PDB Chemical Component D3

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 D3

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.480 1.480
P OP2 1.481 1.609
P OP3 1.610 1.609
P O5' 1.611 1.610
OP2 HOP2 0.950 0.967
OP3 HOP3 0.950 0.968
O5' C5' 1.431 1.428
C5' C4' 1.525 1.530
C5' H5' 1.091 1.090
C5' H5'' 1.091 1.089
C4' O4' 1.456 1.446
C4' C3' 1.533 1.544
C4' H4' 1.090 1.090
O4' C1' 1.434 1.444
C3' O3' 1.435 1.429
C3' C2' 1.498 1.546
C3' H3' 1.091 1.090
O3' HO3' 0.950 0.967
C2' C1' 1.506 1.545
C2' H2' 1.092 1.090
C2' H2'' 1.089 1.090
C1' N1A 1.466 1.466
C1' H1' 1.091 1.090
N1A C2A 1.337 1.351
N1A C5A 1.349 1.367
C2A N3A 1.299 1.303
C2A H2A 1.095 1.080
N3A C4A 1.386 1.349
C4A C5A 1.370 1.358
C4A C1B 1.507 1.482
C5A H5A 1.094 1.079
C1B C2B 1.417 1.392
C1B C6B 1.409 1.395
C2B C3B 1.406 1.387
C2B H2B 1.093 1.079
C3B C4B 1.410 1.389
C3B N 1.411 1.398
C4B C5B 1.392 1.382
C4B H4B 1.078 1.080
C5B C6B 1.385 1.380
C5B H5B 1.074 1.080
C6B H6B 1.084 1.080
N C 1.320 1.347
N HN 0.980 0.970
C O 1.219 1.216
C C1C 1.532 1.477
C1C C2C 1.407 1.396
C1C C6C 1.402 1.396
C2C C3C 1.400 1.380
C2C H2C 1.078 1.079
C3C C4C 1.398 1.384
C3C H3C 1.081 1.080
C4C C5C 1.397 1.383
C4C H4C 1.081 1.080
C5C C6C 1.400 1.380
C5C H5C 1.080 1.080
C6C H6C 1.080 1.080

Bond Angles for D3

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 119.9 109.4
OP1 P OP3 108.3 109.5
OP1 P O5' 108.3 109.4
OP2 P OP3 108.1 109.5
OP2 P O5' 108.2 109.5
P OP2 HOP2 120.0 106.8
OP3 P O5' 102.6 109.5
P OP3 HOP3 108.3 106.8
P O5' C5' 120.7 106.8
O5' C5' C4' 111.5 109.5
O5' C5' H5' 109.0 109.4
O5' C5' H5'' 109.0 109.6
C4' C5' H5' 109.1 109.4
C4' C5' H5'' 109.0 109.4
C5' C4' O4' 110.9 110.4
C5' C4' C3' 110.8 110.7
C5' C4' H4' 109.3 110.3
H5' C5' H5'' 109.1 109.5
O4' C4' C3' 107.4 104.7
O4' C4' H4' 109.2 110.3
C4' O4' C1' 108.1 105.4
C3' C4' H4' 109.2 110.3
C4' C3' O3' 111.9 110.5
C4' C3' C2' 104.2 104.2
C4' C3' H3' 110.0 110.5
O4' C1' C2' 105.7 104.9
O4' C1' N1A 113.2 110.5
O4' C1' H1' 109.5 110.4
O3' C3' C2' 110.6 110.5
O3' C3' H3' 110.0 110.5
C3' O3' HO3' 111.8 106.8
C2' C3' H3' 109.9 110.5
C3' C2' C1' 104.9 104.0
C3' C2' H2' 109.9 110.5
C3' C2' H2'' 110.9 110.5
C1' C2' H2' 110.1 110.5
C1' C2' H2'' 110.3 110.5
C2' C1' N1A 109.6 110.4
C2' C1' H1' 109.0 110.3
H2' C2' H2'' 110.6 110.6
N1A C1' H1' 109.7 110.3
C1' N1A C2A 130.8 126.3
C1' N1A C5A 126.6 126.2
C2A N1A C5A 102.5 107.5
N1A C2A N3A 116.8 109.0
N1A C2A H2A 121.1 125.5
N1A C5A C4A 110.0 106.7
N1A C5A H5A 124.5 126.7
N3A C2A H2A 122.0 125.5
C2A N3A C4A 103.4 109.2
N3A C4A C5A 107.3 107.6
N3A C4A C1B 122.2 126.2
C5A C4A C1B 130.5 126.2
C4A C5A H5A 125.5 126.7
C4A C1B C2B 121.4 120.1
C4A C1B C6B 119.0 120.1
C2B C1B C6B 119.5 119.8
C1B C2B C3B 119.5 119.8
C1B C2B H2B 120.8 120.1
C1B C6B C5B 120.4 120.0
C1B C6B H6B 120.7 120.0
C3B C2B H2B 119.7 120.1
C2B C3B C4B 119.9 120.0
C2B C3B N 119.5 120.0
C4B C3B N 120.6 120.0
C3B C4B C5B 120.1 120.2
C3B C4B H4B 120.8 119.9
C3B N C 121.7 120.0
C3B N HN 119.2 120.0
C5B C4B H4B 119.1 119.9
C4B C5B C6B 120.6 120.2
C4B C5B H5B 120.0 119.9
C6B C5B H5B 119.4 119.9
C5B C6B H6B 118.9 120.0
C N HN 119.1 119.9
N C O 121.9 120.0
N C C1C 117.0 120.1
O C C1C 121.1 120.0
C C1C C2C 120.9 120.2
C C1C C6C 119.5 120.1
C2C C1C C6C 119.6 119.7
C1C C2C C3C 119.9 119.9
C1C C2C H2C 120.4 120.0
C1C C6C C5C 120.1 119.9
C1C C6C H6C 119.9 120.1
C3C C2C H2C 119.6 120.1
C2C C3C C4C 120.1 120.2
C2C C3C H3C 119.9 119.9
C4C C3C H3C 120.0 120.0
C3C C4C C5C 120.0 120.3
C3C C4C H4C 119.8 119.8
C5C C4C H4C 120.1 119.9
C4C C5C C6C 120.1 120.2
C4C C5C H5C 120.0 119.9
C6C C5C H5C 119.9 119.9
C5C C6C H6C 119.9 120.1

Torsion Angles for D3

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 OP3 235.4 120.0
OP2 P OP1 O5' 124.7 240.0
OP1 P OP2 HOP2 180.0 300.0
OP3 P OP1 O5' 249.4 120.0
OP1 P OP3 HOP3 180.0 180.0
OP1 P O5' C5' 67.5 60.0
OP1 P OP2 OP3 124.8 240.0
OP1 P OP2 O5' 235.2 120.0
OP3 P OP2 O5' 110.4 240.0
OP2 P OP3 HOP3 311.4 60.0
OP2 P O5' C5' 296.0 180.0
OP1 P OP3 OP2 228.6 120.0
OP1 P OP3 O5' 114.4 240.0
OP2 P OP3 O5' 245.8 120.0
OP3 P OP2 HOP2 55.3 60.0
OP3 P O5' C5' 181.9 300.0
OP1 P O5' OP2 131.4 240.0
OP1 P O5' OP3 245.5 120.0
OP2 P O5' OP3 114.1 240.0
O5' P OP2 HOP2 304.8 180.0
O5' P OP3 HOP3 65.6 300.0
P O5' C5' C4' 178.1 180.0
P O5' C5' H5' 57.6 60.1
P O5' C5' H5'' 298.6 299.9
HOP2 OP2 P OP3 55.3 60.0
HOP2 OP2 P O5' 304.8 180.0
HOP3 OP3 P O5' 65.6 300.0
C4' C5' O5' H5' 120.5 120.0
C4' C5' O5' H5'' 239.5 240.1
O5' C5' C4' O4' 62.9 61.4
O5' C5' C4' C3' 182.0 176.9
O5' C5' C4' H4' 302.4 299.2
H5' C5' O5' H5'' 119.0 120.1
O5' C5' C4' H5' 239.5 240.0
O5' C5' C4' H5'' 120.4 120.0
H5' C5' C4' H5'' 241.0 240.0
O4' C4' C5' C3' 240.8 244.5
O4' C4' C5' H4' 120.5 122.2
C5' C4' O4' C1' 133.9 159.5
C3' C4' C5' H4' 239.7 237.7
C5' C4' C3' O3' 126.4 98.6
C5' C4' C3' C2' 245.9 217.2
C5' C4' C3' H3' 3.8 336.0
O5' C5' H5' C4' 122.0 120.0
O5' C5' H5' H5'' 241.1 239.9
C4' C5' H5' H5'' 119.0 119.9
H5' C5' C4' O4' 183.4 181.4
H5' C5' C4' C3' 302.6 296.9
H5' C5' C4' H4' 62.9 59.2
O5' C5' H5'' C4' 238.0 240.0
O5' C5' H5'' H5' 119.0 120.1
C4' C5' H5'' H5' 241.0 240.1
H5'' C5' C4' O4' 302.4 301.4
H5'' C5' C4' C3' 61.6 56.9
H5'' C5' C4' H4' 181.9 179.2
O4' C4' C5' H5' 183.4 181.4
O4' C4' C5' H5'' 302.4 301.4
C5' C4' O4' C3' 121.2 119.2
C5' C4' O4' H4' 239.5 237.8
C3' C4' O4' H4' 118.3 118.7
O4' C4' C3' O3' 247.6 217.5
O4' C4' C3' C2' 7.2 336.2
O4' C4' C3' H3' 125.0 94.9
C4' O4' C1' C2' 332.4 319.6
C4' O4' C1' N1A 212.4 200.7
C4' O4' C1' H1' 89.7 78.4
C3' C4' C5' H5' 302.6 296.9
C3' C4' C5' H5'' 61.6 56.9
C5' C4' C3' O4' 238.7 241.0
C5' C4' C3' H4' 120.4 122.3
O4' C4' C3' H4' 241.7 241.3
C3' C4' O4' C1' 12.7 40.3
O3' C3' C4' C2' 240.4 241.3
O3' C3' C4' H3' 122.6 122.6
C4' C3' O3' HO3' 179.9 178.1
C2' C3' C4' H3' 242.2 241.3
C4' C3' C2' C1' 336.7 359.9
C4' C3' C2' H2' 95.0 118.5
C4' C3' C2' H2'' 217.6 241.3
H4' C4' C5' H5' 62.9 59.2
H4' C4' C5' H5'' 181.9 179.2
C5' C4' H4' O4' 121.5 122.2
C5' C4' H4' C3' 238.6 237.4
O4' C4' H4' C3' 117.2 115.2
H4' C4' O4' C1' 254.4 281.6
H4' C4' C3' O3' 6.0 336.2
H4' C4' C3' C2' 125.5 94.9
H4' C4' C3' H3' 243.4 213.6
C1' O4' C4' C3' 12.7 40.3
C1' O4' C4' H4' 254.4 281.6
C3' C2' C1' O4' 31.8 23.9
O4' C1' C2' H2' 273.7 265.3
O4' C1' C2' H2'' 151.3 142.6
C2' C1' O4' N1A 120.0 118.9
C2' C1' O4' H1' 242.7 241.2
N1A C1' O4' H1' 122.7 122.3
O4' C1' N1A C2A 49.3 205.5
O4' C1' N1A C5A 225.0 25.2
O3' C3' C4' H4' 6.0 336.2
C4' C3' O3' C2' 115.8 114.8
C4' C3' O3' H3' 237.4 237.4
C2' C3' O3' H3' 121.7 122.6
O3' C3' C2' C1' 97.1 118.7
O3' C3' C2' H2' 215.4 237.3
O3' C3' C2' H2'' 338.0 0.0
C2' C3' C4' H4' 125.5 94.9
C4' C3' C2' O3' 239.6 241.3
C4' C3' C2' H3' 117.8 118.7
O4' C1' C2' C3' 31.8 23.9
O3' C3' C2' H3' 238.3 237.5
C2' C3' O3' HO3' 64.2 63.3
C1' C2' C3' H2' 241.7 241.4
C1' C2' C3' H2'' 119.1 118.6
C3' C2' C1' N1A 154.1 142.9
C3' C2' C1' H1' 274.2 265.1
H2' C2' C3' H2'' 237.4 237.2
H3' C3' C4' H4' 243.4 213.6
C4' C3' H3' O3' 123.7 122.6
C4' C3' H3' C2' 245.8 245.2
O3' C3' H3' C2' 122.1 122.5
H3' C3' O3' HO3' 302.5 300.8
H3' C3' C2' C1' 218.9 241.2
H3' C3' C2' H2' 337.1 359.8
H3' C3' C2' H2'' 99.7 122.6
HO3' O3' C3' C2' 64.2 63.3
HO3' O3' C3' H3' 302.5 300.8
O4' C1' C2' N1A 237.7 241.0
O4' C1' C2' H1' 117.6 118.9
C1' C2' C3' H3' 218.9 241.2
C3' C2' C1' H2' 118.2 118.6
C3' C2' C1' H2'' 240.5 241.4
H2' C2' C1' H2'' 122.3 122.8
N1A C1' C2' H1' 239.9 237.9
C2' C1' N1A C2A 291.6 90.0
C2' C1' N1A C5A 107.2 269.7
H2' C2' C3' H3' 337.1 359.8
C3' C2' H2' C1' 245.0 245.4
C3' C2' H2' H2'' 122.8 122.7
C1' C2' H2' H2'' 237.8 237.3
H2' C2' C1' N1A 36.0 24.3
H2' C2' C1' H1' 156.0 146.5
H2'' C2' C3' H3' 99.7 122.6
C3' C2' H2'' C1' 115.8 114.6
C3' C2' H2'' H2' 237.8 237.3
C1' C2' H2'' H2' 122.0 122.7
H2'' C2' C1' N1A 273.6 261.6
H2'' C2' C1' H1' 33.7 23.7
O4' C1' N1A C2' 117.7 115.5
O4' C1' N1A H1' 237.4 237.7
N1A C1' C2' H2' 36.0 24.3
N1A C1' C2' H2'' 273.6 261.6
C2' C1' N1A H1' 119.7 122.2
C2A N1A C1' C5A 184.3 180.3
C1' N1A C2A N3A 176.2 180.0
C1' N1A C2A H2A 356.6 360.0
C1' N1A C5A C4A 183.7 179.9
C1' N1A C5A H5A 3.8 0.2
O4' C1' H1' C2' 244.8 244.6
O4' C1' H1' N1A 124.7 122.4
H1' C1' C2' H2' 156.0 146.5
H1' C1' C2' H2'' 33.7 23.7
C2' C1' H1' N1A 239.9 237.8
H1' C1' N1A C2A 171.9 327.8
H1' C1' N1A C5A 347.5 147.6
C2A N1A C1' H1' 171.9 327.8
C1' N1A C2A C5A 176.4 179.8
C2A N1A C5A C4A 0.3 359.7
C2A N1A C5A H5A 180.4 180.0
N3A C2A N1A H2A 179.6 180.0
N1A C2A N3A C4A 0.1 0.0
C5A N1A C1' H1' 347.5 147.6
C1' N1A C5A C2A 183.4 180.2
C5A N1A C2A N3A 359.8 0.2
C5A N1A C2A H2A 180.2 180.2
N3A C4A C5A N1A 359.7 0.4
N1A C5A C4A C1B 177.2 180.1
C4A C5A N1A H5A 179.9 179.7
N3A C2A N1A C5A 359.8 0.2
N1A C2A N3A H2A 180.4 180.0
C2A N3A C4A C5A 0.1 359.8
C2A N3A C4A C1B 182.4 180.0
H2A C2A N1A C5A 180.2 180.2
N1A C2A H2A N3A 179.5 180.0
H2A C2A N3A C4A 179.6 180.0
N1A C5A C4A N3A 359.7 0.4
C4A N3A C2A H2A 179.6 180.0
C5A C4A N3A C1B 177.7 179.8
N3A C4A C5A H5A 179.6 180.0
N3A C4A C1B C2B 346.8 320.0
N3A C4A C1B C6B 164.8 140.3
N1A C5A C4A H5A 180.1 180.3
N3A C4A C5A C1B 182.6 180.2
C5A C4A C1B C2B 169.7 140.2
C5A C4A C1B C6B 347.6 320.6
N3A C4A C1B C5A 177.1 179.7
C1B C4A C5A H5A 357.0 359.8
C2B C1B C4A C6B 182.0 179.7
C4A C1B C2B C3B 178.0 179.8
C4A C1B C2B H2B 358.5 0.2
C4A C1B C6B C5B 181.9 180.0
C4A C1B C6B H6B 1.4 359.9
N1A C5A H5A C4A 179.9 179.6
H5A C5A C4A C1B 357.0 359.8
C4A C1B C2B C6B 178.0 180.3
C2B C1B C6B C5B 359.9 0.3
C2B C1B C6B H6B 179.4 180.2
C3B C2B C1B H2B 179.5 179.5
C1B C2B C3B C4B 360.0 0.5
C1B C2B C3B N 180.6 180.3
C4A C1B C6B C2B 182.0 179.7
C6B C1B C2B C3B 0.1 359.4
C6B C1B C2B H2B 180.6 179.9
C4B C5B C6B C1B 0.1 360.0
C1B C6B C5B H5B 179.9 179.9
C5B C6B C1B H6B 180.5 180.1
C3B C2B C1B C6B 0.1 359.4
C1B C2B C3B H2B 180.5 180.5
C4B C3B C2B N 179.4 180.2
C2B C3B C4B C5B 0.0 359.8
C2B C3B C4B H4B 180.4 179.8
C2B C3B N C 242.4 33.5
C2B C3B N HN 62.1 213.6
H2B C2B C1B C6B 180.6 179.9
C1B C2B H2B C3B 179.5 179.5
H2B C2B C3B C4B 179.5 180.0
H2B C2B C3B N 0.0 359.9
C4B C3B C2B H2B 179.5 180.0
C2B C3B C4B N 180.6 179.8
C4B C3B N C 63.0 213.3
C4B C3B N HN 242.7 33.4
C5B C4B C3B H4B 179.6 180.0
C3B C4B C5B C6B 359.9 359.9
C3B C4B C5B H5B 180.1 180.1
N C3B C2B H2B 0.0 359.9
C2B C3B N C4B 179.4 180.2
N C3B C4B C5B 179.4 180.0
N C3B C4B H4B 359.8 360.0
C N C3B HN 180.3 179.9
C3B N C O 359.8 5.7
C3B N C C1C 179.7 185.5
C1B C6B C5B C4B 0.1 360.0
C5B C4B C3B N 179.4 180.0
C3B C4B C5B H4B 180.4 180.0
C6B C5B C4B H5B 179.8 179.9
C4B C5B C6B H6B 180.6 180.1
H4B C4B C3B N 359.8 360.0
C3B C4B H4B C5B 179.6 180.0
H4B C4B C5B C6B 179.5 179.9
H4B C4B C5B H5B 359.7 0.1
C1B C6B C5B H6B 179.6 179.9
C6B C5B C4B H4B 179.5 179.9
C4B C5B C6B H5B 180.2 180.1
H5B C5B C4B H4B 359.7 0.1
C4B C5B H5B C6B 179.8 179.9
H5B C5B C6B H6B 0.4 360.0
C1B C6B H6B C5B 180.4 180.1
H6B C6B C5B H5B 0.4 360.0
C3B N C HN 179.7 180.1
O C N C1C 180.2 180.2
N C C1C C2C 130.5 180.0
N C C1C C6C 310.6 359.8
C3B N HN C 180.3 179.9
HN N C O 180.1 185.6
HN N C C1C 359.9 5.4
O C N HN 180.1 185.6
N C O C1C 179.8 179.8
O C C1C C2C 310.4 359.9
O C C1C C6C 130.4 179.7
C1C C N HN 359.9 5.4
N C C1C O 180.1 180.2
C2C C1C C C6C 180.0 180.2
C C1C C2C C3C 180.1 180.0
C C1C C2C H2C 0.3 0.0
C C1C C6C C5C 179.9 179.6
C C1C C6C H6C 359.8 0.2
C C1C C2C C6C 180.0 179.8
C2C C1C C6C C5C 359.9 359.4
C2C C1C C6C H6C 179.8 180.0
C3C C2C C1C H2C 179.8 180.0
C1C C2C C3C C4C 0.0 0.1
C1C C2C C3C H3C 179.9 179.9
C C1C C6C C2C 180.0 180.2
C6C C1C C2C C3C 0.0 0.2
C6C C1C C2C H2C 180.3 180.2
C4C C5C C6C C1C 360.0 0.7
C1C C6C C5C H5C 180.0 180.2
C5C C6C C1C H6C 180.1 179.4
C3C C2C C1C C6C 0.0 0.2
C1C C2C C3C H2C 180.2 180.0
C4C C3C C2C H3C 180.1 180.1
C2C C3C C4C C5C 359.9 0.0
C2C C3C C4C H4C 180.0 180.0
H2C C2C C1C C6C 180.3 180.2
C1C C2C H2C C3C 179.8 180.0
H2C C2C C3C C4C 179.8 180.0
H2C C2C C3C H3C 359.7 359.9
C4C C3C C2C H2C 179.8 180.0
C2C C3C C4C H3C 179.9 179.9
C5C C4C C3C H4C 179.9 180.1
C3C C4C C5C C6C 0.1 359.6
C3C C4C C5C H5C 180.1 180.0
H3C C3C C2C H2C 359.7 359.9
C2C C3C H3C C4C 180.1 180.1
H3C C3C C4C C5C 180.0 180.1
H3C C3C C4C H4C 0.2 0.1
C1C C6C C5C C4C 360.0 0.7
C5C C4C C3C H3C 180.0 180.1
C3C C4C C5C H4C 180.1 179.9
C6C C5C C4C H5C 180.0 179.6
C4C C5C C6C H6C 180.1 180.0
H4C C4C C3C H3C 0.2 0.1
C3C C4C H4C C5C 179.9 180.1
H4C C4C C5C C6C 179.9 179.7
H4C C4C C5C H5C 359.9 0.1
C1C C6C C5C H6C 179.9 180.6
C6C C5C C4C H4C 179.9 179.7
C4C C5C C6C H5C 180.0 180.4
H5C C5C C4C H4C 359.9 0.1
C4C C5C H5C C6C 180.0 179.6
H5C C5C C6C H6C 0.1 359.6
C1C C6C H6C C5C 180.1 179.4
H6C C6C C5C H5C 0.1 359.6