PDB Chemical Component 5MC

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 5MC

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.494 1.479
P OP2 1.486 1.609
P OP3 1.608 1.610
P O5' 1.595 1.609
OP2 HOP2 0.950 0.967
OP3 HOP3 0.950 0.966
O5' C5' 1.420 1.428
C5' C4' 1.507 1.529
C5' H5' 1.114 1.090
C5' H5'' 1.115 1.090
C4' O4' 1.454 1.445
C4' C3' 1.512 1.545
C4' H4' 1.115 1.090
O4' C1' 1.420 1.444
C3' O3' 1.414 1.429
C3' C2' 1.519 1.546
C3' H3' 1.116 1.090
O3' HO3' 0.950 0.967
C2' O2' 1.413 1.429
C2' C1' 1.525 1.544
C2' H2' 1.115 1.090
O2' HO2' 0.951 0.967
C1' N1 1.469 1.465
C1' H1' 1.116 1.090
N1 C2 1.394 1.344
N1 C6 1.363 1.363
C2 O2 1.238 1.220
C2 N3 1.347 1.332
N3 C4 1.326 1.327
C4 N4 1.336 1.375
C4 C5 1.418 1.410
N4 HN41 1.020 0.971
N4 HN42 1.020 0.970
C5 C6 1.338 1.354
C5 CM5 1.493 1.507
C6 H6 1.102 1.079
CM5 HM51 1.114 1.090
CM5 HM52 1.116 1.089
CM5 HM53 1.116 1.090

Bond Angles for 5MC

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 119.9 109.5
OP1 P OP3 107.4 109.5
OP1 P O5' 108.2 109.5
OP2 P OP3 108.4 109.4
OP2 P O5' 107.3 109.5
P OP2 HOP2 119.8 106.8
OP3 P O5' 104.8 109.5
P OP3 HOP3 107.3 106.8
P O5' C5' 120.9 106.8
O5' C5' C4' 110.0 109.5
O5' C5' H5' 112.0 109.4
O5' C5' H5'' 112.0 109.4
C4' C5' H5' 112.0 109.5
C4' C5' H5'' 112.0 109.5
C5' C4' O4' 110.0 110.4
C5' C4' C3' 114.2 110.5
C5' C4' H4' 104.0 110.4
H5' C5' H5'' 98.4 109.5
O4' C4' C3' 102.6 104.8
O4' C4' H4' 115.3 110.4
C4' O4' C1' 109.3 105.2
C3' C4' H4' 111.1 110.3
C4' C3' O3' 111.0 110.5
C4' C3' C2' 101.4 104.1
C4' C3' H3' 114.3 110.4
O4' C1' C2' 106.9 104.9
O4' C1' N1 109.1 110.3
O4' C1' H1' 111.7 110.3
O3' C3' C2' 111.2 110.6
O3' C3' H3' 105.0 110.5
C3' O3' HO3' 111.0 106.8
C2' C3' H3' 114.1 110.6
C3' C2' O2' 114.3 110.5
C3' C2' C1' 100.9 104.0
C3' C2' H2' 112.7 110.5
O2' C2' C1' 111.3 110.8
O2' C2' H2' 102.5 110.4
C2' O2' HO2' 114.3 106.8
C1' C2' H2' 115.5 110.4
C2' C1' N1 110.2 110.4
C2' C1' H1' 110.6 110.4
N1 C1' H1' 108.5 110.4
C1' N1 C2 118.3 119.9
C1' N1 C6 121.5 119.8
C2 N1 C6 120.2 120.4
N1 C2 O2 118.9 119.4
N1 C2 N3 119.5 121.1
N1 C6 C5 120.7 119.3
N1 C6 H6 120.6 120.4
O2 C2 N3 121.6 119.5
C2 N3 C4 119.9 120.7
N3 C4 N4 117.7 120.2
N3 C4 C5 121.9 119.6
N4 C4 C5 120.3 120.2
C4 N4 HN41 117.8 120.0
C4 N4 HN42 109.2 120.1
C4 C5 C6 117.7 119.0
C4 C5 CM5 118.9 120.5
HN41 N4 HN42 109.2 119.9
C6 C5 CM5 123.1 120.5
C5 C6 H6 118.7 120.3
C5 CM5 HM51 118.9 109.5
C5 CM5 HM52 108.8 109.5
C5 CM5 HM53 108.8 109.5
HM51 CM5 HM52 108.8 109.4
HM51 CM5 HM53 108.9 109.5
HM52 CM5 HM53 101.2 109.5

Torsion Angles for 5MC

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 OP3 235.9 120.0
OP2 P OP1 O5' 123.4 240.0
OP1 P OP2 HOP2 180.1 300.0
OP3 P OP1 O5' 247.4 120.0
OP1 P OP3 HOP3 179.9 180.0
OP1 P O5' C5' 154.9 60.0
OP1 P OP2 OP3 123.6 240.0
OP1 P OP2 O5' 236.2 120.0
OP3 P OP2 O5' 112.6 240.0
OP2 P OP3 HOP3 310.7 60.0
OP2 P O5' C5' 24.2 180.0
OP1 P OP3 OP2 229.2 120.0
OP1 P OP3 O5' 114.9 240.0
OP2 P OP3 O5' 245.7 120.0
OP3 P OP2 HOP2 56.5 60.0
OP3 P O5' C5' 269.2 300.0
OP1 P O5' OP2 130.6 240.0
OP1 P O5' OP3 245.7 120.1
OP2 P O5' OP3 115.0 240.1
O5' P OP2 HOP2 303.9 180.0
O5' P OP3 HOP3 65.0 300.0
P O5' C5' C4' 168.7 180.0
P O5' C5' H5' 294.0 60.0
P O5' C5' H5'' 43.4 300.0
HOP2 OP2 P OP3 56.5 60.0
HOP2 OP2 P O5' 303.9 180.0
HOP3 OP3 P O5' 65.0 300.0
C4' C5' O5' H5' 234.8 120.1
C4' C5' O5' H5'' 125.3 240.0
O5' C5' C4' O4' 319.6 61.4
O5' C5' C4' C3' 74.2 176.9
O5' C5' C4' H4' 195.5 299.1
H5' C5' O5' H5'' 250.5 120.0
O5' C5' C4' H5' 125.2 240.0
O5' C5' C4' H5'' 234.7 120.0
H5' C5' C4' H5'' 109.5 240.0
O4' C4' C5' C3' 245.3 244.5
O4' C4' C5' H4' 124.0 122.3
C5' C4' O4' C1' 148.4 159.4
C3' C4' C5' H4' 238.7 237.8
C5' C4' C3' O3' 81.3 98.3
C5' C4' C3' C2' 199.6 217.0
C5' C4' C3' H3' 322.8 335.8
O5' C5' H5' C4' 235.9 120.0
O5' C5' H5' H5'' 117.9 240.1
C4' C5' H5' H5'' 242.0 120.0
H5' C5' C4' O4' 194.3 181.4
H5' C5' C4' C3' 309.0 296.9
H5' C5' C4' H4' 70.3 59.1
O5' C5' H5'' C4' 124.1 240.0
O5' C5' H5'' H5' 242.1 119.9
C4' C5' H5'' H5' 117.9 240.0
H5'' C5' C4' O4' 84.8 301.5
H5'' C5' C4' C3' 199.5 56.9
H5'' C5' C4' H4' 320.8 179.2
O4' C4' C5' H5' 194.3 181.4
O4' C4' C5' H5'' 84.8 301.5
C5' C4' O4' C3' 121.9 119.0
C5' C4' O4' H4' 242.8 237.7
C3' C4' O4' H4' 121.0 118.7
O4' C4' C3' O3' 200.3 217.2
O4' C4' C3' C2' 318.5 336.0
O4' C4' C3' H3' 81.7 94.7
C4' O4' C1' C2' 359.3 319.6
C4' O4' C1' N1 240.2 200.7
C4' O4' C1' H1' 120.4 78.5
C3' C4' C5' H5' 309.0 296.9
C3' C4' C5' H5'' 199.5 56.9
C5' C4' C3' O4' 241.0 241.1
C5' C4' C3' H4' 117.3 122.3
O4' C4' C3' H4' 236.2 241.2
C3' C4' O4' C1' 26.5 40.4
O3' C3' C4' C2' 241.8 241.3
O3' C3' C4' H3' 118.6 122.5
C4' C3' O3' HO3' 180.0 180.1
C2' C3' C4' H3' 236.8 241.2
C4' C3' C2' O2' 280.7 241.1
C4' C3' C2' C1' 40.3 0.1
C4' C3' C2' H2' 164.1 118.6
H4' C4' C5' H5' 70.3 59.1
H4' C4' C5' H5'' 320.8 179.2
C5' C4' H4' O4' 120.5 122.3
C5' C4' H4' C3' 236.7 237.6
O4' C4' H4' C3' 116.2 115.3
H4' C4' O4' C1' 265.6 281.7
H4' C4' C3' O3' 324.1 336.0
H4' C4' C3' C2' 82.3 94.7
H4' C4' C3' H3' 205.5 213.5
C1' O4' C4' C3' 26.5 40.4
C1' O4' C4' H4' 265.6 281.7
C3' C2' C1' O4' 334.8 23.9
O2' C2' C1' O4' 96.5 142.6
O4' C1' C2' H2' 213.0 265.3
C2' C1' O4' N1 119.1 118.9
C2' C1' O4' H1' 238.9 241.1
N1 C1' O4' H1' 119.8 122.2
O4' C1' N1 C2 183.7 57.2
O4' C1' N1 C6 3.7 237.0
O3' C3' C4' H4' 324.1 336.0
C4' C3' O3' C2' 112.1 114.7
C4' C3' O3' H3' 236.0 237.5
C2' C3' O3' H3' 123.9 122.8
O3' C3' C2' O2' 38.8 359.8
O3' C3' C2' C1' 158.4 118.8
O3' C3' C2' H2' 282.2 237.3
C2' C3' C4' H4' 82.3 94.7
C4' C3' C2' O3' 241.9 241.3
C4' C3' C2' H3' 123.4 118.6
O4' C1' C2' C3' 334.8 23.9
O3' C3' C2' H3' 241.5 237.3
C2' C3' O3' HO3' 67.9 65.3
O2' C2' C3' C1' 240.4 241.0
O2' C2' C3' H2' 116.6 122.5
C3' C2' O2' HO2' 180.0 298.6
C1' C2' C3' H2' 236.2 241.5
C3' C2' C1' N1 93.2 142.7
C3' C2' C1' H1' 213.1 265.0
H3' C3' C4' H4' 205.5 213.5
C4' C3' H3' O3' 121.9 122.6
C4' C3' H3' C2' 243.9 245.3
O3' C3' H3' C2' 122.0 122.7
H3' C3' O3' HO3' 304.0 302.6
H3' C3' C2' O2' 157.3 122.5
H3' C3' C2' C1' 276.9 241.5
H3' C3' C2' H2' 40.7 0.0
HO3' O3' C3' C2' 67.9 65.3
HO3' O3' C3' H3' 304.0 302.6
O4' C1' C2' O2' 96.5 142.6
O2' C2' C3' H3' 157.3 122.5
C3' C2' O2' C1' 113.6 114.8
C3' C2' O2' H2' 237.7 237.4
C1' C2' O2' H2' 124.1 122.7
O2' C2' C1' N1 214.9 261.5
O2' C2' C1' H1' 334.8 23.8
O4' C1' C2' N1 241.6 241.2
O4' C1' C2' H1' 121.7 118.8
C1' C2' C3' H3' 276.9 241.5
C3' C2' C1' O2' 238.3 241.2
C3' C2' C1' H2' 121.9 118.6
O2' C2' C1' H2' 243.6 237.3
C1' C2' O2' HO2' 66.4 183.8
N1 C1' C2' H1' 240.1 237.7
C2' C1' N1 C2 66.6 301.7
C2' C1' N1 C6 246.7 121.5
H2' C2' C3' H3' 40.7 0.0
C3' C2' H2' O2' 123.4 122.6
C3' C2' H2' C1' 244.7 245.5
O2' C2' H2' C1' 121.3 122.9
H2' C2' O2' HO2' 302.3 61.2
H2' C2' C1' N1 331.3 24.1
H2' C2' C1' H1' 91.2 146.4
HO2' O2' C2' C1' 66.4 183.8
HO2' O2' C2' H2' 302.3 61.2
O4' C1' N1 C2' 117.0 115.5
O4' C1' N1 H1' 238.2 237.8
N1 C1' C2' H2' 331.3 24.1
C2' C1' N1 H1' 121.2 122.3
C2 N1 C1' C6 180.0 180.2
C1' N1 C2 O2 357.8 359.9
C1' N1 C2 N3 178.3 180.0
C1' N1 C6 C5 180.4 180.1
C1' N1 C6 H6 0.3 0.2
O4' C1' H1' C2' 241.1 244.5
O4' C1' H1' N1 120.2 122.1
H1' C1' C2' H2' 91.2 146.4
C2' C1' H1' N1 239.1 237.7
H1' C1' N1 C2 305.5 179.3
H1' C1' N1 C6 125.5 359.2
C2 N1 C1' H1' 305.5 179.3
C1' N1 C2 C6 180.0 179.8
C2 N1 C6 C5 0.4 359.9
C2 N1 C6 H6 180.4 180.0
O2 C2 N1 N3 179.5 179.9
N1 C2 N3 C4 1.1 359.6
C6 N1 C1' H1' 125.5 359.2
C1' N1 C6 C2 180.0 180.2
C6 N1 C2 O2 177.7 180.0
C6 N1 C2 N3 358.3 0.1
C4 C5 C6 N1 1.4 0.3
N1 C6 C5 CM5 187.0 180.0
C5 C6 N1 H6 180.0 179.9
O2 C2 N1 C6 177.7 180.0
N1 C2 O2 N3 180.6 180.1
O2 C2 N3 C4 181.7 179.7
N3 C2 N1 C6 358.3 0.1
N1 C2 N3 O2 179.4 179.9
C2 N3 C4 N4 181.1 180.0
C2 N3 C4 C5 0.7 0.5
N4 C4 N3 C5 180.4 179.5
N3 C4 N4 HN41 180.0 0.1
N3 C4 N4 HN42 54.7 180.0
N3 C4 C5 C6 358.0 359.5
N3 C4 C5 CM5 172.6 179.7
N3 C4 N4 C5 179.6 180.5
N4 C4 C5 C6 177.6 180.0
N4 C4 C5 CM5 352.2 0.3
HN41 N4 C4 HN42 125.3 180.1
N1 C6 C5 C4 1.4 0.3
N3 C4 C5 N4 180.4 179.5
C5 C4 N4 HN41 0.4 179.5
C5 C4 N4 HN42 235.1 359.4
C6 C5 C4 CM5 185.4 179.7
C4 C5 C6 H6 181.4 180.2
C4 C5 CM5 HM51 180.0 359.8
C4 C5 CM5 HM52 305.3 119.7
C4 C5 CM5 HM53 54.7 239.7
HN41 N4 C4 C5 0.4 179.5
C4 N4 HN41 HN42 234.7 179.9
HN42 N4 C4 C5 235.1 359.4
C4 N4 HN42 HN41 130.1 180.1
N1 C6 C5 H6 180.0 180.1
C4 C5 C6 CM5 174.4 180.3
C6 C5 CM5 HM51 354.3 180.0
C6 C5 CM5 HM52 119.6 300.0
C6 C5 CM5 HM53 229.0 60.0
C4 C5 CM5 C6 185.7 179.7
CM5 C5 C6 H6 7.0 359.9
HM51 CM5 C5 HM52 234.7 240.0
HM51 CM5 C5 HM53 125.3 120.0
HM52 CM5 C5 HM53 250.6 240.0
N1 C6 H6 C5 180.0 179.9
H6 C6 C5 CM5 7.0 359.9
C5 CM5 HM51 HM52 125.3 120.0
C5 CM5 HM51 HM53 234.7 240.0
HM52 CM5 HM51 HM53 109.5 120.0
C5 CM5 HM52 HM51 229.0 240.0
C5 CM5 HM52 HM53 114.5 120.0
HM51 CM5 HM52 HM53 245.4 240.0
C5 CM5 HM53 HM51 131.0 120.0
C5 CM5 HM53 HM52 245.5 240.0
HM51 CM5 HM53 HM52 114.5 120.0