MinE07-U-Ph which has one of the worst K d values and docking scores (-13.3 kcal/mol) sits in the binding pocket in a very different conformation, showing that the complete modification hinders the overall binding. MinE07-U-Vi binds in a similar fashion to MinE07 itself, with the vinyl group of fU-Vi(8) slotting between Glu90 and Asn91, while fU-Vi(7) sits between Glu258, Glu 221, and Thr235. MinE07-U-I is also similar overall, but with the iodine of fU-I(7) and fU-I(8) both pointing towards Glu residues which could indicate formation of halogen bonds. MinE07UA sits further into the binding pocket than MinE07 at the 5' and 3' end that interacts via base pairing. This is because of the truncation of 3 nucleotides and the fU-Ph modification at position U2, U3 and U8 distorting the original base pairing, pulling the stands apart allowing them to go deeper into the binding pocket. Due to shape changes in other areas of MinE07UA caused by chemical modifications, the fU-Ph(7) sits deeper into the binding pocket, with the phenyl ring located in empty space between the side chains of Glu90 and Asn91. The full length analogue MinE07UA' binds more weakly since the untruncated duplex cannot protrude as deeply into the EGF binding pocket; it overlays very closely with the unmodified aptamer. MinE07UB is very similar to the parent aptamer, but with the additional possibility of a halogen bond being formed between fU-I(7) and Glu258; the docking model does not handle halogen bonds, so this may explain the difference between the calculated docking energy and the measured K d . Like MinE07UA, MinE07UC also sits further into the binding pocket than MinE07 at the 5' and 3' end from the separation of the original base pairing caused by the truncation of four nucleotides and the modification fU-Vi in U1 position. The fU-Ph at U6 position rotates the molecule slightly allowing the fU-Vi at U7 position to be further into the same binding pocket as MinE07UA, the fU-Vi( ) is predicted to be interacting with Ser222 and Glu258. The phenyl modification at U6 also stops the base pairing that usually occurs in MinE07 between U6 and A12, causing the fU-Ph(6) to sit closer to Ser146, Asp147, Cys195 and Ser196. These extra interactions are lost when the aptamer is in its full-length version