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1 Electronic Supplementary Material (ESI) for Chemical Science. This journal is The Royal Society of Chemistry 2018 Supporting Information for: Cation p interactions in protein-ligand binding: theory and datamining reveal different roles for lysine and arginine Kiran Kumar a and Shin M. Woo a, Thomas Siu a, Wilian A. Cortopassi a, Fernanda Duarte b, and Robert S. Paton a* a Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK b EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK These authors contributed equally to this work fernanda.duarte@ed.ac.uk; robert.paton@chem.ox.ac.uk Table of contents 1 Full citation [C 6 H 6 ][Na] + potential energy curve: basis set dependency PLIP cation π interaction geometric criteria Interactions involving polycyclic aromatic rings van der Waals Surface Representations Minimum energy structures SAPT2+3 energy decomposition DLPNO-CCSD(T)/aug-cc-pVTZ calculated values Orientations of Arg-aromatic interactions Lys-aromatic interactions Effect of methylation Cartesian coordinates S1

2 1 Full citation 50 Gaussian 09, Revision D.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. Marenich, J. Bloino, B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian, J. V. Ortiz, A. F. Izmaylov, J. L. Sonnenberg, D. Williams-Young, F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone, T. Henderson, D. Ranasinghe, V. G. Zakrzewski, J. Gao, N. Rega, G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, K. Throssell, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, J. M. Millam, M. Klene, C. Adamo, R. Cammi, J. W. Ochterski, R. L. Martin, K. Morokuma, O. Farkas, J. B. Foresman, and D. J. Fox, Gaussian, Inc., Wallingford CT, S2

3 2 [C 6 H 6 ][Na] + potential energy curve: basis set dependency Figure S1. CCSD(T)/aug-cc-pVXZ potential energy curve of the [C 6 H 6 ][Na] + complex Basis Set Equilibrium R z (Å) E int aug-cc-pvdz aug-cc-pvtz aug-cc-pvqz S3

4 3 PLIP cation π interaction geometric criteria Figure S2. Geometric criteria used define a cation π interaction. A distance cut-off of 6.0 Å (blue sphere) was defined from the centroid of the aromatic ring, along with a 2.3 Å horizontaloffset cut-off in the plane of the ring (purple cylinder). S4

5 4 Interactions involving polycyclic aromatic rings Figure S3. Examples of polycyclic aromatic rings further sub-classified as a) fused bicyclic ligand, b) sandwich complex, and c) bridged bicyclic ligand cation π interaction. S5

6 5 van der Waals Surface Representations Figure S4. Van der Waals surfaces generated using atomic Bondi radii, for minimum energy geometries along the potential energy curve. S6

7 6 Minimum energy structures Figure S5. SAPT2+3/aug-cc-pVDZ and DLPNO-CCSD(T)/aug-cc-pVTZ E int at the minimum along the potential energy curve. Horizontal offset, R y = 0.00 (Å) for all geometries. S7

8 7 SAPT2+3 energy decomposition Table S1. SAPT2+3/aug-cc-pVDZ decomposition of E int values and DLPNO-CCSD(T)/aug-cc-pVTZ. Energies in kcal mol -1. Complex Electrostatic (E ele ) Exchange (E ee ) Induction (E ind ) Dispersion (E disp ) SAPT2+3 E int CCSD(T) E int A B C D E F G H S8

9 8 DLPNO-CCSD(T)/aug-cc-pVTZ calculated values Table S2. R z (Å) and DLPNO-CCSD(T)/aug-cc-pVTZ calculated E monomer, E complex, and E int of cation π complexes (A) and (B). E p = a.u in the gas phase. (A) NH 4 + E monomer (a.u) (B) NH 4 + E monomer (a.u) R z (Å) (A) [C 6 H 6 ][NH 4 ] + E complex (a.u) E int (B) [C 6 H 6 ][NH 4 ] + E complex (a.u) E int S9

10 Table S3. R z (Å) CPCM-MP2/cc-pVTZ calculated E monomer, E complex, and E int of cation π complex (A) in diethyl ether (dielectric constant = 4.2) and water (dielectric constant = 78.4). R z (Å) E int,ether E int,water S10

11 Table S4. R z (Å) and DLPNO-CCSD(T)/aug-cc-pVTZ calculated E monomer, E complex, and E int of cation π complexes (C) and (D). E p = a.u. (C) Gdm + E monomer (a.u) (D) Gdm + E monomer (a.u) R z (Å) (C) [C 6 H 6 ][Gdm] + E complex (a.u) E int (D) [C 6 H 6 ][Gdm] + E complex (a.u) E int S11

12 Table S5. R z (Å) and CPCM-MP2/cc-pVTZ calculated E monomer, E complex, and E int of cation π complex (C) in diethyl ether (dielectric constant = 4.2) and water (dielectric constant = 78.4). R z (Å) E int,ether E int,water S12

13 Table S6. R z (Å) and DLPNO-CCSD(T)/aug-cc-pVTZ calculated E monomer, E complex, and E int of cation π complexes (E) and (F). E p = a.u. (E) Imi + E monomer (a.u) (F) Imi + E monomer (a.u) R z (Å) (E) [C 6 H 6 ][Imi] + E complex (a.u) E int (kcal mol 1 ) (F) [C 6 H 6 ][Imi] + E complex (a.u) E int ( kcal mol 1 ) S13

14 Table S7. R z (Å) and SMD-MP2/cc-pVTZ calculated E monomer, E complex, and E int of cation π complex (E) in diethyl ether (dielectric constant = 4.2) and water (dielectric constant = 78.4). R z (Å) E int,ether E int,water S14

15 Table S8. R z (Å) and DLPNO-CCSD(T)/aug-cc-pVTZ calculated E monomer, E complex, and E int of cation π complexes (G) and (H). E p = a.u. (G) Imi + E monomer (a.u) (H) Imi + E monomer (a.u) R z (Å) (G) [C 6 H 6 ][Imi] + E complex (a.u) E int (H) [C 6 H 6 ][Imi] + E complex (a.u) E int S15

16 Table S9. R z (Å) SMD-MP2/cc-pVTZ calculated E monomer, E complex, and E int of cation π complex (G) in diethyl ether (dielectric constant = 4.2) and water (dielectric constant = 78.4). R z (Å) E int,ether E int,water S16

17 9 Orientations of Arg-aromatic interactions Figure S6. Empirical distribution of Arg-aromatic complexes found in PDB crystal structures. The interplanar angle between arginine and the aromatic ring is plotted against the intermolecular separation of the two groups. Relative abunance in bins of 10 are shown on the right. interplanar angle ( ) distance (Å) 10 Lys-aromatic interactions S17

18 Figure S7. Empirical distribution of Lys-aromatic small molecule complexes found in PDB crystal structures. Orange points indicate aromatic system belongs to GTP, GDP, ATP, ADP, FAD, NAD, or derivatives. 11 Effect of methylation Figure S8. MP2/cc-pVTZ interaction energy (kcal mol 1 ) as a function of intermolecular separation of cation π complexes: in red, NH 4 + -C 6 H 6 (complex A); in blue CH 3 NH 3 + -C 6 H 6. S18

19 12 Cartesian coordinates Table S10. Cartesian coordinates at DLPNO-CCSD(T)/aug-cc-pVTZ equilibrium separation. (A) (B) Atom X Y Z Atom X Y Z C C C C C C C C C C C C H H H H H H H H H H H H H H H H H H H H S19

20 N N S20

21 (C) (D) Atom X Y Z Atom X Y Z C C C C C C C C C C C C H H H H H H H H H H H H C C N N H H H H N N H H H H N N H H H H S21

22 (E) (F) Atom X Y Z Atom X Y Z C C C C C C C C C C C C H H H H H H H H H H H H C C C C C C N N H H H H H H H H H H N N S22

23 (G) (H) Atom X Y Z Atom X Y Z C C C C C C C C C C C C H H H H H H H H H H H H C C C C C C N N H H H H H H H H H H N N S23

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