ClaRNA

Doublet Group distance statistics: 48780

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Distances from reference structure (by RMSD)

1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,

RMS Distances matrix

Distances graph

Distances from reference structure (by atoms)

Atom Chain Distances
N3 A 0, 0.001, 0.005, 0.008, 0.010 max_d=0.010 avg_d=0.005 std_dev=0.004
C5 A 0, 0.001, 0.006, 0.012, 0.013 max_d=0.013 avg_d=0.006 std_dev=0.005
C4 A 0, 0.000, 0.013, 0.025, 0.033 max_d=0.033 avg_d=0.013 std_dev=0.013
C2 A 0, -0.001, 0.012, 0.025, 0.033 max_d=0.033 avg_d=0.012 std_dev=0.013
C6 A 0, -0.002, 0.011, 0.024, 0.032 max_d=0.032 avg_d=0.011 std_dev=0.013
C1' A 0, -0.001, 0.013, 0.026, 0.035 max_d=0.035 avg_d=0.013 std_dev=0.013
N1 A 0, -0.002, 0.011, 0.025, 0.034 max_d=0.034 avg_d=0.011 std_dev=0.013
O2 A 0, -0.002, 0.026, 0.054, 0.073 max_d=0.073 avg_d=0.026 std_dev=0.028
O4 A 0, 0.016, 0.060, 0.104, 0.125 max_d=0.125 avg_d=0.060 std_dev=0.044
OP1 B 0, 0.212, 0.507, 0.802, 0.730 max_d=0.730 avg_d=0.507 std_dev=0.295
OP2 B 0, 0.262, 0.662, 1.061, 1.073 max_d=1.073 avg_d=0.662 std_dev=0.400
O4' A 0, -0.128, 0.330, 0.788, 1.116 max_d=1.116 avg_d=0.330 std_dev=0.458
C2' A 0, -0.145, 0.337, 0.819, 1.169 max_d=1.169 avg_d=0.337 std_dev=0.482
P B 0, 0.180, 0.760, 1.340, 1.619 max_d=1.619 avg_d=0.760 std_dev=0.580
C4' A 0, -0.177, 0.413, 1.003, 1.432 max_d=1.432 avg_d=0.413 std_dev=0.590
O2' A 0, 0.017, 0.639, 1.262, 1.573 max_d=1.573 avg_d=0.639 std_dev=0.622
C3' A 0, 0.012, 0.732, 1.452, 1.808 max_d=1.808 avg_d=0.732 std_dev=0.720
C5' A 0, -0.172, 0.865, 1.902, 2.619 max_d=2.619 avg_d=0.865 std_dev=1.037
O3' A 0, 0.116, 1.287, 2.458, 2.689 max_d=2.689 avg_d=1.287 std_dev=1.171
O5' A 0, 0.020, 1.240, 2.461, 3.188 max_d=3.188 avg_d=1.240 std_dev=1.220
O5' B 0, 0.206, 1.500, 2.793, 3.515 max_d=3.515 avg_d=1.500 std_dev=1.293
C5' B 0, 0.206, 1.679, 3.153, 3.999 max_d=3.999 avg_d=1.679 std_dev=1.474
P A 0, 0.232, 2.159, 4.087, 4.894 max_d=4.894 avg_d=2.159 std_dev=1.928
C4' B 0, 0.459, 2.536, 4.614, 5.414 max_d=5.414 avg_d=2.536 std_dev=2.078
O4' B 0, 0.585, 2.731, 4.876, 5.284 max_d=5.284 avg_d=2.731 std_dev=2.146
OP1 A 0, 0.042, 2.543, 5.044, 6.357 max_d=6.357 avg_d=2.543 std_dev=2.501
OP2 A 0, 0.303, 2.932, 5.561, 6.728 max_d=6.728 avg_d=2.932 std_dev=2.629
C3' B 0, 0.488, 3.268, 6.048, 7.003 max_d=7.003 avg_d=3.268 std_dev=2.780
C1' B 0, 0.684, 3.649, 6.613, 7.168 max_d=7.168 avg_d=3.649 std_dev=2.964
N9 B 0, 0.649, 3.885, 7.122, 7.632 max_d=7.632 avg_d=3.885 std_dev=3.236
C2' B 0, 0.654, 4.042, 7.430, 8.341 max_d=8.341 avg_d=4.042 std_dev=3.388
O3' B 0, 0.432, 3.900, 7.369, 8.766 max_d=8.766 avg_d=3.900 std_dev=3.469
C8 B 0, 0.710, 4.207, 7.704, 8.249 max_d=8.249 avg_d=4.207 std_dev=3.497
C4 B 0, 0.523, 4.152, 7.781, 8.533 max_d=8.533 avg_d=4.152 std_dev=3.629
N7 B 0, 0.624, 4.552, 8.480, 9.300 max_d=9.300 avg_d=4.552 std_dev=3.928
C5 B 0, 0.520, 4.474, 8.428, 9.267 max_d=9.267 avg_d=4.474 std_dev=3.954
N3 B 0, 0.398, 4.374, 8.349, 9.457 max_d=9.457 avg_d=4.374 std_dev=3.976
O2' B 0, 0.715, 4.867, 9.019, 10.507 max_d=10.507 avg_d=4.867 std_dev=4.152
C6 B 0, 0.408, 4.920, 9.431, 10.567 max_d=10.567 avg_d=4.920 std_dev=4.511
C2 B 0, 0.311, 4.866, 9.420, 10.738 max_d=10.738 avg_d=4.866 std_dev=4.554
N1 B 0, 0.330, 5.066, 9.803, 11.079 max_d=11.079 avg_d=5.066 std_dev=4.737
O6 B 0, 0.371, 5.344, 10.317, 11.732 max_d=11.732 avg_d=5.344 std_dev=4.973
N2 B 0, 0.201, 5.399, 10.597, 12.334 max_d=12.334 avg_d=5.399 std_dev=5.198

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 0.01 0.00 0.01 0.01 0.01 0.01 0.06 0.00 0.01 0.01 0.02 0.01 0.26 0.01 0.00 0.36 0.28 0.24 0.24
C2 0.01 0.00 0.12 0.08 0.01 0.16 0.01 0.32 0.00 0.00 0.00 0.00 0.33 0.29 0.01 0.19 0.26 0.39 0.27 0.14
C2' 0.00 0.12 0.00 0.00 0.04 0.02 0.05 0.14 0.08 0.02 0.10 0.17 0.00 0.04 0.05 0.02 0.43 0.63 0.66 0.54
C3' 0.01 0.08 0.00 0.00 0.24 0.00 0.31 0.02 0.29 0.15 0.14 0.05 0.01 0.01 0.25 0.04 0.07 0.49 0.34 0.25
C4 0.01 0.01 0.04 0.24 0.00 0.11 0.00 0.25 0.00 0.01 0.00 0.01 0.28 0.05 0.00 0.03 0.52 0.14 0.94 0.58
C4' 0.01 0.16 0.02 0.00 0.11 0.00 0.04 0.01 0.01 0.07 0.16 0.21 0.25 0.03 0.12 0.00 0.02 0.23 0.45 0.16
C5 0.01 0.01 0.05 0.31 0.00 0.04 0.00 0.16 0.00 0.01 0.00 0.01 0.20 0.21 0.00 0.12 0.70 0.40 1.19 0.83
C5' 0.06 0.32 0.14 0.02 0.25 0.01 0.16 0.00 0.14 0.15 0.33 0.43 0.12 0.15 0.28 0.02 0.01 0.06 0.17 0.02
C6 0.00 0.00 0.08 0.29 0.00 0.01 0.00 0.14 0.00 0.01 0.00 0.01 0.15 0.19 0.01 0.17 0.71 0.43 0.99 0.77
N1 0.01 0.00 0.02 0.15 0.01 0.07 0.01 0.15 0.01 0.00 0.00 0.00 0.17 0.11 0.01 0.01 0.44 0.20 0.47 0.38
N3 0.01 0.00 0.10 0.14 0.00 0.16 0.00 0.33 0.00 0.00 0.00 0.00 0.35 0.18 0.00 0.14 0.34 0.31 0.54 0.29
O2 0.02 0.00 0.17 0.05 0.01 0.21 0.01 0.43 0.01 0.00 0.00 0.00 0.38 0.49 0.01 0.34 0.06 0.69 0.18 0.17
O2' 0.01 0.33 0.00 0.01 0.28 0.25 0.20 0.12 0.15 0.17 0.35 0.38 0.00 0.08 0.31 0.17 0.21 0.51 0.87 0.45
O3' 0.26 0.29 0.04 0.01 0.05 0.03 0.21 0.15 0.19 0.11 0.18 0.49 0.08 0.00 0.06 0.16 0.41 0.18 0.82 0.42
O4 0.01 0.01 0.05 0.25 0.00 0.12 0.00 0.28 0.01 0.01 0.00 0.01 0.31 0.06 0.00 0.04 0.52 0.13 1.05 0.62
O4' 0.00 0.19 0.02 0.04 0.03 0.00 0.12 0.02 0.17 0.01 0.14 0.34 0.17 0.16 0.04 0.00 0.33 0.19 0.06 0.13
O5' 0.36 0.26 0.43 0.07 0.52 0.02 0.70 0.01 0.71 0.44 0.34 0.06 0.21 0.41 0.52 0.33 0.00 0.01 0.02 0.00
OP1 0.28 0.39 0.63 0.49 0.14 0.23 0.40 0.06 0.43 0.20 0.31 0.69 0.51 0.18 0.13 0.19 0.01 0.00 0.01 0.00
OP2 0.24 0.27 0.66 0.34 0.94 0.45 1.19 0.17 0.99 0.47 0.54 0.18 0.87 0.82 1.05 0.06 0.02 0.01 0.00 0.01
P 0.24 0.14 0.54 0.25 0.58 0.16 0.83 0.02 0.77 0.38 0.29 0.17 0.45 0.42 0.62 0.13 0.00 0.00 0.01 0.00

Atoms distances Chain-A - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N2N3N7N9O2'O3'O4'O5'O6OP1OP2P
C1' 2.05 2.58 2.86 2.43 1.65 1.89 1.28 1.52 1.88 1.05 2.56 3.10 2.19 0.59 1.54 3.49 2.52 1.62 1.03 1.92 0.30 0.34 0.49
C2 1.37 2.49 2.07 1.75 1.11 1.44 0.81 1.29 1.56 0.75 2.41 3.20 1.86 0.18 0.87 2.39 1.67 1.13 0.83 1.55 0.32 0.38 0.49
C2' 2.62 2.85 3.36 2.74 2.24 2.21 1.78 1.73 2.04 1.71 2.65 3.28 2.69 1.29 2.21 4.07 2.83 2.09 1.34 1.87 0.35 0.52 0.71
C3' 2.56 2.49 3.35 2.82 1.97 2.23 1.41 1.73 1.61 1.50 2.24 2.93 2.43 0.97 2.03 4.24 3.06 2.01 1.23 1.48 0.31 0.35 0.59
C4 0.78 2.00 1.31 0.93 0.42 0.81 0.35 0.80 0.98 1.16 1.82 2.91 1.32 0.96 0.48 1.59 0.77 0.59 0.48 1.05 0.20 0.36 0.44
C4' 1.94 2.14 2.80 2.44 1.36 1.84 0.99 1.45 1.61 0.79 2.16 2.61 1.87 0.30 1.34 3.65 2.73 1.47 0.90 1.85 0.35 0.27 0.43
C5 1.09 1.89 1.69 1.25 0.50 1.04 0.11 0.96 0.86 1.17 1.73 2.74 1.27 0.85 0.73 2.09 1.11 0.84 0.62 0.90 0.21 0.37 0.48
C5' 1.54 1.55 2.41 2.09 0.73 1.56 0.47 1.29 1.24 0.64 1.68 2.03 1.22 0.28 0.89 3.26 2.39 1.12 0.79 1.67 0.53 0.46 0.55
C6 1.46 2.07 2.14 1.68 0.92 1.37 0.50 1.19 1.11 1.09 1.96 2.81 1.55 0.59 1.02 2.63 1.61 1.14 0.80 1.10 0.26 0.39 0.52
N1 1.64 2.36 2.38 1.97 1.21 1.58 0.83 1.35 1.49 0.95 2.30 3.02 1.84 0.36 1.15 2.86 1.94 1.31 0.91 1.49 0.30 0.38 0.52
N3 0.87 2.29 1.45 1.13 0.72 0.99 0.49 0.97 1.25 0.90 2.12 3.15 1.61 0.66 0.43 1.70 0.98 0.71 0.58 1.25 0.27 0.39 0.46
O2 1.54 2.78 2.27 2.07 1.45 1.68 1.21 1.47 1.98 0.57 2.77 3.35 2.15 0.24 1.04 2.53 2.02 1.29 0.93 1.95 0.37 0.33 0.45
O2' 3.30 3.51 3.97 3.25 3.04 2.72 2.59 2.16 2.76 2.40 3.28 3.83 3.43 2.07 2.96 4.64 3.30 2.70 1.83 2.53 0.72 0.86 1.09
O3' 3.30 3.01 4.08 3.58 2.63 2.94 1.97 2.34 2.00 2.03 2.60 3.40 3.10 1.50 2.70 5.07 3.93 2.71 1.78 1.72 0.73 0.76 1.03
O4 0.57 1.94 0.96 0.63 0.50 0.53 0.69 0.54 1.04 1.38 1.73 2.87 1.28 1.30 0.58 1.15 0.58 0.35 0.30 1.15 0.13 0.31 0.37
O4' 1.59 2.20 2.46 2.15 1.12 1.60 0.91 1.31 1.72 0.57 2.33 2.74 1.69 0.12 0.99 3.17 2.35 1.18 0.76 1.98 0.42 0.31 0.43
O5' 1.88 1.83 2.71 2.30 1.15 1.80 0.66 1.51 1.11 1.06 1.75 2.36 1.60 0.46 1.34 3.50 2.50 1.45 1.06 1.26 0.49 0.52 0.70
OP1 1.87 0.93 2.59 2.19 0.89 1.76 0.49 1.52 0.22 1.41 0.74 1.38 1.04 1.03 1.39 3.49 2.48 1.45 1.14 0.70 0.82 0.77 0.93
OP2 2.07 1.98 2.81 2.27 1.48 1.81 1.05 1.51 1.07 1.60 1.74 2.53 1.82 1.15 1.70 3.57 2.39 1.58 1.19 0.83 0.60 0.62 0.85
P 1.79 1.63 2.59 2.14 1.05 1.65 0.54 1.37 0.85 1.14 1.51 2.17 1.44 0.62 1.30 3.41 2.35 1.33 0.97 0.97 0.45 0.43 0.65

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 0.04 0.01 0.00 0.02 0.03 0.02 0.00 0.00 0.01 0.25 0.00 0.14 0.01 0.10 0.10 0.11
C2 0.02 0.00 0.31 0.81 0.01 0.70 0.01 1.09 0.01 0.00 0.00 0.00 0.00 0.00 0.01 0.29 0.54 0.47 1.42 0.01 1.61 2.21 1.75
C2' 0.00 0.31 0.00 0.01 0.16 0.02 0.09 0.15 0.15 0.12 0.25 0.37 0.30 0.07 0.03 0.00 0.00 0.02 0.22 0.13 0.18 0.49 0.31
C3' 0.01 0.81 0.01 0.00 0.42 0.00 0.35 0.01 0.45 0.43 0.65 1.00 0.77 0.38 0.20 0.01 0.01 0.02 0.17 0.42 0.28 0.23 0.08
C4 0.01 0.01 0.16 0.42 0.00 0.30 0.00 0.38 0.01 0.00 0.01 0.01 0.00 0.00 0.00 0.20 0.14 0.24 0.45 0.01 0.50 0.91 0.65
C4' 0.01 0.70 0.02 0.00 0.30 0.00 0.12 0.00 0.24 0.42 0.51 0.91 0.68 0.30 0.08 0.27 0.02 0.00 0.01 0.17 0.06 0.23 0.04
C5 0.01 0.01 0.09 0.35 0.00 0.12 0.00 0.12 0.00 0.00 0.01 0.01 0.00 0.00 0.00 0.20 0.12 0.08 0.09 0.00 0.11 0.71 0.24
C5' 0.04 1.09 0.15 0.01 0.38 0.00 0.12 0.00 0.32 0.70 0.77 1.46 0.99 0.53 0.13 0.12 0.18 0.01 0.01 0.19 0.06 0.34 0.01
C6 0.01 0.01 0.15 0.45 0.01 0.24 0.00 0.32 0.00 0.00 0.00 0.01 0.01 0.00 0.01 0.23 0.19 0.18 0.38 0.00 0.45 1.16 0.63
C8 0.00 0.00 0.12 0.43 0.00 0.42 0.00 0.70 0.00 0.00 0.01 0.01 0.00 0.00 0.00 0.19 0.39 0.29 0.98 0.00 0.98 0.89 0.88
N1 0.02 0.00 0.25 0.65 0.01 0.51 0.01 0.77 0.00 0.01 0.00 0.01 0.01 0.00 0.02 0.26 0.37 0.35 1.00 0.01 1.18 1.86 1.34
N2 0.03 0.00 0.37 1.00 0.01 0.91 0.01 1.46 0.01 0.01 0.01 0.00 0.00 0.01 0.01 0.34 0.76 0.58 1.92 0.01 2.26 2.87 2.34
N3 0.02 0.00 0.30 0.77 0.00 0.68 0.00 0.99 0.01 0.00 0.01 0.00 0.00 0.00 0.01 0.27 0.48 0.48 1.27 0.01 1.34 1.77 1.49
N7 0.00 0.00 0.07 0.38 0.00 0.30 0.00 0.53 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.20 0.34 0.17 0.76 0.00 0.82 0.82 0.68
N9 0.00 0.01 0.03 0.20 0.00 0.08 0.00 0.13 0.01 0.00 0.02 0.01 0.01 0.00 0.00 0.13 0.12 0.02 0.21 0.01 0.18 0.22 0.08
O2' 0.01 0.29 0.00 0.01 0.20 0.27 0.20 0.12 0.23 0.19 0.26 0.34 0.27 0.20 0.13 0.00 0.02 0.17 0.09 0.23 0.13 0.52 0.20
O3' 0.25 0.54 0.00 0.01 0.14 0.02 0.12 0.18 0.19 0.39 0.37 0.76 0.48 0.34 0.12 0.02 0.00 0.18 0.35 0.21 0.61 0.12 0.32
O4' 0.00 0.47 0.02 0.02 0.24 0.00 0.08 0.01 0.18 0.29 0.35 0.58 0.48 0.17 0.02 0.17 0.18 0.00 0.11 0.11 0.15 0.15 0.17
O5' 0.14 1.42 0.22 0.17 0.45 0.01 0.09 0.01 0.38 0.98 1.00 1.92 1.27 0.76 0.21 0.09 0.35 0.11 0.00 0.19 0.01 0.01 0.00
O6 0.01 0.01 0.13 0.42 0.01 0.17 0.00 0.19 0.00 0.00 0.01 0.01 0.01 0.00 0.01 0.23 0.21 0.11 0.19 0.00 0.22 1.05 0.41
OP1 0.10 1.61 0.18 0.28 0.50 0.06 0.11 0.06 0.45 0.98 1.18 2.26 1.34 0.82 0.18 0.13 0.61 0.15 0.01 0.22 0.00 0.01 0.00
OP2 0.10 2.21 0.49 0.23 0.91 0.23 0.71 0.34 1.16 0.89 1.86 2.87 1.77 0.82 0.22 0.52 0.12 0.15 0.01 1.05 0.01 0.00 0.01
P 0.11 1.75 0.31 0.08 0.65 0.04 0.24 0.01 0.63 0.88 1.34 2.34 1.49 0.68 0.08 0.20 0.32 0.17 0.00 0.41 0.00 0.01 0.00