ClaRNA

Doublet Group distance statistics: 48772

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Distances from reference structure (by RMSD)

1, 0, 0, 0, 0, 0, 0, 2, 1, 1, 1, 2, 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, 0.004, 0.009, 0.014, 0.017 max_d=0.017 avg_d=0.009 std_dev=0.005
C4 A 0, 0.007, 0.014, 0.021, 0.023 max_d=0.023 avg_d=0.014 std_dev=0.007
N1 A 0, 0.003, 0.010, 0.017, 0.022 max_d=0.022 avg_d=0.010 std_dev=0.007
C6 A 0, 0.006, 0.013, 0.020, 0.022 max_d=0.022 avg_d=0.013 std_dev=0.007
C1' A 0, 0.008, 0.017, 0.027, 0.030 max_d=0.030 avg_d=0.017 std_dev=0.010
N3 A 0, 0.003, 0.013, 0.023, 0.031 max_d=0.031 avg_d=0.013 std_dev=0.010
C2 A 0, 0.008, 0.019, 0.030, 0.035 max_d=0.035 avg_d=0.019 std_dev=0.011
O2 A 0, 0.021, 0.045, 0.069, 0.074 max_d=0.074 avg_d=0.045 std_dev=0.024
O4 A 0, 0.030, 0.069, 0.108, 0.117 max_d=0.117 avg_d=0.069 std_dev=0.039
O4' A 0, 0.101, 0.213, 0.325, 0.415 max_d=0.415 avg_d=0.213 std_dev=0.112
C2' A 0, 0.068, 0.218, 0.369, 0.530 max_d=0.530 avg_d=0.218 std_dev=0.150
C4' A 0, 0.199, 0.494, 0.788, 0.897 max_d=0.897 avg_d=0.494 std_dev=0.294
OP2 B 0, 0.298, 0.600, 0.901, 0.985 max_d=0.985 avg_d=0.600 std_dev=0.302
C3' A 0, 0.414, 0.736, 1.059, 1.047 max_d=1.047 avg_d=0.736 std_dev=0.323
OP1 B 0, 0.497, 0.862, 1.228, 1.383 max_d=1.383 avg_d=0.862 std_dev=0.366
O2' A 0, 0.268, 0.699, 1.130, 1.276 max_d=1.276 avg_d=0.699 std_dev=0.431
P B 0, 0.366, 0.857, 1.347, 1.455 max_d=1.455 avg_d=0.857 std_dev=0.490
C5' A 0, 0.444, 0.963, 1.482, 1.645 max_d=1.645 avg_d=0.963 std_dev=0.519
O5' A 0, 0.790, 1.363, 1.937, 1.958 max_d=1.958 avg_d=1.363 std_dev=0.573
O3' A 0, 0.674, 1.446, 2.219, 2.266 max_d=2.266 avg_d=1.446 std_dev=0.772
P A 0, 1.365, 2.225, 3.085, 2.876 max_d=2.876 avg_d=2.225 std_dev=0.860
OP2 A 0, 0.629, 1.818, 3.006, 3.219 max_d=3.219 avg_d=1.818 std_dev=1.189
O5' B 0, 0.674, 2.098, 3.521, 3.858 max_d=3.858 avg_d=2.098 std_dev=1.423
OP1 A 0, 1.924, 3.448, 4.971, 4.883 max_d=4.883 avg_d=3.448 std_dev=1.524
C5' B 0, 1.023, 3.078, 5.134, 5.600 max_d=5.600 avg_d=3.078 std_dev=2.056
C4' B 0, 1.044, 4.154, 7.265, 8.045 max_d=8.045 avg_d=4.154 std_dev=3.110
O4' B 0, 1.316, 4.941, 8.565, 9.367 max_d=9.367 avg_d=4.941 std_dev=3.624
O3' B 0, 1.681, 5.596, 9.512, 10.422 max_d=10.422 avg_d=5.596 std_dev=3.916
C3' B 0, 0.640, 4.657, 8.675, 9.820 max_d=9.820 avg_d=4.657 std_dev=4.018
C1' B 0, 1.314, 6.021, 10.728, 11.848 max_d=11.848 avg_d=6.021 std_dev=4.707
C2' B 0, 0.900, 5.886, 10.871, 12.255 max_d=12.255 avg_d=5.886 std_dev=4.986
N9 B 0, 1.340, 6.397, 11.454, 12.473 max_d=12.473 avg_d=6.397 std_dev=5.057
C8 B 0, 1.896, 6.974, 12.051, 12.754 max_d=12.754 avg_d=6.974 std_dev=5.078
N3 B 0, 1.462, 6.727, 11.993, 13.177 max_d=13.177 avg_d=6.727 std_dev=5.265
C4 B 0, 1.354, 6.635, 11.916, 13.016 max_d=13.016 avg_d=6.635 std_dev=5.281
O2' B 0, 1.495, 6.789, 12.082, 13.560 max_d=13.560 avg_d=6.789 std_dev=5.294
N7 B 0, 1.872, 7.335, 12.799, 13.370 max_d=13.370 avg_d=7.335 std_dev=5.464
C2 B 0, 1.599, 7.152, 12.704, 13.822 max_d=13.822 avg_d=7.152 std_dev=5.552
C5 B 0, 1.383, 7.006, 12.629, 13.477 max_d=13.477 avg_d=7.006 std_dev=5.623
N1 B 0, 1.739, 7.455, 13.171, 14.215 max_d=14.215 avg_d=7.455 std_dev=5.716
C6 B 0, 1.570, 7.412, 13.254, 14.101 max_d=14.101 avg_d=7.412 std_dev=5.842
N2 B 0, 1.594, 7.436, 13.279, 14.219 max_d=14.219 avg_d=7.436 std_dev=5.842
O6 B 0, 1.606, 7.816, 14.027, 14.591 max_d=14.591 avg_d=7.816 std_dev=6.211

Atoms distances (summary)

atom dist matrix

Atoms distances Chain-A - Chain-A

Atom C1'C2C2'C3'C4C4'C5C5'C6N1N3O2O2'O3'O4O4'O5'OP1OP2P
C1' 0.00 0.02 0.00 0.01 0.01 0.01 0.01 0.09 0.01 0.00 0.02 0.02 0.02 0.32 0.01 0.00 0.22 0.51 0.35 0.29
C2 0.02 0.00 0.09 0.16 0.01 0.03 0.01 0.06 0.01 0.01 0.00 0.00 0.21 0.26 0.01 0.07 0.10 0.72 0.32 0.23
C2' 0.00 0.09 0.00 0.00 0.03 0.01 0.04 0.21 0.06 0.02 0.07 0.14 0.00 0.04 0.04 0.02 0.47 0.63 0.52 0.53
C3' 0.01 0.16 0.00 0.00 0.39 0.00 0.47 0.02 0.43 0.24 0.26 0.03 0.02 0.01 0.42 0.03 0.04 0.15 0.10 0.04
C4 0.01 0.01 0.03 0.39 0.00 0.15 0.01 0.12 0.01 0.01 0.01 0.01 0.36 0.15 0.00 0.03 0.17 0.90 0.50 0.19
C4' 0.01 0.03 0.01 0.00 0.15 0.00 0.22 0.01 0.22 0.08 0.07 0.09 0.32 0.03 0.16 0.00 0.02 0.17 0.27 0.03
C5 0.01 0.01 0.04 0.47 0.01 0.22 0.00 0.17 0.00 0.01 0.01 0.01 0.36 0.32 0.01 0.07 0.21 0.92 0.54 0.20
C5' 0.09 0.06 0.21 0.02 0.12 0.01 0.17 0.00 0.14 0.05 0.07 0.11 0.11 0.22 0.15 0.02 0.01 0.33 0.40 0.01
C6 0.01 0.01 0.06 0.43 0.01 0.22 0.00 0.14 0.00 0.00 0.02 0.01 0.29 0.27 0.01 0.08 0.14 0.82 0.41 0.22
N1 0.00 0.01 0.02 0.24 0.01 0.08 0.01 0.05 0.00 0.00 0.01 0.01 0.20 0.08 0.01 0.01 0.11 0.70 0.32 0.24
N3 0.02 0.00 0.07 0.26 0.01 0.07 0.01 0.07 0.02 0.01 0.00 0.01 0.30 0.11 0.01 0.05 0.09 0.83 0.39 0.20
O2 0.02 0.00 0.14 0.03 0.01 0.09 0.01 0.11 0.01 0.01 0.01 0.00 0.12 0.52 0.01 0.12 0.14 0.65 0.31 0.25
O2' 0.02 0.21 0.00 0.02 0.36 0.32 0.36 0.11 0.29 0.20 0.30 0.12 0.00 0.06 0.40 0.21 0.33 0.50 0.53 0.40
O3' 0.32 0.26 0.04 0.01 0.15 0.03 0.32 0.22 0.27 0.08 0.11 0.52 0.06 0.00 0.19 0.22 0.27 0.73 0.34 0.40
O4 0.01 0.01 0.04 0.42 0.00 0.16 0.01 0.15 0.01 0.01 0.01 0.01 0.40 0.19 0.00 0.04 0.21 0.94 0.59 0.20
O4' 0.00 0.07 0.02 0.03 0.03 0.00 0.07 0.02 0.08 0.01 0.05 0.12 0.21 0.22 0.04 0.00 0.07 0.22 0.32 0.12
O5' 0.22 0.10 0.47 0.04 0.17 0.02 0.21 0.01 0.14 0.11 0.09 0.14 0.33 0.27 0.21 0.07 0.00 0.02 0.01 0.00
OP1 0.51 0.72 0.63 0.15 0.90 0.17 0.92 0.33 0.82 0.70 0.83 0.65 0.50 0.73 0.94 0.22 0.02 0.00 0.01 0.00
OP2 0.35 0.32 0.52 0.10 0.50 0.27 0.54 0.40 0.41 0.32 0.39 0.31 0.53 0.34 0.59 0.32 0.01 0.01 0.00 0.00
P 0.29 0.23 0.53 0.04 0.19 0.03 0.20 0.01 0.22 0.24 0.20 0.25 0.40 0.40 0.20 0.12 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' 0.94 2.88 0.70 0.18 1.89 0.46 2.01 0.48 2.63 1.11 3.03 3.22 2.35 1.56 1.22 0.81 0.41 0.82 0.47 2.77 0.16 0.26 0.19
C2 0.68 2.88 0.53 0.18 1.61 0.44 1.47 0.51 2.05 0.63 2.75 3.39 2.32 0.92 0.83 0.53 0.39 0.67 0.43 1.95 0.14 0.23 0.15
C2' 0.85 2.36 0.64 0.57 1.65 0.35 1.84 0.56 2.30 1.29 2.52 2.63 1.94 1.65 1.18 0.73 0.68 0.73 0.46 2.48 0.16 0.17 0.25
C3' 0.82 2.47 0.54 0.38 1.64 0.38 1.82 0.46 2.35 1.17 2.62 2.82 2.00 1.58 1.10 0.65 0.62 0.75 0.50 2.58 0.20 0.18 0.29
C4 1.10 1.89 0.99 1.25 0.83 1.15 0.70 1.17 0.80 1.65 1.60 2.66 1.41 1.37 1.05 1.04 1.27 1.16 0.58 0.57 0.18 0.13 0.17
C4' 0.94 2.74 0.68 0.23 1.77 0.58 1.91 0.48 2.55 1.04 2.90 3.15 2.23 1.51 1.14 0.87 0.61 0.88 0.48 2.83 0.17 0.22 0.20
C5 1.16 1.81 1.12 1.39 0.94 1.19 0.90 1.19 0.90 1.76 1.58 2.51 1.36 1.58 1.16 1.12 1.39 1.17 0.55 0.77 0.18 0.13 0.14
C5' 0.69 2.39 0.50 0.47 1.33 0.64 1.38 0.64 2.01 0.70 2.46 2.90 1.89 1.07 0.73 0.72 0.78 0.75 0.43 2.25 0.19 0.22 0.20
C6 0.63 2.01 0.69 1.02 0.79 0.84 0.66 0.96 1.14 1.10 1.89 2.65 1.46 1.00 0.58 0.70 1.09 0.73 0.37 1.09 0.17 0.15 0.11
N1 0.50 2.57 0.41 0.47 1.34 0.49 1.27 0.65 1.89 0.66 2.55 3.08 1.99 0.88 0.63 0.49 0.63 0.56 0.36 1.88 0.16 0.20 0.13
N3 0.41 2.39 0.34 0.59 0.97 0.62 0.63 0.76 1.25 0.71 2.11 3.10 1.83 0.49 0.26 0.41 0.72 0.58 0.35 1.07 0.15 0.13 0.11
O2 1.40 3.48 1.17 0.47 2.45 0.75 2.37 0.42 2.85 1.38 3.39 3.79 3.01 1.79 1.69 1.10 0.32 1.24 0.71 2.73 0.14 0.31 0.24
O2' 0.98 2.33 0.77 0.81 1.85 0.42 2.18 0.76 2.61 1.58 2.63 2.44 1.95 2.03 1.42 0.89 1.00 0.73 0.26 2.90 0.40 0.53 0.24
O3' 0.73 2.35 0.35 0.58 1.56 0.55 1.80 0.66 2.35 1.08 2.55 2.68 1.90 1.56 1.01 0.48 0.96 0.70 0.36 2.66 0.40 0.44 0.32
O4 1.71 1.76 1.48 1.62 1.30 1.56 1.33 1.42 1.09 2.34 1.50 2.48 1.45 2.02 1.72 1.54 1.58 1.72 0.88 0.97 0.21 0.20 0.28
O4' 0.99 2.98 0.78 0.25 1.87 0.66 1.95 0.53 2.67 0.92 3.14 3.41 2.41 1.40 1.15 0.95 0.60 0.92 0.49 2.88 0.19 0.29 0.22
O5' 0.56 1.94 0.63 0.93 0.90 0.78 0.94 0.89 1.43 0.94 1.94 2.51 1.45 1.07 0.56 0.66 1.07 0.68 0.39 1.61 0.18 0.18 0.17
OP1 1.76 1.51 1.92 2.24 1.56 1.90 1.78 1.95 1.63 2.29 1.51 1.81 1.44 2.33 1.82 1.80 2.26 1.71 1.19 1.82 0.80 0.78 0.91
OP2 0.93 1.99 0.81 0.97 0.97 0.97 0.79 0.87 1.07 1.14 1.78 2.68 1.57 1.09 0.83 0.85 1.10 1.02 0.59 1.00 0.55 0.52 0.43
P 0.95 1.72 0.97 1.27 0.89 1.11 0.88 1.11 1.10 1.27 1.60 2.33 1.34 1.28 0.88 0.94 1.38 1.03 0.54 1.20 0.28 0.28 0.30

Atoms distances Chain-B - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N2N3N7N9O2'O3'O4'O5'O6OP1OP2P
C1' 0.00 0.02 0.00 0.01 0.01 0.01 0.01 0.10 0.02 0.00 0.02 0.03 0.02 0.01 0.00 0.03 0.35 0.00 0.15 0.02 0.18 0.17 0.20
C2 0.02 0.00 0.37 0.43 0.01 0.69 0.01 1.36 0.00 0.02 0.00 0.00 0.01 0.01 0.02 0.23 0.25 0.57 1.74 0.01 1.78 2.01 1.85
C2' 0.00 0.37 0.00 0.00 0.19 0.01 0.12 0.24 0.19 0.17 0.30 0.45 0.36 0.09 0.03 0.00 0.02 0.02 0.26 0.16 0.26 0.19 0.25
C3' 0.01 0.43 0.00 0.00 0.25 0.01 0.34 0.02 0.35 0.48 0.36 0.57 0.41 0.48 0.23 0.02 0.01 0.02 0.32 0.40 0.29 0.43 0.24
C4 0.01 0.01 0.19 0.25 0.00 0.26 0.00 0.56 0.01 0.01 0.01 0.01 0.01 0.01 0.00 0.10 0.12 0.29 0.85 0.01 0.83 0.88 0.87
C4' 0.01 0.69 0.01 0.01 0.26 0.00 0.06 0.01 0.20 0.44 0.48 0.91 0.66 0.32 0.07 0.31 0.01 0.00 0.02 0.11 0.25 0.19 0.11
C5 0.01 0.01 0.12 0.34 0.00 0.06 0.00 0.22 0.01 0.01 0.01 0.01 0.01 0.00 0.01 0.23 0.13 0.13 0.61 0.01 0.70 0.74 0.67
C5' 0.10 1.36 0.24 0.02 0.56 0.01 0.22 0.00 0.49 0.63 1.00 1.78 1.25 0.44 0.09 0.06 0.26 0.01 0.01 0.32 0.22 0.38 0.01
C6 0.02 0.00 0.19 0.35 0.01 0.20 0.01 0.49 0.00 0.01 0.00 0.01 0.01 0.01 0.01 0.19 0.19 0.24 0.91 0.01 0.98 1.10 0.99
C8 0.00 0.02 0.17 0.48 0.01 0.44 0.01 0.63 0.01 0.00 0.02 0.02 0.01 0.00 0.00 0.40 0.13 0.30 0.64 0.02 0.76 0.91 0.72
N1 0.02 0.00 0.30 0.36 0.01 0.48 0.01 1.00 0.00 0.02 0.00 0.01 0.01 0.01 0.02 0.15 0.21 0.43 1.42 0.01 1.48 1.71 1.54
N2 0.03 0.00 0.45 0.57 0.01 0.91 0.01 1.78 0.01 0.02 0.01 0.00 0.01 0.01 0.02 0.36 0.33 0.68 2.19 0.02 2.36 2.65 2.40
N3 0.02 0.01 0.36 0.41 0.01 0.66 0.01 1.25 0.01 0.01 0.01 0.01 0.00 0.01 0.01 0.23 0.25 0.56 1.54 0.01 1.51 1.62 1.57
N7 0.01 0.01 0.09 0.48 0.01 0.32 0.00 0.44 0.01 0.00 0.01 0.01 0.01 0.00 0.01 0.39 0.18 0.16 0.51 0.02 0.76 0.84 0.65
N9 0.00 0.02 0.03 0.23 0.00 0.07 0.01 0.09 0.01 0.00 0.02 0.02 0.01 0.01 0.00 0.19 0.11 0.01 0.31 0.02 0.34 0.40 0.35
O2' 0.03 0.23 0.00 0.02 0.10 0.31 0.23 0.06 0.19 0.40 0.15 0.36 0.23 0.39 0.19 0.00 0.02 0.21 0.19 0.24 0.27 0.32 0.18
O3' 0.35 0.25 0.02 0.01 0.12 0.01 0.13 0.26 0.19 0.13 0.21 0.33 0.25 0.18 0.11 0.02 0.00 0.25 0.38 0.25 0.48 0.64 0.32
O4' 0.00 0.57 0.02 0.02 0.29 0.00 0.13 0.01 0.24 0.30 0.43 0.68 0.56 0.16 0.01 0.21 0.25 0.00 0.09 0.17 0.20 0.08 0.17
O5' 0.15 1.74 0.26 0.32 0.85 0.02 0.61 0.01 0.91 0.64 1.42 2.19 1.54 0.51 0.31 0.19 0.38 0.09 0.00 0.79 0.02 0.01 0.01
O6 0.02 0.01 0.16 0.40 0.01 0.11 0.01 0.32 0.01 0.02 0.01 0.02 0.01 0.02 0.02 0.24 0.25 0.17 0.79 0.00 0.93 1.02 0.88
OP1 0.18 1.78 0.26 0.29 0.83 0.25 0.70 0.22 0.98 0.76 1.48 2.36 1.51 0.76 0.34 0.27 0.48 0.20 0.02 0.93 0.00 0.01 0.00
OP2 0.17 2.01 0.19 0.43 0.88 0.19 0.74 0.38 1.10 0.91 1.71 2.65 1.62 0.84 0.40 0.32 0.64 0.08 0.01 1.02 0.01 0.00 0.00
P 0.20 1.85 0.25 0.24 0.87 0.11 0.67 0.01 0.99 0.72 1.54 2.40 1.57 0.65 0.35 0.18 0.32 0.17 0.01 0.88 0.00 0.00 0.00