PDB Chemical Component S2M

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 S2M

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O4 C4 1.213 1.227
C4 C5 1.355 1.486
C4 N3 1.328 1.386
C5 C6 1.272 1.339
C5 C5M 1.494 1.495
C6 N1 1.301 1.400
C6 H6 1.104 1.085
C5M H71 1.115 1.089
C5M H72 1.115 1.089
C5M H73 1.114 1.090
N3 C2 1.316 1.394
N3 H3 1.020 1.016
S2 C2 1.664 1.683
C2 N1 1.398 1.421
C5' O5' 1.420 1.416
C5' C4' 1.526 1.523
C5' H5' 1.116 1.092
C5' H5'' 1.115 1.091
O5' P 1.614 1.619
P OP2 1.500 1.617
P OP1 1.505 1.501
P OP3   1.618
OP2 HOP2 0.950 0.980
C4' O4' 1.438 1.444
C4' C3' 1.535 1.523
C4' H4' 1.116 1.095
O4' C1' 1.436 1.437
C1' N1 1.462 1.435
C1' C2' 1.529 1.519
C1' H1' 1.115 1.094
C2' C3' 1.519 1.514
C2' O2' 1.416 1.413
C2' H2' 1.115 1.097
C3' O3' 1.420 1.427
C3' H3' 1.115 1.093
O3' HO3' 0.950 0.969
O2' CA' 1.444 1.424
CA' CB' 1.333 1.516
CA' HA'1 1.114 1.095
CA' HA'2 1.116 1.094
CB' OC' 1.451 1.422
CB' HB'1 1.116 1.094
CB' HB'2 1.115 1.095
OC' CD' 1.431 1.422
CD' HD'1 1.115 1.093
CD' HD'2 1.115 1.092
CD' HD'3 1.115 1.093
OP3 HOP3   0.980

Bond Angles for S2M

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O4 C4 C5 123.7 121.6
O4 C4 N3 118.1 123.7
C5 C4 N3 118.2 114.7
C4 C5 C6 120.9 118.5
C4 C5 C5M 118.9 118.0
C4 N3 C2 124.5 126.9
C4 N3 H3 118.2 116.6
C6 C5 C5M 120.3 123.5
C5 C6 N1 119.7 125.2
C5 C6 H6 119.1 120.0
C5 C5M H71 118.8 109.7
C5 C5M H72 108.8 109.8
C5 C5M H73 108.8 109.7
N1 C6 H6 121.2 114.7
C6 N1 C2 124.1 118.4
C6 N1 C1' 119.3 118.0
H71 C5M H72 108.8 109.3
H71 C5M H73 108.8 109.4
H72 C5M H73 101.3 108.9
C2 N3 H3 117.2 116.6
N3 C2 S2 122.8 118.2
N3 C2 N1 112.5 116.3
S2 C2 N1 124.7 125.5
C2 N1 C1' 116.3 123.5
O5' C5' C4' 110.2 108.6
O5' C5' H5' 112.0 109.2
O5' C5' H5'' 112.0 109.3
C5' O5' P 117.8 118.5
C4' C5' H5' 111.9 110.1
C4' C5' H5'' 111.9 110.1
C5' C4' O4' 108.2 108.2
C5' C4' C3' 114.8 113.3
C5' C4' H4' 106.0 109.3
H5' C5' H5'' 98.4 109.6
O5' P OP2 110.2 103.8
O5' P OP1 107.6 115.0
O5' P OP3   102.9
OP2 P OP1 116.0 115.3
OP2 P OP3   103.3
P OP2 HOP2 110.2 119.0
OP1 P OP3   114.9
P OP3 HOP3   119.0
O4' C4' C3' 107.3 105.9
O4' C4' H4' 113.8 107.7
C4' O4' C1' 108.9 109.2
C3' C4' H4' 106.9 112.2
C4' C3' C2' 101.4 102.1
C4' C3' O3' 111.2 107.9
C4' C3' H3' 114.6 114.5
O4' C1' N1 112.1 109.0
O4' C1' C2' 107.4 106.5
O4' C1' H1' 106.9 108.9
N1 C1' C2' 101.9 112.5
N1 C1' H1' 112.1 107.3
C2' C1' H1' 116.4 112.6
C1' C2' C3' 104.2 102.0
C1' C2' O2' 111.1 112.6
C1' C2' H2' 111.5 111.1
C3' C2' O2' 108.1 112.3
C3' C2' H2' 114.3 110.1
C2' C3' O3' 112.5 110.3
C2' C3' H3' 113.5 114.0
O2' C2' H2' 107.7 108.6
C2' O2' CA' 121.5 111.9
O3' C3' H3' 104.0 107.8
C3' O3' HO3' 111.2 106.4
O2' CA' CB' 119.9 109.0
O2' CA' HA'1 108.5 108.1
O2' CA' HA'2 108.5 108.2
CB' CA' HA'1 108.5 111.2
CB' CA' HA'2 108.5 110.5
CA' CB' OC' 120.7 109.0
CA' CB' HB'1 108.2 111.1
CA' CB' HB'2 108.2 110.5
HA'1 CA' HA'2 101.5 109.7
OC' CB' HB'1 108.2 108.2
OC' CB' HB'2 108.2 108.3
CB' OC' CD' 122.6 111.5
HB'1 CB' HB'2 101.7 109.7
OC' CD' HD'1 122.5 109.5
OC' CD' HD'2 107.5 109.5
OC' CD' HD'3 107.5 108.9
HD'1 CD' HD'2 107.6 110.1
HD'1 CD' HD'3 107.6 109.4
HD'2 CD' HD'3 102.3 109.4

Torsion Angles for S2M

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C5 C4 O4 N3 180.0 180.3
O4 C4 C5 C6 180.4 180.6
O4 C4 C5 C5M 0.3 0.7
O4 C4 N3 C2 180.0 179.6
O4 C4 N3 H3 0.0 359.5
O4 C4 C5 N3 180.0 179.7
C5 C4 N3 C2 0.1 359.3
C5 C4 N3 H3 180.0 179.2
C6 C5 C4 C5M 180.1 179.9
C4 C5 C6 N1 357.7 0.2
C4 C5 C6 H6 177.7 180.1
C4 C5 C5M H71 180.0 240.0
C4 C5 C5M H72 305.2 119.8
C4 C5 C5M H73 54.7 0.2
O4 C4 N3 C5 180.0 180.3
N3 C4 C5 C6 0.4 0.9
N3 C4 C5 C5M 180.3 181.0
C2 N3 C4 H3 180.0 180.1
C4 N3 C2 S2 181.2 178.9
C4 N3 C2 N1 1.2 359.4
C6 C5 C4 N3 0.4 0.9
C4 C5 C6 C5M 179.9 180.1
C6 C5 C5M H71 359.9 60.1
C6 C5 C5M H72 125.1 299.9
C6 C5 C5M H73 234.6 180.3
N1 C6 C5 H6 180.0 180.0
C5 C6 N1 C2 3.9 358.5
C5 C6 N1 C1' 177.7 180.4
C5M C5 C4 N3 180.3 181.0
C4 C5 C5M C6 180.1 179.9
C5M C5 C6 N1 177.8 180.1
C5M C5 C6 H6 357.8 0.1
H71 C5M C5 H72 234.8 120.2
H71 C5M C5 H73 125.3 239.8
H72 C5M C5 H73 250.5 119.6
N1 C6 C5 C5M 177.8 180.1
C5 C6 N1 H6 180.0 180.0
N3 C2 N1 C6 356.8 1.7
S2 C2 N1 C6 176.8 182.2
C2 N1 C6 C1' 186.1 178.1
O4' C1' N1 C6 28.0 32.2
C6 N1 C1' C2' 273.4 274.4
C6 N1 C1' H1' 148.3 150.0
H6 C6 C5 C5M 357.8 0.1
C5 C6 H6 N1 180.0 180.0
H6 C6 N1 C2 183.9 178.5
H6 C6 N1 C1' 357.8 0.4
C5 C5M H71 H72 125.2 239.6
C5 C5M H71 H73 234.8 120.4
H72 C5M H71 H73 109.5 240.8
C5 C5M H72 H71 229.1 120.4
C5 C5M H72 H73 114.5 239.9
H71 C5M H72 H73 245.4 119.5
C5 C5M H73 H71 130.9 239.6
C5 C5M H73 H72 245.4 120.1
H71 C5M H73 H72 114.5 240.6
C4 N3 C2 H3 180.0 179.9
C6 N1 C2 N3 356.8 1.7
S2 C2 N3 N1 179.9 179.6
N3 C2 N1 C1' 182.7 179.6
C4 N3 H3 C2 180.0 180.1
H3 N3 C2 S2 1.2 359.0
H3 N3 C2 N1 181.2 179.5
C6 N1 C2 S2 176.8 182.2
S2 C2 N3 H3 1.2 359.0
N3 C2 S2 N1 180.1 180.5
S2 C2 N1 C1' 2.8 0.1
C2 N1 C6 H6 183.9 178.5
C6 N1 C2 C1' 174.0 182.1
N1 C2 N3 H3 181.2 179.5
N3 C2 N1 S2 179.9 179.5
O4' C1' N1 C2 202.3 214.3
C2 N1 C1' C2' 87.8 96.4
C2 N1 C1' H1' 322.6 332.0
C4' C5' O5' H5' 234.8 239.9
C4' C5' O5' H5'' 125.3 120.1
O5' C5' C4' O4' 288.6 62.4
O5' C5' C4' C3' 48.4 179.5
O5' C5' C4' H4' 166.2 305.4
H5' C5' O5' H5'' 250.5 240.2
C5' O5' P OP2 184.4 53.2
C5' O5' P OP1 57.0 180.1
C5' O5' P OP3   305.8
O5' C5' C4' H5' 125.3 119.5
O5' C5' C4' H5'' 234.7 240.4
C4' C5' O5' P 186.3 180.0
H5' C5' C4' H5'' 109.4 120.9
O4' C4' C5' C3' 240.2 242.9
O4' C4' C5' H4' 122.4 117.0
C5' C4' O4' C1' 142.9 109.0
C3' C4' C5' H4' 242.2 234.1
C5' C4' C3' C2' 208.6 273.1
C5' C4' C3' O3' 88.8 156.8
C5' C4' C3' H3' 331.2 36.8
O5' C5' H5' C4' 235.7 240.8
O5' C5' H5' H5'' 117.9 119.6
H5' C5' O5' P 311.6 300.1
C4' C5' H5' H5'' 242.2 238.8
H5' C5' C4' O4' 163.3 302.9
H5' C5' C4' C3' 283.1 60.0
H5' C5' C4' H4' 40.9 185.9
O5' C5' H5'' C4' 124.3 119.2
O5' C5' H5'' H5' 242.1 240.4
H5'' C5' O5' P 61.1 59.9
C4' C5' H5'' H5' 117.8 121.2
H5'' C5' C4' O4' 53.9 182.0
H5'' C5' C4' C3' 173.7 299.1
H5'' C5' C4' H4' 291.5 65.0
P O5' C5' C4' 186.3 180.0
P O5' C5' H5' 311.6 300.1
P O5' C5' H5'' 61.1 59.9
OP2 P O5' OP1 127.4 233.1
OP2 P O5' OP3   107.4
O5' P OP2 HOP2 180.0 175.4
OP1 P O5' OP3   234.2
O5' P OP3 HOP3   186.2
O5' P OP2 OP1 237.4 126.6
O5' P OP2 OP3   252.9
OP1 P OP2 OP3   126.2
OP2 P OP3 HOP3   78.5
O5' P OP1 OP2 124.0 239.3
O5' P OP1 OP3   119.3
OP2 P OP1 OP3   240.0
OP1 P OP2 HOP2 302.6 48.7
OP1 P OP3 HOP3   312.0
O5' P OP3 OP2   107.7
O5' P OP3 OP1   234.2
OP2 P OP3 OP1   126.5
OP3 P OP2 HOP2   282.5
HOP2 OP2 P OP1 302.6 48.7
HOP2 OP2 P OP3   282.5
O4' C4' C5' H5' 163.3 302.9
O4' C4' C5' H5'' 53.9 182.0
C5' C4' O4' C3' 124.4 121.7
C5' C4' O4' H4' 242.5 241.9
C3' C4' O4' H4' 118.1 120.2
O4' C4' C3' C2' 328.9 31.5
O4' C4' C3' O3' 209.1 275.3
O4' C4' C3' H3' 91.5 155.2
C4' O4' C1' N1 251.0 227.1
C4' O4' C1' C2' 2.2 348.7
C4' O4' C1' H1' 127.8 110.3
C3' C4' C5' H5' 283.1 60.0
C3' C4' C5' H5'' 173.7 299.1
C5' C4' C3' O4' 239.7 241.6
C5' C4' C3' H4' 117.3 124.4
O4' C4' C3' H4' 237.6 242.8
C3' C4' O4' C1' 18.4 347.2
C1' C2' C3' C4' 31.2 322.9
C4' C3' C2' O2' 272.9 202.0
C4' C3' C2' H2' 153.1 80.9
C2' C3' C4' O3' 119.8 116.3
C2' C3' C4' H3' 237.4 236.3
O3' C3' C4' H3' 117.6 120.1
C4' C3' O3' HO3' 180.0 15.2
H4' C4' C5' H5' 40.9 185.9
H4' C4' C5' H5'' 291.5 65.0
C5' C4' H4' O4' 118.8 117.3
C5' C4' H4' C3' 237.0 233.5
O4' C4' H4' C3' 118.2 116.2
H4' C4' O4' C1' 260.4 227.0
H4' C4' C3' C2' 91.3 148.7
H4' C4' C3' O3' 331.6 32.5
H4' C4' C3' H3' 214.0 272.4
C6 N1 C1' O4' 28.0 32.2
C2 N1 C1' O4' 202.3 214.3
C1' O4' C4' C3' 18.4 347.2
C1' O4' C4' H4' 260.4 227.0
N1 C1' O4' C2' 248.9 238.4
N1 C1' O4' H1' 123.2 116.8
C2' C1' O4' H1' 234.4 238.4
O4' C1' C2' C3' 338.1 30.7
O4' C1' C2' O2' 94.3 151.3
O4' C1' C2' H2' 214.4 273.4
C1' N1 C6 H6 357.8 0.4
C6 N1 C1' C2 185.7 177.9
O4' C1' N1 C2' 114.6 117.9
O4' C1' N1 H1' 239.7 242.3
C2' C1' N1 H1' 125.2 124.4
N1 C1' C2' C3' 96.1 150.0
N1 C1' C2' O2' 212.3 270.6
N1 C1' C2' H2' 332.4 32.7
C4' C3' C2' C1' 31.2 322.9
O4' C1' C2' N1 242.0 240.7
O4' C1' C2' H1' 119.8 119.3
N1 C1' C2' H1' 237.7 238.6
C3' C2' C1' O2' 243.8 239.4
C3' C2' C1' H2' 123.7 117.3
C1' C2' C3' O3' 150.1 77.4
C1' C2' C3' H3' 267.8 198.9
O2' C2' C1' H2' 239.9 237.9
C1' C2' O2' CA' 66.1 185.5
O4' C1' H1' N1 123.2 117.8
O4' C1' H1' C2' 240.0 242.1
N1 C1' H1' C2' 116.8 124.3
H1' C1' C2' C3' 218.4 271.5
H1' C1' C2' O2' 334.6 32.1
H1' C1' C2' H2' 94.6 154.2
C2' C3' C4' H4' 91.3 148.7
C4' C3' C2' O3' 241.1 245.5
C4' C3' C2' H3' 123.4 124.0
C3' C2' C1' H1' 218.4 271.5
C1' C2' C3' O2' 118.3 120.8
C1' C2' C3' H2' 238.1 242.0
O2' C2' C3' H2' 119.9 121.1
C3' C2' O2' CA' 179.9 300.0
O3' C3' C2' H3' 242.3 238.5
C2' C3' O3' HO3' 67.1 264.4
O2' C2' C1' H1' 334.6 32.1
C1' C2' O2' C3' 246.2 245.5
C1' C2' O2' H2' 122.3 123.5
C3' C2' O2' H2' 236.1 238.0
O2' C2' C3' O3' 31.8 316.5
O2' C2' C3' H3' 149.5 78.0
C2' O2' CA' CB' 242.7 179.0
C2' O2' CA' HA'1 8.0 300.0
C2' O2' CA' HA'2 117.5 58.8
H2' C2' C1' H1' 94.6 154.2
C1' C2' H2' C3' 117.8 112.3
C1' C2' H2' O2' 237.9 235.6
C3' C2' H2' O2' 120.1 123.3
H2' C2' C3' O3' 271.9 195.4
H2' C2' C3' H3' 29.6 316.9
H2' C2' O2' CA' 303.8 62.0
O3' C3' C4' H4' 331.6 32.5
C4' C3' O3' C2' 112.9 110.7
C4' C3' O3' H3' 236.1 235.8
O3' C3' C2' O2' 31.8 316.5
O3' C3' C2' H2' 271.9 195.4
C2' C3' O3' H3' 123.2 125.1
H3' C3' C4' H4' 214.0 272.4
C4' C3' H3' C2' 244.1 243.0
C4' C3' H3' O3' 121.6 120.1
H3' C3' C2' O2' 149.5 78.0
H3' C3' C2' H2' 29.6 316.9
C2' C3' H3' O3' 237.5 237.2
H3' C3' O3' HO3' 303.9 139.4
HO3' O3' C3' H3' 303.9 139.4
CA' O2' C2' H2' 303.8 62.0
CB' CA' O2' HA'1 234.7 239.0
CB' CA' O2' HA'2 125.2 120.2
O2' CA' CB' OC' 93.0 299.2
O2' CA' CB' HB'1 218.2 180.0
O2' CA' CB' HB'2 327.6 58.0
HA'1 CA' O2' HA'2 250.5 241.3
O2' CA' CB' HA'1 125.3 119.1
O2' CA' CB' HA'2 234.8 241.2
HA'1 CA' CB' HA'2 109.5 122.0
OC' CB' CA' HB'1 234.7 119.2
OC' CB' CA' HB'2 125.3 241.1
CA' CB' OC' CD' 50.0 179.0
HB'1 CB' CA' HB'2 250.6 121.9
O2' CA' HA'1 CB' 228.3 240.3
O2' CA' HA'1 HA'2 114.1 117.8
CB' CA' HA'1 HA'2 245.9 237.5
HA'1 CA' CB' OC' 327.7 180.0
HA'1 CA' CB' HB'1 93.0 60.8
HA'1 CA' CB' HB'2 202.4 298.9
O2' CA' HA'2 CB' 131.7 119.3
O2' CA' HA'2 HA'1 245.8 242.2
CB' CA' HA'2 HA'1 114.1 122.9
HA'2 CA' CB' OC' 218.2 58.0
HA'2 CA' CB' HB'1 343.5 298.8
HA'2 CA' CB' HB'2 92.9 176.9
OC' CB' CA' HA'1 327.7 180.0
OC' CB' CA' HA'2 218.2 58.0
CA' CB' OC' HB'1 125.3 239.0
CA' CB' OC' HB'2 234.7 120.2
HB'1 CB' OC' HB'2 109.4 241.2
CB' OC' CD' HD'1 180.0 268.5
CB' OC' CD' HD'2 305.3 147.7
CB' OC' CD' HD'3 54.7 28.1
HB'1 CB' CA' HA'1 93.0 60.8
HB'1 CB' CA' HA'2 343.5 298.8
CA' CB' HB'1 OC' 227.7 119.7
CA' CB' HB'1 HB'2 113.8 237.6
OC' CB' HB'1 HB'2 246.1 117.9
HB'1 CB' OC' CD' 284.7 300.0
HB'2 CB' CA' HA'1 202.4 298.9
HB'2 CB' CA' HA'2 92.9 176.9
CA' CB' HB'2 OC' 132.3 240.7
CA' CB' HB'2 HB'1 246.2 122.8
OC' CB' HB'2 HB'1 113.8 242.2
HB'2 CB' OC' CD' 175.3 58.8
CD' OC' CB' HB'1 284.7 300.0
CD' OC' CB' HB'2 175.3 58.8
HD'1 CD' OC' HD'2 234.7 120.8
HD'1 CD' OC' HD'3 125.2 240.4
HD'2 CD' OC' HD'3 250.5 119.6
OC' CD' HD'1 HD'2 125.2 239.6
OC' CD' HD'1 HD'3 234.8 119.3
HD'2 CD' HD'1 HD'3 109.5 239.8
OC' CD' HD'2 HD'1 226.2 120.4
OC' CD' HD'2 HD'3 113.1 240.7
HD'1 CD' HD'2 HD'3 246.9 120.3
OC' CD' HD'3 HD'1 133.8 240.3
OC' CD' HD'3 HD'2 246.9 119.7
HD'1 CD' HD'3 HD'2 113.2 239.3