# HAV_dIII-best.pdb # **************************************************************************** DSSR: Software for Defining the (Secondary) Structures of RNA by Xiang-Jun Lu (xiangjun@x3dna.org), beta-r08-on-20130323 The program is currently under active development. As always, we greatly appreciate your feedback! Please report all DSSR-related issues on the 3DNA Forum (http://forum.x3dna.org/), and I strive to promptly respond to any questions posted there. **************************************************************************** Date and time: Sun Oct 11 12:40:56 2026 File name: HAV_dIII-best.pdb no. of DNA/RNA chains: 1 [A=93] no. of nucleotides: 93 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 48 base pair(s) 1 A.C2 A.G65 [C-G] WC 19-XIX cWW cW-W 163.2(...) C3'-endo lambda=48.4; -173.7(anti) C3'-endo lambda=58.5 d(C1'-C1')=10.78 d(N1-N9)=8.96 d(C6-C8)=9.94 tor(N1-C1'-C1'-N9)=-13.6 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.95]; N3-N1(imino)[2.92]; N4(amino)-O6(carbonyl)[3.00]" bp_pars: [-0.38 -0.10 -0.41 -1.34 -20.55 3.85] 2 A.C3 A.U63 [C-U] 00-n/a tWW tW-W -165.9(anti) C3'-endo lambda=32.8; -165.9(anti) C3'-endo lambda=31.1 d(C1'-C1')=11.30 d(N1-N9)=8.68 d(C6-C8)=8.47 tor(N1-C1'-C1'-N9)=-90.5 H-bonds[1]: "N4(amino)-O4(carbonyl)[2.42]" bp_pars: [-1.78 -0.67 -0.74 3.67 -39.48 -57.30] 3 A.C3 A.A64 [C-A] 00-n/a cWW cW-W -165.9(anti) C3'-endo lambda=55.1; -169.7(anti) C3'-endo lambda=41.3 d(C1'-C1')=11.54 d(N1-N9)=9.46 d(C6-C8)=9.57 tor(N1-C1'-C1'-N9)=-22.4 H-bonds[2]: "N3-N6(amino)[2.96]; N4(amino)*N6(amino)[2.57]" bp_pars: [1.13 -0.00 -1.19 -16.34 -21.00 -32.59] 4 A.A4 A.U22 [A-U] WC 20-XX cWW cW-W -160.7(anti) C3'-endo lambda=45.4; -165.7(anti) C3'-endo lambda=54.1 d(C1'-C1')=10.69 d(N1-N9)=8.75 d(C6-C8)=9.65 tor(N1-C1'-C1'-N9)=-57.1 H-bonds[2]: "N6(amino)-O4(carbonyl)[2.70]; N1-N3(imino)[2.70]" bp_pars: [0.03 -0.29 -0.07 5.48 -16.64 -1.86] 5 A.G5 A.C21 [G-C] WC 19-XIX cWW cW-W -153.7(anti) C3'-endo lambda=60.3; -159.0(anti) C3'-endo lambda=59.3 d(C1'-C1')=10.73 d(N1-N9)=9.21 d(C6-C8)=10.17 tor(N1-C1'-C1'-N9)=4.5 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.19]; N1(imino)-N3[3.15]; N2(amino)-O2(carbonyl)[3.08]" bp_pars: [0.11 0.13 -0.51 -4.45 -14.54 2.43] 6 A.G6 A.C20 [G-C] WC 19-XIX cWW cW-W -154.9(anti) C3'-endo lambda=47.5; -167.1(anti) C3'-endo lambda=49.3 d(C1'-C1')=10.61 d(N1-N9)=8.67 d(C6-C8)=9.41 tor(N1-C1'-C1'-N9)=-24.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.34]; N1(imino)-N3[2.54]; N2(amino)-O2(carbonyl)[2.86]" bp_pars: [-0.20 -0.59 0.09 -4.12 -20.34 -8.55] 7 A.G7 A.C19 [G-C] WC 19-XIX cWW cW-W -175.6(anti) C2'-exo lambda=48.5; -161.6(anti) C3'-endo lambda=55.8 d(C1'-C1')=10.45 d(N1-N9)=8.67 d(C6-C8)=9.51 tor(N1-C1'-C1'-N9)=1.7 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.48]; N1(imino)-N3[2.66]; N2(amino)-O2(carbonyl)[2.76]" bp_pars: [-0.42 -0.54 -0.56 -3.94 -9.86 -3.17] 8 A.G7 A.A85 [G+A] 00-n/a cSH cm+M -175.6(anti) C2'-exo lambda=116.6; -152.4(anti) C2'-exo lambda=32.1 d(C1'-C1')=8.71 d(N1-N9)=8.25 d(C6-C8)=8.44 tor(N1-C1'-C1'-N9)=-76.5 H-bonds[1]: "N3-N6(amino)[3.42]" bp_pars: [6.00 -0.23 2.19 -31.52 -3.32 -28.60] 9 A.C8 A.G18 [C-G] WC 19-XIX cWW cW-W -173.6(anti) C3'-endo lambda=58.8; -162.0(anti) C3'-endo lambda=57.1 d(C1'-C1')=10.48 d(N1-N9)=8.91 d(C6-C8)=9.93 tor(N1-C1'-C1'-N9)=0.4 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.69]; N3-N1(imino)[2.93]; N4(amino)-O6(carbonyl)[3.11]" bp_pars: [0.39 -0.08 -0.04 -7.17 -7.95 4.48] 10 A.U9 A.U17 [U-U] 16-XVI cWW cW-W -144.4(anti) C3'-endo lambda=69.4; -149.8(anti) C3'-exo lambda=44.6 d(C1'-C1')=9.36 d(N1-N9)=7.90 d(C6-C8)=8.74 tor(N1-C1'-C1'-N9)=34.1 H-bonds[2]: "O2(carbonyl)-N3(imino)[3.39]; N3(imino)-O4(carbonyl)[2.63]" bp_pars: [3.37 -2.00 -0.18 6.65 -5.71 -8.07] 11 A.C10 A.C15 [C-C] 00-n/a tSH tm-M -165.1(anti) C3'-endo lambda=100.0; -160.1(anti) C3'-endo lambda=17.4 d(C1'-C1')=9.80 d(N1-N9)=8.76 d(C6-C8)=9.29 tor(N1-C1'-C1'-N9)=124.3 H-bonds[1]: "O2(carbonyl)-N4(amino)[3.93]" bp_pars: [7.96 -5.10 -0.70 -7.78 56.54 1.94] 12 A.C12 A.G93 [C-G] WC 19-XIX cWW cW-W -172.5(anti) C3'-endo lambda=53.8; -165.0(anti) C3'-endo lambda=55.0 d(C1'-C1')=10.91 d(N1-N9)=9.18 d(C6-C8)=10.07 tor(N1-C1'-C1'-N9)=-3.0 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.03]; N3-N1(imino)[3.05]; N4(amino)-O6(carbonyl)[3.00]" bp_pars: [-0.10 0.04 0.13 -2.77 -8.83 -2.05] 13 A.C13 A.G92 [C-G] WC 19-XIX cWW cW-W -165.9(anti) C3'-endo lambda=59.6; -151.6(anti) C2'-exo lambda=60.7 d(C1'-C1')=10.23 d(N1-N9)=8.66 d(C6-C8)=9.61 tor(N1-C1'-C1'-N9)=17.8 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.59]; N3-N1(imino)[2.71]; N4(amino)-O6(carbonyl)[2.73]" bp_pars: [0.52 -0.44 -0.52 3.56 -6.82 1.45] 14 A.C14 A.G91 [C-G] WC 19-XIX cWW cW-W -168.1(anti) C3'-endo lambda=53.9; -172.0(anti) C3'-endo lambda=56.8 d(C1'-C1')=10.45 d(N1-N9)=8.79 d(C6-C8)=9.74 tor(N1-C1'-C1'-N9)=-1.2 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.53]; N3-N1(imino)[2.71]; N4(amino)-O6(carbonyl)[2.78]" bp_pars: [-0.00 -0.29 0.27 1.73 -4.92 1.00] 15 A.C15 A.G90 [C-G] WC 19-XIX cWW cW-W -160.1(anti) C3'-endo lambda=65.9; -161.8(anti) C3'-endo lambda=60.3 d(C1'-C1')=10.24 d(N1-N9)=8.88 d(C6-C8)=9.98 tor(N1-C1'-C1'-N9)=6.7 H-bonds[4]: "O2(carbonyl)-N1(imino)[3.25]; O2(carbonyl)-N2(amino)[2.77]; N3-N1(imino)[3.13]; N4(amino)-O6(carbonyl)[3.44]" bp_pars: [1.08 -0.09 -0.54 -0.61 -7.90 9.07] 16 A.G18 A.A87 [G-A] 00-n/a cSW cm-W -162.0(anti) C3'-endo lambda=109.2; -157.1(anti) C3'-endo lambda=54.7 d(C1'-C1')=9.66 d(N1-N9)=9.26 d(C6-C8)=10.86 tor(N1-C1'-C1'-N9)=3.9 H-bonds[1]: "N2(amino)-N1[2.81]" bp_pars: [4.36 0.94 -1.23 -11.90 -8.39 50.48] 17 A.G18 A.U88 [G-U] 00-n/a cSW cm-W -162.0(anti) C3'-endo lambda=123.2; -147.1(anti) C3'-endo lambda=66.1 d(C1'-C1')=6.49 d(N1-N9)=6.77 d(C6-C8)=9.00 tor(N1-C1'-C1'-N9)=19.0 H-bonds[1]: "N2(amino)-O4(carbonyl)[2.87]" bp_pars: [3.14 0.91 1.39 -16.58 -2.90 83.51] 18 A.C19 A.A86 [C-A] 00-n/a cS. cm-. -161.6(anti) C3'-endo lambda=128.1; -159.8(anti) C3'-endo lambda=29.4 d(C1'-C1')=9.35 d(N1-N9)=8.93 d(C6-C8)=10.12 tor(N1-C1'-C1'-N9)=5.0 H-bonds[2]: "O2'(hydroxyl)-N1[3.10]; O2(carbonyl)-N6(amino)[2.75]" bp_pars: [7.04 -1.58 0.20 -20.36 1.94 48.11] 19 A.C20 A.A85 [C-A] 00-n/a cSW cm-W -167.1(anti) C3'-endo lambda=126.6; -152.4(anti) C2'-exo lambda=34.6 d(C1'-C1')=8.34 d(N1-N9)=8.16 d(C6-C8)=9.20 tor(N1-C1'-C1'-N9)=56.9 H-bonds[2]: "O2'(hydroxyl)-N1[3.03]; O2(carbonyl)-N6(amino)[2.62]" bp_pars: [6.61 -2.46 1.34 -23.53 12.85 50.43] 20 A.A23 A.U84 [A-U] WC 20-XX cWW cW-W -165.5(anti) C4'-exo lambda=52.7; -151.9(anti) O4'-endo lambda=54.7 d(C1'-C1')=11.10 d(N1-N9)=9.42 d(C6-C8)=10.40 tor(N1-C1'-C1'-N9)=7.2 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.51]; N1-N3(imino)[3.37]" bp_pars: [0.57 0.44 -0.29 2.65 0.65 1.37] 21 A.G24 A.C83 [G-C] WC 19-XIX cWW cW-W -167.0(anti) C3'-endo lambda=48.8; -163.2(anti) C3'-endo lambda=52.2 d(C1'-C1')=11.07 d(N1-N9)=9.22 d(C6-C8)=10.04 tor(N1-C1'-C1'-N9)=-8.8 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.96]; N1(imino)-N3[3.12]; N2(amino)-O2(carbonyl)[3.31]" bp_pars: [-0.18 0.03 -0.11 5.03 -17.01 -4.26] 22 A.G25 A.U82 [G-U] Wobble 28-XXVIII cWW cW-W -161.7(anti) C3'-endo lambda=47.4; -158.2(anti) C3'-endo lambda=59.6 d(C1'-C1')=10.60 d(N1-N9)=8.89 d(C6-C8)=9.74 tor(N1-C1'-C1'-N9)=-1.4 H-bonds[3]: "O6(carbonyl)-N3(imino)[3.00]; N1(imino)-O2(carbonyl)[3.03]; N2(amino)-O2(carbonyl)[3.20]" bp_pars: [-1.35 -0.36 0.28 3.27 -14.02 -4.25] 23 A.C26 A.G81 [C-G] WC 19-XIX cWW cW-W -164.3(anti) C3'-endo lambda=49.3; -170.2(anti) C3'-endo lambda=48.6 d(C1'-C1')=10.98 d(N1-N9)=9.09 d(C6-C8)=9.93 tor(N1-C1'-C1'-N9)=-24.1 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.18]; N3-N1(imino)[3.12]; N4(amino)-O6(carbonyl)[3.06]" bp_pars: [0.77 -0.10 0.07 7.18 -16.39 -3.47] 24 A.U27 A.A80 [U-A] WC 20-XX cWW cW-W -164.8(anti) C3'-endo lambda=57.1; -167.8(anti) C3'-endo lambda=51.2 d(C1'-C1')=10.38 d(N1-N9)=8.71 d(C6-C8)=9.73 tor(N1-C1'-C1'-N9)=14.7 H-bonds[2]: "N3(imino)-N1[2.84]; O4(carbonyl)-N6(amino)[3.06]" bp_pars: [0.66 -0.24 -0.33 0.14 6.02 3.34] 25 A.C28 A.G79 [C-G] WC 19-XIX cWW cW-W -162.2(anti) C3'-endo lambda=54.2; -166.4(anti) C3'-endo lambda=50.0 d(C1'-C1')=10.83 d(N1-N9)=9.00 d(C6-C8)=9.83 tor(N1-C1'-C1'-N9)=-8.2 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.04]; N3-N1(imino)[2.93]; N4(amino)-O6(carbonyl)[2.78]" bp_pars: [0.38 -0.20 -0.06 2.73 -12.87 -4.52] 26 A.U29 A.G78 [U-G] Wobble 28-XXVIII cWW cW-W -160.2(anti) C3'-endo lambda=64.3; -165.3(anti) C3'-endo lambda=46.4 d(C1'-C1')=10.87 d(N1-N9)=9.18 d(C6-C8)=10.14 tor(N1-C1'-C1'-N9)=-6.4 H-bonds[2]: "O2(carbonyl)-N1(imino)[3.20]; N3(imino)-O6(carbonyl)[3.33]" bp_pars: [1.87 -0.04 -0.16 -2.31 -13.05 1.74] 27 A.G30 A.C41 [G-C] WC 19-XIX cWW cW-W -169.0(anti) C3'-endo lambda=62.3; -176.6(anti) C3'-endo lambda=56.0 d(C1'-C1')=10.74 d(N1-N9)=8.86 d(C6-C8)=9.95 tor(N1-C1'-C1'-N9)=-38.1 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.18]; N1(imino)-N3[2.94]; N2(amino)-O2(carbonyl)[2.72]" bp_pars: [-0.08 -0.08 -0.65 -0.58 -14.40 8.57] 28 A.G30 A.A77 [G-A] 00-n/a cS. cm-. -169.0(anti) C3'-endo lambda=123.6; -151.8(anti) C2'-exo lambda=40.4 d(C1'-C1')=8.80 d(N1-N9)=8.54 d(C6-C8)=9.82 tor(N1-C1'-C1'-N9)=16.7 H-bonds[2]: "O2'(hydroxyl)-N1[2.51]; N3-N6(amino)[2.51]" bp_pars: [6.17 -1.53 1.16 -4.20 -21.73 43.92] 29 A.G31 A.C40 [G-C] WC 19-XIX cWW cW-W -171.3(anti) C3'-endo lambda=51.0; -171.5(anti) C3'-endo lambda=54.0 d(C1'-C1')=10.42 d(N1-N9)=8.68 d(C6-C8)=9.68 tor(N1-C1'-C1'-N9)=-12.8 H-bonds[3]: "O6(carbonyl)-N4(amino)[2.86]; N1(imino)-N3[2.69]; N2(amino)-O2(carbonyl)[2.73]" bp_pars: [-0.16 -0.34 -0.47 -5.96 -24.70 5.93] 30 A.C32 A.G47 [C-G] WC 19-XIX cWW cW-W -160.2(anti) C3'-endo lambda=56.9; -178.8(anti) C3'-endo lambda=46.9 d(C1'-C1')=10.49 d(N1-N9)=8.61 d(C6-C8)=9.61 tor(N1-C1'-C1'-N9)=-6.0 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.38]; N3-N1(imino)[2.67]; N4(amino)-O6(carbonyl)[2.86]" bp_pars: [0.30 -0.45 -0.78 0.62 5.91 2.93] 31 A.C33 A.G46 [C-G] WC 19-XIX cWW cW-W -170.3(anti) C3'-endo lambda=60.3; -161.8(anti) C3'-endo lambda=58.0 d(C1'-C1')=10.32 d(N1-N9)=8.75 d(C6-C8)=9.93 tor(N1-C1'-C1'-N9)=-8.9 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.31]; N3-N1(imino)[2.83]; N4(amino)-O6(carbonyl)[3.30]" bp_pars: [-0.04 -0.03 0.15 -7.63 -9.75 11.42] 32 A.G34 A.C45 [G-C] WC 19-XIX cWW cW-W -157.5(anti) C3'-endo lambda=59.5; -170.2(anti) C3'-endo lambda=58.3 d(C1'-C1')=10.41 d(N1-N9)=8.85 d(C6-C8)=9.91 tor(N1-C1'-C1'-N9)=9.7 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.15]; N1(imino)-N3[2.89]; N2(amino)-O2(carbonyl)[2.52]" bp_pars: [-0.24 -0.10 -0.60 -8.09 1.07 5.98] 33 A.U35 A.G44 [U-G] 00-n/a cWW cW-W -161.9(anti) C3'-endo lambda=57.5; -165.5(anti) C3'-endo lambda=51.9 d(C1'-C1')=10.32 d(N1-N9)=8.62 d(C6-C8)=9.57 tor(N1-C1'-C1'-N9)=6.5 H-bonds[5]: "O2(carbonyl)-N1(imino)[2.93]; O2(carbonyl)-N2(amino)[2.60]; N3(imino)-O6(carbonyl)[3.04]; N3(imino)*N1(imino)[2.87]; O4(carbonyl)*O6(carbonyl)[2.89]" bp_pars: [0.90 -0.48 -0.26 2.72 -1.68 0.33] 34 A.U36 A.G43 [U-G] Wobble 28-XXVIII cWW cW-W -163.0(anti) C3'-endo lambda=66.7; -156.1(anti) C3'-endo lambda=48.5 d(C1'-C1')=10.43 d(N1-N9)=8.91 d(C6-C8)=10.04 tor(N1-C1'-C1'-N9)=-27.2 H-bonds[2]: "O2(carbonyl)-N1(imino)[3.06]; O2(carbonyl)-N2(amino)[2.84]" bp_pars: [1.23 0.01 0.96 -14.52 -23.46 7.62] 35 A.G37 A.C42 [G-C] WC 19-XIX cWW cW-W -168.0(anti) C3'-endo lambda=59.5; -161.3(anti) C3'-endo lambda=53.8 d(C1'-C1')=10.18 d(N1-N9)=8.64 d(C6-C8)=9.79 tor(N1-C1'-C1'-N9)=-6.3 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.11]; N1(imino)-N3[2.77]; N2(amino)-O2(carbonyl)[2.37]" bp_pars: [0.41 -0.20 0.54 -7.99 5.24 10.27] 36 A.G49 A.U76 [G-U] 00-n/a cWW cW-W -163.5(anti) C3'-endo lambda=27.4; -163.4(anti) C3'-endo lambda=27.6 d(C1'-C1')=11.82 d(N1-N9)=9.27 d(C6-C8)=9.17 tor(N1-C1'-C1'-N9)=-6.0 H-bonds[2]: "O6(carbonyl)-N3(imino)[3.17]; N1(imino)-O4(carbonyl)[3.42]" bp_pars: [0.35 -0.28 -2.02 -10.25 -28.71 -40.31] 37 A.U50 A.U76 [U-U] 00-n/a cWW cW-W -166.2(anti) C3'-endo lambda=48.8; -163.4(anti) C3'-endo lambda=49.3 d(C1'-C1')=9.55 d(N1-N9)=7.69 d(C6-C8)=8.53 tor(N1-C1'-C1'-N9)=0.3 H-bonds[2]: "O4(carbonyl)-N3(imino)[3.24]; O4(carbonyl)*O4(carbonyl)[2.42]" bp_pars: [-0.59 -1.54 0.41 -7.56 -11.72 -12.47] 38 A.C51 A.G75 [C-G] WC 19-XIX cWW cW-W -172.5(anti) C3'-endo lambda=42.1; -160.9(anti) C3'-endo lambda=54.5 d(C1'-C1')=10.77 d(N1-N9)=8.79 d(C6-C8)=9.59 tor(N1-C1'-C1'-N9)=-12.3 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.73]; N3-N1(imino)[2.62]; N4(amino)-O6(carbonyl)[2.40]" bp_pars: [-0.49 -0.42 -0.37 8.12 -7.01 -5.30] 39 A.A52 A.U74 [A-U] WC 20-XX cWW cW-W -176.5(anti) C3'-endo lambda=48.5; -166.9(anti) C3'-endo lambda=44.7 d(C1'-C1')=11.76 d(N1-N9)=9.77 d(C6-C8)=10.41 tor(N1-C1'-C1'-N9)=-8.7 H-bonds[2]: "N6(amino)-O4(carbonyl)[3.25]; N1-N3(imino)[3.71]" bp_pars: [-0.52 0.51 -0.28 -1.76 -15.98 -13.16] 40 A.A53 A.C73 [A-C] 00-n/a ... c... -166.3(anti) C3'-endo lambda=47.6; -158.0(anti) C3'-endo lambda=48.2 d(C1'-C1')=10.63 d(N1-N9)=8.59 d(C6-C8)=9.25 tor(N1-C1'-C1'-N9)=-18.7 H-bonds[1]: "N1*N3[2.35]" bp_pars: [0.12 -0.67 -0.25 2.96 -21.37 -10.78] 41 A.C54 A.G72 [C-G] WC 19-XIX cWW cW-W -173.9(anti) C3'-endo lambda=50.7; -168.2(anti) C3'-endo lambda=56.6 d(C1'-C1')=11.11 d(N1-N9)=9.35 d(C6-C8)=10.31 tor(N1-C1'-C1'-N9)=-2.2 H-bonds[3]: "O2(carbonyl)-N2(amino)[3.08]; N3-N1(imino)[3.25]; N4(amino)-O6(carbonyl)[3.29]" bp_pars: [-0.23 0.27 -0.04 0.63 1.69 1.06] 42 A.U55 A.A71 [U-A] WC 20-XX cWW cW-W -163.8(anti) C3'-endo lambda=56.2; -161.0(anti) C3'-endo lambda=59.5 d(C1'-C1')=10.15 d(N1-N9)=8.59 d(C6-C8)=9.66 tor(N1-C1'-C1'-N9)=-2.4 H-bonds[2]: "N3(imino)-N1[2.61]; O4(carbonyl)-N6(amino)[2.92]" bp_pars: [-0.17 -0.26 -0.15 6.58 -5.96 5.86] 43 A.C56 A.G70 [C-G] WC 19-XIX cWW cW-W -166.1(anti) C3'-endo lambda=54.3; -172.1(anti) C3'-endo lambda=55.1 d(C1'-C1')=10.58 d(N1-N9)=8.88 d(C6-C8)=9.94 tor(N1-C1'-C1'-N9)=-9.9 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.67]; N3-N1(imino)[2.87]; N4(amino)-O6(carbonyl)[3.11]" bp_pars: [-0.23 -0.08 -0.28 2.00 -16.98 6.76] 44 A.C57 A.G69 [C-G] WC 19-XIX cWW cW-W -166.0(anti) C3'-endo lambda=57.0; -176.5(anti) C3'-endo lambda=58.6 d(C1'-C1')=10.16 d(N1-N9)=8.65 d(C6-C8)=9.58 tor(N1-C1'-C1'-N9)=26.0 H-bonds[3]: "O2(carbonyl)-N2(amino)[2.56]; N3-N1(imino)[2.71]; N4(amino)-O6(carbonyl)[2.75]" bp_pars: [0.62 -0.46 -0.53 7.32 2.14 0.44] 45 A.A58 A.U68 [A-U] WC 20-XX cWW cW-W -162.0(anti) C3'-endo lambda=61.9; -156.5(anti) C3'-endo lambda=52.5 d(C1'-C1')=10.44 d(N1-N9)=8.84 d(C6-C8)=9.69 tor(N1-C1'-C1'-N9)=7.7 H-bonds[2]: "N6(amino)-O4(carbonyl)[2.63]; N1-N3(imino)[2.74]" bp_pars: [0.43 -0.28 -0.47 -0.77 -16.06 -3.37] 46 A.U59 A.A67 [U-A] WC 20-XX cWW cW-W -173.4(anti) C3'-endo lambda=58.1; -158.3(anti) C3'-endo lambda=57.3 d(C1'-C1')=10.64 d(N1-N9)=9.05 d(C6-C8)=10.12 tor(N1-C1'-C1'-N9)=-6.8 H-bonds[2]: "N3(imino)-N1[3.18]; O4(carbonyl)-N6(amino)[3.43]" bp_pars: [0.19 0.18 -0.58 -8.24 -4.07 5.53] 47 A.G60 A.C66 [G-C] WC 19-XIX cWW cW-W -154.5(anti) C3'-endo lambda=57.1; -169.7(anti) C3'-endo lambda=57.3 d(C1'-C1')=10.63 d(N1-N9)=9.01 d(C6-C8)=10.14 tor(N1-C1'-C1'-N9)=-15.9 H-bonds[3]: "O6(carbonyl)-N4(amino)[3.41]; N1(imino)-N3[3.05]; N2(amino)-O2(carbonyl)[2.59]" bp_pars: [-0.04 0.15 0.19 -3.00 4.23 9.18] 48 A.U63 A.A64 [U+A] Platform 00-n/a cSH cm+M -165.9(anti) C3'-endo lambda=102.5; -169.7(anti) C3'-endo lambda=32.6 d(C1'-C1')=5.79 d(N1-N9)=4.93 d(C6-C8)=4.81 tor(N1-C1'-C1'-N9)=-30.4 H-bonds[2]: "O2(carbonyl)-N6(amino)[2.25]; N3(imino)-N7[3.30]" bp_pars: [3.16 0.32 -0.15 -15.75 -27.60 -17.03] **************************************************************************** List of 5 multiplet(s) 1 nts=3 A.C3+A.U63+A.A64 [CUA] 2 nts=3 A.G6+A.C20+A.A85 [GCA] 3 nts=3 A.G7+A.C19+A.A86 [GCA] 4 nts=3 A.C8+A.G18+A.A87 [CGA] 5 nts=3 A.G30+A.C41+A.A77 [GCA] **************************************************************************** List of 5 helices helix=1[1] bps=6 1 A.A4 A.U22 [A-U] WC 20-XX cWW cW-W 2 A.G5 A.C21 [G-C] WC 19-XIX cWW cW-W 3 A.G6 A.C20 [G-C] WC 19-XIX cWW cW-W 4 A.G7 A.C19 [G-C] WC 19-XIX cWW cW-W 5 A.C8 A.G18 [C-G] WC 19-XIX cWW cW-W 6 A.U9 A.U17 [U-U] 16-XVI cWW cW-W helix=2[1] bps=4 1 A.C12 A.G93 [C-G] WC 19-XIX cWW cW-W 2 A.C13 A.G92 [C-G] WC 19-XIX cWW cW-W 3 A.C14 A.G91 [C-G] WC 19-XIX cWW cW-W 4 A.C15 A.G90 [C-G] WC 19-XIX cWW cW-W helix=3[2] bps=9 1 A.A23 A.U84 [A-U] WC 20-XX cWW cW-W 2 A.G24 A.C83 [G-C] WC 19-XIX cWW cW-W 3 A.G25 A.U82 [G-U] Wobble 28-XXVIII cWW cW-W 4 A.C26 A.G81 [C-G] WC 19-XIX cWW cW-W 5 A.U27 A.A80 [U-A] WC 20-XX cWW cW-W 6 A.C28 A.G79 [C-G] WC 19-XIX cWW cW-W 7 A.U29 A.G78 [U-G] Wobble 28-XXVIII cWW cW-W 8 A.G30 A.C41 [G-C] WC 19-XIX cWW cW-W 9 A.G31 A.C40 [G-C] WC 19-XIX cWW cW-W helix=4[2] bps=6 1 A.C32 A.G47 [C-G] WC 19-XIX cWW cW-W 2 A.C33 A.G46 [C-G] WC 19-XIX cWW cW-W 3 A.G34 A.C45 [G-C] WC 19-XIX cWW cW-W 4 A.U35 A.G44 [U-G] 00-n/a cWW cW-W 5 A.U36 A.G43 [U-G] Wobble 28-XXVIII cWW cW-W 6 A.G37 A.C42 [G-C] WC 19-XIX cWW cW-W helix=5[2] bps=13 1 A.U50 A.U76 [U-U] 00-n/a cWW cW-W 2 A.C51 A.G75 [C-G] WC 19-XIX cWW cW-W 3 A.A52 A.U74 [A-U] WC 20-XX cWW cW-W 4 A.A53 A.C73 [A-C] 00-n/a ... c... 5 A.C54 A.G72 [C-G] WC 19-XIX cWW cW-W 6 A.U55 A.A71 [U-A] WC 20-XX cWW cW-W 7 A.C56 A.G70 [C-G] WC 19-XIX cWW cW-W 8 A.C57 A.G69 [C-G] WC 19-XIX cWW cW-W 9 A.A58 A.U68 [A-U] WC 20-XX cWW cW-W 10 A.U59 A.A67 [U-A] WC 20-XX cWW cW-W 11 A.G60 A.C66 [G-C] WC 19-XIX cWW cW-W 12 A.C2 A.G65 [C-G] WC 19-XIX cWW cW-W 13 A.C3 A.A64 [C-A] 00-n/a cWW cW-W **************************************************************************** List of 8 stems stem=1[#1] bps=5 1 A.A4 A.U22 [A-U] WC 20-XX cWW cW-W 2 A.G5 A.C21 [G-C] WC 19-XIX cWW cW-W 3 A.G6 A.C20 [G-C] WC 19-XIX cWW cW-W 4 A.G7 A.C19 [G-C] WC 19-XIX cWW cW-W 5 A.C8 A.G18 [C-G] WC 19-XIX cWW cW-W stem=2[#2] bps=4 1 A.C12 A.G93 [C-G] WC 19-XIX cWW cW-W 2 A.C13 A.G92 [C-G] WC 19-XIX cWW cW-W 3 A.C14 A.G91 [C-G] WC 19-XIX cWW cW-W 4 A.C15 A.G90 [C-G] WC 19-XIX cWW cW-W stem=3[#3] bps=7 1 A.A23 A.U84 [A-U] WC 20-XX cWW cW-W 2 A.G24 A.C83 [G-C] WC 19-XIX cWW cW-W 3 A.G25 A.U82 [G-U] Wobble 28-XXVIII cWW cW-W 4 A.C26 A.G81 [C-G] WC 19-XIX cWW cW-W 5 A.U27 A.A80 [U-A] WC 20-XX cWW cW-W 6 A.C28 A.G79 [C-G] WC 19-XIX cWW cW-W 7 A.U29 A.G78 [U-G] Wobble 28-XXVIII cWW cW-W stem=4[#3] bps=2 1 A.G30 A.C41 [G-C] WC 19-XIX cWW cW-W 2 A.G31 A.C40 [G-C] WC 19-XIX cWW cW-W stem=5[#4] bps=3 1 A.C32 A.G47 [C-G] WC 19-XIX cWW cW-W 2 A.C33 A.G46 [C-G] WC 19-XIX cWW cW-W 3 A.G34 A.C45 [G-C] WC 19-XIX cWW cW-W stem=6[#4] bps=2 1 A.U36 A.G43 [U-G] Wobble 28-XXVIII cWW cW-W 2 A.G37 A.C42 [G-C] WC 19-XIX cWW cW-W stem=7[#5] bps=2 1 A.C51 A.G75 [C-G] WC 19-XIX cWW cW-W 2 A.A52 A.U74 [A-U] WC 20-XX cWW cW-W stem=8[#5] bps=7 1 A.C54 A.G72 [C-G] WC 19-XIX cWW cW-W 2 A.U55 A.A71 [U-A] WC 20-XX cWW cW-W 3 A.C56 A.G70 [C-G] WC 19-XIX cWW cW-W 4 A.C57 A.G69 [C-G] WC 19-XIX cWW cW-W 5 A.A58 A.U68 [A-U] WC 20-XX cWW cW-W 6 A.U59 A.A67 [U-A] WC 20-XX cWW cW-W 7 A.G60 A.C66 [G-C] WC 19-XIX cWW cW-W **************************************************************************** List of 1 lone WC/wobble pair(s) -1 A.C2 A.G65 [C-G] WC 19-XIX cWW cW-W **************************************************************************** List of 3 coaxial stack(s) 1 Helix#3 contains 2 stems: [#3, #4] 2 Helix#4 contains 2 stems: [#5, #6] 3 Helix#5 contains 2 stems: [#7, #8] **************************************************************************** List of 3 hairpin loop(s) 1 nts=9 UCUCCCCUU closed by pair {A.C8+A.G18 [CG], #1} A.C8+A.U9+A.C10+A.U11+A.C12+A.C13+A.C14+A.C15+A.U16+A.U17+A.G18 [CUCUCCCCUUG] 2 nts=4 CGCC closed by pair {A.G37+A.C42 [GC], #6} A.G37+A.C38+A.G39+A.C40+A.C41+A.C42 [GCGCCC] 3 nts=5 AUUAG closed by pair {A.G60+A.C66 [GC], #8} A.G60+A.A61+A.U62+A.U63+A.A64+A.G65+A.C66 [GAUUAGC] **************************************************************************** List of 2 internal loop(s) 1 symmetric internal loop: 6 nts; [1x1]; linked by [#5, #6] A.G34+A.U35+A.U36+A.G43+A.G44+A.C45 [GUUGGC] 2 symmetric internal loop: 6 nts; [1x1]; linked by [#7, #8] A.A52+A.A53+A.C54+A.G72+A.C73+A.U74 [AACGCU] This structure contains pseudo-knot(s). **************************************************************************** >chain-A #1 RNA* with 93 nts UCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGG .[.(((((...[[[[..)))))((((((([[(((.((..]])).)))...((.(((((((....]))))))).))..))))))).....]]]] DONE!