PDB Chemical Component NMT

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 NMT

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP3 1.462 1.617
P OP2 1.484 1.618
P O5' 1.609 1.619
P OP1   1.501
OP3 HOP3 0.950 0.980
OP2 HOP2 0.950 0.980
O5' C5' 1.420 1.416
N1 C6 1.365 1.390
N1 C2 1.368 1.413
N1 C1' 1.531 1.435
C6 C5 1.327 1.339
C6 H6 1.103 1.086
C2 O2 1.233 1.232
C2 N3 1.383 1.400
N3 C4 1.394 1.386
N3 HN3 1.020 1.017
C4 O4 1.213 1.229
C4 C5 1.449 1.487
C5 C5M 1.506 1.495
C5M H71 1.115 1.089
C5M H72 1.115 1.089
C5M H73 1.115 1.090
C2' C1' 1.452 1.519
C2' C3' 1.511 1.514
C2' O6' 1.386 1.413
C2' H2' 1.115 1.097
C5' C4' 1.465 1.523
C5' H5' 1.115 1.092
C5' H5'' 1.115 1.091
C4' O4' 1.466 1.444
C4' C3' 1.516 1.523
C4' H4' 1.115 1.095
O4' C1' 1.443 1.437
C1' H1' 1.115 1.094
C3' O3' 1.415 1.427
C3' H3' 1.115 1.093
O3' HO3' 0.950 0.969
O6' C7' 1.333 1.437
C7' N8' 1.378 1.465
C7' O7' 1.203 1.427
C7' H7' 1.115 1.097
N8' C9' 1.467 1.456
N8' H8' 1.020 1.019
C9' H9'1 1.115 1.093
C9' H9'2 1.115 1.094
C9' H9'3 1.115 1.093
O7' H1 0.950 0.972

Bond Angles for NMT

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP3 P OP2 121.8 103.3
OP3 P O5' 112.2 103.8
OP3 P OP1   115.3
P OP3 HOP3 121.7 119.0
OP2 P O5' 103.2 102.9
OP2 P OP1   114.9
P OP2 HOP2 121.8 119.0
O5' P OP1   115.0
P O5' C5' 118.5 118.5
O5' C5' C4' 110.4 108.6
O5' C5' H5' 111.9 109.2
O5' C5' H5'' 111.8 109.3
C6 N1 C2 120.7 120.2
C6 N1 C1' 125.0 118.5
N1 C6 C5 125.7 124.5
N1 C6 H6 118.7 114.7
C2 N1 C1' 114.4 121.3
N1 C2 O2 123.0 123.8
N1 C2 N3 114.4 115.1
N1 C1' C2' 111.7 112.5
N1 C1' O4' 106.5 109.0
N1 C1' H1' 110.5 107.3
C5 C6 H6 115.5 120.7
C6 C5 C4 117.5 118.4
C6 C5 C5M 125.7 123.6
O2 C2 N3 122.6 121.1
C2 N3 C4 127.4 127.0
C2 N3 HN3 115.8 116.4
C4 N3 HN3 116.8 116.6
N3 C4 O4 118.2 123.6
N3 C4 C5 114.3 114.8
O4 C4 C5 127.5 121.6
C4 C5 C5M 116.8 118.0
C5 C5M H71 106.5 109.7
C5 C5M H72 125.7 109.8
C5 C5M H73 106.5 109.7
H71 C5M H72 106.5 109.4
H71 C5M H73 103.1 109.4
H72 C5M H73 106.4 108.9
C1' C2' C3' 99.0 102.0
C1' C2' O6' 111.6 112.6
C1' C2' H2' 113.5 111.1
C2' C1' O4' 111.0 106.5
C2' C1' H1' 106.0 112.6
C3' C2' O6' 105.6 112.3
C3' C2' H2' 118.9 110.1
C2' C3' C4' 102.5 102.1
C2' C3' O3' 115.0 110.3
C2' C3' H3' 110.4 114.0
O6' C2' H2' 107.8 108.6
C2' O6' C7' 122.2 113.0
C4' C5' H5' 111.8 110.1
C4' C5' H5'' 111.9 110.1
C5' C4' O4' 109.2 108.2
C5' C4' C3' 116.1 113.3
C5' C4' H4' 103.1 109.3
H5' C5' H5'' 98.5 109.6
O4' C4' C3' 102.2 105.9
O4' C4' H4' 116.8 107.7
C4' O4' C1' 105.7 109.2
C3' C4' H4' 110.0 112.2
C4' C3' O3' 109.1 107.9
C4' C3' H3' 116.2 114.5
O4' C1' H1' 111.2 108.9
O3' C3' H3' 104.0 107.8
C3' O3' HO3' 115.0 106.4
O6' C7' N8' 118.5 110.2
O6' C7' O7' 121.8 110.5
O6' C7' H7' 86.4 107.7
N8' C7' O7' 119.5 112.1
N8' C7' H7' 114.9 108.6
C7' N8' C9' 117.2 112.3
C7' N8' H8' 109.4 109.2
O7' C7' H7' 73.3 107.7
C7' O7' H1 121.8 106.8
C9' N8' H8' 109.4 109.7
N8' C9' H9'1 109.4 110.1
N8' C9' H9'2 117.2 110.2
N8' C9' H9'3 109.4 110.2
H9'1 C9' H9'2 109.4 108.8
H9'1 C9' H9'3 100.8 108.8
H9'2 C9' H9'3 109.4 108.8

Torsion Angles for NMT

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP3 O5' 237.2 107.1
OP2 P OP3 OP1   233.8
OP3 P OP2 HOP2 180.0 78.5
O5' P OP3 OP1   126.6
OP3 P O5' C5' 41.4 53.2
OP3 P OP2 O5' 127.0 252.3
OP3 P OP2 OP1   126.5
OP2 P OP3 HOP3 180.0 282.5
O5' P OP2 OP1   234.2
OP2 P O5' C5' 174.2 305.8
OP3 P O5' OP2 227.2 107.4
OP3 P O5' OP1   233.1
O5' P OP3 HOP3 302.8 175.4
OP2 P O5' OP1   125.8
O5' P OP2 HOP2 53.0 186.2
P O5' C5' C4' 173.3 180.0
P O5' C5' H5' 48.0 300.1
P O5' C5' H5'' 298.5 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' 302.8 175.4
HOP3 OP3 P OP1   48.7
HOP2 OP2 P O5' 53.0 186.2
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' 295.9 62.4
O5' C5' C4' C3' 50.7 179.5
O5' C5' C4' H4' 171.0 305.4
H5' C5' O5' H5'' 109.5 240.2
C2 N1 C6 C1' 180.3 180.1
C6 N1 C2 O2 179.9 180.0
C6 N1 C2 N3 359.4 360.0
C6 N1 C1' C2' 264.9 274.4
C6 N1 C1' O4' 26.3 32.3
C6 N1 C1' H1' 147.2 150.0
C5 C6 N1 H6 180.0 180.0
N1 C6 C5 C4 359.7 0.0
N1 C6 C5 C5M 179.7 180.0
C6 N1 C2 C1' 179.8 179.9
C2 N1 C6 C5 0.6 0.0
C2 N1 C6 H6 180.6 180.0
C2 N1 C1' C2' 84.7 94.3
C2 N1 C1' O4' 206.1 212.2
C2 N1 C1' H1' 327.0 329.9
O2 C2 N1 N3 180.5 180.1
N1 C2 N3 C4 0.4 360.0
N1 C2 N3 HN3 180.4 180.1
C6 N1 C1' C2 180.2 180.1
C1' N1 C6 C5 180.3 180.0
C1' N1 C6 H6 0.3 360.0
C1' N1 C2 O2 0.1 0.1
C1' N1 C2 N3 179.7 180.0
N1 C1' C2' C3' 89.8 150.0
N1 C1' C2' O6' 200.6 270.6
N1 C1' C2' H2' 322.7 32.7
C2' C1' N1 O4' 238.6 242.1
C2' C1' N1 H1' 117.7 124.4
C4' O4' C1' N1 242.0 227.1
O4' C1' N1 H1' 239.1 242.3
C5 C6 N1 C2 0.6 0.0
C5 C6 N1 C1' 180.3 180.0
N1 C6 C5 H6 180.0 180.0
N3 C4 C5 C6 0.1 360.0
O4 C4 C5 C6 180.5 180.0
C4 C5 C6 C5M 180.0 180.0
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 180.6 180.0
H6 C6 N1 C1' 0.3 360.0
N1 C6 H6 C5 180.0 180.0
H6 C6 C5 C4 179.7 180.0
H6 C6 C5 C5M 359.7 360.0
O2 C2 N1 C1' 0.1 0.1
N1 C2 O2 N3 179.5 179.9
O2 C2 N3 C4 179.9 179.9
O2 C2 N3 HN3 359.9 0.0
N3 C2 N1 C1' 179.7 180.0
N1 C2 N3 O2 180.5 180.1
C4 N3 C2 HN3 180.0 179.9
C2 N3 C4 O4 179.5 180.1
C2 N3 C4 C5 359.8 0.1
C6 C5 C4 N3 0.1 360.0
C2 N3 C4 HN3 180.0 180.1
O4 C4 N3 C5 179.6 180.0
N3 C4 C5 C5M 180.1 180.0
C2 N3 HN3 C4 180.0 179.9
HN3 N3 C4 O4 359.5 360.0
HN3 N3 C4 C5 179.9 180.0
C6 C5 C4 O4 180.5 180.0
O4 C4 N3 HN3 359.5 360.0
N3 C4 O4 C5 180.4 180.0
O4 C4 C5 C5M 0.5 360.0
C4 C5 C6 H6 179.7 180.0
C6 C5 C4 C5M 180.0 180.0
C5 C4 N3 HN3 179.9 180.0
N3 C4 C5 O4 179.6 180.0
C4 C5 C5M H71 234.7 244.2
C4 C5 C5M H72 360.0 124.0
C4 C5 C5M H73 125.2 4.4
C5M C5 C6 H6 359.7 360.0
C6 C5 C5M C4 180.0 180.0
H71 C5M C5 H72 234.7 120.2
H71 C5M C5 H73 109.5 239.8
H72 C5M C5 H73 234.8 119.6
C5 C5M H71 H72 136.3 239.5
C5 C5M H71 H73 248.1 120.4
H72 C5M H71 H73 111.8 240.8
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 111.9 239.6
C5 C5M H73 H72 223.7 120.2
H71 C5M H73 H72 111.9 240.5
N1 C1' C2' O4' 118.8 119.3
N1 C1' C2' H1' 239.6 238.6
C3' C2' C1' O6' 249.2 239.4
C3' C2' C1' H2' 127.1 117.3
C1' C2' C3' C4' 42.1 322.9
C1' C2' C3' O3' 160.4 77.4
C1' C2' C3' H3' 277.7 198.9
O6' C2' C1' H2' 237.9 237.9
C1' C2' O6' C7' 70.6 153.5
C4' O4' C1' C2' 3.8 348.7
O4' C1' C2' H1' 120.9 119.3
C1' C2' C3' O6' 115.6 120.8
C1' C2' C3' H2' 236.7 242.0
C3' C2' C1' O4' 331.1 30.7
C3' C2' C1' H1' 210.2 271.5
O6' C2' C3' H2' 121.1 121.1
C3' C2' O6' C7' 177.2 268.0
C5' C4' C3' C2' 200.0 273.1
O4' C4' C3' C2' 318.8 31.5
C2' C3' C4' H4' 83.5 148.7
C4' C3' C2' O3' 241.8 245.5
C4' C3' C2' H3' 124.5 124.0
O3' C3' C2' H3' 242.7 238.5
C2' C3' O3' HO3' 180.0 264.4
C1' C2' O6' C3' 253.4 245.5
C1' C2' O6' H2' 125.3 123.5
O6' C2' C1' O4' 81.9 151.3
O6' C2' C1' H1' 321.0 32.1
C3' C2' O6' H2' 231.9 238.0
O6' C2' C3' C4' 286.5 202.0
O6' C2' C3' O3' 44.8 316.5
O6' C2' C3' H3' 162.1 78.0
C2' O6' C7' N8' 177.4 181.7
C2' O6' C7' O7' 353.2 57.4
C2' O6' C7' H7' 61.0 300.0
C1' C2' H2' C3' 115.8 112.3
C1' C2' H2' O6' 235.8 235.6
H2' C2' C1' O4' 203.9 273.4
H2' C2' C1' H1' 83.1 154.2
C3' C2' H2' O6' 120.0 123.3
H2' C2' C3' C4' 165.4 80.9
H2' C2' C3' O3' 283.7 195.4
H2' C2' C3' H3' 41.0 316.9
H2' C2' O6' C7' 305.3 30.0
O5' C5' C4' H5' 234.7 119.5
O5' C5' C4' H5'' 125.3 240.4
C2' C3' C4' C5' 200.0 273.1
H5' C5' C4' H5'' 250.5 120.9
O4' C4' C5' C3' 245.1 242.9
O4' C4' C5' H4' 124.8 117.0
C5' C4' O4' C1' 146.7 109.0
C3' C4' C5' H4' 239.7 234.1
C5' C4' C3' O3' 77.6 156.8
C5' C4' C3' H3' 320.4 36.8
O5' C5' H5' C4' 124.5 240.8
O5' C5' H5' H5'' 242.3 119.6
C4' C5' H5' H5'' 117.8 238.8
H5' C5' C4' O4' 61.1 302.9
H5' C5' C4' C3' 176.0 60.0
H5' C5' C4' H4' 296.3 185.9
O5' C5' H5'' C4' 235.5 119.2
O5' C5' H5'' H5' 117.8 240.4
C4' C5' H5'' H5' 242.3 121.2
H5'' C5' C4' O4' 170.6 182.0
H5'' C5' C4' C3' 285.5 299.1
H5'' C5' C4' H4' 45.8 65.0
N1 C1' O4' C4' 242.0 227.1
C2' C1' O4' C4' 3.8 348.7
C2' C3' C4' O4' 318.8 31.5
O4' C4' C5' H5' 61.1 302.9
O4' C4' C5' H5'' 170.6 182.0
C5' C4' O4' C3' 123.5 121.7
C5' C4' O4' H4' 243.6 241.9
C3' C4' O4' H4' 120.1 120.2
O4' C4' C3' O3' 196.4 275.3
O4' C4' C3' H3' 79.2 155.2
C4' O4' C1' H1' 121.6 110.3
C4' C3' C2' O6' 286.5 202.0
C4' C3' C2' H2' 165.4 80.9
C2' C3' C4' O3' 122.4 116.3
C2' C3' C4' H3' 239.5 236.3
C3' C4' C5' H5' 176.0 60.0
C3' C4' C5' H5'' 285.5 299.1
C5' C4' C3' O4' 241.2 241.6
C5' C4' C3' H4' 116.5 124.4
O4' C4' C3' H4' 235.3 242.8
C3' C4' O4' C1' 23.2 347.2
O3' C3' C4' H3' 117.2 120.1
C4' C3' O3' HO3' 294.5 15.2
H4' C4' C5' H5' 296.3 185.9
H4' C4' C5' H5'' 45.8 65.0
C5' C4' H4' O4' 119.8 117.3
C5' C4' H4' C3' 235.6 233.5
O4' C4' H4' C3' 115.8 116.2
H4' C4' O4' C1' 263.1 227.0
H4' C4' C3' O3' 321.1 32.5
H4' C4' C3' H3' 203.9 272.4
N1 C1' O4' C2' 238.2 238.4
N1 C1' O4' H1' 120.4 116.8
O4' C1' C2' C3' 331.1 30.7
O4' C1' C2' O6' 81.9 151.3
O4' C1' C2' H2' 203.9 273.4
C2' C1' O4' H1' 242.3 238.4
C1' O4' C4' C3' 23.2 347.2
C1' O4' C4' H4' 263.1 227.0
N1 C1' H1' C2' 121.2 124.3
N1 C1' H1' O4' 241.9 242.2
H1' C1' C2' C3' 210.2 271.5
H1' C1' C2' O6' 321.0 32.1
H1' C1' C2' H2' 83.1 154.2
C2' C1' H1' O4' 120.7 117.9
O3' C3' C2' O6' 44.8 316.5
O3' C3' C2' H2' 283.7 195.4
C2' C3' O3' C4' 245.5 249.3
C2' C3' O3' H3' 120.8 125.1
O3' C3' C4' H4' 321.1 32.5
C4' C3' O3' H3' 235.3 235.8
H3' C3' C2' O6' 162.1 78.0
H3' C3' C2' H2' 41.0 316.9
C2' C3' H3' C4' 116.2 117.0
C2' C3' H3' O3' 236.1 237.2
H3' C3' C4' H4' 203.9 272.4
C4' C3' H3' O3' 119.9 120.1
H3' C3' O3' HO3' 59.1 139.4
HO3' O3' C3' H3' 59.1 139.4
C7' O6' C2' H2' 305.3 30.0
N8' C7' O6' O7' 184.2 124.4
N8' C7' O6' H7' 116.5 241.7
O6' C7' N8' C9' 175.1 57.8
O6' C7' N8' H8' 49.8 179.7
O7' C7' O6' H7' 292.2 117.4
O6' C7' O7' H1 180.0 90.2
O6' C7' N8' O7' 175.9 236.6
O6' C7' N8' H7' 260.1 117.8
O7' C7' N8' H7' 84.2 241.2
N8' C7' O7' H1 355.7 327.0
C9' N8' C7' H8' 125.3 238.1
C7' N8' C9' H9'1 54.8 273.9
C7' N8' C9' H9'2 180.0 153.9
C7' N8' C9' H9'3 305.2 33.8
O6' C7' O7' N8' 184.3 123.3
O6' C7' O7' H7' 74.7 242.6
N8' C7' O7' H7' 250.4 119.3
O7' C7' N8' C9' 359.3 181.2
O7' C7' N8' H8' 234.0 303.1
O6' C7' H7' N8' 119.9 240.7
O6' C7' H7' O7' 235.2 119.2
N8' C7' H7' O7' 115.4 238.5
H7' C7' N8' C9' 275.1 300.0
H7' C7' N8' H8' 149.8 62.0
H7' C7' O7' H1 105.3 207.6
C9' N8' C7' O7' 359.3 181.2
C9' N8' C7' H7' 275.1 300.0
C7' N8' C9' H8' 234.7 121.6
H9'1 C9' N8' H9'2 234.8 120.0
H9'1 C9' N8' H9'3 109.5 240.0
H9'2 C9' N8' H9'3 234.8 120.1
H8' N8' C7' O7' 234.0 303.1
H8' N8' C7' H7' 149.8 62.0
C7' N8' H8' C9' 129.7 236.5
H8' N8' C9' H9'1 180.0 152.2
H8' N8' C9' H9'2 305.3 32.3
H8' N8' C9' H9'3 70.5 272.2
H9'1 C9' N8' H8' 180.0 152.2
N8' C9' H9'1 H9'2 129.6 239.1
N8' C9' H9'1 H9'3 244.8 120.8
H9'2 C9' H9'1 H9'3 115.2 241.7
H9'2 C9' N8' H8' 305.3 32.3
N8' C9' H9'2 H9'1 234.7 120.8
N8' C9' H9'2 H9'3 125.2 239.1
H9'1 C9' H9'2 H9'3 250.5 118.3
H9'3 C9' N8' H8' 70.5 272.2
N8' C9' H9'3 H9'1 115.2 239.2
N8' C9' H9'3 H9'2 230.4 121.0
H9'1 C9' H9'3 H9'2 115.2 241.7
H1 O7' C7' H7' 105.3 207.6