Electronic Supplementary Information
CHARMM all atom force field employs a Lennard-Jones (6-12) function to describe Van der Waals
interactions. This potential is a combination of attractive and repulsive contributions. The repulsive
term describes internuclear electrostatic repulsion and short-range repulsive forces (or exchange
forces) between electrons with the same spin. The attractive term is due to dispersion forces, which
in turn are due to instantaneous dipoles arising during the fluctuations in the electron clouds. The
form of the potential energy function of two interacting atoms is:
 σ 12  σ  6 
VvdW = 4ε   −   
 r  
 r 
Where r is the distance between the two atoms, σ is the collision diameter (the distance at the zero
energy) and ε is the Lennard-Jones well depth. For a q atom and a c atom, these empirical
parameters are expressed from the Lorentz-Berthelot mixing rules:
σ qc =
1
(σ qq + σ cc )
2
ε qc = ε qqε cc
Van der Waals interactions are also important to well describe the interaction between QM and MM
regions in hybrid QM/MM enzyme simulation. The Van der Waals parameters relative to the QM
atoms of the FAAH-oleamide complex, applied in all the simulations performed, are reported in the
table below. These are consistent to those reported in the combined parameter file (CHARMM22
for protein, CHARMM27 for lipid) par_all27_prot_lipid.prm.
For further details see www.charmm.org
PRIVILEGED DOCUMENT FOR REVIEW PURPOSES ONLY
ATOM NAME
O1
C1
N2
H
H1
C18
C2
C3
H6
H7
H4
H5
H2
H3
CB
HB1
HB2
OG
HG1
CE
HE1
HE2
NZ
HZ1
HZ2
CB'
HB1'
HB2'
OG'
HG1'
HQL1
HQS1
HQS2
HQM1
ATOM TYPE
O
CC
NH2
H
H
CTL2
CTL2
CTL2
HAL2
HAL2
HAL2
HAL2
HAL2
HAL2
CT2
HA
HA
OH1
H
CT2
HA
HA
NH2
HC
HC
CT2
HA
HA
OH1
H
HQ
HQ
HQ
HQ
ε (kcal mole-1)
-0.120000
-0.070000
-0.200000
-0.046000
-0.046000
-0.056000
-0.056000
-0.056000
-0.028000
-0.028000
-0.028000
-0.028000
-0.028000
-0.028000
-0.055000
-0.022000
-0.022000
-0.152100
-0.046000
-0.055000
-0.022000
-0.022000
-0.200000
-0.046000
-0.046000
-0.055000
-0.022000
-0.022000
-0.152100
-0.046000
-
σ (Å)
1.700000
2.000000
1.850000
0.224500
0.224500
2.010000
2.010000
2.010000
1.340000
1.340000
1.340000
1.340000
1.340000
1.340000
2.175000
1.320000
1.320000
1.770000
0.224500
2.175000
1.320000
1.320000
1.850000
0.224500
0.224500
2.175000
1.320000
1.320000
1.770000
0.224500
-
PRIVILEGED DOCUMENT FOR REVIEW PURPOSES ONLY
Notes
Oleamide
Oleamide
Oleamide
Oleamide
Oleamide
Oleamide
Oleamide
Oleamide
Oleamide
Oleamide
Oleamide
Oleamide
Oleamide
Oleamide
Ser217
Ser217
Ser217
Ser217
Ser217
Lys142
Lys142
Lys142
Lys142
Lys142
Lys142
Ser241
Ser241
Ser241
Ser241
Ser241
Link atom
Link atom
Link atom
Link atom