PDB Chemical Component N5P

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 N5P

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
OR2 NRO 1.222 1.218
NRO CZ3 1.461 1.480
NRO OR1 1.222 1.218
CZ3 CH2 1.400 1.388
CZ3 CE3 1.388 1.366
CE3 CD2 1.402 1.396
CE3 HE3 1.081 1.080
CD2 CE2 1.417 1.406
CD2 CG 1.435 1.465
CH2 CZ2 1.371 1.378
CH2 HH2 1.080 1.080
CZ2 CE2 1.405 1.392
CZ2 HZ2 1.080 1.080
CE2 NE1 1.370 1.376
NE1 C1' 1.494 1.465
NE1 CD1 1.374 1.368
CD1 CG 1.365 1.343
CD1 HD1 1.080 1.080
CG HG 1.080 1.080
C1' C2' 1.528 1.541
C1' O4' 1.430 1.437
C1' H1' 1.100 1.090
O4' C4' 1.426 1.444
C4' C3' 1.524 1.549
C4' C5' 1.529 1.530
C4' H4' 1.100 1.091
C3' C2' 1.521 1.548
C3' O3' 1.434 1.429
C3' H3' 1.100 1.090
O3' HO3' 0.950 0.967
C2' H2'1 1.100 1.091
C2' H2'2 1.100 1.090
C5' O5' 1.424 1.429
C5' H5'1 1.100 1.090
C5' H5'2 1.100 1.090
O5' PA 1.609 1.610
PA O3A 1.611 1.610
PA O1A 1.512 1.480
PA O2A 1.510 1.610
O2A HO2A 0.950 0.967
O3A PB 1.613 1.609
PB O1B 1.510 1.480
PB O3B 1.611 1.610
PB O2B 1.514 1.610
O2B HO2B 0.950 0.967
O3B PG 1.614 1.610
PG O1G 1.512 1.480
PG O3G 1.514 1.609
PG O2G 1.516 1.610
O3G HOG3 0.950 0.967
O2G HOG2 0.950 0.968

Bond Angles for N5P

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OR2 NRO CZ3 120.6 120.0
OR2 NRO OR1 119.0 120.0
OR1 NRO CZ3 120.4 119.9
NRO CZ3 CH2 118.6 119.7
NRO CZ3 CE3 118.9 119.8
CE3 CZ3 CH2 122.5 120.5
CZ3 CH2 CZ2 120.8 120.7
CZ3 CH2 HH2 119.6 119.7
CZ3 CE3 CD2 118.0 119.7
CZ3 CE3 HE3 121.0 120.1
CD2 CE3 HE3 121.0 120.1
CE3 CD2 CE2 118.8 120.0
CE3 CD2 CG 134.0 134.0
CE2 CD2 CG 107.2 106.1
CD2 CE2 CZ2 122.5 119.3
CD2 CE2 NE1 107.0 107.2
CD2 CG CD1 106.4 107.0
CD2 CG HG 126.8 126.5
CZ2 CH2 HH2 119.6 119.6
CH2 CZ2 CE2 117.4 119.8
CH2 CZ2 HZ2 121.3 120.2
CE2 CZ2 HZ2 121.3 120.1
CZ2 CE2 NE1 130.5 133.5
CE2 NE1 C1' 127.5 125.1
CE2 NE1 CD1 109.5 109.9
CD1 NE1 C1' 123.0 125.0
NE1 C1' C2' 114.2 109.9
NE1 C1' O4' 109.5 109.9
NE1 C1' H1' 105.2 109.9
NE1 CD1 CG 109.9 109.9
NE1 CD1 HD1 125.1 125.0
CG CD1 HD1 125.0 125.0
CD1 CG HG 126.8 126.5
O4' C1' C2' 106.4 107.3
C2' C1' H1' 108.4 109.9
C1' C2' C3' 103.5 104.2
C1' C2' H2'1 111.5 110.5
C1' C2' H2'2 111.5 110.5
O4' C1' H1' 113.3 110.0
C1' O4' C4' 110.5 107.0
O4' C4' C3' 105.0 103.5
O4' C4' C5' 109.3 110.6
O4' C4' H4' 115.1 110.6
C3' C4' C5' 116.1 110.7
C3' C4' H4' 108.1 110.7
C4' C3' C2' 102.0 102.1
C4' C3' O3' 110.5 110.9
C4' C3' H3' 114.2 110.9
C5' C4' H4' 103.7 110.7
C4' C5' O5' 110.6 109.5
C4' C5' H5'1 109.1 109.4
C4' C5' H5'2 109.1 109.5
O3' C3' C2' 111.1 110.9
C2' C3' H3' 113.6 110.9
C3' C2' H2'1 111.5 110.5
C3' C2' H2'2 111.5 110.5
O3' C3' H3' 105.6 110.8
C3' O3' HO3' 109.5 114.0
H2'1 C2' H2'2 107.4 110.5
O5' C5' H5'1 109.1 109.5
O5' C5' H5'2 109.1 109.5
C5' O5' PA 121.2 123.0
H5'1 C5' H5'2 109.8 109.5
O5' PA O3A 107.5 109.5
O5' PA O1A 108.1 109.4
O5' PA O2A 107.4 109.5
O1A PA O3A 107.3 109.5
O2A PA O3A 107.2 109.5
PA O3A PB 122.1 134.0
O1A PA O2A 119.0 109.5
PA O2A HO2A 109.5 114.0
O3A PB O1B 107.9 109.5
O3A PB O3B 101.9 109.5
O3A PB O2B 110.2 109.5
O1B PB O3B 108.1 109.4
O1B PB O2B 119.1 109.4
O2B PB O3B 108.2 109.5
PB O3B PG 122.5 134.0
PB O2B HO2B 109.5 114.0
O3B PG O1G 103.7 109.5
O3B PG O3G 103.6 109.5
O3B PG O2G 106.2 109.5
O3G PG O1G 114.0 109.5
O2G PG O1G 114.4 109.4
O3G PG O2G 113.6 109.4
PG O3G HOG3 109.5 114.0
PG O2G HOG2 109.5 114.0

Torsion Angles for N5P

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OR1 NRO OR2 CZ3 179.7 180.3
OR2 NRO CZ3 CH2 359.4 0.1
OR2 NRO CZ3 CE3 180.2 180.3
OR2 NRO CZ3 OR1 179.7 180.3
CE3 CZ3 NRO CH2 180.8 180.2
NRO CZ3 CH2 CZ2 180.3 180.0
NRO CZ3 CH2 HH2 0.3 359.9
NRO CZ3 CE3 CD2 179.8 180.0
NRO CZ3 CE3 HE3 359.8 0.0
OR2 NRO OR1 CZ3 180.3 179.7
OR1 NRO CZ3 CH2 179.7 179.7
OR1 NRO CZ3 CE3 0.5 360.0
NRO CZ3 CH2 CE3 180.8 180.2
CH2 CZ3 CE3 CD2 0.6 0.2
CH2 CZ3 CE3 HE3 180.6 180.2
CZ2 CH2 CZ3 HH2 180.0 180.1
CZ3 CH2 CZ2 CE2 359.8 359.9
CZ3 CH2 CZ2 HZ2 179.8 180.0
NRO CZ3 CE3 CH2 179.2 179.8
CE3 CZ3 CH2 CZ2 359.5 359.8
CE3 CZ3 CH2 HH2 179.5 179.7
CD2 CE3 CZ3 HE3 180.0 180.0
CZ3 CE3 CD2 CE2 359.9 0.0
CZ3 CE3 CD2 CG 179.9 180.0
CD2 CE3 CZ3 CH2 0.6 0.2
CZ3 CE3 CD2 HE3 180.0 180.0
CE2 CD2 CE3 CG 180.0 180.0
CE3 CD2 CE2 CZ2 359.4 359.7
CE3 CD2 CE2 NE1 180.1 180.0
CE3 CD2 CG CD1 179.9 180.0
CE3 CD2 CG HG 359.9 0.0
HE3 CE3 CZ3 CH2 180.6 180.2
CZ3 CE3 HE3 CD2 180.0 180.0
HE3 CE3 CD2 CE2 179.9 180.0
HE3 CE3 CD2 CG 359.9 360.0
CE2 CD2 CE3 HE3 179.9 180.0
CE3 CD2 CE2 CG 180.0 180.0
CE2 CD2 CG CD1 359.9 360.0
CE2 CD2 CG HG 179.9 180.0
CH2 CZ2 CE2 CD2 0.8 0.3
CD2 CE2 CZ2 HZ2 180.8 180.3
CZ2 CE2 CD2 NE1 179.2 179.7
CD2 CE2 NE1 C1' 179.8 180.0
CD2 CE2 NE1 CD1 359.9 360.0
CG CD2 CE3 HE3 359.9 360.0
CE3 CD2 CG CE2 180.0 180.0
CG CD2 CE2 CZ2 179.4 179.7
CG CD2 CE2 NE1 0.2 0.0
NE1 CD1 CG CD2 0.1 0.0
CD2 CG CD1 HD1 180.0 180.0
CD1 CG CD2 HG 180.0 180.0
CZ3 CH2 CZ2 HH2 180.0 179.9
CD2 CE2 CZ2 CH2 0.8 0.3
CE2 CZ2 CH2 HZ2 180.0 180.0
CH2 CZ2 CE2 NE1 179.8 179.9
CZ3 CH2 HH2 CZ2 180.0 180.1
HH2 CH2 CZ2 CE2 179.8 180.0
HH2 CH2 CZ2 HZ2 359.8 0.0
CZ2 CE2 CD2 CG 179.4 179.7
CD2 CE2 CZ2 NE1 181.0 180.4
CE2 CZ2 CH2 HH2 179.8 180.0
CH2 CZ2 CE2 HZ2 180.0 180.0
CZ2 CE2 NE1 C1' 0.7 0.4
CZ2 CE2 NE1 CD1 180.7 180.3
HZ2 CZ2 CH2 HH2 359.8 0.0
CH2 CZ2 HZ2 CE2 180.0 180.0
HZ2 CZ2 CE2 NE1 359.8 359.9
NE1 CE2 CD2 CG 0.2 0.0
CD2 CE2 NE1 CZ2 179.1 179.6
NE1 CE2 CZ2 HZ2 359.8 359.9
CD1 NE1 CE2 C1' 180.0 180.0
CE2 NE1 C1' C2' 57.5 85.0
CE2 NE1 C1' O4' 176.7 202.8
CE2 NE1 C1' H1' 298.7 324.0
CE2 NE1 CD1 CG 0.1 0.0
CE2 NE1 CD1 HD1 180.1 180.0
CE2 NE1 C1' CD1 180.0 180.0
C1' NE1 CD1 CG 180.1 180.0
C1' NE1 CD1 HD1 0.1 360.0
O4' C1' NE1 C2' 119.2 117.8
C2' C1' NE1 H1' 118.8 121.0
NE1 C1' C2' C3' 140.5 121.5
NE1 C1' C2' H2'1 260.5 240.2
NE1 C1' C2' H2'2 20.5 2.8
O4' C1' NE1 H1' 238.0 238.9
NE1 C1' O4' C4' 238.5 214.1
CD2 CG CD1 NE1 0.1 0.0
CE2 NE1 CD1 C1' 180.0 180.0
CD1 NE1 C1' C2' 237.4 265.0
CD1 NE1 C1' O4' 356.6 22.9
CD1 NE1 C1' H1' 118.7 144.0
CG CD1 NE1 HD1 180.0 180.0
NE1 CD1 CG HG 180.1 180.0
CD2 CG CD1 HG 180.0 180.0
CG CD1 NE1 C1' 180.1 180.0
NE1 CD1 CG HD1 180.0 180.0
HD1 CD1 NE1 C1' 0.1 360.0
NE1 CD1 HD1 CG 180.0 180.0
HD1 CD1 CG HG 0.0 360.0
CD2 CG HG CD1 180.0 180.0
HG CG CD1 HD1 0.0 360.0
NE1 C1' C2' O4' 120.9 119.4
NE1 C1' C2' H1' 243.0 239.0
O4' C1' C2' H1' 122.1 119.5
C2' C1' O4' C4' 2.5 333.5
C4' C3' C2' C1' 327.5 20.9
O3' C3' C2' C1' 85.3 139.1
C1' C2' C3' H3' 204.2 262.7
C3' C2' C1' H2'1 240.0 241.3
C3' C2' C1' H2'2 120.0 118.7
H2'1 C2' C1' H2'2 240.0 237.4
NE1 C1' O4' C2' 236.1 240.6
NE1 C1' O4' H1' 117.1 121.1
C2' C1' O4' H1' 241.0 240.5
O4' C1' C2' C3' 19.5 2.1
O4' C1' C2' H2'1 139.5 120.7
O4' C1' C2' H2'2 259.6 243.3
C1' O4' C4' C3' 336.4 40.0
C1' O4' C4' C5' 101.5 158.6
C1' O4' C4' H4' 217.7 281.5
NE1 C1' H1' C2' 122.6 121.0
NE1 C1' H1' O4' 240.4 238.9
O4' C1' H1' C2' 242.2 242.1
H1' C1' C2' C3' 257.4 242.5
H1' C1' C2' H2'1 17.4 1.2
H1' C1' C2' H2'2 137.4 123.8
H1' C1' O4' C4' 121.5 93.0
C4' O4' C1' C2' 2.5 333.5
C4' O4' C1' H1' 121.5 93.0
C3' C4' O4' C5' 234.9 241.5
C3' C4' O4' H4' 118.7 118.5
O4' C4' C3' C2' 34.6 323.0
O4' C4' C3' O3' 276.4 204.8
O4' C4' C3' H3' 157.6 81.2
C5' C4' O4' H4' 243.8 237.1
O4' C4' C5' O5' 172.3 66.4
O4' C4' C5' H5'1 292.3 186.4
O4' C4' C5' H5'2 52.4 306.4
C1' C2' C3' C4' 327.5 20.9
O4' C4' C3' C5' 120.7 118.5
O4' C4' C3' H4' 236.7 241.5
C5' C4' C3' H4' 115.9 123.0
C3' C4' C5' O5' 290.7 180.5
C3' C4' C5' H5'1 50.7 300.5
C3' C4' C5' H5'2 170.7 60.5
O3' C3' C4' C2' 241.8 241.8
C2' C3' C4' H3' 237.0 241.8
C4' C3' C2' H2'1 207.5 262.2
C4' C3' C2' H2'2 87.5 139.6
O3' C3' C4' H3' 118.8 123.6
C4' C3' O3' HO3' 180.0 180.0
O4' C4' C5' C3' 241.6 245.9
O4' C4' C5' H4' 123.2 122.9
C3' C4' C5' H4' 241.6 237.0
C5' C4' C3' C2' 273.9 204.5
C5' C4' C3' O3' 155.7 86.3
C5' C4' C3' H3' 36.9 322.7
O5' C5' C4' H5'1 240.0 240.0
O5' C5' C4' H5'2 120.0 120.0
C4' C5' O5' PA 190.0 180.0
H5'1 C5' C4' H5'2 240.0 240.0
O4' C4' H4' C3' 116.9 114.1
O4' C4' H4' C5' 240.7 237.1
C3' C4' H4' C5' 123.8 123.0
H4' C4' C3' C2' 157.9 81.5
H4' C4' C3' O3' 39.7 323.3
H4' C4' C3' H3' 280.9 199.7
H4' C4' C5' O5' 49.1 303.6
H4' C4' C5' H5'1 169.1 63.5
H4' C4' C5' H5'2 289.1 183.5
C3' C2' C1' H1' 257.4 242.5
C1' C2' C3' H2'1 120.0 118.7
C1' C2' C3' H2'2 240.0 241.3
C2' C3' C4' C5' 273.9 204.5
C2' C3' C4' H4' 157.9 81.5
C4' C3' C2' O3' 242.2 241.8
C4' C3' C2' H3' 123.4 118.2
O3' C3' C2' H3' 241.1 236.4
C2' C3' O3' HO3' 67.5 67.2
H2'1 C2' C3' H2'2 120.0 122.6
C1' C2' C3' O3' 85.3 139.1
O3' C3' C4' C5' 155.7 86.3
O3' C3' C4' H4' 39.7 323.3
C4' C3' O3' C2' 112.5 112.7
C4' C3' O3' H3' 236.1 236.4
C2' C3' O3' H3' 123.6 123.6
O3' C3' C2' H2'1 325.3 20.4
O3' C3' C2' H2'2 205.3 257.8
H3' C3' C4' C5' 36.9 322.7
H3' C3' C4' H4' 280.9 199.7
C4' C3' H3' C2' 243.6 247.3
C4' C3' H3' O3' 121.6 123.6
O3' C3' H3' C2' 122.0 123.7
H3' C3' C2' H2'1 84.2 144.0
H3' C3' C2' H2'2 324.2 21.4
H3' C3' O3' HO3' 303.9 303.6
HO3' O3' C3' C2' 67.5 67.2
HO3' O3' C3' H3' 303.9 303.6
H2'1 C2' C1' H1' 17.4 1.2
C1' C2' H2'1 C3' 244.8 245.2
C1' C2' H2'1 H2'2 122.4 122.6
H2'1 C2' C3' H3' 84.2 144.0
C3' C2' H2'1 H2'2 237.6 237.4
H2'2 C2' C1' H1' 137.4 123.8
C1' C2' H2'2 C3' 115.2 114.8
C1' C2' H2'2 H2'1 237.5 237.4
H2'2 C2' C3' H3' 324.2 21.4
C3' C2' H2'2 H2'1 122.4 122.6
O5' C5' C4' H4' 49.1 303.6
C4' C5' O5' H5'1 120.0 120.0
C4' C5' O5' H5'2 240.0 240.0
H5'1 C5' O5' H5'2 120.0 120.0
C5' O5' PA O3A 196.0 185.0
C5' O5' PA O1A 311.4 305.0
C5' O5' PA O2A 81.0 64.9
H5'1 C5' C4' H4' 169.1 63.5
C4' C5' H5'1 O5' 239.1 240.0
C4' C5' H5'1 H5'2 119.5 120.0
O5' C5' H5'1 H5'2 240.5 240.0
H5'1 C5' O5' PA 69.9 60.1
H5'2 C5' C4' H4' 289.1 183.5
C4' C5' H5'2 O5' 120.9 120.0
C4' C5' H5'2 H5'1 240.4 240.0
O5' C5' H5'2 H5'1 119.5 120.0
H5'2 C5' O5' PA 309.9 300.0
PA O5' C5' H5'1 69.9 60.1
PA O5' C5' H5'2 309.9 300.0
O1A PA O5' O3A 115.5 120.0
O2A PA O5' O3A 245.0 240.0
O5' PA O3A PB 349.4 165.0
O1A PA O5' O2A 230.5 240.0
O5' PA O2A HO2A 236.9 60.1
O5' PA O3A O1A 116.0 120.0
O5' PA O3A O2A 244.9 240.0
O1A PA O3A O2A 128.9 120.0
O3A PA O2A HO2A 121.7 300.1
PA O3A PB O1B 106.0 45.0
PA O3A PB O3B 219.7 165.0
PA O3A PB O2B 334.4 285.0
O5' PA O1A O3A 244.4 240.0
O5' PA O1A O2A 122.7 120.0
O2A PA O1A O3A 121.7 120.0
O1A PA O3A PB 233.3 45.0
O1A PA O2A HO2A 360.0 180.0
O5' PA O2A O3A 115.2 120.0
O5' PA O2A O1A 237.0 240.0
O1A PA O2A O3A 238.2 240.0
O2A PA O3A PB 104.5 285.0
HO2A O2A PA O3A 121.7 300.1
O1B PB O3A O3B 246.3 240.0
O1B PB O3A O2B 131.6 120.0
O2B PB O3A O3B 114.7 120.0
O3A PB O3B PG 89.6 200.0
O3A PB O2B HO2B 125.4 300.0
O3A PB O1B O3B 109.5 120.0
O3A PB O1B O2B 233.5 240.0
O2B PB O1B O3B 236.0 240.0
O1B PB O3B PG 203.1 320.0
O1B PB O2B HO2B 0.0 180.0
O3A PB O3B O1B 246.5 240.0
O3A PB O3B O2B 116.1 120.0
O1B PB O3B O2B 229.6 240.0
O3B PB O2B HO2B 236.0 60.0
PB O3B PG O1G 99.4 45.0
PB O3B PG O3G 218.7 165.0
PB O3B PG O2G 338.6 285.0
O3A PB O2B O1B 125.4 120.0
O3A PB O2B O3B 249.4 240.0
O1B PB O2B O3B 124.0 120.0
O2B PB O3B PG 333.5 80.0
HO2B O2B PB O3B 236.0 60.0
O3G PG O3B O1G 119.3 120.1
O2G PG O3B O1G 239.2 240.0
O3G PG O3B O2G 240.1 240.0
O3B PG O3G HOG3 248.0 180.0
O3B PG O2G HOG2 113.7 300.0
O3B PG O1G O3G 111.9 120.0
O3B PG O1G O2G 244.9 240.0
O3G PG O1G O2G 133.0 120.0
O1G PG O3G HOG3 360.0 300.0
O1G PG O2G HOG2 360.0 180.0
O3B PG O3G O1G 248.1 240.0
O3B PG O3G O2G 114.7 120.0
O2G PG O3G O1G 133.4 120.0
O3G PG O2G HOG2 226.8 60.0
O3B PG O2G O1G 113.7 120.0
O3B PG O2G O3G 246.9 240.0
O3G PG O2G O1G 226.8 240.0
O2G PG O3G HOG3 133.4 60.0
HOG3 O3G PG O1G 360.0 300.0
HOG3 O3G PG O2G 133.4 60.0
HOG2 O2G PG O1G 360.0 180.0