PDB Chemical Component 2NT

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 2NT

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP3 1.509 1.617
P OP2 1.453 1.618
P O5' 1.590 1.619
P OP1   1.501
OP3 HOP3 0.950 0.980
OP2 HOP2 0.950 0.980
O5' C5' 1.426 1.416
C5' C4' 1.506 1.523
C5' H5' 1.115 1.092
C5' H5'' 1.116 1.091
C4' O4' 1.453 1.444
C4' C3' 1.516 1.523
C4' H4' 1.115 1.095
O4' C1' 1.419 1.437
C1' N1 1.487 1.435
C1' C2' 1.533 1.519
C1' H1' 1.115 1.094
N1 C6 1.384 1.390
N1 C2 1.368 1.413
C6 C5 1.346 1.339
C6 H6 1.103 1.086
C2 O2 1.217 1.232
C2 N3 1.368 1.400
N3 C4 1.370 1.386
N3 HN3 1.020 1.017
C4 O4 1.225 1.228
C4 C5 1.448 1.487
C5 C5M 1.500 1.495
C5M H71 1.116 1.089
C5M H72 1.115 1.089
C5M H73 1.115 1.090
C2' O2' 1.439 1.413
C2' C3' 1.522 1.514
C2' H2' 1.115 1.097
O2' CB' 1.418 1.424
CB' CC' 1.517 1.516
CB' HB'1 1.115 1.095
CB' HB'2 1.115 1.094
CC' OD' 1.424 1.422
CC' HC'1 1.114 1.094
CC' HC'2 1.115 1.095
OD' NE' 1.345 1.456
NE' CF' 1.281 1.457
NE' HE' 1.020 1.019
CF' OG' 1.422 1.422
CF' HF'1 1.115 1.095
CF' HF'2 1.115 1.094
OG' HG' 0.950 0.972
C3' O3' 1.419 1.427
C3' H3' 1.115 1.093
O3' HO3' 0.950 0.968

Bond Angles for 2NT

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP3 P OP2 118.1 103.3
OP3 P O5' 108.4 103.8
OP3 P OP1   115.3
P OP3 HOP3 118.1 119.0
OP2 P O5' 111.0 102.9
OP2 P OP1   114.9
P OP2 HOP2 118.1 119.0
O5' P OP1   115.0
P O5' C5' 120.7 118.5
O5' C5' C4' 110.0 108.6
O5' C5' H5' 112.0 109.2
O5' C5' H5'' 112.0 109.3
C4' C5' H5' 112.0 110.1
C4' C5' H5'' 112.0 110.1
C5' C4' O4' 108.7 108.2
C5' C4' C3' 116.1 113.3
C5' C4' H4' 103.8 109.3
H5' C5' H5'' 98.4 109.6
O4' C4' C3' 104.0 105.9
O4' C4' H4' 116.0 107.7
C4' O4' C1' 109.3 109.2
C3' C4' H4' 108.6 112.2
C4' C3' C2' 102.4 102.1
C4' C3' O3' 113.5 107.9
C4' C3' H3' 113.3 114.5
O4' C1' N1 108.6 109.0
O4' C1' C2' 107.7 106.5
O4' C1' H1' 111.9 108.9
N1 C1' C2' 111.6 112.5
N1 C1' H1' 108.0 107.3
C1' N1 C6 123.2 118.5
C1' N1 C2 115.7 121.3
C2' C1' H1' 109.0 112.6
C1' C2' O2' 105.7 112.6
C1' C2' C3' 100.3 102.0
C1' C2' H2' 116.5 111.1
C6 N1 C2 121.2 120.2
N1 C6 C5 123.1 124.5
N1 C6 H6 119.9 114.7
N1 C2 O2 122.5 123.8
N1 C2 N3 115.0 115.1
C5 C6 H6 117.0 120.7
C6 C5 C4 117.9 118.4
C6 C5 C5M 123.4 123.6
O2 C2 N3 122.5 121.1
C2 N3 C4 127.4 127.0
C2 N3 HN3 116.2 116.4
C4 N3 HN3 116.4 116.6
N3 C4 O4 119.8 123.6
N3 C4 C5 115.3 114.8
O4 C4 C5 124.9 121.6
C4 C5 C5M 118.7 118.0
C5 C5M H71 107.2 109.7
C5 C5M H72 123.4 109.8
C5 C5M H73 107.3 109.7
H71 C5M H72 107.3 109.4
H71 C5M H73 102.5 109.4
H72 C5M H73 107.3 108.9
O2' C2' C3' 106.6 112.3
O2' C2' H2' 111.1 108.6
C2' O2' CB' 118.6 111.9
C3' C2' H2' 115.7 110.1
C2' C3' O3' 114.2 110.3
C2' C3' H3' 112.6 114.0
O2' CB' CC' 105.8 109.0
O2' CB' HB'1 113.6 108.1
O2' CB' HB'2 113.6 108.2
CC' CB' HB'1 113.6 111.2
CC' CB' HB'2 113.6 110.5
CB' CC' OD' 105.8 109.0
CB' CC' HC'1 113.6 111.1
CB' CC' HC'2 113.6 110.5
HB'1 CB' HB'2 96.9 109.7
OD' CC' HC'1 113.6 108.2
OD' CC' HC'2 113.6 108.3
CC' OD' NE' 110.9 107.5
HC'1 CC' HC'2 96.9 109.7
OD' NE' CF' 111.7 105.3
OD' NE' HE' 111.4 101.1
CF' NE' HE' 111.3 109.4
NE' CF' OG' 112.4 113.0
NE' CF' HF'1 111.1 110.9
NE' CF' HF'2 111.1 109.1
OG' CF' HF'1 111.1 108.7
OG' CF' HF'2 111.1 107.5
CF' OG' HG' 112.4 106.7
HF'1 CF' HF'2 99.2 107.4
O3' C3' H3' 101.3 107.8
C3' O3' HO3' 113.5 106.5

Torsion Angles for 2NT

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP3 O5' 232.7 107.1
OP2 P OP3 OP1   233.8
OP3 P OP2 HOP2 180.0 78.5
O5' P OP3 OP1   126.6
OP3 P O5' C5' 49.3 53.2
OP3 P OP2 O5' 126.0 252.3
OP3 P OP2 OP1   126.5
OP2 P OP3 HOP3 180.0 282.5
O5' P OP2 OP1   234.2
OP2 P O5' C5' 180.5 305.8
OP3 P O5' OP2 228.7 107.4
OP3 P O5' OP1   233.1
O5' P OP3 HOP3 307.3 175.4
OP2 P O5' OP1   125.8
O5' P OP2 HOP2 54.0 186.2
P O5' C5' C4' 177.5 180.0
P O5' C5' H5' 52.3 300.1
P O5' C5' H5'' 302.8 59.9
OP3 P OP1 OP2   240.0
OP3 P OP1 O5'   120.7
OP1 P OP3 HOP3   48.7
OP2 P OP1 O5'   240.7
OP1 P OP2 HOP2   312.0
OP1 P O5' C5'   180.1
HOP3 OP3 P OP2 180.0 282.5
HOP3 OP3 P O5' 307.3 175.4
HOP3 OP3 P OP1   48.7
HOP2 OP2 P O5' 54.0 186.2
HOP2 OP2 P OP1   312.0
C5' O5' P OP1   180.1
C4' C5' O5' H5' 125.3 239.9
C4' C5' O5' H5'' 234.7 120.1
O5' C5' C4' O4' 289.1 62.4
O5' C5' C4' C3' 45.8 179.5
O5' C5' C4' H4' 165.0 305.4
H5' C5' O5' H5'' 109.5 240.2
O5' C5' C4' H5' 234.7 119.5
O5' C5' C4' H5'' 125.3 240.4
H5' C5' C4' H5'' 250.5 120.9
O4' C4' C5' C3' 243.2 242.9
O4' C4' C5' H4' 124.1 117.0
C5' C4' O4' C1' 145.0 109.0
C3' C4' C5' H4' 240.9 234.1
C5' C4' C3' C2' 203.1 273.1
C5' C4' C3' O3' 79.4 156.8
C5' C4' C3' H3' 324.6 36.8
O5' C5' H5' C4' 124.2 240.8
O5' C5' H5' H5'' 242.1 119.6
C4' C5' H5' H5'' 117.9 238.8
H5' C5' C4' O4' 54.3 302.9
H5' C5' C4' C3' 171.1 60.0
H5' C5' C4' H4' 290.2 185.9
O5' C5' H5'' C4' 235.8 119.2
O5' C5' H5'' H5' 117.9 240.4
C4' C5' H5'' H5' 242.1 121.2
H5'' C5' C4' O4' 163.8 182.0
H5'' C5' C4' C3' 280.6 299.1
H5'' C5' C4' H4' 39.7 65.0
O4' C4' C5' H5' 54.3 302.9
O4' C4' C5' H5'' 163.8 182.0
C5' C4' O4' C3' 124.3 121.7
C5' C4' O4' H4' 243.5 241.9
C3' C4' O4' H4' 119.2 120.2
O4' C4' C3' C2' 322.5 31.5
O4' C4' C3' O3' 198.8 275.3
O4' C4' C3' H3' 84.0 155.2
C4' O4' C1' N1 243.5 227.1
C4' O4' C1' C2' 4.5 348.7
C4' O4' C1' H1' 124.3 110.3
C3' C4' C5' H5' 171.1 60.0
C3' C4' C5' H5'' 280.6 299.1
C5' C4' C3' O4' 240.6 241.6
C5' C4' C3' H4' 116.5 124.4
O4' C4' C3' H4' 235.9 242.8
C3' C4' O4' C1' 20.7 347.2
C1' C2' C3' C4' 38.8 322.9
O2' C2' C3' C4' 288.9 202.0
C4' C3' C2' H2' 164.9 80.9
C2' C3' C4' O3' 123.7 116.3
C2' C3' C4' H3' 238.5 236.3
O3' C3' C4' H3' 114.8 120.1
C4' C3' O3' HO3' 180.0 276.6
H4' C4' C5' H5' 290.2 185.9
H4' C4' C5' H5'' 39.7 65.0
C5' C4' H4' O4' 119.2 117.3
C5' C4' H4' C3' 235.8 233.5
O4' C4' H4' C3' 116.6 116.2
H4' C4' O4' C1' 261.5 227.0
H4' C4' C3' C2' 86.6 148.7
H4' C4' C3' O3' 322.9 32.5
H4' C4' C3' H3' 208.1 272.4
C1' O4' C4' C3' 20.7 347.2
C1' O4' C4' H4' 261.5 227.0
N1 C1' O4' C2' 239.0 238.4
N1 C1' O4' H1' 119.2 116.8
O4' C1' N1 C6 26.2 32.3
O4' C1' N1 C2 205.1 212.2
C2' C1' O4' H1' 240.2 238.4
O4' C1' C2' O2' 83.2 151.3
O4' C1' C2' C3' 332.6 30.7
O4' C1' C2' H2' 207.0 273.4
O4' C1' N1 C2' 118.6 117.9
O4' C1' N1 H1' 238.4 242.3
C2' C1' N1 H1' 119.8 124.4
N1 C1' C2' O2' 202.4 270.6
N1 C1' C2' C3' 91.8 150.0
N1 C1' C2' H2' 326.2 32.7
C6 N1 C1' C2 181.1 180.1
C1' N1 C6 C5 176.5 180.0
C1' N1 C6 H6 356.5 360.0
C1' N1 C2 O2 0.8 0.1
C1' N1 C2 N3 181.5 180.0
C4' C3' C2' C1' 38.8 322.9
O4' C1' C2' N1 240.9 240.7
O4' C1' C2' H1' 121.6 119.3
N1 C1' C2' H1' 240.8 238.6
C2' C1' N1 C6 267.6 274.4
C2' C1' N1 C2 86.5 94.3
O2' C2' C1' C3' 110.6 120.6
O2' C2' C1' H2' 236.2 237.9
C1' C2' O2' CB' 77.9 185.5
C3' C2' C1' H2' 125.6 117.3
C1' C2' C3' O3' 162.0 77.4
C1' C2' C3' H3' 276.7 198.9
O4' C1' H1' N1 119.6 117.8
O4' C1' H1' C2' 241.0 242.1
N1 C1' H1' C2' 121.4 124.3
H1' C1' N1 C6 147.8 150.0
H1' C1' N1 C2 326.7 329.9
H1' C1' C2' O2' 321.6 32.1
H1' C1' C2' C3' 211.0 271.5
H1' C1' C2' H2' 85.4 154.2
C6 N1 C1' C2' 267.6 274.4
C6 N1 C1' H1' 147.8 150.0
C1' N1 C6 C2 178.8 179.9
C6 N1 C2 O2 179.7 180.0
C6 N1 C2 N3 0.4 360.0
C5 C6 N1 H6 180.0 180.0
N1 C6 C5 C4 1.8 0.0
N1 C6 C5 C5M 182.5 180.0
C2 N1 C1' C2' 86.5 94.3
C2 N1 C1' H1' 326.7 329.9
C1' N1 C2 C6 181.1 180.1
C2 N1 C6 C5 357.7 0.0
C2 N1 C6 H6 177.7 180.0
O2 C2 N1 N3 179.3 180.1
N1 C2 N3 C4 2.1 360.0
N1 C2 N3 HN3 182.1 180.1
C5 C6 N1 C2 357.7 0.0
N1 C6 C5 H6 180.0 180.0
N3 C4 C5 C6 0.5 360.0
O4 C4 C5 C6 181.0 179.9
C4 C5 C6 C5M 179.2 180.0
C6 C5 C5M H71 54.7 64.2
C6 C5 C5M H72 180.0 304.0
C6 C5 C5M H73 305.2 184.4
H6 C6 N1 C2 177.7 180.0
N1 C6 H6 C5 180.0 180.0
H6 C6 C5 C4 181.8 180.0
H6 C6 C5 C5M 2.6 360.0
N1 C2 O2 N3 180.7 179.9
O2 C2 N3 C4 182.8 179.9
O2 C2 N3 HN3 2.7 0.0
N1 C2 N3 O2 179.3 180.1
C4 N3 C2 HN3 180.0 179.9
C2 N3 C4 O4 176.9 180.1
C2 N3 C4 C5 357.5 0.1
C6 C5 C4 N3 0.5 360.0
C2 N3 C4 HN3 180.0 180.1
O4 C4 N3 C5 179.5 180.0
N3 C4 C5 C5M 179.8 180.0
C2 N3 HN3 C4 180.0 179.9
HN3 N3 C4 O4 357.0 0.0
HN3 N3 C4 C5 177.5 180.0
C6 C5 C4 O4 181.0 179.9
O4 C4 N3 HN3 357.0 0.0
N3 C4 O4 C5 180.6 180.0
O4 C4 C5 C5M 0.3 359.9
C4 C5 C6 H6 181.8 180.0
C6 C5 C4 C5M 180.7 180.0
C5 C4 N3 HN3 177.5 180.0
N3 C4 C5 O4 179.4 180.0
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 2.6 360.0
C6 C5 C5M C4 179.2 180.0
H71 C5M C5 H72 234.8 120.2
H71 C5M C5 H73 109.5 239.8
H72 C5M C5 H73 234.7 119.6
C5 C5M H71 H72 134.4 239.5
C5 C5M H71 H73 247.2 120.4
H72 C5M H71 H73 112.8 240.8
C5 C5M H72 H71 234.8 120.4
C5 C5M H72 H73 125.3 239.9
H71 C5M H72 H73 250.5 119.5
C5 C5M H73 H71 112.8 239.6
C5 C5M H73 H72 225.5 120.2
H71 C5M H73 H72 112.8 240.5
C4' C3' C2' O2' 288.9 202.0
O2' C2' C1' H1' 321.6 32.1
C1' C2' O2' C3' 254.0 245.5
C1' C2' O2' H2' 127.2 123.5
C3' C2' O2' H2' 233.2 238.0
O2' C2' C3' O3' 52.1 316.5
O2' C2' C3' H3' 166.9 78.0
C2' O2' CB' CC' 179.8 179.0
C2' O2' CB' HB'1 54.6 300.0
C2' O2' CB' HB'2 305.1 58.8
C2' C3' C4' H4' 86.6 148.7
C4' C3' C2' O3' 236.8 245.5
C4' C3' C2' H3' 122.0 124.0
C3' C2' C1' H1' 211.0 271.5
C1' C2' C3' O2' 109.9 120.8
C1' C2' C3' H2' 233.9 242.0
O2' C2' C3' H2' 124.0 121.1
C3' C2' O2' CB' 183.9 300.0
O3' C3' C2' H3' 245.2 238.5
C2' C3' O3' HO3' 63.1 165.9
H2' C2' C1' H1' 85.4 154.2
C1' C2' H2' O2' 239.0 235.6
C1' C2' H2' C3' 117.4 112.3
O2' C2' H2' C3' 238.4 236.7
H2' C2' O2' CB' 310.7 62.0
H2' C2' C3' O3' 288.1 195.4
H2' C2' C3' H3' 42.9 316.9
CB' O2' C2' C3' 183.9 300.0
CB' O2' C2' H2' 310.7 62.0
CC' CB' O2' HB'1 125.2 239.0
CC' CB' O2' HB'2 234.7 120.2
O2' CB' CC' OD' 289.1 299.2
O2' CB' CC' HC'1 163.9 180.0
O2' CB' CC' HC'2 54.4 58.0
HB'1 CB' O2' HB'2 109.5 241.3
O2' CB' CC' HB'1 234.7 119.1
O2' CB' CC' HB'2 125.3 241.2
HB'1 CB' CC' HB'2 250.6 122.0
OD' CC' CB' HC'1 125.3 119.2
OD' CC' CB' HC'2 234.7 241.1
CB' CC' OD' NE' 190.5 180.0
HC'1 CC' CB' HC'2 109.5 121.9
O2' CB' HB'1 CC' 121.0 240.3
O2' CB' HB'1 HB'2 240.5 117.8
CC' CB' HB'1 HB'2 119.5 237.5
HB'1 CB' CC' OD' 54.4 180.0
HB'1 CB' CC' HC'1 289.1 60.8
HB'1 CB' CC' HC'2 179.7 298.9
O2' CB' HB'2 CC' 239.0 119.3
O2' CB' HB'2 HB'1 119.5 242.2
CC' CB' HB'2 HB'1 240.5 122.9
HB'2 CB' CC' OD' 163.8 58.0
HB'2 CB' CC' HC'1 38.6 298.8
HB'2 CB' CC' HC'2 289.1 176.9
OD' CC' CB' HB'1 54.4 180.0
OD' CC' CB' HB'2 163.8 58.0
CB' CC' OD' HC'1 234.8 239.0
CB' CC' OD' HC'2 125.3 120.2
HC'1 CC' OD' HC'2 250.5 241.2
CC' OD' NE' CF' 195.3 186.1
CC' OD' NE' HE' 70.0 300.0
HC'1 CC' CB' HB'1 289.1 60.8
HC'1 CC' CB' HB'2 38.6 298.8
CB' CC' HC'1 OD' 121.0 119.7
CB' CC' HC'1 HC'2 240.5 237.6
OD' CC' HC'1 HC'2 119.5 117.9
HC'1 CC' OD' NE' 315.7 301.0
HC'2 CC' CB' HB'1 179.7 298.9
HC'2 CC' CB' HB'2 289.1 176.9
CB' CC' HC'2 OD' 239.0 240.7
CB' CC' HC'2 HC'1 119.5 122.8
OD' CC' HC'2 HC'1 240.5 242.2
HC'2 CC' OD' NE' 65.2 59.8
NE' OD' CC' HC'1 315.7 301.0
NE' OD' CC' HC'2 65.2 59.8
CF' NE' OD' HE' 125.2 246.1
OD' NE' CF' OG' 306.1 287.9
OD' NE' CF' HF'1 180.8 50.3
OD' NE' CF' HF'2 71.4 168.4
OD' NE' CF' HE' 234.8 107.9
OG' CF' NE' HF'1 125.3 237.6
OG' CF' NE' HF'2 234.7 119.5
NE' CF' OG' HG' 180.0 51.6
HF'1 CF' NE' HF'2 109.4 241.9
OD' NE' HE' CF' 125.4 249.3
HE' NE' CF' OG' 71.3 180.0
HE' NE' CF' HF'1 306.0 302.4
HE' NE' CF' HF'2 196.6 60.5
OG' CF' NE' HE' 71.3 180.0
NE' CF' OG' HF'1 234.7 123.6
NE' CF' OG' HF'2 125.3 239.5
HF'1 CF' OG' HF'2 250.5 116.0
HF'1 CF' NE' HE' 306.0 302.4
NE' CF' HF'1 OG' 126.0 235.2
NE' CF' HF'1 HF'2 243.0 119.1
OG' CF' HF'1 HF'2 117.0 244.0
HF'1 CF' OG' HG' 305.3 288.0
HF'2 CF' NE' HE' 196.6 60.5
NE' CF' HF'2 OG' 234.0 122.9
NE' CF' HF'2 HF'1 117.0 239.7
OG' CF' HF'2 HF'1 243.0 116.8
HF'2 CF' OG' HG' 54.7 172.1
HG' OG' CF' HF'1 305.3 288.0
HG' OG' CF' HF'2 54.7 172.1
O3' C3' C4' H4' 322.9 32.5
C4' C3' O3' C2' 116.9 110.7
C4' C3' O3' H3' 238.2 235.8
O3' C3' C2' H2' 288.1 195.4
C2' C3' O3' H3' 121.3 125.1
H3' C3' C4' H4' 208.1 272.4
C4' C3' H3' C2' 244.4 243.0
C4' C3' H3' O3' 121.9 120.1
H3' C3' C2' H2' 42.9 316.9
C2' C3' H3' O3' 237.6 237.2
H3' C3' O3' HO3' 301.8 40.8
HO3' O3' C3' H3' 301.8 40.8