PDB Chemical Component SPT

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 SPT

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
S5' C5' 1.787 1.813
S5' P   2.094
N1 C6 1.379 1.389
N1 C2 1.375 1.411
N1 C1' 1.473 1.434
C6 C5 1.334 1.339
C6 H6 1.080 1.086
C2 O2 1.221 1.232
C2 N3 1.372 1.399
N3 C4 1.384 1.387
N3 H3 1.000 1.016
C4 O4 1.222 1.228
C4 C5 1.438 1.487
C5 C5M 1.495 1.495
C5M H71 1.100 1.089
C5M H72 1.100 1.090
C5M H73 1.100 1.090
C2' C1' 1.519 1.520
C2' C3' 1.515 1.511
C2' H2' 1.100 1.097
C2' H2'' 1.100 1.095
C5' C4' 1.511 1.523
C5' H5' 1.100 1.093
C5' H5'' 1.099 1.094
C4' O4' 1.449 1.441
C4' C3' 1.525 1.522
C4' H4' 1.100 1.094
O4' C1' 1.426 1.434
C1' H1' 1.100 1.095
C3' O3' 1.428 1.426
C3' H3' 1.100 1.094
O3' HO3' 0.950 0.973
OP3 P   1.623
OP3 HOP3   0.982
P OP1   1.505
P OP2   1.623
OP2 HOP2   0.980

Bond Angles for SPT

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C5' S5' P   105.1
S5' C5' C4' 110.1 110.5
S5' C5' H5' 109.2 108.9
S5' C5' H5'' 109.1 108.8
S5' P OP3   109.3
S5' P OP1   111.4
S5' P OP2   108.8
C6 N1 C2 121.4 120.4
C6 N1 C1' 120.0 118.4
N1 C6 C5 123.7 124.5
N1 C6 H6 118.1 114.9
C2 N1 C1' 118.6 121.2
N1 C2 O2 123.3 123.8
N1 C2 N3 114.3 115.1
N1 C1' C2' 112.0 112.8
N1 C1' O4' 107.6 109.3
N1 C1' H1' 108.1 107.8
C5 C6 H6 118.2 120.7
C6 C5 C4 118.0 118.3
C6 C5 C5M 123.0 123.6
O2 C2 N3 122.4 121.1
C2 N3 C4 127.1 127.0
C2 N3 H3 116.5 116.4
C4 N3 H3 116.5 116.6
N3 C4 O4 120.0 123.6
N3 C4 C5 115.4 114.8
O4 C4 C5 124.5 121.6
C4 C5 C5M 118.9 118.1
C5 C5M H71 109.5 109.7
C5 C5M H72 109.5 109.8
C5 C5M H73 109.5 109.7
H71 C5M H72 109.5 109.4
H71 C5M H73 109.4 109.4
H72 C5M H73 109.5 108.9
C1' C2' C3' 103.0 102.5
C1' C2' H2' 111.7 110.6
C1' C2' H2'' 113.0 111.7
C2' C1' O4' 106.4 107.4
C2' C1' H1' 109.2 111.5
C3' C2' H2' 111.7 109.7
C3' C2' H2'' 113.1 114.1
C2' C3' C4' 103.4 103.1
C2' C3' O3' 109.5 109.7
C2' C3' H3' 114.0 113.2
H2' C2' H2'' 104.6 108.3
C4' C5' H5' 109.3 110.2
C4' C5' H5'' 109.1 110.1
C5' C4' O4' 109.3 107.9
C5' C4' C3' 113.2 112.9
C5' C4' H4' 105.9 109.5
H5' C5' H5'' 110.0 108.1
O4' C4' C3' 105.7 106.2
O4' C4' H4' 113.4 107.9
C4' O4' C1' 110.6 109.3
C3' C4' H4' 109.5 112.2
C4' C3' O3' 111.2 109.9
C4' C3' H3' 112.3 113.5
O4' C1' H1' 113.5 108.0
O3' C3' H3' 106.5 107.4
C3' O3' HO3' 109.5 107.3
P OP3 HOP3   118.7
OP3 P OP1   112.7
OP3 P OP2   101.5
OP1 P OP2   112.7
P OP2 HOP2   118.7

Torsion Angles for SPT

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C5' S5' P OP3   54.8
C5' S5' P OP1   180.0
C5' S5' P OP2   304.8
C4' C5' S5' H5' 240.0 238.8
C4' C5' S5' H5'' 119.7 121.1
S5' C5' C4' O4' 127.9 63.3
S5' C5' C4' C3' 245.4 180.4
S5' C5' C4' H4' 5.4 306.1
H5' C5' S5' H5'' 239.7 242.3
P S5' C5' C4'   180.0
P S5' C5' H5'   301.2
P S5' C5' H5''   58.9
S5' P OP3 HOP3   172.4
OP3 P S5' OP1   234.8
OP3 P S5' OP2   110.0
OP1 P S5' OP2   235.2
S5' P OP2 HOP2   187.8
C2 N1 C6 C1' 180.1 180.0
C6 N1 C2 O2 179.7 180.0
C6 N1 C2 N3 359.9 360.0
C6 N1 C1' C2' 284.2 273.5
C6 N1 C1' O4' 40.8 32.9
C6 N1 C1' H1' 163.8 150.0
C5 C6 N1 H6 180.0 180.0
N1 C6 C5 C4 359.9 0.0
N1 C6 C5 C5M 179.8 180.0
C6 N1 C2 C1' 179.9 180.0
C2 N1 C6 C5 0.3 0.0
C2 N1 C6 H6 180.3 180.0
C2 N1 C1' C2' 104.0 93.5
C2 N1 C1' O4' 220.7 212.8
C2 N1 C1' H1' 343.7 330.0
O2 C2 N1 N3 179.8 180.0
N1 C2 N3 C4 359.8 360.0
N1 C2 N3 H3 179.8 180.0
C6 N1 C1' C2 180.1 180.0
C1' N1 C6 C5 180.2 180.0
C1' N1 C6 H6 0.2 360.0
C1' N1 C2 O2 359.8 0.0
C1' N1 C2 N3 180.0 180.0
N1 C1' C2' C3' 145.7 147.4
N1 C1' C2' H2' 265.7 30.6
N1 C1' C2' H2'' 23.4 269.9
C2' C1' N1 O4' 243.3 240.6
C2' C1' N1 H1' 120.4 123.5
C4' O4' C1' N1 227.4 228.3
O4' C1' N1 H1' 237.1 242.9
C5 C6 N1 C2 0.3 0.0
C5 C6 N1 C1' 180.2 180.0
N1 C6 C5 H6 180.0 180.0
N3 C4 C5 C6 359.8 359.9
O4 C4 C5 C6 179.7 179.9
C4 C5 C6 C5M 180.1 180.0
C6 C5 C5M H71 194.4 119.7
C6 C5 C5M H72 314.5 359.5
C6 C5 C5M H73 74.5 239.8
H6 C6 N1 C2 180.3 180.0
H6 C6 N1 C1' 0.2 360.0
N1 C6 H6 C5 180.0 180.0
H6 C6 C5 C4 179.9 180.0
H6 C6 C5 C5M 359.8 360.0
O2 C2 N1 C1' 359.8 0.0
N1 C2 O2 N3 180.2 180.0
O2 C2 N3 C4 180.0 179.9
O2 C2 N3 H3 360.0 0.0
N3 C2 N1 C1' 180.0 180.0
N1 C2 N3 O2 179.8 180.0
C4 N3 C2 H3 180.0 179.9
C2 N3 C4 O4 180.5 180.1
C2 N3 C4 C5 0.4 0.1
C6 C5 C4 N3 359.8 359.9
C2 N3 C4 H3 180.0 180.1
O4 C4 N3 C5 180.1 180.0
N3 C4 C5 C5M 179.9 180.0
C2 N3 H3 C4 180.0 179.9
H3 N3 C4 O4 0.5 0.0
H3 N3 C4 C5 180.4 180.0
C6 C5 C4 O4 179.7 179.9
O4 C4 N3 H3 0.5 0.0
N3 C4 O4 C5 179.9 180.0
O4 C4 C5 C5M 359.8 360.0
C4 C5 C6 H6 179.9 180.0
C6 C5 C4 C5M 179.9 180.0
C5 C4 N3 H3 180.4 180.0
N3 C4 C5 O4 180.1 180.0
C4 C5 C5M H71 14.3 299.6
C4 C5 C5M H72 134.3 179.4
C4 C5 C5M H73 254.3 59.8
C5M C5 C6 H6 359.8 360.0
C6 C5 C5M C4 180.1 180.0
H71 C5M C5 H72 239.9 120.2
H71 C5M C5 H73 120.0 239.8
H72 C5M C5 H73 240.0 119.6
C5 C5M H71 H72 120.0 239.6
C5 C5M H71 H73 240.0 120.4
H72 C5M H71 H73 120.0 240.8
C5 C5M H72 H71 239.9 120.4
C5 C5M H72 H73 120.0 239.9
H71 C5M H72 H73 240.1 119.5
C5 C5M H73 H71 120.0 239.6
C5 C5M H73 H72 240.0 120.2
H71 C5M H73 H72 120.0 240.5
N1 C1' C2' O4' 117.4 120.5
N1 C1' C2' H1' 240.3 238.6
C3' C2' C1' H2' 240.0 116.9
C3' C2' C1' H2'' 122.4 237.5
C1' C2' C3' C4' 327.2 326.6
C1' C2' C3' O3' 85.9 83.6
C1' C2' C3' H3' 205.0 203.6
H2' C2' C1' H2'' 242.4 120.7
C4' O4' C1' C2' 347.7 351.0
O4' C1' C2' H1' 122.9 118.1
C1' C2' C3' H2' 120.0 242.5
C1' C2' C3' H2'' 237.6 120.8
C3' C2' C1' O4' 28.3 26.9
C3' C2' C1' H1' 265.4 268.8
H2' C2' C3' H2'' 117.7 238.3
C5' C4' C3' C2' 266.6 271.2
O4' C4' C3' C2' 26.1 29.2
C2' C3' C4' H4' 148.6 146.9
C4' C3' C2' O3' 241.4 242.9
C4' C3' C2' H3' 122.2 123.0
O3' C3' C2' H3' 240.8 240.1
C2' C3' O3' HO3' 148.5 119.3
C1' C2' H2' C3' 245.2 112.3
C1' C2' H2' H2'' 122.6 237.3
H2' C2' C1' O4' 148.3 270.0
H2' C2' C1' H1' 25.4 151.9
C3' C2' H2' H2'' 237.4 125.1
H2' C2' C3' C4' 207.2 84.1
H2' C2' C3' O3' 325.9 201.1
H2' C2' C3' H3' 85.0 321.1
C1' C2' H2'' C3' 116.6 244.4
C1' C2' H2'' H2' 238.3 122.0
H2'' C2' C1' O4' 266.0 149.4
H2'' C2' C1' H1' 143.1 31.3
C3' C2' H2'' H2' 121.7 237.5
H2'' C2' C3' C4' 89.6 205.7
H2'' C2' C3' O3' 208.2 322.8
H2'' C2' C3' H3' 327.4 82.7
C4' C5' S5' P   180.0
S5' C5' C4' H5' 120.0 120.4
S5' C5' C4' H5'' 240.3 239.7
C2' C3' C4' C5' 266.6 271.2
H5' C5' C4' H5'' 120.3 119.3
O4' C4' C5' C3' 242.6 242.9
O4' C4' C5' H4' 122.5 117.1
C5' C4' O4' C1' 113.3 108.6
C3' C4' C5' H4' 240.0 234.2
C5' C4' C3' O3' 149.1 154.2
C5' C4' C3' H3' 29.9 34.0
H5' C5' S5' P   301.2
S5' C5' H5' C4' 239.5 238.6
S5' C5' H5' H5'' 119.7 118.1
C4' C5' H5' H5'' 240.3 239.5
H5' C5' C4' O4' 7.9 302.8
H5' C5' C4' C3' 125.4 60.0
H5' C5' C4' H4' 245.4 185.7
H5'' C5' S5' P   58.9
S5' C5' H5'' C4' 120.4 121.3
S5' C5' H5'' H5' 240.2 241.9
C4' C5' H5'' H5' 119.8 120.5
H5'' C5' C4' O4' 247.7 183.6
H5'' C5' C4' C3' 5.1 300.7
H5'' C5' C4' H4' 125.2 66.5
N1 C1' O4' C4' 227.4 228.3
C2' C1' O4' C4' 347.7 351.0
C2' C3' C4' O4' 26.1 29.2
O4' C4' C5' H5' 7.9 302.8
O4' C4' C5' H5'' 247.7 183.6
C5' C4' O4' C3' 122.1 121.4
C5' C4' O4' H4' 242.1 241.8
C3' C4' O4' H4' 120.0 120.5
O4' C4' C3' O3' 268.7 272.3
O4' C4' C3' H3' 149.4 152.1
C4' O4' C1' H1' 107.8 111.3
C4' C3' C2' H2' 207.2 84.1
C4' C3' C2' H2'' 89.6 205.7
C2' C3' C4' O3' 117.5 116.9
C2' C3' C4' H3' 236.7 237.2
C3' C4' C5' H5' 125.4 60.0
C3' C4' C5' H5'' 5.1 300.7
C5' C4' C3' O4' 240.5 241.9
C5' C4' C3' H4' 118.0 124.3
O4' C4' C3' H4' 237.5 242.4
C3' C4' O4' C1' 351.2 347.3
O3' C3' C4' H3' 119.2 120.2
C4' C3' O3' HO3' 262.1 232.0
H4' C4' C5' H5' 245.4 185.7
H4' C4' C5' H5'' 125.2 66.5
C5' C4' H4' O4' 119.8 117.1
C5' C4' H4' C3' 237.6 233.8
O4' C4' H4' C3' 117.8 116.7
H4' C4' O4' C1' 231.2 226.8
H4' C4' C3' O3' 31.2 29.9
H4' C4' C3' H3' 271.9 269.7
N1 C1' O4' C2' 239.7 237.3
N1 C1' O4' H1' 119.5 117.0
O4' C1' C2' C3' 28.3 26.9
O4' C1' C2' H2' 148.3 270.0
O4' C1' C2' H2'' 266.0 149.4
C2' C1' O4' H1' 239.8 239.7
C1' O4' C4' C3' 351.2 347.3
C1' O4' C4' H4' 231.2 226.8
N1 C1' H1' C2' 122.1 124.3
N1 C1' H1' O4' 240.7 242.0
H1' C1' C2' C3' 265.4 268.8
H1' C1' C2' H2' 25.4 151.9
H1' C1' C2' H2'' 143.1 31.3
C2' C1' H1' O4' 118.6 117.7
O3' C3' C2' H2' 325.9 201.1
O3' C3' C2' H2'' 208.2 322.8
C2' C3' O3' C4' 246.3 247.3
C2' C3' O3' H3' 123.7 123.4
O3' C3' C4' H4' 31.2 29.9
C4' C3' O3' H3' 237.3 236.1
H3' C3' C2' H2' 85.0 321.1
H3' C3' C2' H2'' 327.4 82.7
C2' C3' H3' C4' 117.1 117.1
C2' C3' H3' O3' 239.1 238.7
H3' C3' C4' H4' 271.9 269.7
C4' C3' H3' O3' 122.0 121.7
H3' C3' O3' HO3' 24.8 355.9
HO3' O3' C3' H3' 24.8 355.9
S5' P OP3 OP1   124.4
S5' P OP3 OP2   245.2
OP1 P OP3 OP2   120.8
OP3 P OP2 HOP2   72.7
HOP3 OP3 P OP1   48.0
HOP3 OP3 P OP2   287.2
S5' P OP1 OP3   236.8
S5' P OP1 OP2   122.6
OP1 P OP3 HOP3   48.0
OP3 P OP1 OP2   245.8
OP1 P OP2 HOP2   311.8
S5' P OP2 OP3   115.1
S5' P OP2 OP1   236.0
OP2 P OP3 HOP3   287.2
OP3 P OP2 OP1   120.8