2K0V 3LPV_molA 3LPV_molB 1A84 Morphological Parameter Mean SD Min 25% 50% 75% Max 11.10 29.50 27.60 83.20 tbend 32.91 13.47 1.64 23.60 32.74 42.30 83.52 -0.03 -0.05 -0.10 0.03 shear -0.09 0.31 -1.84 -0.30 -0.08 0.11 0.93 -0.21 -0.12 -0.13 -0.17 stretch 0.02 0.13 -0.37 -0.06 0.01 0.09 0.98 0.00 0.13 0.10 -0.20 stagger 0.10 0.45 -3.16 -0.19 0.10 0.40 1.81 -0.10 -1.30 0.00 6.90 buckle -5.23 13.76 -55.52 -15.09 -5.21 4.75 37.53 -0.60 -13.00 -12.60 -2.00 propel -11.01 11.02 -51.94 -18.50 -11.42 -3.66 25.61 -1.00 2.50 2.60 4.00 opening 2.80 5.35 -25.28 -0.49 2.39 5.67 45.44 -0.77 -2.98 -3.07 -2.11 xdisp -1.95 0.93 -4.88 -2.56 -1.93 -1.33 1.38 -0.07 0.64 0.62 0.38 ydisp -0.01 0.80 -2.77 -0.59 -0.02 0.58 2.42 4.60 14.20 14.80 20.50 inclin 13.68 6.98 -9.92 9.05 13.75 18.49 36.11 -3.80 -2.20 -2.20 -2.90 tip -2.51 9.64 -30.86 -8.87 -2.40 3.97 27.22 2.50 3.30 3.10 10.70 ax-bend 4.27 1.85 0.06 2.96 4.10 5.36 12.15 0.08 -0.03 0.03 -0.06 shift 0.23 0.84 -2.69 -0.36 0.22 0.82 3.85 -0.21 -1.03 -1.03 -0.20 slide -0.51 0.74 -2.51 -1.03 -0.55 -0.07 3.60 3.21 3.23 3.24 3.83 rise 3.40 0.52 2.20 3.07 3.32 3.64 5.72 0.40 1.50 1.50 0.90 tilt 1.36 4.91 -25.19 -1.88 1.34 4.53 23.51 1.40 7.80 8.00 5.40 roll 7.36 14.46 -21.91 -0.83 3.83 9.18 59.71 34.70 32.10 32.20 28.10 twist 30.20 7.63 -28.38 25.53 30.31 35.47 58.53 3.22 2.77 2.76 3.34 h-ris 3.18 0.52 1.61 2.83 3.17 3.50 5.32 35.00 33.60 33.60 32.30 h-twi 31.64 6.74 -30.58 27.59 31.61 35.90 57.16 -47.30 -71.10 -68.90 -66.40 alphaW -71.96 18.04 -307.39 -77.88 -70.06 -62.95 -36.93 -179.60 177.50 177.70 162.80 betaW 169.86 18.09 41.26 163.75 171.14 178.22 300.13 38.10 62.50 61.60 113.50 gammaW 59.39 18.01 4.55 51.39 57.50 64.00 201.67 134.20 90.20 91.60 132.40 deltaW 109.96 21.79 62.37 91.45 109.68 128.68 163.65 172.40 -158.20 -157.70 -177.90 epsilW -167.65 21.72 -336.13 -178.51 -171.41 -163.38 -60.10 -98.50 -75.90 -77.00 -98.90 zetaW -90.76 29.88 -299.73 -95.24 -86.40 -76.81 -43.63 -111.00 -155.00 -153.40 -111.30 chiW -127.62 19.04 -176.07 -141.38 -130.58 -115.29 -53.96 154.20 21.70 17.70 168.90 phaseW 107.97 45.32 0.60 80.11 114.86 139.56 358.54 32.20 40.40 40.70 26.20 ampW 39.56 6.87 5.68 35.24 39.97 44.49 59.51 -38.30 -80.20 -71.80 -90.20 alphaC -75.26 15.66 -285.51 -83.00 -73.04 -65.41 -33.86 -175.60 171.10 173.90 -174.70 betaC 170.69 14.01 70.34 163.03 171.27 179.12 239.61 30.90 62.40 57.90 98.50 gammaC 55.04 11.56 3.05 48.32 54.72 61.63 193.47 142.60 94.10 94.00 136.00 deltaC 118.50 23.13 64.03 97.10 124.19 138.11 160.58 175.50 -150.70 -157.10 171.40 epsilC -160.55 29.65 -203.66 -176.73 -169.20 -159.50 -50.24 -105.80 -83.40 -83.30 -80.00 zetaC -102.51 42.91 -284.62 -100.57 -88.77 -79.50 -42.76 -107.00 -148.70 -147.40 -108.20 chiC -118.79 20.35 -168.95 -134.64 -118.84 -104.22 -17.41 168.20 34.10 34.10 162.70 phaseC 123.93 46.76 1.41 93.45 133.89 155.81 359.86 34.80 45.60 42.90 27.70 ampC 37.84 7.45 2.22 33.20 38.16 42.91 57.58 7.41 9.48 9.60 7.99 minw 8.12 1.98 0.00 6.77 8.10 9.65 12.88 4.52 1.83 1.72 2.73 mind 3.56 1.19 -0.15 2.85 3.77 4.40 7.09 10.22 4.94 5.23 10.12 majw 9.69 5.08 0.00 7.91 11.42 13.34 19.78 5.08 9.67 9.71 11.88 majd 5.22 3.99 -0.94 1.46 4.85 8.90 14.05

Table 2: Sequence-averaged morphological parameters for Cisplatin-DNA using the uncorrelated snap shots from five MD simulations (total length of MD run is 150 ns, RESP charges were used for (NH3)2Ptgg). 2K0V is unplatinated DNA from NMR studies.1A84 numbers refer to the NMR data. 3LPV numbers refer to the X-ray data. The 2K0V, 3LPV and 1A84 numbers highlighted in green are within Mean ± SD values from the MD run. SD is the standard deviation. Min and Max are the minimum and maximum values obtained for that parameter from the MD run. 25%, Median (50%) and 75% are the respective percentiles between Min and Max. tbend is total bend. Ax-bend is a re-rendering of the total bend using the local base-step data. Helical-Rise and Helical-Twist correspond to the translation and rotation of successive base pairs along and around the helical axis. Backbone angles are presented separately for “W” (platinated strand) and “C” (complementary strand). Under Morphological Parameter column, min and maj refer to minor and major grooves and w and d stand for width and depth.