PDB Chemical Component TYD

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 TYD

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
PA O1A 1.518 1.479
PA O2A 1.449 1.610
PA O3A 1.609 1.609
PA O5' 1.603 1.610
O2A HOA2 0.950 0.966
O3A PB 1.618 1.609
PB O1B 1.472 1.480
PB O2B 1.513 1.611
PB O3B 1.462 1.609
O2B HOB2 0.951 0.967
O3B HOB3 0.951 0.966
O5' C5' 1.438 1.428
C5' C4' 1.500 1.529
C5' H5'1 1.115 1.089
C5' H5'2 1.114 1.090
C4' O4' 1.406 1.446
C4' C3' 1.524 1.549
C4' H4' 1.115 1.090
O4' C1' 1.449 1.438
C3' O3' 1.423 1.429
C3' C2' 1.507 1.548
C3' H3' 1.115 1.090
O3' HO3' 0.951 0.967
C2' C1' 1.549 1.540
C2' H2'1 1.116 1.091
C2' H2'2 1.115 1.089
C1' N1 1.484 1.465
C1' H1' 1.115 1.090
N1 C2 1.392 1.344
N1 C6 1.380 1.368
C2 O2 1.228 1.216
C2 N3 1.406 1.346
N3 C4 1.391 1.348
N3 HN3 1.020 0.970
C4 O4 1.226 1.218
C4 C5 1.449 1.415
C5 C5M 1.523 1.507
C5 C6 1.343 1.350
C5M H51 1.115 1.090
C5M H52 1.115 1.090
C5M H53 1.114 1.091
C6 H6 1.103 1.080

Bond Angles for TYD

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1A PA O2A 120.3 109.5
O1A PA O3A 108.3 109.5
O1A PA O5' 109.4 109.5
O2A PA O3A 106.1 109.4
O2A PA O5' 108.0 109.5
PA O2A HOA2 120.3 106.8
O3A PA O5' 103.3 109.5
PA O3A PB 134.8 106.8
PA O5' C5' 118.0 106.8
O3A PB O1B 103.0 109.5
O3A PB O2B 106.6 109.5
O3A PB O3B 103.9 109.5
O1B PB O2B 111.1 109.4
O1B PB O3B 115.2 109.5
O2B PB O3B 115.6 109.4
PB O2B HOB2 106.5 106.8
PB O3B HOB3 103.9 106.9
O5' C5' C4' 110.8 109.5
O5' C5' H5'1 111.7 109.5
O5' C5' H5'2 111.7 109.4
C4' C5' H5'1 111.7 109.4
C4' C5' H5'2 111.7 109.4
C5' C4' O4' 107.3 110.7
C5' C4' C3' 115.6 110.7
C5' C4' H4' 105.1 110.6
H5'1 C5' H5'2 98.7 109.5
O4' C4' C3' 103.6 103.6
O4' C4' H4' 116.9 110.5
C4' O4' C1' 111.0 106.9
C3' C4' H4' 108.8 110.6
C4' C3' O3' 101.4 110.9
C4' C3' C2' 101.4 102.2
C4' C3' H3' 121.4 110.9
O4' C1' C2' 104.4 107.4
O4' C1' N1 108.8 109.8
O4' C1' H1' 114.5 109.9
O3' C3' C2' 115.3 110.9
O3' C3' H3' 108.7 110.8
C3' O3' HO3' 101.5 106.8
C2' C3' H3' 108.8 110.9
C3' C2' C1' 102.4 104.2
C3' C2' H2'1 114.9 110.4
C3' C2' H2'2 114.9 110.6
C1' C2' H2'1 114.9 110.5
C1' C2' H2'2 115.0 110.5
C2' C1' N1 113.0 109.9
C2' C1' H1' 110.3 109.9
H2'1 C2' H2'2 95.5 110.5
N1 C1' H1' 106.0 109.9
C1' N1 C2 119.2 119.7
C1' N1 C6 120.4 119.6
C2 N1 C6 120.2 120.7
N1 C2 O2 121.2 119.6
N1 C2 N3 117.1 120.9
N1 C6 C5 121.9 119.6
N1 C6 H6 120.4 120.2
O2 C2 N3 121.7 119.5
C2 N3 C4 124.6 120.2
C2 N3 HN3 118.3 119.9
C4 N3 HN3 117.1 119.9
N3 C4 O4 119.4 120.3
N3 C4 C5 114.4 119.4
O4 C4 C5 126.2 120.3
C4 C5 C5M 120.4 120.4
C4 C5 C6 121.5 119.1
C5M C5 C6 118.0 120.4
C5 C5M H51 120.4 109.5
C5 C5M H52 108.3 109.5
C5 C5M H53 108.3 109.5
C5 C6 H6 117.6 120.2
H51 C5M H52 108.2 109.4
H51 C5M H53 108.3 109.5
H52 C5M H53 101.7 109.4

Torsion Angles for TYD

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2A PA O1A O3A 237.8 240.0
O2A PA O1A O5' 125.9 120.0
O1A PA O2A HOA2 179.9 180.0
O3A PA O1A O5' 248.1 239.9
O1A PA O3A PB 3.6 300.0
O1A PA O5' C5' 307.6 60.0
O1A PA O2A O3A 123.3 120.0
O1A PA O2A O5' 233.5 240.0
O3A PA O2A O5' 110.2 120.0
O2A PA O3A PB 134.1 60.0
O2A PA O5' C5' 175.0 300.0
O1A PA O3A O2A 229.5 240.0
O1A PA O3A O5' 116.0 120.0
O2A PA O3A O5' 246.4 240.0
O3A PA O2A HOA2 56.7 60.0
O3A PA O5' C5' 62.8 180.1
PA O3A PB O1B 104.9 60.0
PA O3A PB O2B 347.9 180.0
PA O3A PB O3B 225.3 299.9
O1A PA O5' O2A 132.6 120.0
O1A PA O5' O3A 244.8 239.9
O2A PA O5' O3A 112.2 119.9
O5' PA O2A HOA2 306.4 300.0
O5' PA O3A PB 247.7 180.0
PA O5' C5' C4' 228.1 180.0
PA O5' C5' H5'1 353.3 60.0
PA O5' C5' H5'2 102.9 300.0
HOA2 O2A PA O3A 56.7 60.0
HOA2 O2A PA O5' 306.4 300.0
PB O3A PA O5' 247.7 180.0
O1B PB O3A O2B 117.0 240.0
O1B PB O3A O3B 239.5 120.1
O2B PB O3A O3B 122.6 240.1
O3A PB O2B HOB2 180.0 180.0
O3A PB O3B HOB3 180.0 300.0
O3A PB O1B O2B 246.3 120.0
O3A PB O1B O3B 112.4 240.0
O2B PB O1B O3B 226.1 119.9
O1B PB O2B HOB2 68.6 300.0
O1B PB O3B HOB3 291.9 179.9
O3A PB O2B O1B 111.4 240.0
O3A PB O2B O3B 245.1 120.0
O1B PB O2B O3B 133.7 240.0
O2B PB O3B HOB3 63.6 60.0
O3A PB O3B O1B 248.1 120.1
O3A PB O3B O2B 116.4 240.0
O1B PB O3B O2B 228.2 120.0
O3B PB O2B HOB2 294.9 60.0
HOB2 O2B PB O3B 294.9 60.0
C4' C5' O5' H5'1 234.8 120.0
C4' C5' O5' H5'2 125.3 240.0
O5' C5' C4' O4' 303.4 65.7
O5' C5' C4' C3' 58.4 180.0
O5' C5' C4' H4' 178.3 302.9
H5'1 C5' O5' H5'2 250.5 120.0
O5' C5' C4' H5'1 125.2 239.9
O5' C5' C4' H5'2 234.7 120.0
H5'1 C5' C4' H5'2 109.5 240.0
O4' C4' C5' C3' 245.1 245.7
O4' C4' C5' H4' 125.1 122.8
C5' C4' O4' C1' 150.2 158.6
C3' C4' C5' H4' 240.1 237.1
C5' C4' C3' O3' 83.2 86.1
C5' C4' C3' C2' 202.2 204.4
C5' C4' C3' H3' 322.7 322.5
O5' C5' H5'1 C4' 235.3 120.1
O5' C5' H5'1 H5'2 117.6 240.0
C4' C5' H5'1 H5'2 242.4 119.9
H5'1 C5' C4' O4' 178.2 185.8
H5'1 C5' C4' C3' 293.2 300.0
H5'1 C5' C4' H4' 53.1 63.0
O5' C5' H5'2 C4' 124.8 240.0
O5' C5' H5'2 H5'1 242.4 120.0
C4' C5' H5'2 H5'1 117.6 240.1
H5'2 C5' C4' O4' 68.7 305.7
H5'2 C5' C4' C3' 183.7 60.0
H5'2 C5' C4' H4' 303.6 182.9
O4' C4' C5' H5'1 178.2 185.8
O4' C4' C5' H5'2 68.7 305.7
C5' C4' O4' C3' 122.7 118.7
C5' C4' O4' H4' 242.3 237.2
C3' C4' O4' H4' 119.6 118.5
O4' C4' C3' O3' 200.2 204.8
O4' C4' C3' C2' 319.3 323.1
O4' C4' C3' H3' 79.8 81.3
C4' O4' C1' C2' 356.9 333.6
C4' O4' C1' N1 236.0 214.2
C4' O4' C1' H1' 117.6 93.2
C3' C4' C5' H5'1 293.2 300.0
C3' C4' C5' H5'2 183.7 60.0
C5' C4' C3' O4' 242.9 241.3
C5' C4' C3' H4' 117.9 122.9
O4' C4' C3' H4' 235.0 241.6
C3' C4' O4' C1' 27.4 39.9
O3' C3' C4' C2' 240.9 241.7
O3' C3' C4' H3' 120.4 123.6
C4' C3' O3' HO3' 180.0 174.3
C2' C3' C4' H3' 239.5 241.8
C4' C3' C2' C1' 38.0 20.8
C4' C3' C2' H2'1 163.2 262.2
C4' C3' C2' H2'2 272.6 139.6
H4' C4' C5' H5'1 53.1 63.0
H4' C4' C5' H5'2 303.6 182.9
C5' C4' H4' O4' 118.9 122.9
C5' C4' H4' C3' 235.6 237.0
O4' C4' H4' C3' 116.7 114.1
H4' C4' O4' C1' 267.9 281.4
H4' C4' C3' O3' 325.3 323.2
H4' C4' C3' C2' 84.3 81.5
H4' C4' C3' H3' 204.8 199.6
C1' O4' C4' C3' 27.4 39.9
C1' O4' C4' H4' 267.9 281.4
C3' C2' C1' O4' 337.4 2.0
O4' C1' C2' H2'1 212.1 120.6
O4' C1' C2' H2'2 102.6 243.2
C2' C1' O4' N1 120.9 119.5
C2' C1' O4' H1' 239.3 240.5
N1 C1' O4' H1' 118.4 121.0
O4' C1' N1 C2 204.3 58.3
O4' C1' N1 C6 30.4 238.3
O3' C3' C4' H4' 325.3 323.2
C4' C3' O3' C2' 108.5 112.8
C4' C3' O3' H3' 231.0 236.4
C2' C3' O3' H3' 122.5 123.6
O3' C3' C2' C1' 146.5 139.1
O3' C3' C2' H2'1 271.8 20.5
O3' C3' C2' H2'2 21.2 257.8
C2' C3' C4' H4' 84.3 81.5
C4' C3' C2' O3' 251.4 241.7
C4' C3' C2' H3' 129.0 118.2
O4' C1' C2' C3' 337.4 2.0
O3' C3' C2' H3' 237.6 236.5
C2' C3' O3' HO3' 71.4 61.4
C1' C2' C3' H2'1 234.7 118.7
C1' C2' C3' H2'2 125.3 241.3
C3' C2' C1' N1 95.4 121.5
C3' C2' C1' H1' 213.9 242.5
H2'1 C2' C3' H2'2 250.6 122.6
H3' C3' C4' H4' 204.8 199.6
C4' C3' H3' O3' 116.8 123.6
C4' C3' H3' C2' 243.2 247.2
O3' C3' H3' C2' 126.3 123.6
H3' C3' O3' HO3' 309.0 297.9
H3' C3' C2' C1' 269.0 262.6
H3' C3' C2' H2'1 34.2 144.0
H3' C3' C2' H2'2 143.6 21.4
HO3' O3' C3' C2' 71.4 61.4
HO3' O3' C3' H3' 309.0 297.9
O4' C1' C2' N1 241.9 240.5
O4' C1' C2' H1' 123.4 119.5
C1' C2' C3' H3' 269.0 262.6
C3' C2' C1' H2'1 125.3 241.4
C3' C2' C1' H2'2 234.7 118.8
H2'1 C2' C1' H2'2 109.4 237.4
N1 C1' C2' H1' 241.5 239.0
C2' C1' N1 C2 88.9 300.4
C2' C1' N1 C6 274.9 120.3
H2'1 C2' C3' H3' 34.2 144.0
C3' C2' H2'1 C1' 241.6 114.7
C3' C2' H2'1 H2'2 120.7 237.3
C1' C2' H2'1 H2'2 239.2 122.6
H2'1 C2' C1' N1 330.2 240.1
H2'1 C2' C1' H1' 88.7 1.1
H2'2 C2' C3' H3' 143.6 21.4
C3' C2' H2'2 C1' 118.5 245.2
C3' C2' H2'2 H2'1 239.3 122.6
C1' C2' H2'2 H2'1 120.8 237.4
H2'2 C2' C1' N1 220.7 2.7
H2'2 C2' C1' H1' 339.2 123.7
O4' C1' N1 C2' 115.5 118.0
O4' C1' N1 H1' 236.4 239.0
N1 C1' C2' H2'1 330.2 240.1
N1 C1' C2' H2'2 220.7 2.7
C2' C1' N1 H1' 121.0 121.1
C2 N1 C1' C6 173.9 180.1
C1' N1 C2 O2 4.0 359.9
C1' N1 C2 N3 182.9 179.9
C1' N1 C6 C5 180.1 180.0
C1' N1 C6 H6 0.2 0.1
O4' C1' H1' C2' 242.6 242.0
O4' C1' H1' N1 120.0 121.0
H1' C1' C2' H2'1 88.7 1.1
H1' C1' C2' H2'2 339.2 123.7
C2' C1' H1' N1 237.3 239.0
H1' C1' N1 C2 327.9 179.3
H1' C1' N1 C6 154.0 359.2
C2 N1 C1' H1' 327.9 179.3
C1' N1 C2 C6 186.1 179.9
C2 N1 C6 C5 6.3 359.9
C2 N1 C6 H6 186.3 180.0
O2 C2 N1 N3 181.1 180.0
N1 C2 N3 C4 359.2 359.8
N1 C2 N3 HN3 179.1 180.0
C6 N1 C1' H1' 154.0 359.2
C1' N1 C6 C2 173.8 180.1
C6 N1 C2 O2 177.9 180.0
C6 N1 C2 N3 356.8 0.0
C4 C5 C6 N1 354.7 0.3
C5M C5 C6 N1 173.0 180.0
C5 C6 N1 H6 180.0 179.9
O2 C2 N1 C6 177.9 180.0
N1 C2 O2 N3 178.9 180.0
O2 C2 N3 C4 178.1 179.8
O2 C2 N3 HN3 358.0 360.0
N3 C2 N1 C6 356.8 0.0
N1 C2 N3 O2 181.1 180.0
C4 N3 C2 HN3 180.0 179.8
C2 N3 C4 O4 181.6 179.9
C2 N3 C4 C5 1.8 0.5
C2 N3 C4 HN3 180.0 180.2
O4 C4 N3 C5 179.8 179.5
N3 C4 C5 C5M 183.0 179.8
N3 C4 C5 C6 1.2 359.5
C2 N3 HN3 C4 180.0 179.8
HN3 N3 C4 O4 1.6 359.7
HN3 N3 C4 C5 181.8 180.3
O4 C4 N3 HN3 1.6 359.7
N3 C4 O4 C5 180.2 180.5
O4 C4 C5 C5M 3.2 0.3
O4 C4 C5 C6 181.4 180.0
N1 C6 C5 C4 354.7 0.3
C5 C4 N3 HN3 181.8 180.3
N3 C4 C5 O4 179.8 179.5
C5M C5 C4 C6 181.8 180.3
C4 C5 C5M H51 180.0 359.7
C4 C5 C5M H52 305.2 119.7
C4 C5 C5M H53 54.7 239.7
C4 C5 C6 H6 174.7 180.2
N1 C6 C5 C5M 173.0 180.0
C4 C5 C5M C6 178.3 179.7
C5M C5 C6 H6 353.0 359.9
H51 C5M C5 H52 234.8 240.0
H51 C5M C5 H53 125.3 120.0
H52 C5M C5 H53 250.5 240.0
N1 C6 C5 H6 180.0 180.1
C4 C5 C6 C5M 181.7 180.3
C6 C5 C5M H51 1.7 180.0
C6 C5 C5M H52 126.9 300.0
C6 C5 C5M H53 236.4 60.0
H51 C5M C5 C6 1.7 180.0
C5 C5M H51 H52 125.2 120.0
C5 C5M H51 H53 234.7 240.0
H52 C5M H51 H53 109.5 119.9
H52 C5M C5 C6 126.9 300.0
C5 C5M H52 H51 227.9 240.0
C5 C5M H52 H53 113.9 120.0
H51 C5M H52 H53 246.0 240.0
H53 C5M C5 C6 236.4 60.0
C5 C5M H53 H51 132.2 120.1
C5 C5M H53 H52 246.1 240.0
H51 C5M H53 H52 113.9 119.9
N1 C6 H6 C5 180.0 179.9