ClaRNA

Doublet Group distance statistics: 48836

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Distances from reference structure (by RMSD)

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

RMS Distances matrix

Distances graph

Distances from reference structure (by atoms)

Atom Chain Distances
C4 A 0, 0.004, 0.009, 0.014, 0.016 max_d=0.016 avg_d=0.009 std_dev=0.005
N3 A 0, 0.003, 0.009, 0.015, 0.019 max_d=0.019 avg_d=0.009 std_dev=0.006
C5 A 0, 0.004, 0.011, 0.018, 0.018 max_d=0.018 avg_d=0.011 std_dev=0.007
C6 A 0, 0.004, 0.013, 0.021, 0.025 max_d=0.025 avg_d=0.013 std_dev=0.009
C1' A 0, 0.005, 0.015, 0.026, 0.036 max_d=0.036 avg_d=0.015 std_dev=0.011
C2 A 0, 0.003, 0.014, 0.025, 0.035 max_d=0.035 avg_d=0.014 std_dev=0.011
O4 A 0, 0.007, 0.019, 0.030, 0.034 max_d=0.034 avg_d=0.019 std_dev=0.012
N1 A 0, 0.006, 0.021, 0.035, 0.047 max_d=0.047 avg_d=0.021 std_dev=0.015
O2 A 0, -0.001, 0.035, 0.071, 0.113 max_d=0.113 avg_d=0.035 std_dev=0.036
C2' A 0, 0.041, 0.180, 0.319, 0.405 max_d=0.405 avg_d=0.180 std_dev=0.139
O4' A 0, 0.008, 0.152, 0.296, 0.362 max_d=0.362 avg_d=0.152 std_dev=0.144
P B 0, 0.271, 0.601, 0.930, 1.114 max_d=1.114 avg_d=0.601 std_dev=0.329
OP2 B 0, 0.218, 0.581, 0.944, 1.114 max_d=1.114 avg_d=0.581 std_dev=0.363
OP1 B 0, 0.336, 0.714, 1.092, 1.124 max_d=1.124 avg_d=0.714 std_dev=0.378
C4' A 0, 0.063, 0.479, 0.895, 1.070 max_d=1.070 avg_d=0.479 std_dev=0.416
C5' A 0, 0.187, 0.643, 1.100, 1.472 max_d=1.472 avg_d=0.643 std_dev=0.457
O2' A 0, 0.018, 0.640, 1.261, 1.676 max_d=1.676 avg_d=0.640 std_dev=0.622
O5' A 0, 0.115, 0.845, 1.575, 2.167 max_d=2.167 avg_d=0.845 std_dev=0.730
C3' A 0, -0.028, 0.719, 1.467, 1.818 max_d=1.818 avg_d=0.719 std_dev=0.748
OP1 A 0, 1.215, 2.219, 3.222, 2.950 max_d=2.950 avg_d=2.219 std_dev=1.003
O5' B 0, 0.190, 1.351, 2.511, 3.594 max_d=3.594 avg_d=1.351 std_dev=1.160
P A 0, 0.311, 1.566, 2.821, 3.520 max_d=3.520 avg_d=1.566 std_dev=1.255
O3' A 0, -0.194, 1.302, 2.798, 3.491 max_d=3.491 avg_d=1.302 std_dev=1.496
C5' B 0, 0.045, 1.795, 3.544, 5.267 max_d=5.267 avg_d=1.795 std_dev=1.750
OP2 A 0, 1.464, 3.464, 5.464, 6.154 max_d=6.154 avg_d=3.464 std_dev=2.000
C4' B 0, 0.062, 2.744, 5.426, 7.862 max_d=7.862 avg_d=2.744 std_dev=2.682
O4' B 0, 0.002, 3.026, 6.051, 8.859 max_d=8.859 avg_d=3.026 std_dev=3.025
C3' B 0, 0.248, 3.563, 6.878, 8.757 max_d=8.757 avg_d=3.563 std_dev=3.315
C6 B 0, 0.509, 4.031, 7.554, 7.919 max_d=7.919 avg_d=4.031 std_dev=3.522
C1' B 0, 0.216, 3.948, 7.680, 10.152 max_d=10.152 avg_d=3.948 std_dev=3.732
N1 B 0, 0.409, 4.165, 7.921, 9.509 max_d=9.509 avg_d=4.165 std_dev=3.756
C2' B 0, 0.292, 4.201, 8.111, 9.837 max_d=9.837 avg_d=4.201 std_dev=3.910
C5 B 0, 0.580, 4.518, 8.456, 8.840 max_d=8.840 avg_d=4.518 std_dev=3.938
O3' B 0, 0.461, 4.488, 8.516, 9.979 max_d=9.979 avg_d=4.488 std_dev=4.027
C2 B 0, 0.421, 4.663, 8.905, 10.946 max_d=10.946 avg_d=4.663 std_dev=4.242
C4 B 0, 0.638, 5.081, 9.525, 9.574 max_d=9.574 avg_d=5.081 std_dev=4.443
N3 B 0, 0.589, 5.063, 9.536, 10.621 max_d=10.621 avg_d=5.063 std_dev=4.473
O2 B 0, 0.214, 4.828, 9.441, 12.630 max_d=12.630 avg_d=4.828 std_dev=4.613
O2' B 0, 0.297, 5.255, 10.213, 12.140 max_d=12.140 avg_d=5.255 std_dev=4.958
O4 B 0, 0.684, 5.643, 10.602, 11.022 max_d=11.022 avg_d=5.643 std_dev=4.959

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 0.01 0.01 0.01 0.02 0.01 0.06 0.01 0.01 0.02 0.05 0.02 0.29 0.02 0.01 0.16 0.34 0.14 0.14
C2 0.03 0.00 0.09 0.17 0.00 0.05 0.01 0.20 0.01 0.01 0.00 0.00 0.39 0.23 0.01 0.04 0.26 0.59 0.38 0.33
C2' 0.01 0.09 0.00 0.00 0.04 0.01 0.04 0.16 0.06 0.02 0.07 0.15 0.00 0.03 0.04 0.03 0.34 0.53 0.55 0.42
C3' 0.01 0.17 0.00 0.00 0.44 0.00 0.55 0.02 0.50 0.27 0.29 0.11 0.02 0.01 0.46 0.02 0.10 0.40 0.25 0.15
C4 0.01 0.00 0.04 0.44 0.00 0.23 0.01 0.40 0.01 0.01 0.00 0.01 0.43 0.25 0.01 0.03 0.50 1.05 0.87 0.68
C4' 0.02 0.05 0.01 0.00 0.23 0.00 0.30 0.01 0.28 0.12 0.13 0.07 0.29 0.02 0.24 0.00 0.02 0.33 0.18 0.05
C5 0.01 0.01 0.04 0.55 0.01 0.30 0.00 0.44 0.00 0.00 0.01 0.02 0.34 0.47 0.01 0.03 0.54 1.10 0.86 0.70
C5' 0.06 0.20 0.16 0.02 0.40 0.01 0.44 0.00 0.36 0.20 0.30 0.10 0.14 0.20 0.44 0.02 0.01 0.37 0.32 0.02
C6 0.01 0.01 0.06 0.50 0.01 0.28 0.00 0.36 0.00 0.01 0.01 0.02 0.26 0.39 0.01 0.04 0.41 0.83 0.53 0.49
N1 0.01 0.01 0.02 0.27 0.01 0.12 0.00 0.20 0.01 0.00 0.01 0.02 0.26 0.02 0.01 0.01 0.24 0.55 0.28 0.28
N3 0.02 0.00 0.07 0.29 0.00 0.13 0.01 0.30 0.01 0.01 0.00 0.01 0.45 0.08 0.01 0.05 0.39 0.82 0.65 0.51
O2 0.05 0.00 0.15 0.11 0.01 0.07 0.02 0.10 0.02 0.02 0.01 0.00 0.41 0.55 0.01 0.06 0.17 0.47 0.24 0.21
O2' 0.02 0.39 0.00 0.02 0.43 0.29 0.34 0.14 0.26 0.26 0.45 0.41 0.00 0.08 0.47 0.21 0.22 0.44 0.60 0.33
O3' 0.29 0.23 0.03 0.01 0.25 0.02 0.47 0.20 0.39 0.02 0.08 0.55 0.08 0.00 0.30 0.17 0.37 0.69 0.34 0.39
O4 0.02 0.01 0.04 0.46 0.01 0.24 0.01 0.44 0.01 0.01 0.01 0.01 0.47 0.30 0.00 0.03 0.55 1.17 1.03 0.77
O4' 0.01 0.04 0.03 0.02 0.03 0.00 0.03 0.02 0.04 0.01 0.05 0.06 0.21 0.17 0.03 0.00 0.11 0.18 0.16 0.10
O5' 0.16 0.26 0.34 0.10 0.50 0.02 0.54 0.01 0.41 0.24 0.39 0.17 0.22 0.37 0.55 0.11 0.00 0.02 0.02 0.01
OP1 0.34 0.59 0.53 0.40 1.05 0.33 1.10 0.37 0.83 0.55 0.82 0.47 0.44 0.69 1.17 0.18 0.02 0.00 0.01 0.00
OP2 0.14 0.38 0.55 0.25 0.87 0.18 0.86 0.32 0.53 0.28 0.65 0.24 0.60 0.34 1.03 0.16 0.02 0.01 0.00 0.00
P 0.14 0.33 0.42 0.15 0.68 0.05 0.70 0.02 0.49 0.28 0.51 0.21 0.33 0.39 0.77 0.10 0.01 0.00 0.00 0.00

Atoms distances Chain-A - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6N1N3O2O2'O3'O4O4'O5'OP1OP2P
C1' 1.67 1.50 2.48 2.04 1.71 1.49 1.05 1.11 0.87 1.26 1.74 1.71 3.22 2.14 2.28 1.30 0.64 0.31 0.14 0.26
C2 1.09 1.22 1.80 1.45 1.85 1.10 1.26 0.93 0.73 0.87 1.68 1.26 2.19 1.35 2.36 0.86 0.50 0.26 0.16 0.28
C2' 1.95 1.47 2.75 2.12 1.04 1.57 0.70 1.10 1.07 1.48 1.30 1.74 3.60 2.23 1.36 1.49 0.70 0.27 0.15 0.30
C3' 2.23 1.73 3.02 2.43 1.17 1.82 0.82 1.26 1.17 1.70 1.46 2.09 4.03 2.66 1.51 1.72 0.78 0.19 0.17 0.27
C4 0.31 0.73 0.95 0.61 1.61 0.52 1.29 0.57 0.69 0.42 1.28 0.56 1.32 0.52 2.10 0.40 0.29 0.19 0.13 0.32
C4' 1.91 1.57 2.73 2.32 1.57 1.70 0.96 1.22 0.90 1.39 1.64 1.90 3.69 2.60 2.16 1.47 0.69 0.27 0.08 0.25
C5 0.50 0.52 1.28 0.90 1.49 0.67 1.12 0.63 0.51 0.23 1.13 0.37 1.78 0.84 2.07 0.43 0.31 0.18 0.11 0.31
C5' 1.57 1.25 2.42 2.03 1.49 1.44 0.93 1.02 0.62 1.06 1.41 1.55 3.39 2.32 2.17 1.15 0.53 0.26 0.19 0.19
C6 0.84 0.58 1.70 1.29 1.39 0.92 0.90 0.77 0.25 0.34 1.10 0.64 2.31 1.29 2.05 0.61 0.37 0.19 0.12 0.29
N1 1.19 1.07 2.00 1.60 1.63 1.16 1.02 0.93 0.56 0.80 1.47 1.18 2.58 1.59 2.25 0.90 0.50 0.25 0.13 0.28
N3 0.48 0.87 1.17 0.85 1.69 0.66 1.25 0.67 0.58 0.46 1.41 0.79 1.48 0.73 2.16 0.38 0.28 0.19 0.17 0.31
O2 1.51 1.75 2.10 1.81 2.17 1.43 1.53 1.15 1.14 1.36 2.14 1.80 2.40 1.68 2.53 1.26 0.70 0.35 0.16 0.25
O2' 2.42 1.82 3.21 2.50 1.07 1.92 1.11 1.40 1.65 1.98 1.46 2.04 3.99 2.62 1.00 1.88 1.08 0.84 0.56 0.77
O3' 2.89 2.24 3.70 3.12 1.21 2.41 1.06 1.70 1.66 2.26 1.72 2.68 4.80 3.48 1.25 2.28 1.14 0.61 0.31 0.57
O4 0.62 1.09 0.63 0.38 1.79 0.53 1.60 0.57 1.13 0.91 1.50 0.94 0.89 0.35 2.15 0.75 0.43 0.24 0.13 0.33
O4' 1.58 1.59 2.38 2.02 1.99 1.45 1.27 1.08 0.88 1.23 1.95 1.80 3.18 2.21 2.67 1.20 0.59 0.33 0.17 0.26
O5' 1.26 0.75 2.14 1.70 1.16 1.16 0.72 0.81 0.26 0.68 0.92 1.04 3.09 1.92 1.85 0.86 0.38 0.27 0.31 0.19
OP1 1.39 0.63 2.23 1.82 1.00 1.28 0.96 0.95 0.77 0.86 0.47 0.92 3.23 2.12 1.59 1.02 0.75 0.75 0.84 0.72
OP2 1.32 0.89 2.09 1.53 0.85 1.10 0.60 0.79 0.47 0.86 0.73 1.20 3.02 1.67 1.38 0.92 0.52 0.42 0.51 0.37
P 1.12 0.47 1.98 1.51 1.00 1.01 0.69 0.68 0.05 0.51 0.59 0.82 2.96 1.74 1.68 0.72 0.31 0.31 0.43 0.21

Atoms distances Chain-B - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6N1N3O2O2'O3'O4O4'O5'OP1OP2P
C1' 0.00 0.02 0.00 0.02 0.01 0.01 0.02 0.02 0.02 0.01 0.01 0.03 0.02 0.33 0.01 0.00 0.11 0.31 0.15 0.13
C2 0.02 0.00 0.24 0.31 0.00 0.32 0.01 0.55 0.01 0.01 0.00 0.01 0.45 0.27 0.01 0.28 0.56 0.60 0.80 0.55
C2' 0.00 0.24 0.00 0.00 0.04 0.01 0.16 0.17 0.23 0.02 0.18 0.43 0.00 0.03 0.04 0.03 0.26 0.48 0.54 0.36
C3' 0.02 0.31 0.00 0.00 0.49 0.00 0.53 0.01 0.48 0.30 0.40 0.28 0.01 0.01 0.51 0.01 0.19 0.82 0.30 0.34
C4 0.01 0.00 0.04 0.49 0.00 0.27 0.01 0.43 0.01 0.01 0.00 0.01 0.35 0.32 0.01 0.04 0.49 0.58 1.18 0.55
C4' 0.01 0.32 0.01 0.00 0.27 0.00 0.15 0.01 0.10 0.16 0.34 0.36 0.32 0.04 0.29 0.01 0.02 0.35 0.27 0.10
C5 0.02 0.01 0.16 0.53 0.01 0.15 0.00 0.15 0.00 0.01 0.01 0.01 0.25 0.46 0.02 0.18 0.15 0.43 0.86 0.22
C5' 0.02 0.55 0.17 0.01 0.43 0.01 0.15 0.00 0.08 0.22 0.60 0.68 0.13 0.18 0.49 0.04 0.01 0.15 0.40 0.01
C6 0.02 0.01 0.23 0.48 0.01 0.10 0.00 0.08 0.00 0.01 0.01 0.01 0.21 0.39 0.02 0.25 0.06 0.35 0.47 0.08
N1 0.01 0.01 0.02 0.30 0.01 0.16 0.01 0.22 0.01 0.00 0.01 0.02 0.20 0.11 0.01 0.02 0.20 0.42 0.44 0.23
N3 0.01 0.00 0.18 0.40 0.00 0.34 0.01 0.60 0.01 0.01 0.00 0.02 0.46 0.23 0.01 0.20 0.65 0.66 1.11 0.67
O2 0.03 0.01 0.43 0.28 0.01 0.36 0.01 0.68 0.01 0.02 0.02 0.00 0.61 0.53 0.02 0.45 0.66 0.65 0.76 0.62
O2' 0.02 0.45 0.00 0.01 0.35 0.32 0.25 0.13 0.21 0.20 0.46 0.61 0.00 0.07 0.39 0.26 0.12 0.58 0.57 0.29
O3' 0.33 0.27 0.03 0.01 0.32 0.04 0.46 0.18 0.39 0.11 0.23 0.53 0.07 0.00 0.37 0.24 0.38 1.34 0.42 0.69
O4 0.01 0.01 0.04 0.51 0.01 0.29 0.02 0.49 0.02 0.01 0.01 0.02 0.39 0.37 0.00 0.06 0.56 0.62 1.38 0.64
O4' 0.00 0.28 0.03 0.01 0.04 0.01 0.18 0.04 0.25 0.02 0.20 0.45 0.26 0.24 0.06 0.00 0.15 0.12 0.19 0.12
O5' 0.11 0.56 0.26 0.19 0.49 0.02 0.15 0.01 0.06 0.20 0.65 0.66 0.12 0.38 0.56 0.15 0.00 0.03 0.02 0.00
OP1 0.31 0.60 0.48 0.82 0.58 0.35 0.43 0.15 0.35 0.42 0.66 0.65 0.58 1.34 0.62 0.12 0.03 0.00 0.01 0.00
OP2 0.15 0.80 0.54 0.30 1.18 0.27 0.86 0.40 0.47 0.44 1.11 0.76 0.57 0.42 1.38 0.19 0.02 0.01 0.00 0.01
P 0.13 0.55 0.36 0.34 0.55 0.10 0.22 0.01 0.08 0.23 0.67 0.62 0.29 0.69 0.64 0.12 0.00 0.00 0.01 0.00