# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 23:17:41 2021
#   Inital geometry file: a 122 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1nc(N)c2ncn([C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O)c2n1
#
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
 6AT  6AT  '2-(methylsulfanyl)adenosine 5'-(tetrahydrogen triphosphate)'  ligand  51  33  .  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_6AT
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
 6AT  OAI  O  OH1   0  -0.735  -15.3185   -9.6637  16.6595
 6AT  PBE  P  P     0   1.479  -15.3507   -8.0963  16.5319
 6AT  OAH  O  O     0  -0.704  -16.4996   -7.3813  17.1344
 6AT  OAC  O  OH1   0  -0.695  -13.9050   -7.7368  17.0331
 6AT  OAS  O  O2    0  -0.685  -15.2505   -7.7901  14.9307
 6AT  PBG  P  P     0   1.483  -16.2626   -7.9405  13.6953
 6AT  OAK  O  O     0  -0.650  -16.1349   -9.1848  12.9293
 6AT  OAE  O  OH1   0  -0.697  -15.9984   -6.5650  12.9748
 6AT  OAT  O  O2    0  -0.703  -17.7240   -7.7047  14.3532
 6AT  PBF  P  P     0   1.525  -18.5674   -8.7515  15.2739
 6AT  OAJ  O  OH1   0  -0.731  -19.0762   -7.8504  16.4576
 6AT  OAD  O  O     0  -0.701  -17.7671   -9.9573  15.5878
 6AT  O5'  O  O2    0  -0.567  -19.8508   -9.0939  14.4357
 6AT  C5'  C  CH2   0  -0.212  -20.8404   -8.1286  14.0350
 6AT  C4'  C  CH1   0  -0.013  -21.7733   -8.7675  13.0371
 6AT  O4'  O  O2    0  -0.493  -21.0762   -9.0389  11.8218
 6AT  C3'  C  CH1   0  -0.042  -22.4033  -10.0897  13.4834
 6AT  O3'  O  OH1   0  -0.668  -23.7157  -10.1357  12.9848
 6AT  C2'  C  CH1   0  -0.040  -21.5205  -11.1215  12.7728
 6AT  O2'  O  OH1   0  -0.653  -22.1570  -12.3323  12.4928
 6AT  C1'  C  CH1   0   0.211  -21.2101  -10.3877  11.4695
 6AT  N9   N  NR5   0  -0.549  -20.0093  -10.8261  10.8131
 6AT  C8   C  CR15  0   0.114  -18.7195  -10.7397  11.2766
 6AT  N7   N  N     0  -0.445  -17.8446  -11.2241  10.4503
 6AT  C5   C  CR56  0  -0.028  -18.5852  -11.6573   9.3797
 6AT  C4   C  CR56  0   0.498  -19.9343  -11.4143   9.5834
 6AT  N3   N  N     0  -0.471  -20.9263  -11.7002   8.7477
 6AT  C2   C  CR6   0   0.217  -20.4803  -12.2746   7.6402
 6AT  S2   S  S2    0   0.031  -21.7624  -12.6651   6.5024
 6AT  CAA  C  CH3   0  -0.762  -20.8718  -13.4390   5.1406
 6AT  N1   N  N     0  -0.468  -19.2316  -12.5735   7.3114
 6AT  C6   C  CR6   0   0.471  -18.2438  -12.2766   8.1640
 6AT  N6   N  NH2   0  -0.816  -16.9899  -12.5753   7.8308
 6AT  H1   H  HOH1  0   0.509  -16.1765  -10.0581  16.3758
 6AT  H2   H  HOH1  0   0.519  -13.7520   -6.7993  17.2198
 6AT  H3   H  HOH1  0   0.519  -16.1523   -6.5764  12.0189
 6AT  H4   H  HOH1  0   0.511  -18.3151   -7.5110  16.9818
 6AT  H5   H  HCH2  0   0.275  -20.3599   -7.2558  13.5879
 6AT  H6   H  HCH2  0   0.271  -21.4103   -7.8045  14.9068
 6AT  H7   H  HCH1  0   0.279  -22.5623   -8.0305  12.8520
 6AT  H8   H  HCH1  0   0.257  -22.3834  -10.2102  14.5739
 6AT  H9   H  HOH1  0   0.450  -23.9696  -11.0636  12.9102
 6AT  H10  H  HCH1  0   0.256  -20.5978  -11.2699  13.3444
 6AT  H11  H  HOH1  0   0.471  -22.0443  -12.9258  13.2419
 6AT  H12  H  HCH1  0   0.262  -22.0226  -10.5428  10.7504
 6AT  H13  H  HCR5  0   0.278  -18.4838  -10.3023  12.2334
 6AT  H14  H  HCH3  0   0.277  -21.6260  -13.6864   4.3955
 6AT  H15  H  HCH3  0   0.273  -20.1475  -12.7579   4.7021
 6AT  H16  H  HCH3  0   0.272  -20.3740  -14.3512   5.4595
 6AT  H17  H  HNH2  0   0.406  -16.7903  -13.0278   6.9556
 6AT  H18  H  HNH2  0   0.414  -16.2245  -12.3706   8.4489

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
 6AT  CAA  S2   single    1.802  0.020  1.802
 6AT  S2   C2   single    1.758  0.020  1.758
 6AT  N1   C2   aromatic  1.325  0.020  1.325
 6AT  N1   C6   aromatic  1.338  0.020  1.338
 6AT  C2   N3   aromatic  1.325  0.020  1.325
 6AT  N6   C6   single    1.331  0.020  1.331
 6AT  C6   C5   aromatic  1.406  0.020  1.406
 6AT  N3   C4   aromatic  1.328  0.020  1.328
 6AT  C5   C4   aromatic  1.386  0.020  1.386
 6AT  C5   N7   aromatic  1.372  0.020  1.372
 6AT  C4   N9   aromatic  1.365  0.020  1.365
 6AT  N7   C8   aromatic  1.297  0.020  1.297
 6AT  N9   C8   aromatic  1.373  0.020  1.373
 6AT  N9   C1'  single    1.437  0.020  1.437
 6AT  O4'  C1'  single    1.400  0.020  1.400
 6AT  O4'  C4'  single    1.427  0.020  1.427
 6AT  C1'  C2'  single    1.528  0.020  1.528
 6AT  C4'  C5'  single    1.508  0.020  1.508
 6AT  C4'  C3'  single    1.531  0.020  1.531
 6AT  O5'  C5'  single    1.439  0.020  1.439
 6AT  O5'  PBF  single    1.571  0.020  1.571
 6AT  C2'  O2'  single    1.396  0.020  1.396
 6AT  C2'  C3'  single    1.533  0.020  1.533
 6AT  OAD  PBF  double    1.481  0.020  1.481
 6AT  C3'  O3'  single    1.405  0.020  1.405
 6AT  PBF  OAT  single    1.629  0.020  1.629
 6AT  PBF  OAJ  single    1.572  0.020  1.572
 6AT  OAK  PBG  double    1.467  0.020  1.467
 6AT  OAT  PBG  single    1.620  0.020  1.620
 6AT  PBG  OAE  single    1.575  0.020  1.575
 6AT  PBG  OAS  single    1.604  0.020  1.604
 6AT  OAS  PBE  single    1.633  0.020  1.633
 6AT  OAH  PBE  double    1.481  0.020  1.481
 6AT  PBE  OAC  single    1.572  0.020  1.572
 6AT  PBE  OAI  single    1.573  0.020  1.573
 6AT  OAI  H1   single    0.850  0.020  0.980
 6AT  OAC  H2   single    0.850  0.020  0.980
 6AT  OAE  H3   single    0.850  0.020  0.980
 6AT  OAJ  H4   single    0.850  0.020  0.980
 6AT  C5'  H5   single    0.970  0.020  1.090
 6AT  C5'  H6   single    0.970  0.020  1.090
 6AT  C4'  H7   single    0.970  0.020  1.090
 6AT  C3'  H8   single    0.970  0.020  1.090
 6AT  O3'  H9   single    0.850  0.020  0.980
 6AT  C2'  H10  single    0.970  0.020  1.090
 6AT  O2'  H11  single    0.850  0.020  0.980
 6AT  C1'  H12  single    0.970  0.020  1.090
 6AT  C8   H13  single    0.930  0.020  1.080
 6AT  CAA  H14  single    0.970  0.020  1.090
 6AT  CAA  H15  single    0.970  0.020  1.090
 6AT  CAA  H16  single    0.970  0.020  1.090
 6AT  N6   H17  single    0.860  0.020  1.020
 6AT  N6   H18  single    0.860  0.020  1.020

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
 6AT  H1   OAI  PBE  110.95  3.000
 6AT  OAS  PBE  OAC  102.32  3.000
 6AT  OAC  PBE  OAH  118.25  3.000
 6AT  OAS  PBE  OAH  110.84  3.000
 6AT  OAC  PBE  OAI  100.56  3.000
 6AT  OAH  PBE  OAI  117.63  3.000
 6AT  OAS  PBE  OAI  105.37  3.000
 6AT  H2   OAC  PBE  115.36  3.000
 6AT  PBG  OAS  PBE  134.33  3.000
 6AT  OAT  PBG  OAE  102.12  3.000
 6AT  OAE  PBG  OAK  119.17  3.000
 6AT  OAT  PBG  OAK  114.47  3.000
 6AT  OAE  PBG  OAS   99.47  3.000
 6AT  OAT  PBG  OAS  104.05  3.000
 6AT  OAK  PBG  OAS  115.27  3.000
 6AT  H3   OAE  PBG  114.49  3.000
 6AT  PBF  OAT  PBG  127.08  3.000
 6AT  O5'  PBF  OAD  112.16  3.000
 6AT  OAD  PBF  OAJ  118.81  3.000
 6AT  O5'  PBF  OAJ  105.21  3.000
 6AT  OAJ  PBF  OAT  102.99  3.000
 6AT  OAD  PBF  OAT  111.30  3.000
 6AT  O5'  PBF  OAT  105.16  3.000
 6AT  H4   OAJ  PBF  110.38  3.000
 6AT  C5'  O5'  PBF  124.34  3.000
 6AT  H6   C5'  H5   108.64  3.000
 6AT  H6   C5'  C4'  109.36  3.000
 6AT  H5   C5'  C4'  109.87  3.000
 6AT  H6   C5'  O5'  109.63  3.000
 6AT  H5   C5'  O5'  110.33  3.000
 6AT  C4'  C5'  O5'  108.99  3.000
 6AT  H7   C4'  C3'  109.51  3.000
 6AT  H7   C4'  O4'  109.63  3.000
 6AT  C3'  C4'  O4'  106.56  3.000
 6AT  H7   C4'  C5'  105.80  3.000
 6AT  C3'  C4'  C5'  115.31  3.000
 6AT  O4'  C4'  C5'  109.99  3.000
 6AT  C1'  O4'  C4'  110.53  3.000
 6AT  H8   C3'  C2'  112.12  3.000
 6AT  H8   C3'  O3'  111.48  3.000
 6AT  C2'  C3'  O3'  110.58  3.000
 6AT  H8   C3'  C4'  112.15  3.000
 6AT  O3'  C3'  C4'  108.01  3.000
 6AT  C2'  C3'  C4'  102.08  3.000
 6AT  H9   O3'  C3'  107.74  3.000
 6AT  H10  C2'  C1'  109.82  3.000
 6AT  H10  C2'  O2'  111.78  3.000
 6AT  C1'  C2'  O2'  109.76  3.000
 6AT  H10  C2'  C3'  109.54  3.000
 6AT  O2'  C2'  C3'  114.47  3.000
 6AT  C1'  C2'  C3'  100.91  3.000
 6AT  H11  O2'  C2'  108.99  3.000
 6AT  H12  C1'  N9   106.06  3.000
 6AT  H12  C1'  C2'  109.95  3.000
 6AT  N9   C1'  C2'  114.39  3.000
 6AT  H12  C1'  O4'  111.85  3.000
 6AT  C2'  C1'  O4'  105.51  3.000
 6AT  N9   C1'  O4'  109.20  3.000
 6AT  C4   N9   C8   106.23  3.000
 6AT  C8   N9   C1'  127.70  3.000
 6AT  C4   N9   C1'  126.07  3.000
 6AT  H13  C8   N7   124.70  3.000
 6AT  H13  C8   N9   122.04  3.000
 6AT  N7   C8   N9   113.26  3.000
 6AT  C5   N7   C8   104.53  3.000
 6AT  C6   C5   C4   116.14  3.000
 6AT  C4   C5   N7   110.82  3.000
 6AT  C6   C5   N7   133.04  3.000
 6AT  N3   C4   C5   126.65  3.000
 6AT  C5   C4   N9   105.15  3.000
 6AT  N3   C4   N9   128.20  3.000
 6AT  C2   N3   C4   111.58  3.000
 6AT  N1   C2   S2   118.45  3.000
 6AT  N1   C2   N3   128.48  3.000
 6AT  S2   C2   N3   113.07  3.000
 6AT  CAA  S2   C2   102.95  3.000
 6AT  H16  CAA  H15  109.82  3.000
 6AT  H16  CAA  H14  109.11  3.000
 6AT  H15  CAA  H14  109.15  3.000
 6AT  H16  CAA  S2   111.41  3.000
 6AT  H15  CAA  S2   111.42  3.000
 6AT  H14  CAA  S2   105.81  3.000
 6AT  C6   N1   C2   119.16  3.000
 6AT  N6   C6   N1   119.07  3.000
 6AT  N6   C6   C5   122.94  3.000
 6AT  N1   C6   C5   117.99  3.000
 6AT  H18  N6   H17  118.42  3.000
 6AT  H18  N6   C6   121.18  3.000
 6AT  H17  N6   C6   120.39  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
 6AT  CONST_01  C2   N3   C4   N9    180.00   0.0  0
 6AT  CONST_02  C6   C5   C4   N9    180.00   0.0  0
 6AT  CONST_03  N7   C5   C4   N9      0.00   0.0  0
 6AT  CONST_04  C5   N7   C8   N9      0.00   0.0  0
 6AT  CONST_05  C6   C5   N7   C8    180.00   0.0  0
 6AT  CONST_06  C4   C5   N7   C8      0.00   0.0  0
 6AT  CONST_07  N3   C4   N9   C8    180.00   0.0  0
 6AT  CONST_08  C5   C4   N9   C8      0.00   0.0  0
 6AT  CONST_09  N1   C6   C5   N7    180.00   0.0  0
 6AT  CONST_10  N3   C4   C5   N7    180.00   0.0  0
 6AT  CONST_11  C4   N9   C8   N7      0.00   0.0  0
 6AT  CONST_12  C2   N1   C6   C5      0.00   0.0  0
 6AT  CONST_13  C2   N3   C4   C5      0.00   0.0  0
 6AT  CONST_14  N1   C2   N3   C4      0.00   0.0  0
 6AT  CONST_15  N1   C6   C5   C4      0.00   0.0  0
 6AT  CONST_16  C6   N1   C2   N3      0.00   0.0  0
 6AT  CONST_17  C6   C5   C4   N3      0.00   0.0  0
 6AT  CONST_18  N3   C4   N9   C1'     0.00   0.0  0
 6AT  CONST_19  C5   C4   N9   C1'   180.00   0.0  0
 6AT  CONST_20  N7   C8   N9   C1'   180.00   0.0  0
 6AT  CONST_21  N6   C6   C5   N7      0.00   0.0  0
 6AT  CONST_22  S2   C2   N3   C4    180.00   0.0  0
 6AT  CONST_23  N6   C6   C5   C4    180.00   0.0  0
 6AT  CONST_24  N6   C6   N1   C2    180.00   0.0  0
 6AT  CONST_25  C6   N1   C2   S2    180.00   0.0  0
 6AT  CONST_26  H13  C8   N9   C1'     0.00   0.0  0
 6AT  CONST_27  H17  N6   C6   C5    180.00   0.0  0
 6AT  CONST_28  H18  N6   C6   C5      0.00   0.0  0
 6AT  Var_01    N1   C2   S2   CAA     0.82  30.0  2
 6AT  Var_02    C4'  C5'  O5'  PBF   169.39  30.0  3
 6AT  Var_03    H14  CAA  S2   C2   -179.06  30.0  3
 6AT  Var_04    OAK  PBG  OAS  PBE   -95.32  30.0  2
 6AT  Var_05    O5'  PBF  OAT  PBG  -115.46  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
 6AT  chir_03  C4'  O4'  C5'  C3'  positiv
 6AT  chir_04  C3'  O3'  C4'  C2'  positiv
 6AT  chir_05  C2'  O2'  C3'  C1'  positiv
 6AT  chir_06  C1'  O4'  N9   C2'  negativ
 6AT  chir_07  PBG  OAT  OAE  OAS  both
 6AT  chir_08  PBF  OAD  OAT  OAJ  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
 6AT  plan-1  C1'  0.020
 6AT  plan-1  N9   0.020
 6AT  plan-1  C8   0.020
 6AT  plan-1  N7   0.020
 6AT  plan-1  C5   0.020
 6AT  plan-1  C4   0.020
 6AT  plan-1  N3   0.020
 6AT  plan-1  C2   0.020
 6AT  plan-1  S2   0.020
 6AT  plan-1  N1   0.020
 6AT  plan-1  C6   0.020
 6AT  plan-1  N6   0.020
 6AT  plan-1  H13  0.020
 6AT  plan-2  C6   0.020
 6AT  plan-2  N6   0.020
 6AT  plan-2  H17  0.020
 6AT  plan-2  H18  0.020

