PDB Chemical Component EDA

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 EDA

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.484 1.480
P OP2 1.481 1.610
P OP3 1.599 1.610
P O5' 1.594 1.610
OP2 HOP2 0.950 0.967
OP3 HOP3 0.950 0.966
O5' C5' 1.434 1.428
N9 C4 1.382 1.242
N9 C8 1.387 1.396
N9 C1' 1.464 1.469
C4 N3 1.352 1.345
C4 C5 1.386 1.386
N3 C2 1.333 1.299
C2 N1 1.365 1.388
C2 H2 1.103 1.081
N1 C6 1.375 1.409
N1 C10 1.410 1.221
C6 N6 1.332 1.297
C6 C5 1.413 1.457
C10 C11 1.359 1.338
C10 H10 1.103 1.080
C11 N6 1.396 1.364
C11 H11 1.102 1.081
C5 N7 1.398 1.362
N7 C8 1.319 1.296
C8 H8 1.104 1.080
C2' C1' 1.524 1.545
C2' C3' 1.518 1.544
C2' H2' 1.115 1.090
C2' H2'' 1.115 1.090
C5' C4' 1.515 1.530
C5' H5' 1.116 1.090
C5' H5'' 1.115 1.090
C4' O4' 1.443 1.447
C4' C3' 1.527 1.544
C4' H4' 1.116 1.090
O4' C1' 1.421 1.443
C1' H1' 1.115 1.090
C3' O3' 1.431 1.429
C3' H3' 1.115 1.090
O3' HO3' 0.951 0.967

Bond Angles for EDA

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 119.5 109.4
OP1 P OP3 109.7 109.5
OP1 P O5' 109.0 109.5
OP2 P OP3 105.8 109.5
OP2 P O5' 108.1 109.5
P OP2 HOP2 119.4 106.8
OP3 P O5' 103.6 109.5
P OP3 HOP3 109.8 106.9
P O5' C5' 121.7 106.8
O5' C5' C4' 109.7 109.5
O5' C5' H5' 112.2 109.5
O5' C5' H5'' 112.1 109.5
C4 N9 C8 104.7 109.7
C4 N9 C1' 128.0 109.5
N9 C4 N3 126.9 132.1
N9 C4 C5 106.2 107.7
C8 N9 C1' 127.3 109.4
N9 C8 N7 115.1 108.2
N9 C8 H8 124.7 126.0
N9 C1' C2' 113.7 110.4
N9 C1' O4' 107.0 110.4
N9 C1' H1' 107.6 110.3
N3 C4 C5 126.9 120.2
C4 N3 C2 112.2 123.1
C4 C5 C6 117.8 116.9
C4 C5 N7 111.5 107.7
N3 C2 N1 126.5 119.7
N3 C2 H2 115.4 120.1
N1 C2 H2 118.1 120.2
C2 N1 C6 120.7 117.7
C2 N1 C10 137.0 114.9
C6 N1 C10 102.3 109.1
N1 C6 N6 117.7 105.8
N1 C6 C5 115.9 115.0
N1 C10 C11 106.6 108.6
N1 C10 H10 128.0 125.7
N6 C6 C5 126.4 139.1
C6 N6 C11 100.1 106.1
C6 C5 N7 130.7 135.4
C11 C10 H10 125.3 125.7
C10 C11 N6 113.3 108.2
C10 C11 H11 122.2 125.9
N6 C11 H11 124.5 125.9
C5 N7 C8 102.6 106.7
N7 C8 H8 120.2 125.9
C1' C2' C3' 103.8 104.0
C1' C2' H2' 114.3 110.5
C1' C2' H2'' 114.4 110.5
C2' C1' O4' 107.0 104.8
C2' C1' H1' 107.6 110.3
C3' C2' H2' 114.3 110.5
C3' C2' H2'' 114.3 110.5
C2' C3' C4' 102.9 104.2
C2' C3' O3' 110.2 110.5
C2' C3' H3' 113.7 110.5
H2' C2' H2'' 96.2 110.6
C4' C5' H5' 112.1 109.5
C4' C5' H5'' 112.1 109.4
C5' C4' O4' 107.5 110.4
C5' C4' C3' 113.6 110.7
C5' C4' H4' 106.8 110.3
H5' C5' H5'' 98.3 109.4
O4' C4' C3' 105.5 104.7
O4' C4' H4' 114.7 110.4
C4' O4' C1' 110.7 105.3
C3' C4' H4' 108.8 110.2
C4' C3' O3' 110.9 110.5
C4' C3' H3' 113.0 110.5
O4' C1' H1' 114.2 110.4
O3' C3' H3' 106.1 110.4
C3' O3' HO3' 110.2 106.9

Torsion Angles for EDA

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 OP3 237.8 120.0
OP2 P OP1 O5' 124.9 240.0
OP1 P OP2 HOP2 180.0 300.0
OP3 P OP1 O5' 247.2 120.0
OP1 P OP3 HOP3 179.9 180.0
OP1 P O5' C5' 303.4 60.0
OP1 P OP2 OP3 124.2 240.0
OP1 P OP2 O5' 234.6 120.0
OP3 P OP2 O5' 110.4 240.0
OP2 P OP3 HOP3 310.0 60.0
OP2 P O5' C5' 172.1 180.0
OP1 P OP3 OP2 229.9 120.0
OP1 P OP3 O5' 116.3 240.0
OP2 P OP3 O5' 246.4 120.0
OP3 P OP2 HOP2 55.8 60.0
OP3 P O5' C5' 60.2 300.0
OP1 P O5' OP2 131.3 240.0
OP1 P O5' OP3 243.2 120.0
OP2 P O5' OP3 111.9 240.0
O5' P OP2 HOP2 305.4 180.0
O5' P OP3 HOP3 63.6 300.0
P O5' C5' C4' 161.5 180.0
P O5' C5' H5' 286.8 60.0
P O5' C5' H5'' 36.3 300.0
HOP2 OP2 P OP3 55.8 60.0
HOP2 OP2 P O5' 305.4 180.0
HOP3 OP3 P O5' 63.6 300.0
C4' C5' O5' H5' 234.7 120.0
C4' C5' O5' H5'' 125.3 240.0
O5' C5' C4' O4' 299.3 61.4
O5' C5' C4' C3' 55.7 176.9
O5' C5' C4' H4' 175.7 299.2
H5' C5' O5' H5'' 250.6 120.0
C8 N9 C4 C1' 179.8 120.1
C4 N9 C8 N7 359.8 359.5
C4 N9 C8 H8 179.8 179.6
C4 N9 C1' C2' 64.8 292.5
C4 N9 C1' O4' 182.7 47.9
C4 N9 C1' H1' 305.8 170.3
N3 C4 N9 C5 180.2 179.1
N9 C4 N3 C2 179.4 169.8
N9 C4 C5 C6 181.1 178.7
N9 C4 C5 N7 0.6 359.4
C4 N9 C8 C1' 180.2 239.9
C8 N9 C4 N3 180.0 179.8
C8 N9 C4 C5 359.8 0.7
C8 N9 C1' C2' 245.1 172.2
C8 N9 C1' O4' 3.0 287.7
C8 N9 C1' H1' 126.1 50.0
C5 N7 C8 N9 0.5 0.1
N7 C8 N9 H8 180.0 179.9
C4 N9 C1' C8 179.7 120.2
C1' N9 C4 N3 0.2 59.7
C1' N9 C4 C5 180.0 240.6
C1' N9 C8 N7 179.6 119.6
C1' N9 C8 H8 359.6 299.7
N9 C1' C2' C3' 139.7 142.9
N9 C1' C2' H2' 264.9 24.3
N9 C1' C2' H2'' 14.5 261.6
C2' C1' N9 O4' 242.1 244.6
C2' C1' N9 H1' 119.0 122.2
C4' O4' C1' N9 234.3 200.7
O4' C1' N9 H1' 236.9 237.6
N3 C4 N9 C8 180.0 179.8
N3 C4 N9 C1' 0.2 59.7
N9 C4 N3 C5 179.8 181.0
N3 C4 C5 C6 0.9 359.4
N3 C4 C5 N7 180.4 180.1
C4 N3 C2 N1 359.6 0.3
C4 N3 C2 H2 179.6 180.3
C5 C4 N9 C8 359.8 0.7
C5 C4 N9 C1' 180.0 240.6
N9 C4 C5 N3 180.2 179.2
C5 C4 N3 C2 359.7 348.8
N1 C6 C5 C4 359.3 21.5
N6 C6 C5 C4 179.2 200.2
C6 C5 C4 N7 180.5 179.3
C4 C5 N7 C8 359.4 0.3
C2 N3 C4 C5 359.7 348.8
N1 C2 N3 H2 180.0 180.0
N3 C2 N1 C6 0.5 22.1
N3 C2 N1 C10 180.5 152.7
N3 C2 N1 H2 180.0 180.0
C6 N1 C2 C10 180.0 229.3
C2 N1 C6 N6 180.2 148.7
C2 N1 C6 C5 0.1 327.9
C2 N1 C10 C11 179.8 213.9
C2 N1 C10 H10 359.8 34.0
N3 C2 H2 N1 180.0 180.0
H2 C2 N1 C6 180.5 202.1
H2 C2 N1 C10 0.5 332.7
C4 C5 C6 N1 359.3 21.5
C6 N1 C2 H2 180.5 202.1
C2 N1 C6 C10 180.0 133.3
C6 N1 C10 C11 359.9 348.5
C6 N1 C10 H10 179.9 168.6
N6 C6 N1 C5 180.1 180.8
N1 C6 N6 C11 359.9 347.6
N1 C6 C5 N7 179.9 200.5
C10 N1 C2 H2 0.5 332.7
C2 N1 C10 C6 180.0 225.3
C10 N1 C6 N6 0.2 15.5
C10 N1 C6 C5 180.1 194.6
C11 C10 N1 H10 180.0 179.9
N1 C10 C11 N6 0.1 3.7
N1 C10 C11 H11 180.1 183.7
C4 C5 C6 N6 179.2 200.2
N6 C6 N1 C10 0.2 15.5
N1 C6 N6 C5 179.9 178.9
N6 C6 C5 N7 359.8 19.3
C10 C11 N6 C6 0.0 6.2
C6 N6 C11 H11 180.0 186.2
C4 C5 C6 N7 179.4 181.0
C5 C6 N1 C10 180.1 194.6
N1 C6 C5 N6 180.1 181.2
C5 C6 N6 C11 180.0 168.8
C6 C5 N7 C8 178.8 181.2
N1 C10 C11 H10 180.0 180.1
C6 N6 C11 C10 0.0 6.2
N6 C11 C10 H11 180.0 180.0
N1 C10 H10 C11 180.0 179.9
H10 C10 C11 N6 180.1 183.6
H10 C10 C11 H11 0.1 3.6
C11 N6 C6 C5 180.0 168.8
N6 C11 C10 H10 180.1 183.6
C10 C11 N6 H11 180.0 180.0
H11 C11 C10 H10 0.1 3.6
C10 C11 H11 N6 180.0 180.0
N9 C8 N7 C5 0.5 0.1
C4 C5 N7 C6 180.6 179.1
C5 N7 C8 H8 180.5 180.0
N7 C8 N9 C1' 179.6 119.6
N9 C8 N7 H8 180.0 180.1
H8 C8 N9 C1' 359.6 299.7
N9 C8 H8 N7 180.0 179.9
N9 C1' C2' O4' 117.9 118.9
N9 C1' C2' H1' 241.0 237.8
C3' C2' C1' H2' 234.8 118.6
C3' C2' C1' H2'' 125.2 241.3
C1' C2' C3' C4' 329.4 359.9
C1' C2' C3' O3' 87.7 118.7
C1' C2' C3' H3' 206.7 241.2
H2' C2' C1' H2'' 250.5 122.7
C4' O4' C1' C2' 356.6 319.6
O4' C1' C2' H1' 123.1 118.9
C1' C2' C3' H2' 125.2 241.4
C1' C2' C3' H2'' 234.7 118.6
C3' C2' C1' O4' 21.8 24.0
C3' C2' C1' H1' 258.7 265.1
H2' C2' C3' H2'' 109.5 237.3
C5' C4' C3' C2' 271.6 217.3
O4' C4' C3' C2' 29.2 336.2
C2' C3' C4' H4' 152.8 94.9
C4' C3' C2' O3' 241.6 241.2
C4' C3' C2' H3' 122.6 118.7
O3' C3' C2' H3' 241.0 237.5
C2' C3' O3' HO3' 180.0 63.2
C1' C2' H2' C3' 240.5 114.6
C1' C2' H2' H2'' 120.3 237.3
H2' C2' C1' O4' 147.1 265.4
H2' C2' C1' H1' 24.0 146.5
C3' C2' H2' H2'' 239.8 122.7
H2' C2' C3' C4' 204.1 118.6
H2' C2' C3' O3' 322.5 237.3
H2' C2' C3' H3' 81.5 359.8
C1' C2' H2'' C3' 119.5 245.4
C1' C2' H2'' H2' 239.7 122.6
H2'' C2' C1' O4' 256.6 142.7
H2'' C2' C1' H1' 133.5 23.8
C3' C2' H2'' H2' 120.2 237.3
H2'' C2' C3' C4' 94.6 241.3
H2'' C2' C3' O3' 213.0 0.0
H2'' C2' C3' H3' 332.0 122.5
O5' C5' C4' H5' 125.3 240.0
O5' C5' C4' H5'' 234.7 120.1
C2' C3' C4' C5' 271.6 217.3
H5' C5' C4' H5'' 109.4 240.1
O4' C4' C5' C3' 243.6 244.6
O4' C4' C5' H4' 123.6 122.3
C5' C4' O4' C1' 105.2 159.5
C3' C4' C5' H4' 240.0 237.7
C5' C4' C3' O3' 153.7 98.5
C5' C4' C3' H3' 34.7 336.0
O5' C5' H5' C4' 236.1 120.0
O5' C5' H5' H5'' 118.0 239.9
C4' C5' H5' H5'' 242.0 119.9
H5' C5' C4' O4' 174.0 181.4
H5' C5' C4' C3' 290.4 296.9
H5' C5' C4' H4' 50.4 59.2
O5' C5' H5'' C4' 123.9 240.0
O5' C5' H5'' H5' 241.9 120.0
C4' C5' H5'' H5' 118.0 240.0
H5'' C5' C4' O4' 64.6 301.4
H5'' C5' C4' C3' 181.0 56.8
H5'' C5' C4' H4' 301.0 179.1
N9 C1' O4' C4' 234.3 200.7
C2' C1' O4' C4' 356.6 319.6
C2' C3' C4' O4' 29.2 336.2
O4' C4' C5' H5' 174.0 181.4
O4' C4' C5' H5'' 64.6 301.4
C5' C4' O4' C3' 121.6 119.2
C5' C4' O4' H4' 241.4 237.8
C3' C4' O4' H4' 119.8 118.6
O4' C4' C3' O3' 271.3 217.4
O4' C4' C3' H3' 152.3 94.9
C4' O4' C1' H1' 115.4 78.4
C4' C3' C2' H2' 204.1 118.6
C4' C3' C2' H2'' 94.6 241.3
C2' C3' C4' O3' 117.9 118.7
C2' C3' C4' H3' 236.9 241.3
C3' C4' C5' H5' 290.4 296.9
C3' C4' C5' H5'' 181.0 56.8
C5' C4' C3' O4' 242.4 241.1
C5' C4' C3' H4' 118.8 122.4
O4' C4' C3' H4' 236.4 241.3
C3' C4' O4' C1' 343.6 40.3
O3' C3' C4' H3' 119.0 122.5
C4' C3' O3' HO3' 293.3 178.1
H4' C4' C5' H5' 50.4 59.2
H4' C4' C5' H5'' 301.0 179.1
C5' C4' H4' O4' 119.0 122.3
C5' C4' H4' C3' 237.0 237.4
O4' C4' H4' C3' 117.9 115.2
H4' C4' O4' C1' 223.9 281.7
H4' C4' C3' O3' 34.9 336.2
H4' C4' C3' H3' 275.9 213.6
N9 C1' O4' C2' 237.8 241.1
N9 C1' O4' H1' 118.9 122.3
O4' C1' C2' C3' 21.8 24.0
O4' C1' C2' H2' 147.1 265.4
O4' C1' C2' H2'' 256.6 142.7
C2' C1' O4' H1' 241.1 241.2
C1' O4' C4' C3' 343.6 40.3
C1' O4' C4' H4' 223.9 281.7
N9 C1' H1' C2' 122.9 122.2
N9 C1' H1' O4' 241.4 237.6
H1' C1' C2' C3' 258.7 265.1
H1' C1' C2' H2' 24.0 146.5
H1' C1' C2' H2'' 133.5 23.8
C2' C1' H1' O4' 118.5 115.4
O3' C3' C2' H2' 322.5 237.3
O3' C3' C2' H2'' 213.0 0.0
C2' C3' O3' C4' 246.7 245.2
C2' C3' O3' H3' 123.6 122.5
O3' C3' C4' H4' 34.9 336.2
C4' C3' O3' H3' 236.9 237.4
H3' C3' C2' H2' 81.5 359.8
H3' C3' C2' H2'' 332.0 122.5
C2' C3' H3' C4' 116.9 114.8
C2' C3' H3' O3' 238.7 237.4
H3' C3' C4' H4' 275.9 213.6
C4' C3' H3' O3' 121.8 122.6
H3' C3' O3' HO3' 56.4 300.7
HO3' O3' C3' H3' 56.4 300.7