PDB Chemical Component SMT

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 SMT

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.509 1.480
P OP2 1.488 1.610
P OP3   1.609
P O5' 1.588 1.610
OP2 H2P 0.950 0.966
OP3 H3P   0.967
O5' C5' 1.411 1.429
C5' C4' 1.497 1.530
C5' H5' 1.100 1.091
C5' H5'2 1.100 1.089
C4' O4' 1.464 1.437
C4' C3' 1.491 1.542
C4' H4' 1.100 1.090
O4' C1' 1.467 1.445
C3' O3' 1.442 1.429
C3' C2' 1.508 1.548
C3' H3' 1.100 1.089
O3' HO3 0.950 0.967
C2' O2' 1.381 1.430
C2' C1' 1.487 1.549
C2' H2' 1.100 1.090
O2' CA' 1.557 1.429
C1' N1 1.467 1.465
C1' H1' 1.100 1.090
N1 C2 1.394 1.345
N1 C6 1.328 1.368
C2 O2 1.235 1.216
C2 N3 1.330 1.346
N3 C4 1.412 1.349
N3 H3 1.000 0.971
C4 O4 1.265 1.218
C4 C5 1.462 1.416
C5 C5A 1.462 1.507
C5 C6 1.357 1.350
C5A H5A 1.100 1.090
C5A H5A1 1.100 1.090
C5A H5A2 1.100 1.090
C6 H6 1.080 1.080
CA' CB   1.530
CA' HA1 1.100 1.090
CA' HA2 1.100 1.090
CB SC   1.814
CB HB1   1.090
CB HB2   1.090
SC CD   1.814
CD HD1   1.091
CD HD2   1.090
CD HD3   1.090

Bond Angles for SMT

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 119.6 109.5
OP1 P OP3   109.5
OP1 P O5' 110.6 109.5
OP2 P OP3   109.5
OP2 P O5' 106.8 109.4
P OP2 H2P 109.5 114.0
OP3 P O5'   109.5
P OP3 H3P   114.0
P O5' C5' 119.4 123.0
O5' C5' C4' 108.9 109.5
O5' C5' H5' 109.6 109.5
O5' C5' H5'2 109.6 109.5
C4' C5' H5' 109.6 109.4
C4' C5' H5'2 109.6 109.5
C5' C4' O4' 108.5 109.9
C5' C4' C3' 117.8 109.9
C5' C4' H4' 109.3 109.9
H5' C5' H5'2 109.4 109.5
O4' C4' C3' 101.8 107.3
O4' C4' H4' 109.7 109.9
C4' O4' C1' 107.4 107.0
C3' C4' H4' 109.4 110.0
C4' C3' O3' 111.0 110.5
C4' C3' C2' 101.2 104.2
C4' C3' H3' 110.0 110.5
O4' C1' C2' 106.0 103.5
O4' C1' N1 106.0 110.6
O4' C1' H1' 109.4 110.5
O3' C3' C2' 113.9 110.5
O3' C3' H3' 110.7 110.5
C3' O3' HO3 109.5 114.0
C2' C3' H3' 109.7 110.6
C3' C2' O2' 107.5 110.9
C3' C2' C1' 99.8 102.1
C3' C2' H2' 109.7 110.9
O2' C2' C1' 117.3 110.9
O2' C2' H2' 111.6 110.8
C2' O2' CA' 112.2 114.0
C1' C2' H2' 110.0 110.9
C2' C1' N1 116.6 110.7
C2' C1' H1' 109.1 110.6
O2' CA' CB   109.4
O2' CA' HA1 113.9 109.5
O2' CA' HA2 113.9 109.5
N1 C1' H1' 109.4 110.7
C1' N1 C2 115.9 119.7
C1' N1 C6 124.9 119.7
C2 N1 C6 119.2 120.7
N1 C2 O2 120.2 119.6
N1 C2 N3 115.6 120.9
N1 C6 C5 128.6 119.7
N1 C6 H6 115.7 120.2
O2 C2 N3 124.3 119.5
C2 N3 C4 127.2 120.3
C2 N3 H3 116.4 119.8
C4 N3 H3 116.4 119.9
N3 C4 O4 118.1 120.3
N3 C4 C5 115.5 119.4
O4 C4 C5 126.2 120.3
C4 C5 C5A 121.7 120.4
C4 C5 C6 113.7 119.1
C5A C5 C6 124.4 120.5
C5 C5A H5A 109.5 109.5
C5 C5A H5A1 109.4 109.5
C5 C5A H5A2 109.5 109.4
C5 C6 H6 115.7 120.1
H5A C5A H5A1 109.5 109.5
H5A C5A H5A2 109.5 109.4
H5A1 C5A H5A2 109.5 109.4
CB CA' HA1   109.5
CB CA' HA2   109.5
CA' CB SC   109.5
CA' CB HB1   109.5
CA' CB HB2   109.5
HA1 CA' HA2 109.5 109.5
SC CB HB1   109.5
SC CB HB2   109.5
CB SC CD   103.0
HB1 CB HB2   109.4
SC CD HD1   109.5
SC CD HD2   109.5
SC CD HD3   109.5
HD1 CD HD2   109.4
HD1 CD HD3   109.5
HD2 CD HD3   109.5

Torsion Angles for SMT

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 OP3   240.0
OP2 P OP1 O5' 235.3 120.0
OP1 P OP2 H2P 360.0 180.0
OP3 P OP1 O5'   240.0
OP1 P OP3 H3P   300.0
OP1 P O5' C5' 45.7 55.0
OP1 P OP2 OP3   120.0
OP1 P OP2 O5' 126.5 240.0
OP3 P OP2 O5'   120.0
OP2 P OP3 H3P   60.0
OP2 P O5' C5' 177.4 295.0
OP1 P OP3 OP2   240.0
OP1 P OP3 O5'   120.0
OP2 P OP3 O5'   240.0
OP3 P OP2 H2P   60.0
OP3 P O5' C5'   175.0
OP1 P O5' OP2 228.3 120.0
OP1 P O5' OP3   240.0
OP2 P O5' OP3   120.0
O5' P OP2 H2P 233.5 300.0
O5' P OP3 H3P   180.0
P O5' C5' C4' 172.6 180.0
P O5' C5' H5' 292.6 300.0
P O5' C5' H5'2 52.7 60.0
H2P OP2 P OP3   60.0
H2P OP2 P O5' 233.5 300.0
H3P OP3 P O5'   180.0
C4' C5' O5' H5' 240.1 240.0
C4' C5' O5' H5'2 119.9 120.0
O5' C5' C4' O4' 295.3 66.4
O5' C5' C4' C3' 50.1 184.2
O5' C5' C4' H4' 175.7 305.4
H5' C5' O5' H5'2 239.9 240.0
O5' C5' C4' H5' 119.9 120.0
O5' C5' C4' H5'2 240.0 240.0
H5' C5' C4' H5'2 120.1 120.0
O4' C4' C5' C3' 245.2 242.2
O4' C4' C5' H4' 119.6 121.0
C5' C4' O4' C1' 149.7 145.9
C3' C4' C5' H4' 234.4 238.8
C5' C4' C3' O3' 75.7 119.9
C5' C4' C3' C2' 196.9 238.5
C5' C4' C3' H3' 312.9 357.3
O5' C5' H5' C4' 240.5 240.0
O5' C5' H5' H5'2 120.2 120.0
C4' C5' H5' H5'2 239.8 240.0
H5' C5' C4' O4' 175.4 306.5
H5' C5' C4' C3' 290.2 64.3
H5' C5' C4' H4' 55.8 185.4
O5' C5' H5'2 C4' 119.5 120.0
O5' C5' H5'2 H5' 239.8 240.0
C4' C5' H5'2 H5' 120.2 120.0
H5'2 C5' C4' O4' 55.3 186.5
H5'2 C5' C4' C3' 170.1 304.3
H5'2 C5' C4' H4' 295.7 65.4
O4' C4' C5' H5' 175.4 306.5
O4' C4' C5' H5'2 55.3 186.5
C5' C4' O4' C3' 124.9 119.4
C5' C4' O4' H4' 240.7 239.0
C3' C4' O4' H4' 115.8 119.6
O4' C4' C3' O3' 194.1 239.3
O4' C4' C3' C2' 315.3 358.0
O4' C4' C3' H3' 71.3 116.8
C4' O4' C1' C2' 4.8 320.0
C4' O4' C1' N1 240.2 201.4
C4' O4' C1' H1' 122.3 78.4
C3' C4' C5' H5' 290.2 64.3
C3' C4' C5' H5'2 170.1 304.3
C5' C4' C3' O4' 241.6 240.6
C5' C4' C3' H4' 125.5 121.1
O4' C4' C3' H4' 243.9 240.5
C3' C4' O4' C1' 24.9 26.5
O3' C3' C4' C2' 238.8 241.3
O3' C3' C4' H3' 122.8 122.5
C4' C3' O3' HO3 180.0 298.5
C2' C3' C4' H3' 244.0 241.2
C4' C3' C2' O2' 284.2 220.9
C4' C3' C2' C1' 47.1 339.1
C4' C3' C2' H2' 162.7 97.4
H4' C4' C5' H5' 55.8 185.4
H4' C4' C5' H5'2 295.7 65.4
C5' C4' H4' O4' 118.8 121.0
C5' C4' H4' C3' 229.7 238.9
O4' C4' H4' C3' 110.9 117.9
H4' C4' O4' C1' 269.1 266.9
H4' C4' C3' O3' 310.2 358.8
H4' C4' C3' C2' 71.4 117.5
H4' C4' C3' H3' 187.3 236.3
C1' O4' C4' C3' 24.9 26.5
C1' O4' C4' H4' 269.1 266.9
C3' C2' C1' O4' 328.1 37.0
O2' C2' C1' O4' 83.8 155.2
O4' C1' C2' H2' 212.7 278.8
C2' C1' O4' N1 124.6 118.5
C2' C1' O4' H1' 242.5 241.5
N1 C1' O4' H1' 117.9 123.0
O4' C1' N1 C2 202.8 53.6
O4' C1' N1 C6 26.3 233.3
O3' C3' C4' H4' 310.2 358.8
C4' C3' O3' C2' 113.4 114.7
C4' C3' O3' H3' 237.6 237.5
C2' C3' O3' H3' 124.1 122.7
O3' C3' C2' O2' 43.4 339.6
O3' C3' C2' C1' 166.3 97.8
O3' C3' C2' H2' 281.8 216.0
C2' C3' C4' H4' 71.4 117.5
C4' C3' C2' O3' 240.8 241.4
C4' C3' C2' H3' 116.2 118.7
O4' C1' C2' C3' 328.1 37.0
O3' C3' C2' H3' 235.3 237.3
C2' C3' O3' HO3 66.6 183.8
O2' C2' C3' C1' 237.1 241.8
O2' C2' C3' H2' 121.6 123.6
C3' C2' O2' CA' 182.5 268.6
C1' C2' C3' H2' 244.5 241.7
C3' C2' C1' N1 85.8 155.5
C3' C2' C1' H1' 210.3 278.6
H3' C3' C4' H4' 187.3 236.3
C4' C3' H3' O3' 123.1 122.5
C4' C3' H3' C2' 249.5 245.2
O3' C3' H3' C2' 126.5 122.7
H3' C3' O3' HO3 302.4 61.1
H3' C3' C2' O2' 168.1 102.2
H3' C3' C2' C1' 291.0 220.4
H3' C3' C2' H2' 46.5 338.7
HO3 O3' C3' C2' 66.6 183.8
HO3 O3' C3' H3' 302.4 61.1
O4' C1' C2' O2' 83.8 155.2
O2' C2' C3' H3' 168.1 102.2
C3' C2' O2' C1' 111.4 112.8
C3' C2' O2' H2' 239.6 236.4
C1' C2' O2' H2' 128.2 123.6
O2' C2' C1' N1 201.5 273.7
O2' C2' C1' H1' 326.0 36.8
C2' O2' CA' CB   180.0
C2' O2' CA' HA1 44.5 299.9
C2' O2' CA' HA2 171.0 60.0
O4' C1' C2' N1 242.3 241.5
O4' C1' C2' H1' 117.7 118.4
C1' C2' C3' H3' 291.0 220.4
C3' C2' C1' O2' 244.3 241.8
C3' C2' C1' H2' 115.3 118.2
O2' C2' C1' H2' 231.0 236.5
C1' C2' O2' CA' 71.1 155.8
N1 C1' C2' H1' 235.5 236.9
C2' C1' N1 C2 85.1 299.5
C2' C1' N1 C6 268.6 119.2
H2' C2' C3' H3' 46.5 338.7
C3' C2' H2' O2' 119.1 123.6
C3' C2' H2' C1' 251.1 247.2
O2' C2' H2' C1' 132.0 123.6
H2' C2' O2' CA' 302.9 32.2
H2' C2' C1' N1 330.5 37.3
H2' C2' C1' H1' 95.0 160.3
CA' O2' C2' C1' 71.1 155.8
CA' O2' C2' H2' 302.9 32.2
CB CA' O2' HA1   240.0
CB CA' O2' HA2   120.0
O2' CA' CB SC   180.0
O2' CA' CB HB1   300.1
O2' CA' CB HB2   60.0
HA1 CA' O2' HA2 233.4 240.0
O4' C1' N1 C2' 117.7 114.1
O4' C1' N1 H1' 242.1 237.1
N1 C1' C2' H2' 330.5 37.3
C2' C1' N1 H1' 124.4 123.0
C2 N1 C1' C6 176.5 180.3
C1' N1 C2 O2 1.5 360.0
C1' N1 C2 N3 180.3 180.0
C1' N1 C6 C5 178.9 179.7
C1' N1 C6 H6 358.9 360.0
O4' C1' H1' C2' 244.4 246.0
O4' C1' H1' N1 115.7 122.9
H1' C1' C2' H2' 95.0 160.3
C2' C1' H1' N1 231.3 237.0
H1' C1' N1 C2 320.7 176.5
H1' C1' N1 C6 144.2 356.2
C2 N1 C1' H1' 320.7 176.5
C1' N1 C2 C6 183.3 179.7
C2 N1 C6 C5 2.5 359.4
C2 N1 C6 H6 182.5 179.7
O2 C2 N1 N3 181.2 180.0
N1 C2 N3 C4 4.9 360.0
N1 C2 N3 H3 184.9 180.0
C6 N1 C1' H1' 144.2 356.2
C1' N1 C6 C2 176.4 180.3
C6 N1 C2 O2 178.1 180.3
C6 N1 C2 N3 357.0 0.3
C4 C5 C6 N1 356.9 0.6
C5A C5 C6 N1 182.4 180.2
C5 C6 N1 H6 180.0 179.8
O2 C2 N1 C6 178.1 180.3
N1 C2 O2 N3 178.7 180.0
O2 C2 N3 C4 183.7 180.0
O2 C2 N3 H3 3.7 360.0
N3 C2 N1 C6 357.0 0.3
N1 C2 N3 O2 181.2 180.0
C4 N3 C2 H3 180.0 180.0
C2 N3 C4 O4 179.7 180.0
C2 N3 C4 C5 354.4 0.0
C2 N3 C4 H3 180.0 180.0
O4 C4 N3 C5 185.3 180.0
N3 C4 C5 C5A 178.8 180.0
N3 C4 C5 C6 4.1 359.7
C2 N3 H3 C4 180.0 180.0
H3 N3 C4 O4 359.7 0.1
H3 N3 C4 C5 174.4 180.0
O4 C4 N3 H3 359.7 0.1
N3 C4 O4 C5 174.1 180.0
O4 C4 C5 C5A 353.0 0.0
O4 C4 C5 C6 178.3 179.7
N1 C6 C5 C4 356.9 0.6
C5 C4 N3 H3 174.4 180.0
N3 C4 C5 O4 185.7 180.0
C5A C5 C4 C6 174.7 180.3
C4 C5 C5A H5A 180.0 359.9
C4 C5 C5A H5A1 300.0 120.0
C4 C5 C5A H5A2 60.0 240.0
C4 C5 C6 H6 176.9 180.3
N1 C6 C5 C5A 182.4 180.2
C4 C5 C5A C6 185.9 179.7
C5A C5 C6 H6 2.4 360.0
H5A C5A C5 H5A1 240.0 239.9
H5A C5A C5 H5A2 120.0 120.0
H5A1 C5A C5 H5A2 240.0 240.0
N1 C6 C5 H6 180.0 180.2
C4 C5 C6 C5A 174.5 180.3
C6 C5 C5A H5A 354.1 180.3
C6 C5 C5A H5A1 114.1 300.3
C6 C5 C5A H5A2 234.1 60.3
H5A C5A C5 C6 354.1 180.3
C5 C5A H5A H5A1 120.0 120.0
C5 C5A H5A H5A2 240.0 240.0
H5A1 C5A H5A H5A2 120.0 120.0
H5A1 C5A C5 C6 114.1 300.3
C5 C5A H5A1 H5A 240.0 239.9
C5 C5A H5A1 H5A2 120.0 120.0
H5A C5A H5A1 H5A2 240.0 240.0
H5A2 C5A C5 C6 234.1 60.3
C5 C5A H5A2 H5A 120.0 120.0
C5 C5A H5A2 H5A1 240.0 240.0
H5A C5A H5A2 H5A1 120.0 120.0
N1 C6 H6 C5 180.0 179.8
O2' CA' CB HA1   120.0
O2' CA' CB HA2   240.0
HA1 CA' CB HA2   120.0
SC CB CA' HB1   239.9
SC CB CA' HB2   120.0
CA' CB SC CD   180.0
HB1 CB CA' HB2   240.1
O2' CA' HA1 CB   240.0
O2' CA' HA1 HA2 128.8 120.0
CB CA' HA1 HA2   240.0
HA1 CA' CB SC   60.0
HA1 CA' CB HB1   180.1
HA1 CA' CB HB2   300.0
O2' CA' HA2 CB   120.0
O2' CA' HA2 HA1 231.2 240.0
CB CA' HA2 HA1   120.0
HA2 CA' CB SC   300.0
HA2 CA' CB HB1   60.1
HA2 CA' CB HB2   180.0
SC CB CA' HA1   60.0
SC CB CA' HA2   300.0
CA' CB SC HB1   120.1
CA' CB SC HB2   240.0
HB1 CB SC HB2   119.9
CB SC CD HD1   300.0
CB SC CD HD2   60.0
CB SC CD HD3   180.0
HB1 CB CA' HA1   180.1
HB1 CB CA' HA2   60.1
CA' CB HB1 SC   239.9
CA' CB HB1 HB2   120.0
SC CB HB1 HB2   240.1
HB1 CB SC CD   59.9
HB2 CB CA' HA1   300.0
HB2 CB CA' HA2   180.0
CA' CB HB2 SC   120.0
CA' CB HB2 HB1   240.0
SC CB HB2 HB1   120.0
HB2 CB SC CD   300.0
CD SC CB HB1   59.9
CD SC CB HB2   300.0
HD1 CD SC HD2   240.0
HD1 CD SC HD3   120.0
HD2 CD SC HD3   240.0
SC CD HD1 HD2   120.0
SC CD HD1 HD3   240.0
HD2 CD HD1 HD3   120.0
SC CD HD2 HD1   240.0
SC CD HD2 HD3   120.0
HD1 CD HD2 HD3   240.0
SC CD HD3 HD1   120.0
SC CD HD3 HD2   240.0
HD1 CD HD3 HD2   120.0