ClaRNA

Doublet Group distance statistics: 53034

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Distances from reference structure (by RMSD)

1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 2, 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, 0.002, 0.004, 0.007, 0.007 max_d=0.007 avg_d=0.004 std_dev=0.003
C6 A 0, 0.002, 0.007, 0.011, 0.011 max_d=0.011 avg_d=0.007 std_dev=0.004
C1' A 0, 0.004, 0.009, 0.015, 0.014 max_d=0.014 avg_d=0.009 std_dev=0.005
N3 A 0, 0.005, 0.014, 0.023, 0.023 max_d=0.023 avg_d=0.014 std_dev=0.009
N1 A 0, 0.005, 0.014, 0.022, 0.024 max_d=0.024 avg_d=0.014 std_dev=0.009
C5 A 0, 0.003, 0.012, 0.021, 0.023 max_d=0.023 avg_d=0.012 std_dev=0.009
C4 A 0, 0.006, 0.017, 0.027, 0.028 max_d=0.028 avg_d=0.017 std_dev=0.010
N9 A 0, 0.006, 0.017, 0.029, 0.029 max_d=0.029 avg_d=0.017 std_dev=0.011
N6 A 0, 0.003, 0.021, 0.039, 0.039 max_d=0.039 avg_d=0.021 std_dev=0.018
N7 A 0, 0.009, 0.027, 0.045, 0.049 max_d=0.049 avg_d=0.027 std_dev=0.018
C8 A 0, 0.012, 0.032, 0.052, 0.055 max_d=0.055 avg_d=0.032 std_dev=0.020
P B 0, 0.142, 0.577, 1.012, 1.029 max_d=1.029 avg_d=0.577 std_dev=0.435
OP2 B 0, 0.153, 0.669, 1.185, 1.291 max_d=1.291 avg_d=0.669 std_dev=0.516
OP1 B 0, 0.119, 0.642, 1.166, 1.380 max_d=1.380 avg_d=0.642 std_dev=0.524
O4' A 0, -0.102, 0.529, 1.160, 1.596 max_d=1.596 avg_d=0.529 std_dev=0.631
C2' A 0, -0.098, 0.564, 1.225, 1.679 max_d=1.679 avg_d=0.564 std_dev=0.662
O5' A 0, -0.036, 0.737, 1.511, 1.937 max_d=1.937 avg_d=0.737 std_dev=0.773
OP2 A 0, -0.061, 0.871, 1.802, 2.438 max_d=2.438 avg_d=0.871 std_dev=0.931
O2' A 0, 0.025, 0.986, 1.948, 2.422 max_d=2.422 avg_d=0.986 std_dev=0.961
C3' A 0, 0.039, 1.004, 1.969, 2.311 max_d=2.311 avg_d=1.004 std_dev=0.965
C4' A 0, -0.145, 0.838, 1.820, 2.437 max_d=2.437 avg_d=0.838 std_dev=0.983
P A 0, 0.148, 1.141, 2.133, 2.164 max_d=2.164 avg_d=1.141 std_dev=0.993
C5' A 0, -0.386, 1.036, 2.458, 3.484 max_d=3.484 avg_d=1.036 std_dev=1.422
O3' A 0, 0.105, 1.529, 2.953, 3.041 max_d=3.041 avg_d=1.529 std_dev=1.424
O5' B 0, 0.126, 1.875, 3.623, 3.840 max_d=3.840 avg_d=1.875 std_dev=1.749
OP1 A 0, 0.171, 1.928, 3.686, 4.254 max_d=4.254 avg_d=1.928 std_dev=1.757
C5' B 0, -0.013, 2.573, 5.160, 6.169 max_d=6.169 avg_d=2.573 std_dev=2.587
C4' B 0, 0.043, 3.789, 7.535, 8.426 max_d=8.426 avg_d=3.789 std_dev=3.746
O4' B 0, 0.102, 4.221, 8.340, 8.743 max_d=8.743 avg_d=4.221 std_dev=4.119
C3' B 0, 0.084, 4.476, 8.868, 9.716 max_d=9.716 avg_d=4.476 std_dev=4.392
C8 B 0, 0.073, 4.540, 9.007, 9.833 max_d=9.833 avg_d=4.540 std_dev=4.467
C2' B 0, 0.162, 4.944, 9.726, 10.062 max_d=10.062 avg_d=4.944 std_dev=4.782
C1' B 0, 0.149, 5.014, 9.880, 9.966 max_d=9.966 avg_d=5.014 std_dev=4.866
N7 B 0, 0.017, 5.014, 10.010, 11.145 max_d=11.145 avg_d=5.014 std_dev=4.997
N9 B 0, 0.130, 5.136, 10.141, 10.304 max_d=10.304 avg_d=5.136 std_dev=5.006
O3' B 0, 0.053, 5.246, 10.438, 11.865 max_d=11.865 avg_d=5.246 std_dev=5.193
O2' B 0, 0.253, 5.742, 11.231, 11.484 max_d=11.484 avg_d=5.742 std_dev=5.489
C5 B 0, 0.081, 5.966, 11.852, 12.453 max_d=12.453 avg_d=5.966 std_dev=5.886
C4 B 0, 0.121, 6.060, 11.999, 12.061 max_d=12.061 avg_d=6.060 std_dev=5.939
C6 B 0, 0.081, 6.899, 13.717, 14.364 max_d=14.364 avg_d=6.899 std_dev=6.818
N3 B 0, 0.120, 6.973, 13.827, 14.501 max_d=14.501 avg_d=6.973 std_dev=6.853
N6 B 0, 0.027, 7.002, 13.977, 15.352 max_d=15.352 avg_d=7.002 std_dev=6.975
C2 B 0, 0.118, 7.779, 15.440, 16.073 max_d=16.073 avg_d=7.779 std_dev=7.661
N1 B 0, 0.114, 7.799, 15.485, 15.509 max_d=15.509 avg_d=7.799 std_dev=7.686

Atoms distances (summary)

atom dist matrix

Atoms distances Chain-A - Chain-A

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N3N6N7N9O2'O3'O4'O5'OP1OP2P
C1' 0.00 0.01 0.01 0.00 0.01 0.01 0.01 0.07 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.02 0.31 0.00 0.28 0.41 0.14 0.27
C2 0.01 0.00 0.42 0.38 0.00 0.05 0.00 0.04 0.00 0.01 0.00 0.00 0.00 0.01 0.01 0.25 0.49 0.19 0.39 0.71 0.15 0.45
C2' 0.01 0.42 0.00 0.00 0.22 0.01 0.12 0.20 0.21 0.18 0.34 0.41 0.16 0.08 0.02 0.00 0.01 0.01 0.60 0.77 0.49 0.68
C3' 0.00 0.38 0.00 0.00 0.30 0.01 0.36 0.02 0.40 0.38 0.40 0.34 0.42 0.40 0.23 0.02 0.01 0.02 0.33 0.14 0.37 0.32
C4 0.01 0.00 0.22 0.30 0.00 0.05 0.01 0.03 0.01 0.01 0.01 0.00 0.01 0.01 0.00 0.18 0.24 0.11 0.39 0.64 0.15 0.41
C4' 0.01 0.05 0.01 0.01 0.05 0.00 0.10 0.01 0.09 0.16 0.06 0.05 0.11 0.15 0.07 0.31 0.02 0.00 0.01 0.17 0.17 0.03
C5 0.01 0.00 0.12 0.36 0.01 0.10 0.00 0.06 0.00 0.01 0.01 0.01 0.00 0.01 0.01 0.25 0.12 0.06 0.43 0.70 0.17 0.46
C5' 0.07 0.04 0.20 0.02 0.03 0.01 0.06 0.00 0.06 0.07 0.05 0.04 0.09 0.09 0.02 0.10 0.23 0.01 0.00 0.34 0.31 0.02
C6 0.01 0.00 0.21 0.40 0.01 0.09 0.00 0.06 0.00 0.01 0.00 0.01 0.00 0.01 0.01 0.24 0.22 0.10 0.45 0.74 0.16 0.50
C8 0.01 0.01 0.18 0.38 0.01 0.16 0.01 0.07 0.01 0.00 0.01 0.01 0.02 0.01 0.00 0.34 0.24 0.09 0.42 0.65 0.20 0.40
N1 0.01 0.00 0.34 0.40 0.01 0.06 0.01 0.05 0.00 0.01 0.00 0.01 0.00 0.01 0.01 0.22 0.37 0.15 0.42 0.74 0.15 0.49
N3 0.01 0.00 0.41 0.34 0.00 0.05 0.01 0.04 0.01 0.01 0.01 0.00 0.01 0.01 0.01 0.25 0.48 0.19 0.36 0.64 0.14 0.40
N6 0.01 0.00 0.16 0.42 0.01 0.11 0.00 0.09 0.00 0.02 0.00 0.01 0.00 0.01 0.01 0.27 0.20 0.07 0.46 0.76 0.18 0.52
N7 0.01 0.01 0.08 0.40 0.01 0.15 0.01 0.09 0.01 0.01 0.01 0.01 0.01 0.00 0.00 0.35 0.21 0.04 0.45 0.70 0.20 0.45
N9 0.01 0.01 0.02 0.23 0.00 0.07 0.01 0.02 0.01 0.00 0.01 0.01 0.01 0.00 0.00 0.19 0.08 0.02 0.37 0.57 0.16 0.36
O2' 0.02 0.25 0.00 0.02 0.18 0.31 0.25 0.10 0.24 0.34 0.22 0.25 0.27 0.35 0.19 0.00 0.02 0.22 0.32 0.69 0.26 0.48
O3' 0.31 0.49 0.01 0.01 0.24 0.02 0.12 0.23 0.22 0.24 0.37 0.48 0.20 0.21 0.08 0.02 0.00 0.22 0.26 0.24 0.56 0.22
O4' 0.00 0.19 0.01 0.02 0.11 0.00 0.06 0.01 0.10 0.09 0.15 0.19 0.07 0.04 0.02 0.22 0.22 0.00 0.03 0.31 0.10 0.09
O5' 0.28 0.39 0.60 0.33 0.39 0.01 0.43 0.00 0.45 0.42 0.42 0.36 0.46 0.45 0.37 0.32 0.26 0.03 0.00 0.03 0.03 0.01
OP1 0.41 0.71 0.77 0.14 0.64 0.17 0.70 0.34 0.74 0.65 0.74 0.64 0.76 0.70 0.57 0.69 0.24 0.31 0.03 0.00 0.01 0.01
OP2 0.14 0.15 0.49 0.37 0.15 0.17 0.17 0.31 0.16 0.20 0.15 0.14 0.18 0.20 0.16 0.26 0.56 0.10 0.03 0.01 0.00 0.01
P 0.27 0.45 0.68 0.32 0.41 0.03 0.46 0.02 0.50 0.40 0.49 0.40 0.52 0.45 0.36 0.48 0.22 0.09 0.01 0.01 0.01 0.00

Atoms distances Chain-A - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N3N6N7N9O2'O3'O4'O5'OP1OP2P
C1' 0.91 1.31 1.39 1.62 0.85 1.05 0.58 0.85 0.68 0.44 1.02 1.31 0.59 0.55 0.65 1.20 1.71 0.62 0.34 0.20 0.36 0.18
C2 0.62 0.84 0.69 0.70 0.74 0.52 0.88 0.60 0.85 1.06 0.80 0.82 0.98 1.13 0.76 0.36 0.45 0.62 0.15 0.28 0.29 0.26
C2' 0.82 0.84 1.29 1.42 0.46 0.90 0.18 0.47 0.08 0.44 0.44 0.91 0.37 0.55 0.41 1.40 1.62 0.63 0.72 0.38 0.32 0.52
C3' 1.23 1.37 1.71 1.85 0.93 1.27 0.47 0.77 0.52 0.33 0.97 1.42 0.17 0.20 0.80 1.84 2.13 0.93 0.88 0.43 0.18 0.45
C4 0.49 0.86 0.73 0.88 0.64 0.52 0.77 0.56 0.78 0.92 0.77 0.83 0.92 1.03 0.61 0.38 0.78 0.45 0.03 0.24 0.33 0.23
C4' 1.25 1.76 1.67 1.90 1.18 1.31 0.76 0.93 0.92 0.33 1.40 1.73 0.63 0.32 0.91 1.59 2.15 0.91 0.59 0.20 0.20 0.04
C5 0.66 0.85 0.38 0.42 0.89 0.34 1.14 0.43 1.12 1.32 0.95 0.79 1.31 1.44 0.94 0.19 0.28 0.75 0.22 0.31 0.33 0.27
C5' 1.02 1.61 1.40 1.64 1.00 1.09 0.62 0.77 0.79 0.18 1.27 1.55 0.54 0.24 0.72 1.31 1.88 0.71 0.50 0.17 0.17 0.04
C6 1.03 1.07 0.53 0.31 1.21 0.57 1.46 0.53 1.42 1.65 1.22 1.02 1.60 1.74 1.29 0.64 0.26 1.11 0.42 0.37 0.32 0.30
C8 0.41 0.82 0.59 0.81 0.64 0.40 0.85 0.46 0.86 1.00 0.79 0.76 1.05 1.14 0.62 0.29 0.81 0.44 0.08 0.25 0.35 0.23
N1 0.99 1.01 0.60 0.43 1.13 0.62 1.34 0.59 1.29 1.56 1.12 0.98 1.44 1.61 1.21 0.60 0.24 1.06 0.42 0.37 0.30 0.30
N3 0.60 0.95 0.96 1.09 0.65 0.71 0.63 0.71 0.66 0.73 0.77 0.94 0.72 0.83 0.56 0.63 0.97 0.47 0.15 0.22 0.31 0.22
N6 1.44 1.43 0.84 0.56 1.62 0.86 1.87 0.66 1.84 2.03 1.62 1.39 2.01 2.12 1.70 1.10 0.73 1.49 0.61 0.43 0.33 0.33
N7 0.62 0.84 0.30 0.41 0.88 0.27 1.16 0.38 1.15 1.33 0.96 0.76 1.36 1.46 0.92 0.17 0.40 0.72 0.22 0.30 0.34 0.26
N9 0.54 0.97 0.92 1.13 0.62 0.66 0.65 0.62 0.69 0.74 0.79 0.94 0.80 0.87 0.51 0.64 1.13 0.39 0.13 0.22 0.35 0.21
O2' 1.05 1.00 1.59 1.69 0.67 1.07 0.24 0.66 0.21 0.27 0.61 1.09 0.20 0.31 0.61 1.69 1.82 0.78 0.69 0.22 0.03 0.29
O3' 2.09 2.16 2.59 2.70 1.76 2.07 1.27 1.49 1.31 1.03 1.76 2.24 0.93 0.82 1.63 2.77 3.02 1.72 1.44 0.82 0.59 0.75
O4' 1.22 1.80 1.59 1.85 1.25 1.34 0.93 1.13 1.08 0.61 1.49 1.75 0.87 0.66 0.99 1.33 1.99 0.95 0.51 0.39 0.48 0.32
O5' 0.88 1.47 1.25 1.56 0.98 1.03 0.81 0.97 0.93 0.67 1.24 1.40 0.86 0.77 0.76 0.95 1.69 0.67 0.35 0.47 0.56 0.39
OP1 0.63 0.97 0.66 0.98 0.80 0.72 0.94 0.97 0.95 1.07 0.94 0.89 1.05 1.15 0.80 0.20 0.91 0.75 0.38 0.68 0.79 0.68
OP2 0.82 1.56 1.10 1.40 0.96 0.93 0.74 0.81 0.90 0.55 1.29 1.45 0.77 0.64 0.69 0.79 1.53 0.63 0.30 0.30 0.33 0.19
P 0.73 1.31 0.99 1.32 0.90 0.85 0.86 0.92 0.95 0.85 1.15 1.23 0.95 0.94 0.75 0.60 1.39 0.65 0.26 0.47 0.62 0.48

Atoms distances Chain-B - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N3N6N7N9O2'O3'O4'O5'OP1OP2P
C1' 0.00 0.08 0.00 0.01 0.03 0.01 0.01 0.02 0.02 0.03 0.06 0.07 0.01 0.01 0.00 0.01 0.36 0.00 0.17 0.18 0.20 0.05
C2 0.08 0.00 0.48 0.29 0.02 0.28 0.01 0.27 0.00 0.01 0.01 0.01 0.01 0.01 0.02 0.32 0.25 0.49 0.36 0.27 0.40 0.18
C2' 0.00 0.48 0.00 0.00 0.29 0.01 0.17 0.15 0.27 0.17 0.39 0.47 0.22 0.06 0.05 0.00 0.02 0.03 0.54 0.56 0.44 0.50
C3' 0.01 0.29 0.00 0.00 0.32 0.01 0.42 0.03 0.44 0.37 0.37 0.24 0.50 0.44 0.26 0.02 0.01 0.02 0.35 0.42 0.05 0.26
C4 0.03 0.02 0.29 0.32 0.00 0.06 0.00 0.10 0.01 0.01 0.03 0.00 0.01 0.00 0.00 0.02 0.15 0.24 0.31 0.21 0.48 0.21
C4' 0.01 0.28 0.01 0.01 0.06 0.00 0.15 0.01 0.09 0.40 0.14 0.29 0.20 0.36 0.13 0.30 0.02 0.00 0.01 0.15 0.29 0.03
C5 0.01 0.01 0.17 0.42 0.00 0.15 0.00 0.30 0.01 0.02 0.02 0.01 0.02 0.00 0.01 0.23 0.06 0.07 0.45 0.45 0.80 0.49
C5' 0.02 0.27 0.15 0.03 0.10 0.01 0.30 0.00 0.24 0.57 0.13 0.30 0.40 0.57 0.19 0.12 0.21 0.02 0.01 0.17 0.37 0.02
C6 0.02 0.00 0.27 0.44 0.01 0.09 0.01 0.24 0.00 0.02 0.01 0.01 0.00 0.01 0.01 0.13 0.09 0.17 0.44 0.43 0.86 0.47
C8 0.03 0.01 0.17 0.37 0.01 0.40 0.02 0.57 0.02 0.00 0.01 0.00 0.05 0.00 0.01 0.58 0.07 0.31 0.60 0.63 0.80 0.65
N1 0.06 0.01 0.39 0.37 0.03 0.14 0.02 0.13 0.01 0.01 0.00 0.01 0.02 0.01 0.02 0.12 0.16 0.36 0.37 0.25 0.64 0.27
N3 0.07 0.01 0.47 0.24 0.00 0.29 0.01 0.30 0.01 0.00 0.01 0.00 0.01 0.00 0.02 0.36 0.29 0.50 0.35 0.31 0.27 0.19
N6 0.01 0.01 0.22 0.50 0.01 0.20 0.02 0.40 0.00 0.05 0.02 0.01 0.00 0.05 0.03 0.24 0.13 0.08 0.54 0.65 1.09 0.67
N7 0.01 0.01 0.06 0.44 0.00 0.36 0.00 0.57 0.01 0.00 0.01 0.00 0.05 0.00 0.00 0.53 0.10 0.19 0.65 0.74 1.02 0.76
N9 0.00 0.02 0.05 0.26 0.00 0.13 0.01 0.19 0.01 0.01 0.02 0.02 0.03 0.00 0.00 0.22 0.13 0.01 0.31 0.25 0.43 0.25
O2' 0.01 0.32 0.00 0.02 0.02 0.30 0.23 0.12 0.13 0.58 0.12 0.36 0.24 0.53 0.22 0.00 0.02 0.21 0.29 0.34 0.50 0.34
O3' 0.36 0.25 0.02 0.01 0.15 0.02 0.06 0.21 0.09 0.07 0.16 0.29 0.13 0.10 0.13 0.02 0.00 0.22 0.25 0.43 0.28 0.28
O4' 0.00 0.49 0.03 0.02 0.24 0.00 0.07 0.02 0.17 0.31 0.36 0.50 0.08 0.19 0.01 0.21 0.22 0.00 0.08 0.04 0.41 0.16
O5' 0.17 0.36 0.54 0.35 0.31 0.01 0.45 0.01 0.44 0.60 0.37 0.35 0.54 0.65 0.31 0.29 0.25 0.08 0.00 0.01 0.02 0.00
OP1 0.18 0.27 0.56 0.42 0.21 0.15 0.45 0.17 0.43 0.63 0.25 0.31 0.65 0.74 0.25 0.34 0.43 0.04 0.01 0.00 0.01 0.00
OP2 0.20 0.40 0.44 0.05 0.48 0.29 0.80 0.37 0.86 0.80 0.64 0.27 1.09 1.02 0.43 0.50 0.28 0.41 0.02 0.01 0.00 0.01
P 0.05 0.18 0.50 0.26 0.21 0.03 0.49 0.02 0.47 0.65 0.27 0.19 0.67 0.76 0.25 0.34 0.28 0.16 0.00 0.00 0.01 0.00