ClaRNA

Doublet Group distance statistics: 51407

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Distances from reference structure (by RMSD)

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

RMS Distances matrix

Distances graph

Distances from reference structure (by atoms)

Atom Chain Distances
C2 A 0, 0.003, 0.006, 0.009, 0.010 max_d=0.010 avg_d=0.006 std_dev=0.003
C5 A 0, 0.007, 0.012, 0.018, 0.022 max_d=0.022 avg_d=0.012 std_dev=0.006
C6 A 0, 0.007, 0.015, 0.023, 0.025 max_d=0.025 avg_d=0.015 std_dev=0.008
C1' A 0, 0.007, 0.015, 0.023, 0.030 max_d=0.030 avg_d=0.015 std_dev=0.008
N1 A 0, 0.006, 0.015, 0.024, 0.032 max_d=0.032 avg_d=0.015 std_dev=0.009
N3 A 0, 0.006, 0.015, 0.024, 0.036 max_d=0.036 avg_d=0.015 std_dev=0.009
N2 A 0, 0.014, 0.024, 0.033, 0.037 max_d=0.037 avg_d=0.024 std_dev=0.009
N7 A 0, 0.012, 0.023, 0.034, 0.038 max_d=0.038 avg_d=0.023 std_dev=0.011
C4 A 0, 0.008, 0.019, 0.030, 0.044 max_d=0.044 avg_d=0.019 std_dev=0.011
O6 A 0, 0.017, 0.029, 0.042, 0.043 max_d=0.043 avg_d=0.029 std_dev=0.013
N9 A 0, 0.012, 0.025, 0.038, 0.047 max_d=0.047 avg_d=0.025 std_dev=0.013
C8 A 0, 0.016, 0.034, 0.053, 0.071 max_d=0.071 avg_d=0.034 std_dev=0.018
OP2 B 0, 0.271, 0.628, 0.985, 1.049 max_d=1.049 avg_d=0.628 std_dev=0.357
OP1 B 0, 0.496, 0.912, 1.329, 1.480 max_d=1.480 avg_d=0.912 std_dev=0.416
P B 0, 0.309, 0.789, 1.270, 1.338 max_d=1.338 avg_d=0.789 std_dev=0.481
O5' B 0, 0.330, 0.914, 1.499, 1.642 max_d=1.642 avg_d=0.914 std_dev=0.584
C2' A 0, 0.021, 0.634, 1.248, 1.527 max_d=1.527 avg_d=0.634 std_dev=0.613
O4' A 0, 0.025, 0.639, 1.253, 1.523 max_d=1.523 avg_d=0.639 std_dev=0.614
O2' A 0, 0.214, 0.959, 1.703, 1.978 max_d=1.978 avg_d=0.959 std_dev=0.744
C4' A 0, 0.065, 1.053, 2.041, 2.412 max_d=2.412 avg_d=1.053 std_dev=0.988
N1 B 0, 0.521, 1.536, 2.550, 3.248 max_d=3.248 avg_d=1.536 std_dev=1.014
C3' A 0, -0.024, 1.015, 2.054, 2.362 max_d=2.362 avg_d=1.015 std_dev=1.039
C6 B 0, 0.595, 1.674, 2.753, 3.477 max_d=3.477 avg_d=1.674 std_dev=1.079
C2 B 0, 0.413, 1.505, 2.596, 3.018 max_d=3.018 avg_d=1.505 std_dev=1.091
O2 B 0, 0.405, 1.516, 2.626, 3.055 max_d=3.055 avg_d=1.516 std_dev=1.110
C1' B 0, 0.644, 1.775, 2.906, 3.770 max_d=3.770 avg_d=1.775 std_dev=1.131
O4' B 0, 0.573, 1.758, 2.943, 3.674 max_d=3.674 avg_d=1.758 std_dev=1.185
C2' B 0, 0.736, 1.927, 3.118, 4.042 max_d=4.042 avg_d=1.927 std_dev=1.191
C5 B 0, 0.512, 1.734, 2.956, 3.626 max_d=3.626 avg_d=1.734 std_dev=1.222
C3' B 0, 0.613, 1.898, 3.183, 3.991 max_d=3.991 avg_d=1.898 std_dev=1.285
C5' A 0, 0.144, 1.432, 2.721, 3.349 max_d=3.349 avg_d=1.432 std_dev=1.289
C5' B 0, 0.430, 1.757, 3.084, 3.722 max_d=3.722 avg_d=1.757 std_dev=1.327
C4' B 0, 0.555, 1.893, 3.231, 3.957 max_d=3.957 avg_d=1.893 std_dev=1.338
O3' A 0, 0.045, 1.440, 2.835, 3.190 max_d=3.190 avg_d=1.440 std_dev=1.395
N3 B 0, 0.335, 1.751, 3.167, 3.515 max_d=3.515 avg_d=1.751 std_dev=1.416
O2' B 0, 0.967, 2.420, 3.873, 4.837 max_d=4.837 avg_d=2.420 std_dev=1.453
C4 B 0, 0.342, 1.832, 3.322, 3.784 max_d=3.784 avg_d=1.832 std_dev=1.490
O3' B 0, 0.592, 2.218, 3.845, 4.535 max_d=4.535 avg_d=2.218 std_dev=1.626
O5' A 0, 0.426, 2.053, 3.680, 4.292 max_d=4.292 avg_d=2.053 std_dev=1.627
P A 0, 0.543, 2.368, 4.193, 4.893 max_d=4.893 avg_d=2.368 std_dev=1.825
N4 B 0, 0.326, 2.268, 4.210, 4.657 max_d=4.657 avg_d=2.268 std_dev=1.942
OP2 A 0, 0.552, 2.609, 4.665, 5.435 max_d=5.435 avg_d=2.609 std_dev=2.056
OP1 A 0, 0.628, 3.057, 5.486, 6.105 max_d=6.105 avg_d=3.057 std_dev=2.429

Atoms distances (summary)

atom dist matrix

Atoms distances Chain-A - Chain-A

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 0.07 0.02 0.01 0.01 0.01 0.01 0.01 0.01 0.03 0.31 0.00 0.41 0.02 0.46 0.48 0.41
C2 0.01 0.00 0.39 0.31 0.01 0.10 0.01 0.14 0.00 0.01 0.00 0.00 0.00 0.01 0.01 0.16 0.15 0.29 0.63 0.01 0.64 1.06 0.73
C2' 0.00 0.39 0.00 0.00 0.21 0.01 0.10 0.20 0.19 0.19 0.31 0.47 0.38 0.09 0.02 0.00 0.02 0.01 0.23 0.14 0.23 0.27 0.10
C3' 0.01 0.31 0.00 0.00 0.33 0.01 0.42 0.02 0.45 0.38 0.40 0.27 0.26 0.44 0.28 0.02 0.01 0.02 0.28 0.49 0.31 0.18 0.17
C4 0.01 0.01 0.21 0.33 0.00 0.03 0.00 0.03 0.01 0.00 0.01 0.01 0.00 0.00 0.00 0.09 0.04 0.15 0.80 0.01 0.84 1.09 0.86
C4' 0.01 0.10 0.01 0.01 0.03 0.00 0.14 0.00 0.10 0.30 0.02 0.18 0.11 0.27 0.12 0.33 0.02 0.00 0.01 0.15 0.21 0.31 0.05
C5 0.01 0.01 0.10 0.42 0.00 0.14 0.00 0.12 0.01 0.01 0.01 0.01 0.01 0.00 0.01 0.26 0.14 0.05 1.07 0.01 1.17 1.48 1.19
C5' 0.07 0.14 0.20 0.02 0.03 0.00 0.12 0.00 0.10 0.28 0.05 0.22 0.15 0.27 0.07 0.10 0.23 0.01 0.01 0.16 0.38 0.35 0.01
C6 0.02 0.00 0.19 0.45 0.01 0.10 0.01 0.10 0.00 0.02 0.00 0.01 0.01 0.02 0.02 0.20 0.15 0.11 1.06 0.00 1.19 1.60 1.22
C8 0.01 0.01 0.19 0.38 0.00 0.30 0.01 0.28 0.02 0.00 0.01 0.01 0.01 0.00 0.00 0.46 0.21 0.21 1.24 0.02 1.30 1.35 1.27
N1 0.01 0.00 0.31 0.40 0.01 0.02 0.01 0.05 0.00 0.01 0.00 0.01 0.00 0.01 0.01 0.05 0.07 0.22 0.85 0.01 0.92 1.37 0.99
N2 0.01 0.00 0.47 0.27 0.01 0.18 0.01 0.22 0.01 0.01 0.01 0.00 0.01 0.01 0.01 0.30 0.25 0.36 0.48 0.01 0.45 0.94 0.57
N3 0.01 0.00 0.38 0.26 0.00 0.11 0.01 0.15 0.01 0.01 0.00 0.01 0.00 0.01 0.01 0.18 0.20 0.29 0.55 0.01 0.56 0.88 0.62
N7 0.01 0.01 0.09 0.44 0.00 0.27 0.00 0.27 0.02 0.00 0.01 0.01 0.01 0.00 0.01 0.45 0.27 0.12 1.31 0.02 1.46 1.68 1.44
N9 0.01 0.01 0.02 0.28 0.00 0.12 0.01 0.07 0.02 0.00 0.01 0.01 0.01 0.01 0.00 0.21 0.04 0.01 0.83 0.02 0.86 0.94 0.83
O2' 0.03 0.16 0.00 0.02 0.09 0.33 0.26 0.10 0.20 0.46 0.05 0.30 0.18 0.45 0.21 0.00 0.03 0.25 0.26 0.29 0.31 0.34 0.11
O3' 0.31 0.15 0.02 0.01 0.04 0.02 0.14 0.23 0.15 0.21 0.07 0.25 0.20 0.27 0.04 0.03 0.00 0.22 0.23 0.23 0.43 0.09 0.21
O4' 0.00 0.29 0.01 0.02 0.15 0.00 0.05 0.01 0.11 0.21 0.22 0.36 0.29 0.12 0.01 0.25 0.22 0.00 0.36 0.07 0.47 0.57 0.44
O5' 0.41 0.63 0.23 0.28 0.80 0.01 1.07 0.01 1.06 1.24 0.85 0.48 0.55 1.31 0.83 0.26 0.23 0.36 0.00 1.19 0.01 0.01 0.00
O6 0.02 0.01 0.14 0.49 0.01 0.15 0.01 0.16 0.00 0.02 0.01 0.01 0.01 0.02 0.02 0.29 0.23 0.07 1.19 0.00 1.39 1.83 1.41
OP1 0.46 0.64 0.23 0.31 0.84 0.21 1.17 0.38 1.19 1.30 0.92 0.45 0.56 1.46 0.86 0.31 0.43 0.47 0.01 1.39 0.00 0.01 0.01
OP2 0.48 1.06 0.27 0.18 1.09 0.31 1.48 0.35 1.60 1.35 1.37 0.94 0.88 1.68 0.94 0.34 0.09 0.57 0.01 1.83 0.01 0.00 0.01
P 0.41 0.73 0.10 0.17 0.86 0.05 1.19 0.01 1.22 1.27 0.99 0.57 0.62 1.44 0.83 0.11 0.21 0.44 0.00 1.41 0.01 0.01 0.00

Atoms distances Chain-A - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6N1N3N4O2O2'O3'O4'O5'OP1OP2P
C1' 0.61 1.21 0.40 0.44 1.61 0.62 1.21 0.92 0.86 0.87 1.57 2.04 1.20 0.38 0.58 0.53 0.13 0.13 0.13 0.11
C2 0.52 1.12 0.42 0.34 1.56 0.50 1.34 0.80 0.95 0.86 1.43 1.82 1.03 0.34 0.36 0.36 0.14 0.14 0.13 0.12
C2' 1.20 1.85 0.91 0.56 2.16 0.72 1.70 0.81 1.37 1.47 2.17 2.55 1.88 0.93 0.32 0.97 0.62 0.49 0.50 0.50
C3' 0.87 1.44 0.49 0.33 1.75 0.56 1.35 0.78 1.05 1.11 1.75 2.13 1.45 0.51 0.43 0.75 0.47 0.47 0.47 0.47
C4 0.60 1.21 0.43 0.35 1.67 0.52 1.36 0.82 0.96 0.91 1.55 2.03 1.15 0.37 0.42 0.45 0.17 0.15 0.15 0.14
C4' 0.51 1.12 0.31 0.63 1.55 0.68 1.12 1.00 0.77 0.77 1.50 2.02 1.10 0.30 0.95 0.51 0.15 0.13 0.12 0.11
C5 0.61 1.22 0.46 0.33 1.66 0.45 1.41 0.70 1.01 0.94 1.54 2.00 1.14 0.37 0.34 0.42 0.22 0.17 0.19 0.19
C5' 0.52 1.16 0.30 0.63 1.60 0.66 1.19 0.98 0.82 0.81 1.54 2.07 1.13 0.30 0.99 0.50 0.17 0.14 0.14 0.13
C6 0.59 1.17 0.48 0.34 1.62 0.38 1.43 0.60 1.04 0.94 1.48 1.91 1.08 0.36 0.29 0.38 0.24 0.17 0.21 0.22
C8 0.64 1.25 0.43 0.35 1.67 0.51 1.33 0.78 0.96 0.94 1.59 2.05 1.21 0.39 0.42 0.48 0.20 0.16 0.18 0.17
N1 0.54 1.12 0.46 0.34 1.56 0.39 1.39 0.63 1.01 0.89 1.42 1.81 1.02 0.34 0.30 0.32 0.20 0.16 0.18 0.18
N2 0.46 1.02 0.41 0.35 1.40 0.54 1.20 0.88 0.86 0.78 1.30 1.60 0.93 0.32 0.37 0.34 0.11 0.14 0.14 0.14
N3 0.56 1.17 0.41 0.38 1.63 0.57 1.34 0.88 0.93 0.88 1.51 1.96 1.11 0.36 0.45 0.45 0.13 0.14 0.12 0.11
N7 0.64 1.24 0.46 0.33 1.67 0.46 1.39 0.70 1.00 0.96 1.57 2.03 1.18 0.39 0.35 0.46 0.24 0.18 0.20 0.21
N9 0.62 1.23 0.42 0.38 1.66 0.55 1.31 0.85 0.93 0.91 1.58 2.06 1.20 0.38 0.48 0.49 0.16 0.15 0.15 0.14
O2' 1.07 1.74 0.87 0.53 1.95 0.65 1.40 0.82 1.13 1.30 2.06 2.36 1.83 0.92 0.32 0.82 0.36 0.19 0.20 0.16
O3' 0.45 0.93 0.27 0.64 1.17 0.63 0.78 0.94 0.56 0.61 1.22 1.56 0.97 0.23 0.93 0.49 0.18 0.12 0.13 0.10
O4' 0.43 0.94 0.42 0.78 1.42 0.85 1.01 1.17 0.66 0.62 1.34 1.91 0.91 0.45 1.08 0.54 0.34 0.28 0.28 0.30
O5' 0.92 1.38 0.56 0.61 1.78 0.81 1.52 1.04 1.22 1.15 1.69 2.16 1.31 0.54 0.80 0.92 0.69 0.85 0.83 0.85
O6 0.60 1.15 0.50 0.37 1.59 0.34 1.43 0.48 1.07 0.95 1.44 1.86 1.05 0.37 0.29 0.39 0.28 0.19 0.23 0.27
OP1 0.84 1.32 0.43 0.51 1.74 0.68 1.50 0.90 1.18 1.10 1.64 2.11 1.25 0.42 0.81 0.85 0.69 0.93 0.89 0.92
OP2 1.27 1.65 0.85 0.66 1.96 0.98 1.78 1.10 1.53 1.48 1.88 2.23 1.60 0.83 0.41 1.27 1.32 1.57 1.47 1.52
P 0.97 1.44 0.55 0.51 1.84 0.76 1.60 0.96 1.29 1.22 1.74 2.19 1.37 0.53 0.62 0.96 0.84 1.06 1.00 1.03

Atoms distances Chain-B - Chain-B

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 0.06 0.01 0.01 0.01 0.01 0.02 0.00 0.01 0.00 0.30 0.34 0.33 0.34
C2 0.01 0.00 0.09 0.10 0.00 0.03 0.00 0.13 0.00 0.01 0.00 0.01 0.01 0.07 0.12 0.02 0.57 0.59 0.79 0.63
C2' 0.00 0.09 0.00 0.00 0.04 0.01 0.02 0.03 0.04 0.02 0.08 0.05 0.14 0.00 0.01 0.00 0.30 0.36 0.31 0.30
C3' 0.01 0.10 0.00 0.00 0.06 0.00 0.05 0.02 0.06 0.04 0.10 0.07 0.14 0.01 0.01 0.02 0.38 0.50 0.26 0.34
C4 0.01 0.00 0.04 0.06 0.00 0.06 0.00 0.22 0.00 0.00 0.00 0.00 0.01 0.04 0.08 0.02 0.76 0.86 1.14 0.89
C4' 0.00 0.03 0.01 0.00 0.06 0.00 0.09 0.00 0.09 0.04 0.04 0.07 0.06 0.04 0.02 0.00 0.01 0.18 0.15 0.05
C5 0.01 0.00 0.02 0.05 0.00 0.09 0.00 0.26 0.00 0.00 0.00 0.00 0.01 0.02 0.05 0.02 0.76 0.88 1.11 0.90
C5' 0.06 0.13 0.03 0.02 0.22 0.00 0.26 0.00 0.23 0.15 0.17 0.24 0.08 0.04 0.06 0.03 0.00 0.32 0.36 0.01
C6 0.01 0.00 0.04 0.06 0.00 0.09 0.00 0.23 0.00 0.00 0.00 0.01 0.01 0.02 0.06 0.02 0.66 0.73 0.85 0.75
N1 0.01 0.01 0.02 0.04 0.00 0.04 0.00 0.15 0.00 0.00 0.01 0.01 0.01 0.02 0.04 0.01 0.53 0.56 0.68 0.59
N3 0.01 0.00 0.08 0.10 0.00 0.04 0.00 0.17 0.00 0.01 0.00 0.01 0.01 0.07 0.13 0.02 0.69 0.74 1.00 0.77
N4 0.01 0.01 0.05 0.07 0.00 0.07 0.00 0.24 0.01 0.01 0.01 0.00 0.01 0.05 0.10 0.02 0.82 0.96 1.27 0.97
O2 0.02 0.01 0.14 0.14 0.01 0.06 0.01 0.08 0.01 0.01 0.01 0.01 0.00 0.12 0.17 0.02 0.48 0.49 0.67 0.53
O2' 0.00 0.07 0.00 0.01 0.04 0.04 0.02 0.04 0.02 0.02 0.07 0.05 0.12 0.00 0.03 0.03 0.06 0.11 0.11 0.09
O3' 0.01 0.12 0.01 0.01 0.08 0.02 0.05 0.06 0.06 0.04 0.13 0.10 0.17 0.03 0.00 0.01 0.35 0.57 0.23 0.35
O4' 0.00 0.02 0.00 0.02 0.02 0.00 0.02 0.03 0.02 0.01 0.02 0.02 0.02 0.03 0.01 0.00 0.25 0.37 0.15 0.31
O5' 0.30 0.57 0.30 0.38 0.76 0.01 0.76 0.00 0.66 0.53 0.69 0.82 0.48 0.06 0.35 0.25 0.00 0.02 0.02 0.01
OP1 0.34 0.59 0.36 0.50 0.86 0.18 0.88 0.32 0.73 0.56 0.74 0.96 0.49 0.11 0.57 0.37 0.02 0.00 0.01 0.00
OP2 0.33 0.79 0.31 0.26 1.14 0.15 1.11 0.36 0.85 0.68 1.00 1.27 0.67 0.11 0.23 0.15 0.02 0.01 0.00 0.00
P 0.34 0.63 0.30 0.34 0.89 0.05 0.90 0.01 0.75 0.59 0.77 0.97 0.53 0.09 0.35 0.31 0.01 0.00 0.00 0.00