PDB Chemical Component RTP

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 RTP

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
PG O1G 1.492 1.480
PG O2G 1.491 1.610
PG O3G 1.491 1.609
PG O3B 1.616 1.611
O2G HOG2 0.950 0.966
O3G HOG3 0.950 0.968
O3B PB 1.614 1.610
PB O1B 1.488 1.480
PB O2B 1.480 1.610
PB O3A 1.595 1.611
O2B HOB2 0.950 0.967
O3A PA 1.596 1.610
PA O1A 1.487 1.480
PA O2A 1.485 1.610
PA O5' 1.589 1.610
O2A HOA2 0.950 0.967
O5' C5' 1.417 1.428
C5' C4' 1.503 1.530
C5' H5'1 1.115 1.090
C5' H5'2 1.115 1.090
C4' O4' 1.453 1.444
C4' C3' 1.514 1.545
C4' H4' 1.115 1.090
O4' C1' 1.426 1.445
C1' N1 1.458 1.466
C1' C2' 1.531 1.545
C1' H1' 1.115 1.090
N1 N2 1.365 1.288
N1 C5 1.371 1.346
N2 C3 1.390 1.315
N3 C6 1.397 1.348
N3 HN31 1.020 0.970
N3 HN32 1.021 0.970
C6 O3 1.236 1.215
C6 C3 1.414 1.479
C3 N4 1.392 1.345
N4 C5 1.303 1.309
C5 H5 1.103 1.080
C2' O2' 1.417 1.429
C2' C3' 1.513 1.547
C2' H2' 1.115 1.090
O2' HO2' 0.950 0.967
C3' O3' 1.421 1.429
C3' H3' 1.115 1.090
O3' HO3' 0.950 0.967

Bond Angles for RTP

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1G PG O2G 117.5 109.5
O1G PG O3G 103.6 109.5
O1G PG O3B 106.3 109.5
O2G PG O3G 117.9 109.5
O2G PG O3B 105.1 109.5
PG O2G HOG2 117.5 106.8
O3G PG O3B 105.3 109.5
PG O3G HOG3 103.6 106.8
PG O3B PB 144.1 106.8
O3B PB O1B 109.8 109.5
O3B PB O2B 108.1 109.5
O3B PB O3A 106.4 109.4
O1B PB O2B 119.0 109.5
O1B PB O3A 106.6 109.5
O2B PB O3A 106.2 109.5
PB O2B HOB2 108.1 106.8
PB O3A PA 133.4 106.8
O3A PA O1A 109.8 109.5
O3A PA O2A 108.9 109.5
O3A PA O5' 99.3 109.5
O1A PA O2A 119.9 109.5
O1A PA O5' 108.8 109.5
O2A PA O5' 108.2 109.5
PA O2A HOA2 108.9 106.8
PA O5' C5' 120.1 106.8
O5' C5' C4' 110.0 109.4
O5' C5' H5'1 112.0 109.5
O5' C5' H5'2 112.0 109.5
C4' C5' H5'1 112.0 109.4
C4' C5' H5'2 112.0 109.5
C5' C4' O4' 109.7 110.4
C5' C4' C3' 115.5 110.4
C5' C4' H4' 103.5 110.3
H5'1 C5' H5'2 98.4 109.5
O4' C4' C3' 103.5 104.8
O4' C4' H4' 115.5 110.4
C4' O4' C1' 110.2 105.3
C3' C4' H4' 109.7 110.4
C4' C3' C2' 105.2 104.1
C4' C3' O3' 111.6 110.5
C4' C3' H3' 111.9 110.5
O4' C1' N1 107.8 110.4
O4' C1' C2' 107.8 104.9
O4' C1' H1' 112.7 110.4
N1 C1' C2' 112.5 110.4
N1 C1' H1' 108.1 110.3
C1' N1 N2 126.1 125.7
C1' N1 C5 127.4 125.7
C2' C1' H1' 108.1 110.4
C1' C2' O2' 109.1 110.8
C1' C2' C3' 99.7 104.0
C1' C2' H2' 117.0 110.4
N2 N1 C5 106.5 108.5
N1 N2 C3 106.0 108.7
N1 C5 N4 113.1 107.6
N1 C5 H5 125.6 126.2
N2 C3 C6 125.1 126.0
N2 C3 N4 109.5 107.9
C6 N3 HN31 120.1 120.0
C6 N3 HN32 111.7 120.0
N3 C6 O3 120.1 120.0
N3 C6 C3 111.7 120.0
HN31 N3 HN32 128.2 120.0
O3 C6 C3 128.2 120.0
C6 C3 N4 125.4 126.1
C3 N4 C5 104.9 107.3
N4 C5 H5 121.2 126.2
O2' C2' C3' 112.8 110.5
O2' C2' H2' 104.9 110.4
C2' O2' HO2' 109.1 106.8
C3' C2' H2' 113.6 110.5
C2' C3' O3' 112.4 110.5
C2' C3' H3' 111.1 110.6
O3' C3' H3' 104.7 110.5
C3' O3' HO3' 111.6 106.8

Torsion Angles for RTP

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2G PG O1G O3G 132.0 120.0
O2G PG O1G O3B 242.6 240.0
O1G PG O2G HOG2 180.0 300.0
O3G PG O1G O3B 110.7 120.0
O1G PG O3G HOG3 180.0 180.0
O1G PG O3B PB 130.2 45.0
O1G PG O2G O3G 234.8 240.0
O1G PG O2G O3B 118.0 120.0
O3G PG O2G O3B 243.2 240.0
O2G PG O3G HOG3 48.2 60.0
O2G PG O3B PB 255.5 165.0
O1G PG O3G O2G 131.8 120.0
O1G PG O3G O3B 248.5 240.0
O2G PG O3G O3B 116.8 120.0
O3G PG O2G HOG2 305.1 60.0
O3G PG O3B PB 20.7 285.0
O1G PG O3B O2G 234.7 240.0
O1G PG O3B O3G 109.5 120.0
O2G PG O3B O3G 234.8 240.0
O3B PG O2G HOG2 62.0 180.0
O3B PG O3G HOG3 291.5 300.0
PG O3B PB O1B 42.0 319.9
PG O3B PB O2B 173.3 80.0
PG O3B PB O3A 287.0 200.0
HOG2 O2G PG O3G 305.1 60.0
HOG2 O2G PG O3B 62.0 180.0
HOG3 O3G PG O3B 291.5 300.0
O1B PB O3B O2B 228.7 239.9
O1B PB O3B O3A 115.0 119.9
O2B PB O3B O3A 246.3 240.0
O3B PB O2B HOB2 180.0 59.9
O3B PB O3A PA 98.8 165.0
O3B PB O1B O2B 125.2 120.1
O3B PB O1B O3A 245.1 240.1
O2B PB O1B O3A 119.9 120.0
O1B PB O2B HOB2 306.0 180.0
O1B PB O3A PA 341.7 45.1
O3B PB O2B O1B 234.0 240.0
O3B PB O2B O3A 113.8 120.0
O1B PB O2B O3A 239.9 240.0
O2B PB O3A PA 213.8 285.0
O3B PB O3A O1B 117.1 119.9
O3B PB O3A O2B 245.0 240.0
O1B PB O3A O2B 127.9 120.0
O3A PB O2B HOB2 66.1 300.0
PB O3A PA O1A 103.2 45.0
PB O3A PA O2A 330.2 285.0
PB O3A PA O5' 217.2 165.0
HOB2 O2B PB O3A 66.1 300.0
O1A PA O3A O2A 133.0 120.0
O1A PA O3A O5' 246.0 240.0
O2A PA O3A O5' 113.0 120.0
O3A PA O2A HOA2 180.0 300.0
O3A PA O5' C5' 65.7 185.0
O3A PA O1A O2A 232.9 240.0
O3A PA O1A O5' 107.8 120.0
O2A PA O1A O5' 234.8 240.0
O1A PA O2A HOA2 52.5 180.0
O1A PA O5' C5' 180.5 305.0
O3A PA O2A O1A 127.5 120.0
O3A PA O2A O5' 253.0 240.0
O1A PA O2A O5' 125.5 120.0
O2A PA O5' C5' 312.2 65.0
O3A PA O5' O1A 245.3 240.0
O3A PA O5' O2A 113.5 120.0
O1A PA O5' O2A 228.3 240.0
O5' PA O2A HOA2 287.0 60.0
PA O5' C5' C4' 235.3 180.0
PA O5' C5' H5'1 110.0 60.1
PA O5' C5' H5'2 0.6 300.0
HOA2 O2A PA O5' 287.0 60.0
C4' C5' O5' H5'1 125.3 120.0
C4' C5' O5' H5'2 234.7 240.0
O5' C5' C4' O4' 287.9 66.5
O5' C5' C4' C3' 44.3 181.9
O5' C5' C4' H4' 164.1 304.2
H5'1 C5' O5' H5'2 109.4 120.1
O5' C5' C4' H5'1 234.7 240.0
O5' C5' C4' H5'2 125.3 120.0
H5'1 C5' C4' H5'2 250.6 240.0
O4' C4' C5' C3' 243.6 244.6
O4' C4' C5' H4' 123.8 122.3
C5' C4' O4' C1' 138.0 159.5
C3' C4' C5' H4' 240.2 237.7
C5' C4' C3' C2' 207.8 217.0
C5' C4' C3' O3' 85.6 98.4
C5' C4' C3' H3' 328.6 335.8
O5' C5' H5'1 C4' 124.2 119.9
O5' C5' H5'1 H5'2 242.1 239.9
C4' C5' H5'1 H5'2 117.9 120.0
H5'1 C5' C4' O4' 53.2 186.5
H5'1 C5' C4' C3' 169.6 301.9
H5'1 C5' C4' H4' 289.4 64.2
O5' C5' H5'2 C4' 235.8 240.0
O5' C5' H5'2 H5'1 117.9 120.1
C4' C5' H5'2 H5'1 242.1 240.0
H5'2 C5' C4' O4' 162.6 306.5
H5'2 C5' C4' C3' 279.0 61.9
H5'2 C5' C4' H4' 38.9 184.2
O4' C4' C5' H5'1 53.2 186.5
O4' C4' C5' H5'2 162.6 306.5
C5' C4' O4' C3' 123.7 118.9
C5' C4' O4' H4' 243.6 237.8
C3' C4' O4' H4' 119.8 118.8
O4' C4' C3' C2' 327.6 335.9
O4' C4' C3' O3' 205.4 217.2
O4' C4' C3' H3' 88.4 94.7
C4' O4' C1' N1 247.5 200.6
C4' O4' C1' C2' 9.1 319.5
C4' O4' C1' H1' 128.3 78.4
C3' C4' C5' H5'1 169.6 301.9
C3' C4' C5' H5'2 279.0 61.9
C5' C4' C3' O4' 240.2 241.1
C5' C4' C3' H4' 116.4 122.3
O4' C4' C3' H4' 236.2 241.1
C3' C4' O4' C1' 14.3 40.5
C1' C2' C3' C4' 36.5 0.1
O2' C2' C3' C4' 280.9 241.2
C4' C3' C2' H2' 161.7 118.7
C2' C3' C4' O3' 122.2 118.7
C2' C3' C4' H3' 239.2 241.3
O3' C3' C4' H3' 117.0 122.6
C4' C3' O3' HO3' 180.0 180.0
H4' C4' C5' H5'1 289.4 64.2
H4' C4' C5' H5'2 38.9 184.2
C5' C4' H4' O4' 119.9 122.3
C5' C4' H4' C3' 236.3 237.7
O4' C4' H4' C3' 116.4 115.4
H4' C4' O4' C1' 254.4 281.7
H4' C4' C3' C2' 91.4 94.8
H4' C4' C3' O3' 329.2 336.1
H4' C4' C3' H3' 212.2 213.5
C1' O4' C4' C3' 14.3 40.5
C1' O4' C4' H4' 254.4 281.7
N1 C1' O4' C2' 238.4 241.1
N1 C1' O4' H1' 119.2 122.3
O4' C1' N1 N2 222.9 62.3
O4' C1' N1 C5 42.9 242.0
C2' C1' O4' H1' 240.8 241.1
O4' C1' C2' O2' 90.2 142.6
O4' C1' C2' C3' 331.9 23.9
O4' C1' C2' H2' 209.0 265.3
O4' C1' N1 C2' 118.7 115.5
O4' C1' N1 H1' 237.9 237.7
C2' C1' N1 H1' 119.3 122.2
N1 C1' C2' O2' 208.9 261.5
N1 C1' C2' C3' 90.5 142.7
N1 C1' C2' H2' 327.7 24.2
N2 N1 C1' C5 180.0 180.3
C1' N1 N2 C3 180.2 180.2
C1' N1 C5 N4 179.9 180.0
C1' N1 C5 H5 360.0 360.0
C4' C3' C2' C1' 36.5 0.1
O4' C1' C2' N1 241.3 241.1
O4' C1' C2' H1' 122.1 118.9
N1 C1' C2' H1' 240.8 237.8
C2' C1' N1 N2 104.2 306.9
C2' C1' N1 C5 284.2 126.6
O2' C2' C1' C3' 118.4 118.7
O2' C2' C1' H2' 241.2 237.3
C1' C2' O2' HO2' 180.0 65.3
C3' C2' C1' H2' 122.9 118.6
C1' C2' C3' O3' 158.1 118.8
C1' C2' C3' H3' 275.1 241.5
O4' C1' H1' N1 119.0 122.3
O4' C1' H1' C2' 241.0 244.5
N1 C1' H1' C2' 122.0 122.2
H1' C1' N1 N2 345.0 184.6
H1' C1' N1 C5 165.0 4.3
H1' C1' C2' O2' 328.1 23.7
H1' C1' C2' C3' 209.8 265.0
H1' C1' C2' H2' 86.9 146.4
N2 N1 C1' C2' 104.2 306.9
N2 N1 C1' H1' 345.0 184.6
C1' N1 N2 C5 180.0 179.8
N2 N1 C5 N4 359.9 359.8
N2 N1 C5 H5 180.0 179.7
N1 N2 C3 C6 179.8 179.8
N1 N2 C3 N4 359.8 359.6
C5 N1 C1' C2' 284.2 126.6
C5 N1 C1' H1' 165.0 4.3
C1' N1 C5 N2 180.0 180.2
C5 N1 N2 C3 0.2 0.4
C3 N4 C5 N1 359.9 360.0
N4 C5 N1 H5 180.0 180.1
C3 N2 N1 C5 0.2 0.4
N3 C6 C3 N2 0.8 179.7
O3 C6 C3 N2 181.1 359.7
C6 C3 N2 N4 180.0 180.3
N2 C3 N4 C5 0.2 0.3
N2 C3 C6 N3 0.8 179.7
HN31 N3 C6 HN32 180.2 180.3
O3 C6 N3 C3 179.7 180.0
N3 C6 C3 N4 180.9 0.0
C6 N3 HN31 HN32 179.7 179.7
HN31 N3 C6 O3 180.0 0.0
HN31 N3 C6 C3 0.2 180.0
C6 N3 HN32 HN31 180.3 180.3
HN32 N3 C6 O3 359.7 179.7
HN32 N3 C6 C3 180.0 359.7
N2 C3 C6 O3 181.1 359.7
O3 C6 N3 HN31 180.0 0.0
O3 C6 N3 HN32 359.7 179.7
N3 C6 O3 C3 180.3 180.0
O3 C6 C3 N4 1.2 180.0
N2 C3 C6 N4 180.0 179.7
C3 C6 N3 HN31 0.2 180.0
C3 C6 N3 HN32 180.0 359.7
N3 C6 C3 O3 179.7 180.0
C6 C3 N4 C5 180.1 180.0
N1 C5 N4 C3 359.9 360.0
N2 C3 N4 C6 180.0 180.3
C3 N4 C5 H5 179.9 180.0
N1 C5 N4 H5 180.0 179.9
N1 C5 H5 N4 180.0 180.1
C4' C3' C2' O2' 280.9 241.2
O2' C2' C1' H1' 328.1 23.7
C1' C2' O2' C3' 250.2 245.3
C1' C2' O2' H2' 126.1 122.7
C3' C2' O2' H2' 235.9 237.4
O2' C2' C3' O3' 42.5 359.8
O2' C2' C3' H3' 159.5 122.5
C2' C3' C4' H4' 91.4 94.8
C4' C3' C2' O3' 238.3 241.3
C4' C3' C2' H3' 121.3 118.7
C3' C2' C1' H1' 209.8 265.0
C1' C2' C3' O2' 115.6 118.9
C1' C2' C3' H2' 234.8 241.5
O2' C2' C3' H2' 119.2 122.5
C3' C2' O2' HO2' 289.8 180.0
O3' C3' C2' H3' 243.0 237.3
C2' C3' O3' HO3' 62.1 65.4
H2' C2' C1' H1' 86.9 146.4
C1' C2' H2' O2' 239.0 237.1
C1' C2' H2' C3' 115.4 114.5
O2' C2' H2' C3' 236.4 237.4
H2' C2' O2' HO2' 53.9 302.6
H2' C2' C3' O3' 283.4 237.3
H2' C2' C3' H3' 40.4 360.0
HO2' O2' C2' C3' 289.8 180.0
HO2' O2' C2' H2' 53.9 302.6
O3' C3' C4' H4' 329.2 336.1
C4' C3' O3' C2' 117.9 114.7
C4' C3' O3' H3' 238.7 237.4
O3' C3' C2' H2' 283.4 237.3
C2' C3' O3' H3' 120.8 122.7
H3' C3' C4' H4' 212.2 213.5
C4' C3' H3' C2' 242.7 245.3
C4' C3' H3' O3' 121.1 122.6
H3' C3' C2' H2' 40.4 360.0
C2' C3' H3' O3' 238.4 237.3
H3' C3' O3' HO3' 301.3 302.6
HO3' O3' C3' H3' 301.3 302.6