PDB Chemical Component PYD
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 PYD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N1' |
C2' |
1.358 |
1.317 |
| N1' |
C6' |
1.371 |
1.324 |
| C2' |
CM2 |
1.462 |
1.507 |
| C2' |
N3' |
1.319 |
1.317 |
| CM2 |
HM21 |
1.115 |
1.089 |
| CM2 |
HM22 |
1.115 |
1.090 |
| CM2 |
HM23 |
1.114 |
1.089 |
| N3' |
C4' |
1.382 |
1.329 |
| C4' |
N4' |
1.302 |
1.385 |
| C4' |
C5' |
1.439 |
1.396 |
| N4' |
HN41 |
1.020 |
0.970 |
| N4' |
HN42 |
1.019 |
0.971 |
| C5' |
C6' |
1.356 |
1.381 |
| C5' |
C7' |
1.522 |
1.507 |
| C6' |
HC6' |
1.103 |
1.080 |
| C7' |
HC71 |
1.114 |
1.090 |
| C7' |
HC72 |
1.116 |
1.089 |
| C7' |
HC73 |
1.114 |
1.089 |
Bond Angles for PYD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2' |
N1' |
C6' |
120.3 |
121.1 |
| N1' |
C2' |
CM2 |
116.7 |
119.1 |
| N1' |
C2' |
N3' |
122.5 |
121.8 |
| N1' |
C6' |
C5' |
121.3 |
119.2 |
| N1' |
C6' |
HC6' |
119.9 |
120.4 |
| CM2 |
C2' |
N3' |
120.7 |
119.1 |
| C2' |
CM2 |
HM21 |
116.7 |
109.5 |
| C2' |
CM2 |
HM22 |
109.5 |
109.4 |
| C2' |
CM2 |
HM23 |
109.6 |
109.5 |
| C2' |
N3' |
C4' |
118.2 |
120.7 |
| HM21 |
CM2 |
HM22 |
109.6 |
109.4 |
| HM21 |
CM2 |
HM23 |
109.6 |
109.5 |
| HM22 |
CM2 |
HM23 |
100.6 |
109.5 |
| N3' |
C4' |
N4' |
116.5 |
120.6 |
| N3' |
C4' |
C5' |
121.6 |
118.9 |
| N4' |
C4' |
C5' |
121.9 |
120.5 |
| C4' |
N4' |
HN41 |
116.6 |
120.0 |
| C4' |
N4' |
HN42 |
109.7 |
120.0 |
| C4' |
C5' |
C6' |
116.1 |
118.3 |
| C4' |
C5' |
C7' |
122.2 |
120.9 |
| HN41 |
N4' |
HN42 |
109.7 |
119.9 |
| C6' |
C5' |
C7' |
121.7 |
120.8 |
| C5' |
C6' |
HC6' |
118.8 |
120.4 |
| C5' |
C7' |
HC71 |
122.2 |
109.4 |
| C5' |
C7' |
HC72 |
107.7 |
109.5 |
| C5' |
C7' |
HC73 |
107.7 |
109.5 |
| HC71 |
C7' |
HC72 |
107.7 |
109.4 |
| HC71 |
C7' |
HC73 |
107.7 |
109.4 |
| HC72 |
C7' |
HC73 |
102.1 |
109.5 |
Torsion Angles for PYD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2' |
N1' |
C6' |
C5' |
0.6 |
-0.0 |
| C2' |
N1' |
C6' |
HC6' |
180.6 |
180.0 |
| CM2 |
C2' |
N1' |
N3' |
180.0 |
179.8 |
| N1' |
C2' |
CM2 |
HM21 |
180.0 |
90.0 |
| N1' |
C2' |
CM2 |
HM22 |
305.2 |
209.9 |
| N1' |
C2' |
CM2 |
HM23 |
54.7 |
329.9 |
| N1' |
C2' |
N3' |
C4' |
0.9 |
359.5 |
| C6' |
N1' |
C2' |
CM2 |
178.8 |
180.0 |
| C6' |
N1' |
C2' |
N3' |
358.7 |
0.2 |
| C4' |
C5' |
C6' |
N1' |
0.3 |
0.0 |
| N1' |
C6' |
C5' |
C7' |
180.1 |
180.0 |
| C5' |
C6' |
N1' |
HC6' |
179.9 |
180.0 |
| CM2 |
C2' |
N1' |
C6' |
178.8 |
180.0 |
| N1' |
C2' |
CM2 |
N3' |
180.0 |
180.2 |
| CM2 |
C2' |
N3' |
C4' |
180.9 |
179.7 |
| HM21 |
CM2 |
C2' |
HM22 |
234.8 |
240.1 |
| HM21 |
CM2 |
C2' |
HM23 |
125.3 |
120.1 |
| HM22 |
CM2 |
C2' |
HM23 |
250.5 |
240.0 |
| N3' |
C2' |
N1' |
C6' |
358.7 |
0.2 |
| N1' |
C2' |
N3' |
CM2 |
180.0 |
179.8 |
| N3' |
C2' |
CM2 |
HM21 |
0.0 |
269.8 |
| N3' |
C2' |
CM2 |
HM22 |
125.2 |
29.8 |
| N3' |
C2' |
CM2 |
HM23 |
234.7 |
149.8 |
| C2' |
N3' |
C4' |
N4' |
179.7 |
180.2 |
| C2' |
N3' |
C4' |
C5' |
0.0 |
0.5 |
| HM21 |
CM2 |
C2' |
N3' |
0.0 |
269.8 |
| C2' |
CM2 |
HM21 |
HM22 |
125.2 |
120.0 |
| C2' |
CM2 |
HM21 |
HM23 |
234.7 |
239.9 |
| HM22 |
CM2 |
HM21 |
HM23 |
109.5 |
120.0 |
| HM22 |
CM2 |
C2' |
N3' |
125.2 |
29.8 |
| C2' |
CM2 |
HM22 |
HM21 |
230.8 |
240.0 |
| C2' |
CM2 |
HM22 |
HM23 |
115.4 |
120.0 |
| HM21 |
CM2 |
HM22 |
HM23 |
244.6 |
240.0 |
| HM23 |
CM2 |
C2' |
N3' |
234.7 |
149.8 |
| C2' |
CM2 |
HM23 |
HM21 |
129.3 |
120.1 |
| C2' |
CM2 |
HM23 |
HM22 |
244.7 |
240.0 |
| HM21 |
CM2 |
HM23 |
HM22 |
115.4 |
119.9 |
| N4' |
C4' |
N3' |
C5' |
179.7 |
179.7 |
| N3' |
C4' |
N4' |
HN41 |
180.1 |
0.3 |
| N3' |
C4' |
N4' |
HN42 |
54.7 |
180.3 |
| N3' |
C4' |
C5' |
C6' |
359.4 |
359.7 |
| N3' |
C4' |
C5' |
C7' |
179.6 |
179.8 |
| N3' |
C4' |
N4' |
C5' |
180.3 |
180.3 |
| N4' |
C4' |
C5' |
C6' |
179.7 |
180.0 |
| N4' |
C4' |
C5' |
C7' |
360.0 |
0.0 |
| HN41 |
N4' |
C4' |
HN42 |
125.4 |
179.9 |
| N1' |
C6' |
C5' |
C4' |
0.3 |
0.0 |
| N3' |
C4' |
C5' |
N4' |
179.7 |
179.7 |
| C5' |
C4' |
N4' |
HN41 |
359.8 |
180.0 |
| C5' |
C4' |
N4' |
HN42 |
234.4 |
0.0 |
| C6' |
C5' |
C4' |
C7' |
179.7 |
180.0 |
| C4' |
C5' |
C6' |
HC6' |
180.3 |
180.0 |
| C4' |
C5' |
C7' |
HC71 |
180.0 |
270.0 |
| C4' |
C5' |
C7' |
HC72 |
305.3 |
29.9 |
| C4' |
C5' |
C7' |
HC73 |
54.7 |
150.0 |
| HN41 |
N4' |
C4' |
C5' |
359.8 |
180.0 |
| C4' |
N4' |
HN41 |
HN42 |
234.6 |
180.1 |
| HN42 |
N4' |
C4' |
C5' |
234.4 |
0.0 |
| C4' |
N4' |
HN42 |
HN41 |
129.2 |
179.9 |
| N1' |
C6' |
C5' |
HC6' |
180.1 |
180.0 |
| C4' |
C5' |
C6' |
C7' |
180.3 |
180.0 |
| C6' |
C5' |
C7' |
HC71 |
0.3 |
90.0 |
| C6' |
C5' |
C7' |
HC72 |
125.5 |
210.0 |
| C6' |
C5' |
C7' |
HC73 |
235.0 |
330.1 |
| C4' |
C5' |
C7' |
C6' |
179.7 |
180.0 |
| C7' |
C5' |
C6' |
HC6' |
360.0 |
-0.0 |
| HC71 |
C7' |
C5' |
HC72 |
234.8 |
240.1 |
| HC71 |
C7' |
C5' |
HC73 |
125.3 |
120.0 |
| HC72 |
C7' |
C5' |
HC73 |
250.6 |
239.9 |
| N1' |
C6' |
HC6' |
C5' |
179.9 |
180.0 |
| HC6' |
C6' |
C5' |
C7' |
360.0 |
-0.0 |
| C5' |
C7' |
HC71 |
HC72 |
125.2 |
120.0 |
| C5' |
C7' |
HC71 |
HC73 |
234.7 |
240.0 |
| HC72 |
C7' |
HC71 |
HC73 |
109.4 |
120.0 |
| C5' |
C7' |
HC72 |
HC71 |
226.5 |
240.1 |
| C5' |
C7' |
HC72 |
HC73 |
113.2 |
120.1 |
| HC71 |
C7' |
HC72 |
HC73 |
246.8 |
240.1 |
| C5' |
C7' |
HC73 |
HC71 |
133.6 |
120.0 |
| C5' |
C7' |
HC73 |
HC72 |
246.8 |
239.9 |
| HC71 |
C7' |
HC73 |
HC72 |
113.2 |
119.9 |