C5L
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| OP2 | P | doub | 1.48Å | 1.48Å | |
| O5' | P | sing | 1.61Å | 1.60Å | |
| P | OP3 | sing | 1.61Å | 1.60Å | |
| P | OP1 | sing | 1.61Å | 1.49Å | |
| C2 | N1 | sing | 1.35Å | 1.40Å | |
| C6 | N1 | sing | 1.36Å | 1.37Å | |
| N1 | C1' | sing | 1.47Å | 1.48Å | |
| N3 | C2 | sing | 1.33Å | 1.35Å | |
| C2 | O2 | doub | 1.22Å | 1.23Å | |
| C4 | N3 | doub | 1.33Å | 1.31Å | |
| N4 | C4 | sing | 1.38Å | 1.30Å | |
| C4 | C5 | sing | 1.41Å | 1.44Å | |
| H41 | N4 | sing | 0.97Å | 1.00Å | |
| H42 | N4 | sing | 0.97Å | 1.00Å | |
| C7 | C5 | sing | 1.51Å | 1.52Å | |
| C5 | C6 | doub | 1.35Å | 1.35Å | |
| C6 | H6 | sing | 1.08Å | 1.08Å | |
| H72 | C7 | sing | 1.09Å | 1.10Å | |
| H73 | C7 | sing | 1.09Å | 1.10Å | |
| C7 | H71 | sing | 1.09Å | 1.10Å | |
| H1' | C1' | sing | 1.09Å | 1.10Å | |
| C1' | C2' | sing | 1.55Å | 1.52Å | |
| C1' | O4' | sing | 1.44Å | 1.42Å | |
| H2' | C2' | sing | 1.09Å | 1.10Å | |
| C2' | O2' | sing | 1.43Å | 1.43Å | |
| C2' | C3' | sing | 1.55Å | 1.53Å | |
| CA' | O2' | sing | 1.43Å | 1.42Å | |
| H3' | C3' | sing | 1.09Å | 1.10Å | |
| C3' | C4' | sing | 1.54Å | 1.53Å | |
| C3' | O3' | sing | 1.43Å | 1.42Å | |
| O3' | HO3' | sing | 0.97Å | 0.95Å | |
| O4' | C4' | sing | 1.44Å | 1.43Å | |
| C4' | C5' | sing | 1.53Å | 1.54Å | |
| C4' | H4' | sing | 1.09Å | 1.10Å | |
| O5' | C5' | sing | 1.43Å | 1.42Å | |
| C5' | H5' | sing | 1.09Å | 1.10Å | |
| C5' | H5'' | sing | 1.09Å | 1.10Å | |
| HCA1 | CA' | sing | 1.09Å | 1.10Å | |
| HCA2 | CA' | sing | 1.09Å | 1.10Å | |
| CA' | CB' | sing | 1.53Å | 1.53Å | |
| OC' | CB' | sing | 1.43Å | 1.43Å | |
| CB' | HCB2 | sing | 1.09Å | 1.10Å | |
| CB' | HCB1 | sing | 1.09Å | 1.10Å | |
| CD' | OC' | sing | 1.43Å | 1.42Å | |
| HCD1 | CD' | sing | 1.09Å | 1.10Å | |
| HCD2 | CD' | sing | 1.09Å | 1.10Å | |
| CD' | HCD3 | sing | 1.09Å | 1.10Å | |
| OP1 | HOP1 | sing | 0.97Å | 0.95Å | |
| OP3 | HOP3 | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| OP2 | P | O5' | 107.9° | 109.5° |
| OP2 | P | OP3 | 107.8° | 109.5° |
| OP2 | P | OP1 | 118.7° | 109.4° |
| O5' | P | OP3 | 105.2° | 109.5° |
| O5' | P | OP1 | 108.6° | 109.5° |
| P | O5' | C5' | 122.4° | 123.0° |
| OP3 | P | OP1 | 107.8° | 109.5° |
| P | OP3 | HOP3 | 109.5° | 114.0° |
| P | OP1 | HOP1 | 109.5° | 114.0° |
| C2 | N1 | C6 | 120.3° | 120.4° |
| C2 | N1 | C1' | 117.4° | 119.9° |
| N1 | C2 | N3 | 120.8° | 121.1° |
| N1 | C2 | O2 | 122.3° | 119.4° |
| C6 | N1 | C1' | 122.3° | 119.8° |
| N1 | C6 | C5 | 120.1° | 119.2° |
| N1 | C6 | H6 | 120.0° | 120.4° |
| N1 | C1' | H1' | 107.9° | 110.6° |
| N1 | C1' | C2' | 114.0° | 110.6° |
| N1 | C1' | O4' | 111.8° | 110.6° |
| N3 | C2 | O2 | 116.9° | 119.5° |
| C2 | N3 | C4 | 118.1° | 120.7° |
| N3 | C4 | N4 | 112.2° | 120.2° |
| N3 | C4 | C5 | 124.2° | 119.6° |
| N4 | C4 | C5 | 123.6° | 120.2° |
| C4 | N4 | H41 | 120.0° | 120.0° |
| C4 | N4 | H42 | 120.0° | 120.0° |
| C4 | C5 | C7 | 123.5° | 120.5° |
| C4 | C5 | C6 | 116.4° | 119.0° |
| H41 | N4 | H42 | 120.0° | 120.0° |
| C7 | C5 | C6 | 120.0° | 120.5° |
| C5 | C7 | H72 | 109.5° | 109.5° |
| C5 | C7 | H73 | 109.5° | 109.5° |
| C5 | C7 | H71 | 109.5° | 109.5° |
| C5 | C6 | H6 | 120.0° | 120.4° |
| H72 | C7 | H73 | 109.5° | 109.4° |
| H72 | C7 | H71 | 109.5° | 109.5° |
| H73 | C7 | H71 | 109.4° | 109.5° |
| H1' | C1' | C2' | 107.4° | 110.6° |
| H1' | C1' | O4' | 108.7° | 110.8° |
| C2' | C1' | O4' | 106.9° | 103.5° |
| C1' | C2' | H2' | 110.7° | 110.9° |
| C1' | C2' | O2' | 109.6° | 110.9° |
| C1' | C2' | C3' | 102.0° | 102.1° |
| C1' | O4' | C4' | 109.0° | 107.0° |
| H2' | C2' | O2' | 112.1° | 110.8° |
| H2' | C2' | C3' | 110.6° | 111.0° |
| O2' | C2' | C3' | 111.4° | 110.9° |
| C2' | O2' | CA' | 113.5° | 114.0° |
| C2' | C3' | H3' | 109.4° | 110.5° |
| C2' | C3' | C4' | 99.9° | 104.2° |
| C2' | C3' | O3' | 112.8° | 110.5° |
| O2' | CA' | HCA1 | 109.4° | 109.5° |
| O2' | CA' | HCA2 | 109.4° | 109.4° |
| O2' | CA' | CB' | 109.6° | 109.5° |
| H3' | C3' | C4' | 109.4° | 110.5° |
| H3' | C3' | O3' | 111.0° | 110.5° |
| C4' | C3' | O3' | 113.8° | 110.5° |
| C3' | C4' | O4' | 106.5° | 107.3° |
| C3' | C4' | C5' | 114.0° | 109.9° |
| C3' | C4' | H4' | 107.5° | 109.9° |
| C3' | O3' | HO3' | 109.5° | 114.0° |
| O4' | C4' | C5' | 112.4° | 109.9° |
| O4' | C4' | H4' | 108.9° | 110.0° |
| C5' | C4' | H4' | 107.4° | 109.9° |
| C4' | C5' | O5' | 111.3° | 109.5° |
| C4' | C5' | H5' | 109.0° | 109.4° |
| C4' | C5' | H5'' | 109.0° | 109.5° |
| O5' | C5' | H5' | 109.0° | 109.5° |
| O5' | C5' | H5'' | 109.0° | 109.5° |
| H5' | C5' | H5'' | 109.5° | 109.5° |
| HCA1 | CA' | HCA2 | 109.5° | 109.5° |
| HCA1 | CA' | CB' | 109.4° | 109.5° |
| HCA2 | CA' | CB' | 109.5° | 109.5° |
| CA' | CB' | OC' | 113.3° | 109.5° |
| CA' | CB' | HCB2 | 108.5° | 109.5° |
| CA' | CB' | HCB1 | 108.5° | 109.5° |
| OC' | CB' | HCB2 | 108.5° | 109.5° |
| OC' | CB' | HCB1 | 108.5° | 109.5° |
| CB' | OC' | CD' | 114.7° | 114.0° |
| HCB2 | CB' | HCB1 | 109.5° | 109.4° |
| OC' | CD' | HCD1 | 109.5° | 109.5° |
| OC' | CD' | HCD2 | 109.5° | 109.4° |
| OC' | CD' | HCD3 | 109.5° | 109.5° |
| HCD1 | CD' | HCD2 | 109.5° | 109.5° |
| HCD1 | CD' | HCD3 | 109.4° | 109.5° |
| HCD2 | CD' | HCD3 | 109.5° | 109.4° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| OP2 | P | O5' | OP3 | 114.9° | 120.0° |
| OP2 | P | O5' | OP1 | 129.9° | 119.9° |
| OP2 | P | OP3 | OP1 | 129.3° | 120.0° |
| OP2 | P | O5' | C5' | 173.8° | 55.0° |
| OP2 | P | OP1 | HOP1 | 0.0° | 180.0° |
| OP2 | P | OP3 | HOP3 | 0.0° | 60.0° |
| O5' | P | OP3 | OP1 | 115.8° | 120.0° |
| P | O5' | C5' | C4' | 176.6° | 180.0° |
| P | O5' | C5' | H5' | 56.3° | 60.0° |
| P | O5' | C5' | H5'' | 63.1° | 60.0° |
| O5' | P | OP1 | HOP1 | 123.7° | 60.0° |
| O5' | P | OP3 | HOP3 | 115.0° | 180.0° |
| OP3 | P | O5' | C5' | 71.3° | 175.0° |
| OP3 | P | OP1 | HOP1 | 122.8° | 60.0° |
| OP1 | P | O5' | C5' | 43.9° | 64.9° |
| OP1 | P | OP3 | HOP3 | 129.2° | 60.0° |
| C2 | N1 | C6 | C1' | 179.6° | 179.8° |
| N1 | C2 | N3 | O2 | 180.0° | 179.9° |
| N1 | C2 | N3 | C4 | 2.7° | 0.0° |
| C2 | N1 | C6 | C5 | 2.6° | 0.5° |
| C2 | N1 | C6 | H6 | 177.5° | 180.0° |
| C2 | N1 | C1' | H1' | 33.1° | 172.1° |
| C2 | N1 | C1' | C2' | 86.1° | 65.0° |
| C2 | N1 | C1' | O4' | 152.6° | 49.0° |
| C6 | N1 | C2 | N3 | 4.6° | 0.2° |
| C6 | N1 | C2 | O2 | 175.4° | 179.7° |
| N1 | C6 | C5 | C4 | 1.0° | 0.6° |
| N1 | C6 | C5 | C7 | 177.3° | 179.7° |
| N1 | C6 | C5 | H6 | 180.0° | 179.5° |
| C6 | N1 | C1' | H1' | 146.5° | 8.1° |
| C6 | N1 | C1' | C2' | 94.3° | 114.8° |
| C6 | N1 | C1' | O4' | 27.0° | 131.2° |
| C1' | N1 | C2 | N3 | 175.1° | 180.0° |
| C1' | N1 | C2 | O2 | 5.0° | 0.1° |
| C1' | N1 | C6 | C5 | 177.0° | 179.7° |
| C1' | N1 | C6 | H6 | 3.0° | 0.2° |
| N1 | C1' | H1' | C2' | 123.3° | 122.9° |
| N1 | C1' | H1' | O4' | 121.4° | 123.0° |
| N1 | C1' | C2' | O4' | 124.1° | 118.4° |
| N1 | C1' | C2' | H2' | 23.3° | 37.2° |
| N1 | C1' | C2' | O2' | 147.4° | 86.3° |
| N1 | C1' | C2' | C3' | 94.4° | 155.5° |
| N1 | C1' | O4' | C4' | 117.6° | 158.5° |
| C2 | N3 | C4 | N4 | 178.8° | 180.0° |
| C2 | N3 | C4 | C5 | 1.1° | 0.1° |
| O2 | C2 | N3 | C4 | 177.3° | 179.9° |
| N3 | C4 | N4 | C5 | 179.9° | 179.9° |
| N3 | C4 | N4 | H41 | 0.0° | 0.0° |
| N3 | C4 | N4 | H42 | 180.0° | 179.9° |
| N3 | C4 | C5 | C7 | 179.1° | 179.9° |
| N3 | C4 | C5 | C6 | 2.9° | 0.4° |
| C4 | N4 | H41 | H42 | 180.0° | 180.0° |
| N4 | C4 | C5 | C7 | 0.8° | 0.0° |
| N4 | C4 | C5 | C6 | 176.9° | 179.7° |
| C5 | C4 | N4 | H41 | 179.9° | 180.0° |
| C5 | C4 | N4 | H42 | 0.1° | 0.0° |
| C4 | C5 | C7 | C6 | 176.0° | 179.7° |
| C4 | C5 | C6 | H6 | 179.0° | 180.0° |
| C4 | C5 | C7 | H72 | 180.0° | 120.0° |
| C4 | C5 | C7 | H73 | 60.0° | 120.0° |
| C4 | C5 | C7 | H71 | 60.0° | 0.1° |
| C7 | C5 | C6 | H6 | 2.7° | 0.3° |
| C5 | C7 | H72 | H73 | 120.0° | 120.0° |
| C5 | C7 | H72 | H71 | 120.0° | 120.0° |
| C5 | C7 | H73 | H71 | 120.0° | 120.0° |
| C6 | C5 | C7 | H72 | 3.9° | 59.7° |
| C6 | C5 | C7 | H73 | 124.0° | 60.3° |
| C6 | C5 | C7 | H71 | 116.1° | 179.7° |
| H72 | C7 | H73 | H71 | 120.0° | 120.0° |
| H1' | C1' | C2' | O4' | 116.5° | 118.7° |
| H1' | C1' | C2' | H2' | 96.2° | 160.1° |
| H1' | C1' | C2' | O2' | 27.9° | 36.6° |
| H1' | C1' | C2' | C3' | 146.1° | 81.6° |
| H1' | C1' | O4' | C4' | 123.4° | 78.5° |
| C1' | C2' | H2' | O2' | 122.7° | 123.6° |
| C1' | C2' | H2' | C3' | 112.3° | 112.8° |
| C1' | C2' | O2' | C3' | 112.1° | 112.7° |
| C1' | C2' | O2' | CA' | 86.5° | 150.0° |
| C1' | C2' | C3' | H3' | 76.8° | 139.6° |
| C1' | C2' | C3' | C4' | 37.9° | 20.9° |
| C1' | C2' | C3' | O3' | 159.2° | 97.8° |
| C2' | C1' | O4' | C4' | 7.8° | 40.1° |
| O4' | C1' | C2' | H2' | 147.4° | 81.2° |
| O4' | C1' | C2' | O2' | 88.5° | 155.2° |
| O4' | C1' | C2' | C3' | 29.6° | 37.1° |
| C1' | O4' | C4' | C3' | 17.5° | 26.5° |
| C1' | O4' | C4' | C5' | 143.0° | 146.0° |
| C1' | O4' | C4' | H4' | 98.1° | 92.9° |
| H2' | C2' | O2' | C3' | 124.5° | 123.7° |
| H2' | C2' | O2' | CA' | 36.8° | 26.4° |
| H2' | C2' | C3' | H3' | 41.0° | 21.3° |
| H2' | C2' | C3' | C4' | 155.7° | 97.3° |
| H2' | C2' | C3' | O3' | 83.0° | 143.9° |
| O2' | C2' | C3' | H3' | 166.4° | 102.3° |
| O2' | C2' | C3' | C4' | 78.9° | 139.1° |
| O2' | C2' | C3' | O3' | 42.3° | 20.3° |
| C2' | O2' | CA' | HCA1 | 65.3° | 60.0° |
| C2' | O2' | CA' | HCA2 | 54.6° | 60.0° |
| C2' | O2' | CA' | CB' | 174.7° | 180.0° |
| C3' | C2' | O2' | CA' | 161.3° | 97.4° |
| C2' | C3' | H3' | C4' | 108.5° | 114.8° |
| C2' | C3' | H3' | O3' | 125.1° | 122.6° |
| C2' | C3' | C4' | O3' | 120.5° | 118.7° |
| C2' | C3' | O3' | HO3' | 180.0° | 180.0° |
| C2' | C3' | C4' | O4' | 34.9° | 2.0° |
| C2' | C3' | C4' | C5' | 159.4° | 121.4° |
| C2' | C3' | C4' | H4' | 81.6° | 117.6° |
| O2' | CA' | HCA1 | HCA2 | 119.9° | 120.0° |
| O2' | CA' | HCA1 | CB' | 120.1° | 120.0° |
| O2' | CA' | HCA2 | CB' | 120.1° | 120.0° |
| O2' | CA' | CB' | OC' | 179.9° | 65.0° |
| O2' | CA' | CB' | HCB2 | 59.4° | 55.0° |
| O2' | CA' | CB' | HCB1 | 59.5° | 174.9° |
| H3' | C3' | C4' | O3' | 124.7° | 122.6° |
| H3' | C3' | O3' | HO3' | 56.8° | 57.4° |
| H3' | C3' | C4' | O4' | 79.9° | 116.7° |
| H3' | C3' | C4' | C5' | 44.6° | 2.8° |
| H3' | C3' | C4' | H4' | 163.6° | 123.8° |
| C4' | C3' | O3' | HO3' | 67.0° | 65.2° |
| C3' | C4' | O4' | C5' | 125.5° | 119.4° |
| C3' | C4' | O4' | H4' | 115.6° | 119.5° |
| C3' | C4' | C5' | H4' | 119.0° | 121.0° |
| C3' | C4' | C5' | O5' | 56.6° | 175.0° |
| C3' | C4' | C5' | H5' | 176.9° | 55.0° |
| C3' | C4' | C5' | H5'' | 63.6° | 65.0° |
| O3' | C3' | C4' | O4' | 155.4° | 120.7° |
| O3' | C3' | C4' | C5' | 80.1° | 119.8° |
| O3' | C3' | C4' | H4' | 38.9° | 1.2° |
| O4' | C4' | C5' | H4' | 119.7° | 121.2° |
| O4' | C4' | C5' | O5' | 64.7° | 67.2° |
| O4' | C4' | C5' | H5' | 55.6° | 172.8° |
| O4' | C4' | C5' | H5'' | 175.1° | 52.8° |
| C4' | C5' | O5' | H5' | 120.3° | 120.0° |
| C4' | C5' | O5' | H5'' | 120.2° | 120.0° |
| C4' | C5' | H5' | H5'' | 119.1° | 120.0° |
| H4' | C4' | C5' | O5' | 175.6° | 54.0° |
| H4' | C4' | C5' | H5' | 64.1° | 66.0° |
| H4' | C4' | C5' | H5'' | 55.3° | 174.0° |
| O5' | C5' | H5' | H5'' | 119.2° | 120.0° |
| HCA1 | CA' | HCA2 | CB' | 120.0° | 120.0° |
| HCA1 | CA' | CB' | OC' | 60.1° | 55.0° |
| HCA1 | CA' | CB' | HCB2 | 179.4° | 175.0° |
| HCA1 | CA' | CB' | HCB1 | 60.5° | 65.0° |
| HCA2 | CA' | CB' | OC' | 59.9° | 175.0° |
| HCA2 | CA' | CB' | HCB2 | 60.6° | 65.0° |
| HCA2 | CA' | CB' | HCB1 | 179.5° | 55.0° |
| CA' | CB' | OC' | HCB2 | 120.5° | 120.0° |
| CA' | CB' | OC' | HCB1 | 120.6° | 120.0° |
| CA' | CB' | HCB2 | HCB1 | 118.3° | 120.0° |
| CA' | CB' | OC' | CD' | 65.3° | 180.0° |
| OC' | CB' | HCB2 | HCB1 | 118.3° | 120.0° |
| CB' | OC' | CD' | HCD1 | 180.0° | 180.0° |
| CB' | OC' | CD' | HCD2 | 60.0° | 60.0° |
| CB' | OC' | CD' | HCD3 | 60.0° | 59.9° |
| HCB2 | CB' | OC' | CD' | 55.2° | 60.0° |
| HCB1 | CB' | OC' | CD' | 174.1° | 60.0° |
| OC' | CD' | HCD1 | HCD2 | 120.0° | 120.0° |
| OC' | CD' | HCD1 | HCD3 | 120.0° | 120.0° |
| OC' | CD' | HCD2 | HCD3 | 120.0° | 119.9° |
| HCD1 | CD' | HCD2 | HCD3 | 120.0° | 120.1° |
