ClaRNA

Doublet Group distance statistics: 48589

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Distances from reference structure (by RMSD)

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

RMS Distances matrix

Distances graph

Distances from reference structure (by atoms)

Atom Chain Distances
N3 A 0, 0.003, 0.010, 0.016, 0.018 max_d=0.018 avg_d=0.010 std_dev=0.007
C5 A 0, 0.004, 0.015, 0.026, 0.030 max_d=0.030 avg_d=0.015 std_dev=0.011
N1 A 0, 0.006, 0.026, 0.045, 0.056 max_d=0.056 avg_d=0.026 std_dev=0.020
C6 A 0, 0.010, 0.034, 0.058, 0.074 max_d=0.074 avg_d=0.034 std_dev=0.024
C2 A 0, 0.013, 0.037, 0.062, 0.075 max_d=0.075 avg_d=0.037 std_dev=0.024
C1' A 0, 0.012, 0.036, 0.061, 0.074 max_d=0.074 avg_d=0.036 std_dev=0.024
C4 A 0, 0.012, 0.037, 0.062, 0.076 max_d=0.076 avg_d=0.037 std_dev=0.025
O2 A 0, 0.030, 0.084, 0.139, 0.165 max_d=0.165 avg_d=0.084 std_dev=0.054
O4 A 0, 0.061, 0.148, 0.234, 0.269 max_d=0.269 avg_d=0.148 std_dev=0.087
O4' A 0, 0.119, 0.361, 0.604, 0.630 max_d=0.630 avg_d=0.361 std_dev=0.242
P B 0, 0.176, 0.475, 0.774, 0.880 max_d=0.880 avg_d=0.475 std_dev=0.299
C4' A 0, 0.168, 0.533, 0.899, 0.941 max_d=0.941 avg_d=0.533 std_dev=0.365
C2' A 0, 0.136, 0.511, 0.886, 0.904 max_d=0.904 avg_d=0.511 std_dev=0.375
OP2 B 0, 0.272, 0.682, 1.092, 1.107 max_d=1.107 avg_d=0.682 std_dev=0.410
OP1 B 0, 0.165, 0.599, 1.033, 1.162 max_d=1.162 avg_d=0.599 std_dev=0.434
O5' B 0, 0.314, 0.790, 1.266, 1.502 max_d=1.502 avg_d=0.790 std_dev=0.476
C3' A 0, 0.217, 0.700, 1.184, 1.291 max_d=1.291 avg_d=0.700 std_dev=0.483
C5' A 0, 0.271, 0.809, 1.346, 1.422 max_d=1.422 avg_d=0.809 std_dev=0.538
O2' A 0, 0.195, 1.004, 1.814, 1.799 max_d=1.799 avg_d=1.004 std_dev=0.810
O3' A 0, 0.390, 1.212, 2.035, 2.252 max_d=2.252 avg_d=1.212 std_dev=0.823
C5' B 0, 0.777, 1.661, 2.545, 2.504 max_d=2.504 avg_d=1.661 std_dev=0.884
O5' A 0, -0.012, 1.144, 2.301, 3.364 max_d=3.364 avg_d=1.144 std_dev=1.156
C4' B 0, 0.319, 1.544, 2.770, 3.691 max_d=3.691 avg_d=1.544 std_dev=1.225
O4' B 0, 0.370, 1.796, 3.222, 3.925 max_d=3.925 avg_d=1.796 std_dev=1.426
P A 0, -0.033, 1.525, 3.083, 4.502 max_d=4.502 avg_d=1.525 std_dev=1.558
OP2 A 0, 0.054, 1.668, 3.282, 4.744 max_d=4.744 avg_d=1.668 std_dev=1.614
OP1 A 0, -0.038, 1.593, 3.225, 4.720 max_d=4.720 avg_d=1.593 std_dev=1.632
C3' B 0, -0.684, 1.490, 3.663, 5.813 max_d=5.813 avg_d=1.490 std_dev=2.174
C1' B 0, -0.037, 2.163, 4.363, 6.374 max_d=6.374 avg_d=2.163 std_dev=2.200
N3 B 0, 2.046, 4.434, 6.822, 6.595 max_d=6.595 avg_d=4.434 std_dev=2.388
O3' B 0, -0.096, 2.426, 4.947, 7.312 max_d=7.312 avg_d=2.426 std_dev=2.522
N9 B 0, 0.638, 3.209, 5.781, 7.487 max_d=7.487 avg_d=3.209 std_dev=2.572
C2' B 0, -0.183, 2.530, 5.243, 7.791 max_d=7.791 avg_d=2.530 std_dev=2.713
C4 B 0, 1.098, 3.838, 6.579, 7.622 max_d=7.622 avg_d=3.838 std_dev=2.741
C2 B 0, 2.655, 5.709, 8.764, 8.051 max_d=8.051 avg_d=5.709 std_dev=3.055
C8 B 0, 1.692, 4.759, 7.826, 9.364 max_d=9.364 avg_d=4.759 std_dev=3.067
O2' B 0, 0.312, 3.633, 6.953, 9.877 max_d=9.877 avg_d=3.633 std_dev=3.320
N2 B 0, 3.303, 6.897, 10.491, 9.828 max_d=9.828 avg_d=6.897 std_dev=3.594
N7 B 0, 1.957, 5.612, 9.266, 10.722 max_d=10.722 avg_d=5.612 std_dev=3.655
C5 B 0, 1.157, 4.830, 8.504, 9.637 max_d=9.637 avg_d=4.830 std_dev=3.674
N1 B 0, 2.469, 6.221, 9.974, 9.381 max_d=9.381 avg_d=6.221 std_dev=3.753
C6 B 0, 1.507, 5.821, 10.135, 10.647 max_d=10.647 avg_d=5.821 std_dev=4.314
O6 B 0, 1.590, 6.844, 12.097, 12.672 max_d=12.672 avg_d=6.844 std_dev=5.254

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 0.03 0.00 0.01 0.02 0.00 0.01 0.08 0.01 0.01 0.02 0.06 0.02 0.28 0.02 0.01 0.43 0.66 0.17 0.11
C2 0.03 0.00 0.09 0.11 0.01 0.04 0.02 0.10 0.01 0.01 0.00 0.01 0.22 0.24 0.01 0.09 0.57 0.44 0.52 0.35
C2' 0.00 0.09 0.00 0.00 0.08 0.01 0.15 0.18 0.16 0.03 0.06 0.19 0.00 0.02 0.09 0.02 0.53 0.88 0.42 0.38
C3' 0.01 0.11 0.00 0.00 0.34 0.00 0.42 0.01 0.39 0.19 0.22 0.10 0.01 0.00 0.36 0.02 0.20 0.77 0.48 0.37
C4 0.02 0.01 0.08 0.34 0.00 0.10 0.00 0.08 0.01 0.01 0.00 0.01 0.31 0.20 0.00 0.03 0.77 0.11 0.96 0.76
C4' 0.00 0.04 0.01 0.00 0.10 0.00 0.14 0.01 0.13 0.06 0.05 0.11 0.27 0.02 0.10 0.00 0.01 0.68 0.42 0.36
C5 0.01 0.02 0.15 0.42 0.00 0.14 0.00 0.07 0.01 0.02 0.00 0.03 0.33 0.37 0.01 0.04 0.83 0.21 1.02 0.86
C5' 0.08 0.10 0.18 0.01 0.08 0.01 0.07 0.00 0.06 0.07 0.09 0.15 0.09 0.19 0.08 0.02 0.01 0.08 0.20 0.02
C6 0.01 0.01 0.16 0.39 0.01 0.13 0.01 0.06 0.00 0.01 0.01 0.02 0.28 0.31 0.01 0.06 0.79 0.11 0.81 0.70
N1 0.01 0.01 0.03 0.19 0.01 0.06 0.02 0.07 0.01 0.00 0.00 0.03 0.18 0.11 0.01 0.02 0.62 0.35 0.51 0.38
N3 0.02 0.00 0.06 0.22 0.00 0.05 0.00 0.09 0.01 0.00 0.00 0.00 0.26 0.12 0.01 0.07 0.66 0.25 0.73 0.53
O2 0.06 0.01 0.19 0.10 0.01 0.11 0.03 0.15 0.02 0.03 0.00 0.00 0.27 0.51 0.01 0.16 0.46 0.65 0.35 0.20
O2' 0.02 0.22 0.00 0.01 0.31 0.27 0.33 0.09 0.28 0.18 0.26 0.27 0.00 0.05 0.33 0.17 0.24 1.40 0.66 0.67
O3' 0.28 0.24 0.02 0.00 0.20 0.02 0.37 0.19 0.31 0.11 0.12 0.51 0.05 0.00 0.24 0.19 0.29 1.34 1.27 1.01
O4 0.02 0.01 0.09 0.36 0.00 0.10 0.01 0.08 0.01 0.01 0.01 0.01 0.33 0.24 0.00 0.04 0.80 0.17 1.07 0.85
O4' 0.01 0.09 0.02 0.02 0.03 0.00 0.04 0.02 0.06 0.02 0.07 0.16 0.17 0.19 0.04 0.00 0.27 0.48 0.06 0.03
O5' 0.43 0.57 0.53 0.20 0.77 0.01 0.83 0.01 0.79 0.62 0.66 0.46 0.24 0.29 0.80 0.27 0.00 0.01 0.01 0.01
OP1 0.66 0.44 0.88 0.77 0.11 0.68 0.21 0.08 0.11 0.35 0.25 0.65 1.40 1.34 0.17 0.48 0.01 0.00 0.01 0.00
OP2 0.17 0.52 0.42 0.48 0.96 0.42 1.02 0.20 0.81 0.51 0.73 0.35 0.66 1.27 1.07 0.06 0.01 0.01 0.00 0.01
P 0.11 0.35 0.38 0.37 0.76 0.36 0.86 0.02 0.70 0.38 0.53 0.20 0.67 1.01 0.85 0.03 0.01 0.00 0.01 0.00

Atoms distances Chain-A - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N2N3N7N9O2'O3'O4'O5'O6OP1OP2P
C1' 1.17 3.12 1.10 0.52 2.55 0.41 2.86 0.52 3.31 1.88 3.41 3.12 2.66 2.45 1.88 1.32 0.29 0.80 0.43 3.45 0.30 0.42 0.37
C2 0.77 2.74 0.20 0.55 2.23 0.85 2.77 0.93 3.32 1.70 3.24 2.68 2.21 2.43 1.55 0.65 0.83 0.88 0.35 3.62 0.35 0.26 0.31
C2' 1.02 2.98 1.08 0.62 2.30 0.09 2.60 0.32 3.13 1.62 3.27 3.09 2.47 2.19 1.63 1.39 0.68 0.52 0.22 3.33 0.16 0.45 0.32
C3' 1.03 2.66 1.22 0.78 2.08 0.31 2.29 0.58 2.69 1.49 2.84 2.80 2.27 1.94 1.53 1.53 0.87 0.56 0.62 2.83 0.51 1.06 0.87
C4 0.70 1.99 0.58 0.98 1.57 1.13 1.98 1.19 2.33 1.32 2.29 2.03 1.60 1.87 1.12 0.87 1.13 0.99 0.34 2.56 0.36 0.19 0.27
C4' 1.39 2.82 1.66 1.11 2.29 0.47 2.41 0.39 2.73 1.72 2.91 2.95 2.51 2.08 1.81 2.01 1.13 0.77 0.49 2.80 0.24 0.71 0.55
C5 0.50 1.84 0.22 0.30 1.51 0.72 1.82 0.90 2.08 1.27 2.07 1.84 1.52 1.70 1.10 0.73 0.44 0.72 0.34 2.23 0.34 0.29 0.33
C5' 1.52 2.45 1.93 1.48 2.06 0.68 2.07 0.38 2.28 1.59 2.45 2.58 2.27 1.81 1.73 2.32 1.66 0.85 0.44 2.30 0.18 0.65 0.43
C6 0.79 2.20 0.66 0.25 1.91 0.44 2.19 0.63 2.46 1.52 2.45 2.15 1.89 1.96 1.44 1.02 0.12 0.69 0.39 2.58 0.31 0.37 0.36
N1 0.89 2.70 0.62 0.19 2.28 0.55 2.67 0.69 3.08 1.73 3.06 2.63 2.27 2.33 1.66 0.94 0.20 0.77 0.38 3.24 0.32 0.34 0.35
N3 0.76 2.38 0.49 0.97 1.92 1.12 2.44 1.14 2.93 1.52 2.83 2.36 1.90 2.23 1.33 0.82 1.24 1.01 0.35 3.26 0.36 0.20 0.29
O2 0.81 3.02 0.26 0.60 2.37 0.87 2.96 0.93 3.67 1.76 3.62 2.99 2.39 2.55 1.61 0.62 0.92 0.90 0.35 4.08 0.36 0.25 0.31
O2' 1.17 3.49 1.18 0.64 2.60 0.16 2.94 0.23 3.58 1.82 3.82 3.70 2.86 2.45 1.85 1.38 0.61 0.65 0.22 3.83 0.39 0.29 0.20
O3' 1.02 2.73 1.27 0.81 2.04 0.35 2.22 0.68 2.66 1.41 2.87 2.95 2.30 1.85 1.48 1.65 0.96 0.54 0.70 2.80 0.68 1.31 1.07
O4 0.97 1.86 1.12 1.37 1.40 1.36 1.70 1.36 2.03 1.19 2.06 2.00 1.51 1.62 1.07 1.28 1.44 1.17 0.37 2.26 0.36 0.15 0.21
O4' 1.41 2.94 1.54 0.91 2.50 0.52 2.66 0.50 2.97 1.92 3.08 2.95 2.64 2.33 1.97 1.80 0.68 0.90 0.54 3.02 0.38 0.50 0.44
O5' 2.17 2.73 2.58 2.33 2.52 1.55 2.52 1.25 2.66 2.17 2.76 2.77 2.62 2.32 2.30 2.87 2.45 1.60 1.24 2.67 1.04 0.72 0.85
OP1 2.59 3.13 2.74 2.51 2.80 2.03 2.67 1.57 2.80 2.30 3.02 3.30 3.05 2.38 2.57 3.04 2.92 2.16 1.40 2.73 0.88 0.96 0.90
OP2 2.70 2.91 2.98 2.99 2.76 2.47 2.66 2.19 2.73 2.45 2.85 2.97 2.88 2.48 2.65 3.16 3.17 2.36 1.97 2.67 1.51 1.36 1.48
P 2.83 3.16 3.11 2.99 2.97 2.36 2.87 1.97 2.96 2.59 3.10 3.23 3.11 2.65 2.81 3.35 3.30 2.37 1.80 2.90 1.37 1.19 1.29

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 0.09 0.01 0.01 0.01 0.03 0.02 0.01 0.00 0.01 0.28 0.00 0.18 0.02 0.24 0.29 0.16
C2 0.02 0.00 0.42 0.44 0.01 0.39 0.00 0.68 0.00 0.01 0.00 0.00 0.00 0.00 0.01 0.33 0.17 0.36 0.53 0.00 0.91 0.63 0.61
C2' 0.00 0.42 0.00 0.00 0.21 0.00 0.09 0.20 0.18 0.23 0.32 0.51 0.42 0.13 0.02 0.00 0.02 0.02 0.49 0.14 0.45 0.54 0.47
C3' 0.01 0.44 0.00 0.00 0.32 0.01 0.32 0.03 0.40 0.12 0.44 0.46 0.38 0.21 0.17 0.01 0.00 0.01 0.36 0.40 0.15 0.39 0.28
C4 0.01 0.01 0.21 0.32 0.00 0.21 0.00 0.33 0.01 0.00 0.01 0.01 0.00 0.01 0.00 0.16 0.11 0.19 0.15 0.02 0.51 0.36 0.16
C4' 0.01 0.39 0.00 0.01 0.21 0.00 0.15 0.00 0.22 0.15 0.33 0.48 0.36 0.11 0.06 0.25 0.01 0.00 0.01 0.21 0.22 0.19 0.02
C5 0.01 0.00 0.09 0.32 0.00 0.15 0.00 0.27 0.01 0.01 0.01 0.00 0.01 0.00 0.01 0.23 0.13 0.08 0.14 0.02 0.63 0.42 0.19
C5' 0.09 0.68 0.20 0.03 0.33 0.00 0.27 0.00 0.39 0.28 0.57 0.84 0.59 0.23 0.14 0.06 0.18 0.02 0.01 0.36 0.34 0.31 0.01
C6 0.01 0.00 0.18 0.40 0.01 0.22 0.01 0.39 0.00 0.02 0.00 0.00 0.00 0.02 0.02 0.21 0.17 0.15 0.25 0.01 0.73 0.41 0.28
C8 0.01 0.01 0.23 0.12 0.00 0.15 0.01 0.28 0.02 0.00 0.02 0.01 0.00 0.01 0.00 0.40 0.09 0.18 0.38 0.04 0.72 0.64 0.48
N1 0.01 0.00 0.32 0.44 0.01 0.33 0.01 0.57 0.00 0.02 0.00 0.00 0.00 0.01 0.01 0.23 0.19 0.27 0.43 0.00 0.86 0.51 0.48
N2 0.03 0.00 0.51 0.46 0.01 0.48 0.00 0.84 0.00 0.01 0.00 0.00 0.00 0.00 0.01 0.46 0.19 0.43 0.72 0.01 1.18 0.87 0.88
N3 0.02 0.00 0.42 0.38 0.00 0.36 0.01 0.59 0.00 0.00 0.00 0.00 0.00 0.01 0.01 0.32 0.14 0.36 0.41 0.00 0.70 0.53 0.47
N7 0.01 0.00 0.13 0.21 0.01 0.11 0.00 0.23 0.02 0.01 0.01 0.00 0.01 0.00 0.01 0.39 0.10 0.09 0.29 0.04 0.76 0.62 0.42
N9 0.00 0.01 0.02 0.17 0.00 0.06 0.01 0.14 0.02 0.00 0.01 0.01 0.01 0.01 0.00 0.19 0.12 0.01 0.14 0.03 0.43 0.38 0.18
O2' 0.01 0.33 0.00 0.01 0.16 0.25 0.23 0.06 0.21 0.40 0.23 0.46 0.32 0.39 0.19 0.00 0.03 0.17 0.48 0.25 0.53 0.54 0.49
O3' 0.28 0.17 0.02 0.00 0.11 0.01 0.13 0.18 0.17 0.09 0.19 0.19 0.14 0.10 0.12 0.03 0.00 0.19 0.39 0.20 0.19 0.57 0.38
O4' 0.00 0.36 0.02 0.01 0.19 0.00 0.08 0.02 0.15 0.18 0.27 0.43 0.36 0.09 0.01 0.17 0.19 0.00 0.19 0.11 0.44 0.14 0.16
O5' 0.18 0.53 0.49 0.36 0.15 0.01 0.14 0.01 0.25 0.38 0.43 0.72 0.41 0.29 0.14 0.48 0.39 0.19 0.00 0.26 0.02 0.02 0.00
O6 0.02 0.00 0.14 0.40 0.02 0.21 0.02 0.36 0.01 0.04 0.00 0.01 0.00 0.04 0.03 0.25 0.20 0.11 0.26 0.00 0.80 0.44 0.31
OP1 0.24 0.91 0.45 0.15 0.51 0.22 0.63 0.34 0.73 0.72 0.86 1.18 0.70 0.76 0.43 0.53 0.19 0.44 0.02 0.80 0.00 0.01 0.00
OP2 0.29 0.63 0.54 0.39 0.36 0.19 0.42 0.31 0.41 0.64 0.51 0.87 0.53 0.62 0.38 0.54 0.57 0.14 0.02 0.44 0.01 0.00 0.00
P 0.16 0.61 0.47 0.28 0.16 0.02 0.19 0.01 0.28 0.48 0.48 0.88 0.47 0.42 0.18 0.49 0.38 0.16 0.00 0.31 0.00 0.00 0.00