# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun  2 19:25:05 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 5'-azido-8-[(2-{[2-(3-bromophenyl)ethyl]amino}-2-oxoethyl)sulfanyl]-5'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n([C@@H]3O[C@H](CN=[N+]=[N-])[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
 5A9  5A9  5'-azido-8-[(2-{[2-(3-bromophenyl)ethyl]amino}-2-oxoethyl)sulfanyl]-5'-deoxyadenosine  ligand  57  35  .  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_5A9
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
 5A9  C4   C   CR56   0   0.490   5.2476  -1.7288   0.6085
 5A9  C5   C   CR56   0   0.009   4.3792  -2.7852   0.8111
 5A9  C6   C   CR6    0   0.448   4.9664  -4.0264   1.1102
 5A9  C8   C   CR5    0   0.326   3.1536  -1.1131   0.3868
 5A9  N1   N   N      0  -0.471   6.3024  -4.0868   1.1756
 5A9  N3   N   N      0  -0.459   6.5741  -1.7706   0.6677
 5A9  CBC  C   CR16   0  -0.279  -6.3531  -0.7778  -0.0049
 5A9  CBD  C   CR6    0  -0.090  -7.5931  -0.2040  -0.2407
 5A9  BR   BR  BR     0  -0.051  -8.6337   0.3780   1.2268
 5A9  CBE  C   CR16   0  -0.246  -8.0882  -0.0504  -1.5268
 5A9  CAX  C   CR16   0  -0.234  -7.3116  -0.4881  -2.5909
 5A9  CAW  C   CR16   0  -0.300  -6.0692  -1.0642  -2.3703
 5A9  CAV  C   CR6    0   0.126  -5.5787  -1.2152  -1.0766
 5A9  CAM  C   CH2    0  -0.563  -4.2157  -1.7981  -0.8294
 5A9  CAL  C   CH2    0  -0.233  -3.1560  -0.7017  -0.8238
 5A9  NAK  N   NH1    0  -0.644  -1.8465  -1.2675  -0.5696
 5A9  CAJ  C   C      0   0.577  -0.7770  -0.5111  -0.3076
 5A9  OAB  O   O      0  -0.485  -0.8040   0.7099  -0.2612
 5A9  CAI  C   CH2    0  -0.683   0.5036  -1.2820  -0.0533
 5A9  SAH  S   S2     0   0.084   1.8052  -0.0410   0.1328
 5A9  N7   N   N      0  -0.459   3.0762  -2.3800   0.6745
 5A9  N6   N   NH2    0  -0.818   4.2502  -5.1298   1.3341
 5A9  C2   C   CR16   0   0.043   7.0126  -2.9851   0.9583
 5A9  N9   N   NR5    0  -0.583   4.4491  -0.6498   0.3327
 5A9  CAR  C   CH1    0   0.186   4.9374   0.6546  -0.0418
 5A9  OAS  O   O2     0  -0.492   4.1547   1.6177   0.6129
 5A9  CAZ  C   CH1    0  -0.048   4.8888   0.9630  -1.5554
 5A9  OAY  O   OH1    0  -0.666   6.1696   1.3445  -1.9714
 5A9  CBA  C   CH1    0  -0.022   3.9019   2.1472  -1.6372
 5A9  OBF  O   OH1    0  -0.657   4.2682   3.1016  -2.5943
 5A9  CAT  C   CH1    0   0.028   3.9958   2.7410  -0.2337
 5A9  CAU  C   CH2    0  -0.340   2.7691   3.5291   0.1750
 5A9  NBB  N   N      0  -0.354   2.8664   4.0621   1.5352
 5A9  NBG  N   N      1   0.355   3.5179   5.0814   1.6744
 5A9  NBI  N   N     -1  -0.217   4.0926   6.0177   1.9125
 5A9  H2   H   HCR6   0   0.279  -9.0563   0.3968  -1.7074
 5A9  H3   H   HCR6   0   0.269  -7.6858  -0.3774  -3.6001
 5A9  H4   H   HCR6   0   0.258  -5.4787  -1.4045  -3.2123
 5A9  H5   H   HCH2   0   0.266  -4.2007  -2.3239   0.1284
 5A9  H6   H   HCH2   0   0.266  -3.9830  -2.5319  -1.6051
 5A9  H7   H   HCH2   0   0.246  -3.1642  -0.1731  -1.7816
 5A9  H8   H   HCH2   0   0.249  -3.3886   0.0329  -0.0500
 5A9  H9   H   HNH1   0   0.412  -1.7357  -2.2672  -0.6366
 5A9  H10  H   HCH2   0   0.321   0.4171  -1.8803   0.8548
 5A9  H11  H   HCH2   0   0.316   0.7261  -1.9594  -0.8789
 5A9  H12  H   HNH2   0   0.411   3.2485  -5.1238   1.2576
 5A9  H13  H   HNH2   0   0.403   4.7103  -6.0062   1.5091
 5A9  H14  H   HCR6   0   0.253   8.0890  -3.1010   1.0263
 5A9  H15  H   HCH1   0   0.275   5.9808   0.6913   0.2876
 5A9  H16  H   HCH1   0   0.255   4.5290   0.0943  -2.1207
 5A9  H17  H   HOH1   0   0.451   6.0631   2.0716  -2.6000
 5A9  H18  H   HCH1   0   0.253   2.8909   1.7665  -1.8149
 5A9  H19  H   HOH1   0   0.473   3.8248   2.9006  -3.4244
 5A9  H20  H   HCH1   0   0.253   4.8856   3.3866  -0.1814
 5A9  H21  H   HCH2   0   0.274   2.6091   4.3246  -0.5579
 5A9  H22  H   HCH2   0   0.267   1.8880   2.8895   0.1661
 5A9  H1   H   HCR6   0   0.274  -5.9810  -0.8951   1.0055

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
 5A9  OBF  CBA  single    1.400  0.020  1.400
 5A9  NBB  CAU  single    1.464  0.020  1.464
 5A9  NBB  NBG  double    1.218  0.020  1.218
 5A9  CBA  CAT  single    1.527  0.020  1.527
 5A9  CBA  CAZ  single    1.544  0.020  1.544
 5A9  CAU  CAT  single    1.514  0.020  1.514
 5A9  OAY  CAZ  single    1.400  0.020  1.400
 5A9  CAT  OAS  single    1.416  0.020  1.416
 5A9  NBG  NBI  double    1.124  0.020  1.124
 5A9  CAZ  CAR  single    1.545  0.020  1.545
 5A9  OAS  CAR  single    1.403  0.020  1.403
 5A9  CAR  N9   single    1.442  0.020  1.442
 5A9  SAH  C8   single    1.741  0.020  1.741
 5A9  SAH  CAI  single    1.808  0.020  1.808
 5A9  N9   C8   aromatic  1.377  0.020  1.377
 5A9  N9   C4   aromatic  1.370  0.020  1.370
 5A9  C8   N7   aromatic  1.301  0.020  1.301
 5A9  N3   C4   aromatic  1.328  0.020  1.328
 5A9  N3   C2   aromatic  1.324  0.020  1.324
 5A9  C4   C5   aromatic  1.383  0.020  1.383
 5A9  CAI  CAJ  single    1.516  0.020  1.516
 5A9  CAX  CBE  aromatic  1.388  0.020  1.388
 5A9  CAX  CAW  aromatic  1.387  0.020  1.387
 5A9  CBE  CBD  aromatic  1.387  0.020  1.387
 5A9  C2   N1   aromatic  1.329  0.020  1.329
 5A9  OAB  CAJ  double    1.222  0.020  1.222
 5A9  N7   C5   aromatic  1.371  0.020  1.371
 5A9  C5   C6   aromatic  1.405  0.020  1.405
 5A9  CAJ  NAK  single    1.336  0.020  1.336
 5A9  CAW  CAV  aromatic  1.392  0.020  1.392
 5A9  CBD  BR   single    1.891  0.020  1.891
 5A9  CBD  CBC  aromatic  1.386  0.020  1.386
 5A9  N1   C6   aromatic  1.339  0.020  1.339
 5A9  C6   N6   single    1.334  0.020  1.334
 5A9  NAK  CAL  single    1.449  0.020  1.449
 5A9  CAV  CBC  aromatic  1.393  0.020  1.393
 5A9  CAV  CAM  single    1.503  0.020  1.503
 5A9  CAL  CAM  single    1.525  0.020  1.525
 5A9  CBC  H1   single    0.930  0.020  1.080
 5A9  CBE  H2   single    0.930  0.020  1.080
 5A9  CAX  H3   single    0.930  0.020  1.080
 5A9  CAW  H4   single    0.930  0.020  1.080
 5A9  CAM  H5   single    0.970  0.020  1.090
 5A9  CAM  H6   single    0.970  0.020  1.090
 5A9  CAL  H7   single    0.970  0.020  1.090
 5A9  CAL  H8   single    0.970  0.020  1.090
 5A9  NAK  H9   single    0.860  0.020  1.020
 5A9  CAI  H10  single    0.970  0.020  1.090
 5A9  CAI  H11  single    0.970  0.020  1.090
 5A9  N6   H12  single    0.860  0.020  1.020
 5A9  N6   H13  single    0.860  0.020  1.020
 5A9  C2   H14  single    0.930  0.020  1.080
 5A9  CAR  H15  single    0.970  0.020  1.090
 5A9  CAZ  H16  single    0.970  0.020  1.090
 5A9  OAY  H17  single    0.850  0.020  0.980
 5A9  CBA  H18  single    0.970  0.020  1.090
 5A9  OBF  H19  single    0.850  0.020  0.980
 5A9  CAT  H20  single    0.970  0.020  1.090
 5A9  CAU  H21  single    0.970  0.020  1.090
 5A9  CAU  H22  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
 5A9  N9   C4   N3   127.99  3.000
 5A9  N3   C4   C5   126.63  3.000
 5A9  N9   C4   C5   105.37  3.000
 5A9  N7   C5   C6   132.78  3.000
 5A9  C6   C5   C4   116.33  3.000
 5A9  N7   C5   C4   110.89  3.000
 5A9  N6   C6   N1   119.35  3.000
 5A9  N6   C6   C5   122.81  3.000
 5A9  N1   C6   C5   117.85  3.000
 5A9  N9   C8   N7   113.09  3.000
 5A9  N7   C8   SAH  125.84  3.000
 5A9  N9   C8   SAH  121.04  3.000
 5A9  C2   N1   C6   119.21  3.000
 5A9  C2   N3   C4   111.69  3.000
 5A9  H1   CBC  CAV  119.53  3.000
 5A9  H1   CBC  CBD  120.71  3.000
 5A9  CAV  CBC  CBD  119.76  3.000
 5A9  CBE  CBD  BR   119.29  3.000
 5A9  BR   CBD  CBC  119.18  3.000
 5A9  CBE  CBD  CBC  121.53  3.000
 5A9  H2   CBE  CAX  120.21  3.000
 5A9  H2   CBE  CBD  121.35  3.000
 5A9  CAX  CBE  CBD  118.44  3.000
 5A9  H3   CAX  CAW  120.04  3.000
 5A9  H3   CAX  CBE  119.29  3.000
 5A9  CAW  CAX  CBE  120.67  3.000
 5A9  H4   CAW  CAV  119.76  3.000
 5A9  H4   CAW  CAX  119.67  3.000
 5A9  CAV  CAW  CAX  120.57  3.000
 5A9  CAM  CAV  CAW  120.97  3.000
 5A9  CAM  CAV  CBC  119.97  3.000
 5A9  CAW  CAV  CBC  119.03  3.000
 5A9  H6   CAM  H5   107.23  3.000
 5A9  H6   CAM  CAL  109.72  3.000
 5A9  H5   CAM  CAL  109.47  3.000
 5A9  H6   CAM  CAV  109.68  3.000
 5A9  H5   CAM  CAV  110.07  3.000
 5A9  CAL  CAM  CAV  110.61  3.000
 5A9  H8   CAL  H7   107.08  3.000
 5A9  H8   CAL  NAK  109.32  3.000
 5A9  H7   CAL  NAK  110.43  3.000
 5A9  H8   CAL  CAM  109.77  3.000
 5A9  H7   CAL  CAM  109.82  3.000
 5A9  NAK  CAL  CAM  110.36  3.000
 5A9  H9   NAK  CAJ  119.11  3.000
 5A9  H9   NAK  CAL  118.36  3.000
 5A9  CAJ  NAK  CAL  122.47  3.000
 5A9  CAI  CAJ  OAB  121.35  3.000
 5A9  OAB  CAJ  NAK  123.74  3.000
 5A9  CAI  CAJ  NAK  114.91  3.000
 5A9  H11  CAI  H10  107.80  3.000
 5A9  H11  CAI  SAH  110.93  3.000
 5A9  H10  CAI  SAH  110.35  3.000
 5A9  H11  CAI  CAJ  111.17  3.000
 5A9  H10  CAI  CAJ  110.58  3.000
 5A9  SAH  CAI  CAJ  106.04  3.000
 5A9  CAI  SAH  C8    98.62  3.000
 5A9  C8   N7   C5   104.66  3.000
 5A9  H13  N6   H12  118.35  3.000
 5A9  H13  N6   C6   120.29  3.000
 5A9  H12  N6   C6   121.16  3.000
 5A9  H14  C2   N3   116.14  3.000
 5A9  H14  C2   N1   115.57  3.000
 5A9  N3   C2   N1   128.29  3.000
 5A9  CAR  N9   C8   129.28  3.000
 5A9  C8   N9   C4   105.98  3.000
 5A9  CAR  N9   C4   124.55  3.000
 5A9  H15  CAR  CAZ  108.54  3.000
 5A9  H15  CAR  OAS  111.61  3.000
 5A9  CAZ  CAR  OAS  107.61  3.000
 5A9  H15  CAR  N9   105.95  3.000
 5A9  OAS  CAR  N9   108.10  3.000
 5A9  CAZ  CAR  N9   115.09  3.000
 5A9  CAT  OAS  CAR  109.16  3.000
 5A9  H16  CAZ  CBA  111.74  3.000
 5A9  H16  CAZ  OAY  111.27  3.000
 5A9  CBA  CAZ  OAY  111.11  3.000
 5A9  H16  CAZ  CAR  110.91  3.000
 5A9  OAY  CAZ  CAR  108.46  3.000
 5A9  CBA  CAZ  CAR  103.01  3.000
 5A9  H17  OAY  CAZ  107.29  3.000
 5A9  H18  CBA  CAT  109.94  3.000
 5A9  H18  CBA  OBF  111.57  3.000
 5A9  CAT  CBA  OBF  110.31  3.000
 5A9  H18  CBA  CAZ  109.41  3.000
 5A9  CAT  CBA  CAZ  102.14  3.000
 5A9  OBF  CBA  CAZ  113.07  3.000
 5A9  H19  OBF  CBA  109.06  3.000
 5A9  H20  CAT  CAU  109.69  3.000
 5A9  H20  CAT  CBA  108.75  3.000
 5A9  CAU  CAT  CBA  113.62  3.000
 5A9  H20  CAT  OAS  110.26  3.000
 5A9  CAU  CAT  OAS  110.03  3.000
 5A9  CBA  CAT  OAS  104.36  3.000
 5A9  H22  CAU  H21  107.67  3.000
 5A9  H22  CAU  NBB  105.97  3.000
 5A9  H21  CAU  NBB  111.56  3.000
 5A9  H22  CAU  CAT  110.34  3.000
 5A9  H21  CAU  CAT  108.44  3.000
 5A9  NBB  CAU  CAT  112.73  3.000
 5A9  NBG  NBB  CAU  116.52  3.000
 5A9  NBI  NBG  NBB  174.25  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
 5A9  CONST_01  N7   C8   N9   C4      0.00   0.0  0
 5A9  CONST_02  N1   C2   N3   C4      0.00   0.0  0
 5A9  CONST_03  C8   N7   C5   C4      0.00   0.0  0
 5A9  CONST_04  N1   C6   C5   C4      0.00   0.0  0
 5A9  CONST_05  C8   N9   C4   C5      0.00   0.0  0
 5A9  CONST_06  C2   N3   C4   C5      0.00   0.0  0
 5A9  CONST_07  N9   C8   N7   C5      0.00   0.0  0
 5A9  CONST_08  C2   N1   C6   C5      0.00   0.0  0
 5A9  CONST_09  N9   C4   C5   C6    180.00   0.0  0
 5A9  CONST_10  N3   C4   C5   C6      0.00   0.0  0
 5A9  CONST_11  C8   N7   C5   C6    180.00   0.0  0
 5A9  CONST_12  N3   C2   N1   C6      0.00   0.0  0
 5A9  CONST_13  N3   C4   N9   C8    180.00   0.0  0
 5A9  CONST_14  N7   C5   C6   N1    180.00   0.0  0
 5A9  CONST_15  N7   C5   C4   N3    180.00   0.0  0
 5A9  CONST_16  CAX  CBE  CBD  CBC     0.00   0.0  0
 5A9  CONST_17  CAX  CAW  CAV  CBC     0.00   0.0  0
 5A9  CONST_18  CAW  CAX  CBE  CBD     0.00   0.0  0
 5A9  CONST_19  CAW  CAV  CBC  CBD     0.00   0.0  0
 5A9  CONST_20  CAV  CAW  CAX  CBE     0.00   0.0  0
 5A9  CONST_21  CAV  CBC  CBD  CBE     0.00   0.0  0
 5A9  CONST_22  N9   C4   C5   N7      0.00   0.0  0
 5A9  CONST_23  N9   C4   N3   C2    180.00   0.0  0
 5A9  CONST_24  CAR  N9   C4   C5    180.00   0.0  0
 5A9  CONST_25  CAR  N9   C4   N3      0.00   0.0  0
 5A9  CONST_26  CAR  N9   C8   N7    180.00   0.0  0
 5A9  CONST_27  SAH  C8   N9   C4    180.00   0.0  0
 5A9  CONST_28  N6   C6   C5   C4    180.00   0.0  0
 5A9  CONST_29  SAH  C8   N7   C5    180.00   0.0  0
 5A9  CONST_30  CAM  CAV  CBC  CBD   180.00   0.0  0
 5A9  CONST_31  CAX  CBE  CBD  BR    180.00   0.0  0
 5A9  CONST_32  CAV  CBC  CBD  BR    180.00   0.0  0
 5A9  CONST_33  CAM  CAV  CAW  CAX   180.00   0.0  0
 5A9  CONST_34  CAR  N9   C8   SAH     0.00   0.0  0
 5A9  CONST_35  N6   C6   C5   N7      0.00   0.0  0
 5A9  CONST_36  C2   N1   C6   N6    180.00   0.0  0
 5A9  CONST_37  H14  C2   N3   C4    180.00   0.0  0
 5A9  CONST_38  H2   CBE  CBD  CBC   180.00   0.0  0
 5A9  CONST_39  H4   CAW  CAV  CBC   180.00   0.0  0
 5A9  CONST_40  H3   CAX  CBE  CBD   180.00   0.0  0
 5A9  CONST_41  H1   CBC  CBD  CBE   180.00   0.0  0
 5A9  CONST_42  H12  N6   C6   C5      0.00   0.0  0
 5A9  CONST_43  H13  N6   C6   C5    180.00   0.0  0
 5A9  CONST_44  CAI  CAJ  NAK  CAL   180.00   0.0  0
 5A9  CONST_45  OAB  CAJ  NAK  CAL     0.00   0.0  0
 5A9  CONST_46  H9   NAK  CAJ  OAB   180.00   0.0  0
 5A9  Var_01    CAL  CAM  CAV  CBC   -88.72  30.0  2
 5A9  Var_02    N9   C8   SAH  CAI   167.48  30.0  2
 5A9  Var_03    CAJ  CAI  SAH  C8   -179.24  30.0  3
 5A9  Var_04    NAK  CAL  CAM  CAV   179.33  30.0  1
 5A9  Var_05    CAJ  NAK  CAL  CAM  -169.39  30.0  2
 5A9  Var_06    SAH  CAI  CAJ  NAK   175.36  30.0  1
 5A9  Var_07    H21  CAU  NBB  NBG   -42.03  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
 5A9  chir_01  CAR  CAZ  OAS  N9   negativ
 5A9  chir_02  CAZ  OAY  CBA  CAR  positiv
 5A9  chir_03  CBA  OBF  CAT  CAZ  positiv
 5A9  chir_04  CAT  OAS  CBA  CAU  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
 5A9  plan-1  CBC  0.020
 5A9  plan-1  CBD  0.020
 5A9  plan-1  BR   0.020
 5A9  plan-1  CBE  0.020
 5A9  plan-1  CAX  0.020
 5A9  plan-1  CAW  0.020
 5A9  plan-1  CAV  0.020
 5A9  plan-1  CAM  0.020
 5A9  plan-1  H2   0.020
 5A9  plan-1  H3   0.020
 5A9  plan-1  H4   0.020
 5A9  plan-1  H1   0.020
 5A9  plan-2  C4   0.020
 5A9  plan-2  C5   0.020
 5A9  plan-2  C6   0.020
 5A9  plan-2  C8   0.020
 5A9  plan-2  N1   0.020
 5A9  plan-2  N3   0.020
 5A9  plan-2  SAH  0.020
 5A9  plan-2  N7   0.020
 5A9  plan-2  N6   0.020
 5A9  plan-2  C2   0.020
 5A9  plan-2  N9   0.020
 5A9  plan-2  CAR  0.020
 5A9  plan-2  H14  0.020
 5A9  plan-3  C6   0.020
 5A9  plan-3  N6   0.020
 5A9  plan-3  H12  0.020
 5A9  plan-3  H13  0.020
 5A9  plan-4  CAL  0.020
 5A9  plan-4  NAK  0.020
 5A9  plan-4  CAJ  0.020
 5A9  plan-4  OAB  0.020
 5A9  plan-4  CAI  0.020
 5A9  plan-4  H9   0.020
 5A9  plan-5  CAU  0.020
 5A9  plan-5  NBB  0.020
 5A9  plan-5  NBG  0.020
 5A9  plan-5  NBI  0.020

