PDB Chemical Component PPD
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 PPD
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N1 |
C2 |
1.334 |
1.317 |
| N1 |
C6 |
1.351 |
1.318 |
| C2 |
C2A |
1.512 |
1.507 |
| C2 |
C3 |
1.402 |
1.387 |
| C2A |
H2A1 |
1.115 |
1.089 |
| C2A |
H2A2 |
1.115 |
1.090 |
| C2A |
H2A3 |
1.116 |
1.090 |
| C3 |
O3 |
1.345 |
1.359 |
| C3 |
C4 |
1.395 |
1.392 |
| O3 |
HO3 |
0.950 |
0.967 |
| C4 |
C4A |
1.428 |
1.507 |
| C4 |
C5 |
1.406 |
1.384 |
| C4A |
N |
1.477 |
1.467 |
| C4A |
H4A1 |
1.116 |
1.091 |
| C4A |
H4A2 |
1.114 |
1.089 |
| C5 |
C6 |
1.358 |
1.382 |
| C5 |
C5A |
1.553 |
1.507 |
| C6 |
H6 |
1.103 |
1.080 |
| C5A |
O4P |
1.414 |
1.429 |
| C5A |
H5A1 |
1.115 |
1.089 |
| C5A |
H5A2 |
1.114 |
1.090 |
| O4P |
P |
1.585 |
1.609 |
| P |
O1P |
1.471 |
1.480 |
| P |
O2P |
1.544 |
1.609 |
| P |
O3P |
1.467 |
1.609 |
| O2P |
HOP2 |
0.950 |
0.967 |
| O3P |
HOP3 |
0.950 |
0.968 |
| N |
CA |
1.473 |
1.469 |
| N |
HN |
1.020 |
1.009 |
| CA |
CB |
1.503 |
1.529 |
| CA |
C |
1.478 |
1.507 |
| CA |
HA |
1.116 |
1.090 |
| CB |
CG |
1.510 |
1.507 |
| CB |
HB1 |
1.115 |
1.090 |
| CB |
HB2 |
1.115 |
1.090 |
| CG |
OD1 |
1.257 |
1.207 |
| CG |
OD2 |
1.269 |
1.343 |
| OD2 |
HOD |
0.950 |
0.966 |
| C |
O |
1.252 |
1.208 |
| C |
OXT |
1.270 |
1.342 |
| OXT |
HXT |
0.950 |
0.968 |
Bond Angles for PPD
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
125.6 |
121.8 |
| N1 |
C2 |
C2A |
118.2 |
119.7 |
| N1 |
C2 |
C3 |
116.6 |
120.7 |
| N1 |
C6 |
C5 |
118.0 |
120.9 |
| N1 |
C6 |
H6 |
120.7 |
119.6 |
| C2A |
C2 |
C3 |
125.2 |
119.6 |
| C2 |
C2A |
H2A1 |
118.3 |
109.5 |
| C2 |
C2A |
H2A2 |
109.1 |
109.5 |
| C2 |
C2A |
H2A3 |
109.1 |
109.5 |
| C2 |
C3 |
O3 |
115.6 |
120.5 |
| C2 |
C3 |
C4 |
121.2 |
119.1 |
| H2A1 |
C2A |
H2A2 |
109.1 |
109.5 |
| H2A1 |
C2A |
H2A3 |
109.0 |
109.5 |
| H2A2 |
C2A |
H2A3 |
101.0 |
109.4 |
| O3 |
C3 |
C4 |
123.2 |
120.4 |
| C3 |
O3 |
HO3 |
115.7 |
106.8 |
| C3 |
C4 |
C4A |
122.6 |
120.9 |
| C3 |
C4 |
C5 |
117.4 |
118.3 |
| C4A |
C4 |
C5 |
120.0 |
120.8 |
| C4 |
C4A |
N |
108.3 |
109.5 |
| C4 |
C4A |
H4A1 |
112.6 |
109.5 |
| C4 |
C4A |
H4A2 |
112.7 |
109.4 |
| C4 |
C5 |
C6 |
121.2 |
119.3 |
| C4 |
C5 |
C5A |
118.2 |
120.4 |
| N |
C4A |
H4A1 |
112.7 |
109.5 |
| N |
C4A |
H4A2 |
112.6 |
109.6 |
| C4A |
N |
CA |
121.6 |
106.7 |
| C4A |
N |
HN |
107.8 |
106.7 |
| H4A1 |
C4A |
H4A2 |
97.8 |
109.4 |
| C6 |
C5 |
C5A |
120.3 |
120.3 |
| C5 |
C6 |
H6 |
121.2 |
119.6 |
| C5 |
C5A |
O4P |
111.1 |
109.5 |
| C5 |
C5A |
H5A1 |
111.6 |
109.5 |
| C5 |
C5A |
H5A2 |
111.6 |
109.5 |
| O4P |
C5A |
H5A1 |
111.6 |
109.5 |
| O4P |
C5A |
H5A2 |
111.6 |
109.4 |
| C5A |
O4P |
P |
124.5 |
106.9 |
| H5A1 |
C5A |
H5A2 |
98.9 |
109.4 |
| O4P |
P |
O1P |
104.6 |
109.4 |
| O4P |
P |
O2P |
104.1 |
109.5 |
| O4P |
P |
O3P |
110.8 |
109.5 |
| O1P |
P |
O2P |
114.6 |
109.5 |
| O1P |
P |
O3P |
114.0 |
109.4 |
| O2P |
P |
O3P |
108.3 |
109.5 |
| P |
O2P |
HOP2 |
104.1 |
106.8 |
| P |
O3P |
HOP3 |
110.8 |
106.7 |
| CA |
N |
HN |
107.9 |
106.7 |
| N |
CA |
CB |
112.6 |
109.5 |
| N |
CA |
C |
109.7 |
109.5 |
| N |
CA |
HA |
107.8 |
109.5 |
| CB |
CA |
C |
111.4 |
109.4 |
| CB |
CA |
HA |
106.0 |
109.5 |
| CA |
CB |
CG |
115.1 |
109.5 |
| CA |
CB |
HB1 |
110.2 |
109.5 |
| CA |
CB |
HB2 |
110.1 |
109.5 |
| C |
CA |
HA |
109.1 |
109.5 |
| CA |
C |
O |
118.6 |
120.0 |
| CA |
C |
OXT |
117.5 |
120.0 |
| CG |
CB |
HB1 |
110.2 |
109.4 |
| CG |
CB |
HB2 |
110.2 |
109.5 |
| CB |
CG |
OD1 |
117.6 |
120.0 |
| CB |
CG |
OD2 |
121.4 |
120.0 |
| HB1 |
CB |
HB2 |
100.0 |
109.5 |
| OD1 |
CG |
OD2 |
121.0 |
120.0 |
| CG |
OD2 |
HOD |
121.4 |
120.0 |
| O |
C |
OXT |
123.8 |
120.0 |
| C |
OXT |
HXT |
117.5 |
120.0 |
Torsion Angles for PPD
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
C5 |
359.9 |
360.0 |
| C2 |
N1 |
C6 |
H6 |
179.9 |
179.9 |
| C2A |
C2 |
N1 |
C3 |
181.0 |
179.6 |
| N1 |
C2 |
C2A |
H2A1 |
179.9 |
90.0 |
| N1 |
C2 |
C2A |
H2A2 |
305.3 |
210.0 |
| N1 |
C2 |
C2A |
H2A3 |
54.7 |
330.0 |
| N1 |
C2 |
C3 |
O3 |
179.0 |
180.0 |
| N1 |
C2 |
C3 |
C4 |
1.4 |
359.4 |
| C6 |
N1 |
C2 |
C2A |
180.9 |
180.0 |
| C6 |
N1 |
C2 |
C3 |
359.9 |
0.3 |
| C4 |
C5 |
C6 |
N1 |
358.8 |
360.0 |
| N1 |
C6 |
C5 |
C5A |
184.5 |
180.0 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
180.1 |
| C2A |
C2 |
N1 |
C6 |
180.9 |
180.0 |
| N1 |
C2 |
C2A |
C3 |
179.0 |
180.4 |
| C2A |
C2 |
C3 |
O3 |
358.0 |
0.3 |
| C2A |
C2 |
C3 |
C4 |
180.4 |
179.7 |
| H2A1 |
C2A |
C2 |
H2A2 |
234.6 |
240.0 |
| H2A1 |
C2A |
C2 |
H2A3 |
125.2 |
120.0 |
| H2A2 |
C2A |
C2 |
H2A3 |
250.6 |
240.0 |
| C3 |
C2 |
N1 |
C6 |
359.9 |
0.3 |
| N1 |
C2 |
C3 |
C2A |
181.0 |
179.6 |
| C3 |
C2 |
C2A |
H2A1 |
1.0 |
269.7 |
| C3 |
C2 |
C2A |
H2A2 |
126.4 |
29.7 |
| C3 |
C2 |
C2A |
H2A3 |
235.8 |
149.6 |
| O3 |
C3 |
C2 |
C4 |
177.6 |
180.6 |
| C2 |
C3 |
O3 |
HO3 |
179.9 |
269.4 |
| C2 |
C3 |
C4 |
C4A |
179.6 |
180.3 |
| C2 |
C3 |
C4 |
C5 |
357.4 |
0.6 |
| H2A1 |
C2A |
C2 |
C3 |
1.0 |
269.7 |
| C2 |
C2A |
H2A1 |
H2A2 |
125.4 |
120.0 |
| C2 |
C2A |
H2A1 |
H2A3 |
234.7 |
240.0 |
| H2A2 |
C2A |
H2A1 |
H2A3 |
109.4 |
120.0 |
| H2A2 |
C2A |
C2 |
C3 |
126.4 |
29.7 |
| C2 |
C2A |
H2A2 |
H2A1 |
229.5 |
240.0 |
| C2 |
C2A |
H2A2 |
H2A3 |
114.8 |
120.0 |
| H2A1 |
C2A |
H2A2 |
H2A3 |
245.3 |
240.0 |
| H2A3 |
C2A |
C2 |
C3 |
235.8 |
149.6 |
| C2 |
C2A |
H2A3 |
H2A1 |
130.4 |
120.0 |
| C2 |
C2A |
H2A3 |
H2A2 |
245.2 |
240.0 |
| H2A1 |
C2A |
H2A3 |
H2A2 |
114.8 |
120.0 |
| C2 |
C3 |
O3 |
C4 |
182.5 |
179.4 |
| O3 |
C3 |
C4 |
C4A |
2.2 |
359.7 |
| O3 |
C3 |
C4 |
C5 |
180.0 |
180.0 |
| C2 |
C3 |
C4 |
O3 |
177.4 |
180.6 |
| C4 |
C3 |
O3 |
HO3 |
357.4 |
90.0 |
| C4A |
C4 |
C3 |
C5 |
182.2 |
179.7 |
| C3 |
C4 |
C4A |
N |
326.2 |
270.3 |
| C3 |
C4 |
C4A |
H4A1 |
91.4 |
30.3 |
| C3 |
C4 |
C4A |
H4A2 |
200.9 |
150.2 |
| C3 |
C4 |
C5 |
C6 |
2.5 |
359.7 |
| C3 |
C4 |
C5 |
C5A |
176.9 |
179.7 |
| HO3 |
O3 |
C3 |
C4 |
357.4 |
90.0 |
| C3 |
C4 |
C4A |
C5 |
177.8 |
180.3 |
| C4A |
C4 |
C5 |
C6 |
180.4 |
180.0 |
| C4A |
C4 |
C5 |
C5A |
354.8 |
0.0 |
| N |
C4A |
C4 |
H4A1 |
234.7 |
240.0 |
| N |
C4A |
C4 |
H4A2 |
125.3 |
120.1 |
| C4 |
C4A |
N |
CA |
166.5 |
180.0 |
| C4 |
C4A |
N |
HN |
41.2 |
293.8 |
| H4A1 |
C4A |
C4 |
H4A2 |
250.6 |
240.1 |
| N1 |
C6 |
C5 |
C4 |
358.8 |
360.0 |
| C3 |
C4 |
C5 |
C4A |
182.1 |
179.7 |
| C5 |
C4 |
C4A |
N |
148.4 |
90.0 |
| C5 |
C4 |
C4A |
H4A1 |
273.7 |
210.0 |
| C5 |
C4 |
C4A |
H4A2 |
23.1 |
329.9 |
| C6 |
C5 |
C4 |
C5A |
185.6 |
180.0 |
| C4 |
C5 |
C6 |
H6 |
178.8 |
180.1 |
| C4 |
C5 |
C5A |
O4P |
77.9 |
179.9 |
| C4 |
C5 |
C5A |
H5A1 |
203.1 |
300.1 |
| C4 |
C5 |
C5A |
H5A2 |
312.7 |
60.0 |
| N |
C4A |
C4 |
C5 |
148.4 |
90.0 |
| C4 |
C4A |
N |
H4A1 |
125.2 |
120.0 |
| C4 |
C4A |
N |
H4A2 |
234.7 |
240.0 |
| H4A1 |
C4A |
N |
H4A2 |
109.5 |
120.0 |
| CA |
N |
C4A |
HN |
125.2 |
246.2 |
| C4A |
N |
CA |
CB |
56.7 |
150.0 |
| C4A |
N |
CA |
C |
181.4 |
270.0 |
| C4A |
N |
CA |
HA |
300.1 |
30.0 |
| H4A1 |
C4A |
C4 |
C5 |
273.7 |
210.0 |
| C4 |
C4A |
H4A1 |
N |
237.1 |
240.0 |
| C4 |
C4A |
H4A1 |
H4A2 |
118.6 |
119.9 |
| N |
C4A |
H4A1 |
H4A2 |
241.4 |
239.9 |
| H4A1 |
C4A |
N |
CA |
41.2 |
60.0 |
| H4A1 |
C4A |
N |
HN |
276.0 |
173.8 |
| H4A2 |
C4A |
C4 |
C5 |
23.1 |
329.9 |
| C4 |
C4A |
H4A2 |
N |
122.9 |
120.1 |
| C4 |
C4A |
H4A2 |
H4A1 |
241.5 |
240.1 |
| N |
C4A |
H4A2 |
H4A1 |
118.6 |
120.0 |
| H4A2 |
C4A |
N |
CA |
291.8 |
300.0 |
| H4A2 |
C4A |
N |
HN |
166.5 |
53.8 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
179.9 |
| C4 |
C5 |
C6 |
C5A |
174.3 |
180.0 |
| C6 |
C5 |
C5A |
O4P |
252.4 |
360.0 |
| C6 |
C5 |
C5A |
H5A1 |
17.6 |
120.1 |
| C6 |
C5 |
C5A |
H5A2 |
127.2 |
240.0 |
| C4 |
C5 |
C5A |
C6 |
185.5 |
180.0 |
| C5A |
C5 |
C6 |
H6 |
4.5 |
0.0 |
| O4P |
C5A |
C5 |
H5A1 |
234.8 |
239.9 |
| O4P |
C5A |
C5 |
H5A2 |
125.2 |
119.9 |
| C5 |
C5A |
O4P |
P |
178.7 |
180.0 |
| H5A1 |
C5A |
C5 |
H5A2 |
250.4 |
240.1 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
180.1 |
| H6 |
C6 |
C5 |
C5A |
4.5 |
0.0 |
| C5 |
C5A |
O4P |
H5A1 |
125.2 |
120.1 |
| C5 |
C5A |
O4P |
H5A2 |
234.8 |
240.0 |
| H5A1 |
C5A |
O4P |
H5A2 |
109.6 |
119.9 |
| C5A |
O4P |
P |
O1P |
214.7 |
60.0 |
| C5A |
O4P |
P |
O2P |
94.0 |
180.0 |
| C5A |
O4P |
P |
O3P |
337.9 |
300.1 |
| C5 |
C5A |
H5A1 |
O4P |
235.1 |
239.9 |
| C5 |
C5A |
H5A1 |
H5A2 |
117.6 |
120.0 |
| O4P |
C5A |
H5A1 |
H5A2 |
242.5 |
240.1 |
| H5A1 |
C5A |
O4P |
P |
53.5 |
59.9 |
| C5 |
C5A |
H5A2 |
O4P |
124.9 |
120.0 |
| C5 |
C5A |
H5A2 |
H5A1 |
242.4 |
240.0 |
| O4P |
C5A |
H5A2 |
H5A1 |
117.5 |
120.0 |
| H5A2 |
C5A |
O4P |
P |
303.9 |
299.9 |
| P |
O4P |
C5A |
H5A1 |
53.5 |
59.9 |
| P |
O4P |
C5A |
H5A2 |
303.9 |
299.9 |
| O1P |
P |
O4P |
O2P |
120.6 |
240.0 |
| O1P |
P |
O4P |
O3P |
236.8 |
119.9 |
| O2P |
P |
O4P |
O3P |
116.2 |
239.9 |
| O4P |
P |
O2P |
HOP2 |
180.0 |
180.0 |
| O4P |
P |
O3P |
HOP3 |
180.0 |
299.9 |
| O4P |
P |
O1P |
O2P |
246.7 |
120.0 |
| O4P |
P |
O1P |
O3P |
121.1 |
240.0 |
| O2P |
P |
O1P |
O3P |
234.5 |
120.0 |
| O1P |
P |
O2P |
HOP2 |
66.3 |
299.9 |
| O1P |
P |
O3P |
HOP3 |
297.7 |
180.0 |
| O4P |
P |
O2P |
O1P |
113.6 |
240.0 |
| O4P |
P |
O2P |
O3P |
242.1 |
120.1 |
| O1P |
P |
O2P |
O3P |
128.4 |
240.0 |
| O2P |
P |
O3P |
HOP3 |
66.5 |
60.0 |
| O4P |
P |
O3P |
O1P |
242.4 |
119.9 |
| O4P |
P |
O3P |
O2P |
113.5 |
239.9 |
| O1P |
P |
O3P |
O2P |
231.2 |
120.0 |
| O3P |
P |
O2P |
HOP2 |
297.9 |
59.9 |
| HOP2 |
O2P |
P |
O3P |
297.9 |
59.9 |
| CA |
N |
C4A |
H4A1 |
41.2 |
60.0 |
| CA |
N |
C4A |
H4A2 |
291.8 |
300.0 |
| C4A |
N |
CA |
HN |
234.8 |
113.8 |
| CB |
CA |
N |
C |
235.3 |
240.0 |
| CB |
CA |
N |
HA |
116.5 |
120.0 |
| N |
CA |
CB |
CG |
56.3 |
300.0 |
| N |
CA |
CB |
HB1 |
181.6 |
60.0 |
| N |
CA |
CB |
HB2 |
291.0 |
180.0 |
| C |
CA |
N |
HA |
241.3 |
240.0 |
| N |
CA |
C |
O |
7.6 |
150.0 |
| N |
CA |
C |
OXT |
185.0 |
330.0 |
| HN |
N |
C4A |
H4A1 |
276.0 |
173.8 |
| HN |
N |
C4A |
H4A2 |
166.5 |
53.8 |
| C4A |
N |
HN |
CA |
133.0 |
246.2 |
| HN |
N |
CA |
CB |
181.9 |
36.2 |
| HN |
N |
CA |
C |
306.6 |
156.2 |
| HN |
N |
CA |
HA |
65.3 |
276.2 |
| CB |
CA |
N |
HN |
181.9 |
36.2 |
| N |
CA |
CB |
C |
123.8 |
120.0 |
| N |
CA |
CB |
HA |
242.3 |
240.0 |
| C |
CA |
CB |
HA |
118.6 |
120.0 |
| CB |
CA |
C |
O |
133.0 |
270.0 |
| CB |
CA |
C |
OXT |
310.4 |
90.1 |
| CG |
CB |
CA |
HB1 |
234.7 |
240.1 |
| CG |
CB |
CA |
HB2 |
125.3 |
120.0 |
| CA |
CB |
CG |
OD1 |
201.0 |
360.0 |
| CA |
CB |
CG |
OD2 |
23.9 |
180.0 |
| HB1 |
CB |
CA |
HB2 |
250.6 |
239.9 |
| C |
CA |
N |
HN |
306.6 |
156.2 |
| N |
CA |
C |
CB |
234.6 |
240.0 |
| N |
CA |
C |
HA |
117.9 |
120.0 |
| CB |
CA |
C |
HA |
243.3 |
240.0 |
| C |
CA |
CB |
CG |
292.6 |
180.0 |
| C |
CA |
CB |
HB1 |
57.9 |
300.0 |
| C |
CA |
CB |
HB2 |
167.3 |
60.0 |
| O |
C |
CA |
OXT |
182.7 |
179.9 |
| CA |
C |
OXT |
HXT |
180.1 |
180.0 |
| HA |
CA |
N |
HN |
65.3 |
276.2 |
| N |
CA |
HA |
CB |
120.8 |
120.1 |
| N |
CA |
HA |
C |
240.9 |
240.0 |
| CB |
CA |
HA |
C |
120.1 |
119.9 |
| HA |
CA |
CB |
CG |
174.0 |
60.1 |
| HA |
CA |
CB |
HB1 |
299.3 |
180.0 |
| HA |
CA |
CB |
HB2 |
48.7 |
300.1 |
| HA |
CA |
C |
O |
249.7 |
30.0 |
| HA |
CA |
C |
OXT |
67.0 |
210.0 |
| CG |
CB |
CA |
C |
292.6 |
180.0 |
| CG |
CB |
CA |
HA |
174.0 |
60.1 |
| CA |
CB |
CG |
HB1 |
125.3 |
120.0 |
| CA |
CB |
CG |
HB2 |
234.8 |
239.9 |
| HB1 |
CB |
CG |
HB2 |
109.5 |
120.0 |
| OD1 |
CG |
CB |
OD2 |
177.1 |
179.9 |
| CB |
CG |
OD2 |
HOD |
180.0 |
180.0 |
| HB1 |
CB |
CA |
C |
57.9 |
300.0 |
| HB1 |
CB |
CA |
HA |
299.3 |
180.0 |
| CA |
CB |
HB1 |
CG |
232.0 |
240.1 |
| CA |
CB |
HB1 |
HB2 |
115.9 |
120.1 |
| CG |
CB |
HB1 |
HB2 |
244.0 |
240.0 |
| HB1 |
CB |
CG |
OD1 |
75.7 |
240.0 |
| HB1 |
CB |
CG |
OD2 |
258.6 |
60.1 |
| HB2 |
CB |
CA |
C |
167.3 |
60.0 |
| HB2 |
CB |
CA |
HA |
48.7 |
300.1 |
| CA |
CB |
HB2 |
CG |
128.0 |
120.0 |
| CA |
CB |
HB2 |
HB1 |
244.1 |
239.9 |
| CG |
CB |
HB2 |
HB1 |
116.1 |
119.9 |
| HB2 |
CB |
CG |
OD1 |
326.2 |
120.0 |
| HB2 |
CB |
CG |
OD2 |
149.2 |
300.1 |
| OD1 |
CG |
CB |
HB1 |
75.7 |
240.0 |
| OD1 |
CG |
CB |
HB2 |
326.2 |
120.0 |
| CB |
CG |
OD1 |
OD2 |
182.9 |
180.1 |
| OD1 |
CG |
OD2 |
HOD |
3.1 |
0.1 |
| OD2 |
CG |
CB |
HB1 |
258.6 |
60.1 |
| OD2 |
CG |
CB |
HB2 |
149.2 |
300.1 |
| CB |
CG |
OD2 |
OD1 |
177.0 |
179.9 |
| O |
C |
CA |
HA |
249.7 |
30.0 |
| CA |
C |
O |
OXT |
177.1 |
180.1 |
| O |
C |
OXT |
HXT |
357.2 |
0.0 |
| OXT |
C |
CA |
HA |
67.0 |
210.0 |
| CA |
C |
OXT |
O |
182.8 |
179.9 |