5SE
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| P | O5' | sing | 1.61Å | 1.57Å | |
| N1 | C1' | sing | 1.47Å | 1.43Å | |
| N1 | C2 | sing | 1.35Å | 1.39Å | |
| C2 | O2 | doub | 1.22Å | 1.22Å | |
| N3 | C2 | sing | 1.33Å | 1.35Å | |
| C4 | N3 | doub | 1.33Å | 1.30Å | |
| N4 | C4 | sing | 1.38Å | 1.32Å | |
| N4 | HN4 | sing | 0.97Å | 1.00Å | |
| N4 | HN4A | sing | 0.97Å | 1.00Å | |
| C5 | C4 | sing | 1.41Å | 1.42Å | |
| C5 | C6 | doub | 1.35Å | 1.33Å | |
| C6 | N1 | sing | 1.36Å | 1.34Å | |
| C6 | H6 | sing | 1.08Å | 1.08Å | |
| C1' | H1' | sing | 1.09Å | 1.10Å | |
| OP3 | P | sing | 1.61Å | 1.47Å | |
| OP3 | HOP3 | sing | 0.97Å | 0.95Å | |
| C2' | C1' | sing | 1.54Å | 1.50Å | |
| C2' | H2' | sing | 1.09Å | 1.10Å | |
| C2' | H2'A | sing | 1.09Å | 1.10Å | |
| OP2 | P | sing | 1.61Å | 1.45Å | |
| OP2 | HOP2 | sing | 0.97Å | 0.95Å | |
| C3' | C2' | sing | 1.55Å | 1.50Å | |
| C3' | C4' | sing | 1.55Å | 1.51Å | |
| C3' | H3' | sing | 1.09Å | 1.10Å | |
| O3' | C3' | sing | 1.43Å | 1.42Å | |
| O3' | HO3' | sing | 0.97Å | 0.95Å | |
| C4' | O4' | sing | 1.45Å | 1.44Å | |
| C4' | H4' | sing | 1.09Å | 1.10Å | |
| O4' | C1' | sing | 1.44Å | 1.41Å | |
| C5' | C4' | sing | 1.53Å | 1.52Å | |
| C5' | H5' | sing | 1.09Å | 1.10Å | |
| C5' | H5'A | sing | 1.09Å | 1.10Å | |
| O5' | C5' | sing | 1.43Å | 1.39Å | |
| CA5 | SE5 | sing | 1.96Å | 1.97Å | |
| CA5 | HA5 | sing | 1.09Å | 1.10Å | |
| CA5 | HA5A | sing | 1.09Å | 1.10Å | |
| CA5 | HA5B | sing | 1.09Å | 1.10Å | |
| SE5 | C5 | sing | 1.96Å | 1.92Å | |
| P | OP1 | doub | 1.48Å | 1.72Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| O5' | P | OP3 | 105.6° | 109.5° |
| O5' | P | OP2 | 109.7° | 109.5° |
| P | O5' | C5' | 121.4° | 123.0° |
| O5' | P | OP1 | 159.7° | 109.5° |
| C1' | N1 | C2 | 118.3° | 119.8° |
| C1' | N1 | C6 | 121.2° | 119.9° |
| N1 | C1' | H1' | 107.4° | 109.8° |
| N1 | C1' | C2' | 117.2° | 109.9° |
| N1 | C1' | O4' | 104.9° | 109.9° |
| N1 | C2 | O2 | 117.9° | 119.4° |
| N1 | C2 | N3 | 121.7° | 121.1° |
| C2 | N1 | C6 | 120.3° | 120.3° |
| O2 | C2 | N3 | 120.4° | 119.5° |
| C2 | N3 | C4 | 118.3° | 120.7° |
| N3 | C4 | N4 | 116.0° | 120.1° |
| N3 | C4 | C5 | 120.5° | 119.6° |
| C4 | N4 | HN4 | 120.0° | 120.0° |
| C4 | N4 | HN4A | 120.0° | 120.0° |
| N4 | C4 | C5 | 123.4° | 120.2° |
| HN4 | N4 | HN4A | 120.0° | 120.0° |
| C4 | C5 | C6 | 121.0° | 119.0° |
| C4 | C5 | SE5 | 119.7° | 120.5° |
| C5 | C6 | N1 | 118.1° | 119.3° |
| C5 | C6 | H6 | 120.9° | 120.4° |
| C6 | C5 | SE5 | 119.3° | 120.5° |
| N1 | C6 | H6 | 121.0° | 120.4° |
| H1' | C1' | C2' | 103.0° | 109.8° |
| H1' | C1' | O4' | 115.8° | 109.9° |
| P | OP3 | HOP3 | 109.5° | 114.0° |
| OP3 | P | OP2 | 122.3° | 109.5° |
| OP3 | P | OP1 | 85.9° | 109.4° |
| C1' | C2' | H2' | 114.5° | 110.5° |
| C1' | C2' | H2'A | 114.5° | 110.5° |
| C1' | C2' | C3' | 95.3° | 104.2° |
| C2' | C1' | O4' | 109.1° | 107.4° |
| H2' | C2' | H2'A | 104.0° | 110.4° |
| H2' | C2' | C3' | 114.5° | 110.5° |
| H2'A | C2' | C3' | 114.5° | 110.6° |
| P | OP2 | HOP2 | 109.5° | 114.0° |
| OP2 | P | OP1 | 76.2° | 109.5° |
| C2' | C3' | C4' | 102.1° | 102.1° |
| C2' | C3' | H3' | 115.4° | 110.9° |
| C2' | C3' | O3' | 109.6° | 110.9° |
| C4' | C3' | H3' | 112.1° | 110.9° |
| C4' | C3' | O3' | 112.9° | 110.9° |
| C3' | C4' | O4' | 97.0° | 103.6° |
| C3' | C4' | H4' | 113.1° | 110.7° |
| C3' | C4' | C5' | 116.4° | 110.6° |
| H3' | C3' | O3' | 105.0° | 110.8° |
| C3' | O3' | HO3' | 109.5° | 113.9° |
| O4' | C4' | H4' | 120.1° | 110.5° |
| C4' | O4' | C1' | 107.7° | 106.8° |
| O4' | C4' | C5' | 108.9° | 110.6° |
| H4' | C4' | C5' | 102.1° | 110.7° |
| C4' | C5' | H5' | 111.3° | 109.4° |
| C4' | C5' | H5'A | 111.3° | 109.5° |
| C4' | C5' | O5' | 104.1° | 109.4° |
| H5' | C5' | H5'A | 107.6° | 109.5° |
| H5' | C5' | O5' | 111.3° | 109.5° |
| H5'A | C5' | O5' | 111.3° | 109.5° |
| SE5 | CA5 | HA5 | 109.5° | 109.5° |
| SE5 | CA5 | HA5A | 109.5° | 109.5° |
| SE5 | CA5 | HA5B | 109.4° | 109.5° |
| CA5 | SE5 | C5 | 108.6° | 101.0° |
| HA5 | CA5 | HA5A | 109.4° | 109.5° |
| HA5 | CA5 | HA5B | 109.5° | 109.5° |
| HA5A | CA5 | HA5B | 109.5° | 109.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O5' | P | OP3 | OP2 | 126.1° | 120.0° |
| O5' | P | OP3 | OP1 | 163.0° | 120.0° |
| O5' | P | OP3 | HOP3 | 163.0° | 60.0° |
| O5' | P | OP2 | OP1 | 159.7° | 120.0° |
| O5' | P | OP2 | HOP2 | 159.7° | 180.0° |
| P | O5' | C5' | C4' | 179.4° | 180.0° |
| P | O5' | C5' | H5' | 60.6° | 60.0° |
| P | O5' | C5' | H5'A | 59.4° | 60.0° |
| C1' | N1 | C2 | C6 | 175.6° | 179.7° |
| C1' | N1 | C2 | O2 | 4.3° | 0.0° |
| C1' | N1 | C2 | N3 | 176.5° | 180.0° |
| C1' | N1 | C6 | C5 | 176.1° | 179.7° |
| C1' | N1 | C6 | H6 | 3.9° | 0.3° |
| N1 | C1' | H1' | C2' | 124.3° | 121.0° |
| N1 | C1' | H1' | O4' | 116.7° | 121.0° |
| N1 | C1' | C2' | O4' | 118.9° | 119.6° |
| N1 | C1' | C2' | H2' | 148.1° | 119.8° |
| N1 | C1' | C2' | H2'A | 28.1° | 2.6° |
| N1 | C1' | C2' | C3' | 91.8° | 121.5° |
| N1 | C1' | O4' | C4' | 131.1° | 145.9° |
| N1 | C2 | O2 | N3 | 179.3° | 180.0° |
| N1 | C2 | N3 | C4 | 0.3° | 0.0° |
| C2 | N1 | C6 | C5 | 0.6° | 0.6° |
| C2 | N1 | C6 | H6 | 179.4° | 180.0° |
| C2 | N1 | C1' | H1' | 37.7° | 174.4° |
| C2 | N1 | C1' | C2' | 77.5° | 64.7° |
| C2 | N1 | C1' | O4' | 161.4° | 53.3° |
| O2 | C2 | N3 | C4 | 179.5° | 180.0° |
| O2 | C2 | N1 | C6 | 179.9° | 179.7° |
| C2 | N3 | C4 | N4 | 180.0° | 179.9° |
| C2 | N3 | C4 | C5 | 0.6° | 0.0° |
| N3 | C2 | N1 | C6 | 0.9° | 0.3° |
| N3 | C4 | N4 | C5 | 179.4° | 179.9° |
| N3 | C4 | N4 | HN4 | 0.0° | 5.9° |
| N3 | C4 | N4 | HN4A | 180.0° | 174.1° |
| N3 | C4 | C5 | C6 | 0.9° | 0.3° |
| N3 | C4 | C5 | SE5 | 178.8° | 180.0° |
| C4 | N4 | HN4 | HN4A | 180.0° | 180.0° |
| N4 | C4 | C5 | C6 | 179.8° | 179.7° |
| N4 | C4 | C5 | SE5 | 1.8° | 0.1° |
| HN4 | N4 | C4 | C5 | 179.4° | 174.2° |
| HN4A | N4 | C4 | C5 | 0.6° | 5.8° |
| C4 | C5 | C6 | SE5 | 177.9° | 179.7° |
| C4 | C5 | C6 | N1 | 0.2° | 0.6° |
| C4 | C5 | C6 | H6 | 179.8° | 180.0° |
| C4 | C5 | SE5 | CA5 | 74.0° | 85.7° |
| C5 | C6 | N1 | H6 | 180.0° | 179.4° |
| C6 | C5 | SE5 | CA5 | 104.0° | 94.6° |
| C6 | N1 | C1' | H1' | 137.8° | 6.0° |
| C6 | N1 | C1' | C2' | 107.0° | 115.0° |
| C6 | N1 | C1' | O4' | 14.2° | 127.0° |
| N1 | C6 | C5 | SE5 | 178.1° | 179.7° |
| H6 | C6 | C5 | SE5 | 1.9° | 0.3° |
| H1' | C1' | C2' | O4' | 123.5° | 119.5° |
| H1' | C1' | C2' | H2' | 30.5° | 1.1° |
| H1' | C1' | C2' | H2'A | 89.5° | 123.6° |
| H1' | C1' | C2' | C3' | 150.6° | 117.6° |
| H1' | C1' | O4' | C4' | 110.8° | 93.2° |
| OP3 | P | OP2 | OP1 | 76.0° | 120.0° |
| OP3 | P | OP2 | HOP2 | 76.0° | 60.0° |
| OP3 | P | O5' | C5' | 36.4° | 65.0° |
| HOP3 | OP3 | P | OP2 | 70.9° | 60.0° |
| HOP3 | OP3 | P | OP1 | 0.0° | 180.0° |
| C1' | C2' | H2' | H2'A | 125.7° | 122.5° |
| C1' | C2' | H2' | C3' | 108.6° | 114.8° |
| C1' | C2' | H2'A | C3' | 108.6° | 114.8° |
| C1' | C2' | C3' | C4' | 48.0° | 20.9° |
| C1' | C2' | C3' | H3' | 73.8° | 97.3° |
| C1' | C2' | C3' | O3' | 168.0° | 139.1° |
| C2' | C1' | O4' | C4' | 4.8° | 26.3° |
| H2' | C2' | H2'A | C3' | 125.7° | 122.6° |
| H2' | C2' | C3' | C4' | 72.0° | 97.8° |
| H2' | C2' | C3' | H3' | 166.1° | 144.0° |
| H2' | C2' | C3' | O3' | 47.9° | 20.4° |
| H2' | C2' | C1' | O4' | 93.0° | 120.6° |
| H2'A | C2' | C3' | C4' | 168.1° | 139.6° |
| H2'A | C2' | C3' | H3' | 46.2° | 21.4° |
| H2'A | C2' | C3' | O3' | 72.0° | 102.2° |
| H2'A | C2' | C1' | O4' | 147.0° | 116.9° |
| OP2 | P | O5' | C5' | 169.9° | 175.0° |
| HOP2 | OP2 | P | OP1 | 0.0° | 59.9° |
| C2' | C3' | C4' | H3' | 124.1° | 118.2° |
| C2' | C3' | C4' | O3' | 117.5° | 118.2° |
| C2' | C3' | H3' | O3' | 120.7° | 123.7° |
| C2' | C3' | O3' | HO3' | 180.0° | 61.5° |
| C2' | C3' | C4' | O4' | 52.3° | 37.0° |
| C2' | C3' | C4' | H4' | 74.7° | 81.4° |
| C3' | C2' | C1' | O4' | 27.1° | 1.9° |
| C2' | C3' | C4' | C5' | 167.6° | 155.5° |
| C4' | C3' | H3' | O3' | 123.0° | 123.6° |
| C4' | C3' | O3' | HO3' | 67.0° | 174.1° |
| C3' | C4' | O4' | H4' | 121.9° | 118.5° |
| C3' | C4' | O4' | C5' | 121.1° | 118.5° |
| C3' | C4' | H4' | C5' | 125.9° | 123.0° |
| C3' | C4' | O4' | C1' | 34.2° | 39.9° |
| C3' | C4' | C5' | H5' | 172.8° | 55.0° |
| C3' | C4' | C5' | H5'A | 67.2° | 65.0° |
| C3' | C4' | C5' | O5' | 52.8° | 175.0° |
| H3' | C3' | O3' | HO3' | 55.5° | 62.2° |
| H3' | C3' | C4' | O4' | 71.7° | 81.2° |
| H3' | C3' | C4' | H4' | 161.3° | 160.4° |
| H3' | C3' | C4' | C5' | 43.5° | 37.3° |
| O3' | C3' | C4' | O4' | 169.9° | 155.2° |
| O3' | C3' | C4' | H4' | 42.9° | 36.8° |
| O3' | C3' | C4' | C5' | 74.9° | 86.3° |
| O4' | C4' | H4' | C5' | 120.5° | 122.9° |
| O4' | C4' | C5' | H5' | 64.5° | 169.2° |
| O4' | C4' | C5' | H5'A | 175.6° | 49.2° |
| O4' | C4' | C5' | O5' | 55.6° | 70.8° |
| H4' | C4' | O4' | C1' | 87.7° | 78.7° |
| H4' | C4' | C5' | H5' | 63.5° | 68.0° |
| H4' | C4' | C5' | H5'A | 56.5° | 172.0° |
| H4' | C4' | C5' | O5' | 176.5° | 52.0° |
| C1' | O4' | C4' | C5' | 155.3° | 158.4° |
| C4' | C5' | H5' | H5'A | 122.1° | 120.0° |
| C4' | C5' | H5' | O5' | 115.7° | 119.9° |
| C4' | C5' | H5'A | O5' | 115.6° | 120.0° |
| H5' | C5' | H5'A | O5' | 122.2° | 120.1° |
| C5' | O5' | P | OP1 | 86.4° | 55.0° |
| SE5 | CA5 | HA5 | HA5A | 120.0° | 120.0° |
| SE5 | CA5 | HA5 | HA5B | 120.0° | 120.0° |
| SE5 | CA5 | HA5A | HA5B | 120.0° | 120.0° |
| HA5 | CA5 | HA5A | HA5B | 120.0° | 120.0° |
| HA5 | CA5 | SE5 | C5 | 180.0° | 55.0° |
| HA5A | CA5 | SE5 | C5 | 60.0° | 65.0° |
| HA5B | CA5 | SE5 | C5 | 60.0° | 175.0° |
