PDB Chemical Component M5D
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 M5D
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N24 |
C23 |
1.137 |
1.136 |
| C18 |
C16 |
1.531 |
1.530 |
| C18 |
C19 |
1.533 |
1.530 |
| C21 |
C19 |
1.529 |
1.530 |
| C23 |
C2 |
1.429 |
1.432 |
| C16 |
C19 |
1.533 |
1.530 |
| C16 |
C14 |
1.515 |
1.507 |
| C30 |
N28 |
1.463 |
1.464 |
| N28 |
N27 |
1.396 |
1.400 |
| N28 |
C29 |
1.341 |
1.346 |
| C2 |
N3 |
1.333 |
1.332 |
| C2 |
C1 |
1.421 |
1.407 |
| N27 |
C26 |
1.305 |
1.305 |
| C29 |
C25 |
1.370 |
1.367 |
| C26 |
C25 |
1.409 |
1.411 |
| C25 |
C1 |
1.486 |
1.481 |
| N3 |
C4 |
1.318 |
1.316 |
| C1 |
N6 |
1.337 |
1.329 |
| C14 |
O15 |
1.220 |
1.212 |
| C14 |
N11 |
1.368 |
1.348 |
| C4 |
C5 |
1.415 |
1.399 |
| N6 |
C5 |
1.339 |
1.326 |
| C5 |
N7 |
1.411 |
1.386 |
| C9 |
N11 |
1.484 |
1.471 |
| C9 |
C22 |
1.532 |
1.531 |
| C9 |
C8 |
1.548 |
1.532 |
| N11 |
C12 |
1.481 |
1.470 |
| N7 |
C8 |
1.490 |
1.469 |
| N7 |
C13 |
1.488 |
1.469 |
| C13 |
C12 |
1.539 |
1.533 |
| C4 |
H1 |
1.080 |
1.080 |
| C8 |
H2 |
1.100 |
1.090 |
| C8 |
H3 |
1.100 |
1.089 |
| C12 |
H4 |
1.100 |
1.090 |
| C12 |
H5 |
1.100 |
1.090 |
| C16 |
H6 |
1.100 |
1.089 |
| C18 |
H7 |
1.100 |
1.090 |
| C18 |
H8 |
1.100 |
1.090 |
| C19 |
H9 |
1.100 |
1.090 |
| C21 |
H10 |
1.100 |
1.091 |
| C21 |
H11 |
1.100 |
1.090 |
| C21 |
H12 |
1.100 |
1.089 |
| C30 |
H13 |
1.100 |
1.090 |
| C30 |
H14 |
1.100 |
1.091 |
| C30 |
H15 |
1.100 |
1.090 |
| C9 |
H16 |
1.100 |
1.089 |
| C13 |
H17 |
1.100 |
1.090 |
| C13 |
H18 |
1.099 |
1.090 |
| C22 |
H19 |
1.100 |
1.090 |
| C22 |
H20 |
1.100 |
1.090 |
| C22 |
H21 |
1.100 |
1.090 |
| C26 |
H22 |
1.079 |
1.080 |
| C29 |
H23 |
1.080 |
1.080 |
Bond Angles for M5D
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C18 |
C16 |
C19 |
60.0 |
60.0 |
| C18 |
C16 |
C14 |
118.6 |
117.5 |
| C18 |
C16 |
H6 |
116.4 |
117.5 |
| C16 |
C19 |
C18 |
59.9 |
60.0 |
| C19 |
C18 |
H7 |
120.0 |
117.5 |
| C19 |
C18 |
H8 |
120.0 |
117.5 |
| C18 |
C19 |
H9 |
116.1 |
117.5 |
| C21 |
C19 |
H9 |
116.1 |
115.5 |
| C23 |
C2 |
N3 |
117.5 |
120.1 |
| C19 |
C16 |
C14 |
116.6 |
117.5 |
| C19 |
C16 |
H6 |
116.4 |
117.5 |
| C16 |
C19 |
H9 |
116.1 |
117.5 |
| C16 |
C14 |
O15 |
117.4 |
120.0 |
| C16 |
C14 |
N11 |
122.4 |
119.9 |
| C14 |
C16 |
H6 |
116.7 |
115.6 |
| C30 |
N28 |
N27 |
126.4 |
125.8 |
| C30 |
N28 |
C29 |
125.0 |
125.9 |
| N28 |
C30 |
H13 |
109.5 |
109.5 |
| N28 |
C30 |
H14 |
109.5 |
109.5 |
| N28 |
C30 |
H15 |
109.5 |
109.5 |
| N28 |
C29 |
H23 |
126.1 |
126.2 |
| C2 |
N3 |
C4 |
121.7 |
120.1 |
| C2 |
C1 |
N6 |
118.5 |
119.7 |
| N27 |
C26 |
H22 |
125.6 |
126.0 |
| N3 |
C4 |
H1 |
119.5 |
119.9 |
| C1 |
N6 |
C5 |
122.9 |
119.9 |
| C4 |
C5 |
N7 |
122.9 |
119.9 |
| C5 |
C4 |
H1 |
119.5 |
119.8 |
| N6 |
C5 |
N7 |
120.0 |
119.9 |
| C5 |
N7 |
C8 |
121.8 |
111.0 |
| C5 |
N7 |
C13 |
122.5 |
111.0 |
| N11 |
C9 |
C22 |
110.7 |
109.6 |
| N11 |
C9 |
H16 |
108.8 |
109.6 |
| C22 |
C9 |
H16 |
108.2 |
109.8 |
| C9 |
C22 |
H19 |
109.5 |
109.4 |
| C9 |
C22 |
H20 |
109.5 |
109.5 |
| C9 |
C22 |
H21 |
109.5 |
109.4 |
| C9 |
C8 |
H2 |
109.7 |
109.5 |
| C9 |
C8 |
H3 |
109.7 |
109.5 |
| N11 |
C12 |
H4 |
110.0 |
109.6 |
| N11 |
C12 |
H5 |
110.0 |
109.6 |
| N7 |
C8 |
H2 |
109.7 |
109.5 |
| N7 |
C8 |
H3 |
109.7 |
109.5 |
| N7 |
C13 |
H17 |
109.2 |
109.5 |
| N7 |
C13 |
H18 |
109.2 |
109.5 |
| C13 |
C12 |
H4 |
110.0 |
109.6 |
| C13 |
C12 |
H5 |
110.0 |
109.7 |
| H2 |
C8 |
H3 |
109.4 |
109.5 |
| H4 |
C12 |
H5 |
109.5 |
109.6 |
| H7 |
C18 |
H8 |
109.5 |
115.6 |
| H10 |
C21 |
H11 |
109.5 |
109.5 |
| H10 |
C21 |
H12 |
109.4 |
109.5 |
| H11 |
C21 |
H12 |
109.5 |
109.5 |
| H13 |
C30 |
H14 |
109.5 |
109.5 |
| H13 |
C30 |
H15 |
109.4 |
109.5 |
| H14 |
C30 |
H15 |
109.5 |
109.4 |
| H17 |
C13 |
H18 |
109.4 |
109.5 |
| H19 |
C22 |
H20 |
109.5 |
109.5 |
| H19 |
C22 |
H21 |
109.5 |
109.5 |
| H20 |
C22 |
H21 |
109.5 |
109.5 |
Torsion Angles for M5D
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C16 |
C19 |
C18 |
C16 |
-0.0 |
360.0 |
| C19 |
C16 |
C18 |
C14 |
105.9 |
107.5 |
| C19 |
C16 |
C18 |
H6 |
253.3 |
252.5 |
| C18 |
C16 |
C19 |
H9 |
253.6 |
252.5 |
| C18 |
C16 |
C14 |
O15 |
344.2 |
68.6 |
| C18 |
C16 |
C14 |
N11 |
163.6 |
248.6 |
| C14 |
C16 |
C18 |
H6 |
147.4 |
145.0 |
| C19 |
C18 |
C16 |
C19 |
360.0 |
-0.0 |
| C19 |
C18 |
C16 |
C14 |
254.1 |
252.5 |
| C19 |
C18 |
C16 |
H6 |
106.7 |
107.5 |
| C21 |
C19 |
C18 |
H9 |
143.6 |
145.0 |
| C18 |
C19 |
C16 |
C14 |
109.3 |
107.5 |
| C18 |
C19 |
C16 |
H6 |
253.3 |
252.5 |
| C16 |
C19 |
C18 |
H9 |
253.6 |
252.5 |
| H7 |
C18 |
C19 |
H8 |
141.1 |
145.0 |
| C21 |
C19 |
C18 |
H7 |
140.5 |
145.0 |
| C21 |
C19 |
C18 |
H8 |
359.4 |
0.0 |
| C18 |
C19 |
C21 |
H9 |
216.4 |
214.3 |
| C21 |
C19 |
C16 |
C14 |
215.5 |
215.0 |
| C21 |
C19 |
C16 |
H6 |
359.6 |
360.0 |
| C16 |
C19 |
C21 |
H9 |
147.3 |
145.7 |
| C23 |
C2 |
N3 |
C4 |
180.1 |
179.9 |
| C23 |
C2 |
C1 |
N6 |
179.4 |
180.0 |
| C18 |
C16 |
C19 |
C14 |
250.7 |
252.5 |
| C18 |
C16 |
C19 |
H6 |
106.7 |
107.5 |
| C16 |
C19 |
C18 |
H7 |
250.5 |
252.5 |
| C16 |
C19 |
C18 |
H8 |
109.5 |
107.5 |
| C18 |
C19 |
C16 |
H9 |
106.4 |
107.5 |
| C21 |
C19 |
C16 |
H9 |
212.7 |
215.0 |
| C19 |
C16 |
C14 |
O15 |
275.4 |
0.0 |
| C19 |
C16 |
C14 |
N11 |
94.9 |
180.0 |
| C14 |
C16 |
C19 |
H6 |
215.9 |
215.0 |
| C18 |
C16 |
C14 |
C19 |
68.7 |
68.6 |
| C18 |
C16 |
C14 |
H6 |
212.7 |
214.3 |
| C14 |
C16 |
C19 |
C18 |
109.3 |
107.5 |
| C19 |
C16 |
C14 |
H6 |
143.9 |
145.7 |
| C14 |
C16 |
C19 |
H9 |
2.8 |
360.0 |
| C30 |
N28 |
C29 |
H23 |
0.2 |
0.1 |
| H13 |
C30 |
N28 |
H14 |
240.0 |
240.0 |
| H13 |
C30 |
N28 |
H15 |
120.0 |
120.1 |
| H14 |
C30 |
N28 |
H15 |
240.0 |
240.1 |
| C30 |
N28 |
N27 |
C29 |
179.2 |
180.2 |
| N27 |
N28 |
C30 |
H13 |
360.0 |
90.1 |
| N27 |
N28 |
C30 |
H14 |
120.0 |
210.1 |
| N27 |
N28 |
C30 |
H15 |
240.0 |
330.0 |
| N28 |
N27 |
C26 |
H22 |
180.1 |
180.0 |
| C30 |
N28 |
C29 |
N27 |
180.7 |
179.8 |
| C29 |
N28 |
C30 |
H13 |
179.1 |
270.3 |
| C29 |
N28 |
C30 |
H14 |
299.1 |
30.3 |
| C29 |
N28 |
C30 |
H15 |
59.1 |
150.2 |
| N3 |
C2 |
C1 |
N6 |
359.7 |
0.0 |
| C2 |
N3 |
C4 |
H1 |
180.2 |
180.0 |
| C2 |
C1 |
N6 |
C5 |
0.8 |
0.0 |
| C30 |
N28 |
N27 |
C26 |
179.6 |
180.0 |
| C30 |
N28 |
C29 |
C25 |
180.2 |
180.2 |
| N3 |
C4 |
C5 |
N7 |
180.6 |
179.9 |
| C5 |
C4 |
N3 |
H1 |
180.0 |
180.1 |
| C1 |
N6 |
C5 |
N7 |
178.9 |
180.0 |
| C16 |
C14 |
O15 |
N11 |
179.5 |
180.0 |
| O15 |
C14 |
C16 |
H6 |
131.5 |
214.4 |
| C16 |
C14 |
N11 |
O15 |
180.6 |
180.0 |
| N11 |
C14 |
C16 |
H6 |
311.0 |
34.3 |
| C14 |
N11 |
C9 |
C22 |
276.7 |
350.9 |
| C14 |
N11 |
C9 |
H16 |
35.4 |
111.5 |
| C14 |
N11 |
C12 |
H4 |
7.2 |
248.5 |
| C14 |
N11 |
C12 |
H5 |
127.9 |
8.9 |
| C2 |
N3 |
C4 |
C5 |
0.3 |
0.0 |
| N3 |
C4 |
C5 |
H1 |
180.0 |
179.9 |
| C1 |
N6 |
C5 |
C4 |
359.2 |
360.0 |
| N6 |
C5 |
C4 |
N7 |
179.6 |
180.1 |
| C4 |
C5 |
N7 |
C8 |
165.6 |
0.0 |
| C4 |
C5 |
N7 |
C13 |
346.8 |
124.3 |
| C4 |
C5 |
N6 |
N7 |
180.3 |
179.9 |
| N6 |
C5 |
C4 |
H1 |
180.2 |
180.0 |
| N6 |
C5 |
N7 |
C8 |
345.9 |
180.0 |
| N6 |
C5 |
N7 |
C13 |
167.2 |
304.2 |
| N7 |
C5 |
C4 |
H1 |
0.6 |
360.0 |
| C5 |
N7 |
C8 |
H2 |
123.4 |
307.2 |
| C5 |
N7 |
C8 |
H3 |
3.1 |
67.3 |
| C5 |
N7 |
C13 |
H17 |
277.8 |
52.8 |
| C5 |
N7 |
C13 |
H18 |
37.5 |
292.7 |
| C16 |
C14 |
N11 |
C9 |
1.3 |
184.9 |
| C22 |
C9 |
N11 |
H16 |
241.3 |
239.5 |
| N11 |
C9 |
C22 |
H19 |
180.0 |
66.4 |
| N11 |
C9 |
C22 |
H20 |
300.0 |
186.4 |
| N11 |
C9 |
C22 |
H21 |
60.0 |
306.4 |
| N11 |
C9 |
C8 |
H2 |
83.6 |
186.2 |
| N11 |
C9 |
C8 |
H3 |
203.8 |
66.2 |
| C9 |
N11 |
C12 |
H4 |
185.9 |
68.5 |
| C9 |
N11 |
C12 |
H5 |
306.6 |
188.9 |
| N11 |
C9 |
C22 |
H16 |
119.1 |
120.5 |
| C22 |
C9 |
C8 |
H2 |
320.5 |
66.5 |
| C22 |
C9 |
C8 |
H3 |
80.8 |
306.5 |
| H19 |
C22 |
C9 |
H20 |
240.0 |
240.0 |
| H19 |
C22 |
C9 |
H21 |
120.0 |
120.0 |
| H20 |
C22 |
C9 |
H21 |
240.0 |
240.0 |
| N7 |
C8 |
C9 |
H2 |
240.1 |
119.9 |
| N7 |
C8 |
C9 |
H3 |
119.9 |
240.0 |
| H2 |
C8 |
C9 |
H3 |
239.7 |
120.0 |
| C13 |
C12 |
N11 |
H4 |
240.3 |
240.3 |
| C13 |
C12 |
N11 |
H5 |
119.7 |
119.9 |
| H4 |
C12 |
N11 |
H5 |
239.3 |
239.6 |
| C5 |
N7 |
C8 |
C13 |
181.2 |
124.1 |
| C9 |
C8 |
N7 |
H2 |
119.9 |
240.1 |
| C9 |
C8 |
N7 |
H3 |
240.1 |
120.0 |
| H2 |
C8 |
N7 |
H3 |
120.3 |
239.9 |
| C5 |
N7 |
C13 |
C8 |
178.8 |
235.9 |
| C13 |
N7 |
C8 |
H2 |
302.2 |
183.1 |
| C13 |
N7 |
C8 |
H3 |
182.0 |
303.2 |
| N7 |
C13 |
C12 |
H4 |
200.6 |
294.1 |
| N7 |
C13 |
C12 |
H5 |
79.9 |
173.7 |
| H17 |
C13 |
N7 |
H18 |
240.4 |
120.1 |
| C5 |
N7 |
C13 |
C12 |
157.7 |
172.8 |
| N11 |
C12 |
C13 |
H4 |
119.7 |
119.7 |
| N11 |
C12 |
C13 |
H5 |
240.3 |
240.2 |
| H4 |
C12 |
C13 |
H5 |
120.7 |
120.5 |
| H1 |
C4 |
C5 |
N7 |
0.6 |
360.0 |
| C9 |
C8 |
H2 |
H3 |
120.4 |
240.0 |
| N7 |
C8 |
H2 |
H3 |
239.6 |
120.1 |
| C9 |
C8 |
H3 |
H2 |
239.6 |
120.0 |
| N7 |
C8 |
H3 |
H2 |
120.4 |
239.9 |
| N11 |
C12 |
H4 |
H5 |
121.0 |
120.4 |
| C13 |
C12 |
H4 |
H5 |
239.0 |
239.5 |
| N11 |
C12 |
H5 |
H4 |
239.0 |
239.6 |
| C13 |
C12 |
H5 |
H4 |
121.0 |
120.5 |
| C18 |
C16 |
H6 |
C19 |
292.1 |
291.4 |
| C18 |
C16 |
H6 |
C14 |
148.1 |
145.7 |
| H6 |
C16 |
C19 |
C18 |
253.3 |
252.5 |
| C19 |
C16 |
H6 |
C14 |
216.0 |
214.3 |
| H6 |
C16 |
C19 |
H9 |
146.9 |
145.0 |
| H6 |
C16 |
C14 |
O15 |
131.5 |
214.4 |
| H6 |
C16 |
C14 |
N11 |
311.0 |
34.3 |
| H7 |
C18 |
C16 |
C19 |
109.5 |
107.5 |
| H7 |
C18 |
C16 |
C14 |
3.6 |
360.0 |
| H7 |
C18 |
C16 |
H6 |
216.1 |
214.9 |
| C19 |
C18 |
H7 |
H8 |
215.3 |
214.3 |
| H7 |
C18 |
C19 |
H9 |
357.0 |
0.0 |
| H8 |
C18 |
C16 |
C19 |
250.5 |
252.5 |
| H8 |
C18 |
C16 |
C14 |
144.6 |
145.1 |
| H8 |
C18 |
C16 |
H6 |
357.2 |
0.0 |
| C19 |
C18 |
H8 |
H7 |
144.7 |
145.7 |
| H8 |
C18 |
C19 |
H9 |
215.9 |
215.0 |
| C16 |
C19 |
H9 |
C18 |
67.6 |
68.6 |
| H9 |
C19 |
C18 |
H7 |
357.0 |
0.0 |
| H9 |
C19 |
C18 |
H8 |
215.9 |
215.0 |
| H9 |
C19 |
C16 |
C14 |
2.8 |
360.0 |
| H9 |
C19 |
C16 |
H6 |
146.9 |
145.0 |
| H10 |
C21 |
C19 |
H9 |
323.5 |
274.3 |
| H11 |
C21 |
H10 |
H12 |
120.0 |
120.1 |
| H11 |
C21 |
C19 |
H9 |
83.5 |
34.3 |
| H10 |
C21 |
H11 |
H12 |
240.0 |
239.9 |
| H12 |
C21 |
C19 |
H9 |
203.6 |
154.3 |
| H10 |
C21 |
H12 |
H11 |
120.0 |
120.1 |
| H13 |
C30 |
N28 |
N27 |
360.0 |
90.1 |
| H13 |
C30 |
N28 |
C29 |
179.1 |
270.3 |
| N28 |
C30 |
H13 |
H14 |
120.0 |
120.0 |
| N28 |
C30 |
H13 |
H15 |
240.0 |
239.9 |
| H14 |
C30 |
H13 |
H15 |
120.0 |
119.9 |
| H14 |
C30 |
N28 |
N27 |
120.0 |
210.1 |
| H14 |
C30 |
N28 |
C29 |
299.1 |
30.3 |
| N28 |
C30 |
H14 |
H13 |
240.0 |
240.0 |
| N28 |
C30 |
H14 |
H15 |
120.0 |
120.0 |
| H13 |
C30 |
H14 |
H15 |
240.1 |
240.0 |
| H15 |
C30 |
N28 |
N27 |
240.0 |
330.0 |
| H15 |
C30 |
N28 |
C29 |
59.1 |
150.2 |
| N28 |
C30 |
H15 |
H13 |
120.0 |
120.0 |
| N28 |
C30 |
H15 |
H14 |
240.0 |
240.0 |
| H13 |
C30 |
H15 |
H14 |
120.0 |
120.0 |
| N11 |
C9 |
H16 |
C22 |
239.7 |
239.5 |
| H16 |
C9 |
C22 |
H19 |
60.9 |
306.0 |
| H16 |
C9 |
C22 |
H20 |
180.9 |
65.9 |
| H16 |
C9 |
C22 |
H21 |
300.9 |
186.0 |
| H16 |
C9 |
C8 |
H2 |
202.1 |
305.9 |
| H16 |
C9 |
C8 |
H3 |
322.3 |
185.9 |
| N7 |
C13 |
H17 |
H18 |
119.5 |
240.0 |
| H17 |
C13 |
C12 |
H4 |
80.4 |
54.1 |
| H17 |
C13 |
C12 |
H5 |
319.7 |
293.6 |
| N7 |
C13 |
H18 |
H17 |
240.5 |
120.0 |
| H18 |
C13 |
C12 |
H4 |
320.7 |
174.2 |
| H18 |
C13 |
C12 |
H5 |
200.1 |
53.7 |
| H19 |
C22 |
C9 |
H16 |
60.9 |
306.0 |
| C9 |
C22 |
H19 |
H20 |
120.0 |
120.0 |
| C9 |
C22 |
H19 |
H21 |
240.0 |
240.1 |
| H20 |
C22 |
H19 |
H21 |
120.0 |
120.1 |
| H20 |
C22 |
C9 |
H16 |
180.9 |
65.9 |
| C9 |
C22 |
H20 |
H19 |
240.0 |
240.0 |
| C9 |
C22 |
H20 |
H21 |
120.0 |
120.0 |
| H19 |
C22 |
H20 |
H21 |
240.0 |
240.0 |
| H21 |
C22 |
C9 |
H16 |
300.9 |
186.0 |
| C9 |
C22 |
H21 |
H19 |
120.0 |
120.0 |
| C9 |
C22 |
H21 |
H20 |
240.0 |
240.0 |
| H19 |
C22 |
H21 |
H20 |
120.0 |
120.0 |