PDB Chemical Component 5CM

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 5CM

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
N1 C2 1.405 1.345
N1 C6 1.365 1.363
N1 C1' 1.469 1.465
C2 N3 1.354 1.332
C2 O2 1.234 1.220
N3 C4 1.324 1.327
C4 C5 1.439 1.409
C4 N4 1.331 1.376
C5 C5A 1.488 1.507
C5 C6 1.339 1.353
C5A H5A1 1.115 1.090
C5A H5A2 1.115 1.090
C5A H5A3 1.114 1.090
C6 H6 1.103 1.079
N4 HN41 1.020 0.970
N4 HN42 1.021 0.970
C1' C2' 1.502 1.541
C1' O4' 1.420 1.437
C1' H1' 1.116 1.091
C2' C3' 1.513 1.547
C2' H2' 1.115 1.090
C2' H2'' 1.115 1.090
C3' C4' 1.521 1.549
C3' O3' 1.409 1.429
C3' H3' 1.114 1.090
C4' O4' 1.453 1.445
C4' C5' 1.508 1.530
C4' H4' 1.114 1.089
O3' HO3' 0.949 0.967
C5' O5' 1.440 1.428
C5' H5' 1.115 1.089
C5' H5'' 1.115 1.090
O5' P 1.584 1.610
P OP1 1.507 1.479
P OP2 1.501 1.610
P OP3 1.596 1.609
OP2 HOP2 0.949 0.966
OP3 HOP3 0.949 0.966

Bond Angles for 5CM

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C2 N1 C6 120.1 120.4
C2 N1 C1' 119.0 119.8
N1 C2 N3 119.7 121.1
N1 C2 O2 118.6 119.5
C6 N1 C1' 120.8 119.8
N1 C6 C5 120.7 119.3
N1 C6 H6 120.6 120.4
N1 C1' C2' 104.3 109.9
N1 C1' O4' 108.8 109.9
N1 C1' H1' 112.6 109.9
N3 C2 O2 121.7 119.5
C2 N3 C4 119.8 120.7
N3 C4 C5 121.8 119.6
N3 C4 N4 117.6 120.2
C5 C4 N4 120.5 120.2
C4 C5 C5A 119.3 120.5
C4 C5 C6 117.8 119.0
C4 N4 HN41 117.6 120.0
C4 N4 HN42 109.3 120.0
C5A C5 C6 122.9 120.5
C5 C5A H5A1 119.3 109.5
C5 C5A H5A2 108.6 109.5
C5 C5A H5A3 108.6 109.5
C5 C6 H6 118.7 120.4
H5A1 C5A H5A2 108.7 109.5
H5A1 C5A H5A3 108.7 109.5
H5A2 C5A H5A3 101.4 109.5
HN41 N4 HN42 109.3 120.0
C2' C1' O4' 107.5 107.4
C2' C1' H1' 113.7 109.8
C1' C2' C3' 106.3 104.2
C1' C2' H2' 113.4 110.5
C1' C2' H2'' 113.4 110.5
O4' C1' H1' 109.6 109.9
C1' O4' C4' 111.5 106.9
C3' C2' H2' 113.4 110.4
C3' C2' H2'' 113.4 110.5
C2' C3' C4' 106.7 102.1
C2' C3' O3' 109.2 110.9
C2' C3' H3' 115.7 110.9
H2' C2' H2'' 97.1 110.5
C4' C3' O3' 119.7 110.9
C4' C3' H3' 104.3 110.9
C3' C4' O4' 105.1 103.6
C3' C4' C5' 109.7 110.7
C3' C4' H4' 111.0 110.6
O3' C3' H3' 101.5 110.8
C3' O3' HO3' 109.2 106.8
O4' C4' C5' 105.6 110.8
O4' C4' H4' 114.7 110.5
C5' C4' H4' 110.4 110.5
C4' C5' O5' 109.1 109.6
C4' C5' H5' 112.3 109.5
C4' C5' H5'' 112.3 109.4
O5' C5' H5' 112.3 109.5
O5' C5' H5'' 112.4 109.4
C5' O5' P 120.9 106.8
H5' C5' H5'' 98.1 109.4
O5' P OP1 106.6 109.5
O5' P OP2 110.6 109.5
O5' P OP3 101.7 109.5
OP1 P OP2 119.4 109.5
OP1 P OP3 110.9 109.5
OP2 P OP3 106.2 109.4
P OP2 HOP2 110.6 106.8
P OP3 HOP3 101.7 106.9

Torsion Angles for 5CM

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C6 N1 C2 C1' 176.5 180.1
C2 N1 C6 C5 355.8 360.0
C2 N1 C6 H6 175.9 180.0
C2 N1 C1' C2' 116.7 300.3
C2 N1 C1' O4' 231.2 58.3
C2 N1 C1' H1' 353.0 179.4
N3 C2 N1 O2 180.1 180.0
N1 C2 N3 C4 359.1 359.7
C2 N1 C6 C1' 183.5 179.9
C6 N1 C2 N3 3.5 0.0
C6 N1 C2 O2 183.4 180.1
C6 N1 C1' C2' 300.2 120.2
C6 N1 C1' O4' 54.7 238.3
C6 N1 C1' H1' 176.4 359.3
C4 C5 C6 N1 2.2 0.2
C5A C5 C6 N1 183.0 180.0
C5 C6 N1 H6 180.0 180.0
C2 N1 C1' C6 176.5 180.1
C1' N1 C2 N3 187.0 180.0
C1' N1 C2 O2 6.8 360.0
C1' N1 C6 C5 172.3 180.0
C1' N1 C6 H6 352.3 0.1
C2' C1' N1 O4' 245.5 242.0
C2' C1' N1 H1' 123.8 120.9
N1 C1' C2' C3' 121.4 121.5
N1 C1' C2' H2' 246.7 240.1
N1 C1' C2' H2'' 356.1 2.8
O4' C1' N1 H1' 238.3 239.0
N1 C1' O4' C4' 232.6 214.2
N3 C2 N1 C6 3.5 0.0
N3 C2 N1 C1' 187.0 180.0
N1 C2 N3 O2 179.8 180.0
C2 N3 C4 C5 359.0 0.5
C2 N3 C4 N4 178.6 180.0
O2 C2 N1 C6 183.4 180.1
O2 C2 N1 C1' 6.8 360.0
N1 C2 O2 N3 180.2 180.0
O2 C2 N3 C4 179.2 179.7
C4 N3 C2 O2 179.2 179.7
C5 C4 N3 N4 180.3 180.6
N3 C4 C5 C5A 179.6 179.7
N3 C4 C5 C6 0.4 359.5
N3 C4 N4 HN41 180.0 0.1
N3 C4 N4 HN42 54.7 180.0
N1 C6 C5 C4 2.2 0.2
N3 C4 C5 N4 179.7 179.4
C5 C4 N4 HN41 359.7 179.5
C5 C4 N4 HN42 234.4 359.4
C5A C5 C4 C6 179.2 180.2
C4 C5 C5A H5A1 180.0 359.7
C4 C5 C5A H5A2 305.3 119.7
C4 C5 C5A H5A3 54.7 239.7
C4 C5 C6 H6 182.2 180.2
N3 C4 N4 C5 180.3 180.6
N4 C4 C5 C5A 360.0 0.3
N4 C4 C5 C6 180.8 180.1
HN41 N4 C4 HN42 125.3 180.1
N1 C6 C5 C5A 183.0 180.0
C5A C5 C4 N4 360.0 0.3
C4 C5 C5A C6 180.8 179.8
C5A C5 C6 H6 3.0 360.0
H5A1 C5A C5 H5A2 234.7 240.0
H5A1 C5A C5 H5A3 125.3 120.0
H5A2 C5A C5 H5A3 250.5 240.0
C5 C6 N1 C1' 172.3 180.0
N1 C6 C5 H6 180.0 180.0
C6 C5 C4 N4 180.8 180.1
C4 C5 C6 C5A 179.2 180.2
C6 C5 C5A H5A1 359.2 180.0
C6 C5 C5A H5A2 124.4 300.0
C6 C5 C5A H5A3 233.9 60.0
H5A1 C5A C5 C6 359.2 180.0
C5 C5A H5A1 H5A2 125.2 120.0
C5 C5A H5A1 H5A3 234.8 240.0
H5A2 C5A H5A1 H5A3 109.5 120.0
H5A2 C5A C5 C6 124.4 300.0
C5 C5A H5A2 H5A1 228.7 240.0
C5 C5A H5A2 H5A3 114.3 120.0
H5A1 C5A H5A2 H5A3 245.6 240.0
H5A3 C5A C5 C6 233.9 60.0
C5 C5A H5A3 H5A1 131.3 120.0
C5 C5A H5A3 H5A2 245.7 240.0
H5A1 C5A H5A3 H5A2 114.4 120.0
H6 C6 N1 C1' 352.3 0.1
N1 C6 H6 C5 180.0 180.0
C4 N4 HN41 HN42 234.7 179.9
C4 N4 HN42 HN41 130.0 180.1
N1 C1' C2' O4' 115.4 119.5
N1 C1' C2' H1' 237.0 239.1
O4' C1' C2' H1' 121.6 119.5
C2' C1' O4' C4' 345.0 333.7
C3' C2' C1' H2' 234.8 241.4
C3' C2' C1' H2'' 125.3 118.7
C1' C2' C3' C4' 4.4 20.9
C1' C2' C3' O3' 135.1 139.2
C1' C2' C3' H3' 248.9 262.7
H2' C2' C1' H2'' 250.5 237.3
N1 C1' O4' C2' 247.6 240.5
N1 C1' O4' H1' 123.5 121.0
C2' C1' O4' H1' 235.9 240.5
O4' C1' C2' C3' 6.0 2.0
O4' C1' C2' H2' 131.2 120.6
O4' C1' C2' H2'' 240.7 243.2
C3' C4' O4' C1' 17.5 39.9
C1' O4' C4' C5' 133.5 158.6
C1' O4' C4' H4' 255.4 281.3
N1 C1' H1' C2' 118.3 121.0
N1 C1' H1' O4' 238.7 239.0
C2' C1' H1' O4' 120.4 118.0
H1' C1' C2' C3' 244.4 242.4
H1' C1' C2' H2' 9.7 1.1
H1' C1' C2' H2'' 119.1 123.7
H1' C1' O4' C4' 109.1 93.2
C3' C2' C1' O4' 6.0 2.0
C3' C2' C1' H1' 244.4 242.4
C1' C2' C3' H2' 125.2 118.7
C1' C2' C3' H2'' 234.7 241.3
H2' C2' C3' H2'' 109.5 122.6
C4' C3' C2' O3' 229.3 241.7
C4' C3' C2' H3' 115.6 118.2
C2' C3' C4' O4' 347.1 323.1
C2' C3' C4' C5' 234.0 204.3
C2' C3' C4' H4' 111.6 81.5
O3' C3' C2' H3' 246.3 236.5
C2' C3' O3' HO3' 179.9 61.4
H2' C2' C1' O4' 131.2 120.6
H2' C2' C1' H1' 9.7 1.1
C1' C2' H2' C3' 238.6 245.3
C1' C2' H2' H2'' 119.3 122.7
C3' C2' H2' H2'' 240.7 237.4
H2' C2' C3' C4' 239.2 262.2
H2' C2' C3' O3' 9.9 20.5
H2' C2' C3' H3' 123.6 144.0
H2'' C2' C1' O4' 240.7 243.2
H2'' C2' C1' H1' 119.1 123.7
C1' C2' H2'' C3' 121.4 114.8
C1' C2' H2'' H2' 240.7 237.3
C3' C2' H2'' H2' 119.3 122.6
H2'' C2' C3' C4' 129.7 139.6
H2'' C2' C3' O3' 260.4 257.9
H2'' C2' C3' H3' 14.1 21.4
C1' O4' C4' C3' 17.5 39.9
C4' C3' C2' H2' 239.2 262.2
C4' C3' C2' H2'' 129.7 139.6
C2' C3' C4' O3' 124.5 118.2
C2' C3' C4' H3' 237.0 241.8
O3' C3' C4' H3' 112.5 123.6
C4' C3' O3' HO3' 303.3 174.2
O4' C4' C3' C5' 113.2 118.7
O4' C4' C3' H4' 235.5 241.6
C5' C4' C3' H4' 122.3 122.8
C3' C4' C5' O5' 33.5 180.0
C3' C4' C5' H5' 158.7 300.1
C3' C4' C5' H5'' 268.2 60.0
O3' C3' C2' H2' 9.9 20.5
O3' C3' C2' H2'' 260.4 257.9
C2' C3' O3' C4' 236.7 247.2
C2' C3' O3' H3' 122.7 123.6
C4' C3' O3' H3' 246.0 236.4
O3' C3' C4' O4' 222.6 204.8
O3' C3' C4' C5' 109.4 86.1
O3' C3' C4' H4' 347.1 323.2
H3' C3' C2' H2' 123.6 144.0
H3' C3' C2' H2'' 14.1 21.4
C2' C3' H3' C4' 116.9 112.7
C2' C3' H3' O3' 241.9 236.4
C4' C3' H3' O3' 125.0 123.7
H3' C3' C4' O4' 110.1 81.3
H3' C3' C4' C5' 357.0 322.5
H3' C3' C4' H4' 234.7 199.7
H3' C3' O3' HO3' 57.2 297.8
C4' O4' C1' H1' 109.1 93.2
O4' C4' C3' O3' 222.6 204.8
O4' C4' C3' H3' 110.1 81.3
C3' C4' O4' C5' 244.0 241.3
C3' C4' O4' H4' 122.1 118.5
C5' C4' O4' H4' 238.1 237.2
O4' C4' C5' O5' 280.6 65.7
O4' C4' C5' H5' 45.9 185.8
O4' C4' C5' H5'' 155.4 305.7
C5' C4' C3' O3' 109.4 86.1
C5' C4' C3' H3' 357.0 322.5
C3' C4' C5' O4' 112.8 114.3
C3' C4' C5' H4' 237.4 237.1
O4' C4' C5' H4' 124.6 122.8
O5' C5' C4' H5' 234.7 239.9
O5' C5' C4' H5'' 125.3 120.0
C4' C5' O5' P 184.7 180.0
H5' C5' C4' H5'' 250.5 240.1
H4' C4' C3' O3' 347.1 323.2
H4' C4' C3' H3' 234.7 199.7
C3' C4' H4' O4' 241.1 245.9
C3' C4' H4' C5' 121.9 122.9
O4' C4' H4' C5' 240.8 237.1
H4' C4' C5' O5' 156.1 302.9
H4' C4' C5' H5' 281.3 63.0
H4' C4' C5' H5'' 30.8 182.9
HO3' O3' C3' H3' 57.2 297.8
O5' C5' C4' H4' 156.1 302.9
C4' C5' O5' H5' 125.2 120.1
C4' C5' O5' H5'' 234.8 240.0
H5' C5' O5' H5'' 109.5 119.9
C5' O5' P OP1 189.1 60.0
C5' O5' P OP2 57.8 180.0
C5' O5' P OP3 305.3 300.0
H5' C5' C4' H4' 281.3 63.0
C4' C5' H5' O5' 236.5 239.9
C4' C5' H5' H5'' 118.2 119.9
O5' C5' H5' H5'' 241.7 240.1
H5' C5' O5' P 59.4 60.0
H5'' C5' C4' H4' 30.8 182.9
C4' C5' H5'' O5' 123.5 120.1
C4' C5' H5'' H5' 241.8 240.0
O5' C5' H5'' H5' 118.3 120.0
H5'' C5' O5' P 309.9 300.0
P O5' C5' H5' 59.4 60.0
P O5' C5' H5'' 309.9 300.0
OP1 P O5' OP2 131.3 240.0
OP1 P O5' OP3 243.8 120.1
OP2 P O5' OP3 112.5 240.1
O5' P OP2 HOP2 180.0 180.0
O5' P OP3 HOP3 180.0 300.1
O5' P OP1 OP2 233.8 120.0
O5' P OP1 OP3 109.9 240.0
OP2 P OP1 OP3 236.1 120.0
OP1 P OP2 HOP2 55.7 300.0
OP1 P OP3 HOP3 293.1 180.0
O5' P OP2 OP1 124.3 240.0
O5' P OP2 OP3 250.4 120.0
OP1 P OP2 OP3 126.2 240.0
OP2 P OP3 HOP3 64.3 60.0
O5' P OP3 OP1 247.0 120.0
O5' P OP3 OP2 115.8 240.0
OP1 P OP3 OP2 228.8 120.0
OP3 P OP2 HOP2 289.5 60.0
HOP2 OP2 P OP3 289.5 60.0