suppmat1515.doc 1074KB Jun 05 2011 09:30:54 PM
Development of a Polarizable Force Field For Proteins via Ab
Initio Quantum Chemistry: First Generation Model and Gas
Phase Tests
George A. Kaminski, Harry A. Stern, B. J. Berne, and Richard A. Friesner
Department of Chemistry, Columbia University, New York, New York 10027
Yixiang X. Cao, Robert B. Murphy, Ruhong Zhou, and Thomas A. Halgren,
Shrödinger, Inc., 120 West 45th Street, Tower 45, 8th Floor, New York, NY 10036
Supporting Materials
Listed below are parameters for all the dipeptides, also used in the alanine
tetrapeptide and PDB proteins. Values for the parameters that are not listed (bond
stretching, angle bending, some torsional parameters) are taken directly from the OPLSAA (Jorgensen, W.L.; Maxwell D.S.; TiradoRives, J. J. Am. Chem. Soc., 1996, 113,
11225-11236).
All the di- and tetrapeptide backbone parameters are the same, taken from the
alanine dipeptide set with no further adjustments.
Table S1. Lennard-Jones Parameters
Atom
CT, CT1, CP1
C, CG1, CO3
HC
N
O
OH
CA, CR, CV, CW, C*, CB9, CN, CX
HA
SH, S
NA, NB
OH6
O2
N3A
NA, protonated histidine
CA8
N2
Table S2. Torsional Parameters, kcal/mol
Angle
Alanine and all backbones
C-N-CT1-CT
C-CT1-N-C
N-C-CT1-N
CT-CT1-C-N
Serine
N-CT1-CT-OH
CT1-CT-OH-HO
C-CT1-CT-OH
Phenylalanine
CA-CA-CT-CT1
C-CT1-CT-CA
CA-CT-CT1-N
Cysteine
N-CT1-CT-SH
CT1-CT-SH-HS
C-CT1-CT-SH
Asparagine
C-CT-CT1-N
CT1-CT-C-N
C-CT-CT1-C
Glutamine
CT-CT-CT1-N
C-CT-CT-CT1
, Å
3.50
3.75
2.50
3.30
3.16
3.25
3.55
2.42
3.60
3.25
3.20
2.96
3.00
3.05
2.25
3.20
, kcal/mol
0.066
0.105
0.030
0.280
0.280
0.280
0.070
0.030
0.425
0.170
0.190
0.210
0.080
0.160
0.050
0.100
V1
V2
V3
-2.485
-0.330
-6.976
-3.642
1.191
-1.113
2.821
0.519
-0.773
1.276
-0.613
0.382
-2.165
1.502
-4.700
1.510
-1.728
-1.110
0.580
1.581
0.194
-0.530
1.315
-2.221
0.519
0.578
2.173
-1.744
-0.741
-0.301
-6.995
-1.201
-6.647
1.715
-1.809
-0.703
-0.860
0.832
0.962
5.632
-3.060
-2.114
3.182
-0.115
0.935
4.353
-0.418
-2.618
3.925
-0.733
0.958
-0.517
-3.374
0.037
C-CT1-CT-CT
CT-CT-C-N
Histidine
CV-CT-CT1-N
CT1-CT-CV-NB
CT1-CT-CV-CW
C-CT1-CT-CV
Leucine
CT-CT-CT1-N
C-CT1-CT-CT
CT-CT-CT-CT1
Isoleucine
CT-CT-CT1-N
C-CT1-CT-CT
CT-CT-CT-CT1, CT-CT-CT-CT
Valine
CT-CT-CT1-N
C-CT1-CT-CT
Methionine
CT-CT-CT1-N
CT1-CT-CT-S
C-CT1-CT-CT
CT-CT-S-CT
Tryptophan
C*-CT-CT1-N
CT1-CT-C*-CW
CB9-C*-CT-CT1
C-CT1-CT-C*
Threonine
N-CT1-CT-OH
CT1-CT-OH-HO
C-CT1-CT-OH
Tyrosine
CA-CT-CT1-N
CA-CA-CT-CT1
C-CT1-CT-CA
CA-CA-OH6-HO
Aspartic Acid
CG1-CT-CT1-N
CT1-CT-CG1-O2
C-CT1-CT-CG1
Glutamic Aced
CT-CT-CT1-N
CO3-CT-CT-CT1
CT-CT-CO3-O2
C_CT1-CT-CT
0.539
-0.471
1.424
-0.431
4.422
-0.078
-1.116
0.061
0.000
-1.944
0.691
0.231
0.000
-0.466
-0.173
-0.362
0.000
0.012
5.246
1.509
0.335
0.874
0.255
0.302
-2.843
2.827
0.141
-5.102
-6.975
1.888
2.334
2.498
-0.269
1.578
-0.597
0.591
-6.039
-2.690
1.446
0.846
0.286
0.271
-12.673
-0.430
-2.883
-2.184
0.981
0.135
1.175
-2.478
-2.634
-0.173
2.906
1.612
-1.493
-1.380
0.000
-1.079
1.386
0.572
0.000
0.419
-1.883
0.048
0.000
1.849
-9.964
1.502
-16.848
0.906
-1.728
0.682
-2.414
1.581
1.346
0.283
0.000
-0.917
0.000
1.336
0.000
0.517
3.943
-3.733
0.000
3.706
0.000
3.712
0.000
-3.900
1.813
0.695
4.331
0.301
0.000
-0.822
-1.513
-3.404
0.000
-2.371
0.871
0.201
0.820
0.314
0.963
0.117
0.000
0.000
Lysine
CT-CT-CT1-N
C-CT1-CT-CT
CT-CT-CT-N3A
Protonated Histidine
CX-CT-CT1-N
CT1-CT-CX-NA
CT1-CT-CX-CX
C-CT1-CT-CX
Agrinine
CT-CT-CT1-N
CT-CT-CT-CT1
CT-CT-CT-N2
CA8-N2-CT-CT
C-CT1-CT-CT
-3.264
-1.027
2.144
-0.211
-0.426
-1.352
0.430
0.133
2.069
-5.864
-0.139
0.000
-1.000
1.304
-0.558
0.000
0.272
-0.513
-1.320
0.000
1.133
2.359
-0.775
0.673
-1.697
2.416
0.813
0.807
0.987
0.542
-0.689
-0.568
-1.792
-2.000
0.542
1.860
Tables S3 and S4 list electrostatic parameters. Please note that we used a
scaling factor of 1.0 for the electrostatic 1,4-interactions, unlike the 0.5 value
for the van-der-Waals ones.
For the fixed bond charge increments – as an example – O236_X0 bci value of 0.326463
means an electron transfer from O to X (negative resulting charge on X)
Dipole means internal electrostatic field, resulting in a point “permanent dipole”
located on the first atom in the pair, dipole means internal electrostatic field, resulting
in a point “permanent dipole” located on the second atom in the pair. A positive value
means field producing a dipole directed toward the other atom in the pair, a negative
value – away from the other atom.
Table S3. Fixed Bond Charge Increments, in e, and Dipole s, in (kcal/mol)1/2·Å-3/2.
Atom Pair
Bond Charge Increment
Dipole /
Alanine
C135_C224
0.097985
0.607132 / 0.116592
C135_C235
-0.0480366
0.153272 / 0.373441
C135_H140
-0.110953
-0.755875 / C224_C235
-0.00735223
-0.152324 / 0.279954
C224_H140
-0.209973
-2.04571 / C224_N238
0.208593
1.63831 / 0.396263
C235_N238
-0.0327599
0.64934 / -0.0116159
C235_O236
0.227873
-1.56473 / C242_H140
-0.0998559
-0.379682 / C242_N238
0.220074
0.273629 / 0.0340511
H241_N238
0.258316
- / 0.56991
O236_X0 (lone pair)
0.326463
-
Serine
C157_C224
C157_H140
C157_O154
H155_O154
O154_X0
Phenylalanine
C145_C149
C145_H146
C149_C224
C149_H140
C145_C145
Cysteine
C206_C224
C206_H140
C206_S200
H204_S200
S200_X0
Asparagine
C136_C224
C136_C235
C136_H140
C235_N237
C235_O236 (side chain)
H240_N237
O236_X0 (side chain)
Glutamine
C136_C224
C136_C235
C136_H140
C235_N237
C235_O236 (side chain)
H240_N237
O236_X0 (side chain)
C136_C136
Histidine
C224_C505
C505_C507
C505_H140
C506_H146
C506_N503
C506_N511
C507_C508
C507_N511
C508_H146
C508_N503
0.116725
-0.136309
-0.110053
0.122747
0.600477
2.18762 / -0.131951
0.608399 / 0.643742 / -1.97661
-6.441 / -8.67218
-
-0.0673306
-0.102698
0.0200496
-0.0596082
-
0.000229846 / -0.000239204
0.000403568 / -0.00005505 / 0.00123112
0.000327497 / -0.000633269
-0.0534597
-0.109281
0.0903085
0.130253
0.017169
0.00563573 / -0.00236531
0.0153869 / -0.020398 / -0.00595555
- / 0.00719557
-
0.196372
-0.13411
-0.097974
-0.102893
0.273747
0.407637
0.240195
0.977204 / -1.89449
-0.237043 / 1.45552
-0.418817 / 0.370868 / 3.17608
-0.634036 / - / -0.298673
-
0.0437679
0.164519
0.0337042
-0.196311
0.480364
0.199717
0.120912
-
0.0013247 / 0.00270597
-0.00533217 / 0.0133523
0.000494025 / 0.011942 / -0.00849117
-0.0241726 / - / 0.00956328
0.00306502
0.0100364
0.0599774
-0.0641425
-0.114389
-0.131173
0.191382
-0.160069
0.0813819
-0.102242
-0.0811045
0.00107392 / 0.00139211
-0.00551098 / -0.00017132
0.00456435 / 0.0052744 / 0.00644356 / -0.00586025
-0.0120094 / 0.00528713
0.000912032 / -0.0106541
-0.000800828 / 0.00207551
0.00826427 / 0.00137659 / -0.00505754
H504_N503
Leucine
C135_C137
C136_C137
C136_C224
C136_H140
C137_H140
Isoleucine
C135_C136
C135_C137
C136_C137
C136_C224
C136_H140
C137_C224
C137_H140
Valine
C135_C137
C137_C224
C137_H140
Methionine
C136_C210
C136_C224
C136_H140
C209_H140
C209_S202
C210_H140
C210_S202
S202_X0
Proline
C136_C245
C136_C246
C136_H140
C235_C246
C235_N239
C245_H140
C245_N239
C246_H140
C246_N239
C136_C136
Tryptophan
C136_C224
C136_C500
C136_H140
C145_C501
C145_C502
C145_H146
0.161869
- / 0.00916099
-0.146868
-0.124146
0.0166872
-0.0678362
0.116302
0.033175 / 0.000333922
0.000621941 /0.0000245489
-0.000208909 / -0.00630183
-0.000535165 / -0.000450057 / -
0.0
-0.146868
-0.124146
0.0166872
-0.0678362
0.0
0.116302
0.0 / 0.0
0.033175 / 0.000333922
0.000621941 / 0.0000245489
-0.000208909 / -0.00630183
-0.000535165 / 0.0 / 0.0
-0.000450057 / -
0.0723389
0.104525
-0.00657239
1.23919 / 0.148709
-0.0868066 / -0.229779
-0.0740794 / -
0.0935418
0.0208381
-0.162903
-0.243665
-0.155553
-0.125907
0.0600352
0.449691
1.38705 / 0.444529
0.801983 / 0.810454
-2.42772 / 0.291426 / 0.0724554 / 0.802467
-0.317935 / -0.151669 / -1.37233
-
0.0729211
0.0957254
-0.0532278
-0.0176697
-0.0136698
-0.0116227
0.26151
-0.0779027
0.201598
-
0.635282 / -0.233324
0.163052 / 0.216856
-0.996827 / 0.0542661 / -0.073014
1.0433 / 0.278585
-0.321562 / 0.603253 / 0.288494
-0.613241 / 0.52365 / -0.668299
0.234194
-0.00548767
0.0528376
-0.0265289
-0.00191486
0.0173216
-0.0768596
0.000517722 / -0.000759049
-0.00284223 / 0.000798661
0.00261878 / 0.00572442 / -0.000158477
-0.0015452 / -0.00160748
0.0000488274 / -
C500_C501
C500_C514
C501_C502
C502_N503
C514_H146
C514_N503
H504_N503
C145_C145
Threonine
C135_C158
C158_C224
C158_H140
C158_O154
H155_O154
O154_X0
Tyrosine
C145_C149
C145_C166
C145_H146
C149_C224
C149_H140
C166_O167
H168_O167
O167_X0
C145_C145
Aspartic Acid. Formal
charge of –0.5 on O272
C224_C274
C271_C274
C271_O272
C274_H140
O272_X0
Glutamic Acid. Formal
charge of –0.5 on O272
C136_C224
C136_C274
C136_H140
C271_C274
C271_O272
C274_H140
O272_X0
Lysine. Formal charge of
+1.0 on N287
C136_C224
C136_C292
C136_H140
0.0772466
-0.0572644
-0.0224854
-0.164221
-0.063842
-0.0521954
0.241869
-
-0.00130709 / 0.000248156
0.000327291 / -0.0000533602
-0.0000905563 / -0.00552142
0.00678851 / -0.0165872
0.0000442391 / 0.00000607413 / -0.0061889
- / 0.0196599
-0.00465174
0.112878
0.0992506
-0.204639
-0.10328
0.316595
0.239077
1.14045 / 0.737352
1.98056 / 0.588577
-2.43919 / -0.308812 / 3.56155
-1.58336 / -3.89152
-
-0.00579876
-0.0304862
-0.121312
0.0154813
-0.0160531
0.0325574
0.254649
0.159654
-
-0.00000790066 / -0.00221347
0.00000958763 / -0.00378592
0.0000371821 / -0.00019629 / 0.00140221
0.00271868 / 0.00219646 / -0.0000376123
-0.0977027
0.0304503
0.1368
0.0696202
0.0748858
0.00507626 / -0.00648952
0.000875131 / 0.00783434
-0.000819109 / 0.00660001
-0.00140657 / -
0.0786512
-0.0825442
-0.0606561
0.143842
0.171253
0.0288231
0.125131
-0.00324192 / 0.00701377
0.0122969 / 0.0212826
-0.0103197 / -0.135622 / -0.0297912
0.124577 / 0.0071406 / -
0.00763358
0.0604499
-0.0343106
-0.024419 / -0.0851402
-0.0659708 / -0.053823
-0.175439 / -
C292_H140
C292_N287
H290_N287
C136_C136
Protonated Histidine.
Formal charge of +0.5
on N512
C224_C505
C505_C510
C505_H140
C509_H146
C509_N512
C510_H146
C510_N512
H513_N512
C510_C510
Arginine. Formal charge
of +1.0 on C302
C136_C224
C136_C308
C136_H140
C302_N300
C302_N303
C307_C308
C307_H140
C307_N303
C308_H140
H301_N300
H304_N303
-0.0282786
0.397861
0.341731
-
0.03601 / 0.0180809 / 0.114811
- / -0.113318
0.244323
-0.0298412
0.185721
-0.15159
-0.230999
0.0689035
-0.103774
0.155405
0.297322
-
0.32426 / 0.884187
0.106838 / 0.0102203
-1.10232 / 0.0178131 / -0.0214623 / -0.0158379
0.0273401 / 0.0286613 / -0.0193385
- / 0.0208468
-0.0858125
-0.00283199
-0.0342771
0.0592934
-0.10473
0.00782999
-0.0918754
0.092882
-0.0280027
-0.0876708
0.217723
0.0997339
0.000661955 / -0.000863189
0.00201562 / -0.00164835
-0.00287667 / 0.000889051 / -0.00918126
-0.00082715 / -0.000867548
0.00793005 / -0.00502689
-0.0117669 / 0.00315085 / -0.00211463
0.00743096 / - / 0.00991513
- / 0.00312121
Table S4. Inverse Polarizabilities, Å-3
Atom
Alanine
C135
C224
C235
C242
N238
Serine
C157
H155
O154
Phenylalanine
C145
C149
1/
0.515642
0.691837
0.525854
0.485997
1.40464
0.509135
3.70039
2.31814
10.0
10.0
Cysteine
C206
S200
Asparagine
C136
N237
Glutamine
C136
N237
Histidine
C505
C506
C507
C508
N503
N511
Leucine
C136
C137
Isoleucine
C136
C137
Valine
C137
Methionine
C136
C209
C210
S202
Proline
C136
C245
C246
N239
Tryptophan
C136
C145
C500
C501
C502
C514
N503
Threonine
C158
H155
O154
0.417752
0.497968
0.584073
1.28334
0.804315
1.18945
0.391962
0.758618
5.70968
0.719624
1.01387
1.01298
10.0
10.0
10.0
10.0
1.71809
1.26937
0.583708
2.67492
0.831939
0.596225
0.558897
0.491165
0.760093
0.312904
0.69451
2.19726
12.5098
0.798391
100.0
0.540221
1.1167
3.08747
1.63216
Tyrosine
C145
C149
C166
Aspartic Acid
C271
C274
O272
Glutamic Acid
C136
C271
C274
Lysine
C136
C292
N287
Protonated Histidine
C505
C509
C510
N512
Arginine
C136
C302
C307
C308
N300
N303
100.0
0.30056
0.312942
0.753218
0.487163
1.39829
1.51783
0.301317
0.631377
0.807484
1.14114
0.555973
0.57413
0.870782
0.882096
1.41498
0.643049
1.61209
0.456629
0.579122
0.747804
1.18755
Initio Quantum Chemistry: First Generation Model and Gas
Phase Tests
George A. Kaminski, Harry A. Stern, B. J. Berne, and Richard A. Friesner
Department of Chemistry, Columbia University, New York, New York 10027
Yixiang X. Cao, Robert B. Murphy, Ruhong Zhou, and Thomas A. Halgren,
Shrödinger, Inc., 120 West 45th Street, Tower 45, 8th Floor, New York, NY 10036
Supporting Materials
Listed below are parameters for all the dipeptides, also used in the alanine
tetrapeptide and PDB proteins. Values for the parameters that are not listed (bond
stretching, angle bending, some torsional parameters) are taken directly from the OPLSAA (Jorgensen, W.L.; Maxwell D.S.; TiradoRives, J. J. Am. Chem. Soc., 1996, 113,
11225-11236).
All the di- and tetrapeptide backbone parameters are the same, taken from the
alanine dipeptide set with no further adjustments.
Table S1. Lennard-Jones Parameters
Atom
CT, CT1, CP1
C, CG1, CO3
HC
N
O
OH
CA, CR, CV, CW, C*, CB9, CN, CX
HA
SH, S
NA, NB
OH6
O2
N3A
NA, protonated histidine
CA8
N2
Table S2. Torsional Parameters, kcal/mol
Angle
Alanine and all backbones
C-N-CT1-CT
C-CT1-N-C
N-C-CT1-N
CT-CT1-C-N
Serine
N-CT1-CT-OH
CT1-CT-OH-HO
C-CT1-CT-OH
Phenylalanine
CA-CA-CT-CT1
C-CT1-CT-CA
CA-CT-CT1-N
Cysteine
N-CT1-CT-SH
CT1-CT-SH-HS
C-CT1-CT-SH
Asparagine
C-CT-CT1-N
CT1-CT-C-N
C-CT-CT1-C
Glutamine
CT-CT-CT1-N
C-CT-CT-CT1
, Å
3.50
3.75
2.50
3.30
3.16
3.25
3.55
2.42
3.60
3.25
3.20
2.96
3.00
3.05
2.25
3.20
, kcal/mol
0.066
0.105
0.030
0.280
0.280
0.280
0.070
0.030
0.425
0.170
0.190
0.210
0.080
0.160
0.050
0.100
V1
V2
V3
-2.485
-0.330
-6.976
-3.642
1.191
-1.113
2.821
0.519
-0.773
1.276
-0.613
0.382
-2.165
1.502
-4.700
1.510
-1.728
-1.110
0.580
1.581
0.194
-0.530
1.315
-2.221
0.519
0.578
2.173
-1.744
-0.741
-0.301
-6.995
-1.201
-6.647
1.715
-1.809
-0.703
-0.860
0.832
0.962
5.632
-3.060
-2.114
3.182
-0.115
0.935
4.353
-0.418
-2.618
3.925
-0.733
0.958
-0.517
-3.374
0.037
C-CT1-CT-CT
CT-CT-C-N
Histidine
CV-CT-CT1-N
CT1-CT-CV-NB
CT1-CT-CV-CW
C-CT1-CT-CV
Leucine
CT-CT-CT1-N
C-CT1-CT-CT
CT-CT-CT-CT1
Isoleucine
CT-CT-CT1-N
C-CT1-CT-CT
CT-CT-CT-CT1, CT-CT-CT-CT
Valine
CT-CT-CT1-N
C-CT1-CT-CT
Methionine
CT-CT-CT1-N
CT1-CT-CT-S
C-CT1-CT-CT
CT-CT-S-CT
Tryptophan
C*-CT-CT1-N
CT1-CT-C*-CW
CB9-C*-CT-CT1
C-CT1-CT-C*
Threonine
N-CT1-CT-OH
CT1-CT-OH-HO
C-CT1-CT-OH
Tyrosine
CA-CT-CT1-N
CA-CA-CT-CT1
C-CT1-CT-CA
CA-CA-OH6-HO
Aspartic Acid
CG1-CT-CT1-N
CT1-CT-CG1-O2
C-CT1-CT-CG1
Glutamic Aced
CT-CT-CT1-N
CO3-CT-CT-CT1
CT-CT-CO3-O2
C_CT1-CT-CT
0.539
-0.471
1.424
-0.431
4.422
-0.078
-1.116
0.061
0.000
-1.944
0.691
0.231
0.000
-0.466
-0.173
-0.362
0.000
0.012
5.246
1.509
0.335
0.874
0.255
0.302
-2.843
2.827
0.141
-5.102
-6.975
1.888
2.334
2.498
-0.269
1.578
-0.597
0.591
-6.039
-2.690
1.446
0.846
0.286
0.271
-12.673
-0.430
-2.883
-2.184
0.981
0.135
1.175
-2.478
-2.634
-0.173
2.906
1.612
-1.493
-1.380
0.000
-1.079
1.386
0.572
0.000
0.419
-1.883
0.048
0.000
1.849
-9.964
1.502
-16.848
0.906
-1.728
0.682
-2.414
1.581
1.346
0.283
0.000
-0.917
0.000
1.336
0.000
0.517
3.943
-3.733
0.000
3.706
0.000
3.712
0.000
-3.900
1.813
0.695
4.331
0.301
0.000
-0.822
-1.513
-3.404
0.000
-2.371
0.871
0.201
0.820
0.314
0.963
0.117
0.000
0.000
Lysine
CT-CT-CT1-N
C-CT1-CT-CT
CT-CT-CT-N3A
Protonated Histidine
CX-CT-CT1-N
CT1-CT-CX-NA
CT1-CT-CX-CX
C-CT1-CT-CX
Agrinine
CT-CT-CT1-N
CT-CT-CT-CT1
CT-CT-CT-N2
CA8-N2-CT-CT
C-CT1-CT-CT
-3.264
-1.027
2.144
-0.211
-0.426
-1.352
0.430
0.133
2.069
-5.864
-0.139
0.000
-1.000
1.304
-0.558
0.000
0.272
-0.513
-1.320
0.000
1.133
2.359
-0.775
0.673
-1.697
2.416
0.813
0.807
0.987
0.542
-0.689
-0.568
-1.792
-2.000
0.542
1.860
Tables S3 and S4 list electrostatic parameters. Please note that we used a
scaling factor of 1.0 for the electrostatic 1,4-interactions, unlike the 0.5 value
for the van-der-Waals ones.
For the fixed bond charge increments – as an example – O236_X0 bci value of 0.326463
means an electron transfer from O to X (negative resulting charge on X)
Dipole means internal electrostatic field, resulting in a point “permanent dipole”
located on the first atom in the pair, dipole means internal electrostatic field, resulting
in a point “permanent dipole” located on the second atom in the pair. A positive value
means field producing a dipole directed toward the other atom in the pair, a negative
value – away from the other atom.
Table S3. Fixed Bond Charge Increments, in e, and Dipole s, in (kcal/mol)1/2·Å-3/2.
Atom Pair
Bond Charge Increment
Dipole /
Alanine
C135_C224
0.097985
0.607132 / 0.116592
C135_C235
-0.0480366
0.153272 / 0.373441
C135_H140
-0.110953
-0.755875 / C224_C235
-0.00735223
-0.152324 / 0.279954
C224_H140
-0.209973
-2.04571 / C224_N238
0.208593
1.63831 / 0.396263
C235_N238
-0.0327599
0.64934 / -0.0116159
C235_O236
0.227873
-1.56473 / C242_H140
-0.0998559
-0.379682 / C242_N238
0.220074
0.273629 / 0.0340511
H241_N238
0.258316
- / 0.56991
O236_X0 (lone pair)
0.326463
-
Serine
C157_C224
C157_H140
C157_O154
H155_O154
O154_X0
Phenylalanine
C145_C149
C145_H146
C149_C224
C149_H140
C145_C145
Cysteine
C206_C224
C206_H140
C206_S200
H204_S200
S200_X0
Asparagine
C136_C224
C136_C235
C136_H140
C235_N237
C235_O236 (side chain)
H240_N237
O236_X0 (side chain)
Glutamine
C136_C224
C136_C235
C136_H140
C235_N237
C235_O236 (side chain)
H240_N237
O236_X0 (side chain)
C136_C136
Histidine
C224_C505
C505_C507
C505_H140
C506_H146
C506_N503
C506_N511
C507_C508
C507_N511
C508_H146
C508_N503
0.116725
-0.136309
-0.110053
0.122747
0.600477
2.18762 / -0.131951
0.608399 / 0.643742 / -1.97661
-6.441 / -8.67218
-
-0.0673306
-0.102698
0.0200496
-0.0596082
-
0.000229846 / -0.000239204
0.000403568 / -0.00005505 / 0.00123112
0.000327497 / -0.000633269
-0.0534597
-0.109281
0.0903085
0.130253
0.017169
0.00563573 / -0.00236531
0.0153869 / -0.020398 / -0.00595555
- / 0.00719557
-
0.196372
-0.13411
-0.097974
-0.102893
0.273747
0.407637
0.240195
0.977204 / -1.89449
-0.237043 / 1.45552
-0.418817 / 0.370868 / 3.17608
-0.634036 / - / -0.298673
-
0.0437679
0.164519
0.0337042
-0.196311
0.480364
0.199717
0.120912
-
0.0013247 / 0.00270597
-0.00533217 / 0.0133523
0.000494025 / 0.011942 / -0.00849117
-0.0241726 / - / 0.00956328
0.00306502
0.0100364
0.0599774
-0.0641425
-0.114389
-0.131173
0.191382
-0.160069
0.0813819
-0.102242
-0.0811045
0.00107392 / 0.00139211
-0.00551098 / -0.00017132
0.00456435 / 0.0052744 / 0.00644356 / -0.00586025
-0.0120094 / 0.00528713
0.000912032 / -0.0106541
-0.000800828 / 0.00207551
0.00826427 / 0.00137659 / -0.00505754
H504_N503
Leucine
C135_C137
C136_C137
C136_C224
C136_H140
C137_H140
Isoleucine
C135_C136
C135_C137
C136_C137
C136_C224
C136_H140
C137_C224
C137_H140
Valine
C135_C137
C137_C224
C137_H140
Methionine
C136_C210
C136_C224
C136_H140
C209_H140
C209_S202
C210_H140
C210_S202
S202_X0
Proline
C136_C245
C136_C246
C136_H140
C235_C246
C235_N239
C245_H140
C245_N239
C246_H140
C246_N239
C136_C136
Tryptophan
C136_C224
C136_C500
C136_H140
C145_C501
C145_C502
C145_H146
0.161869
- / 0.00916099
-0.146868
-0.124146
0.0166872
-0.0678362
0.116302
0.033175 / 0.000333922
0.000621941 /0.0000245489
-0.000208909 / -0.00630183
-0.000535165 / -0.000450057 / -
0.0
-0.146868
-0.124146
0.0166872
-0.0678362
0.0
0.116302
0.0 / 0.0
0.033175 / 0.000333922
0.000621941 / 0.0000245489
-0.000208909 / -0.00630183
-0.000535165 / 0.0 / 0.0
-0.000450057 / -
0.0723389
0.104525
-0.00657239
1.23919 / 0.148709
-0.0868066 / -0.229779
-0.0740794 / -
0.0935418
0.0208381
-0.162903
-0.243665
-0.155553
-0.125907
0.0600352
0.449691
1.38705 / 0.444529
0.801983 / 0.810454
-2.42772 / 0.291426 / 0.0724554 / 0.802467
-0.317935 / -0.151669 / -1.37233
-
0.0729211
0.0957254
-0.0532278
-0.0176697
-0.0136698
-0.0116227
0.26151
-0.0779027
0.201598
-
0.635282 / -0.233324
0.163052 / 0.216856
-0.996827 / 0.0542661 / -0.073014
1.0433 / 0.278585
-0.321562 / 0.603253 / 0.288494
-0.613241 / 0.52365 / -0.668299
0.234194
-0.00548767
0.0528376
-0.0265289
-0.00191486
0.0173216
-0.0768596
0.000517722 / -0.000759049
-0.00284223 / 0.000798661
0.00261878 / 0.00572442 / -0.000158477
-0.0015452 / -0.00160748
0.0000488274 / -
C500_C501
C500_C514
C501_C502
C502_N503
C514_H146
C514_N503
H504_N503
C145_C145
Threonine
C135_C158
C158_C224
C158_H140
C158_O154
H155_O154
O154_X0
Tyrosine
C145_C149
C145_C166
C145_H146
C149_C224
C149_H140
C166_O167
H168_O167
O167_X0
C145_C145
Aspartic Acid. Formal
charge of –0.5 on O272
C224_C274
C271_C274
C271_O272
C274_H140
O272_X0
Glutamic Acid. Formal
charge of –0.5 on O272
C136_C224
C136_C274
C136_H140
C271_C274
C271_O272
C274_H140
O272_X0
Lysine. Formal charge of
+1.0 on N287
C136_C224
C136_C292
C136_H140
0.0772466
-0.0572644
-0.0224854
-0.164221
-0.063842
-0.0521954
0.241869
-
-0.00130709 / 0.000248156
0.000327291 / -0.0000533602
-0.0000905563 / -0.00552142
0.00678851 / -0.0165872
0.0000442391 / 0.00000607413 / -0.0061889
- / 0.0196599
-0.00465174
0.112878
0.0992506
-0.204639
-0.10328
0.316595
0.239077
1.14045 / 0.737352
1.98056 / 0.588577
-2.43919 / -0.308812 / 3.56155
-1.58336 / -3.89152
-
-0.00579876
-0.0304862
-0.121312
0.0154813
-0.0160531
0.0325574
0.254649
0.159654
-
-0.00000790066 / -0.00221347
0.00000958763 / -0.00378592
0.0000371821 / -0.00019629 / 0.00140221
0.00271868 / 0.00219646 / -0.0000376123
-0.0977027
0.0304503
0.1368
0.0696202
0.0748858
0.00507626 / -0.00648952
0.000875131 / 0.00783434
-0.000819109 / 0.00660001
-0.00140657 / -
0.0786512
-0.0825442
-0.0606561
0.143842
0.171253
0.0288231
0.125131
-0.00324192 / 0.00701377
0.0122969 / 0.0212826
-0.0103197 / -0.135622 / -0.0297912
0.124577 / 0.0071406 / -
0.00763358
0.0604499
-0.0343106
-0.024419 / -0.0851402
-0.0659708 / -0.053823
-0.175439 / -
C292_H140
C292_N287
H290_N287
C136_C136
Protonated Histidine.
Formal charge of +0.5
on N512
C224_C505
C505_C510
C505_H140
C509_H146
C509_N512
C510_H146
C510_N512
H513_N512
C510_C510
Arginine. Formal charge
of +1.0 on C302
C136_C224
C136_C308
C136_H140
C302_N300
C302_N303
C307_C308
C307_H140
C307_N303
C308_H140
H301_N300
H304_N303
-0.0282786
0.397861
0.341731
-
0.03601 / 0.0180809 / 0.114811
- / -0.113318
0.244323
-0.0298412
0.185721
-0.15159
-0.230999
0.0689035
-0.103774
0.155405
0.297322
-
0.32426 / 0.884187
0.106838 / 0.0102203
-1.10232 / 0.0178131 / -0.0214623 / -0.0158379
0.0273401 / 0.0286613 / -0.0193385
- / 0.0208468
-0.0858125
-0.00283199
-0.0342771
0.0592934
-0.10473
0.00782999
-0.0918754
0.092882
-0.0280027
-0.0876708
0.217723
0.0997339
0.000661955 / -0.000863189
0.00201562 / -0.00164835
-0.00287667 / 0.000889051 / -0.00918126
-0.00082715 / -0.000867548
0.00793005 / -0.00502689
-0.0117669 / 0.00315085 / -0.00211463
0.00743096 / - / 0.00991513
- / 0.00312121
Table S4. Inverse Polarizabilities, Å-3
Atom
Alanine
C135
C224
C235
C242
N238
Serine
C157
H155
O154
Phenylalanine
C145
C149
1/
0.515642
0.691837
0.525854
0.485997
1.40464
0.509135
3.70039
2.31814
10.0
10.0
Cysteine
C206
S200
Asparagine
C136
N237
Glutamine
C136
N237
Histidine
C505
C506
C507
C508
N503
N511
Leucine
C136
C137
Isoleucine
C136
C137
Valine
C137
Methionine
C136
C209
C210
S202
Proline
C136
C245
C246
N239
Tryptophan
C136
C145
C500
C501
C502
C514
N503
Threonine
C158
H155
O154
0.417752
0.497968
0.584073
1.28334
0.804315
1.18945
0.391962
0.758618
5.70968
0.719624
1.01387
1.01298
10.0
10.0
10.0
10.0
1.71809
1.26937
0.583708
2.67492
0.831939
0.596225
0.558897
0.491165
0.760093
0.312904
0.69451
2.19726
12.5098
0.798391
100.0
0.540221
1.1167
3.08747
1.63216
Tyrosine
C145
C149
C166
Aspartic Acid
C271
C274
O272
Glutamic Acid
C136
C271
C274
Lysine
C136
C292
N287
Protonated Histidine
C505
C509
C510
N512
Arginine
C136
C302
C307
C308
N300
N303
100.0
0.30056
0.312942
0.753218
0.487163
1.39829
1.51783
0.301317
0.631377
0.807484
1.14114
0.555973
0.57413
0.870782
0.882096
1.41498
0.643049
1.61209
0.456629
0.579122
0.747804
1.18755