Supplementary materials for
An Improved Fragment-based Quantum Mechanical
Method for Calculation of Electrostatic Solvation Energy
of Proteins
Xiangyu Jia1, Xianwei Wang1, Jinfeng Liu1, John Z.H. Zhang1,2, Ye Mei1,* and Xiao He1,*
1
State Key Laboratory of Precision Spectroscopy, Department of Physics and Institute of
Theoretical and Computational Science, East China Normal University, Shanghai 200062,
China
2
Joint Research Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062,
China
* To whom correspondence should be addressed: ymei@phy.ecnu.edu.cn (Y. Mei);
xiaohe@phy.ecnu.edu.cn (X. He)
Table S1. Electrostatic solvation energies in kcal/mol from the full system CPCM,
EE-GMFCC-CPCM_Amber94 and EE-GMFCC-CPCM_PPC calculations, respectively, at the
HF/6-31G* level. EE-GMFCC-CPCM_Amber94 and EE-GMFCC-CPCM_PPC represent the
fragment calculations performed with the electrostatically embedded Amber94 charges and with
the polarized protein-specific charges (PPCs), respectively.
Protein
(pdb id)
1LE1
2I9M
2GB1
1L2Y
1WN8
2XL1
1VTP
1BBA
2KCF
No. of
No. of
Energy
Full
EE-GMFCC-CPCM
EE-GMFCC-CPCM
_Amber94a
_PPCa
tesserae
atoms
component
system
10756
218
G(es)
-188.37
-189.40 (-1.03)
-189.70(-1.33)
E(wfd)
21.64
18.26 (-3.38)
18.71(-2.93)
G(ele)
-166.73
-171.14 (-4.41)
-170.99(-4.26)
G(es)
-264.63
-266.47 (-1.84)
-269.12(-4.49)
E(wfd)
27.48
28.18 (0.70)
28.48(1.00)
G(ele)
-237.15
-238.29 (-1.14)
-240.64(-3.49)
G(es)
-482.72
-483.84 (-1.12)
-483.92(-1.20)
E(wfd)
43.02
40.90 (-2.12)
40.92(-2.10)
G(ele)
-439.70
-442.94 (-3.24)
-443.00(-3.30)
G(es)
-372.86
-374.33 (-1.47)
-374.71(-1.85)
E(wfd)
48.08
45.45 (-2.63)
46.75(-1.33)
G(ele)
-324.78
-328.88 (-4.10)
-327.96(-3.18)
G(es)
-285.43
-286.70 (-1.27)
-288.64(-3.21)
E(wfd)
27.44
27.71 (0.27)
26.06(-1.38)
G(ele)
-257.99
-258.99 (-1.00)
-262.58(-4.59)
G(es)
-203.88
-205.70 (-1.82)
-207.69(-3.81)
E(wfd)
26.87
20.80 (-6.07)
21.53(-5.34)
G(e
-177.02
-184.90 (-7.88)
-186.16(-9.14)
G(es)
-882.48
-882.71 (-0.23)
-886.44(-3.96)
E(wfd)
100.86
96.46 (-4.40)
98.01(-2.85)
G(ele)
-781.62
-786.24 (-4.62)
-788.43(-6.81)
G(es)
-698.31
-695.68 (2.63)
-695.36(2.95)
E(wfd)
75.06
73.57 (-1.49)
71.53(-3.53)
G(ele)
-623.25
-622.11 (1.14)
-623.83(-0.58)
G(es)
-745.74
-745.67 (0.07)
-745.25(0.49)
E(wfd)
60.27
59.27 (-1.00)
57.21(-3.06)
14360
14013
16642
19701
12369
27004
36259
29995
246
247
304
354
243
396
582
576
2F21
32205
1BHI
32358
2Y0Q
32003
RMSD
MUE
aData
603
591
803
G(ele)
-685.46
-686.40 (-0.94)
-688.04(-2.58)
G(es)
-711.35
-705.98 (5.37)
-705.73(5.62)
E(wfd)
86.56
86.19 (-0.37)
83.48(-3.08)
G(ele)
-624.79
-619.79 (5.00)
-622.25(2.54)
G(es)
-597.68
-595.40 (2.28)
-596.02(1.66)
E(wfd)
69.58
69.79 (0.21)
68.71(-0.87)
G(ele)
-528.10
-525.61 (2.49)
-527.31(0.79)
G(es)
-571.71
-569.43 (2.28)
-575.20(-3.49)
E(wfd)
68.24
70.39 (2.15)
67.90(-0.34)
G(ele)
-503.47
-499.04 (4.43)
-507.30(-3.83)
G(es)
2.22
3.20
E(wfd)
2.70
2.68
G(ele)
3.93
4.39
G(es)
1.78
2.51
E(wfd)
2.07
2.32
G(ele)
3.36
3.76
in parentheses represent the errors with respect to the full system calculations.