ClaRNA

Doublet Group distance statistics: 48177

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Distances from reference structure (by RMSD)

1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1, 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, 0.012, 0.015 max_d=0.015 avg_d=0.007 std_dev=0.005
N1 A 0, 0.005, 0.016, 0.028, 0.034 max_d=0.034 avg_d=0.016 std_dev=0.012
C5 A 0, 0.001, 0.014, 0.028, 0.035 max_d=0.035 avg_d=0.014 std_dev=0.014
C2 A 0, 0.012, 0.026, 0.040, 0.040 max_d=0.040 avg_d=0.026 std_dev=0.014
C4 A 0, 0.012, 0.027, 0.042, 0.045 max_d=0.045 avg_d=0.027 std_dev=0.015
C1' A 0, 0.012, 0.027, 0.042, 0.047 max_d=0.047 avg_d=0.027 std_dev=0.015
C6 A 0, 0.010, 0.026, 0.042, 0.050 max_d=0.050 avg_d=0.026 std_dev=0.016
O2 A 0, 0.030, 0.073, 0.116, 0.128 max_d=0.128 avg_d=0.073 std_dev=0.043
N4 A 0, 0.034, 0.081, 0.127, 0.142 max_d=0.142 avg_d=0.081 std_dev=0.046
O2' B 0, 0.092, 0.258, 0.425, 0.424 max_d=0.424 avg_d=0.258 std_dev=0.166
C2' A 0, -0.159, 0.500, 1.159, 1.804 max_d=1.804 avg_d=0.500 std_dev=0.659
O4' A 0, -0.226, 0.461, 1.147, 1.813 max_d=1.813 avg_d=0.461 std_dev=0.687
O2' A 0, -0.192, 0.542, 1.275, 1.991 max_d=1.991 avg_d=0.542 std_dev=0.733
C2' B 0, 0.304, 1.043, 1.782, 2.084 max_d=2.084 avg_d=1.043 std_dev=0.739
C4' A 0, -0.289, 0.681, 1.651, 2.584 max_d=2.584 avg_d=0.681 std_dev=0.970
C3' A 0, -0.286, 0.755, 1.797, 2.810 max_d=2.810 avg_d=0.755 std_dev=1.042
C3' B 0, 0.457, 1.632, 2.807, 3.135 max_d=3.135 avg_d=1.632 std_dev=1.175
O3' A 0, -0.355, 1.065, 2.485, 3.863 max_d=3.863 avg_d=1.065 std_dev=1.420
C5' A 0, -0.533, 1.192, 2.916, 4.597 max_d=4.597 avg_d=1.192 std_dev=1.725
O3' B 0, 0.620, 2.390, 4.160, 4.525 max_d=4.525 avg_d=2.390 std_dev=1.770
O5' A 0, -0.570, 1.336, 3.241, 5.093 max_d=5.093 avg_d=1.336 std_dev=1.905
C1' B 0, 0.696, 2.725, 4.754, 4.812 max_d=4.812 avg_d=2.725 std_dev=2.029
C4' B 0, 0.769, 2.963, 5.157, 5.287 max_d=5.287 avg_d=2.963 std_dev=2.194
O5' B 0, 0.603, 2.882, 5.161, 5.648 max_d=5.648 avg_d=2.882 std_dev=2.279
OP1 B 0, 0.689, 3.009, 5.330, 6.257 max_d=6.257 avg_d=3.009 std_dev=2.321
C5' B 0, 0.733, 3.210, 5.688, 6.308 max_d=6.308 avg_d=3.210 std_dev=2.477
P A 0, -0.714, 1.825, 4.364, 6.841 max_d=6.841 avg_d=1.825 std_dev=2.539
OP1 A 0, -0.597, 2.039, 4.674, 7.218 max_d=7.218 avg_d=2.039 std_dev=2.635
P B 0, 0.466, 3.146, 5.825, 7.587 max_d=7.587 avg_d=3.146 std_dev=2.680
O4' B 0, 0.893, 3.580, 6.267, 6.561 max_d=6.561 avg_d=3.580 std_dev=2.687
N9 B 0, 0.894, 3.625, 6.355, 6.361 max_d=6.361 avg_d=3.625 std_dev=2.731
OP2 A 0, -0.800, 2.348, 5.497, 8.577 max_d=8.577 avg_d=2.348 std_dev=3.149
C8 B 0, 1.016, 4.280, 7.544, 7.900 max_d=7.900 avg_d=4.280 std_dev=3.264
OP2 B 0, -0.085, 3.210, 6.504, 9.398 max_d=9.398 avg_d=3.210 std_dev=3.295
C4 B 0, 1.085, 4.445, 7.806, 7.702 max_d=7.702 avg_d=4.445 std_dev=3.361
N3 B 0, 1.114, 4.523, 7.932, 8.107 max_d=8.107 avg_d=4.523 std_dev=3.409
N7 B 0, 1.254, 5.384, 9.514, 9.862 max_d=9.862 avg_d=5.384 std_dev=4.130
C5 B 0, 1.314, 5.508, 9.703, 9.403 max_d=9.403 avg_d=5.508 std_dev=4.194
C2 B 0, 1.362, 5.676, 9.989, 10.447 max_d=10.447 avg_d=5.676 std_dev=4.313
C6 B 0, 1.568, 6.649, 11.731, 11.858 max_d=11.858 avg_d=6.649 std_dev=5.081
N1 B 0, 1.578, 6.685, 11.793, 12.337 max_d=12.337 avg_d=6.685 std_dev=5.108
N6 B 0, 1.807, 7.807, 13.806, 13.748 max_d=13.748 avg_d=7.807 std_dev=6.000

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 0.02 0.00 0.01 0.02 0.01 0.02 0.01 0.02 0.01 0.01 0.02 0.04 0.01 0.02 0.00 0.03 0.08 0.21 0.14
C2 0.02 0.00 0.23 0.14 0.01 0.13 0.02 0.24 0.01 0.01 0.00 0.01 0.01 0.21 0.20 0.24 0.20 0.47 0.40 0.29
C2' 0.00 0.23 0.00 0.01 0.06 0.02 0.13 0.02 0.20 0.03 0.19 0.07 0.40 0.00 0.03 0.01 0.03 0.18 0.13 0.03
C3' 0.01 0.14 0.01 0.00 0.10 0.01 0.06 0.02 0.04 0.07 0.14 0.11 0.18 0.03 0.01 0.01 0.04 0.20 0.14 0.05
C4 0.02 0.01 0.06 0.10 0.00 0.05 0.01 0.09 0.01 0.01 0.00 0.01 0.01 0.04 0.13 0.01 0.14 0.42 0.53 0.30
C4' 0.01 0.13 0.02 0.01 0.05 0.00 0.19 0.01 0.23 0.04 0.10 0.06 0.26 0.08 0.02 0.00 0.01 0.20 0.10 0.04
C5 0.02 0.02 0.13 0.06 0.01 0.19 0.00 0.34 0.01 0.01 0.01 0.03 0.02 0.19 0.04 0.21 0.41 0.24 0.94 0.59
C5' 0.01 0.24 0.02 0.02 0.09 0.01 0.34 0.00 0.38 0.07 0.19 0.09 0.44 0.08 0.04 0.01 0.01 0.31 0.19 0.02
C6 0.02 0.01 0.20 0.04 0.01 0.23 0.01 0.38 0.00 0.01 0.01 0.02 0.02 0.23 0.03 0.29 0.45 0.18 0.84 0.59
N1 0.01 0.01 0.03 0.07 0.01 0.04 0.01 0.07 0.01 0.00 0.01 0.02 0.02 0.03 0.08 0.01 0.10 0.21 0.35 0.23
N3 0.01 0.00 0.19 0.14 0.00 0.10 0.01 0.19 0.01 0.01 0.00 0.01 0.01 0.16 0.20 0.18 0.17 0.55 0.39 0.29
N4 0.02 0.01 0.07 0.11 0.01 0.06 0.03 0.09 0.02 0.02 0.01 0.00 0.01 0.05 0.15 0.02 0.14 0.48 0.57 0.30
O2 0.04 0.01 0.40 0.18 0.01 0.26 0.02 0.44 0.02 0.02 0.01 0.01 0.00 0.42 0.27 0.43 0.38 0.58 0.64 0.47
O2' 0.01 0.21 0.00 0.03 0.04 0.08 0.19 0.08 0.23 0.03 0.16 0.05 0.42 0.00 0.05 0.06 0.05 0.17 0.11 0.07
O3' 0.02 0.20 0.03 0.01 0.13 0.02 0.04 0.04 0.03 0.08 0.20 0.15 0.27 0.05 0.00 0.02 0.06 0.31 0.22 0.14
O4' 0.00 0.24 0.01 0.01 0.01 0.00 0.21 0.01 0.29 0.01 0.18 0.02 0.43 0.06 0.02 0.00 0.06 0.08 0.22 0.15
O5' 0.03 0.20 0.03 0.04 0.14 0.01 0.41 0.01 0.45 0.10 0.17 0.14 0.38 0.05 0.06 0.06 0.00 0.01 0.02 0.00
OP1 0.08 0.47 0.18 0.20 0.42 0.20 0.24 0.31 0.18 0.21 0.55 0.48 0.58 0.17 0.31 0.08 0.01 0.00 0.01 0.01
OP2 0.21 0.40 0.13 0.14 0.53 0.10 0.94 0.19 0.84 0.35 0.39 0.57 0.64 0.11 0.22 0.22 0.02 0.01 0.00 0.00
P 0.14 0.29 0.03 0.05 0.30 0.04 0.59 0.02 0.59 0.23 0.29 0.30 0.47 0.07 0.14 0.15 0.00 0.01 0.00 0.00

Atoms distances Chain-A - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N3N6N7N9O2'O3'O4'O5'OP1OP2P
C1' 0.47 1.86 0.10 0.40 1.51 0.45 2.18 0.32 2.60 1.68 2.36 1.41 3.17 2.29 1.14 0.24 0.99 0.50 0.94 1.22 1.67 1.22
C2 0.47 2.02 0.06 0.42 1.51 0.61 1.99 0.48 2.41 1.39 2.37 1.58 2.78 1.92 1.06 0.22 0.85 0.45 0.51 0.94 1.03 0.72
C2' 0.46 1.95 0.32 0.21 1.63 0.32 2.39 0.60 2.80 1.94 2.50 1.47 3.46 2.58 1.28 0.23 0.80 0.43 1.27 1.62 2.16 1.66
C3' 0.21 1.61 0.14 0.38 1.22 0.40 1.94 0.48 2.29 1.63 2.03 1.17 2.91 2.21 0.93 0.30 1.06 0.38 1.20 1.62 2.13 1.62
C4 0.44 1.62 0.06 0.40 1.30 0.58 1.67 0.43 1.93 1.22 1.86 1.33 2.15 1.63 0.95 0.21 0.78 0.41 0.47 0.86 0.82 0.61
C4' 0.33 1.40 0.14 0.64 1.02 0.66 1.68 0.39 2.05 1.35 1.82 1.02 2.64 1.91 0.72 0.39 1.32 0.59 0.96 1.30 1.74 1.28
C5 0.43 1.35 0.10 0.37 1.25 0.39 1.78 0.26 1.96 1.49 1.71 1.08 2.27 1.92 1.01 0.23 0.91 0.42 0.86 1.07 1.33 1.03
C5' 0.49 1.16 0.36 0.89 0.64 0.93 1.23 0.58 1.56 0.99 1.41 0.84 2.10 1.47 0.36 0.53 1.58 0.81 0.88 1.22 1.53 1.14
C6 0.45 1.52 0.13 0.39 1.37 0.39 2.00 0.33 2.27 1.65 1.97 1.18 2.71 2.18 1.09 0.24 0.99 0.47 1.00 1.22 1.62 1.24
N1 0.46 1.79 0.09 0.39 1.46 0.46 2.06 0.30 2.43 1.57 2.23 1.38 2.90 2.13 1.09 0.23 0.93 0.47 0.81 1.10 1.44 1.05
N3 0.47 2.00 0.08 0.46 1.47 0.70 1.84 0.62 2.22 1.23 2.25 1.60 2.48 1.71 1.01 0.20 0.81 0.45 0.36 0.88 0.73 0.53
N4 0.43 1.51 0.11 0.46 1.20 0.73 1.41 0.62 1.63 0.98 1.65 1.30 1.76 1.30 0.85 0.19 0.74 0.44 0.28 0.79 0.42 0.39
O2 0.49 2.24 0.06 0.44 1.60 0.67 2.07 0.59 2.57 1.37 2.60 1.72 2.96 1.94 1.09 0.21 0.85 0.46 0.42 0.93 0.95 0.64
O2' 0.64 2.26 0.43 0.22 1.90 0.33 2.70 0.71 3.20 2.15 2.90 1.71 3.94 2.86 1.50 0.24 0.73 0.56 1.38 1.70 2.31 1.79
O3' 0.23 1.71 0.21 0.32 1.28 0.36 2.02 0.64 2.39 1.74 2.14 1.24 3.06 2.33 0.99 0.30 1.01 0.40 1.37 1.85 2.41 1.88
O4' 0.47 1.47 0.17 0.67 1.14 0.73 1.75 0.40 2.12 1.33 1.90 1.11 2.67 1.89 0.82 0.36 1.29 0.70 0.81 1.05 1.46 1.04
O5' 0.54 1.14 0.44 0.91 0.50 0.93 0.99 0.56 1.29 0.82 1.24 0.86 1.75 1.25 0.17 0.60 1.61 0.82 0.82 1.20 1.44 1.08
OP1 0.50 1.27 0.31 0.73 0.64 0.83 1.13 0.85 1.38 1.16 1.41 0.84 1.75 1.44 0.56 0.52 1.38 0.73 1.40 1.95 1.99 1.72
OP2 1.40 1.74 1.31 1.67 1.06 1.73 0.83 1.33 1.15 0.52 1.55 1.57 1.21 0.54 0.92 1.33 2.25 1.60 0.87 0.93 0.31 0.57
P 0.87 1.30 0.73 1.22 0.52 1.28 0.66 0.91 1.02 0.46 1.23 1.07 1.34 0.80 0.29 0.84 1.90 1.14 0.86 1.18 1.13 0.93

Atoms distances Chain-B - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N3N6N7N9O2'O3'O4'O5'OP1OP2P
C1' 0.00 0.05 0.00 0.01 0.03 0.00 0.01 0.12 0.03 0.03 0.04 0.06 0.02 0.02 0.00 0.01 0.30 0.01 0.30 0.30 0.27 0.12
C2 0.05 0.00 0.48 0.85 0.01 0.50 0.01 0.74 0.01 0.01 0.00 0.01 0.01 0.02 0.01 0.10 0.62 0.21 1.03 1.82 1.68 1.46
C2' 0.00 0.48 0.00 0.00 0.24 0.01 0.08 0.24 0.18 0.26 0.35 0.49 0.10 0.16 0.01 0.00 0.01 0.01 0.63 0.63 0.17 0.41
C3' 0.01 0.85 0.00 0.00 0.52 0.01 0.43 0.02 0.57 0.22 0.75 0.80 0.52 0.26 0.21 0.03 0.01 0.02 0.24 0.55 0.42 0.24
C4 0.03 0.01 0.24 0.52 0.00 0.28 0.00 0.39 0.02 0.01 0.02 0.00 0.02 0.01 0.00 0.16 0.25 0.11 0.67 0.98 0.93 0.79
C4' 0.00 0.50 0.01 0.01 0.28 0.00 0.21 0.01 0.31 0.14 0.43 0.45 0.26 0.08 0.07 0.32 0.02 0.00 0.01 0.28 0.42 0.12
C5 0.01 0.01 0.08 0.43 0.00 0.21 0.00 0.30 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.30 0.19 0.07 0.63 0.77 0.81 0.67
C5' 0.12 0.74 0.24 0.02 0.39 0.01 0.30 0.00 0.46 0.30 0.66 0.65 0.39 0.18 0.16 0.09 0.25 0.03 0.01 0.15 0.29 0.02
C6 0.03 0.01 0.18 0.57 0.02 0.31 0.01 0.46 0.00 0.02 0.01 0.00 0.01 0.02 0.02 0.28 0.34 0.12 0.80 1.15 1.21 1.00
C8 0.03 0.01 0.26 0.22 0.01 0.14 0.01 0.30 0.02 0.00 0.02 0.01 0.01 0.01 0.01 0.37 0.23 0.12 0.54 0.40 0.51 0.49
N1 0.04 0.00 0.35 0.75 0.02 0.43 0.01 0.66 0.01 0.02 0.00 0.01 0.02 0.02 0.02 0.18 0.52 0.18 0.99 1.64 1.62 1.37
N3 0.06 0.01 0.49 0.80 0.00 0.45 0.01 0.65 0.00 0.01 0.01 0.00 0.01 0.01 0.01 0.09 0.54 0.20 0.89 1.55 1.37 1.22
N6 0.02 0.01 0.10 0.52 0.02 0.26 0.01 0.39 0.01 0.01 0.02 0.01 0.00 0.01 0.02 0.36 0.32 0.09 0.74 0.99 1.06 0.88
N7 0.02 0.02 0.16 0.26 0.01 0.08 0.01 0.18 0.02 0.01 0.02 0.01 0.01 0.00 0.00 0.40 0.18 0.07 0.47 0.33 0.41 0.38
N9 0.00 0.01 0.01 0.21 0.00 0.07 0.01 0.16 0.02 0.01 0.02 0.01 0.02 0.00 0.00 0.20 0.05 0.01 0.43 0.40 0.37 0.29
O2' 0.01 0.10 0.00 0.03 0.16 0.32 0.30 0.09 0.28 0.37 0.18 0.09 0.36 0.40 0.20 0.00 0.04 0.22 0.39 0.54 0.26 0.31
O3' 0.30 0.62 0.01 0.01 0.25 0.02 0.19 0.25 0.34 0.23 0.52 0.54 0.32 0.18 0.05 0.04 0.00 0.23 0.09 0.74 0.61 0.42
O4' 0.01 0.21 0.01 0.02 0.11 0.00 0.07 0.03 0.12 0.12 0.18 0.20 0.09 0.07 0.01 0.22 0.23 0.00 0.10 0.20 0.53 0.27
O5' 0.30 1.03 0.63 0.24 0.67 0.01 0.63 0.01 0.80 0.54 0.99 0.89 0.74 0.47 0.43 0.39 0.09 0.10 0.00 0.01 0.01 0.01
OP1 0.30 1.82 0.63 0.55 0.98 0.28 0.77 0.15 1.15 0.40 1.64 1.55 0.99 0.33 0.40 0.54 0.74 0.20 0.01 0.00 0.02 0.01
OP2 0.27 1.68 0.17 0.42 0.93 0.42 0.81 0.29 1.21 0.51 1.62 1.37 1.06 0.41 0.37 0.26 0.61 0.53 0.01 0.02 0.00 0.00
P 0.12 1.46 0.41 0.24 0.79 0.12 0.67 0.02 1.00 0.49 1.37 1.22 0.88 0.38 0.29 0.31 0.42 0.27 0.01 0.01 0.00 0.00