Supporting Information
Ttile: Relative Solvation Free Energies Calculated Using an Ab Initio QM/MM-Based Free Energy Perturbation Method: Dependence of Results on Simulation Length.
M. Rami Reddy* and Mark D. Erion
Metabasis Therapeutics, Inc.
11119 North Torrey Pines Road, La Jolla, CA92037, USA
Table 1. Partial atomic charges and optimized geometries of all the solute molecules.
Molecule# 1: Methanol
Atom Res X Y Z Charge
ATOM 1 C MOH 1 .656 -.020 .000 .3206
ATOM 2 H MOH 1 1.013 -.544 -.883 -.0387
ATOM 3 H MOH 1 1.077 .976 -.001 .0260
ATOM 4 H MOH 1 1.013 -.543 .884 -.0387
ATOM 5 O MOH 1 -.737 .121 .000 -.6935
ATOM 6 H MOH 1 -1.140 -.736 .000 .4244
Molecule# 2: Ethane
Atom Res X Y Z Charge
ATOM 1 C ETA 1 -.764 .000 .000 -.1730
ATOM 2 H ETA 1 -1.157 .877 -.506 .0670
ATOM 3 H ETA 1 -1.157 -.877 -.506 .0585
ATOM 4 H ETA 1 -1.156 .000 1.012 .0475
ATOM 5 C ETA 1 .764 .000 .000 -.1698
ATOM 6 H ETA 1 1.157 .877 .505 .0685
ATOM 7 H ETA 1 1.157 -.876 .507 .0551
ATOM 8 H ETA 1 1.156 -.001 -1.012 .0462
Molecule# 3: Acetamide
Atom Res X Y Z Charge
ATOM 1 H ACN 1 -1.621 -.677 .989 .1063
ATOM 2 C ACN 1 -1.361 -.312 .000 -.4269
ATOM 3 H ACN 1 -1.524 -1.116 -.710 .1174
ATOM 4 H ACN 1 -2.001 .523 -.242 .1118
ATOM 5 C ACN 1 .079 .153 -.008 .9892
ATOM 6 O ACN 1 .386 1.311 .006 -.6666
ATOM 7 N ACN 1 1.005 -.840 -.032 -1.1089
ATOM 8 H ACN 1 1.960 -.587 .086 .4484
ATOM 9 H ACN 1 .756 -1.792 .104 .4291
Molecule# 4: Acetone
Atom Res X Y Z Charge
ATOM 1 H ACE 1 -1.336 -1.250 .874 .0917
ATOM 2 C ACE 1 -1.288 -.608 .000 -.3762
ATOM 3 H ACE 1 -1.335 -1.250 -.874 .0917
ATOM 4 H ACE 1 -2.134 .066 .000 .1036
ATOM 5 C ACE 1 .000 .188 .000 .7664
ATOM 6 O ACE 1 .000 1.380 .000 -.5882
ATOM 7 C ACE 1 1.288 -.608 .000 -.3762
ATOM 8 H ACE 1 2.134 .066 .000 .1036
ATOM 9 H ACE 1 1.336 -1.250 .874 .0917
ATOM 10 H ACE 1 1.335 -1.250 -.874 .0917
Molecule# 5: Phenol
Atom Res X Y Z Charge
ATOM 1 C PEN 1 .934 -.025 .000 .5173
ATOM 2 C PEN 1 .265 1.189 .000 -.3993
ATOM 3 C PEN 1 -1.122 1.209 .000 .0256
ATOM 4 C PEN 1 -1.844 .030 .000 -.2232
ATOM 5 C PEN 1 -1.162 -1.180 .000 -.0280
ATOM 6 C PEN 1 .219 -1.215 .000 -.3042
ATOM 7 H PEN 1 .821 2.112 .001 .1500
ATOM 8 H PEN 1 -1.633 2.155 .000 .0958
ATOM 9 H PEN 1 -2.919 .049 .000 .1187
ATOM 10 H PEN 1 -1.712 -2.105 .000 .1046
ATOM 11 H PEN 1 .756 -2.145 .001 .1689
ATOM 12 O PEN 1 2.284 -.109 -.001 -.6725
ATOM 13 H PEN 1 2.673 .755 .002 .4463
Molecule# 7: Benzene
Atom Res X Y Z Charge
ATOM 1 C BEN 1 -.167 -1.376 .000 -.1135
ATOM 2 C BEN 1 -1.275 -.543 .000 -.0857
ATOM 3 C BEN 1 -1.108 .833 .000 -.1077
ATOM 4 C BEN 1 .167 1.376 .000 -.1135
ATOM 5 C BEN 1 1.275 .543 .000 -.0857
ATOM 6 C BEN 1 1.108 -.833 .000 -.1077
ATOM 7 H BEN 1 -.297 -2.444 .000 .1057
ATOM 8 H BEN 1 -2.265 -.965 .000 .0969
ATOM 9 H BEN 1 -1.968 1.479 .000 .1042
ATOM 10H BEN 1 .297 2.444 .000 .1057
ATOM 11 H BEN 1 2.265 .965 .000 .0969
ATOM 12 H BEN 1 1.968 -1.479 .000 .1042
Molecule# 8: 1,1,1 Trichloroethane
Atom Res X Y Z Charge
ATOM 1 C CL3 1 .000 .000 .243 .0129
ATOM 2 Cl CL3 1 -.074 1.670 -.361 .0000
ATOM 3 Cl CL3 1 1.484 -.771 -.361 .0000
ATOM 4 Cl CL3 1 -1.409 -.900 -.361 .0000
ATOM 5 C CL3 1 .000 .000 1.764 -.2908
ATOM 6 H CL3 1 -.905 .470 2.124 .1405
ATOM 7 H CL3 1 .045 -1.019 2.124 .1398
ATOM 8 H CL3 1 .860 .549 2.124 .1402
Molecule# 9: Phenylalanine(Phe)
Atom Res X Y Z Charge
ATOM 1 N PHE 1 -2.475 1.613 -.329 -.5424
ATOM 2 H PHE 1 -2.270 2.316 -1.018 .3300
ATOM 3 H PHE 1 -3.337 1.058 -.548 .3202
ATOM 4 H PHE 1 -2.610 2.062 .562 .3190
ATOM 5 C PHE 1 -1.472 .484 -.257 .3967
ATOM 6 H PHE 1 -1.024 .431 -1.240 -.0515
ATOM 7 C PHE 1 -.399 .721 .819 -.3404
ATOM 8 H PHE 1 -.373 1.776 1.079 .0737
ATOM 9 H PHE 1 -.683 .176 1.711 .0989
ATOM 10 C PHE 1 .999 .313 .389 .2623
ATOM 11 C PHE 1 1.980 1.276 . 193 -.2676
ATOM 12 H PHE 1 1.751 2.316 .356 .1158
ATOM 13 C PHE 1 1.320 -1.027 .184 -.2599
ATOM 14 H PHE 1 .563 -1.775 .326 .1663
ATOM 15 C PHE 1 3.260 .918 -.200 -.0466
ATOM 16 H PHE 1 4.008 1.677 -.344 .1014
ATOM 17 C PHE 1 2.599 -1.383 -.210 -.0225
ATOM 18 H PHE 1 2.835 -2.421 -.365 .0987
ATOM 19 C PHE 1 3.573 -.415 -.404 -.1830
ATOM 20 H PHE 1 4.565 -.698 -.708 .1199
ATOM 21 C PHE 1 -2.378 -.789 -.061 .7515
ATOM 22 O PHE 1 -3.565 -.566 -.353 -.7511
ATOM 23 O PHE 1 -1.809 -1.784 .325 -.6894
Molecule# 10: Isoleucine(Ile)
Atom Res X Y Z Charge
ATOM 1 N ILE 1 1.499 -1.553 -.532 -.5807
ATOM 2 H ILE 1 1.792 -1.943 -1.410 .3494
ATOM 3 H ILE 1 2.311 -1.086 -.032 .3488
ATOM 4 H ILE 1 1.103 -2.286 .030 .3238
ATOM 5 C ILE 1 .606 -.338 -.671 .0578
ATOM 6 H ILE 1 .508 -.141 -1.730 .0319
ATOM 7 C ILE 1 -.778 -.594 -.050 .2463
ATOM 8 H ILE 1 -1.109 -1.572 -.409 -.0584
ATOM 9 C ILE 1 -.708 -.640 1.482 -.2496
ATOM 10 H ILE 1 -1.644 -.988 1.903 .0579
ATOM 11 H ILE 1 .069 -1.311 1.842 .0368
ATOM 12 H ILE 1 -.495 .344 1.881 .0907
ATOM 13 C ILE 1 -1.793 .440 -.566 -.0077
ATOM 14 H ILE 1 -1.479 1.426 -.250 .0459
ATOM 15 H ILE 1 -1.757 .439 1.654 -.0182
ATOM 16 C ILE 1 -3.232 .167 -.129 -.1155
ATOM 17 H ILE 1 -3.908 .864 -.614 .0412
ATOM 18 H ILE 1 -3.549 -.838 -.397 .0138
ATOM 19 H ILE 1 -3.364 .284 .941 .0288
ATOM 20 C ILE 1 1.447 .816 -.010 .8408
ATOM 21 O ILE 1 2.539 .412 .431 -.7623
ATOM 22 O ILE 1 .934 1.910 -.020 -.7218