PDB Chemical Component NDU

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 NDU

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.483 1.480
P OP2 1.492 1.610
P OP3 1.488 1.610
P O5' 1.590 1.610
O5' C5' 1.402 1.429
C5' C4' 1.516 1.530
C4' C3' 1.525 1.545
C4' O4' 1.441 1.445
C3' O3' 1.420 1.429
C3' C2' 1.519 1.545
C2' C1' 1.537 1.544
C1' O4' 1.452 1.444
C1' N1 1.496 1.465
N1 C2 1.453 1.343
N1 C6 1.617 1.464
C2 O2 1.196 1.215
C2 N3 1.406 1.343
N3 C4 1.421 1.346
C4 O4 1.211 1.212
C4 C5 1.591 1.509
C5 C6 1.636 1.534
C5 N5 1.399 1.464
N5 O51 1.247 1.218
N5 O52 1.251 1.218
OP2 HP2 0.950 0.967
OP3 HP3 0.950 0.967
C5' H51' 1.100 1.090
C5' H52' 1.100 1.091
C4' H4' 1.100 1.089
C3' H3' 1.100 1.089
O3' HA 0.950 0.968
C2' H21' 1.100 1.090
C2' H22' 1.099 1.090
C1' H1' 1.100 1.090
C6 H611 1.100 1.090
C6 H612 1.100 1.090
N3 H3 1.000 0.970
C5 H5 1.100 1.090

Bond Angles for NDU

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 112.8 109.4
OP1 P OP3 108.2 109.5
OP1 P O5' 112.5 109.5
OP2 P OP3 119.0 109.5
OP2 P O5' 98.2 109.5
P OP2 HP2 109.5 114.0
OP3 P O5' 105.6 109.5
P OP3 HP3 109.5 114.0
P O5' C5' 133.4 123.0
O5' C5' C4' 113.2 109.4
O5' C5' H51' 108.2 109.4
O5' C5' H52' 107.4 109.5
C5' C4' C3' 121.4 110.4
C5' C4' O4' 111.8 110.3
C4' C5' H51' 108.2 109.5
C4' C5' H52' 107.4 109.5
C5' C4' H4' 97.0 110.4
C3' C4' O4' 102.8 104.8
C4' C3' O3' 113.5 110.5
C4' C3' C2' 104.7 104.0
C3' C4' H4' 107.1 110.4
C4' C3' H3' 111.0 110.5
C4' O4' C1' 111.5 105.2
O4' C4' H4' 117.6 110.4
O3' C3' C2' 112.1 110.5
O3' C3' H3' 103.3 110.5
C3' O3' HA 109.5 114.0
C3' C2' C1' 101.5 104.1
C2' C3' H3' 112.4 110.6
C3' C2' H21' 112.2 110.5
C3' C2' H22' 113.9 110.5
C2' C1' O4' 106.1 104.8
C2' C1' N1 109.8 110.4
C1' C2' H21' 112.2 110.5
C1' C2' H22' 113.9 110.5
C2' C1' H1' 119.1 110.4
O4' C1' N1 124.9 110.3
O4' C1' H1' 101.0 110.4
C1' N1 C2 126.0 119.6
C1' N1 C6 105.7 119.5
N1 C1' H1' 96.5 110.4
C2 N1 C6 123.6 120.9
N1 C2 O2 123.6 119.1
N1 C2 N3 118.4 121.6
N1 C6 C5 111.7 109.3
N1 C6 H611 108.7 109.5
N1 C6 H612 108.2 109.5
O2 C2 N3 118.0 119.2
C2 N3 C4 127.6 121.0
C2 N3 H3 116.2 119.6
N3 C4 O4 122.5 120.1
N3 C4 C5 117.0 119.9
C4 N3 H3 116.2 119.5
O4 C4 C5 120.6 120.0
C4 C5 C6 116.8 109.1
C4 C5 N5 124.1 109.5
C4 C5 H5 87.2 109.5
C6 C5 N5 117.7 109.7
C5 C6 H611 108.7 109.6
C5 C6 H612 108.2 109.4
C6 C5 H5 112.5 109.4
C5 N5 O51 122.7 120.0
C5 N5 O52 127.0 120.0
N5 C5 H5 83.6 109.6
O51 N5 O52 110.3 119.9
H51' C5' H52' 112.4 109.5
H21' C2' H22' 103.5 110.5
H611 C6 H612 111.3 109.5

Torsion Angles for NDU

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 OP3 133.8 240.0
OP2 P OP1 O5' 250.0 120.0
OP1 P OP2 HP2 261.5 60.0
OP3 P OP1 O5' 116.2 240.0
OP1 P OP3 HP3 47.8 180.0
OP1 P O5' C5' 172.4 305.0
OP1 P OP2 OP3 231.7 120.0
OP1 P OP2 O5' 118.7 240.0
OP3 P OP2 O5' 247.0 120.0
OP2 P OP3 HP3 277.3 300.0
OP2 P O5' C5' 291.3 185.0
OP1 P OP3 OP2 130.4 240.0
OP1 P OP3 O5' 239.3 120.0
OP2 P OP3 O5' 108.9 240.0
OP3 P OP2 HP2 29.9 300.0
OP3 P O5' C5' 54.6 65.0
OP1 P O5' OP2 241.1 120.0
OP1 P O5' OP3 117.8 240.0
OP2 P O5' OP3 236.7 120.0
O5' P OP2 HP2 142.8 180.0
O5' P OP3 HP3 168.4 60.0
P O5' C5' C4' 154.2 180.0
P O5' C5' H51' 274.2 300.0
P O5' C5' H52' 35.9 60.0
O5' C5' C4' C3' 286.1 185.0
O5' C5' C4' O4' 164.6 69.6
C4' C5' O5' H51' 240.0 240.0
C4' C5' O5' H52' 118.4 120.0
O5' C5' C4' H4' 41.1 307.3
H51' C5' O5' H52' 238.4 240.0
O5' C5' C4' H51' 120.0 120.0
O5' C5' C4' H52' 241.6 240.0
C3' C4' C5' O4' 121.6 115.3
C5' C4' C3' O3' 146.4 98.6
C5' C4' C3' C2' 269.0 217.2
C3' C4' C5' H4' 245.1 237.7
C5' C4' C3' H3' 30.5 336.0
C5' C4' O4' C1' 111.7 159.3
O4' C4' C5' H4' 123.5 122.4
H51' C5' C4' H52' 121.6 120.0
C5' C4' C3' O4' 234.2 241.2
C3' C4' C5' H51' 166.1 65.0
C3' C4' C5' H52' 44.5 305.0
C5' C4' C3' H4' 109.7 122.3
C3' C4' O4' C1' 339.8 40.5
O4' C4' C3' H4' 235.5 241.1
O3' C3' C4' C2' 237.4 241.4
O3' C3' C4' H3' 115.9 122.6
C4' C3' O3' HA 135.1 180.0
C4' C3' C2' C1' 324.5 0.0
C2' C3' C4' H3' 238.5 241.2
C4' C3' C2' H21' 84.5 118.7
C4' C3' C2' H22' 201.7 241.3
C5' C4' O4' C3' 131.8 118.8
O4' C4' C5' H51' 44.5 309.7
O4' C4' C5' H52' 282.9 189.6
C5' C4' O4' H4' 249.1 237.7
O4' C4' C3' O3' 272.2 217.4
O4' C4' C3' C2' 34.8 336.0
C3' C4' O4' H4' 117.3 118.9
O4' C4' C3' H3' 156.3 94.8
C2' C1' O4' C4' 357.9 319.5
C4' O4' C1' N1 228.8 200.7
C4' O4' C1' H1' 122.8 78.3
O3' C3' C4' O4' 272.2 217.4
C4' C3' O3' C2' 118.4 114.6
O3' C3' C4' H4' 36.7 336.3
C4' C3' O3' H3' 239.7 237.4
O3' C3' C2' C1' 88.0 118.6
C2' C3' O3' H3' 121.3 122.8
O3' C3' C2' H21' 208.0 237.3
O3' C3' C2' H22' 325.2 359.9
C2' C3' C4' O4' 34.8 336.0
C4' C3' C2' O3' 236.5 241.4
C2' C3' C4' H4' 159.3 94.9
C4' C3' C2' H3' 120.6 118.7
O3' C3' C2' H3' 244.1 237.3
C2' C3' O3' HA 16.8 65.4
C3' C2' C1' O4' 23.4 24.0
C3' C2' C1' N1 160.8 142.8
C1' C2' C3' H21' 240.0 241.3
C1' C2' C3' H22' 122.8 118.7
C3' C2' C1' H1' 270.5 265.1
H21' C2' C3' H22' 242.8 237.4
C4' O4' C1' C2' 357.9 319.5
C1' C2' C3' H3' 203.9 241.3
C3' C2' C1' H21' 120.0 118.7
C3' C2' C1' H22' 237.2 241.3
O4' C1' C2' N1 222.5 241.2
O4' C1' C2' H1' 112.8 118.9
C2' C1' N1 C2 85.5 295.0
C2' C1' N1 C6 241.9 114.7
N1 C1' C2' H1' 250.3 237.7
H21' C2' C1' H22' 117.2 122.7
C1' O4' C4' H4' 222.6 281.6
C2' C1' O4' N1 129.1 118.8
O4' C1' C2' H21' 263.3 265.3
O4' C1' C2' H22' 146.2 142.7
C2' C1' O4' H1' 235.1 241.1
O4' C1' N1 C2 213.1 50.4
O4' C1' N1 C6 9.5 230.1
N1 C1' O4' H1' 106.0 122.3
C2' C1' N1 O4' 232.4 244.6
N1 C1' C2' H21' 40.8 24.1
N1 C1' C2' H22' 283.6 261.4
C2' C1' N1 H1' 124.1 122.3
O4' C1' N1 H1' 251.7 237.7
C2 N1 C1' C6 203.7 180.3
C1' N1 C2 O2 323.1 5.7
C1' N1 C2 N3 142.9 185.7
C1' N1 C6 C5 214.5 144.0
C1' N1 C6 H611 334.5 264.2
C1' N1 C6 H612 95.5 24.2
C1' N1 C2 C6 152.3 179.7
C2 N1 C1' H1' 321.4 172.7
C2 N1 C6 C5 11.5 323.7
C2 N1 C6 H611 131.5 83.8
C2 N1 C6 H612 252.5 203.9
O2 C2 N1 N3 180.2 180.0
N1 C2 N3 C4 15.5 12.0
N1 C2 N3 H3 195.5 192.0
C1' N1 C6 C2 203.0 180.3
C6 N1 C1' H1' 117.7 352.4
C6 N1 C2 O2 170.7 186.0
C6 N1 C2 N3 350.5 6.0
C4 C5 C6 N1 342.5 47.0
N1 C6 C5 N5 175.7 287.1
C5 C6 N1 H611 240.0 239.9
C5 C6 N1 H612 119.0 119.8
N1 C6 C5 H5 81.1 166.8
H611 C6 N1 H612 239.0 239.9
O2 C2 N1 C6 170.7 186.0
N1 C2 O2 N3 179.8 180.0
O2 C2 N3 C4 195.3 192.0
O2 C2 N3 H3 15.3 12.0
N3 C2 N1 C6 350.5 6.0
N1 C2 N3 O2 180.2 180.0
C2 N3 C4 O4 157.8 184.4
C2 N3 C4 C5 337.4 4.5
C4 N3 C2 H3 180.0 180.0
C2 N3 C4 H3 180.0 180.0
O4 C4 N3 C5 180.4 180.0
N3 C4 C5 C6 22.9 325.6
N3 C4 C5 N5 188.8 85.7
N3 C4 C5 H5 269.1 205.8
N3 C4 O4 C5 179.6 180.0
O4 C4 N3 H3 337.8 4.4
O4 C4 C5 C6 202.5 145.6
O4 C4 C5 N5 8.4 265.7
O4 C4 C5 H5 88.7 25.9
N1 C6 C5 C4 342.5 47.0
N3 C4 C5 O4 180.4 180.0
C5 C4 N3 H3 157.4 184.5
C6 C5 C4 N5 194.1 239.9
C4 C5 C6 H611 222.5 287.0
C4 C5 C6 H612 101.5 166.9
C6 C5 C4 H5 113.8 119.7
C4 C5 N5 O51 13.0 120.0
C4 C5 N5 O52 193.2 299.9
N5 C5 C4 H5 279.7 239.8
N1 C6 C5 H611 120.0 120.0
N1 C6 C5 H612 241.0 240.1
C4 C5 C6 N5 166.8 120.0
C4 C5 C6 H5 261.4 240.2
C6 C5 N5 O51 178.8 239.8
C6 C5 N5 O52 358.9 59.7
N5 C5 C6 H5 94.6 120.2
H611 C6 C5 H612 121.0 120.1
C4 C5 N5 C6 194.2 240.3
C4 C5 N5 H5 82.2 120.1
N5 C5 C6 H611 55.7 167.0
N5 C5 C6 H612 294.7 46.9
C6 C5 N5 H5 247.9 239.8
O51 N5 C5 O52 179.8 180.1
C5 N5 O51 O52 180.1 179.9
O51 N5 C5 H5 290.8 359.9
C5 N5 O52 O51 179.9 180.1
O52 N5 C5 H5 111.0 179.8
HP2 OP2 P OP3 29.9 300.0
HP2 OP2 P O5' 142.8 180.0
HP3 OP3 P O5' 168.4 60.0
O5' C5' H51' C4' 236.9 240.0
O5' C5' H51' H52' 118.5 120.0
H51' C5' C4' C3' 166.1 65.0
H51' C5' C4' O4' 44.5 309.7
C4' C5' H51' H52' 241.6 240.0
H51' C5' C4' H4' 281.0 187.3
O5' C5' H52' C4' 122.1 120.0
O5' C5' H52' H51' 241.0 240.0
H52' C5' C4' C3' 44.5 305.0
H52' C5' C4' O4' 282.9 189.6
C4' C5' H52' H51' 118.9 120.1
H52' C5' C4' H4' 159.4 67.3
C5' C4' H4' C3' 234.0 237.7
C5' C4' H4' O4' 119.1 122.3
H4' C4' C5' H51' 281.0 187.3
H4' C4' C5' H52' 159.4 67.3
C3' C4' H4' O4' 245.1 244.6
H4' C4' C3' O3' 36.7 336.3
H4' C4' C3' C2' 159.3 94.9
H4' C4' C3' H3' 280.8 213.7
H4' C4' O4' C1' 222.6 281.6
H3' C3' C4' O4' 156.3 94.8
C4' C3' H3' O3' 122.0 122.6
C4' C3' H3' C2' 243.1 245.3
H3' C3' C4' H4' 280.8 213.7
O3' C3' H3' C2' 121.1 122.7
H3' C3' O3' HA 255.5 302.7
H3' C3' C2' C1' 203.9 241.3
H3' C3' C2' H21' 323.9 360.0
H3' C3' C2' H22' 81.1 122.6
HA O3' C3' C2' 16.8 65.4
HA O3' C3' H3' 255.5 302.7
C3' C2' H21' C1' 246.4 245.3
H21' C2' C3' H3' 323.9 360.0
C3' C2' H21' H22' 123.2 122.6
H21' C2' C1' O4' 263.3 265.3
H21' C2' C1' N1 40.8 24.1
C1' C2' H21' H22' 236.8 237.3
H21' C2' C1' H1' 150.5 146.4
C3' C2' H22' C1' 115.7 114.7
H22' C2' C3' H3' 81.1 122.6
C3' C2' H22' H21' 237.9 237.4
H22' C2' C1' O4' 146.2 142.7
H22' C2' C1' N1 283.6 261.4
C1' C2' H22' H21' 122.1 122.7
H22' C2' C1' H1' 33.3 23.8
C2' C1' H1' O4' 115.5 115.4
C2' C1' H1' N1 243.1 237.7
H1' C1' C2' H21' 150.5 146.4
H1' C1' C2' H22' 33.3 23.8
O4' C1' H1' N1 127.5 122.3
H1' C1' N1 C2 321.4 172.7
H1' C1' N1 C6 117.7 352.4
N1 C6 H611 C5 238.1 240.1
N1 C6 H611 H612 119.1 120.1
H611 C6 C5 N5 55.7 167.0
C5 C6 H611 H612 241.0 240.0
H611 C6 C5 H5 321.1 46.8
N1 C6 H612 C5 121.2 119.8
N1 C6 H612 H611 240.6 239.9
H612 C6 C5 N5 294.7 46.9
C5 C6 H612 H611 119.4 120.2
H612 C6 C5 H5 200.1 286.7
C2 N3 H3 C4 180.0 180.0
H3 N3 C4 O4 337.8 4.4
H3 N3 C4 C5 157.4 184.5
C4 C5 H5 C6 117.9 119.5
C4 C5 H5 N5 235.2 239.9
C6 C5 H5 N5 117.3 120.4
H5 C5 C6 H611 321.1 46.8
H5 C5 C6 H612 200.1 286.7
H5 C5 N5 O51 290.8 359.9
H5 C5 N5 O52 111.0 179.8