PDB Chemical Component B9H
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 B9H
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
OP2 |
P |
1.494 |
1.610 |
C5' |
C4' |
1.505 |
1.530 |
C5' |
O5' |
1.406 |
1.429 |
C4' |
O4' |
1.422 |
1.437 |
C4' |
C3' |
1.507 |
1.542 |
P |
O5' |
1.570 |
1.611 |
P |
OP1 |
1.495 |
1.480 |
O4' |
C1' |
1.424 |
1.444 |
O2' |
C21 |
1.418 |
1.429 |
O2' |
C2' |
1.415 |
1.429 |
C1' |
C2' |
1.529 |
1.549 |
C1' |
N1 |
1.476 |
1.465 |
C3' |
O3' |
1.453 |
1.429 |
C3' |
C2' |
1.507 |
1.548 |
N1 |
C6 |
1.340 |
1.386 |
N1 |
C2 |
1.393 |
1.340 |
C6 |
C5 |
1.378 |
1.320 |
O2 |
C2 |
1.241 |
1.216 |
C2 |
N3 |
1.406 |
1.348 |
C5 |
C4 |
1.373 |
1.514 |
N3 |
C4 |
1.400 |
1.473 |
N3 |
C31 |
1.465 |
1.465 |
C4 |
N4 |
1.349 |
1.469 |
C32 |
C31 |
1.517 |
1.530 |
C32 |
C33 |
1.509 |
1.530 |
C4 |
H1 |
1.100 |
1.090 |
C5 |
H2 |
1.080 |
1.080 |
C6 |
H3 |
1.080 |
1.079 |
C32 |
H4 |
1.100 |
1.090 |
C32 |
H5 |
1.100 |
1.090 |
C1' |
H6 |
1.101 |
1.090 |
C2' |
H7 |
1.100 |
1.090 |
C3' |
H8 |
1.100 |
1.090 |
C31 |
H9 |
1.100 |
1.090 |
C31 |
H10 |
1.100 |
1.090 |
C33 |
H11 |
1.100 |
1.090 |
C33 |
H12 |
1.100 |
1.090 |
C33 |
H13 |
1.100 |
1.091 |
C4' |
H14 |
1.101 |
1.090 |
C5' |
H15 |
1.100 |
1.090 |
C5' |
H16 |
1.100 |
1.090 |
N4 |
H17 |
1.000 |
1.009 |
N4 |
H18 |
1.001 |
1.010 |
O3' |
H20 |
0.950 |
0.967 |
OP2 |
H22 |
0.950 |
0.967 |
C21 |
H23 |
1.100 |
1.090 |
C21 |
H24 |
1.100 |
1.090 |
C21 |
H25 |
1.100 |
1.090 |
P |
OP3 |
1.599 |
1.610 |
OP3 |
H19 |
0.950 |
0.967 |
Bond Angles for B9H
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
P |
OP2 |
H22 |
109.5 |
114.0 |
OP2 |
P |
OP3 |
109.8 |
109.5 |
C5' |
C4' |
O4' |
111.0 |
109.9 |
C5' |
C4' |
H14 |
110.1 |
110.0 |
O5' |
C5' |
H15 |
110.2 |
109.5 |
O5' |
C5' |
H16 |
110.2 |
109.4 |
O4' |
C4' |
H14 |
111.4 |
109.9 |
C4' |
C3' |
O3' |
119.1 |
110.5 |
C4' |
C3' |
H8 |
103.7 |
110.6 |
O4' |
C1' |
H6 |
109.5 |
110.7 |
O2' |
C21 |
H23 |
109.5 |
109.5 |
O2' |
C21 |
H24 |
109.5 |
109.5 |
O2' |
C21 |
H25 |
109.5 |
109.5 |
O2' |
C2' |
H7 |
114.4 |
110.8 |
C2' |
C1' |
N1 |
113.2 |
110.6 |
C2' |
C1' |
H6 |
108.1 |
110.6 |
C1' |
C2' |
H7 |
112.5 |
111.0 |
N1 |
C1' |
H6 |
108.8 |
110.6 |
O3' |
C3' |
H8 |
104.3 |
110.5 |
C3' |
O3' |
H20 |
109.5 |
114.0 |
C3' |
C2' |
H7 |
112.9 |
110.9 |
N1 |
C6 |
H3 |
118.5 |
119.4 |
N1 |
C2 |
N3 |
120.3 |
121.8 |
C6 |
C5 |
H2 |
120.1 |
121.0 |
C2 |
N3 |
C4 |
119.1 |
118.3 |
C2 |
N3 |
C31 |
122.4 |
120.8 |
C5 |
C4 |
N4 |
119.8 |
107.9 |
C5 |
C4 |
H1 |
90.1 |
107.9 |
N3 |
C4 |
N4 |
120.9 |
107.9 |
N3 |
C4 |
H1 |
90.1 |
107.9 |
N3 |
C31 |
H9 |
107.9 |
109.5 |
N3 |
C31 |
H10 |
107.9 |
109.4 |
N4 |
C4 |
H1 |
90.1 |
107.7 |
C4 |
N4 |
H17 |
109.5 |
111.1 |
C4 |
N4 |
H18 |
109.5 |
111.0 |
C31 |
C32 |
C33 |
112.8 |
109.5 |
C31 |
C32 |
H4 |
108.6 |
109.5 |
C31 |
C32 |
H5 |
108.6 |
109.5 |
C32 |
C31 |
H9 |
107.9 |
109.5 |
C32 |
C31 |
H10 |
107.9 |
109.5 |
C33 |
C32 |
H4 |
108.6 |
109.4 |
C33 |
C32 |
H5 |
108.6 |
109.4 |
C32 |
C33 |
H11 |
109.5 |
109.5 |
C32 |
C33 |
H12 |
109.5 |
109.5 |
C32 |
C33 |
H13 |
109.5 |
109.5 |
H4 |
C32 |
H5 |
109.5 |
109.5 |
H9 |
C31 |
H10 |
109.5 |
109.5 |
H11 |
C33 |
H12 |
109.5 |
109.5 |
H11 |
C33 |
H13 |
109.5 |
109.5 |
H12 |
C33 |
H13 |
109.5 |
109.4 |
H15 |
C5' |
H16 |
109.5 |
109.4 |
H17 |
N4 |
H18 |
109.5 |
111.0 |
H23 |
C21 |
H24 |
109.4 |
109.5 |
H23 |
C21 |
H25 |
109.5 |
109.5 |
H24 |
C21 |
H25 |
109.5 |
109.5 |
P |
OP3 |
H19 |
109.5 |
114.0 |
Torsion Angles for B9H
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP2 |
P |
OP3 |
H19 |
128.0 |
60.0 |
O4' |
C4' |
C5' |
H14 |
123.9 |
121.2 |
C5' |
C4' |
C3' |
O3' |
54.8 |
119.9 |
C5' |
C4' |
C3' |
H8 |
299.6 |
357.3 |
O5' |
C5' |
C4' |
O4' |
291.4 |
66.5 |
O5' |
C5' |
C4' |
H14 |
167.6 |
305.3 |
H15 |
C5' |
O5' |
H16 |
121.0 |
120.0 |
C5' |
C4' |
O4' |
H14 |
236.9 |
238.8 |
O4' |
C4' |
C3' |
O3' |
173.6 |
239.3 |
O4' |
C4' |
C3' |
H8 |
58.4 |
116.7 |
C4' |
O4' |
C1' |
H6 |
115.3 |
78.5 |
O3' |
C3' |
C4' |
H8 |
115.2 |
122.6 |
C4' |
C3' |
O3' |
H20 |
180.0 |
294.7 |
C4' |
C3' |
C2' |
H7 |
166.5 |
97.4 |
P |
O5' |
C5' |
H15 |
41.6 |
60.0 |
P |
O5' |
C5' |
H16 |
280.7 |
300.0 |
C2' |
C1' |
O4' |
H6 |
244.3 |
241.4 |
O4' |
C1' |
C2' |
H7 |
210.0 |
278.8 |
N1 |
C1' |
O4' |
H6 |
121.1 |
122.9 |
C21 |
O2' |
C2' |
H7 |
326.0 |
26.3 |
H23 |
C21 |
O2' |
H24 |
240.0 |
240.0 |
H23 |
C21 |
O2' |
H25 |
120.0 |
120.0 |
H24 |
C21 |
O2' |
H25 |
240.0 |
240.0 |
O2' |
C2' |
C1' |
H6 |
326.2 |
36.6 |
C1' |
C2' |
O2' |
H7 |
126.0 |
123.7 |
C3' |
C2' |
O2' |
H7 |
233.6 |
236.4 |
O4' |
C1' |
C2' |
H6 |
116.6 |
118.6 |
O2' |
C2' |
C1' |
H7 |
232.9 |
236.4 |
N1 |
C1' |
C2' |
H6 |
239.3 |
237.1 |
C3' |
C2' |
C1' |
H7 |
120.2 |
118.2 |
O4' |
C1' |
N1 |
H6 |
238.5 |
237.0 |
C2' |
C1' |
N1 |
H6 |
120.3 |
122.9 |
N1 |
C1' |
C2' |
H7 |
332.6 |
37.3 |
C1' |
N1 |
C6 |
H3 |
358.7 |
360.0 |
C1' |
N1 |
C2 |
N3 |
180.2 |
180.0 |
C4' |
C3' |
O3' |
H8 |
245.0 |
237.3 |
O3' |
C3' |
C2' |
H7 |
301.0 |
216.0 |
O2' |
C2' |
C3' |
H7 |
127.3 |
123.5 |
C3' |
C2' |
C1' |
N1 |
92.9 |
155.5 |
C3' |
C2' |
C1' |
H6 |
213.6 |
278.4 |
C1' |
C2' |
C3' |
H7 |
240.0 |
241.7 |
C6 |
N1 |
C2 |
N3 |
0.6 |
0.0 |
N1 |
C6 |
C5 |
H2 |
181.7 |
179.9 |
N1 |
C2 |
N3 |
C4 |
0.6 |
0.0 |
N1 |
C2 |
N3 |
C31 |
178.7 |
179.9 |
C6 |
C5 |
C4 |
N4 |
179.4 |
121.9 |
C6 |
C5 |
C4 |
H1 |
269.5 |
238.1 |
C2 |
N3 |
C4 |
N4 |
179.6 |
238.0 |
C2 |
N3 |
C4 |
H1 |
89.4 |
121.9 |
C2 |
N3 |
C31 |
H9 |
188.9 |
330.0 |
C2 |
N3 |
C31 |
H10 |
307.1 |
210.0 |
C2 |
N3 |
C4 |
C5 |
359.3 |
360.0 |
N3 |
C4 |
C5 |
N4 |
180.3 |
238.1 |
N3 |
C4 |
C5 |
H1 |
90.1 |
121.9 |
N4 |
C4 |
C5 |
H1 |
269.8 |
243.9 |
C5 |
C4 |
N4 |
H17 |
180.0 |
56.3 |
C5 |
C4 |
N4 |
H18 |
300.0 |
180.2 |
C2 |
N3 |
C4 |
C31 |
178.1 |
179.9 |
C5 |
C4 |
N3 |
N4 |
179.7 |
122.0 |
C5 |
C4 |
N3 |
H1 |
269.9 |
238.1 |
N4 |
C4 |
N3 |
H1 |
90.2 |
116.1 |
N3 |
C4 |
N4 |
H17 |
359.7 |
183.8 |
N3 |
C4 |
N4 |
H18 |
119.7 |
307.7 |
C2 |
N3 |
C31 |
C4 |
181.9 |
180.1 |
C31 |
N3 |
C4 |
N4 |
1.4 |
58.1 |
C31 |
N3 |
C4 |
H1 |
271.3 |
302.0 |
N3 |
C31 |
C32 |
H4 |
282.6 |
299.9 |
N3 |
C31 |
C32 |
H5 |
41.6 |
60.0 |
C32 |
C31 |
N3 |
H9 |
239.1 |
120.0 |
C32 |
C31 |
N3 |
H10 |
120.9 |
240.0 |
H9 |
C31 |
N3 |
H10 |
241.8 |
120.0 |
C5 |
C4 |
N4 |
H1 |
90.1 |
116.3 |
N3 |
C4 |
N4 |
H1 |
269.8 |
243.8 |
H17 |
N4 |
C4 |
H18 |
240.0 |
236.0 |
C2 |
N3 |
C31 |
C32 |
68.0 |
90.0 |
N3 |
C31 |
C32 |
H9 |
120.9 |
240.0 |
N3 |
C31 |
C32 |
H10 |
239.1 |
119.9 |
C33 |
C32 |
C31 |
H4 |
239.5 |
240.0 |
C33 |
C32 |
C31 |
H5 |
120.5 |
120.0 |
C31 |
C32 |
C33 |
H11 |
180.0 |
179.9 |
C31 |
C32 |
C33 |
H12 |
300.0 |
300.0 |
C31 |
C32 |
C33 |
H13 |
60.0 |
59.9 |
H4 |
C32 |
C31 |
H5 |
241.0 |
240.0 |
H9 |
C31 |
C32 |
H10 |
118.2 |
240.0 |
C31 |
C32 |
C33 |
H4 |
120.5 |
120.0 |
C31 |
C32 |
C33 |
H5 |
239.5 |
240.0 |
C33 |
C32 |
C31 |
H9 |
41.2 |
300.0 |
C33 |
C32 |
C31 |
H10 |
283.0 |
60.0 |
H4 |
C32 |
C33 |
H5 |
119.0 |
120.0 |
H11 |
C33 |
C32 |
H12 |
240.0 |
239.9 |
H11 |
C33 |
C32 |
H13 |
120.0 |
120.0 |
H12 |
C33 |
C32 |
H13 |
240.0 |
240.1 |
C5 |
C4 |
H1 |
N4 |
240.2 |
243.7 |
N3 |
C4 |
H1 |
N4 |
120.9 |
116.2 |
H1 |
C4 |
N4 |
H17 |
89.9 |
300.0 |
H1 |
C4 |
N4 |
H18 |
209.9 |
64.0 |
H2 |
C5 |
C4 |
N4 |
359.4 |
302.0 |
H2 |
C5 |
C4 |
H1 |
89.5 |
58.1 |
H3 |
C6 |
C5 |
H2 |
1.7 |
359.9 |
C31 |
C32 |
H4 |
C33 |
236.9 |
240.0 |
C31 |
C32 |
H4 |
H5 |
118.5 |
120.1 |
H4 |
C32 |
C31 |
H9 |
161.7 |
60.0 |
H4 |
C32 |
C31 |
H10 |
43.5 |
180.0 |
C33 |
C32 |
H4 |
H5 |
241.5 |
240.1 |
H4 |
C32 |
C33 |
H11 |
59.5 |
59.9 |
H4 |
C32 |
C33 |
H12 |
179.5 |
180.0 |
H4 |
C32 |
C33 |
H13 |
299.5 |
299.9 |
C31 |
C32 |
H5 |
C33 |
123.1 |
120.0 |
C31 |
C32 |
H5 |
H4 |
241.5 |
240.0 |
H5 |
C32 |
C31 |
H9 |
280.7 |
180.0 |
H5 |
C32 |
C31 |
H10 |
162.5 |
300.0 |
C33 |
C32 |
H5 |
H4 |
118.4 |
119.9 |
H5 |
C32 |
C33 |
H11 |
300.5 |
300.0 |
H5 |
C32 |
C33 |
H12 |
60.5 |
60.0 |
H5 |
C32 |
C33 |
H13 |
180.5 |
180.0 |
C2' |
C1' |
H6 |
N1 |
236.6 |
237.1 |
H6 |
C1' |
C2' |
H7 |
93.3 |
160.2 |
H7 |
C2' |
C1' |
N1 |
332.6 |
37.3 |
H7 |
C2' |
C1' |
H6 |
93.3 |
160.2 |
C4' |
C3' |
H8 |
O3' |
125.4 |
122.6 |
H8 |
C3' |
O3' |
H20 |
295.0 |
57.4 |
H8 |
C3' |
C2' |
H7 |
60.1 |
338.6 |
N3 |
C31 |
H9 |
H10 |
117.2 |
240.0 |
H9 |
C31 |
C32 |
C33 |
41.2 |
300.0 |
H9 |
C31 |
C32 |
H4 |
161.7 |
60.0 |
H9 |
C31 |
C32 |
H5 |
280.7 |
180.0 |
C32 |
C31 |
H9 |
H10 |
242.8 |
120.0 |
N3 |
C31 |
H10 |
H9 |
242.8 |
120.0 |
H10 |
C31 |
C32 |
C33 |
283.0 |
60.0 |
H10 |
C31 |
C32 |
H4 |
43.5 |
180.0 |
H10 |
C31 |
C32 |
H5 |
162.5 |
300.0 |
C32 |
C31 |
H10 |
H9 |
117.2 |
240.0 |
H11 |
C33 |
C32 |
H4 |
59.5 |
59.9 |
H11 |
C33 |
C32 |
H5 |
300.5 |
300.0 |
C32 |
C33 |
H11 |
H12 |
120.0 |
120.1 |
C32 |
C33 |
H11 |
H13 |
240.0 |
240.0 |
H12 |
C33 |
H11 |
H13 |
120.0 |
119.9 |
H12 |
C33 |
C32 |
H4 |
179.5 |
180.0 |
H12 |
C33 |
C32 |
H5 |
60.5 |
60.0 |
C32 |
C33 |
H12 |
H11 |
240.0 |
239.9 |
C32 |
C33 |
H12 |
H13 |
120.0 |
120.0 |
H11 |
C33 |
H12 |
H13 |
240.0 |
240.1 |
H13 |
C33 |
C32 |
H4 |
299.5 |
299.9 |
H13 |
C33 |
C32 |
H5 |
180.5 |
180.0 |
C32 |
C33 |
H13 |
H11 |
120.0 |
120.0 |
C32 |
C33 |
H13 |
H12 |
240.0 |
240.0 |
H11 |
C33 |
H13 |
H12 |
120.0 |
120.0 |
C5' |
C4' |
H14 |
O4' |
123.6 |
121.1 |
H14 |
C4' |
C3' |
O3' |
292.2 |
358.8 |
H14 |
C4' |
C3' |
H8 |
177.0 |
236.2 |
H15 |
C5' |
C4' |
O4' |
50.9 |
186.5 |
H15 |
C5' |
C4' |
H14 |
287.1 |
65.3 |
O5' |
C5' |
H15 |
H16 |
238.6 |
240.0 |
H16 |
C5' |
C4' |
O4' |
171.9 |
306.5 |
H16 |
C5' |
C4' |
H14 |
48.1 |
185.3 |
O5' |
C5' |
H16 |
H15 |
121.4 |
120.0 |
H17 |
N4 |
C4 |
H1 |
89.9 |
300.0 |
C4 |
N4 |
H17 |
H18 |
120.0 |
124.0 |
H18 |
N4 |
C4 |
H1 |
209.9 |
64.0 |
C4 |
N4 |
H18 |
H17 |
240.0 |
236.0 |
H20 |
O3' |
C3' |
H8 |
295.0 |
57.4 |
H22 |
OP2 |
P |
OP3 |
231.6 |
60.0 |
O2' |
C21 |
H23 |
H24 |
120.0 |
120.0 |
O2' |
C21 |
H23 |
H25 |
240.0 |
240.0 |
H24 |
C21 |
H23 |
H25 |
120.0 |
120.0 |
O2' |
C21 |
H24 |
H23 |
240.0 |
240.0 |
O2' |
C21 |
H24 |
H25 |
120.0 |
120.0 |
H23 |
C21 |
H24 |
H25 |
240.0 |
240.0 |
O2' |
C21 |
H25 |
H23 |
120.0 |
120.0 |
O2' |
C21 |
H25 |
H24 |
240.0 |
240.0 |
H23 |
C21 |
H25 |
H24 |
120.0 |
120.0 |
OP3 |
P |
OP2 |
H22 |
231.6 |
60.0 |