PDB Chemical Component 2ST

The following tables include covalent bond distance, bond angle and torsion angle values for the experimental model and ideal geometries stored in the definition for this chemical component.

Bond Distances for 2ST

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
OP3 P 1.611  
OP3 HOP3 0.950  
P OP1 1.468  
P OP2 1.491  
P O5' 1.592  
OP2 HOP2 0.950  
O5' C5' 1.414  
N1 C6 1.389  
N1 C2 1.389  
N1 C1' 1.500  
C6 C5 1.400  
C6 H6 1.080  
C2 O2 1.220  
C2 N3 1.372  
N3 C4 1.386  
N3 HN3 1.001  
C4 O4 1.222  
C4 C5 1.500  
C5 C5A 1.504  
C5A H5A1 1.100  
C5A H5A2 1.100  
C5A H5A3 1.100  
C2' C1' 1.502  
C2' C3' 1.519  
C2' SE 2.058  
C2' H2' 1.100  
C5' C4' 1.506  
C5' H5' 1.100  
C5' H5'' 1.100  
C4' O4' 1.444  
C4' C3' 1.514  
C4' H4' 1.100  
O4' C1' 1.444  
C1' H1' 1.100  
C3' O3' 1.368  
C3' H3' 1.100  
SE CA' 1.960  
CA' HA'1 1.100  
CA' HA'2 1.101  
CA' HA'3 1.100  
O3' HO3' 0.950  

Bond Angles for 2ST

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
P OP3 HOP3 104.3  
OP3 P OP1 104.3  
OP3 P OP2 110.9  
OP3 P O5' 104.8  
OP1 P OP2 121.1  
OP1 P O5' 107.3  
OP2 P O5' 107.3  
P OP2 HOP2 110.9  
P O5' C5' 119.9  
O5' C5' C4' 110.3  
O5' C5' H5' 109.2  
O5' C5' H5'' 109.0  
C6 N1 C2 121.0  
C6 N1 C1' 124.2  
N1 C6 C5 122.7  
N1 C6 H6 118.6  
C2 N1 C1' 114.8  
N1 C2 O2 121.9  
N1 C2 N3 116.7  
N1 C1' C2' 107.2  
N1 C1' O4' 103.0  
N1 C1' H1' 114.3  
C5 C6 H6 118.6  
C6 C5 C4 117.3  
C6 C5 C5A 123.8  
O2 C2 N3 121.4  
C2 N3 C4 127.6  
C2 N3 HN3 116.2  
C4 N3 HN3 116.2  
N3 C4 O4 120.0  
N3 C4 C5 114.7  
O4 C4 C5 125.3  
C4 C5 C5A 118.9  
C5 C5A H5A1 109.5  
C5 C5A H5A2 109.4  
C5 C5A H5A3 109.4  
H5A1 C5A H5A2 109.5  
H5A1 C5A H5A3 109.5  
H5A2 C5A H5A3 109.5  
C1' C2' C3' 101.1  
C1' C2' SE 104.5  
C1' C2' H2' 118.2  
C2' C1' O4' 107.1  
C2' C1' H1' 110.5  
C3' C2' SE 111.3  
C3' C2' H2' 112.2  
C2' C3' C4' 101.8  
C2' C3' O3' 108.9  
C2' C3' H3' 116.2  
SE C2' H2' 109.1  
C2' SE CA' 99.6  
C4' C5' H5' 109.2  
C4' C5' H5'' 109.0  
C5' C4' O4' 107.4  
C5' C4' C3' 117.1  
C5' C4' H4' 103.6  
H5' C5' H5'' 110.1  
O4' C4' C3' 101.5  
O4' C4' H4' 118.7  
C4' O4' C1' 108.7  
C3' C4' H4' 109.2  
C4' C3' O3' 113.7  
C4' C3' H3' 111.6  
O4' C1' H1' 114.2  
O3' C3' H3' 104.9  
C3' O3' HO3' 109.5  
SE CA' HA'1 109.5  
SE CA' HA'2 109.5  
SE CA' HA'3 109.4  
HA'1 CA' HA'2 109.5  
HA'1 CA' HA'3 109.4  
HA'2 CA' HA'3 109.5  

Torsion Angles for 2ST

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP3 OP2 131.9  
OP1 P OP3 O5' 247.4  
OP2 P OP3 O5' 115.5  
OP3 P OP2 HOP2 180.0  
OP3 P O5' C5' 294.8  
HOP3 OP3 P OP1 180.0  
HOP3 OP3 P OP2 48.1  
HOP3 OP3 P O5' 292.7  
OP1 P OP3 HOP3 180.0  
OP3 P OP1 OP2 234.3  
OP3 P OP1 O5' 110.9  
OP2 P OP1 O5' 236.6  
OP1 P OP2 HOP2 57.4  
OP1 P O5' C5' 45.3  
OP2 P OP3 HOP3 48.1  
OP3 P OP2 OP1 122.6  
OP3 P OP2 O5' 246.0  
OP1 P OP2 O5' 123.4  
OP2 P O5' C5' 176.8  
O5' P OP3 HOP3 292.7  
OP3 P O5' OP1 249.5  
OP3 P O5' OP2 118.0  
OP1 P O5' OP2 228.5  
O5' P OP2 HOP2 294.0  
P O5' C5' C4' 174.6  
P O5' C5' H5' 54.6  
P O5' C5' H5'' 294.3  
HOP2 OP2 P O5' 294.0  
C4' C5' O5' H5' 120.0  
C4' C5' O5' H5'' 240.4  
O5' C5' C4' O4' 294.0  
O5' C5' C4' C3' 47.3  
O5' C5' C4' H4' 167.6  
H5' C5' O5' H5'' 120.4  
C2 N1 C6 C1' 180.8  
C6 N1 C2 O2 176.0  
C6 N1 C2 N3 357.4  
C6 N1 C1' C2' 267.3  
C6 N1 C1' O4' 20.1  
C6 N1 C1' H1' 144.6  
C5 C6 N1 H6 180.0  
N1 C6 C5 C4 0.7  
N1 C6 C5 C5A 180.3  
C6 N1 C2 C1' 179.3  
C2 N1 C6 C5 1.4  
C2 N1 C6 H6 181.4  
C2 N1 C1' C2' 86.6  
C2 N1 C1' O4' 199.4  
C2 N1 C1' H1' 323.8  
O2 C2 N1 N3 178.5  
N1 C2 N3 C4 1.7  
N1 C2 N3 HN3 181.7  
C6 N1 C1' C2 180.8  
C1' N1 C6 C5 180.6  
C1' N1 C6 H6 0.6  
C1' N1 C2 O2 356.7  
C1' N1 C2 N3 178.2  
N1 C1' C2' C3' 87.5  
N1 C1' C2' SE 203.2  
N1 C1' C2' H2' 324.7  
C2' C1' N1 O4' 247.2  
C2' C1' N1 H1' 122.8  
C4' O4' C1' N1 242.4  
O4' C1' N1 H1' 235.6  
C5 C6 N1 C2 1.4  
C5 C6 N1 C1' 180.6  
N1 C6 C5 H6 180.0  
N3 C4 C5 C6 358.5  
O4 C4 C5 C6 177.9  
C4 C5 C6 C5A 180.4  
C6 C5 C5A H5A1 60.1  
C6 C5 C5A H5A2 180.2  
C6 C5 C5A H5A3 300.1  
H6 C6 N1 C2 181.4  
H6 C6 N1 C1' 0.6  
N1 C6 H6 C5 180.0  
H6 C6 C5 C4 180.7  
H6 C6 C5 C5A 0.3  
O2 C2 N1 C1' 356.7  
N1 C2 O2 N3 181.5  
O2 C2 N3 C4 183.1  
O2 C2 N3 HN3 3.1  
N3 C2 N1 C1' 178.2  
N1 C2 N3 O2 178.5  
C4 N3 C2 HN3 180.0  
C2 N3 C4 O4 180.9  
C2 N3 C4 C5 0.4  
C6 C5 C4 N3 358.5  
C2 N3 C4 HN3 180.0  
O4 C4 N3 C5 180.5  
N3 C4 C5 C5A 178.9  
C2 N3 HN3 C4 180.0  
HN3 N3 C4 O4 0.8  
HN3 N3 C4 C5 180.4  
C6 C5 C4 O4 177.9  
O4 C4 N3 HN3 0.8  
N3 C4 O4 C5 179.5  
O4 C4 C5 C5A 358.4  
C4 C5 C6 H6 180.7  
C6 C5 C4 C5A 179.6  
C5 C4 N3 HN3 180.4  
N3 C4 C5 O4 180.5  
C4 C5 C5A H5A1 239.7  
C4 C5 C5A H5A2 359.7  
C4 C5 C5A H5A3 119.7  
C5A C5 C6 H6 0.3  
C6 C5 C5A C4 180.4  
H5A1 C5A C5 H5A2 240.0  
H5A1 C5A C5 H5A3 120.0  
H5A2 C5A C5 H5A3 240.0  
C5 C5A H5A1 H5A2 120.0  
C5 C5A H5A1 H5A3 240.0  
H5A2 C5A H5A1 H5A3 120.0  
C5 C5A H5A2 H5A1 240.0  
C5 C5A H5A2 H5A3 119.9  
H5A1 C5A H5A2 H5A3 240.0  
C5 C5A H5A3 H5A1 120.0  
C5 C5A H5A3 H5A2 240.0  
H5A1 C5A H5A3 H5A2 120.0  
N1 C1' C2' O4' 109.9  
N1 C1' C2' H1' 234.9  
C3' C2' C1' SE 244.3  
C3' C2' C1' H2' 122.8  
C1' C2' C3' C4' 40.0  
C1' C2' C3' O3' 160.4  
C1' C2' C3' H3' 278.5  
SE C2' C1' H2' 238.5  
C1' C2' SE CA' 82.5  
C4' O4' C1' C2' 355.2  
O4' C1' C2' H1' 125.0  
C1' C2' C3' SE 110.5  
C1' C2' C3' H2' 233.1  
C3' C2' C1' O4' 337.6  
C3' C2' C1' H1' 212.6  
SE C2' C3' H2' 122.6  
C3' C2' SE CA' 190.8  
C5' C4' C3' C2' 200.1  
O4' C4' C3' C2' 316.6  
C2' C3' C4' H4' 82.8  
C4' C3' C2' O3' 239.6  
C4' C3' C2' H3' 121.5  
O3' C3' C2' H3' 241.9  
C2' C3' O3' HO3' 344.9  
C1' C2' SE C3' 251.7  
C1' C2' SE H2' 127.3  
SE C2' C1' O4' 93.3  
SE C2' C1' H1' 328.3  
C3' C2' SE H2' 235.7  
SE C2' C3' C4' 289.5  
SE C2' C3' O3' 49.9  
SE C2' C3' H3' 168.0  
C2' SE CA' HA'1 305.7  
C2' SE CA' HA'2 65.7  
C2' SE CA' HA'3 185.8  
C1' C2' H2' C3' 117.0  
C1' C2' H2' SE 240.9  
H2' C2' C1' O4' 214.8  
H2' C2' C1' H1' 89.8  
C3' C2' H2' SE 123.8  
H2' C2' C3' C4' 166.9  
H2' C2' C3' O3' 287.3  
H2' C2' C3' H3' 45.4  
H2' C2' SE CA' 315.1  
O5' C5' C4' H5' 240.0  
O5' C5' C4' H5'' 119.6  
C2' C3' C4' C5' 200.1  
H5' C5' C4' H5'' 239.6  
O4' C4' C5' C3' 246.7  
O4' C4' C5' H4' 126.4  
C5' C4' O4' C1' 153.5  
C3' C4' C5' H4' 239.7  
C5' C4' C3' O3' 83.2  
C5' C4' C3' H3' 324.8  
O5' C5' H5' C4' 120.7  
O5' C5' H5' H5'' 240.4  
C4' C5' H5' H5'' 119.7  
H5' C5' C4' O4' 54.0  
H5' C5' C4' C3' 167.3  
H5' C5' C4' H4' 287.6  
O5' C5' H5'' C4' 239.6  
O5' C5' H5'' H5' 119.8  
C4' C5' H5'' H5' 240.2  
H5'' C5' C4' O4' 174.3  
H5'' C5' C4' C3' 287.6  
H5'' C5' C4' H4' 47.9  
N1 C1' O4' C4' 242.4  
C2' C1' O4' C4' 355.2  
C2' C3' C4' O4' 316.6  
O4' C4' C5' H5' 54.0  
O4' C4' C5' H5'' 174.3  
C5' C4' O4' C3' 123.4  
C5' C4' O4' H4' 243.1  
C3' C4' O4' H4' 119.7  
O4' C4' C3' O3' 199.7  
O4' C4' C3' H3' 81.3  
C4' O4' C1' H1' 118.0  
C4' C3' C2' SE 289.5  
C4' C3' C2' H2' 166.9  
C2' C3' C4' O3' 116.9  
C2' C3' C4' H3' 235.3  
C3' C4' C5' H5' 167.3  
C3' C4' C5' H5'' 287.6  
C5' C4' C3' O4' 243.5  
C5' C4' C3' H4' 117.3  
O4' C4' C3' H4' 233.8  
C3' C4' O4' C1' 30.0  
O3' C3' C4' H3' 118.4  
C4' C3' O3' HO3' 97.6  
H4' C4' C5' H5' 287.6  
H4' C4' C5' H5'' 47.9  
C5' C4' H4' O4' 118.9  
C5' C4' H4' C3' 234.5  
O4' C4' H4' C3' 115.6  
H4' C4' O4' C1' 270.4  
H4' C4' C3' O3' 325.9  
H4' C4' C3' H3' 207.5  
N1 C1' O4' C2' 247.2  
N1 C1' O4' H1' 124.5  
O4' C1' C2' C3' 337.6  
O4' C1' C2' SE 93.3  
O4' C1' C2' H2' 214.8  
C2' C1' O4' H1' 237.3  
C1' O4' C4' C3' 30.0  
C1' O4' C4' H4' 270.4  
N1 C1' H1' C2' 120.9  
N1 C1' H1' O4' 241.8  
H1' C1' C2' C3' 212.6  
H1' C1' C2' SE 328.3  
H1' C1' C2' H2' 89.8  
C2' C1' H1' O4' 120.9  
O3' C3' C2' SE 49.9  
O3' C3' C2' H2' 287.3  
C2' C3' O3' C4' 247.3  
C2' C3' O3' H3' 125.1  
O3' C3' C4' H4' 325.9  
C4' C3' O3' H3' 237.8  
H3' C3' C2' SE 168.0  
H3' C3' C2' H2' 45.4  
C2' C3' H3' C4' 116.2  
C2' C3' H3' O3' 239.7  
H3' C3' C4' H4' 207.5  
C4' C3' H3' O3' 123.6  
H3' C3' O3' HO3' 219.9  
CA' SE C2' H2' 315.1  
HA'1 CA' SE HA'2 240.0  
HA'1 CA' SE HA'3 119.9  
HA'2 CA' SE HA'3 240.0  
SE CA' HA'1 HA'2 120.0  
SE CA' HA'1 HA'3 240.0  
HA'2 CA' HA'1 HA'3 120.0  
SE CA' HA'2 HA'1 240.0  
SE CA' HA'2 HA'3 120.0  
HA'1 CA' HA'2 HA'3 240.0  
SE CA' HA'3 HA'1 120.0  
SE CA' HA'3 HA'2 240.0  
HA'1 CA' HA'3 HA'2 120.0  
HO3' O3' C3' H3' 219.9