# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 03:02:51 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: 5'-O-[(R)-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}(sulfanyl)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](S)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
#
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
 TAT  TAT  5'-O-[(R)-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}(sulfanyl)phosphoryl]adenosine  ligand  47  31  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TAT
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
 TAT  N1   N  N     0  -0.474  55.1545  -17.7917  54.2071
 TAT  C2   C  CR16  0   0.047  54.9574  -16.5065  54.4852
 TAT  N3   N  N     0  -0.461  55.6712  -15.4636  54.0984
 TAT  C4   C  CR56  0   0.502  56.7025  -15.8225  53.3355
 TAT  C5   C  CR56  0  -0.005  57.0332  -17.1155  52.9629
 TAT  C6   C  CR6   0   0.461  56.1937  -18.1397  53.4404
 TAT  N6   N  NH2   0  -0.816  56.3998  -19.4272  53.1630
 TAT  N7   N  N     0  -0.453  58.1552  -17.1294  52.1740
 TAT  C8   C  CR15  0   0.117  58.4916  -15.8799  52.0767
 TAT  N9   N  NR5   0  -0.543  57.6528  -15.0312  52.7479
 TAT  PA   P  P     0   1.268  56.1092   -9.8869  56.4171
 TAT  PB   P  P     0   1.496  58.0766   -9.4633  58.5996
 TAT  PG   P  P     0   1.482  57.6186   -6.6041  59.1235
 TAT  C1'  C  CH1   0   0.211  57.8042  -13.6034  52.8342
 TAT  O1A  O  OH1   0  -0.719  56.3507   -6.7325  60.0589
 TAT  O1B  O  O     0  -0.648  59.5186   -9.7175  58.5365
 TAT  S1G  S  S2    0  -0.316  54.4968   -9.1521  57.4812
 TAT  C2'  C  CH1   0  -0.023  56.5645  -12.8152  52.4129
 TAT  O2'  O  OH1   0  -0.655  56.5560  -12.6783  51.0273
 TAT  O2A  O  O     0  -0.646  56.6297   -9.0048  55.3567
 TAT  O2B  O  OH1   0  -0.717  57.3294   -9.7488  59.9623
 TAT  O2G  O  O     0  -0.664  57.7180   -5.4480  58.2251
 TAT  C3'  C  CH1   0  -0.040  56.7195  -11.5259  53.2224
 TAT  O3'  O  OH1   0  -0.667  57.5774  -10.6583  52.5335
 TAT  O3A  O  O2    0  -0.683  57.2454  -10.3067  57.5069
 TAT  O3B  O  O2    0  -0.708  57.5867   -7.9800  58.2332
 TAT  O3G  O  OH1   0  -0.729  58.7533   -6.8690  60.1965
 TAT  C4'  C  CH1   0  -0.058  57.3601  -12.0550  54.5124
 TAT  O4'  O  O2    0  -0.490  58.0702  -13.2381  54.1607
 TAT  C5'  C  CH2   0  -0.208  56.3679  -12.4302  55.6075
 TAT  O5'  O  O2    0  -0.566  55.5536  -11.3150  56.0212
 TAT  H1   H  HCR6  0   0.254  54.0983  -16.2904  55.1111
 TAT  H2   H  HNH2  0   0.404  55.7490  -20.1249  53.4801
 TAT  H3   H  HNH2  0   0.412  57.1503  -19.7146  52.5599
 TAT  H4   H  HCR5  0   0.302  59.3414  -15.5006  51.5277
 TAT  H5   H  HCH1  0   0.265  58.6466  -13.3483  52.1807
 TAT  H6   H  HOH1  0   0.512  55.5755   -6.2368  59.7617
 TAT  H7   H  HSH1  0   0.278  54.6342   -7.9003  57.0269
 TAT  H8   H  HCH1  0   0.263  55.6662  -13.3291  52.7742
 TAT  H9   H  HOH1  0   0.464  55.6872  -12.3703  50.7520
 TAT  H10  H  HOH1  0   0.515  57.8004  -10.3420  60.5653
 TAT  H11  H  HCH1  0   0.256  55.7459  -11.0604  53.4101
 TAT  H12  H  HOH1  0   0.452  57.6444   -9.8467  53.0484
 TAT  H13  H  HOH1  0   0.515  59.6507   -6.6513  59.9074
 TAT  H14  H  HCH1  0   0.261  58.0884  -11.3342  54.8992
 TAT  H15  H  HCH2  0   0.279  55.6684  -13.1862  55.2547
 TAT  H16  H  HCH2  0   0.271  56.8961  -12.8322  56.4739

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
 TAT  C2   N1   aromatic  1.330  0.020  1.330
 TAT  C2   N3   aromatic  1.322  0.020  1.322
 TAT  N1   C6   aromatic  1.338  0.020  1.338
 TAT  N3   C4   aromatic  1.332  0.020  1.332
 TAT  O2'  C2'  single    1.392  0.020  1.392
 TAT  O3'  C3'  single    1.401  0.020  1.401
 TAT  C6   N6   single    1.333  0.020  1.333
 TAT  C6   C5   aromatic  1.408  0.020  1.408
 TAT  C4   C5   aromatic  1.386  0.020  1.386
 TAT  C4   N9   aromatic  1.369  0.020  1.369
 TAT  C5   N7   aromatic  1.372  0.020  1.372
 TAT  C1'  N9   single    1.438  0.020  1.438
 TAT  C1'  C2'  single    1.528  0.020  1.528
 TAT  C1'  O4'  single    1.401  0.020  1.401
 TAT  N9   C8   aromatic  1.369  0.020  1.369
 TAT  C2'  C3'  single    1.530  0.020  1.530
 TAT  N7   C8   aromatic  1.298  0.020  1.298
 TAT  C3'  C4'  single    1.534  0.020  1.534
 TAT  O4'  C4'  single    1.424  0.020  1.424
 TAT  C4'  C5'  single    1.525  0.020  1.525
 TAT  O2A  PA   double    1.474  0.020  1.474
 TAT  C5'  O5'  single    1.441  0.020  1.441
 TAT  O5'  PA   single    1.583  0.020  1.583
 TAT  PA   O3A  single    1.629  0.020  1.629
 TAT  PA   S1G  single    2.067  0.020  2.067
 TAT  O3A  PB   single    1.611  0.020  1.611
 TAT  O1B  PB   double    1.465  0.020  1.465
 TAT  PB   O3B  single    1.605  0.020  1.605
 TAT  PB   O2B  single    1.580  0.020  1.580
 TAT  O3B  PG   single    1.639  0.020  1.639
 TAT  O2G  PG   double    1.468  0.020  1.468
 TAT  O1A  PG   single    1.581  0.020  1.581
 TAT  PG   O3G  single    1.584  0.020  1.584
 TAT  C2   H1   single    0.930  0.020  1.080
 TAT  N6   H2   single    0.860  0.020  1.020
 TAT  N6   H3   single    0.860  0.020  1.020
 TAT  C8   H4   single    0.930  0.020  1.080
 TAT  C1'  H5   single    0.970  0.020  1.090
 TAT  O1A  H6   single    0.850  0.020  0.980
 TAT  S1G  H7   single    1.200  0.020  1.300
 TAT  C2'  H8   single    0.970  0.020  1.090
 TAT  O2'  H9   single    0.850  0.020  0.980
 TAT  O2B  H10  single    0.850  0.020  0.980
 TAT  C3'  H11  single    0.970  0.020  1.090
 TAT  O3'  H12  single    0.850  0.020  0.980
 TAT  O3G  H13  single    0.850  0.020  0.980
 TAT  C4'  H14  single    0.970  0.020  1.090
 TAT  C5'  H15  single    0.970  0.020  1.090
 TAT  C5'  H16  single    0.970  0.020  1.090

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
 TAT  C6   N1   C2   119.12  3.000
 TAT  H1   C2   N3   116.07  3.000
 TAT  H1   C2   N1   115.51  3.000
 TAT  N3   C2   N1   128.42  3.000
 TAT  C4   N3   C2   111.91  3.000
 TAT  N9   C4   C5   104.97  3.000
 TAT  N9   C4   N3   128.86  3.000
 TAT  C5   C4   N3   126.17  3.000
 TAT  N7   C5   C6   132.49  3.000
 TAT  N7   C5   C4   111.06  3.000
 TAT  C6   C5   C4   116.45  3.000
 TAT  N6   C6   C5   122.68  3.000
 TAT  C5   C6   N1   117.93  3.000
 TAT  N6   C6   N1   119.39  3.000
 TAT  H3   N6   H2   118.31  3.000
 TAT  H3   N6   C6   121.11  3.000
 TAT  H2   N6   C6   120.30  3.000
 TAT  C8   N7   C5   104.21  3.000
 TAT  H4   C8   N9   120.89  3.000
 TAT  H4   C8   N7   125.45  3.000
 TAT  N9   C8   N7   113.66  3.000
 TAT  C1'  N9   C8   125.47  3.000
 TAT  C8   N9   C4   106.10  3.000
 TAT  C1'  N9   C4   128.39  3.000
 TAT  O5'  PA   O3A  100.35  3.000
 TAT  O3A  PA   O2A  112.89  3.000
 TAT  O5'  PA   O2A  118.94  3.000
 TAT  O3A  PA   S1G  106.93  3.000
 TAT  O5'  PA   S1G  100.12  3.000
 TAT  O2A  PA   S1G  115.66  3.000
 TAT  O3B  PB   O3A   99.87  3.000
 TAT  O3B  PB   O2B  102.68  3.000
 TAT  O3A  PB   O2B  104.26  3.000
 TAT  O2B  PB   O1B  118.11  3.000
 TAT  O3B  PB   O1B  116.80  3.000
 TAT  O3A  PB   O1B  112.81  3.000
 TAT  O3G  PG   O3B  103.97  3.000
 TAT  O3G  PG   O2G  119.87  3.000
 TAT  O3B  PG   O2G  109.28  3.000
 TAT  O3G  PG   O1A   99.21  3.000
 TAT  O2G  PG   O1A  118.72  3.000
 TAT  O3B  PG   O1A  103.74  3.000
 TAT  H5   C1'  O4'  110.96  3.000
 TAT  H5   C1'  C2'  109.82  3.000
 TAT  O4'  C1'  C2'  106.29  3.000
 TAT  H5   C1'  N9   106.03  3.000
 TAT  O4'  C1'  N9   109.61  3.000
 TAT  C2'  C1'  N9   114.21  3.000
 TAT  H6   O1A  PG   114.79  3.000
 TAT  H7   S1G  PA    94.46  3.000
 TAT  H8   C2'  C3'  107.68  3.000
 TAT  H8   C2'  O2'  111.67  3.000
 TAT  C3'  C2'  O2'  116.37  3.000
 TAT  H8   C2'  C1'  109.39  3.000
 TAT  C3'  C2'  C1'  101.92  3.000
 TAT  O2'  C2'  C1'  109.27  3.000
 TAT  H9   O2'  C2'  108.77  3.000
 TAT  H10  O2B  PB   114.70  3.000
 TAT  H11  C3'  C4'  111.94  3.000
 TAT  H11  C3'  O3'  111.42  3.000
 TAT  C4'  C3'  O3'  111.79  3.000
 TAT  H11  C3'  C2'  111.02  3.000
 TAT  C4'  C3'  C2'  101.33  3.000
 TAT  O3'  C3'  C2'  108.88  3.000
 TAT  H12  O3'  C3'  107.54  3.000
 TAT  PB   O3A  PA   132.73  3.000
 TAT  PG   O3B  PB   130.24  3.000
 TAT  H13  O3G  PG   115.10  3.000
 TAT  H14  C4'  C5'  109.94  3.000
 TAT  H14  C4'  O4'  107.60  3.000
 TAT  C5'  C4'  O4'  107.31  3.000
 TAT  H14  C4'  C3'  110.34  3.000
 TAT  C5'  C4'  C3'  114.65  3.000
 TAT  O4'  C4'  C3'  106.68  3.000
 TAT  C4'  O4'  C1'  110.84  3.000
 TAT  H16  C5'  H15  108.20  3.000
 TAT  H16  C5'  O5'  109.30  3.000
 TAT  H15  C5'  O5'  105.50  3.000
 TAT  H16  C5'  C4'  110.24  3.000
 TAT  H15  C5'  C4'  110.87  3.000
 TAT  O5'  C5'  C4'  112.54  3.000
 TAT  C5'  O5'  PA   124.86  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
 TAT  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 TAT  CONST_02  C4   C5   C6   N1     0.00   0.0  0
 TAT  CONST_03  N7   C5   C6   N1   180.00   0.0  0
 TAT  CONST_04  C5   C6   N1   C2     0.00   0.0  0
 TAT  CONST_05  C5   C4   N3   C2     0.00   0.0  0
 TAT  CONST_06  N9   C4   N3   C2   180.00   0.0  0
 TAT  CONST_07  C6   N1   C2   N3     0.00   0.0  0
 TAT  CONST_08  C6   C5   C4   N3     0.00   0.0  0
 TAT  CONST_09  N7   C5   C4   N3   180.00   0.0  0
 TAT  CONST_10  C8   N9   C4   N3   180.00   0.0  0
 TAT  CONST_11  C8   N7   C5   C4     0.00   0.0  0
 TAT  CONST_12  N7   C8   N9   C4     0.00   0.0  0
 TAT  CONST_13  C8   N9   C4   C5     0.00   0.0  0
 TAT  CONST_14  N9   C8   N7   C5     0.00   0.0  0
 TAT  CONST_15  N9   C4   C5   C6   180.00   0.0  0
 TAT  CONST_16  C8   N7   C5   C6   180.00   0.0  0
 TAT  CONST_17  N9   C4   C5   N7     0.00   0.0  0
 TAT  CONST_18  C1'  N9   C4   N3     0.00   0.0  0
 TAT  CONST_19  C1'  N9   C4   C5   180.00   0.0  0
 TAT  CONST_20  C1'  N9   C8   N7   180.00   0.0  0
 TAT  CONST_21  N6   C6   N1   C2   180.00   0.0  0
 TAT  CONST_22  N6   C6   C5   C4   180.00   0.0  0
 TAT  CONST_23  N7   C5   C6   N6     0.00   0.0  0
 TAT  CONST_24  H1   C2   N3   C4   180.00   0.0  0
 TAT  CONST_25  H4   C8   N9   C4   180.00   0.0  0
 TAT  CONST_26  H2   N6   C6   N1     0.00   0.0  0
 TAT  CONST_27  H3   N6   C6   N1   180.00   0.0  0
 TAT  Var_01    C4'  C5'  O5'  PA   -49.73  30.0  2
 TAT  Var_02    O1B  PB   O3A  PA  -130.41  30.0  3
 TAT  Var_03    O2A  PA   O3A  PB    66.35  30.0  2
 TAT  Var_04    O2G  PG   O3B  PB   151.66  30.0  3
 TAT  Var_05    O3A  PB   O3B  PG   160.06  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
 TAT  chir_03  C1'  N9   C2'  O4'  negativ
 TAT  chir_04  C2'  O2'  C3'  C1'  positiv
 TAT  chir_05  C3'  O3'  C4'  C2'  positiv
 TAT  chir_06  C4'  O4'  C3'  C5'  negativ
 TAT  chir_07  PA   O5'  O3A  S1G  both
 TAT  chir_08  PB   O1B  O3B  O2B  both

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
 TAT  plan-1  N1   0.020
 TAT  plan-1  C2   0.020
 TAT  plan-1  N3   0.020
 TAT  plan-1  C4   0.020
 TAT  plan-1  C5   0.020
 TAT  plan-1  C6   0.020
 TAT  plan-1  N6   0.020
 TAT  plan-1  N7   0.020
 TAT  plan-1  C8   0.020
 TAT  plan-1  N9   0.020
 TAT  plan-1  C1'  0.020
 TAT  plan-1  H1   0.020
 TAT  plan-1  H4   0.020
 TAT  plan-2  C6   0.020
 TAT  plan-2  N6   0.020
 TAT  plan-2  H2   0.020
 TAT  plan-2  H3   0.020

