PDB Chemical Component 6J2
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 6J2
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O2 |
C2 |
1.253 |
1.220 |
| N3 |
C2 |
1.339 |
1.340 |
| N3 |
C4 |
1.371 |
1.354 |
| C2 |
N1 |
1.348 |
1.329 |
| O4 |
C4 |
1.236 |
1.217 |
| C4 |
C4A |
1.493 |
1.470 |
| N1 |
C10 |
1.325 |
1.327 |
| C4A |
C10 |
1.461 |
1.466 |
| C4A |
C5 |
1.404 |
1.382 |
| C10 |
N10 |
1.404 |
1.363 |
| C5 |
C5A |
1.411 |
1.413 |
| N10 |
C1' |
1.479 |
1.465 |
| N10 |
C9A |
1.410 |
1.379 |
| O4' |
C4' |
1.460 |
1.429 |
| C5A |
C9A |
1.458 |
1.411 |
| C5A |
C6 |
1.417 |
1.408 |
| C1' |
C2' |
1.498 |
1.530 |
| C9A |
C9 |
1.405 |
1.391 |
| C4' |
C5' |
1.512 |
1.530 |
| C4' |
C3' |
1.524 |
1.530 |
| C6 |
C7 |
1.389 |
1.360 |
| C9 |
C8 |
1.352 |
1.384 |
| C5' |
O5' |
1.372 |
1.429 |
| C7 |
C8 |
1.373 |
1.397 |
| C8 |
O8M |
1.366 |
1.356 |
| O3' |
C3' |
1.426 |
1.429 |
| C3' |
C2' |
1.533 |
1.529 |
| C2' |
O2' |
1.419 |
1.429 |
| O1P |
P |
1.547 |
1.480 |
| O5' |
P |
1.571 |
1.610 |
| P |
O2P |
1.451 |
1.610 |
| P |
O3P |
1.632 |
1.610 |
| O3P |
C1I |
1.450 |
1.429 |
| C1I |
C2I |
1.543 |
1.531 |
| C1I |
C3I |
1.522 |
1.507 |
| C3I |
O3I |
1.242 |
1.209 |
| C1I |
H16 |
1.100 |
1.090 |
| C2I |
H17 |
1.100 |
1.090 |
| C2I |
H18 |
1.100 |
1.089 |
| C2I |
H19 |
1.100 |
1.090 |
| O2P |
H20 |
0.950 |
0.967 |
| C5' |
H21 |
1.100 |
1.090 |
| C5' |
H22 |
1.100 |
1.090 |
| C4' |
H23 |
1.101 |
1.090 |
| O4' |
H24 |
0.950 |
0.967 |
| C3' |
H25 |
1.100 |
1.090 |
| O3' |
H26 |
0.950 |
0.968 |
| C2' |
H27 |
1.100 |
1.090 |
| O2' |
H28 |
0.950 |
0.967 |
| C1' |
H29 |
1.100 |
1.090 |
| C1' |
H30 |
1.100 |
1.090 |
| C9 |
H31 |
1.080 |
1.080 |
| O8M |
H32 |
0.950 |
0.967 |
| C7 |
H33 |
1.080 |
1.080 |
| C6 |
H34 |
1.080 |
1.080 |
| C5 |
H35 |
1.080 |
1.080 |
| N3 |
H37 |
1.000 |
0.971 |
| C3I |
OXT |
1.296 |
1.341 |
| OXT |
HXT |
0.950 |
0.967 |
Bond Angles for 6J2
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N3 |
H37 |
118.6 |
119.4 |
| C4A |
C5 |
H35 |
121.7 |
120.6 |
| N10 |
C1' |
H29 |
108.2 |
109.5 |
| N10 |
C1' |
H30 |
108.2 |
109.5 |
| N10 |
C9A |
C9 |
120.8 |
119.7 |
| O4' |
C4' |
C3' |
114.1 |
109.4 |
| O4' |
C4' |
H23 |
108.6 |
109.5 |
| C5A |
C6 |
H34 |
120.9 |
120.0 |
| C1' |
C2' |
H27 |
108.4 |
109.5 |
| C9A |
C9 |
C8 |
120.2 |
119.9 |
| C9A |
C9 |
H31 |
119.9 |
120.0 |
| C4' |
C5' |
H21 |
109.0 |
109.4 |
| C4' |
C5' |
H22 |
109.0 |
109.4 |
| C4' |
C3' |
C2' |
111.1 |
109.5 |
| C3' |
C4' |
H23 |
107.8 |
109.5 |
| C4' |
C3' |
H25 |
110.0 |
109.4 |
| C6 |
C7 |
H33 |
118.6 |
119.7 |
| C9 |
C8 |
O8M |
118.0 |
119.8 |
| C8 |
C9 |
H31 |
119.9 |
120.0 |
| C8 |
O8M |
H32 |
109.5 |
114.0 |
| O3' |
C3' |
C2' |
107.6 |
109.5 |
| O3' |
C3' |
H25 |
111.4 |
109.4 |
| C3' |
C2' |
O2' |
111.1 |
109.5 |
| C2' |
C3' |
H25 |
109.8 |
109.5 |
| C3' |
C2' |
H27 |
108.0 |
109.5 |
| O2' |
C2' |
H27 |
109.5 |
109.5 |
| C2' |
O2' |
H28 |
109.5 |
114.0 |
| O1P |
P |
O2P |
121.3 |
109.4 |
| P |
O2P |
H20 |
109.5 |
114.0 |
| O3P |
C1I |
H16 |
109.0 |
109.5 |
| C2I |
C1I |
H16 |
107.9 |
109.5 |
| C1I |
C2I |
H17 |
109.5 |
109.5 |
| C1I |
C2I |
H18 |
109.5 |
109.5 |
| C1I |
C2I |
H19 |
109.5 |
109.4 |
| C1I |
C3I |
OXT |
111.2 |
120.0 |
| O3I |
C3I |
OXT |
126.3 |
120.0 |
| H17 |
C2I |
H18 |
109.5 |
109.5 |
| H17 |
C2I |
H19 |
109.5 |
109.4 |
| H18 |
C2I |
H19 |
109.4 |
109.5 |
| H21 |
C5' |
H22 |
109.5 |
109.5 |
| H29 |
C1' |
H30 |
109.5 |
109.5 |
| C3I |
OXT |
HXT |
109.5 |
117.0 |
Torsion Angles for 6J2
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O2 |
C2 |
N3 |
H37 |
2.4 |
0.3 |
| C4 |
C4A |
C5 |
H35 |
352.2 |
0.3 |
| C10 |
C4A |
C5 |
H35 |
172.1 |
179.8 |
| C10 |
N10 |
C1' |
H29 |
40.6 |
149.7 |
| C10 |
N10 |
C1' |
H30 |
159.1 |
29.7 |
| C5 |
C5A |
C6 |
H34 |
358.6 |
359.9 |
| N10 |
C1' |
C2' |
H27 |
49.1 |
60.0 |
| H29 |
C1' |
N10 |
H30 |
241.5 |
120.0 |
| C9A |
N10 |
C1' |
H29 |
216.6 |
330.0 |
| C9A |
N10 |
C1' |
H30 |
335.1 |
210.0 |
| N10 |
C9A |
C9 |
C8 |
179.2 |
180.0 |
| N10 |
C9A |
C9 |
H31 |
359.2 |
360.0 |
| O4' |
C4' |
C5' |
H21 |
59.4 |
305.0 |
| O4' |
C4' |
C5' |
H22 |
178.8 |
185.0 |
| O4' |
C4' |
C3' |
C2' |
325.8 |
300.0 |
| C3' |
C4' |
O4' |
H23 |
120.2 |
120.0 |
| O4' |
C4' |
C3' |
H25 |
87.6 |
60.1 |
| C5A |
C9A |
C9 |
H31 |
182.3 |
180.0 |
| C5A |
C6 |
C7 |
H33 |
181.2 |
180.0 |
| C1' |
C2' |
C3' |
H25 |
180.6 |
60.0 |
| C3' |
C2' |
C1' |
H27 |
119.4 |
120.0 |
| O2' |
C2' |
C1' |
H27 |
241.9 |
240.0 |
| C1' |
C2' |
O2' |
H28 |
180.0 |
300.0 |
| C9A |
C9 |
C8 |
O8M |
180.5 |
180.0 |
| C8 |
C9 |
C9A |
H31 |
180.0 |
180.1 |
| H21 |
C5' |
C4' |
H22 |
240.6 |
120.0 |
| O4' |
C4' |
C3' |
H23 |
239.3 |
240.0 |
| C3' |
C4' |
C5' |
H21 |
184.7 |
65.0 |
| C3' |
C4' |
C5' |
H22 |
304.1 |
305.0 |
| O3' |
C3' |
C4' |
C2' |
242.9 |
240.0 |
| O3' |
C3' |
C4' |
H25 |
121.1 |
119.9 |
| C4' |
C3' |
C2' |
O2' |
182.2 |
60.0 |
| C2' |
C3' |
C4' |
H25 |
238.2 |
240.0 |
| C4' |
C3' |
C2' |
H27 |
62.1 |
300.0 |
| C9A |
C9 |
C8 |
H31 |
180.0 |
179.9 |
| C9 |
C8 |
O8M |
H32 |
180.0 |
89.9 |
| C7 |
C8 |
C9 |
H31 |
178.8 |
180.0 |
| C7 |
C8 |
O8M |
H32 |
1.7 |
270.0 |
| O8M |
C8 |
C9 |
H31 |
0.5 |
0.0 |
| C4' |
C3' |
O3' |
C2' |
119.4 |
120.1 |
| O3' |
C3' |
C4' |
H23 |
329.3 |
300.0 |
| C4' |
C3' |
O3' |
H25 |
239.9 |
240.1 |
| O3' |
C3' |
C2' |
O2' |
298.9 |
180.0 |
| C2' |
C3' |
O3' |
H25 |
120.4 |
120.0 |
| O3' |
C3' |
C2' |
H27 |
178.8 |
60.0 |
| C1' |
C2' |
C3' |
H27 |
240.3 |
240.0 |
| C2' |
C3' |
C4' |
H23 |
86.4 |
60.0 |
| C4' |
C3' |
C2' |
H25 |
121.9 |
120.0 |
| O3' |
C3' |
C2' |
H25 |
238.6 |
240.0 |
| O2' |
C2' |
C3' |
H27 |
120.1 |
120.0 |
| C3' |
C2' |
O2' |
H28 |
303.5 |
60.0 |
| C1' |
C2' |
O2' |
H27 |
117.4 |
120.0 |
| O2' |
C2' |
C3' |
H25 |
60.3 |
300.0 |
| C3' |
C2' |
O2' |
H27 |
240.8 |
240.0 |
| O1P |
P |
O2P |
H20 |
0.0 |
180.1 |
| O5' |
P |
O2P |
H20 |
133.6 |
300.0 |
| P |
O3P |
C1I |
H16 |
339.3 |
360.0 |
| C2I |
C1I |
O3P |
H16 |
121.9 |
120.0 |
| O3P |
C1I |
C2I |
H17 |
180.0 |
59.9 |
| O3P |
C1I |
C2I |
H18 |
300.0 |
180.0 |
| O3P |
C1I |
C2I |
H19 |
60.0 |
300.0 |
| O3P |
C1I |
C3I |
OXT |
137.9 |
175.3 |
| O3P |
C1I |
C2I |
H16 |
237.5 |
239.9 |
| C2I |
C1I |
C3I |
OXT |
263.8 |
295.3 |
| H17 |
C2I |
C1I |
H18 |
240.0 |
239.9 |
| H17 |
C2I |
C1I |
H19 |
120.0 |
119.9 |
| H18 |
C2I |
C1I |
H19 |
240.0 |
240.0 |
| O3I |
C3I |
C1I |
OXT |
186.9 |
179.7 |
| C1I |
C3I |
OXT |
HXT |
187.3 |
179.8 |
| C1I |
C3I |
O3I |
OXT |
172.0 |
180.3 |
| O3I |
C3I |
OXT |
HXT |
0.0 |
0.1 |
| H16 |
C1I |
C2I |
H17 |
302.5 |
180.0 |
| H16 |
C1I |
C2I |
H18 |
62.5 |
300.1 |
| H16 |
C1I |
C2I |
H19 |
182.5 |
60.1 |
| H16 |
C1I |
C3I |
OXT |
21.2 |
55.3 |
| H17 |
C2I |
C1I |
H16 |
302.5 |
180.0 |
| C1I |
C2I |
H17 |
H18 |
120.0 |
120.0 |
| C1I |
C2I |
H17 |
H19 |
240.0 |
240.1 |
| H18 |
C2I |
H17 |
H19 |
120.0 |
120.1 |
| H18 |
C2I |
C1I |
H16 |
62.5 |
300.1 |
| C1I |
C2I |
H18 |
H17 |
240.0 |
240.0 |
| C1I |
C2I |
H18 |
H19 |
120.0 |
120.0 |
| H17 |
C2I |
H18 |
H19 |
240.0 |
240.0 |
| H19 |
C2I |
C1I |
H16 |
182.5 |
60.1 |
| C1I |
C2I |
H19 |
H17 |
120.0 |
119.9 |
| C1I |
C2I |
H19 |
H18 |
240.0 |
240.0 |
| H17 |
C2I |
H19 |
H18 |
120.0 |
120.1 |
| C4' |
C5' |
H21 |
H22 |
119.1 |
240.1 |
| C4' |
C5' |
H22 |
H21 |
240.9 |
120.0 |
| O4' |
C4' |
H23 |
C3' |
124.1 |
120.0 |
| H23 |
C4' |
C5' |
H21 |
300.9 |
185.0 |
| H23 |
C4' |
C5' |
H22 |
60.3 |
65.0 |
| H23 |
C4' |
C3' |
C2' |
86.4 |
60.0 |
| H23 |
C4' |
C3' |
H25 |
208.2 |
180.0 |
| H24 |
O4' |
C4' |
C3' |
90.8 |
300.0 |
| H24 |
O4' |
C4' |
H23 |
330.6 |
180.0 |
| C4' |
C3' |
H25 |
C2' |
237.4 |
240.0 |
| H25 |
C3' |
C4' |
H23 |
208.2 |
180.0 |
| O3' |
C3' |
H25 |
C2' |
119.1 |
120.0 |
| H25 |
C3' |
C2' |
O2' |
60.3 |
300.0 |
| H25 |
C3' |
C2' |
H27 |
300.2 |
180.0 |
| H26 |
O3' |
C3' |
C2' |
60.5 |
300.0 |
| H26 |
O3' |
C3' |
H25 |
300.1 |
180.0 |
| C3' |
C2' |
H27 |
O2' |
121.1 |
120.0 |
| H27 |
C2' |
C3' |
H25 |
300.2 |
180.0 |
| H27 |
C2' |
O2' |
H28 |
62.7 |
180.0 |
| H28 |
O2' |
C2' |
H27 |
62.7 |
180.0 |
| N10 |
C1' |
H29 |
H30 |
117.7 |
240.0 |
| H29 |
C1' |
C2' |
H27 |
288.4 |
180.0 |
| N10 |
C1' |
H30 |
H29 |
242.3 |
120.0 |
| H30 |
C1' |
C2' |
H27 |
169.8 |
300.0 |
| C9A |
C9 |
H31 |
C8 |
180.0 |
180.1 |
| H31 |
C9 |
C8 |
O8M |
0.5 |
0.0 |
| H34 |
C6 |
C7 |
H33 |
1.2 |
0.1 |