PDB Chemical Component T4S
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 T4S
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
OP3 |
P |
1.614 |
|
OP3 |
HOP3 |
0.950 |
|
P |
OP1 |
1.502 |
|
P |
OP2 |
1.448 |
|
P |
O5' |
1.598 |
|
OP2 |
HOP2 |
0.950 |
|
O5' |
C5' |
1.418 |
|
N1 |
C1' |
1.501 |
|
N1 |
C6 |
1.372 |
|
N1 |
C2 |
1.387 |
|
C6 |
C5 |
1.374 |
|
C6 |
H6 |
1.080 |
|
C2 |
O2 |
1.222 |
|
C2 |
N3 |
1.389 |
|
N3 |
C4 |
1.391 |
|
C4 |
C5 |
1.470 |
|
C4 |
SE |
1.723 |
|
SE |
HSE |
1.500 |
|
C5 |
C5A |
1.495 |
|
C5A |
H5A1 |
1.100 |
|
C5A |
H5A2 |
1.099 |
|
C5A |
H5A3 |
1.100 |
|
C2' |
C3' |
1.520 |
|
C2' |
C1' |
1.509 |
|
C2' |
H2' |
1.100 |
|
C2' |
H2'' |
1.100 |
|
C5' |
C4' |
1.511 |
|
C5' |
H5' |
1.100 |
|
C5' |
H5'' |
1.100 |
|
C4' |
C3' |
1.520 |
|
C4' |
O4' |
1.451 |
|
C4' |
H4' |
1.100 |
|
O4' |
C1' |
1.436 |
|
C1' |
H1' |
1.100 |
|
C3' |
O3' |
1.405 |
|
C3' |
H3' |
1.100 |
|
O3' |
HO3' |
0.951 |
|
Bond Angles for T4S
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
P |
OP3 |
HOP3 |
109.5 |
|
OP3 |
P |
OP1 |
105.3 |
|
OP3 |
P |
OP2 |
112.1 |
|
OP3 |
P |
O5' |
103.3 |
|
OP1 |
P |
OP2 |
119.4 |
|
OP1 |
P |
O5' |
109.2 |
|
OP2 |
P |
O5' |
106.4 |
|
P |
OP2 |
HOP2 |
109.5 |
|
P |
O5' |
C5' |
120.2 |
|
O5' |
C5' |
C4' |
111.1 |
|
O5' |
C5' |
H5' |
108.9 |
|
O5' |
C5' |
H5'' |
108.6 |
|
C6 |
N1 |
C1' |
121.5 |
|
C2 |
N1 |
C1' |
116.9 |
|
N1 |
C1' |
C2' |
107.3 |
|
N1 |
C1' |
O4' |
100.6 |
|
N1 |
C1' |
H1' |
115.7 |
|
C6 |
N1 |
C2 |
121.6 |
|
N1 |
C6 |
C5 |
123.5 |
|
N1 |
C6 |
H6 |
118.3 |
|
N1 |
C2 |
O2 |
122.7 |
|
N1 |
C2 |
N3 |
115.2 |
|
C5 |
C6 |
H6 |
118.3 |
|
C6 |
C5 |
C4 |
117.7 |
|
C6 |
C5 |
C5A |
123.2 |
|
O2 |
C2 |
N3 |
122.1 |
|
C2 |
N3 |
C4 |
126.9 |
|
N3 |
C4 |
C5 |
115.1 |
|
N3 |
C4 |
SE |
125.4 |
|
SE |
C4 |
C5 |
119.5 |
|
C4 |
C5 |
C5A |
119.0 |
|
C4 |
SE |
HSE |
109.5 |
|
C5 |
C5A |
H5A1 |
109.5 |
|
C5 |
C5A |
H5A2 |
109.5 |
|
C5 |
C5A |
H5A3 |
109.5 |
|
H5A1 |
C5A |
H5A2 |
109.4 |
|
H5A1 |
C5A |
H5A3 |
109.5 |
|
H5A2 |
C5A |
H5A3 |
109.5 |
|
C1' |
C2' |
C3' |
105.0 |
|
C3' |
C2' |
H2' |
111.0 |
|
C3' |
C2' |
H2'' |
112.0 |
|
C2' |
C3' |
C4' |
104.0 |
|
C2' |
C3' |
O3' |
109.1 |
|
C2' |
C3' |
H3' |
114.5 |
|
C1' |
C2' |
H2' |
111.0 |
|
C1' |
C2' |
H2'' |
112.0 |
|
C2' |
C1' |
O4' |
107.5 |
|
C2' |
C1' |
H1' |
109.6 |
|
H2' |
C2' |
H2'' |
106.1 |
|
C4' |
C5' |
H5' |
108.9 |
|
C4' |
C5' |
H5'' |
108.5 |
|
C5' |
C4' |
C3' |
114.0 |
|
C5' |
C4' |
O4' |
109.1 |
|
C5' |
C4' |
H4' |
105.2 |
|
H5' |
C5' |
H5'' |
110.8 |
|
O4' |
C4' |
C3' |
104.7 |
|
C3' |
C4' |
H4' |
109.5 |
|
C4' |
C3' |
O3' |
112.7 |
|
C4' |
C3' |
H3' |
110.8 |
|
O4' |
C4' |
H4' |
114.5 |
|
C4' |
O4' |
C1' |
109.9 |
|
O4' |
C1' |
H1' |
115.5 |
|
O3' |
C3' |
H3' |
105.9 |
|
C3' |
O3' |
HO3' |
109.5 |
|
Torsion Angles for T4S
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP1 |
P |
OP3 |
OP2 |
131.4 |
|
OP1 |
P |
OP3 |
O5' |
245.5 |
|
OP2 |
P |
OP3 |
O5' |
114.1 |
|
OP3 |
P |
OP2 |
HOP2 |
124.4 |
|
OP3 |
P |
O5' |
C5' |
306.1 |
|
HOP3 |
OP3 |
P |
OP1 |
200.3 |
|
HOP3 |
OP3 |
P |
OP2 |
69.0 |
|
HOP3 |
OP3 |
P |
O5' |
314.8 |
|
OP1 |
P |
OP3 |
HOP3 |
200.3 |
|
OP3 |
P |
OP1 |
OP2 |
233.0 |
|
OP3 |
P |
OP1 |
O5' |
110.4 |
|
OP2 |
P |
OP1 |
O5' |
237.3 |
|
OP1 |
P |
OP2 |
HOP2 |
0.6 |
|
OP1 |
P |
O5' |
C5' |
57.8 |
|
OP2 |
P |
OP3 |
HOP3 |
69.0 |
|
OP3 |
P |
OP2 |
OP1 |
123.8 |
|
OP3 |
P |
OP2 |
O5' |
247.8 |
|
OP1 |
P |
OP2 |
O5' |
124.0 |
|
OP2 |
P |
O5' |
C5' |
188.0 |
|
O5' |
P |
OP3 |
HOP3 |
314.8 |
|
OP3 |
P |
O5' |
OP1 |
248.3 |
|
OP3 |
P |
O5' |
OP2 |
118.2 |
|
OP1 |
P |
O5' |
OP2 |
229.8 |
|
O5' |
P |
OP2 |
HOP2 |
236.6 |
|
P |
O5' |
C5' |
C4' |
182.8 |
|
P |
O5' |
C5' |
H5' |
302.8 |
|
P |
O5' |
C5' |
H5'' |
63.5 |
|
HOP2 |
OP2 |
P |
O5' |
236.6 |
|
C4' |
C5' |
O5' |
H5' |
240.0 |
|
C4' |
C5' |
O5' |
H5'' |
119.3 |
|
O5' |
C5' |
C4' |
C3' |
41.6 |
|
O5' |
C5' |
C4' |
O4' |
284.9 |
|
O5' |
C5' |
C4' |
H4' |
161.6 |
|
H5' |
C5' |
O5' |
H5'' |
239.3 |
|
C6 |
N1 |
C1' |
C2 |
181.5 |
|
C1' |
N1 |
C6 |
C5 |
177.4 |
|
C1' |
N1 |
C6 |
H6 |
357.4 |
|
C1' |
N1 |
C2 |
O2 |
359.7 |
|
C1' |
N1 |
C2 |
N3 |
181.0 |
|
N1 |
C1' |
C2' |
C3' |
96.3 |
|
N1 |
C1' |
C2' |
H2' |
336.3 |
|
N1 |
C1' |
C2' |
H2'' |
217.9 |
|
C2' |
C1' |
N1 |
O4' |
247.7 |
|
C2' |
C1' |
N1 |
H1' |
122.6 |
|
C4' |
O4' |
C1' |
N1 |
239.8 |
|
O4' |
C1' |
N1 |
H1' |
234.9 |
|
C2 |
N1 |
C6 |
C1' |
181.6 |
|
C6 |
N1 |
C1' |
C2' |
272.7 |
|
C6 |
N1 |
C1' |
O4' |
25.0 |
|
C6 |
N1 |
C1' |
H1' |
150.1 |
|
C6 |
N1 |
C2 |
O2 |
178.1 |
|
C6 |
N1 |
C2 |
N3 |
359.5 |
|
C5 |
C6 |
N1 |
H6 |
180.0 |
|
N1 |
C6 |
C5 |
C4 |
1.5 |
|
N1 |
C6 |
C5 |
C5A |
181.5 |
|
C6 |
N1 |
C2 |
C1' |
178.5 |
|
C2 |
N1 |
C1' |
C2' |
91.1 |
|
C2 |
N1 |
C1' |
O4' |
203.4 |
|
C2 |
N1 |
C1' |
H1' |
328.5 |
|
C2 |
N1 |
C6 |
C5 |
359.0 |
|
C2 |
N1 |
C6 |
H6 |
179.0 |
|
O2 |
C2 |
N1 |
N3 |
178.7 |
|
N1 |
C2 |
N3 |
C4 |
1.7 |
|
C5 |
C6 |
N1 |
C1' |
177.4 |
|
C5 |
C6 |
N1 |
C2 |
359.0 |
|
N1 |
C6 |
C5 |
H6 |
180.0 |
|
N3 |
C4 |
C5 |
C6 |
359.6 |
|
SE |
C4 |
C5 |
C6 |
179.9 |
|
C4 |
C5 |
C6 |
C5A |
180.0 |
|
C6 |
C5 |
C5A |
H5A1 |
235.8 |
|
C6 |
C5 |
C5A |
H5A2 |
355.8 |
|
C6 |
C5 |
C5A |
H5A3 |
115.8 |
|
H6 |
C6 |
N1 |
C1' |
357.4 |
|
H6 |
C6 |
N1 |
C2 |
179.0 |
|
N1 |
C6 |
H6 |
C5 |
180.0 |
|
H6 |
C6 |
C5 |
C4 |
181.5 |
|
H6 |
C6 |
C5 |
C5A |
1.4 |
|
O2 |
C2 |
N1 |
C1' |
359.7 |
|
N1 |
C2 |
O2 |
N3 |
181.4 |
|
O2 |
C2 |
N3 |
C4 |
183.0 |
|
N3 |
C2 |
N1 |
C1' |
181.0 |
|
N1 |
C2 |
N3 |
O2 |
178.7 |
|
C2 |
N3 |
C4 |
C5 |
358.8 |
|
C2 |
N3 |
C4 |
SE |
178.5 |
|
C6 |
C5 |
C4 |
N3 |
359.6 |
|
SE |
C4 |
N3 |
C5 |
179.7 |
|
N3 |
C4 |
C5 |
C5A |
179.6 |
|
N3 |
C4 |
SE |
HSE |
229.5 |
|
C4 |
C5 |
C6 |
H6 |
181.5 |
|
C6 |
C5 |
C4 |
C5A |
180.0 |
|
N3 |
C4 |
C5 |
SE |
179.7 |
|
C5 |
C4 |
SE |
HSE |
49.2 |
|
C4 |
C5 |
C5A |
H5A1 |
55.8 |
|
C4 |
C5 |
C5A |
H5A2 |
175.8 |
|
C4 |
C5 |
C5A |
H5A3 |
295.8 |
|
C6 |
C5 |
C4 |
SE |
179.9 |
|
N3 |
C4 |
SE |
C5 |
180.3 |
|
SE |
C4 |
C5 |
C5A |
359.9 |
|
HSE |
SE |
C4 |
C5 |
49.2 |
|
C5A |
C5 |
C6 |
H6 |
1.4 |
|
C6 |
C5 |
C5A |
C4 |
180.0 |
|
H5A1 |
C5A |
C5 |
H5A2 |
240.0 |
|
H5A1 |
C5A |
C5 |
H5A3 |
120.0 |
|
H5A2 |
C5A |
C5 |
H5A3 |
240.0 |
|
C5 |
C5A |
H5A1 |
H5A2 |
120.0 |
|
C5 |
C5A |
H5A1 |
H5A3 |
240.0 |
|
H5A2 |
C5A |
H5A1 |
H5A3 |
120.0 |
|
C5 |
C5A |
H5A2 |
H5A1 |
239.9 |
|
C5 |
C5A |
H5A2 |
H5A3 |
120.0 |
|
H5A1 |
C5A |
H5A2 |
H5A3 |
240.0 |
|
C5 |
C5A |
H5A3 |
H5A1 |
120.1 |
|
C5 |
C5A |
H5A3 |
H5A2 |
240.0 |
|
H5A1 |
C5A |
H5A3 |
H5A2 |
119.9 |
|
C1' |
C2' |
C3' |
H2' |
240.0 |
|
C1' |
C2' |
C3' |
H2'' |
121.7 |
|
C3' |
C2' |
C1' |
O4' |
348.8 |
|
C3' |
C2' |
C1' |
H1' |
222.6 |
|
H2' |
C2' |
C3' |
H2'' |
241.7 |
|
C5' |
C4' |
C3' |
C2' |
210.9 |
|
O4' |
C4' |
C3' |
C2' |
330.0 |
|
C2' |
C3' |
C4' |
H4' |
93.3 |
|
C4' |
C3' |
C2' |
O3' |
239.5 |
|
C4' |
C3' |
C2' |
H3' |
121.1 |
|
O3' |
C3' |
C2' |
H3' |
241.6 |
|
C2' |
C3' |
O3' |
HO3' |
196.9 |
|
N1 |
C1' |
C2' |
O4' |
107.5 |
|
N1 |
C1' |
C2' |
H1' |
233.7 |
|
C3' |
C2' |
C1' |
H2' |
120.0 |
|
C3' |
C2' |
C1' |
H2'' |
238.3 |
|
C1' |
C2' |
C3' |
C4' |
25.1 |
|
C1' |
C2' |
C3' |
O3' |
145.6 |
|
C1' |
C2' |
C3' |
H3' |
264.0 |
|
H2' |
C2' |
C1' |
H2'' |
118.3 |
|
C4' |
O4' |
C1' |
C2' |
351.9 |
|
O4' |
C1' |
C2' |
H1' |
126.2 |
|
C1' |
C2' |
H2' |
C3' |
116.3 |
|
C3' |
C2' |
H2' |
H2'' |
121.8 |
|
H2' |
C2' |
C3' |
C4' |
145.1 |
|
H2' |
C2' |
C3' |
O3' |
265.6 |
|
H2' |
C2' |
C3' |
H3' |
24.0 |
|
C1' |
C2' |
H2' |
H2'' |
238.2 |
|
H2' |
C2' |
C1' |
O4' |
228.8 |
|
H2' |
C2' |
C1' |
H1' |
102.6 |
|
C1' |
C2' |
H2'' |
C3' |
242.4 |
|
C3' |
C2' |
H2'' |
H2' |
238.8 |
|
H2'' |
C2' |
C3' |
C4' |
263.4 |
|
H2'' |
C2' |
C3' |
O3' |
23.9 |
|
H2'' |
C2' |
C3' |
H3' |
142.3 |
|
C1' |
C2' |
H2'' |
H2' |
121.2 |
|
H2'' |
C2' |
C1' |
O4' |
110.5 |
|
H2'' |
C2' |
C1' |
H1' |
344.2 |
|
O5' |
C5' |
C4' |
H5' |
120.0 |
|
O5' |
C5' |
C4' |
H5'' |
240.7 |
|
C2' |
C3' |
C4' |
C5' |
210.9 |
|
H5' |
C5' |
C4' |
H5'' |
120.7 |
|
O4' |
C4' |
C5' |
C3' |
243.4 |
|
C3' |
C4' |
C5' |
H4' |
239.9 |
|
C5' |
C4' |
C3' |
O3' |
92.9 |
|
C5' |
C4' |
C3' |
H3' |
334.3 |
|
O4' |
C4' |
C5' |
H4' |
123.3 |
|
C5' |
C4' |
O4' |
C1' |
146.5 |
|
O5' |
C5' |
H5' |
C4' |
238.6 |
|
O5' |
C5' |
H5' |
H5'' |
119.3 |
|
C4' |
C5' |
H5' |
H5'' |
240.7 |
|
H5' |
C5' |
C4' |
C3' |
281.6 |
|
H5' |
C5' |
C4' |
O4' |
164.9 |
|
H5' |
C5' |
C4' |
H4' |
41.6 |
|
O5' |
C5' |
H5'' |
C4' |
120.9 |
|
O5' |
C5' |
H5'' |
H5' |
240.5 |
|
C4' |
C5' |
H5'' |
H5' |
119.5 |
|
H5'' |
C5' |
C4' |
C3' |
160.9 |
|
H5'' |
C5' |
C4' |
O4' |
44.2 |
|
H5'' |
C5' |
C4' |
H4' |
281.0 |
|
C4' |
C3' |
C2' |
H2' |
145.1 |
|
C4' |
C3' |
C2' |
H2'' |
263.4 |
|
C2' |
C3' |
C4' |
O3' |
118.0 |
|
C2' |
C3' |
C4' |
H3' |
236.5 |
|
C3' |
C4' |
C5' |
H5' |
281.6 |
|
C3' |
C4' |
C5' |
H5'' |
160.9 |
|
C5' |
C4' |
C3' |
O4' |
240.8 |
|
C5' |
C4' |
C3' |
H4' |
117.6 |
|
O4' |
C4' |
C3' |
H4' |
236.8 |
|
C3' |
C4' |
O4' |
C1' |
24.0 |
|
O3' |
C3' |
C4' |
H3' |
118.6 |
|
C4' |
C3' |
O3' |
HO3' |
311.9 |
|
N1 |
C1' |
O4' |
C4' |
239.8 |
|
C2' |
C3' |
C4' |
O4' |
330.0 |
|
C2' |
C1' |
O4' |
C4' |
351.9 |
|
O4' |
C4' |
C5' |
H5' |
164.9 |
|
O4' |
C4' |
C5' |
H5'' |
44.2 |
|
C5' |
C4' |
O4' |
C3' |
122.5 |
|
C5' |
C4' |
O4' |
H4' |
242.4 |
|
C3' |
C4' |
O4' |
H4' |
120.0 |
|
O4' |
C4' |
C3' |
O3' |
212.1 |
|
O4' |
C4' |
C3' |
H3' |
93.5 |
|
C4' |
O4' |
C1' |
H1' |
114.6 |
|
H4' |
C4' |
C5' |
H5' |
41.6 |
|
H4' |
C4' |
C5' |
H5'' |
281.0 |
|
C5' |
C4' |
H4' |
C3' |
237.0 |
|
C5' |
C4' |
H4' |
O4' |
119.7 |
|
O4' |
C4' |
H4' |
C3' |
117.2 |
|
H4' |
C4' |
C3' |
O3' |
335.3 |
|
H4' |
C4' |
C3' |
H3' |
216.7 |
|
H4' |
C4' |
O4' |
C1' |
264.1 |
|
N1 |
C1' |
O4' |
C2' |
247.9 |
|
N1 |
C1' |
O4' |
H1' |
125.2 |
|
O4' |
C1' |
C2' |
C3' |
348.8 |
|
O4' |
C1' |
C2' |
H2' |
228.8 |
|
O4' |
C1' |
C2' |
H2'' |
110.5 |
|
C2' |
C1' |
O4' |
H1' |
237.3 |
|
C1' |
O4' |
C4' |
C3' |
24.0 |
|
C1' |
O4' |
C4' |
H4' |
264.1 |
|
N1 |
C1' |
H1' |
C2' |
121.4 |
|
N1 |
C1' |
H1' |
O4' |
243.0 |
|
H1' |
C1' |
C2' |
C3' |
222.6 |
|
H1' |
C1' |
C2' |
H2' |
102.6 |
|
H1' |
C1' |
C2' |
H2'' |
344.2 |
|
C2' |
C1' |
H1' |
O4' |
121.6 |
|
O3' |
C3' |
C2' |
H2' |
265.6 |
|
O3' |
C3' |
C2' |
H2'' |
23.9 |
|
C2' |
C3' |
O3' |
C4' |
245.1 |
|
C2' |
C3' |
O3' |
H3' |
123.7 |
|
O3' |
C3' |
C4' |
H4' |
335.3 |
|
C4' |
C3' |
O3' |
H3' |
238.6 |
|
H3' |
C3' |
C2' |
H2' |
24.0 |
|
H3' |
C3' |
C2' |
H2'' |
142.3 |
|
C2' |
C3' |
H3' |
C4' |
117.2 |
|
C2' |
C3' |
H3' |
O3' |
239.8 |
|
H3' |
C3' |
C4' |
H4' |
216.7 |
|
C4' |
C3' |
H3' |
O3' |
122.6 |
|
H3' |
C3' |
O3' |
HO3' |
73.3 |
|
HO3' |
O3' |
C3' |
H3' |
73.3 |
|