ClaRNA

Doublet Group distance statistics: 51855

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Distances from reference structure (by RMSD)

1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 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, 0.010, 0.018, 0.016 max_d=0.016 avg_d=0.010 std_dev=0.007
C6 A 0, 0.004, 0.015, 0.025, 0.023 max_d=0.023 avg_d=0.015 std_dev=0.010
C4 A 0, 0.004, 0.015, 0.026, 0.025 max_d=0.025 avg_d=0.015 std_dev=0.011
N3 A 0, 0.002, 0.015, 0.029, 0.032 max_d=0.032 avg_d=0.015 std_dev=0.013
C2 A 0, 0.006, 0.021, 0.036, 0.035 max_d=0.035 avg_d=0.021 std_dev=0.015
N1 A 0, 0.006, 0.021, 0.037, 0.034 max_d=0.034 avg_d=0.021 std_dev=0.015
C1' A 0, 0.006, 0.025, 0.045, 0.047 max_d=0.047 avg_d=0.025 std_dev=0.019
O2 A 0, 0.010, 0.034, 0.058, 0.052 max_d=0.052 avg_d=0.034 std_dev=0.024
O4 A 0, 0.013, 0.058, 0.103, 0.109 max_d=0.109 avg_d=0.058 std_dev=0.045
O4' A 0, 0.001, 0.123, 0.244, 0.288 max_d=0.288 avg_d=0.123 std_dev=0.122
C2' A 0, 0.053, 0.194, 0.334, 0.331 max_d=0.331 avg_d=0.194 std_dev=0.141
C4' A 0, 0.116, 0.522, 0.928, 0.990 max_d=0.990 avg_d=0.522 std_dev=0.406
P B 0, 0.187, 0.655, 1.122, 1.063 max_d=1.063 avg_d=0.655 std_dev=0.468
C5' A 0, 0.263, 0.897, 1.532, 1.361 max_d=1.361 avg_d=0.897 std_dev=0.634
O2' A 0, 0.315, 1.077, 1.839, 1.623 max_d=1.623 avg_d=1.077 std_dev=0.762
OP1 B 0, 0.195, 0.961, 1.726, 1.873 max_d=1.873 avg_d=0.961 std_dev=0.765
OP2 B 0, 0.074, 0.855, 1.636, 1.888 max_d=1.888 avg_d=0.855 std_dev=0.781
C3' A 0, 0.361, 1.264, 2.168, 2.053 max_d=2.053 avg_d=1.264 std_dev=0.903
O5' A 0, 0.366, 1.275, 2.185, 2.055 max_d=2.055 avg_d=1.275 std_dev=0.909
OP1 A 0, -0.143, 0.926, 1.996, 2.424 max_d=2.424 avg_d=0.926 std_dev=1.069
P A 0, 0.425, 1.497, 2.570, 2.458 max_d=2.458 avg_d=1.497 std_dev=1.073
O5' B 0, 0.183, 1.638, 3.093, 3.535 max_d=3.535 avg_d=1.638 std_dev=1.455
O3' A 0, 0.719, 2.470, 4.220, 3.854 max_d=3.854 avg_d=2.470 std_dev=1.750
OP2 A 0, 0.699, 2.451, 4.203, 3.989 max_d=3.989 avg_d=2.451 std_dev=1.752
C5' B 0, 0.668, 3.126, 5.585, 6.007 max_d=6.007 avg_d=3.126 std_dev=2.459
C3' B 0, 0.888, 3.795, 6.702, 7.062 max_d=7.062 avg_d=3.795 std_dev=2.907
C4' B 0, 1.031, 4.294, 7.556, 7.903 max_d=7.903 avg_d=4.294 std_dev=3.263
C2' B 0, 1.174, 4.648, 8.122, 8.350 max_d=8.350 avg_d=4.648 std_dev=3.474
O3' B 0, 1.330, 4.861, 8.392, 8.283 max_d=8.283 avg_d=4.861 std_dev=3.531
O4' B 0, 1.191, 4.874, 8.556, 8.899 max_d=8.899 avg_d=4.874 std_dev=3.682
C8 B 0, 0.605, 4.619, 8.632, 9.785 max_d=9.785 avg_d=4.619 std_dev=4.013
C1' B 0, 1.250, 5.320, 9.391, 9.884 max_d=9.884 avg_d=5.320 std_dev=4.071
O2' B 0, 1.703, 5.939, 10.175, 9.589 max_d=9.589 avg_d=5.939 std_dev=4.236
N9 B 0, 0.954, 5.217, 9.479, 10.442 max_d=10.442 avg_d=5.217 std_dev=4.263
N7 B 0, 1.043, 5.757, 10.471, 11.547 max_d=11.547 avg_d=5.757 std_dev=4.714
C4 B 0, 1.368, 6.517, 11.665, 12.587 max_d=12.587 avg_d=6.517 std_dev=5.148
C5 B 0, 1.435, 6.806, 12.177, 13.129 max_d=13.129 avg_d=6.806 std_dev=5.371
N3 B 0, 1.815, 7.699, 13.583, 14.283 max_d=14.283 avg_d=7.699 std_dev=5.884
C6 B 0, 2.010, 8.404, 14.798, 15.495 max_d=15.495 avg_d=8.404 std_dev=6.394
C2 B 0, 2.188, 8.912, 15.637, 16.240 max_d=16.240 avg_d=8.912 std_dev=6.724
N6 B 0, 2.344, 9.318, 16.292, 16.776 max_d=16.776 avg_d=9.318 std_dev=6.974
N1 B 0, 2.314, 9.316, 16.317, 16.880 max_d=16.880 avg_d=9.316 std_dev=7.002

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 0.02 0.02 0.01 0.01 0.03 0.01 0.01 0.02 0.02 0.01 0.19 0.02 0.00 0.14 0.09 0.28 0.09
C2 0.02 0.00 0.06 0.15 0.00 0.07 0.01 0.10 0.00 0.00 0.00 0.00 0.23 0.18 0.01 0.01 0.33 0.12 0.57 0.28
C2' 0.00 0.06 0.00 0.00 0.06 0.01 0.06 0.11 0.05 0.04 0.07 0.07 0.00 0.04 0.06 0.00 0.13 0.23 0.27 0.16
C3' 0.02 0.15 0.00 0.00 0.35 0.00 0.42 0.01 0.39 0.20 0.24 0.07 0.01 0.01 0.37 0.02 0.23 0.42 0.30 0.29
C4 0.02 0.00 0.06 0.35 0.00 0.18 0.00 0.23 0.00 0.01 0.01 0.01 0.22 0.27 0.00 0.03 0.45 0.34 0.83 0.38
C4' 0.01 0.07 0.01 0.00 0.18 0.00 0.22 0.00 0.21 0.11 0.12 0.02 0.20 0.02 0.19 0.00 0.03 0.12 0.02 0.01
C5 0.01 0.01 0.06 0.42 0.00 0.22 0.00 0.26 0.00 0.01 0.01 0.01 0.15 0.40 0.01 0.05 0.44 0.46 0.78 0.36
C5' 0.03 0.10 0.11 0.01 0.23 0.00 0.26 0.00 0.21 0.11 0.17 0.05 0.08 0.13 0.25 0.01 0.01 0.17 0.11 0.02
C6 0.01 0.00 0.05 0.39 0.00 0.21 0.00 0.21 0.00 0.00 0.01 0.00 0.10 0.34 0.01 0.06 0.37 0.37 0.60 0.27
N1 0.01 0.00 0.04 0.20 0.01 0.11 0.01 0.11 0.00 0.00 0.01 0.00 0.14 0.11 0.01 0.02 0.30 0.17 0.49 0.21
N3 0.02 0.00 0.07 0.24 0.01 0.12 0.01 0.17 0.01 0.01 0.00 0.00 0.25 0.16 0.02 0.01 0.41 0.19 0.72 0.35
O2 0.02 0.00 0.07 0.07 0.01 0.02 0.01 0.05 0.00 0.00 0.00 0.00 0.25 0.36 0.02 0.03 0.28 0.11 0.49 0.27
O2' 0.01 0.23 0.00 0.01 0.22 0.20 0.15 0.08 0.10 0.14 0.25 0.25 0.00 0.07 0.23 0.16 0.21 0.10 0.26 0.15
O3' 0.19 0.18 0.04 0.01 0.27 0.02 0.40 0.13 0.34 0.11 0.16 0.36 0.07 0.00 0.31 0.14 0.25 0.67 0.30 0.40
O4 0.02 0.01 0.06 0.37 0.00 0.19 0.01 0.25 0.01 0.01 0.02 0.02 0.23 0.31 0.00 0.03 0.48 0.39 0.91 0.43
O4' 0.00 0.01 0.00 0.02 0.03 0.00 0.05 0.01 0.06 0.02 0.01 0.03 0.16 0.14 0.03 0.00 0.06 0.24 0.11 0.09
O5' 0.14 0.33 0.13 0.23 0.45 0.03 0.44 0.01 0.37 0.30 0.41 0.28 0.21 0.25 0.48 0.06 0.00 0.02 0.02 0.00
OP1 0.09 0.12 0.23 0.42 0.34 0.12 0.46 0.17 0.37 0.17 0.19 0.11 0.10 0.67 0.39 0.24 0.02 0.00 0.02 0.00
OP2 0.28 0.57 0.27 0.30 0.83 0.02 0.78 0.11 0.60 0.49 0.72 0.49 0.26 0.30 0.91 0.11 0.02 0.02 0.00 0.00
P 0.09 0.28 0.16 0.29 0.38 0.01 0.36 0.02 0.27 0.21 0.35 0.27 0.15 0.40 0.43 0.09 0.00 0.00 0.00 0.00

Atoms distances Chain-A - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N3N6N7N9O2'O3'O4'O5'OP1OP2P
C1' 1.43 2.04 1.54 1.16 1.81 1.03 1.81 0.90 1.91 1.54 2.02 1.92 1.83 1.64 1.62 1.31 1.05 1.30 0.65 0.20 0.16 0.16
C2 1.57 2.43 1.69 1.20 2.22 0.98 2.50 0.75 2.67 2.16 2.62 2.19 2.80 2.47 1.97 1.59 1.21 1.29 0.52 0.24 0.18 0.07
C2' 1.42 1.75 1.53 1.21 1.57 1.15 1.43 1.06 1.45 1.28 1.63 1.72 1.29 1.24 1.46 1.31 1.07 1.37 0.81 0.03 0.28 0.29
C3' 1.08 1.43 1.23 0.91 1.15 0.88 0.96 0.81 1.06 0.69 1.30 1.39 0.89 0.64 1.00 1.13 0.73 1.02 0.74 0.25 0.32 0.49
C4 1.06 2.03 1.38 0.90 1.65 0.61 1.97 0.53 2.19 1.80 2.24 1.67 2.40 2.09 1.45 1.45 1.06 0.74 0.20 0.29 0.11 0.05
C4' 0.75 1.24 0.95 0.63 0.92 0.58 0.76 0.53 0.89 0.44 1.13 1.16 0.76 0.45 0.73 0.77 0.47 0.70 0.43 0.50 0.32 0.35
C5 0.78 1.78 1.18 0.75 1.31 0.47 1.53 0.49 1.80 1.35 1.95 1.42 1.93 1.54 1.09 1.22 0.90 0.50 0.10 0.32 0.10 0.09
C5' 0.10 0.66 0.48 0.21 0.34 0.05 0.31 0.09 0.49 0.19 0.64 0.53 0.50 0.22 0.10 0.25 0.17 0.06 0.17 0.79 0.56 0.42
C6 0.92 1.66 1.25 0.80 1.33 0.51 1.46 0.44 1.63 1.31 1.75 1.41 1.68 1.43 1.16 1.17 0.83 0.67 0.23 0.31 0.11 0.06
N1 1.34 2.01 1.52 1.07 1.80 0.84 1.95 0.68 2.05 1.73 2.09 1.83 2.07 1.90 1.63 1.38 1.03 1.11 0.48 0.26 0.16 0.07
N3 1.41 2.32 1.60 1.09 2.07 0.81 2.43 0.62 2.62 2.15 2.55 2.02 2.85 2.51 1.85 1.59 1.18 1.08 0.38 0.27 0.16 0.02
O2 1.82 2.89 1.84 1.37 2.60 1.20 2.90 0.94 3.16 2.37 3.12 2.61 3.30 2.74 2.26 1.71 1.38 1.55 0.64 0.21 0.21 0.12
O2' 1.66 2.03 1.60 1.36 1.80 1.47 1.58 1.38 1.63 1.31 1.85 2.03 1.42 1.29 1.63 1.39 1.21 1.70 0.94 0.22 0.26 0.35
O3' 1.54 1.74 1.56 1.33 1.54 1.43 1.33 1.35 1.37 1.08 1.58 1.75 1.19 1.04 1.42 1.59 1.17 1.54 1.33 0.88 0.78 1.14
O4 0.96 2.09 1.32 0.86 1.60 0.60 1.97 0.56 2.26 1.78 2.35 1.65 2.53 2.11 1.38 1.48 1.11 0.64 0.14 0.29 0.09 0.06
O4' 1.00 1.65 1.18 0.83 1.34 0.70 1.31 0.64 1.45 1.00 1.62 1.52 1.38 1.09 1.13 0.93 0.71 0.90 0.41 0.44 0.16 0.14
O5' 0.37 0.76 0.83 0.50 0.42 0.29 0.39 0.26 0.61 0.30 0.79 0.59 0.62 0.19 0.31 0.65 0.41 0.34 0.07 0.58 0.33 0.14
OP1 0.86 0.06 1.18 0.95 0.35 0.88 0.23 0.80 0.14 0.69 0.17 0.24 0.28 0.42 0.64 1.10 0.90 0.93 0.54 0.51 0.30 0.34
OP2 0.47 0.52 0.84 0.46 0.12 0.46 0.24 0.39 0.55 0.32 0.67 0.26 0.71 0.05 0.25 0.85 0.44 0.56 0.12 0.66 0.47 0.19
P 0.67 0.24 0.98 0.74 0.16 0.69 0.09 0.61 0.24 0.59 0.36 0.02 0.37 0.33 0.48 0.90 0.71 0.75 0.36 0.70 0.10 0.20

Atoms distances Chain-B - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N3N6N7N9O2'O3'O4'O5'OP1OP2P
C1' 0.00 0.02 0.01 0.01 0.01 0.01 0.01 0.12 0.02 0.00 0.02 0.02 0.02 0.01 0.00 0.03 0.25 0.00 0.14 0.21 0.26 0.11
C2 0.02 0.00 0.38 0.26 0.01 0.16 0.01 0.27 0.00 0.01 0.00 0.00 0.00 0.01 0.01 0.36 0.39 0.33 0.61 0.65 1.05 0.74
C2' 0.01 0.38 0.00 0.00 0.21 0.01 0.11 0.12 0.19 0.16 0.30 0.37 0.15 0.07 0.03 0.00 0.01 0.03 0.48 0.46 0.86 0.56
C3' 0.01 0.26 0.00 0.00 0.29 0.01 0.45 0.03 0.43 0.61 0.33 0.23 0.52 0.61 0.33 0.01 0.00 0.01 0.37 0.33 0.53 0.38
C4 0.01 0.01 0.21 0.29 0.00 0.12 0.00 0.47 0.00 0.00 0.00 0.00 0.01 0.00 0.00 0.21 0.12 0.15 0.65 0.68 0.77 0.64
C4' 0.01 0.16 0.01 0.01 0.12 0.00 0.34 0.01 0.25 0.64 0.06 0.18 0.37 0.59 0.29 0.27 0.02 0.00 0.06 0.12 0.14 0.01
C5 0.01 0.01 0.11 0.45 0.00 0.34 0.00 0.77 0.01 0.01 0.01 0.01 0.02 0.00 0.01 0.33 0.14 0.04 0.86 0.96 0.99 0.84
C5' 0.12 0.27 0.12 0.03 0.47 0.01 0.77 0.00 0.70 1.03 0.46 0.22 0.87 1.07 0.56 0.09 0.11 0.01 0.02 0.09 0.20 0.03
C6 0.02 0.00 0.19 0.43 0.00 0.25 0.01 0.70 0.00 0.01 0.00 0.00 0.00 0.01 0.01 0.30 0.12 0.12 0.89 1.02 1.23 0.95
C8 0.00 0.01 0.16 0.61 0.00 0.64 0.01 1.03 0.01 0.00 0.01 0.00 0.03 0.00 0.00 0.56 0.42 0.22 0.78 0.91 0.43 0.62
N1 0.02 0.00 0.30 0.33 0.00 0.06 0.01 0.46 0.00 0.01 0.00 0.01 0.01 0.01 0.01 0.29 0.23 0.25 0.77 0.87 1.24 0.89
N3 0.02 0.00 0.37 0.23 0.00 0.18 0.01 0.22 0.00 0.00 0.01 0.00 0.00 0.01 0.01 0.36 0.40 0.34 0.51 0.50 0.81 0.59
N6 0.02 0.00 0.15 0.52 0.01 0.37 0.02 0.87 0.00 0.03 0.01 0.00 0.00 0.03 0.02 0.35 0.21 0.05 1.00 1.21 1.38 1.08
N7 0.01 0.01 0.07 0.61 0.00 0.59 0.00 1.07 0.01 0.00 0.01 0.01 0.03 0.00 0.00 0.54 0.39 0.14 0.94 1.10 0.81 0.85
N9 0.00 0.01 0.03 0.33 0.00 0.29 0.01 0.56 0.01 0.00 0.01 0.01 0.02 0.00 0.00 0.24 0.06 0.02 0.54 0.59 0.43 0.44
O2' 0.03 0.36 0.00 0.01 0.21 0.27 0.33 0.09 0.30 0.56 0.29 0.36 0.35 0.54 0.24 0.00 0.03 0.34 0.31 0.28 0.84 0.40
O3' 0.25 0.39 0.01 0.00 0.12 0.02 0.14 0.11 0.12 0.42 0.23 0.40 0.21 0.39 0.06 0.03 0.00 0.11 0.32 0.16 0.51 0.29
O4' 0.00 0.33 0.03 0.01 0.15 0.00 0.04 0.01 0.12 0.22 0.25 0.34 0.05 0.14 0.02 0.34 0.11 0.00 0.12 0.33 0.08 0.15
O5' 0.14 0.61 0.48 0.37 0.65 0.06 0.86 0.02 0.89 0.78 0.77 0.51 1.00 0.94 0.54 0.31 0.32 0.12 0.00 0.01 0.02 0.01
OP1 0.21 0.65 0.46 0.33 0.68 0.12 0.96 0.09 1.02 0.91 0.87 0.50 1.21 1.10 0.59 0.28 0.16 0.33 0.01 0.00 0.01 0.00
OP2 0.26 1.05 0.86 0.53 0.77 0.14 0.99 0.20 1.23 0.43 1.24 0.81 1.38 0.81 0.43 0.84 0.51 0.08 0.02 0.01 0.00 0.00
P 0.11 0.74 0.56 0.38 0.64 0.01 0.84 0.03 0.95 0.62 0.89 0.59 1.08 0.85 0.44 0.40 0.29 0.15 0.01 0.00 0.00 0.00