PDB Chemical Component N5I

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 N5I

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O3P P 1.607 1.617
O3P HOP3 0.950 0.981
OR2 NRO 1.223 1.255
NRO OR1 1.222 1.254
NRO CZ3 1.460 1.421
CZ3 CH2 1.405 1.394
CZ3 CE3 1.387 1.399
CE3 CD2 1.401 1.410
CE3 HE3 1.080 1.087
CD2 CE2 1.417 1.396
CD2 CG 1.432 1.423
CH2 CZ2 1.372 1.398
CH2 HH2 1.080 1.088
CZ2 CE2 1.408 1.399
CZ2 HZ2 1.080 1.085
CE2 NE1 1.369 1.381
NE1 C1' 1.494 1.459
NE1 CD1 1.371 1.373
CD1 CG 1.359 1.376
CD1 HD1 1.080 1.081
CG HG 1.080 1.081
C1' C2' 1.525 1.522
C1' O4' 1.429 1.439
C1' H1' 1.100 1.095
O4' C4' 1.429 1.443
C4' C3' 1.524 1.525
C4' C5' 1.525 1.523
C4' H4' 1.100 1.095
C3' O3' 1.431 1.425
C3' C2' 1.521 1.512
C3' H3' 1.100 1.093
O3' H3T 0.950 0.969
C2' H2'1 1.100 1.097
C2' H2'2 1.100 1.094
C5' O5' 1.425 1.417
C5' H5'1 1.100 1.090
C5' H5'2 1.100 1.091
O5' P 1.612 1.619
P O1P 1.520 1.501
P O2P 1.516 1.617
O2P HOP2 0.950 0.981

Bond Angles for N5I

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
P O3P HOP3 109.5 118.9
O3P P O5' 101.3 103.7
O3P P O1P 110.2 115.3
O3P P O2P 107.3 103.3
OR2 NRO OR1 119.0 122.1
OR2 NRO CZ3 120.5 118.9
OR1 NRO CZ3 120.5 119.0
NRO CZ3 CH2 118.8 119.7
NRO CZ3 CE3 118.6 119.5
CE3 CZ3 CH2 122.5 120.8
CZ3 CH2 CZ2 120.7 121.0
CZ3 CH2 HH2 119.7 120.3
CZ3 CE3 CD2 118.0 119.2
CZ3 CE3 HE3 121.0 120.8
CD2 CE3 HE3 121.0 120.0
CE3 CD2 CE2 118.8 118.8
CE3 CD2 CG 133.9 134.1
CE2 CD2 CG 107.3 107.1
CD2 CE2 CZ2 122.6 122.7
CD2 CE2 NE1 106.8 107.4
CD2 CG CD1 106.4 107.7
CD2 CG HG 126.8 126.9
CZ2 CH2 HH2 119.6 118.6
CH2 CZ2 CE2 117.3 117.5
CH2 CZ2 HZ2 121.3 120.7
CE2 CZ2 HZ2 121.3 121.7
CZ2 CE2 NE1 130.6 129.9
CE2 NE1 C1' 127.4 125.8
CE2 NE1 CD1 109.4 109.6
CD1 NE1 C1' 123.1 124.6
NE1 C1' C2' 114.6 114.3
NE1 C1' O4' 109.8 110.0
NE1 C1' H1' 104.6 105.9
NE1 CD1 CG 110.1 108.2
NE1 CD1 HD1 124.9 120.8
CG CD1 HD1 124.9 131.0
CD1 CG HG 126.8 125.4
O4' C1' C2' 105.7 106.7
C2' C1' H1' 108.7 111.7
C1' C2' C3' 101.7 101.6
C1' C2' H2'1 112.1 110.5
C1' C2' H2'2 113.8 111.7
O4' C1' H1' 113.6 108.1
C1' O4' C4' 110.4 108.7
O4' C4' C3' 106.0 106.8
O4' C4' C5' 109.5 108.0
O4' C4' H4' 113.5 107.7
C3' C4' C5' 114.3 112.7
C3' C4' H4' 108.6 112.0
C4' C3' O3' 110.2 109.6
C4' C3' C2' 102.2 103.2
C4' C3' H3' 114.4 114.0
C5' C4' H4' 105.1 109.4
C4' C5' O5' 110.4 108.7
C4' C5' H5'1 109.2 110.1
C4' C5' H5'2 108.9 110.1
O3' C3' C2' 111.5 108.4
O3' C3' H3' 105.6 107.8
C3' O3' H3T 109.5 106.6
C2' C3' H3' 113.2 113.7
C3' C2' H2'1 112.2 110.0
C3' C2' H2'2 113.8 114.2
H2'1 C2' H2'2 103.7 108.7
O5' C5' H5'1 109.1 109.2
O5' C5' H5'2 109.0 109.2
C5' O5' P 122.0 118.5
H5'1 C5' H5'2 110.2 109.6
O5' P O1P 109.3 115.0
O5' P O2P 108.6 102.9
O2P P O1P 118.7 115.0
P O2P HOP2 109.5 118.9

Torsion Angles for N5I

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C5' O5' P O3P 139.7 53.2
O5' P O3P O1P 244.3 126.6
O5' P O3P O2P 113.8 252.9
O2P P O3P O1P 130.6 233.7
O3P P O2P HOP2 169.7 78.5
HOP3 O3P P O5' 149.9 175.4
HOP3 O3P P O1P 265.5 48.8
HOP3 O3P P O2P 36.1 282.5
OR1 NRO OR2 CZ3 180.1 180.0
OR2 NRO CZ3 CH2 0.0 360.0
OR2 NRO CZ3 CE3 180.2 180.0
OR2 NRO OR1 CZ3 179.9 180.0
OR1 NRO CZ3 CH2 180.0 180.0
OR1 NRO CZ3 CE3 0.1 0.0
OR2 NRO CZ3 OR1 180.1 180.0
CE3 CZ3 NRO CH2 180.1 180.0
NRO CZ3 CH2 CZ2 179.8 180.0
NRO CZ3 CH2 HH2 359.8 0.0
NRO CZ3 CE3 CD2 180.2 180.0
NRO CZ3 CE3 HE3 0.2 359.9
NRO CZ3 CH2 CE3 180.1 180.0
CH2 CZ3 CE3 CD2 0.3 0.1
CH2 CZ3 CE3 HE3 180.3 179.9
CZ2 CH2 CZ3 HH2 180.0 179.9
CZ3 CH2 CZ2 CE2 0.2 0.0
CZ3 CH2 CZ2 HZ2 180.2 180.0
NRO CZ3 CE3 CH2 179.9 180.0
CE3 CZ3 CH2 CZ2 359.7 359.9
CE3 CZ3 CH2 HH2 179.7 180.0
CD2 CE3 CZ3 HE3 180.0 180.1
CZ3 CE3 CD2 CE2 359.8 360.0
CZ3 CE3 CD2 CG 180.5 180.0
CD2 CE3 CZ3 CH2 0.3 0.1
CZ3 CE3 CD2 HE3 180.0 179.9
CE2 CD2 CE3 CG 179.3 180.0
CE3 CD2 CE2 CZ2 0.1 360.0
CE3 CD2 CE2 NE1 180.2 180.0
CE3 CD2 CG CD1 180.0 180.0
CE3 CD2 CG HG 0.0 360.0
HE3 CE3 CZ3 CH2 180.3 179.9
CZ3 CE3 HE3 CD2 180.0 180.1
HE3 CE3 CD2 CE2 179.8 180.1
HE3 CE3 CD2 CG 0.5 0.1
CE2 CD2 CE3 HE3 179.8 180.1
CE3 CD2 CE2 CG 180.5 180.0
CE2 CD2 CG CD1 0.6 360.0
CE2 CD2 CG HG 180.7 180.0
CH2 CZ2 CE2 CD2 359.9 0.0
CD2 CE2 CZ2 HZ2 179.9 180.1
CZ2 CE2 CD2 NE1 179.9 180.0
CD2 CE2 NE1 C1' 179.8 180.0
CD2 CE2 NE1 CD1 359.9 360.0
CG CD2 CE3 HE3 0.5 0.1
CE3 CD2 CG CE2 179.4 180.0
CG CD2 CE2 CZ2 179.6 180.0
CG CD2 CE2 NE1 359.7 0.0
NE1 CD1 CG CD2 359.3 0.0
CD2 CG CD1 HD1 179.3 180.0
CD1 CG CD2 HG 180.0 180.0
CZ3 CH2 CZ2 HH2 180.0 180.1
CD2 CE2 CZ2 CH2 359.9 0.0
CE2 CZ2 CH2 HZ2 180.0 180.0
CH2 CZ2 CE2 NE1 179.8 180.0
CZ3 CH2 HH2 CZ2 180.0 179.9
HH2 CH2 CZ2 CE2 180.2 180.0
HH2 CH2 CZ2 HZ2 0.2 359.9
CZ2 CE2 CD2 CG 179.6 180.0
CD2 CE2 CZ2 NE1 180.1 180.0
CE2 CZ2 CH2 HH2 180.2 180.0
CH2 CZ2 CE2 HZ2 180.0 180.0
CZ2 CE2 NE1 C1' 359.9 0.0
CZ2 CE2 NE1 CD1 180.0 180.0
HZ2 CZ2 CH2 HH2 0.2 359.9
CH2 CZ2 HZ2 CE2 180.0 180.0
HZ2 CZ2 CE2 NE1 359.8 0.0
NE1 CE2 CD2 CG 359.7 0.0
CD2 CE2 NE1 CZ2 179.9 180.0
NE1 CE2 CZ2 HZ2 359.8 0.0
CD1 NE1 CE2 C1' 180.1 180.0
CE2 NE1 C1' C2' 70.7 93.4
CE2 NE1 C1' O4' 189.5 213.5
CE2 NE1 C1' H1' 311.8 330.0
CE2 NE1 CD1 CG 0.5 360.0
CE2 NE1 CD1 HD1 180.5 180.0
CE2 NE1 C1' CD1 180.1 180.0
C1' NE1 CD1 CG 180.6 180.0
C1' NE1 CD1 HD1 0.6 360.0
O4' C1' NE1 C2' 118.8 120.0
C2' C1' NE1 H1' 118.9 123.5
NE1 C1' C2' C3' 89.0 154.5
NE1 C1' C2' H2'1 209.0 37.8
NE1 C1' C2' H2'2 326.2 276.7
O4' C1' NE1 H1' 237.7 243.5
NE1 C1' O4' C4' 250.2 218.2
CD2 CG CD1 NE1 359.3 0.0
CE2 NE1 CD1 C1' 179.9 180.0
CD1 NE1 C1' C2' 250.6 273.4
CD1 NE1 C1' O4' 9.4 33.5
CD1 NE1 C1' H1' 131.6 150.0
CG CD1 NE1 HD1 180.0 180.0
NE1 CD1 CG HG 179.3 180.0
CD2 CG CD1 HG 180.0 180.0
CG CD1 NE1 C1' 180.6 180.0
NE1 CD1 CG HD1 180.0 180.0
HD1 CD1 NE1 C1' 0.6 360.0
NE1 CD1 HD1 CG 180.0 180.0
HD1 CD1 CG HG 359.3 360.0
CD2 CG HG CD1 180.0 180.0
HG CG CD1 HD1 359.3 360.0
NE1 C1' C2' O4' 121.0 121.8
NE1 C1' C2' H1' 243.4 239.7
O4' C1' C2' H1' 122.4 117.9
C2' C1' O4' C4' 14.3 342.7
C4' C3' C2' C1' 36.7 325.2
O3' C3' C2' C1' 154.4 81.3
C1' C2' C3' H3' 273.2 201.2
C3' C2' C1' H2'1 240.0 116.7
C3' C2' C1' H2'2 122.8 237.8
H2'1 C2' C1' H2'2 242.8 121.1
NE1 C1' O4' C2' 235.9 235.5
NE1 C1' O4' H1' 116.7 115.2
C2' C1' O4' H1' 240.9 239.7
O4' C1' C2' C3' 328.0 32.7
O4' C1' C2' H2'1 88.0 276.0
O4' C1' C2' H2'2 205.2 154.9
C1' O4' C4' C3' 9.7 354.5
C1' O4' C4' C5' 133.5 116.0
C1' O4' C4' H4' 250.5 234.0
NE1 C1' H1' C2' 122.9 125.1
NE1 C1' H1' O4' 240.3 242.2
O4' C1' H1' C2' 242.6 242.9
H1' C1' C2' C3' 205.6 274.8
H1' C1' C2' H2'1 325.6 158.1
H1' C1' C2' H2'2 82.8 37.0
H1' C1' O4' C4' 133.4 103.1
C4' O4' C1' C2' 14.3 342.7
C4' O4' C1' H1' 133.4 103.1
C3' C4' O4' C5' 236.2 238.5
C3' C4' O4' H4' 119.1 120.5
O4' C4' C3' O3' 212.0 270.6
O4' C4' C3' C2' 330.6 25.9
O4' C4' C3' H3' 93.2 149.7
C5' C4' O4' H4' 242.9 242.0
O4' C4' C5' O5' 46.1 61.8
O4' C4' C5' H5'1 166.1 302.2
O4' C4' C5' H5'2 286.5 181.3
C1' C2' C3' C4' 36.7 325.2
O4' C4' C3' C5' 120.7 118.5
O4' C4' C3' H4' 237.7 242.3
C5' C4' C3' H4' 117.0 123.8
C3' C4' C5' O5' 164.9 179.5
C3' C4' C5' H5'1 284.9 60.0
C3' C4' C5' H5'2 45.2 299.1
O3' C3' C4' C2' 241.4 244.7
O3' C3' C4' H3' 118.7 120.9
C4' C3' O3' H3T 12.8 46.6
C2' C3' C4' H3' 237.3 236.3
C4' C3' C2' H2'1 276.7 82.2
C4' C3' C2' H2'2 159.4 204.8
O4' C4' C5' C3' 241.2 242.3
O4' C4' C5' H4' 122.3 117.0
C3' C4' C5' H4' 241.0 234.7
C5' C4' C3' O3' 91.2 152.1
C5' C4' C3' C2' 209.8 267.4
C5' C4' C3' H3' 332.5 31.2
O5' C5' C4' H5'1 240.0 119.6
O5' C5' C4' H5'2 119.6 240.5
C4' C5' O5' P 241.1 180.0
H5'1 C5' C4' H5'2 239.6 120.9
O4' C4' H4' C3' 117.6 117.2
O4' C4' H4' C5' 240.3 242.8
C3' C4' H4' C5' 122.7 125.7
H4' C4' C3' O3' 334.2 28.3
H4' C4' C3' C2' 92.9 143.6
H4' C4' C3' H3' 215.5 267.4
H4' C4' C5' O5' 283.9 304.8
H4' C4' C5' H5'1 43.8 185.3
H4' C4' C5' H5'2 164.2 64.3
C1' C2' C3' O3' 154.4 81.3
O3' C3' C4' C5' 91.2 152.1
O3' C3' C4' H4' 334.2 28.3
C4' C3' O3' C2' 112.7 111.9
C4' C3' O3' H3' 236.0 235.4
C2' C3' O3' H3' 123.3 123.5
O3' C3' C2' H2'1 34.4 198.4
O3' C3' C2' H2'2 277.1 320.9
C3' C2' C1' H1' 205.6 274.8
C1' C2' C3' H2'1 120.0 243.0
C1' C2' C3' H2'2 237.2 120.4
C2' C3' C4' C5' 209.8 267.4
C2' C3' C4' H4' 92.9 143.6
C4' C3' C2' O3' 242.3 243.8
C4' C3' C2' H3' 123.5 123.9
O3' C3' C2' H3' 241.2 240.1
C2' C3' O3' H3T 260.1 294.7
H2'1 C2' C3' H2'2 117.3 237.5
H3' C3' C4' C5' 332.5 31.2
H3' C3' C4' H4' 215.5 267.4
C4' C3' H3' O3' 121.3 121.9
C4' C3' H3' C2' 243.5 242.1
O3' C3' H3' C2' 122.2 120.2
H3' C3' O3' H3T 136.8 171.2
H3' C3' C2' H2'1 153.2 318.3
H3' C3' C2' H2'2 36.0 80.8
H3T O3' C3' C2' 260.1 294.7
H3T O3' C3' H3' 136.8 171.2
H2'1 C2' C1' H1' 325.6 158.1
C1' C2' H2'1 C3' 246.3 111.4
C1' C2' H2'1 H2'2 123.1 237.1
H2'1 C2' C3' H3' 153.2 318.3
C3' C2' H2'1 H2'2 236.8 125.7
H2'2 C2' C1' H1' 82.8 37.0
C1' C2' H2'2 C3' 115.8 245.4
C1' C2' H2'2 H2'1 237.9 122.1
H2'2 C2' C3' H3' 36.0 80.8
C3' C2' H2'2 H2'1 122.1 236.7
O3P P O5' C5' 139.7 53.2
O5' C5' C4' H4' 283.9 304.8
C4' C5' O5' H5'1 120.0 239.9
C4' C5' O5' H5'2 240.4 120.1
H5'1 C5' O5' H5'2 120.4 240.2
C5' O5' P O1P 23.4 180.0
C5' O5' P O2P 252.5 305.8
H5'1 C5' C4' H4' 43.8 185.3
C4' C5' H5'1 O5' 239.2 119.2
C4' C5' H5'1 H5'2 119.6 238.8
O5' C5' H5'1 H5'2 240.4 119.6
H5'1 C5' O5' P 121.1 300.1
H5'2 C5' C4' H4' 164.2 64.3
C4' C5' H5'2 O5' 120.5 240.8
C4' C5' H5'2 H5'1 240.2 121.2
O5' C5' H5'2 H5'1 119.7 240.4
H5'2 C5' O5' P 0.7 59.9
O5' P O3P HOP3 149.9 175.4
O3P P O5' O1P 116.3 233.2
O3P P O5' O2P 247.2 107.4
P O5' C5' H5'1 121.1 300.1
P O5' C5' H5'2 0.7 59.9
O2P P O5' O1P 229.1 125.8
O5' P O2P HOP2 60.9 186.1
O1P P O3P HOP3 265.5 48.8
O3P P O1P O5' 249.5 120.6
O3P P O1P O2P 124.2 239.9
O5' P O1P O2P 234.8 119.3
O1P P O2P HOP2 295.3 312.0
O2P P O3P HOP3 36.1 282.5
O3P P O2P O5' 108.8 252.3
O3P P O2P O1P 234.4 126.5
O5' P O2P O1P 125.6 234.2
HOP2 O2P P O1P 295.3 312.0