PDB Chemical Component 8DT

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 8DT

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O3' C3' 1.439 1.429
C3' C4' 1.490 1.550
C3' C2' 1.516 1.548
C4' C5' 1.495 1.530
C4' O4' 1.443 1.443
OP1 P 1.511 1.480
C2' C1' 1.533 1.541
C5' O5' 1.434 1.429
O4' C1' 1.411 1.438
C1' N1 1.447 1.464
O5' P 1.634 1.609
P OP2 1.526 1.610
O2 C2 1.245 1.216
N1 C2 1.367 1.343
N1 C6 1.336 1.365
C2 N3 1.373 1.345
C6 C5 1.387 1.366
N3 C4 1.369 1.349
C5 C4 1.378 1.470
C5 C7 1.489 1.477
C4 O4 1.258 1.217
C7 C1 1.331 1.327
C1 C3 1.512 1.507
C3 N9 1.460 1.465
N9 C32 1.350 1.348
O34 C32 1.268 1.213
C32 C33 1.544 1.507
OP2 H2 0.950 0.967
C5' H3 1.100 1.091
C5' H4 1.100 1.090
C4' H5 1.100 1.090
C3' H6 1.100 1.090
O3' H7 0.951 0.968
C2' H8 1.100 1.090
C2' H9 1.101 1.091
C1' H10 1.100 1.090
C6 H11 1.080 1.080
N3 H12 1.000 0.969
C7 H13 1.080 1.080
C1 H14 1.080 1.080
C3 H15 1.100 1.090
C3 H16 1.100 1.090
N9 H17 1.000 0.970
C33 H18 1.100 1.090
C33 H19 1.100 1.090
C33 H20 1.100 1.090
P OP3 1.542 1.610
OP3 H1 0.950 0.968

Bond Angles for 8DT

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O3' C3' C2' 105.3 110.9
O3' C3' H6 112.9 110.8
C3' C4' O4' 106.5 103.5
C3' C4' H5 108.1 110.7
C3' C2' C1' 102.0 104.2
C2' C3' H6 111.7 110.9
C3' C2' H8 111.3 110.5
C3' C2' H9 111.3 110.5
C4' C5' H3 108.0 109.5
C4' C5' H4 108.1 109.5
C4' O4' C1' 110.7 107.0
O4' C4' H5 108.7 110.6
OP1 P OP2 108.7 109.4
OP1 P OP3 128.2 109.5
C2' C1' O4' 104.5 107.3
C2' C1' N1 114.8 109.9
C1' C2' H8 111.3 110.5
C1' C2' H9 111.3 110.5
C2' C1' H10 108.6 109.9
O4' C1' N1 108.9 109.9
O4' C1' H10 110.3 109.8
C1' N1 C2 120.0 119.3
C1' N1 C6 119.2 119.3
N1 C1' H10 109.7 110.0
O5' P OP3 106.9 109.5
P OP2 H2 109.5 114.0
OP2 P OP3 111.1 109.5
O2 C2 N3 122.4 119.0
C6 N1 C2 120.6 121.4
N1 C2 N3 120.7 121.9
N1 C6 C5 120.4 119.5
N1 C6 H11 119.8 120.2
C2 N3 C4 118.6 120.3
C2 N3 H12 120.7 119.9
C6 C5 C4 118.6 118.3
C6 C5 C7 115.9 120.8
C5 C6 H11 119.8 120.3
N3 C4 O4 119.5 120.7
C4 N3 H12 120.7 119.9
C5 C7 C1 124.0 120.0
C5 C7 H13 118.0 120.0
C7 C1 C3 123.4 120.0
C1 C7 H13 118.0 120.0
C7 C1 H14 118.3 120.0
C1 C3 N9 101.0 109.4
C3 C1 H14 118.3 120.0
C1 C3 H15 111.5 109.5
C1 C3 H16 111.5 109.5
C3 N9 C32 127.7 120.0
N9 C3 H15 111.5 109.5
N9 C3 H16 111.5 109.4
C3 N9 H17 116.2 120.0
N9 C32 C33 111.3 120.0
C32 N9 H17 116.2 119.9
O34 C32 C33 125.8 120.0
C32 C33 H18 109.5 109.4
C32 C33 H19 109.5 109.5
C32 C33 H20 109.5 109.5
H3 C5' H4 109.5 109.5
H8 C2' H9 109.5 110.5
H15 C3 H16 109.5 109.5
H18 C33 H19 109.4 109.5
H18 C33 H20 109.5 109.5
H19 C33 H20 109.5 109.4
P OP3 H1 109.5 114.0

Torsion Angles for 8DT

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O3' C3' C4' O4' 271.0 204.8
O3' C3' C4' H5 27.7 323.4
O3' C3' C2' C1' 82.2 139.1
C2' C3' O3' H6 122.1 123.6
O3' C3' C2' H8 201.0 257.7
O3' C3' C2' H9 323.4 20.4
C3' C4' C5' H3 163.4 60.6
C3' C4' C5' H4 281.7 300.6
C3' C4' O4' C1' 357.8 40.0
O4' C4' C3' H5 243.3 241.4
O3' C3' C2' H6 237.1 236.4
C2' C3' C4' O4' 23.4 323.0
C2' C3' C4' H5 140.1 81.6
C3' C2' C1' O4' 33.4 2.0
C3' C2' C1' N1 152.6 121.5
C1' C2' C3' H8 241.2 241.3
C1' C2' C3' H9 118.8 118.7
C3' C2' C1' H10 275.8 242.7
H8 C2' C3' H9 237.5 237.4
H3 C5' C4' H4 241.6 120.0
C3' C4' O4' H5 116.2 118.6
O4' C4' C5' H3 43.1 306.5
O4' C4' C5' H4 161.5 186.5
C2' C1' O4' C4' 340.1 333.5
C4' O4' C1' N1 217.0 214.1
C4' O4' C1' H10 96.6 92.9
O5' P OP1 OP3 240.8 240.0
OP1 P OP2 H2 0.0 180.0
OP2 P OP1 OP3 138.6 120.0
OP1 P OP3 H1 360.0 60.0
C1' C2' C3' H6 205.1 262.7
C3' C2' C1' H8 118.8 118.7
C3' C2' C1' H9 241.2 241.3
C4' O4' C1' C2' 340.1 333.5
O4' C1' C2' N1 240.8 240.5
O4' C1' C2' H10 117.7 119.4
C2' C1' N1 C2 118.5 295.0
C2' C1' N1 C6 294.0 115.3
N1 C1' C2' H10 236.8 238.8
H8 C2' C1' H9 122.4 122.6
C5' O5' P OP3 286.8 185.0
C1' O4' C4' H5 241.6 281.4
C2' C1' O4' N1 123.1 119.5
O4' C1' C2' H8 274.7 243.3
O4' C1' C2' H9 152.2 120.7
C2' C1' O4' H10 243.5 240.6
O4' C1' N1 C2 235.2 52.8
O4' C1' N1 C6 50.7 233.1
N1 C1' O4' H10 120.4 121.2
C2' C1' N1 O4' 243.3 242.2
N1 C1' C2' H8 33.8 2.8
N1 C1' C2' H9 271.4 240.1
C2' C1' N1 H10 122.6 121.1
O4' C1' N1 H10 239.3 238.9
C6 N1 C1' C2 175.5 180.3
C1' N1 C2 N3 177.6 180.0
C1' N1 C6 C5 180.4 180.0
C1' N1 C6 H11 0.4 360.0
OP1 P O5' OP3 134.2 120.0
O5' P OP2 H2 258.1 60.0
OP2 P O5' OP3 244.7 240.0
O5' P OP3 H1 115.5 180.0
OP1 P OP2 OP3 213.9 240.0
O5' P OP2 OP3 112.0 120.0
OP2 P OP3 H1 222.2 300.1
N1 C2 O2 N3 178.6 179.9
O2 C2 N3 C4 178.8 180.0
O2 C2 N3 H12 358.8 359.9
C1' N1 C2 C6 175.4 180.3
C2 N1 C1' H10 355.9 173.9
O2 C2 N1 N3 181.4 180.1
C2 N1 C6 C5 355.9 0.3
C2 N1 C6 H11 175.9 180.3
N1 C2 N3 C4 0.3 0.0
N1 C2 N3 H12 180.2 180.0
C1' N1 C6 C2 184.5 179.7
C6 N1 C1' H10 171.4 354.2
C6 N1 C2 N3 2.2 359.7
N1 C6 C5 C4 3.6 359.9
N1 C6 C5 C7 181.9 180.0
C5 C6 N1 H11 180.0 180.0
C2 N3 C4 O4 180.5 180.1
C4 N3 C2 H12 180.0 180.0
C5 C6 N1 C2 355.9 0.3
N1 C6 C5 H11 180.0 180.0
C6 C5 C7 C1 184.8 174.4
C6 C5 C7 H13 4.9 354.4
C2 N3 C4 H12 180.0 180.0
C6 C5 C4 N3 358.9 359.8
C6 C5 C4 C7 178.2 180.0
C4 C5 C6 H11 183.6 180.0
C5 C4 N3 H12 179.3 180.2
C6 C5 C7 C4 181.8 180.0
C7 C5 C6 H11 1.9 360.0
C5 C7 C1 C3 176.8 185.0
C1 C7 C5 H13 180.0 179.9
C5 C7 C1 H14 356.8 5.1
C6 C5 C4 O4 177.6 180.0
O4 C4 N3 H12 0.5 0.1
C5 C7 C1 H13 180.0 180.1
C7 C1 C3 N9 177.8 125.0
C3 C1 C7 H14 180.0 179.9
C7 C1 C3 H15 296.4 245.0
C7 C1 C3 H16 59.1 5.1
C3 C1 C7 H13 356.8 5.0
C7 C1 C3 H14 180.0 180.1
C1 C3 N9 C32 104.4 180.0
N9 C3 C1 H15 241.4 240.0
N9 C3 C1 H16 118.6 120.0
C1 C3 N9 H17 284.4 0.0
H15 C3 C1 H16 237.2 240.0
N9 C3 C1 H14 357.8 305.0
C1 C3 N9 H15 118.6 120.0
C1 C3 N9 H16 241.4 240.0
C3 N9 C32 C33 192.3 180.0
C32 N9 C3 H17 180.0 179.9
H15 C3 N9 H16 122.8 120.0
C32 N9 C3 H15 345.8 60.0
C32 N9 C3 H16 223.0 300.0
C3 N9 C32 H17 180.0 180.1
O34 C32 N9 C33 178.9 180.1
N9 C32 C33 H18 178.9 60.1
N9 C32 C33 H19 298.8 180.1
N9 C32 C33 H20 58.8 300.0
N9 C32 O34 C33 181.3 179.9
O34 C32 N9 H17 191.2 180.0
O34 C32 C33 H18 0.0 240.0
O34 C32 C33 H19 120.0 360.0
O34 C32 C33 H20 240.0 119.9
C33 C32 N9 H17 12.3 359.9
H18 C33 C32 H19 240.0 240.0
H18 C33 C32 H20 120.0 120.0
H19 C33 C32 H20 240.0 240.0
H2 OP2 P OP3 146.1 300.0
C4' C5' H3 H4 117.5 240.0
C4' C5' H4 H3 242.6 120.0
C3' C4' H5 O4' 244.7 245.8
H5 C4' C5' H3 285.7 183.6
H5 C4' C5' H4 44.1 63.6
H5 C4' O4' C1' 241.6 281.4
O3' C3' H6 C2' 118.4 123.7
H6 C3' C4' O4' 143.9 81.2
H6 C3' C4' H5 260.5 199.8
H6 C3' C2' C1' 205.1 262.7
H6 C3' C2' H8 323.8 21.3
H6 C3' C2' H9 86.3 144.0
H7 O3' C3' C2' 68.7 67.3
H7 O3' C3' H6 306.7 303.6
C3' C2' H8 C1' 247.0 245.2
H8 C2' C3' H6 323.8 21.3
C3' C2' H8 H9 123.5 122.6
H8 C2' C1' O4' 274.7 243.3
H8 C2' C1' N1 33.8 2.8
C1' C2' H8 H9 236.5 237.4
H8 C2' C1' H10 157.0 124.0
C3' C2' H9 C1' 113.0 114.8
H9 C2' C3' H6 86.3 144.0
C3' C2' H9 H8 236.5 237.4
H9 C2' C1' O4' 152.2 120.7
H9 C2' C1' N1 271.4 240.1
C1' C2' H9 H8 123.5 122.6
H9 C2' C1' H10 34.6 1.3
C2' C1' H10 O4' 113.9 117.8
C2' C1' H10 N1 233.8 238.9
H10 C1' C2' H8 157.0 124.0
H10 C1' C2' H9 34.6 1.3
O4' C1' H10 N1 119.9 121.1
H10 C1' N1 C2 355.9 173.9
H10 C1' N1 C6 171.4 354.2
H11 C6 N1 C2 175.9 180.3
N1 C6 H11 C5 180.0 180.0
H11 C6 C5 C4 183.6 180.0
H11 C6 C5 C7 1.9 360.0
C2 N3 H12 C4 180.0 180.0
H12 N3 C4 O4 0.5 0.1
C5 C7 H13 C1 180.0 179.9
H13 C7 C1 C3 356.8 5.0
H13 C7 C1 H14 176.8 185.0
C7 C1 H14 C3 180.0 179.9
H14 C1 C7 H13 176.8 185.0
H14 C1 C3 N9 357.8 305.0
H14 C1 C3 H15 116.4 65.0
H14 C1 C3 H16 239.1 185.0
C1 C3 H15 N9 247.9 240.0
H15 C3 C1 H14 116.4 65.0
C1 C3 H15 H16 123.9 120.0
H15 C3 N9 C32 345.8 60.0
N9 C3 H15 H16 236.1 240.0
H15 C3 N9 H17 165.8 240.1
C1 C3 H16 N9 112.1 120.0
H16 C3 C1 H14 239.1 185.0
C1 C3 H16 H15 236.1 240.0
H16 C3 N9 C32 223.0 300.0
N9 C3 H16 H15 123.9 120.0
H16 C3 N9 H17 43.1 120.0
C3 N9 H17 C32 180.0 179.9
H17 N9 C3 H15 165.8 240.1
H17 N9 C3 H16 43.1 120.0
H17 N9 C32 C33 12.3 359.9
C32 C33 H18 H19 120.0 120.0
C32 C33 H18 H20 240.0 240.0
H19 C33 H18 H20 120.0 120.0
C32 C33 H19 H18 240.0 240.0
C32 C33 H19 H20 120.0 120.0
H18 C33 H19 H20 240.0 240.0
C32 C33 H20 H18 120.0 120.0
C32 C33 H20 H19 240.0 240.0
H18 C33 H20 H19 120.0 120.0
OP1 P OP3 OP2 137.8 119.9
OP3 P OP2 H2 146.1 300.0