PDB Chemical Component NMS

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 NMS

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP2 1.447 1.617
P OP1 1.452 1.501
P O5' 1.565 1.619
P OP3   1.618
OP2 HOP2 0.950 0.980
O5' C5' 1.417 1.416
N1 C6 1.367 1.390
N1 C2 1.362 1.413
N1 C1' 1.463 1.435
C6 C5 1.331 1.339
C6 H6 1.103 1.086
C2 O2 1.216 1.232
C2 N3 1.372 1.400
N3 C4 1.372 1.386
N3 HN3 1.020 1.017
C4 O4 1.198 1.229
C4 C5 1.446 1.487
C5 C5M 1.503 1.495
C5M H71 1.115 1.089
C5M H72 1.115 1.089
C5M H73 1.115 1.090
C2' C1' 1.445 1.519
C2' C3' 1.493 1.514
C2' O6' 1.398 1.413
C2' H2' 1.115 1.097
C5' C4' 1.499 1.523
C5' H5' 1.115 1.092
C5' H5'' 1.115 1.091
C4' O4' 1.475 1.444
C4' C3' 1.487 1.523
C4' H4' 1.115 1.095
O4' C1' 1.436 1.437
C1' H1' 1.115 1.094
C3' O3' 1.410 1.427
C3' H3' 1.115 1.093
O3' HO3' 0.950 0.969
O6' C7' 1.447 1.424
C7' C8' 1.499 1.513
C7' H7'1 1.115 1.094
C7' H7'2 1.115 1.094
C8' O8' 1.204 1.227
C8' N9' 1.371 1.386
N9' C10 1.465 1.445
N9' H9' 1.020 1.016
C10 H101 1.115 1.094
C10 H102 1.115 1.093
C10 H103 1.115 1.093
OP3 HOP3   0.980

Bond Angles for NMS

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 122.5 115.3
OP2 P O5' 111.5 103.8
OP2 P OP3   103.3
P OP2 HOP2 122.5 119.0
OP1 P O5' 103.9 115.0
OP1 P OP3   114.9
O5' P OP3   102.9
P O5' C5' 117.3 118.5
P OP3 HOP3   119.0
O5' C5' C4' 106.0 108.6
O5' C5' H5' 113.5 109.2
O5' C5' H5'' 113.5 109.3
C6 N1 C2 122.0 120.2
C6 N1 C1' 124.6 118.5
N1 C6 C5 122.4 124.5
N1 C6 H6 120.2 114.7
C2 N1 C1' 113.3 121.3
N1 C2 O2 124.4 123.8
N1 C2 N3 115.4 115.1
N1 C1' C2' 112.8 112.5
N1 C1' O4' 105.8 109.0
N1 C1' H1' 108.6 107.3
C5 C6 H6 117.4 120.7
C6 C5 C4 118.9 118.4
C6 C5 C5M 121.6 123.6
O2 C2 N3 120.2 121.1
C2 N3 C4 126.0 127.0
C2 N3 HN3 117.0 116.4
C4 N3 HN3 117.0 116.6
N3 C4 O4 118.7 123.6
N3 C4 C5 115.3 114.8
O4 C4 C5 126.0 121.6
C4 C5 C5M 119.5 118.0
C5 C5M H71 107.9 109.7
C5 C5M H72 121.6 109.8
C5 C5M H73 107.9 109.7
H71 C5M H72 107.9 109.4
H71 C5M H73 102.0 109.4
H72 C5M H73 107.9 108.9
C1' C2' C3' 103.0 102.0
C1' C2' O6' 106.8 112.6
C1' C2' H2' 118.4 111.1
C2' C1' O4' 105.6 106.5
C2' C1' H1' 108.7 112.6
C3' C2' O6' 117.6 112.3
C3' C2' H2' 107.7 110.1
C2' C3' C4' 98.4 102.1
C2' C3' O3' 112.5 110.3
C2' C3' H3' 115.5 114.0
O6' C2' H2' 104.0 108.6
C2' O6' C7' 106.2 111.9
C4' C5' H5' 113.5 110.1
C4' C5' H5'' 113.5 110.1
C5' C4' O4' 105.2 108.2
C5' C4' C3' 120.3 113.3
C5' C4' H4' 103.1 109.3
H5' C5' H5'' 97.0 109.6
O4' C4' C3' 102.0 105.9
O4' C4' H4' 121.1 107.7
C4' O4' C1' 106.9 109.2
C3' C4' H4' 106.3 112.2
C4' C3' O3' 111.8 107.9
C4' C3' H3' 116.1 114.5
O4' C1' H1' 115.4 108.9
O3' C3' H3' 102.9 107.8
C3' O3' HO3' 112.5 106.4
O6' C7' C8' 107.3 110.7
O6' C7' H7'1 113.0 108.5
O6' C7' H7'2 113.0 109.2
C8' C7' H7'1 113.0 109.3
C8' C7' H7'2 113.0 110.1
C7' C8' O8' 124.0 122.8
C7' C8' N9' 112.6 111.6
H7'1 C7' H7'2 97.4 109.0
O8' C8' N9' 123.4 125.6
C8' N9' C10 116.3 123.0
C8' N9' H9' 118.8 118.5
C10 N9' H9' 124.8 118.5
N9' C10 H101 109.7 110.1
N9' C10 H102 116.3 110.2
N9' C10 H103 109.7 110.2
H101 C10 H102 109.7 108.9
H101 C10 H103 100.4 108.8
H102 C10 H103 109.7 108.7

Torsion Angles for NMS

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 O5' 236.1 233.4
OP1 P OP2 OP3   126.2
O5' P OP2 OP3   252.9
OP2 P O5' C5' 48.5 53.2
OP2 P OP3 HOP3   78.5
OP2 P OP1 O5' 127.3 120.7
OP2 P OP1 OP3   240.0
OP1 P OP2 HOP2 180.0 48.7
O5' P OP1 OP3   119.3
OP1 P O5' C5' 182.4 180.1
OP1 P OP3 HOP3   312.0
OP2 P O5' OP1 226.1 233.1
OP2 P O5' OP3   107.4
O5' P OP2 HOP2 303.9 175.4
OP1 P O5' OP3   234.2
O5' P OP3 HOP3   186.2
P O5' C5' C4' 181.8 180.0
P O5' C5' H5' 56.5 300.1
P O5' C5' H5'' 307.0 59.9
OP2 P OP3 OP1   126.5
OP2 P OP3 O5'   252.3
OP3 P OP2 HOP2   282.5
OP1 P OP3 O5'   125.8
OP3 P O5' C5'   305.8
HOP2 OP2 P OP1 180.0 48.7
HOP2 OP2 P O5' 303.9 175.4
HOP2 OP2 P OP3   282.5
C5' O5' P OP3   305.8
C4' C5' O5' H5' 125.3 239.9
C4' C5' O5' H5'' 234.7 120.1
O5' C5' C4' O4' 287.5 62.4
O5' C5' C4' C3' 41.6 179.5
O5' C5' C4' H4' 159.7 305.4
H5' C5' O5' H5'' 109.5 240.2
C2 N1 C6 C1' 181.0 180.1
C6 N1 C2 O2 179.7 180.0
C6 N1 C2 N3 359.1 360.0
C6 N1 C1' C2' 270.0 274.4
C6 N1 C1' O4' 25.0 32.3
C6 N1 C1' H1' 149.4 150.0
C5 C6 N1 H6 180.0 180.0
N1 C6 C5 C4 359.1 0.0
N1 C6 C5 C5M 179.9 180.0
C6 N1 C2 C1' 179.1 179.9
C2 N1 C6 C5 1.0 0.0
C2 N1 C6 H6 181.0 180.0
C2 N1 C1' C2' 89.0 94.3
C2 N1 C1' O4' 204.0 212.2
C2 N1 C1' H1' 328.5 329.9
O2 C2 N1 N3 180.6 180.1
N1 C2 N3 C4 0.8 360.0
N1 C2 N3 HN3 180.8 180.1
C6 N1 C1' C2 180.9 180.1
C1' N1 C6 C5 179.9 180.0
C1' N1 C6 H6 360.0 360.0
C1' N1 C2 O2 0.6 0.1
C1' N1 C2 N3 180.0 180.0
N1 C1' C2' C3' 83.5 150.0
N1 C1' C2' O6' 208.1 270.6
N1 C1' C2' H2' 324.8 32.7
C2' C1' N1 O4' 245.0 242.1
C2' C1' N1 H1' 120.6 124.4
C4' O4' C1' N1 243.1 227.1
O4' C1' N1 H1' 235.6 242.3
C5 C6 N1 C2 1.0 0.0
C5 C6 N1 C1' 179.9 180.0
N1 C6 C5 H6 180.0 180.0
N3 C4 C5 C6 0.7 360.0
O4 C4 C5 C6 179.9 180.0
C4 C5 C6 C5M 179.3 180.0
C6 C5 C5M H71 54.7 64.2
C6 C5 C5M H72 180.0 304.0
C6 C5 C5M H73 305.3 184.4
H6 C6 N1 C2 181.0 180.0
H6 C6 N1 C1' 360.0 360.0
N1 C6 H6 C5 180.0 180.0
H6 C6 C5 C4 179.1 180.0
H6 C6 C5 C5M 359.9 360.0
O2 C2 N1 C1' 0.6 0.1
N1 C2 O2 N3 179.4 179.9
O2 C2 N3 C4 180.3 179.9
O2 C2 N3 HN3 0.3 0.0
N3 C2 N1 C1' 180.0 180.0
N1 C2 N3 O2 180.6 180.1
C4 N3 C2 HN3 180.0 179.9
C2 N3 C4 O4 180.0 180.1
C2 N3 C4 C5 359.2 0.1
C6 C5 C4 N3 0.7 360.0
C2 N3 C4 HN3 180.0 180.1
O4 C4 N3 C5 180.7 180.0
N3 C4 C5 C5M 180.0 180.0
C2 N3 HN3 C4 180.0 179.9
HN3 N3 C4 O4 360.0 360.0
HN3 N3 C4 C5 179.3 180.0
C6 C5 C4 O4 179.9 180.0
O4 C4 N3 HN3 360.0 360.0
N3 C4 O4 C5 179.2 180.0
O4 C4 C5 C5M 359.2 360.0
C4 C5 C6 H6 179.1 180.0
C6 C5 C4 C5M 180.7 180.0
C5 C4 N3 HN3 179.3 180.0
N3 C4 C5 O4 180.8 180.0
C4 C5 C5M H71 235.5 244.2
C4 C5 C5M H72 0.7 124.0
C4 C5 C5M H73 126.0 4.4
C5M C5 C6 H6 359.9 360.0
C6 C5 C5M C4 179.3 180.0
H71 C5M C5 H72 234.7 120.2
H71 C5M C5 H73 109.5 239.8
H72 C5M C5 H73 234.7 119.6
C5 C5M H71 H72 133.0 239.5
C5 C5M H71 H73 246.6 120.4
H72 C5M H71 H73 113.5 240.8
C5 C5M H72 H71 234.7 120.4
C5 C5M H72 H73 125.2 239.9
H71 C5M H72 H73 250.5 119.5
C5 C5M H73 H71 113.5 239.6
C5 C5M H73 H72 227.0 120.2
H71 C5M H73 H72 113.5 240.5
N1 C1' C2' O4' 115.1 119.3
N1 C1' C2' H1' 239.5 238.6
C3' C2' C1' O6' 235.5 239.4
C3' C2' C1' H2' 118.7 117.3
C1' C2' C3' C4' 47.1 322.9
C1' C2' C3' O3' 165.1 77.4
C1' C2' C3' H3' 282.8 198.9
O6' C2' C1' H2' 243.2 237.9
C1' C2' O6' C7' 67.7 185.5
C4' O4' C1' C2' 2.9 348.7
O4' C1' C2' H1' 124.4 119.3
C1' C2' C3' O6' 117.1 120.8
C1' C2' C3' H2' 234.1 242.0
C3' C2' C1' O4' 328.5 30.7
C3' C2' C1' H1' 204.0 271.5
O6' C2' C3' H2' 117.0 121.1
C3' C2' O6' C7' 182.7 300.0
C5' C4' C3' C2' 199.8 273.1
O4' C4' C3' C2' 315.6 31.5
C2' C3' C4' H4' 83.3 148.7
C4' C3' C2' O3' 242.1 245.5
C4' C3' C2' H3' 124.3 124.0
O3' C3' C2' H3' 242.2 238.5
C2' C3' O3' HO3' 180.0 264.4
C1' C2' O6' C3' 245.0 245.5
C1' C2' O6' H2' 126.0 123.5
O6' C2' C1' O4' 93.0 151.3
O6' C2' C1' H1' 328.6 32.1
C3' C2' O6' H2' 241.0 238.0
O6' C2' C3' C4' 290.0 202.0
O6' C2' C3' O3' 47.9 316.5
O6' C2' C3' H3' 165.7 78.0
C2' O6' C7' C8' 132.0 180.0
C2' O6' C7' H7'1 6.7 60.1
C2' O6' C7' H7'2 257.2 301.4
C1' C2' H2' C3' 116.2 112.3
C1' C2' H2' O6' 241.7 235.6
H2' C2' C1' O4' 209.8 273.4
H2' C2' C1' H1' 85.3 154.2
C3' C2' H2' O6' 125.5 123.3
H2' C2' C3' C4' 173.0 80.9
H2' C2' C3' O3' 291.0 195.4
H2' C2' C3' H3' 48.7 316.9
H2' C2' O6' C7' 301.7 62.0
O5' C5' C4' H5' 234.7 119.5
O5' C5' C4' H5'' 125.3 240.4
C2' C3' C4' C5' 199.8 273.1
H5' C5' C4' H5'' 250.5 120.9
O4' C4' C5' C3' 245.9 242.9
O4' C4' C5' H4' 127.8 117.0
C5' C4' O4' C1' 153.2 109.0
C3' C4' C5' H4' 241.9 234.1
C5' C4' C3' O3' 81.3 156.8
C5' C4' C3' H3' 323.6 36.8
O5' C5' H5' C4' 121.2 240.8
O5' C5' H5' H5'' 240.6 119.6
C4' C5' H5' H5'' 119.4 238.8
H5' C5' C4' O4' 52.8 302.9
H5' C5' C4' C3' 166.9 60.0
H5' C5' C4' H4' 284.9 185.9
O5' C5' H5'' C4' 238.9 119.2
O5' C5' H5'' H5' 119.4 240.4
C4' C5' H5'' H5' 240.6 121.2
H5'' C5' C4' O4' 162.2 182.0
H5'' C5' C4' C3' 276.4 299.1
H5'' C5' C4' H4' 34.4 65.0
N1 C1' O4' C4' 243.1 227.1
C2' C1' O4' C4' 2.9 348.7
C2' C3' C4' O4' 315.6 31.5
O4' C4' C5' H5' 52.8 302.9
O4' C4' C5' H5'' 162.2 182.0
C5' C4' O4' C3' 126.3 121.7
C5' C4' O4' H4' 243.9 241.9
C3' C4' O4' H4' 117.6 120.2
O4' C4' C3' O3' 197.1 275.3
O4' C4' C3' H3' 79.4 155.2
C4' O4' C1' H1' 123.0 110.3
C4' C3' C2' O6' 290.0 202.0
C4' C3' C2' H2' 173.0 80.9
C2' C3' C4' O3' 118.4 116.3
C2' C3' C4' H3' 236.2 236.3
C3' C4' C5' H5' 166.9 60.0
C3' C4' C5' H5'' 276.4 299.1
C5' C4' C3' O4' 244.2 241.6
C5' C4' C3' H4' 116.4 124.4
O4' C4' C3' H4' 232.2 242.8
C3' C4' O4' C1' 26.8 347.2
O3' C3' C4' H3' 117.7 120.1
C4' C3' O3' HO3' 289.7 15.2
H4' C4' C5' H5' 284.9 185.9
H4' C4' C5' H5'' 34.4 65.0
C5' C4' H4' O4' 117.1 117.3
C5' C4' H4' C3' 232.6 233.5
O4' C4' H4' C3' 115.4 116.2
H4' C4' O4' C1' 269.2 227.0
H4' C4' C3' O3' 324.9 32.5
H4' C4' C3' H3' 207.2 272.4
N1 C1' O4' C2' 240.2 238.4
N1 C1' O4' H1' 120.1 116.8
O4' C1' C2' C3' 328.5 30.7
O4' C1' C2' O6' 93.0 151.3
O4' C1' C2' H2' 209.8 273.4
C2' C1' O4' H1' 239.9 238.4
C1' O4' C4' C3' 26.8 347.2
C1' O4' C4' H4' 269.2 227.0
N1 C1' H1' C2' 123.1 124.3
N1 C1' H1' O4' 241.5 242.2
H1' C1' C2' C3' 204.0 271.5
H1' C1' C2' O6' 328.6 32.1
H1' C1' C2' H2' 85.3 154.2
C2' C1' H1' O4' 118.4 117.9
O3' C3' C2' O6' 47.9 316.5
O3' C3' C2' H2' 291.0 195.4
C2' C3' O3' C4' 250.3 249.3
C2' C3' O3' H3' 125.0 125.1
O3' C3' C4' H4' 324.9 32.5
C4' C3' O3' H3' 234.7 235.8
H3' C3' C2' O6' 165.7 78.0
H3' C3' C2' H2' 48.7 316.9
C2' C3' H3' C4' 114.5 117.0
C2' C3' H3' O3' 237.0 237.2
H3' C3' C4' H4' 207.2 272.4
C4' C3' H3' O3' 122.5 120.1
H3' C3' O3' HO3' 55.0 139.4
HO3' O3' C3' H3' 55.0 139.4
C7' O6' C2' H2' 301.7 62.0
C8' C7' O6' H7'1 125.3 119.9
C8' C7' O6' H7'2 234.7 238.6
O6' C7' C8' O8' 181.2 0.6
O6' C7' C8' N9' 359.4 180.6
H7'1 C7' O6' H7'2 109.5 118.7
O6' C7' C8' H7'1 234.7 240.6
O6' C7' C8' H7'2 125.3 120.9
H7'1 C7' C8' H7'2 250.6 240.3
O8' C8' C7' N9' 181.7 180.0
C7' C8' N9' C10 178.6 180.0
C7' C8' N9' H9' 358.6 0.1
O6' C7' H7'1 C8' 122.1 120.7
O6' C7' H7'1 H7'2 241.0 241.1
C8' C7' H7'1 H7'2 118.9 120.4
H7'1 C7' C8' O8' 306.4 120.0
H7'1 C7' C8' N9' 124.7 300.0
O6' C7' H7'2 C8' 237.8 238.3
O6' C7' H7'2 H7'1 118.9 118.4
C8' C7' H7'2 H7'1 241.1 240.1
H7'2 C7' C8' O8' 55.9 239.7
H7'2 C7' C8' N9' 234.1 59.7
O8' C8' C7' H7'1 306.4 120.0
O8' C8' C7' H7'2 55.9 239.7
C7' C8' O8' N9' 178.1 180.0
O8' C8' N9' C10 356.9 360.0
O8' C8' N9' H9' 176.9 180.1
N9' C8' C7' H7'1 124.7 300.0
N9' C8' C7' H7'2 234.1 59.7
C7' C8' N9' O8' 181.7 180.0
C10 N9' C8' H9' 180.0 179.9
C8' N9' C10 H101 54.7 150.3
C8' N9' C10 H102 180.0 30.2
C8' N9' C10 H103 305.3 270.3
C8' N9' C10 H9' 180.0 180.1
H101 C10 N9' H102 234.8 120.1
H101 C10 N9' H103 109.5 240.0
H102 C10 N9' H103 234.7 120.0
C8' N9' H9' C10 180.0 179.9
H9' N9' C10 H101 234.8 330.2
H9' N9' C10 H102 0.0 210.1
H9' N9' C10 H103 125.3 90.2
H101 C10 N9' H9' 234.8 330.2
N9' C10 H101 H102 129.0 239.1
N9' C10 H101 H103 244.5 120.8
H102 C10 H101 H103 115.5 241.7
H102 C10 N9' H9' 0.0 210.1
N9' C10 H102 H101 234.7 120.8
N9' C10 H102 H103 125.3 239.1
H101 C10 H102 H103 250.6 118.3
H103 C10 N9' H9' 125.3 90.2
N9' C10 H103 H101 115.5 239.3
N9' C10 H103 H102 231.0 120.9
H101 C10 H103 H102 115.5 241.6