PDB Chemical Component D3N
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 D3N
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
O3' |
C3' |
1.482 |
1.429 |
C2' |
C3' |
1.525 |
1.549 |
C2' |
C1' |
1.503 |
1.540 |
C3' |
C4' |
1.496 |
1.549 |
C1' |
N1 |
1.443 |
1.465 |
C1' |
O4' |
1.419 |
1.437 |
O2 |
C2 |
1.238 |
1.216 |
N1 |
C2 |
1.349 |
1.347 |
N1 |
C6 |
1.408 |
1.393 |
C2 |
N3 |
1.358 |
1.347 |
C7 |
C6 |
1.347 |
1.376 |
C7 |
C8 |
1.409 |
1.394 |
C6 |
C5 |
1.414 |
1.410 |
C4' |
O4' |
1.401 |
1.444 |
C4' |
C5' |
1.514 |
1.530 |
C8 |
C9 |
1.364 |
1.363 |
N3 |
C4 |
1.410 |
1.393 |
C5 |
C4 |
1.380 |
1.409 |
C5 |
C10 |
1.414 |
1.412 |
C4 |
C13 |
1.403 |
1.376 |
C9 |
C10 |
1.373 |
1.405 |
C10 |
C11 |
1.412 |
1.405 |
C13 |
C12 |
1.404 |
1.393 |
C5' |
O5' |
1.387 |
1.429 |
C11 |
C12 |
1.374 |
1.364 |
O5' |
P |
1.611 |
1.610 |
O2P |
P |
1.460 |
1.480 |
P |
O1P |
1.504 |
1.610 |
O1P |
H1 |
0.950 |
0.967 |
C5' |
H3 |
1.099 |
1.090 |
C5' |
H4 |
1.100 |
1.090 |
C4' |
H5 |
1.100 |
1.091 |
C3' |
H6 |
1.100 |
1.090 |
O3' |
H7 |
0.950 |
0.967 |
C2' |
H8 |
1.101 |
1.090 |
C2' |
H9 |
1.100 |
1.091 |
C1' |
H10 |
1.100 |
1.090 |
N3 |
H11 |
1.000 |
0.970 |
C7 |
H12 |
1.080 |
1.080 |
C8 |
H13 |
1.080 |
1.080 |
C9 |
H14 |
1.080 |
1.080 |
C11 |
H15 |
1.080 |
1.080 |
C12 |
H16 |
1.080 |
1.080 |
C13 |
H17 |
1.080 |
1.080 |
P |
OP3 |
|
1.611 |
OP3 |
H2 |
|
0.967 |
Bond Angles for D3N
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
O3' |
C3' |
H6 |
112.0 |
110.8 |
C2' |
C3' |
H6 |
111.3 |
110.9 |
C2' |
C1' |
N1 |
120.6 |
109.9 |
C1' |
C2' |
H8 |
110.5 |
110.5 |
C1' |
C2' |
H9 |
110.5 |
110.5 |
C2' |
C1' |
H10 |
107.6 |
109.9 |
C3' |
C4' |
H5 |
109.8 |
110.8 |
C1' |
N1 |
C2 |
119.2 |
119.8 |
C1' |
N1 |
C6 |
116.8 |
119.9 |
N1 |
C1' |
H10 |
108.3 |
109.8 |
O2 |
C2 |
N3 |
120.1 |
118.8 |
C2 |
N1 |
C6 |
123.8 |
120.4 |
N1 |
C2 |
N3 |
117.1 |
122.4 |
N1 |
C6 |
C5 |
117.2 |
118.7 |
C2 |
N3 |
C4 |
123.8 |
120.4 |
C2 |
N3 |
H11 |
118.1 |
119.8 |
C7 |
C8 |
C9 |
123.0 |
121.5 |
C8 |
C7 |
H12 |
120.2 |
119.8 |
C7 |
C8 |
H13 |
118.5 |
119.3 |
C6 |
C5 |
C10 |
120.9 |
120.2 |
O4' |
C4' |
H5 |
111.2 |
110.6 |
C4' |
C5' |
H3 |
108.9 |
109.5 |
C4' |
C5' |
H4 |
108.8 |
109.4 |
C8 |
C9 |
C10 |
118.4 |
119.9 |
C9 |
C8 |
H13 |
118.5 |
119.3 |
C8 |
C9 |
H14 |
120.8 |
120.1 |
N3 |
C4 |
C13 |
120.2 |
122.2 |
C4 |
N3 |
H11 |
118.1 |
119.8 |
C5 |
C4 |
C13 |
122.2 |
119.1 |
C5 |
C10 |
C9 |
119.6 |
118.9 |
C5 |
C10 |
C11 |
118.9 |
118.9 |
C4 |
C13 |
C12 |
119.1 |
120.4 |
C4 |
C13 |
H17 |
120.5 |
119.8 |
C9 |
C10 |
C11 |
121.5 |
122.2 |
C10 |
C9 |
H14 |
120.8 |
120.0 |
C10 |
C11 |
C12 |
121.9 |
119.8 |
C10 |
C11 |
H15 |
119.1 |
120.1 |
C13 |
C12 |
H16 |
120.3 |
119.3 |
C12 |
C11 |
H15 |
119.1 |
120.1 |
C11 |
C12 |
H16 |
120.4 |
119.2 |
O5' |
P |
OP3 |
|
109.5 |
O2P |
P |
OP3 |
|
109.5 |
P |
O1P |
H1 |
109.5 |
113.9 |
H3 |
C5' |
H4 |
109.5 |
109.5 |
H8 |
C2' |
H9 |
109.5 |
110.5 |
P |
OP3 |
H2 |
|
113.9 |
Torsion Angles for D3N
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
C2' |
C3' |
O3' |
H6 |
127.3 |
123.6 |
O3' |
C3' |
C4' |
H5 |
342.1 |
323.4 |
O3' |
C3' |
C2' |
H6 |
232.3 |
236.4 |
C2' |
C3' |
C4' |
H5 |
101.2 |
81.6 |
C1' |
C2' |
C3' |
H6 |
250.4 |
262.7 |
C2' |
C1' |
N1 |
C2 |
309.7 |
291.7 |
C2' |
C1' |
N1 |
C6 |
134.2 |
111.4 |
N1 |
C1' |
C2' |
H10 |
235.3 |
239.1 |
H8 |
C2' |
C1' |
H9 |
121.3 |
122.7 |
O4' |
C4' |
C3' |
H5 |
238.5 |
241.4 |
C3' |
C4' |
C5' |
H3 |
326.7 |
60.5 |
C3' |
C4' |
C5' |
H4 |
86.0 |
300.5 |
N1 |
C1' |
C2' |
H8 |
0.4 |
2.8 |
N1 |
C1' |
C2' |
H9 |
239.1 |
240.1 |
C2' |
C1' |
N1 |
H10 |
124.4 |
121.0 |
C2 |
N1 |
C1' |
C6 |
175.5 |
180.3 |
C1' |
N1 |
C2 |
N3 |
184.1 |
180.0 |
C1' |
N1 |
C6 |
C5 |
175.3 |
179.8 |
C1' |
O4' |
C4' |
H5 |
261.7 |
281.4 |
O2 |
C2 |
N1 |
C6 |
179.5 |
180.3 |
N1 |
C2 |
O2 |
N3 |
179.7 |
179.9 |
O2 |
C2 |
N3 |
C4 |
181.4 |
180.0 |
O2 |
C2 |
N3 |
H11 |
1.3 |
360.0 |
C1' |
N1 |
C2 |
C6 |
184.9 |
179.7 |
C2 |
N1 |
C1' |
H10 |
185.4 |
170.7 |
O2 |
C2 |
N1 |
N3 |
180.3 |
180.1 |
C2 |
N1 |
C6 |
C5 |
0.0 |
359.5 |
N1 |
C2 |
N3 |
C4 |
1.7 |
0.1 |
N1 |
C2 |
N3 |
H11 |
181.7 |
180.0 |
C1' |
N1 |
C6 |
C2 |
175.3 |
180.3 |
C6 |
N1 |
C1' |
H10 |
9.9 |
350.4 |
C6 |
N1 |
C2 |
N3 |
359.2 |
0.2 |
N1 |
C6 |
C5 |
C10 |
179.4 |
180.3 |
N3 |
C2 |
N1 |
C6 |
359.2 |
0.2 |
C2 |
N3 |
C4 |
C13 |
179.2 |
179.9 |
C4 |
N3 |
C2 |
H11 |
180.0 |
180.0 |
C7 |
C6 |
C5 |
C10 |
359.7 |
0.1 |
C7 |
C8 |
C9 |
C10 |
358.6 |
359.4 |
C9 |
C8 |
C7 |
H13 |
180.0 |
180.0 |
C7 |
C8 |
C9 |
H14 |
178.5 |
180.0 |
C6 |
C5 |
C4 |
C13 |
179.9 |
179.8 |
C6 |
C5 |
C10 |
C9 |
358.8 |
359.4 |
C6 |
C5 |
C10 |
C11 |
178.7 |
180.2 |
C3' |
C4' |
O4' |
H5 |
120.6 |
118.7 |
O4' |
C4' |
C5' |
H3 |
208.8 |
306.4 |
O4' |
C4' |
C5' |
H4 |
328.1 |
186.4 |
H3 |
C5' |
C4' |
H4 |
240.7 |
120.0 |
C9 |
C8 |
C7 |
H12 |
179.9 |
180.0 |
C7 |
C8 |
C9 |
H13 |
180.0 |
180.0 |
C5 |
C10 |
C9 |
C8 |
2.0 |
0.9 |
C8 |
C9 |
C10 |
C11 |
182.2 |
180.0 |
C10 |
C9 |
C8 |
H14 |
180.0 |
179.5 |
C2 |
N3 |
C4 |
H11 |
180.0 |
180.0 |
C5 |
C4 |
N3 |
C13 |
179.0 |
180.0 |
N3 |
C4 |
C13 |
C12 |
179.8 |
180.0 |
N3 |
C4 |
C13 |
H17 |
359.8 |
0.0 |
N1 |
C6 |
C5 |
C4 |
359.9 |
0.5 |
N3 |
C4 |
C5 |
C13 |
181.0 |
180.0 |
C5 |
C4 |
N3 |
H11 |
178.3 |
180.0 |
C5 |
C4 |
C13 |
C12 |
0.8 |
360.0 |
C5 |
C4 |
C13 |
H17 |
180.8 |
180.0 |
C8 |
C9 |
C10 |
C5 |
2.0 |
0.9 |
C10 |
C5 |
C4 |
C13 |
0.4 |
360.0 |
C9 |
C10 |
C5 |
C11 |
180.2 |
179.1 |
C5 |
C10 |
C9 |
H14 |
182.0 |
180.3 |
C5 |
C10 |
C11 |
C12 |
2.1 |
360.0 |
C5 |
C10 |
C11 |
H15 |
182.1 |
180.0 |
C13 |
C4 |
N3 |
H11 |
359.2 |
360.0 |
C4 |
C13 |
C12 |
H16 |
179.4 |
180.1 |
C10 |
C9 |
C8 |
H13 |
178.6 |
179.4 |
C8 |
C9 |
C10 |
H14 |
180.0 |
180.5 |
C5 |
C10 |
C9 |
C11 |
179.8 |
180.9 |
C9 |
C10 |
C11 |
C12 |
182.0 |
180.9 |
C9 |
C10 |
C11 |
H15 |
2.0 |
0.9 |
C5 |
C10 |
C11 |
C9 |
180.2 |
179.1 |
C11 |
C10 |
C9 |
H14 |
2.2 |
359.4 |
C12 |
C11 |
C10 |
H15 |
180.0 |
180.0 |
C10 |
C11 |
C12 |
H16 |
179.1 |
180.0 |
C4 |
C13 |
C12 |
H17 |
180.0 |
180.0 |
C13 |
C12 |
C11 |
H15 |
179.1 |
180.0 |
C11 |
C12 |
C13 |
H16 |
180.0 |
179.9 |
C5' |
O5' |
P |
OP3 |
|
175.0 |
C4 |
C13 |
C12 |
C11 |
359.4 |
0.0 |
C10 |
C11 |
C12 |
H15 |
180.0 |
180.0 |
C13 |
C12 |
C11 |
H16 |
180.0 |
180.1 |
O2P |
P |
O5' |
OP3 |
|
240.0 |
O5' |
P |
O1P |
H1 |
231.8 |
300.0 |
O5' |
P |
OP3 |
H2 |
|
180.1 |
O5' |
P |
O2P |
OP3 |
|
120.0 |
O2P |
P |
O1P |
H1 |
360.0 |
180.0 |
O2P |
P |
OP3 |
H2 |
|
300.0 |
C4' |
C5' |
H3 |
H4 |
118.9 |
240.0 |
C4' |
C5' |
H4 |
H3 |
241.1 |
120.0 |
H5 |
C4' |
C5' |
H3 |
88.2 |
183.6 |
H5 |
C4' |
C5' |
H4 |
207.5 |
63.6 |
H6 |
C3' |
C4' |
H5 |
221.5 |
199.7 |
H7 |
O3' |
C3' |
H6 |
52.6 |
303.7 |
H8 |
C2' |
C3' |
H6 |
9.8 |
21.4 |
H8 |
C2' |
C1' |
N1 |
0.4 |
2.8 |
C1' |
C2' |
H8 |
H9 |
238.1 |
237.4 |
H8 |
C2' |
C1' |
H10 |
125.1 |
123.7 |
H9 |
C2' |
C3' |
H6 |
131.1 |
144.0 |
H9 |
C2' |
C1' |
N1 |
239.1 |
240.1 |
C1' |
C2' |
H9 |
H8 |
121.9 |
122.7 |
H9 |
C2' |
C1' |
H10 |
3.8 |
1.1 |
C2' |
C1' |
H10 |
N1 |
228.2 |
239.0 |
H10 |
C1' |
C2' |
H8 |
125.1 |
123.7 |
H10 |
C1' |
C2' |
H9 |
3.8 |
1.1 |
H10 |
C1' |
N1 |
C2 |
185.4 |
170.7 |
H10 |
C1' |
N1 |
C6 |
9.9 |
350.4 |
C2 |
N3 |
H11 |
C4 |
180.0 |
180.0 |
H11 |
N3 |
C4 |
C13 |
359.2 |
360.0 |
H12 |
C7 |
C8 |
C9 |
179.9 |
180.0 |
H12 |
C7 |
C8 |
H13 |
359.9 |
360.0 |
C7 |
C8 |
H13 |
C9 |
180.0 |
180.0 |
H13 |
C8 |
C7 |
H12 |
359.9 |
360.0 |
H13 |
C8 |
C9 |
C10 |
178.6 |
179.4 |
H13 |
C8 |
C9 |
H14 |
358.5 |
360.0 |
C8 |
C9 |
H14 |
C10 |
180.0 |
179.5 |
H14 |
C9 |
C8 |
H13 |
358.5 |
360.0 |
H14 |
C9 |
C10 |
C11 |
2.2 |
359.4 |
C10 |
C11 |
H15 |
C12 |
180.0 |
180.0 |
H15 |
C11 |
C12 |
H16 |
359.1 |
359.9 |
H16 |
C12 |
C11 |
H15 |
359.1 |
359.9 |
C4 |
C13 |
H17 |
C12 |
180.0 |
180.0 |
H17 |
C13 |
C12 |
H16 |
359.4 |
0.0 |
OP3 |
P |
O1P |
H1 |
|
60.0 |