PDB Chemical Component 0AP

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 0AP

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.478 1.480
P OP2 1.481 1.610
P O5' 1.589 1.610
P OP3 1.614 1.610
O5' C5' 1.425 1.429
C5' C4' 1.510 1.530
C5' H5'1 1.100 1.090
C5' H5'2 1.100 1.090
C4' O4' 1.449 1.444
C4' C3' 1.531 1.549
C4' H4' 1.100 1.090
O4' C1' 1.425 1.437
C3' O3' 1.432 1.429
C3' C2' 1.519 1.549
C3' H3' 1.100 1.090
O3' P1 1.599 1.611
P1 O11 1.481 1.480
P1 O21 1.485 1.610
P1 O31 1.595 1.610
C2' C1' 1.523 1.541
C2' H2'1 1.100 1.091
C2' H2'2 1.100 1.090
C1' N1 1.481 1.464
C1' H1' 1.100 1.090
N1 C2 1.400 1.346
N1 C6 1.365 1.362
C2 O2 1.229 1.220
C2 N3 1.350 1.332
N3 C4 1.327 1.327
C4 N4 1.321 1.376
C4 C5 1.427 1.410
N4 H4N1 1.001 0.970
N4 H4N2 1.000 0.970
C5 C6 1.344 1.354
OP2 H10 0.950 0.967
O21 H11 0.950 0.967
O31 H12 0.950 0.967
C5 H13 1.080 1.081
C6 H14 1.080 1.081
OP3 H15 0.950 0.967

Bond Angles for 0AP

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 119.8 109.4
OP1 P O5' 108.0 109.5
OP1 P OP3 104.6 109.5
OP2 P O5' 106.5 109.4
OP2 P OP3 112.5 109.4
P OP2 H10 109.5 114.0
O5' P OP3 104.4 109.5
P O5' C5' 120.9 123.0
P OP3 H15 109.5 114.0
O5' C5' C4' 110.4 109.5
O5' C5' H5'1 109.1 109.5
O5' C5' H5'2 108.9 109.5
C4' C5' H5'1 109.2 109.5
C4' C5' H5'2 108.9 109.5
C5' C4' O4' 109.7 110.6
C5' C4' C3' 111.7 110.6
C5' C4' H4' 106.5 110.6
H5'1 C5' H5'2 110.3 109.4
O4' C4' C3' 105.2 103.5
O4' C4' H4' 112.9 110.6
C4' O4' C1' 109.4 107.0
C3' C4' H4' 110.9 110.8
C4' C3' O3' 107.5 110.9
C4' C3' C2' 102.3 102.1
C4' C3' H3' 115.3 111.0
O4' C1' C2' 106.8 107.3
O4' C1' N1 109.2 109.9
O4' C1' H1' 116.2 109.9
O3' C3' C2' 109.8 110.9
O3' C3' H3' 108.5 110.8
C3' O3' P1 120.5 123.0
C2' C3' H3' 113.2 110.9
C3' C2' C1' 100.6 104.2
C3' C2' H2'1 112.6 110.5
C3' C2' H2'2 114.4 110.5
O3' P1 O11 106.0 109.5
O3' P1 O21 107.9 109.4
O3' P1 O31 103.1 109.5
O11 P1 O21 118.7 109.5
O11 P1 O31 110.1 109.5
O21 P1 O31 109.7 109.5
P1 O21 H11 109.5 114.0
P1 O31 H12 109.5 114.0
C1' C2' H2'1 112.5 110.5
C1' C2' H2'2 114.4 110.5
C2' C1' N1 120.6 109.9
C2' C1' H1' 103.5 109.8
H2'1 C2' H2'2 102.8 110.5
N1 C1' H1' 100.9 110.0
C1' N1 C2 118.6 119.8
C1' N1 C6 121.3 119.9
C2 N1 C6 120.0 120.3
N1 C2 O2 119.0 119.5
N1 C2 N3 119.6 121.1
N1 C6 C5 120.9 119.3
N1 C6 H14 119.6 120.3
O2 C2 N3 121.3 119.4
C2 N3 C4 119.9 120.7
N3 C4 N4 117.4 120.2
N3 C4 C5 122.0 119.6
N4 C4 C5 120.6 120.2
C4 N4 H4N1 110.4 119.9
C4 N4 H4N2 124.8 120.1
C4 C5 C6 117.4 119.0
C4 C5 H13 121.3 120.5
H4N1 N4 H4N2 124.8 120.0
C6 C5 H13 121.3 120.5
C5 C6 H14 119.5 120.4

Torsion Angles for 0AP

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 O5' 238.0 240.0
OP2 P OP1 OP3 127.2 120.0
OP1 P OP2 H10 291.3 300.0
O5' P OP1 OP3 249.3 239.9
OP1 P O5' C5' 357.0 55.1
OP1 P OP3 H15 162.9 180.0
OP1 P OP2 O5' 122.7 120.0
OP1 P OP2 OP3 236.5 240.0
O5' P OP2 OP3 113.8 120.0
OP2 P O5' C5' 126.8 175.0
OP2 P OP3 H15 31.4 60.0
OP1 P O5' OP2 230.1 240.0
OP1 P O5' OP3 110.9 120.1
OP2 P O5' OP3 240.8 240.0
O5' P OP2 H10 168.5 180.0
O5' P OP3 H15 276.3 300.1
P O5' C5' C4' 83.0 180.0
P O5' C5' H5'1 203.0 300.0
P O5' C5' H5'2 323.4 59.9
OP1 P OP3 OP2 131.6 120.0
OP1 P OP3 O5' 246.6 239.9
OP2 P OP3 O5' 115.1 120.0
OP3 P OP2 H10 54.7 60.0
OP3 P O5' C5' 246.1 295.0
C5' O5' P OP3 246.1 295.0
C4' C5' O5' H5'1 240.0 239.9
C4' C5' O5' H5'2 119.6 120.0
O5' C5' C4' O4' 50.1 66.4
O5' C5' C4' C3' 166.4 180.5
O5' C5' C4' H4' 287.7 303.6
H5'1 C5' O5' H5'2 239.6 240.1
O5' C5' C4' H5'1 120.0 120.0
O5' C5' C4' H5'2 240.4 240.0
H5'1 C5' C4' H5'2 120.4 120.0
O4' C4' C5' C3' 243.7 245.9
O4' C4' C5' H4' 122.5 122.8
C5' C4' O4' C1' 109.8 158.6
C3' C4' C5' H4' 238.7 236.9
C5' C4' C3' O3' 156.7 86.3
C5' C4' C3' C2' 272.3 204.5
C5' C4' C3' H3' 35.6 322.7
O5' C5' H5'1 C4' 239.2 239.9
O5' C5' H5'1 H5'2 119.6 119.9
C4' C5' H5'1 H5'2 240.4 240.0
H5'1 C5' C4' O4' 290.2 306.4
H5'1 C5' C4' C3' 46.4 60.5
H5'1 C5' C4' H4' 167.7 183.6
O5' C5' H5'2 C4' 120.5 120.0
O5' C5' H5'2 H5'1 240.3 240.1
C4' C5' H5'2 H5'1 119.8 120.0
H5'2 C5' C4' O4' 169.7 186.4
H5'2 C5' C4' C3' 286.0 300.5
H5'2 C5' C4' H4' 47.3 63.6
O4' C4' C5' H5'1 290.2 306.4
O4' C4' C5' H5'2 169.7 186.4
C5' C4' O4' C3' 120.3 118.5
C5' C4' O4' H4' 241.4 237.2
C3' C4' O4' H4' 121.1 118.7
O4' C4' C3' O3' 275.7 204.8
O4' C4' C3' C2' 31.3 323.0
O4' C4' C3' H3' 154.6 81.2
C4' O4' C1' C2' 345.3 333.5
C4' O4' C1' N1 213.4 214.1
C4' O4' C1' H1' 100.2 92.9
C3' C4' C5' H5'1 46.4 60.5
C3' C4' C5' H5'2 286.0 300.5
C5' C4' C3' O4' 241.0 241.5
C5' C4' C3' H4' 118.7 123.0
O4' C4' C3' H4' 237.7 241.5
C3' C4' O4' C1' 349.5 40.1
O3' C3' C4' C2' 244.4 241.9
O3' C3' C4' H3' 121.1 123.7
C4' C3' O3' P1 207.1 240.0
C2' C3' C4' H3' 236.7 241.8
C4' C3' C2' C1' 321.4 20.9
C4' C3' C2' H2'1 81.4 139.6
C4' C3' C2' H2'2 198.3 262.2
H4' C4' C5' H5'1 167.7 183.6
H4' C4' C5' H5'2 47.3 63.6
C5' C4' H4' O4' 120.5 122.8
C5' C4' H4' C3' 238.2 237.0
O4' C4' H4' C3' 117.8 114.2
H4' C4' O4' C1' 228.4 281.4
H4' C4' C3' O3' 38.0 323.4
H4' C4' C3' C2' 153.6 81.5
H4' C4' C3' H3' 276.9 199.7
C1' O4' C4' C3' 349.5 40.1
C1' O4' C4' H4' 228.4 281.4
C3' C2' C1' O4' 33.6 2.0
O4' C1' C2' H2'1 273.6 243.4
O4' C1' C2' H2'2 156.7 120.7
C2' C1' O4' N1 131.9 119.4
C2' C1' O4' H1' 245.1 240.6
N1 C1' O4' H1' 113.2 121.2
O4' C1' N1 C2 210.8 53.5
O4' C1' N1 C6 27.8 233.3
O3' C3' C4' H4' 38.0 323.4
C4' C3' O3' C2' 110.5 112.7
C4' C3' O3' H3' 234.7 236.3
C2' C3' O3' H3' 124.2 123.6
O3' C3' C2' C1' 75.3 139.1
O3' C3' C2' H2'1 195.3 257.8
O3' C3' C2' H2'2 312.2 20.4
C3' O3' P1 O11 152.5 54.9
C3' O3' P1 O21 280.7 174.9
C3' O3' P1 O31 36.8 294.9
C2' C3' C4' H4' 153.6 81.5
C4' C3' C2' O3' 246.1 241.8
C4' C3' C2' H3' 124.7 118.2
O4' C1' C2' C3' 33.6 2.0
O3' C3' C2' H3' 238.6 236.4
C2' C3' O3' P1 96.5 127.4
C1' C2' C3' H2'1 240.0 241.3
C1' C2' C3' H2'2 123.1 118.7
C3' C2' C1' N1 158.9 121.5
C3' C2' C1' H1' 270.5 242.6
H2'1 C2' C3' H2'2 243.1 237.4
H3' C3' C4' H4' 276.9 199.7
C4' C3' H3' O3' 120.6 123.7
C4' C3' H3' C2' 242.7 247.3
O3' C3' H3' C2' 122.1 123.6
H3' C3' O3' P1 332.3 3.7
H3' C3' C2' C1' 196.7 262.7
H3' C3' C2' H2'1 316.7 21.3
H3' C3' C2' H2'2 73.6 143.9
P1 O3' C3' C2' 96.5 127.4
P1 O3' C3' H3' 332.3 3.7
O11 P1 O3' O21 231.8 240.0
O11 P1 O3' O31 115.7 120.0
O21 P1 O3' O31 243.9 240.0
O3' P1 O21 H11 67.6 179.9
O3' P1 O31 H12 155.8 300.0
O3' P1 O11 O21 121.5 120.0
O3' P1 O11 O31 249.1 240.0
O21 P1 O11 O31 127.7 120.1
O11 P1 O21 H11 188.1 299.9
O11 P1 O31 H12 43.0 180.0
O3' P1 O21 O11 239.5 240.0
O3' P1 O21 O31 111.7 120.0
O11 P1 O21 O31 232.2 239.9
O21 P1 O31 H12 270.6 60.0
O3' P1 O31 O11 112.7 120.0
O3' P1 O31 O21 245.2 240.0
O11 P1 O31 O21 132.5 120.0
O31 P1 O21 H11 315.9 60.0
O4' C1' C2' N1 234.7 240.5
O4' C1' C2' H1' 123.2 119.4
C1' C2' C3' H3' 196.7 262.7
C3' C2' C1' H2'1 120.0 118.6
C3' C2' C1' H2'2 236.9 241.3
H2'1 C2' C1' H2'2 116.9 122.7
N1 C1' C2' H1' 248.4 238.9
C2' C1' N1 C2 86.7 295.6
C2' C1' N1 C6 263.7 115.5
H2'1 C2' C3' H3' 316.7 21.3
C3' C2' H2'1 C1' 247.2 245.2
C3' C2' H2'1 H2'2 123.6 122.6
C1' C2' H2'1 H2'2 236.4 237.3
H2'1 C2' C1' N1 38.9 2.8
H2'1 C2' C1' H1' 150.4 124.0
H2'2 C2' C3' H3' 73.6 143.9
C3' C2' H2'2 C1' 115.3 114.8
C3' C2' H2'2 H2'1 237.6 237.4
C1' C2' H2'2 H2'1 122.3 122.6
H2'2 C2' C1' N1 282.0 240.2
H2'2 C2' C1' H1' 33.5 1.3
O4' C1' N1 C2' 124.2 117.8
O4' C1' N1 H1' 237.1 238.9
N1 C1' C2' H2'1 38.9 2.8
N1 C1' C2' H2'2 282.0 240.2
C2' C1' N1 H1' 113.0 121.0
C2 N1 C1' C6 183.0 180.2
C1' N1 C2 O2 354.8 0.1
C1' N1 C2 N3 174.3 180.0
C1' N1 C6 C5 186.3 179.7
C1' N1 C6 H14 6.3 359.9
O4' C1' H1' C2' 243.3 242.2
O4' C1' H1' N1 117.9 121.2
H1' C1' C2' H2'1 150.4 124.0
H1' C1' C2' H2'2 33.5 1.3
C2' C1' H1' N1 234.6 239.0
H1' C1' N1 C2 333.7 174.6
H1' C1' N1 C6 150.7 354.5
C2 N1 C1' H1' 333.7 174.6
C1' N1 C2 C6 177.0 179.8
C2 N1 C6 C5 3.2 359.5
C2 N1 C6 H14 183.2 179.7
O2 C2 N1 N3 180.5 180.1
N1 C2 N3 C4 0.4 0.1
C6 N1 C1' H1' 150.7 354.5
C1' N1 C6 C2 183.0 180.2
C6 N1 C2 O2 177.8 180.3
C6 N1 C2 N3 357.3 0.2
C4 C5 C6 N1 358.6 0.5
N1 C6 C5 H13 178.6 180.3
C5 C6 N1 H14 180.0 179.8
O2 C2 N1 C6 177.8 180.3
N1 C2 O2 N3 179.5 179.9
O2 C2 N3 C4 179.9 180.0
N3 C2 N1 C6 357.3 0.2
N1 C2 N3 O2 180.5 180.1
C2 N3 C4 N4 181.7 180.0
C2 N3 C4 C5 1.5 359.9
N4 C4 N3 C5 180.2 180.1
N3 C4 N4 H4N1 180.0 360.0
N3 C4 N4 H4N2 360.0 180.0
N3 C4 C5 C6 359.0 359.8
N3 C4 C5 H13 179.0 180.0
N3 C4 N4 C5 179.8 179.9
N4 C4 C5 C6 178.8 179.7
N4 C4 C5 H13 358.8 359.9
H4N1 N4 C4 H4N2 180.0 180.0
N1 C6 C5 C4 358.6 0.5
N3 C4 C5 N4 180.2 180.1
C5 C4 N4 H4N1 0.2 180.0
C5 C4 N4 H4N2 180.2 0.0
C6 C5 C4 H13 180.0 179.8
C4 C5 C6 H14 178.6 180.3
H4N1 N4 C4 C5 0.2 180.0
C4 N4 H4N1 H4N2 180.0 180.0
H4N2 N4 C4 C5 180.2 0.0
C4 N4 H4N2 H4N1 180.0 180.0
N1 C6 C5 H14 180.0 180.2
C4 C5 C6 H13 180.0 180.2
H10 OP2 P O5' 168.5 180.0
H10 OP2 P OP3 54.7 60.0
H11 O21 P1 O31 315.9 60.0
C4 C5 H13 C6 180.0 179.8
H13 C5 C6 H14 358.6 0.1
N1 C6 H14 C5 180.0 179.8
H14 C6 C5 H13 358.6 0.1