Supporting Information for: Validating computer simulations of
enantioselective catalysis; Reproducing the large steric and entropic
contributions in Candida Antarctica lipase B
Table S1. The EVB charges used in the present calculations
atom name
His 224
CG
ND1
HD1
CE1
HE1
NE2
CD2
HD2
Seryl-butanoylester CB
HB1
HB2
OG
C11
O14
C13
H20
H21
C17
H22
H23
C18
H24
H25
H26
Phenylethanole
C28
C16
C33
C34
H35
C36
H37
C38
1
2
3
0.151
-0.413
0.397
0.271
0.131
-0.673
-0.001
0.137
0.369
0.042
0.042
-0.500
0.924
-0.706
-0.430
0.116
0.116
0.290
-0.039
-0.039
-0.416
0.068
0.068
0.068
-0.367
0.447
0.086
-0.229
0.170
-0.151
0.156
-0.149
0.292
-0.249
0.408
0.081
0.253
-0.163
-0.298
0.272
0.369
0.042
0.042
-0.500
0.924
-0.706
-0.430
0.116
0.116
0.290
-0.039
-0.039
-0.416
0.068
0.068
0.068
-0.250
0.680
0.005
-0.230
0.156
-0.150
0.142
0.011
0.292
-0.249
0.408
0.081
0.253
-0.163
-0.298
0.272
0.365
-0.049
-0.049
-0.584
0.728
-0.897
-0.229
0.030
0.030
0.358
-0.070
-0.070
-0.369
0.070
0.070
0.070
-0.355
0.552
0.008
-0.224
0.148
-0.135
0.149
-0.201
1
H39
C40
H41
C42
H43
O15
H29
H30
H31
H27
H10
0.171
-0.151
0.156
-0.229
0.170
0.827
0.083
0.083
0.083
-0.005
0.503
0.149
-0.150
0.141
-0.230
0.156
-1.318
0.023
0.023
0.023
-0.181
0.404
0.156
-0.135
0.149
-0.224
0.148
-0.632
0.072
0.072
0.072
-0.024
0.404
Table S2. Morse bond parameters: M (b)  DM (1  e   (b b0 ) ) 2
Bond type
DM
b0

C0-H0
C0-O0
O0-C+
C+-C0
C+-N+
C+-C+
N+-H+
C+-H+
O0-H0
C0-OC0-C0
100.4
93.0
93.0
96.0
94.0
96.0
98.3
100.4
102.0
93.0
96.0
1.10
1.50
1.25
1.40
1.40
1.40
1.10
1.10
0.96
1.40
1.54
2.0
0.8
2.0
2.0
2.0
2.0
2.0
2.0
2.0
2.0
0.8
Table S3. Angle parameters: V ( ) 
1
k (   0 ) 2
2
Angle type
1
k
2
0
H0-C0-H0
H0-C0-O0
C+-C0-C0
C+-C0-H0
H0-C0-C0
C0-C0-C0
O0-C0-C+
O0-C+-O0
O0-C+-C0
50.0
50.0
50.0
50.0
50.0
50.0
50.0
50.0
50.0
109.5
109.5
109.5
109.5
109.5
109.5
109.5
120.0
120.0
2
N+-C+-C+
O0-C+-O0
C+-N+-H+
N+-C+-H+
N+-C+-N+
C+-C+-H+
C0-C+-C+
C+-C+-C+
C+-N+-C+
C0-O0-H0
50.0
50.0
50.0
50.0
50.0
50.0
50.0
50.0
90.0
80.0
120.0
120.0
120.0
120.0
120.0
120.0
120.0
120.0
120.0
120.0
Table S4. Torsion angle parameters: V  k (1  cos(n  0 ))
Angle type
k
n
0
*-C0-O0-*
*-C0-C+-*
*-O0-C+-*
*-C+-N+-*
*-C+-C+-*
*-C0-C0-*
2.0
2.0
15.0
15.0
15.0
1.0
3.0
3.0
2.0
2.0
2.0
3.0
0.0
0.0
180.0
180.0
180.0
0.0
Table S5. Improper torsion angle parameters: V  k (1  cos(n  0 ))
Angle type
k
n
0
*-O0-O0-*
*-N+-H+-*
*-C+-N+-*
*-C0-C+-*
*-C+-H+-*
*-C+-C+-*
15.0
15.0
15.0
15.0
15.0
15.0
2.0
2.0
2.0
2.0
2.0
2.0
180.0
180.0
180.0
180.0
180.0
180.0
Table S6. Nonbonded parameters (repulsion function): Vnb  Ce  r
Atom type
O--C0
O0-C0
O0-O0
O0-OO--H0
O0-H0
C

19999.0
19999.0
30000.0
30000.0
4000.0
4000.0
3.8
3.8
3.0
3.0
4.0
4.0
3
 
 *
Table S7. Nonbonded parameters (van der Waals): Vnb   *  r
 r
Atom type
H0
C0
C+
N+
O0
O-
 r  
12
r*
*
7.0
632.0
632.0
774.0
774.0
1400.0
0.0
24.0
24.0
24.0
24.0
24.0
*
2 r
6
Table S8. EVB mapping parameters used in the present calculations.
EVB mapping parameters  1   2
 2  3
Hij  Aij e  ( r r0 )
10.3
35.0
   i   j
80.0
45.0
Table S9. Calculated free energies (in kcal/mol) for perturbing the restraints from K=10.0
to 0.03 for both chemical reactions and both the RS and the TS of each enantiomer
complexed to the WT. The individual free energy contribution for the PT and NA are
given for each enantiomer using GPT,Relax and GNA,Relax and their sum providing the
total barrier gcat,calc,relax. Additionally the barriers obtained without the free energy of
removing the restraints are given in column labeled gcat,calc.
run1
run2
run3
run4
AVG
STDEV
MUE
run1
run2
run
run4
AVG
STDEV
MUE
GPT,Relax
WT-R
(RS1)
-6.0
-6.2
-6.1
-5.5
-6.0
0.3
0.2
GPT,Relax
WT-S
(RS1)
-5.9
-5.4
-5.7
-5.8
-5.7
0.2
0.1
GPT,Relax
WT-R
(TS1)
-6.9
-6.6
-6.3
-6.9
-6.7
0.3
0.1
GPT,Relax
WT-S
(TS1)
-6.5
-6.3
-6.7
-6.9
-6.6
0.3
0.1
GNA,Relax
WT-R
(RS2)
-5.4
-5.7
-5.3
-5.9
-5.6
0.3
0.1
GNA,Relax
WT-S
(RS2)
-5.5
-5.8
-5.3
-5.9
-5.6
0.3
0.1
GNA,Relax
WT-R
(TS2)
-6.9
-7.1
-6.6
-6.3
-6.7
0.4
0.2
GNA,Relax
WT-S
(TS2)
-6.9
-7.2
-7.3
-7.0
-7.1
0.2
0.1
GPT,Relax
WT-R
GNA,Relax
WT-R
gcat,calc,relax
WT-R
gcat,calc
WT-R
9.2
10.7
9.9
9.1
9.7
0.4
0.2
GPT,Relax
WT-S
4.4
4.9
5.6
5.1
5
0.7
0.3
13.6
15.6
15.5
14.2
14.7
1.0
0.5
gNA,Relax
WT-S
gcat,calc,relax
WT-S
16.0
17.4
17.0
16.0
16.6
1.1
0.5
gcat,calc
WT-S
11.2
13.3
10.0
10.7
11.3
1.4
0.7
11.9
9.3
9.2
10.6
10.3
1.0
0.5
23.1
22.6
19.2
21.3
21.6
2.5
1.2
25.1
24.9
22.2
23.5
23.9
2.5
1.3
4
Figures
Figure S1. The three resonance structures (  i ) used to describe the deacylation reaction
of CalB.  1 ,  2 and  3 describe the reactant state, the product of the proton transfer step
and the tetrahedral intermediate, respectively.
Figure S2. Thermodynamic cycle for calculating the “relaxed” free energies of the RS
and TS of the PT and the NA. The top horizontal arrows reflect the free energy provided
by the EVB at K=10.0, while the vertical arrows indicate the perturbation of the restraints
towards 0.03. Finally, the bottom horizontal arrow provides us with the relaxed total
barrier g cat ,calc ,relax .
5
Figure S3. Diagram of the calculated activation barriers (in kcal/mol ) for the PT
(RS1 and TS1 in the figure) and NA (RS2 and TS2 in the figure) for the WT and in
solution using the EVB method. Here the barriers are given with and without the
specialized restraint relaxation treatment (not for the solution).
6
7