PDB Chemical Component N5M

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 N5M

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O4 N5 1.223 1.218
N5 O3 1.222 1.219
N5 C5 1.447 1.480
C5 C4 1.393 1.409
C5 C6 1.390 1.354
C4 N4 1.356 1.376
C4 N3 1.354 1.327
N3 C2 1.355 1.332
C2 O2 1.253 1.220
C2 N1 1.356 1.345
C6 N1 1.344 1.362
N1 C1' 1.472 1.465
C1' O4' 1.437 1.444
C1' C2' 1.525 1.545
O4' C4' 1.433 1.444
C2' O2' 1.430 1.429
C2' C3' 1.517 1.545
C3' O3' 1.432 1.429
C3' C4' 1.518 1.545
C4' C5' 1.527 1.529
C5' O5' 1.429 1.429
O5' P 1.616 1.611
P OP2 1.512 1.480
P OP1 1.513 1.610
P OP3 1.600 1.610
N4 HN4 1.000 0.970
N4 HN4A 1.000 0.970
C6 H6 1.080 1.080
C1' H1' 1.100 1.090
C2' H2' 1.100 1.090
O2' HO2' 0.950 0.967
C3' H3' 1.100 1.090
O3' HO3' 0.950 0.967
C4' H4' 1.100 1.091
C5' H5' 1.100 1.090
C5' H5'A 1.100 1.090
OP1 HOP1 0.950 0.968
OP3 HOP3 0.950 0.967

Bond Angles for N5M

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O4 N5 O3 119.2 119.9
O4 N5 C5 119.3 120.1
O3 N5 C5 121.5 120.0
N5 C5 C4 123.2 120.5
N5 C5 C6 118.4 120.5
C4 C5 C6 118.4 119.0
C5 C4 N4 121.8 120.2
C5 C4 N3 119.1 119.6
C5 C6 N1 121.0 119.3
C5 C6 H6 119.5 120.4
N4 C4 N3 119.0 120.2
C4 N4 HN4 109.8 120.0
C4 N4 HN4A 125.1 120.0
C4 N3 C2 121.2 120.7
N3 C2 O2 118.3 119.4
N3 C2 N1 120.6 121.1
O2 C2 N1 121.2 119.5
C2 N1 C6 119.8 120.4
C2 N1 C1' 121.6 119.8
C6 N1 C1' 118.6 119.8
N1 C6 H6 119.5 120.4
N1 C1' O4' 111.4 110.4
N1 C1' C2' 109.9 110.4
N1 C1' H1' 107.1 110.4
O4' C1' C2' 106.9 104.8
C1' O4' C4' 110.0 105.3
O4' C1' H1' 110.0 110.3
C1' C2' O2' 108.8 110.6
C1' C2' C3' 105.4 104.1
C2' C1' H1' 111.6 110.4
C1' C2' H2' 113.2 110.5
O4' C4' C3' 105.8 104.8
O4' C4' C5' 112.7 110.4
O4' C4' H4' 111.1 110.3
O2' C2' C3' 111.2 110.6
O2' C2' H2' 107.5 110.5
C2' O2' HO2' 109.5 114.0
C2' C3' O3' 111.7 110.5
C2' C3' C4' 103.8 104.1
C3' C2' H2' 110.9 110.6
C2' C3' H3' 112.2 110.5
O3' C3' C4' 110.9 110.5
O3' C3' H3' 105.3 110.4
C3' O3' HO3' 109.5 114.0
C3' C4' C5' 112.9 110.4
C4' C3' H3' 113.0 110.7
C3' C4' H4' 110.9 110.4
C4' C5' O5' 112.2 109.4
C5' C4' H4' 103.6 110.4
C4' C5' H5' 108.6 109.5
C4' C5' H5'A 108.0 109.5
C5' O5' P 115.9 123.0
O5' C5' H5' 108.6 109.5
O5' C5' H5'A 107.9 109.5
O5' P OP2 85.2 109.5
O5' P OP1 115.9 109.5
O5' P OP3 105.7 109.4
OP2 P OP1 129.4 109.5
OP2 P OP3 110.0 109.5
OP1 P OP3 107.4 109.5
P OP1 HOP1 109.5 114.0
P OP3 HOP3 109.5 114.0
HN4 N4 HN4A 125.1 120.0
H5' C5' H5'A 111.7 109.4

Torsion Angles for N5M

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O3 N5 O4 C5 180.3 180.3
O4 N5 C5 C4 159.3 174.6
O4 N5 C5 C6 339.4 354.3
O4 N5 O3 C5 179.7 179.7
O3 N5 C5 C4 339.0 354.3
O3 N5 C5 C6 159.2 174.0
O4 N5 C5 O3 180.3 180.3
C4 C5 N5 C6 179.8 180.3
N5 C5 C4 N4 0.1 0.0
N5 C5 C4 N3 180.1 180.0
N5 C5 C6 N1 179.8 179.8
N5 C5 C6 H6 359.8 359.9
N5 C5 C4 C6 180.2 179.7
C4 C5 C6 N1 360.0 359.5
C4 C5 C6 H6 180.0 179.7
N4 C4 C5 N3 180.0 180.1
C5 C4 N4 HN4 180.0 5.5
C5 C4 N4 HN4A 0.0 185.4
C5 C4 N3 C2 0.1 0.1
N5 C5 C6 C4 179.8 180.3
C6 C5 C4 N4 179.9 180.3
C6 C5 C4 N3 359.9 0.2
C2 N1 C6 C5 0.1 0.5
C5 C6 N1 C1' 179.8 180.2
N1 C6 C5 H6 180.0 179.8
N4 C4 C5 C6 179.9 180.3
C5 C4 N4 N3 180.0 179.9
N4 C4 N3 C2 180.1 180.0
HN4 N4 C4 HN4A 180.0 180.1
N3 C4 C5 C6 359.9 0.2
C5 C4 N3 N4 180.0 180.1
N3 C4 N4 HN4 360.0 185.5
N3 C4 N4 HN4A 180.0 5.5
C4 N3 C2 O2 179.9 180.0
C4 N3 C2 N1 359.9 359.9
O2 C2 N3 N1 180.0 180.1
N3 C2 N1 C6 360.0 359.8
N3 C2 N1 C1' 180.2 180.1
N3 C2 O2 N1 180.0 179.9
O2 C2 N1 C6 180.0 179.8
O2 C2 N1 C1' 0.2 360.0
C5 C6 N1 C2 0.1 0.5
N3 C2 N1 O2 180.0 180.1
C6 N1 C2 C1' 179.8 179.8
C2 N1 C6 H6 180.1 180.3
C2 N1 C1' O4' 200.3 53.6
C2 N1 C1' C2' 82.0 298.2
C2 N1 C1' H1' 320.6 175.8
C5 C6 N1 H6 180.0 180.2
C2 N1 C6 C1' 180.2 180.2
C6 N1 C1' O4' 20.5 233.8
C6 N1 C1' C2' 262.2 118.4
C6 N1 C1' H1' 140.9 356.0
C2 N1 C1' C6 179.8 179.8
C1' N1 C6 H6 359.8 0.1
O4' C1' N1 C2' 118.3 115.4
N1 C1' O4' C4' 228.7 200.7
O4' C1' N1 H1' 239.6 237.8
N1 C1' C2' O2' 232.9 261.5
N1 C1' C2' C3' 113.6 142.8
C2' C1' N1 H1' 121.4 122.4
N1 C1' C2' H2' 352.4 24.0
N1 C1' O4' C2' 240.0 241.1
N1 C1' O4' H1' 118.6 122.3
O4' C1' C2' O2' 111.9 142.6
O4' C1' C2' C3' 352.6 23.9
C2' C1' O4' H1' 238.7 241.1
O4' C1' C2' H2' 231.3 265.2
C1' O4' C4' C3' 25.5 40.5
C1' O4' C4' C5' 149.4 159.3
C1' O4' C4' H4' 265.1 281.7
N1 C1' C2' O4' 121.1 118.9
N1 C1' C2' H1' 241.4 237.7
C2' C1' O4' C4' 348.7 319.6
O4' C1' C2' H1' 120.3 118.8
O2' C2' C1' C3' 119.3 118.7
O2' C2' C1' H2' 240.6 237.4
C1' C2' O2' HO2' 200.2 180.0
C1' C2' C3' O3' 141.4 118.7
C1' C2' C3' C4' 21.9 0.0
C3' C2' C1' H2' 121.3 118.7
C1' C2' C3' H3' 259.5 241.2
C4' O4' C1' C2' 348.7 319.6
C4' O4' C1' H1' 110.0 78.4
C2' C3' C4' O4' 331.1 336.0
O3' C3' C4' O4' 210.9 217.4
C3' C4' O4' C5' 236.1 241.2
O4' C4' C3' H3' 92.9 94.7
C3' C4' O4' H4' 120.4 118.8
O4' C4' C5' O5' 311.5 66.4
C5' C4' O4' H4' 244.3 237.7
O4' C4' C5' H5' 71.5 186.4
O4' C4' C5' H5'A 192.7 306.5
C1' C2' O2' C3' 244.4 245.3
O2' C2' C1' H1' 351.5 23.8
C1' C2' O2' H2' 122.9 122.6
O2' C2' C3' O3' 23.7 360.0
O2' C2' C3' C4' 264.2 241.3
C3' C2' O2' H2' 238.5 237.3
O2' C2' C3' H3' 141.8 122.5
C1' C2' C3' O2' 117.7 118.7
C3' C2' C1' H1' 232.3 265.1
C1' C2' C3' H2' 237.2 241.4
O4' C4' C3' C2' 331.1 336.0
O2' C2' C3' H2' 119.5 122.7
C3' C2' O2' HO2' 315.8 294.7
O3' C3' C2' C4' 119.5 118.7
O3' C3' C2' H3' 241.9 237.5
C2' C3' O3' HO3' 147.4 61.5
C2' C3' C4' C5' 207.3 217.1
C4' C3' C2' H3' 122.4 118.8
C2' C3' C4' H4' 91.6 94.8
O4' C4' C3' O3' 210.9 217.4
C2' C3' O3' C4' 244.7 245.4
O3' C3' C2' H2' 264.2 237.3
C2' C3' O3' H3' 122.1 122.5
O3' C3' C4' C5' 87.2 98.5
C4' C3' O3' H3' 237.4 237.2
O3' C3' C4' H4' 331.5 336.2
O4' C4' C3' C5' 123.8 118.9
O4' C4' C3' H4' 239.5 241.2
C2' C3' C4' O3' 120.1 118.6
C4' C3' C2' H2' 144.6 118.7
C2' C3' C4' H3' 238.1 241.3
O3' C3' C4' H3' 118.0 122.7
C4' C3' O3' HO3' 262.7 176.1
C3' C4' C5' O5' 71.3 181.8
C5' C4' C3' H4' 115.7 122.3
C3' C4' C5' H5' 191.3 301.8
C3' C4' C5' H5'A 312.5 61.9
O4' C4' C5' C3' 240.2 244.6
O4' C4' C5' H4' 120.2 122.3
C5' C4' C3' H3' 329.2 335.9
C3' C4' C5' H4' 240.0 237.7
C4' C5' O5' P 178.6 180.0
O5' C5' C4' H5' 240.0 240.0
O5' C5' C4' H5'A 118.8 120.0
H5' C5' C4' H5'A 238.8 240.0
O5' C5' C4' H4' 191.3 304.1
C4' C5' O5' H5' 120.0 120.1
C4' C5' O5' H5'A 241.2 240.0
C5' O5' P OP2 171.1 55.0
C5' O5' P OP1 39.3 175.0
C5' O5' P OP3 280.5 295.0
H5' C5' O5' H5'A 121.2 119.9
P O5' C5' H5' 58.6 60.0
P O5' C5' H5'A 297.4 300.0
OP2 P O5' OP1 131.8 240.0
OP2 P O5' OP3 250.6 120.0
OP1 P O5' OP3 118.7 240.0
O5' P OP1 HOP1 166.3 180.0
O5' P OP3 HOP3 152.2 300.0
O5' P OP2 OP1 240.2 120.0
O5' P OP2 OP3 105.0 240.0
OP1 P OP2 OP3 224.8 120.0
OP2 P OP1 HOP1 60.3 300.0
OP2 P OP3 HOP3 242.7 180.0
O5' P OP1 OP2 106.1 240.0
O5' P OP1 OP3 242.2 119.9
OP2 P OP1 OP3 136.1 240.0
OP1 P OP3 HOP3 28.0 59.9
O5' P OP3 OP2 269.5 120.0
O5' P OP3 OP1 124.2 240.0
OP2 P OP3 OP1 214.8 120.0
OP3 P OP1 HOP1 284.2 60.1
HN4 N4 C4 N3 360.0 185.5
C4 N4 HN4 HN4A 180.0 179.9
HN4A N4 C4 N3 180.0 5.5
C4 N4 HN4A HN4 180.0 180.1
C5 C6 H6 N1 180.0 179.8
H6 C6 N1 C1' 359.8 0.1
N1 C1' H1' O4' 238.7 237.7
N1 C1' H1' C2' 120.3 122.4
O4' C1' H1' C2' 241.5 244.6
H1' C1' O4' C4' 110.0 78.4
H1' C1' C2' O2' 351.5 23.8
H1' C1' C2' C3' 232.3 265.1
H1' C1' C2' H2' 111.0 146.4
C1' C2' H2' O2' 239.8 237.4
C1' C2' H2' C3' 118.1 114.7
H2' C2' C1' H1' 111.0 146.4
O2' C2' H2' C3' 238.3 237.3
H2' C2' O2' HO2' 77.3 57.5
H2' C2' C3' O3' 264.2 237.3
H2' C2' C3' C4' 144.6 118.7
H2' C2' C3' H3' 22.2 359.8
HO2' O2' C2' C3' 315.8 294.7
HO2' O2' C2' H2' 77.3 57.5
C2' C3' H3' O3' 238.2 237.5
C2' C3' H3' C4' 117.0 114.8
H3' C3' C2' H2' 22.2 359.8
O3' C3' H3' C4' 238.8 237.3
H3' C3' O3' HO3' 25.3 298.9
H3' C3' C4' C5' 329.2 335.9
H3' C3' C4' H4' 213.4 213.5
HO3' O3' C3' C4' 262.7 176.1
HO3' O3' C3' H3' 25.3 298.9
O4' C4' H4' C3' 117.3 115.4
O4' C4' H4' C5' 238.7 237.6
C3' C4' H4' C5' 121.4 122.3
H4' C4' C3' H3' 213.4 213.5
H4' C4' C5' O5' 191.3 304.1
H4' C4' C5' H5' 311.3 64.1
H4' C4' C5' H5'A 72.5 184.2
C4' C5' H5' O5' 237.8 240.0
H5' C5' C4' H4' 311.3 64.1
C4' C5' H5' H5'A 118.9 120.0
H5' C5' O5' P 58.6 60.0
O5' C5' H5' H5'A 241.1 240.0
C4' C5' H5'A O5' 121.5 120.0
H5'A C5' C4' H4' 72.5 184.2
C4' C5' H5'A H5' 240.7 239.9
H5'A C5' O5' P 297.4 300.0
O5' C5' H5'A H5' 119.2 120.0
HOP1 OP1 P OP3 284.2 60.1