PDB Chemical Component JMH
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 JMH
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| OP1 |
P |
1.507 |
1.480 |
| N4 |
C4 |
1.353 |
1.309 |
| P |
OP2 |
1.506 |
1.610 |
| P |
O5' |
1.588 |
1.609 |
| C5 |
C4 |
1.385 |
1.469 |
| C5 |
C6 |
1.389 |
1.346 |
| C4 |
N3 |
1.403 |
1.386 |
| C6 |
N1 |
1.339 |
1.372 |
| O4' |
C1' |
1.415 |
1.444 |
| O4' |
C4' |
1.450 |
1.438 |
| N3 |
C31 |
1.464 |
1.465 |
| N3 |
C2 |
1.405 |
1.347 |
| O5' |
C5' |
1.418 |
1.429 |
| C5' |
C4' |
1.505 |
1.529 |
| N1 |
C2 |
1.412 |
1.342 |
| N1 |
C1' |
1.484 |
1.465 |
| C2 |
O2 |
1.249 |
1.216 |
| C1' |
C2' |
1.532 |
1.550 |
| C4' |
C3' |
1.513 |
1.541 |
| C3' |
C2' |
1.521 |
1.548 |
| C3' |
O3' |
1.414 |
1.430 |
| C2' |
O2' |
1.419 |
1.429 |
| P |
OP3 |
1.604 |
1.610 |
| C5 |
H1 |
1.080 |
1.080 |
| C1' |
H2 |
1.100 |
1.090 |
| C2' |
H3 |
1.100 |
1.090 |
| C3' |
H4 |
1.100 |
1.089 |
| C4' |
H6 |
1.100 |
1.090 |
| C5' |
H7 |
1.100 |
1.090 |
| C5' |
H8 |
1.100 |
1.090 |
| C6 |
H9 |
1.080 |
1.080 |
| C31 |
H10 |
1.100 |
1.090 |
| C31 |
H11 |
1.100 |
1.090 |
| C31 |
H12 |
1.100 |
1.090 |
| N4 |
H13 |
1.000 |
0.970 |
| O2' |
H16 |
0.950 |
0.967 |
| O3' |
H17 |
0.950 |
0.966 |
| OP2 |
H18 |
0.950 |
0.967 |
| OP3 |
H19 |
0.950 |
0.968 |
Bond Angles for JMH
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP2 |
119.8 |
109.5 |
| OP1 |
P |
OP3 |
108.1 |
109.4 |
| P |
OP2 |
H18 |
109.5 |
113.9 |
| C4 |
C5 |
C6 |
120.4 |
118.5 |
| C5 |
C4 |
N3 |
119.3 |
118.4 |
| C4 |
C5 |
H1 |
119.8 |
120.7 |
| C6 |
C5 |
H1 |
119.8 |
120.8 |
| C5 |
C6 |
H9 |
119.2 |
119.9 |
| C4 |
N3 |
C31 |
120.4 |
120.2 |
| O4' |
C1' |
H2 |
110.0 |
110.8 |
| O4' |
C4' |
H6 |
109.8 |
109.8 |
| N3 |
C31 |
H10 |
109.5 |
109.5 |
| N3 |
C31 |
H11 |
109.5 |
109.5 |
| N3 |
C31 |
H12 |
109.4 |
109.5 |
| N3 |
C2 |
O2 |
119.1 |
119.2 |
| O5' |
C5' |
H7 |
109.0 |
109.4 |
| O5' |
C5' |
H8 |
109.1 |
109.5 |
| C5' |
C4' |
H6 |
109.0 |
109.9 |
| C2 |
N1 |
C1' |
119.3 |
119.1 |
| N1 |
C2 |
O2 |
120.9 |
119.2 |
| N1 |
C1' |
C2' |
112.6 |
110.6 |
| N1 |
C1' |
H2 |
109.0 |
110.5 |
| C1' |
C2' |
O2' |
108.1 |
110.9 |
| C2' |
C1' |
H2 |
108.4 |
110.6 |
| C1' |
C2' |
H3 |
111.5 |
111.0 |
| C4' |
C3' |
O3' |
113.7 |
110.5 |
| C4' |
C3' |
H4 |
108.2 |
110.6 |
| C3' |
C2' |
O2' |
110.7 |
110.9 |
| C3' |
C2' |
H3 |
111.6 |
110.9 |
| O3' |
C3' |
H4 |
109.6 |
110.4 |
| C3' |
O3' |
H17 |
109.5 |
114.0 |
| O2' |
C2' |
H3 |
113.3 |
110.8 |
| C2' |
O2' |
H16 |
109.5 |
114.0 |
| P |
OP3 |
H19 |
109.5 |
114.0 |
| H7 |
C5' |
H8 |
109.5 |
109.5 |
| H10 |
C31 |
H11 |
109.4 |
109.5 |
| H10 |
C31 |
H12 |
109.5 |
109.5 |
| H11 |
C31 |
H12 |
109.5 |
109.5 |
Torsion Angles for JMH
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP2 |
H18 |
360.0 |
180.0 |
| OP1 |
P |
OP3 |
H19 |
0.0 |
60.0 |
| N4 |
C4 |
C5 |
H1 |
359.9 |
0.5 |
| OP1 |
P |
OP2 |
OP3 |
124.3 |
240.0 |
| P |
O5' |
C5' |
H7 |
277.7 |
60.1 |
| P |
O5' |
C5' |
H8 |
37.2 |
300.1 |
| C6 |
C5 |
C4 |
H1 |
180.0 |
179.5 |
| C4 |
C5 |
C6 |
H9 |
180.4 |
180.4 |
| C5 |
C4 |
N3 |
C31 |
179.8 |
180.0 |
| C6 |
C5 |
C4 |
N3 |
359.8 |
359.4 |
| C4 |
C5 |
C6 |
H1 |
180.0 |
180.5 |
| N3 |
C4 |
C5 |
C6 |
359.8 |
359.4 |
| N3 |
C4 |
C5 |
H1 |
179.8 |
179.9 |
| C4 |
N3 |
C31 |
H10 |
180.0 |
65.1 |
| C4 |
N3 |
C31 |
H11 |
300.0 |
185.1 |
| C4 |
N3 |
C31 |
H12 |
60.0 |
305.0 |
| C4 |
N3 |
C2 |
O2 |
179.8 |
180.0 |
| C6 |
N1 |
C2 |
O2 |
180.3 |
179.7 |
| C6 |
N1 |
C1' |
H2 |
139.7 |
172.4 |
| N1 |
C1' |
O4' |
H2 |
119.7 |
122.9 |
| C2' |
C1' |
O4' |
H2 |
242.3 |
241.4 |
| O4' |
C1' |
C2' |
H3 |
218.1 |
278.8 |
| C4' |
O4' |
C1' |
H2 |
116.1 |
78.5 |
| C5' |
C4' |
O4' |
H6 |
239.9 |
238.9 |
| O4' |
C4' |
C3' |
H4 |
73.9 |
116.7 |
| C31 |
N3 |
C2 |
O2 |
0.0 |
0.4 |
| H10 |
C31 |
N3 |
H11 |
240.0 |
240.0 |
| H10 |
C31 |
N3 |
H12 |
120.0 |
120.0 |
| H11 |
C31 |
N3 |
H12 |
240.0 |
240.0 |
| N1 |
C2 |
N3 |
O2 |
180.2 |
180.0 |
| O5' |
C5' |
C4' |
H6 |
166.8 |
306.1 |
| H7 |
C5' |
O5' |
H8 |
240.5 |
120.0 |
| O4' |
C4' |
C5' |
H6 |
120.6 |
121.1 |
| C5' |
C4' |
C3' |
O3' |
75.6 |
119.8 |
| C5' |
C4' |
C3' |
H4 |
313.6 |
357.2 |
| N3 |
C2 |
N1 |
O2 |
179.8 |
180.0 |
| C2 |
N1 |
C1' |
C2' |
80.1 |
115.0 |
| C2 |
N1 |
C1' |
H2 |
319.8 |
352.1 |
| O4' |
C1' |
N1 |
H2 |
239.7 |
237.0 |
| C1' |
N1 |
C2 |
O2 |
0.3 |
0.1 |
| N1 |
C1' |
C2' |
O2' |
213.5 |
273.7 |
| C2' |
C1' |
N1 |
H2 |
120.3 |
122.9 |
| N1 |
C1' |
C2' |
H3 |
338.6 |
37.3 |
| O2 |
C2 |
N1 |
C1' |
0.3 |
0.1 |
| O4' |
C1' |
C2' |
H2 |
118.8 |
118.7 |
| N1 |
C1' |
C2' |
H2 |
239.3 |
237.2 |
| C3' |
C2' |
C1' |
O2' |
243.8 |
241.8 |
| C3' |
C2' |
C1' |
H3 |
118.7 |
118.2 |
| O2' |
C2' |
C1' |
H3 |
234.9 |
236.4 |
| C1' |
C2' |
O2' |
H16 |
180.0 |
180.0 |
| C4' |
C3' |
C2' |
O2' |
283.7 |
220.9 |
| C4' |
C3' |
C2' |
H3 |
156.6 |
97.4 |
| O3' |
C3' |
C4' |
H4 |
122.1 |
122.6 |
| C4' |
C3' |
O3' |
H17 |
180.0 |
176.2 |
| C1' |
C2' |
C3' |
O2' |
114.3 |
118.2 |
| C3' |
C2' |
C1' |
H2 |
218.0 |
278.4 |
| C1' |
C2' |
C3' |
H3 |
241.5 |
241.7 |
| O2' |
C2' |
C3' |
H3 |
127.2 |
123.5 |
| C3' |
C2' |
O2' |
H16 |
289.7 |
292.7 |
| C4' |
C3' |
O3' |
H4 |
238.7 |
237.3 |
| O3' |
C3' |
C2' |
O2' |
47.1 |
339.6 |
| O3' |
C3' |
C2' |
H3 |
280.0 |
216.1 |
| O2' |
C2' |
C1' |
H2 |
334.2 |
36.6 |
| C1' |
C2' |
O2' |
H3 |
124.1 |
123.7 |
| C3' |
C2' |
O2' |
H3 |
233.8 |
236.4 |
| OP1 |
P |
OP3 |
OP2 |
229.0 |
120.0 |
| OP3 |
P |
OP2 |
H18 |
235.7 |
300.0 |
| C4 |
C5 |
H1 |
C6 |
180.0 |
179.5 |
| H1 |
C5 |
C4 |
N3 |
179.8 |
179.9 |
| H1 |
C5 |
C6 |
H9 |
0.4 |
359.9 |
| N1 |
C1' |
H2 |
C2' |
122.9 |
122.9 |
| H2 |
C1' |
C2' |
O2' |
334.2 |
36.6 |
| H2 |
C1' |
C2' |
H3 |
99.3 |
160.1 |
| C1' |
C2' |
H3 |
O2' |
237.8 |
236.4 |
| H3 |
C2' |
C1' |
H2 |
99.3 |
160.1 |
| C3' |
C2' |
H3 |
O2' |
125.7 |
123.6 |
| H3 |
C2' |
O2' |
H16 |
55.9 |
56.3 |
| C4' |
C3' |
H4 |
O3' |
124.6 |
122.6 |
| H4 |
C3' |
C2' |
O2' |
169.7 |
102.1 |
| H4 |
C3' |
C2' |
H3 |
42.6 |
338.6 |
| H4 |
C3' |
O3' |
H17 |
301.3 |
298.9 |
| H6 |
C4' |
C3' |
O3' |
312.5 |
358.7 |
| H6 |
C4' |
C3' |
H4 |
190.5 |
236.1 |
| O5' |
C5' |
H7 |
H8 |
119.2 |
240.0 |
| H7 |
C5' |
C4' |
H6 |
46.6 |
66.0 |
| O5' |
C5' |
H8 |
H7 |
240.8 |
119.9 |
| H8 |
C5' |
C4' |
H6 |
287.1 |
186.0 |
| H9 |
C6 |
C5 |
H1 |
0.4 |
359.9 |
| N3 |
C31 |
H10 |
H11 |
120.0 |
120.0 |
| N3 |
C31 |
H10 |
H12 |
240.0 |
240.0 |
| H11 |
C31 |
H10 |
H12 |
120.0 |
120.0 |
| N3 |
C31 |
H11 |
H10 |
240.0 |
240.0 |
| N3 |
C31 |
H11 |
H12 |
120.0 |
120.0 |
| H10 |
C31 |
H11 |
H12 |
240.0 |
240.0 |
| N3 |
C31 |
H12 |
H10 |
120.0 |
120.0 |
| N3 |
C31 |
H12 |
H11 |
240.0 |
240.0 |
| H10 |
C31 |
H12 |
H11 |
120.0 |
120.0 |
| H16 |
O2' |
C2' |
H3 |
55.9 |
56.3 |
| H17 |
O3' |
C3' |
H4 |
301.3 |
298.9 |