PDB Chemical Component DDY

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 DDY

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
C4 C5 1.401 1.410
C4 N4 1.332 1.376
C4 N3 1.406 1.327
PB O3B 1.596 1.480
PB O1B 1.476 1.610
PB O2B 1.474 1.610
PB O3A 1.631 1.610
PA O3A 1.623 1.610
PA O1A 1.467 1.480
PA O2A 1.478 1.610
PA O5' 1.605 1.610
C2 O2 1.232 1.221
C2 N1 1.416 1.345
C2 N3 1.405 1.331
C5 C6 1.403 1.354
C5 H5 1.079 1.080
O1B H1B 0.950 0.967
O2B H2B 0.950 0.967
O2A H2A 0.950 0.967
O5' C5' 1.430 1.429
C5' C4' 1.534 1.530
C5' H5'1 1.100 1.089
C5' H5'2 1.100 1.091
C4' O4' 1.456 1.444
C4' C3' 1.335 1.550
C4' H4' 1.100 1.090
O4' C1' 1.455 1.438
C3' C2' 1.319 1.549
C3' H3'1 1.100 1.090
C3' H3'2 1.100 1.090
C2' C1' 1.327 1.541
C2' H2'1 1.100 1.090
C2' H2'2 1.100 1.090
C1' N1 1.497 1.465
C1' H1' 1.101 1.089
N1 C6 1.416 1.363
C6 H6 1.080 1.080
N4 HN41 1.000 0.970
N4 HN42 1.000 0.970

Bond Angles for DDY

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C5 C4 N4 120.1 120.2
C5 C4 N3 120.4 119.6
C4 C5 C6 119.7 119.0
C4 C5 H5 120.1 120.5
N4 C4 N3 119.5 120.2
C4 N4 HN41 120.0 120.0
C4 N4 HN42 120.0 120.0
C4 N3 C2 120.4 120.7
O3B PB O1B 107.2 109.5
O3B PB O2B 108.8 109.5
O3B PB O3A 104.2 109.5
O1B PB O2B 117.8 109.5
O1B PB O3A 110.8 109.5
PB O1B H1B 109.5 114.0
O2B PB O3A 107.2 109.5
PB O2B H2B 109.5 114.0
PB O3A PA 125.6 134.0
O3A PA O1A 111.7 109.5
O3A PA O2A 107.9 109.4
O3A PA O5' 100.4 109.5
O1A PA O2A 117.6 109.4
O1A PA O5' 109.6 109.5
O2A PA O5' 108.2 109.5
PA O2A H2A 109.5 114.0
PA O5' C5' 122.5 123.0
O2 C2 N1 120.5 119.4
O2 C2 N3 119.9 119.4
N1 C2 N3 119.6 121.1
C2 N1 C1' 120.0 119.9
C2 N1 C6 119.5 120.3
C6 C5 H5 120.1 120.5
C5 C6 N1 120.4 119.2
C5 C6 H6 119.8 120.4
O5' C5' C4' 108.8 109.4
O5' C5' H5'1 109.7 109.5
O5' C5' H5'2 109.7 109.5
C4' C5' H5'1 109.7 109.5
C4' C5' H5'2 109.7 109.4
C5' C4' O4' 111.6 110.6
C5' C4' C3' 109.0 110.6
C5' C4' H4' 106.6 110.6
H5'1 C5' H5'2 109.3 109.5
O4' C4' C3' 103.3 103.5
O4' C4' H4' 112.0 110.6
C4' O4' C1' 104.6 107.0
C3' C4' H4' 114.4 110.7
C4' C3' C2' 111.9 102.1
C4' C3' H3'1 108.7 110.9
C4' C3' H3'2 108.7 110.9
O4' C1' C2' 103.8 107.3
O4' C1' N1 113.4 109.9
O4' C1' H1' 112.5 109.9
C2' C3' H3'1 108.6 110.9
C2' C3' H3'2 108.7 110.8
C3' C2' C1' 111.5 104.2
C3' C2' H2'1 108.8 110.5
C3' C2' H2'2 108.8 110.5
H3'1 C3' H3'2 110.3 110.8
C1' C2' H2'1 108.8 110.5
C1' C2' H2'2 108.8 110.5
C2' C1' N1 114.3 109.9
C2' C1' H1' 111.5 109.9
H2'1 C2' H2'2 110.1 110.6
N1 C1' H1' 101.6 110.0
C1' N1 C6 120.4 119.8
N1 C6 H6 119.8 120.4
HN41 N4 HN42 120.0 120.0

Torsion Angles for DDY

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
N4 C4 C5 N3 179.3 180.3
C5 C4 N4 HN41 180.7 360.0
C5 C4 N4 HN42 0.8 180.0
C5 C4 N3 C2 0.2 0.0
C6 C5 C4 H5 180.0 180.0
C4 C5 C6 N1 359.8 0.0
C4 C5 C6 H6 179.9 180.0
C5 C4 N4 N3 180.7 179.7
N4 C4 C5 C6 179.0 180.0
N4 C4 C5 H5 359.0 360.0
N4 C4 N3 C2 180.9 179.7
HN41 N4 C4 HN42 180.0 180.0
C5 C4 N3 N4 179.3 180.3
N3 C4 C5 C6 359.8 359.7
N3 C4 C5 H5 179.8 179.7
N3 C4 N4 HN41 0.0 180.3
N3 C4 N4 HN42 180.0 0.3
O2 C2 N3 C4 181.0 179.8
N1 C2 N3 C4 0.3 0.6
O1B PB O3B O2B 231.6 240.0
O1B PB O3B O3A 117.5 120.0
O3B PB O1B H1B 0.0 60.0
O2B PB O3B O3A 245.9 240.0
O3B PB O2B H2B 360.0 180.0
O3B PB O3A PA 47.8 320.0
O3B PB O1B O2B 123.0 120.0
O3B PB O1B O3A 246.9 240.0
O2B PB O1B O3A 123.9 120.0
O1B PB O2B H2B 122.2 300.0
O1B PB O3A PA 292.9 200.1
O3B PB O2B O1B 237.8 240.0
O3B PB O2B O3A 112.2 120.0
O1B PB O2B O3A 234.3 240.0
O2B PB O1B H1B 237.0 300.0
O2B PB O3A PA 163.1 80.1
O3B PB O3A O1B 115.0 120.0
O3B PB O3A O2B 244.8 240.0
O1B PB O3A O2B 129.8 120.0
O3A PB O1B H1B 113.1 180.0
O3A PB O2B H2B 247.8 60.0
PB O3A PA O1A 43.2 44.9
PB O3A PA O2A 272.4 285.0
PB O3A PA O5' 159.3 165.0
O1A PA O3A O2A 130.8 119.9
O1A PA O3A O5' 243.9 240.0
O2A PA O3A O5' 113.1 120.0
O3A PA O2A H2A 127.4 300.0
O3A PA O5' C5' 238.3 184.9
O3A PA O1A O2A 234.4 240.0
O3A PA O1A O5' 110.3 120.0
O2A PA O1A O5' 235.9 240.0
O1A PA O2A H2A 0.0 180.0
O1A PA O5' C5' 356.0 305.0
O3A PA O2A O1A 127.4 120.0
O3A PA O2A O5' 252.3 240.0
O1A PA O2A O5' 124.8 120.0
O2A PA O5' C5' 125.4 65.0
O3A PA O5' O1A 242.3 240.0
O3A PA O5' O2A 112.9 120.0
O1A PA O5' O2A 230.5 240.0
O5' PA O2A H2A 235.2 60.0
PA O5' C5' C4' 199.2 180.0
PA O5' C5' H5'1 319.2 300.0
PA O5' C5' H5'2 79.2 60.1
C4 N3 C2 O2 181.0 179.8
N1 C2 O2 N3 180.7 179.2
O2 C2 N1 C1' 354.3 360.0
O2 C2 N1 C6 178.6 179.9
C4 N3 C2 N1 0.3 0.6
O2 C2 N1 N3 179.3 180.8
C5 C6 N1 C2 0.6 0.6
O4' C1' N1 C2 201.6 53.5
C2' C1' N1 C2 82.8 295.7
C2 N1 C1' H1' 322.6 174.6
C1' N1 C2 C6 175.7 180.0
C2 N1 C6 H6 180.6 180.6
O2 C2 N3 N1 180.7 179.2
N3 C2 N1 C1' 175.0 179.2
N3 C2 N1 C6 359.3 359.1
C6 C5 C4 N4 179.0 180.0
C6 C5 C4 N3 359.8 359.7
C4 C5 C6 H5 180.0 180.0
C2 N1 C6 C5 0.6 0.6
C1' N1 C6 C5 184.9 180.5
N1 C6 C5 H6 180.0 180.1
H5 C5 C4 N4 359.0 360.0
H5 C5 C4 N3 179.8 179.7
C4 C5 H5 C6 180.0 180.0
H5 C5 C6 N1 179.8 180.0
H5 C5 C6 H6 359.9 360.0
H1B O1B PB O2B 237.0 300.0
H1B O1B PB O3A 113.1 180.0
H2B O2B PB O3A 247.8 60.0
H2A O2A PA O5' 235.2 60.0
C4' C5' O5' H5'1 240.0 240.0
C4' C5' O5' H5'2 120.0 119.9
O5' C5' C4' O4' 302.1 66.5
O5' C5' C4' C3' 55.6 180.5
O5' C5' C4' H4' 179.5 303.6
H5'1 C5' O5' H5'2 240.0 240.0
O5' C5' C4' H5'1 120.0 120.1
O5' C5' C4' H5'2 240.0 240.0
H5'1 C5' C4' H5'2 120.0 120.0
O4' C4' C5' C3' 246.5 245.9
O4' C4' C5' H4' 122.5 122.9
C5' C4' O4' C1' 137.4 158.6
C3' C4' C5' H4' 236.0 236.9
C5' C4' C3' C2' 228.5 204.5
C5' C4' C3' H3'1 348.5 322.7
C5' C4' C3' H3'2 108.5 86.3
O5' C5' H5'1 C4' 240.6 240.0
O5' C5' H5'1 H5'2 120.3 120.0
C4' C5' H5'1 H5'2 239.8 240.1
H5'1 C5' C4' O4' 182.1 306.4
H5'1 C5' C4' C3' 295.6 60.5
H5'1 C5' C4' H4' 59.5 183.5
O5' C5' H5'2 C4' 119.4 119.9
O5' C5' H5'2 H5'1 239.7 239.9
C4' C5' H5'2 H5'1 120.3 120.0
H5'2 C5' C4' O4' 62.1 186.5
H5'2 C5' C4' C3' 175.6 300.5
H5'2 C5' C4' H4' 299.5 63.6
O4' C4' C5' H5'1 182.1 306.4
O4' C4' C5' H5'2 62.1 186.5
C5' C4' O4' C3' 117.0 118.5
C5' C4' O4' H4' 240.6 237.1
C3' C4' O4' H4' 123.6 118.6
O4' C4' C3' C2' 347.2 323.0
O4' C4' C3' H3'1 107.2 81.2
O4' C4' C3' H3'2 227.2 204.8
C4' O4' C1' C2' 339.0 333.5
C4' O4' C1' N1 214.4 214.1
C4' O4' C1' H1' 99.7 92.9
C3' C4' C5' H5'1 295.6 60.5
C3' C4' C5' H5'2 175.6 300.5
C5' C4' C3' O4' 241.2 241.5
C5' C4' C3' H4' 119.2 123.0
O4' C4' C3' H4' 238.0 241.5
C3' C4' O4' C1' 20.4 40.1
C2' C3' C4' H3'1 240.0 241.8
C2' C3' C4' H3'2 120.0 118.1
C4' C3' C2' C1' 359.1 20.9
C4' C3' C2' H2'1 119.2 139.6
C4' C3' C2' H2'2 239.1 262.3
H3'1 C3' C4' H3'2 240.0 236.4
H4' C4' C5' H5'1 59.5 183.5
H4' C4' C5' H5'2 299.5 63.6
C5' C4' H4' O4' 122.3 122.9
C5' C4' H4' C3' 239.4 237.0
O4' C4' H4' C3' 117.2 114.1
H4' C4' O4' C1' 256.8 281.5
H4' C4' C3' C2' 109.2 81.5
H4' C4' C3' H3'1 229.2 199.7
H4' C4' C3' H3'2 349.2 323.4
C2 N1 C1' O4' 201.6 53.5
C1' O4' C4' C3' 20.4 40.1
C1' O4' C4' H4' 256.8 281.5
C3' C2' C1' O4' 14.1 2.0
O4' C1' C2' H2'1 254.1 243.4
O4' C1' C2' H2'2 134.1 120.7
C2' C1' O4' N1 124.6 119.4
C2' C1' O4' H1' 239.3 240.6
N1 C1' O4' H1' 114.6 121.2
O4' C1' N1 C6 17.2 233.6
C2' C3' C4' H4' 109.2 81.5
C4' C3' C2' H3'1 120.0 118.3
C4' C3' C2' H3'2 240.0 241.8
O4' C1' C2' C3' 14.1 2.0
H3'1 C3' C2' H3'2 120.0 123.6
C1' C2' C3' H2'1 240.0 241.3
C1' C2' C3' H2'2 120.0 118.6
C3' C2' C1' N1 138.1 121.4
C3' C2' C1' H1' 252.7 242.6
H2'1 C2' C3' H2'2 240.0 237.3
H3'1 C3' C4' H4' 229.2 199.7
C4' C3' H3'1 C2' 238.0 247.2
C4' C3' H3'1 H3'2 119.0 123.7
C2' C3' H3'1 H3'2 241.0 236.4
H3'1 C3' C2' C1' 239.1 262.6
H3'1 C3' C2' H2'1 359.2 21.3
H3'1 C3' C2' H2'2 119.1 144.0
H3'2 C3' C4' H4' 349.2 323.4
C4' C3' H3'2 C2' 122.0 112.7
C4' C3' H3'2 H3'1 241.0 236.3
C2' C3' H3'2 H3'1 119.0 123.6
H3'2 C3' C2' C1' 119.1 139.1
H3'2 C3' C2' H2'1 239.2 257.7
H3'2 C3' C2' H2'2 359.1 20.4
C2 N1 C1' C2' 82.8 295.7
O4' C1' C2' N1 236.0 240.6
O4' C1' C2' H1' 121.4 119.4
C1' C2' C3' H3'1 239.1 262.6
C1' C2' C3' H3'2 119.1 139.1
C3' C2' C1' H2'1 120.0 118.7
C3' C2' C1' H2'2 240.0 241.3
H2'1 C2' C1' H2'2 120.0 122.7
N1 C1' C2' H1' 245.4 238.8
C2' C1' N1 C6 258.5 115.8
H2'1 C2' C3' H3'1 359.2 21.3
H2'1 C2' C3' H3'2 239.2 257.7
C3' C2' H2'1 C1' 238.3 245.3
C3' C2' H2'1 H2'2 119.2 122.7
C1' C2' H2'1 H2'2 240.9 237.4
H2'1 C2' C1' N1 18.1 2.8
H2'1 C2' C1' H1' 132.7 123.9
H2'2 C2' C3' H3'1 119.1 144.0
H2'2 C2' C3' H3'2 359.1 20.4
C3' C2' H2'2 C1' 121.7 114.7
C3' C2' H2'2 H2'1 240.8 237.4
C1' C2' H2'2 H2'1 119.2 122.6
H2'2 C2' C1' N1 258.2 240.1
H2'2 C2' C1' H1' 12.7 1.3
C1' N1 C2 N3 175.0 179.2
C2 N1 C1' C6 184.4 180.0
C5 C6 N1 C1' 184.9 180.5
O4' C1' N1 C2' 118.7 117.8
O4' C1' N1 H1' 239.0 238.9
N1 C1' C2' H2'1 18.1 2.8
N1 C1' C2' H2'2 258.2 240.1
C2' C1' N1 H1' 120.3 121.1
C1' N1 C6 H6 4.9 0.6
O4' C1' H1' C2' 243.8 242.2
O4' C1' H1' N1 121.6 121.1
H1' C1' C2' H2'1 132.7 123.9
H1' C1' C2' H2'2 12.7 1.3
C2' C1' H1' N1 237.8 238.9
H1' C1' N1 C6 138.2 354.6
C6 N1 C2 N3 359.3 359.1
C2 N1 C6 C1' 175.7 180.0
N1 C6 C5 H5 179.8 180.0
C5 C6 N1 H6 180.0 179.9
C6 N1 C1' H1' 138.2 354.6
H6 C6 C5 H5 359.9 360.0
C5 C6 H6 N1 180.0 180.1
HN41 N4 C4 N3 0.0 180.3
C4 N4 HN41 HN42 180.0 180.0
HN42 N4 C4 N3 180.0 0.3
C4 N4 HN42 HN41 180.0 180.0