PDB Chemical Component SAJ

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 SAJ

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O2C C2C 1.402 1.429
O2 C2 1.224 1.216
O3C C3C 1.407 1.430
C2C C3C 1.522 1.545
C2C C1C 1.520 1.545
C2 N3 1.351 1.346
C2 N1 1.424 1.345
N3 C4 1.354 1.348
C3C C4C 1.529 1.544
C1C N1 1.471 1.465
C1C O4C 1.401 1.444
N1 C6 1.371 1.368
C4 O4 1.244 1.217
C4 C5 1.420 1.416
C6 C5 1.398 1.350
O4C C4C 1.416 1.445
C4C C5C 1.524 1.530
O5C C5C 1.410 1.430
O5C PA 1.556 1.610
O1A PA 1.484 1.480
PA O3A 1.616 1.610
PA O2A 1.475 1.610
O3A PB 1.655 1.610
PB O2B 1.486 1.480
PB O1B 1.438 1.611
PB O1' 1.690 1.610
O1' C1' 1.504 1.429
C1' C2' 1.482 1.531
C1' O5' 1.431 1.429
C2' N2' 1.463 1.465
C2' C3' 1.548 1.532
O7' C7' 1.232 1.212
O5' C5' 1.473 1.429
C7' N2' 1.427 1.349
C7' C8' 1.540 1.507
C3' O3' 1.420 1.429
C3' C4' 1.543 1.531
C5' C4' 1.531 1.531
C5' C6' 1.512 1.507
C4' O4' 1.379 1.429
O6B C6' 1.370 1.207
C6' O6A 1.366 1.343
N3 H1 1.001 0.970
C5 H2 1.080 1.080
C6 H3 1.080 1.080
C1C H4 1.100 1.090
C2C H5 1.100 1.090
O2C H6 0.950 0.967
C3C H7 1.100 1.090
C4C H8 1.100 1.090
O3C H9 0.950 0.967
C5C H10 1.100 1.089
C5C H11 1.100 1.090
O2A H12 0.950 0.967
O1B H13 0.950 0.967
C1' H14 1.100 1.090
C2' H15 1.100 1.090
N2' H16 1.000 0.970
C8' H17 1.100 1.090
C8' H18 1.100 1.090
C8' H19 1.100 1.089
C3' H20 1.100 1.090
O3' H21 0.950 0.968
C4' H22 1.100 1.091
O4' H23 0.950 0.966
C5' H24 1.100 1.090
O6A H25 0.950 0.968

Bond Angles for SAJ

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O2C C2C C3C 113.9 110.6
O2C C2C H5 110.3 110.5
O3C C3C H7 112.2 110.5
C2C C3C C4C 102.8 104.1
C3C C2C H5 108.6 110.5
C2C C3C H7 110.4 110.5
C2C C1C O4C 104.4 104.8
C2C C1C H4 106.8 110.5
C2 N3 C4 126.0 120.2
C2 N3 H1 117.0 119.9
C2 N1 C6 117.8 120.6
N3 C4 O4 123.4 120.3
N3 C4 C5 117.9 119.4
C4 N3 H1 117.0 119.9
C3C C4C C5C 112.2 110.3
C4C C3C H7 110.4 110.6
C3C C4C H8 109.1 110.4
C1C O4C C4C 112.7 105.2
O4C C1C H4 108.3 110.4
N1 C6 C5 123.9 119.7
N1 C6 H3 118.0 120.2
C5 C4 O4 118.7 120.3
C4 C5 H2 121.5 120.5
C6 C5 H2 121.6 120.4
O4C C4C C5C 110.2 110.4
O4C C4C H8 110.7 110.5
C5C C4C H8 109.2 110.3
C4C C5C H10 109.3 109.5
C4C C5C H11 109.3 109.5
O5C C5C H10 109.4 109.5
O5C C5C H11 109.4 109.5
O5C PA O3A 99.5 109.4
O5C PA O2A 108.2 109.5
O1A PA O3A 111.6 109.5
O1A PA O2A 118.6 109.5
O2A PA O3A 109.0 109.4
PA O3A PB 133.0 134.0
PA O2A H12 109.5 114.0
O3A PB O2B 109.9 109.5
O3A PB O1B 109.4 109.5
O3A PB O1' 113.0 109.5
O1B PB O2B 112.8 109.5
O2B PB O1' 95.9 109.5
O1B PB O1' 115.3 109.4
PB O1B H13 109.5 114.0
PB O1' C1' 115.6 123.0
O1' C1' C2' 105.2 109.5
O1' C1' O5' 101.0 109.5
O1' C1' H14 110.7 109.5
C2' C1' O5' 116.4 109.4
C1' C2' N2' 107.8 109.6
C1' C2' C3' 110.8 109.1
C2' C1' H14 111.0 109.4
C1' C2' H15 110.7 109.5
C1' O5' C5' 114.0 114.1
O5' C1' H14 111.8 109.5
N2' C2' C3' 106.7 109.5
N2' C2' H15 111.0 109.6
C2' N2' H16 119.6 120.0
C2' C3' O3' 111.7 109.5
C2' C3' C4' 112.2 109.0
C3' C2' H15 109.8 109.5
C2' C3' H20 107.9 109.6
O7' C7' C8' 119.0 120.1
O5' C5' C6' 108.2 109.5
O5' C5' H24 109.5 109.5
C7' N2' H16 119.6 120.0
C7' C8' H17 109.5 109.5
C7' C8' H18 109.4 109.4
C7' C8' H19 109.5 109.5
O3' C3' C4' 107.5 109.5
O3' C3' H20 109.5 109.6
C3' O3' H21 109.5 114.0
C3' C4' O4' 111.3 109.6
C4' C3' H20 107.9 109.6
C3' C4' H22 107.3 109.5
C5' C4' H22 107.4 109.6
C5' C6' O6A 114.7 120.0
C6' C5' H24 109.0 109.5
O4' C4' H22 109.4 109.5
C4' O4' H23 109.5 114.0
C6' O6A H25 109.5 117.0
H10 C5C H11 109.5 109.5
H17 C8' H18 109.5 109.4
H17 C8' H19 109.5 109.5
H18 C8' H19 109.5 109.5

Torsion Angles for SAJ

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2C C2C C3C C4C 205.7 241.4
C3C C2C O2C H5 237.6 237.3
O2C C2C C3C H7 88.0 122.6
O2C C2C C1C O4C 155.7 142.7
O2C C2C C1C H4 41.1 23.8
O2 C2 N3 H1 359.2 0.1
O3C C3C C2C H5 199.0 237.3
C2C C3C O3C H7 124.7 122.6
O3C C3C C4C C5C 142.4 98.6
C4C C3C O3C H7 237.6 237.2
O3C C3C C4C H8 21.3 336.4
O2C C2C C3C H5 123.3 122.7
O3C C3C C2C H7 234.3 237.4
C3C C2C C1C O4C 32.8 24.0
C3C C2C C1C H4 278.2 265.1
C2C C3C C4C C5C 261.1 217.2
C4C C3C C2C H7 117.7 118.7
C2C C3C C4C H8 140.1 95.0
C2C C1C O4C C4C 339.3 319.5
O4C C1C C2C H4 114.6 118.9
N3 C2 N1 C6 0.6 0.1
C2 N3 C4 O4 180.2 179.9
C2 N3 C4 C5 0.2 0.1
C4 N3 C2 H1 180.0 179.9
C2 N1 C6 C5 359.5 359.9
C2 N1 C6 H3 179.5 180.0
C2 N3 C4 H1 180.0 180.1
C5 C4 N3 O4 180.0 180.1
N3 C4 C5 H2 180.0 179.9
O3C C3C C4C H7 123.5 122.7
C4C C3C C2C H5 82.4 118.7
C2C C3C C4C H7 242.2 241.3
C1C O4C C4C C3C 359.6 40.5
O4C C4C C3C C5C 120.0 118.8
O4C C4C C3C H8 241.1 241.0
C5C C4C C3C H8 121.1 122.2
C3C C4C C5C H10 172.6 305.0
C3C C4C C5C H11 292.4 65.0
C1C N1 C6 H3 0.2 0.4
C2C C1C O4C H4 246.5 241.0
C1C O4C C4C C5C 120.9 159.4
C1C O4C C4C H8 241.7 281.6
N1 C6 C5 H2 180.1 180.1
N3 C4 O4 C5 180.0 180.1
O4 C4 N3 H1 0.3 359.9
O4 C4 C5 H2 360.0 0.0
N3 C4 C5 O4 180.0 179.9
C5 C4 N3 H1 180.2 180.0
N1 C6 C5 C4 0.1 0.1
C6 C5 C4 H2 180.0 180.0
N1 C6 C5 H3 180.0 180.1
C6 C5 C4 O4 180.0 180.1
C4 C5 C6 H2 180.0 180.0
C3C C4C O4C C5C 238.7 241.2
O4C C4C C3C H7 138.9 94.6
C3C C4C O4C H8 117.9 119.0
C4C O4C C1C H4 92.8 78.5
C5C C4C O4C H8 239.2 237.8
O4C C4C C5C H10 55.3 189.6
O4C C4C C5C H11 175.1 309.6
C5C C4C C3C H7 18.9 335.8
C3C C4C C5C H8 239.0 237.7
O4C C4C C5C H8 121.7 122.4
O5C C5C C4C H10 239.9 240.0
O5C C5C C4C H11 120.1 120.0
H10 C5C C4C H11 240.2 240.0
O5C C5C C4C H8 173.5 307.2
C4C C5C O5C H10 120.1 120.0
C4C C5C O5C H11 239.9 240.0
H10 C5C O5C H11 119.9 120.0
PA O5C C5C H10 34.1 60.0
PA O5C C5C H11 274.3 300.0
O1A PA O5C O3A 116.6 120.0
O1A PA O5C O2A 230.3 240.0
O2A PA O5C O3A 246.3 240.0
O5C PA O3A PB 249.4 165.0
O5C PA O2A H12 236.4 60.0
O5C PA O1A O3A 251.5 240.0
O5C PA O1A O2A 123.6 120.0
O2A PA O1A O3A 127.9 120.0
O1A PA O3A PB 135.3 45.0
O1A PA O2A H12 0.0 180.0
O5C PA O3A O2A 246.9 240.0
O1A PA O3A O2A 132.9 120.0
O3A PA O2A H12 129.1 300.0
PA O3A PB O2B 182.4 45.0
PA O3A PB O1B 58.0 285.0
PA O3A PB O1' 288.1 165.0
O5C PA O2A O3A 107.2 120.0
O1A PA O2A O3A 230.9 240.0
O2A PA O3A PB 2.4 285.0
O1B PB O3A O2B 235.6 240.0
O2B PB O3A O1' 254.3 240.0
O1B PB O3A O1' 129.9 120.0
O3A PB O1B H13 122.7 300.0
O3A PB O1' C1' 104.2 185.0
O3A PB O2B O1B 237.6 240.0
O3A PB O2B O1' 117.0 120.0
O1B PB O2B O1' 239.4 240.0
O2B PB O1B H13 0.0 180.0
O2B PB O1' C1' 218.7 305.0
O3A PB O1B O2B 122.6 120.0
O3A PB O1B O1' 231.4 240.0
O2B PB O1B O1' 108.8 120.0
O1B PB O1' C1' 337.4 65.0
O3A PB O1' O2B 245.5 240.0
O3A PB O1' O1B 126.8 120.0
O1B PB O1' O2B 118.7 120.0
O1' PB O1B H13 251.3 60.0
PB O1' C1' C2' 213.5 210.0
PB O1' C1' O5' 92.0 90.0
PB O1' C1' H14 333.5 330.0
C2' C1' O1' O5' 121.5 119.9
O1' C1' C2' N2' 176.7 177.7
O1' C1' C2' C3' 293.2 297.6
C2' C1' O1' H14 240.0 240.0
O1' C1' C2' H15 55.1 57.5
O1' C1' O5' C5' 59.0 58.8
O5' C1' O1' H14 118.6 120.1
O1' C1' C2' O5' 249.2 240.0
O1' C1' C2' H14 119.8 120.0
C2' C1' O5' C5' 305.8 298.8
O5' C1' C2' H14 230.6 240.0
N2' C2' C1' C3' 243.6 240.1
N2' C2' C1' H15 121.6 120.2
C1' C2' N2' H16 35.6 95.0
C1' C2' C3' O3' 193.6 183.1
C1' C2' C3' C4' 314.4 303.0
C3' C2' C1' H15 238.0 240.1
C1' C2' C3' H20 73.2 63.0
O1' C1' O5' C2' 113.2 120.0
O1' C1' O5' H14 242.2 239.9
O5' C1' C2' N2' 287.5 297.7
O5' C1' C2' C3' 44.0 57.6
C2' C1' O5' H14 129.1 119.9
O5' C1' C2' H15 166.0 177.6
C1' O5' C5' C6' 185.2 181.1
C1' O5' C5' H24 303.9 301.2
N2' C2' C1' O5' 287.5 297.7
C1' C2' N2' C3' 119.0 119.7
N2' C2' C1' H14 57.0 57.7
C1' C2' N2' H15 238.6 239.8
N2' C2' C3' O3' 310.7 303.1
N2' C2' C3' C4' 71.5 62.9
C3' C2' N2' H15 119.6 120.2
N2' C2' C3' H20 190.3 182.9
C7' N2' C2' H16 180.0 180.1
C3' C2' C1' O5' 44.0 57.6
C1' C2' C3' N2' 242.9 240.1
C3' C2' C1' H14 173.4 177.6
C1' C2' C3' H15 122.5 119.9
N2' C2' C3' H15 239.7 239.8
C3' C2' N2' H16 276.5 335.3
O3' C3' C2' C4' 239.2 240.1
O3' C3' C2' H20 120.5 120.2
C2' C3' O3' H21 180.0 180.0
C2' C3' C4' O4' 180.7 176.9
C4' C3' C2' H20 241.2 240.0
C2' C3' C4' H22 300.4 297.0
O7' C7' N2' H16 179.8 180.0
O7' C7' C8' H17 360.0 240.0
O7' C7' C8' H18 120.0 360.0
O7' C7' C8' H19 240.0 120.0
C5' O5' C1' H14 176.8 178.8
O5' C5' C4' H22 54.1 62.4
O5' C5' C6' O6A 313.6 175.1
C6' C5' O5' H24 241.3 239.9
C7' N2' C2' C3' 96.5 155.4
C7' N2' C2' H15 337.0 35.2
C2' N2' C7' H16 180.0 179.9
C8' C7' N2' H16 359.9 0.1
H17 C8' C7' H18 240.0 240.0
H17 C8' C7' H19 120.0 120.0
H18 C8' C7' H19 240.0 240.0
C2' C3' O3' C4' 123.5 119.6
O3' C3' C2' H15 71.1 63.2
C2' C3' O3' H20 240.5 239.8
O3' C3' C4' O4' 303.8 296.7
C4' C3' O3' H20 117.0 120.3
O3' C3' C4' H22 63.5 56.8
C2' C3' C4' O3' 236.8 240.2
C4' C3' C2' H15 191.9 183.1
C2' C3' C4' H20 118.7 119.9
O3' C3' C4' H20 241.9 239.8
C4' C3' O3' H21 56.5 60.4
C5' C4' C3' H22 115.9 120.0
O4' C4' C3' H22 240.3 239.9
C3' C4' O4' H23 180.0 180.0
C1' O5' C5' C4' 61.4 61.2
C5' C4' C3' H20 297.6 297.1
C3' C4' C5' H22 244.1 240.1
O4' C4' C5' H22 120.4 120.1
C5' C4' O4' H23 302.3 299.7
O5' C5' C6' H24 119.0 120.1
C6' C5' C4' H22 294.3 302.4
C5' C6' O6A H25 180.9 180.0
O4' C4' C3' H20 61.9 57.0
C3' C4' O4' H22 118.4 120.1
C5' C4' O4' H22 240.8 239.8
O6B C6' C5' H24 15.3 235.1
O6B C6' O6A H25 0.0 359.9
O6A C6' C5' H24 194.6 55.0
C2 N3 H1 C4 180.0 179.9
H1 N3 C4 O4 0.3 359.9
H1 N3 C4 C5 180.2 180.0
H2 C5 C4 O4 360.0 0.0
N1 C6 H3 C5 180.0 179.9
H3 C6 C5 H2 0.1 360.0
C2C C1C H4 O4C 111.9 115.5
H4 C1C O4C C4C 92.8 78.5
O2C C2C H5 C3C 234.5 237.2
H5 C2C C3C C4C 82.4 118.7
H5 C2C C3C H7 324.7 359.9
H5 C2C C1C O4C 278.0 265.3
H5 C2C C1C H4 163.4 146.4
H6 O2C C2C C3C 180.0 298.6
H6 O2C C2C H5 302.4 61.3
C2C C3C H7 C4C 113.0 114.7
H7 C3C C2C H5 324.7 359.9
H7 C3C C4C C5C 18.9 335.8
H7 C3C C4C H8 257.9 213.6
C3C C4C H8 C5C 122.9 122.2
H8 C4C C3C H7 257.9 213.6
O4C C4C H8 C5C 238.6 237.7
H8 C4C C5C H10 293.6 67.3
H8 C4C C5C H11 53.4 187.3
H9 O3C C3C H7 55.3 298.9
H10 C5C C4C H8 293.6 67.3
C4C C5C H10 H11 119.8 120.0
O5C C5C H10 H11 240.2 240.0
H11 C5C C4C H8 53.4 187.3
C4C C5C H11 H10 240.2 240.0
O5C C5C H11 H10 119.8 120.0
H12 O2A PA O3A 129.1 300.0
H13 O1B PB O2B 0.0 180.0
H13 O1B PB O1' 251.3 60.0
O1' C1' H14 C2' 243.6 240.0
O1' C1' H14 O5' 111.8 120.1
C2' C1' H14 O5' 228.1 240.1
H14 C1' C2' N2' 57.0 57.7
H14 C1' C2' C3' 173.4 177.6
H14 C1' C2' H15 295.4 297.5
H14 C1' O5' C5' 176.8 178.8
H15 C2' C1' O5' 166.0 177.6
C1' C2' H15 N2' 119.7 120.2
C1' C2' H15 C3' 237.4 240.3
H15 C2' C1' H14 295.4 297.5
N2' C2' H15 C3' 117.7 120.1
H15 C2' N2' H16 157.0 215.1
H15 C2' C3' O3' 71.1 63.2
H15 C2' C3' C4' 191.9 183.1
H15 C2' C3' H20 310.6 303.1
H16 N2' C2' C3' 276.5 335.3
H16 N2' C2' H15 157.0 215.1
C7' C8' H17 H18 120.0 119.9
C7' C8' H17 H19 240.0 240.0
H18 C8' H17 H19 120.0 120.0
C7' C8' H18 H17 240.0 240.0
C7' C8' H18 H19 120.0 120.0
H17 C8' H18 H19 240.0 240.0
C7' C8' H19 H17 120.0 120.1
C7' C8' H19 H18 240.0 240.0
H17 C8' H19 H18 120.0 120.0
C2' C3' H20 O3' 121.8 120.2
C2' C3' H20 C4' 238.6 240.4
H20 C3' C2' H15 310.6 303.1
O3' C3' H20 C4' 116.8 120.2
H20 C3' O3' H21 299.5 300.2
H20 C3' C4' O4' 61.9 57.0
H20 C3' C4' H22 181.6 177.1
H21 O3' C3' C4' 56.5 60.4
H21 O3' C3' H20 299.5 300.2
C3' C4' H22 O4' 239.1 239.9
H22 C4' C3' H20 181.6 177.1
H22 C4' O4' H23 61.6 59.9
H23 O4' C4' H22 61.6 59.9
O5' C5' H24 C6' 241.8 239.9
H24 C5' C4' H22 172.0 182.3
H24 C5' C6' O6A 194.6 55.0