PDB Chemical Component EMA

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 EMA

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
PG O1G 1.463 1.609
PG O2G 1.447 1.479
PG O3G 1.486 1.610
PG O3B 1.611 1.610
O1G H1G 0.950 0.967
O3G H3G 0.950 0.967
PB O1B 1.499 1.479
PB O2B 1.466 1.609
PB O3B 1.639 1.610
PB O3A 1.576 1.611
O2B H2B 0.950 0.967
PA O1A 1.473 1.480
PA O2A 1.486 1.610
PA O3A 1.598 1.609
PA C5' 1.604 1.823
O2A H2A 0.949 0.966
C5' O5' 1.493 1.428
C5' H5'1 1.115 1.090
C5' H5'2 1.116 1.090
O5' C4' 1.532 1.429
C4' C1' 1.606 1.530
C4' H4'1 1.116 1.090
C4' H4'2 1.115 1.090
C1' N9 1.570 1.465
C1' H1'1 1.115 1.090
C1' H1'2 1.115 1.090
N9 C8 1.437 1.363
N9 C4 1.343 1.371
C8 N7 1.372 1.302
C8 H8 1.103 1.080
N7 C5 1.362 1.354
C5 C6 1.439 1.405
C5 C4 1.351 1.404
C6 N6 1.319 1.384
C6 N1 1.355 1.328
N6 HN61 1.020 0.970
N6 HN62 1.020 0.970
N1 C2 1.339 1.320
C2 N3 1.354 1.316
C2 H2 1.104 1.079
N3 C4 1.417 1.329

Bond Angles for EMA

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1G PG O2G 115.0 109.5
O1G PG O3G 113.8 109.5
O1G PG O3B 104.1 109.5
PG O1G H1G 115.1 106.8
O2G PG O3G 114.4 109.5
O2G PG O3B 99.2 109.5
O3G PG O3B 108.4 109.4
PG O3G H3G 113.8 106.8
PG O3B PB 133.4 106.8
O1B PB O2B 118.3 109.5
O1B PB O3B 108.6 109.5
O1B PB O3A 107.6 109.5
O2B PB O3B 108.8 109.5
O2B PB O3A 113.1 109.4
PB O2B H2B 118.2 106.8
O3B PB O3A 98.6 109.4
PB O3A PA 135.9 106.8
O1A PA O2A 119.0 109.5
O1A PA O3A 104.5 109.5
O1A PA C5' 104.7 109.4
O2A PA O3A 112.2 109.5
O2A PA C5' 110.0 109.5
PA O2A H2A 119.0 106.7
O3A PA C5' 105.5 109.5
PA C5' O5' 133.2 109.5
PA C5' H5'1 104.0 109.5
PA C5' H5'2 104.0 109.5
O5' C5' H5'1 104.1 109.4
O5' C5' H5'2 104.1 109.4
C5' O5' C4' 116.1 106.8
H5'1 C5' H5'2 104.7 109.5
O5' C4' C1' 115.6 109.5
O5' C4' H4'1 110.0 109.5
O5' C4' H4'2 110.0 109.4
C1' C4' H4'1 110.0 109.5
C1' C4' H4'2 110.0 109.4
C4' C1' N9 128.3 109.5
C4' C1' H1'1 105.6 109.5
C4' C1' H1'2 105.6 109.4
H4'1 C4' H4'2 100.2 109.5
N9 C1' H1'1 105.7 109.5
N9 C1' H1'2 105.7 109.4
C1' N9 C8 138.7 126.3
C1' N9 C4 117.9 126.3
H1'1 C1' H1'2 103.7 109.5
C8 N9 C4 103.4 107.4
N9 C8 N7 110.6 110.0
N9 C8 H8 126.6 125.0
N9 C4 C5 110.8 106.0
N9 C4 N3 123.1 134.9
N7 C8 H8 122.8 125.0
C8 N7 C5 104.4 109.4
N7 C5 C6 133.1 134.7
N7 C5 C4 110.7 107.1
C6 C5 C4 116.1 118.2
C5 C6 N6 120.5 120.8
C5 C6 N1 119.4 118.4
C5 C4 N3 126.0 119.1
N6 C6 N1 120.0 120.8
C6 N6 HN61 120.5 120.0
C6 N6 HN62 108.2 120.0
C6 N1 C2 119.4 121.2
HN61 N6 HN62 108.2 120.0
N1 C2 N3 127.0 122.4
N1 C2 H2 115.9 118.8
N3 C2 H2 117.1 118.8
C2 N3 C4 111.9 120.7

Torsion Angles for EMA

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2G PG O1G O3G 134.8 240.0
O2G PG O1G O3B 252.6 120.0
O3G PG O1G O3B 117.9 240.0
O1G PG O3G H3G 180.0 60.1
O1G PG O3B PB 62.5 180.0
O1G PG O2G O3G 225.5 120.0
O1G PG O2G O3B 110.4 239.9
O2G PG O1G H1G 180.0 300.0
O3G PG O2G O3B 244.9 120.0
O2G PG O3G H3G 45.0 180.0
O2G PG O3B PB 181.3 60.0
O1G PG O3G O2G 135.0 240.0
O1G PG O3G O3B 244.6 120.0
O3G PG O1G H1G 45.3 60.0
O2G PG O3G O3B 109.6 240.0
O3G PG O3B PB 301.0 300.0
O1G PG O3B O2G 241.1 120.0
O1G PG O3B O3G 121.5 240.0
O3B PG O1G H1G 287.4 180.0
O2G PG O3B O3G 240.3 120.0
O3B PG O3G H3G 295.3 300.0
O1B PB O3B PG 309.4 299.9
O2B PB O3B PG 79.4 60.0
PG O3B PB O3A 197.5 180.0
H1G O1G PG O2G 180.0 300.0
H1G O1G PG O3G 45.3 60.0
H1G O1G PG O3B 287.4 180.0
H3G O3G PG O3B 295.3 300.0
PG O3B PB O1B 309.4 299.9
O2B PB O1B O3B 235.5 239.9
O2B PB O1B O3A 129.6 120.0
O1B PB O2B H2B 180.0 180.0
O3B PB O1B O3A 254.2 240.1
O1B PB O3A PA 303.8 60.0
PG O3B PB O2B 79.4 60.0
O1B PB O2B O3B 124.4 120.0
O1B PB O2B O3A 232.9 240.0
O3B PB O2B O3A 108.5 120.0
O2B PB O3A PA 171.3 300.0
O1B PB O3B O2B 230.0 239.9
O1B PB O3B O3A 112.0 120.0
O2B PB O3B O3A 241.9 240.0
O3B PB O2B H2B 55.6 60.0
O3B PB O3A PA 56.5 180.0
O1B PB O3A O2B 132.5 120.0
O1B PB O3A O3B 247.3 240.1
O2B PB O3A O3B 114.8 120.0
O3A PB O2B H2B 307.1 300.0
O1A PA O3A PB 292.0 300.0
O2A PA O3A PB 62.3 60.0
PB O3A PA C5' 182.0 180.0
H2B O2B PB O3B 55.6 60.0
H2B O2B PB O3A 307.1 300.0
PB O3A PA O1A 292.0 300.0
O2A PA O1A O3A 233.9 239.9
O2A PA O1A C5' 123.3 120.0
O1A PA O2A H2A 180.0 180.0
O3A PA O1A C5' 249.4 240.0
O1A PA C5' O5' 181.0 60.0
O1A PA C5' H5'1 306.3 180.0
O1A PA C5' H5'2 55.8 300.0
PB O3A PA O2A 62.3 60.0
O1A PA O2A O3A 122.3 120.1
O1A PA O2A C5' 239.4 240.0
O3A PA O2A C5' 117.0 120.0
O2A PA C5' O5' 52.1 300.0
O2A PA C5' H5'1 177.4 60.0
O2A PA C5' H5'2 286.8 180.1
O1A PA O3A O2A 229.8 240.0
O1A PA O3A C5' 110.0 120.0
O2A PA O3A C5' 240.3 240.0
O3A PA O2A H2A 57.7 60.0
O3A PA C5' O5' 290.9 180.0
O3A PA C5' H5'1 56.2 300.0
O3A PA C5' H5'2 165.7 60.0
O1A PA C5' O2A 128.9 120.0
O1A PA C5' O3A 250.1 240.0
O2A PA C5' O3A 121.1 120.0
C5' PA O2A H2A 300.7 300.0
O5' C5' PA H5'1 234.7 240.0
O5' C5' PA H5'2 125.3 120.0
PA C5' O5' C4' 290.9 89.9
H5'1 C5' PA H5'2 250.6 239.9
H2A O2A PA O3A 57.7 60.0
H2A O2A PA C5' 300.7 300.0
PA C5' O5' H5'1 125.3 120.0
PA C5' O5' H5'2 234.7 240.0
H5'1 C5' O5' H5'2 109.5 120.0
C5' O5' C4' C1' 198.2 180.0
C5' O5' C4' H4'1 323.5 300.1
C5' O5' C4' H4'2 72.9 60.1
PA C5' H5'1 O5' 217.9 240.0
PA C5' H5'1 H5'2 108.9 120.1
O5' C5' H5'1 H5'2 251.0 240.1
H5'1 C5' O5' C4' 165.6 329.9
PA C5' H5'2 O5' 142.1 120.0
PA C5' H5'2 H5'1 251.1 240.0
O5' C5' H5'2 H5'1 109.0 119.9
H5'2 C5' O5' C4' 56.2 209.9
C4' O5' C5' H5'1 165.6 329.9
C4' O5' C5' H5'2 56.2 209.9
C1' C4' O5' H4'1 234.7 239.9
C1' C4' O5' H4'2 125.3 119.9
O5' C4' C1' N9 2.3 180.0
O5' C4' C1' H1'1 127.5 300.1
O5' C4' C1' H1'2 237.0 60.1
H4'1 C4' O5' H4'2 250.5 240.0
O5' C4' C1' H4'1 125.3 120.1
O5' C4' C1' H4'2 234.7 240.1
H4'1 C4' C1' H4'2 109.4 120.0
N9 C1' C4' H1'1 234.7 240.0
N9 C1' C4' H1'2 125.3 119.9
C4' C1' N9 C8 323.9 90.0
C4' C1' N9 C4 146.5 270.1
H1'1 C1' C4' H1'2 250.6 239.9
O5' C4' H4'1 C1' 231.6 239.9
O5' C4' H4'1 H4'2 115.8 119.9
C1' C4' H4'1 H4'2 244.2 240.0
H4'1 C4' C1' N9 237.0 59.9
H4'1 C4' C1' H1'1 2.3 180.0
H4'1 C4' C1' H1'2 111.7 300.0
O5' C4' H4'2 C1' 128.4 120.0
O5' C4' H4'2 H4'1 244.2 240.0
C1' C4' H4'2 H4'1 115.8 120.0
H4'2 C4' C1' N9 127.6 299.9
H4'2 C4' C1' H1'1 252.8 60.0
H4'2 C4' C1' H1'2 2.2 180.0
N9 C1' C4' H4'1 237.0 59.9
N9 C1' C4' H4'2 127.6 299.9
C4' C1' N9 H1'1 125.2 120.0
C4' C1' N9 H1'2 234.7 240.1
H1'1 C1' N9 H1'2 109.5 120.1
C8 N9 C1' C4 177.4 180.0
C1' N9 C8 N7 178.7 180.0
C1' N9 C8 H8 358.7 359.9
C1' N9 C4 C5 181.8 180.3
C1' N9 C4 N3 358.5 359.9
H1'1 C1' C4' H4'1 2.3 180.0
H1'1 C1' C4' H4'2 252.8 60.0
C4' C1' H1'1 N9 221.7 240.0
C4' C1' H1'1 H1'2 110.8 120.0
N9 C1' H1'1 H1'2 249.1 240.0
H1'1 C1' N9 C8 198.7 330.0
H1'1 C1' N9 C4 21.3 150.1
H1'2 C1' C4' H4'1 111.7 300.0
H1'2 C1' C4' H4'2 2.2 180.0
C4' C1' H1'2 N9 138.3 120.0
C4' C1' H1'2 H1'1 249.2 240.0
N9 C1' H1'2 H1'1 110.9 120.0
H1'2 C1' N9 C8 89.2 210.0
H1'2 C1' N9 C4 271.8 30.0
C8 N9 C1' H1'1 198.7 330.0
C8 N9 C1' H1'2 89.2 210.0
C1' N9 C8 C4 182.4 180.0
C8 N9 C4 C5 3.5 0.3
C8 N9 C4 N3 180.3 180.0
N7 C8 N9 H8 179.9 180.1
N9 C8 N7 C5 2.4 359.7
C4 N9 C1' H1'1 21.3 150.1
C4 N9 C1' H1'2 271.8 30.0
C1' N9 C4 C8 178.2 180.0
C4 N9 C8 N7 356.3 0.0
C4 N9 C8 H8 176.4 179.9
N7 C5 C4 N9 357.7 359.5
C6 C5 C4 N9 175.1 180.3
C5 C4 N9 N3 183.2 180.3
C2 N3 C4 N9 183.0 180.0
N7 C8 N9 C4 356.3 0.0
N9 C8 N7 H8 180.1 179.9
C8 N7 C5 C6 183.1 179.5
C8 N7 C5 C4 359.8 0.5
H8 C8 N9 C4 176.4 179.9
N9 C8 H8 N7 179.9 180.1
H8 C8 N7 C5 182.3 179.8
N9 C4 C5 N7 357.7 359.5
C5 N7 C8 H8 182.3 179.8
C6 C5 N7 C4 183.3 179.0
N7 C5 C6 N6 357.1 0.8
N7 C5 C6 N1 180.1 180.5
N7 C5 C4 N3 181.1 179.8
N9 C4 C5 C6 175.1 180.3
N7 C5 C6 C4 176.6 181.1
C6 C5 C4 N3 358.4 0.6
N6 C6 C5 N1 177.0 180.2
C5 C6 N6 HN61 180.0 179.8
C5 C6 N6 HN62 54.8 359.5
C5 C6 N1 C2 356.8 0.3
N9 C4 C5 N3 176.7 179.7
N7 C5 C4 C6 182.7 179.2
C4 C5 C6 N6 180.5 179.7
C4 C5 C6 N1 3.6 359.4
C2 N3 C4 C5 359.3 359.7
N6 C6 C5 C4 180.5 179.7
C5 C6 N6 N1 183.1 179.7
N6 C6 N1 C2 179.8 180.0
HN61 N6 C6 HN62 125.2 180.3
N1 C6 C5 C4 3.6 359.4
C5 C6 N1 N6 177.0 180.2
N1 C6 N6 HN61 356.9 0.0
N1 C6 N6 HN62 231.7 179.7
C6 N1 C2 N3 0.7 360.0
C6 N1 C2 H2 180.7 180.0
HN61 N6 C6 N1 356.9 0.0
C6 N6 HN61 HN62 234.8 179.7
HN62 N6 C6 N1 231.7 179.7
C6 N6 HN62 HN61 132.1 180.3
N3 C2 N1 H2 179.9 179.9
N1 C2 N3 C4 1.3 0.0
N9 C4 N3 C2 183.0 180.0
C5 C4 N3 C2 359.3 359.7
N1 C2 N3 H2 180.1 180.1
N1 C2 H2 N3 180.0 179.9
H2 C2 N3 C4 181.2 180.0
N9 C4 N3 C5 183.7 180.4
C4 N3 C2 H2 181.2 180.0