PDB Chemical Component 678
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 678
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C1 |
C2 |
1.418 |
1.401 |
| C1 |
C6 |
1.424 |
1.391 |
| C1 |
C7 |
1.429 |
1.478 |
| C2 |
C3 |
1.396 |
1.365 |
| C2 |
HC2 |
1.076 |
1.080 |
| C3 |
C4 |
1.364 |
1.393 |
| C3 |
HC3 |
1.079 |
1.080 |
| C4 |
C5 |
1.332 |
1.410 |
| C4 |
N3 |
1.321 |
1.375 |
| C5 |
C6 |
1.397 |
1.394 |
| C5 |
CN4 |
1.340 |
1.464 |
| C6 |
HC6 |
1.083 |
1.081 |
| C7 |
N1 |
1.318 |
1.332 |
| C7 |
N2 |
1.317 |
1.332 |
| N1 |
HH11 |
0.998 |
0.969 |
| N1 |
HH12 |
0.998 |
0.970 |
| N2 |
HH21 |
1.000 |
0.970 |
| N2 |
HH22 |
0.999 |
0.969 |
| N3 |
C8 |
1.330 |
1.376 |
| N3 |
HN3 |
0.973 |
0.970 |
| CN4 |
C8 |
1.378 |
1.355 |
| CN4 |
HCN4 |
1.070 |
1.080 |
| C8 |
C1' |
1.427 |
1.479 |
| C1' |
C2' |
1.426 |
1.395 |
| C1' |
C6' |
1.375 |
1.400 |
| C2' |
C3' |
1.413 |
1.380 |
| C2' |
HC2' |
1.079 |
1.079 |
| C3' |
CV' |
1.566 |
1.507 |
| C3' |
C4' |
1.383 |
1.384 |
| CV' |
CW' |
1.520 |
1.507 |
| CV' |
H31B |
1.067 |
1.090 |
| CV' |
H31A |
1.077 |
1.089 |
| CW' |
OX' |
1.212 |
1.220 |
| CW' |
OY' |
1.221 |
1.220 |
| C4' |
C5' |
1.373 |
1.382 |
| C4' |
HC4' |
1.084 |
1.080 |
| C5' |
C6' |
1.394 |
1.386 |
| C5' |
BR5' |
1.922 |
1.891 |
| C6' |
O6' |
1.372 |
1.358 |
Bond Angles for 678
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
C1 |
C6 |
116.1 |
120.1 |
| C2 |
C1 |
C7 |
121.4 |
120.0 |
| C1 |
C2 |
C3 |
122.9 |
120.7 |
| C1 |
C2 |
HC2 |
119.2 |
119.6 |
| C6 |
C1 |
C7 |
122.5 |
120.0 |
| C1 |
C6 |
C5 |
119.6 |
119.4 |
| C1 |
C6 |
HC6 |
120.6 |
120.3 |
| C1 |
C7 |
N1 |
121.4 |
120.0 |
| C1 |
C7 |
N2 |
121.1 |
120.0 |
| C3 |
C2 |
HC2 |
117.9 |
119.7 |
| C2 |
C3 |
C4 |
116.8 |
120.3 |
| C2 |
C3 |
HC3 |
121.5 |
119.9 |
| C4 |
C3 |
HC3 |
121.7 |
119.9 |
| C3 |
C4 |
C5 |
123.9 |
119.6 |
| C3 |
C4 |
N3 |
128.6 |
133.0 |
| C5 |
C4 |
N3 |
107.4 |
107.4 |
| C4 |
C5 |
C6 |
120.6 |
120.0 |
| C4 |
C5 |
CN4 |
106.0 |
106.2 |
| C4 |
N3 |
C8 |
113.4 |
109.9 |
| C4 |
N3 |
HN3 |
123.2 |
125.0 |
| C6 |
C5 |
CN4 |
133.4 |
133.8 |
| C5 |
C6 |
HC6 |
119.8 |
120.3 |
| C5 |
CN4 |
C8 |
111.7 |
106.9 |
| C5 |
CN4 |
HCN4 |
125.1 |
126.5 |
| N1 |
C7 |
N2 |
117.4 |
120.0 |
| C7 |
N1 |
HH11 |
119.5 |
120.0 |
| C7 |
N1 |
HH12 |
120.7 |
120.0 |
| C7 |
N2 |
HH21 |
122.2 |
120.0 |
| C7 |
N2 |
HH22 |
118.2 |
120.0 |
| HH11 |
N1 |
HH12 |
119.8 |
120.0 |
| HH21 |
N2 |
HH22 |
119.6 |
120.0 |
| C8 |
N3 |
HN3 |
123.3 |
125.1 |
| N3 |
C8 |
CN4 |
101.5 |
109.6 |
| N3 |
C8 |
C1' |
125.3 |
125.2 |
| C8 |
CN4 |
HCN4 |
123.2 |
126.6 |
| CN4 |
C8 |
C1' |
132.7 |
125.2 |
| C8 |
C1' |
C2' |
121.8 |
120.1 |
| C8 |
C1' |
C6' |
122.8 |
120.1 |
| C2' |
C1' |
C6' |
115.4 |
119.7 |
| C1' |
C2' |
C3' |
123.5 |
119.9 |
| C1' |
C2' |
HC2' |
120.1 |
120.1 |
| C1' |
C6' |
C5' |
121.0 |
119.7 |
| C1' |
C6' |
O6' |
119.9 |
120.1 |
| C3' |
C2' |
HC2' |
116.4 |
120.1 |
| C2' |
C3' |
CV' |
118.4 |
119.8 |
| C2' |
C3' |
C4' |
118.5 |
120.3 |
| CV' |
C3' |
C4' |
123.1 |
119.9 |
| C3' |
CV' |
CW' |
116.3 |
109.4 |
| C3' |
CV' |
H31B |
108.9 |
109.5 |
| C3' |
CV' |
H31A |
109.0 |
109.5 |
| C3' |
C4' |
C5' |
118.2 |
120.4 |
| C3' |
C4' |
HC4' |
122.9 |
119.8 |
| CW' |
CV' |
H31B |
108.0 |
109.4 |
| CW' |
CV' |
H31A |
109.7 |
109.5 |
| CV' |
CW' |
OX' |
116.4 |
120.0 |
| CV' |
CW' |
OY' |
117.6 |
120.0 |
| H31B |
CV' |
H31A |
104.2 |
109.5 |
| OX' |
CW' |
OY' |
125.8 |
119.9 |
| C5' |
C4' |
HC4' |
118.9 |
119.9 |
| C4' |
C5' |
C6' |
123.5 |
120.1 |
| C4' |
C5' |
BR5' |
119.7 |
120.0 |
| C6' |
C5' |
BR5' |
116.8 |
119.9 |
| C5' |
C6' |
O6' |
119.1 |
120.2 |
Torsion Angles for 678
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C6 |
C1 |
C2 |
C7 |
180.4 |
180.2 |
| C2 |
C1 |
C6 |
C5 |
359.5 |
359.6 |
| C2 |
C1 |
C6 |
HC6 |
179.4 |
179.6 |
| C2 |
C1 |
C7 |
N1 |
181.5 |
180.0 |
| C2 |
C1 |
C7 |
N2 |
1.9 |
360.0 |
| C3 |
C2 |
C1 |
HC2 |
181.2 |
180.0 |
| C1 |
C2 |
C3 |
C4 |
359.7 |
0.1 |
| C1 |
C2 |
C3 |
HC3 |
179.9 |
180.0 |
| C2 |
C1 |
C6 |
C7 |
179.6 |
179.8 |
| C6 |
C1 |
C2 |
C3 |
0.9 |
0.2 |
| C6 |
C1 |
C2 |
HC2 |
179.7 |
180.2 |
| C6 |
C1 |
C7 |
N1 |
1.0 |
359.8 |
| C6 |
C1 |
C7 |
N2 |
181.4 |
179.8 |
| C4 |
C5 |
C6 |
C1 |
359.7 |
0.4 |
| C1 |
C6 |
C5 |
CN4 |
179.9 |
180.2 |
| C5 |
C6 |
C1 |
HC6 |
180.0 |
179.9 |
| C2 |
C1 |
C7 |
C6 |
180.5 |
180.2 |
| C7 |
C1 |
C2 |
C3 |
180.4 |
180.0 |
| C7 |
C1 |
C2 |
HC2 |
359.3 |
0.0 |
| C7 |
C1 |
C6 |
C5 |
179.9 |
179.8 |
| C7 |
C1 |
C6 |
HC6 |
359.8 |
359.8 |
| N1 |
C7 |
C1 |
N2 |
179.6 |
180.0 |
| C1 |
C7 |
N1 |
HH11 |
0.4 |
180.0 |
| C1 |
C7 |
N1 |
HH12 |
179.3 |
0.0 |
| C1 |
C7 |
N2 |
HH21 |
358.8 |
0.0 |
| C1 |
C7 |
N2 |
HH22 |
180.3 |
179.7 |
| C3 |
C2 |
C1 |
C6 |
0.9 |
0.2 |
| C3 |
C2 |
C1 |
C7 |
180.4 |
180.0 |
| C1 |
C2 |
C3 |
HC2 |
178.8 |
180.0 |
| C4 |
C3 |
C2 |
HC3 |
179.8 |
180.1 |
| C2 |
C3 |
C4 |
C5 |
359.3 |
359.9 |
| C2 |
C3 |
C4 |
N3 |
181.0 |
180.0 |
| HC2 |
C2 |
C1 |
C6 |
179.7 |
180.2 |
| HC2 |
C2 |
C1 |
C7 |
359.3 |
0.0 |
| C1 |
C2 |
HC2 |
C3 |
181.1 |
180.0 |
| HC2 |
C2 |
C3 |
C4 |
180.9 |
180.0 |
| HC2 |
C2 |
C3 |
HC3 |
1.1 |
360.0 |
| C4 |
C3 |
C2 |
HC2 |
180.9 |
180.0 |
| C2 |
C3 |
C4 |
HC3 |
180.2 |
179.9 |
| C5 |
C4 |
C3 |
N3 |
178.3 |
180.0 |
| C3 |
C4 |
C5 |
C6 |
1.0 |
359.8 |
| C3 |
C4 |
C5 |
CN4 |
180.8 |
180.0 |
| C3 |
C4 |
N3 |
C8 |
179.1 |
180.0 |
| C3 |
C4 |
N3 |
HN3 |
358.9 |
360.0 |
| HC3 |
C3 |
C2 |
HC2 |
1.1 |
360.0 |
| C2 |
C3 |
HC3 |
C4 |
179.8 |
180.1 |
| HC3 |
C3 |
C4 |
C5 |
179.1 |
180.0 |
| HC3 |
C3 |
C4 |
N3 |
0.8 |
0.1 |
| C1 |
C6 |
C5 |
C4 |
359.7 |
0.4 |
| C5 |
C4 |
C3 |
HC3 |
179.1 |
180.0 |
| C3 |
C4 |
C5 |
N3 |
181.4 |
180.0 |
| C5 |
C4 |
N3 |
C8 |
0.6 |
0.0 |
| C5 |
C4 |
N3 |
HN3 |
180.4 |
180.0 |
| C6 |
C5 |
C4 |
CN4 |
180.2 |
179.8 |
| C4 |
C5 |
C6 |
HC6 |
179.7 |
180.4 |
| C4 |
C5 |
CN4 |
C8 |
0.4 |
0.0 |
| C4 |
C5 |
CN4 |
HCN4 |
180.7 |
180.0 |
| N3 |
C4 |
C3 |
HC3 |
0.8 |
0.1 |
| C3 |
C4 |
N3 |
C5 |
178.5 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
179.6 |
179.8 |
| N3 |
C4 |
C5 |
CN4 |
359.4 |
360.0 |
| C8 |
N3 |
C4 |
HN3 |
180.2 |
180.0 |
| C4 |
N3 |
C8 |
CN4 |
359.6 |
360.0 |
| C4 |
N3 |
C8 |
C1' |
172.2 |
180.0 |
| C5 |
C6 |
C1 |
C7 |
179.9 |
179.8 |
| C1 |
C6 |
C5 |
HC6 |
180.0 |
180.1 |
| C6 |
C5 |
C4 |
N3 |
179.6 |
179.8 |
| C4 |
C5 |
C6 |
CN4 |
179.8 |
180.3 |
| C6 |
C5 |
CN4 |
C8 |
180.1 |
180.3 |
| C6 |
C5 |
CN4 |
HCN4 |
0.5 |
0.3 |
| CN4 |
C5 |
C4 |
N3 |
359.4 |
360.0 |
| C4 |
C5 |
CN4 |
C6 |
180.2 |
179.8 |
| CN4 |
C5 |
C6 |
HC6 |
359.9 |
0.1 |
| N3 |
C8 |
CN4 |
C5 |
360.0 |
0.0 |
| C8 |
CN4 |
C5 |
HCN4 |
179.7 |
180.0 |
| C5 |
CN4 |
C8 |
C1' |
188.2 |
180.0 |
| HC6 |
C6 |
C1 |
C7 |
359.8 |
359.8 |
| C1 |
C6 |
HC6 |
C5 |
180.0 |
179.9 |
| HC6 |
C6 |
C5 |
CN4 |
359.9 |
0.1 |
| C1 |
C7 |
N1 |
N2 |
180.4 |
180.0 |
| N1 |
C7 |
N2 |
HH21 |
179.2 |
180.0 |
| N1 |
C7 |
N2 |
HH22 |
0.6 |
359.7 |
| HH11 |
N1 |
C7 |
HH12 |
181.2 |
180.0 |
| C1 |
C7 |
N2 |
N1 |
179.6 |
180.0 |
| N2 |
C7 |
N1 |
HH11 |
180.1 |
0.0 |
| N2 |
C7 |
N1 |
HH12 |
358.9 |
180.0 |
| HH21 |
N2 |
C7 |
HH22 |
178.6 |
180.3 |
| HH11 |
N1 |
C7 |
N2 |
180.1 |
0.0 |
| C7 |
N1 |
HH11 |
HH12 |
178.8 |
180.0 |
| HH12 |
N1 |
C7 |
N2 |
358.9 |
180.0 |
| C7 |
N1 |
HH12 |
HH11 |
181.2 |
180.0 |
| C7 |
N2 |
HH21 |
HH22 |
181.5 |
179.7 |
| C7 |
N2 |
HH22 |
HH21 |
178.6 |
180.3 |
| C4 |
N3 |
C8 |
HN3 |
179.8 |
180.0 |
| C5 |
CN4 |
C8 |
N3 |
360.0 |
0.0 |
| N3 |
C8 |
CN4 |
HCN4 |
179.7 |
180.0 |
| CN4 |
C8 |
N3 |
C1' |
187.4 |
180.0 |
| N3 |
C8 |
C1' |
C2' |
189.5 |
320.0 |
| N3 |
C8 |
C1' |
C6' |
9.6 |
139.7 |
| C4 |
N3 |
HN3 |
C8 |
180.2 |
180.0 |
| HN3 |
N3 |
C8 |
CN4 |
179.8 |
180.0 |
| HN3 |
N3 |
C8 |
C1' |
352.4 |
360.0 |
| C5 |
CN4 |
C8 |
HCN4 |
180.3 |
180.0 |
| CN4 |
C8 |
N3 |
HN3 |
179.8 |
180.0 |
| N3 |
C8 |
CN4 |
C1' |
171.8 |
180.0 |
| CN4 |
C8 |
C1' |
C2' |
359.6 |
140.0 |
| CN4 |
C8 |
C1' |
C6' |
179.7 |
319.7 |
| C5 |
CN4 |
HCN4 |
C8 |
179.7 |
180.0 |
| HCN4 |
CN4 |
C8 |
C1' |
7.9 |
0.0 |
| C1' |
C8 |
N3 |
HN3 |
352.4 |
360.0 |
| N3 |
C8 |
C1' |
CN4 |
189.9 |
180.0 |
| C1' |
C8 |
CN4 |
HCN4 |
7.9 |
0.0 |
| C2' |
C1' |
C8 |
C6' |
180.0 |
180.3 |
| C8 |
C1' |
C2' |
C3' |
180.0 |
180.0 |
| C8 |
C1' |
C2' |
HC2' |
359.6 |
360.0 |
| C8 |
C1' |
C6' |
C5' |
180.3 |
179.7 |
| C8 |
C1' |
C6' |
O6' |
0.9 |
0.3 |
| C8 |
C1' |
C2' |
C6' |
180.0 |
179.7 |
| C2' |
C1' |
C6' |
C5' |
0.3 |
359.4 |
| C2' |
C1' |
C6' |
O6' |
181.0 |
180.0 |
| C3' |
C2' |
C1' |
HC2' |
180.3 |
180.0 |
| C1' |
C2' |
C3' |
CV' |
179.6 |
180.0 |
| C1' |
C2' |
C3' |
C4' |
360.0 |
360.0 |
| C8 |
C1' |
C6' |
C2' |
180.0 |
180.3 |
| C6' |
C1' |
C2' |
C3' |
359.9 |
0.3 |
| C6' |
C1' |
C2' |
HC2' |
179.6 |
180.3 |
| C4' |
C5' |
C6' |
C1' |
359.5 |
0.7 |
| C1' |
C6' |
C5' |
BR5' |
179.8 |
180.3 |
| C5' |
C6' |
C1' |
O6' |
179.4 |
179.4 |
| C3' |
C2' |
C1' |
C6' |
359.9 |
0.3 |
| C1' |
C2' |
C3' |
HC2' |
179.7 |
180.0 |
| CV' |
C3' |
C2' |
C4' |
179.7 |
180.0 |
| C2' |
C3' |
CV' |
CW' |
176.7 |
90.0 |
| C2' |
C3' |
CV' |
H31B |
299.0 |
330.1 |
| C2' |
C3' |
CV' |
H31A |
52.1 |
210.1 |
| C2' |
C3' |
C4' |
C5' |
359.9 |
0.1 |
| C2' |
C3' |
C4' |
HC4' |
180.3 |
180.0 |
| HC2' |
C2' |
C1' |
C6' |
179.6 |
180.3 |
| C1' |
C2' |
HC2' |
C3' |
180.3 |
180.0 |
| HC2' |
C2' |
C3' |
CV' |
359.9 |
359.9 |
| HC2' |
C2' |
C3' |
C4' |
180.3 |
180.0 |
| CV' |
C3' |
C2' |
HC2' |
359.9 |
359.9 |
| C2' |
C3' |
CV' |
C4' |
180.4 |
180.0 |
| CV' |
C3' |
C4' |
C5' |
180.3 |
180.1 |
| CV' |
C3' |
C4' |
HC4' |
0.6 |
360.0 |
| CW' |
CV' |
C3' |
H31B |
237.7 |
119.9 |
| CW' |
CV' |
C3' |
H31A |
124.6 |
240.0 |
| C3' |
CV' |
CW' |
OX' |
78.1 |
0.0 |
| C3' |
CV' |
CW' |
OY' |
254.9 |
180.0 |
| H31B |
CV' |
C3' |
H31A |
246.9 |
120.0 |
| C4' |
C3' |
C2' |
HC2' |
180.3 |
180.0 |
| C2' |
C3' |
C4' |
CV' |
179.6 |
180.0 |
| C4' |
C3' |
CV' |
CW' |
356.4 |
270.0 |
| C4' |
C3' |
CV' |
H31B |
118.6 |
150.1 |
| C4' |
C3' |
CV' |
H31A |
231.7 |
30.1 |
| C5' |
C4' |
C3' |
HC4' |
179.6 |
180.1 |
| C3' |
C4' |
C5' |
C6' |
0.4 |
359.6 |
| C3' |
C4' |
C5' |
BR5' |
180.1 |
180.0 |
| CW' |
CV' |
C3' |
C4' |
356.4 |
270.0 |
| C3' |
CV' |
CW' |
H31B |
122.8 |
240.0 |
| C3' |
CV' |
CW' |
H31A |
235.7 |
120.0 |
| H31B |
CV' |
CW' |
H31A |
113.0 |
240.0 |
| OX' |
CW' |
CV' |
OY' |
183.1 |
180.0 |
| H31B |
CV' |
C3' |
C4' |
118.6 |
150.1 |
| C3' |
CV' |
H31B |
CW' |
232.8 |
120.0 |
| C3' |
CV' |
H31B |
H31A |
116.2 |
240.0 |
| CW' |
CV' |
H31B |
H31A |
243.4 |
120.0 |
| H31B |
CV' |
CW' |
OX' |
315.3 |
120.0 |
| H31B |
CV' |
CW' |
OY' |
132.2 |
300.0 |
| H31A |
CV' |
C3' |
C4' |
231.7 |
30.1 |
| C3' |
CV' |
H31A |
CW' |
128.4 |
240.0 |
| C3' |
CV' |
H31A |
H31B |
243.8 |
120.0 |
| CW' |
CV' |
H31A |
H31B |
115.4 |
240.0 |
| H31A |
CV' |
CW' |
OX' |
202.4 |
240.0 |
| H31A |
CV' |
CW' |
OY' |
19.2 |
60.0 |
| OX' |
CW' |
CV' |
H31B |
315.3 |
120.0 |
| OX' |
CW' |
CV' |
H31A |
202.4 |
240.0 |
| CV' |
CW' |
OX' |
OY' |
176.6 |
180.0 |
| OY' |
CW' |
CV' |
H31B |
132.2 |
300.0 |
| OY' |
CW' |
CV' |
H31A |
19.2 |
60.0 |
| CV' |
CW' |
OY' |
OX' |
183.5 |
180.0 |
| C1' |
C6' |
C5' |
C4' |
359.5 |
0.7 |
| C3' |
C4' |
C5' |
HC4' |
180.4 |
179.9 |
| C6' |
C5' |
C4' |
BR5' |
180.3 |
179.6 |
| C4' |
C5' |
C6' |
O6' |
178.9 |
180.0 |
| C3' |
C4' |
HC4' |
C5' |
179.6 |
180.1 |
| HC4' |
C4' |
C5' |
C6' |
180.0 |
179.7 |
| HC4' |
C4' |
C5' |
BR5' |
359.7 |
0.1 |
| C1' |
C6' |
C5' |
O6' |
180.6 |
180.6 |
| C6' |
C5' |
C4' |
HC4' |
180.0 |
179.7 |
| C4' |
C5' |
C6' |
BR5' |
179.7 |
180.4 |
| BR5' |
C5' |
C4' |
HC4' |
359.7 |
0.1 |
| C4' |
C5' |
BR5' |
C6' |
180.3 |
179.6 |
| BR5' |
C5' |
C6' |
O6' |
359.2 |
359.6 |
| C1' |
C6' |
O6' |
C5' |
179.4 |
179.4 |
| O6' |
C6' |
C5' |
BR5' |
359.2 |
359.6 |