PDB Chemical Component SVY

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 SVY

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
N CA 1.459 1.469
CA C 1.547 1.507
C O 1.235 1.208
CA CB 1.530 1.530
CB OG 1.413 1.429
C1 C2 1.535 1.530
C1 C3 1.540 1.530
C1' C2' 1.520 1.529
C1' C3' 1.522 1.530
OG P 1.609 1.610
C1 O1P 1.453 1.429
P O1P 1.644 1.610
C1' O2P 1.424 1.430
P O2P 1.613 1.609
P O3P 1.599 1.480
C OXT 1.336 1.343
N HN1 1.000 1.009
N HN2 1.000 1.009
CA HA 1.100 1.090
CB HBC1 1.100 1.089
CB HBC2 1.100 1.089
OXT HOT 0.950 0.967
C1 H1 1.101 1.090
C2 H2C1 1.100 1.090
C2 H2C2 1.100 1.091
C2 H2C3 1.100 1.091
C3 H3C1 1.100 1.090
C3 H3C2 1.100 1.090
C3 H3C3 1.100 1.090
C1' H1' 1.100 1.089
C2' H2'1 1.100 1.090
C2' H2'2 1.100 1.090
C2' H2'3 1.100 1.091
C3' H3'1 1.100 1.090
C3' H3'2 1.100 1.091
C3' H3'3 1.100 1.090

Bond Angles for SVY

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
N CA C 110.4 109.5
N CA CB 109.2 109.5
CA N HN1 109.5 110.9
CA N HN2 109.5 111.0
N CA HA 108.8 109.4
CA C O 119.5 120.0
C CA CB 112.7 109.5
CA C OXT 118.2 120.0
C CA HA 107.7 109.5
O C OXT 122.2 120.0
CA CB OG 112.0 109.4
CB CA HA 107.9 109.5
CA CB HBC1 108.8 109.5
CA CB HBC2 108.8 109.5
CB OG P 113.4 123.0
OG CB HBC1 108.8 109.5
OG CB HBC2 108.9 109.5
C2 C1 C3 110.2 109.5
C2 C1 O1P 109.9 109.4
C2 C1 H1 106.9 109.5
C1 C2 H2C1 109.5 109.5
C1 C2 H2C2 109.5 109.4
C1 C2 H2C3 109.4 109.4
C3 C1 O1P 114.7 109.5
C3 C1 H1 106.9 109.5
C1 C3 H3C1 109.5 109.5
C1 C3 H3C2 109.4 109.5
C1 C3 H3C3 109.5 109.5
C2' C1' C3' 110.9 109.4
C2' C1' O2P 108.6 109.5
C2' C1' H1' 109.0 109.5
C1' C2' H2'1 109.5 109.5
C1' C2' H2'2 109.4 109.5
C1' C2' H2'3 109.4 109.5
C3' C1' O2P 109.1 109.5
C3' C1' H1' 109.0 109.5
C1' C3' H3'1 109.5 109.5
C1' C3' H3'2 109.5 109.4
C1' C3' H3'3 109.4 109.5
OG P O1P 145.5 109.5
OG P O2P 77.1 109.5
OG P O3P 101.9 109.5
C1 O1P P 127.0 123.0
O1P C1 H1 107.9 109.5
O1P P O2P 104.9 109.5
O1P P O3P 110.9 109.5
C1' O2P P 122.7 123.0
O2P C1' H1' 110.3 109.4
O2P P O3P 102.5 109.5
C OXT HOT 109.5 116.9
HN1 N HN2 109.4 111.0
HBC1 CB HBC2 109.4 109.5
H2C1 C2 H2C2 109.5 109.5
H2C1 C2 H2C3 109.5 109.5
H2C2 C2 H2C3 109.5 109.4
H3C1 C3 H3C2 109.5 109.5
H3C1 C3 H3C3 109.4 109.5
H3C2 C3 H3C3 109.5 109.5
H2'1 C2' H2'2 109.5 109.5
H2'1 C2' H2'3 109.5 109.4
H2'2 C2' H2'3 109.5 109.4
H3'1 C3' H3'2 109.5 109.5
H3'1 C3' H3'3 109.5 109.5
H3'2 C3' H3'3 109.5 109.5

Torsion Angles for SVY

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
N CA C O 57.7 340.0
C CA N CB 124.4 120.0
N CA C OXT 238.1 160.0
C CA N HA 242.0 240.0
N CA CB OG 199.6 295.0
CB CA N HA 117.6 120.0
N CA CB HBC1 320.0 55.0
N CA CB HBC2 79.2 175.1
HN1 N CA HN2 240.0 236.1
N CA C CB 237.6 240.0
C CA N HN1 180.0 296.1
C CA N HN2 300.0 60.0
N CA C HA 118.7 120.0
O C CA OXT 179.5 180.0
C CA CB OG 76.6 175.0
CB CA C HA 241.1 240.0
C CA CB HBC1 197.0 295.0
C CA CB HBC2 316.2 55.0
CA C OXT HOT 179.5 180.0
O C CA CB 180.1 100.0
CA C O OXT 180.5 180.0
O C CA HA 299.0 220.0
O C OXT HOT 0.0 360.0
N CA CB C 123.0 120.0
CB CA N HN1 55.6 176.1
CB CA N HN2 175.6 299.9
N CA CB HA 241.8 240.0
CB CA C O 180.1 100.0
CB CA C OXT 0.6 280.0
C CA CB HA 118.8 120.0
CA CB OG P 209.4 180.0
OG CB CA HBC1 239.6 240.0
OG CB CA HBC2 120.4 120.0
HBC1 CB CA HBC2 240.8 240.0
OG CB CA HA 317.8 55.0
CA CB OG HBC1 120.4 120.0
CA CB OG HBC2 239.6 240.0
CB OG P O1P 251.4 65.0
CB OG P O2P 153.9 185.0
CB OG P O3P 53.5 305.0
HBC1 CB OG HBC2 119.2 120.1
C3 C1 C2 O1P 127.4 240.0
C3 C1 C2 H1 244.2 120.0
C2 C1 C3 H3C1 180.0 60.0
C2 C1 C3 H3C2 300.0 180.0
C2 C1 C3 H3C3 60.0 300.0
C2 C1 O1P P 148.0 124.3
O1P C1 C2 H1 116.9 240.0
H2C1 C2 C1 H2C2 240.0 239.9
H2C1 C2 C1 H2C3 120.0 120.1
H2C2 C2 C1 H2C3 240.0 240.1
C2 C1 C3 O1P 235.3 120.0
C2 C1 C3 H1 115.8 240.0
C3 C1 C2 H2C1 180.0 175.1
C3 C1 C2 H2C2 300.0 295.1
C3 C1 C2 H2C3 60.0 55.0
C3 C1 O1P P 23.1 244.4
O1P C1 C3 H1 240.5 120.0
H3C1 C3 C1 H3C2 240.0 240.0
H3C1 C3 C1 H3C3 120.0 120.0
H3C2 C3 C1 H3C3 240.0 240.0
C3' C1' C2' O2P 119.9 240.0
C3' C1' C2' H1' 240.1 120.0
C2' C1' C3' H3'1 180.0 60.0
C2' C1' C3' H3'2 300.0 180.0
C2' C1' C3' H3'3 60.0 300.0
C2' C1' O2P P 214.2 115.1
O2P C1' C2' H1' 120.2 240.0
H2'1 C2' C1' H2'2 240.0 239.9
H2'1 C2' C1' H2'3 120.0 119.9
H2'2 C2' C1' H2'3 240.0 240.0
C2' C1' C3' O2P 240.4 120.0
C2' C1' C3' H1' 119.9 240.0
C3' C1' C2' H2'1 180.0 304.9
C3' C1' C2' H2'2 300.0 65.0
C3' C1' C2' H2'3 60.0 184.9
C3' C1' O2P P 93.2 235.1
O2P C1' C3' H1' 239.5 120.0
H3'1 C3' C1' H3'2 240.0 240.0
H3'1 C3' C1' H3'3 120.0 120.0
H3'2 C3' C1' H3'3 240.0 240.0
P OG CB HBC1 89.0 60.0
P OG CB HBC2 329.8 300.0
C1 O1P P OG 67.2 294.2
O1P P OG O2P 97.5 240.0
O1P P OG O3P 197.8 120.0
C1' O2P P OG 94.8 175.6
O2P P OG O3P 100.3 240.0
C2 C1 O1P C3 124.8 240.0
C2 C1 O1P H1 243.8 120.0
O1P C1 C2 H2C1 52.6 295.1
O1P C1 C2 H2C2 172.7 55.2
O1P C1 C2 H2C3 292.7 175.0
C3 C1 O1P H1 118.9 240.0
O1P C1 C3 H3C1 304.7 300.0
O1P C1 C3 H3C2 64.7 60.0
O1P C1 C3 H3C3 184.7 180.0
OG P O1P C1 67.2 294.2
C1 O1P P O2P 156.0 174.3
C1 O1P P O3P 266.0 54.2
OG P O1P O2P 271.3 120.0
OG P O1P O3P 161.3 240.0
P O1P C1 H1 264.2 4.4
C1' O2P P O1P 310.3 295.6
O2P P O1P O3P 250.0 120.0
C2' C1' O2P C3' 121.0 240.0
C2' C1' O2P H1' 240.7 120.0
O2P C1' C2' H2'1 60.1 64.9
O2P C1' C2' H2'2 180.1 185.0
O2P C1' C2' H2'3 300.1 304.9
C3' C1' O2P H1' 119.7 240.0
O2P C1' C3' H3'1 299.5 300.0
O2P C1' C3' H3'2 59.5 60.0
O2P C1' C3' H3'3 179.5 180.0
OG P O2P C1' 94.8 175.6
O1P P O2P C1' 310.3 295.6
C1' O2P P O3P 194.4 55.6
OG P O2P O1P 144.5 240.0
OG P O2P O3P 260.4 120.0
O1P P O2P O3P 115.9 240.0
P O2P C1' H1' 333.5 355.0
OG P O3P O1P 190.7 120.0
OG P O3P O2P 79.2 240.0
O1P P O3P O2P 248.5 120.0
CA C OXT O 179.5 180.0
OXT C CA CB 0.6 280.0
OXT C CA HA 119.5 40.0
HN1 N CA C 180.0 296.1
HN1 N CA CB 55.6 176.1
CA N HN1 HN2 120.0 123.9
HN1 N CA HA 298.0 56.1
HN2 N CA C 300.0 60.0
HN2 N CA CB 175.6 299.9
CA N HN2 HN1 240.0 236.1
HN2 N CA HA 58.0 180.0
N CA HA C 240.3 240.0
N CA HA CB 118.4 120.0
HA CA N HN1 298.0 56.1
HA CA N HN2 58.0 180.0
HA CA C O 299.0 220.0
C CA HA CB 238.1 240.0
HA CA C OXT 119.5 40.0
HA CA CB OG 317.8 55.0
HA CA CB HBC1 78.2 175.0
HA CA CB HBC2 197.4 295.0
CA CB HBC1 OG 237.7 240.0
HBC1 CB CA HA 78.2 175.0
CA CB HBC1 HBC2 118.8 120.0
HBC1 CB OG P 89.0 60.0
OG CB HBC1 HBC2 241.2 240.0
CA CB HBC2 OG 122.3 120.0
HBC2 CB CA HA 197.4 295.0
CA CB HBC2 HBC1 241.2 240.0
HBC2 CB OG P 329.8 300.0
OG CB HBC2 HBC1 118.8 120.0
C2 C1 H1 C3 242.0 120.0
C2 C1 H1 O1P 118.2 240.1
H1 C1 C2 H2C1 295.8 55.1
H1 C1 C2 H2C2 55.8 175.1
H1 C1 C2 H2C3 175.8 295.0
C3 C1 H1 O1P 236.2 120.0
H1 C1 C3 H3C1 64.2 180.0
H1 C1 C3 H3C2 184.2 300.0
H1 C1 C3 H3C3 304.2 60.0
H1 C1 O1P P 264.2 4.4
H2C1 C2 C1 C3 180.0 175.1
H2C1 C2 C1 O1P 52.6 295.1
H2C1 C2 C1 H1 295.8 55.1
C1 C2 H2C1 H2C2 120.0 120.0
C1 C2 H2C1 H2C3 240.0 240.0
H2C2 C2 H2C1 H2C3 120.0 120.0
H2C2 C2 C1 C3 300.0 295.1
H2C2 C2 C1 O1P 172.7 55.2
H2C2 C2 C1 H1 55.8 175.1
C1 C2 H2C2 H2C1 240.0 240.0
C1 C2 H2C2 H2C3 120.0 119.9
H2C1 C2 H2C2 H2C3 240.0 239.9
H2C3 C2 C1 C3 60.0 55.0
H2C3 C2 C1 O1P 292.7 175.0
H2C3 C2 C1 H1 175.8 295.0
C1 C2 H2C3 H2C1 120.0 120.0
C1 C2 H2C3 H2C2 240.0 240.1
H2C1 C2 H2C3 H2C2 120.0 120.1
H3C1 C3 C1 O1P 304.7 300.0
H3C1 C3 C1 H1 64.2 180.0
C1 C3 H3C1 H3C2 120.0 120.0
C1 C3 H3C1 H3C3 240.0 240.0
H3C2 C3 H3C1 H3C3 120.0 120.0
H3C2 C3 C1 O1P 64.7 60.0
H3C2 C3 C1 H1 184.2 300.0
C1 C3 H3C2 H3C1 240.0 240.0
C1 C3 H3C2 H3C3 120.0 120.0
H3C1 C3 H3C2 H3C3 240.0 240.0
H3C3 C3 C1 O1P 184.7 180.0
H3C3 C3 C1 H1 304.2 60.0
C1 C3 H3C3 H3C1 120.0 120.0
C1 C3 H3C3 H3C2 240.0 240.0
H3C1 C3 H3C3 H3C2 120.0 120.0
C2' C1' H1' C3' 238.9 120.0
C2' C1' H1' O2P 119.1 240.0
H1' C1' C2' H2'1 299.9 184.9
H1' C1' C2' H2'2 59.9 305.0
H1' C1' C2' H2'3 179.9 64.9
C3' C1' H1' O2P 240.2 120.0
H1' C1' C3' H3'1 60.1 180.1
H1' C1' C3' H3'2 180.1 300.0
H1' C1' C3' H3'3 300.1 60.0
H1' C1' O2P P 333.5 355.0
H2'1 C2' C1' C3' 180.0 304.9
H2'1 C2' C1' O2P 60.1 64.9
H2'1 C2' C1' H1' 299.9 184.9
C1' C2' H2'1 H2'2 120.0 120.1
C1' C2' H2'1 H2'3 240.0 240.0
H2'2 C2' H2'1 H2'3 120.0 119.9
H2'2 C2' C1' C3' 300.0 65.0
H2'2 C2' C1' O2P 180.1 185.0
H2'2 C2' C1' H1' 59.9 305.0
C1' C2' H2'2 H2'1 240.0 239.9
C1' C2' H2'2 H2'3 120.0 120.0
H2'1 C2' H2'2 H2'3 240.0 240.1
H2'3 C2' C1' C3' 60.0 184.9
H2'3 C2' C1' O2P 300.1 304.9
H2'3 C2' C1' H1' 179.9 64.9
C1' C2' H2'3 H2'1 120.0 120.0
C1' C2' H2'3 H2'2 240.0 240.0
H2'1 C2' H2'3 H2'2 120.0 120.0
H3'1 C3' C1' O2P 299.5 300.0
H3'1 C3' C1' H1' 60.1 180.1
C1' C3' H3'1 H3'2 120.0 120.0
C1' C3' H3'1 H3'3 240.0 240.0
H3'2 C3' H3'1 H3'3 120.0 120.0
H3'2 C3' C1' O2P 59.5 60.0
H3'2 C3' C1' H1' 180.1 300.0
C1' C3' H3'2 H3'1 240.0 240.0
C1' C3' H3'2 H3'3 120.0 120.0
H3'1 C3' H3'2 H3'3 240.0 240.0
H3'3 C3' C1' O2P 179.5 180.0
H3'3 C3' C1' H1' 300.1 60.0
C1' C3' H3'3 H3'1 120.0 120.0
C1' C3' H3'3 H3'2 240.0 240.0
H3'1 C3' H3'3 H3'2 120.0 120.0