# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 23:02:06 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate
#   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
 T99  T99  '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate'  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_T99
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
 T99  PA   P  P     0   1.266  -28.2786  75.5666  -105.1519
 T99  PB   P  P     0   1.524  -27.5152  73.3005  -106.8376
 T99  PG   P  P     0   1.472  -27.6535  71.0741  -104.9563
 T99  C5'  C  CH2   0  -0.210  -30.7423  76.5778  -105.4015
 T99  O5'  O  O2    0  -0.568  -29.5945  75.9261  -105.9657
 T99  C4'  C  CH1   0  -0.041  -31.2871  75.8519  -104.1763
 T99  O4'  O  O2    0  -0.491  -32.4974  76.5119  -103.8116
 T99  C3'  C  CH1   0  -0.049  -31.6289  74.3685  -104.4207
 T99  O3'  O  OH1   0  -0.671  -31.3523  73.5748  -103.2998
 T99  C2'  C  CH1   0  -0.005  -33.1373  74.4333  -104.6243
 T99  O2'  O  OH1   0  -0.647  -33.7655  73.2199  -104.3691
 T99  C1'  C  CH1   0   0.178  -33.5209  75.5622  -103.6634
 T99  N1   N  N     0  -0.474  -38.1090  76.8803  -101.8546
 T99  O1A  O  O     0  -0.683  -27.7294  70.0680  -106.0250
 T99  O1B  O  O     0  -0.643  -26.6481  73.0972  -108.0000
 T99  S1G  S  S2    0  -0.321  -27.3476  77.3949  -104.9380
 T99  C2   C  CR16  0   0.048  -37.1017  76.2116  -101.3004
 T99  O2A  O  O     0  -0.645  -28.4169  74.7624  -103.9228
 T99  O2B  O  OH1   0  -0.735  -29.0532  72.9459  -106.9597
 T99  O2G  O  OH1   0  -0.710  -26.6726  70.8446  -103.7384
 T99  N3   N  N     0  -0.456  -35.9353  75.8916  -101.8344
 T99  O3A  O  O2    0  -0.662  -27.4435  74.8378  -106.3359
 T99  O3B  O  O2    0  -0.693  -27.1220  72.5249  -105.4964
 T99  O3G  O  OH1   0  -0.720  -28.9817  71.4370  -104.1760
 T99  C4   C  CR56  0   0.492  -35.8312  76.3304  -103.0852
 T99  C5   C  CR56  0  -0.010  -36.7885  77.0368  -103.7944
 T99  C6   C  CR6   0   0.461  -37.9890  77.3140  -103.1145
 T99  N6   N  NH2   0  -0.815  -39.0011  77.9746  -103.6786
 T99  N7   N  N     0  -0.447  -36.3403  77.3344  -105.0567
 T99  C8   C  CR15  0   0.112  -35.1501  76.8194  -105.1081
 T99  N9   N  NR5   0  -0.546  -34.7795  76.1896  -103.9477
 T99  H1   H  HCH2  0   0.275  -30.4938  77.6126  -105.1540
 T99  H2   H  HCH2  0   0.266  -31.4815  76.5884  -106.2022
 T99  H3   H  HCH1  0   0.267  -30.5846  75.9396  -103.3433
 T99  H4   H  HCH1  0   0.257  -31.1337  73.9789  -105.3158
 T99  H5   H  HOH1  0   0.453  -30.3941  73.5531  -103.1924
 T99  H6   H  HCH1  0   0.250  -33.3150  74.7764  -105.6533
 T99  H7   H  HOH1  0   0.464  -34.6360  73.2314  -104.7782
 T99  H8   H  HCH1  0   0.266  -33.5861  75.1824  -102.6373
 T99  H9   H  HSH1  0   0.285  -26.5914  77.0246  -103.8960
 T99  H11  H  HOH1  0   0.518  -29.4425  73.0713  -107.8379
 T99  H12  H  HOH1  0   0.513  -25.7815  70.5547  -103.9808
 T99  H13  H  HOH1  0   0.511  -29.7781  71.0113  -104.5210
 T99  H14  H  HNH2  0   0.404  -39.8099  78.2195  -103.1337
 T99  H15  H  HNH2  0   0.411  -38.9044  78.3838  -104.5914
 T99  H16  H  HCR5  0   0.299  -34.4909  76.8723  -105.9619
 T99  H10  H  HCR6  0   0.254  -37.2631  75.8899  -100.2771

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
 T99  O1B  PB   double    1.464  0.020  1.464
 T99  O2B  PB   single    1.583  0.020  1.583
 T99  PB   O3A  single    1.619  0.020  1.619
 T99  PB   O3B  single    1.598  0.020  1.598
 T99  O1A  PG   double    1.470  0.020  1.470
 T99  O3A  PA   single    1.622  0.020  1.622
 T99  O3B  PG   single    1.637  0.020  1.637
 T99  O5'  C5'  single    1.436  0.020  1.436
 T99  O5'  PA   single    1.588  0.020  1.588
 T99  PG   O3G  single    1.583  0.020  1.583
 T99  PG   O2G  single    1.581  0.020  1.581
 T99  C5'  C4'  single    1.525  0.020  1.525
 T99  N7   C8   aromatic  1.298  0.020  1.298
 T99  N7   C5   aromatic  1.372  0.020  1.372
 T99  C8   N9   aromatic  1.371  0.020  1.371
 T99  PA   S1G  single    2.063  0.020  2.063
 T99  PA   O2A  double    1.475  0.020  1.475
 T99  C2'  C3'  single    1.523  0.020  1.523
 T99  C2'  O2'  single    1.390  0.020  1.390
 T99  C2'  C1'  single    1.531  0.020  1.531
 T99  C4'  C3'  single    1.542  0.020  1.542
 T99  C4'  O4'  single    1.426  0.020  1.426
 T99  N6   C6   single    1.334  0.020  1.334
 T99  C3'  O3'  single    1.401  0.020  1.401
 T99  C5   C6   aromatic  1.407  0.020  1.407
 T99  C5   C4   aromatic  1.385  0.020  1.385
 T99  N9   C1'  single    1.435  0.020  1.435
 T99  N9   C4   aromatic  1.367  0.020  1.367
 T99  O4'  C1'  single    1.404  0.020  1.404
 T99  C6   N1   aromatic  1.338  0.020  1.338
 T99  C4   N3   aromatic  1.330  0.020  1.330
 T99  N1   C2   aromatic  1.330  0.020  1.330
 T99  N3   C2   aromatic  1.322  0.020  1.322
 T99  C5'  H1   single    0.970  0.020  1.090
 T99  C5'  H2   single    0.970  0.020  1.090
 T99  C4'  H3   single    0.970  0.020  1.090
 T99  C3'  H4   single    0.970  0.020  1.090
 T99  O3'  H5   single    0.850  0.020  0.980
 T99  C2'  H6   single    0.970  0.020  1.090
 T99  O2'  H7   single    0.850  0.020  0.980
 T99  C1'  H8   single    0.970  0.020  1.090
 T99  S1G  H9   single    1.200  0.020  1.300
 T99  C2   H10  single    0.930  0.020  1.080
 T99  O2B  H11  single    0.850  0.020  0.980
 T99  O2G  H12  single    0.850  0.020  0.980
 T99  O3G  H13  single    0.850  0.020  0.980
 T99  N6   H14  single    0.860  0.020  1.020
 T99  N6   H15  single    0.860  0.020  1.020
 T99  C8   H16  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
 T99  O3A  PA   O2A  114.30  3.000
 T99  O2A  PA   S1G  116.04  3.000
 T99  O3A  PA   S1G  103.98  3.000
 T99  O2A  PA   O5'  118.20  3.000
 T99  S1G  PA   O5'  103.09  3.000
 T99  O3A  PA   O5'   98.87  3.000
 T99  O3B  PB   O3A  100.94  3.000
 T99  O3B  PB   O2B  101.24  3.000
 T99  O3A  PB   O2B  106.24  3.000
 T99  O3B  PB   O1B  116.94  3.000
 T99  O3A  PB   O1B  110.59  3.000
 T99  O2B  PB   O1B  118.88  3.000
 T99  O3G  PG   O3B  103.41  3.000
 T99  O3G  PG   O2G  100.03  3.000
 T99  O3B  PG   O2G  100.45  3.000
 T99  O2G  PG   O1A  119.53  3.000
 T99  O3G  PG   O1A  118.18  3.000
 T99  O3B  PG   O1A  112.56  3.000
 T99  H2   C5'  H1   108.15  3.000
 T99  H2   C5'  C4'  110.66  3.000
 T99  H1   C5'  C4'  110.50  3.000
 T99  H2   C5'  O5'  104.95  3.000
 T99  H1   C5'  O5'  109.70  3.000
 T99  C4'  C5'  O5'  112.67  3.000
 T99  C5'  O5'  PA   124.32  3.000
 T99  H3   C4'  C3'  109.90  3.000
 T99  H3   C4'  O4'  108.26  3.000
 T99  C3'  C4'  O4'  107.31  3.000
 T99  H3   C4'  C5'  110.15  3.000
 T99  O4'  C4'  C5'  106.77  3.000
 T99  C3'  C4'  C5'  114.20  3.000
 T99  C1'  O4'  C4'  109.43  3.000
 T99  H4   C3'  C2'  110.72  3.000
 T99  H4   C3'  O3'  111.30  3.000
 T99  C2'  C3'  O3'  109.06  3.000
 T99  H4   C3'  C4'  111.82  3.000
 T99  O3'  C3'  C4'  111.99  3.000
 T99  C2'  C3'  C4'  101.52  3.000
 T99  H5   O3'  C3'  107.34  3.000
 T99  H6   C2'  C1'  108.47  3.000
 T99  H6   C2'  O2'  111.79  3.000
 T99  C1'  C2'  O2'  114.53  3.000
 T99  H6   C2'  C3'  107.36  3.000
 T99  C1'  C2'  C3'  101.27  3.000
 T99  O2'  C2'  C3'  112.69  3.000
 T99  H7   O2'  C2'  108.69  3.000
 T99  H8   C1'  N9   106.55  3.000
 T99  H8   C1'  C2'  110.29  3.000
 T99  N9   C1'  C2'  114.69  3.000
 T99  H8   C1'  O4'  112.12  3.000
 T99  N9   C1'  O4'  108.83  3.000
 T99  C2'  C1'  O4'  104.47  3.000
 T99  C6   N1   C2   119.18  3.000
 T99  H9   S1G  PA    95.19  3.000
 T99  H10  C2   N3   116.14  3.000
 T99  H10  C2   N1   115.44  3.000
 T99  N3   C2   N1   128.43  3.000
 T99  H11  O2B  PB   115.55  3.000
 T99  H12  O2G  PG   114.96  3.000
 T99  C4   N3   C2   111.66  3.000
 T99  PB   O3A  PA   129.07  3.000
 T99  PG   O3B  PB   128.83  3.000
 T99  H13  O3G  PG   114.49  3.000
 T99  N9   C4   C5   105.14  3.000
 T99  N9   C4   N3   128.29  3.000
 T99  C5   C4   N3   126.57  3.000
 T99  N7   C5   C6   132.87  3.000
 T99  C6   C5   C4   116.28  3.000
 T99  N7   C5   C4   110.85  3.000
 T99  N6   C6   C5   122.72  3.000
 T99  C5   C6   N1   117.88  3.000
 T99  N6   C6   N1   119.40  3.000
 T99  H15  N6   H14  118.06  3.000
 T99  H15  N6   C6   120.85  3.000
 T99  H14  N6   C6   120.12  3.000
 T99  C8   N7   C5   104.47  3.000
 T99  H16  C8   N9   121.77  3.000
 T99  H16  C8   N7   124.86  3.000
 T99  N9   C8   N7   113.36  3.000
 T99  C8   N9   C4   106.18  3.000
 T99  C4   N9   C1'  126.50  3.000
 T99  C8   N9   C1'  127.27  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
 T99  CONST_01  N7   C5   C6   N1   180.00   0.0  0
 T99  CONST_02  C4   C5   C6   N1     0.00   0.0  0
 T99  CONST_03  C4   N3   C2   N1     0.00   0.0  0
 T99  CONST_04  C5   C6   N1   C2     0.00   0.0  0
 T99  CONST_05  C5   C4   N3   C2     0.00   0.0  0
 T99  CONST_06  N9   C4   N3   C2   180.00   0.0  0
 T99  CONST_07  N7   C5   C4   N3   180.00   0.0  0
 T99  CONST_08  C6   C5   C4   N3     0.00   0.0  0
 T99  CONST_09  C8   N9   C4   N3   180.00   0.0  0
 T99  CONST_10  C6   N1   C2   N3     0.00   0.0  0
 T99  CONST_11  C8   N7   C5   C4     0.00   0.0  0
 T99  CONST_12  N7   C8   N9   C4     0.00   0.0  0
 T99  CONST_13  N9   C8   N7   C5     0.00   0.0  0
 T99  CONST_14  C8   N9   C4   C5     0.00   0.0  0
 T99  CONST_15  C8   N7   C5   C6   180.00   0.0  0
 T99  CONST_16  N9   C4   C5   C6   180.00   0.0  0
 T99  CONST_17  N9   C4   C5   N7     0.00   0.0  0
 T99  CONST_18  N7   C8   N9   C1'  180.00   0.0  0
 T99  CONST_19  C5   C4   N9   C1'  180.00   0.0  0
 T99  CONST_20  N3   C4   N9   C1'    0.00   0.0  0
 T99  CONST_21  N6   C6   N1   C2   180.00   0.0  0
 T99  CONST_22  N6   C6   C5   C4   180.00   0.0  0
 T99  CONST_23  N7   C5   C6   N6     0.00   0.0  0
 T99  CONST_24  H16  C8   N9   C1'    0.00   0.0  0
 T99  CONST_25  H10  C2   N3   C4   180.00   0.0  0
 T99  CONST_26  H14  N6   C6   N1     0.00   0.0  0
 T99  CONST_27  H15  N6   C6   N1   180.00   0.0  0
 T99  Var_01    C4'  C5'  O5'  PA   -54.67  30.0  3
 T99  Var_02    O1B  PB   O3A  PA   176.12  30.0  1
 T99  Var_03    O5'  PA   O3A  PB   -84.18  30.0  3
 T99  Var_04    O1A  PG   O3B  PB    42.40  30.0  3
 T99  Var_05    O3A  PA   O5'  C5'  178.43  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
 T99  chir_03  C4'  C5'  C3'  O4'  positiv
 T99  chir_04  C3'  O3'  C2'  C4'  negativ
 T99  chir_05  C2'  O2'  C1'  C3'  negativ
 T99  chir_06  C1'  O4'  N9   C2'  negativ
 T99  chir_07  PA   O5'  S1G  O2A  both
 T99  chir_08  PB   O2B  O3A  O3B  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
 T99  plan-1  C1'  0.020
 T99  plan-1  N1   0.020
 T99  plan-1  C2   0.020
 T99  plan-1  N3   0.020
 T99  plan-1  C4   0.020
 T99  plan-1  C5   0.020
 T99  plan-1  C6   0.020
 T99  plan-1  N6   0.020
 T99  plan-1  N7   0.020
 T99  plan-1  C8   0.020
 T99  plan-1  N9   0.020
 T99  plan-1  H16  0.020
 T99  plan-1  H10  0.020
 T99  plan-2  C6   0.020
 T99  plan-2  N6   0.020
 T99  plan-2  H14  0.020
 T99  plan-2  H15  0.020

