PDB Chemical Component TDL

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 TDL

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O1B PB 1.506 1.480
PB O2B 1.510 1.610
PB O3B 1.510 1.611
PB O3A 1.643 1.610
O2B H2B 0.950 0.967
O3B H3B 0.950 0.967
O3A PA 1.622 1.610
PA O1A 1.492 1.480
PA O2A 1.516 1.611
PA O7 1.589 1.610
O2A H2A 0.950 0.966
O7 C7 1.428 1.429
C7 C6 1.521 1.530
C7 H71 1.100 1.090
C7 H72 1.100 1.090
C6 C5 1.512 1.507
C6 H61 1.100 1.091
C6 H62 1.100 1.090
C5 S1 1.739 1.762
C5 C4 1.412 1.336
S1 C2 1.758 1.710
C4 CM4 1.519 1.507
C4 N3 1.375 1.318
CM4 HM41 1.100 1.090
CM4 HM42 1.100 1.090
CM4 HM43 1.100 1.090
N3 C2 1.393 1.290
N3 C7' 1.496 1.466
C2 CLA 1.535 1.507
CLA OL1 1.420 1.429
CLA CLB 1.543 1.530
CLA CLC 1.580 1.508
OL1 HL1 0.950 0.967
CLB HLB1 1.100 1.090
CLB HLB2 1.100 1.090
CLB HLB3 1.100 1.090
CLC OL2 1.281 1.343
CLC OL3 1.288 1.208
OL2 HL2 0.951 0.967
C7' C5' 1.562 1.507
C7' H7'1 1.100 1.089
C7' H7'2 1.100 1.090
C5' C6' 1.417 1.381
C5' C4' 1.416 1.396
C6' N1' 1.354 1.325
C6' H6' 1.080 1.079
N1' C2' 1.353 1.318
C2' CM2 1.512 1.507
C2' N3' 1.343 1.318
CM2 HM21 1.100 1.089
CM2 HM22 1.100 1.090
CM2 HM23 1.100 1.090
N3' C4' 1.369 1.330
C4' N4' 1.368 1.385
N4' H4'1 1.000 0.969
N4' H4'2 1.000 0.970

Bond Angles for TDL

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1B PB O2B 114.6 109.5
O1B PB O3B 114.3 109.5
O1B PB O3A 105.4 109.5
O2B PB O3B 115.5 109.4
O2B PB O3A 98.6 109.5
PB O2B H2B 109.5 114.0
O3B PB O3A 106.1 109.4
PB O3B H3B 109.5 114.0
PB O3A PA 130.0 134.0
O3A PA O1A 111.1 109.5
O3A PA O2A 107.4 109.4
O3A PA O7 102.5 109.5
O1A PA O2A 116.4 109.4
O1A PA O7 110.3 109.5
O2A PA O7 108.1 109.5
PA O2A H2A 109.5 114.0
PA O7 C7 118.6 123.0
O7 C7 C6 103.3 109.4
O7 C7 H71 112.9 109.5
O7 C7 H72 111.6 109.5
C6 C7 H71 112.9 109.5
C6 C7 H72 111.6 109.4
C7 C6 C5 119.1 109.5
C7 C6 H61 104.2 109.5
C7 C6 H62 106.4 109.5
H71 C7 H72 104.8 109.5
C5 C6 H61 104.1 109.5
C5 C6 H62 106.4 109.5
C6 C5 S1 117.7 126.0
C6 C5 C4 132.0 126.0
H61 C6 H62 117.3 109.4
S1 C5 C4 110.2 107.9
C5 S1 C2 90.6 90.3
C5 C4 CM4 120.2 122.8
C5 C4 N3 115.2 114.5
S1 C2 N3 112.5 110.2
S1 C2 CLA 123.4 124.9
CM4 C4 N3 124.5 122.8
C4 CM4 HM41 109.5 109.4
C4 CM4 HM42 109.5 109.5
C4 CM4 HM43 109.5 109.4
C4 N3 C2 111.4 117.2
C4 N3 C7' 120.8 121.4
HM41 CM4 HM42 109.5 109.5
HM41 CM4 HM43 109.5 109.5
HM42 CM4 HM43 109.4 109.5
C2 N3 C7' 127.7 121.4
N3 C2 CLA 123.6 124.9
N3 C7' C5' 108.5 109.5
N3 C7' H7'1 110.0 109.5
N3 C7' H7'2 109.8 109.5
C2 CLA OL1 114.2 109.5
C2 CLA CLB 114.6 109.5
C2 CLA CLC 106.1 109.5
OL1 CLA CLB 108.1 109.4
OL1 CLA CLC 105.8 109.5
CLA OL1 HL1 109.5 114.0
CLB CLA CLC 107.5 109.5
CLA CLB HLB1 109.4 109.5
CLA CLB HLB2 109.4 109.4
CLA CLB HLB3 109.5 109.5
CLA CLC OL2 121.9 120.0
CLA CLC OL3 122.6 120.0
HLB1 CLB HLB2 109.5 109.5
HLB1 CLB HLB3 109.5 109.5
HLB2 CLB HLB3 109.5 109.4
OL2 CLC OL3 115.4 120.0
CLC OL2 HL2 109.5 117.0
C5' C7' H7'1 110.0 109.5
C5' C7' H7'2 109.8 109.4
C7' C5' C6' 119.4 120.8
C7' C5' C4' 125.2 120.8
H7'1 C7' H7'2 108.7 109.5
C6' C5' C4' 115.4 118.4
C5' C6' N1' 122.2 119.2
C5' C6' H6' 118.9 120.5
C5' C4' N3' 120.0 118.9
C5' C4' N4' 124.6 120.6
N1' C6' H6' 118.9 120.4
C6' N1' C2' 120.1 121.0
N1' C2' CM2 121.6 119.1
N1' C2' N3' 120.3 121.9
CM2 C2' N3' 118.0 119.1
C2' CM2 HM21 109.4 109.5
C2' CM2 HM22 109.5 109.4
C2' CM2 HM23 109.5 109.4
C2' N3' C4' 121.9 120.6
HM21 CM2 HM22 109.5 109.5
HM21 CM2 HM23 109.4 109.5
HM22 CM2 HM23 109.5 109.4
N3' C4' N4' 115.4 120.5
C4' N4' H4'1 109.5 120.0
C4' N4' H4'2 109.5 120.0
H4'1 N4' H4'2 109.4 120.0

Torsion Angles for TDL

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2B PB O1B O3B 223.5 240.0
O2B PB O1B O3A 107.3 120.0
O1B PB O2B H2B 131.3 59.9
O3B PB O1B O3A 243.9 240.0
O1B PB O3B H3B 38.2 180.0
O1B PB O3A PA 250.4 320.0
O1B PB O2B O3B 136.0 120.0
O1B PB O2B O3A 248.6 239.9
O3B PB O2B O3A 112.6 120.0
O2B PB O3B H3B 174.3 300.0
O2B PB O3A PA 131.9 200.0
O1B PB O3B O2B 223.9 240.0
O1B PB O3B O3A 115.8 120.0
O2B PB O3B O3A 251.9 240.0
O3B PB O2B H2B 355.3 299.9
O3B PB O3A PA 12.0 80.1
O1B PB O3A O2B 118.6 120.0
O1B PB O3A O3B 238.4 240.0
O2B PB O3A O3B 119.8 119.9
O3A PB O2B H2B 242.7 180.0
O3A PB O3B H3B 282.4 60.0
PB O3A PA O1A 321.0 44.9
PB O3A PA O2A 192.5 285.0
PB O3A PA O7 78.8 165.0
H2B O2B PB O3B 355.3 299.9
H2B O2B PB O3A 242.7 180.0
H3B O3B PB O3A 282.4 60.0
O1A PA O3A O2A 128.4 120.0
O1A PA O3A O7 242.2 239.9
O2A PA O3A O7 113.8 120.0
O3A PA O2A H2A 359.9 300.0
O3A PA O7 C7 73.5 185.0
O3A PA O1A O2A 236.6 240.0
O3A PA O1A O7 113.0 120.1
O2A PA O1A O7 236.4 240.0
O1A PA O2A H2A 234.6 180.0
O1A PA O7 C7 191.9 305.1
O3A PA O2A O1A 125.3 120.0
O3A PA O2A O7 250.1 240.0
O1A PA O2A O7 124.8 120.0
O2A PA O7 C7 320.2 65.0
O3A PA O7 O1A 241.6 240.0
O3A PA O7 O2A 113.3 120.0
O1A PA O7 O2A 231.7 240.0
O7 PA O2A H2A 109.9 60.0
PA O7 C7 C6 191.4 180.0
PA O7 C7 H71 69.2 299.9
PA O7 C7 H72 311.4 60.0
H2A O2A PA O7 109.9 60.0
C6 C7 O7 H71 122.3 240.0
C6 C7 O7 H72 240.0 120.0
O7 C7 C6 C5 192.0 180.0
O7 C7 C6 H61 76.6 300.0
O7 C7 C6 H62 312.0 60.0
H71 C7 O7 H72 117.7 239.9
O7 C7 C6 H71 237.7 120.0
O7 C7 C6 H72 120.0 240.0
H71 C7 C6 H72 242.3 120.1
C5 C6 C7 H61 115.4 240.0
C5 C6 C7 H62 240.0 120.0
C7 C6 C5 S1 287.8 270.0
C7 C6 C5 C4 110.8 89.7
H61 C6 C7 H62 124.6 240.0
O7 C7 H71 C6 116.7 240.0
O7 C7 H71 H72 238.3 120.0
C6 C7 H71 H72 121.6 240.0
H71 C7 C6 C5 314.2 60.0
H71 C7 C6 H61 198.8 180.0
H71 C7 C6 H62 74.2 300.0
O7 C7 H72 C6 245.0 120.0
O7 C7 H72 H71 122.5 240.0
C6 C7 H72 H71 237.5 120.0
H72 C7 C6 C5 71.9 300.0
H72 C7 C6 H61 316.6 60.0
H72 C7 C6 H62 191.9 179.9
C5 C6 C7 H71 314.2 60.0
C5 C6 C7 H72 71.9 300.0
C7 C6 C5 H61 244.6 120.0
C7 C6 C5 H62 120.0 240.0
H61 C6 C5 H62 235.4 119.9
S1 C5 C6 C4 177.0 180.4
C6 C5 S1 C2 182.0 179.9
C6 C5 C4 CM4 356.5 0.0
C6 C5 C4 N3 177.9 180.1
H61 C6 C7 H71 198.8 180.0
H61 C6 C7 H72 316.6 60.0
C7 C6 H61 C5 125.5 240.0
C7 C6 H61 H62 242.7 120.0
C5 C6 H61 H62 117.3 240.0
H61 C6 C5 S1 43.2 150.0
H61 C6 C5 C4 226.2 329.6
H62 C6 C7 H71 74.2 300.0
H62 C6 C7 H72 191.9 179.9
C7 C6 H62 C5 232.1 120.1
C7 C6 H62 H61 116.1 240.0
C5 C6 H62 H61 244.0 119.9
H62 C6 C5 S1 167.8 30.1
H62 C6 C5 C4 350.8 209.7
S1 C5 C6 H61 43.2 150.0
S1 C5 C6 H62 167.8 30.1
C6 C5 S1 C4 182.4 179.7
S1 C5 C4 CM4 179.3 179.7
S1 C5 C4 N3 0.7 359.8
C5 S1 C2 N3 359.9 359.8
C5 S1 C2 CLA 172.3 180.0
C4 C5 C6 H61 226.2 329.6
C4 C5 C6 H62 350.8 209.7
C6 C5 C4 S1 177.2 180.3
C4 C5 S1 C2 359.7 0.2
CM4 C4 C5 N3 178.6 179.9
C5 C4 CM4 HM41 145.9 90.0
C5 C4 CM4 HM42 25.9 210.0
C5 C4 CM4 HM43 266.0 330.0
C5 C4 N3 C2 359.2 0.1
C5 C4 N3 C7' 177.3 180.0
C2 S1 C5 C4 359.7 0.2
C4 N3 C2 S1 0.5 0.1
S1 C2 N3 C7' 182.5 180.2
N3 C2 S1 CLA 187.6 179.9
S1 C2 CLA OL1 144.1 128.5
S1 C2 CLA CLB 18.7 8.6
S1 C2 CLA CLC 260.2 248.5
C5 C4 CM4 N3 181.5 180.1
CM4 C4 N3 C2 180.7 180.1
CM4 C4 N3 C7' 358.8 0.0
HM41 CM4 C4 HM42 120.0 240.0
HM41 CM4 C4 HM43 240.0 120.0
HM42 CM4 C4 HM43 120.0 240.0
C5 C4 N3 CM4 178.6 179.9
S1 C2 N3 C4 0.5 0.1
N3 C4 CM4 HM41 324.4 269.9
N3 C4 CM4 HM42 204.4 29.9
N3 C4 CM4 HM43 84.5 149.9
C2 N3 C4 C7' 181.9 180.1
C4 N3 C2 CLA 188.1 180.0
C4 N3 C7' C5' 286.5 96.5
C4 N3 C7' H7'1 166.2 216.5
C4 N3 C7' H7'2 46.5 336.6
HM41 CM4 C4 N3 324.4 269.9
C4 CM4 HM41 HM42 240.0 120.0
C4 CM4 HM41 HM43 120.0 240.1
HM42 CM4 HM41 HM43 240.0 120.1
HM42 CM4 C4 N3 204.4 29.9
C4 CM4 HM42 HM41 120.0 240.1
C4 CM4 HM42 HM43 240.0 120.0
HM41 CM4 HM42 HM43 120.0 239.9
HM43 CM4 C4 N3 84.5 149.9
C4 CM4 HM43 HM41 240.0 119.9
C4 CM4 HM43 HM42 120.0 240.0
HM41 CM4 HM43 HM42 240.0 120.1
S1 C2 N3 CLA 172.4 180.1
C4 N3 C2 C7' 177.9 179.9
C2 N3 C7' C5' 104.3 276.4
C2 N3 C7' H7'1 343.9 36.4
C2 N3 C7' H7'2 224.3 156.5
N3 C2 CLA OL1 315.6 308.7
N3 C2 CLA CLB 190.2 188.7
N3 C2 CLA CLC 71.8 68.7
C4 N3 C7' C2 182.2 180.1
C7' N3 C2 CLA 10.2 0.1
C5' C7' N3 H7'1 120.4 240.0
C5' C7' N3 H7'2 240.0 120.0
N3 C7' C5' C6' 116.7 332.5
N3 C7' C5' C4' 297.6 152.3
H7'1 C7' N3 H7'2 119.6 239.9
S1 C2 CLA N3 188.5 179.9
CLA C2 N3 C7' 10.2 0.1
OL1 CLA C2 CLB 125.4 120.0
OL1 CLA C2 CLC 243.9 240.0
C2 CLA OL1 HL1 257.8 86.2
CLB CLA C2 CLC 118.5 120.0
C2 CLA CLB HLB1 141.9 60.0
C2 CLA CLB HLB2 21.9 180.0
C2 CLA CLB HLB3 261.9 299.9
C2 CLA CLC OL2 109.0 209.2
C2 CLA CLC OL3 288.6 29.3
C2 CLA OL1 CLB 231.2 240.0
C2 CLA OL1 CLC 116.3 120.0
CLB CLA OL1 CLC 245.1 240.0
OL1 CLA CLB HLB1 13.4 300.0
OL1 CLA CLB HLB2 253.4 60.0
OL1 CLA CLB HLB3 133.3 179.9
OL1 CLA CLC OL2 230.7 329.2
OL1 CLA CLC OL3 50.3 149.3
C2 CLA CLB OL1 128.5 120.0
C2 CLA CLB CLC 242.3 240.0
OL1 CLA CLB CLC 113.8 120.0
CLB CLA OL1 HL1 26.6 206.2
CLB CLA CLC OL2 346.0 89.2
CLB CLA CLC OL3 165.6 269.3
HLB1 CLB CLA HLB2 120.0 240.0
HLB1 CLB CLA HLB3 240.0 120.1
HLB2 CLB CLA HLB3 120.0 240.1
C2 CLA CLC OL1 238.3 240.0
C2 CLA CLC CLB 123.1 120.0
OL1 CLA CLC CLB 244.7 240.0
CLC CLA OL1 HL1 141.5 326.2
CLC CLA CLB HLB1 259.6 180.0
CLC CLA CLB HLB2 139.6 300.0
CLC CLA CLB HLB3 19.6 60.0
OL2 CLC CLA OL3 180.4 179.9
CLA CLC OL2 HL2 179.6 180.5
HL1 OL1 CLA CLB 26.6 206.2
HL1 OL1 CLA CLC 141.5 326.2
HLB1 CLB CLA CLC 259.6 180.0
CLA CLB HLB1 HLB2 240.0 120.0
CLA CLB HLB1 HLB3 120.0 240.0
HLB2 CLB HLB1 HLB3 240.0 120.0
HLB2 CLB CLA CLC 139.6 300.0
CLA CLB HLB2 HLB1 120.0 240.0
CLA CLB HLB2 HLB3 240.0 120.0
HLB1 CLB HLB2 HLB3 120.0 240.0
HLB3 CLB CLA CLC 19.6 60.0
CLA CLB HLB3 HLB1 240.0 120.0
CLA CLB HLB3 HLB2 120.0 240.1
HLB1 CLB HLB3 HLB2 240.0 120.0
CLA CLC OL2 OL3 179.6 180.1
CLA CLC OL3 OL2 180.4 179.9
OL3 CLC OL2 HL2 360.0 0.5
HL2 OL2 CLC OL3 360.0 0.5
N3 C7' C5' H7'1 239.6 120.0
N3 C7' C5' H7'2 120.0 240.0
H7'1 C7' C5' H7'2 240.4 120.0
C6' C5' C7' C4' 179.1 180.3
C7' C5' C6' N1' 180.3 180.0
C7' C5' C6' H6' 0.3 360.0
C7' C5' C4' N3' 179.4 179.8
C7' C5' C4' N4' 358.5 0.0
N3 C7' H7'1 C5' 119.5 240.0
N3 C7' H7'1 H7'2 239.7 120.0
C5' C7' H7'1 H7'2 120.3 240.0
H7'1 C7' C5' C6' 237.0 212.6
H7'1 C7' C5' C4' 57.9 32.3
N3 C7' H7'2 C5' 240.8 120.0
N3 C7' H7'2 H7'1 120.4 240.0
C5' C7' H7'2 H7'1 239.6 120.0
H7'2 C7' C5' C6' 356.7 92.5
H7'2 C7' C5' C4' 177.6 272.3
C6' C5' C7' H7'1 237.0 212.6
C6' C5' C7' H7'2 356.7 92.5
C7' C5' C6' C4' 180.8 179.7
C6' C5' C4' N3' 0.2 359.5
C6' C5' C4' N4' 179.4 179.7
N1' C6' C5' H6' 180.0 180.0
C5' C6' N1' C2' 0.7 360.0
C4' C5' C7' H7'1 57.9 32.3
C4' C5' C7' H7'2 177.6 272.3
C7' C5' C4' C6' 179.1 180.3
C4' C5' C6' N1' 359.5 0.3
C4' C5' C6' H6' 179.5 180.2
C2' N3' C4' C5' 359.9 0.5
N3' C4' C5' N4' 180.9 179.7
C5' C4' N4' H4'1 119.2 13.1
C5' C4' N4' H4'2 359.2 193.1
N1' C6' C5' C4' 359.5 0.3
C5' C6' N1' H6' 180.0 180.0
C6' N1' C2' CM2 179.2 180.0
C6' N1' C2' N3' 359.4 360.0
H6' C6' C5' C4' 179.5 180.2
C5' C6' H6' N1' 180.0 180.0
H6' C6' N1' C2' 180.7 180.0
C2' N1' C6' H6' 180.7 180.0
CM2 C2' N1' N3' 179.8 180.1
N1' C2' CM2 HM21 69.8 90.0
N1' C2' CM2 HM22 309.8 210.0
N1' C2' CM2 HM23 189.8 329.9
N1' C2' N3' C4' 0.3 359.8
N1' C2' CM2 N3' 180.2 179.9
CM2 C2' N3' C4' 180.5 179.7
HM21 CM2 C2' HM22 120.0 240.0
HM21 CM2 C2' HM23 240.0 120.1
HM22 CM2 C2' HM23 120.0 240.1
C5' C4' N3' C2' 359.9 0.5
N1' C2' N3' CM2 179.8 180.1
N3' C2' CM2 HM21 249.6 270.1
N3' C2' CM2 HM22 129.6 30.1
N3' C2' CM2 HM23 9.6 150.0
C2' N3' C4' N4' 180.6 180.2
HM21 CM2 C2' N3' 249.6 270.1
C2' CM2 HM21 HM22 240.0 120.0
C2' CM2 HM21 HM23 120.0 240.0
HM22 CM2 HM21 HM23 240.0 120.0
HM22 CM2 C2' N3' 129.6 30.1
C2' CM2 HM22 HM21 120.0 240.0
C2' CM2 HM22 HM23 240.0 119.9
HM21 CM2 HM22 HM23 120.0 240.0
HM23 CM2 C2' N3' 9.6 150.0
C2' CM2 HM23 HM21 240.0 120.1
C2' CM2 HM23 HM22 120.0 240.1
HM21 CM2 HM23 HM22 240.0 120.0
C5' C4' N3' N4' 179.2 180.3
N3' C4' N4' H4'1 298.4 193.4
N3' C4' N4' H4'2 178.4 13.4
C5' C4' N4' N3' 180.8 179.7
H4'1 N4' C4' H4'2 120.0 180.0
C4' N4' H4'1 H4'2 240.0 180.0
C4' N4' H4'2 H4'1 120.0 180.0