ClaRNA

Doublet Group distance statistics: 54278

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Distances from reference structure (by RMSD)

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

RMS Distances matrix

Distances graph

Distances from reference structure (by atoms)

Atom Chain Distances
N3 A 0, 0.002, 0.007, 0.011, 0.014 max_d=0.014 avg_d=0.007 std_dev=0.005
C5 A 0, 0.004, 0.009, 0.014, 0.016 max_d=0.016 avg_d=0.009 std_dev=0.005
C6 A 0, 0.005, 0.012, 0.020, 0.023 max_d=0.023 avg_d=0.012 std_dev=0.008
C4 A 0, 0.003, 0.011, 0.018, 0.022 max_d=0.022 avg_d=0.011 std_dev=0.008
C2 A 0, 0.007, 0.015, 0.023, 0.024 max_d=0.024 avg_d=0.015 std_dev=0.008
C1' A 0, 0.007, 0.015, 0.024, 0.026 max_d=0.026 avg_d=0.015 std_dev=0.009
N1 A 0, 0.009, 0.020, 0.031, 0.031 max_d=0.031 avg_d=0.020 std_dev=0.011
O2 A 0, 0.019, 0.040, 0.060, 0.058 max_d=0.058 avg_d=0.040 std_dev=0.020
N4 A 0, 0.007, 0.028, 0.048, 0.062 max_d=0.062 avg_d=0.028 std_dev=0.021
C2' B 0, 0.227, 0.671, 1.116, 1.168 max_d=1.168 avg_d=0.671 std_dev=0.445
C3' B 0, 0.314, 0.779, 1.244, 1.292 max_d=1.292 avg_d=0.779 std_dev=0.465
O4' A 0, 0.158, 0.687, 1.216, 1.240 max_d=1.240 avg_d=0.687 std_dev=0.529
C2' A 0, 0.158, 0.727, 1.297, 1.321 max_d=1.321 avg_d=0.727 std_dev=0.570
C4' B 0, 0.305, 0.959, 1.612, 1.491 max_d=1.491 avg_d=0.959 std_dev=0.653
O3' B 0, 0.308, 0.983, 1.659, 2.028 max_d=2.028 avg_d=0.983 std_dev=0.676
O2' B 0, 0.424, 1.106, 1.788, 1.848 max_d=1.848 avg_d=1.106 std_dev=0.682
C3' A 0, 0.274, 1.081, 1.887, 1.755 max_d=1.755 avg_d=1.081 std_dev=0.807
C4' A 0, 0.269, 1.077, 1.886, 1.845 max_d=1.845 avg_d=1.077 std_dev=0.809
O4' B 0, 0.249, 1.102, 1.955, 2.094 max_d=2.094 avg_d=1.102 std_dev=0.853
O5' B 0, 0.167, 1.048, 1.929, 2.472 max_d=2.472 avg_d=1.048 std_dev=0.881
O2' A 0, 0.288, 1.304, 2.320, 2.345 max_d=2.345 avg_d=1.304 std_dev=1.016
C5' B 0, 0.156, 1.185, 2.214, 2.974 max_d=2.974 avg_d=1.185 std_dev=1.029
C5' A 0, 0.358, 1.402, 2.446, 2.506 max_d=2.506 avg_d=1.402 std_dev=1.044
O3' A 0, 0.375, 1.566, 2.757, 2.865 max_d=2.865 avg_d=1.566 std_dev=1.191
C1' B 0, 0.461, 1.655, 2.849, 2.883 max_d=2.883 avg_d=1.655 std_dev=1.194
P B 0, 0.001, 1.378, 2.756, 3.920 max_d=3.920 avg_d=1.378 std_dev=1.378
OP1 B 0, -0.584, 1.153, 2.889, 4.613 max_d=4.613 avg_d=1.153 std_dev=1.737
OP2 B 0, 0.364, 2.144, 3.923, 4.855 max_d=4.855 avg_d=2.144 std_dev=1.780
O5' A 0, 1.226, 3.111, 4.996, 4.762 max_d=4.762 avg_d=3.111 std_dev=1.885
N9 B 0, 0.682, 2.571, 4.461, 4.228 max_d=4.228 avg_d=2.571 std_dev=1.889
C8 B 0, 0.718, 2.796, 4.873, 4.686 max_d=4.686 avg_d=2.796 std_dev=2.078
P A 0, 1.132, 3.730, 6.328, 5.999 max_d=5.999 avg_d=3.730 std_dev=2.598
OP1 A 0, 1.478, 4.145, 6.812, 6.725 max_d=6.725 avg_d=4.145 std_dev=2.667
C4 B 0, 0.943, 3.898, 6.853, 6.330 max_d=6.330 avg_d=3.898 std_dev=2.955
OP2 A 0, 1.178, 4.207, 7.236, 6.888 max_d=6.888 avg_d=4.207 std_dev=3.029
N7 B 0, 0.971, 4.074, 7.177, 6.707 max_d=6.707 avg_d=4.074 std_dev=3.103
N3 B 0, 1.053, 4.519, 7.985, 7.548 max_d=7.548 avg_d=4.519 std_dev=3.466
C5 B 0, 1.089, 4.674, 8.259, 7.854 max_d=7.854 avg_d=4.674 std_dev=3.585
C2 B 0, 1.315, 5.827, 10.339, 9.520 max_d=9.520 avg_d=5.827 std_dev=4.512
C6 B 0, 1.350, 6.092, 10.835, 10.610 max_d=10.610 avg_d=6.092 std_dev=4.742
N1 B 0, 1.436, 6.521, 11.606, 11.276 max_d=11.276 avg_d=6.521 std_dev=5.085
N2 B 0, 1.478, 6.696, 11.913, 11.169 max_d=11.169 avg_d=6.696 std_dev=5.217
O6 B 0, 1.522, 7.033, 12.545, 12.375 max_d=12.375 avg_d=7.033 std_dev=5.512

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 0.01 0.00 0.01 0.01 0.00 0.01 0.05 0.01 0.01 0.01 0.01 0.01 0.02 0.28 0.00 0.27 0.31 0.50 0.29
C2 0.01 0.00 0.15 0.15 0.00 0.02 0.01 0.05 0.00 0.00 0.00 0.00 0.00 0.09 0.21 0.11 0.51 0.56 0.92 0.64
C2' 0.00 0.15 0.00 0.00 0.03 0.01 0.13 0.17 0.17 0.02 0.11 0.03 0.27 0.00 0.02 0.02 0.09 0.23 0.37 0.10
C3' 0.01 0.15 0.00 0.00 0.31 0.01 0.35 0.01 0.32 0.18 0.23 0.33 0.09 0.01 0.00 0.02 0.14 0.26 0.32 0.10
C4 0.01 0.00 0.03 0.31 0.00 0.15 0.00 0.16 0.00 0.00 0.00 0.00 0.00 0.35 0.08 0.03 0.90 1.06 1.42 1.15
C4' 0.00 0.02 0.01 0.01 0.15 0.00 0.24 0.01 0.25 0.08 0.04 0.16 0.14 0.25 0.00 0.01 0.01 0.33 0.27 0.08
C5 0.01 0.01 0.13 0.35 0.00 0.24 0.00 0.26 0.00 0.00 0.00 0.00 0.01 0.47 0.21 0.13 1.04 1.18 1.52 1.29
C5' 0.05 0.05 0.17 0.01 0.16 0.01 0.26 0.00 0.24 0.06 0.05 0.18 0.16 0.07 0.19 0.02 0.00 0.38 0.30 0.01
C6 0.01 0.00 0.17 0.32 0.00 0.25 0.00 0.24 0.00 0.00 0.00 0.00 0.00 0.44 0.18 0.17 0.93 0.96 1.23 1.07
N1 0.01 0.00 0.02 0.18 0.00 0.08 0.00 0.06 0.00 0.00 0.01 0.00 0.00 0.19 0.11 0.01 0.59 0.60 0.88 0.68
N3 0.01 0.00 0.11 0.23 0.00 0.04 0.00 0.05 0.00 0.01 0.00 0.00 0.00 0.18 0.11 0.07 0.69 0.79 1.17 0.88
N4 0.01 0.00 0.03 0.33 0.00 0.16 0.00 0.18 0.00 0.00 0.00 0.00 0.00 0.38 0.11 0.03 0.98 1.21 1.57 1.28
O2 0.01 0.00 0.27 0.09 0.00 0.14 0.01 0.16 0.00 0.00 0.00 0.00 0.00 0.22 0.40 0.22 0.30 0.36 0.71 0.38
O2' 0.02 0.09 0.00 0.01 0.35 0.25 0.47 0.07 0.44 0.19 0.18 0.38 0.22 0.00 0.03 0.17 0.13 0.27 0.34 0.08
O3' 0.28 0.21 0.02 0.00 0.08 0.00 0.21 0.19 0.18 0.11 0.11 0.11 0.40 0.03 0.00 0.17 0.23 0.33 0.33 0.15
O4' 0.00 0.11 0.02 0.02 0.03 0.01 0.13 0.02 0.17 0.01 0.07 0.03 0.22 0.17 0.17 0.00 0.30 0.39 0.39 0.29
O5' 0.27 0.51 0.09 0.14 0.90 0.01 1.04 0.00 0.93 0.59 0.69 0.98 0.30 0.13 0.23 0.30 0.00 0.02 0.03 0.00
OP1 0.31 0.56 0.23 0.26 1.06 0.33 1.18 0.38 0.96 0.60 0.79 1.21 0.36 0.27 0.33 0.39 0.02 0.00 0.01 0.00
OP2 0.50 0.92 0.37 0.32 1.42 0.27 1.52 0.30 1.23 0.88 1.17 1.57 0.71 0.34 0.33 0.39 0.03 0.01 0.00 0.00
P 0.29 0.64 0.10 0.10 1.15 0.08 1.29 0.01 1.07 0.68 0.88 1.28 0.38 0.08 0.15 0.29 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' 0.09 1.64 0.17 0.41 1.13 0.58 1.70 0.52 2.13 1.17 1.99 1.84 1.22 1.73 0.67 0.65 0.52 0.41 0.41 2.55 0.52 1.02 0.58
C2 0.17 1.12 0.15 0.38 0.62 0.50 0.91 0.56 1.18 0.69 1.22 1.35 0.83 0.97 0.30 0.58 0.45 0.31 0.53 1.38 0.80 1.20 0.79
C2' 0.10 1.91 0.20 0.12 1.32 0.32 1.96 0.36 2.43 1.47 2.24 2.23 1.44 2.08 0.86 0.47 0.27 0.27 0.50 2.93 0.52 0.95 0.61
C3' 0.56 1.81 0.65 0.83 0.98 0.96 1.63 0.78 2.30 0.93 2.16 2.19 1.33 1.61 0.31 1.13 0.94 0.81 0.18 2.95 0.53 0.66 0.29
C4 0.23 0.56 0.14 0.36 0.24 0.45 0.35 0.61 0.51 0.34 0.59 0.68 0.41 0.41 0.07 0.50 0.44 0.23 0.57 0.59 0.88 1.17 0.83
C4' 0.43 1.90 0.64 0.86 1.17 0.95 1.83 0.78 2.54 0.96 2.43 2.09 1.33 1.69 0.50 1.16 0.99 0.73 0.20 3.13 0.39 0.71 0.27
C5 0.18 0.63 0.15 0.39 0.46 0.52 0.74 0.58 0.83 0.68 0.75 0.68 0.46 0.86 0.33 0.55 0.45 0.27 0.47 0.95 0.64 0.94 0.64
C5' 0.47 2.11 0.77 1.00 1.32 1.05 1.99 0.89 2.81 0.93 2.78 2.22 1.43 1.71 0.57 1.29 1.13 0.78 0.31 3.37 0.50 0.60 0.27
C6 0.10 1.12 0.16 0.40 0.88 0.56 1.32 0.53 1.51 1.02 1.36 1.18 0.85 1.41 0.58 0.61 0.48 0.35 0.41 1.72 0.52 0.92 0.56
N1 0.11 1.29 0.16 0.40 0.87 0.55 1.31 0.54 1.60 0.97 1.51 1.46 0.97 1.38 0.52 0.62 0.48 0.36 0.46 1.88 0.61 1.05 0.65
N3 0.22 0.83 0.14 0.36 0.37 0.45 0.51 0.58 0.73 0.41 0.86 1.01 0.61 0.53 0.10 0.53 0.44 0.26 0.57 0.84 0.92 1.26 0.87
N4 0.29 0.52 0.12 0.33 0.33 0.35 0.32 0.63 0.47 0.10 0.55 0.57 0.43 0.15 0.21 0.41 0.44 0.19 0.64 0.52 1.06 1.25 0.96
O2 0.18 1.28 0.15 0.38 0.68 0.50 0.96 0.55 1.28 0.69 1.37 1.56 0.94 0.99 0.31 0.59 0.46 0.33 0.54 1.52 0.83 1.26 0.82
O2' 0.48 2.02 0.61 0.35 1.54 0.19 2.22 0.50 2.58 1.94 2.33 2.35 1.55 2.51 1.23 0.39 0.26 0.35 0.95 3.09 0.82 1.33 1.02
O3' 0.73 1.83 0.83 0.92 0.83 0.97 1.39 0.70 2.05 0.87 2.01 2.40 1.39 1.47 0.12 1.36 1.10 0.85 0.06 2.71 0.41 0.58 0.19
O4' 0.25 1.77 0.44 0.70 1.20 0.81 1.79 0.68 2.35 1.03 2.24 1.88 1.27 1.67 0.62 0.95 0.82 0.57 0.28 2.80 0.36 0.88 0.41
O5' 1.31 1.63 1.61 1.85 0.76 1.93 1.33 1.75 2.25 0.12 2.29 1.81 1.06 0.97 0.40 2.05 1.92 1.65 1.21 2.91 1.42 1.27 1.17
OP1 1.75 1.01 2.27 2.53 0.10 2.45 0.91 2.26 1.88 0.46 1.88 1.17 0.37 0.69 0.72 2.75 2.76 1.99 1.81 2.65 2.20 1.65 1.82
OP2 1.88 1.29 2.31 2.52 0.31 2.56 0.70 2.41 1.68 0.61 1.99 1.57 0.52 0.23 0.89 2.67 2.46 2.18 1.95 2.17 2.16 1.86 1.92
P 1.70 1.29 2.16 2.41 0.36 2.42 0.95 2.25 1.94 0.32 2.06 1.48 0.59 0.57 0.68 2.61 2.52 2.01 1.75 2.59 2.00 1.65 1.71

Atoms distances Chain-B - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N2N3N7N9O2'O3'O4'O5'O6OP1OP2P
C1' 0.00 0.01 0.00 0.01 0.01 0.01 0.01 0.11 0.02 0.01 0.02 0.01 0.01 0.01 0.01 0.03 0.27 0.00 0.25 0.04 0.20 0.26 0.18
C2 0.01 0.00 0.47 0.93 0.01 0.65 0.00 1.00 0.00 0.01 0.00 0.01 0.00 0.00 0.01 0.33 0.97 0.27 1.68 0.01 1.97 2.34 1.97
C2' 0.00 0.47 0.00 0.00 0.24 0.02 0.13 0.10 0.21 0.20 0.37 0.56 0.45 0.10 0.02 0.00 0.10 0.02 0.17 0.15 0.27 0.24 0.21
C3' 0.01 0.93 0.00 0.00 0.46 0.01 0.36 0.01 0.48 0.59 0.72 1.17 0.89 0.49 0.22 0.02 0.01 0.01 0.34 0.45 0.33 0.31 0.32
C4 0.01 0.01 0.24 0.46 0.00 0.32 0.00 0.56 0.01 0.00 0.01 0.01 0.00 0.00 0.01 0.29 0.38 0.14 0.86 0.02 1.11 1.18 0.94
C4' 0.01 0.65 0.02 0.01 0.32 0.00 0.32 0.01 0.37 0.50 0.50 0.84 0.63 0.46 0.20 0.21 0.01 0.01 0.01 0.40 0.19 0.12 0.07
C5 0.01 0.00 0.13 0.36 0.00 0.32 0.00 0.70 0.01 0.01 0.01 0.01 0.00 0.00 0.01 0.36 0.12 0.10 0.64 0.02 1.42 1.10 0.91
C5' 0.11 1.00 0.10 0.01 0.56 0.01 0.70 0.00 0.78 0.89 0.86 1.28 0.88 0.92 0.46 0.08 0.13 0.01 0.01 0.86 0.09 0.22 0.01
C6 0.02 0.00 0.21 0.48 0.01 0.37 0.01 0.78 0.00 0.02 0.00 0.01 0.00 0.02 0.02 0.39 0.30 0.15 0.91 0.01 1.64 1.56 1.22
C8 0.01 0.01 0.20 0.59 0.00 0.50 0.01 0.89 0.02 0.00 0.01 0.01 0.01 0.00 0.00 0.24 0.53 0.12 0.49 0.03 1.48 0.53 0.83
N1 0.02 0.00 0.37 0.72 0.01 0.50 0.01 0.86 0.00 0.01 0.00 0.01 0.00 0.01 0.02 0.39 0.69 0.21 1.36 0.01 1.80 2.13 1.67
N2 0.01 0.01 0.56 1.17 0.01 0.84 0.01 1.28 0.01 0.01 0.01 0.00 0.01 0.01 0.02 0.32 1.30 0.32 2.06 0.00 2.60 2.94 2.56
N3 0.01 0.00 0.45 0.89 0.00 0.63 0.00 0.88 0.00 0.01 0.00 0.01 0.00 0.00 0.01 0.27 0.89 0.27 1.51 0.01 1.59 1.86 1.63
N7 0.01 0.00 0.10 0.49 0.00 0.46 0.00 0.92 0.02 0.00 0.01 0.01 0.00 0.00 0.00 0.33 0.40 0.08 0.51 0.03 1.76 0.75 0.97
N9 0.01 0.01 0.02 0.22 0.01 0.20 0.01 0.46 0.02 0.00 0.02 0.02 0.01 0.00 0.00 0.20 0.06 0.03 0.30 0.03 0.78 0.51 0.42
O2' 0.03 0.33 0.00 0.02 0.29 0.21 0.36 0.08 0.39 0.24 0.39 0.32 0.27 0.33 0.20 0.00 0.19 0.23 0.26 0.41 0.33 0.26 0.27
O3' 0.27 0.97 0.10 0.01 0.38 0.01 0.12 0.13 0.30 0.53 0.69 1.30 0.89 0.40 0.06 0.19 0.00 0.14 0.58 0.21 0.39 0.50 0.47
O4' 0.00 0.27 0.02 0.01 0.14 0.01 0.10 0.01 0.15 0.12 0.21 0.32 0.27 0.08 0.03 0.23 0.14 0.00 0.39 0.14 0.14 0.15 0.29
O5' 0.25 1.68 0.17 0.34 0.86 0.01 0.64 0.01 0.91 0.49 1.36 2.06 1.51 0.51 0.30 0.26 0.58 0.39 0.00 0.82 0.01 0.01 0.00
O6 0.04 0.01 0.15 0.45 0.02 0.40 0.02 0.86 0.01 0.03 0.01 0.00 0.01 0.03 0.03 0.41 0.21 0.14 0.82 0.00 1.86 1.52 1.25
OP1 0.20 1.97 0.27 0.33 1.11 0.19 1.42 0.09 1.64 1.48 1.80 2.60 1.59 1.76 0.78 0.33 0.39 0.14 0.01 1.86 0.00 0.01 0.00
OP2 0.26 2.34 0.24 0.31 1.18 0.12 1.10 0.22 1.56 0.53 2.13 2.94 1.86 0.75 0.51 0.26 0.50 0.15 0.01 1.52 0.01 0.00 0.00
P 0.18 1.97 0.21 0.32 0.94 0.07 0.91 0.01 1.22 0.83 1.67 2.56 1.63 0.97 0.42 0.27 0.47 0.29 0.00 1.25 0.00 0.00 0.00