# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 19:22:54 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 5'-thioadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CS)[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
 A4D  A4D  '5'-thioadenosine         '  ligand  32  19  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_A4D
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
 A4D  N1    N  N     0  -0.474  -4.4054  -0.3168  -0.0101
 A4D  C2    C  CR16  0   0.039  -3.6655  -1.2947   0.5063
 A4D  N3    N  N     0  -0.458  -2.3588  -1.3201   0.7032
 A4D  C4    C  CR56  0   0.487  -1.7829  -0.1841   0.3131
 A4D  C5    C  CR56  0  -0.002  -2.4166   0.9192  -0.2358
 A4D  C6    C  CR6   0   0.458  -3.8112   0.8175  -0.3977
 A4D  N6    N  NH2   0  -0.816  -4.5518   1.8002  -0.9111
 A4D  N7    N  N     0  -0.450  -1.5132   1.9117  -0.5081
 A4D  C8    C  CR15  0   0.103  -0.3677   1.4192  -0.1348
 A4D  N9    N  NR5   0  -0.537  -0.4617   0.1493   0.3657
 A4D  OAB   O  OH1   0  -0.656   2.8553  -2.1189  -1.5533
 A4D  OAC   O  OH1   0  -0.663   1.4638  -2.8941   0.7063
 A4D  OAK   O  O     0  -0.495   1.7649   0.0450   1.0247
 A4D  CAO   C  CR15  0  -0.027   1.9875  -1.2063  -0.9455
 A4D  CAP   C  CR15  0  -0.044   0.9188  -1.8552  -0.0586
 A4D  CAQ   C  CR15  0   0.054   2.7471  -0.3494   0.0669
 A4D  CAR   C  CR15  0   0.175   0.5974  -0.7058   0.8935
 A4D  H2    H  HCR6  0   0.252  -4.2107  -2.1849   0.8019
 A4D  HN6   H  HNH2  0   0.404  -5.5417   1.6771  -1.0364
 A4D  HN6A  H  HNH2  0   0.411  -4.1304   2.6494  -1.2432
 A4D  H8    H  HCR5  0   0.293   0.5715   1.9469  -0.1877
 A4D  HOAB  H  HOH1  0   0.470   2.4566  -2.4289  -2.3729
 A4D  HOAC  H  HOH1  0   0.453   2.0611  -3.3966   0.1385
 A4D  HSAD  H  HSH1  0   0.227   4.9543   2.5903   0.0715
 A4D  HAO   H  HCR5  0   0.247   1.4979  -0.5612  -1.6868
 A4D  HAP   H  HCR5  0   0.263   0.0389  -2.1827  -0.6248
 A4D  HAQ   H  HCR5  0   0.254   3.5099  -0.9558   0.5688
 A4D  HAR   H  HCR5  0   0.288   0.2656  -1.0713   1.8690
 A4D  CAG   C  CH2   0  -0.583   3.4034   0.8719  -0.5339
 A4D  HAG   H  HCH2  0   0.265   2.7034   1.4302  -1.1565
 A4D  SAD   S  S2    0  -0.236   4.0426   1.9384   0.8003
 A4D  HAGA  H  HCH2  0   0.297   4.2326   0.5472  -1.1615

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
 A4D  N1   C2    aromatic  1.331  0.020  1.331
 A4D  N1   C6    aromatic  1.338  0.020  1.338
 A4D  C2   N3    aromatic  1.322  0.020  1.322
 A4D  N3   C4    aromatic  1.332  0.020  1.332
 A4D  C4   C5    aromatic  1.386  0.020  1.386
 A4D  C4   N9    aromatic  1.364  0.020  1.364
 A4D  C5   C6    aromatic  1.408  0.020  1.408
 A4D  C5   N7    aromatic  1.369  0.020  1.369
 A4D  C6   N6    single    1.333  0.020  1.333
 A4D  N7   C8    aromatic  1.302  0.020  1.302
 A4D  C8   N9    aromatic  1.368  0.020  1.368
 A4D  N9   CAR   single    1.460  0.020  1.460
 A4D  OAB  CAO   single    1.398  0.020  1.398
 A4D  OAC  CAP   single    1.400  0.020  1.400
 A4D  SAD  CAG   single    1.824  0.020  1.824
 A4D  CAG  CAQ   single    1.511  0.020  1.511
 A4D  OAK  CAQ   single    1.427  0.020  1.427
 A4D  OAK  CAR   single    1.394  0.020  1.394
 A4D  CAO  CAP   single    1.533  0.020  1.533
 A4D  CAO  CAQ   single    1.529  0.020  1.529
 A4D  CAP  CAR   single    1.527  0.020  1.527
 A4D  C2   H2    single    0.930  0.020  1.080
 A4D  N6   HN6   single    0.860  0.020  1.020
 A4D  N6   HN6A  single    0.860  0.020  1.020
 A4D  C8   H8    single    0.930  0.020  1.080
 A4D  OAB  HOAB  single    0.850  0.020  0.980
 A4D  OAC  HOAC  single    0.850  0.020  0.980
 A4D  SAD  HSAD  single    1.200  0.020  1.300
 A4D  CAG  HAG   single    0.970  0.020  1.090
 A4D  CAG  HAGA  single    0.970  0.020  1.090
 A4D  CAO  HAO   single    0.970  0.020  1.090
 A4D  CAP  HAP   single    0.970  0.020  1.090
 A4D  CAQ  HAQ   single    0.970  0.020  1.090
 A4D  CAR  HAR   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
 A4D  C6    N1   C2   119.25  3.000
 A4D  H2    C2   N3   116.14  3.000
 A4D  H2    C2   N1   115.42  3.000
 A4D  N3    C2   N1   128.44  3.000
 A4D  C4    N3   C2   111.56  3.000
 A4D  N9    C4   C5   105.29  3.000
 A4D  N9    C4   N3   128.03  3.000
 A4D  C5    C4   N3   126.68  3.000
 A4D  N7    C5   C6   133.08  3.000
 A4D  N7    C5   C4   110.75  3.000
 A4D  C6    C5   C4   116.17  3.000
 A4D  N6    C6   C5   122.77  3.000
 A4D  N6    C6   N1   119.33  3.000
 A4D  C5    C6   N1   117.90  3.000
 A4D  HN6A  N6   HN6  118.38  3.000
 A4D  HN6A  N6   C6   121.16  3.000
 A4D  HN6   N6   C6   120.31  3.000
 A4D  C8    N7   C5   104.43  3.000
 A4D  H8    C8   N9   122.13  3.000
 A4D  H8    C8   N7   124.55  3.000
 A4D  N9    C8   N7   113.31  3.000
 A4D  CAR   N9   C8   128.76  3.000
 A4D  CAR   N9   C4   125.00  3.000
 A4D  C8    N9   C4   106.23  3.000
 A4D  HOAB  OAB  CAO  108.86  3.000
 A4D  HOAC  OAC  CAP  107.81  3.000
 A4D  CAR   OAK  CAQ  111.37  3.000
 A4D  HAO   CAO  CAQ  109.84  3.000
 A4D  HAO   CAO  CAP  109.17  3.000
 A4D  CAQ   CAO  CAP  101.57  3.000
 A4D  HAO   CAO  OAB  111.52  3.000
 A4D  CAQ   CAO  OAB  110.21  3.000
 A4D  CAP   CAO  OAB  114.07  3.000
 A4D  HAP   CAP  CAR  112.21  3.000
 A4D  HAP   CAP  CAO  112.78  3.000
 A4D  CAR   CAP  CAO  100.89  3.000
 A4D  HAP   CAP  OAC  111.89  3.000
 A4D  CAR   CAP  OAC  107.45  3.000
 A4D  CAO   CAP  OAC  111.02  3.000
 A4D  HAQ   CAQ  CAO  109.81  3.000
 A4D  HAQ   CAQ  OAK  108.93  3.000
 A4D  CAO   CAQ  OAK  104.91  3.000
 A4D  HAQ   CAQ  CAG  109.08  3.000
 A4D  CAO   CAQ  CAG  113.93  3.000
 A4D  OAK   CAQ  CAG  110.02  3.000
 A4D  HAR   CAR  CAP  111.63  3.000
 A4D  HAR   CAR  OAK  110.50  3.000
 A4D  CAP   CAR  OAK  106.73  3.000
 A4D  HAR   CAR  N9   107.35  3.000
 A4D  CAP   CAR  N9   111.60  3.000
 A4D  OAK   CAR  N9   109.03  3.000
 A4D  HAGA  CAG  HAG  108.20  3.000
 A4D  HAGA  CAG  CAQ  108.59  3.000
 A4D  HAG   CAG  CAQ  111.23  3.000
 A4D  HAGA  CAG  SAD  109.20  3.000
 A4D  HAG   CAG  SAD  110.07  3.000
 A4D  CAQ   CAG  SAD  109.51  3.000
 A4D  HSAD  SAD  CAG   97.20  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
 A4D  CONST_01  C4    N3  C2  N1    0.00  0.0  0
 A4D  CONST_02  C4    C5  C6  N1    0.00  0.0  0
 A4D  CONST_03  N7    C5  C6  N1  180.00  0.0  0
 A4D  CONST_04  C5    C6  N1  C2    0.00  0.0  0
 A4D  CONST_05  C5    C4  N3  C2    0.00  0.0  0
 A4D  CONST_06  N9    C4  N3  C2  180.00  0.0  0
 A4D  CONST_07  C6    N1  C2  N3    0.00  0.0  0
 A4D  CONST_08  C6    C5  C4  N3    0.00  0.0  0
 A4D  CONST_09  N7    C5  C4  N3  180.00  0.0  0
 A4D  CONST_10  C8    N9  C4  N3  180.00  0.0  0
 A4D  CONST_11  C8    N7  C5  C4    0.00  0.0  0
 A4D  CONST_12  N7    C8  N9  C4    0.00  0.0  0
 A4D  CONST_13  C8    N9  C4  C5    0.00  0.0  0
 A4D  CONST_14  N9    C8  N7  C5    0.00  0.0  0
 A4D  CONST_15  N9    C4  C5  C6  180.00  0.0  0
 A4D  CONST_16  C8    N7  C5  C6  180.00  0.0  0
 A4D  CONST_17  N9    C4  C5  N7    0.00  0.0  0
 A4D  CONST_18  CAR   N9  C4  N3    0.00  0.0  0
 A4D  CONST_19  CAR   N9  C4  C5  180.00  0.0  0
 A4D  CONST_20  CAR   N9  C8  N7  180.00  0.0  0
 A4D  CONST_21  N6    C6  N1  C2  180.00  0.0  0
 A4D  CONST_22  N6    C6  C5  C4  180.00  0.0  0
 A4D  CONST_23  N7    C5  C6  N6    0.00  0.0  0
 A4D  CONST_24  H2    C2  N3  C4  180.00  0.0  0
 A4D  CONST_25  H8    C8  N9  C4  180.00  0.0  0
 A4D  CONST_26  HN6   N6  C6  N1    0.00  0.0  0
 A4D  CONST_27  HN6A  N6  C6  N1  180.00  0.0  0

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
 A4D  chir_01  CAO  OAB  CAP  CAQ  negativ
 A4D  chir_02  CAP  OAC  CAR  CAO  negativ
 A4D  chir_03  CAQ  OAK  CAO  CAG  negativ
 A4D  chir_04  CAR  OAK  N9   CAP  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
 A4D  plan-1  N1    0.020
 A4D  plan-1  C2    0.020
 A4D  plan-1  N3    0.020
 A4D  plan-1  C4    0.020
 A4D  plan-1  C5    0.020
 A4D  plan-1  C6    0.020
 A4D  plan-1  N6    0.020
 A4D  plan-1  N7    0.020
 A4D  plan-1  C8    0.020
 A4D  plan-1  N9    0.020
 A4D  plan-1  CAR   0.020
 A4D  plan-1  H2    0.020
 A4D  plan-1  H8    0.020
 A4D  plan-2  C6    0.020
 A4D  plan-2  N6    0.020
 A4D  plan-2  HN6   0.020
 A4D  plan-2  HN6A  0.020

