PDB Chemical Component DH3

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 DH3

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
N4 C4 1.415 1.385
N4 HN41 1.000 0.969
N4 HN42 1.000 0.970
C4 N3 1.363 1.329
C4 C5 1.441 1.397
N3 C2 1.371 1.324
C2 N2 1.412 1.384
C2 N1 1.360 1.325
N2 HN21 1.000 0.970
N2 HN22 0.999 0.970
N1 C6 1.360 1.324
C6 C5 1.425 1.381
C6 H6 1.080 1.080
C5 C51 1.587 1.508
C51 C1' 1.557 1.507
C51 H511 1.100 1.090
C51 H512 1.100 1.090
C1' C6' 1.437 1.379
C1' C2' 1.413 1.383
C6' C52 1.435 1.395
C6' H6' 1.080 1.081
C52 C53 1.483 1.432
C52 C4' 1.433 1.398
C53 C54 1.193 1.174
C54 C1 1.257 1.473
C1 C3 1.291 1.530
C1 H11 1.100 1.090
C1 H12 1.101 1.090
C3 C7 1.458 1.530
C3 H31 1.100 1.090
C3 H32 1.100 1.090
C7 C8 1.495 1.507
C7 H71 1.100 1.090
C7 H72 1.100 1.090
C8 O10 1.220 1.342
C8 O9 1.222 1.208
O9 HO9 0.950  
C4' O5 1.414 1.360
C4' C3' 1.433 1.389
O5 C5' 1.568 1.429
C5' H5'1 1.100 1.090
C5' H5'2 1.100 1.090
C5' H5'3 1.100 1.091
C3' O4 1.392 1.360
C3' C2' 1.417 1.386
O4 C4B 1.716 1.429
C4B H4'1 1.099 1.090
C4B H4'2 1.100 1.090
C4B H4'3 1.100 1.090
C2' H2' 1.080 1.080

Bond Angles for DH3

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C4 N4 HN41 109.5 120.0
C4 N4 HN42 109.5 120.0
N4 C4 N3 118.1 120.5
N4 C4 C5 121.6 120.5
HN41 N4 HN42 109.4 120.0
N3 C4 C5 120.3 119.0
C4 N3 C2 121.8 120.7
C4 C5 C6 115.6 118.5
C4 C5 C51 111.4 120.7
N3 C2 N2 119.4 119.2
N3 C2 N1 119.3 121.6
N2 C2 N1 121.3 119.2
C2 N2 HN21 125.2 120.0
C2 N2 HN22 109.6 120.0
C2 N1 C6 121.8 120.9
HN21 N2 HN22 125.2 120.0
N1 C6 C5 121.2 119.3
N1 C6 H6 119.4 120.4
C5 C6 H6 119.4 120.3
C6 C5 C51 133.0 120.8
C5 C51 C1' 110.2 109.4
C5 C51 H511 109.0 109.5
C5 C51 H512 109.2 109.4
C1' C51 H511 109.1 109.5
C1' C51 H512 109.2 109.5
C51 C1' C6' 123.2 119.9
C51 C1' C2' 117.7 119.9
H511 C51 H512 110.1 109.5
C6' C1' C2' 119.1 120.3
C1' C6' C52 118.7 120.0
C1' C6' H6' 120.7 120.0
C1' C2' C3' 122.6 120.3
C1' C2' H2' 118.7 119.9
C52 C6' H6' 120.6 120.0
C6' C52 C53 118.4 120.2
C6' C52 C4' 121.6 119.7
C53 C52 C4' 120.0 120.1
C52 C53 C54 164.4 179.9
C52 C4' O5 119.1 120.2
C52 C4' C3' 118.7 119.7
C53 C54 C1 172.5 179.9
C54 C1 C3 144.1 109.5
C54 C1 H11 92.0 109.4
C54 C1 H12 99.2 109.4
C3 C1 H11 92.0 109.5
C3 C1 H12 99.2 109.5
C1 C3 C7 124.4 109.5
C1 C3 H31 101.3 109.5
C1 C3 H32 104.7 109.5
H11 C1 H12 142.3 109.6
C7 C3 H31 101.2 109.4
C7 C3 H32 104.8 109.5
C3 C7 C8 152.3 109.5
C3 C7 H71 89.5 109.5
C3 C7 H72 97.0 109.5
H31 C3 H32 122.1 109.4
C8 C7 H71 89.5 109.5
C8 C7 H72 97.1 109.4
C7 C8 O10 120.4 120.0
C7 C8 O9 120.2 120.0
H71 C7 H72 151.4 109.5
O10 C8 O9 119.4 120.0
C8 O9 HO9 109.5  
O5 C4' C3' 122.1 120.1
C4' O5 C5' 133.4 106.8
C4' C3' O4 120.9 120.0
C4' C3' C2' 119.2 120.0
O5 C5' H5'1 109.4 109.5
O5 C5' H5'2 109.5 109.4
O5 C5' H5'3 109.5 109.4
H5'1 C5' H5'2 109.5 109.5
H5'1 C5' H5'3 109.5 109.5
H5'2 C5' H5'3 109.5 109.5
O4 C3' C2' 119.9 120.0
C3' O4 C4B 117.1 106.8
C3' C2' H2' 118.7 119.8
O4 C4B H4'1 109.5 109.4
O4 C4B H4'2 109.5 109.4
O4 C4B H4'3 109.5 109.4
H4'1 C4B H4'2 109.5 109.5
H4'1 C4B H4'3 109.4 109.5
H4'2 C4B H4'3 109.5 109.5

Torsion Angles for DH3

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
HN41 N4 C4 HN42 120.0 179.9
N3 C4 N4 C5 180.1 180.4
N4 C4 N3 C2 180.0 180.0
N4 C4 C5 C6 179.8 180.0
N4 C4 C5 C51 359.3 0.2
C4 N4 HN41 HN42 240.0 180.1
HN41 N4 C4 N3 173.6 359.9
HN41 N4 C4 C5 353.5 179.5
C4 N4 HN42 HN41 120.0 179.9
HN42 N4 C4 N3 53.6 180.0
HN42 N4 C4 C5 233.5 359.6
N3 C4 N4 HN41 173.6 359.9
N3 C4 N4 HN42 53.6 180.0
N4 C4 N3 C5 179.9 179.6
N3 C4 C5 C6 359.7 359.6
N3 C4 C5 C51 179.3 179.8
C4 N3 C2 N2 180.2 179.7
C4 N3 C2 N1 359.9 359.8
C5 C4 N4 HN41 353.5 179.5
C5 C4 N4 HN42 233.5 359.6
N4 C4 C5 N3 180.1 180.4
C5 C4 N3 C2 0.1 0.4
N1 C6 C5 C4 0.4 0.2
C4 C5 C6 H6 180.4 180.2
C6 C5 C4 C51 180.5 179.8
C4 C5 C51 C1' 177.2 84.8
C4 C5 C51 H511 57.5 324.8
C4 C5 C51 H512 297.2 204.8
C2 N3 C4 C5 0.1 0.4
N2 C2 N3 N1 180.3 179.9
N3 C2 N2 HN21 179.9 180.0
N3 C2 N2 HN22 359.9 0.1
N3 C2 N1 C6 0.3 360.0
N3 C2 N2 N1 179.7 180.1
N2 C2 N1 C6 180.0 180.0
HN21 N2 C2 HN22 180.0 179.9
N3 C2 N1 N2 180.3 179.9
N1 C2 N2 HN21 0.2 359.9
N1 C2 N2 HN22 180.1 180.0
C2 N1 C6 C5 359.6 0.0
C2 N1 C6 H6 179.6 180.0
HN21 N2 C2 N1 0.2 359.9
C2 N2 HN21 HN22 180.0 180.1
HN22 N2 C2 N1 180.1 180.0
C2 N2 HN22 HN21 180.0 179.9
C4 C5 C6 N1 0.4 0.2
C5 C6 N1 H6 180.0 180.0
N1 C6 C5 C51 181.0 180.0
C4 C5 C6 C51 179.4 180.2
N1 C6 C5 H6 180.0 180.0
C6 C5 C51 C1' 356.6 265.0
C6 C5 C51 H511 236.9 145.0
C6 C5 C51 H512 116.6 25.0
N1 C6 H6 C5 180.0 180.0
H6 C6 C5 C51 1.0 0.0
C4 C5 C51 C6 180.6 179.8
C51 C5 C6 H6 1.0 0.0
C1' C51 C5 H511 119.7 120.0
C1' C51 C5 H512 240.0 240.0
C5 C51 C1' C6' 74.2 270.0
C5 C51 C1' C2' 254.2 90.0
H511 C51 C5 H512 120.3 120.0
C5 C51 C1' H511 240.3 240.0
C5 C51 C1' H512 120.0 120.0
H511 C51 C1' H512 239.7 239.9
C6' C1' C51 C2' 180.0 180.0
C51 C1' C6' C52 180.4 180.0
C51 C1' C6' H6' 0.4 0.1
C51 C1' C2' C3' 179.7 179.9
C51 C1' C2' H2' 359.7 0.0
C5 C51 H511 C1' 120.4 119.9
C5 C51 H511 H512 240.2 240.0
C1' C51 H511 H512 119.8 120.1
H511 C51 C1' C6' 193.9 29.9
H511 C51 C1' C2' 13.8 210.0
C5 C51 H512 C1' 239.4 240.1
C5 C51 H512 H511 119.7 120.0
C1' C51 H512 H511 240.3 239.9
H512 C51 C1' C6' 314.2 150.0
H512 C51 C1' C2' 134.2 330.1
C6' C1' C51 H511 193.9 29.9
C6' C1' C51 H512 314.2 150.0
C51 C1' C6' C2' 180.0 180.0
C6' C1' C2' C3' 359.6 360.0
C6' C1' C2' H2' 179.7 180.1
C52 C6' C1' H6' 180.0 179.9
C1' C6' C52 C53 179.6 180.1
C1' C6' C52 C4' 359.5 359.8
C2' C1' C51 H511 13.8 210.0
C2' C1' C51 H512 134.2 330.1
C51 C1' C2' C6' 180.0 180.0
C2' C1' C6' C52 0.5 360.0
C2' C1' C6' H6' 180.5 180.0
C4' C3' C2' C1' 0.2 0.3
O4 C3' C2' C1' 180.0 180.0
C3' C2' C1' H2' 180.0 179.9
C52 C6' C1' C2' 0.5 360.0
C1' C6' C52 H6' 180.0 180.1
C53 C52 C6' C4' 180.1 180.3
C6' C52 C53 C54 87.8 341.3
C6' C52 C4' O5 179.9 180.0
C6' C52 C4' C3' 0.4 0.5
H6' C6' C1' C2' 180.5 180.0
C1' C6' H6' C52 180.0 179.9
H6' C6' C52 C53 359.6 0.0
H6' C6' C52 C4' 179.5 179.7
C53 C52 C6' H6' 359.6 0.0
C6' C52 C53 C4' 179.9 179.7
C53 C52 C4' O5 359.8 359.7
C53 C52 C4' C3' 180.3 180.2
C52 C53 C54 C1 8.5 182.5
C4' C52 C6' H6' 179.5 179.7
C6' C52 C4' C53 180.1 180.3
C4' C52 C53 C54 267.9 161.6
O5 C4' C52 C3' 179.6 179.5
C52 C4' O5 C5' 246.9 90.0
C52 C4' C3' O4 180.0 179.8
C52 C4' C3' C2' 359.8 359.5
C54 C53 C52 C4' 267.9 161.6
C53 C54 C1 C3 262.2 16.2
C53 C54 C1 H11 166.0 136.2
C53 C54 C1 H12 22.2 256.3
C3 C1 C54 H11 96.2 240.0
C3 C1 C54 H12 240.0 120.0
C54 C1 C3 C7 359.8 180.0
C54 C1 C3 H31 247.6 300.0
C54 C1 C3 H32 119.8 60.0
H11 C1 C54 H12 143.8 240.0
C54 C1 C3 H11 263.8 119.9
C54 C1 C3 H12 120.0 240.1
H11 C1 C3 H12 216.2 120.1
C7 C3 C1 H31 112.2 240.0
C7 C3 C1 H32 240.0 120.0
C1 C3 C7 C8 126.9 180.0
C1 C3 C7 H71 39.0 300.0
C1 C3 C7 H72 246.9 60.0
H31 C3 C1 H32 127.8 240.0
C54 C1 H11 C3 144.4 240.0
C54 C1 H11 H12 252.2 120.0
C3 C1 H11 H12 107.8 239.9
H11 C1 C3 C7 95.9 60.1
H11 C1 C3 H31 343.7 180.0
H11 C1 C3 H32 215.9 300.1
C54 C1 H12 C3 210.9 120.0
C54 C1 H12 H11 105.4 240.0
C3 C1 H12 H11 254.5 120.1
H12 C1 C3 C7 239.8 299.9
H12 C1 C3 H31 127.6 59.9
H12 C1 C3 H32 359.8 179.9
C7 C3 C1 H11 95.9 60.1
C7 C3 C1 H12 239.8 299.9
C1 C3 C7 H31 247.8 120.0
C1 C3 C7 H32 120.0 240.0
H31 C3 C7 H32 232.2 119.9
C8 C7 C3 H71 87.9 240.0
C8 C7 C3 H72 240.0 119.9
C3 C7 C8 O10 46.8 179.9
C3 C7 C8 O9 227.0 0.0
H71 C7 C3 H72 152.1 240.0
H31 C3 C1 H11 343.7 180.0
H31 C3 C1 H12 127.6 59.9
C1 C3 H31 C7 128.8 240.0
C1 C3 H31 H32 244.4 120.1
C7 C3 H31 H32 115.6 240.1
H31 C3 C7 C8 239.1 59.9
H31 C3 C7 H71 151.2 180.0
H31 C3 C7 H72 359.1 300.0
H32 C3 C1 H11 215.9 300.1
H32 C3 C1 H12 359.8 179.9
C1 C3 H32 C7 227.7 120.0
C1 C3 H32 H31 113.8 239.9
C7 C3 H32 H31 246.2 119.9
H32 C3 C7 C8 6.9 300.0
H32 C3 C7 H71 279.0 60.0
H32 C3 C7 H72 126.9 180.1
C8 C7 C3 H31 239.1 59.9
C8 C7 C3 H32 6.9 300.0
C3 C7 C8 H71 272.1 120.0
C3 C7 C8 H72 120.0 240.0
H71 C7 C8 H72 207.9 120.0
O10 C8 C7 O9 179.8 179.9
C7 C8 O9 HO9 179.8  
H71 C7 C3 H31 151.2 180.0
H71 C7 C3 H32 279.0 60.0
C3 C7 H71 C8 152.3 240.0
C3 C7 H71 H72 256.2 120.0
C8 C7 H71 H72 103.9 240.1
H71 C7 C8 O10 134.7 59.9
H71 C7 C8 O9 314.9 240.0
H72 C7 C3 H31 359.1 300.0
H72 C7 C3 H32 126.9 180.1
C3 C7 H72 C8 203.9 120.0
C3 C7 H72 H71 101.9 240.0
C8 C7 H72 H71 258.0 120.0
H72 C7 C8 O10 286.8 300.0
H72 C7 C8 O9 107.0 120.0
O10 C8 C7 H71 134.7 59.9
O10 C8 C7 H72 286.8 300.0
C7 C8 O10 O9 180.2 180.1
O10 C8 O9 HO9 0.0  
O9 C8 C7 H71 314.9 240.0
O9 C8 C7 H72 107.0 120.0
C7 C8 O9 O10 179.8 179.9
C52 C4' O5 C3' 180.4 180.5
O5 C4' C3' O4 0.4 0.3
O5 C4' C3' C2' 180.2 180.0
C4' O5 C5' H5'1 341.1 60.0
C4' O5 C5' H5'2 221.1 180.0
C4' O5 C5' H5'3 101.1 300.0
C1' C2' C3' C4' 0.2 0.3
C52 C4' C3' O5 179.6 179.5
C3' C4' O5 C5' 66.5 269.5
O4 C3' C4' C2' 180.2 180.3
C4' C3' O4 C4B 74.6 179.7
C4' C3' C2' H2' 180.2 180.2
C5' O5 C4' C3' 66.5 269.5
H5'1 C5' O5 H5'2 120.0 239.9
H5'1 C5' O5 H5'3 240.0 120.0
H5'2 C5' O5 H5'3 120.0 240.0
O5 C5' H5'1 H5'2 240.0 120.0
O5 C5' H5'1 H5'3 120.0 240.0
H5'2 C5' H5'1 H5'3 240.0 120.0
O5 C5' H5'2 H5'1 120.0 240.0
O5 C5' H5'2 H5'3 240.0 119.9
H5'1 C5' H5'2 H5'3 120.0 240.0
O5 C5' H5'3 H5'1 240.0 120.0
O5 C5' H5'3 H5'2 120.0 240.1
H5'1 C5' H5'3 H5'2 240.0 120.1
C1' C2' C3' O4 180.0 180.0
C4' C3' O4 C2' 179.8 179.7
O4 C3' C2' H2' 0.0 359.9
C3' O4 C4B H4'1 7.2 180.0
C3' O4 C4B H4'2 247.1 300.0
C3' O4 C4B H4'3 127.1 60.0
C1' C2' C3' H2' 180.0 180.1
C4' C3' C2' O4 180.2 180.3
C2' C3' O4 C4B 254.8 0.1
C4B O4 C3' C2' 254.8 0.1
H4'1 C4B O4 H4'2 120.0 240.0
H4'1 C4B O4 H4'3 240.0 120.0
H4'2 C4B O4 H4'3 120.0 240.0
O4 C4B H4'1 H4'2 240.0 119.9
O4 C4B H4'1 H4'3 120.0 240.1
H4'2 C4B H4'1 H4'3 240.0 120.1
O4 C4B H4'2 H4'1 120.0 240.0
O4 C4B H4'2 H4'3 240.0 120.0
H4'1 C4B H4'2 H4'3 120.0 239.9
O4 C4B H4'3 H4'1 240.0 120.0
O4 C4B H4'3 H4'2 120.0 240.1
H4'1 C4B H4'3 H4'2 240.0 120.1
C1' C2' H2' C3' 180.0 179.9