PDB Chemical Component DDG

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 DDG

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
OP3 P 1.607 1.610
OP3 HOP3 0.951 0.967
P OP1 1.484 1.479
P OP2 1.481 1.608
P O5' 1.602 1.610
OP2 HOP2 0.951 0.967
O5' C5' 1.419 1.429
C5' C4' 1.508 1.530
C5' H5' 1.116 1.090
C5' H5'' 1.115 1.089
C4' O4' 1.451 1.446
C4' C3' 1.517 1.550
C4' H4' 1.115 1.089
O4' C1' 1.418 1.436
C3' C2' 1.525 1.547
C3' H3'1 1.116 1.091
C3' H3'2 1.115 1.091
C2' C1' 1.527 1.540
C2' H2' 1.115 1.091
C2' H2'' 1.115 1.089
C1' N9 1.460 1.465
C1' H1' 1.114 1.090
N9 C8 1.376 1.364
N9 C4 1.369 1.368
C8 N7 1.302 1.301
C8 H8 1.104 1.080
N7 C5 1.387 1.356
C5 C6 1.418 1.414
C5 C4 1.378 1.399
C6 O6 1.236 1.219
C6 N1 1.392 1.351
N1 C2 1.379 1.362
N1 H1 1.019 0.970
C2 N2 1.346 1.374
C2 N3 1.318 1.314
N2 H21 1.020 0.969
N2 H22 1.020 0.970
N3 C4 1.351 1.338

Bond Angles for DDG

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
P OP3 HOP3 108.7 106.8
OP3 P OP1 108.8 109.4
OP3 P OP2 105.3 109.5
OP3 P O5' 105.2 109.5
OP1 P OP2 119.6 109.5
OP1 P O5' 107.5 109.4
OP2 P O5' 109.6 109.5
P OP2 HOP2 105.4 106.8
P O5' C5' 119.3 106.8
O5' C5' C4' 110.8 109.5
O5' C5' H5' 111.7 109.4
O5' C5' H5'' 111.7 109.5
C4' C5' H5' 111.8 109.5
C4' C5' H5'' 111.8 109.5
C5' C4' O4' 110.4 110.8
C5' C4' C3' 116.1 110.6
C5' C4' H4' 102.8 110.6
H5' C5' H5'' 98.7 109.4
O4' C4' C3' 104.8 103.5
O4' C4' H4' 114.5 110.6
C4' O4' C1' 109.7 106.9
C3' C4' H4' 108.6 110.6
C4' C3' C2' 102.1 102.1
C4' C3' H3'1 115.0 110.9
C4' C3' H3'2 115.0 110.9
O4' C1' C2' 107.2 107.4
O4' C1' N9 108.8 109.9
O4' C1' H1' 112.0 109.9
C2' C3' H3'1 115.1 110.9
C2' C3' H3'2 115.0 110.9
C3' C2' C1' 101.8 104.2
C3' C2' H2' 115.1 110.5
C3' C2' H2'' 115.1 110.5
H3'1 C3' H3'2 95.4 110.8
C1' C2' H2' 115.2 110.5
C1' C2' H2'' 115.2 110.4
C2' C1' N9 111.4 110.0
C2' C1' H1' 109.5 109.8
H2' C2' H2'' 95.3 110.6
N9 C1' H1' 107.9 109.9
C1' N9 C8 127.8 126.2
C1' N9 C4 125.8 126.3
C8 N9 C4 106.4 107.5
N9 C8 N7 113.1 109.8
N9 C8 H8 125.9 125.1
N9 C4 C5 105.4 106.2
N9 C4 N3 125.7 134.2
N7 C8 H8 121.0 125.1
C8 N7 C5 104.3 109.4
N7 C5 C6 130.3 134.2
N7 C5 C4 110.8 107.2
C6 C5 C4 118.8 118.6
C5 C6 O6 128.6 120.8
C5 C6 N1 111.4 118.4
C5 C4 N3 128.9 119.7
O6 C6 N1 119.9 120.8
C6 N1 C2 125.1 120.3
C6 N1 H1 118.0 119.8
C2 N1 H1 116.9 119.9
N1 C2 N2 116.5 119.0
N1 C2 N3 123.9 121.9
N2 C2 N3 119.6 119.0
C2 N2 H21 116.5 119.9
C2 N2 H22 109.7 120.0
C2 N3 C4 111.9 121.1
H21 N2 H22 109.7 120.1

Torsion Angles for DDG

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP3 OP2 230.7 240.0
OP1 P OP3 O5' 114.9 119.9
OP2 P OP3 O5' 244.2 239.9
OP3 P OP2 HOP2 180.0 60.0
OP3 P O5' C5' 298.7 180.0
HOP3 OP3 P OP1 180.0 299.9
HOP3 OP3 P OP2 309.3 60.0
HOP3 OP3 P O5' 65.1 180.0
OP1 P OP3 HOP3 180.0 299.9
OP3 P OP1 OP2 121.0 120.0
OP3 P OP1 O5' 246.6 240.1
OP2 P OP1 O5' 125.6 120.1
OP1 P OP2 HOP2 302.7 180.0
OP1 P O5' C5' 182.9 60.1
OP2 P OP3 HOP3 309.3 60.0
OP3 P OP2 OP1 237.3 240.0
OP3 P OP2 O5' 112.7 120.0
OP1 P OP2 O5' 235.4 240.0
OP2 P O5' C5' 51.5 300.0
O5' P OP3 HOP3 65.1 180.0
OP3 P O5' OP1 115.8 119.9
OP3 P O5' OP2 247.2 240.0
OP1 P O5' OP2 131.4 120.1
O5' P OP2 HOP2 67.3 300.0
P O5' C5' C4' 183.7 179.9
P O5' C5' H5' 309.0 59.9
P O5' C5' H5'' 58.4 300.0
HOP2 OP2 P O5' 67.3 300.0
C4' C5' O5' H5' 234.7 120.0
C4' C5' O5' H5'' 125.3 239.9
O5' C5' C4' O4' 282.3 65.8
O5' C5' C4' C3' 41.4 180.0
O5' C5' C4' H4' 159.8 302.9
H5' C5' O5' H5'' 250.6 119.9
O5' C5' C4' H5' 125.2 240.0
O5' C5' C4' H5'' 234.7 120.0
H5' C5' C4' H5'' 109.5 240.0
O4' C4' C5' C3' 240.9 245.8
O4' C4' C5' H4' 122.6 122.9
C5' C4' O4' C1' 144.8 158.5
C3' C4' C5' H4' 241.6 237.1
C5' C4' C3' C2' 203.2 204.4
C5' C4' C3' H3'1 328.5 86.1
C5' C4' C3' H3'2 77.9 322.6
O5' C5' H5' C4' 235.3 120.0
O5' C5' H5' H5'' 117.6 240.1
C4' C5' H5' H5'' 242.3 120.1
H5' C5' C4' O4' 157.1 185.8
H5' C5' C4' C3' 276.2 300.0
H5' C5' C4' H4' 34.6 62.9
O5' C5' H5'' C4' 124.8 240.0
O5' C5' H5'' H5' 242.4 119.9
C4' C5' H5'' H5' 117.7 240.0
H5'' C5' C4' O4' 47.6 305.8
H5'' C5' C4' C3' 166.7 60.0
H5'' C5' C4' H4' 285.0 182.9
O4' C4' C5' H5' 157.1 185.8
O4' C4' C5' H5'' 47.6 305.8
C5' C4' O4' C3' 125.7 118.6
C5' C4' O4' H4' 244.6 237.1
C3' C4' O4' H4' 118.9 118.5
O4' C4' C3' C2' 325.3 323.0
O4' C4' C3' H3'1 90.6 204.8
O4' C4' C3' H3'2 200.0 81.2
C4' O4' C1' C2' 4.8 333.6
C4' O4' C1' N9 244.2 214.1
C4' O4' C1' H1' 124.9 93.1
C3' C4' C5' H5' 276.2 300.0
C3' C4' C5' H5'' 166.7 60.0
C5' C4' C3' O4' 237.9 241.3
C5' C4' C3' H4' 115.1 122.9
O4' C4' C3' H4' 237.2 241.6
C3' C4' O4' C1' 19.0 39.9
C2' C3' C4' H3'1 234.7 118.2
C2' C3' C4' H3'2 125.3 241.8
C4' C3' C2' C1' 36.5 20.9
C4' C3' C2' H2' 161.8 262.2
C4' C3' C2' H2'' 271.2 139.6
H3'1 C3' C4' H3'2 250.6 123.6
H4' C4' C5' H5' 34.6 62.9
H4' C4' C5' H5'' 285.0 182.9
C5' C4' H4' O4' 119.8 123.0
C5' C4' H4' C3' 236.5 237.1
O4' C4' H4' C3' 116.7 114.1
H4' C4' O4' C1' 260.2 281.4
H4' C4' C3' C2' 88.0 81.5
H4' C4' C3' H3'1 213.4 323.2
H4' C4' C3' H3'2 322.8 199.7
C1' O4' C4' C3' 19.0 39.9
C1' O4' C4' H4' 260.2 281.4
C3' C2' C1' O4' 333.7 2.0
O4' C1' C2' H2' 208.5 120.6
O4' C1' C2' H2'' 99.0 243.3
C2' C1' O4' N9 120.6 119.6
C2' C1' O4' H1' 239.9 240.5
N9 C1' O4' H1' 119.3 121.0
O4' C1' N9 C8 28.0 28.3
O4' C1' N9 C4 206.8 208.2
C2' C3' C4' H4' 88.0 81.5
C4' C3' C2' H3'1 125.3 241.8
C4' C3' C2' H3'2 234.7 118.2
O4' C1' C2' C3' 333.7 2.0
H3'1 C3' C2' H3'2 109.4 236.4
C1' C2' C3' H2' 234.7 118.7
C1' C2' C3' H2'' 125.3 241.4
C3' C2' C1' N9 92.7 121.5
C3' C2' C1' H1' 212.0 242.5
H2' C2' C3' H2'' 250.6 122.7
H3'1 C3' C4' H4' 213.4 323.2
C4' C3' H3'1 C2' 241.8 112.7
C4' C3' H3'1 H3'2 120.9 236.4
C2' C3' H3'1 H3'2 239.1 123.6
H3'1 C3' C2' C1' 271.2 139.1
H3'1 C3' C2' H2' 36.5 20.4
H3'1 C3' C2' H2'' 145.9 257.8
H3'2 C3' C4' H4' 322.8 199.7
C4' C3' H3'2 C2' 118.2 247.3
C4' C3' H3'2 H3'1 239.1 123.6
C2' C3' H3'2 H3'1 120.9 236.3
H3'2 C3' C2' C1' 161.8 262.7
H3'2 C3' C2' H2' 287.1 144.0
H3'2 C3' C2' H2'' 36.5 21.3
O4' C1' C2' N9 241.0 240.5
O4' C1' C2' H1' 121.7 119.5
C1' C2' C3' H3'1 271.2 139.1
C1' C2' C3' H3'2 161.8 262.7
C3' C2' C1' H2' 125.3 241.3
C3' C2' C1' H2'' 234.7 118.7
H2' C2' C1' H2'' 109.5 237.4
N9 C1' C2' H1' 240.7 239.0
C2' C1' N9 C8 270.0 270.3
C2' C1' N9 C4 88.8 90.2
H2' C2' C3' H3'1 36.5 20.4
H2' C2' C3' H3'2 287.1 144.0
C3' C2' H2' C1' 242.0 114.8
C3' C2' H2' H2'' 121.0 237.4
C1' C2' H2' H2'' 238.9 122.6
H2' C2' C1' N9 327.4 240.2
H2' C2' C1' H1' 86.7 1.2
H2'' C2' C3' H3'1 145.9 257.8
H2'' C2' C3' H3'2 36.5 21.3
C3' C2' H2'' C1' 118.0 245.2
C3' C2' H2'' H2' 239.0 122.6
C1' C2' H2'' H2' 121.0 237.4
H2'' C2' C1' N9 217.9 2.8
H2'' C2' C1' H1' 337.2 123.8
O4' C1' N9 C2' 118.0 118.0
O4' C1' N9 H1' 238.2 239.0
N9 C1' C2' H2' 327.4 240.2
N9 C1' C2' H2'' 217.9 2.8
C2' C1' N9 H1' 120.2 121.0
C8 N9 C1' C4 181.2 180.1
C1' N9 C8 N7 178.3 179.9
C1' N9 C8 H8 358.3 0.0
C1' N9 C4 C5 181.3 180.0
C1' N9 C4 N3 1.2 0.1
O4' C1' H1' C2' 241.2 242.0
O4' C1' H1' N9 119.8 121.0
H1' C1' C2' H2' 86.7 1.2
H1' C1' C2' H2'' 337.2 123.8
C2' C1' H1' N9 238.6 238.9
H1' C1' N9 C8 149.8 149.3
H1' C1' N9 C4 328.6 329.2
C8 N9 C1' H1' 149.8 149.3
C1' N9 C8 C4 179.0 179.9
C8 N9 C4 C5 0.3 360.0
C8 N9 C4 N3 180.2 180.0
N7 C8 N9 H8 180.0 179.9
N9 C8 N7 C5 0.8 360.0
C4 N9 C1' H1' 328.6 329.2
C1' N9 C4 C8 181.0 180.1
C4 N9 C8 N7 359.3 0.0
C4 N9 C8 H8 179.4 180.1
N7 C5 C4 N9 0.2 0.0
C6 C5 C4 N9 180.4 180.0
C5 C4 N9 N3 180.1 179.9
C2 N3 C4 N9 180.0 180.0
N7 C8 N9 C4 359.3 0.0
N9 C8 N7 H8 180.0 180.1
C8 N7 C5 C6 179.2 180.0
C8 N7 C5 C4 359.4 360.0
H8 C8 N9 C4 179.4 180.1
N9 C8 H8 N7 180.0 179.9
H8 C8 N7 C5 180.7 179.9
N9 C4 C5 N7 0.2 0.0
C5 N7 C8 H8 180.7 179.9
C6 C5 N7 C4 179.8 180.0
N7 C5 C6 O6 359.7 0.0
N7 C5 C6 N1 179.8 179.7
N7 C5 C4 N3 180.3 180.0
N9 C4 C5 C6 180.4 180.0
N7 C5 C6 C4 180.2 180.0
C6 C5 C4 N3 0.5 0.0
O6 C6 C5 N1 179.9 180.3
C5 C6 N1 C2 0.2 0.6
C5 C6 N1 H1 180.2 180.0
N9 C4 C5 N3 179.9 180.0
N7 C5 C4 C6 179.8 180.0
C4 C5 C6 O6 179.5 180.0
C4 C5 C6 N1 359.6 359.7
C2 N3 C4 C5 359.8 0.0
O6 C6 C5 C4 179.5 180.0
C5 C6 O6 N1 180.1 179.7
O6 C6 N1 C2 180.3 180.3
O6 C6 N1 H1 0.3 359.7
N1 C6 C5 C4 359.6 359.7
C5 C6 N1 O6 179.9 180.3
C2 N1 C6 H1 180.0 180.6
C6 N1 C2 N2 180.0 179.7
C6 N1 C2 N3 0.1 359.4
C6 N1 C2 H1 180.0 179.4
N2 C2 N1 N3 179.9 180.3
N1 C2 N2 H21 180.0 179.7
N1 C2 N2 H22 54.7 359.4
N1 C2 N3 C4 359.9 0.3
C6 N1 H1 C2 180.0 180.6
H1 N1 C2 N2 360.0 0.3
H1 N1 C2 N3 180.1 180.0
N2 C2 N1 H1 360.0 0.3
N1 C2 N2 N3 180.1 179.7
N2 C2 N3 C4 180.0 180.0
H21 N2 C2 H22 125.2 180.3
N9 C4 N3 C2 180.0 180.0
C5 C4 N3 C2 359.8 0.0
N3 C2 N1 H1 180.1 180.0
N1 C2 N3 N2 179.9 180.3
N3 C2 N2 H21 359.9 360.0
N3 C2 N2 H22 234.7 179.7
H21 N2 C2 N3 359.9 360.0
C2 N2 H21 H22 234.8 179.7
H22 N2 C2 N3 234.7 179.7
C2 N2 H22 H21 129.1 180.3
N9 C4 N3 C5 180.1 179.9