PDB Chemical Component STP

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 STP

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
PG O1G 1.478 1.500
PG O2G 1.490 1.616
PG O3G 1.591 1.616
PG O3B 1.604 1.616
O2G HOG2 0.950 0.981
O3G HOG3 0.950 0.981
PB O1B 1.479 1.500
PB O2B 1.488 1.617
PB O3B 1.566 1.615
PB O3A 1.667 1.614
O2B HOB2 0.950 0.982
PA S1A 1.485 1.942
PA O2A 1.492 1.623
PA O3A 1.622 1.620
PA O5' 1.601 1.623
O2A HOA2 0.950 0.981
O5' C5'   1.417
C5' C4'   1.518
C5' H5'1   1.094
C5' H5'2   1.094
C4' O4'   1.437
C4' C3'   1.521
C4' H4'   1.097
O4' C1'   1.442
C3' O3'   1.412
C3' C2'   1.512
C3' H3'   1.096
O3' HO3'   0.972
C2' C1'   1.521
C2' H2'1   1.097
C2' H2'2   1.094
C1' N9   1.458
C1' H1'   1.095
N9 C8   1.372
N9 C4   1.369
C8 N7   1.317
C8 H8   1.082
N7 C5   1.373
C5 C6   1.391
C5 C4   1.386
C6 N6   1.406
C6 N1   1.355
N6 HN61   1.003
N6 HN62   1.002
N1 C2   1.355
C2 N3   1.351
C2 H2   1.084
N3 C4   1.342

Bond Angles for STP

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1G PG O2G 118.4 115.1
O1G PG O3G 109.1 115.1
O1G PG O3B 107.8 114.3
O2G PG O3G 110.0 103.7
O2G PG O3B 110.8 103.7
PG O2G HOG2 109.5 119.0
O3G PG O3B 98.9 103.5
PG O3G HOG3 109.5 118.9
PG O3B PB 129.2 132.0
O1B PB O2B 118.2 114.9
O1B PB O3B 105.9 115.3
O1B PB O3A 108.6 116.1
O2B PB O3B 107.9 103.3
O2B PB O3A 112.9 104.0
PB O2B HOB2 109.5 118.9
O3B PB O3A 101.7 101.5
PB O3A PA 140.2 132.4
S1A PA O2A 116.3 114.7
S1A PA O3A 109.9 116.4
S1A PA O5' 109.8 116.8
O2A PA O3A 108.8 101.8
O2A PA O5' 109.1 101.2
PA O2A HOA2 109.5 118.7
O3A PA O5' 101.9 103.7
PA O5' C5'   119.6
O5' C5' C4'   109.0
O5' C5' H5'1   108.8
O5' C5' H5'2   108.8
C4' C5' H5'1   110.6
C4' C5' H5'2   110.6
C5' C4' O4'   109.6
C5' C4' C3'   113.4
C5' C4' H4'   108.7
H5'1 C5' H5'2   109.1
O4' C4' C3'   106.0
O4' C4' H4'   107.9
C4' O4' C1'   108.2
C3' C4' H4'   111.1
C4' C3' O3'   112.4
C4' C3' C2'   101.6
C4' C3' H3'   111.6
O4' C1' C2'   107.2
O4' C1' N9   109.5
O4' C1' H1'   107.9
O3' C3' C2'   111.3
O3' C3' H3'   109.3
C3' O3' HO3'   107.3
C2' C3' H3'   110.4
C3' C2' C1'   101.6
C3' C2' H2'1   110.7
C3' C2' H2'2   113.0
C1' C2' H2'1   111.8
C1' C2' H2'2   112.9
C2' C1' N9   114.2
C2' C1' H1'   111.7
H2'1 C2' H2'2   106.9
N9 C1' H1'   106.1
C1' N9 C8   126.2
C1' N9 C4   127.0
C8 N9 C4   106.8
N9 C8 N7   112.3
N9 C8 H8   122.1
N9 C4 C5   105.3
N9 C4 N3   127.4
N7 C8 H8   125.6
C8 N7 C5   104.9
N7 C5 C6   132.4
N7 C5 C4   110.7
C6 C5 C4   116.9
C5 C6 N6   120.7
C5 C6 N1   119.1
C5 C4 N3   127.2
N6 C6 N1   120.2
C6 N6 HN61   119.4
C6 N6 HN62   119.4
C6 N1 C2   117.5
HN61 N6 HN62   120.9
N1 C2 N3   128.8
N1 C2 H2   115.6
N3 C2 H2   115.6
C2 N3 C4   110.4

Torsion Angles for STP

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2G PG O1G O3G 126.8 120.5
O2G PG O1G O3B 233.3 240.1
O1G PG O2G HOG2 16.8 312.2
O3G PG O1G O3B 106.4 119.6
O1G PG O3G HOG3 114.8 47.9
O1G PG O3B PB 3.2 60.0
O1G PG O2G O3G 233.6 233.4
O1G PG O2G O3B 125.3 125.6
O3G PG O2G O3B 251.7 252.1
O2G PG O3G HOG3 343.4 281.3
O2G PG O3B PB 134.3 186.1
O1G PG O3G O2G 131.5 126.6
O1G PG O3G O3B 247.6 234.6
O2G PG O3G O3B 116.1 108.0
O3G PG O2G HOG2 143.2 78.8
O3G PG O3B PB 249.8 294.1
O1G PG O3B O2G 228.9 233.9
O1G PG O3B O3G 113.4 125.9
O2G PG O3B O3G 244.5 252.0
O3B PG O2G HOG2 251.5 186.6
O3B PG O3G HOG3 227.2 173.3
O1B PB O3B PG 225.5 300.0
O2B PB O3B PG 353.0 66.2
PG O3B PB O3A 112.0 173.7
HOG2 O2G PG O3G 143.2 78.8
HOG2 O2G PG O3B 251.5 186.6
HOG3 O3G PG O3B 227.2 173.3
PG O3B PB O1B 225.5 300.0
O2B PB O1B O3B 238.9 240.0
O2B PB O1B O3A 130.4 121.6
O1B PB O2B HOB2 275.2 49.1
O3B PB O1B O3A 251.5 241.6
O1B PB O3A PA 148.6 300.0
PG O3B PB O2B 353.0 66.2
O1B PB O2B O3B 120.0 126.4
O1B PB O2B O3A 231.6 232.0
O3B PB O2B O3A 111.6 105.6
O2B PB O3A PA 15.4 172.8
O1B PB O3B O2B 232.5 233.8
O1B PB O3B O3A 113.5 126.3
O2B PB O3B O3A 241.0 252.5
O3B PB O2B HOB2 155.2 282.7
O3B PB O3A PA 260.0 65.7
O1B PB O3A O2B 133.2 127.2
O1B PB O3A O3B 248.6 234.2
O2B PB O3A O3B 115.4 107.0
O3A PB O2B HOB2 43.6 177.1
S1A PA O3A PB 43.4 174.5
O2A PA O3A PB 171.8 300.0
PB O3A PA O5' 286.9 44.8
HOB2 O2B PB O3B 155.2 282.7
HOB2 O2B PB O3A 43.6 177.1
PB O3A PA S1A 43.4 174.5
O2A PA S1A O3A 235.8 241.3
O2A PA S1A O5' 124.4 118.2
S1A PA O2A HOA2 63.0 286.8
O3A PA S1A O5' 248.6 236.8
S1A PA O5' C5'   65.3
PB O3A PA O2A 171.8 300.0
S1A PA O2A O3A 124.8 126.6
S1A PA O2A O5' 235.2 233.3
O3A PA O2A O5' 110.4 106.7
O2A PA O5' C5'   300.0
S1A PA O3A O2A 231.6 234.5
S1A PA O3A O5' 116.4 129.8
O2A PA O3A O5' 244.9 255.2
O3A PA O2A HOA2 298.3 160.3
O3A PA O5' C5'   194.7
S1A PA O5' O2A 128.5 125.3
S1A PA O5' O3A 243.5 230.5
O2A PA O5' O3A 114.9 105.2
O5' PA O2A HOA2 187.8 53.5
PA O5' C5' C4'   120.0
PA O5' C5' H5'1   240.6
PA O5' C5' H5'2   359.4
HOA2 O2A PA O3A 298.3 160.3
HOA2 O2A PA O5' 187.8 53.5
C4' C5' O5' H5'1   239.4
C4' C5' O5' H5'2   120.6
O5' C5' C4' O4'   297.8
O5' C5' C4' C3'   179.5
O5' C5' C4' H4'   55.5
H5'1 C5' O5' H5'2   241.2
O5' C5' C4' H5'1   119.6
O5' C5' C4' H5'2   240.5
H5'1 C5' C4' H5'2   121.0
O4' C4' C5' C3'   118.3
O4' C4' C5' H4'   242.3
C5' C4' O4' C1'   219.9
C3' C4' C5' H4'   124.1
C5' C4' C3' O3'   274.4
C5' C4' C3' C2'   155.3
C5' C4' C3' H3'   37.7
O5' C5' H5'1 C4'   240.3
O5' C5' H5'1 H5'2   118.5
C4' C5' H5'1 H5'2   238.2
H5'1 C5' C4' O4'   178.3
H5'1 C5' C4' C3'   60.0
H5'1 C5' C4' H4'   295.9
O5' C5' H5'2 C4'   119.6
O5' C5' H5'2 H5'1   241.4
C4' C5' H5'2 H5'1   121.8
H5'2 C5' C4' O4'   57.3
H5'2 C5' C4' C3'   299.0
H5'2 C5' C4' H4'   175.0
O4' C4' C5' H5'1   178.3
O4' C4' C5' H5'2   57.3
C5' C4' O4' C3'   237.3
C5' C4' O4' H4'   118.2
C3' C4' O4' H4'   240.9
O4' C4' C3' O3'   154.1
O4' C4' C3' C2'   35.0
O4' C4' C3' H3'   277.4
C4' O4' C1' C2'   352.5
C4' O4' C1' N9   228.1
C4' O4' C1' H1'   113.0
C3' C4' C5' H5'1   60.0
C3' C4' C5' H5'2   299.0
C5' C4' C3' O4'   120.3
C5' C4' C3' H4'   237.3
O4' C4' C3' H4'   117.0
C3' C4' O4' C1'   342.7
O3' C3' C4' C2'   119.1
O3' C3' C4' H3'   236.7
C4' C3' O3' HO3'   295.8
C2' C3' C4' H3'   117.7
C4' C3' C2' C1'   322.1
C4' C3' C2' H2'1   81.0
C4' C3' C2' H2'2   200.9
H4' C4' C5' H5'1   295.9
H4' C4' C5' H5'2   175.0
C5' C4' H4' O4'   241.3
C5' C4' H4' C3'   125.4
O4' C4' H4' C3'   244.2
H4' C4' O4' C1'   101.8
H4' C4' C3' O3'   37.1
H4' C4' C3' C2'   278.1
H4' C4' C3' H3'   160.4
C1' O4' C4' C3'   342.7
C1' O4' C4' H4'   101.8
C3' C2' C1' O4'   29.0
O4' C1' C2' H2'1   270.9
O4' C1' C2' H2'2   150.3
C2' C1' O4' N9   124.5
C2' C1' O4' H1'   239.6
N9 C1' O4' H1'   115.1
O4' C1' N9 C8   33.7
O4' C1' N9 C4   213.8
O3' C3' C4' H4'   37.1
C4' C3' O3' C2'   246.8
C4' C3' O3' H3'   124.5
C2' C3' O3' H3'   237.7
O3' C3' C2' C1'   202.2
O3' C3' C2' H2'1   321.1
O3' C3' C2' H2'2   81.1
C2' C3' C4' H4'   278.1
C4' C3' C2' O3'   119.8
C4' C3' C2' H3'   241.5
O4' C1' C2' C3'   29.0
O3' C3' C2' H3'   121.6
C2' C3' O3' HO3'   49.0
C1' C2' C3' H2'1   241.1
C1' C2' C3' H2'2   121.2
C3' C2' C1' N9   150.6
C3' C2' C1' H1'   271.0
H2'1 C2' C3' H2'2   240.1
H3' C3' C4' H4'   160.4
C4' C3' H3' O3'   235.0
C4' C3' H3' C2'   112.2
O3' C3' H3' C2'   237.2
H3' C3' O3' HO3'   171.3
H3' C3' C2' C1'   80.6
H3' C3' C2' H2'1   199.5
H3' C3' C2' H2'2   319.4
HO3' O3' C3' C2'   49.0
HO3' O3' C3' H3'   171.3
O4' C1' C2' N9   238.5
O4' C1' C2' H1'   118.0
C1' C2' C3' H3'   80.6
C3' C2' C1' H2'1   118.1
C3' C2' C1' H2'2   238.7
H2'1 C2' C1' H2'2   120.6
N9 C1' C2' H1'   239.6
C2' C1' N9 C8   273.4
C2' C1' N9 C4   93.5
H2'1 C2' C3' H3'   199.5
C3' C2' H2'1 C1'   247.5
C3' C2' H2'1 H2'2   123.5
C1' C2' H2'1 H2'2   236.0
H2'1 C2' C1' N9   32.4
H2'1 C2' C1' H1'   152.9
H2'2 C2' C3' H3'   319.4
C3' C2' H2'2 C1'   114.6
C3' C2' H2'2 H2'1   237.9
C1' C2' H2'2 H2'1   123.3
H2'2 C2' C1' N9   271.9
H2'2 C2' C1' H1'   32.3
O4' C1' N9 C2'   120.2
O4' C1' N9 H1'   243.7
N9 C1' C2' H2'1   32.4
N9 C1' C2' H2'2   271.9
C2' C1' N9 H1'   123.5
C8 N9 C1' C4   179.9
C1' N9 C8 N7   180.0
C1' N9 C8 H8   0.0
C1' N9 C4 C5   179.9
C1' N9 C4 N3   359.9
O4' C1' H1' C2'   242.4
O4' C1' H1' N9   117.3
H1' C1' C2' H2'1   152.9
H1' C1' C2' H2'2   32.3
C2' C1' H1' N9   234.9
H1' C1' N9 C8   150.0
H1' C1' N9 C4   330.1
C8 N9 C1' H1'   150.0
C1' N9 C8 C4   180.1
C8 N9 C4 C5   0.0
C8 N9 C4 N3   180.0
N7 C8 N9 H8   180.0
N9 C8 N7 C5   0.1
C4 N9 C1' H1'   330.1
C1' N9 C4 C8   179.9
C4 N9 C8 N7   360.0
C4 N9 C8 H8   180.0
N7 C5 C4 N9   0.0
C6 C5 C4 N9   180.0
C5 C4 N9 N3   180.0
C2 N3 C4 N9   180.0
N7 C8 N9 C4   360.0
N9 C8 N7 H8   180.0
C8 N7 C5 C6   180.0
C8 N7 C5 C4   359.9
H8 C8 N9 C4   180.0
N9 C8 H8 N7   180.0
H8 C8 N7 C5   180.0
N9 C4 C5 N7   0.0
C5 N7 C8 H8   180.0
C6 C5 N7 C4   180.1
N7 C5 C6 N6   359.9
N7 C5 C6 N1   179.9
N7 C5 C4 N3   180.0
N9 C4 C5 C6   180.0
N7 C5 C6 C4   179.9
C6 C5 C4 N3   360.0
N6 C6 C5 N1   180.0
C5 C6 N6 HN61   97.3
C5 C6 N6 HN62   283.5
C5 C6 N1 C2   360.0
N9 C4 C5 N3   180.0
N7 C5 C4 C6   180.1
C4 C5 C6 N6   180.0
C4 C5 C6 N1   0.0
C2 N3 C4 C5   0.0
N6 C6 C5 C4   180.0
C5 C6 N6 N1   180.0
N6 C6 N1 C2   180.0
HN61 N6 C6 HN62   173.8
N1 C6 C5 C4   0.0
C5 C6 N1 N6   180.0
N1 C6 N6 HN61   277.3
N1 C6 N6 HN62   103.5
C6 N1 C2 N3   0.0
C6 N1 C2 H2   180.0
HN61 N6 C6 N1   277.3
C6 N6 HN61 HN62   186.3
HN62 N6 C6 N1   103.5
C6 N6 HN62 HN61   173.7
N3 C2 N1 H2   180.1
N1 C2 N3 C4   360.0
N9 C4 N3 C2   180.0
C5 C4 N3 C2   0.0
N1 C2 N3 H2   179.9
N1 C2 H2 N3   180.1
H2 C2 N3 C4   180.0
N9 C4 N3 C5   180.0
C4 N3 C2 H2   180.0