PDB Chemical Component NP

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 NP

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
C1' C2' 1.394 1.383
C1' C6' 1.388 1.382
C1' C1 1.530 1.508
C2' C3' 1.389 1.381
C2' H2' 1.102 1.080
C3' C4' 1.384 1.387
C3' H3' 1.103 1.079
C4' O4' 1.382 1.359
C4' C5' 1.420 1.387
O4' HO4' 0.951 0.967
C5' N5' 1.353 1.480
C5' C6' 1.417 1.382
N5' ON1 1.298 1.217
N5' ON2 1.288 1.218
C6' H6' 1.103 1.080
C1 C2 1.522 1.507
C1 H11 1.115 1.089
C1 H12 1.115 1.090
C2 O2 1.247 1.212
C2 N3 1.334 1.347
N3 C4 1.466 1.464
N3 HN3 1.019 0.970
C4 C5 1.563 1.529
C4 H41 1.115 1.089
C4 H42 1.116 1.091
C5 C6 1.558 1.529
C5 H51 1.114 1.090
C5 H52 1.115 1.089
C6 C7 1.545 1.529
C6 H61 1.115 1.091
C6 H62 1.114 1.090
C7 C8 1.528 1.530
C7 H71 1.115 1.090
C7 H72 1.115 1.090
C8 C9 1.544 1.507
C8 H81 1.116 1.090
C8 H82 1.114 1.089
C9 O3 1.234 1.208
C9 O4 1.242 1.343
O4 HO4 0.950 0.967

Bond Angles for NP

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C2' C1' C6' 118.9 120.1
C2' C1' C1 119.5 119.9
C1' C2' C3' 121.4 120.0
C1' C2' H2' 119.5 120.0
C6' C1' C1 121.6 120.0
C1' C6' C5' 120.7 120.1
C1' C6' H6' 118.6 120.0
C1' C1 C2 106.2 109.5
C1' C1 H11 113.4 109.4
C1' C1 H12 113.4 109.4
C3' C2' H2' 119.2 120.0
C2' C3' C4' 120.6 120.0
C2' C3' H3' 119.9 120.0
C4' C3' H3' 119.5 120.1
C3' C4' O4' 114.0 120.1
C3' C4' C5' 119.2 119.9
O4' C4' C5' 126.8 120.0
C4' O4' HO4' 114.0 106.8
C4' C5' N5' 117.7 120.0
C4' C5' C6' 119.2 119.9
N5' C5' C6' 123.0 120.1
C5' N5' ON1 118.8 120.0
C5' N5' ON2 125.8 120.0
C5' C6' H6' 120.6 119.9
ON1 N5' ON2 114.5 120.0
C2 C1 H11 113.5 109.5
C2 C1 H12 113.4 109.5
C1 C2 O2 85.8 120.0
C1 C2 N3 158.3 120.0
H11 C1 H12 97.0 109.5
O2 C2 N3 72.5 120.0
C2 N3 C4 132.9 120.0
C2 N3 HN3 107.3 120.0
C4 N3 HN3 119.7 120.0
N3 C4 C5 113.3 109.5
N3 C4 H41 110.8 109.5
N3 C4 H42 110.8 109.5
C5 C4 H41 110.8 109.5
C5 C4 H42 110.8 109.4
C4 C5 C6 121.8 109.6
C4 C5 H51 107.8 109.5
C4 C5 H52 107.8 109.4
H41 C4 H42 99.5 109.4
C6 C5 H51 107.8 109.5
C6 C5 H52 107.8 109.5
C5 C6 C7 121.2 109.6
C5 C6 H61 108.1 109.4
C5 C6 H62 108.1 109.5
H51 C5 H52 102.1 109.4
C7 C6 H61 108.0 109.5
C7 C6 H62 108.0 109.5
C6 C7 C8 118.2 109.5
C6 C7 H71 109.1 109.5
C6 C7 H72 109.1 109.5
H61 C6 H62 101.9 109.4
C8 C7 H71 109.0 109.4
C8 C7 H72 109.1 109.5
C7 C8 C9 117.3 109.5
C7 C8 H81 109.4 109.4
C7 C8 H82 109.4 109.5
H71 C7 H72 100.9 109.4
C9 C8 H81 109.4 109.4
C9 C8 H82 109.4 109.5
C8 C9 O3 118.0 120.0
C8 C9 O4 121.9 120.0
H81 C8 H82 100.7 109.5
O3 C9 O4 120.0 119.9
C9 O4 HO4 121.9 120.0

Torsion Angles for NP

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C6' C1' C2' C1 181.7 180.2
C2' C1' C6' C5' 359.8 359.5
C2' C1' C6' H6' 179.7 180.0
C2' C1' C1 C2 298.9 90.0
C2' C1' C1 H11 64.2 330.0
C2' C1' C1 H12 173.7 210.0
C3' C2' C1' H2' 180.0 180.0
C1' C2' C3' C4' 1.2 0.0
C1' C2' C3' H3' 181.2 180.0
C2' C1' C6' C1 178.3 179.8
C6' C1' C2' C3' 359.0 0.2
C6' C1' C2' H2' 179.0 180.2
C6' C1' C1 C2 117.2 269.8
C6' C1' C1 H11 242.5 149.7
C6' C1' C1 H12 352.0 29.7
C4' C5' C6' C1' 1.2 0.5
N5' C5' C6' C1' 183.4 180.3
C5' C6' C1' H6' 180.0 179.4
C2' C1' C1 C6' 181.7 180.2
C1 C1' C2' C3' 177.4 180.0
C1 C1' C2' H2' 357.3 360.0
C1 C1' C6' C5' 181.5 179.7
C1 C1' C6' H6' 1.4 0.3
C2 C1 C1' H11 234.7 120.0
C2 C1 C1' H12 125.2 240.0
C1' C1 C2 O2 141.3 360.0
C1' C1 C2 N3 139.1 180.0
H11 C1 C1' H12 250.5 120.0
C3' C2' C1' C6' 359.0 0.2
C3' C2' C1' C1 177.4 180.0
C1' C2' C3' H2' 180.0 180.0
C4' C3' C2' H3' 180.0 180.0
C2' C3' C4' O4' 178.6 180.0
C2' C3' C4' C5' 359.7 360.0
H2' C2' C1' C6' 179.0 180.2
H2' C2' C1' C1 357.3 360.0
C1' C2' H2' C3' 180.0 180.0
H2' C2' C3' C4' 181.3 180.0
H2' C2' C3' H3' 1.3 0.0
C4' C3' C2' H2' 181.3 180.0
C2' C3' C4' H3' 180.0 180.0
O4' C4' C3' C5' 178.9 180.0
C3' C4' O4' HO4' 180.0 90.0
C3' C4' C5' N5' 177.0 180.0
C3' C4' C5' C6' 359.1 359.7
H3' C3' C2' H2' 1.3 0.0
C2' C3' H3' C4' 180.0 180.0
H3' C3' C4' O4' 358.6 0.0
H3' C3' C4' C5' 179.7 180.0
O4' C4' C3' H3' 358.6 0.0
C3' C4' O4' C5' 181.2 180.0
O4' C4' C5' N5' 358.2 360.0
O4' C4' C5' C6' 180.4 179.7
C1' C6' C5' C4' 1.2 0.5
C5' C4' C3' H3' 179.7 180.0
C3' C4' C5' O4' 178.7 180.0
C5' C4' O4' HO4' 358.8 270.0
N5' C5' C4' C6' 177.8 180.3
C4' C5' N5' ON1 182.3 0.1
C4' C5' N5' ON2 14.3 180.0
C4' C5' C6' H6' 181.2 180.0
HO4' O4' C4' C5' 358.8 270.0
C1' C6' C5' N5' 183.4 180.3
C4' C5' N5' C6' 182.3 179.7
N5' C5' C6' H6' 3.5 359.7
ON1 N5' C5' ON2 168.0 180.1
C5' C6' C1' C1 181.5 179.7
C1' C6' C5' H6' 180.0 180.6
C4' C5' C6' N5' 177.7 180.3
C6' C5' N5' ON1 0.0 180.3
C6' C5' N5' ON2 192.1 0.2
ON1 N5' C5' C6' 0.0 180.3
C5' N5' ON1 ON2 190.7 179.9
ON2 N5' C5' C6' 192.1 0.2
C5' N5' ON2 ON1 168.4 180.1
H6' C6' C1' C1 1.4 0.3
C1' C6' H6' C5' 180.0 179.4
C1' C1 C2 H11 125.3 240.0
C1' C1 C2 H12 234.8 120.0
H11 C1 C2 H12 109.5 239.9
O2 C2 C1 N3 2.3 180.0
C1 C2 N3 C4 183.4 180.0
C1 C2 N3 HN3 3.4 360.0
C1' C1 H11 C2 238.7 120.0
C1' C1 H11 H12 119.3 240.0
C2 C1 H11 H12 240.6 120.1
H11 C1 C2 O2 16.1 120.0
H11 C1 C2 N3 13.8 300.0
C1' C1 H12 C2 121.3 240.0
C1' C1 H12 H11 240.7 120.0
C2 C1 H12 H11 119.4 239.9
H12 C1 C2 O2 266.6 240.0
H12 C1 C2 N3 264.3 60.0
O2 C2 C1 H11 16.1 120.0
O2 C2 C1 H12 266.6 240.0
C1 C2 O2 N3 180.9 180.0
O2 C2 N3 C4 181.0 0.0
O2 C2 N3 HN3 1.0 180.0
N3 C2 C1 H11 13.8 300.0
N3 C2 C1 H12 264.3 60.0
C1 C2 N3 O2 2.4 180.0
C4 N3 C2 HN3 180.0 180.0
C2 N3 C4 C5 75.1 180.0
C2 N3 C4 H41 200.4 59.9
C2 N3 C4 H42 309.9 300.0
C2 N3 C4 HN3 180.0 180.0
C5 C4 N3 H41 234.7 120.1
C5 C4 N3 H42 125.2 240.0
N3 C4 C5 C6 313.2 180.0
N3 C4 C5 H51 78.4 59.9
N3 C4 C5 H52 187.9 300.0
H41 C4 N3 H42 250.5 119.9
C2 N3 HN3 C4 180.0 180.0
HN3 N3 C4 C5 255.1 0.0
HN3 N3 C4 H41 20.4 239.9
HN3 N3 C4 H42 129.9 120.0
C5 C4 N3 HN3 255.1 0.0
N3 C4 C5 H41 125.3 239.9
N3 C4 C5 H42 234.8 120.0
H41 C4 C5 H42 109.5 240.1
C6 C5 C4 H51 234.8 120.0
C6 C5 C4 H52 125.2 239.9
C4 C5 C6 C7 298.7 180.0
C4 C5 C6 H61 63.9 60.0
C4 C5 C6 H62 173.5 300.1
H51 C5 C4 H52 250.5 119.9
H41 C4 N3 HN3 20.4 239.9
N3 C4 H41 C5 233.4 120.1
N3 C4 H41 H42 116.7 240.0
C5 C4 H41 H42 243.3 119.9
H41 C4 C5 C6 187.9 300.0
H41 C4 C5 H51 313.1 180.0
H41 C4 C5 H52 62.7 60.1
H42 C4 N3 HN3 129.9 120.0
N3 C4 H42 C5 126.6 239.9
N3 C4 H42 H41 243.3 120.0
C5 C4 H42 H41 116.7 240.0
H42 C4 C5 C6 78.4 59.9
H42 C4 C5 H51 203.6 299.9
H42 C4 C5 H52 313.2 180.0
C6 C5 C4 H41 187.9 300.0
C6 C5 C4 H42 78.4 59.9
C4 C5 C6 H51 125.3 240.0
C4 C5 C6 H52 234.8 120.0
H51 C5 C6 H52 109.5 240.0
C7 C6 C5 H61 234.8 120.0
C7 C6 C5 H62 125.3 239.9
C5 C6 C7 C8 276.3 180.0
C5 C6 C7 H71 41.6 60.0
C5 C6 C7 H72 151.0 300.0
H61 C6 C5 H62 250.5 119.9
H51 C5 C4 H41 313.1 180.0
H51 C5 C4 H42 203.6 299.9
C4 C5 H51 C6 226.8 120.1
C4 C5 H51 H52 113.4 240.1
C6 C5 H51 H52 246.6 120.0
H51 C5 C6 C7 173.4 300.0
H51 C5 C6 H61 298.6 180.0
H51 C5 C6 H62 48.2 60.1
H52 C5 C4 H41 62.7 60.1
H52 C5 C4 H42 313.2 180.0
C4 C5 H52 C6 133.2 239.9
C4 C5 H52 H51 246.5 119.9
C6 C5 H52 H51 113.4 240.0
H52 C5 C6 C7 64.0 59.9
H52 C5 C6 H61 189.2 299.9
H52 C5 C6 H62 298.7 180.1
C7 C6 C5 H51 173.4 300.0
C7 C6 C5 H52 64.0 59.9
C5 C6 C7 H61 125.2 240.0
C5 C6 C7 H62 234.7 120.1
H61 C6 C7 H62 109.5 240.1
C8 C7 C6 H71 234.7 120.0
C8 C7 C6 H72 125.3 240.0
C6 C7 C8 C9 88.7 180.0
C6 C7 C8 H81 214.0 60.0
C6 C7 C8 H82 323.4 300.1
H71 C7 C6 H72 250.6 120.0
H61 C6 C5 H51 298.6 180.0
H61 C6 C5 H52 189.2 299.9
C5 C6 H61 C7 227.3 120.1
C5 C6 H61 H62 113.7 240.1
C7 C6 H61 H62 246.4 120.0
H61 C6 C7 C8 151.1 300.0
H61 C6 C7 H71 276.3 180.0
H61 C6 C7 H72 25.8 60.0
H62 C6 C5 H51 48.2 60.1
H62 C6 C5 H52 298.7 180.1
C5 C6 H62 C7 132.7 239.9
C5 C6 H62 H61 246.3 119.9
C7 C6 H62 H61 113.6 240.0
H62 C6 C7 C8 41.6 59.9
H62 C6 C7 H71 166.9 299.9
H62 C6 C7 H72 276.3 179.9
C8 C7 C6 H61 151.1 300.0
C8 C7 C6 H62 41.6 59.9
C6 C7 C8 H71 125.3 240.0
C6 C7 C8 H72 234.7 120.1
H71 C7 C8 H72 109.4 240.1
C9 C8 C7 H81 234.7 119.9
C9 C8 C7 H82 125.3 239.9
C7 C8 C9 O3 135.1 0.1
C7 C8 C9 O4 312.1 180.0
H81 C8 C7 H82 250.6 120.0
H71 C7 C6 H61 276.3 180.0
H71 C7 C6 H62 166.9 299.9
C6 C7 H71 C8 229.6 120.0
C6 C7 H71 H72 114.8 240.0
C8 C7 H71 H72 245.2 119.9
H71 C7 C8 C9 323.4 300.0
H71 C7 C8 H81 88.6 180.1
H71 C7 C8 H82 198.1 60.1
H72 C7 C6 H61 25.8 60.0
H72 C7 C6 H62 276.3 179.9
C6 C7 H72 C8 130.4 239.9
C6 C7 H72 H71 245.1 120.0
C8 C7 H72 H71 114.7 240.1
H72 C7 C8 C9 214.0 59.9
H72 C7 C8 H81 339.3 300.0
H72 C7 C8 H82 88.7 180.0
C9 C8 C7 H71 323.4 300.0
C9 C8 C7 H72 214.0 59.9
C7 C8 C9 H81 125.3 240.1
C7 C8 C9 H82 234.7 120.1
H81 C8 C9 H82 109.5 240.0
O3 C9 C8 O4 183.0 180.0
C8 C9 O4 HO4 180.0 180.1
H81 C8 C7 H71 88.6 180.1
H81 C8 C7 H72 339.3 300.0
C7 C8 H81 C9 230.3 120.0
C7 C8 H81 H82 115.1 240.0
C9 C8 H81 H82 244.9 120.0
H81 C8 C9 O3 9.9 120.0
H81 C8 C9 O4 186.8 299.9
H82 C8 C7 H71 198.1 60.1
H82 C8 C7 H72 88.7 180.0
C7 C8 H82 C9 129.7 239.9
C7 C8 H82 H81 244.9 119.9
C9 C8 H82 H81 115.1 240.0
H82 C8 C9 O3 260.4 240.0
H82 C8 C9 O4 77.4 59.9
O3 C9 C8 H81 9.9 120.0
O3 C9 C8 H82 260.4 240.0
C8 C9 O3 O4 177.0 180.0
O3 C9 O4 HO4 356.9 0.0
O4 C9 C8 H81 186.8 299.9
O4 C9 C8 H82 77.4 59.9
C8 C9 O4 O3 183.1 180.0