ClaRNA

Doublet Group distance statistics: 48646

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Distances from reference structure (by RMSD)

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

RMS Distances matrix

Distances graph

Distances from reference structure (by atoms)

Atom Chain Distances
C5 A 0, 0.003, 0.012, 0.020, 0.018 max_d=0.018 avg_d=0.012 std_dev=0.008
N3 A 0, 0.006, 0.020, 0.034, 0.030 max_d=0.030 avg_d=0.020 std_dev=0.014
N1 A 0, 0.006, 0.024, 0.042, 0.043 max_d=0.043 avg_d=0.024 std_dev=0.018
C2 A 0, 0.004, 0.022, 0.041, 0.045 max_d=0.045 avg_d=0.022 std_dev=0.018
C4 A 0, 0.007, 0.028, 0.048, 0.047 max_d=0.047 avg_d=0.028 std_dev=0.020
C6 A 0, 0.006, 0.029, 0.052, 0.056 max_d=0.056 avg_d=0.029 std_dev=0.023
C1' A 0, 0.011, 0.037, 0.063, 0.056 max_d=0.056 avg_d=0.037 std_dev=0.026
O2 A 0, 0.017, 0.060, 0.102, 0.094 max_d=0.094 avg_d=0.060 std_dev=0.042
O4 A 0, 0.042, 0.145, 0.247, 0.231 max_d=0.231 avg_d=0.145 std_dev=0.103
P B 0, 0.179, 0.623, 1.067, 1.003 max_d=1.003 avg_d=0.623 std_dev=0.444
OP1 B 0, 0.209, 0.760, 1.311, 1.290 max_d=1.290 avg_d=0.760 std_dev=0.551
OP2 B 0, 0.046, 0.775, 1.505, 1.752 max_d=1.752 avg_d=0.775 std_dev=0.729
O4' A 0, -0.223, 0.948, 2.119, 2.598 max_d=2.598 avg_d=0.948 std_dev=1.171
C2' A 0, -0.124, 1.087, 2.297, 2.776 max_d=2.776 avg_d=1.087 std_dev=1.210
O5' B 0, 0.571, 1.952, 3.333, 2.989 max_d=2.989 avg_d=1.952 std_dev=1.381
O2' A 0, 0.081, 1.572, 3.063, 3.575 max_d=3.575 avg_d=1.572 std_dev=1.491
C4' A 0, -0.252, 1.285, 2.822, 3.446 max_d=3.446 avg_d=1.285 std_dev=1.537
C3' A 0, -0.148, 1.616, 3.379, 4.069 max_d=4.069 avg_d=1.616 std_dev=1.764
C5' B 0, 0.881, 3.009, 5.138, 4.542 max_d=4.542 avg_d=3.009 std_dev=2.128
O3' A 0, 0.172, 2.436, 4.701, 5.455 max_d=5.455 avg_d=2.436 std_dev=2.265
C5' A 0, -0.717, 2.219, 5.155, 6.368 max_d=6.368 avg_d=2.219 std_dev=2.936
C4' B 0, 1.324, 4.571, 7.819, 7.236 max_d=7.236 avg_d=4.571 std_dev=3.247
O5' A 0, -0.852, 2.668, 6.189, 7.642 max_d=7.642 avg_d=2.668 std_dev=3.520
C3' B 0, 1.564, 5.341, 9.117, 8.046 max_d=8.046 avg_d=5.341 std_dev=3.776
O4' B 0, 1.631, 5.582, 9.533, 8.582 max_d=8.582 avg_d=5.582 std_dev=3.951
O3' B 0, 1.633, 5.649, 9.665, 8.980 max_d=8.980 avg_d=5.649 std_dev=4.016
C8 B 0, 1.569, 5.639, 9.709, 9.456 max_d=9.456 avg_d=5.639 std_dev=4.070
N7 B 0, 1.572, 5.968, 10.365, 10.463 max_d=10.463 avg_d=5.968 std_dev=4.397
N9 B 0, 1.927, 6.711, 11.495, 10.811 max_d=10.811 avg_d=6.711 std_dev=4.784
C1' B 0, 1.984, 6.773, 11.563, 10.181 max_d=10.181 avg_d=6.773 std_dev=4.790
P A 0, -0.994, 3.814, 8.623, 10.597 max_d=10.597 avg_d=3.814 std_dev=4.809
OP1 A 0, -0.087, 4.723, 9.534, 11.325 max_d=11.325 avg_d=4.723 std_dev=4.811
C2' B 0, 2.007, 6.857, 11.707, 10.421 max_d=10.421 avg_d=6.857 std_dev=4.850
OP2 A 0, -0.095, 5.031, 10.157, 12.066 max_d=12.066 avg_d=5.031 std_dev=5.126
C5 B 0, 1.951, 7.315, 12.678, 12.710 max_d=12.710 avg_d=7.315 std_dev=5.363
O2' B 0, 2.185, 7.690, 13.195, 12.584 max_d=12.584 avg_d=7.690 std_dev=5.505
C4 B 0, 2.213, 7.842, 13.471, 12.950 max_d=12.950 avg_d=7.842 std_dev=5.629
N6 B 0, 1.905, 8.012, 14.118, 14.810 max_d=14.810 avg_d=8.012 std_dev=6.107
C6 B 0, 2.136, 8.297, 14.458, 14.748 max_d=14.748 avg_d=8.297 std_dev=6.161
N3 B 0, 2.654, 9.252, 15.849, 14.923 max_d=14.923 avg_d=9.252 std_dev=6.597
N1 B 0, 2.596, 9.690, 16.784, 16.786 max_d=16.786 avg_d=9.690 std_dev=7.094
C2 B 0, 2.833, 10.084, 17.335, 16.737 max_d=16.737 avg_d=10.084 std_dev=7.251

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 0.05 0.00 0.02 0.04 0.00 0.03 0.05 0.01 0.02 0.05 0.05 0.02 0.33 0.05 0.00 0.08 0.29 0.43 0.16
C2 0.05 0.00 0.07 0.08 0.02 0.35 0.01 0.62 0.01 0.01 0.02 0.00 0.16 0.15 0.04 0.40 0.68 1.41 1.07 0.97
C2' 0.00 0.07 0.00 0.00 0.10 0.02 0.11 0.17 0.10 0.03 0.08 0.13 0.00 0.05 0.11 0.02 0.38 0.54 0.50 0.44
C3' 0.02 0.08 0.00 0.00 0.23 0.01 0.36 0.03 0.36 0.16 0.09 0.27 0.02 0.01 0.24 0.02 0.04 0.11 0.08 0.02
C4 0.04 0.02 0.10 0.23 0.00 0.08 0.01 0.11 0.01 0.03 0.01 0.03 0.45 0.08 0.00 0.02 0.25 0.59 0.73 0.21
C4' 0.00 0.35 0.02 0.01 0.08 0.00 0.39 0.01 0.46 0.06 0.23 0.73 0.29 0.02 0.07 0.00 0.02 0.24 0.30 0.02
C5 0.03 0.01 0.11 0.36 0.01 0.39 0.00 0.63 0.00 0.03 0.00 0.02 0.59 0.14 0.03 0.30 0.91 0.33 1.31 0.93
C5' 0.05 0.62 0.17 0.03 0.11 0.01 0.63 0.00 0.69 0.05 0.44 1.26 0.13 0.24 0.11 0.00 0.01 0.39 0.35 0.02
C6 0.01 0.01 0.10 0.36 0.01 0.46 0.00 0.69 0.00 0.00 0.02 0.01 0.55 0.18 0.02 0.40 0.95 0.43 1.15 0.94
N1 0.02 0.01 0.03 0.16 0.03 0.06 0.03 0.05 0.00 0.00 0.02 0.01 0.24 0.17 0.03 0.01 0.13 0.41 0.49 0.14
N3 0.05 0.02 0.08 0.09 0.01 0.23 0.00 0.44 0.02 0.02 0.00 0.03 0.26 0.08 0.03 0.28 0.45 1.36 0.90 0.78
O2 0.05 0.00 0.13 0.27 0.03 0.73 0.02 1.26 0.01 0.01 0.03 0.00 0.34 0.20 0.06 0.72 1.47 2.22 1.95 1.87
O2' 0.02 0.16 0.00 0.02 0.45 0.29 0.59 0.13 0.55 0.24 0.26 0.34 0.00 0.07 0.48 0.20 0.26 0.46 0.41 0.34
O3' 0.33 0.15 0.05 0.01 0.08 0.02 0.14 0.24 0.18 0.17 0.08 0.20 0.07 0.00 0.05 0.20 0.18 0.54 0.19 0.26
O4 0.05 0.04 0.11 0.24 0.00 0.07 0.03 0.11 0.02 0.03 0.03 0.06 0.48 0.05 0.00 0.02 0.24 0.67 0.80 0.22
O4' 0.00 0.40 0.02 0.02 0.02 0.00 0.30 0.00 0.40 0.01 0.28 0.72 0.20 0.20 0.02 0.00 0.11 0.19 0.41 0.05
O5' 0.08 0.68 0.38 0.04 0.25 0.02 0.91 0.01 0.95 0.13 0.45 1.47 0.26 0.18 0.24 0.11 0.00 0.03 0.02 0.01
OP1 0.29 1.41 0.54 0.11 0.59 0.24 0.33 0.39 0.43 0.41 1.36 2.22 0.46 0.54 0.67 0.19 0.03 0.00 0.03 0.00
OP2 0.43 1.07 0.50 0.08 0.73 0.30 1.31 0.35 1.15 0.49 0.90 1.95 0.41 0.19 0.80 0.41 0.02 0.03 0.00 0.00
P 0.16 0.97 0.44 0.02 0.21 0.02 0.93 0.02 0.94 0.14 0.78 1.87 0.34 0.26 0.22 0.05 0.01 0.00 0.00 0.00

Atoms distances Chain-A - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N3N6N7N9O2'O3'O4'O5'OP1OP2P
C1' 1.61 2.93 2.09 1.48 2.19 0.85 1.88 0.65 2.21 0.96 2.73 2.70 1.87 1.06 1.63 2.14 1.57 0.89 0.30 0.29 0.13 0.16
C2 0.96 2.39 1.34 0.91 1.78 0.41 1.87 0.68 2.30 0.88 2.52 2.05 2.33 1.29 1.22 1.23 0.96 0.39 0.37 0.26 0.12 0.19
C2' 1.14 2.27 1.68 1.19 1.47 0.76 1.09 0.93 1.41 0.56 2.01 2.05 1.03 0.48 1.04 1.84 1.40 0.69 0.44 0.53 0.31 0.39
C3' 1.69 2.36 2.35 1.89 1.72 1.26 1.17 0.81 1.31 0.75 1.93 2.31 0.80 0.56 1.42 2.59 2.23 1.13 0.63 0.25 0.42 0.38
C4 0.44 1.69 0.75 0.53 1.33 0.24 1.62 0.64 1.92 0.90 1.91 1.39 2.09 1.40 0.89 0.43 0.51 0.17 0.47 0.19 0.10 0.24
C4' 2.48 3.13 3.23 2.64 2.48 1.89 1.82 1.11 1.94 1.27 2.61 3.15 1.37 1.03 2.14 3.49 2.97 1.79 1.07 0.62 0.56 0.72
C5 0.64 1.61 0.93 0.70 1.34 0.26 1.50 0.61 1.70 0.93 1.74 1.41 1.75 1.29 0.99 0.67 0.68 0.18 0.35 0.25 0.10 0.22
C5' 2.92 3.01 3.82 3.42 2.54 2.63 1.78 1.82 1.76 1.50 2.39 3.17 1.13 1.09 2.39 4.17 3.95 2.34 1.72 1.37 1.04 1.33
C6 1.08 2.00 1.44 1.09 1.66 0.53 1.62 0.64 1.81 0.97 1.99 1.85 1.71 1.20 1.28 1.28 1.10 0.51 0.28 0.29 0.11 0.18
N1 1.21 2.44 1.62 1.15 1.90 0.58 1.82 0.67 2.14 0.94 2.42 2.20 1.99 1.20 1.39 1.54 1.21 0.58 0.31 0.30 0.13 0.18
N3 0.61 2.01 0.96 0.64 1.52 0.25 1.76 0.67 2.17 0.87 2.24 1.67 2.34 1.38 0.99 0.73 0.66 0.18 0.45 0.22 0.11 0.22
O2 1.04 2.65 1.44 0.95 1.87 0.46 1.92 0.69 2.47 0.84 2.79 2.23 2.51 1.22 1.25 1.39 1.03 0.45 0.38 0.26 0.13 0.19
O2' 1.02 2.20 1.38 1.09 1.29 1.09 1.00 1.59 1.30 1.03 1.95 1.88 1.00 0.95 0.98 1.56 1.18 0.97 1.07 1.26 0.82 1.02
O3' 1.47 2.17 2.09 1.67 1.48 1.17 0.99 1.03 1.12 0.79 1.74 2.08 0.68 0.69 1.21 2.40 2.02 1.02 0.58 0.30 0.06 0.12
O4 0.35 1.55 0.63 0.52 1.23 0.37 1.57 0.60 1.87 0.90 1.82 1.24 2.10 1.42 0.80 0.31 0.50 0.37 0.52 0.10 0.06 0.24
O4' 2.55 3.43 3.16 2.51 2.84 1.76 2.30 0.98 2.47 1.60 3.03 3.40 2.00 1.51 2.41 3.24 2.63 1.78 0.94 0.46 0.42 0.60
O5' 2.80 2.51 3.68 3.56 2.28 2.79 1.56 2.14 1.43 1.51 1.94 2.75 0.82 1.03 2.28 3.89 4.13 2.39 2.07 1.85 1.45 1.73
OP1 2.35 1.68 3.35 3.48 1.48 2.82 0.70 2.28 0.65 0.84 1.10 1.98 0.72 0.23 1.61 3.81 4.50 2.12 1.96 2.03 1.17 1.62
OP2 3.16 2.47 3.92 4.18 2.45 3.61 1.82 3.25 1.60 2.04 1.97 2.76 1.08 1.50 2.62 4.09 4.84 3.01 3.11 3.11 2.28 2.75
P 3.07 2.38 3.97 4.12 2.27 3.42 1.52 2.85 1.32 1.67 1.79 2.70 0.78 1.08 2.41 4.26 4.96 2.82 2.64 2.55 1.80 2.26

Atoms distances Chain-B - Chain-B

Atom C1'C2C2'C3'C4C4'C5C5'C6C8N1N3N6N7N9O2'O3'O4'O5'OP1OP2P
C1' 0.00 0.06 0.00 0.01 0.03 0.01 0.01 0.01 0.02 0.01 0.05 0.07 0.01 0.01 0.00 0.00 0.01 0.01 0.19 0.19 0.46 0.16
C2 0.06 0.00 0.06 0.07 0.00 0.04 0.01 0.03 0.01 0.01 0.00 0.00 0.00 0.01 0.02 0.18 0.08 0.05 0.46 0.18 1.19 0.63
C2' 0.00 0.06 0.00 0.00 0.03 0.02 0.04 0.01 0.04 0.04 0.05 0.06 0.04 0.05 0.02 0.00 0.02 0.01 0.32 0.32 0.54 0.15
C3' 0.01 0.07 0.00 0.00 0.10 0.00 0.15 0.02 0.15 0.15 0.11 0.05 0.18 0.18 0.09 0.01 0.00 0.01 0.44 0.21 0.55 0.25
C4 0.03 0.00 0.03 0.10 0.00 0.05 0.00 0.05 0.00 0.02 0.01 0.00 0.01 0.00 0.01 0.08 0.11 0.02 0.44 0.23 1.11 0.64
C4' 0.01 0.04 0.02 0.00 0.05 0.00 0.10 0.01 0.09 0.12 0.05 0.04 0.13 0.14 0.06 0.06 0.02 0.00 0.01 0.40 0.03 0.15
C5 0.01 0.01 0.04 0.15 0.00 0.10 0.00 0.12 0.00 0.00 0.00 0.00 0.02 0.00 0.00 0.05 0.17 0.01 0.50 0.47 1.37 0.87
C5' 0.01 0.03 0.01 0.02 0.05 0.01 0.12 0.00 0.12 0.13 0.07 0.02 0.18 0.16 0.05 0.05 0.02 0.02 0.01 0.06 0.07 0.02
C6 0.02 0.01 0.04 0.15 0.00 0.09 0.00 0.12 0.00 0.00 0.00 0.00 0.00 0.01 0.01 0.09 0.17 0.01 0.52 0.50 1.48 0.91
C8 0.01 0.01 0.04 0.15 0.02 0.12 0.00 0.13 0.00 0.00 0.01 0.02 0.03 0.00 0.00 0.03 0.15 0.04 0.44 0.47 1.16 0.81
N1 0.05 0.00 0.05 0.11 0.01 0.05 0.00 0.07 0.00 0.01 0.00 0.00 0.01 0.01 0.02 0.15 0.12 0.03 0.51 0.36 1.39 0.80
N3 0.07 0.00 0.06 0.05 0.00 0.04 0.00 0.02 0.00 0.02 0.00 0.00 0.00 0.00 0.03 0.16 0.06 0.06 0.42 0.09 1.02 0.52
N6 0.01 0.00 0.04 0.18 0.01 0.13 0.02 0.18 0.00 0.03 0.01 0.00 0.00 0.04 0.02 0.07 0.21 0.03 0.53 0.64 1.61 1.03
N7 0.01 0.01 0.05 0.18 0.00 0.14 0.00 0.16 0.01 0.00 0.01 0.00 0.04 0.00 0.01 0.02 0.19 0.04 0.50 0.62 1.43 0.98
N9 0.00 0.02 0.02 0.09 0.01 0.06 0.00 0.05 0.01 0.00 0.02 0.03 0.02 0.01 0.00 0.02 0.09 0.01 0.37 0.18 0.92 0.55
O2' 0.00 0.18 0.00 0.01 0.08 0.06 0.05 0.05 0.09 0.03 0.15 0.16 0.07 0.02 0.02 0.00 0.02 0.05 0.03 0.78 0.09 0.31
O3' 0.01 0.08 0.02 0.00 0.11 0.02 0.17 0.02 0.17 0.15 0.12 0.06 0.21 0.19 0.09 0.02 0.00 0.01 0.38 0.45 0.38 0.08
O4' 0.01 0.05 0.01 0.01 0.02 0.00 0.01 0.02 0.01 0.04 0.03 0.06 0.03 0.04 0.01 0.05 0.01 0.00 0.05 0.23 0.13 0.07
O5' 0.19 0.46 0.32 0.44 0.44 0.01 0.50 0.01 0.52 0.44 0.51 0.42 0.53 0.50 0.37 0.03 0.38 0.05 0.00 0.03 0.01 0.01
OP1 0.19 0.18 0.32 0.21 0.23 0.40 0.47 0.06 0.50 0.47 0.36 0.09 0.64 0.62 0.18 0.78 0.45 0.23 0.03 0.00 0.00 0.01
OP2 0.46 1.19 0.54 0.55 1.11 0.03 1.37 0.07 1.48 1.16 1.39 1.02 1.61 1.43 0.92 0.09 0.38 0.13 0.01 0.00 0.00 0.00
P 0.16 0.63 0.15 0.25 0.64 0.15 0.87 0.02 0.91 0.81 0.80 0.52 1.03 0.98 0.55 0.31 0.08 0.07 0.01 0.01 0.00 0.00