PDB Chemical Component UTP

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 UTP

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
PA O1A 1.486 1.480
PA O2A 1.488 1.611
PA O3A 1.622 1.610
PA O5' 1.583 1.610
O2A H2A 0.950 0.967
O3A PB 1.582 1.611
O5' C5' 1.415 1.429
PB O1B 1.453 1.610
PB O2B 1.439 1.480
PB O3B 1.593 1.610
O1B H1B 0.950 0.967
O3B PG 1.583 1.609
PG O1G 1.532 1.610
PG O2G 1.508 1.480
PG O3G 1.521 1.610
O1G H1G 0.950 0.967
O3G H3G 0.950 0.967
C5' C4' 1.500 1.530
C5' H5'1 1.100 1.089
C5' H5'2 1.100 1.090
C4' O4' 1.454 1.447
C4' C3' 1.523 1.545
C4' H4' 1.100 1.090
O4' C1' 1.406 1.444
C1' C2' 1.529 1.545
C1' N1 1.474 1.465
C1' H1' 1.100 1.090
C2' O2' 1.408 1.429
C2' C3' 1.531 1.545
C2' H2' 1.100 1.090
O2' HA 0.950 0.967
C3' O3' 1.424 1.428
C3' H3' 1.100 1.090
O3' HB 0.950 0.967
N1 C6 1.375 1.368
N1 C2 1.388 1.346
C6 C5 1.340 1.351
C6 H6 1.080 1.080
C2 O2 1.220 1.216
C2 N3 1.377 1.346
N3 C4 1.384 1.349
N3 H3 1.000 0.969
C4 O4 1.239 1.218
C4 C5 1.435 1.416
C5 H5 1.080 1.080

Bond Angles for UTP

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1A PA O2A 120.1 109.5
O1A PA O3A 110.2 109.5
O1A PA O5' 110.3 109.5
O2A PA O3A 108.0 109.4
O2A PA O5' 108.3 109.5
PA O2A H2A 109.5 106.8
O3A PA O5' 97.5 109.5
PA O3A PB 131.8 106.8
PA O5' C5' 120.0 106.8
O3A PB O1B 116.1 109.5
O3A PB O2B 104.7 109.4
O3A PB O3B 98.9 109.5
O5' C5' C4' 109.8 109.4
O5' C5' H5'1 109.3 109.5
O5' C5' H5'2 109.3 109.5
O1B PB O2B 118.3 109.5
O1B PB O3B 106.5 109.5
PB O1B H1B 109.5 106.8
O2B PB O3B 110.6 109.5
PB O3B PG 130.9 106.8
O3B PG O1G 107.1 109.5
O3B PG O2G 103.2 109.5
O3B PG O3G 109.0 109.5
O1G PG O2G 113.7 109.4
O1G PG O3G 111.3 109.4
PG O1G H1G 109.5 106.8
O2G PG O3G 112.2 109.5
PG O3G H3G 109.5 106.9
C4' C5' H5'1 109.3 109.5
C4' C5' H5'2 109.4 109.5
C5' C4' O4' 109.2 110.4
C5' C4' C3' 113.9 110.7
C5' C4' H4' 105.6 110.4
H5'1 C5' H5'2 109.7 109.5
O4' C4' C3' 106.4 104.7
O4' C4' H4' 113.3 110.3
C4' O4' C1' 108.4 105.4
C3' C4' H4' 108.5 110.3
C4' C3' C2' 103.4 104.2
C4' C3' O3' 110.0 110.5
C4' C3' H3' 114.1 110.5
O4' C1' C2' 103.2 104.8
O4' C1' N1 109.0 110.5
O4' C1' H1' 115.4 110.4
C2' C1' N1 113.8 110.3
C2' C1' H1' 110.6 110.4
C1' C2' O2' 111.5 110.6
C1' C2' C3' 101.7 104.0
C1' C2' H2' 114.6 110.6
N1 C1' H1' 105.1 110.3
C1' N1 C6 121.5 119.7
C1' N1 C2 117.7 119.7
O2' C2' C3' 113.3 110.4
O2' C2' H2' 103.3 110.5
C2' O2' HA 109.5 106.8
C3' C2' H2' 112.9 110.5
C2' C3' O3' 112.5 110.5
C2' C3' H3' 111.7 110.5
O3' C3' H3' 105.3 110.5
C3' O3' HB 109.5 106.9
C6 N1 C2 120.8 120.6
N1 C6 C5 122.7 119.7
N1 C6 H6 118.6 120.1
N1 C2 O2 122.7 119.5
N1 C2 N3 115.1 121.0
C5 C6 H6 118.7 120.1
C6 C5 C4 119.9 119.1
C6 C5 H5 120.0 120.4
O2 C2 N3 122.2 119.5
C2 N3 C4 126.9 120.2
C2 N3 H3 116.5 119.9
C4 N3 H3 116.5 119.9
N3 C4 O4 119.6 120.3
N3 C4 C5 114.5 119.4
O4 C4 C5 125.8 120.3
C4 C5 H5 120.1 120.5

Torsion Angles for UTP

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2A PA O1A O3A 126.4 120.0
O2A PA O1A O5' 233.0 240.0
O1A PA O2A H2A 49.2 180.0
O3A PA O1A O5' 106.6 120.0
O1A PA O3A PB 105.3 45.0
O1A PA O5' C5' 180.3 305.0
O1A PA O2A O3A 232.6 240.0
O1A PA O2A O5' 127.9 120.0
O3A PA O2A O5' 255.4 240.0
O2A PA O3A PB 332.4 285.0
O2A PA O5' C5' 313.6 65.0
O1A PA O3A O2A 133.0 120.0
O1A PA O3A O5' 245.1 240.0
O2A PA O3A O5' 112.1 120.0
O3A PA O2A H2A 176.6 300.0
O3A PA O5' C5' 65.4 185.0
PA O3A PB O1B 12.7 80.0
PA O3A PB O2B 240.3 320.0
PA O3A PB O3B 126.1 200.0
O1A PA O5' O2A 226.6 240.0
O1A PA O5' O3A 114.9 120.0
O2A PA O5' O3A 248.2 240.0
O5' PA O2A H2A 281.2 60.0
O5' PA O3A PB 220.3 165.0
PA O5' C5' C4' 206.0 180.0
PA O5' C5' H5'1 86.2 60.0
PA O5' C5' H5'2 326.0 300.0
H2A O2A PA O3A 176.6 300.0
H2A O2A PA O5' 281.2 60.0
PB O3A PA O5' 220.3 165.0
O1B PB O3A O2B 132.4 120.0
O1B PB O3A O3B 246.6 240.0
O3A PB O1B H1B 340.2 60.0
O2B PB O3A O3B 114.2 120.0
O3A PB O3B PG 182.7 165.0
C4' C5' O5' H5'1 119.9 120.0
C4' C5' O5' H5'2 240.0 240.0
O5' C5' C4' O4' 71.4 66.5
O5' C5' C4' C3' 190.2 181.9
O5' C5' C4' H4' 309.2 304.2
H5'1 C5' O5' H5'2 120.1 120.0
O3A PB O1B O2B 234.2 240.0
O3A PB O1B O3B 109.0 120.0
O2B PB O1B O3B 234.8 240.0
O1B PB O3B PG 303.4 285.0
O3A PB O2B O1B 131.1 120.0
O3A PB O2B O3B 254.4 240.0
O1B PB O2B O3B 123.2 120.0
O2B PB O1B H1B 106.0 180.0
O2B PB O3B PG 73.2 45.0
O3A PB O3B O1B 239.2 240.0
O3A PB O3B O2B 109.5 120.0
O1B PB O3B O2B 230.2 240.0
O3B PB O1B H1B 231.2 300.0
PB O3B PG O1G 159.6 80.0
PB O3B PG O2G 279.8 320.0
PB O3B PG O3G 39.2 200.0
H1B O1B PB O2B 106.0 180.0
H1B O1B PB O3B 231.2 300.0
O1G PG O3B O2G 239.8 120.0
O1G PG O3B O3G 120.4 240.0
O3B PG O1G H1G 156.1 60.0
O2G PG O3B O3G 240.6 120.0
O3B PG O3G H3G 20.6 180.0
O3B PG O1G O2G 113.2 240.0
O3B PG O1G O3G 241.0 120.0
O2G PG O1G O3G 127.8 240.0
O1G PG O3G H3G 262.8 300.0
O3B PG O2G O1G 244.4 120.0
O3B PG O2G O3G 117.1 240.0
O1G PG O2G O3G 232.7 119.9
O2G PG O1G H1G 42.9 180.0
O2G PG O3G H3G 134.2 60.0
O3B PG O3G O1G 117.8 240.0
O3B PG O3G O2G 246.4 120.0
O1G PG O3G O2G 128.6 240.1
O3G PG O1G H1G 275.1 300.0
H1G O1G PG O2G 42.9 180.0
H1G O1G PG O3G 275.1 300.0
O5' C5' C4' H5'1 240.1 240.0
O5' C5' C4' H5'2 120.0 120.0
H5'1 C5' C4' H5'2 239.9 240.0
O4' C4' C5' C3' 241.1 244.6
O4' C4' C5' H4' 122.2 122.2
C5' C4' O4' C1' 141.7 159.5
C3' C4' C5' H4' 241.0 237.6
C5' C4' C3' C2' 247.9 217.3
C5' C4' C3' O3' 127.4 98.5
C5' C4' C3' H3' 9.4 335.9
O5' C5' H5'1 C4' 120.2 120.0
O5' C5' H5'1 H5'2 240.1 240.0
C4' C5' H5'1 H5'2 119.9 120.0
H5'1 C5' C4' O4' 191.2 186.5
H5'1 C5' C4' C3' 310.1 301.9
H5'1 C5' C4' H4' 69.1 64.3
O5' C5' H5'2 C4' 239.7 240.1
O5' C5' H5'2 H5'1 119.9 120.1
C4' C5' H5'2 H5'1 240.1 240.0
H5'2 C5' C4' O4' 311.4 306.5
H5'2 C5' C4' C3' 70.2 61.9
H5'2 C5' C4' H4' 189.2 184.3
O4' C4' C5' H5'1 191.2 186.5
O4' C4' C5' H5'2 311.4 306.5
C5' C4' O4' C3' 123.4 119.1
C5' C4' O4' H4' 242.6 237.8
C3' C4' O4' H4' 119.1 118.6
O4' C4' C3' C2' 8.3 336.2
O4' C4' C3' O3' 247.9 217.5
O4' C4' C3' H3' 129.8 94.9
C4' O4' C1' C2' 322.9 319.5
C4' O4' C1' N1 201.6 200.7
C4' O4' C1' H1' 83.7 78.4
C3' C4' C5' H5'1 310.1 301.9
C3' C4' C5' H5'2 70.2 61.9
C5' C4' C3' O4' 239.5 241.1
C5' C4' C3' H4' 117.3 122.4
O4' C4' C3' H4' 237.8 241.3
C3' C4' O4' C1' 18.2 40.4
C1' C2' C3' C4' 330.9 359.9
O2' C2' C3' C4' 211.1 241.1
C4' C3' C2' H2' 94.2 118.6
C2' C3' C4' O3' 120.4 118.8
C2' C3' C4' H3' 238.5 241.4
O3' C3' C4' H3' 118.1 122.6
C4' C3' O3' HB 141.0 178.1
H4' C4' C5' H5'1 69.1 64.3
H4' C4' C5' H5'2 189.2 184.3
C5' C4' H4' O4' 119.5 122.3
C5' C4' H4' C3' 237.5 237.4
O4' C4' H4' C3' 117.9 115.2
H4' C4' O4' C1' 259.1 281.7
H4' C4' C3' C2' 130.6 94.9
H4' C4' C3' O3' 10.1 336.1
H4' C4' C3' H3' 252.1 213.5
C1' O4' C4' C3' 18.2 40.4
C1' O4' C4' H4' 259.1 281.7
C2' C1' O4' N1 121.3 118.8
C2' C1' O4' H1' 239.2 241.1
O4' C1' C2' O2' 161.8 142.7
O4' C1' C2' C3' 40.8 24.0
O4' C1' C2' H2' 278.7 265.4
N1 C1' O4' H1' 117.9 122.3
O4' C1' N1 C6 49.8 230.4
O4' C1' N1 C2 228.4 50.2
C4' C3' C2' C1' 330.9 359.9
O4' C1' C2' N1 242.1 241.1
O4' C1' C2' H1' 124.0 118.9
N1 C1' C2' H1' 241.9 237.8
C2' C1' N1 C6 295.2 115.0
C2' C1' N1 C2 113.8 294.8
O2' C2' C1' C3' 121.0 118.6
O2' C2' C1' H2' 243.1 237.2
C1' C2' O2' HA 87.2 183.9
C3' C2' C1' H2' 122.1 118.6
C1' C2' C3' O3' 89.6 118.6
C1' C2' C3' H3' 207.8 241.2
O4' C1' N1 C2' 114.6 115.4
O4' C1' N1 H1' 235.8 237.7
C2' C1' N1 H1' 121.2 122.2
N1 C1' C2' O2' 279.8 261.6
N1 C1' C2' C3' 158.8 143.0
N1 C1' C2' H2' 36.7 24.3
C6 N1 C1' C2 181.4 180.2
C1' N1 C6 C5 176.6 180.0
C1' N1 C6 H6 356.6 360.0
C1' N1 C2 O2 4.4 0.2
C1' N1 C2 N3 183.9 179.8
O4' C1' H1' C2' 243.3 244.6
O4' C1' H1' N1 120.0 122.4
C2' C1' H1' N1 236.7 237.8
H1' C1' C2' O2' 37.8 23.7
H1' C1' C2' C3' 276.8 265.1
H1' C1' C2' H2' 154.8 146.5
H1' C1' N1 C6 174.0 352.7
H1' C1' N1 C2 352.6 172.5
C4' C3' C2' O2' 211.1 241.1
O2' C2' C1' N1 279.8 261.6
O2' C2' C1' H1' 37.8 23.7
C1' C2' O2' C3' 246.0 245.4
C1' C2' O2' H2' 123.6 122.8
C3' C2' O2' H2' 237.6 237.4
O2' C2' C3' O3' 329.9 359.9
O2' C2' C3' H3' 88.0 122.5
C2' C3' C4' H4' 130.6 94.9
C4' C3' C2' O3' 241.3 241.2
C4' C3' C2' H3' 123.1 118.7
C3' C2' C1' N1 158.8 143.0
C3' C2' C1' H1' 276.8 265.1
C1' C2' C3' O2' 119.7 118.7
C1' C2' C3' H2' 236.7 241.3
O2' C2' C3' H2' 117.0 122.6
C3' C2' O2' HA 201.2 298.5
O3' C3' C2' H3' 241.8 237.4
C2' C3' O3' HB 26.2 63.3
H2' C2' C1' N1 36.7 24.3
H2' C2' C1' H1' 154.8 146.5
C1' C2' H2' O2' 238.5 237.2
C1' C2' H2' C3' 115.8 114.6
O2' C2' H2' C3' 237.3 237.5
H2' C2' O2' HA 323.7 61.1
H2' C2' C3' O3' 212.9 237.3
H2' C2' C3' H3' 331.1 359.9
HA O2' C2' C3' 201.2 298.5
HA O2' C2' H2' 323.7 61.1
O3' C3' C4' H4' 10.1 336.1
C4' C3' O3' C2' 114.8 114.8
C4' C3' O3' H3' 236.6 237.4
O3' C3' C2' H2' 212.9 237.3
C2' C3' O3' H3' 121.8 122.6
H3' C3' C4' H4' 252.1 213.5
C4' C3' H3' C2' 243.2 245.2
C4' C3' H3' O3' 120.8 122.6
H3' C3' C2' H2' 331.1 359.9
C2' C3' H3' O3' 237.6 237.4
H3' C3' O3' HB 264.4 300.7
HB O3' C3' H3' 264.4 300.7
C6 N1 C1' H1' 174.0 352.7
C1' N1 C6 C2 178.6 179.8
C6 N1 C2 O2 183.1 180.0
C6 N1 C2 N3 2.5 359.6
C5 C6 N1 H6 180.0 180.0
N1 C6 C5 C4 359.8 360.0
N1 C6 C5 H5 179.8 180.0
C2 N1 C1' H1' 352.6 172.5
C1' N1 C2 C6 181.4 180.2
C2 N1 C6 C5 358.0 0.2
C2 N1 C6 H6 178.0 180.2
O2 C2 N1 N3 180.6 180.4
N1 C2 N3 C4 358.9 0.4
N1 C2 N3 H3 178.8 180.2
C5 C6 N1 C2 358.0 0.2
N1 C6 C5 H6 180.0 180.0
N3 C4 C5 C6 1.5 0.0
O4 C4 C5 C6 185.1 180.0
C4 C5 C6 H5 180.0 180.0
H6 C6 N1 C2 178.0 180.2
N1 C6 H6 C5 180.0 180.0
H6 C6 C5 C4 179.8 180.0
H6 C6 C5 H5 359.8 0.0
N1 C2 O2 N3 179.4 179.6
O2 C2 N3 C4 178.3 180.0
O2 C2 N3 H3 358.3 359.9
N1 C2 N3 O2 180.6 180.4
C4 N3 C2 H3 180.0 180.1
C2 N3 C4 O4 175.9 179.8
C2 N3 C4 C5 359.2 359.8
C6 C5 C4 N3 1.5 0.0
C2 N3 C4 H3 180.0 179.9
O4 C4 N3 C5 176.7 180.0
N3 C4 C5 H5 181.5 180.0
C2 N3 H3 C4 180.0 180.1
H3 N3 C4 O4 355.9 359.9
H3 N3 C4 C5 179.2 179.9
C6 C5 C4 O4 185.1 180.0
O4 C4 N3 H3 355.9 359.9
N3 C4 O4 C5 183.7 180.0
O4 C4 C5 H5 5.0 0.0
C4 C5 C6 H6 179.8 180.0
C6 C5 C4 H5 180.0 180.0
C5 C4 N3 H3 179.2 179.9
N3 C4 C5 O4 176.4 180.0
H5 C5 C6 H6 359.8 0.0
C6 C5 H5 C4 180.0 180.0