PDB Chemical Component RDG
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 RDG
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
O6 |
C6 |
1.348 |
1.220 |
N1 |
C6 |
1.362 |
1.351 |
N1 |
C2 |
1.349 |
1.364 |
N2 |
C2 |
1.428 |
1.372 |
N2 |
C11 |
1.436 |
1.465 |
C6 |
C5 |
1.425 |
1.415 |
O7 |
C12 |
1.330 |
1.343 |
O7 |
C10 |
1.324 |
1.343 |
C2 |
N3 |
1.350 |
1.314 |
C11 |
C10 |
1.520 |
1.507 |
C12 |
C7 |
1.393 |
1.345 |
C10 |
C9 |
1.400 |
1.344 |
C5 |
C4 |
1.372 |
1.399 |
C5 |
N7 |
1.395 |
1.355 |
N3 |
C4 |
1.391 |
1.338 |
C4 |
N9 |
1.381 |
1.369 |
C7 |
C9 |
1.456 |
1.414 |
N7 |
C8 |
1.337 |
1.301 |
N9 |
C8 |
1.352 |
1.366 |
N9 |
C1' |
1.544 |
1.464 |
C1' |
O4' |
1.493 |
1.445 |
C1' |
C2' |
1.525 |
1.544 |
O4' |
C4' |
1.378 |
1.445 |
OP1 |
P |
1.505 |
1.479 |
C2' |
C3' |
1.457 |
1.546 |
C4' |
C5' |
1.482 |
1.530 |
C4' |
C3' |
1.488 |
1.546 |
C5' |
O5' |
1.375 |
1.430 |
OP3 |
P |
1.606 |
1.610 |
C3' |
O3' |
1.382 |
1.429 |
P |
O5' |
1.576 |
1.610 |
P |
OP2 |
1.548 |
1.610 |
OP3 |
H1 |
0.950 |
0.966 |
OP2 |
H2 |
0.950 |
0.968 |
C5' |
H3 |
1.100 |
1.090 |
C5' |
H4 |
1.100 |
1.091 |
C4' |
H5 |
1.100 |
1.090 |
C3' |
H6 |
1.101 |
1.090 |
O3' |
HO3' |
0.950 |
0.967 |
C2' |
H8 |
1.100 |
1.090 |
C2' |
H9 |
1.100 |
1.090 |
C1' |
H10 |
1.100 |
1.090 |
C8 |
H12 |
1.080 |
1.080 |
N2 |
H13 |
1.000 |
0.970 |
C11 |
H14 |
1.100 |
1.090 |
C11 |
H15 |
1.100 |
1.089 |
C9 |
H16 |
1.080 |
1.080 |
C12 |
H17 |
1.080 |
1.080 |
C7 |
H18 |
1.080 |
1.081 |
N1 |
H11 |
1.000 |
0.969 |
Bond Angles for RDG
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
O6 |
C6 |
C5 |
118.5 |
120.8 |
N1 |
C6 |
C5 |
118.9 |
118.4 |
C6 |
N1 |
H11 |
119.1 |
119.9 |
N2 |
C11 |
C10 |
115.3 |
109.5 |
C11 |
N2 |
H13 |
119.8 |
120.0 |
N2 |
C11 |
H14 |
108.0 |
109.5 |
N2 |
C11 |
H15 |
108.0 |
109.5 |
C6 |
C5 |
N7 |
133.9 |
134.1 |
O7 |
C12 |
C7 |
109.9 |
108.4 |
O7 |
C12 |
H17 |
125.1 |
125.8 |
C11 |
C10 |
C9 |
125.9 |
125.8 |
C10 |
C11 |
H14 |
108.0 |
109.4 |
C10 |
C11 |
H15 |
108.0 |
109.5 |
C7 |
C12 |
H17 |
125.0 |
125.8 |
C12 |
C7 |
H18 |
127.9 |
126.6 |
C10 |
C9 |
H16 |
126.9 |
126.6 |
C5 |
N7 |
C8 |
107.5 |
109.3 |
C4 |
N9 |
C8 |
109.2 |
107.5 |
C7 |
C9 |
H16 |
126.9 |
126.6 |
N9 |
C8 |
N7 |
109.1 |
109.8 |
N7 |
C8 |
H12 |
125.5 |
125.1 |
N9 |
C8 |
H12 |
125.4 |
125.1 |
N9 |
C1' |
H10 |
104.6 |
110.5 |
O4' |
C1' |
H10 |
105.1 |
110.4 |
C1' |
C2' |
H8 |
110.7 |
110.5 |
C1' |
C2' |
H9 |
110.7 |
110.6 |
O4' |
C4' |
H5 |
111.1 |
110.5 |
OP1 |
P |
O5' |
115.2 |
109.5 |
C2' |
C3' |
H6 |
110.7 |
110.6 |
C4' |
C5' |
H3 |
107.7 |
109.5 |
C4' |
C5' |
H4 |
107.7 |
109.5 |
C4' |
C3' |
O3' |
110.6 |
110.5 |
C3' |
C4' |
H5 |
109.4 |
110.3 |
C4' |
C3' |
H6 |
110.2 |
110.5 |
OP3 |
P |
O5' |
103.9 |
109.5 |
OP3 |
P |
OP2 |
115.5 |
109.5 |
P |
OP3 |
H1 |
109.5 |
114.0 |
O3' |
C3' |
H6 |
111.9 |
110.5 |
C3' |
O3' |
HO3' |
109.5 |
113.9 |
P |
OP2 |
H2 |
109.5 |
114.0 |
H3 |
C5' |
H4 |
109.4 |
109.5 |
H8 |
C2' |
H9 |
109.5 |
110.4 |
H14 |
C11 |
H15 |
109.5 |
109.5 |
Torsion Angles for RDG
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
N1 |
C6 |
O6 |
C5 |
180.6 |
179.9 |
O6 |
C6 |
N1 |
H11 |
359.6 |
0.1 |
O6 |
C6 |
C5 |
N7 |
0.6 |
359.9 |
O6 |
C6 |
N1 |
C5 |
179.4 |
180.1 |
N1 |
C6 |
C5 |
N7 |
180.0 |
180.0 |
N2 |
C11 |
C10 |
C9 |
253.7 |
90.0 |
C10 |
C11 |
N2 |
H14 |
239.2 |
240.0 |
C10 |
C11 |
N2 |
H15 |
120.9 |
120.0 |
H14 |
C11 |
N2 |
H15 |
241.7 |
240.0 |
C5 |
C6 |
N1 |
H11 |
180.2 |
180.0 |
C6 |
C5 |
N7 |
C8 |
179.5 |
180.0 |
C7 |
C12 |
O7 |
H17 |
180.0 |
180.2 |
O7 |
C12 |
C7 |
H18 |
180.1 |
180.1 |
O7 |
C10 |
C11 |
H14 |
312.1 |
149.7 |
O7 |
C10 |
C11 |
H15 |
193.8 |
29.7 |
O7 |
C10 |
C9 |
H16 |
180.3 |
180.3 |
C10 |
C11 |
N2 |
H13 |
277.1 |
0.1 |
N2 |
C11 |
C10 |
H14 |
120.8 |
120.0 |
N2 |
C11 |
C10 |
H15 |
239.1 |
240.0 |
C11 |
C10 |
C9 |
H16 |
359.6 |
0.0 |
H14 |
C11 |
C10 |
H15 |
118.3 |
120.0 |
O7 |
C12 |
C7 |
H17 |
180.0 |
179.8 |
C12 |
C7 |
C9 |
H16 |
179.8 |
179.8 |
C9 |
C10 |
C11 |
H14 |
132.9 |
330.0 |
C9 |
C10 |
C11 |
H15 |
14.6 |
210.0 |
C7 |
C9 |
C10 |
H16 |
180.0 |
180.0 |
C5 |
C4 |
N9 |
C8 |
0.2 |
360.0 |
N9 |
C8 |
N7 |
C5 |
0.4 |
0.0 |
C5 |
N7 |
C8 |
H12 |
180.3 |
180.3 |
N3 |
C4 |
N9 |
C8 |
180.3 |
180.0 |
C4 |
N9 |
C8 |
N7 |
359.7 |
360.0 |
C4 |
N9 |
C8 |
H12 |
179.7 |
179.8 |
C4 |
N9 |
C1' |
H10 |
22.2 |
326.2 |
C10 |
C9 |
C7 |
H16 |
180.0 |
180.0 |
N9 |
C8 |
N7 |
H12 |
180.0 |
179.8 |
C5 |
N7 |
C8 |
N9 |
0.4 |
0.0 |
N7 |
C8 |
N9 |
H12 |
180.0 |
180.2 |
C8 |
N9 |
C1' |
H10 |
201.3 |
145.8 |
O4' |
C1' |
N9 |
H10 |
244.4 |
237.7 |
N9 |
C1' |
C2' |
H8 |
263.6 |
24.1 |
N9 |
C1' |
C2' |
H9 |
25.3 |
261.5 |
N9 |
C1' |
O4' |
H10 |
115.3 |
122.4 |
O4' |
C1' |
C2' |
H8 |
130.8 |
265.3 |
O4' |
C1' |
C2' |
H9 |
252.5 |
142.7 |
C1' |
O4' |
C4' |
H5 |
206.4 |
281.6 |
C1' |
C2' |
C3' |
H6 |
209.4 |
241.3 |
H8 |
C2' |
C1' |
H9 |
238.4 |
122.6 |
O4' |
C4' |
C5' |
H3 |
348.1 |
309.6 |
O4' |
C4' |
C5' |
H4 |
106.0 |
189.6 |
C3' |
C4' |
O4' |
H5 |
117.1 |
118.9 |
O4' |
C4' |
C3' |
H6 |
161.7 |
94.8 |
OP3 |
P |
OP1 |
O5' |
245.4 |
120.0 |
OP1 |
P |
OP3 |
H1 |
360.0 |
60.0 |
OP1 |
P |
OP2 |
H2 |
360.0 |
180.0 |
C2' |
C3' |
C4' |
H5 |
161.8 |
95.0 |
C4' |
C3' |
C2' |
H6 |
117.8 |
118.6 |
O3' |
C3' |
C2' |
H6 |
235.9 |
237.3 |
C2' |
C3' |
O3' |
HO3' |
180.0 |
65.4 |
H3 |
C5' |
C4' |
H4 |
242.1 |
120.1 |
O4' |
C4' |
C3' |
H5 |
241.7 |
241.0 |
C2' |
C3' |
C4' |
H6 |
241.8 |
241.2 |
C3' |
C4' |
C5' |
H3 |
102.9 |
65.0 |
C3' |
C4' |
C5' |
H4 |
220.8 |
305.0 |
O3' |
C3' |
C4' |
H6 |
124.2 |
122.6 |
C4' |
C3' |
O3' |
HO3' |
293.3 |
180.0 |
OP1 |
P |
OP3 |
O5' |
122.0 |
240.0 |
OP3 |
P |
OP2 |
H2 |
239.4 |
300.0 |
C2' |
C3' |
O3' |
H6 |
123.5 |
122.8 |
O3' |
C3' |
C4' |
H5 |
44.1 |
336.4 |
C4' |
C3' |
O3' |
H6 |
236.7 |
237.4 |
OP3 |
P |
O5' |
OP2 |
238.0 |
120.0 |
O5' |
P |
OP3 |
H1 |
238.0 |
180.0 |
O5' |
P |
OP2 |
H2 |
125.1 |
60.0 |
OP3 |
P |
OP2 |
O5' |
114.3 |
240.0 |
OP2 |
P |
OP3 |
H1 |
122.5 |
300.0 |
H1 |
OP3 |
P |
O5' |
238.0 |
180.0 |
H1 |
OP3 |
P |
OP2 |
122.5 |
300.0 |
C4' |
C5' |
H3 |
H4 |
116.8 |
239.9 |
C4' |
C5' |
H4 |
H3 |
243.2 |
120.1 |
H5 |
C4' |
C5' |
H3 |
226.9 |
187.2 |
H5 |
C4' |
C5' |
H4 |
344.8 |
67.2 |
H5 |
C4' |
C3' |
O3' |
44.1 |
336.4 |
H5 |
C4' |
C3' |
H6 |
279.9 |
213.7 |
C4' |
C3' |
H6 |
O3' |
123.5 |
122.6 |
H6 |
C3' |
C4' |
H5 |
279.9 |
213.7 |
H6 |
C3' |
O3' |
HO3' |
56.6 |
302.6 |
HO3' |
O3' |
C3' |
H6 |
56.6 |
302.6 |
C1' |
C2' |
H8 |
H9 |
122.4 |
237.2 |
H8 |
C2' |
C3' |
H6 |
90.2 |
0.1 |
C1' |
C2' |
H9 |
H8 |
237.6 |
122.7 |
H9 |
C2' |
C3' |
H6 |
328.6 |
122.5 |
H10 |
C1' |
C2' |
H8 |
21.1 |
146.5 |
H10 |
C1' |
C2' |
H9 |
142.7 |
23.9 |
N9 |
C8 |
H12 |
N7 |
180.0 |
180.3 |
H13 |
N2 |
C11 |
C10 |
277.1 |
0.1 |
H13 |
N2 |
C11 |
H14 |
37.9 |
120.0 |
H13 |
N2 |
C11 |
H15 |
156.2 |
240.1 |
N2 |
C11 |
H14 |
C10 |
234.7 |
240.0 |
H14 |
C11 |
N2 |
H13 |
37.9 |
120.0 |
N2 |
C11 |
H14 |
H15 |
117.4 |
120.0 |
H14 |
C11 |
C10 |
C9 |
132.9 |
330.0 |
C10 |
C11 |
H14 |
H15 |
242.7 |
240.0 |
N2 |
C11 |
H15 |
C10 |
125.3 |
120.0 |
H15 |
C11 |
N2 |
H13 |
156.2 |
240.1 |
N2 |
C11 |
H15 |
H14 |
242.6 |
240.0 |
H15 |
C11 |
C10 |
C9 |
14.6 |
210.0 |
C10 |
C11 |
H15 |
H14 |
117.3 |
120.0 |
O7 |
C12 |
H17 |
C7 |
180.0 |
180.2 |
H17 |
C12 |
C7 |
H18 |
0.0 |
0.3 |
H18 |
C7 |
C12 |
H17 |
0.0 |
0.3 |
H18 |
C7 |
C9 |
H16 |
359.8 |
359.7 |
H11 |
N1 |
C6 |
C5 |
180.2 |
180.0 |