PDB Chemical Component D16

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 D16

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
N1 C2 1.434 1.343
N1 C8A 1.397 1.381
N1 HN1 1.000 0.970
C2 CM2 1.500 1.507
C2 N3 1.419 1.304
CM2 HM21 1.100 1.090
CM2 HM22 1.100 1.090
CM2 HM23 1.100 1.091
N3 C4 1.418 1.347
C4 O4 1.209 1.219
C4 C4A 1.520 1.474
C4A C5 1.409 1.393
C4A C8A 1.431 1.407
C5 C6 1.444 1.379
C5 H5 1.080 1.080
C6 C7 1.443 1.387
C6 C9 1.589 1.507
C7 C8 1.428 1.379
C7 H7 1.079 1.081
C8 C8A 1.412 1.388
C8 H8 1.080 1.080
C9 N10 1.557 1.465
C9 H91 1.100 1.090
C9 H92 1.100 1.089
N10 C14 1.450 1.386
N10 CP1 1.474 1.465
C11 S13 1.737 1.758
C11 C16 1.350 1.369
C11 C 1.547 1.418
S13 C14 1.738 1.706
C14 C15 1.358 1.360
C15 C16 1.390 1.370
C15 H15 1.080 1.080
C16 H16 1.080 1.081
C O 1.253 1.218
C N 1.384 1.348
N CA 1.475 1.464
N HN 1.000 0.970
CA CB 1.589 1.530
CA CT 1.584 1.507
CA HA 1.100 1.090
CB CG 1.595 1.530
CB HB1 1.100 1.090
CB HB2 1.100 1.090
CG CD 1.579 1.507
CG HG1 1.100 1.091
CG HG2 1.100 1.090
CD OE1 1.242 1.209
CD OE2 1.252 1.342
OE2 HOE2 0.950 0.967
CT O1 1.249 1.209
CT O2 1.242 1.342
O2 HO2 0.950 0.968
CP1 HP11 1.100 1.091
CP1 HP12 1.100 1.090
CP1 HP13 1.100 1.090

Bond Angles for D16

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C2 N1 C8A 122.2 120.5
C2 N1 HN1 118.9 119.8
N1 C2 CM2 121.0 118.3
N1 C2 N3 118.9 123.4
C8A N1 HN1 118.9 119.7
N1 C8A C4A 119.3 118.4
N1 C8A C8 117.7 122.0
CM2 C2 N3 120.1 118.3
C2 CM2 HM21 109.5 109.5
C2 CM2 HM22 109.5 109.5
C2 CM2 HM23 109.5 109.5
C2 N3 C4 123.0 121.7
HM21 CM2 HM22 109.5 109.5
HM21 CM2 HM23 109.5 109.5
HM22 CM2 HM23 109.5 109.4
N3 C4 O4 122.1 121.0
N3 C4 C4A 116.0 118.1
O4 C4 C4A 122.0 121.0
C4 C4A C5 122.5 122.1
C4 C4A C8A 120.4 117.9
C5 C4A C8A 117.1 120.1
C4A C5 C6 123.3 119.4
C4A C5 H5 118.4 120.3
C4A C8A C8 122.9 119.6
C6 C5 H5 118.4 120.3
C5 C6 C7 116.9 120.5
C5 C6 C9 121.7 119.7
C7 C6 C9 121.4 119.8
C6 C7 C8 121.3 120.7
C6 C7 H7 119.3 119.7
C6 C9 N10 118.8 109.5
C6 C9 H91 107.1 109.4
C6 C9 H92 107.1 109.5
C8 C7 H7 119.4 119.6
C7 C8 C8A 118.6 119.7
C7 C8 H8 120.7 120.1
C8A C8 H8 120.7 120.2
N10 C9 H91 107.1 109.5
N10 C9 H92 107.1 109.5
C9 N10 C14 122.4 120.0
C9 N10 CP1 116.7 120.0
H91 C9 H92 109.5 109.5
C14 N10 CP1 120.5 120.0
N10 C14 S13 127.2 124.6
N10 C14 C15 124.7 124.6
N10 CP1 HP11 109.5 109.4
N10 CP1 HP12 109.5 109.5
N10 CP1 HP13 109.5 109.5
S13 C11 C16 110.4 109.4
S13 C11 C 118.9 125.3
C11 S13 C14 92.6 91.6
C16 C11 C 130.7 125.3
C11 C16 C15 112.6 113.5
C11 C16 H16 123.7 123.2
C11 C O 118.7 120.0
C11 C N 117.5 120.0
S13 C14 C15 108.0 110.8
C14 C15 C16 116.4 114.7
C14 C15 H15 121.8 122.7
C16 C15 H15 121.8 122.7
C15 C16 H16 123.7 123.2
O C N 123.3 120.0
C N CA 118.6 120.0
C N HN 120.7 120.0
CA N HN 120.7 120.0
N CA CB 114.1 109.5
N CA CT 108.2 109.5
N CA HA 106.0 109.5
CB CA CT 117.7 109.5
CB CA HA 104.8 109.4
CA CB CG 123.0 109.5
CA CB HB1 106.0 109.5
CA CB HB2 106.0 109.5
CT CA HA 104.9 109.5
CA CT O1 116.0 120.0
CA CT O2 116.0 120.0
CG CB HB1 106.0 109.4
CG CB HB2 106.0 109.4
CB CG CD 113.8 109.5
CB CG HG1 108.4 109.4
CB CG HG2 108.4 109.5
HB1 CB HB2 109.4 109.5
CD CG HG1 108.4 109.5
CD CG HG2 108.4 109.5
CG CD OE1 115.6 120.0
CG CD OE2 116.5 120.0
HG1 CG HG2 109.4 109.5
OE1 CD OE2 127.9 120.0
CD OE2 HOE2 109.5 117.0
O1 CT O2 128.0 120.0
CT O2 HO2 109.5 117.0
HP11 CP1 HP12 109.5 109.4
HP11 CP1 HP13 109.5 109.5
HP12 CP1 HP13 109.4 109.5

Torsion Angles for D16

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C8A N1 C2 HN1 180.0 180.3
C2 N1 C8A C4A 0.1 360.0
C2 N1 C8A C8 179.8 180.0
CM2 C2 N1 N3 180.2 180.1
N1 C2 CM2 HM21 179.8 89.9
N1 C2 CM2 HM22 299.8 210.0
N1 C2 CM2 HM23 59.8 329.9
N1 C2 N3 C4 359.9 0.0
C2 N1 C8A HN1 180.0 179.7
C8A N1 C2 CM2 180.3 180.1
C8A N1 C2 N3 0.1 360.0
C4 C4A C8A N1 359.7 0.1
C5 C4A C8A N1 179.7 180.0
C4A C8A N1 C8 180.3 179.9
C7 C8 C8A N1 180.3 180.0
N1 C8A C8 H8 0.4 0.1
C2 N1 HN1 C8A 180.0 180.3
HN1 N1 C2 CM2 0.3 359.8
HN1 N1 C2 N3 180.1 179.7
HN1 N1 C8A C4A 180.1 180.3
HN1 N1 C8A C8 359.8 0.3
CM2 C2 N1 C8A 180.3 180.1
CM2 C2 N1 HN1 0.3 359.8
N1 C2 CM2 N3 179.8 179.9
CM2 C2 N3 C4 179.7 179.9
HM21 CM2 C2 HM22 240.0 239.9
HM21 CM2 C2 HM23 120.0 120.0
HM22 CM2 C2 HM23 240.0 240.1
N3 C2 N1 C8A 0.1 360.0
N3 C2 N1 HN1 180.1 179.7
N1 C2 N3 CM2 180.2 180.1
N3 C2 CM2 HM21 0.0 270.0
N3 C2 CM2 HM22 120.0 30.1
N3 C2 CM2 HM23 240.0 150.0
C2 N3 C4 O4 180.0 180.0
C2 N3 C4 C4A 359.9 0.0
HM21 CM2 C2 N3 0.0 270.0
C2 CM2 HM21 HM22 120.0 120.1
C2 CM2 HM21 HM23 240.0 240.0
HM22 CM2 HM21 HM23 120.0 119.9
HM22 CM2 C2 N3 120.0 30.1
C2 CM2 HM22 HM21 240.0 239.9
C2 CM2 HM22 HM23 120.0 120.0
HM21 CM2 HM22 HM23 240.0 240.1
HM23 CM2 C2 N3 240.0 150.0
C2 CM2 HM23 HM21 120.0 120.1
C2 CM2 HM23 HM22 240.0 240.0
HM21 CM2 HM23 HM22 120.0 120.0
O4 C4 N3 C4A 180.1 179.9
N3 C4 C4A C5 180.3 180.0
N3 C4 C4A C8A 0.3 359.9
N3 C4 O4 C4A 179.9 180.1
O4 C4 C4A C5 0.2 0.1
O4 C4 C4A C8A 180.2 180.0
N1 C8A C4A C4 359.7 0.1
N3 C4 C4A O4 180.1 179.9
C5 C4A C4 C8A 180.0 180.1
C4 C4A C5 C6 179.8 179.9
C4 C4A C5 H5 359.8 359.9
C4 C4A C8A C8 180.0 180.0
N1 C8A C4A C5 179.7 180.0
C4 C4A C5 C8A 180.0 179.9
C5 C4A C8A C8 360.0 360.0
C6 C5 C4A H5 180.0 180.0
C4A C5 C6 C7 0.3 0.1
C4A C5 C6 C9 180.4 180.0
C4A C8A N1 HN1 180.1 180.3
N1 C8A C4A C8 179.7 180.1
C4 C4A C8A C5 180.0 180.1
C8A C4A C5 C6 359.9 360.0
C8A C4A C5 H5 179.8 180.0
C7 C8 C8A C4A 0.1 0.1
C4A C8A C8 H8 180.1 180.1
C6 C5 C4A C8A 359.9 360.0
C4A C5 C6 H5 180.0 180.0
C7 C6 C5 C9 179.8 180.1
C5 C6 C7 C8 359.8 360.0
C5 C6 C7 H7 179.8 179.9
C5 C6 C9 N10 20.8 90.0
C5 C6 C9 H91 142.1 210.0
C5 C6 C9 H92 259.5 330.0
H5 C5 C4A C8A 179.8 180.0
C4A C5 H5 C6 180.0 180.0
H5 C5 C6 C7 180.3 180.0
H5 C5 C6 C9 0.5 360.0
C7 C6 C5 H5 180.3 180.0
C5 C6 C7 C9 180.2 179.9
C7 C6 C9 N10 201.0 270.0
C7 C6 C9 H91 322.3 30.0
C7 C6 C9 H92 79.7 150.0
C8 C7 C6 H7 180.0 180.1
C6 C7 C8 C8A 0.1 360.0
C6 C7 C8 H8 180.1 179.9
C9 C6 C5 H5 0.5 360.0
C5 C6 C9 C7 179.8 180.1
C9 C6 C7 C8 179.6 180.0
C9 C6 C7 H7 359.6 360.0
N10 C9 C6 H91 238.7 240.0
N10 C9 C6 H92 121.3 120.0
C6 C9 N10 C14 62.9 89.9
C6 C9 N10 CP1 235.9 270.0
H91 C9 C6 H92 242.6 240.0
N1 C8A C8 C7 180.3 180.0
C4A C8A C8 C7 0.1 0.1
C8 C7 C6 C9 179.6 180.0
C6 C7 C8 H7 180.0 179.9
C8A C8 C7 H8 180.0 180.0
H7 C7 C6 C9 359.6 360.0
C6 C7 H7 C8 180.0 180.1
H7 C7 C8 C8A 180.1 180.0
H7 C7 C8 H8 0.1 360.0
C8 C8A N1 HN1 359.8 0.3
N1 C8A C8 C4A 180.3 179.9
C8A C8 C7 H7 180.1 180.0
C7 C8 C8A H8 180.0 180.0
H8 C8 C7 H7 0.1 360.0
C7 C8 H8 C8A 180.0 180.0
C6 C9 N10 H91 121.3 120.0
C6 C9 N10 H92 238.7 240.0
H91 C9 N10 H92 117.4 120.0
C14 N10 C9 CP1 187.0 180.0
C9 N10 C14 S13 9.9 0.1
C9 N10 C14 C15 188.0 180.0
C9 N10 CP1 HP11 180.0 90.0
C9 N10 CP1 HP12 300.0 209.9
C9 N10 CP1 HP13 60.0 330.0
C6 C9 H91 N10 231.6 240.0
C6 C9 H91 H92 115.8 120.0
N10 C9 H91 H92 244.3 240.0
H91 C9 N10 C14 301.6 330.0
H91 C9 N10 CP1 114.6 150.0
C6 C9 H92 N10 128.4 120.0
C6 C9 H92 H91 244.2 240.1
N10 C9 H92 H91 115.8 120.0
H92 C9 N10 C14 184.2 210.0
H92 C9 N10 CP1 357.2 30.0
C14 N10 C9 H91 301.6 330.0
C14 N10 C9 H92 184.2 210.0
C9 N10 C14 CP1 172.7 180.0
C14 N10 CP1 HP11 353.1 270.0
C14 N10 CP1 HP12 113.1 30.0
C14 N10 CP1 HP13 233.1 150.1
C11 S13 C14 N10 177.5 180.0
S13 C14 N10 C15 181.9 180.0
N10 C14 C15 C16 182.7 180.0
N10 C14 C15 H15 2.7 360.0
CP1 N10 C9 H91 114.6 150.0
CP1 N10 C9 H92 357.2 30.0
C9 N10 CP1 C14 186.9 180.0
CP1 N10 C14 S13 197.1 180.0
CP1 N10 C14 C15 15.2 360.0
HP11 CP1 N10 HP12 240.0 240.0
HP11 CP1 N10 HP13 120.0 120.0
HP12 CP1 N10 HP13 240.0 239.9
N10 C14 S13 C11 177.5 180.0
C16 C11 S13 C 180.3 180.3
S13 C11 C16 C15 360.0 0.0
S13 C11 C16 H16 180.0 180.0
S13 C11 C O 7.4 180.0
S13 C11 C N 180.2 0.1
C11 S13 C14 C15 359.1 360.0
S13 C11 C16 C 179.7 179.7
C16 C11 S13 C14 0.5 360.0
C16 C11 C O 187.1 359.7
C16 C11 C N 359.9 179.8
C14 C15 C16 C11 359.3 360.0
C11 C16 C15 H15 179.2 180.0
C15 C16 C11 H16 180.0 180.0
S13 C11 C C16 180.3 180.3
C C11 S13 C14 180.3 179.7
C C11 C16 C15 180.3 180.3
C C11 C16 H16 0.3 0.3
O C C11 N 187.2 180.0
C11 C N CA 183.1 180.0
C11 C N HN 3.1 360.0
S13 C14 N10 CP1 197.1 180.0
N10 C14 S13 C15 178.4 180.0
C14 S13 C11 C16 0.5 360.0
C14 S13 C11 C 180.3 179.7
S13 C14 C15 C16 1.1 0.0
S13 C14 C15 H15 181.1 180.0
C15 C14 N10 CP1 15.2 360.0
N10 C14 C15 S13 181.6 180.0
C11 C16 C15 C14 359.3 360.0
C16 C15 C14 H15 180.0 180.1
C14 C15 C16 H16 179.2 180.0
C15 C16 C11 C 180.3 180.3
C11 C16 C15 H16 180.0 180.0
C14 C15 C16 H15 180.0 179.9
C14 C15 H15 C16 180.0 180.1
H15 C15 C16 H16 359.2 0.0
H16 C16 C11 C 0.3 0.3
C11 C16 H16 C15 180.0 180.0
H16 C16 C15 H15 359.2 0.0
C11 C O N 172.4 180.0
O C N CA 355.6 0.0
O C N HN 175.6 180.0
C11 C N O 187.5 180.0
CA N C HN 180.0 180.0
C N CA CB 92.6 155.0
C N CA CT 225.7 275.0
C N CA HA 337.7 35.0
C N CA HN 180.0 180.0
CB CA N CT 226.9 240.0
CB CA N HA 114.8 119.9
N CA CB CG 289.2 295.0
N CA CB HB1 51.0 55.0
N CA CB HB2 167.3 175.0
CT CA N HA 247.9 239.9
N CA CT O1 290.5 0.0
N CA CT O2 110.2 180.0
C N HN CA 180.0 180.0
HN N CA CB 272.6 335.0
HN N CA CT 45.7 95.0
HN N CA HA 157.7 215.1
CB CA N HN 272.6 335.0
N CA CB CT 128.4 120.0
N CA CB HA 244.5 240.0
CT CA CB HA 116.0 120.0
CB CA CT O1 61.7 120.0
CB CA CT O2 241.4 300.0
CG CB CA HB1 238.1 240.0
CG CB CA HB2 121.9 120.0
CA CB CG CD 207.3 180.0
CA CB CG HG1 328.0 300.0
CA CB CG HG2 86.7 60.0
HB1 CB CA HB2 243.8 240.0
CT CA N HN 45.7 95.0
N CA CT CB 228.8 240.0
N CA CT HA 112.8 120.0
CB CA CT HA 244.0 240.0
CT CA CB CG 160.7 175.0
CT CA CB HB1 282.6 295.0
CT CA CB HB2 38.8 55.0
O1 CT CA O2 180.3 180.0
CA CT O2 HO2 180.3 180.0
HA CA N HN 157.7 215.1
N CA HA CB 121.0 120.0
N CA HA CT 245.6 239.9
CB CA HA CT 124.6 120.0
HA CA CB CG 44.7 55.0
HA CA CB HB1 166.6 175.0
HA CA CB HB2 282.8 295.0
HA CA CT O1 177.7 240.0
HA CA CT O2 357.4 60.0
CG CB CA CT 160.7 175.0
CG CB CA HA 44.7 55.0
CA CB CG HB1 121.9 120.0
CA CB CG HB2 238.1 240.0
HB1 CB CG HB2 116.3 120.0
CD CG CB HG1 239.3 240.0
CD CG CB HG2 120.7 120.1
CB CG CD OE1 138.9 0.0
CB CG CD OE2 318.9 180.0
HG1 CG CB HG2 241.3 240.0
HB1 CB CA CT 282.6 295.0
HB1 CB CA HA 166.6 175.0
CA CB HB1 CG 227.8 240.0
CA CB HB1 HB2 113.9 120.0
CG CB HB1 HB2 246.0 240.1
HB1 CB CG CD 85.5 60.0
HB1 CB CG HG1 206.2 180.0
HB1 CB CG HG2 324.8 299.9
HB2 CB CA CT 38.8 55.0
HB2 CB CA HA 282.8 295.0
CA CB HB2 CG 132.2 120.0
CA CB HB2 HB1 246.1 240.0
CG CB HB2 HB1 114.0 120.0
HB2 CB CG CD 329.2 300.0
HB2 CB CG HG1 89.9 60.0
HB2 CB CG HG2 208.5 180.0
CD CG CB HB1 85.5 60.0
CD CG CB HB2 329.2 300.0
CB CG CD HG1 120.6 120.0
CB CG CD HG2 239.4 240.0
HG1 CG CD HG2 118.7 120.0
OE1 CD CG OE2 180.0 180.0
CG CD OE2 HOE2 180.0 180.0
HG1 CG CB HB1 206.2 180.0
HG1 CG CB HB2 89.9 60.0
CB CG HG1 CD 236.0 240.0
CB CG HG1 HG2 118.0 120.0
CD CG HG1 HG2 242.0 240.0
HG1 CG CD OE1 18.3 240.1
HG1 CG CD OE2 198.3 60.0
HG2 CG CB HB1 324.8 299.9
HG2 CG CB HB2 208.5 180.0
CB CG HG2 CD 124.0 120.1
CB CG HG2 HG1 242.0 240.1
CD CG HG2 HG1 118.0 120.0
HG2 CG CD OE1 259.6 120.0
HG2 CG CD OE2 79.6 300.0
OE1 CD CG HG1 18.3 240.1
OE1 CD CG HG2 259.6 120.0
CG CD OE1 OE2 180.0 180.0
OE1 CD OE2 HOE2 0.0 359.9
OE2 CD CG HG1 198.3 60.0
OE2 CD CG HG2 79.6 300.0
CG CD OE2 OE1 180.0 180.0
O1 CT CA HA 177.7 240.0
CA CT O1 O2 179.7 180.0
O1 CT O2 HO2 0.0 360.0
O2 CT CA HA 357.4 60.0
CA CT O2 O1 180.3 180.0
N10 CP1 HP11 HP12 120.0 120.0
N10 CP1 HP11 HP13 240.0 240.0
HP12 CP1 HP11 HP13 120.0 120.0
N10 CP1 HP12 HP11 240.0 240.0
N10 CP1 HP12 HP13 120.0 120.0
HP11 CP1 HP12 HP13 240.0 240.0
N10 CP1 HP13 HP11 120.0 119.9
N10 CP1 HP13 HP12 240.0 239.9
HP11 CP1 HP13 HP12 120.0 120.0