PDB Chemical Component 3TD

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 3TD

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P O5' 1.523 1.610
P OP1 1.512 1.610
P OP2 1.478 1.480
N1 C2 1.353 1.347
N1 C6 1.351 1.367
N1 HN1 1.000 0.970
C2 O2 1.254 1.216
C2 N3 1.373 1.346
N3 C4 1.378 1.348
N3 C10 1.450 1.465
C4 O4 1.255 1.218
C4 C5 1.420 1.416
C5 C6 1.409 1.351
C5 C1' 1.495 1.507
C6 H6 1.080 1.080
C1' C2' 1.540 1.541
C1' O4' 1.437 1.437
C1' H1' 1.100 1.091
C10 H10 1.099 1.090
C10 H10A 1.100 1.090
C10 H10B 1.100 1.090
C2' O2' 1.427 1.429
C2' C3' 1.538 1.548
C2' H2' 1.100 1.090
O2' HO2' 0.950 0.967
C3' O3' 1.429 1.429
C3' C4' 1.555 1.550
C3' H3' 1.100 1.090
O3' HO3' 0.950 0.967
C4' O4' 1.437 1.444
C4' C5' 1.548 1.530
C4' H4' 1.100 1.090
C5' O5' 1.339 1.430
C5' H5' 1.100 1.090
C5' H5'A 1.100 1.090
P O9 1.511 1.610
OP1 H14 0.950 0.967
O9 H15 0.950 0.967

Bond Angles for 3TD

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O5' P OP1 109.0 109.5
O5' P OP2 110.0 109.5
P O5' C5' 125.2 123.0
O5' P O9 109.5 109.4
OP1 P OP2 109.8 109.5
OP1 P O9 109.1 109.5
P OP1 H14 109.5 114.0
OP2 P O9 109.5 109.5
C2 N1 C6 121.5 120.6
C2 N1 HN1 119.2 119.6
N1 C2 O2 116.0 119.5
N1 C2 N3 121.1 120.9
C6 N1 HN1 119.2 119.8
N1 C6 C5 120.8 119.7
N1 C6 H6 119.6 120.2
O2 C2 N3 123.0 119.6
C2 N3 C4 118.7 120.3
C2 N3 C10 120.1 119.9
C4 N3 C10 121.2 119.8
N3 C4 O4 120.3 120.4
N3 C4 C5 121.5 119.4
N3 C10 H10 109.5 109.4
N3 C10 H10A 109.4 109.5
N3 C10 H10B 109.4 109.5
O4 C4 C5 118.2 120.3
C4 C5 C6 116.4 119.1
C4 C5 C1' 123.0 120.5
C6 C5 C1' 120.6 120.5
C5 C6 H6 119.6 120.1
C5 C1' C2' 112.5 109.9
C5 C1' O4' 113.2 109.9
C5 C1' H1' 109.1 109.9
C2' C1' O4' 103.4 107.3
C2' C1' H1' 108.5 109.9
C1' C2' O2' 112.6 110.5
C1' C2' C3' 103.1 104.2
C1' C2' H2' 108.7 110.4
O4' C1' H1' 109.9 110.0
C1' O4' C4' 107.5 107.0
H10 C10 H10A 109.5 109.5
H10 C10 H10B 109.5 109.5
H10A C10 H10B 109.5 109.5
O2' C2' C3' 113.3 110.6
O2' C2' H2' 110.2 110.4
C2' O2' HO2' 109.5 114.0
C3' C2' H2' 108.7 110.6
C2' C3' O3' 112.1 110.9
C2' C3' C4' 103.8 102.1
C2' C3' H3' 109.5 111.0
O3' C3' C4' 111.0 110.9
O3' C3' H3' 111.0 110.8
C3' O3' HO3' 109.5 114.0
C4' C3' H3' 109.3 110.9
C3' C4' O4' 106.7 103.5
C3' C4' C5' 113.2 110.6
C3' C4' H4' 108.2 110.6
O4' C4' C5' 110.7 110.6
O4' C4' H4' 109.8 110.5
C5' C4' H4' 108.3 110.7
C4' C5' O5' 111.1 109.5
C4' C5' H5' 109.1 109.4
C4' C5' H5'A 109.1 109.5
O5' C5' H5' 109.1 109.4
O5' C5' H5'A 109.1 109.5
H5' C5' H5'A 109.5 109.5
P O9 H15 109.5 113.9

Torsion Angles for 3TD

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP1 P O5' OP2 239.6 240.0
OP1 P O5' O9 119.3 120.0
O5' P OP1 H14 120.5 300.1
OP2 P O5' O9 239.6 240.0
C4' C5' O5' P 178.3 180.0
P O5' C5' H5' 58.0 60.0
P O5' C5' H5'A 298.5 300.0
O5' P O9 H15 239.3 180.0
O5' P OP1 OP2 120.5 120.0
OP1 P O5' C5' 298.9 294.9
O5' P OP1 O9 240.5 240.1
OP2 P OP1 O9 120.0 120.0
OP1 P O9 H15 120.1 60.0
O5' P OP2 OP1 240.1 240.0
OP2 P O5' C5' 59.3 55.0
O5' P OP2 O9 120.3 120.0
OP1 P OP2 O9 240.3 240.0
OP2 P OP1 H14 360.0 180.1
OP2 P O9 H15 360.0 300.0
C6 N1 C2 HN1 180.0 180.3
C2 N1 C6 C5 359.4 0.0
C2 N1 C6 H6 179.4 180.0
O2 C2 N1 N3 179.6 180.0
N1 C2 N3 C4 1.4 360.0
N1 C2 N3 C10 180.2 180.0
C2 N1 C6 HN1 180.0 179.7
C6 N1 C2 O2 179.2 180.0
C6 N1 C2 N3 359.6 360.0
C4 C5 C6 N1 0.6 360.0
N1 C6 C5 C1' 179.1 180.0
C5 C6 N1 H6 180.0 180.1
C2 N1 HN1 C6 180.0 180.3
HN1 N1 C2 O2 359.2 359.7
HN1 N1 C2 N3 179.5 179.7
HN1 N1 C6 C5 179.5 180.3
HN1 N1 C6 H6 359.5 0.2
O2 C2 N1 C6 179.2 180.0
O2 C2 N1 HN1 359.2 359.7
N1 C2 O2 N3 180.4 180.0
O2 C2 N3 C4 181.8 180.0
O2 C2 N3 C10 0.6 360.0
N3 C2 N1 C6 359.6 360.0
N3 C2 N1 HN1 179.5 179.7
N1 C2 N3 O2 179.6 180.0
C4 N3 C2 C10 181.1 180.0
C2 N3 C4 O4 178.9 180.0
C2 N3 C4 C5 358.7 0.0
C2 N3 C10 H10 180.0 360.0
C2 N3 C10 H10A 300.0 120.0
C2 N3 C10 H10B 60.0 240.0
C2 N3 C4 C10 178.9 180.0
C4 N3 C10 H10 358.8 180.0
C4 N3 C10 H10A 118.9 300.0
C4 N3 C10 H10B 238.8 60.0
O4 C4 N3 C5 180.2 180.0
N3 C4 C5 C6 0.4 360.0
N3 C4 C5 C1' 181.9 180.0
C2 N3 C10 C4 181.2 180.0
C10 N3 C4 O4 0.0 0.0
C10 N3 C4 C5 179.8 180.0
H10 C10 N3 H10A 240.0 240.0
H10 C10 N3 H10B 120.0 120.0
H10A C10 N3 H10B 240.0 240.0
O4 C4 N3 C10 0.0 0.0
N3 C4 O4 C5 179.8 180.0
O4 C4 C5 C6 180.2 180.0
O4 C4 C5 C1' 1.7 360.0
N1 C6 C5 C4 0.6 360.0
C5 C4 N3 C10 179.8 180.0
N3 C4 C5 O4 180.2 180.0
C6 C5 C4 C1' 178.5 180.0
C4 C5 C6 H6 180.6 180.1
C4 C5 C1' C2' 89.7 295.0
C4 C5 C1' O4' 206.5 52.8
C4 C5 C1' H1' 329.2 173.9
C5 C6 N1 HN1 179.5 180.3
N1 C6 C5 H6 180.0 179.9
C4 C5 C6 C1' 181.5 180.0
C6 C5 C1' C2' 271.3 115.0
C6 C5 C1' O4' 28.1 232.8
C6 C5 C1' H1' 150.8 353.9
C4 C5 C1' C6 178.4 180.0
C1' C5 C6 H6 359.1 0.1
C2' C1' C5 O4' 243.2 242.1
C2' C1' C5 H1' 120.5 121.0
C5 C1' C2' O2' 281.2 240.2
C5 C1' C2' C3' 158.8 121.4
C5 C1' C2' H2' 43.6 2.7
O4' C1' C5 H1' 237.3 238.9
C5 C1' O4' C4' 198.2 214.1
H6 C6 N1 HN1 359.5 0.2
N1 C6 H6 C5 180.0 180.1
H6 C6 C5 C1' 359.1 0.1
C5 C1' C2' O4' 122.5 119.5
C5 C1' C2' H1' 239.2 239.0
O4' C1' C2' H1' 116.7 119.5
C2' C1' O4' C4' 320.2 333.5
O2' C2' C1' C3' 122.4 118.8
O2' C2' C1' H2' 237.6 237.5
C1' C2' O2' HO2' 180.0 180.0
C3' C2' C1' H2' 115.2 118.7
C1' C2' C3' O3' 99.9 139.1
C1' C2' C3' C4' 340.1 20.9
C1' C2' C3' H3' 223.5 262.7
C5 C1' O4' C2' 238.0 240.5
C5 C1' O4' H1' 122.2 121.0
C2' C1' O4' H1' 244.3 240.5
O4' C1' C2' O2' 158.7 120.7
O4' C1' C2' C3' 36.3 2.0
O4' C1' C2' H2' 281.1 243.2
C3' C4' O4' C1' 26.9 40.0
C1' O4' C4' C5' 150.4 158.5
C1' O4' C4' H4' 269.9 281.6
C5 C1' H1' C2' 122.9 121.0
C5 C1' H1' O4' 235.4 238.9
C2' C1' H1' O4' 112.5 117.9
H1' C1' C2' O2' 42.0 1.2
H1' C1' C2' C3' 279.6 242.4
H1' C1' C2' H2' 164.4 123.7
H1' C1' O4' C4' 75.9 93.0
N3 C10 H10 H10A 120.0 120.0
N3 C10 H10 H10B 240.0 240.0
H10A C10 H10 H10B 120.0 120.0
N3 C10 H10A H10 240.0 240.0
N3 C10 H10A H10B 120.0 120.0
H10 C10 H10A H10B 240.0 240.0
N3 C10 H10B H10 120.0 120.0
N3 C10 H10B H10A 240.0 240.0
H10 C10 H10B H10A 120.0 120.0
O2' C2' C1' O4' 158.7 120.7
O2' C2' C1' H1' 42.0 1.2
C1' C2' O2' C3' 243.5 245.2
C1' C2' O2' H2' 121.5 122.5
C3' C2' O2' H2' 238.0 237.3
O2' C2' C3' O3' 338.0 20.4
O2' C2' C3' C4' 218.2 262.2
O2' C2' C3' H3' 101.6 143.9
C3' C2' C1' O4' 36.3 2.0
C3' C2' C1' H1' 279.6 242.4
C1' C2' C3' O2' 121.9 118.7
C1' C2' C3' H2' 244.8 241.3
O2' C2' C3' H2' 122.9 122.6
C3' C2' O2' HO2' 296.5 294.8
O3' C3' C2' C4' 119.9 118.2
O3' C3' C2' H3' 236.4 236.4
C2' C3' O3' HO3' 180.0 61.5
C4' C3' C2' H3' 116.6 118.3
C2' C3' C4' O4' 357.1 323.0
C2' C3' C4' C5' 235.1 204.5
C2' C3' C4' H4' 115.1 81.4
H2' C2' C1' O4' 281.1 243.2
H2' C2' C1' H1' 164.4 123.7
C1' C2' H2' O2' 236.2 237.4
C1' C2' H2' C3' 111.5 114.8
O2' C2' H2' C3' 235.3 237.3
H2' C2' O2' HO2' 58.5 57.5
H2' C2' C3' O3' 215.1 257.8
H2' C2' C3' C4' 95.3 139.6
H2' C2' C3' H3' 338.7 21.3
HO2' O2' C2' C3' 296.5 294.8
HO2' O2' C2' H2' 58.5 57.5
O3' C3' C2' H2' 215.1 257.8
C2' C3' O3' C4' 244.5 247.3
C2' C3' O3' H3' 122.7 123.7
C4' C3' O3' H3' 238.3 236.4
O3' C3' C4' O4' 236.6 204.8
O3' C3' C4' C5' 114.6 86.3
O3' C3' C4' H4' 354.6 323.2
C1' O4' C4' C3' 26.9 40.0
C4' C3' C2' H2' 95.3 139.6
C2' C3' C4' O3' 120.6 118.2
C2' C3' C4' H3' 243.3 241.7
O3' C3' C4' H3' 122.8 123.6
C4' C3' O3' HO3' 295.5 174.2
O4' C4' C3' C5' 122.0 118.5
O4' C4' C3' H4' 242.0 241.6
C5' C4' C3' H4' 120.0 123.1
C3' C4' C5' O5' 180.5 185.0
C3' C4' C5' H5' 300.7 304.9
C3' C4' C5' H5'A 60.2 64.9
H3' C3' C2' H2' 338.7 21.3
C2' C3' H3' O3' 235.8 236.4
C2' C3' H3' C4' 113.0 112.8
O3' C3' H3' C4' 237.2 236.4
H3' C3' O3' HO3' 57.3 297.8
H3' C3' C4' O4' 113.8 81.3
H3' C3' C4' C5' 351.8 322.8
H3' C3' C4' H4' 231.8 199.7
HO3' O3' C3' C4' 295.5 174.2
HO3' O3' C3' H3' 57.3 297.8
C4' O4' C1' H1' 75.9 93.0
O4' C4' C3' H3' 113.8 81.3
C3' C4' O4' C5' 236.5 241.5
C3' C4' O4' H4' 117.0 118.5
C5' C4' O4' H4' 240.5 237.0
O4' C4' C5' O5' 60.8 70.9
O4' C4' C5' H5' 181.0 190.9
O4' C4' C5' H5'A 300.5 310.9
P O5' C5' C4' 178.3 180.0
C5' C4' C3' H3' 351.8 322.8
C3' C4' C5' O4' 119.7 114.0
C3' C4' C5' H4' 240.1 237.0
O4' C4' C5' H4' 120.4 122.9
O5' C5' C4' H5' 239.8 240.0
O5' C5' C4' H5'A 120.2 120.0
H5' C5' C4' H5'A 240.5 240.0
H4' C4' C3' H3' 231.8 199.7
C3' C4' H4' O4' 244.0 246.0
C3' C4' H4' C5' 123.0 123.0
O4' C4' H4' C5' 239.0 237.0
H4' C4' C5' O5' 300.4 308.0
H4' C4' C5' H5' 60.7 68.0
H4' C4' C5' H5'A 180.2 188.0
C5' O5' P OP1 298.9 294.9
C5' O5' P OP2 59.3 55.0
C5' O5' P O9 179.7 175.0
O5' C5' C4' H4' 300.4 308.0
C4' C5' O5' H5' 120.2 120.0
C4' C5' O5' H5'A 239.7 239.9
H5' C5' O5' H5'A 119.5 120.0
H5' C5' C4' H4' 60.7 68.0
C4' C5' H5' O5' 238.5 240.0
C4' C5' H5' H5'A 119.3 120.0
O5' C5' H5' H5'A 240.7 240.0
H5'A C5' C4' H4' 180.2 188.0
C4' C5' H5'A O5' 121.5 120.1
C4' C5' H5'A H5' 240.7 240.0
O5' C5' H5'A H5' 119.3 120.0
O5' P O9 OP1 119.2 120.0
O5' P O9 OP2 239.4 240.0
O9 P O5' C5' 179.7 175.0
OP1 P O9 OP2 120.1 120.0
O9 P OP1 H14 240.0 60.0
H14 OP1 P OP2 360.0 180.1
H14 OP1 P O9 240.0 60.0