PDB Chemical Component HN1

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 HN1

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
C C1 1.442 1.530
C C3 1.557 1.523
P OP1 1.487 1.479
P OP3 1.490 1.610
P O5' 1.604 1.610
C1 N1 1.521 1.467
N1 C6 1.451 1.357
N1 C2 1.401 1.378
C2 N3 1.338 1.388
N2 C2 1.312 1.296
C3 N2 1.462 1.450
C3 C7 1.563 1.530
N3 C4 1.372 1.381
C4 N9 1.363 1.345
C5 C4 1.381 1.402
C5 N7 1.406 1.341
C6 C5 1.458 1.466
O6 C6 1.237 1.217
C7 O10 1.458 1.430
N7 C8 1.314 1.306
C8 N9 1.371 1.370
C9 C7 1.555 1.530
C9 C10 1.551 1.530
N9 C1' 1.473 1.464
C1' C2' 1.528 1.541
C10 C11 1.549 1.530
O11 C1 1.421 1.429
C12 C11 1.543 1.530
C12 C13 1.538 1.530
C2' C3' 1.521 1.548
C3' O3' 1.427 1.430
C4' C3' 1.523 1.550
O4' C1' 1.412 1.437
O4' C4' 1.435 1.444
C5' C4' 1.506 1.530
C5' O5' 1.422 1.429
P OP2 1.720 1.611
C H 1.100 1.089
C HA 1.100 1.091
C1 H31 1.100 1.090
C3 H3 1.100 1.091
N3 HN3 1.000 0.970
C7 H7 1.100 1.090
C8 H8 1.080 1.080
C9 H9 1.100 1.091
C9 H9A 1.100 1.090
C1' H1' 1.100 1.090
C10 H10 1.100 1.090
C10 H10A 1.100 1.090
O10 HO10 0.950 0.966
C11 H11 1.100 1.089
C11 H11A 1.100 1.090
O11 H16 0.950 0.967
C12 H12 1.100 1.090
C12 H12A 1.100 1.090
C13 H13 1.100 1.090
C13 H13A 1.100 1.089
C13 H13B 1.100 1.090
OP3 HOP3 0.950 0.967
C2' H2' 1.100 1.090
C2' H2'A 1.100 1.091
C3' H3' 1.100 1.089
O3' HO3' 0.951 0.968
C4' H4' 1.100 1.090
C5' H5' 1.100 1.089
C5' H5'A 1.100 1.090
OP2 HOP2 0.950 0.967

Bond Angles for HN1

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C1 C C3 118.2 110.3
C C1 N1 118.9 108.3
C1 C H 106.6 109.4
C1 C HA 106.7 109.3
C C1 H31 104.5 109.7
C C3 N2 112.5 112.9
C C3 C7 113.2 108.8
C3 C H 106.6 109.3
C3 C HA 106.6 109.3
C C3 H3 104.1 108.7
OP1 P OP3 120.0 109.5
OP1 P O5' 108.7 109.5
OP1 P OP2 115.2 109.5
OP3 P O5' 108.2 109.5
OP3 P OP2 97.9 109.4
P OP3 HOP3 109.5 114.0
P O5' C5' 118.2 123.0
O5' P OP2 105.8 109.5
C1 N1 C6 120.7 119.4
C1 N1 C2 119.2 118.8
N1 C1 H31 102.0 109.7
C2 N1 C6 120.2 121.8
N1 C6 C5 114.7 116.0
N1 C2 N3 125.4 120.9
N2 C2 N3 113.2 118.5
C2 N3 C4 114.1 116.5
C2 N3 HN3 122.9 121.8
C3 C7 O10 109.1 109.5
C7 C3 H3 109.3 108.7
C3 C7 H7 107.9 109.5
N3 C4 N9 125.3 133.5
C4 N3 HN3 123.0 121.7
C5 C4 N9 107.0 106.5
C4 N9 C8 105.8 107.5
C4 N9 C1' 125.4 126.3
C6 C5 N7 132.5 132.6
C5 N7 C8 103.7 109.0
C9 C7 O10 108.8 109.4
O10 C7 H7 111.1 109.5
C7 O10 HO10 109.5 114.0
N7 C8 N9 113.9 109.6
N7 C8 H8 123.0 125.2
C8 N9 C1' 128.8 126.3
N9 C8 H8 123.0 125.2
C9 C7 H7 108.1 109.5
C9 C10 C11 113.3 109.5
C10 C9 H9 107.5 109.5
C10 C9 H9A 107.5 109.5
C9 C10 H10 108.2 109.5
C9 C10 H10A 108.2 109.4
N9 C1' C2' 114.4 109.9
N9 C1' H1' 107.0 109.9
C1' C2' C3' 104.0 104.2
C2' C1' H1' 107.4 109.9
C1' C2' H2' 111.3 110.6
C1' C2' H2'A 111.3 110.4
C11 C10 H10 108.2 109.5
C11 C10 H10A 108.2 109.5
C10 C11 H11 108.4 109.5
C10 C11 H11A 108.4 109.4
O11 C1 H31 115.0 109.7
C12 C11 H11 108.4 109.5
C12 C11 H11A 108.4 109.5
C13 C12 H12 108.2 109.5
C13 C12 H12A 108.2 109.5
C12 C13 H13 109.5 109.5
C12 C13 H13A 109.5 109.5
C12 C13 H13B 109.5 109.4
C2' C3' O3' 114.1 110.9
C3' C2' H2' 111.4 110.5
C3' C2' H2'A 111.4 110.5
C2' C3' H3' 110.0 111.0
O3' C3' H3' 104.6 110.8
C3' O3' HO3' 109.5 114.0
C4' C3' H3' 114.4 110.9
O4' C1' H1' 114.8 109.9
O4' C4' H4' 113.4 110.6
C5' C4' H4' 103.0 110.5
O5' C5' H5' 108.8 109.5
O5' C5' H5'A 108.8 109.5
P OP2 HOP2 109.5 114.0
H C HA 112.2 109.2
H9 C9 H9A 111.4 109.4
H10 C10 H10A 110.7 109.5
H11 C11 H11A 110.5 109.5
H12 C12 H12A 110.7 109.5
H13 C13 H13A 109.5 109.6
H13 C13 H13B 109.5 109.5
H13A C13 H13B 109.5 109.5
H2' C2' H2'A 107.5 110.5
H5' C5' H5'A 110.2 109.5

Torsion Angles for HN1

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C1 C C3 N2 341.3 321.7
C1 C C3 C7 219.0 200.8
C3 C C1 H 240.0 239.7
C3 C C1 HA 120.0 120.2
C1 C C3 H3 100.4 82.5
C C1 N1 C6 178.0 133.7
C C1 N1 C2 357.9 314.4
N1 C1 C H31 247.1 240.3
O11 C1 C H31 122.4 120.6
H C C1 HA 240.0 240.5
C3 C C1 N1 11.9 54.8
C1 C C3 H 120.0 120.3
C1 C C3 HA 240.0 239.8
C3 C C1 H31 124.8 174.5
C C3 C7 O10 165.0 60.0
C7 C3 C H3 118.6 118.3
C C3 C7 H7 44.3 300.0
H C C3 HA 120.0 119.5
OP3 P OP1 O5' 234.9 240.0
OP3 P OP1 OP2 116.5 119.9
OP1 P OP3 HOP3 360.0 300.0
OP1 P O5' C5' 47.7 55.0
O5' P OP1 OP2 241.6 240.0
OP1 P OP2 HOP2 360.0 180.0
OP1 P OP3 O5' 125.3 120.0
OP1 P OP3 OP2 234.8 240.0
OP3 P O5' C5' 179.4 175.0
O5' P OP3 OP2 109.5 120.0
OP3 P OP2 HOP2 231.5 60.0
OP1 P O5' OP3 228.3 240.0
OP1 P O5' OP2 124.2 120.0
OP3 P O5' OP2 255.9 240.1
O5' P OP3 HOP3 234.7 180.0
P O5' C5' H5' 40.2 60.1
P O5' C5' H5'A 280.2 300.0
O5' P OP2 HOP2 120.0 300.0
N1 C1 C C3 11.9 54.8
N1 C1 C H 131.9 175.0
N1 C1 C HA 252.0 294.6
C C1 N1 H31 114.2 119.7
C2 N1 C1 C6 179.9 180.7
C1 N1 C6 C5 180.5 182.7
C1 N1 C2 N3 179.8 195.7
O11 C1 N1 H31 237.8 239.4
C1 N1 C6 C2 179.9 180.8
C6 N1 C1 H31 63.8 13.9
C6 N1 C2 N3 359.8 16.4
N1 C6 C5 N7 179.4 170.0
C1 N1 C2 C6 180.1 179.2
C2 N1 C1 H31 243.7 194.7
C2 N1 C6 C5 0.5 2.0
N2 C2 N1 N3 180.0 181.1
N1 C2 N3 C4 359.7 333.4
N1 C2 N3 HN3 179.7 153.4
N3 C2 N1 C6 359.8 16.4
C2 N3 C4 N9 180.3 198.4
C4 N3 C2 HN3 180.0 180.0
C C3 N2 C2 18.2 9.3
N2 C2 N1 C6 179.8 197.5
N1 C2 N2 N3 180.0 178.9
N2 C2 N3 C4 179.7 152.3
N2 C2 N3 HN3 359.7 332.3
C C3 N2 C7 234.6 239.1
N2 C3 C H 221.3 201.4
N2 C3 C HA 101.3 81.9
C C3 N2 H3 115.6 120.8
C3 N2 C2 N3 170.9 184.2
C C3 C7 N2 125.0 123.4
C7 C3 C H 99.0 80.5
C7 C3 C HA 339.0 321.0
C C3 C7 H3 244.5 241.7
C9 C7 C3 O10 120.5 120.0
O10 C7 C3 H7 120.7 120.0
C3 C7 O10 HO10 180.0 59.9
C9 C7 C3 H7 241.2 240.0
C2 N3 C4 HN3 180.0 180.0
C5 C4 N3 N9 180.2 180.0
N3 C4 N9 C8 180.0 180.5
N3 C4 N9 C1' 0.3 0.4
N9 C4 N3 HN3 0.3 18.5
N7 C8 N9 C4 0.2 359.8
C8 N9 C4 C1' 179.7 180.1
C4 N9 C8 H8 180.3 179.7
C4 N9 C1' C2' 108.9 85.1
C4 N9 C1' H1' 350.1 324.0
N1 C6 C5 C4 359.7 350.4
N3 C4 C5 N9 179.8 180.0
C5 C4 N3 HN3 180.5 198.4
C5 C4 N9 C8 359.8 0.5
C5 C4 N9 C1' 180.1 180.4
N7 C5 C4 N9 0.1 359.5
C5 N7 C8 N9 359.9 359.9
C5 N7 C8 H8 179.8 180.0
C6 C5 C4 N9 179.9 179.1
C6 C5 N7 C8 180.3 180.8
O6 C6 C5 N7 359.7 350.0
O10 C7 C3 H3 280.5 178.3
C3 C7 O10 H7 241.2 240.0
C9 C7 O10 H7 118.9 120.0
C4 N9 C8 N7 0.2 359.8
N7 C8 N9 C1' 179.9 179.8
N9 C8 N7 H8 180.0 179.9
C4 N9 C8 C1' 180.3 179.9
N7 C8 N9 H8 180.0 180.1
C8 N9 C1' C2' 289.2 265.0
C8 N9 C1' H1' 170.4 144.0
C3 C7 C9 O10 239.4 240.0
C9 C7 C3 H3 41.0 298.3
C3 C7 C9 H7 118.7 120.0
O10 C7 C9 H7 239.3 240.0
C9 C7 O10 HO10 57.6 299.9
C10 C9 C7 O10 326.0 295.0
C10 C9 C7 H7 86.7 55.0
C11 C10 C9 H10 240.0 239.9
C11 C10 C9 H10A 120.0 120.0
C9 C10 C11 H11 357.2 300.0
C9 C10 C11 H11A 117.2 60.0
H9 C9 C10 H9A 120.0 119.9
H10 C10 C9 H10A 240.0 240.0
C4 N9 C1' C8 179.6 180.1
C1' N9 C8 H8 359.9 359.8
N9 C1' C2' C3' 136.0 121.4
C2' C1' N9 H1' 118.8 121.0
N9 C1' C2' H2' 256.0 240.2
N9 C1' C2' H2'A 16.0 2.8
O4' C1' N9 H1' 236.5 238.9
N9 C1' C2' H1' 241.4 238.9
C1' C2' C3' O3' 125.1 139.1
C3' C2' C1' H2' 240.0 241.2
C3' C2' C1' H2'A 120.0 118.6
C1' C2' C3' H3' 242.3 262.7
O4' C1' C2' H1' 123.4 119.5
H2' C2' C1' H2'A 240.0 237.4
C11 C10 C9 H9 174.7 59.9
C11 C10 C9 H9A 54.8 300.0
C9 C10 C11 H10 120.0 120.1
C9 C10 C11 H10A 240.0 240.1
C12 C11 C10 H11 240.0 240.0
C12 C11 C10 H11A 120.0 120.0
H10 C10 C11 H10A 119.9 120.0
H11 C11 C10 H11A 240.0 240.0
O11 C1 C H 7.3 55.4
O11 C1 C HA 127.3 174.9
C C1 O11 H31 244.3 239.4
N1 C1 O11 H31 114.1 120.6
C12 C11 C10 H10 117.2 60.0
C12 C11 C10 H10A 357.2 300.0
C10 C11 C12 H11 120.0 120.0
C10 C11 C12 H11A 240.0 240.1
H11 C11 C12 H11A 120.0 120.1
C13 C12 C11 H11 49.2 60.0
C13 C12 C11 H11A 289.2 300.0
H12 C12 C13 H12A 120.0 120.0
H13 C13 C12 H13A 240.0 239.9
H13 C13 C12 H13B 120.0 120.0
H13A C13 C12 H13B 240.0 240.1
C3' C2' C1' H1' 254.6 242.5
C1' C2' C3' H2' 120.0 118.8
C1' C2' C3' H2'A 240.0 241.4
O3' C3' C2' H3' 242.8 236.4
C2' C3' O3' HO3' 180.0 61.5
C4' C3' C2' H3' 123.1 118.3
H2' C2' C3' H2'A 120.0 122.6
O3' C3' C2' H2' 5.1 20.3
O3' C3' C2' H2'A 245.1 257.7
C2' C3' O3' H3' 120.3 123.7
C4' C3' O3' H3' 236.8 236.4
C4' C3' C2' H2' 245.4 262.2
C4' C3' C2' H2'A 125.4 139.5
C2' C3' C4' H3' 239.8 241.7
O3' C3' C4' H3' 117.2 123.6
C4' C3' O3' HO3' 296.6 174.2
N9 C1' O4' H1' 118.5 121.1
C2' C1' O4' H1' 241.3 240.6
O4' C1' C2' H2' 138.0 120.7
O4' C1' C2' H2'A 258.0 243.3
O4' C4' C3' H3' 93.6 81.3
C4' O4' C1' H1' 82.8 93.0
C5' C4' O4' H4' 244.4 237.1
P O5' C5' C4' 160.2 180.0
C5' C4' C3' H3' 331.1 322.6
O4' C4' C5' H4' 121.9 122.9
C5' O5' P OP2 283.5 295.0
O5' C5' C4' H4' 174.2 307.9
H5' C5' O5' H5'A 120.0 120.1
OP1 P OP2 OP3 128.5 120.0
OP1 P OP2 O5' 240.0 240.0
OP3 P OP2 O5' 111.5 120.0
OP2 P OP3 HOP3 125.2 60.0
OP2 P O5' C5' 283.5 295.0
C1 C H C3 232.8 239.1
H C C1 N1 131.9 175.0
C1 C H HA 116.4 119.6
H C C1 H31 244.8 294.8
H C C3 N2 221.3 201.4
H C C3 C7 99.0 80.5
C3 C H HA 243.6 240.5
H C C3 H3 340.4 322.2
C1 C HA C3 127.2 120.8
HA C C1 N1 252.0 294.6
C1 C HA H 243.6 240.4
HA C C1 H31 4.8 54.3
HA C C3 N2 101.3 81.9
HA C C3 C7 339.0 321.0
C3 C HA H 116.4 119.6
HA C C3 H3 220.4 202.7
H31 C1 C C3 124.8 174.5
C C1 H31 N1 235.5 241.1
H31 C1 C H 244.8 294.8
H31 C1 C HA 4.8 54.3
H31 C1 N1 C6 63.8 13.9
H31 C1 N1 C2 243.7 194.7
C C3 H3 N2 239.2 236.7
C C3 H3 C7 121.2 118.3
H3 C3 C H 340.4 322.2
H3 C3 C HA 220.4 202.7
H3 C3 C7 O10 280.5 178.3
H3 C3 C7 H7 159.8 58.3
C2 N3 HN3 C4 180.0 180.0
HN3 N3 C4 N9 0.3 18.5
C3 C7 H7 O10 119.5 120.0
H7 C7 C3 H3 159.8 58.3
C9 C7 H7 O10 240.7 240.0
H7 C7 O10 HO10 298.7 180.0
N7 C8 H8 N9 180.0 179.9
H8 C8 N9 C1' 359.9 359.8
H9 C9 C7 O10 85.9 55.0
H9 C9 C7 H7 206.7 175.0
H9 C9 C10 C11 174.7 59.9
C10 C9 H9 H9A 242.5 240.0
H9 C9 C10 H10 294.7 180.0
H9 C9 C10 H10A 54.7 300.0
H9A C9 C7 O10 205.9 175.0
H9A C9 C7 H7 326.7 295.0
H9A C9 C10 C11 54.8 300.0
C10 C9 H9A H9 117.5 120.0
H9A C9 C10 H10 174.8 60.1
H9A C9 C10 H10A 294.8 180.0
N9 C1' H1' C2' 123.3 121.0
H1' C1' C2' C3' 254.6 242.5
H1' C1' C2' H2' 14.6 1.2
H1' C1' C2' H2'A 134.6 123.8
C9 C10 H10 C11 236.8 240.0
H10 C10 C9 H9 294.7 180.0
H10 C10 C9 H9A 174.8 60.1
C9 C10 H10 H10A 118.5 120.0
C11 C10 H10 H10A 241.6 240.0
H10 C10 C11 H11 237.2 180.0
H10 C10 C11 H11A 357.2 300.0
C9 C10 H10A C11 123.2 120.0
H10A C10 C9 H9 54.7 300.0
H10A C10 C9 H9A 294.8 180.0
C9 C10 H10A H10 241.5 240.0
C11 C10 H10A H10 118.4 120.0
H10A C10 C11 H11 117.2 60.0
H10A C10 C11 H11A 237.2 180.0
HO10 O10 C7 H7 298.7 180.0
H11 C11 C10 H10 237.2 180.0
H11 C11 C10 H10A 117.2 60.0
C10 C11 H11 H11A 118.7 119.9
C12 C11 H11 H11A 241.3 239.9
H11A C11 C10 H10 357.2 300.0
H11A C11 C10 H10A 237.2 180.0
C10 C11 H11A H11 241.4 240.0
C12 C11 H11A H11 118.7 120.1
H16 O11 C1 H31 291.0 300.6
H12 C12 C11 H11 169.2 180.0
H12 C12 C11 H11A 49.2 59.9
C13 C12 H12 H12A 241.6 240.0
H12 C12 C13 H13 60.0 60.0
H12 C12 C13 H13A 180.0 180.1
H12 C12 C13 H13B 300.0 300.0
H12A C12 C11 H11 289.2 300.0
H12A C12 C11 H11A 169.2 179.9
C13 C12 H12A H12 118.4 120.0
H12A C12 C13 H13 300.0 300.0
H12A C12 C13 H13A 60.0 60.1
H12A C12 C13 H13B 180.0 180.0
H13 C13 C12 H12 60.0 60.0
H13 C13 C12 H12A 300.0 300.0
C12 C13 H13 H13A 120.0 120.0
C12 C13 H13 H13B 240.0 240.1
H13A C13 H13 H13B 120.0 120.0
H13A C13 C12 H12 180.0 180.1
H13A C13 C12 H12A 60.0 60.1
C12 C13 H13A H13 240.0 240.0
C12 C13 H13A H13B 120.0 119.9
H13 C13 H13A H13B 240.0 239.9
H13B C13 C12 H12 300.0 300.0
H13B C13 C12 H12A 180.0 180.0
C12 C13 H13B H13 120.0 120.0
C12 C13 H13B H13A 240.0 240.1
H13 C13 H13B H13A 120.0 120.1
HOP3 OP3 P O5' 234.7 180.0
HOP3 OP3 P OP2 125.2 60.0
C1' C2' H2' C3' 244.5 245.2
H2' C2' C1' H1' 14.6 1.2
C1' C2' H2' H2'A 122.2 122.6
H2' C2' C3' O3' 5.1 20.3
C3' C2' H2' H2'A 237.7 237.4
H2' C2' C3' H3' 122.3 143.9
C1' C2' H2'A C3' 115.5 114.7
H2'A C2' C1' H1' 134.6 123.8
C1' C2' H2'A H2' 237.8 237.4
H2'A C2' C3' O3' 245.1 257.7
C3' C2' H2'A H2' 122.3 122.6
H2'A C2' C3' H3' 2.3 21.3
C2' C3' H3' O3' 237.0 236.4
H3' C3' C2' H2' 122.3 143.9
H3' C3' C2' H2'A 2.3 21.3
H3' C3' O3' HO3' 59.7 297.8
HO3' O3' C3' H3' 59.7 297.8
H4' C4' C3' H3' 215.6 199.7
H5' C5' C4' H4' 294.2 67.9
O5' C5' H5' H5'A 240.8 239.9
H5'A C5' C4' H4' 54.2 187.9
O5' C5' H5'A H5' 119.2 120.1