PDB Chemical Component OMC

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 OMC

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
N1 C2 1.379 1.344
N1 C6 1.366 1.362
N1 C1' 1.457 1.465
C2 N3 1.354 1.332
C2 O2 1.239 1.220
N3 C4 1.337 1.327
C4 C5 1.424 1.410
C4 N4 1.340 1.375
C5 C6 1.337 1.354
C5 H5 1.103 1.080
C6 H6 1.102 1.080
N4 HN41 1.020 0.971
N4 HN42 1.020 0.970
C1' C2' 1.524 1.550
C1' O4' 1.414 1.443
C1' H1' 1.115 1.090
C2' O2' 1.445 1.429
C2' C3' 1.521 1.547
C2' H2' 1.115 1.089
O2' CM2 1.449 1.428
CM2 HM21 1.114 1.090
CM2 HM22 1.116 1.090
CM2 HM23 1.115 1.090
C3' C4' 1.517 1.540
C3' O3' 1.422 1.429
C3' H3' 1.116 1.090
C4' O4' 1.450 1.437
C4' C5' 1.502 1.530
C4' H4' 1.115 1.090
O3' HO3' 0.950 0.966
C5' O5' 1.421 1.427
C5' H5' 1.116 1.090
C5' H5'' 1.115 1.090
O5' P 1.593 1.610
P OP1 1.488 1.480
P OP2 1.489 1.609
P OP3 1.611 1.609
OP2 HOP2 0.951 0.967
OP3 HOP3 0.951 0.966

Bond Angles for OMC

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C2 N1 C6 120.7 120.4
C2 N1 C1' 118.3 119.8
N1 C2 N3 119.4 121.1
N1 C2 O2 118.4 119.5
C6 N1 C1' 121.0 119.8
N1 C6 C5 121.0 119.3
N1 C6 H6 120.6 120.4
N1 C1' C2' 111.1 110.8
N1 C1' O4' 108.5 110.6
N1 C1' H1' 108.2 110.5
N3 C2 O2 122.2 119.4
C2 N3 C4 119.8 120.7
N3 C4 C5 121.8 119.6
N3 C4 N4 118.4 120.2
C5 C4 N4 119.9 120.2
C4 C5 C6 117.3 119.0
C4 C5 H5 124.3 120.5
C4 N4 HN41 118.4 120.0
C4 N4 HN42 109.0 120.1
C6 C5 H5 118.4 120.5
C5 C6 H6 118.4 120.3
HN41 N4 HN42 108.9 120.0
C2' C1' O4' 107.0 103.5
C2' C1' H1' 109.7 110.6
C1' C2' O2' 108.5 110.9
C1' C2' C3' 101.0 102.1
C1' C2' H2' 116.7 110.9
O4' C1' H1' 112.3 110.6
C1' O4' C4' 109.7 107.0
O2' C2' C3' 113.4 110.9
O2' C2' H2' 105.2 110.8
C2' O2' CM2 119.4 106.8
C3' C2' H2' 112.2 111.0
C2' C3' C4' 101.8 104.2
C2' C3' O3' 111.9 110.5
C2' C3' H3' 113.4 110.5
O2' CM2 HM21 119.4 109.5
O2' CM2 HM22 108.6 109.5
O2' CM2 HM23 108.7 109.5
HM21 CM2 HM22 108.6 109.5
HM21 CM2 HM23 108.7 109.4
HM22 CM2 HM23 101.3 109.4
C4' C3' O3' 110.9 110.7
C4' C3' H3' 114.4 110.5
C3' C4' O4' 104.1 107.3
C3' C4' C5' 114.5 109.9
C3' C4' H4' 109.6 109.8
O3' C3' H3' 104.7 110.4
C3' O3' HO3' 111.9 106.8
O4' C4' C5' 108.8 110.0
O4' C4' H4' 115.2 109.9
C5' C4' H4' 105.0 109.9
C4' C5' O5' 110.0 109.5
C4' C5' H5' 112.0 109.4
C4' C5' H5'' 112.0 109.4
O5' C5' H5' 112.0 109.5
O5' C5' H5'' 112.0 109.5
C5' O5' P 120.3 106.9
H5' C5' H5'' 98.4 109.4
O5' P OP1 109.0 109.4
O5' P OP2 108.1 109.5
O5' P OP3 104.1 109.5
OP1 P OP2 120.0 109.4
OP1 P OP3 107.7 109.5
OP2 P OP3 106.7 109.5
P OP2 HOP2 108.1 106.8
P OP3 HOP3 104.2 106.8

Torsion Angles for OMC

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C6 N1 C2 C1' 179.0 179.7
C2 N1 C6 C5 358.7 0.3
C2 N1 C6 H6 178.7 180.3
C2 N1 C1' C2' 97.8 304.1
C2 N1 C1' O4' 215.2 58.2
C2 N1 C1' H1' 337.3 181.1
N3 C2 N1 O2 180.0 179.4
N1 C2 N3 C4 359.4 0.6
C2 N1 C6 C1' 181.1 180.3
C6 N1 C2 N3 1.5 359.4
C6 N1 C2 O2 181.5 180.0
C6 N1 C1' C2' 278.8 124.4
C6 N1 C1' O4' 36.2 238.6
C6 N1 C1' H1' 158.3 1.5
C4 C5 C6 N1 0.2 359.9
N1 C6 C5 H5 180.1 180.0
C5 C6 N1 H6 180.0 180.0
C2 N1 C1' C6 179.0 179.7
C1' N1 C2 N3 182.6 179.7
C1' N1 C2 O2 2.5 0.3
C1' N1 C6 C5 177.6 180.0
C1' N1 C6 H6 357.6 360.0
C2' C1' N1 O4' 242.6 245.8
C2' C1' N1 H1' 120.5 122.9
N1 C1' C2' O2' 209.1 273.8
N1 C1' C2' C3' 89.6 155.6
N1 C1' C2' H2' 327.7 37.3
O4' C1' N1 H1' 237.9 237.1
N1 C1' O4' C4' 246.1 201.3
N3 C2 N1 C6 1.5 359.4
N3 C2 N1 C1' 182.6 179.7
N1 C2 N3 O2 180.0 180.6
C2 N3 C4 C5 359.5 359.6
C2 N3 C4 N4 179.3 179.7
O2 C2 N1 C6 181.5 180.0
O2 C2 N1 C1' 2.5 0.3
N1 C2 O2 N3 180.0 179.4
O2 C2 N3 C4 179.5 180.0
C4 N3 C2 O2 179.5 180.0
C5 C4 N3 N4 180.2 179.9
N3 C4 C5 C6 0.8 0.1
N3 C4 C5 H5 180.8 180.0
N3 C4 N4 HN41 180.0 360.0
N3 C4 N4 HN42 54.8 179.9
N1 C6 C5 C4 0.2 359.9
N3 C4 C5 N4 179.8 180.1
C5 C4 N4 HN41 359.8 180.1
C5 C4 N4 HN42 234.6 359.9
C6 C5 C4 H5 180.0 180.0
C4 C5 C6 H6 180.2 180.0
N3 C4 N4 C5 180.2 179.9
N4 C4 C5 C6 180.9 180.0
N4 C4 C5 H5 1.0 360.0
HN41 N4 C4 HN42 125.2 180.1
C5 C6 N1 C1' 177.6 180.0
N1 C6 C5 H6 180.0 180.0
C6 C5 C4 N4 180.9 180.0
C4 C5 C6 H5 180.0 180.0
H5 C5 C4 N4 1.0 360.0
C4 C5 H5 C6 180.0 180.0
H5 C5 C6 H6 0.1 0.0
H6 C6 N1 C1' 357.6 360.0
N1 C6 H6 C5 180.0 180.0
H6 C6 C5 H5 0.1 0.0
C4 N4 HN41 HN42 234.8 179.9
C4 N4 HN42 HN41 130.5 180.1
N1 C1' C2' O4' 118.2 118.6
N1 C1' C2' H1' 240.3 237.1
O4' C1' C2' H1' 122.1 118.5
C2' C1' O4' C4' 6.1 320.0
O2' C2' C1' C3' 119.4 118.2
O2' C2' C1' H2' 241.4 236.4
C1' C2' O2' CM2 78.1 152.9
C3' C2' C1' H2' 122.0 118.2
C1' C2' C3' C4' 39.0 339.1
C1' C2' C3' O3' 157.4 98.0
C1' C2' C3' H3' 275.6 220.4
N1 C1' O4' C2' 240.0 241.3
N1 C1' O4' H1' 119.6 122.8
C2' C1' O4' H1' 239.5 241.5
O4' C1' C2' O2' 90.8 155.2
O4' C1' C2' C3' 331.4 37.0
O4' C1' C2' H2' 209.4 278.8
C3' C4' O4' C1' 19.3 26.5
C1' O4' C4' C5' 141.8 146.0
C1' O4' C4' H4' 259.3 267.1
N1 C1' H1' C2' 121.4 123.1
N1 C1' H1' O4' 240.3 237.1
C2' C1' H1' O4' 118.9 114.0
H1' C1' C2' O2' 328.7 36.7
H1' C1' C2' C3' 209.3 278.5
H1' C1' C2' H2' 87.3 160.3
H1' C1' O4' C4' 126.5 78.5
O2' C2' C1' O4' 90.8 155.2
O2' C2' C1' H1' 328.7 36.7
C1' C2' O2' C3' 248.6 247.3
C1' C2' O2' H2' 125.6 123.6
C3' C2' O2' H2' 237.0 236.3
O2' C2' C3' C4' 283.1 220.9
O2' C2' C3' O3' 41.6 339.8
O2' C2' C3' H3' 159.8 102.2
C2' O2' CM2 HM21 180.0 180.0
C2' O2' CM2 HM22 305.3 300.0
C2' O2' CM2 HM23 54.7 60.1
C3' C2' C1' O4' 331.4 37.0
C3' C2' C1' H1' 209.3 278.5
C1' C2' C3' O2' 115.9 118.2
C1' C2' C3' H2' 234.9 241.8
O2' C2' C3' H2' 119.0 123.6
C3' C2' O2' CM2 189.4 265.6
C4' C3' C2' O3' 241.6 241.1
C4' C3' C2' H3' 123.4 118.7
C2' C3' C4' O4' 323.5 358.0
C2' C3' C4' C5' 204.9 238.4
C2' C3' C4' H4' 87.3 117.4
O3' C3' C2' H3' 241.8 237.6
C2' C3' O3' HO3' 180.0 180.0
H2' C2' C1' O4' 209.4 278.8
H2' C2' C1' H1' 87.3 160.3
C1' C2' H2' O2' 239.7 236.4
C1' C2' H2' C3' 115.9 112.7
O2' C2' H2' C3' 236.3 236.3
H2' C2' O2' CM2 312.4 29.3
H2' C2' C3' C4' 164.1 97.3
H2' C2' C3' O3' 282.5 216.2
H2' C2' C3' H3' 40.7 338.6
CM2 O2' C2' C3' 189.4 265.6
CM2 O2' C2' H2' 312.4 29.3
HM21 CM2 O2' HM22 234.8 239.9
HM21 CM2 O2' HM23 125.3 119.9
HM22 CM2 O2' HM23 250.6 240.0
O2' CM2 HM21 HM22 125.2 120.1
O2' CM2 HM21 HM23 234.7 240.0
HM22 CM2 HM21 HM23 109.4 119.9
O2' CM2 HM22 HM21 228.7 239.9
O2' CM2 HM22 HM23 114.3 120.0
HM21 CM2 HM22 HM23 245.7 240.1
O2' CM2 HM23 HM21 131.4 120.0
O2' CM2 HM23 HM22 245.7 239.9
HM21 CM2 HM23 HM22 114.3 120.0
C1' O4' C4' C3' 19.3 26.5
C4' C3' C2' H2' 164.1 97.3
C2' C3' C4' O3' 119.2 118.8
C2' C3' C4' H3' 237.4 241.3
O3' C3' C4' H3' 118.2 122.6
C4' C3' O3' HO3' 292.9 294.8
O4' C4' C3' C5' 118.6 119.6
O4' C4' C3' H4' 236.3 240.6
C5' C4' C3' H4' 117.6 121.0
C3' C4' C5' O5' 48.3 180.0
C3' C4' C5' H5' 173.5 300.0
C3' C4' C5' H5'' 283.0 60.0
O3' C3' C2' H2' 282.5 216.2
C2' C3' O3' C4' 247.1 245.1
C2' C3' O3' H3' 123.2 122.5
C4' C3' O3' H3' 236.1 237.4
O3' C3' C4' O4' 204.3 239.2
O3' C3' C4' C5' 85.7 119.6
O3' C3' C4' H4' 328.1 358.6
H3' C3' C2' H2' 40.7 338.6
C2' C3' H3' C4' 116.1 114.8
C2' C3' H3' O3' 237.7 237.5
C4' C3' H3' O3' 121.6 122.7
H3' C3' C4' O4' 86.1 116.7
H3' C3' C4' C5' 327.5 357.1
H3' C3' C4' H4' 209.9 236.1
H3' C3' O3' HO3' 56.8 57.5
C4' O4' C1' H1' 126.5 78.5
O4' C4' C3' O3' 204.3 239.2
O4' C4' C3' H3' 86.1 116.7
C3' C4' O4' C5' 237.5 240.4
C3' C4' O4' H4' 120.0 119.4
C5' C4' O4' H4' 242.5 239.0
O4' C4' C5' O5' 292.3 62.1
O4' C4' C5' H5' 57.6 182.1
O4' C4' C5' H5'' 167.1 302.0
C5' C4' C3' O3' 85.7 119.6
C5' C4' C3' H3' 327.5 357.1
C3' C4' C5' O4' 116.0 118.0
C3' C4' C5' H4' 239.8 239.0
O4' C4' C5' H4' 123.8 121.1
O5' C5' C4' H5' 234.8 240.0
O5' C5' C4' H5'' 125.3 120.1
C4' C5' O5' P 180.5 180.0
H5' C5' C4' H5'' 250.5 240.1
H4' C4' C3' O3' 328.1 358.6
H4' C4' C3' H3' 209.9 236.1
C3' C4' H4' O4' 243.0 242.2
C3' C4' H4' C5' 123.4 121.0
O4' C4' H4' C5' 240.4 238.9
H4' C4' C5' O5' 168.5 301.0
H4' C4' C5' H5' 293.7 61.0
H4' C4' C5' H5'' 43.2 180.9
HO3' O3' C3' H3' 56.8 57.5
O5' C5' C4' H4' 168.5 301.0
C4' C5' O5' H5' 125.3 120.0
C4' C5' O5' H5'' 234.7 240.0
H5' C5' O5' H5'' 109.5 120.0
C5' O5' P OP1 174.0 60.0
C5' O5' P OP2 41.9 180.0
C5' O5' P OP3 288.7 300.0
H5' C5' C4' H4' 293.7 61.0
C4' C5' H5' O5' 235.9 240.0
C4' C5' H5' H5'' 118.0 119.9
O5' C5' H5' H5'' 242.1 240.0
H5' C5' O5' P 55.3 60.0
H5'' C5' C4' H4' 43.2 180.9
C4' C5' H5'' O5' 124.1 120.1
C4' C5' H5'' H5' 242.0 240.1
O5' C5' H5'' H5' 117.9 120.0
H5'' C5' O5' P 305.8 300.0
P O5' C5' H5' 55.3 60.0
P O5' C5' H5'' 305.8 300.0
OP1 P O5' OP2 132.1 240.0
OP1 P O5' OP3 245.3 120.0
OP2 P O5' OP3 113.2 239.9
O5' P OP2 HOP2 180.0 180.1
O5' P OP3 HOP3 180.0 299.9
O5' P OP1 OP2 234.6 120.0
O5' P OP1 OP3 112.4 240.0
OP2 P OP1 OP3 237.8 120.0
OP1 P OP2 HOP2 54.2 300.0
OP1 P OP3 HOP3 295.7 180.0
O5' P OP2 OP1 125.9 240.1
O5' P OP2 OP3 248.5 120.1
OP1 P OP2 OP3 122.7 240.0
OP2 P OP3 HOP3 65.8 60.0
O5' P OP3 OP1 244.3 119.9
O5' P OP3 OP2 114.2 239.9
OP1 P OP3 OP2 229.9 120.0
OP3 P OP2 HOP2 291.5 60.0
HOP2 OP2 P OP3 291.5 60.0