PDB Chemical Component 3DB
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 3DB
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
C1 |
C2 |
1.395 |
1.382 |
C1 |
C6 |
1.386 |
1.382 |
C2 |
C3 |
1.389 |
1.383 |
C3 |
C4 |
1.390 |
1.383 |
C4 |
C5 |
1.395 |
1.383 |
C5 |
C6 |
1.385 |
1.382 |
C6 |
S1 |
1.612 |
1.762 |
S1 |
O1 |
1.469 |
1.421 |
S1 |
O2 |
1.481 |
1.421 |
S1 |
N1 |
1.505 |
1.656 |
N1 |
C7 |
1.355 |
1.386 |
C7 |
S2 |
1.711 |
1.765 |
C7 |
N2 |
1.354 |
1.303 |
S2 |
C8 |
1.723 |
1.765 |
N2 |
N3 |
1.424 |
1.262 |
N3 |
C8 |
1.351 |
1.293 |
C8 |
S3 |
1.660 |
1.761 |
S3 |
O3 |
1.432 |
1.422 |
S3 |
O4 |
1.410 |
1.421 |
S3 |
N4 |
1.602 |
1.656 |
C1 |
H1 |
1.080 |
1.080 |
C2 |
H2 |
1.080 |
1.080 |
C3 |
H3 |
1.080 |
1.079 |
C4 |
H4 |
1.080 |
1.080 |
C5 |
H5 |
1.080 |
1.081 |
N1 |
HN1 |
1.000 |
0.970 |
N4 |
HN4 |
1.000 |
0.970 |
N4 |
HN4A |
1.000 |
0.970 |
Bond Angles for 3DB
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
C2 |
C1 |
C6 |
118.8 |
120.0 |
C1 |
C2 |
C3 |
119.2 |
120.0 |
C2 |
C1 |
H1 |
120.6 |
120.0 |
C1 |
C2 |
H2 |
120.4 |
120.0 |
C1 |
C6 |
C5 |
122.3 |
120.0 |
C1 |
C6 |
S1 |
117.7 |
120.0 |
C6 |
C1 |
H1 |
120.6 |
120.0 |
C2 |
C3 |
C4 |
121.7 |
120.0 |
C3 |
C2 |
H2 |
120.4 |
120.0 |
C2 |
C3 |
H3 |
119.2 |
120.0 |
C3 |
C4 |
C5 |
119.1 |
120.0 |
C4 |
C3 |
H3 |
119.1 |
120.0 |
C3 |
C4 |
H4 |
120.5 |
120.0 |
C4 |
C5 |
C6 |
118.9 |
120.0 |
C5 |
C4 |
H4 |
120.4 |
120.1 |
C4 |
C5 |
H5 |
120.5 |
119.9 |
C5 |
C6 |
S1 |
120.0 |
120.0 |
C6 |
C5 |
H5 |
120.5 |
120.0 |
C6 |
S1 |
O1 |
104.6 |
106.4 |
C6 |
S1 |
O2 |
108.2 |
106.4 |
C6 |
S1 |
N1 |
106.2 |
107.2 |
O1 |
S1 |
O2 |
110.5 |
123.1 |
O1 |
S1 |
N1 |
117.4 |
106.4 |
O2 |
S1 |
N1 |
109.4 |
106.4 |
S1 |
N1 |
C7 |
128.7 |
120.0 |
S1 |
N1 |
HN1 |
103.5 |
120.0 |
N1 |
C7 |
S2 |
122.9 |
126.2 |
N1 |
C7 |
N2 |
124.8 |
126.2 |
C7 |
N1 |
HN1 |
103.5 |
120.0 |
S2 |
C7 |
N2 |
112.3 |
107.7 |
C7 |
S2 |
C8 |
90.9 |
88.9 |
C7 |
N2 |
N3 |
112.5 |
117.6 |
S2 |
C8 |
N3 |
112.4 |
107.8 |
S2 |
C8 |
S3 |
122.0 |
126.1 |
N2 |
N3 |
C8 |
112.0 |
118.0 |
N3 |
C8 |
S3 |
124.7 |
126.1 |
C8 |
S3 |
O3 |
106.4 |
106.4 |
C8 |
S3 |
O4 |
109.8 |
106.4 |
C8 |
S3 |
N4 |
108.1 |
107.2 |
O3 |
S3 |
O4 |
112.9 |
123.1 |
O3 |
S3 |
N4 |
108.5 |
106.4 |
O4 |
S3 |
N4 |
111.0 |
106.4 |
S3 |
N4 |
HN4 |
109.5 |
120.0 |
S3 |
N4 |
HN4A |
109.4 |
120.0 |
HN4 |
N4 |
HN4A |
109.5 |
120.0 |
Torsion Angles for 3DB
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
C2 |
C1 |
C6 |
C5 |
359.0 |
0.1 |
C2 |
C1 |
C6 |
S1 |
180.3 |
180.0 |
C6 |
C1 |
C2 |
H1 |
180.0 |
180.3 |
C1 |
C2 |
C3 |
C4 |
0.7 |
359.9 |
C3 |
C2 |
C1 |
H2 |
180.0 |
180.1 |
C1 |
C2 |
C3 |
H3 |
180.7 |
179.9 |
C6 |
C1 |
C2 |
C3 |
0.4 |
0.0 |
C2 |
C1 |
C6 |
H1 |
180.0 |
179.7 |
C6 |
C1 |
C2 |
H2 |
180.4 |
179.9 |
C4 |
C5 |
C6 |
C1 |
0.5 |
359.9 |
C5 |
C6 |
C1 |
S1 |
178.7 |
180.1 |
C1 |
C6 |
C5 |
H5 |
180.5 |
180.0 |
C1 |
C6 |
S1 |
O1 |
28.9 |
203.6 |
C1 |
C6 |
S1 |
O2 |
146.7 |
336.5 |
C1 |
C6 |
S1 |
N1 |
264.1 |
90.0 |
C3 |
C2 |
C1 |
C6 |
0.4 |
0.0 |
C3 |
C2 |
C1 |
H1 |
180.4 |
179.7 |
C1 |
C2 |
C3 |
H2 |
180.0 |
179.9 |
C2 |
C3 |
C4 |
C5 |
358.8 |
360.0 |
C4 |
C3 |
C2 |
H3 |
180.0 |
180.0 |
C2 |
C3 |
C4 |
H4 |
178.8 |
180.0 |
C4 |
C3 |
C2 |
H2 |
180.7 |
180.1 |
C2 |
C3 |
C4 |
H3 |
180.0 |
180.0 |
C3 |
C4 |
C5 |
C6 |
0.6 |
0.1 |
C5 |
C4 |
C3 |
H4 |
180.0 |
180.0 |
C3 |
C4 |
C5 |
H5 |
180.6 |
180.0 |
C1 |
C6 |
C5 |
C4 |
0.5 |
359.9 |
C5 |
C4 |
C3 |
H3 |
178.8 |
180.0 |
C3 |
C4 |
C5 |
H4 |
180.0 |
180.0 |
C4 |
C5 |
C6 |
S1 |
179.1 |
180.0 |
C6 |
C5 |
C4 |
H5 |
180.0 |
180.1 |
C1 |
C6 |
C5 |
S1 |
181.3 |
179.9 |
C5 |
C6 |
C1 |
H1 |
179.0 |
180.4 |
C6 |
C5 |
C4 |
H4 |
180.6 |
180.1 |
C4 |
C5 |
C6 |
H5 |
180.0 |
179.9 |
C5 |
C6 |
S1 |
O1 |
210.1 |
23.5 |
C5 |
C6 |
S1 |
O2 |
328.0 |
156.4 |
C5 |
C6 |
S1 |
N1 |
85.4 |
269.9 |
C1 |
C6 |
S1 |
C5 |
178.7 |
180.1 |
S1 |
C6 |
C1 |
H1 |
0.3 |
0.3 |
S1 |
C6 |
C5 |
H5 |
359.1 |
0.1 |
O1 |
S1 |
C6 |
O2 |
242.2 |
227.1 |
O1 |
S1 |
C6 |
N1 |
124.8 |
113.6 |
O2 |
S1 |
C6 |
N1 |
242.6 |
246.5 |
C6 |
S1 |
N1 |
C7 |
99.6 |
65.0 |
C6 |
S1 |
N1 |
HN1 |
219.6 |
245.0 |
C6 |
S1 |
O1 |
O2 |
116.3 |
123.0 |
C6 |
S1 |
O1 |
N1 |
242.7 |
245.9 |
O2 |
S1 |
O1 |
N1 |
126.4 |
122.9 |
O1 |
S1 |
N1 |
C7 |
343.1 |
311.5 |
O1 |
S1 |
N1 |
HN1 |
103.1 |
131.4 |
C6 |
S1 |
O2 |
O1 |
246.0 |
237.0 |
C6 |
S1 |
O2 |
N1 |
115.3 |
114.1 |
O1 |
S1 |
O2 |
N1 |
229.3 |
237.1 |
O2 |
S1 |
N1 |
C7 |
216.2 |
178.6 |
O2 |
S1 |
N1 |
HN1 |
336.2 |
358.5 |
C6 |
S1 |
N1 |
O1 |
116.5 |
113.6 |
C6 |
S1 |
N1 |
O2 |
243.4 |
246.5 |
O1 |
S1 |
N1 |
O2 |
126.9 |
132.9 |
S1 |
N1 |
C7 |
S2 |
30.5 |
180.0 |
S1 |
N1 |
C7 |
N2 |
209.2 |
359.6 |
C7 |
N1 |
S1 |
HN1 |
240.0 |
180.0 |
S1 |
N1 |
C7 |
HN1 |
120.0 |
180.0 |
S2 |
C7 |
N1 |
N2 |
181.3 |
180.4 |
N1 |
C7 |
S2 |
C8 |
178.8 |
180.0 |
N1 |
C7 |
N2 |
N3 |
180.8 |
180.0 |
N1 |
C7 |
S2 |
N2 |
178.8 |
179.7 |
S2 |
C7 |
N1 |
HN1 |
270.5 |
0.0 |
S2 |
C7 |
N2 |
N3 |
359.6 |
359.7 |
C7 |
S2 |
C8 |
N3 |
0.4 |
359.8 |
C7 |
S2 |
C8 |
S3 |
191.0 |
180.0 |
N1 |
C7 |
N2 |
S2 |
181.2 |
180.3 |
N2 |
C7 |
N1 |
HN1 |
89.1 |
179.7 |
N2 |
C7 |
S2 |
C8 |
360.0 |
0.3 |
C7 |
N2 |
N3 |
C8 |
0.7 |
0.1 |
C8 |
S2 |
C7 |
N2 |
360.0 |
0.3 |
N2 |
N3 |
C8 |
S2 |
359.3 |
0.1 |
N3 |
C8 |
S2 |
S3 |
169.5 |
179.7 |
S2 |
C8 |
S3 |
O3 |
254.9 |
293.5 |
S2 |
C8 |
S3 |
O4 |
17.4 |
66.4 |
S2 |
C8 |
S3 |
N4 |
138.6 |
180.0 |
S2 |
C8 |
N3 |
N2 |
359.3 |
0.1 |
N2 |
N3 |
C8 |
S3 |
168.4 |
179.9 |
S2 |
C8 |
N3 |
S3 |
190.9 |
180.3 |
N3 |
C8 |
S3 |
O3 |
86.8 |
113.8 |
N3 |
C8 |
S3 |
O4 |
209.3 |
246.7 |
N3 |
C8 |
S3 |
N4 |
330.5 |
0.3 |
S2 |
C8 |
S3 |
N3 |
168.1 |
179.7 |
O3 |
S3 |
C8 |
O4 |
237.5 |
227.1 |
O3 |
S3 |
C8 |
N4 |
116.3 |
113.5 |
O4 |
S3 |
C8 |
N4 |
238.8 |
246.5 |
C8 |
S3 |
N4 |
HN4 |
325.0 |
360.0 |
C8 |
S3 |
N4 |
HN4A |
85.1 |
180.0 |
C8 |
S3 |
O3 |
O4 |
120.5 |
123.0 |
C8 |
S3 |
O3 |
N4 |
244.0 |
245.9 |
O4 |
S3 |
O3 |
N4 |
123.4 |
122.9 |
O3 |
S3 |
N4 |
HN4 |
210.1 |
246.4 |
O3 |
S3 |
N4 |
HN4A |
330.1 |
66.5 |
C8 |
S3 |
O4 |
O3 |
241.4 |
237.0 |
C8 |
S3 |
O4 |
N4 |
119.4 |
114.1 |
O3 |
S3 |
O4 |
N4 |
238.0 |
237.1 |
O4 |
S3 |
N4 |
HN4 |
85.5 |
113.5 |
O4 |
S3 |
N4 |
HN4A |
205.5 |
293.6 |
C8 |
S3 |
N4 |
O3 |
115.0 |
113.5 |
C8 |
S3 |
N4 |
O4 |
239.6 |
246.4 |
O3 |
S3 |
N4 |
O4 |
124.6 |
132.9 |
HN4 |
N4 |
S3 |
HN4A |
240.0 |
180.0 |
C2 |
C1 |
H1 |
C6 |
180.0 |
180.3 |
H1 |
C1 |
C2 |
C3 |
180.4 |
179.7 |
H1 |
C1 |
C2 |
H2 |
0.4 |
359.6 |
H1 |
C1 |
C6 |
C5 |
179.0 |
180.4 |
H1 |
C1 |
C6 |
S1 |
0.3 |
0.3 |
H2 |
C2 |
C1 |
C6 |
180.4 |
179.9 |
C1 |
C2 |
H2 |
C3 |
180.0 |
180.1 |
H2 |
C2 |
C1 |
H1 |
0.4 |
359.6 |
H2 |
C2 |
C3 |
C4 |
180.7 |
180.1 |
H2 |
C2 |
C3 |
H3 |
0.7 |
0.0 |
C2 |
C3 |
H3 |
C4 |
180.0 |
180.0 |
H3 |
C3 |
C2 |
H2 |
0.7 |
0.0 |
H3 |
C3 |
C4 |
C5 |
178.8 |
180.0 |
H3 |
C3 |
C4 |
H4 |
358.8 |
0.0 |
C3 |
C4 |
H4 |
C5 |
180.0 |
180.0 |
H4 |
C4 |
C3 |
H3 |
358.8 |
0.0 |
H4 |
C4 |
C5 |
C6 |
180.6 |
180.1 |
H4 |
C4 |
C5 |
H5 |
0.6 |
360.0 |
C4 |
C5 |
H5 |
C6 |
180.0 |
180.1 |
H5 |
C5 |
C4 |
H4 |
0.6 |
360.0 |
H5 |
C5 |
C6 |
S1 |
359.1 |
0.1 |
S1 |
N1 |
HN1 |
C7 |
224.1 |
180.0 |
HN1 |
N1 |
C7 |
S2 |
270.5 |
0.0 |
HN1 |
N1 |
C7 |
N2 |
89.1 |
179.7 |
S3 |
N4 |
HN4 |
HN4A |
120.0 |
180.0 |
S3 |
N4 |
HN4A |
HN4 |
240.0 |
180.0 |