# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 13:28:31 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 8-[(2-{[2-(3-bromophenyl)ethyl]amino}-2-oxoethyl)sulfanyl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)c(SCC(=O)NCCc4cccc(Br)c4)nc12
#
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
 5AK  5AK  8-[(2-{[2-(3-bromophenyl)ethyl]amino}-2-oxoethyl)sulfanyl]adenosine  ligand  56  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5AK
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
 5AK  C4   C   CR56  0   0.492  -5.4100  -1.2503   0.0730
 5AK  C5   C   CR56  0   0.009  -4.5875  -2.3607   0.0308
 5AK  C6   C   CR6   0   0.447  -5.2201  -3.6114   0.1302
 5AK  C8   C   CR5   0   0.336  -3.3011  -0.6905  -0.1468
 5AK  N1   N   N     0  -0.471  -6.5529  -3.6302   0.2522
 5AK  N3   N   N     0  -0.456  -6.7331  -1.2509   0.1899
 5AK  CAK  C   CR16  0  -0.279   6.2613  -0.5294   0.0747
 5AK  CAW  C   CR6   0  -0.090   7.5174   0.0212  -0.1288
 5AK  BR   BR  BR    0  -0.051   8.5229   0.6004   1.3641
 5AK  CAI  C   CR16  0  -0.246   8.0538   0.1540  -1.4007
 5AK  CAG  C   CR16  0  -0.235   7.3023  -0.2809  -2.4838
 5AK  CAJ  C   CR16  0  -0.300   6.0440  -0.8333  -2.2955
 5AK  CAY  C   CR6   0   0.127   5.5120  -0.9633  -1.0160
 5AK  CAN  C   CH2   0  -0.566   4.1317  -1.5199  -0.8071
 5AK  CAM  C   CH2   0  -0.232   3.0944  -0.4029  -0.8242
 5AK  NAS  N   NH1   0  -0.645   1.7656  -0.9466  -0.6259
 5AK  CAV  C   C     0   0.579   0.6856  -0.1689  -0.5174
 5AK  OAB  O   O     0  -0.484   0.7183   1.0512  -0.5802
 5AK  CAO  C   CH2   0  -0.679  -0.6181  -0.9114  -0.2983
 5AK  SAU  S   S2    0   0.067  -1.9149   0.3455  -0.3314
 5AK  N7   N   N     0  -0.461  -3.2745  -1.9906  -0.1114
 5AK  N6   N   NH2   0  -0.818  -4.5495  -4.7654   0.0942
 5AK  C2   C   CR16  0   0.042  -7.2176  -2.4796   0.2708
 5AK  N9   N   NR5   0  -0.588  -4.5719  -0.1711  -0.0380
 5AK  C1'  C   CH1   0   0.210  -5.0046   1.2030   0.0078
 5AK  O4'  O   O2    0  -0.504  -4.3485   1.9345  -0.9862
 5AK  C4'  C   CH1   0  -0.033  -4.1755   3.2958  -0.5547
 5AK  C5'  C   CH2   0  -0.185  -2.6992   3.6602  -0.5383
 5AK  O5'  O   OH1   0  -0.667  -2.0654   3.4311  -1.7705
 5AK  C3'  C   CH1   0  -0.059  -4.8124   3.3888   0.8371
 5AK  O3'  O   OH1   0  -0.666  -6.1745   3.7226   0.7952
 5AK  C2'  C   CH1   0   0.004  -4.6996   1.9375   1.3100
 5AK  O2'  O   OH1   0  -0.651  -5.5861   1.5308   2.3000
 5AK  H2   H   HCR6  0   0.279   9.0345   0.5830  -1.5557
 5AK  H3   H   HCR6  0   0.269   7.7086  -0.1864  -3.4821
 5AK  H4   H   HCR6  0   0.259   5.4732  -1.1712  -3.1519
 5AK  H5   H   HCH2  0   0.267   3.9045  -2.2449  -1.5925
 5AK  H6   H   HCH2  0   0.266   4.0826  -2.0505   0.1471
 5AK  H7   H   HCH2  0   0.248   3.3164   0.3208  -0.0362
 5AK  H8   H   HCH2  0   0.247   3.1427   0.1336  -1.7757
 5AK  H9   H   HNH1  0   0.413   1.6554  -1.9480  -0.5913
 5AK  H10  H   HCH2  0   0.319  -0.7861  -1.6535  -1.0792
 5AK  H11  H   HCH2  0   0.323  -0.6102  -1.4303   0.6612
 5AK  H12  H   HNH2  0   0.403  -5.0334  -5.6353   0.2351
 5AK  H13  H   HNH2  0   0.410  -3.5449  -4.7791   0.0815
 5AK  H14  H   HCR6  0   0.252  -8.2948  -2.5629   0.3666
 5AK  H15  H   HCH1  0   0.264  -6.0891   1.1740  -0.1507
 5AK  H16  H   HCH1  0   0.255  -4.6967   3.9461  -1.2656
 5AK  H17  H   HCH2  0   0.243  -2.6244   4.7296  -0.3275
 5AK  H18  H   HCH2  0   0.206  -2.1902   3.1390   0.2833
 5AK  H19  H   HOH1  0   0.448  -1.9570   2.4801  -1.8797
 5AK  H20  H   HCH1  0   0.254  -4.2492   4.0744   1.4841
 5AK  H21  H   HOH1  0   0.457  -6.2581   4.6084   0.4285
 5AK  H22  H   HCH1  0   0.237  -3.6539   1.7508   1.5942
 5AK  H23  H   HOH1  0   0.464  -5.2978   1.8933   3.1434
 5AK  H1   H   HCR6  0   0.274   5.8577  -0.6315   1.0746

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
 5AK  CAN  CAM  single    1.524  0.020  1.524
 5AK  CAN  CAY  single    1.503  0.020  1.503
 5AK  CAM  NAS  single    1.449  0.020  1.449
 5AK  CAY  CAK  aromatic  1.393  0.020  1.393
 5AK  CAY  CAJ  aromatic  1.392  0.020  1.392
 5AK  CAK  CAW  aromatic  1.387  0.020  1.387
 5AK  NAS  CAV  single    1.335  0.020  1.335
 5AK  N6   C6   single    1.335  0.020  1.335
 5AK  CAJ  CAG  aromatic  1.387  0.020  1.387
 5AK  OAB  CAV  double    1.222  0.020  1.222
 5AK  CAV  CAO  single    1.516  0.020  1.516
 5AK  CAW  BR   single    1.891  0.020  1.891
 5AK  CAW  CAI  aromatic  1.387  0.020  1.387
 5AK  C6   N1   aromatic  1.339  0.020  1.339
 5AK  C6   C5   aromatic  1.405  0.020  1.405
 5AK  CAG  CAI  aromatic  1.388  0.020  1.388
 5AK  N1   C2   aromatic  1.329  0.020  1.329
 5AK  N7   C5   aromatic  1.372  0.020  1.372
 5AK  N7   C8   aromatic  1.301  0.020  1.301
 5AK  CAO  SAU  single    1.806  0.020  1.806
 5AK  C5   C4   aromatic  1.383  0.020  1.383
 5AK  C8   SAU  single    1.740  0.020  1.740
 5AK  C8   N9   aromatic  1.377  0.020  1.377
 5AK  C2   N3   aromatic  1.323  0.020  1.323
 5AK  C4   N3   aromatic  1.328  0.020  1.328
 5AK  C4   N9   aromatic  1.371  0.020  1.371
 5AK  N9   C1'  single    1.441  0.020  1.441
 5AK  O4'  C1'  single    1.398  0.020  1.398
 5AK  O4'  C4'  single    1.438  0.020  1.438
 5AK  C1'  C2'  single    1.526  0.020  1.526
 5AK  C2'  C3'  single    1.531  0.020  1.531
 5AK  C2'  O2'  single    1.390  0.020  1.390
 5AK  C5'  C4'  single    1.521  0.020  1.521
 5AK  C5'  O5'  single    1.404  0.020  1.404
 5AK  C4'  C3'  single    1.533  0.020  1.533
 5AK  C3'  O3'  single    1.403  0.020  1.403
 5AK  CAK  H1   single    0.930  0.020  1.080
 5AK  CAI  H2   single    0.930  0.020  1.080
 5AK  CAG  H3   single    0.930  0.020  1.080
 5AK  CAJ  H4   single    0.930  0.020  1.080
 5AK  CAN  H5   single    0.970  0.020  1.090
 5AK  CAN  H6   single    0.970  0.020  1.090
 5AK  CAM  H7   single    0.970  0.020  1.090
 5AK  CAM  H8   single    0.970  0.020  1.090
 5AK  NAS  H9   single    0.860  0.020  1.020
 5AK  CAO  H10  single    0.970  0.020  1.090
 5AK  CAO  H11  single    0.970  0.020  1.090
 5AK  N6   H12  single    0.860  0.020  1.020
 5AK  N6   H13  single    0.860  0.020  1.020
 5AK  C2   H14  single    0.930  0.020  1.080
 5AK  C1'  H15  single    0.970  0.020  1.090
 5AK  C4'  H16  single    0.970  0.020  1.090
 5AK  C5'  H17  single    0.970  0.020  1.090
 5AK  C5'  H18  single    0.970  0.020  1.090
 5AK  O5'  H19  single    0.850  0.020  0.980
 5AK  C3'  H20  single    0.970  0.020  1.090
 5AK  O3'  H21  single    0.850  0.020  0.980
 5AK  C2'  H22  single    0.970  0.020  1.090
 5AK  O2'  H23  single    0.850  0.020  0.980

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
 5AK  N9   C4   N3   128.06  3.000
 5AK  N9   C4   C5   105.43  3.000
 5AK  N3   C4   C5   126.51  3.000
 5AK  N7   C5   C6   132.73  3.000
 5AK  N7   C5   C4   110.85  3.000
 5AK  C6   C5   C4   116.42  3.000
 5AK  N6   C6   N1   119.37  3.000
 5AK  N1   C6   C5   117.86  3.000
 5AK  N6   C6   C5   122.77  3.000
 5AK  N9   C8   N7   113.18  3.000
 5AK  N9   C8   SAU  121.25  3.000
 5AK  N7   C8   SAU  125.56  3.000
 5AK  C2   N1   C6   119.15  3.000
 5AK  C2   N3   C4   111.75  3.000
 5AK  H1   CAK  CAY  119.55  3.000
 5AK  H1   CAK  CAW  120.70  3.000
 5AK  CAY  CAK  CAW  119.75  3.000
 5AK  CAI  CAW  BR   119.29  3.000
 5AK  CAI  CAW  CAK  121.54  3.000
 5AK  BR   CAW  CAK  119.18  3.000
 5AK  H2   CAI  CAG  120.22  3.000
 5AK  H2   CAI  CAW  121.34  3.000
 5AK  CAG  CAI  CAW  118.44  3.000
 5AK  H3   CAG  CAJ  120.04  3.000
 5AK  H3   CAG  CAI  119.29  3.000
 5AK  CAJ  CAG  CAI  120.66  3.000
 5AK  H4   CAJ  CAY  119.75  3.000
 5AK  H4   CAJ  CAG  119.67  3.000
 5AK  CAY  CAJ  CAG  120.58  3.000
 5AK  CAN  CAY  CAJ  120.90  3.000
 5AK  CAJ  CAY  CAK  119.03  3.000
 5AK  CAN  CAY  CAK  120.04  3.000
 5AK  H6   CAN  H5   107.23  3.000
 5AK  H6   CAN  CAM  109.57  3.000
 5AK  H5   CAN  CAM  109.67  3.000
 5AK  H6   CAN  CAY  110.03  3.000
 5AK  H5   CAN  CAY  109.68  3.000
 5AK  CAM  CAN  CAY  110.61  3.000
 5AK  H8   CAM  H7   107.07  3.000
 5AK  H8   CAM  NAS  110.10  3.000
 5AK  H7   CAM  NAS  109.64  3.000
 5AK  H8   CAM  CAN  109.83  3.000
 5AK  H7   CAM  CAN  109.82  3.000
 5AK  NAS  CAM  CAN  110.33  3.000
 5AK  H9   NAS  CAV  119.17  3.000
 5AK  H9   NAS  CAM  118.53  3.000
 5AK  CAV  NAS  CAM  122.29  3.000
 5AK  CAO  CAV  OAB  121.29  3.000
 5AK  CAO  CAV  NAS  114.96  3.000
 5AK  OAB  CAV  NAS  123.75  3.000
 5AK  H11  CAO  H10  107.90  3.000
 5AK  H11  CAO  SAU  110.63  3.000
 5AK  H10  CAO  SAU  110.48  3.000
 5AK  H11  CAO  CAV  110.72  3.000
 5AK  H10  CAO  CAV  111.24  3.000
 5AK  SAU  CAO  CAV  105.90  3.000
 5AK  CAO  SAU  C8    98.96  3.000
 5AK  C8   N7   C5   104.65  3.000
 5AK  H13  N6   H12  118.11  3.000
 5AK  H13  N6   C6   120.95  3.000
 5AK  H12  N6   C6   120.16  3.000
 5AK  H14  C2   N3   116.13  3.000
 5AK  H14  C2   N1   115.56  3.000
 5AK  N3   C2   N1   128.31  3.000
 5AK  C1'  N9   C8   129.73  3.000
 5AK  C1'  N9   C4   124.36  3.000
 5AK  C8   N9   C4   105.88  3.000
 5AK  H15  C1'  C2'  109.50  3.000
 5AK  H15  C1'  O4'  112.05  3.000
 5AK  C2'  C1'  O4'  105.14  3.000
 5AK  H15  C1'  N9   105.49  3.000
 5AK  C2'  C1'  N9   115.22  3.000
 5AK  O4'  C1'  N9   109.60  3.000
 5AK  C4'  O4'  C1'  109.78  3.000
 5AK  H16  C4'  C3'  110.82  3.000
 5AK  H16  C4'  C5'  109.07  3.000
 5AK  C3'  C4'  C5'  112.26  3.000
 5AK  H16  C4'  O4'  108.05  3.000
 5AK  C3'  C4'  O4'  106.25  3.000
 5AK  C5'  C4'  O4'  110.28  3.000
 5AK  H18  C5'  H17  106.77  3.000
 5AK  H18  C5'  O5'  111.70  3.000
 5AK  H17  C5'  O5'  107.33  3.000
 5AK  H18  C5'  C4'  110.15  3.000
 5AK  H17  C5'  C4'  107.64  3.000
 5AK  O5'  C5'  C4'  112.93  3.000
 5AK  H19  O5'  C5'  108.13  3.000
 5AK  H20  C3'  C2'  111.85  3.000
 5AK  H20  C3'  O3'  111.52  3.000
 5AK  C2'  C3'  O3'  107.84  3.000
 5AK  H20  C3'  C4'  111.08  3.000
 5AK  O3'  C3'  C4'  112.99  3.000
 5AK  C2'  C3'  C4'  101.09  3.000
 5AK  H21  O3'  C3'  108.35  3.000
 5AK  H22  C2'  O2'  111.89  3.000
 5AK  H22  C2'  C3'  108.12  3.000
 5AK  O2'  C2'  C3'  116.78  3.000
 5AK  H22  C2'  C1'  109.20  3.000
 5AK  O2'  C2'  C1'  109.85  3.000
 5AK  C3'  C2'  C1'  100.25  3.000
 5AK  H23  O2'  C2'  108.85  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
 5AK  CONST_01  N1   C6   C5   C4      0.00   0.0  0
 5AK  CONST_02  C8   N7   C5   C4      0.00   0.0  0
 5AK  CONST_03  N1   C2   N3   C4      0.00   0.0  0
 5AK  CONST_04  N7   C8   N9   C4      0.00   0.0  0
 5AK  CONST_05  C2   N1   C6   C5      0.00   0.0  0
 5AK  CONST_06  N9   C8   N7   C5      0.00   0.0  0
 5AK  CONST_07  C2   N3   C4   C5      0.00   0.0  0
 5AK  CONST_08  C8   N9   C4   C5      0.00   0.0  0
 5AK  CONST_09  N3   C2   N1   C6      0.00   0.0  0
 5AK  CONST_10  C8   N7   C5   C6    180.00   0.0  0
 5AK  CONST_11  N3   C4   C5   C6      0.00   0.0  0
 5AK  CONST_12  N9   C4   C5   C6    180.00   0.0  0
 5AK  CONST_13  N3   C4   N9   C8    180.00   0.0  0
 5AK  CONST_14  N7   C5   C6   N1    180.00   0.0  0
 5AK  CONST_15  N7   C5   C4   N3    180.00   0.0  0
 5AK  CONST_16  CAG  CAJ  CAY  CAK     0.00   0.0  0
 5AK  CONST_17  CAG  CAI  CAW  CAK     0.00   0.0  0
 5AK  CONST_18  CAJ  CAY  CAK  CAW     0.00   0.0  0
 5AK  CONST_19  CAJ  CAG  CAI  CAW     0.00   0.0  0
 5AK  CONST_20  CAY  CAK  CAW  CAI     0.00   0.0  0
 5AK  CONST_21  CAY  CAJ  CAG  CAI     0.00   0.0  0
 5AK  CONST_22  N9   C4   C5   N7      0.00   0.0  0
 5AK  CONST_23  N9   C4   N3   C2    180.00   0.0  0
 5AK  CONST_24  C1'  N9   C4   C5    180.00   0.0  0
 5AK  CONST_25  C1'  N9   C4   N3      0.00   0.0  0
 5AK  CONST_26  C1'  N9   C8   N7    180.00   0.0  0
 5AK  CONST_27  N6   C6   C5   C4    180.00   0.0  0
 5AK  CONST_28  SAU  C8   N9   C4    180.00   0.0  0
 5AK  CONST_29  SAU  C8   N7   C5    180.00   0.0  0
 5AK  CONST_30  CAN  CAY  CAK  CAW   180.00   0.0  0
 5AK  CONST_31  CAY  CAK  CAW  BR    180.00   0.0  0
 5AK  CONST_32  CAG  CAI  CAW  BR    180.00   0.0  0
 5AK  CONST_33  CAN  CAY  CAJ  CAG   180.00   0.0  0
 5AK  CONST_34  C1'  N9   C8   SAU     0.00   0.0  0
 5AK  CONST_35  N6   C6   C5   N7      0.00   0.0  0
 5AK  CONST_36  C2   N1   C6   N6    180.00   0.0  0
 5AK  CONST_37  H14  C2   N3   C4    180.00   0.0  0
 5AK  CONST_38  H4   CAJ  CAY  CAK   180.00   0.0  0
 5AK  CONST_39  H2   CAI  CAW  CAK   180.00   0.0  0
 5AK  CONST_40  H3   CAG  CAI  CAW   180.00   0.0  0
 5AK  CONST_41  H1   CAK  CAW  CAI   180.00   0.0  0
 5AK  CONST_42  H12  N6   C6   C5    180.00   0.0  0
 5AK  CONST_43  H13  N6   C6   C5      0.00   0.0  0
 5AK  CONST_44  OAB  CAV  NAS  CAM     0.00   0.0  0
 5AK  CONST_45  CAO  CAV  NAS  CAM   180.00   0.0  0
 5AK  CONST_46  H9   NAS  CAV  OAB   180.00   0.0  0
 5AK  Var_01    CAM  CAN  CAY  CAK    87.90  30.0  2
 5AK  Var_02    N7   C8   SAU  CAO    -4.48  30.0  1
 5AK  Var_03    CAV  CAO  SAU  C8    177.39  30.0  1
 5AK  Var_04    NAS  CAM  CAN  CAY   179.84  30.0  3
 5AK  Var_05    CAV  NAS  CAM  CAN   175.82  30.0  3
 5AK  Var_06    SAU  CAO  CAV  NAS  -175.22  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
 5AK  chir_01  C1'  N9   O4'  C2'  positiv
 5AK  chir_02  C4'  O4'  C3'  C5'  negativ
 5AK  chir_03  C3'  O3'  C4'  C2'  positiv
 5AK  chir_04  C2'  O2'  C3'  C1'  positiv

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
 5AK  plan-1  CAK  0.020
 5AK  plan-1  CAW  0.020
 5AK  plan-1  BR   0.020
 5AK  plan-1  CAI  0.020
 5AK  plan-1  CAG  0.020
 5AK  plan-1  CAJ  0.020
 5AK  plan-1  CAY  0.020
 5AK  plan-1  CAN  0.020
 5AK  plan-1  H2   0.020
 5AK  plan-1  H3   0.020
 5AK  plan-1  H4   0.020
 5AK  plan-1  H1   0.020
 5AK  plan-2  C4   0.020
 5AK  plan-2  C5   0.020
 5AK  plan-2  C6   0.020
 5AK  plan-2  C8   0.020
 5AK  plan-2  N1   0.020
 5AK  plan-2  N3   0.020
 5AK  plan-2  SAU  0.020
 5AK  plan-2  N7   0.020
 5AK  plan-2  N6   0.020
 5AK  plan-2  C2   0.020
 5AK  plan-2  N9   0.020
 5AK  plan-2  C1'  0.020
 5AK  plan-2  H14  0.020
 5AK  plan-3  C6   0.020
 5AK  plan-3  N6   0.020
 5AK  plan-3  H12  0.020
 5AK  plan-3  H13  0.020
 5AK  plan-4  CAM  0.020
 5AK  plan-4  NAS  0.020
 5AK  plan-4  CAV  0.020
 5AK  plan-4  OAB  0.020
 5AK  plan-4  CAO  0.020
 5AK  plan-4  H9   0.020

