ClaRNA

Doublet Group distance statistics: 54272

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Distances from reference structure (by RMSD)

1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 3, 1, 0, 0, 0, 0, 0, 0, 0, 0,

RMS Distances matrix

Distances graph

Distances from reference structure (by atoms)

Atom Chain Distances
C5 A 0, 0.003, 0.005, 0.008, 0.008 max_d=0.008 avg_d=0.005 std_dev=0.003
N1 A 0, 0.007, 0.013, 0.019, 0.017 max_d=0.017 avg_d=0.013 std_dev=0.006
N3 A 0, 0.001, 0.007, 0.012, 0.018 max_d=0.018 avg_d=0.007 std_dev=0.006
C6 A 0, 0.005, 0.011, 0.017, 0.020 max_d=0.020 avg_d=0.011 std_dev=0.006
C4 A 0, 0.003, 0.010, 0.017, 0.022 max_d=0.022 avg_d=0.010 std_dev=0.007
C2 A 0, 0.002, 0.010, 0.018, 0.024 max_d=0.024 avg_d=0.010 std_dev=0.008
C1' A 0, 0.002, 0.013, 0.024, 0.033 max_d=0.033 avg_d=0.013 std_dev=0.011
O2 A 0, 0.009, 0.024, 0.040, 0.049 max_d=0.049 avg_d=0.024 std_dev=0.016
N4 A 0, 0.003, 0.027, 0.050, 0.075 max_d=0.075 avg_d=0.027 std_dev=0.023
O4' A 0, 0.013, 0.157, 0.301, 0.453 max_d=0.453 avg_d=0.157 std_dev=0.144
C2' A 0, -0.037, 0.170, 0.378, 0.618 max_d=0.618 avg_d=0.170 std_dev=0.208
C4' A 0, 0.059, 0.290, 0.521, 0.757 max_d=0.757 avg_d=0.290 std_dev=0.231
O2' A 0, 0.011, 0.298, 0.584, 0.913 max_d=0.913 avg_d=0.298 std_dev=0.287
C3' A 0, 0.027, 0.322, 0.618, 0.946 max_d=0.946 avg_d=0.322 std_dev=0.295
C5' A 0, 0.081, 0.490, 0.898, 1.329 max_d=1.329 avg_d=0.490 std_dev=0.409
O2' B 0, 0.210, 0.655, 1.100, 1.412 max_d=1.412 avg_d=0.655 std_dev=0.445
C3' B 0, 0.518, 0.992, 1.466, 1.391 max_d=1.391 avg_d=0.992 std_dev=0.474
O3' A 0, -0.017, 0.481, 0.979, 1.552 max_d=1.552 avg_d=0.481 std_dev=0.498
C2' B 0, 0.478, 0.987, 1.496, 1.401 max_d=1.401 avg_d=0.987 std_dev=0.509
O5' A 0, -0.052, 0.933, 1.918, 3.070 max_d=3.070 avg_d=0.933 std_dev=0.985
C4' B 0, 0.782, 1.776, 2.770, 3.387 max_d=3.387 avg_d=1.776 std_dev=0.994
O3' B 0, 0.024, 1.102, 2.180, 3.421 max_d=3.421 avg_d=1.102 std_dev=1.078
C1' B 0, 1.403, 2.560, 3.717, 3.205 max_d=3.205 avg_d=2.560 std_dev=1.157
OP1 A 0, -0.136, 1.063, 2.262, 3.687 max_d=3.687 avg_d=1.063 std_dev=1.199
C5' B 0, 0.568, 1.851, 3.134, 4.323 max_d=4.323 avg_d=1.851 std_dev=1.283
O4' B 0, 1.524, 2.833, 4.142, 3.983 max_d=3.983 avg_d=2.833 std_dev=1.309
O5' B 0, 1.441, 2.838, 4.234, 4.677 max_d=4.677 avg_d=2.838 std_dev=1.396
P A 0, -0.382, 1.139, 2.659, 4.503 max_d=4.503 avg_d=1.139 std_dev=1.521
N9 B 0, 2.097, 3.822, 5.547, 4.792 max_d=4.792 avg_d=3.822 std_dev=1.725
OP2 A 0, -0.326, 1.655, 3.635, 6.005 max_d=6.005 avg_d=1.655 std_dev=1.980
C8 B 0, 2.542, 4.612, 6.683, 5.668 max_d=5.668 avg_d=4.612 std_dev=2.071
P B 0, 2.009, 4.137, 6.265, 7.266 max_d=7.266 avg_d=4.137 std_dev=2.128
C4 B 0, 2.686, 4.871, 7.056, 5.999 max_d=5.999 avg_d=4.871 std_dev=2.185
N3 B 0, 2.766, 5.031, 7.296, 6.586 max_d=6.586 avg_d=5.031 std_dev=2.265
OP1 B 0, 1.631, 4.109, 6.587, 8.572 max_d=8.572 avg_d=4.109 std_dev=2.478
N7 B 0, 3.271, 5.934, 8.597, 7.317 max_d=7.317 avg_d=5.934 std_dev=2.663
OP2 B 0, 3.318, 6.006, 8.694, 7.299 max_d=7.299 avg_d=6.006 std_dev=2.688
C5 B 0, 3.330, 6.043, 8.757, 7.461 max_d=7.461 avg_d=6.043 std_dev=2.714
C2 B 0, 3.430, 6.275, 9.120, 8.552 max_d=8.552 avg_d=6.275 std_dev=2.845
N2 B 0, 3.583, 6.787, 9.991, 10.393 max_d=10.393 avg_d=6.787 std_dev=3.204
N1 B 0, 4.025, 7.299, 10.573, 9.296 max_d=9.296 avg_d=7.299 std_dev=3.274
C6 B 0, 4.058, 7.347, 10.636, 8.946 max_d=8.946 avg_d=7.347 std_dev=3.289
O6 B 0, 4.738, 8.578, 12.419, 10.452 max_d=10.452 avg_d=8.578 std_dev=3.841

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 0.00 0.02 0.01 0.01 0.02 0.01 0.01 0.02 0.02 0.03 0.01 0.02 0.00 0.19 0.25 0.38 0.06
C2 0.02 0.00 0.08 0.07 0.00 0.02 0.01 0.06 0.01 0.01 0.00 0.01 0.00 0.07 0.10 0.04 0.38 0.30 0.28 0.22
C2' 0.00 0.08 0.00 0.00 0.04 0.01 0.10 0.01 0.11 0.02 0.04 0.04 0.17 0.00 0.02 0.01 0.27 0.28 0.11 0.18
C3' 0.00 0.07 0.00 0.00 0.05 0.00 0.13 0.02 0.14 0.03 0.04 0.06 0.15 0.01 0.00 0.00 0.34 0.31 0.07 0.26
C4 0.02 0.00 0.04 0.05 0.00 0.05 0.00 0.11 0.00 0.01 0.00 0.00 0.01 0.04 0.06 0.03 0.53 0.40 0.14 0.46
C4' 0.01 0.02 0.01 0.00 0.05 0.00 0.07 0.00 0.07 0.03 0.02 0.06 0.04 0.05 0.01 0.00 0.01 0.18 0.35 0.05
C5 0.01 0.01 0.10 0.13 0.00 0.07 0.00 0.13 0.00 0.01 0.00 0.01 0.01 0.08 0.16 0.03 0.55 0.45 0.13 0.53
C5' 0.02 0.06 0.01 0.02 0.11 0.00 0.13 0.00 0.11 0.07 0.08 0.13 0.03 0.04 0.02 0.00 0.00 0.24 0.34 0.01
C6 0.01 0.01 0.11 0.14 0.00 0.07 0.00 0.11 0.00 0.00 0.00 0.01 0.01 0.08 0.16 0.04 0.48 0.41 0.16 0.41
N1 0.01 0.01 0.02 0.03 0.01 0.03 0.01 0.07 0.00 0.00 0.01 0.01 0.01 0.02 0.02 0.02 0.36 0.32 0.28 0.23
N3 0.02 0.00 0.04 0.04 0.00 0.02 0.00 0.08 0.00 0.01 0.00 0.01 0.00 0.04 0.06 0.04 0.46 0.34 0.20 0.33
N4 0.02 0.01 0.04 0.06 0.00 0.06 0.01 0.13 0.01 0.01 0.01 0.00 0.01 0.04 0.08 0.03 0.56 0.42 0.16 0.52
O2 0.03 0.00 0.17 0.15 0.01 0.04 0.01 0.03 0.01 0.01 0.00 0.01 0.00 0.15 0.21 0.06 0.29 0.24 0.35 0.12
O2' 0.01 0.07 0.00 0.01 0.04 0.05 0.08 0.04 0.08 0.02 0.04 0.04 0.15 0.00 0.05 0.03 0.11 0.22 0.20 0.05
O3' 0.02 0.10 0.02 0.00 0.06 0.01 0.16 0.02 0.16 0.02 0.06 0.08 0.21 0.05 0.00 0.01 0.26 0.27 0.20 0.24
O4' 0.00 0.04 0.01 0.00 0.03 0.00 0.03 0.00 0.04 0.02 0.04 0.03 0.06 0.03 0.01 0.00 0.03 0.18 0.57 0.10
O5' 0.19 0.38 0.27 0.34 0.53 0.01 0.55 0.00 0.48 0.36 0.46 0.56 0.29 0.11 0.26 0.03 0.00 0.01 0.00 0.00
OP1 0.25 0.30 0.28 0.31 0.40 0.18 0.45 0.24 0.41 0.32 0.34 0.42 0.24 0.22 0.27 0.18 0.01 0.00 0.00 0.00
OP2 0.38 0.28 0.11 0.07 0.14 0.35 0.13 0.34 0.16 0.28 0.20 0.16 0.35 0.20 0.20 0.57 0.00 0.00 0.00 0.00
P 0.06 0.22 0.18 0.26 0.46 0.05 0.53 0.01 0.41 0.23 0.33 0.52 0.12 0.05 0.24 0.10 0.00 0.00 0.00 0.00

Atoms distances Chain-A - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N2N3N7N9O2'O3'O4'O5'O6OP1OP2P
C1' 0.49 0.48 0.17 0.11 0.34 0.57 0.36 0.85 0.30 0.62 0.37 0.71 0.42 0.53 0.47 0.17 0.75 0.78 1.45 0.29 2.28 1.95 2.12
C2 0.36 1.32 0.16 0.10 0.58 0.47 0.47 0.62 0.74 0.48 1.14 1.77 1.05 0.34 0.32 0.18 0.55 0.55 0.97 0.68 2.08 1.30 1.64
C2' 0.71 0.31 0.43 0.31 0.49 1.03 0.51 1.39 0.40 0.76 0.29 0.37 0.37 0.68 0.65 0.35 0.32 1.13 2.04 0.40 2.98 2.73 2.86
C3' 0.89 0.74 0.51 0.40 0.85 1.21 0.86 1.61 0.82 0.93 0.76 0.67 0.79 0.91 0.89 0.33 0.29 1.38 2.28 0.83 2.96 2.85 3.00
C4 0.27 1.73 0.14 0.10 0.87 0.34 0.73 0.37 1.06 0.40 1.51 2.18 1.44 0.36 0.36 0.18 0.38 0.34 0.44 0.99 1.58 0.53 0.98
C4' 0.74 0.85 0.26 0.08 0.88 0.75 0.93 1.14 0.94 0.90 0.90 0.80 0.84 0.94 0.85 0.17 0.80 1.14 1.88 0.97 2.21 2.33 2.37
C5 0.32 1.12 0.14 0.11 0.55 0.35 0.43 0.39 0.62 0.45 0.93 1.41 0.97 0.33 0.30 0.15 0.51 0.43 0.47 0.55 1.49 0.54 0.96
C5' 0.84 1.33 0.25 0.13 1.23 0.65 1.27 1.00 1.35 1.06 1.37 1.31 1.26 1.18 1.07 0.14 0.97 1.23 1.64 1.37 1.67 1.87 1.88
C6 0.43 0.67 0.16 0.12 0.32 0.46 0.28 0.58 0.33 0.55 0.53 0.92 0.57 0.43 0.37 0.15 0.69 0.64 0.86 0.29 1.78 1.05 1.39
N1 0.42 0.82 0.16 0.11 0.36 0.50 0.30 0.69 0.40 0.55 0.66 1.14 0.67 0.42 0.37 0.17 0.67 0.66 1.10 0.35 2.08 1.44 1.73
N3 0.30 1.74 0.15 0.10 0.83 0.39 0.71 0.48 1.07 0.42 1.54 2.26 1.40 0.35 0.35 0.19 0.43 0.41 0.68 1.00 1.85 0.88 1.30
N4 0.24 2.21 0.13 0.10 1.17 0.25 1.04 0.24 1.46 0.36 1.99 2.72 1.82 0.50 0.50 0.19 0.22 0.21 0.21 1.38 1.33 0.28 0.66
O2 0.37 1.35 0.16 0.10 0.58 0.49 0.48 0.69 0.76 0.49 1.18 1.82 1.05 0.35 0.32 0.18 0.56 0.57 1.11 0.71 2.23 1.56 1.84
O2' 0.68 0.36 0.41 0.29 0.52 0.99 0.54 1.42 0.44 0.74 0.35 0.40 0.42 0.68 0.65 0.34 0.34 1.10 2.17 0.44 3.07 3.09 3.06
O3' 1.05 1.18 0.67 0.66 1.14 1.51 1.13 2.05 1.15 1.06 1.17 1.18 1.18 1.10 1.09 0.44 0.07 1.60 2.82 1.15 3.44 3.69 3.71
O4' 0.48 0.41 0.11 0.30 0.49 0.37 0.56 0.65 0.51 0.69 0.43 0.44 0.42 0.68 0.56 0.16 1.06 0.74 1.31 0.54 1.84 1.73 1.83
O5' 0.21 0.98 0.54 0.81 0.78 0.06 0.88 0.48 1.03 0.59 1.06 1.00 0.83 0.78 0.55 0.86 1.72 0.66 1.06 1.08 1.00 1.30 1.27
OP1 0.11 1.72 0.75 1.23 1.19 0.66 1.38 0.41 1.72 0.66 1.87 1.81 1.36 1.07 0.66 0.97 1.97 0.26 0.34 1.81 0.50 0.64 0.42
OP2 0.39 1.07 0.65 1.06 1.01 0.22 1.17 0.15 1.27 0.93 1.22 1.00 0.94 1.12 0.82 0.97 1.73 0.63 0.20 1.33 0.10 0.31 0.26
P 0.09 1.02 0.96 1.40 0.74 0.61 0.91 0.32 1.11 0.49 1.15 1.03 0.79 0.76 0.41 1.21 2.24 0.22 0.28 1.19 0.25 0.47 0.36

Atoms distances Chain-B - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N2N3N7N9O2'O3'O4'O5'O6OP1OP2P
C1' 0.00 0.03 0.00 0.01 0.01 0.00 0.01 0.07 0.02 0.00 0.03 0.03 0.02 0.01 0.00 0.01 0.20 0.00 0.37 0.02 0.34 0.63 0.26
C2 0.03 0.00 0.20 0.86 0.01 0.85 0.01 1.30 0.00 0.01 0.00 0.00 0.01 0.01 0.02 0.38 0.58 0.53 0.87 0.00 1.06 0.60 0.74
C2' 0.00 0.20 0.00 0.00 0.12 0.01 0.09 0.15 0.14 0.05 0.18 0.23 0.18 0.03 0.03 0.00 0.01 0.01 0.56 0.13 0.31 0.67 0.32
C3' 0.01 0.86 0.00 0.00 0.52 0.00 0.44 0.01 0.60 0.10 0.78 0.97 0.78 0.19 0.20 0.01 0.00 0.02 0.29 0.55 0.43 0.16 0.01
C4 0.01 0.01 0.12 0.52 0.00 0.41 0.00 0.51 0.01 0.00 0.01 0.01 0.01 0.00 0.01 0.27 0.28 0.26 0.24 0.01 0.41 0.78 0.34
C4' 0.00 0.85 0.01 0.00 0.41 0.00 0.24 0.00 0.41 0.27 0.68 1.05 0.80 0.11 0.06 0.22 0.02 0.00 0.01 0.33 0.57 0.10 0.21
C5 0.01 0.01 0.09 0.44 0.00 0.24 0.00 0.24 0.01 0.00 0.01 0.01 0.00 0.00 0.01 0.25 0.29 0.10 0.44 0.01 0.30 1.32 0.72
C5' 0.07 1.30 0.15 0.01 0.51 0.00 0.24 0.00 0.53 0.55 1.00 1.71 1.16 0.33 0.05 0.07 0.15 0.01 0.01 0.39 0.10 0.10 0.02
C6 0.02 0.00 0.14 0.60 0.01 0.41 0.01 0.53 0.00 0.01 0.00 0.00 0.00 0.01 0.01 0.30 0.44 0.21 0.27 0.00 0.31 1.11 0.55
C8 0.00 0.01 0.05 0.10 0.00 0.27 0.00 0.55 0.01 0.00 0.01 0.01 0.01 0.00 0.00 0.10 0.08 0.26 1.16 0.01 0.78 1.98 1.35
N1 0.03 0.00 0.18 0.78 0.01 0.68 0.01 1.00 0.00 0.01 0.00 0.00 0.01 0.01 0.02 0.36 0.56 0.39 0.53 0.00 0.68 0.61 0.42
N2 0.03 0.00 0.23 0.97 0.01 1.05 0.01 1.71 0.00 0.01 0.00 0.00 0.01 0.01 0.02 0.42 0.68 0.64 1.34 0.01 1.51 1.08 1.23
N3 0.02 0.01 0.18 0.78 0.01 0.80 0.00 1.16 0.00 0.01 0.01 0.01 0.00 0.01 0.01 0.36 0.45 0.54 0.75 0.00 1.01 0.51 0.66
N7 0.01 0.01 0.03 0.19 0.00 0.11 0.00 0.33 0.01 0.00 0.01 0.01 0.01 0.00 0.00 0.16 0.12 0.14 1.00 0.01 0.79 2.04 1.34
N9 0.00 0.02 0.03 0.20 0.01 0.06 0.01 0.05 0.01 0.00 0.02 0.02 0.01 0.00 0.00 0.14 0.03 0.01 0.55 0.01 0.19 1.11 0.61
O2' 0.01 0.38 0.00 0.01 0.27 0.22 0.25 0.07 0.30 0.10 0.36 0.42 0.36 0.16 0.14 0.00 0.03 0.13 0.24 0.28 0.79 0.31 0.18
O3' 0.20 0.58 0.01 0.00 0.28 0.02 0.29 0.15 0.44 0.08 0.56 0.68 0.45 0.12 0.03 0.03 0.00 0.14 0.20 0.44 0.96 0.43 0.47
O4' 0.00 0.53 0.01 0.02 0.26 0.00 0.10 0.01 0.21 0.26 0.39 0.64 0.54 0.14 0.01 0.13 0.14 0.00 0.16 0.14 0.38 0.33 0.14
O5' 0.37 0.87 0.56 0.29 0.24 0.01 0.44 0.01 0.27 1.16 0.53 1.34 0.75 1.00 0.55 0.24 0.20 0.16 0.00 0.37 0.00 0.01 0.00
O6 0.02 0.00 0.13 0.55 0.01 0.33 0.01 0.39 0.00 0.01 0.00 0.01 0.00 0.01 0.01 0.28 0.44 0.14 0.37 0.00 0.38 1.41 0.77
OP1 0.34 1.06 0.31 0.43 0.41 0.57 0.30 0.10 0.31 0.78 0.68 1.51 1.01 0.79 0.19 0.79 0.96 0.38 0.00 0.38 0.00 0.00 0.00
OP2 0.63 0.60 0.67 0.16 0.78 0.10 1.32 0.10 1.11 1.98 0.61 1.08 0.51 2.04 1.11 0.31 0.43 0.33 0.01 1.41 0.00 0.00 0.00
P 0.26 0.74 0.32 0.01 0.34 0.21 0.72 0.02 0.55 1.35 0.42 1.23 0.66 1.34 0.61 0.18 0.47 0.14 0.00 0.77 0.00 0.00 0.00