PDB Chemical Component TDP

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 TDP

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
N1' C2' 1.389 1.318
N1' C6' 1.375 1.325
C2' C2A 1.502 1.507
C2' N3' 1.328 1.318
C2A H2A1 1.115 1.090
C2A H2A2 1.116 1.090
C2A H2A3 1.114 1.090
N3' C4' 1.392 1.330
C4' N4' 1.331 1.385
C4' C5' 1.442 1.396
N4' H4'1 1.019 0.970
N4' H4'2 1.020 0.970
C5' C6' 1.361 1.381
C5' C35 1.525 1.507
C6' H6' 1.103 1.080
C35 N3 1.538 1.465
C35 H351 1.115 1.090
C35 H352 1.115 1.090
N3 C2 1.326 1.313
N3 C4 1.397 1.316
C2 S1 1.665 1.737
C2 H2 1.102 1.080
S1 C5 1.715 1.787
C5 C4 1.390 1.358
C5 C5A 1.484 1.507
C4 C4A 1.485 1.507
C4A H4A1 1.116 1.090
C4A H4A2 1.114 1.089
C4A H4A3 1.115 1.090
C5A C5B 1.512 1.530
C5A H5A1 1.115 1.091
C5A H5A2 1.115 1.090
C5B O5G 1.390 1.429
C5B H5B1 1.115 1.090
C5B H5B2 1.115 1.090
O5G P1 1.585 1.610
P1 O11 1.552 1.609
P1 O12 1.453 1.610
P1 O13 1.484 1.480
O11 P2 1.606 1.611
O13 H13 0.951  
P2 O21 1.535 1.610
P2 O22 1.457 1.545
P2 O23 1.514 1.545
O23 H23 0.949  

Bond Angles for TDP

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C2' N1' C6' 118.7 121.0
N1' C2' C2A 121.3 119.1
N1' C2' N3' 121.2 121.8
N1' C6' C5' 123.7 119.2
N1' C6' H6' 118.7 120.4
C2A C2' N3' 117.5 119.1
C2' C2A H2A1 121.4 109.5
C2' C2A H2A2 108.0 109.5
C2' C2A H2A3 108.0 109.5
C2' N3' C4' 120.3 120.7
H2A1 C2A H2A2 107.9 109.5
H2A1 C2A H2A3 108.0 109.4
H2A2 C2A H2A3 101.9 109.5
N3' C4' N4' 115.7 120.5
N3' C4' C5' 120.6 118.9
N4' C4' C5' 123.7 120.6
C4' N4' H4'1 115.7 119.9
C4' N4' H4'2 109.9 120.0
C4' C5' C6' 115.5 118.3
C4' C5' C35 122.4 120.8
H4'1 N4' H4'2 110.0 120.0
C6' C5' C35 122.0 120.8
C5' C6' H6' 117.7 120.4
C5' C35 N3 109.8 109.5
C5' C35 H351 112.1 109.5
C5' C35 H352 112.1 109.5
N3 C35 H351 112.1 109.4
N3 C35 H352 112.1 109.5
C35 N3 C2 118.7 119.2
C35 N3 C4 129.9 119.3
H351 C35 H352 98.4 109.5
C2 N3 C4 111.4 121.5
N3 C2 S1 115.6 102.2
N3 C2 H2 112.0 128.9
N3 C4 C5 111.9 118.4
N3 C4 C4A 124.1 120.8
S1 C2 H2 132.4 128.9
C2 S1 C5 90.4 97.4
S1 C5 C4 110.8 100.6
S1 C5 C5A 118.5 129.7
C4 C5 C5A 130.7 129.7
C5 C4 C4A 124.1 120.8
C5 C5A C5B 114.3 109.5
C5 C5A H5A1 110.5 109.5
C5 C5A H5A2 110.4 109.5
C4 C4A H4A1 124.1 109.4
C4 C4A H4A2 107.1 109.4
C4 C4A H4A3 107.1 109.5
H4A1 C4A H4A2 107.0 109.5
H4A1 C4A H4A3 107.0 109.5
H4A2 C4A H4A3 102.6 109.6
C5B C5A H5A1 110.4 109.4
C5B C5A H5A2 110.4 109.5
C5A C5B O5G 111.3 109.5
C5A C5B H5B1 111.6 109.4
C5A C5B H5B2 111.6 109.5
H5A1 C5A H5A2 99.9 109.4
O5G C5B H5B1 111.5 109.5
O5G C5B H5B2 111.5 109.5
C5B O5G P1 134.8 106.8
H5B1 C5B H5B2 98.8 109.4
O5G P1 O11 100.3 109.5
O5G P1 O12 111.1 109.4
O5G P1 O13 106.4 109.5
O11 P1 O12 111.5 109.5
O11 P1 O13 106.6 109.5
P1 O11 P2 133.7 106.8
O12 P1 O13 119.1 109.4
P1 O13 H13 106.5  
O11 P2 O21 105.5 109.4
O11 P2 O22 106.7 109.4
O11 P2 O23 101.8 109.5
O21 P2 O22 123.2 109.5
O21 P2 O23 107.6 109.5
O22 P2 O23 109.9 109.5
P2 O23 H23 101.8  

Torsion Angles for TDP

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C2' N1' C6' C5' 360.0 359.9
C2' N1' C6' H6' 179.9 180.0
C2A C2' N1' N3' 180.1 179.6
N1' C2' C2A H2A1 180.0 90.0
N1' C2' C2A H2A2 305.2 210.1
N1' C2' C2A H2A3 54.7 330.0
N1' C2' N3' C4' 359.9 359.4
C6' N1' C2' C2A 180.2 180.0
C6' N1' C2' N3' 0.1 0.4
C4' C5' C6' N1' 359.9 0.1
N1' C6' C5' C35 180.3 180.1
C5' C6' N1' H6' 180.0 179.9
C2A C2' N1' C6' 180.2 180.0
N1' C2' C2A N3' 179.9 180.4
C2A C2' N3' C4' 179.9 179.7
H2A1 C2A C2' H2A2 234.8 239.9
H2A1 C2A C2' H2A3 125.3 120.0
H2A2 C2A C2' H2A3 250.5 240.0
N3' C2' N1' C6' 0.1 0.4
N1' C2' N3' C2A 180.1 179.6
N3' C2' C2A H2A1 0.1 269.6
N3' C2' C2A H2A2 125.3 29.7
N3' C2' C2A H2A3 234.8 149.7
C2' N3' C4' N4' 179.9 180.3
C2' N3' C4' C5' 359.9 0.6
H2A1 C2A C2' N3' 0.1 269.6
C2' C2A H2A1 H2A2 125.2 120.0
C2' C2A H2A1 H2A3 234.7 240.0
H2A2 C2A H2A1 H2A3 109.4 120.0
H2A2 C2A C2' N3' 125.3 29.7
C2' C2A H2A2 H2A1 227.2 240.0
C2' C2A H2A2 H2A3 113.6 120.0
H2A1 C2A H2A2 H2A3 246.5 240.0
H2A3 C2A C2' N3' 234.8 149.7
C2' C2A H2A3 H2A1 132.9 120.0
C2' C2A H2A3 H2A2 246.4 240.0
H2A1 C2A H2A3 H2A2 113.5 120.0
N4' C4' N3' C5' 180.0 179.7
N3' C4' N4' H4'1 180.0 180.3
N3' C4' N4' H4'2 54.7 0.3
N3' C4' C5' C6' 0.1 359.7
N3' C4' C5' C35 179.8 179.7
N3' C4' N4' C5' 180.0 180.3
N4' C4' C5' C6' 180.1 180.0
N4' C4' C5' C35 359.8 360.0
H4'1 N4' C4' H4'2 125.3 180.0
N1' C6' C5' C4' 359.9 0.1
N3' C4' C5' N4' 180.0 179.7
C5' C4' N4' H4'1 0.0 0.0
C5' C4' N4' H4'2 234.7 180.0
C6' C5' C4' C35 180.3 180.0
C4' C5' C6' H6' 179.9 180.0
C4' C5' C35 N3 289.1 85.1
C4' C5' C35 H351 54.4 205.0
C4' C5' C35 H352 163.9 325.1
H4'1 N4' C4' C5' 0.0 0.0
C4' N4' H4'1 H4'2 234.7 180.0
H4'2 N4' C4' C5' 234.7 180.0
C4' N4' H4'2 H4'1 128.5 180.0
N1' C6' C5' H6' 180.0 180.1
C4' C5' C6' C35 179.7 180.0
C6' C5' C35 N3 108.8 265.0
C6' C5' C35 H351 234.0 25.0
C6' C5' C35 H352 343.5 145.0
C4' C5' C35 C6' 180.4 180.0
C35 C5' C6' H6' 0.3 360.0
N3 C35 C5' H351 234.8 240.1
N3 C35 C5' H352 125.3 120.0
C5' C35 N3 C2 97.8 266.0
C5' C35 N3 C4 278.6 85.7
H351 C35 C5' H352 250.5 239.9
N1' C6' H6' C5' 180.0 179.9
H6' C6' C5' C35 0.3 360.0
C5' C35 N3 H351 125.2 119.9
C5' C35 N3 H352 234.8 240.0
H351 C35 N3 H352 109.5 120.0
C2 N3 C35 C4 179.3 180.3
C35 N3 C2 S1 180.8 180.0
C35 N3 C2 H2 0.7 359.9
C35 N3 C4 C5 179.1 179.7
C35 N3 C4 C4A 359.4 0.2
C5' C35 H351 N3 236.0 240.1
C5' C35 H351 H352 118.0 120.1
N3 C35 H351 H352 242.0 240.0
H351 C35 N3 C2 332.6 146.1
H351 C35 N3 C4 153.3 325.8
C5' C35 H352 N3 124.0 120.0
C5' C35 H352 H351 242.0 240.0
N3 C35 H352 H351 118.0 120.0
H352 C35 N3 C2 223.1 26.0
H352 C35 N3 C4 43.8 205.7
C2 N3 C35 H351 332.6 146.1
C2 N3 C35 H352 223.1 26.0
C35 N3 C2 C4 180.6 179.7
C2 N3 C4 C5 359.8 359.4
C2 N3 C4 C4A 180.1 179.9
S1 C2 N3 H2 180.0 180.1
N3 C2 S1 C5 359.9 360.0
C4 N3 C35 H351 153.3 325.8
C4 N3 C35 H352 43.8 205.7
C35 N3 C4 C2 179.3 180.3
C4 N3 C2 S1 0.2 0.3
C4 N3 C2 H2 180.1 180.2
S1 C5 C4 N3 0.2 0.4
N3 C4 C5 C5A 180.7 180.2
C5 C4 N3 C4A 179.6 179.5
N3 C4 C4A H4A1 180.0 275.1
N3 C4 C4A H4A2 305.3 35.0
N3 C4 C4A H4A3 54.8 155.1
S1 C2 N3 C4 0.2 0.3
N3 C2 S1 H2 179.9 179.9
C2 S1 C5 C4 359.9 359.8
C2 S1 C5 C5A 179.5 180.0
H2 C2 N3 C4 180.1 180.2
N3 C2 H2 S1 180.1 180.1
H2 C2 S1 C5 180.0 180.1
N3 C4 C5 S1 0.2 0.4
C5 S1 C2 H2 180.0 180.1
C4 C5 S1 C5A 180.4 179.8
S1 C5 C4 C4A 179.8 180.0
S1 C5 C5A C5B 275.6 270.0
S1 C5 C5A H5A1 40.9 30.0
S1 C5 C5A H5A2 150.4 150.0
N3 C4 C5 C4A 180.4 180.5
S1 C5 C4 C5A 179.5 180.2
C4 C5 C5A C5B 95.1 90.3
C4 C5 C5A H5A1 220.3 210.3
C4 C5 C5A H5A2 329.9 330.2
C5 C4 C4A H4A1 0.4 95.6
C5 C4 C4A H4A2 125.7 215.5
C5 C4 C4A H4A3 235.2 335.6
S1 C5 C5A C4 180.5 179.7
C5A C5 C4 C4A 0.3 359.8
C5B C5A C5 H5A1 234.8 240.0
C5B C5A C5 H5A2 125.2 120.1
C5 C5A C5B O5G 162.7 180.0
C5 C5A C5B H5B1 288.0 300.0
C5 C5A C5B H5B2 37.5 59.9
H5A1 C5A C5 H5A2 250.4 240.1
N3 C4 C4A C5 179.6 179.5
C4A C4 C5 C5A 0.3 359.8
H4A1 C4A C4 H4A2 234.7 240.1
H4A1 C4A C4 H4A3 125.2 120.0
H4A2 C4A C4 H4A3 250.5 239.9
C4 C4A H4A1 H4A2 125.3 119.9
C4 C4A H4A1 H4A3 234.8 240.0
H4A2 C4A H4A1 H4A3 109.4 120.1
C4 C4A H4A2 H4A1 225.0 240.1
C4 C4A H4A2 H4A3 112.6 120.0
H4A1 C4A H4A2 H4A3 247.5 239.9
C4 C4A H4A3 H4A1 134.9 119.9
C4 C4A H4A3 H4A2 247.4 240.0
H4A1 C4A H4A3 H4A2 112.5 120.0
C5 C5A C5B H5A1 125.3 120.0
C5 C5A C5B H5A2 234.8 239.9
H5A1 C5A C5B H5A2 109.5 119.9
O5G C5B C5A H5B1 234.7 240.0
O5G C5B C5A H5B2 125.3 120.1
C5A C5B O5G P1 197.5 180.0
H5B1 C5B C5A H5B2 250.5 240.1
C5 C5A H5A1 C5B 232.6 240.0
C5 C5A H5A1 H5A2 116.3 120.0
C5B C5A H5A1 H5A2 243.8 240.0
H5A1 C5A C5B O5G 37.5 60.0
H5A1 C5A C5B H5B1 162.7 180.0
H5A1 C5A C5B H5B2 272.2 299.9
C5 C5A H5A2 C5B 127.4 120.1
C5 C5A H5A2 H5A1 243.7 240.0
C5B C5A H5A2 H5A1 116.2 119.9
H5A2 C5A C5B O5G 288.0 300.1
H5A2 C5A C5B H5B1 53.2 60.1
H5A2 C5A C5B H5B2 162.7 180.0
O5G C5B C5A H5A1 37.5 60.0
O5G C5B C5A H5A2 288.0 300.1
C5A C5B O5G H5B1 125.3 120.0
C5A C5B O5G H5B2 234.7 239.9
H5B1 C5B O5G H5B2 109.4 120.0
C5B O5G P1 O11 89.7 185.0
C5B O5G P1 O12 207.7 65.0
C5B O5G P1 O13 338.8 305.0
H5B1 C5B C5A H5A1 162.7 180.0
H5B1 C5B C5A H5A2 53.2 60.1
C5A C5B H5B1 O5G 234.9 240.0
C5A C5B H5B1 H5B2 117.5 120.0
O5G C5B H5B1 H5B2 242.6 240.0
H5B1 C5B O5G P1 72.2 60.0
H5B2 C5B C5A H5A1 272.2 299.9
H5B2 C5B C5A H5A2 162.7 180.0
C5A C5B H5B2 O5G 125.1 120.1
C5A C5B H5B2 H5B1 242.5 240.1
O5G C5B H5B2 H5B1 117.4 120.0
H5B2 C5B O5G P1 322.8 300.0
P1 O5G C5B H5B1 72.2 60.0
P1 O5G C5B H5B2 322.8 300.0
O11 P1 O5G O12 242.0 120.0
O11 P1 O5G O13 110.9 240.0
O5G P1 O11 P2 66.9 165.0
O12 P1 O5G O13 228.9 120.0
O5G P1 O13 H13 180.0  
O5G P1 O11 O12 117.7 240.0
O5G P1 O11 O13 249.2 120.0
O12 P1 O11 O13 131.6 240.0
O11 P1 O13 H13 73.6  
P1 O11 P2 O21 151.1 165.0
P1 O11 P2 O22 283.6 285.0
P1 O11 P2 O23 38.8 45.0
O5G P1 O12 O11 249.0 120.0
O5G P1 O12 O13 124.2 240.0
O11 P1 O12 O13 235.2 120.0
O12 P1 O11 P2 309.2 285.0
O12 P1 O13 H13 306.5  
O5G P1 O13 O11 106.4 240.0
O5G P1 O13 O12 233.6 120.0
O11 P1 O13 O12 127.1 240.0
O13 P1 O11 P2 177.7 45.0
P2 O11 P1 O12 309.2 285.0
P2 O11 P1 O13 177.7 45.0
O21 P2 O11 O22 227.5 240.0
O21 P2 O11 O23 112.3 120.0
O22 P2 O11 O23 244.8 240.0
O11 P2 O23 H23 180.0  
O11 P2 O21 O22 122.5 119.9
O11 P2 O21 O23 251.9 240.0
O22 P2 O21 O23 129.4 120.1
O21 P2 O23 H23 69.3  
O11 P2 O22 O21 238.0 240.1
O11 P2 O22 O23 109.6 120.0
O21 P2 O22 O23 231.5 239.9
O22 P2 O23 H23 292.7  
O11 P2 O23 O21 110.7 120.0
O11 P2 O23 O22 247.2 240.0
O21 P2 O23 O22 136.6 120.0