PDB Chemical Component XYD
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 XYD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C1 |
C2 |
1.566 |
1.388 |
| C1 |
C6 |
1.543 |
1.389 |
| C1 |
N |
1.347 |
1.397 |
| C2 |
C3 |
1.565 |
1.381 |
| C2 |
C9 |
1.535 |
1.507 |
| C3 |
C4 |
1.533 |
1.382 |
| C3 |
H3 |
1.102 |
1.080 |
| C4 |
C5 |
1.540 |
1.382 |
| C4 |
H4 |
1.102 |
1.081 |
| C5 |
C6 |
1.544 |
1.380 |
| C5 |
C8 |
1.523 |
1.507 |
| C6 |
H6 |
1.103 |
1.080 |
| N |
H1N |
1.021 |
0.970 |
| N |
H2N |
1.020 |
0.969 |
| C8 |
H81 |
1.116 |
1.090 |
| C8 |
H82 |
1.115 |
1.090 |
| C8 |
H83 |
1.114 |
1.089 |
| C9 |
H91 |
1.115 |
1.090 |
| C9 |
H92 |
1.116 |
1.090 |
| C9 |
H93 |
1.115 |
1.089 |
Bond Angles for XYD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
C1 |
C6 |
121.9 |
119.9 |
| C2 |
C1 |
N |
122.6 |
120.1 |
| C1 |
C2 |
C3 |
116.8 |
119.9 |
| C1 |
C2 |
C9 |
123.3 |
120.0 |
| C6 |
C1 |
N |
115.5 |
120.0 |
| C1 |
C6 |
C5 |
118.6 |
119.9 |
| C1 |
C6 |
H6 |
120.6 |
120.0 |
| C1 |
N |
H1N |
122.6 |
120.0 |
| C1 |
N |
H2N |
107.6 |
119.9 |
| C3 |
C2 |
C9 |
119.9 |
120.1 |
| C2 |
C3 |
C4 |
122.3 |
120.1 |
| C2 |
C3 |
H3 |
119.9 |
119.9 |
| C2 |
C9 |
H91 |
123.4 |
109.4 |
| C2 |
C9 |
H92 |
107.3 |
109.5 |
| C2 |
C9 |
H93 |
107.3 |
109.5 |
| C4 |
C3 |
H3 |
117.8 |
120.0 |
| C3 |
C4 |
C5 |
118.7 |
120.1 |
| C3 |
C4 |
H4 |
120.4 |
119.9 |
| C5 |
C4 |
H4 |
120.8 |
120.0 |
| C4 |
C5 |
C6 |
121.7 |
120.1 |
| C4 |
C5 |
C8 |
117.0 |
119.9 |
| C6 |
C5 |
C8 |
121.3 |
120.0 |
| C5 |
C6 |
H6 |
120.8 |
120.1 |
| C5 |
C8 |
H81 |
117.0 |
109.5 |
| C5 |
C8 |
H82 |
109.5 |
109.5 |
| C5 |
C8 |
H83 |
109.5 |
109.5 |
| H1N |
N |
H2N |
107.5 |
120.1 |
| H81 |
C8 |
H82 |
109.4 |
109.4 |
| H81 |
C8 |
H83 |
109.5 |
109.5 |
| H82 |
C8 |
H83 |
100.7 |
109.5 |
| H91 |
C9 |
H92 |
107.3 |
109.5 |
| H91 |
C9 |
H93 |
107.4 |
109.4 |
| H92 |
C9 |
H93 |
102.4 |
109.5 |
Torsion Angles for XYD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C6 |
C1 |
C2 |
N |
180.3 |
179.9 |
| C2 |
C1 |
C6 |
C5 |
0.6 |
0.4 |
| C2 |
C1 |
C6 |
H6 |
180.6 |
180.0 |
| C2 |
C1 |
N |
H1N |
180.0 |
180.0 |
| C2 |
C1 |
N |
H2N |
54.7 |
0.0 |
| C3 |
C2 |
C1 |
C9 |
179.4 |
180.0 |
| C1 |
C2 |
C3 |
C4 |
359.8 |
-0.0 |
| C1 |
C2 |
C3 |
H3 |
179.8 |
180.0 |
| C1 |
C2 |
C9 |
H91 |
180.0 |
270.0 |
| C1 |
C2 |
C9 |
H92 |
305.3 |
30.0 |
| C1 |
C2 |
C9 |
H93 |
54.7 |
150.1 |
| C2 |
C1 |
C6 |
N |
179.8 |
180.1 |
| C6 |
C1 |
C2 |
C3 |
0.3 |
359.8 |
| C6 |
C1 |
C2 |
C9 |
180.9 |
179.8 |
| C6 |
C1 |
N |
H1N |
359.7 |
0.1 |
| C6 |
C1 |
N |
H2N |
234.5 |
180.2 |
| C4 |
C5 |
C6 |
C1 |
358.4 |
359.6 |
| C1 |
C6 |
C5 |
C8 |
179.2 |
179.8 |
| C5 |
C6 |
C1 |
H6 |
180.0 |
180.4 |
| C2 |
C1 |
N |
C6 |
180.2 |
179.9 |
| N |
C1 |
C2 |
C3 |
180.0 |
180.0 |
| N |
C1 |
C2 |
C9 |
0.7 |
360.0 |
| N |
C1 |
C6 |
C5 |
180.8 |
180.2 |
| N |
C1 |
C6 |
H6 |
0.8 |
359.9 |
| H1N |
N |
C1 |
H2N |
125.2 |
180.0 |
| C3 |
C2 |
C1 |
C6 |
0.3 |
359.8 |
| C3 |
C2 |
C1 |
N |
180.0 |
180.0 |
| C1 |
C2 |
C3 |
C9 |
180.6 |
180.0 |
| C3 |
C2 |
C9 |
H91 |
0.7 |
90.0 |
| C3 |
C2 |
C9 |
H92 |
125.9 |
210.0 |
| C3 |
C2 |
C9 |
H93 |
235.3 |
330.1 |
| C4 |
C3 |
C2 |
H3 |
180.0 |
180.0 |
| C2 |
C3 |
C4 |
C5 |
359.2 |
-0.0 |
| C2 |
C3 |
C4 |
H4 |
179.2 |
180.0 |
| C9 |
C2 |
C1 |
C6 |
180.9 |
179.8 |
| C9 |
C2 |
C1 |
N |
0.7 |
360.0 |
| C1 |
C2 |
C9 |
C3 |
179.4 |
180.0 |
| C9 |
C2 |
C3 |
C4 |
179.2 |
180.0 |
| C9 |
C2 |
C3 |
H3 |
359.2 |
360.0 |
| H91 |
C9 |
C2 |
H92 |
234.7 |
240.0 |
| H91 |
C9 |
C2 |
H93 |
125.4 |
120.0 |
| H92 |
C9 |
C2 |
H93 |
250.6 |
239.9 |
| C4 |
C3 |
C2 |
C9 |
179.2 |
180.0 |
| C2 |
C3 |
C4 |
H3 |
180.0 |
180.0 |
| C5 |
C4 |
C3 |
H4 |
180.0 |
180.0 |
| C3 |
C4 |
C5 |
C6 |
1.7 |
0.2 |
| C3 |
C4 |
C5 |
C8 |
180.9 |
180.0 |
| H3 |
C3 |
C2 |
C9 |
359.2 |
-0.0 |
| C2 |
C3 |
H3 |
C4 |
180.0 |
180.0 |
| H3 |
C3 |
C4 |
C5 |
179.2 |
180.0 |
| H3 |
C3 |
C4 |
H4 |
359.2 |
-0.0 |
| C1 |
C6 |
C5 |
C4 |
358.4 |
359.6 |
| C5 |
C4 |
C3 |
H3 |
179.2 |
180.0 |
| C3 |
C4 |
C5 |
H4 |
180.0 |
180.0 |
| C6 |
C5 |
C4 |
C8 |
180.8 |
180.1 |
| C4 |
C5 |
C6 |
H6 |
178.4 |
180.0 |
| C4 |
C5 |
C8 |
H81 |
180.0 |
90.0 |
| C4 |
C5 |
C8 |
H82 |
305.2 |
209.9 |
| C4 |
C5 |
C8 |
H83 |
54.7 |
330.0 |
| H4 |
C4 |
C3 |
H3 |
359.2 |
360.0 |
| C3 |
C4 |
H4 |
C5 |
180.0 |
180.0 |
| H4 |
C4 |
C5 |
C6 |
181.7 |
180.2 |
| H4 |
C4 |
C5 |
C8 |
0.9 |
0.0 |
| C5 |
C6 |
C1 |
N |
180.8 |
180.2 |
| C1 |
C6 |
C5 |
H6 |
180.0 |
179.6 |
| C6 |
C5 |
C4 |
H4 |
181.7 |
180.2 |
| C4 |
C5 |
C6 |
C8 |
179.1 |
179.9 |
| C6 |
C5 |
C8 |
H81 |
359.2 |
269.8 |
| C6 |
C5 |
C8 |
H82 |
124.4 |
29.7 |
| C6 |
C5 |
C8 |
H83 |
233.9 |
149.8 |
| C8 |
C5 |
C4 |
H4 |
0.9 |
0.0 |
| C4 |
C5 |
C8 |
C6 |
180.8 |
180.1 |
| C8 |
C5 |
C6 |
H6 |
359.2 |
0.1 |
| H81 |
C8 |
C5 |
H82 |
234.8 |
240.1 |
| H81 |
C8 |
C5 |
H83 |
125.3 |
120.0 |
| H82 |
C8 |
C5 |
H83 |
250.5 |
239.9 |
| H6 |
C6 |
C1 |
N |
0.8 |
359.9 |
| C1 |
C6 |
H6 |
C5 |
180.0 |
180.4 |
| H6 |
C6 |
C5 |
C8 |
359.2 |
0.1 |
| C1 |
N |
H1N |
H2N |
234.7 |
180.0 |
| C1 |
N |
H2N |
H1N |
133.8 |
180.0 |
| C5 |
C8 |
H81 |
H82 |
125.2 |
120.0 |
| C5 |
C8 |
H81 |
H83 |
234.7 |
240.0 |
| H82 |
C8 |
H81 |
H83 |
109.5 |
120.0 |
| C5 |
C8 |
H82 |
H81 |
230.5 |
240.1 |
| C5 |
C8 |
H82 |
H83 |
115.3 |
120.1 |
| H81 |
C8 |
H82 |
H83 |
244.8 |
240.0 |
| C5 |
C8 |
H83 |
H81 |
129.5 |
120.0 |
| C5 |
C8 |
H83 |
H82 |
244.7 |
239.9 |
| H81 |
C8 |
H83 |
H82 |
115.2 |
119.9 |
| C2 |
C9 |
H91 |
H92 |
125.3 |
120.0 |
| C2 |
C9 |
H91 |
H93 |
234.7 |
240.0 |
| H92 |
C9 |
H91 |
H93 |
109.4 |
120.0 |
| C2 |
C9 |
H92 |
H91 |
225.6 |
240.0 |
| C2 |
C9 |
H92 |
H93 |
112.7 |
120.1 |
| H91 |
C9 |
H92 |
H93 |
247.2 |
240.0 |
| C2 |
C9 |
H93 |
H91 |
134.5 |
119.9 |
| C2 |
C9 |
H93 |
H92 |
247.2 |
240.0 |
| H91 |
C9 |
H93 |
H92 |
112.8 |
120.0 |