ClaRNA

Doublet Group distance statistics: 52305

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Distances from reference structure (by RMSD)

2, 0, 1, 0, 0, 0, 2, 0, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0,

RMS Distances matrix

Distances graph

Distances from reference structure (by atoms)

Atom Chain Distances
C4 A 0, 0.006, 0.011, 0.016, 0.019 max_d=0.019 avg_d=0.011 std_dev=0.005
C6 A 0, 0.007, 0.013, 0.019, 0.020 max_d=0.020 avg_d=0.013 std_dev=0.006
C5 A 0, 0.002, 0.008, 0.014, 0.021 max_d=0.021 avg_d=0.008 std_dev=0.006
N1 A 0, 0.004, 0.011, 0.018, 0.022 max_d=0.022 avg_d=0.011 std_dev=0.007
N3 A 0, 0.001, 0.009, 0.017, 0.028 max_d=0.028 avg_d=0.009 std_dev=0.008
C1' A 0, 0.004, 0.014, 0.023, 0.036 max_d=0.036 avg_d=0.014 std_dev=0.010
C2 A 0, 0.007, 0.017, 0.028, 0.038 max_d=0.038 avg_d=0.017 std_dev=0.010
N4 A 0, 0.016, 0.031, 0.046, 0.048 max_d=0.048 avg_d=0.031 std_dev=0.015
O2 A 0, 0.014, 0.043, 0.072, 0.109 max_d=0.109 avg_d=0.043 std_dev=0.029
O4' A 0, 0.166, 0.496, 0.826, 0.820 max_d=0.820 avg_d=0.496 std_dev=0.330
C2' A 0, 0.172, 0.530, 0.889, 0.933 max_d=0.933 avg_d=0.530 std_dev=0.359
P B 0, 0.108, 0.521, 0.934, 1.144 max_d=1.144 avg_d=0.521 std_dev=0.413
OP2 B 0, 0.062, 0.482, 0.902, 1.205 max_d=1.205 avg_d=0.482 std_dev=0.420
OP1 B 0, 0.166, 0.657, 1.149, 1.468 max_d=1.468 avg_d=0.657 std_dev=0.491
C4' A 0, 0.251, 0.916, 1.582, 1.656 max_d=1.656 avg_d=0.916 std_dev=0.665
O2' A 0, 0.307, 1.026, 1.744, 1.796 max_d=1.796 avg_d=1.026 std_dev=0.718
C3' A 0, 0.184, 0.948, 1.711, 1.859 max_d=1.859 avg_d=0.948 std_dev=0.764
C5' A 0, 0.405, 1.196, 1.987, 1.993 max_d=1.993 avg_d=1.196 std_dev=0.791
O3' A 0, 0.043, 1.397, 2.751, 3.075 max_d=3.075 avg_d=1.397 std_dev=1.354
O5' A 0, 0.327, 1.824, 3.320, 4.103 max_d=4.103 avg_d=1.824 std_dev=1.497
O5' B 0, -0.395, 1.312, 3.019, 4.243 max_d=4.243 avg_d=1.312 std_dev=1.707
OP1 A 0, -0.212, 1.690, 3.592, 4.819 max_d=4.819 avg_d=1.690 std_dev=1.902
P A 0, 0.256, 2.347, 4.439, 5.691 max_d=5.691 avg_d=2.347 std_dev=2.091
C5' B 0, -0.281, 2.126, 4.534, 6.128 max_d=6.128 avg_d=2.126 std_dev=2.407
OP2 A 0, 0.725, 3.671, 6.616, 7.814 max_d=7.814 avg_d=3.671 std_dev=2.945
C4' B 0, -0.523, 2.930, 6.384, 8.783 max_d=8.783 avg_d=2.930 std_dev=3.454
O4' B 0, -0.414, 3.461, 7.337, 9.815 max_d=9.815 avg_d=3.461 std_dev=3.876
C3' B 0, -0.887, 3.032, 6.951, 9.741 max_d=9.741 avg_d=3.032 std_dev=3.919
C8 B 0, -0.752, 3.365, 7.482, 9.425 max_d=9.425 avg_d=3.365 std_dev=4.117
C2' B 0, -0.555, 3.855, 8.265, 11.286 max_d=11.286 avg_d=3.855 std_dev=4.410
O3' B 0, -0.824, 3.712, 8.248, 11.444 max_d=11.444 avg_d=3.712 std_dev=4.536
C1' B 0, -0.556, 4.008, 8.572, 11.519 max_d=11.519 avg_d=4.008 std_dev=4.564
N9 B 0, -0.636, 3.981, 8.598, 11.142 max_d=11.142 avg_d=3.981 std_dev=4.617
N7 B 0, -0.914, 3.882, 8.679, 10.529 max_d=10.529 avg_d=3.882 std_dev=4.796
O2' B 0, -0.653, 4.743, 10.138, 13.844 max_d=13.844 avg_d=4.743 std_dev=5.396
C4 B 0, -0.730, 4.778, 10.286, 13.040 max_d=13.040 avg_d=4.778 std_dev=5.508
C5 B 0, -0.958, 4.668, 10.294, 12.603 max_d=12.603 avg_d=4.668 std_dev=5.626
N3 B 0, -0.635, 5.631, 11.898, 15.232 max_d=15.232 avg_d=5.631 std_dev=6.267
C6 B 0, -1.020, 5.554, 12.127, 14.552 max_d=14.552 avg_d=5.554 std_dev=6.573
O6 B 0, -1.026, 5.922, 12.869, 15.084 max_d=15.084 avg_d=5.922 std_dev=6.947
C2 B 0, -0.730, 6.298, 13.326, 16.719 max_d=16.719 avg_d=6.298 std_dev=7.028
N1 B 0, -0.918, 6.261, 13.439, 16.395 max_d=16.395 avg_d=6.261 std_dev=7.179
N2 B 0, -0.662, 7.195, 15.052, 18.998 max_d=18.998 avg_d=7.195 std_dev=7.857

Atoms distances (summary)

atom dist matrix

Atoms distances Chain-A - Chain-A

Atom C1'C2C2'C3'C4C4'C5C5'C6N1N3N4O2O2'O3'O4'O5'OP1OP2P
C1' 0.00 0.02 0.00 0.01 0.02 0.00 0.01 0.06 0.01 0.01 0.02 0.02 0.04 0.01 0.30 0.00 0.14 0.13 0.22 0.13
C2 0.02 0.00 0.16 0.26 0.01 0.08 0.01 0.12 0.01 0.01 0.00 0.01 0.00 0.28 0.14 0.06 0.45 0.29 0.75 0.45
C2' 0.00 0.16 0.00 0.01 0.04 0.01 0.10 0.20 0.14 0.03 0.13 0.05 0.28 0.00 0.01 0.02 0.26 0.51 0.39 0.28
C3' 0.01 0.26 0.01 0.00 0.42 0.00 0.43 0.02 0.37 0.25 0.35 0.46 0.17 0.02 0.01 0.01 0.42 0.70 0.60 0.44
C4 0.02 0.01 0.04 0.42 0.00 0.21 0.01 0.28 0.01 0.01 0.01 0.00 0.00 0.38 0.21 0.03 0.74 0.51 1.18 0.80
C4' 0.00 0.08 0.01 0.00 0.21 0.00 0.27 0.00 0.25 0.12 0.14 0.23 0.03 0.30 0.02 0.00 0.01 0.34 0.18 0.13
C5 0.01 0.01 0.10 0.43 0.01 0.27 0.00 0.34 0.00 0.01 0.01 0.01 0.01 0.38 0.29 0.09 0.80 0.50 1.14 0.83
C5' 0.06 0.12 0.20 0.02 0.28 0.00 0.34 0.00 0.28 0.13 0.19 0.32 0.08 0.09 0.19 0.02 0.01 0.39 0.36 0.01
C6 0.01 0.01 0.14 0.37 0.01 0.25 0.00 0.28 0.00 0.00 0.01 0.01 0.01 0.32 0.22 0.12 0.67 0.34 0.82 0.62
N1 0.01 0.01 0.03 0.25 0.01 0.12 0.01 0.13 0.00 0.00 0.01 0.01 0.02 0.22 0.10 0.02 0.43 0.23 0.60 0.40
N3 0.02 0.00 0.13 0.35 0.01 0.14 0.01 0.19 0.01 0.01 0.00 0.01 0.01 0.35 0.10 0.04 0.60 0.41 1.01 0.64
N4 0.02 0.01 0.05 0.46 0.00 0.23 0.01 0.32 0.01 0.01 0.01 0.00 0.01 0.41 0.26 0.03 0.80 0.60 1.36 0.92
O2 0.04 0.00 0.28 0.17 0.00 0.03 0.01 0.08 0.01 0.02 0.01 0.01 0.00 0.31 0.32 0.11 0.32 0.22 0.62 0.33
O2' 0.01 0.28 0.00 0.02 0.38 0.30 0.38 0.09 0.32 0.22 0.35 0.41 0.31 0.00 0.03 0.23 0.30 0.37 0.47 0.29
O3' 0.30 0.14 0.01 0.01 0.21 0.02 0.29 0.19 0.22 0.10 0.10 0.26 0.32 0.03 0.00 0.21 0.45 0.98 0.77 0.59
O4' 0.00 0.06 0.02 0.01 0.03 0.00 0.09 0.02 0.12 0.02 0.04 0.03 0.11 0.23 0.21 0.00 0.11 0.17 0.15 0.19
O5' 0.14 0.45 0.26 0.42 0.74 0.01 0.80 0.01 0.67 0.43 0.60 0.80 0.32 0.30 0.45 0.11 0.00 0.02 0.01 0.00
OP1 0.13 0.29 0.51 0.70 0.51 0.34 0.50 0.39 0.34 0.23 0.41 0.60 0.22 0.37 0.98 0.17 0.02 0.00 0.01 0.01
OP2 0.22 0.75 0.39 0.60 1.18 0.18 1.14 0.36 0.82 0.60 1.01 1.36 0.62 0.47 0.77 0.15 0.01 0.01 0.00 0.01
P 0.13 0.45 0.28 0.44 0.80 0.13 0.83 0.01 0.62 0.40 0.64 0.92 0.33 0.29 0.59 0.19 0.00 0.01 0.01 0.00

Atoms distances Chain-A - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N2N3N7N9O2'O3'O4'O5'O6OP1OP2P
C1' 1.36 1.08 2.17 2.28 0.99 1.80 1.41 1.62 1.81 1.03 1.49 1.06 1.01 1.54 0.95 2.73 2.63 1.15 0.56 2.44 0.30 0.35 0.20
C2 0.52 1.87 1.01 1.18 1.61 0.92 2.36 1.08 2.89 1.61 2.54 1.72 1.39 2.41 1.15 1.36 1.42 0.23 0.15 3.55 0.30 0.35 0.23
C2' 1.42 1.17 2.22 2.41 1.07 1.89 1.51 1.62 1.92 1.09 1.58 1.16 1.10 1.65 1.01 2.81 2.90 1.21 0.60 2.57 0.23 0.27 0.09
C3' 2.25 1.44 3.00 3.21 1.43 2.67 1.33 2.26 1.53 1.30 1.37 1.59 1.67 1.40 1.59 3.63 3.77 2.05 1.30 2.01 0.55 0.44 0.70
C4 0.47 1.72 0.56 0.70 1.57 0.60 2.21 0.86 2.56 1.64 2.24 1.57 1.35 2.35 1.19 0.75 0.85 0.20 0.14 3.02 0.30 0.33 0.25
C4' 2.49 1.65 3.30 3.37 1.58 2.75 1.15 2.28 1.18 1.25 1.26 1.89 1.94 1.09 1.76 4.00 3.87 2.21 1.22 1.48 0.39 0.28 0.54
C5 0.77 0.81 1.38 1.54 0.76 1.33 1.27 1.36 1.55 0.93 1.24 0.69 0.61 1.46 0.62 1.61 1.66 0.72 0.42 2.00 0.30 0.35 0.21
C5' 3.13 2.28 3.88 3.91 2.17 3.25 1.46 2.61 1.26 1.63 1.66 2.59 2.62 1.17 2.34 4.60 4.46 2.80 1.55 1.04 0.48 0.31 0.71
C6 1.24 0.79 1.96 2.11 0.78 1.73 1.13 1.61 1.42 0.86 1.11 0.77 0.79 1.30 0.80 2.32 2.31 1.11 0.58 1.92 0.30 0.35 0.21
N1 0.96 1.13 1.71 1.86 1.01 1.48 1.60 1.44 2.02 1.11 1.67 1.01 0.87 1.74 0.81 2.14 2.12 0.82 0.41 2.63 0.30 0.35 0.20
N3 0.66 2.26 0.53 0.63 2.00 0.50 2.73 0.81 3.22 1.94 2.88 2.12 1.79 2.77 1.49 0.74 0.82 0.32 0.19 3.81 0.30 0.32 0.26
N4 0.96 2.15 0.40 0.17 2.04 0.22 2.59 0.52 2.83 2.10 2.57 2.02 1.84 2.73 1.68 0.32 0.13 0.72 0.42 3.14 0.27 0.26 0.30
O2 0.58 2.26 0.93 1.08 1.89 0.81 2.68 1.01 3.33 1.79 2.99 2.13 1.70 2.66 1.35 1.30 1.35 0.16 0.12 4.07 0.30 0.34 0.23
O2' 1.28 1.37 2.12 2.28 1.20 1.72 1.75 1.47 2.24 1.20 1.88 1.34 1.18 1.87 1.00 2.78 2.82 1.00 0.45 2.95 0.43 0.51 0.29
O3' 2.27 1.50 3.04 3.27 1.43 2.72 1.38 2.27 1.66 1.25 1.48 1.67 1.69 1.43 1.57 3.73 3.94 2.08 1.31 2.22 0.54 0.36 0.66
O4' 1.97 1.26 2.80 2.82 1.21 2.25 1.05 1.93 1.24 1.00 1.13 1.43 1.47 1.09 1.35 3.44 3.15 1.71 0.83 1.69 0.31 0.34 0.31
O5' 3.35 2.27 3.99 4.18 2.25 3.67 1.49 3.06 1.18 1.80 1.61 2.52 2.65 1.19 2.51 4.53 4.66 3.17 2.02 0.75 0.76 0.67 1.11
OP1 3.77 2.89 4.18 4.28 2.72 3.82 1.88 2.90 1.60 2.06 2.15 3.25 3.26 1.49 2.88 4.84 5.10 3.51 2.06 1.01 0.74 0.57 1.02
OP2 3.77 2.67 4.10 4.39 2.66 4.27 1.93 3.59 1.63 2.25 2.06 2.90 3.03 1.62 2.93 4.41 4.89 3.80 2.79 1.11 1.36 1.39 1.76
P 3.87 2.78 4.31 4.53 2.74 4.14 1.93 3.34 1.59 2.24 2.08 3.05 3.17 1.60 2.99 4.81 5.22 3.73 2.43 0.98 1.09 0.94 1.42

Atoms distances Chain-B - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N2N3N7N9O2'O3'O4'O5'O6OP1OP2P
C1' 0.00 0.07 0.01 0.01 0.03 0.01 0.02 0.08 0.05 0.01 0.06 0.08 0.06 0.01 0.00 0.03 0.29 0.00 0.20 0.05 0.32 0.25 0.15
C2 0.07 0.00 0.32 0.27 0.02 0.04 0.00 0.11 0.01 0.02 0.01 0.00 0.01 0.01 0.03 0.36 0.12 0.18 0.29 0.02 0.50 0.72 0.21
C2' 0.01 0.32 0.00 0.01 0.16 0.01 0.10 0.21 0.16 0.16 0.26 0.38 0.31 0.09 0.03 0.01 0.03 0.02 0.36 0.14 0.51 0.20 0.34
C3' 0.01 0.27 0.01 0.00 0.25 0.00 0.32 0.03 0.35 0.25 0.32 0.26 0.23 0.32 0.20 0.03 0.02 0.02 0.33 0.37 0.54 0.20 0.27
C4 0.03 0.02 0.16 0.25 0.00 0.03 0.01 0.09 0.03 0.01 0.02 0.02 0.01 0.00 0.01 0.22 0.04 0.10 0.30 0.03 0.49 0.67 0.19
C4' 0.01 0.04 0.01 0.00 0.03 0.00 0.08 0.00 0.07 0.14 0.03 0.06 0.04 0.13 0.06 0.29 0.04 0.00 0.01 0.09 0.22 0.19 0.01
C5 0.02 0.00 0.10 0.32 0.01 0.08 0.00 0.09 0.02 0.01 0.01 0.01 0.01 0.00 0.01 0.28 0.10 0.04 0.36 0.02 0.58 0.89 0.23
C5' 0.08 0.11 0.21 0.03 0.09 0.00 0.09 0.00 0.09 0.15 0.09 0.13 0.11 0.13 0.09 0.08 0.18 0.02 0.01 0.10 0.38 0.36 0.02
C6 0.05 0.01 0.16 0.35 0.03 0.07 0.02 0.09 0.00 0.02 0.01 0.01 0.02 0.01 0.03 0.31 0.12 0.07 0.37 0.01 0.61 0.98 0.25
C8 0.01 0.02 0.16 0.25 0.01 0.14 0.01 0.15 0.02 0.00 0.02 0.02 0.01 0.00 0.00 0.32 0.12 0.11 0.33 0.02 0.54 0.72 0.17
N1 0.06 0.01 0.26 0.32 0.02 0.03 0.01 0.09 0.01 0.02 0.00 0.01 0.02 0.01 0.04 0.33 0.07 0.13 0.34 0.01 0.56 0.89 0.23
N2 0.08 0.00 0.38 0.26 0.02 0.06 0.01 0.13 0.01 0.02 0.01 0.00 0.02 0.01 0.04 0.44 0.19 0.21 0.27 0.02 0.47 0.68 0.20
N3 0.06 0.01 0.31 0.23 0.01 0.04 0.01 0.11 0.02 0.01 0.02 0.02 0.00 0.01 0.03 0.31 0.16 0.17 0.26 0.03 0.45 0.59 0.18
N7 0.01 0.01 0.09 0.32 0.00 0.13 0.00 0.13 0.01 0.00 0.01 0.01 0.01 0.00 0.01 0.33 0.17 0.06 0.38 0.02 0.62 0.96 0.23
N9 0.00 0.03 0.03 0.20 0.01 0.06 0.01 0.09 0.03 0.00 0.04 0.04 0.03 0.01 0.00 0.18 0.06 0.01 0.27 0.04 0.45 0.53 0.16
O2' 0.03 0.36 0.01 0.03 0.22 0.29 0.28 0.08 0.31 0.32 0.33 0.44 0.31 0.33 0.18 0.00 0.08 0.21 0.37 0.33 0.59 0.19 0.34
O3' 0.29 0.12 0.03 0.02 0.04 0.04 0.10 0.18 0.12 0.12 0.07 0.19 0.16 0.17 0.06 0.08 0.00 0.23 0.36 0.18 0.85 0.33 0.43
O4' 0.00 0.18 0.02 0.02 0.10 0.00 0.04 0.02 0.07 0.11 0.13 0.21 0.17 0.06 0.01 0.21 0.23 0.00 0.06 0.05 0.15 0.17 0.08
O5' 0.20 0.29 0.36 0.33 0.30 0.01 0.36 0.01 0.37 0.33 0.34 0.27 0.26 0.38 0.27 0.37 0.36 0.06 0.00 0.39 0.02 0.02 0.01
O6 0.05 0.02 0.14 0.37 0.03 0.09 0.02 0.10 0.01 0.02 0.01 0.02 0.03 0.02 0.04 0.33 0.18 0.05 0.39 0.00 0.65 1.11 0.27
OP1 0.32 0.50 0.51 0.54 0.49 0.22 0.58 0.38 0.61 0.54 0.56 0.47 0.45 0.62 0.45 0.59 0.85 0.15 0.02 0.65 0.00 0.01 0.01
OP2 0.25 0.72 0.20 0.20 0.67 0.19 0.89 0.36 0.98 0.72 0.89 0.68 0.59 0.96 0.53 0.19 0.33 0.17 0.02 1.11 0.01 0.00 0.01
P 0.15 0.21 0.34 0.27 0.19 0.01 0.23 0.02 0.25 0.17 0.23 0.20 0.18 0.23 0.16 0.34 0.43 0.08 0.01 0.27 0.01 0.01 0.00