PDB Chemical Component IPL
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 IPL
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N1 |
C2 |
1.427 |
1.369 |
| N1 |
C8 |
1.301 |
1.377 |
| N1 |
HN1 |
1.019 |
0.969 |
| C2 |
C3 |
1.352 |
1.343 |
| C2 |
H2 |
1.103 |
1.080 |
| C3 |
C9 |
1.411 |
1.464 |
| C3 |
C3' |
1.518 |
1.507 |
| C4 |
C5 |
1.445 |
1.367 |
| C4 |
C9 |
1.445 |
1.396 |
| C4 |
H4 |
1.104 |
1.080 |
| C5 |
C6 |
1.415 |
1.388 |
| C5 |
H5 |
1.104 |
1.080 |
| C6 |
C7 |
1.417 |
1.378 |
| C6 |
H6 |
1.103 |
1.080 |
| C7 |
C8 |
1.405 |
1.390 |
| C7 |
H7 |
1.102 |
1.080 |
| C8 |
C9 |
1.450 |
1.407 |
| C1' |
C2' |
1.492 |
1.530 |
| C1' |
O4P |
1.284 |
1.428 |
| C1' |
H1'1 |
1.115 |
1.089 |
| C1' |
H1'2 |
1.116 |
1.090 |
| C2' |
C3' |
1.495 |
1.528 |
| C2' |
H2'1 |
1.115 |
1.090 |
| C2' |
H2'2 |
1.115 |
1.090 |
| C3' |
H3'1 |
1.115 |
1.090 |
| C3' |
H3'2 |
1.115 |
1.089 |
| P |
O1P |
1.488 |
1.479 |
| P |
O2P |
1.571 |
1.610 |
| P |
O3P |
1.470 |
1.609 |
| P |
O4P |
1.525 |
1.611 |
| O2P |
HOP2 |
0.949 |
0.966 |
| O3P |
HOP3 |
0.949 |
0.967 |
Bond Angles for IPL
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C8 |
109.9 |
109.9 |
| C2 |
N1 |
HN1 |
128.8 |
125.1 |
| N1 |
C2 |
C3 |
107.8 |
109.9 |
| N1 |
C2 |
H2 |
128.2 |
125.0 |
| C8 |
N1 |
HN1 |
121.3 |
125.0 |
| N1 |
C8 |
C7 |
127.6 |
133.5 |
| N1 |
C8 |
C9 |
108.1 |
107.1 |
| C3 |
C2 |
H2 |
124.0 |
125.1 |
| C2 |
C3 |
C9 |
108.2 |
107.0 |
| C2 |
C3 |
C3' |
126.7 |
126.5 |
| C9 |
C3 |
C3' |
125.1 |
126.5 |
| C3 |
C9 |
C4 |
134.9 |
134.0 |
| C3 |
C9 |
C8 |
106.0 |
106.1 |
| C3 |
C3' |
C2' |
111.8 |
109.5 |
| C3 |
C3' |
H3'1 |
111.4 |
109.5 |
| C3 |
C3' |
H3'2 |
111.4 |
109.5 |
| C5 |
C4 |
C9 |
117.8 |
119.8 |
| C5 |
C4 |
H4 |
121.1 |
120.1 |
| C4 |
C5 |
C6 |
121.8 |
120.5 |
| C4 |
C5 |
H5 |
120.2 |
119.8 |
| C9 |
C4 |
H4 |
121.2 |
120.1 |
| C4 |
C9 |
C8 |
118.1 |
119.9 |
| C6 |
C5 |
H5 |
118.0 |
119.7 |
| C5 |
C6 |
C7 |
121.1 |
120.7 |
| C5 |
C6 |
H6 |
119.3 |
119.6 |
| C7 |
C6 |
H6 |
119.5 |
119.7 |
| C6 |
C7 |
C8 |
117.7 |
119.8 |
| C6 |
C7 |
H7 |
121.6 |
120.1 |
| C8 |
C7 |
H7 |
120.7 |
120.2 |
| C7 |
C8 |
C9 |
123.5 |
119.4 |
| C2' |
C1' |
O4P |
119.7 |
109.5 |
| C2' |
C1' |
H1'1 |
108.5 |
109.5 |
| C2' |
C1' |
H1'2 |
108.5 |
109.5 |
| C1' |
C2' |
C3' |
138.1 |
109.5 |
| C1' |
C2' |
H2'1 |
102.4 |
109.4 |
| C1' |
C2' |
H2'2 |
102.5 |
109.4 |
| O4P |
C1' |
H1'1 |
108.6 |
109.4 |
| O4P |
C1' |
H1'2 |
108.6 |
109.5 |
| C1' |
O4P |
P |
137.6 |
106.8 |
| H1'1 |
C1' |
H1'2 |
101.4 |
109.5 |
| C3' |
C2' |
H2'1 |
102.5 |
109.5 |
| C3' |
C2' |
H2'2 |
102.5 |
109.5 |
| C2' |
C3' |
H3'1 |
111.3 |
109.5 |
| C2' |
C3' |
H3'2 |
111.4 |
109.5 |
| H2'1 |
C2' |
H2'2 |
105.7 |
109.5 |
| H3'1 |
C3' |
H3'2 |
99.0 |
109.4 |
| O1P |
P |
O2P |
106.4 |
109.4 |
| O1P |
P |
O3P |
116.3 |
109.5 |
| O1P |
P |
O4P |
111.8 |
109.5 |
| O2P |
P |
O3P |
113.0 |
109.5 |
| O2P |
P |
O4P |
106.7 |
109.5 |
| P |
O2P |
HOP2 |
106.4 |
106.8 |
| O3P |
P |
O4P |
102.4 |
109.5 |
| P |
O3P |
HOP3 |
116.3 |
106.8 |
Torsion Angles for IPL
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C8 |
N1 |
C2 |
HN1 |
180.0 |
180.1 |
| C2 |
N1 |
C8 |
C7 |
190.0 |
180.0 |
| C2 |
N1 |
C8 |
C9 |
359.7 |
359.7 |
| C3 |
C2 |
N1 |
H2 |
180.0 |
180.0 |
| N1 |
C2 |
C3 |
C9 |
359.6 |
0.3 |
| N1 |
C2 |
C3 |
C3' |
176.3 |
179.9 |
| C2 |
N1 |
C8 |
HN1 |
180.0 |
179.9 |
| C8 |
N1 |
C2 |
C3 |
0.4 |
360.0 |
| C8 |
N1 |
C2 |
H2 |
180.4 |
180.0 |
| C3 |
C9 |
C8 |
N1 |
0.1 |
0.4 |
| C4 |
C9 |
C8 |
N1 |
189.8 |
179.7 |
| C6 |
C7 |
C8 |
N1 |
168.1 |
180.0 |
| N1 |
C8 |
C7 |
H7 |
348.1 |
359.9 |
| C7 |
C8 |
N1 |
C9 |
190.3 |
180.3 |
| C2 |
N1 |
HN1 |
C8 |
180.0 |
180.1 |
| HN1 |
N1 |
C2 |
C3 |
180.4 |
179.9 |
| HN1 |
N1 |
C2 |
H2 |
0.4 |
360.0 |
| HN1 |
N1 |
C8 |
C7 |
10.0 |
0.1 |
| HN1 |
N1 |
C8 |
C9 |
179.7 |
179.8 |
| C3 |
C2 |
N1 |
C8 |
0.4 |
360.0 |
| C3 |
C2 |
N1 |
HN1 |
180.4 |
179.9 |
| N1 |
C2 |
C3 |
H2 |
180.0 |
180.0 |
| C9 |
C3 |
C2 |
C3' |
183.4 |
180.3 |
| C2 |
C3 |
C9 |
C4 |
168.0 |
180.5 |
| C2 |
C3 |
C9 |
C8 |
0.2 |
359.6 |
| C2 |
C3 |
C3' |
C2' |
82.3 |
90.1 |
| C2 |
C3 |
C3' |
H3'1 |
207.5 |
330.1 |
| C2 |
C3 |
C3' |
H3'2 |
317.0 |
210.1 |
| H2 |
C2 |
N1 |
C8 |
180.4 |
180.0 |
| H2 |
C2 |
N1 |
HN1 |
0.4 |
360.0 |
| N1 |
C2 |
H2 |
C3 |
180.0 |
180.0 |
| H2 |
C2 |
C3 |
C9 |
179.6 |
180.2 |
| H2 |
C2 |
C3 |
C3' |
356.3 |
359.9 |
| N1 |
C8 |
C9 |
C3 |
0.1 |
0.4 |
| C9 |
C3 |
C2 |
H2 |
179.6 |
180.2 |
| C2 |
C3 |
C9 |
C3' |
176.7 |
179.7 |
| C9 |
C3 |
C3' |
C2' |
258.4 |
269.7 |
| C9 |
C3 |
C3' |
H3'1 |
23.6 |
149.7 |
| C9 |
C3 |
C3' |
H3'2 |
133.1 |
29.7 |
| C5 |
C4 |
C9 |
C3 |
193.7 |
179.5 |
| C3 |
C9 |
C4 |
H4 |
13.8 |
359.3 |
| C4 |
C9 |
C3 |
C8 |
167.8 |
180.9 |
| C7 |
C8 |
C9 |
C3 |
170.3 |
180.2 |
| C3' |
C3 |
C2 |
H2 |
356.3 |
359.9 |
| C2 |
C3 |
C3' |
C9 |
183.9 |
180.4 |
| C3' |
C3 |
C9 |
C4 |
351.3 |
0.8 |
| C3' |
C3 |
C9 |
C8 |
183.5 |
179.9 |
| C1' |
C2' |
C3' |
C3 |
39.2 |
180.0 |
| C3 |
C3' |
C2' |
H2'1 |
274.0 |
60.0 |
| C3 |
C3' |
C2' |
H2'2 |
164.5 |
300.0 |
| C2' |
C3' |
C3 |
H3'1 |
234.8 |
120.0 |
| C2' |
C3' |
C3 |
H3'2 |
125.3 |
239.9 |
| H3'1 |
C3' |
C3 |
H3'2 |
250.5 |
119.9 |
| C3 |
C9 |
C4 |
C5 |
193.7 |
179.5 |
| C9 |
C4 |
C5 |
H4 |
180.0 |
179.8 |
| C5 |
C4 |
C9 |
C8 |
0.5 |
0.5 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
180.1 |
| C4 |
C5 |
C6 |
C7 |
0.8 |
359.9 |
| C4 |
C5 |
C6 |
H6 |
180.9 |
180.0 |
| N1 |
C8 |
C9 |
C4 |
189.8 |
179.7 |
| C4 |
C9 |
C3 |
C3' |
351.3 |
0.8 |
| C3 |
C9 |
C4 |
C8 |
193.3 |
179.0 |
| C5 |
C4 |
C9 |
H4 |
180.0 |
180.2 |
| C9 |
C4 |
C5 |
C6 |
359.1 |
359.8 |
| C9 |
C4 |
C5 |
H5 |
179.2 |
179.7 |
| C7 |
C8 |
C9 |
C4 |
360.0 |
359.4 |
| C5 |
C4 |
H4 |
C9 |
180.0 |
179.8 |
| H4 |
C4 |
C5 |
C6 |
179.1 |
180.0 |
| H4 |
C4 |
C5 |
H5 |
359.1 |
359.9 |
| H4 |
C4 |
C9 |
C8 |
180.5 |
180.3 |
| C6 |
C5 |
C4 |
C9 |
359.1 |
359.8 |
| C6 |
C5 |
C4 |
H4 |
179.1 |
180.0 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
179.9 |
| C7 |
C6 |
C5 |
H6 |
180.0 |
179.9 |
| C5 |
C6 |
C7 |
C8 |
359.6 |
0.0 |
| C5 |
C6 |
C7 |
H7 |
179.7 |
180.1 |
| H5 |
C5 |
C4 |
C9 |
179.2 |
179.7 |
| H5 |
C5 |
C4 |
H4 |
359.1 |
359.9 |
| C4 |
C5 |
H5 |
C6 |
180.0 |
180.1 |
| H5 |
C5 |
C6 |
C7 |
180.8 |
180.0 |
| H5 |
C5 |
C6 |
H6 |
0.8 |
0.1 |
| N1 |
C8 |
C7 |
C6 |
168.1 |
180.0 |
| C7 |
C6 |
C5 |
H5 |
180.8 |
180.0 |
| C5 |
C6 |
C7 |
H6 |
180.0 |
180.1 |
| C8 |
C7 |
C6 |
H7 |
180.0 |
179.9 |
| C6 |
C7 |
C8 |
C9 |
359.9 |
0.3 |
| H6 |
C6 |
C5 |
H5 |
0.8 |
0.1 |
| C5 |
C6 |
H6 |
C7 |
180.0 |
179.9 |
| H6 |
C6 |
C7 |
C8 |
179.6 |
180.0 |
| H6 |
C6 |
C7 |
H7 |
359.7 |
0.1 |
| C7 |
C8 |
N1 |
HN1 |
10.0 |
0.1 |
| N1 |
C8 |
C7 |
C9 |
168.2 |
179.7 |
| C3 |
C9 |
C8 |
C7 |
170.3 |
180.2 |
| C4 |
C9 |
C8 |
C7 |
360.0 |
359.4 |
| C8 |
C7 |
C6 |
H6 |
179.6 |
180.0 |
| C6 |
C7 |
C8 |
H7 |
180.0 |
180.1 |
| H7 |
C7 |
C6 |
H6 |
359.7 |
0.1 |
| C6 |
C7 |
H7 |
C8 |
180.0 |
179.9 |
| H7 |
C7 |
C8 |
C9 |
179.9 |
180.2 |
| C9 |
C8 |
N1 |
HN1 |
179.7 |
179.8 |
| N1 |
C8 |
C9 |
C7 |
189.8 |
180.2 |
| C8 |
C9 |
C3 |
C3' |
183.5 |
179.9 |
| C3 |
C9 |
C8 |
C4 |
170.3 |
180.7 |
| C8 |
C9 |
C4 |
H4 |
180.5 |
180.3 |
| C9 |
C8 |
C7 |
H7 |
179.9 |
180.2 |
| C3 |
C3' |
C2' |
C1' |
39.2 |
180.0 |
| O4P |
C1' |
C2' |
H1'1 |
234.7 |
119.9 |
| O4P |
C1' |
C2' |
H1'2 |
125.3 |
240.0 |
| C2' |
C1' |
O4P |
P |
182.8 |
180.0 |
| H1'1 |
C1' |
C2' |
H1'2 |
250.6 |
120.0 |
| C3' |
C2' |
C1' |
H2'1 |
234.7 |
240.0 |
| C3' |
C2' |
C1' |
H2'2 |
125.3 |
120.0 |
| C1' |
C2' |
C3' |
H3'1 |
274.0 |
300.0 |
| C1' |
C2' |
C3' |
H3'2 |
164.5 |
60.0 |
| H2'1 |
C2' |
C1' |
H2'2 |
250.6 |
240.1 |
| C2' |
C1' |
O4P |
H1'1 |
125.3 |
240.0 |
| C2' |
C1' |
O4P |
H1'2 |
234.7 |
120.0 |
| O4P |
C1' |
C2' |
C3' |
233.2 |
180.0 |
| O4P |
C1' |
C2' |
H2'1 |
358.5 |
300.0 |
| O4P |
C1' |
C2' |
H2'2 |
107.9 |
59.9 |
| H1'1 |
C1' |
O4P |
H1'2 |
109.5 |
240.0 |
| O1P |
P |
O4P |
C1' |
7.7 |
300.0 |
| O2P |
P |
O4P |
C1' |
123.6 |
180.0 |
| O3P |
P |
O4P |
C1' |
242.5 |
60.0 |
| C2' |
C1' |
H1'1 |
O4P |
228.4 |
120.0 |
| C2' |
C1' |
H1'1 |
H1'2 |
114.2 |
240.0 |
| H1'1 |
C1' |
C2' |
C3' |
358.5 |
60.0 |
| H1'1 |
C1' |
C2' |
H2'1 |
123.8 |
180.1 |
| H1'1 |
C1' |
C2' |
H2'2 |
233.2 |
300.0 |
| O4P |
C1' |
H1'1 |
H1'2 |
245.8 |
120.0 |
| H1'1 |
C1' |
O4P |
P |
57.5 |
300.0 |
| C2' |
C1' |
H1'2 |
O4P |
131.6 |
240.0 |
| C2' |
C1' |
H1'2 |
H1'1 |
245.8 |
120.0 |
| H1'2 |
C1' |
C2' |
C3' |
107.9 |
300.0 |
| H1'2 |
C1' |
C2' |
H2'1 |
233.2 |
60.0 |
| H1'2 |
C1' |
C2' |
H2'2 |
342.6 |
180.0 |
| O4P |
C1' |
H1'2 |
H1'1 |
114.2 |
240.1 |
| H1'2 |
C1' |
O4P |
P |
308.1 |
60.0 |
| C3 |
C3' |
C2' |
H3'1 |
125.3 |
240.0 |
| C3 |
C3' |
C2' |
H3'2 |
234.7 |
120.0 |
| C3' |
C2' |
C1' |
O4P |
233.2 |
180.0 |
| C3' |
C2' |
C1' |
H1'1 |
358.5 |
60.0 |
| C3' |
C2' |
C1' |
H1'2 |
107.9 |
300.0 |
| C1' |
C2' |
C3' |
H2'1 |
125.3 |
120.0 |
| C1' |
C2' |
C3' |
H2'2 |
234.7 |
240.0 |
| H2'1 |
C2' |
C3' |
H2'2 |
109.5 |
120.0 |
| H3'1 |
C3' |
C2' |
H3'2 |
109.4 |
240.1 |
| H2'1 |
C2' |
C1' |
O4P |
358.5 |
300.0 |
| H2'1 |
C2' |
C1' |
H1'1 |
123.8 |
180.1 |
| H2'1 |
C2' |
C1' |
H1'2 |
233.2 |
60.0 |
| C1' |
C2' |
H2'1 |
C3' |
214.0 |
240.0 |
| C1' |
C2' |
H2'1 |
H2'2 |
107.0 |
119.9 |
| C3' |
C2' |
H2'1 |
H2'2 |
253.0 |
239.9 |
| H2'1 |
C2' |
C3' |
H3'1 |
148.7 |
180.0 |
| H2'1 |
C2' |
C3' |
H3'2 |
39.2 |
300.0 |
| H2'2 |
C2' |
C1' |
O4P |
107.9 |
59.9 |
| H2'2 |
C2' |
C1' |
H1'1 |
233.2 |
300.0 |
| H2'2 |
C2' |
C1' |
H1'2 |
342.6 |
180.0 |
| C1' |
C2' |
H2'2 |
C3' |
146.0 |
120.0 |
| C1' |
C2' |
H2'2 |
H2'1 |
253.1 |
240.1 |
| C3' |
C2' |
H2'2 |
H2'1 |
107.0 |
120.1 |
| H2'2 |
C2' |
C3' |
H3'1 |
39.2 |
60.0 |
| H2'2 |
C2' |
C3' |
H3'2 |
289.8 |
179.9 |
| C3 |
C3' |
H3'1 |
C2' |
234.5 |
120.0 |
| C3 |
C3' |
H3'1 |
H3'2 |
117.3 |
240.0 |
| H3'1 |
C3' |
C2' |
H2'1 |
148.7 |
180.0 |
| H3'1 |
C3' |
C2' |
H2'2 |
39.2 |
60.0 |
| C2' |
C3' |
H3'1 |
H3'2 |
242.8 |
120.0 |
| C3 |
C3' |
H3'2 |
C2' |
125.5 |
240.0 |
| C3 |
C3' |
H3'2 |
H3'1 |
242.7 |
120.0 |
| H3'2 |
C3' |
C2' |
H2'1 |
39.2 |
300.0 |
| H3'2 |
C3' |
C2' |
H2'2 |
289.8 |
179.9 |
| C2' |
C3' |
H3'2 |
H3'1 |
117.2 |
240.0 |
| C1' |
O4P |
P |
O1P |
7.7 |
300.0 |
| O2P |
P |
O1P |
O3P |
126.8 |
240.0 |
| O2P |
P |
O1P |
O4P |
243.9 |
120.0 |
| O1P |
P |
O2P |
HOP2 |
180.0 |
60.1 |
| O3P |
P |
O1P |
O4P |
117.1 |
239.9 |
| O1P |
P |
O3P |
HOP3 |
180.0 |
180.0 |
| C1' |
O4P |
P |
O2P |
123.6 |
180.0 |
| O1P |
P |
O2P |
O3P |
231.2 |
120.0 |
| O1P |
P |
O2P |
O4P |
119.5 |
240.0 |
| O3P |
P |
O2P |
O4P |
248.3 |
120.0 |
| O2P |
P |
O3P |
HOP3 |
56.5 |
300.0 |
| C1' |
O4P |
P |
O3P |
242.5 |
60.0 |
| O1P |
P |
O3P |
O2P |
123.5 |
240.0 |
| O1P |
P |
O3P |
O4P |
237.8 |
120.0 |
| O2P |
P |
O3P |
O4P |
114.4 |
240.0 |
| O3P |
P |
O2P |
HOP2 |
308.8 |
300.0 |
| P |
O4P |
C1' |
H1'1 |
57.5 |
300.0 |
| P |
O4P |
C1' |
H1'2 |
308.1 |
60.0 |
| O1P |
P |
O4P |
O2P |
244.1 |
119.9 |
| O1P |
P |
O4P |
O3P |
125.2 |
239.9 |
| O2P |
P |
O4P |
O3P |
241.1 |
120.0 |
| O4P |
P |
O2P |
HOP2 |
60.5 |
180.0 |
| O4P |
P |
O3P |
HOP3 |
302.2 |
60.0 |
| HOP2 |
O2P |
P |
O3P |
308.8 |
300.0 |
| HOP2 |
O2P |
P |
O4P |
60.5 |
180.0 |
| HOP3 |
O3P |
P |
O4P |
302.2 |
60.0 |