PDB Chemical Component V5A

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 V5A

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O2' C2' 1.415 1.429
O3' C3' 1.425 1.428
C3' C2' 1.536 1.548
C3' C4' 1.533 1.541
C2' C1' 1.525 1.550
C1' N9 1.463 1.465
C1' O4' 1.405 1.443
C4' O4' 1.446 1.437
C4' C5' 1.512 1.530
N9 C8 1.363 1.363
N9 C4 1.376 1.371
C5' O5' 1.425 1.429
O5' V 1.669 1.840
C8 N7 1.305 1.301
OV2 V 1.570 1.839
C4 N3 1.333 1.328
C4 C5 1.405 1.406
V OV1 1.565 1.583
N3 C2 1.321 1.317
N7 C5 1.357 1.355
C5 C6 1.408 1.405
C2 N1 1.325 1.320
C6 N1 1.327 1.330
C6 N6 1.381 1.384
OV2 H1 0.950 0.967
C5' H2 1.100 1.090
C5' H3 1.100 1.090
C4' H4 1.100 1.090
C3' H5 1.100 1.090
O3' H6 0.950 0.967
C2' H7 1.100 1.091
O2' H8 0.950 0.967
C1' H9 1.100 1.090
C8 H10 1.080 1.081
C2 H11 1.080 1.080
N6 H12 1.000 0.969
N6 H13 1.000 0.970

Bond Angles for V5A

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O2' C2' C1' 111.7 111.0
O2' C2' H7 110.4 110.8
O3' C3' C2' 109.4 110.5
O3' C3' H5 112.3 110.5
C3' C2' C1' 102.6 102.1
C2' C3' H5 110.6 110.5
C3' C2' H7 108.7 110.9
C3' C4' O4' 106.6 107.3
C3' C4' H4 107.6 110.0
C2' C1' N9 114.4 110.6
C2' C1' O4' 105.3 103.5
C1' C2' H7 108.9 110.9
C2' C1' H9 109.2 110.6
O4' C1' N9 106.8 110.7
C1' N9 C8 125.8 126.3
C1' N9 C4 126.7 126.3
N9 C1' H9 110.1 110.5
C4' O4' C1' 109.3 107.0
O4' C1' H9 110.9 110.8
O4' C4' H4 108.7 109.9
C4' C5' H2 109.2 109.4
C4' C5' H3 109.2 109.4
C4 N9 C8 107.5 107.5
N9 C8 N7 109.9 110.0
N9 C8 H10 125.1 125.0
N9 C4 N3 135.3 135.0
N9 C4 C5 106.0 106.0
OV2 V OV1 121.1 120.0
V OV2 H1 109.5 114.0
C5 C4 N3 118.7 119.0
C4 N3 C2 120.7 120.7
C4 C5 C6 118.4 118.2
N3 C2 N1 122.5 122.5
N3 C2 H11 118.7 118.8
N7 C5 C6 134.5 134.7
C5 C6 N1 118.8 118.5
C5 C6 N6 120.5 120.8
N1 C2 H11 118.7 118.8
C6 N6 H12 109.5 120.0
C6 N6 H13 109.5 120.0
H2 C5' H3 109.5 109.5
H12 N6 H13 109.5 120.0

Torsion Angles for V5A

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C3' C2' O2' C1' 115.9 112.7
O2' C2' C3' H5 96.3 102.2
C3' C2' O2' H7 237.1 236.4
O2' C2' C1' N9 274.2 273.8
O2' C2' C1' O4' 157.2 155.2
C1' C2' O2' H7 121.3 123.6
O2' C2' C1' H9 38.1 36.6
O3' C3' C2' C1' 93.1 97.9
C2' C3' O3' H5 123.3 122.6
O3' C3' C2' H7 208.2 216.0
O3' C3' C4' O4' 248.8 239.3
O3' C3' C4' H4 5.3 358.8
O2' C2' C3' C1' 238.9 241.7
O2' C2' C3' H7 123.8 123.6
O3' C3' C2' H5 235.7 237.4
C2' C3' C4' O4' 5.6 358.0
C2' C3' C4' H4 122.1 117.5
C3' C2' C1' N9 151.4 155.5
C3' C2' C1' O4' 34.4 37.0
C1' C2' C3' H7 244.8 241.8
C3' C2' C1' H9 275.3 278.3
C3' C4' O4' C1' 16.8 26.5
O4' C4' C3' H4 243.5 240.5
C3' C4' C5' H2 10.2 64.3
C3' C4' C5' H3 129.9 304.3
O2' C2' C1' H7 237.8 236.4
C1' C2' C3' H5 217.4 220.5
C3' C2' C1' H7 115.0 118.2
O4' C1' C2' N9 243.0 241.5
C2' C1' N9 C8 329.8 265.0
C2' C1' N9 C4 152.3 85.2
N9 C1' C2' H9 236.2 237.2
C4' O4' C1' C2' 327.5 320.0
O4' C1' C2' H9 119.2 118.6
C2' C1' N9 O4' 243.8 245.9
N9 C1' C2' H7 36.4 37.4
C2' C1' N9 H9 123.3 122.8
C4' O4' C1' N9 205.4 201.4
O4' C1' N9 H9 239.5 236.9
C4 N9 C1' C8 182.4 180.2
C1' N9 C8 N7 181.4 179.8
C1' N9 C8 H10 1.4 359.9
C1' N9 C4 N3 358.7 0.1
C1' N9 C4 C5 178.3 180.0
C2' C1' O4' N9 122.1 118.5
O4' C1' C2' H7 279.4 278.8
C2' C1' O4' H9 242.0 241.5
O4' C1' N9 C8 86.0 19.1
O4' C1' N9 C4 268.4 199.3
N9 C1' O4' H9 119.9 123.0
C1' O4' C4' H4 261.1 266.9
C3' C4' O4' H4 115.8 119.6
C2' C1' O4' C4' 327.5 320.0
C4' O4' C1' H9 85.5 78.5
O4' C4' C5' H2 249.3 306.5
O4' C4' C5' H3 9.0 186.5
H2 C5' C4' H3 240.3 120.0
C1' N9 C8 C4 182.1 180.2
C8 N9 C1' H9 206.5 142.2
C8 N9 C4 N3 180.7 180.3
C8 N9 C4 C5 0.3 0.2
C1' N9 C4 C8 177.9 179.8
C4 N9 C1' H9 28.9 322.4
C4 N9 C8 N7 359.3 359.6
C4 N9 C8 H10 179.3 179.7
C5 C4 N9 N3 179.6 179.9
N9 C4 N3 C2 180.2 180.0
N9 C4 C5 C6 179.8 180.1
O5' V OV2 H1 184.4 180.0
N9 C8 N7 H10 180.0 180.1
C8 N7 C5 C6 179.8 179.7
N3 C4 N9 C8 180.7 180.3
N9 C4 N3 C5 179.6 179.9
N3 C4 C5 C6 359.5 360.0
C4 N3 C2 N1 359.8 359.9
C4 N3 C2 H11 179.8 180.0
C5 C4 N9 C8 0.3 0.2
N9 C4 C5 N3 180.3 180.1
C5 C4 N3 C2 0.6 0.1
N7 C5 C4 C6 180.3 180.0
C4 C5 C6 N1 0.0 359.9
C4 C5 C6 N6 180.5 180.1
OV1 V OV2 H1 0.0 360.0
N1 C2 N3 H11 180.0 179.9
N9 C8 N7 C5 0.8 0.4
N7 C5 C4 N3 179.8 179.9
C4 C5 N7 C6 179.7 180.1
N7 C5 C6 N1 179.7 180.0
N7 C5 C6 N6 0.1 0.1
C6 C5 C4 N3 359.5 360.0
C5 C6 N6 H12 179.6 359.9
C5 C6 N6 H13 299.6 180.0
N3 C2 N1 H11 180.0 180.1
C5 C6 N1 C2 0.3 0.1
C5 C6 N1 N6 180.4 180.1
C6 N1 C2 H11 179.8 180.0
C5 C6 N6 N1 179.6 179.9
H12 N6 C6 H13 240.0 180.0
H1 OV2 V OV1 0.0 360.0
C4' C5' H2 H3 119.5 240.0
C4' C5' H3 H2 240.5 119.9
C3' C4' H4 O4' 244.9 242.1
H4 C4' O4' C1' 261.1 266.9
H4 C4' C5' H2 130.9 185.4
H4 C4' C5' H3 250.6 65.5
O3' C3' H5 C2' 122.6 122.6
H5 C3' C2' C1' 217.4 220.5
H5 C3' C2' H7 332.5 338.6
H5 C3' C4' O4' 124.6 116.7
H5 C3' C4' H4 241.1 236.2
H6 O3' C3' C2' 180.0 61.5
H6 O3' C3' H5 56.7 298.9
O2' C2' H7 C1' 123.0 123.7
C3' C2' H7 C1' 249.0 247.3
H7 C2' C3' H5 332.5 338.6
H7 C2' C1' N9 36.4 37.4
H7 C2' C1' O4' 279.4 278.8
H7 C2' C1' H9 160.2 160.2
H8 O2' C2' C1' 64.1 185.8
H8 O2' C2' H7 302.9 62.2
C2' C1' H9 N9 233.6 237.1
C2' C1' H9 O4' 115.6 114.1
H9 C1' C2' H7 160.2 160.2
O4' C1' H9 N9 118.0 123.0
H9 C1' N9 C8 206.5 142.2
H9 C1' N9 C4 28.9 322.4
N9 C8 H10 N7 180.0 179.9
N3 C2 H11 N1 180.0 179.9
C6 N6 H12 H13 120.0 180.0
C6 N6 H13 H12 240.0 180.0