PDB Chemical Component M5M

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 M5M

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.482 1.501
P OP2 1.483 1.617
P O5' 1.599 1.619
P OP3   1.618
N2' C6' 1.330 1.381
N2' C2' 1.453 1.436
N2' HN'2 1.019 1.015
C6' C7' 1.503 1.493
C6' O8' 1.233 1.226
C7' H7'1 1.115 1.102
C7' H7'2 1.115 1.102
C7' H7'3 1.115 1.101
OP2 HOP2 0.950 0.981
O5' C5' 1.430 1.418
C5' C4' 1.517 1.523
C5' H5' 1.115 1.093
C5' H5'' 1.114 1.092
C4' O4' 1.450 1.442
C4' C3' 1.523 1.523
C4' H4' 1.114 1.095
O4' C1' 1.418 1.438
C1' N1 1.465 1.436
C1' C2' 1.528 1.523
C1' H1' 1.114 1.095
N1 C6 1.365 1.384
N1 C2 1.391 1.416
C6 C5 1.335 1.331
C6 H6 1.103 1.084
C2 O2 1.238 1.232
C2 N3 1.347 1.384
N3 C4 1.331 1.307
C4 N4 1.334 1.376
C4 C5 1.423 1.487
N4 HN41 1.020 0.992
N4 HN42 1.020 0.992
C5 H5 1.103 1.082
C2' C3' 1.523 1.518
C2' H2' 1.116 1.096
C3' O3' 1.426 1.428
C3' H3' 1.116 1.094
O3' HO3' 0.951 0.974
OP3 HOP3   0.981

Bond Angles for M5M

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 119.5 115.3
OP1 P O5' 108.5 115.0
OP1 P OP3   115.0
OP2 P O5' 110.5 103.8
OP2 P OP3   103.3
P OP2 HOP2 119.5 118.9
O5' P OP3   102.8
P O5' C5' 120.0 118.5
P OP3 HOP3   118.9
C6' N2' C2' 124.3 123.1
C6' N2' HN'2 113.1 118.5
N2' C6' C7' 115.1 114.0
N2' C6' O8' 123.0 126.5
C2' N2' HN'2 122.6 118.4
N2' C2' C1' 108.5 113.3
N2' C2' C3' 108.1 114.0
N2' C2' H2' 108.6 107.0
C7' C6' O8' 121.9 119.5
C6' C7' H7'1 115.1 112.4
C6' C7' H7'2 110.1 112.4
C6' C7' H7'3 110.2 115.3
H7'1 C7' H7'2 110.2 105.3
H7'1 C7' H7'3 110.2 105.3
H7'2 C7' H7'3 100.1 105.2
O5' C5' C4' 111.4 108.9
O5' C5' H5' 111.4 109.0
O5' C5' H5'' 111.5 109.0
C4' C5' H5' 111.5 110.3
C4' C5' H5'' 111.5 110.4
C5' C4' O4' 109.3 108.2
C5' C4' C3' 118.5 113.3
C5' C4' H4' 101.6 109.3
H5' C5' H5'' 98.9 109.3
O4' C4' C3' 103.8 105.8
O4' C4' H4' 116.9 107.7
C4' O4' C1' 109.5 109.4
C3' C4' H4' 107.3 112.2
C4' C3' C2' 101.6 102.4
C4' C3' O3' 112.0 108.7
C4' C3' H3' 113.2 113.6
O4' C1' N1 108.2 108.9
O4' C1' C2' 107.3 107.0
O4' C1' H1' 112.9 107.9
N1 C1' C2' 112.6 112.7
N1 C1' H1' 107.6 107.5
C1' N1 C6 121.1 118.6
C1' N1 C2 118.6 121.8
C2' C1' H1' 108.5 112.6
C1' C2' C3' 101.0 102.4
C1' C2' H2' 114.9 110.6
C6 N1 C2 120.4 119.6
N1 C6 C5 120.9 122.6
N1 C6 H6 120.7 116.2
N1 C2 O2 118.7 121.1
N1 C2 N3 119.5 118.7
C5 C6 H6 118.4 121.2
C6 C5 C4 117.5 116.3
C6 C5 H5 118.3 123.1
O2 C2 N3 121.8 120.2
C2 N3 C4 119.8 121.1
N3 C4 N4 118.0 120.2
N3 C4 C5 122.0 121.6
N4 C4 C5 120.1 118.2
C4 N4 HN41 118.0 118.0
C4 N4 HN42 109.2 118.1
C4 C5 H5 124.2 120.6
HN41 N4 HN42 109.2 123.9
C3' C2' H2' 115.2 109.5
C2' C3' O3' 110.0 111.1
C2' C3' H3' 115.1 113.4
O3' C3' H3' 105.2 107.4
C3' O3' HO3' 112.0 107.3

Torsion Angles for M5M

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 O5' 232.1 120.7
OP2 P OP1 OP3   239.9
OP1 P OP2 HOP2 180.0 48.8
O5' P OP1 OP3   119.2
OP1 P O5' C5' 46.6 180.1
OP1 P OP3 HOP3   311.9
OP1 P OP2 O5' 127.0 233.3
OP1 P OP2 OP3   126.3
O5' P OP2 OP3   253.0
OP2 P O5' C5' 179.5 53.2
OP2 P OP3 HOP3   78.4
OP1 P O5' OP2 227.1 126.9
OP1 P O5' OP3   234.3
OP2 P O5' OP3   107.4
O5' P OP2 HOP2 53.0 175.5
O5' P OP3 HOP3   186.2
P O5' C5' C4' 161.2 180.0
P O5' C5' H5' 286.4 300.3
P O5' C5' H5'' 35.9 59.6
OP1 P OP3 OP2   233.5
OP1 P OP3 O5'   125.7
OP2 P OP3 O5'   252.3
OP3 P OP2 HOP2   282.5
OP3 P O5' C5'   305.8
C2' N2' C6' HN'2 180.0 179.9
C6' N2' C2' C1' 115.3 92.2
C6' N2' C2' C3' 224.1 208.8
C6' N2' C2' H2' 349.8 330.1
C7' C6' N2' O8' 181.6 180.0
N2' C6' C7' H7'1 180.0 120.7
N2' C6' C7' H7'2 305.3 239.4
N2' C6' C7' H7'3 54.7 0.0
C6' N2' C2' HN'2 180.0 180.1
C2' N2' C6' C7' 144.9 179.9
C2' N2' C6' O8' 323.2 359.9
C4' C3' C2' N2' 285.1 202.4
O4' C1' C2' N2' 86.5 149.6
N1 C1' C2' N2' 205.4 269.3
N2' C2' C1' H1' 324.3 31.2
C1' C2' N2' C3' 251.2 243.4
C1' C2' N2' H2' 125.5 122.1
C3' C2' N2' H2' 234.3 238.7
N2' C2' C3' O3' 43.8 318.3
N2' C2' C3' H3' 162.4 79.5
C6' N2' HN'2 C2' 180.0 179.9
HN'2 N2' C6' C7' 324.9 0.0
HN'2 N2' C6' O8' 143.2 180.0
HN'2 N2' C2' C1' 295.3 272.1
HN'2 N2' C2' C3' 44.1 28.7
HN'2 N2' C2' H2' 169.8 149.9
C7' C6' N2' C2' 144.9 179.9
C7' C6' N2' HN'2 324.9 0.0
N2' C6' C7' O8' 178.4 180.0
H7'1 C7' C6' H7'2 234.8 241.4
H7'1 C7' C6' H7'3 125.3 120.7
H7'2 C7' C6' H7'3 250.5 239.3
O8' C6' N2' C2' 323.2 359.9
O8' C6' N2' HN'2 143.2 180.0
N2' C6' O8' C7' 181.8 180.0
O8' C6' C7' H7'1 1.7 300.8
O8' C6' C7' H7'2 126.9 59.4
O8' C6' C7' H7'3 236.3 180.1
H7'1 C7' C6' O8' 1.7 300.8
C6' C7' H7'1 H7'2 125.2 122.7
C6' C7' H7'1 H7'3 234.7 233.7
H7'2 C7' H7'1 H7'3 109.5 110.9
H7'2 C7' C6' O8' 126.9 59.4
C6' C7' H7'2 H7'1 232.0 237.3
C6' C7' H7'2 H7'3 116.0 126.3
H7'1 C7' H7'2 H7'3 243.9 249.0
H7'3 C7' C6' O8' 236.3 180.1
C6' C7' H7'3 H7'1 128.0 124.5
C6' C7' H7'3 H7'2 244.0 235.5
H7'1 C7' H7'3 H7'2 116.0 111.0
HOP2 OP2 P O5' 53.0 175.5
HOP2 OP2 P OP3   282.5
C5' O5' P OP3   305.8
C4' C5' O5' H5' 234.8 239.7
C4' C5' O5' H5'' 125.3 120.4
O5' C5' C4' O4' 304.9 62.4
O5' C5' C4' C3' 63.5 179.5
O5' C5' C4' H4' 180.7 305.4
H5' C5' O5' H5'' 250.5 240.7
O5' C5' C4' H5' 125.2 119.5
O5' C5' C4' H5'' 234.7 240.4
H5' C5' C4' H5'' 109.5 120.9
O4' C4' C5' C3' 241.4 243.0
O4' C4' C5' H4' 124.1 117.1
C5' C4' O4' C1' 149.3 105.5
C3' C4' C5' H4' 242.8 234.1
C5' C4' C3' C2' 200.5 273.7
C5' C4' C3' O3' 83.2 156.1
C5' C4' C3' H3' 324.5 36.5
O5' C5' H5' C4' 234.8 240.6
O5' C5' H5' H5'' 117.4 119.1
C4' C5' H5' H5'' 242.6 238.5
H5' C5' C4' O4' 179.7 302.9
H5' C5' C4' C3' 298.3 60.0
H5' C5' C4' H4' 55.5 185.9
O5' C5' H5'' C4' 125.2 119.5
O5' C5' H5'' H5' 242.6 241.0
C4' C5' H5'' H5' 117.4 121.4
H5'' C5' C4' O4' 70.1 182.1
H5'' C5' C4' C3' 188.8 299.1
H5'' C5' C4' H4' 306.0 65.0
O4' C4' C5' H5' 179.7 302.9
O4' C4' C5' H5'' 70.1 182.1
C5' C4' O4' C3' 127.4 121.7
C5' C4' O4' H4' 245.4 241.9
C3' C4' O4' H4' 118.0 120.2
O4' C4' C3' C2' 322.0 32.1
O4' C4' C3' O3' 204.6 274.5
O4' C4' C3' H3' 85.9 154.9
C4' O4' C1' N1 241.7 231.4
C4' O4' C1' C2' 3.4 353.5
C4' O4' C1' H1' 122.8 115.0
N2' C2' C3' C4' 285.1 202.4
C3' C4' C5' H5' 298.3 60.0
C3' C4' C5' H5'' 188.8 299.1
C5' C4' C3' O4' 238.6 241.6
C5' C4' C3' H4' 114.2 124.3
O4' C4' C3' H4' 235.6 242.7
C3' C4' O4' C1' 21.9 343.8
C1' C2' C3' C4' 38.9 325.1
C4' C3' C2' H2' 163.4 82.5
C2' C3' C4' O3' 117.3 117.7
C2' C3' C4' H3' 236.1 237.3
O3' C3' C4' H3' 118.7 119.6
C4' C3' O3' HO3' 180.0 215.6
H4' C4' C5' H5' 55.5 185.9
H4' C4' C5' H5'' 306.0 65.0
C5' C4' H4' O4' 118.9 117.4
C5' C4' H4' C3' 234.9 233.5
O4' C4' H4' C3' 116.1 116.1
H4' C4' O4' C1' 263.9 223.6
H4' C4' C3' C2' 86.4 149.4
H4' C4' C3' O3' 329.0 31.7
H4' C4' C3' H3' 210.3 272.1
N2' C2' C1' O4' 86.5 149.6
C1' O4' C4' C3' 21.9 343.8
C1' O4' C4' H4' 263.9 223.6
N1 C1' O4' C2' 238.3 237.9
N1 C1' O4' H1' 118.9 116.4
O4' C1' N1 C6 12.3 33.3
O4' C1' N1 C2 191.8 213.3
C2' C1' O4' H1' 240.6 238.5
O4' C1' C2' C3' 333.0 26.3
O4' C1' C2' H2' 208.3 269.7
N2' C2' C1' N1 205.4 269.3
O4' C1' N1 C2' 118.3 118.6
O4' C1' N1 H1' 237.8 243.3
C2' C1' N1 H1' 119.5 124.7
N1 C1' C2' C3' 91.8 146.0
N1 C1' C2' H2' 327.2 29.4
C6 N1 C1' C2 180.5 180.0
C1' N1 C6 C5 178.4 180.0
C1' N1 C6 H6 358.4 359.9
C1' N1 C2 O2 1.9 0.0
C1' N1 C2 N3 181.8 180.0
C1' C2' N2' HN'2 295.3 272.1
N2' C2' C1' C3' 113.5 123.2
N2' C2' C1' H2' 238.2 239.9
C4' C3' C2' C1' 38.9 325.1
O4' C1' C2' N1 241.2 240.3
O4' C1' C2' H1' 122.2 118.4
N1 C1' C2' H1' 241.1 238.1
C2' C1' N1 C6 254.0 274.7
C2' C1' N1 C2 73.4 94.7
C3' C2' C1' H2' 124.7 116.6
C1' C2' C3' O3' 157.7 81.1
C1' C2' C3' H3' 276.3 202.2
O4' C1' H1' N1 119.2 117.3
O4' C1' H1' C2' 241.3 242.1
N1 C1' H1' C2' 122.0 124.8
H1' C1' N1 C6 134.5 150.0
H1' C1' N1 C2 314.0 329.9
H1' C1' C2' C3' 210.8 267.9
H1' C1' C2' H2' 86.1 151.3
C6 N1 C1' C2' 254.0 274.7
C6 N1 C1' H1' 134.5 150.0
C1' N1 C6 C2 179.4 180.0
C6 N1 C2 O2 181.3 180.0
C6 N1 C2 N3 1.2 360.0
C5 C6 N1 H6 180.0 180.1
N1 C6 C5 C4 359.9 360.0
N1 C6 C5 H5 180.0 179.9
C2 N1 C1' C2' 73.4 94.7
C2 N1 C1' H1' 314.0 329.9
C1' N1 C2 C6 180.5 180.0
C2 N1 C6 C5 359.0 0.0
C2 N1 C6 H6 179.0 180.0
O2 C2 N1 N3 180.1 180.0
N1 C2 N3 C4 359.8 360.0
C5 C6 N1 C2 359.0 0.0
N1 C6 C5 H6 180.0 179.9
N3 C4 C5 C6 1.1 360.0
N4 C4 C5 C6 181.5 180.0
C4 C5 C6 H5 180.0 180.0
H6 C6 N1 C2 179.0 180.0
N1 C6 H6 C5 180.0 180.1
H6 C6 C5 C4 179.9 180.1
H6 C6 C5 H5 359.9 0.0
N1 C2 O2 N3 179.9 180.0
O2 C2 N3 C4 179.6 180.0
N1 C2 N3 O2 180.1 180.0
C2 N3 C4 N4 178.7 180.0
C2 N3 C4 C5 359.1 0.0
C6 C5 C4 N3 1.1 360.0
N4 C4 N3 C5 179.6 180.0
N3 C4 N4 HN41 180.0 235.1
N3 C4 N4 HN42 54.7 55.0
N3 C4 C5 H5 181.0 180.0
C6 C5 C4 N4 181.5 180.0
N3 C4 N4 C5 180.4 180.0
N4 C4 C5 H5 1.4 0.0
HN41 N4 C4 HN42 125.3 180.1
C4 C5 C6 H6 179.9 180.1
C6 C5 C4 H5 180.0 180.0
N3 C4 C5 N4 179.6 180.0
C5 C4 N4 HN41 359.6 55.1
C5 C4 N4 HN42 234.3 235.0
HN41 N4 C4 C5 359.6 55.1
C4 N4 HN41 HN42 234.7 179.9
HN42 N4 C4 C5 234.3 235.0
C4 N4 HN42 HN41 130.3 180.1
H5 C5 C6 H6 359.9 0.0
C6 C5 H5 C4 180.0 180.1
C3' C2' N2' HN'2 44.1 28.7
N2' C2' C3' C1' 246.1 237.2
N2' C2' C3' H2' 121.7 119.9
C2' C3' C4' H4' 86.4 149.4
C4' C3' C2' O3' 241.2 244.0
C4' C3' C2' H3' 122.6 122.9
C3' C2' C1' H1' 210.8 267.9
C1' C2' C3' H2' 235.5 242.6
O3' C3' C2' H3' 241.4 238.8
C2' C3' O3' HO3' 67.9 103.5
H2' C2' N2' HN'2 169.8 149.9
N2' C2' H2' C1' 121.7 123.8
N2' C2' H2' C3' 238.6 236.0
H2' C2' C1' H1' 86.1 151.3
C1' C2' H2' C3' 116.8 112.2
H2' C2' C3' O3' 282.2 198.5
H2' C2' C3' H3' 40.8 319.6
O3' C3' C4' H4' 329.0 31.7
C4' C3' O3' C2' 112.2 112.0
C4' C3' O3' H3' 236.7 236.6
O3' C3' C2' H2' 282.2 198.5
C2' C3' O3' H3' 124.5 124.6
H3' C3' C4' H4' 210.3 272.1
C4' C3' H3' C2' 243.8 243.5
C4' C3' H3' O3' 122.6 120.3
H3' C3' C2' H2' 40.8 319.6
C2' C3' H3' O3' 238.8 236.8
H3' C3' O3' HO3' 303.3 338.9
HO3' O3' C3' H3' 303.3 338.9