PDB Chemical Component THD

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 THD

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
N1' C2' 1.348 1.318
N1' C6' 1.393 1.325
C2' CM2 1.449 1.507
C2' N3' 1.326 1.317
CM2 HM21 1.115 1.091
CM2 HM22 1.115 1.090
CM2 HM23 1.115 1.090
N3' C4' 1.402 1.330
C4' N4' 1.331 1.385
C4' C5' 1.462 1.396
N4' H4'1 1.103 0.970
N4' H4'2 1.103 0.970
C5' C6' 1.372 1.381
C5' C7' 1.540 1.507
C6' H6' 1.103 1.080
C7' N3 1.560 1.465
C7' H7'1 1.115 1.089
C7' H7'2 1.115 1.089
N3 C2 1.402 1.401
N3 C4 1.354 1.368
C2 S1 1.717 1.786
C2 C8 1.273 1.336
S1 C5 1.690 1.785
C5 C4 1.371 1.329
C5 C6 1.516 1.507
C4 CM4 1.492 1.507
CM4 HM41 1.115 1.090
CM4 HM42 1.115 1.090
CM4 HM43 1.115 1.090
C6 C7 1.472 1.530
C6 H6C1 1.114 1.090
C6 H6C2 1.115 1.090
C7 O7 1.428 1.429
C7 H7C1 1.115 1.089
C7 H7C2 1.115 1.090
O7 PA 1.542 1.609
PA O1A 1.505 1.609
PA O2A 1.434 1.480
PA O3A 1.614 1.609
O1A HO1A 0.950 0.966
O3A PB 1.611 1.609
PB O1B 1.454 1.479
PB O2B 1.456 1.610
PB O3B 1.484 1.610
O2B HO2B 0.950 0.966
O3B HO3B 0.950 0.967
C8 O9 1.254 1.365
C8 C9 1.451 1.506
O9 H9 0.950 0.967
C9 O10 1.415 1.428
C9 H9C1 1.115 1.090
C9 H9C2 1.116 1.090
O10 H10 0.950 0.967

Bond Angles for THD

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C2' N1' C6' 120.4 121.0
N1' C2' CM2 118.4 119.1
N1' C2' N3' 120.8 121.8
N1' C6' C5' 123.5 119.2
N1' C6' H6' 118.3 120.4
CM2 C2' N3' 120.8 119.1
C2' CM2 HM21 118.4 109.5
C2' CM2 HM22 109.0 109.5
C2' CM2 HM23 109.0 109.5
C2' N3' C4' 120.8 120.7
HM21 CM2 HM22 109.0 109.4
HM21 CM2 HM23 109.0 109.5
HM22 CM2 HM23 101.1 109.5
N3' C4' N4' 114.4 120.5
N3' C4' C5' 120.8 118.9
N4' C4' C5' 124.8 120.6
C4' N4' H4'1 114.4 120.0
C4' N4' H4'2 124.8 120.0
C4' C5' C6' 113.7 118.3
C4' C5' C7' 125.4 120.8
H4'1 N4' H4'2 120.8 120.0
C6' C5' C7' 120.8 120.8
C5' C6' H6' 118.3 120.4
C5' C7' N3 109.4 109.5
C5' C7' H7'1 112.2 109.5
C5' C7' H7'2 112.3 109.4
N3 C7' H7'1 112.2 109.5
N3 C7' H7'2 112.2 109.5
C7' N3 C2 128.2 121.1
C7' N3 C4 120.6 121.2
H7'1 C7' H7'2 98.2 109.4
C2 N3 C4 111.2 117.7
N3 C2 S1 111.1 101.2
N3 C2 C8 116.1 129.4
N3 C4 C5 115.0 120.4
N3 C4 CM4 121.3 119.8
S1 C2 C8 132.3 129.3
C2 S1 C5 91.5 98.0
C2 C8 O9 132.8 120.0
C2 C8 C9 107.7 120.0
S1 C5 C4 111.2 102.6
S1 C5 C6 122.0 128.7
C4 C5 C6 126.8 128.8
C5 C4 CM4 123.7 119.8
C5 C6 C7 116.0 109.5
C5 C6 H6C1 109.8 109.5
C5 C6 H6C2 109.8 109.4
C4 CM4 HM41 121.3 109.5
C4 CM4 HM42 108.0 109.5
C4 CM4 HM43 108.0 109.5
HM41 CM4 HM42 108.0 109.5
HM41 CM4 HM43 108.0 109.5
HM42 CM4 HM43 101.9 109.5
C7 C6 H6C1 109.9 109.5
C7 C6 H6C2 109.8 109.5
C6 C7 O7 105.5 109.5
C6 C7 H7C1 113.7 109.4
C6 C7 H7C2 113.7 109.5
H6C1 C6 H6C2 100.4 109.5
O7 C7 H7C1 113.7 109.5
O7 C7 H7C2 113.7 109.5
C7 O7 PA 117.2 106.8
H7C1 C7 H7C2 96.8 109.5
O7 PA O1A 117.4 109.5
O7 PA O2A 96.4 109.5
O7 PA O3A 108.7 109.5
O1A PA O2A 117.8 109.5
O1A PA O3A 116.2 109.5
PA O1A HO1A 117.5 106.8
O2A PA O3A 96.9 109.5
PA O3A PB 146.0 106.9
O3A PB O1B 95.6 109.5
O3A PB O2B 105.9 109.6
O3A PB O3B 109.5 109.4
O1B PB O2B 111.7 109.5
O1B PB O3B 119.3 109.5
O2B PB O3B 112.6 109.4
PB O2B HO2B 105.9 106.9
PB O3B HO3B 109.5 106.9
O9 C8 C9 119.5 120.0
C8 O9 H9 132.8 106.8
C8 C9 O10 110.0 109.5
C8 C9 H9C1 112.0 109.4
C8 C9 H9C2 112.0 109.5
O10 C9 H9C1 112.0 109.4
O10 C9 H9C2 112.0 109.4
C9 O10 H10 110.0 106.9
H9C1 C9 H9C2 98.4 109.5

Torsion Angles for THD

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C2' N1' C6' C5' 359.9 360.0
C2' N1' C6' H6' 179.9 180.0
CM2 C2' N1' N3' 179.9 179.7
N1' C2' CM2 HM21 180.0 90.1
N1' C2' CM2 HM22 54.7 210.0
N1' C2' CM2 HM23 305.3 330.0
N1' C2' N3' C4' 359.6 359.4
C6' N1' C2' CM2 180.2 180.0
C6' N1' C2' N3' 0.3 0.3
C4' C5' C6' N1' 359.9 0.0
N1' C6' C5' C7' 180.0 180.0
C5' C6' N1' H6' 180.0 180.0
CM2 C2' N1' C6' 180.2 180.0
N1' C2' CM2 N3' 180.1 180.3
CM2 C2' N3' C4' 179.7 179.7
HM21 CM2 C2' HM22 125.3 240.1
HM21 CM2 C2' HM23 234.7 120.0
HM22 CM2 C2' HM23 109.5 240.0
N3' C2' N1' C6' 0.3 0.3
N1' C2' N3' CM2 179.9 179.7
N3' C2' CM2 HM21 359.9 269.8
N3' C2' CM2 HM22 234.6 29.7
N3' C2' CM2 HM23 125.2 149.7
C2' N3' C4' N4' 180.2 180.2
C2' N3' C4' C5' 0.1 0.6
HM21 CM2 C2' N3' 359.9 269.8
C2' CM2 HM21 HM22 234.7 120.0
C2' CM2 HM21 HM23 125.3 240.0
HM22 CM2 HM21 HM23 250.5 120.0
HM22 CM2 C2' N3' 234.6 29.7
C2' CM2 HM22 HM21 130.6 240.0
C2' CM2 HM22 HM23 245.3 120.0
HM21 CM2 HM22 HM23 114.7 240.0
HM23 CM2 C2' N3' 125.2 149.7
C2' CM2 HM23 HM21 229.4 120.0
C2' CM2 HM23 HM22 114.7 240.0
HM21 CM2 HM23 HM22 245.3 119.9
N4' C4' N3' C5' 180.0 179.6
N3' C4' N4' H4'1 180.0 0.4
N3' C4' N4' H4'2 360.0 180.3
N3' C4' C5' C6' 0.1 359.7
N3' C4' C5' C7' 180.0 179.7
N3' C4' N4' C5' 180.0 180.4
N4' C4' C5' C6' 180.1 180.0
N4' C4' C5' C7' 360.0 0.1
H4'1 N4' C4' H4'2 180.0 180.1
N1' C6' C5' C4' 359.9 0.0
N3' C4' C5' N4' 180.0 179.6
C5' C4' N4' H4'1 0.0 180.0
C5' C4' N4' H4'2 180.0 359.9
C6' C5' C4' C7' 180.1 180.0
C4' C5' C6' H6' 179.9 180.0
C4' C5' C7' N3 303.9 180.0
C4' C5' C7' H7'1 178.6 300.0
C4' C5' C7' H7'2 69.1 59.9
H4'1 N4' C4' C5' 0.0 180.0
C4' N4' H4'1 H4'2 180.0 179.9
H4'2 N4' C4' C5' 180.0 359.9
C4' N4' H4'2 H4'1 180.0 180.1
N1' C6' C5' H6' 180.0 180.0
C4' C5' C6' C7' 179.9 180.0
C6' C5' C7' N3 123.8 0.0
C6' C5' C7' H7'1 358.5 120.1
C6' C5' C7' H7'2 249.0 240.0
C4' C5' C7' C6' 180.1 180.0
C7' C5' C6' H6' 360.0 0.0
N3 C7' C5' H7'1 125.2 240.0
N3 C7' C5' H7'2 234.8 120.1
C5' C7' N3 C2 94.8 274.4
C5' C7' N3 C4 277.2 94.9
H7'1 C7' C5' H7'2 109.5 240.1
N1' C6' H6' C5' 180.0 180.0
H6' C6' C5' C7' 360.0 0.0
C5' C7' N3 H7'1 234.7 120.0
C5' C7' N3 H7'2 125.3 240.0
H7'1 C7' N3 H7'2 250.5 120.0
C2 N3 C7' C4 177.6 179.6
C7' N3 C2 S1 183.4 180.0
C7' N3 C2 C8 10.1 0.4
C7' N3 C4 C5 177.3 180.0
C7' N3 C4 CM4 357.2 359.9
C5' C7' H7'1 N3 123.7 240.0
C5' C7' H7'1 H7'2 241.8 119.9
N3 C7' H7'1 H7'2 118.1 239.9
H7'1 C7' N3 C2 220.1 154.4
H7'1 C7' N3 C4 42.5 334.9
C5' C7' H7'2 N3 236.3 120.0
C5' C7' H7'2 H7'1 118.2 240.1
N3 C7' H7'2 H7'1 241.9 120.1
H7'2 C7' N3 C2 329.6 34.4
H7'2 C7' N3 C4 151.9 214.8
C2 N3 C7' H7'1 220.1 154.4
C2 N3 C7' H7'2 329.6 34.4
C7' N3 C2 C4 182.2 180.4
C2 N3 C4 C5 359.4 0.4
C2 N3 C4 CM4 179.2 180.3
S1 C2 N3 C8 173.3 179.6
N3 C2 S1 C5 358.9 0.4
N3 C2 C8 O9 0.6 5.1
N3 C2 C8 C9 180.7 185.1
C4 N3 C7' H7'1 42.5 334.9
C4 N3 C7' H7'2 151.9 214.8
C7' N3 C4 C2 178.0 179.6
C4 N3 C2 S1 1.2 359.5
C4 N3 C2 C8 187.9 180.0
S1 C5 C4 N3 359.8 360.0
N3 C4 C5 C6 180.2 180.0
C5 C4 N3 CM4 180.2 180.1
N3 C4 CM4 HM41 180.0 180.0
N3 C4 CM4 HM42 54.8 300.0
N3 C4 CM4 HM43 305.3 60.0
S1 C2 N3 C4 1.2 359.5
N3 C2 S1 C8 188.1 180.4
S1 C2 C8 O9 189.0 185.6
S1 C2 C8 C9 9.1 5.7
C2 S1 C5 C4 0.8 359.8
C2 S1 C5 C6 180.3 179.8
C8 C2 N3 C4 187.9 180.0
N3 C2 C8 S1 171.6 179.4
C8 C2 S1 C5 170.8 179.9
O9 C8 C2 C9 179.8 179.9
C2 C8 O9 H9 180.0 115.2
C2 C8 C9 O10 113.3 120.0
C2 C8 C9 H9C1 348.0 239.9
C2 C8 C9 H9C2 238.5 360.0
N3 C4 C5 S1 359.8 360.0
C5 S1 C2 C8 170.8 179.9
C4 C5 S1 C6 180.4 180.0
S1 C5 C4 CM4 180.0 180.0
S1 C5 C6 C7 10.0 270.0
S1 C5 C6 H6C1 244.7 30.1
S1 C5 C6 H6C2 135.3 150.1
N3 C4 C5 CM4 179.8 179.9
S1 C5 C4 C6 179.5 180.0
C4 C5 C6 C7 189.5 90.0
C4 C5 C6 H6C1 64.2 210.1
C4 C5 C6 H6C2 314.8 330.1
C5 C4 CM4 HM41 359.8 360.0
C5 C4 CM4 HM42 234.5 120.0
C5 C4 CM4 HM43 125.0 240.0
S1 C5 C6 C4 180.5 180.0
C6 C5 C4 CM4 0.4 0.0
C7 C6 C5 H6C1 125.3 240.0
C7 C6 C5 H6C2 234.7 120.0
C5 C6 C7 O7 204.0 180.0
C5 C6 C7 H7C1 78.7 300.0
C5 C6 C7 H7C2 329.3 60.0
H6C1 C6 C5 H6C2 109.5 240.0
N3 C4 CM4 C5 180.2 180.1
CM4 C4 C5 C6 0.4 0.0
HM41 CM4 C4 HM42 125.2 240.0
HM41 CM4 C4 HM43 234.7 120.0
HM42 CM4 C4 HM43 109.5 240.0
C4 CM4 HM41 HM42 234.8 120.0
C4 CM4 HM41 HM43 125.2 240.0
HM42 CM4 HM41 HM43 250.5 120.0
C4 CM4 HM42 HM41 132.8 240.0
C4 CM4 HM42 HM43 246.4 120.0
HM41 CM4 HM42 HM43 113.6 240.0
C4 CM4 HM43 HM41 227.2 120.1
C4 CM4 HM43 HM42 113.6 240.0
HM41 CM4 HM43 HM42 246.4 120.0
C5 C6 C7 H6C1 234.7 120.0
C5 C6 C7 H6C2 125.3 240.1
H6C1 C6 C7 H6C2 250.5 120.1
O7 C7 C6 H7C1 125.3 240.0
O7 C7 C6 H7C2 234.7 120.0
C6 C7 O7 PA 122.7 180.0
H7C1 C7 C6 H7C2 109.4 240.0
C5 C6 H6C1 C7 128.7 240.0
C5 C6 H6C1 H6C2 244.4 119.9
C7 C6 H6C1 H6C2 115.6 239.9
H6C1 C6 C7 O7 329.2 60.0
H6C1 C6 C7 H7C1 204.0 180.0
H6C1 C6 C7 H7C2 94.5 300.0
C5 C6 H6C2 C7 231.3 119.9
C5 C6 H6C2 H6C1 115.6 240.0
C7 C6 H6C2 H6C1 244.3 120.1
H6C2 C6 C7 O7 78.7 299.9
H6C2 C6 C7 H7C1 313.5 59.9
H6C2 C6 C7 H7C2 204.0 179.9
O7 C7 C6 H6C1 329.2 60.0
O7 C7 C6 H6C2 78.7 299.9
C6 C7 O7 H7C1 234.7 120.0
C6 C7 O7 H7C2 125.3 240.0
H7C1 C7 O7 H7C2 250.5 120.0
C7 O7 PA O1A 291.0 60.0
C7 O7 PA O2A 165.0 300.0
C7 O7 PA O3A 65.5 180.0
H7C1 C7 C6 H6C1 204.0 180.0
H7C1 C7 C6 H6C2 313.5 59.9
C6 C7 H7C1 O7 120.8 240.0
C6 C7 H7C1 H7C2 240.4 120.0
O7 C7 H7C1 H7C2 119.6 240.0
H7C1 C7 O7 PA 247.9 60.0
H7C2 C7 C6 H6C1 94.5 300.0
H7C2 C7 C6 H6C2 204.0 179.9
C6 C7 H7C2 O7 239.2 120.0
C6 C7 H7C2 H7C1 119.6 240.0
O7 C7 H7C2 H7C1 240.4 120.0
H7C2 C7 O7 PA 357.4 300.0
PA O7 C7 H7C1 247.9 60.0
PA O7 C7 H7C2 357.4 300.0
O1A PA O7 O2A 125.9 120.0
O1A PA O7 O3A 225.4 240.0
O7 PA O1A HO1A 180.0 60.0
O2A PA O7 O3A 99.5 120.0
O7 PA O3A PB 36.7 180.0
O7 PA O1A O2A 245.4 240.0
O7 PA O1A O3A 131.2 120.0
O2A PA O1A O3A 245.8 240.0
O1A PA O3A PB 171.9 300.1
O7 PA O2A O1A 125.7 120.0
O7 PA O2A O3A 250.2 240.0
O1A PA O2A O3A 124.5 120.0
O2A PA O1A HO1A 294.6 180.0
O2A PA O3A PB 297.5 60.1
O7 PA O3A O1A 224.8 240.0
O7 PA O3A O2A 99.2 120.0
O1A PA O3A O2A 234.4 240.0
O3A PA O1A HO1A 48.8 300.0
PA O3A PB O1B 90.2 59.9
PA O3A PB O2B 204.7 180.0
PA O3A PB O3B 326.3 300.0
HO1A O1A PA O2A 294.6 180.0
HO1A O1A PA O3A 48.8 300.0
O1B PB O3A O2B 245.5 239.9
O1B PB O3A O3B 123.8 119.9
O2B PB O3A O3B 238.3 240.1
O3A PB O2B HO2B 180.0 180.0
O3A PB O3B HO3B 180.0 300.0
O3A PB O1B O2B 109.6 120.1
O3A PB O1B O3B 243.9 240.1
O2B PB O1B O3B 134.4 119.9
O1B PB O2B HO2B 282.9 300.1
O1B PB O3B HO3B 71.5 180.0
O3A PB O2B O1B 257.2 239.9
O3A PB O2B O3B 119.6 119.9
O1B PB O2B O3B 222.5 240.0
O2B PB O3B HO3B 297.5 60.0
O3A PB O3B O1B 108.5 120.0
O3A PB O3B O2B 242.5 240.0
O1B PB O3B O2B 134.0 120.0
O3B PB O2B HO2B 60.4 60.1
HO2B O2B PB O3B 60.4 60.1
C2 C8 O9 C9 180.2 180.1
O9 C8 C9 O10 293.4 300.0
O9 C8 C9 H9C1 168.1 60.0
O9 C8 C9 H9C2 58.6 180.0
C2 C8 C9 O9 179.9 179.9
C9 C8 O9 H9 359.8 295.1
O10 C9 C8 H9C1 125.3 240.1
O10 C9 C8 H9C2 234.8 120.0
C8 C9 O10 H10 180.0 180.0
H9C1 C9 C8 H9C2 109.5 239.9
H9 O9 C8 C9 359.8 295.1
C8 C9 O10 H9C1 234.7 120.0
C8 C9 O10 H9C2 125.3 240.0
H9C1 C9 O10 H9C2 250.6 120.0
C8 C9 H9C1 O10 124.2 240.0
C8 C9 H9C1 H9C2 242.1 120.1
O10 C9 H9C1 H9C2 117.9 240.0
H9C1 C9 O10 H10 305.3 60.0
C8 C9 H9C2 O10 235.9 120.0
C8 C9 H9C2 H9C1 117.9 240.0
O10 C9 H9C2 H9C1 242.1 119.9
H9C2 C9 O10 H10 54.8 300.0
H10 O10 C9 H9C1 305.3 60.0
H10 O10 C9 H9C2 54.8 300.0