PDB Chemical Component VC6
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 VC6
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
O2 |
C2 |
1.195 |
1.220 |
C2 |
N3 |
1.323 |
1.333 |
C2 |
N1 |
1.323 |
1.345 |
C2' |
C1' |
1.575 |
1.550 |
C2' |
C3' |
1.551 |
1.553 |
N3 |
C4 |
1.325 |
1.327 |
C1' |
N1 |
1.473 |
1.466 |
C1' |
O4' |
1.310 |
1.437 |
N1 |
C6 |
1.327 |
1.362 |
O3' |
C3' |
1.479 |
1.428 |
C3' |
C4' |
1.326 |
1.544 |
C4 |
N4 |
1.445 |
1.376 |
C4 |
C5 |
1.380 |
1.410 |
O4' |
C4' |
1.598 |
1.433 |
C6 |
C5 |
1.386 |
1.354 |
C4' |
C5' |
1.493 |
1.530 |
O2B |
PB |
1.496 |
1.480 |
C5' |
O5' |
1.401 |
1.429 |
PB |
O3A |
1.632 |
1.610 |
PB |
O1B |
1.518 |
1.610 |
PB |
C3B |
1.871 |
1.823 |
O3A |
PA |
1.637 |
1.610 |
O5' |
PA |
1.632 |
1.611 |
F4B |
C3B |
1.389 |
1.398 |
C3B |
CL1 |
1.756 |
1.803 |
C3B |
PG |
1.872 |
1.824 |
PA |
O2A |
1.488 |
1.479 |
PA |
O1A |
1.498 |
1.611 |
O3G |
PG |
1.489 |
1.480 |
PG |
O2G |
1.519 |
1.610 |
PG |
O1G |
1.504 |
1.609 |
N4 |
H1 |
1.000 |
0.971 |
N4 |
H2 |
1.000 |
0.970 |
C5 |
H3 |
1.080 |
1.080 |
C6 |
H4 |
1.080 |
1.080 |
C1' |
H5 |
1.100 |
1.090 |
C2' |
H6 |
1.100 |
1.091 |
C2' |
H7 |
1.100 |
1.090 |
C3' |
H8 |
1.100 |
1.090 |
O3' |
H9 |
0.950 |
0.967 |
C4' |
H10 |
1.101 |
1.090 |
C5' |
H11 |
1.100 |
1.090 |
C5' |
H12 |
1.100 |
1.090 |
O1A |
H13 |
0.950 |
0.966 |
O1B |
H14 |
0.950 |
0.967 |
O2G |
H15 |
0.950 |
0.967 |
O1G |
H16 |
0.950 |
0.967 |
Bond Angles for VC6
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
O2 |
C2 |
N1 |
118.8 |
119.5 |
C2' |
C1' |
O4' |
103.7 |
105.1 |
C2' |
C1' |
H5 |
108.6 |
110.4 |
C2' |
C3' |
C4' |
102.6 |
102.3 |
C3' |
C2' |
H6 |
110.5 |
111.1 |
C3' |
C2' |
H7 |
110.5 |
111.2 |
C2' |
C3' |
H8 |
105.7 |
110.8 |
C1' |
O4' |
C4' |
103.2 |
109.9 |
O4' |
C1' |
H5 |
112.5 |
110.3 |
N1 |
C6 |
H4 |
119.7 |
120.4 |
O3' |
C3' |
C4' |
118.4 |
110.9 |
O3' |
C3' |
H8 |
106.5 |
110.9 |
C3' |
C4' |
O4' |
111.9 |
107.6 |
C3' |
C4' |
C5' |
125.9 |
109.8 |
C4' |
C3' |
H8 |
108.4 |
110.8 |
C3' |
C4' |
H10 |
102.6 |
109.8 |
N4 |
C4 |
C5 |
118.6 |
120.2 |
C4 |
N4 |
H1 |
120.0 |
120.0 |
C4 |
N4 |
H2 |
120.0 |
120.0 |
C4 |
C5 |
H3 |
121.5 |
120.5 |
O4' |
C4' |
C5' |
110.5 |
109.8 |
O4' |
C4' |
H10 |
100.4 |
109.8 |
C6 |
C5 |
H3 |
121.5 |
120.5 |
C4' |
C5' |
O5' |
90.2 |
109.5 |
C5' |
C4' |
H10 |
101.2 |
109.9 |
C4' |
C5' |
H11 |
114.1 |
109.5 |
C4' |
C5' |
H12 |
114.0 |
109.5 |
O2B |
PB |
C3B |
108.6 |
109.5 |
C5' |
O5' |
PA |
118.3 |
123.0 |
O5' |
C5' |
H11 |
114.1 |
109.5 |
O5' |
C5' |
H12 |
114.1 |
109.5 |
O1B |
PB |
C3B |
111.7 |
109.5 |
PB |
O1B |
H14 |
109.5 |
114.0 |
PB |
C3B |
CL1 |
107.4 |
109.5 |
PB |
C3B |
PG |
110.0 |
109.4 |
O5' |
PA |
O2A |
111.2 |
109.5 |
O5' |
PA |
O1A |
105.8 |
109.4 |
F4B |
C3B |
PG |
112.2 |
109.5 |
CL1 |
C3B |
PG |
107.5 |
109.5 |
C3B |
PG |
O2G |
107.7 |
109.5 |
C3B |
PG |
O1G |
109.5 |
109.5 |
O1A |
PA |
O2A |
114.1 |
109.5 |
PA |
O1A |
H13 |
109.5 |
114.0 |
O2G |
PG |
O1G |
109.6 |
109.5 |
PG |
O2G |
H15 |
109.5 |
114.0 |
PG |
O1G |
H16 |
109.5 |
114.0 |
H1 |
N4 |
H2 |
120.0 |
120.0 |
H6 |
C2' |
H7 |
109.5 |
111.0 |
H11 |
C5' |
H12 |
109.5 |
109.4 |
Torsion Angles for VC6
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
C2 |
N1 |
C6 |
H4 |
181.2 |
179.7 |
C2' |
C1' |
O4' |
C4' |
35.2 |
335.5 |
O4' |
C1' |
C2' |
H5 |
119.8 |
119.0 |
C3' |
C2' |
C1' |
O4' |
328.0 |
36.5 |
C3' |
C2' |
C1' |
H5 |
208.2 |
277.5 |
O3' |
C3' |
C2' |
C4' |
129.6 |
118.2 |
O3' |
C3' |
C2' |
H8 |
243.1 |
236.4 |
C2' |
C3' |
C4' |
O4' |
9.1 |
21.4 |
C2' |
C3' |
C4' |
C5' |
148.2 |
140.9 |
C4' |
C3' |
C2' |
H8 |
113.5 |
118.2 |
C2' |
C3' |
C4' |
H10 |
262.2 |
261.8 |
H6 |
C2' |
C3' |
H7 |
121.4 |
124.2 |
N3 |
C4 |
N4 |
H1 |
0.0 |
179.7 |
N3 |
C4 |
N4 |
H2 |
180.0 |
359.7 |
N3 |
C4 |
C5 |
H3 |
179.2 |
180.3 |
C1' |
N1 |
C6 |
H4 |
357.9 |
0.0 |
C2' |
C1' |
O4' |
H5 |
242.9 |
240.9 |
C3' |
C4' |
O4' |
C1' |
328.9 |
1.7 |
C1' |
O4' |
C4' |
C5' |
183.4 |
242.2 |
C1' |
O4' |
C4' |
H10 |
77.2 |
121.3 |
N1 |
C6 |
C5 |
H3 |
179.7 |
180.0 |
C2' |
C3' |
O3' |
C4' |
238.7 |
247.1 |
O3' |
C3' |
C2' |
H6 |
22.0 |
326.2 |
O3' |
C3' |
C2' |
H7 |
260.7 |
202.0 |
C2' |
C3' |
O3' |
H8 |
116.4 |
123.6 |
O3' |
C3' |
C4' |
O4' |
241.9 |
263.2 |
O3' |
C3' |
C4' |
C5' |
21.0 |
22.7 |
C4' |
C3' |
O3' |
H8 |
237.7 |
236.4 |
O3' |
C3' |
C4' |
H10 |
135.0 |
143.6 |
C4' |
C3' |
C2' |
H6 |
252.4 |
208.0 |
C4' |
C3' |
C2' |
H7 |
131.0 |
83.8 |
C2' |
C3' |
C4' |
H8 |
248.5 |
241.8 |
C1' |
O4' |
C4' |
C3' |
328.9 |
1.7 |
O3' |
C3' |
C4' |
H8 |
121.3 |
123.6 |
O4' |
C4' |
C3' |
C5' |
220.9 |
240.5 |
O4' |
C4' |
C3' |
H10 |
106.9 |
119.5 |
C3' |
C4' |
C5' |
O5' |
124.0 |
175.0 |
C5' |
C4' |
C3' |
H10 |
246.0 |
239.0 |
C3' |
C4' |
C5' |
H11 |
240.6 |
295.0 |
C3' |
C4' |
C5' |
H12 |
7.4 |
55.0 |
N4 |
C4 |
C5 |
H3 |
0.5 |
360.0 |
H1 |
N4 |
C4 |
H2 |
180.0 |
180.0 |
C5 |
C4 |
N4 |
H1 |
178.8 |
0.0 |
C5 |
C4 |
N4 |
H2 |
358.7 |
180.0 |
C6 |
C5 |
C4 |
H3 |
180.0 |
180.1 |
C4' |
O4' |
C1' |
H5 |
152.3 |
94.6 |
C3' |
C4' |
O4' |
C5' |
145.5 |
119.5 |
O4' |
C4' |
C3' |
H8 |
120.6 |
139.5 |
C3' |
C4' |
O4' |
H10 |
251.7 |
240.5 |
O4' |
C4' |
C5' |
O5' |
263.6 |
293.1 |
C5' |
C4' |
O4' |
H10 |
106.2 |
121.0 |
O4' |
C4' |
C5' |
H11 |
20.2 |
53.2 |
O4' |
C4' |
C5' |
H12 |
147.0 |
173.1 |
C4 |
C5 |
C6 |
H3 |
180.0 |
179.9 |
C3' |
C4' |
C5' |
O4' |
220.4 |
241.9 |
C5' |
C4' |
C3' |
H8 |
259.7 |
259.0 |
C3' |
C4' |
C5' |
H10 |
114.7 |
120.9 |
O4' |
C4' |
C5' |
H10 |
254.3 |
239.1 |
C4' |
C5' |
O5' |
PA |
244.8 |
180.0 |
O5' |
C5' |
C4' |
H11 |
243.4 |
240.0 |
O5' |
C5' |
C4' |
H12 |
116.6 |
120.0 |
H11 |
C5' |
C4' |
H12 |
233.2 |
240.0 |
O1B |
PB |
O2B |
C3B |
236.5 |
240.0 |
O2B |
PB |
O1B |
H14 |
0.0 |
180.0 |
O2B |
PB |
C3B |
CL1 |
98.3 |
180.0 |
O2B |
PB |
C3B |
PG |
215.0 |
300.0 |
O5' |
C5' |
C4' |
H10 |
9.3 |
54.1 |
C4' |
C5' |
O5' |
H11 |
116.6 |
120.0 |
C4' |
C5' |
O5' |
H12 |
243.4 |
240.0 |
C5' |
O5' |
PA |
O2A |
161.8 |
305.0 |
C5' |
O5' |
PA |
O1A |
286.1 |
65.0 |
H11 |
C5' |
O5' |
H12 |
126.8 |
120.0 |
O2B |
PB |
O1B |
C3B |
121.8 |
120.0 |
O1B |
PB |
C3B |
CL1 |
221.8 |
300.0 |
O1B |
PB |
C3B |
PG |
338.5 |
60.0 |
C3B |
PB |
O1B |
H14 |
238.3 |
60.0 |
F4B |
C3B |
PB |
PG |
126.0 |
120.0 |
CL1 |
C3B |
PB |
PG |
243.3 |
240.0 |
PB |
C3B |
PG |
O2G |
320.1 |
60.0 |
PB |
C3B |
PG |
O1G |
201.0 |
180.0 |
O3A |
PA |
O1A |
H13 |
123.2 |
300.0 |
PA |
O5' |
C5' |
H11 |
128.2 |
59.9 |
PA |
O5' |
C5' |
H12 |
1.4 |
300.0 |
O1A |
PA |
O5' |
O2A |
124.3 |
120.0 |
O5' |
PA |
O1A |
H13 |
237.5 |
60.0 |
PB |
C3B |
F4B |
PG |
235.2 |
240.0 |
CL1 |
C3B |
F4B |
PG |
117.6 |
120.0 |
F4B |
C3B |
PG |
O2G |
193.9 |
300.0 |
F4B |
C3B |
PG |
O1G |
74.8 |
60.0 |
PB |
C3B |
CL1 |
PG |
118.3 |
120.0 |
F4B |
C3B |
CL1 |
PG |
239.4 |
240.0 |
CL1 |
C3B |
PG |
O2G |
76.7 |
180.0 |
CL1 |
C3B |
PG |
O1G |
317.6 |
300.0 |
PB |
C3B |
PG |
CL1 |
243.4 |
240.0 |
O2G |
PG |
C3B |
O1G |
119.1 |
240.0 |
C3B |
PG |
O2G |
H15 |
118.6 |
60.0 |
C3B |
PG |
O1G |
H16 |
240.0 |
180.0 |
O5' |
PA |
O2A |
O1A |
119.5 |
120.0 |
O2A |
PA |
O1A |
H13 |
0.0 |
180.0 |
O5' |
PA |
O1A |
O2A |
237.5 |
240.0 |
O3G |
PG |
O2G |
H15 |
0.0 |
180.0 |
O3G |
PG |
O1G |
H16 |
360.0 |
60.0 |
C3B |
PG |
O2G |
O1G |
241.0 |
120.0 |
O2G |
PG |
O1G |
H16 |
122.1 |
300.0 |
C3B |
PG |
O1G |
O2G |
117.9 |
240.0 |
O1G |
PG |
O2G |
H15 |
237.6 |
300.0 |
H1 |
N4 |
C4 |
C5 |
178.8 |
0.0 |
C4 |
N4 |
H1 |
H2 |
180.0 |
180.0 |
H2 |
N4 |
C4 |
C5 |
358.7 |
180.0 |
C4 |
N4 |
H2 |
H1 |
180.0 |
180.0 |
H4 |
C6 |
C5 |
H3 |
359.7 |
0.0 |
C2' |
C1' |
H5 |
O4' |
114.1 |
115.8 |
H5 |
C1' |
O4' |
C4' |
152.3 |
94.6 |
H6 |
C2' |
C1' |
O4' |
87.3 |
154.4 |
H6 |
C2' |
C1' |
H5 |
327.6 |
35.4 |
H6 |
C2' |
C3' |
C4' |
252.4 |
208.0 |
C3' |
C2' |
H6 |
H7 |
238.1 |
235.7 |
H6 |
C2' |
C3' |
H8 |
138.9 |
89.8 |
H7 |
C2' |
C1' |
O4' |
208.7 |
278.5 |
H7 |
C2' |
C1' |
H5 |
88.9 |
159.5 |
H7 |
C2' |
C3' |
C4' |
131.0 |
83.8 |
C3' |
C2' |
H7 |
H6 |
121.9 |
124.3 |
H7 |
C2' |
C3' |
H8 |
17.5 |
325.6 |
C2' |
C3' |
H8 |
C4' |
109.4 |
112.8 |
H8 |
C3' |
C2' |
H6 |
138.9 |
89.8 |
H8 |
C3' |
C2' |
H7 |
17.5 |
325.6 |
O3' |
C3' |
H8 |
C4' |
231.6 |
236.4 |
H8 |
C3' |
C4' |
O4' |
120.6 |
139.5 |
H8 |
C3' |
C4' |
C5' |
259.7 |
259.0 |
H8 |
C3' |
C4' |
H10 |
13.7 |
20.0 |
H9 |
O3' |
C3' |
C4' |
274.5 |
174.3 |
H9 |
O3' |
C3' |
H8 |
36.8 |
297.9 |
C3' |
C4' |
H10 |
O4' |
115.5 |
118.2 |
C3' |
C4' |
H10 |
C5' |
229.0 |
239.1 |
H10 |
C4' |
C3' |
H8 |
13.7 |
20.0 |
O4' |
C4' |
H10 |
C5' |
113.5 |
120.9 |
H10 |
C4' |
C5' |
O5' |
9.3 |
54.1 |
H10 |
C4' |
C5' |
H11 |
125.9 |
174.1 |
H10 |
C4' |
C5' |
H12 |
252.7 |
294.1 |
C4' |
C5' |
H11 |
O5' |
258.3 |
240.0 |
H11 |
C5' |
C4' |
H10 |
125.9 |
174.1 |
C4' |
C5' |
H11 |
H12 |
129.1 |
120.0 |
H11 |
C5' |
O5' |
PA |
128.2 |
59.9 |
O5' |
C5' |
H11 |
H12 |
230.8 |
240.0 |
C4' |
C5' |
H12 |
O5' |
101.7 |
120.0 |
H12 |
C5' |
C4' |
H10 |
252.7 |
294.1 |
C4' |
C5' |
H12 |
H11 |
230.9 |
240.0 |
H12 |
C5' |
O5' |
PA |
1.4 |
300.0 |
O5' |
C5' |
H12 |
H11 |
129.2 |
120.0 |
H13 |
O1A |
PA |
O2A |
0.0 |
180.0 |
H14 |
O1B |
PB |
C3B |
238.3 |
60.0 |
H15 |
O2G |
PG |
O1G |
237.6 |
300.0 |