ClaRNA

Doublet Group distance statistics: 53339

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Distances from reference structure (by RMSD)

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

RMS Distances matrix

Distances graph

Distances from reference structure (by atoms)

Atom Chain Distances
C2 A 0, 0.003, 0.009, 0.016, 0.019 max_d=0.019 avg_d=0.009 std_dev=0.007
C6 A 0, 0.003, 0.011, 0.019, 0.022 max_d=0.022 avg_d=0.011 std_dev=0.008
C1' A 0, 0.006, 0.017, 0.028, 0.027 max_d=0.027 avg_d=0.017 std_dev=0.011
N2 A 0, 0.008, 0.019, 0.030, 0.027 max_d=0.027 avg_d=0.019 std_dev=0.011
N1 A 0, 0.008, 0.019, 0.031, 0.031 max_d=0.031 avg_d=0.019 std_dev=0.012
N3 A 0, 0.008, 0.022, 0.036, 0.035 max_d=0.035 avg_d=0.022 std_dev=0.014
C4 A 0, 0.006, 0.023, 0.040, 0.048 max_d=0.048 avg_d=0.023 std_dev=0.017
N9 A 0, 0.009, 0.027, 0.044, 0.049 max_d=0.049 avg_d=0.027 std_dev=0.017
C5 A 0, -0.001, 0.018, 0.038, 0.051 max_d=0.051 avg_d=0.018 std_dev=0.019
O6 A 0, 0.004, 0.040, 0.075, 0.097 max_d=0.097 avg_d=0.040 std_dev=0.036
C8 A 0, 0.001, 0.040, 0.078, 0.104 max_d=0.104 avg_d=0.040 std_dev=0.039
N7 A 0, 0.000, 0.040, 0.080, 0.106 max_d=0.106 avg_d=0.040 std_dev=0.040
C6 B 0, 0.126, 0.345, 0.563, 0.537 max_d=0.537 avg_d=0.345 std_dev=0.218
C5 B 0, 0.161, 0.391, 0.622, 0.558 max_d=0.558 avg_d=0.391 std_dev=0.230
C4 B 0, 0.153, 0.430, 0.707, 0.673 max_d=0.673 avg_d=0.430 std_dev=0.277
N1 B 0, 0.195, 0.488, 0.780, 0.780 max_d=0.780 avg_d=0.488 std_dev=0.293
O4 B 0, 0.148, 0.476, 0.805, 0.786 max_d=0.786 avg_d=0.476 std_dev=0.328
N3 B 0, 0.236, 0.580, 0.925, 0.903 max_d=0.903 avg_d=0.580 std_dev=0.344
C1' B 0, 0.180, 0.582, 0.985, 1.138 max_d=1.138 avg_d=0.582 std_dev=0.403
C2 B 0, 0.204, 0.629, 1.053, 1.198 max_d=1.198 avg_d=0.629 std_dev=0.425
O2 B 0, 0.155, 0.794, 1.432, 1.784 max_d=1.784 avg_d=0.794 std_dev=0.638
C2' B 0, 0.620, 1.708, 2.795, 2.654 max_d=2.654 avg_d=1.708 std_dev=1.088
O4' B 0, 0.370, 1.463, 2.556, 2.523 max_d=2.523 avg_d=1.463 std_dev=1.093
O4' A 0, 0.140, 1.272, 2.403, 2.400 max_d=2.400 avg_d=1.272 std_dev=1.132
C2' A 0, 0.109, 1.368, 2.628, 2.629 max_d=2.629 avg_d=1.368 std_dev=1.259
O2' B 0, 0.804, 2.103, 3.401, 3.192 max_d=3.192 avg_d=2.103 std_dev=1.299
C4' B 0, 0.314, 1.741, 3.168, 3.160 max_d=3.160 avg_d=1.741 std_dev=1.427
C4' A 0, 0.275, 1.863, 3.450, 3.438 max_d=3.438 avg_d=1.863 std_dev=1.588
C3' B 0, 0.402, 2.129, 3.856, 3.840 max_d=3.840 avg_d=2.129 std_dev=1.727
C3' A 0, 0.259, 2.057, 3.856, 3.851 max_d=3.851 avg_d=2.057 std_dev=1.799
O2' A 0, 0.040, 2.035, 4.030, 4.033 max_d=4.033 avg_d=2.035 std_dev=1.995
O3' A 0, 0.407, 2.560, 4.714, 4.698 max_d=4.698 avg_d=2.560 std_dev=2.154
O3' B 0, 0.594, 2.948, 5.302, 5.269 max_d=5.269 avg_d=2.948 std_dev=2.354
C5' B 0, 0.728, 3.341, 5.955, 5.909 max_d=5.909 avg_d=3.341 std_dev=2.613
O5' B 0, 1.634, 4.463, 7.292, 6.919 max_d=6.919 avg_d=4.463 std_dev=2.829
C5' A 0, 0.465, 3.385, 6.306, 6.286 max_d=6.286 avg_d=3.385 std_dev=2.920
O5' A 0, 0.449, 4.152, 7.856, 7.843 max_d=7.843 avg_d=4.152 std_dev=3.704
P B 0, 2.313, 6.351, 10.388, 9.862 max_d=9.862 avg_d=6.351 std_dev=4.037
OP1 B 0, 2.650, 6.829, 11.008, 10.255 max_d=10.255 avg_d=6.829 std_dev=4.179
OP2 B 0, 2.084, 6.828, 11.571, 11.270 max_d=11.270 avg_d=6.828 std_dev=4.743
P A 0, 0.669, 5.765, 10.861, 10.837 max_d=10.837 avg_d=5.765 std_dev=5.096
OP2 A 0, 0.738, 6.048, 11.357, 11.331 max_d=11.331 avg_d=6.048 std_dev=5.310
OP1 A 0, 0.938, 6.681, 12.424, 12.382 max_d=12.382 avg_d=6.681 std_dev=5.743

Atoms distances (summary)

atom dist matrix

Atoms distances Chain-A - Chain-A

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N2N3N7N9O2'O3'O4'O5'O6OP1OP2P
C1' 0.00 0.01 0.00 0.01 0.01 0.01 0.00 0.05 0.01 0.00 0.01 0.01 0.01 0.00 0.00 0.02 0.26 0.00 0.37 0.01 0.38 0.20 0.33
C2 0.01 0.00 0.38 0.40 0.01 0.55 0.00 1.05 0.00 0.01 0.00 0.00 0.00 0.00 0.01 0.43 0.36 0.33 0.43 0.01 0.61 0.90 0.66
C2' 0.00 0.38 0.00 0.00 0.18 0.00 0.08 0.21 0.17 0.18 0.29 0.46 0.38 0.10 0.02 0.00 0.01 0.01 0.02 0.13 0.06 0.28 0.07
C3' 0.01 0.40 0.00 0.00 0.06 0.00 0.27 0.02 0.15 0.68 0.18 0.63 0.41 0.60 0.27 0.02 0.01 0.02 0.03 0.25 0.12 0.14 0.02
C4 0.01 0.01 0.18 0.06 0.00 0.16 0.00 0.35 0.01 0.00 0.01 0.00 0.00 0.00 0.00 0.37 0.14 0.16 0.41 0.01 0.39 0.30 0.36
C4' 0.01 0.55 0.00 0.00 0.16 0.00 0.09 0.01 0.07 0.54 0.34 0.76 0.54 0.43 0.14 0.29 0.01 0.00 0.01 0.07 0.18 0.17 0.01
C5 0.00 0.00 0.08 0.27 0.00 0.09 0.00 0.09 0.01 0.00 0.01 0.00 0.00 0.00 0.00 0.44 0.12 0.04 0.96 0.01 1.01 1.06 1.02
C5' 0.05 1.05 0.21 0.02 0.35 0.01 0.09 0.00 0.21 0.80 0.69 1.43 0.99 0.66 0.14 0.05 0.18 0.01 0.01 0.09 0.37 0.29 0.01
C6 0.01 0.00 0.17 0.15 0.01 0.07 0.01 0.21 0.00 0.01 0.00 0.00 0.00 0.01 0.01 0.52 0.10 0.11 0.72 0.01 0.76 0.79 0.76
C8 0.00 0.01 0.18 0.68 0.00 0.54 0.00 0.80 0.01 0.00 0.01 0.00 0.00 0.00 0.00 0.26 0.32 0.23 1.73 0.01 1.79 1.89 1.83
N1 0.01 0.00 0.29 0.18 0.01 0.34 0.01 0.69 0.00 0.01 0.00 0.00 0.00 0.01 0.01 0.51 0.21 0.24 0.14 0.01 0.16 0.26 0.15
N2 0.01 0.00 0.46 0.63 0.00 0.76 0.00 1.43 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.39 0.51 0.41 0.96 0.01 1.29 1.70 1.33
N3 0.01 0.00 0.38 0.41 0.00 0.54 0.00 0.99 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.34 0.38 0.34 0.40 0.01 0.52 0.80 0.57
N7 0.00 0.00 0.10 0.60 0.00 0.43 0.00 0.66 0.01 0.00 0.01 0.00 0.00 0.00 0.00 0.38 0.32 0.14 1.67 0.01 1.84 2.04 1.88
N9 0.00 0.01 0.02 0.27 0.00 0.14 0.00 0.14 0.01 0.00 0.01 0.01 0.01 0.00 0.00 0.24 0.06 0.01 0.84 0.01 0.84 0.77 0.83
O2' 0.02 0.43 0.00 0.02 0.37 0.29 0.44 0.05 0.52 0.26 0.51 0.39 0.34 0.38 0.24 0.00 0.06 0.23 0.06 0.55 0.10 0.37 0.05
O3' 0.26 0.36 0.01 0.01 0.14 0.01 0.12 0.18 0.10 0.32 0.21 0.51 0.38 0.32 0.06 0.06 0.00 0.16 0.03 0.15 0.23 0.06 0.08
O4' 0.00 0.33 0.01 0.02 0.16 0.00 0.04 0.01 0.11 0.23 0.24 0.41 0.34 0.14 0.01 0.23 0.16 0.00 0.33 0.06 0.41 0.13 0.30
O5' 0.37 0.43 0.02 0.03 0.41 0.01 0.96 0.01 0.72 1.73 0.14 0.96 0.40 1.67 0.84 0.06 0.03 0.33 0.00 0.98 0.01 0.01 0.00
O6 0.01 0.01 0.13 0.25 0.01 0.07 0.01 0.09 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.55 0.15 0.06 0.98 0.00 1.11 1.22 1.11
OP1 0.38 0.61 0.06 0.12 0.39 0.18 1.01 0.37 0.76 1.79 0.16 1.29 0.52 1.84 0.84 0.10 0.23 0.41 0.01 1.11 0.00 0.00 0.00
OP2 0.20 0.90 0.28 0.14 0.30 0.17 1.06 0.29 0.79 1.89 0.26 1.70 0.80 2.04 0.77 0.37 0.06 0.13 0.01 1.22 0.00 0.00 0.00
P 0.33 0.66 0.07 0.02 0.36 0.01 1.02 0.01 0.76 1.83 0.15 1.33 0.57 1.88 0.83 0.05 0.08 0.30 0.00 1.11 0.00 0.00 0.00

Atoms distances Chain-A - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6N1N3O2O2'O3'O4O4'O5'OP1OP2P
C1' 0.40 0.20 0.60 0.25 0.25 0.86 0.29 1.29 0.09 0.18 0.12 0.35 0.68 0.58 0.36 1.26 1.63 1.76 2.30 2.09
C2 0.42 0.33 0.20 0.11 0.08 0.49 0.06 0.69 0.14 0.31 0.17 0.42 0.22 0.30 0.29 0.79 0.67 0.83 1.52 1.01
C2' 0.90 0.73 0.14 0.31 0.56 1.40 0.66 1.99 0.82 0.83 0.61 0.73 0.41 0.18 0.44 1.80 2.28 2.55 3.28 2.92
C3' 0.32 0.26 0.78 0.39 0.28 0.80 0.41 1.51 0.43 0.31 0.23 0.30 1.06 0.93 0.25 1.19 2.05 2.76 3.18 2.98
C4 0.45 0.30 0.39 0.35 0.22 0.43 0.22 0.59 0.02 0.27 0.13 0.44 0.33 0.59 0.36 0.89 0.68 0.74 1.32 0.98
C4' 0.51 0.35 1.60 1.22 0.19 0.08 0.25 0.65 0.33 0.38 0.25 0.40 1.92 1.78 0.12 0.43 1.28 2.00 2.30 2.17
C5 0.48 0.37 0.32 0.53 0.17 0.12 0.15 0.21 0.06 0.31 0.17 0.54 0.25 0.72 0.31 0.61 0.62 0.91 0.64 0.73
C5' 1.09 0.63 2.30 2.10 0.11 0.98 0.19 0.30 0.48 0.72 0.34 0.79 2.70 2.86 0.10 0.35 0.40 1.21 1.54 1.35
C6 0.47 0.43 0.20 0.43 0.08 0.06 0.03 0.27 0.15 0.35 0.25 0.57 0.29 0.58 0.23 0.46 0.80 1.31 0.59 0.95
C8 0.44 0.25 0.60 0.78 0.25 0.14 0.26 0.19 0.09 0.20 0.15 0.45 0.39 1.05 0.35 0.77 0.50 0.51 0.66 0.63
N1 0.45 0.40 0.16 0.22 0.05 0.25 0.02 0.30 0.18 0.35 0.25 0.49 0.21 0.39 0.22 0.58 0.58 1.05 0.86 0.77
N2 0.38 0.30 0.15 0.07 0.02 0.59 0.04 0.88 0.17 0.29 0.17 0.37 0.22 0.15 0.22 0.80 0.79 0.94 1.86 1.21
N3 0.41 0.28 0.32 0.14 0.18 0.61 0.19 0.90 0.06 0.27 0.11 0.39 0.35 0.37 0.36 0.94 0.92 0.98 1.86 1.33
N7 0.47 0.32 0.43 0.80 0.20 0.11 0.19 0.41 0.03 0.25 0.15 0.54 0.30 1.01 0.30 0.51 0.79 0.97 0.58 0.83
N9 0.44 0.25 0.55 0.45 0.26 0.51 0.28 0.70 0.07 0.21 0.13 0.41 0.48 0.74 0.37 1.03 0.88 0.89 1.44 1.19
O2' 1.64 1.39 0.77 1.32 1.10 2.34 1.23 2.99 1.51 1.55 1.21 1.38 0.46 0.82 0.89 2.61 3.10 3.16 4.06 3.58
O3' 0.78 0.55 0.25 0.25 0.51 1.47 0.67 2.26 0.78 0.70 0.48 0.54 0.56 0.30 0.42 1.74 2.93 3.87 3.83 3.95
O4' 0.58 0.45 1.60 1.21 0.54 0.11 0.69 0.47 0.72 0.58 0.44 0.35 1.76 1.60 0.51 0.36 0.99 1.38 1.80 1.65
O5' 1.64 1.37 2.79 2.71 0.65 1.54 0.55 0.87 0.86 1.30 1.04 1.64 3.01 3.40 0.43 0.94 0.38 0.91 1.14 0.93
O6 0.46 0.44 0.19 0.51 0.09 0.19 0.06 0.60 0.18 0.35 0.29 0.60 0.43 0.63 0.14 0.24 1.21 1.87 0.92 1.46
OP1 2.13 1.67 3.24 3.34 0.65 2.37 0.54 1.75 0.99 1.59 1.19 2.10 3.64 4.35 0.32 1.62 0.96 0.42 0.44 0.31
OP2 1.93 1.62 2.95 3.29 0.44 2.40 0.24 2.07 0.71 1.42 1.09 2.15 3.07 4.02 0.15 1.60 1.62 0.58 0.62 0.76
P 2.18 1.75 3.31 3.51 0.73 2.47 0.62 1.91 1.07 1.67 1.26 2.16 3.54 4.42 0.40 1.70 1.23 0.11 0.35 0.31

Atoms distances Chain-B - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6N1N3O2O2'O3'O4O4'O5'OP1OP2P
C1' 0.00 0.03 0.00 0.01 0.01 0.01 0.00 0.01 0.01 0.01 0.03 0.05 0.02 0.02 0.01 0.00 0.19 0.71 0.24 0.22
C2 0.03 0.00 0.12 0.23 0.01 0.35 0.01 0.54 0.01 0.00 0.00 0.00 0.25 0.20 0.01 0.33 1.08 1.89 0.54 1.20
C2' 0.00 0.12 0.00 0.00 0.02 0.01 0.09 0.01 0.12 0.02 0.08 0.21 0.00 0.03 0.01 0.00 0.26 0.50 0.16 0.23
C3' 0.01 0.23 0.00 0.00 0.11 0.01 0.35 0.03 0.39 0.06 0.13 0.51 0.02 0.00 0.10 0.00 0.31 0.30 0.13 0.22
C4 0.01 0.01 0.02 0.11 0.00 0.11 0.01 0.22 0.00 0.00 0.01 0.02 0.04 0.10 0.00 0.05 0.46 1.22 0.66 0.55
C4' 0.01 0.35 0.01 0.01 0.11 0.00 0.42 0.00 0.48 0.05 0.22 0.71 0.05 0.03 0.11 0.00 0.01 0.23 0.10 0.04
C5 0.00 0.01 0.09 0.35 0.01 0.42 0.00 0.71 0.00 0.00 0.01 0.01 0.24 0.30 0.00 0.30 0.30 0.57 1.35 0.55
C5' 0.01 0.54 0.01 0.03 0.22 0.00 0.71 0.00 0.76 0.10 0.36 1.15 0.05 0.06 0.22 0.01 0.01 0.07 0.06 0.02
C6 0.01 0.01 0.12 0.39 0.00 0.48 0.00 0.76 0.00 0.00 0.01 0.01 0.27 0.31 0.00 0.38 0.37 0.41 1.29 0.57
N1 0.01 0.00 0.02 0.06 0.00 0.05 0.00 0.10 0.00 0.00 0.00 0.01 0.02 0.04 0.01 0.02 0.35 0.97 0.40 0.38
N3 0.03 0.00 0.08 0.13 0.01 0.22 0.01 0.36 0.01 0.00 0.00 0.01 0.17 0.11 0.01 0.20 0.97 1.86 0.40 1.12
O2 0.05 0.00 0.21 0.51 0.02 0.71 0.01 1.15 0.01 0.01 0.01 0.00 0.48 0.43 0.02 0.63 1.71 2.64 1.35 1.97
O2' 0.02 0.25 0.00 0.02 0.04 0.05 0.24 0.05 0.27 0.02 0.17 0.48 0.00 0.05 0.04 0.03 0.07 0.34 0.10 0.08
O3' 0.02 0.20 0.03 0.00 0.10 0.03 0.30 0.06 0.31 0.04 0.11 0.43 0.05 0.00 0.09 0.02 0.21 0.05 0.12 0.12
O4 0.01 0.01 0.01 0.10 0.00 0.11 0.00 0.22 0.00 0.01 0.01 0.02 0.04 0.09 0.00 0.05 0.52 1.31 0.69 0.62
O4' 0.00 0.33 0.00 0.00 0.05 0.00 0.30 0.01 0.38 0.02 0.20 0.63 0.03 0.02 0.05 0.00 0.05 0.61 0.21 0.12
O5' 0.19 1.08 0.26 0.31 0.46 0.01 0.30 0.01 0.37 0.35 0.97 1.71 0.07 0.21 0.52 0.05 0.00 0.01 0.02 0.01
OP1 0.71 1.89 0.50 0.30 1.22 0.23 0.57 0.07 0.41 0.97 1.86 2.64 0.34 0.05 1.31 0.61 0.01 0.00 0.01 0.00
OP2 0.24 0.54 0.16 0.13 0.66 0.10 1.35 0.06 1.29 0.40 0.40 1.35 0.10 0.12 0.69 0.21 0.02 0.01 0.00 0.00
P 0.22 1.20 0.23 0.22 0.55 0.04 0.55 0.02 0.57 0.38 1.12 1.97 0.08 0.12 0.62 0.12 0.01 0.00 0.00 0.00