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Table 5 Components of the free energies (in kcal/rnol) calculated according to the MM/GBSA model. The constant term x const is 13.699 kcal/mol

From: Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes.

Original base Mutated ΔGexp ΔGcalc Coul vdW GB P H HB
T3-A39 C-G 0.400 0.115 -79.691 -33.547 50.408 30.607 37.296 -18.658
  G-C 0.600 0.525 -79.292 -33.467 50.226 30.690 37.327 -18.658
  A-T 0.400 1.165 -78.394 -33.432 49.648 30.588 37.181 -18.125
A4-T38 C-G 1.000 0.777 -81.129 -33.803 51.302 30.367 37.934 -17.592
  T-A 1.400 1.036 -81.246 -33.723 51.482 30.201 38.215 -17.592
  G-C 1.100 1.613 -79.949 -33.852 50.681 30.609 38.017 -17.592
C5-G37 T-A 0.800 2.136 -80.893 -33.864 51.109 30.552 39.125 -17.592
  A-T 0.600 0.996 -79.955 -33.842 50.645 30.484 38.090 -18.125
  G-C 0.700 0.377 -81.302 -33.810 51.382 30.589 37.944 -18.125
C6-G36 T-A 0.900. 1.362 -80.476 -33.730 50.877 30.661 38.456 -18.125
  A-T 1.000 0.622 -79.641 -33.667 50.411 30.314 38.163 -18.658
  G-C 0.600 1.110 -80.186 -33.579 50.678 30.491 38.132 -18.125
T7-A35 G-C 0.400 -0.082 -80.781 -33.792 51.084 30.579 37.254 -18.125
  A-T -0.200 0.318 -80.382 -33.960 50.847 30.200 38.038 -18.125
  C-G 0.900 1.146 -80.387 -33.817 50.873 30.729 37.641 -17.592
C8-G34 T-A 0.500 1.350 -80.849 -33.862 51.113 30.593 38.247 -17.592
  A-T 3.600 3.360 -77.402 -33.305 49.165 30.110 38.152 -17.059
  G-C 3.400 2.435 -78.703 -33.834 49.920 30.582 37.829 -17.059
T9-A33 A-T 2.800 2.732 -78.808 -33.818 50.131 30.297 38.289 -17.059
  G-C 1.000 1.489 -79.210 -34.213 50.394 30.812 37.599 -17.592
  C-G 0.300 0.714 -80.866 -33.839 51.216 30.778 37.851 -18.125
G10-C32 A-T 0.400 1.868 -79.605 -33.008 50.347 30.450 38.110 -18.125
  T-A 0.500 1.034 -80.384 -34.230 50.938 30.722 38.414 -18.125
  C-G 0.200 -0.182 -81.436 -34.074 51.523 30.789 37.975 -18.658
G11-C31 C-G 1.400 1.533 -78.037 -33.806 49.387 30.408 38.007 -18.125
  A-T 1.100 1.009 -79.919 -33.894 50.529 30.555 38.163 -18.125
  T-A 2.300 0.731 -78.332 -33.617 49.511 30.299 38.362 -19.191
C12-G30 G-C 2.500 3.881 -78.666 -33.416 50.051 30.575 38.163 -16.526
  A-T 2.500 2.061 -78.455 -33.360 49.873 30.306 37.588 -17.592
  T-A 2.700 2.656 -78.889 -33.693 50.116 30.223 38.257 -17.059
G13-C29 A-T 2.900 1.744 -79.600 -33.700 50.381 30.624 37.933 -17.592
  C-G 3.400 1.941 -80.240 -33.646 50.825 30.805 38.090 -17.592
  T-A 3.200 2.131 -79.467 -33.720 50.343 30.737 38.665 -18.125
G14-G28 C-G 3.700 3.688 -78.059 -33.822 49.562 30.408 38.425 -16.526
  T-A 3.700 2.495 -78.334 -33.204 49.700 30.231 37.996 -17.592
  A-T 3.100 1.703 -80.426 -33.916 50.878 30.593 38.467 -17.592
T15-A27 G-C 2.900 1.755 -79.475 -33.371 50.375 30.884 37.766 -18.125
  A-T 2.000 1.946 -79.417 -33.359 50.311 30.820 37.484 -17.592
  C-G 2.500 1.088 -80.371 -33.422 50.848 30.775 37.683 -18.125
G16-C26 C-G 0.900 1.507 -79.347 -33.801 50.310 30.514 37.724 -17.592
  T-A 1.000 1.411 -79.452 -33.016 50.268 30.302 37.735 -18.125
  A-T 0.600 1.490 -79.733 -33.915 50.492 30.521 38.550 -18.125
A17-T25 C-G 0.200 0.100 -81.783 -33.375 51.717 30.952 37.014 -18.125
  T-A -0.100 0.258 -81.595 -33.370 51.621 30.858 37.171 -18.125
  G-C -0.200 0.741 -79.839 -33.332 50.528 30.608 37.202 -18.125
T18-A24 C-G 2.000 1.549 -81.158 -33.893 51.430 30.971 38.090 -17.592
  A-T 2.800 1.747 -81.528 -33.712 51.592 30.487 37.735 -16.526
  G-C 1.100 1.382 -80.583 -33.977 51.012 30.627 38.195 -17.592
A19-T23 T-A 0.400 1.602 -78.329 -33.474 49.625 30.680 37.526 -18.125
  C-G 0.500 0.917 -79.871 -33.472 50.549 30.684 37.453 -18.125
  G-C 0.400 0.878 -80.353 -33.573 50.784 30.669 37.777 -18.125
wild- type -- 0.000 1.120 -79.937 -33.811 50.610 30.593 38.090 -18.125