ClaRNA

Doublet Group distance statistics: 48184

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Distances from reference structure (by RMSD)

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

RMS Distances matrix

Distances graph

Distances from reference structure (by atoms)

Atom Chain Distances
C4 A 0, 0.001, 0.005, 0.009, 0.009 max_d=0.009 avg_d=0.005 std_dev=0.004
N3 A 0, -0.001, 0.005, 0.010, 0.013 max_d=0.013 avg_d=0.005 std_dev=0.006
C2 A 0, 0.002, 0.008, 0.014, 0.016 max_d=0.016 avg_d=0.008 std_dev=0.006
C1' A 0, 0.000, 0.009, 0.017, 0.020 max_d=0.020 avg_d=0.009 std_dev=0.009
C6 A 0, -0.001, 0.008, 0.018, 0.021 max_d=0.021 avg_d=0.008 std_dev=0.009
C5 A 0, -0.002, 0.009, 0.021, 0.025 max_d=0.025 avg_d=0.009 std_dev=0.011
N1 A 0, -0.002, 0.011, 0.025, 0.030 max_d=0.030 avg_d=0.011 std_dev=0.013
N4 A 0, 0.002, 0.019, 0.036, 0.042 max_d=0.042 avg_d=0.019 std_dev=0.017
O2 A 0, 0.003, 0.031, 0.058, 0.067 max_d=0.067 avg_d=0.031 std_dev=0.028
O4' A 0, -0.009, 0.052, 0.112, 0.137 max_d=0.137 avg_d=0.052 std_dev=0.061
C4' A 0, -0.023, 0.077, 0.177, 0.219 max_d=0.219 avg_d=0.077 std_dev=0.100
C2' A 0, -0.030, 0.090, 0.209, 0.258 max_d=0.258 avg_d=0.090 std_dev=0.119
C5' A 0, -0.056, 0.159, 0.373, 0.462 max_d=0.462 avg_d=0.159 std_dev=0.214
O2' A 0, -0.051, 0.173, 0.396, 0.488 max_d=0.488 avg_d=0.173 std_dev=0.223
C3' A 0, -0.059, 0.168, 0.396, 0.490 max_d=0.490 avg_d=0.168 std_dev=0.227
O3' A 0, -0.116, 0.322, 0.759, 0.940 max_d=0.940 avg_d=0.322 std_dev=0.437
C1' B 0, -0.116, 0.357, 0.829, 1.024 max_d=1.024 avg_d=0.357 std_dev=0.472
C2' B 0, -0.132, 0.394, 0.919, 1.136 max_d=1.136 avg_d=0.394 std_dev=0.525
N9 B 0, -0.169, 0.493, 1.154, 1.427 max_d=1.427 avg_d=0.493 std_dev=0.661
O2' B 0, -0.219, 0.598, 1.415, 1.753 max_d=1.753 avg_d=0.598 std_dev=0.817
O3' B 0, -0.219, 0.627, 1.474, 1.825 max_d=1.825 avg_d=0.627 std_dev=0.847
C3' B 0, -0.231, 0.648, 1.526, 1.890 max_d=1.890 avg_d=0.648 std_dev=0.878
O4' B 0, -0.309, 0.838, 1.984, 2.459 max_d=2.459 avg_d=0.838 std_dev=1.147
O5' A 0, -0.318, 0.833, 1.985, 2.462 max_d=2.462 avg_d=0.833 std_dev=1.151
C4' B 0, -0.327, 0.868, 2.063, 2.557 max_d=2.557 avg_d=0.868 std_dev=1.195
C4 B 0, -0.366, 0.967, 2.300, 2.851 max_d=2.851 avg_d=0.967 std_dev=1.333
C8 B 0, -0.376, 0.997, 2.370, 2.939 max_d=2.939 avg_d=0.997 std_dev=1.373
N7 B 0, -0.381, 1.013, 2.407, 2.984 max_d=2.984 avg_d=1.013 std_dev=1.394
C5 B 0, -0.394, 1.040, 2.473, 3.067 max_d=3.067 avg_d=1.040 std_dev=1.433
P A 0, -0.411, 1.039, 2.488, 3.089 max_d=3.089 avg_d=1.039 std_dev=1.450
OP2 A 0, -0.456, 1.159, 2.775, 3.444 max_d=3.444 avg_d=1.159 std_dev=1.615
OP1 A 0, -0.471, 1.166, 2.803, 3.481 max_d=3.481 avg_d=1.166 std_dev=1.637
C5' B 0, -0.557, 1.432, 3.420, 4.244 max_d=4.244 avg_d=1.432 std_dev=1.988
C6 B 0, -0.642, 1.645, 3.933, 4.880 max_d=4.880 avg_d=1.645 std_dev=2.287
N3 B 0, -0.652, 1.662, 3.976, 4.935 max_d=4.935 avg_d=1.662 std_dev=2.314
N6 B 0, -0.679, 1.736, 4.151, 5.151 max_d=5.151 avg_d=1.736 std_dev=2.415
O5' B 0, -0.797, 2.000, 4.797, 5.956 max_d=5.956 avg_d=2.000 std_dev=2.797
N1 B 0, -0.916, 2.310, 5.537, 6.873 max_d=6.873 avg_d=2.310 std_dev=3.226
C2 B 0, -0.920, 2.313, 5.545, 6.883 max_d=6.883 avg_d=2.313 std_dev=3.232
P B 0, -1.185, 2.928, 7.041, 8.744 max_d=8.744 avg_d=2.928 std_dev=4.113
OP2 B 0, -1.250, 3.088, 7.426, 9.223 max_d=9.223 avg_d=3.088 std_dev=4.338
OP1 B 0, -1.472, 3.624, 8.720, 10.831 max_d=10.831 avg_d=3.624 std_dev=5.096

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 0.00 0.00 0.03 0.01 0.01 0.02 0.01 0.01 0.01 0.00 0.02 0.02 0.00 0.00 0.00 0.39 0.40 0.25 0.39
C2 0.00 0.00 0.01 0.06 0.01 0.02 0.01 0.01 0.01 0.00 0.00 0.01 0.00 0.06 0.06 0.02 0.69 0.71 0.71 0.74
C2' 0.00 0.01 0.00 0.01 0.04 0.01 0.07 0.01 0.07 0.04 0.01 0.05 0.06 0.00 0.01 0.00 0.26 0.26 0.08 0.23
C3' 0.03 0.06 0.01 0.00 0.13 0.00 0.17 0.00 0.16 0.10 0.08 0.15 0.01 0.01 0.01 0.02 0.19 0.22 0.08 0.14
C4 0.01 0.01 0.04 0.13 0.00 0.04 0.00 0.00 0.00 0.00 0.01 0.01 0.02 0.00 0.18 0.02 0.94 1.03 1.08 1.04
C4' 0.01 0.02 0.01 0.00 0.04 0.00 0.05 0.01 0.05 0.03 0.02 0.06 0.01 0.08 0.02 0.00 0.01 0.16 0.21 0.03
C5 0.02 0.01 0.07 0.17 0.00 0.05 0.00 0.00 0.00 0.00 0.01 0.01 0.02 0.05 0.23 0.02 0.98 1.06 1.06 1.06
C5' 0.01 0.01 0.01 0.00 0.00 0.01 0.00 0.00 0.00 0.01 0.01 0.02 0.02 0.08 0.04 0.00 0.00 0.30 0.40 0.01
C6 0.01 0.01 0.07 0.16 0.00 0.05 0.00 0.00 0.00 0.00 0.00 0.01 0.01 0.05 0.20 0.01 0.87 0.88 0.77 0.87
N1 0.01 0.00 0.04 0.10 0.00 0.03 0.00 0.01 0.00 0.00 0.01 0.01 0.01 0.01 0.10 0.01 0.67 0.67 0.58 0.68
N3 0.00 0.00 0.01 0.08 0.01 0.02 0.01 0.01 0.00 0.01 0.00 0.01 0.01 0.05 0.11 0.02 0.82 0.87 0.92 0.90
N4 0.02 0.01 0.05 0.15 0.01 0.06 0.01 0.02 0.01 0.01 0.01 0.00 0.02 0.01 0.22 0.03 1.00 1.16 1.23 1.15
O2 0.02 0.00 0.06 0.01 0.02 0.01 0.02 0.02 0.01 0.01 0.01 0.02 0.00 0.13 0.04 0.01 0.55 0.56 0.59 0.61
O2' 0.00 0.06 0.00 0.01 0.00 0.08 0.05 0.08 0.05 0.01 0.05 0.01 0.13 0.00 0.04 0.04 0.10 0.11 0.03 0.10
O3' 0.00 0.06 0.01 0.01 0.18 0.02 0.23 0.04 0.20 0.10 0.11 0.22 0.04 0.04 0.00 0.02 0.09 0.02 0.27 0.09
O4' 0.00 0.02 0.00 0.02 0.02 0.00 0.02 0.00 0.01 0.01 0.02 0.03 0.01 0.04 0.02 0.00 0.29 0.35 0.11 0.30
O5' 0.39 0.69 0.26 0.19 0.94 0.01 0.98 0.00 0.87 0.67 0.82 1.00 0.55 0.10 0.09 0.29 0.00 0.00 0.02 0.01
OP1 0.40 0.71 0.26 0.22 1.03 0.16 1.06 0.30 0.88 0.67 0.87 1.16 0.56 0.11 0.02 0.35 0.00 0.00 0.00 0.00
OP2 0.25 0.71 0.08 0.08 1.08 0.21 1.06 0.40 0.77 0.58 0.92 1.23 0.59 0.03 0.27 0.11 0.02 0.00 0.00 0.01
P 0.39 0.74 0.23 0.14 1.04 0.03 1.06 0.01 0.87 0.68 0.90 1.15 0.61 0.10 0.09 0.30 0.01 0.00 0.01 0.00

Atoms distances Chain-A - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N3N6N7N9O2'O3'O4'O5'OP1OP2P
C1' 0.11 1.30 0.48 0.40 0.78 0.09 0.80 0.10 1.09 0.23 1.31 1.04 1.10 0.49 0.38 0.27 0.42 0.16 0.51 0.91 1.53 1.09
C2 0.16 0.76 0.47 0.28 0.53 0.13 0.56 0.23 0.70 0.27 0.78 0.63 0.72 0.41 0.32 0.46 0.28 0.14 0.67 1.17 1.98 1.42
C2' 0.13 1.67 0.55 0.39 0.93 0.17 0.91 0.24 1.27 0.16 1.63 1.34 1.25 0.46 0.41 0.38 0.40 0.23 0.69 1.28 1.74 1.32
C3' 0.20 2.00 0.64 0.54 1.13 0.04 1.10 0.06 1.54 0.23 1.96 1.61 1.51 0.58 0.53 0.35 0.55 0.14 0.46 0.94 1.28 0.95
C4 0.20 0.40 0.44 0.24 0.39 0.07 0.45 0.16 0.48 0.35 0.45 0.35 0.53 0.42 0.32 0.49 0.20 0.04 0.50 0.83 1.71 1.15
C4' 0.10 1.75 0.50 0.52 1.00 0.01 1.03 0.07 1.43 0.24 1.77 1.38 1.45 0.58 0.45 0.11 0.54 0.13 0.26 0.53 0.95 0.65
C5 0.18 0.72 0.47 0.37 0.56 0.02 0.61 0.02 0.72 0.35 0.76 0.61 0.76 0.50 0.37 0.30 0.35 0.04 0.30 0.51 1.22 0.78
C5' 0.02 1.76 0.40 0.52 0.98 0.01 1.03 0.16 1.46 0.20 1.80 1.36 1.49 0.57 0.40 0.11 0.54 0.14 0.10 0.20 0.54 0.32
C6 0.14 1.04 0.47 0.40 0.69 0.04 0.73 0.02 0.93 0.30 1.06 0.86 0.95 0.51 0.39 0.24 0.40 0.09 0.34 0.60 1.24 0.82
N1 0.13 1.03 0.47 0.35 0.66 0.10 0.69 0.13 0.90 0.26 1.05 0.84 0.92 0.46 0.36 0.33 0.36 0.14 0.53 0.92 1.62 1.13
N3 0.19 0.46 0.44 0.21 0.39 0.13 0.44 0.26 0.50 0.30 0.50 0.39 0.53 0.39 0.30 0.53 0.19 0.10 0.68 1.15 2.06 1.45
N4 0.25 0.02 0.39 0.14 0.21 0.04 0.30 0.19 0.24 0.40 0.11 0.04 0.31 0.40 0.29 0.56 0.04 0.04 0.48 0.76 1.71 1.14
O2 0.15 0.76 0.47 0.26 0.52 0.16 0.54 0.29 0.69 0.24 0.78 0.63 0.71 0.38 0.31 0.50 0.27 0.16 0.78 1.38 2.19 1.61
O2' 0.13 1.73 0.54 0.38 0.96 0.19 0.94 0.27 1.34 0.17 1.71 1.37 1.32 0.48 0.42 0.37 0.39 0.25 0.75 1.38 1.83 1.41
O3' 0.33 2.43 0.76 0.64 1.39 0.03 1.34 0.01 1.86 0.32 2.38 1.96 1.81 0.71 0.68 0.47 0.62 0.04 0.41 0.98 1.19 0.90
O4' 0.11 1.37 0.46 0.50 0.83 0.02 0.89 0.10 1.19 0.29 1.42 1.08 1.23 0.57 0.41 0.12 0.52 0.09 0.24 0.45 1.03 0.67
O5' 1.00 2.69 1.41 1.55 1.92 1.04 1.91 1.18 2.32 1.07 2.68 2.34 2.29 1.41 1.34 0.88 1.55 0.86 0.93 0.78 0.52 0.72
OP1 1.34 3.41 1.69 1.94 2.48 1.44 2.53 1.67 3.06 1.50 3.48 2.93 3.06 1.93 1.77 1.00 1.88 1.26 1.53 1.53 1.50 1.53
OP2 1.21 2.65 1.62 1.93 2.06 1.44 2.03 1.66 2.35 1.27 2.64 2.39 2.30 1.57 1.53 0.92 1.91 1.20 1.51 1.52 1.40 1.48
P 1.16 2.84 1.55 1.83 2.11 1.34 2.13 1.56 2.53 1.29 2.86 2.48 2.51 1.64 1.53 0.89 1.82 1.12 1.39 1.41 1.25 1.35

Atoms distances Chain-B - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N3N6N7N9O2'O3'O4'O5'OP1OP2P
C1' 0.00 0.08 0.01 0.00 0.03 0.00 0.02 0.02 0.03 0.01 0.07 0.07 0.01 0.00 0.01 0.01 0.04 0.00 0.12 0.06 0.24 0.19
C2 0.08 0.00 0.26 0.80 0.02 0.77 0.01 1.19 0.01 0.00 0.00 0.01 0.00 0.02 0.02 0.04 0.77 0.47 0.77 0.51 0.29 0.30
C2' 0.01 0.26 0.00 0.00 0.11 0.01 0.03 0.01 0.09 0.11 0.19 0.27 0.03 0.08 0.01 0.00 0.03 0.00 0.11 0.21 0.16 0.15
C3' 0.00 0.80 0.00 0.00 0.31 0.01 0.05 0.00 0.23 0.45 0.56 0.80 0.07 0.33 0.05 0.01 0.00 0.01 0.12 0.37 0.16 0.16
C4 0.03 0.02 0.11 0.31 0.00 0.33 0.00 0.51 0.01 0.01 0.03 0.00 0.00 0.01 0.01 0.02 0.27 0.23 0.15 0.05 0.77 0.29
C4' 0.00 0.77 0.01 0.01 0.33 0.00 0.10 0.00 0.27 0.41 0.57 0.75 0.11 0.28 0.02 0.07 0.02 0.01 0.01 0.04 0.30 0.13
C5 0.02 0.01 0.03 0.05 0.00 0.10 0.00 0.20 0.00 0.01 0.01 0.02 0.01 0.01 0.01 0.02 0.02 0.08 0.19 0.48 1.39 0.80
C5' 0.02 1.19 0.01 0.00 0.51 0.00 0.20 0.00 0.46 0.56 0.92 1.11 0.24 0.38 0.02 0.07 0.04 0.02 0.00 0.28 0.10 0.02
C6 0.03 0.01 0.09 0.23 0.01 0.27 0.00 0.46 0.00 0.01 0.00 0.01 0.00 0.02 0.01 0.01 0.19 0.18 0.04 0.32 1.32 0.63
C8 0.01 0.00 0.11 0.45 0.01 0.41 0.01 0.56 0.01 0.00 0.01 0.00 0.04 0.00 0.00 0.08 0.41 0.28 0.88 1.01 1.77 1.37
N1 0.07 0.00 0.19 0.56 0.03 0.57 0.01 0.92 0.00 0.01 0.00 0.01 0.01 0.01 0.03 0.01 0.53 0.36 0.49 0.17 0.78 0.10
N3 0.07 0.01 0.27 0.80 0.00 0.75 0.02 1.11 0.01 0.00 0.01 0.00 0.01 0.02 0.02 0.05 0.74 0.47 0.70 0.49 0.16 0.32
N6 0.01 0.00 0.03 0.07 0.00 0.11 0.01 0.24 0.00 0.04 0.01 0.01 0.00 0.04 0.01 0.02 0.02 0.08 0.20 0.65 1.73 0.98
N7 0.00 0.02 0.08 0.33 0.01 0.28 0.01 0.38 0.02 0.00 0.01 0.02 0.04 0.00 0.00 0.06 0.34 0.16 0.75 1.05 1.99 1.43
N9 0.01 0.02 0.01 0.05 0.01 0.02 0.01 0.02 0.01 0.00 0.03 0.02 0.01 0.00 0.00 0.02 0.04 0.00 0.26 0.34 0.90 0.59
O2' 0.01 0.04 0.00 0.01 0.02 0.07 0.02 0.07 0.01 0.08 0.01 0.05 0.02 0.06 0.02 0.00 0.08 0.04 0.06 0.01 0.31 0.10
O3' 0.04 0.77 0.03 0.00 0.27 0.02 0.02 0.04 0.19 0.41 0.53 0.74 0.02 0.34 0.04 0.08 0.00 0.03 0.04 0.35 0.22 0.06
O4' 0.00 0.47 0.00 0.01 0.23 0.01 0.08 0.02 0.18 0.28 0.36 0.47 0.08 0.16 0.00 0.04 0.03 0.00 0.08 0.03 0.04 0.08
O5' 0.12 0.77 0.11 0.12 0.15 0.01 0.19 0.00 0.04 0.88 0.49 0.70 0.20 0.75 0.26 0.06 0.04 0.08 0.00 0.01 0.03 0.01
OP1 0.06 0.51 0.21 0.37 0.05 0.04 0.48 0.28 0.32 1.01 0.17 0.49 0.65 1.05 0.34 0.01 0.35 0.03 0.01 0.00 0.00 0.00
OP2 0.24 0.29 0.16 0.16 0.77 0.30 1.39 0.10 1.32 1.77 0.78 0.16 1.73 1.99 0.90 0.31 0.22 0.04 0.03 0.00 0.00 0.00
P 0.19 0.30 0.15 0.16 0.29 0.13 0.80 0.02 0.63 1.37 0.10 0.32 0.98 1.43 0.59 0.10 0.06 0.08 0.01 0.00 0.00 0.00