ClaRNA

Doublet Group distance statistics: 53577

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Distances from reference structure (by RMSD)

1, 2, 1, 3, 2, 0, 0, 0, 0, 2, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0,

RMS Distances matrix

Distances graph

Distances from reference structure (by atoms)

Atom Chain Distances
C6 A 0, 0.002, 0.009, 0.015, 0.021 max_d=0.021 avg_d=0.009 std_dev=0.007
N1 A 0, 0.009, 0.018, 0.028, 0.035 max_d=0.035 avg_d=0.018 std_dev=0.010
C2 A 0, 0.008, 0.020, 0.031, 0.046 max_d=0.046 avg_d=0.020 std_dev=0.011
N3 A 0, 0.009, 0.021, 0.033, 0.048 max_d=0.048 avg_d=0.021 std_dev=0.012
C1' A 0, 0.013, 0.025, 0.038, 0.047 max_d=0.047 avg_d=0.025 std_dev=0.012
C5 A 0, 0.006, 0.022, 0.037, 0.055 max_d=0.055 avg_d=0.022 std_dev=0.016
C4 A 0, 0.006, 0.022, 0.039, 0.052 max_d=0.052 avg_d=0.022 std_dev=0.017
N9 A 0, 0.005, 0.027, 0.050, 0.076 max_d=0.076 avg_d=0.027 std_dev=0.022
O6 A 0, 0.006, 0.033, 0.060, 0.092 max_d=0.092 avg_d=0.033 std_dev=0.027
N2 A 0, 0.016, 0.044, 0.072, 0.123 max_d=0.123 avg_d=0.044 std_dev=0.028
N7 A 0, 0.019, 0.055, 0.090, 0.133 max_d=0.133 avg_d=0.055 std_dev=0.036
C8 A 0, 0.013, 0.054, 0.094, 0.136 max_d=0.136 avg_d=0.054 std_dev=0.041
P B 0, 0.102, 0.403, 0.705, 1.002 max_d=1.002 avg_d=0.403 std_dev=0.301
OP1 B 0, 0.110, 0.496, 0.882, 1.393 max_d=1.393 avg_d=0.496 std_dev=0.386
O5' B 0, 0.114, 0.616, 1.119, 1.623 max_d=1.623 avg_d=0.616 std_dev=0.502
OP2 B 0, 0.003, 0.579, 1.156, 1.816 max_d=1.816 avg_d=0.579 std_dev=0.577
O4' A 0, -0.240, 0.528, 1.296, 2.308 max_d=2.308 avg_d=0.528 std_dev=0.768
C2' A 0, -0.237, 0.532, 1.301, 2.314 max_d=2.314 avg_d=0.532 std_dev=0.769
C2' B 0, 0.006, 1.015, 2.025, 2.739 max_d=2.739 avg_d=1.015 std_dev=1.009
C5' B 0, -0.017, 0.999, 2.016, 2.797 max_d=2.797 avg_d=0.999 std_dev=1.017
O2' A 0, -0.365, 0.677, 1.718, 3.195 max_d=3.195 avg_d=0.677 std_dev=1.042
C3' B 0, -0.033, 1.070, 2.172, 2.956 max_d=2.956 avg_d=1.070 std_dev=1.102
C3' A 0, -0.314, 0.818, 1.950, 3.147 max_d=3.147 avg_d=0.818 std_dev=1.132
C4' A 0, -0.335, 0.852, 2.040, 3.398 max_d=3.398 avg_d=0.852 std_dev=1.188
O3' B 0, -0.086, 1.225, 2.536, 3.584 max_d=3.584 avg_d=1.225 std_dev=1.311
O3' A 0, -0.329, 1.052, 2.433, 3.410 max_d=3.410 avg_d=1.052 std_dev=1.381
C4' B 0, -0.125, 1.308, 2.741, 3.836 max_d=3.836 avg_d=1.308 std_dev=1.433
O2' B 0, -0.155, 1.286, 2.727, 4.028 max_d=4.028 avg_d=1.286 std_dev=1.441
C1' B 0, -0.131, 1.444, 3.020, 4.096 max_d=4.096 avg_d=1.444 std_dev=1.575
C5' A 0, -0.491, 1.275, 3.040, 5.286 max_d=5.286 avg_d=1.275 std_dev=1.766
O4' B 0, -0.214, 1.575, 3.365, 4.625 max_d=4.625 avg_d=1.575 std_dev=1.789
N9 B 0, -0.190, 1.637, 3.464, 4.768 max_d=4.768 avg_d=1.637 std_dev=1.827
N3 B 0, -0.151, 1.744, 3.638, 4.967 max_d=4.967 avg_d=1.744 std_dev=1.895
C4 B 0, -0.239, 1.835, 3.910, 5.369 max_d=5.369 avg_d=1.835 std_dev=2.074
C2 B 0, -0.228, 1.993, 4.214, 5.870 max_d=5.870 avg_d=1.993 std_dev=2.221
C8 B 0, -0.341, 1.982, 4.305, 5.888 max_d=5.888 avg_d=1.982 std_dev=2.323
O5' A 0, -0.695, 1.706, 4.107, 6.383 max_d=6.383 avg_d=1.706 std_dev=2.401
C5 B 0, -0.455, 2.338, 5.131, 6.922 max_d=6.922 avg_d=2.338 std_dev=2.793
N1 B 0, -0.444, 2.440, 5.324, 7.617 max_d=7.617 avg_d=2.440 std_dev=2.884
N7 B 0, -0.529, 2.482, 5.493, 7.388 max_d=7.388 avg_d=2.482 std_dev=3.011
C6 B 0, -0.578, 2.691, 5.960, 8.140 max_d=8.140 avg_d=2.691 std_dev=3.269
P A 0, -0.923, 2.380, 5.684, 8.460 max_d=8.460 avg_d=2.380 std_dev=3.304
OP2 A 0, -1.061, 2.572, 6.205, 9.922 max_d=9.922 avg_d=2.572 std_dev=3.633
OP1 A 0, -1.013, 2.750, 6.512, 9.728 max_d=9.728 avg_d=2.750 std_dev=3.763
N6 B 0, -0.826, 3.322, 7.470, 10.236 max_d=10.236 avg_d=3.322 std_dev=4.148

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 0.04 0.00 0.01 0.02 0.01 0.01 0.07 0.02 0.01 0.03 0.06 0.04 0.01 0.00 0.02 0.31 0.01 0.26 0.01 0.25 0.48 0.31
C2 0.04 0.00 0.43 0.34 0.01 0.25 0.00 0.35 0.00 0.01 0.00 0.00 0.00 0.00 0.01 0.31 0.27 0.43 0.32 0.01 0.35 0.49 0.40
C2' 0.00 0.43 0.00 0.00 0.24 0.01 0.15 0.19 0.24 0.18 0.36 0.50 0.41 0.06 0.03 0.00 0.02 0.01 0.32 0.20 0.24 0.47 0.32
C3' 0.01 0.34 0.00 0.00 0.33 0.00 0.43 0.02 0.47 0.34 0.42 0.30 0.28 0.42 0.26 0.01 0.01 0.02 0.32 0.51 0.31 0.28 0.19
C4 0.02 0.01 0.24 0.33 0.00 0.08 0.00 0.16 0.00 0.00 0.01 0.01 0.00 0.00 0.01 0.07 0.19 0.22 0.51 0.00 0.47 0.59 0.50
C4' 0.01 0.25 0.01 0.00 0.08 0.00 0.12 0.00 0.10 0.30 0.15 0.36 0.24 0.26 0.11 0.30 0.03 0.00 0.01 0.13 0.21 0.34 0.18
C5 0.01 0.00 0.15 0.43 0.00 0.12 0.00 0.18 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.19 0.25 0.10 0.79 0.00 0.75 0.90 0.80
C5' 0.07 0.35 0.19 0.02 0.16 0.00 0.18 0.00 0.19 0.36 0.26 0.48 0.33 0.34 0.12 0.10 0.20 0.01 0.01 0.22 0.22 0.27 0.01
C6 0.02 0.00 0.24 0.47 0.00 0.10 0.00 0.19 0.00 0.01 0.00 0.01 0.00 0.01 0.01 0.12 0.30 0.19 0.75 0.00 0.74 0.88 0.77
C8 0.01 0.01 0.18 0.34 0.00 0.30 0.00 0.36 0.01 0.00 0.01 0.01 0.01 0.00 0.00 0.48 0.16 0.23 1.00 0.01 0.91 1.07 1.03
N1 0.03 0.00 0.36 0.42 0.01 0.15 0.00 0.26 0.00 0.01 0.00 0.01 0.00 0.01 0.01 0.16 0.28 0.34 0.52 0.01 0.51 0.62 0.52
N2 0.06 0.00 0.50 0.30 0.01 0.36 0.01 0.48 0.01 0.01 0.01 0.00 0.01 0.01 0.02 0.46 0.32 0.53 0.23 0.02 0.37 0.52 0.46
N3 0.04 0.00 0.41 0.28 0.00 0.24 0.00 0.33 0.00 0.01 0.00 0.01 0.00 0.00 0.01 0.31 0.27 0.42 0.27 0.01 0.31 0.49 0.38
N7 0.01 0.00 0.06 0.42 0.00 0.26 0.00 0.34 0.01 0.00 0.01 0.01 0.00 0.00 0.00 0.42 0.26 0.12 1.06 0.01 1.03 1.26 1.14
N9 0.00 0.01 0.03 0.26 0.01 0.11 0.00 0.12 0.01 0.00 0.01 0.02 0.01 0.00 0.00 0.19 0.11 0.01 0.59 0.01 0.51 0.62 0.56
O2' 0.02 0.31 0.00 0.01 0.07 0.30 0.19 0.10 0.12 0.48 0.16 0.46 0.31 0.42 0.19 0.00 0.04 0.21 0.24 0.18 0.11 0.56 0.24
O3' 0.31 0.27 0.02 0.01 0.19 0.03 0.25 0.20 0.30 0.16 0.28 0.32 0.27 0.26 0.11 0.04 0.00 0.22 0.33 0.37 0.56 0.35 0.29
O4' 0.01 0.43 0.01 0.02 0.22 0.00 0.10 0.01 0.19 0.23 0.34 0.53 0.42 0.12 0.01 0.21 0.22 0.00 0.22 0.14 0.31 0.54 0.33
O5' 0.26 0.32 0.32 0.32 0.51 0.01 0.79 0.01 0.75 1.00 0.52 0.23 0.27 1.06 0.59 0.24 0.33 0.22 0.00 0.88 0.02 0.01 0.00
O6 0.01 0.01 0.20 0.51 0.00 0.13 0.00 0.22 0.00 0.01 0.01 0.02 0.01 0.01 0.01 0.18 0.37 0.14 0.88 0.00 0.92 1.09 0.95
OP1 0.25 0.35 0.24 0.31 0.47 0.21 0.75 0.22 0.74 0.91 0.51 0.37 0.31 1.03 0.51 0.11 0.56 0.31 0.02 0.92 0.00 0.01 0.00
OP2 0.48 0.49 0.47 0.28 0.59 0.34 0.90 0.27 0.88 1.07 0.62 0.52 0.49 1.26 0.62 0.56 0.35 0.54 0.01 1.09 0.01 0.00 0.00
P 0.31 0.40 0.32 0.19 0.50 0.18 0.80 0.01 0.77 1.03 0.52 0.46 0.38 1.14 0.56 0.24 0.29 0.33 0.00 0.95 0.00 0.00 0.00

Atoms distances Chain-A - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N3N6N7N9O2'O3'O4'O5'OP1OP2P
C1' 0.85 1.64 0.29 0.26 1.63 0.49 2.22 0.43 2.47 1.97 2.14 1.34 3.00 2.47 1.45 0.79 0.36 1.17 0.50 0.23 0.40 0.35
C2 0.61 1.09 0.41 0.28 1.14 0.42 1.55 0.36 1.65 1.46 1.40 0.91 1.95 1.79 1.05 0.71 0.30 0.97 0.42 0.20 0.39 0.30
C2' 0.48 1.20 0.76 0.63 1.16 0.34 1.70 0.34 1.95 1.45 1.66 0.92 2.45 1.90 0.98 1.27 0.74 0.80 0.30 0.56 0.48 0.32
C3' 0.83 1.73 0.29 0.25 1.63 0.47 2.18 0.38 2.49 1.84 2.23 1.40 3.03 2.34 1.39 0.81 0.33 1.10 0.38 0.50 0.40 0.26
C4 0.66 1.30 0.41 0.30 1.31 0.37 1.81 0.33 1.98 1.63 1.70 1.06 2.39 2.04 1.17 0.77 0.35 0.99 0.42 0.23 0.40 0.30
C4' 1.34 2.24 0.37 0.49 2.18 0.94 2.79 0.85 3.09 2.46 2.78 1.90 3.67 2.99 1.95 0.45 0.37 1.61 0.90 0.41 0.63 0.63
C5 0.54 1.15 0.47 0.35 1.15 0.30 1.60 0.26 1.76 1.43 1.51 0.92 2.13 1.80 1.01 0.74 0.36 0.86 0.36 0.25 0.43 0.29
C5' 1.46 2.38 0.57 0.67 2.31 1.07 2.92 1.01 3.23 2.56 2.92 2.03 3.82 3.11 2.07 0.49 0.58 1.70 1.06 0.53 0.77 0.76
C6 0.44 0.95 0.51 0.36 0.95 0.27 1.33 0.24 1.46 1.19 1.26 0.76 1.77 1.51 0.84 0.68 0.33 0.74 0.32 0.26 0.43 0.28
C8 0.64 1.37 0.42 0.34 1.36 0.32 1.88 0.28 2.10 1.66 1.82 1.10 2.57 2.10 1.19 0.80 0.40 0.95 0.39 0.25 0.42 0.30
N1 0.47 0.92 0.48 0.32 0.94 0.32 1.30 0.28 1.40 1.20 1.19 0.75 1.66 1.48 0.84 0.66 0.31 0.80 0.36 0.23 0.43 0.29
N2 0.65 1.03 0.38 0.26 1.11 0.50 1.48 0.43 1.53 1.46 1.30 0.89 1.77 1.74 1.05 0.67 0.28 1.03 0.46 0.17 0.31 0.29
N3 0.71 1.30 0.37 0.27 1.35 0.44 1.83 0.38 1.98 1.69 1.69 1.08 2.36 2.09 1.22 0.76 0.32 1.06 0.45 0.21 0.37 0.31
N7 0.55 1.21 0.47 0.37 1.20 0.28 1.67 0.24 1.86 1.47 1.61 0.97 2.27 1.87 1.04 0.76 0.39 0.85 0.35 0.26 0.43 0.28
N9 0.72 1.45 0.37 0.30 1.45 0.39 1.99 0.34 2.20 1.77 1.90 1.17 2.67 2.22 1.28 0.80 0.38 1.04 0.44 0.23 0.41 0.31
O2' 0.70 1.27 0.93 0.81 1.27 0.54 1.76 0.46 1.97 1.57 1.68 1.04 2.44 1.99 1.13 1.42 0.94 0.97 0.40 0.43 0.47 0.32
O3' 1.30 2.18 0.37 0.48 2.06 0.88 2.57 0.68 2.87 2.20 2.64 1.86 3.38 2.68 1.82 0.51 0.41 1.54 0.66 0.41 0.44 0.41
O4' 1.35 2.18 0.34 0.45 2.17 0.96 2.79 0.90 3.06 2.52 2.71 1.86 3.63 3.04 1.98 0.40 0.33 1.64 1.01 0.49 0.81 0.80
O5' 1.23 2.28 0.34 0.46 2.15 0.76 2.77 0.62 3.12 2.33 2.84 1.91 3.71 2.91 1.87 0.38 0.41 1.41 0.69 0.33 0.39 0.37
O6 0.34 0.82 0.55 0.39 0.81 0.22 1.14 0.21 1.27 0.99 1.09 0.65 1.54 1.28 0.69 0.64 0.33 0.61 0.27 0.29 0.42 0.26
OP1 1.61 2.72 0.73 0.86 2.56 1.11 3.16 0.90 3.53 2.69 3.27 2.33 4.12 3.27 2.25 0.30 0.83 1.75 0.97 0.28 0.62 0.60
OP2 1.58 2.62 0.82 0.95 2.48 1.09 3.05 0.86 3.37 2.61 3.12 2.27 3.90 3.16 2.20 0.47 0.98 1.69 1.00 0.37 0.72 0.66
P 1.65 2.76 0.77 0.89 2.61 1.13 3.22 0.92 3.58 2.76 3.31 2.38 4.17 3.35 2.31 0.32 0.86 1.78 1.03 0.31 0.69 0.66

Atoms distances Chain-B - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N3N6N7N9O2'O3'O4'O5'OP1OP2P
C1' 0.00 0.03 0.01 0.02 0.02 0.02 0.02 0.08 0.02 0.01 0.03 0.03 0.02 0.02 0.01 0.02 0.34 0.00 0.20 0.19 0.18 0.17
C2 0.03 0.00 0.25 0.26 0.01 0.09 0.01 0.14 0.00 0.01 0.00 0.00 0.01 0.01 0.01 0.23 0.29 0.07 0.31 0.30 0.44 0.38
C2' 0.01 0.25 0.00 0.00 0.14 0.03 0.07 0.20 0.13 0.10 0.20 0.25 0.09 0.06 0.02 0.00 0.02 0.02 0.55 0.44 0.81 0.57
C3' 0.02 0.26 0.00 0.00 0.25 0.01 0.32 0.01 0.34 0.27 0.31 0.21 0.37 0.32 0.20 0.03 0.01 0.04 0.20 0.17 0.39 0.20
C4 0.02 0.01 0.14 0.25 0.00 0.09 0.00 0.16 0.01 0.00 0.01 0.00 0.01 0.01 0.00 0.27 0.20 0.04 0.31 0.32 0.37 0.37
C4' 0.02 0.09 0.03 0.01 0.09 0.00 0.12 0.01 0.13 0.12 0.11 0.08 0.14 0.14 0.08 0.33 0.03 0.01 0.01 0.09 0.05 0.06
C5 0.02 0.01 0.07 0.32 0.00 0.12 0.00 0.21 0.00 0.00 0.00 0.00 0.01 0.00 0.01 0.35 0.13 0.02 0.37 0.42 0.50 0.48
C5' 0.08 0.14 0.20 0.01 0.16 0.01 0.21 0.00 0.22 0.22 0.18 0.11 0.25 0.25 0.15 0.15 0.26 0.03 0.01 0.09 0.02 0.03
C6 0.02 0.00 0.13 0.34 0.01 0.13 0.00 0.22 0.00 0.01 0.00 0.00 0.00 0.01 0.01 0.37 0.16 0.04 0.39 0.44 0.57 0.51
C8 0.01 0.01 0.10 0.27 0.00 0.12 0.00 0.22 0.01 0.00 0.00 0.00 0.02 0.00 0.01 0.30 0.08 0.05 0.35 0.40 0.39 0.43
N1 0.03 0.00 0.20 0.31 0.01 0.11 0.00 0.18 0.00 0.00 0.00 0.00 0.01 0.00 0.01 0.31 0.22 0.06 0.36 0.38 0.52 0.46
N3 0.03 0.00 0.25 0.21 0.00 0.08 0.00 0.11 0.00 0.00 0.00 0.00 0.01 0.01 0.01 0.18 0.32 0.07 0.28 0.26 0.36 0.32
N6 0.02 0.01 0.09 0.37 0.01 0.14 0.01 0.25 0.00 0.02 0.01 0.01 0.00 0.02 0.01 0.41 0.16 0.03 0.42 0.50 0.65 0.57
N7 0.02 0.01 0.06 0.32 0.01 0.14 0.00 0.25 0.01 0.00 0.00 0.01 0.02 0.00 0.01 0.37 0.12 0.03 0.40 0.48 0.55 0.53
N9 0.01 0.01 0.02 0.20 0.00 0.08 0.01 0.15 0.01 0.01 0.01 0.01 0.01 0.01 0.00 0.22 0.15 0.01 0.27 0.29 0.26 0.31
O2' 0.02 0.23 0.00 0.03 0.27 0.33 0.35 0.15 0.37 0.30 0.31 0.18 0.41 0.37 0.22 0.00 0.03 0.19 0.37 0.19 0.83 0.41
O3' 0.34 0.29 0.02 0.01 0.20 0.03 0.13 0.26 0.16 0.08 0.22 0.32 0.16 0.12 0.15 0.03 0.00 0.21 0.22 0.35 0.24 0.23
O4' 0.00 0.07 0.02 0.04 0.04 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.03 0.03 0.01 0.19 0.21 0.00 0.12 0.18 0.21 0.20
O5' 0.20 0.31 0.55 0.20 0.31 0.01 0.37 0.01 0.39 0.35 0.36 0.28 0.42 0.40 0.27 0.37 0.22 0.12 0.00 0.01 0.01 0.00
OP1 0.19 0.30 0.44 0.17 0.32 0.09 0.42 0.09 0.44 0.40 0.38 0.26 0.50 0.48 0.29 0.19 0.35 0.18 0.01 0.00 0.00 0.00
OP2 0.18 0.44 0.81 0.39 0.37 0.05 0.50 0.02 0.57 0.39 0.52 0.36 0.65 0.55 0.26 0.83 0.24 0.21 0.01 0.00 0.00 0.00
P 0.17 0.38 0.57 0.20 0.37 0.06 0.48 0.03 0.51 0.43 0.46 0.32 0.57 0.53 0.31 0.41 0.23 0.20 0.00 0.00 0.00 0.00