 TET  C4    C  CH1    0  -0.011  47.0584  21.5510  41.9766
 TET  C15   C  CH1    0  -0.073  45.7530  22.3597  42.0522
 TET  C12   C  CH2    0  -0.179  46.8939  20.0635  41.7381
 TET  O14   O  OH1    0  -0.670  45.8581  23.4517  42.9344
 TET  O4    O  O2     0  -0.634  46.0433  19.8435  40.6389
 TET  P1    P  P      0   1.377  46.0275  18.4093  39.8241
 TET  O5    O  O      0  -0.777  46.2909  17.2824  40.7747
 TET  O6    O  OP    -1  -0.777  46.8449  18.5610  38.5787
 TET  O7    O  O2     0  -0.743  44.4346  18.3476  39.4484
 TET  P2    P  P      0   1.379  43.3732  19.4681  38.8796
 TET  O8    O  O2     0  -0.633  42.7991  20.1139  40.2905
 TET  O9    O  O      0  -0.782  42.2797  18.6959  38.2137
 TET  O10   O  OP    -1  -0.773  44.0842  20.5824  38.1842
 TET  C10   C  CH1    0   0.280  41.8104  19.4638  41.0351
 TET  C18   C  CH1    0  -0.142  41.0115  20.5036  41.8340
 TET  C13   C  CH1    0   0.008  41.7784  21.0749  43.0377
 TET  C20   C  CH1    0   0.032  42.4234  19.9306  43.8192
 TET  C16   C  CH1    0  -0.035  43.2014  19.0053  42.8786
 TET  C17   C  CH2    0  -0.202  43.8668  17.8393  43.5756
 TET  N3    N  NH1    0  -0.643  40.5633  21.5605  40.9689
 TET  O21   O  O2     0  -0.520  40.8591  21.7410  43.8768
 TET  O22   O  OH1    0  -0.665  43.3070  20.4739  44.7722
 TET  O23   O  O2     0  -0.497  42.3429  18.4898  41.8772
 TET  O24   O  OH1    0  -0.670  42.9073  17.0747  44.2677
 TET  O12   O  O      0  -0.520  38.5513  20.6547  40.4628
 TET  C8    C  CH3    0  -0.796  39.0963  22.7870  39.5178
 TET  C11   C  CT     0   0.345  40.9376  23.1230  44.1456
 TET  C19   C  CH2    0  -0.057  42.2217  23.4734  44.8933
 TET  O13   O  O2     0  -0.670  40.7374  23.8897  43.0016
 TET  P3    P  P      0   1.305  41.8114  24.7412  42.0033
 TET  O15   O  O      0  -0.840  40.8528  25.5499  41.1519
 TET  O16   O  OP    -1  -0.852  42.5224  23.6155  41.1877
 TET  O17   O  OP    -1  -0.837  42.7560  25.5239  42.8912
 TET  C14   C  C      0   0.363  39.7097  23.4665  45.0675
 TET  O18   O  OC    -1  -0.593  38.8189  22.6138  45.2040
 TET  O19   O  O      0  -0.613  39.7357  24.6178  45.5428
 TET  F1    F  F      0  -0.392  42.1772  22.8614  46.1502
 TET  HN1   H  HNR6   0   0.420  48.1971  24.9142  36.3322
 TET  H5    H  HCR6   0   0.338  47.0868  21.0315  38.8178
 TET  H6    H  HCR6   0   0.278  47.5468  20.7611  36.4456
 TET  H2    H  HCH1   0   0.254  47.4019  24.1427  40.6229
 TET  H4    H  HCH1   0   0.246  47.6143  21.6521  42.9168
 TET  H15   H  HCH1   0   0.252  44.9056  21.7199  42.3235
 TET  H121  H  HCH2   0   0.229  47.8854  19.6212  41.5876
 TET  H122  H  HCH2   0   0.217  46.4790  19.6192  42.6504
 TET  HO4   H  HOH1   0   0.451  45.9282  23.1090  43.8308
 TET  H10   H  HCH1   0   0.227  41.1226  18.9327  40.3709
 TET  H18   H  HCH1   0   0.247  40.1364  19.9748  42.2229
 TET  H13   H  HCH1   0   0.245  42.5652  21.7417  42.6704
 TET  H20   H  HCH1   0   0.214  41.6219  19.3576  44.3031
 TET  H16   H  HCH1   0   0.239  44.0139  19.5857  42.4233
 TET  H171  H  HCH2   0   0.211  44.3978  17.2484  42.8184
 TET  H172  H  HCH2   0   0.200  44.6338  18.2426  44.2477
 TET  HN3   H  HNH1   0   0.422  41.2068  22.3542  40.8679
 TET  HO2   H  HOH1   0   0.452  43.2871  19.9313  45.5645
 TET  H24   H  HOH1   0   0.454  43.3683  16.3890  44.7586
 TET  H81   H  HCH3   0   0.246  38.0308  23.0095  39.5215
 TET  H82   H  HCH3   0   0.248  39.6442  23.6670  39.8524
 TET  H83   H  HCH3   0   0.256  39.3838  22.5808  38.4848
 TET  H191  H  HCH2   0   0.192  43.1232  23.1298  44.3850
 TET  H192  H  HCH2   0   0.204  42.2936  24.5445  45.0444
 TET  O11   O  OH1    0  -0.720  44.9064  24.0636  40.4423
 TET  C7    C  C      0   0.493  39.3683  21.5677  40.3679
 TET  HO1   H  HOH1   0   0.468  43.9478  23.8953  40.7239
 TET  H9    H  HCH1   0   0.235  45.2606  22.0803  39.9992

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
 TET  C1   N1    single  1.389  0.020  1.389
 TET  C1   C6    single  1.440  0.020  1.440
 TET  C1   O1    double  1.217  0.020  1.217
 TET  N1   C3    single  1.372  0.020  1.372
 TET  N1   HN1   single  0.860  0.020  1.020
 TET  C3   N2    single  1.380  0.020  1.380
 TET  C3   O2    double  1.213  0.020  1.213
 TET  N2   C5    single  1.365  0.020  1.365
 TET  N2   C2    single  1.461  0.020  1.461
 TET  C5   C6    double  1.343  0.020  1.343
 TET  C5   H5    single  0.930  0.020  1.080
 TET  C6   H6    single  0.930  0.020  1.080
 TET  C9   C2    single  1.528  0.020  1.528
 TET  C9   C15   single  1.533  0.020  1.533
 TET  C9   O11   single  1.380  0.020  1.380
 TET  C9   H9    single  0.970  0.020  1.090
 TET  C2   O3    single  1.398  0.020  1.398
 TET  C2   H2    single  0.970  0.020  1.090
 TET  O3   C4    single  1.431  0.020  1.431
 TET  C4   C15   single  1.537  0.020  1.537
 TET  C4   C12   single  1.515  0.020  1.515
 TET  C4   H4    single  0.970  0.020  1.090
 TET  C15  O14   single  1.408  0.020  1.408
 TET  C15  H15   single  0.970  0.020  1.090
 TET  C12  O4    single  1.407  0.020  1.407
 TET  C12  H121  single  0.970  0.020  1.090
 TET  C12  H122  single  0.970  0.020  1.090
 TET  O14  HO4   single  0.850  0.020  0.980
 TET  O11  HO1   single  0.850  0.020  0.980
 TET  O4   P1    single  1.650  0.020  1.650
 TET  P1   O5    deloc   1.498  0.020  1.498
 TET  P1   O6    deloc   1.497  0.020  1.497
 TET  P1   O7    single  1.638  0.020  1.638
 TET  O7   P2    single  1.645  0.020  1.645
 TET  P2   O8    single  1.655  0.020  1.655
 TET  P2   O9    deloc   1.495  0.020  1.495
 TET  P2   O10   deloc   1.494  0.020  1.494
 TET  O8   C10   single  1.398  0.020  1.398
 TET  C10  C18   single  1.536  0.020  1.536
 TET  C10  O23   single  1.393  0.020  1.393
 TET  C10  H10   single  0.970  0.020  1.090
 TET  C18  C13   single  1.537  0.020  1.537
 TET  C18  N3    single  1.437  0.020  1.437
 TET  C18  H18   single  0.970  0.020  1.090
 TET  C13  C20   single  1.528  0.020  1.528
 TET  C13  O21   single  1.412  0.020  1.412
 TET  C13  H13   single  0.970  0.020  1.090
 TET  C20  C16   single  1.532  0.020  1.532
 TET  C20  O22   single  1.409  0.020  1.409
 TET  C20  H20   single  0.970  0.020  1.090
 TET  C16  C17   single  1.513  0.020  1.513
 TET  C16  O23   single  1.416  0.020  1.416
 TET  C16  H16   single  0.970  0.020  1.090
 TET  C17  O24   single  1.409  0.020  1.409
 TET  C17  H171  single  0.970  0.020  1.090
 TET  C17  H172  single  0.970  0.020  1.090
 TET  C7   N3    single  1.338  0.020  1.338
 TET  C7   O12   double  1.229  0.020  1.229
 TET  C7   C8    single  1.511  0.020  1.511
 TET  N3   HN3   single  0.860  0.020  1.020
 TET  O21  C11   single  1.410  0.020  1.410
 TET  O22  HO2   single  0.850  0.020  0.980
 TET  O24  H24   single  0.850  0.020  0.980
 TET  C8   H81   single  0.970  0.020  1.090
 TET  C8   H82   single  0.970  0.020  1.090
 TET  C8   H83   single  0.970  0.020  1.090
 TET  C11  C19   single  1.527  0.020  1.527
 TET  C11  O13   single  1.392  0.020  1.392
 TET  C11  C14   single  1.573  0.020  1.573
 TET  C19  F1    single  1.399  0.020  1.399
 TET  C19  H191  single  0.970  0.020  1.090
 TET  C19  H192  single  0.970  0.020  1.090
 TET  O13  P3    single  1.696  0.020  1.696
 TET  P3   O15   deloc   1.516  0.020  1.516
 TET  P3   O16   deloc   1.561  0.020  1.561
 TET  P3   O17   deloc   1.514  0.020  1.514
 TET  C14  O18   deloc   1.241  0.020  1.241
 TET  C14  O19   deloc   1.246  0.020  1.246

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
 TET  O1    C1   C6    126.45  3.000
 TET  O1    C1   N1    120.40  3.000
 TET  C6    C1   N1    113.14  3.000
 TET  HN1   N1   C3    114.94  3.000
 TET  HN1   N1   C1    116.70  3.000
 TET  C3    N1   C1    128.36  3.000
 TET  O2    C3   N2    123.83  3.000
 TET  O2    C3   N1    121.76  3.000
 TET  N2    C3   N1    114.42  3.000
 TET  C2    N2   C5    119.34  3.000
 TET  C2    N2   C3    119.61  3.000
 TET  C5    N2   C3    121.04  3.000
 TET  H5    C5   C6    120.40  3.000
 TET  H5    C5   N2    116.21  3.000
 TET  C6    C5   N2    123.39  3.000
 TET  H6    C6   C5    120.16  3.000
 TET  H6    C6   C1    120.19  3.000
 TET  C5    C6   C1    119.65  3.000
 TET  H9    C9   O11   112.22  3.000
 TET  H9    C9   C15   106.88  3.000
 TET  O11   C9   C15   117.53  3.000
 TET  H9    C9   C2    108.61  3.000
 TET  O11   C9   C2    110.01  3.000
 TET  C15   C9   C2    100.75  3.000
 TET  H2    C2   O3    111.47  3.000
 TET  H2    C2   C9    109.97  3.000
 TET  O3    C2   C9    106.64  3.000
 TET  H2    C2   N2    106.52  3.000
 TET  O3    C2   N2    108.60  3.000
 TET  C9    C2   N2    113.71  3.000
 TET  C4    O3   C2    110.67  3.000
 TET  H4    C4   C12   106.28  3.000
 TET  H4    C4   C15   109.86  3.000
 TET  C12   C4   C15   115.59  3.000
 TET  H4    C4   O3    108.28  3.000
 TET  C12   C4   O3    110.65  3.000
 TET  C15   C4   O3    106.04  3.000
 TET  H15   C15  O14   110.82  3.000
 TET  H15   C15  C4    111.20  3.000
 TET  O14   C15  C4    112.05  3.000
 TET  H15   C15  C9    112.12  3.000
 TET  O14   C15  C9    108.33  3.000
 TET  C4    C15  C9    102.01  3.000
 TET  H122  C12  H121  107.05  3.000
 TET  H122  C12  O4    110.97  3.000
 TET  H121  C12  O4    112.12  3.000
 TET  H122  C12  C4    107.93  3.000
 TET  H121  C12  C4    108.63  3.000
 TET  O4    C12  C4    110.00  3.000
 TET  HO4   O14  C15   108.24  3.000
 TET  P1    O4   C12   121.84  3.000
 TET  O7    P1   O6    110.12  3.000
 TET  O7    P1   O5    106.75  3.000
 TET  O6    P1   O5    120.54  3.000
 TET  O7    P1   O4     98.94  3.000
 TET  O6    P1   O4    108.51  3.000
 TET  O5    P1   O4    109.82  3.000
 TET  P2    O7   P1    132.94  3.000
 TET  O10   P2   O9    121.74  3.000
 TET  O10   P2   O8    105.73  3.000
 TET  O9    P2   O8    109.13  3.000
 TET  O10   P2   O7    111.22  3.000
 TET  O9    P2   O7    105.91  3.000
 TET  O8    P2   O7    101.24  3.000
 TET  C10   O8   P2    121.20  3.000
 TET  H10   C10  O23   105.54  3.000
 TET  H10   C10  C18   108.51  3.000
 TET  O23   C10  C18   110.97  3.000
 TET  H10   C10  O8    110.31  3.000
 TET  O23   C10  O8    112.13  3.000
 TET  C18   C10  O8    109.28  3.000
 TET  H18   C18  N3    108.66  3.000
 TET  H18   C18  C13   107.48  3.000
 TET  N3    C18  C13   110.71  3.000
 TET  H18   C18  C10   105.89  3.000
 TET  N3    C18  C10   110.30  3.000
 TET  C13   C18  C10   113.54  3.000
 TET  H13   C13  O21   112.34  3.000
 TET  H13   C13  C20   108.92  3.000
 TET  O21   C13  C20   108.91  3.000
 TET  H13   C13  C18   108.79  3.000
 TET  O21   C13  C18   108.41  3.000
 TET  C20   C13  C18   109.43  3.000
 TET  H20   C20  O22   111.17  3.000
 TET  H20   C20  C16   109.04  3.000
 TET  O22   C20  C16   109.26  3.000
 TET  H20   C20  C13   107.94  3.000
 TET  O22   C20  C13   108.78  3.000
 TET  C16   C20  C13   110.65  3.000
 TET  H16   C16  O23   110.36  3.000
 TET  H16   C16  C17   105.85  3.000
 TET  O23   C16  C17   108.17  3.000
 TET  H16   C16  C20   108.14  3.000
 TET  O23   C16  C20   110.26  3.000
 TET  C17   C16  C20   113.96  3.000
 TET  H172  C17  H171  106.41  3.000
 TET  H172  C17  O24   112.01  3.000
 TET  H171  C17  O24   112.10  3.000
 TET  H172  C17  C16   107.85  3.000
 TET  H171  C17  C16   108.06  3.000
 TET  O24   C17  C16   110.19  3.000
 TET  HN3   N3   C7    120.77  3.000
 TET  HN3   N3   C18   115.60  3.000
 TET  C7    N3   C18   123.57  3.000
 TET  C11   O21  C13   122.65  3.000
 TET  HO2   O22  C20   109.10  3.000
 TET  C16   O23  C10   113.87  3.000
 TET  H24   O24  C17   108.15  3.000
 TET  H83   C8   H82   108.10  3.000
 TET  H83   C8   H81   107.43  3.000
 TET  H82   C8   H81   109.03  3.000
 TET  H83   C8   C7    109.42  3.000
 TET  H82   C8   C7    112.87  3.000
 TET  H81   C8   C7    109.83  3.000
 TET  C14   C11  O13   104.43  3.000
 TET  C14   C11  C19   108.62  3.000
 TET  O13   C11  C19   113.40  3.000
 TET  C14   C11  O21   106.39  3.000
 TET  O13   C11  O21   112.04  3.000
 TET  C19   C11  O21   111.41  3.000
 TET  H192  C19  H191  108.75  3.000
 TET  H192  C19  F1    108.01  3.000
 TET  H191  C19  F1    107.90  3.000
 TET  H192  C19  C11   110.53  3.000
 TET  H191  C19  C11   113.25  3.000
 TET  F1    C19  C11   108.24  3.000
 TET  P3    O13  C11   132.03  3.000
 TET  O17   P3   O16   113.26  3.000
 TET  O17   P3   O15   116.62  3.000
 TET  O16   P3   O15   112.28  3.000
 TET  O17   P3   O13   108.03  3.000
 TET  O16   P3   O13   103.53  3.000
 TET  O15   P3   O13   101.42  3.000
 TET  O19   C14  O18   127.45  3.000
 TET  O19   C14  C11   114.14  3.000
 TET  O18   C14  C11   118.35  3.000
 TET  HO1   O11  C9    108.73  3.000
 TET  C8    C7   O12   121.55  3.000
 TET  C8    C7   N3    114.70  3.000
 TET  O12   C7   N3    123.73  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
 TET  CONST_01  N2    C3   N1   C1      0.00   0.0  0
 TET  CONST_02  C5    N2   C3   N1      0.00   0.0  0
 TET  CONST_03  C2    N2   C3   N1    180.00   0.0  0
 TET  CONST_04  C6    C1   N1   C3      0.00   0.0  0
 TET  CONST_05  O2    C3   N1   C1    180.00   0.0  0
 TET  CONST_06  O1    C1   N1   C3    180.00   0.0  0
 TET  CONST_07  O2    C3   N2   C5    180.00   0.0  0
 TET  CONST_08  C2    N2   C3   O2      0.00   0.0  0
 TET  CONST_09  HN1   N1   C3   N2    180.00   0.0  0
 TET  CONST_10  O12   C7   N3   C18     0.00   0.0  0
 TET  CONST_11  C8    C7   N3   C18   180.00   0.0  0
 TET  CONST_12  HN3   N3   C7   O12   180.00   0.0  0
 TET  Var_01    O5    P1   O4   C12    33.91  30.0  3
 TET  Var_02    O8    P2   O7   P1    -89.55  30.0  3
 TET  Var_03    O15   P3   O13  C11  -168.73  30.0  3
 TET  Var_04    H121  C12  O4   P1     39.35  30.0  1
 TET  Var_05    H81   C8   C7   N3   -148.97  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
 TET  chir_01  C9   C2   C15  O11  negativ
 TET  chir_02  C2   O3   N2   C9   negativ
 TET  chir_03  C4   O3   C12  C15  positiv
 TET  chir_04  C15  O14  C4   C9   positiv
 TET  chir_07  C10  O8   C18  O23  positiv
 TET  chir_08  C18  N3   C13  C10  positiv
 TET  chir_09  C13  O21  C20  C18  negativ
 TET  chir_10  C20  O22  C13  C16  negativ
 TET  chir_11  C16  O23  C20  C17  negativ
 TET  chir_12  C11  O21  C14  C19  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
 TET  plan-1  C1   0.020
 TET  plan-1  N1   0.020
 TET  plan-1  C3   0.020
 TET  plan-1  N2   0.020
 TET  plan-1  C5   0.020
 TET  plan-1  C6   0.020
 TET  plan-1  O1   0.020
 TET  plan-1  O2   0.020
 TET  plan-1  C2   0.020
 TET  plan-1  HN1  0.020
 TET  plan-1  H5   0.020
 TET  plan-1  H6   0.020
 TET  plan-2  C18  0.020
 TET  plan-2  N3   0.020
 TET  plan-2  O12  0.020
 TET  plan-2  C8   0.020
 TET  plan-2  HN3  0.020
 TET  plan-2  C7   0.020
 TET  plan-3  C11  0.020
 TET  plan-3  C14  0.020
 TET  plan-3  O18  0.020
 TET  plan-3  O19  0.020

