PDB Chemical Component T39
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 T39
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| CD' |
OC' |
1.450 |
1.429 |
| OC' |
CB' |
1.449 |
1.429 |
| CB' |
CA' |
1.452 |
1.530 |
| CA' |
O2' |
1.440 |
1.429 |
| O2' |
C2' |
1.414 |
1.429 |
| O3' |
C3' |
1.423 |
1.430 |
| C2' |
C3' |
1.515 |
1.548 |
| C2' |
C1' |
1.533 |
1.549 |
| C3' |
C4' |
1.527 |
1.541 |
| O2 |
C2 |
1.218 |
1.215 |
| C4' |
O4' |
1.453 |
1.438 |
| C4' |
C5' |
1.504 |
1.531 |
| C1' |
O4' |
1.425 |
1.445 |
| C1' |
N1 |
1.483 |
1.465 |
| C2 |
N1 |
1.385 |
1.345 |
| C2 |
N3 |
1.361 |
1.346 |
| N1 |
C6 |
1.384 |
1.369 |
| C5' |
O5' |
1.437 |
1.429 |
| N3 |
C4 |
1.376 |
1.349 |
| O5' |
P |
1.596 |
1.611 |
| C6 |
C5 |
1.339 |
1.350 |
| C4 |
C5 |
1.444 |
1.416 |
| C4 |
O4 |
1.225 |
1.218 |
| C5 |
C7 |
1.503 |
1.506 |
| OP1 |
P |
1.473 |
1.480 |
| P |
OP2 |
1.479 |
1.610 |
| P |
OP3 |
1.597 |
1.610 |
| OP2 |
HOP2 |
0.950 |
0.967 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'' |
1.100 |
1.090 |
| C4' |
H4' |
1.100 |
1.090 |
| C3' |
H3' |
1.100 |
1.089 |
| O3' |
HO3' |
0.950 |
0.967 |
| C2' |
H7 |
1.100 |
1.090 |
| C1' |
H1' |
1.100 |
1.090 |
| N3 |
H3 |
1.000 |
0.970 |
| C7 |
H71 |
1.100 |
1.090 |
| C7 |
H72 |
1.100 |
1.090 |
| C7 |
H73 |
1.100 |
1.090 |
| C6 |
H6 |
1.080 |
1.080 |
| CA' |
HCA2 |
1.100 |
1.091 |
| CA' |
HCA1 |
1.100 |
1.089 |
| CD' |
HCD1 |
1.100 |
1.090 |
| CD' |
HCD2 |
1.100 |
1.090 |
| CD' |
HCD3 |
1.100 |
1.090 |
| CB' |
HCB1 |
1.100 |
1.090 |
| CB' |
HCB2 |
1.100 |
1.090 |
| OP3 |
HOP3 |
0.950 |
0.967 |
Bond Angles for T39
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| CD' |
OC' |
CB' |
116.0 |
114.0 |
| OC' |
CD' |
HCD1 |
109.5 |
109.5 |
| OC' |
CD' |
HCD2 |
109.5 |
109.5 |
| OC' |
CD' |
HCD3 |
109.5 |
109.5 |
| OC' |
CB' |
HCB1 |
108.7 |
109.4 |
| OC' |
CB' |
HCB2 |
108.7 |
109.5 |
| CB' |
CA' |
HCA2 |
109.1 |
109.4 |
| CB' |
CA' |
HCA1 |
109.1 |
109.5 |
| O2' |
C2' |
C1' |
111.0 |
110.9 |
| O2' |
C2' |
H7 |
112.5 |
110.8 |
| O3' |
C3' |
H3' |
110.8 |
110.4 |
| C2' |
C3' |
H3' |
109.4 |
110.5 |
| C2' |
C1' |
N1 |
111.9 |
110.6 |
| C1' |
C2' |
H7 |
110.7 |
110.9 |
| C2' |
C1' |
H1' |
108.5 |
110.7 |
| C3' |
C4' |
H4' |
108.5 |
110.0 |
| O2 |
C2 |
N3 |
121.1 |
119.6 |
| O4' |
C4' |
H4' |
109.5 |
109.9 |
| C4' |
C5' |
H5' |
109.1 |
109.5 |
| C4' |
C5' |
H5'' |
109.1 |
109.5 |
| C1' |
N1 |
C6 |
121.8 |
119.7 |
| N1 |
C1' |
H1' |
109.1 |
110.7 |
| C2 |
N1 |
C6 |
121.2 |
120.6 |
| C2 |
N3 |
C4 |
127.2 |
120.3 |
| C2 |
N3 |
H3 |
116.4 |
119.9 |
| N1 |
C6 |
C5 |
123.0 |
119.7 |
| N1 |
C6 |
H6 |
118.5 |
120.2 |
| N3 |
C4 |
C5 |
115.6 |
119.4 |
| N3 |
C4 |
O4 |
119.0 |
120.3 |
| C4 |
N3 |
H3 |
116.4 |
119.8 |
| O5' |
P |
OP3 |
104.4 |
109.5 |
| O4 |
C4 |
C5 |
125.5 |
120.3 |
| C4 |
C5 |
C7 |
119.1 |
120.5 |
| C5 |
C7 |
H71 |
109.5 |
109.5 |
| C5 |
C7 |
H72 |
109.5 |
109.5 |
| C5 |
C7 |
H73 |
109.5 |
109.5 |
| OP1 |
P |
OP2 |
119.1 |
109.5 |
| OP1 |
P |
OP3 |
104.2 |
109.5 |
| OP2 |
P |
OP3 |
108.2 |
109.5 |
| P |
OP2 |
HOP2 |
109.5 |
114.0 |
| P |
OP3 |
HOP3 |
109.5 |
114.0 |
| H5' |
C5' |
H5'' |
109.5 |
109.5 |
| H71 |
C7 |
H72 |
109.4 |
109.4 |
| H71 |
C7 |
H73 |
109.5 |
109.4 |
| H72 |
C7 |
H73 |
109.5 |
109.4 |
| HCA2 |
CA' |
HCA1 |
109.5 |
109.5 |
| HCD1 |
CD' |
HCD2 |
109.5 |
109.4 |
| HCD1 |
CD' |
HCD3 |
109.4 |
109.4 |
| HCD2 |
CD' |
HCD3 |
109.5 |
109.5 |
| HCB1 |
CB' |
HCB2 |
109.5 |
109.4 |
Torsion Angles for T39
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| CD' |
OC' |
CB' |
HCB1 |
46.8 |
60.0 |
| CD' |
OC' |
CB' |
HCB2 |
165.9 |
300.1 |
| HCD1 |
CD' |
OC' |
HCD2 |
240.0 |
240.1 |
| HCD1 |
CD' |
OC' |
HCD3 |
120.0 |
119.9 |
| HCD2 |
CD' |
OC' |
HCD3 |
240.0 |
239.9 |
| CB' |
OC' |
CD' |
HCD1 |
180.0 |
300.0 |
| CB' |
OC' |
CD' |
HCD2 |
300.0 |
59.9 |
| CB' |
OC' |
CD' |
HCD3 |
60.0 |
180.0 |
| OC' |
CB' |
CA' |
HCA2 |
86.6 |
305.0 |
| OC' |
CB' |
CA' |
HCA1 |
206.1 |
185.0 |
| HCB1 |
CB' |
OC' |
HCB2 |
240.8 |
119.9 |
| HCA2 |
CA' |
CB' |
HCA1 |
240.5 |
120.0 |
| CA' |
O2' |
C2' |
H7 |
305.4 |
32.3 |
| O2' |
C2' |
C3' |
H3' |
168.0 |
102.2 |
| O2' |
C2' |
C1' |
N1 |
209.4 |
273.7 |
| C1' |
C2' |
O2' |
H7 |
124.7 |
123.6 |
| O2' |
C2' |
C1' |
H1' |
329.9 |
36.8 |
| C2' |
C3' |
O3' |
H3' |
122.0 |
122.6 |
| O3' |
C3' |
C4' |
H4' |
316.4 |
358.7 |
| O3' |
C3' |
C2' |
H3' |
237.2 |
237.4 |
| C2' |
C3' |
C4' |
H4' |
76.1 |
117.4 |
| O2' |
C2' |
C1' |
H7 |
234.2 |
236.5 |
| C1' |
C2' |
C3' |
H3' |
285.3 |
220.4 |
| C2' |
C1' |
N1 |
C6 |
266.7 |
115.0 |
| N1 |
C1' |
C2' |
H1' |
239.5 |
236.9 |
| O4' |
C4' |
C3' |
H4' |
243.8 |
240.5 |
| C3' |
C4' |
C5' |
H5' |
172.5 |
64.3 |
| C3' |
C4' |
C5' |
H5'' |
292.0 |
304.2 |
| O2 |
C2 |
N1 |
C6 |
179.1 |
180.3 |
| O2 |
C2 |
N3 |
C4 |
181.0 |
180.0 |
| O2 |
C2 |
N3 |
H3 |
0.9 |
360.0 |
| C3' |
C4' |
O4' |
H4' |
115.5 |
119.6 |
| O4' |
C4' |
C5' |
H5' |
55.4 |
306.5 |
| O4' |
C4' |
C5' |
H5'' |
175.0 |
186.5 |
| H5' |
C5' |
C4' |
H5'' |
240.4 |
120.0 |
| C1' |
O4' |
C4' |
H4' |
267.3 |
266.9 |
| N1 |
C1' |
C2' |
H7 |
335.2 |
37.2 |
| C2' |
C1' |
N1 |
H1' |
120.2 |
123.0 |
| C2 |
N1 |
C1' |
C6 |
180.6 |
180.3 |
| C1' |
N1 |
C6 |
C5 |
180.4 |
179.8 |
| C1' |
N1 |
C6 |
H6 |
0.4 |
0.1 |
| C1' |
N1 |
C2 |
C6 |
179.4 |
179.7 |
| C2 |
N1 |
C1' |
H1' |
327.2 |
172.3 |
| C2 |
N1 |
C6 |
C5 |
359.7 |
359.5 |
| C2 |
N1 |
C6 |
H6 |
179.8 |
179.8 |
| N3 |
C2 |
N1 |
C6 |
359.6 |
0.3 |
| C2 |
N3 |
C4 |
C5 |
0.1 |
360.0 |
| C2 |
N3 |
C4 |
O4 |
180.2 |
180.0 |
| C4 |
N3 |
C2 |
H3 |
180.0 |
180.0 |
| C6 |
N1 |
C1' |
H1' |
146.5 |
352.0 |
| C5' |
O5' |
P |
OP3 |
295.0 |
185.0 |
| C2 |
N3 |
C4 |
H3 |
180.0 |
180.0 |
| O4 |
C4 |
N3 |
C5 |
180.1 |
180.1 |
| N3 |
C4 |
C5 |
C7 |
179.6 |
180.0 |
| OP1 |
P |
O5' |
OP3 |
111.5 |
120.0 |
| OP2 |
P |
O5' |
OP3 |
244.3 |
240.0 |
| O5' |
P |
OP2 |
HOP2 |
231.9 |
60.0 |
| O5' |
P |
OP3 |
HOP3 |
115.8 |
180.0 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.4 |
| C6 |
C5 |
C7 |
H71 |
180.0 |
180.3 |
| C6 |
C5 |
C7 |
H72 |
300.0 |
300.3 |
| C6 |
C5 |
C7 |
H73 |
60.0 |
60.3 |
| N1 |
C6 |
C5 |
C4 |
0.8 |
0.5 |
| N3 |
C4 |
C5 |
O4 |
180.1 |
180.1 |
| C5 |
C4 |
N3 |
H3 |
180.1 |
180.0 |
| C4 |
C5 |
C7 |
H71 |
359.7 |
0.1 |
| C4 |
C5 |
C7 |
H72 |
119.6 |
120.1 |
| C4 |
C5 |
C7 |
H73 |
239.7 |
240.0 |
| N3 |
C4 |
O4 |
C5 |
179.9 |
179.9 |
| O4 |
C4 |
N3 |
H3 |
0.3 |
0.1 |
| O4 |
C4 |
C5 |
C7 |
359.5 |
359.9 |
| N1 |
C6 |
C5 |
C7 |
180.5 |
180.3 |
| H71 |
C7 |
C5 |
H72 |
240.0 |
240.0 |
| H71 |
C7 |
C5 |
H73 |
120.0 |
120.0 |
| H72 |
C7 |
C5 |
H73 |
240.0 |
240.0 |
| O5' |
P |
OP1 |
OP3 |
248.4 |
240.0 |
| OP2 |
P |
OP1 |
OP3 |
120.7 |
120.0 |
| OP1 |
P |
OP2 |
HOP2 |
0.0 |
180.0 |
| OP1 |
P |
OP3 |
HOP3 |
360.0 |
60.0 |
| O5' |
P |
OP2 |
OP3 |
113.2 |
120.0 |
| OP1 |
P |
OP2 |
OP3 |
241.3 |
239.9 |
| OP2 |
P |
OP3 |
HOP3 |
232.3 |
300.0 |
| OP1 |
P |
OP3 |
OP2 |
127.7 |
120.0 |
| OP3 |
P |
OP2 |
HOP2 |
118.7 |
300.0 |
| HOP2 |
OP2 |
P |
OP3 |
118.7 |
300.0 |
| C4' |
C5' |
H5' |
H5'' |
119.3 |
240.0 |
| C4' |
C5' |
H5'' |
H5' |
240.7 |
120.0 |
| H4' |
C4' |
C5' |
H5' |
295.9 |
185.4 |
| H4' |
C4' |
C5' |
H5'' |
55.4 |
65.4 |
| H3' |
C3' |
C4' |
H4' |
191.7 |
236.2 |
| HO3' |
O3' |
C3' |
H3' |
58.0 |
61.1 |
| O2' |
C2' |
H7 |
C1' |
124.9 |
123.6 |
| H7 |
C2' |
C3' |
H3' |
42.3 |
338.6 |
| H7 |
C2' |
C1' |
N1 |
335.2 |
37.2 |
| H7 |
C2' |
C1' |
H1' |
95.7 |
160.3 |
| C2' |
C1' |
H1' |
N1 |
237.8 |
237.0 |
| H1' |
C1' |
C2' |
H7 |
95.7 |
160.3 |
| H1' |
C1' |
N1 |
C6 |
146.5 |
352.0 |
| C2 |
N3 |
H3 |
C4 |
180.0 |
180.0 |
| H3 |
N3 |
C4 |
C5 |
180.1 |
180.0 |
| H3 |
N3 |
C4 |
O4 |
0.3 |
0.1 |
| C5 |
C7 |
H71 |
H72 |
120.0 |
120.0 |
| C5 |
C7 |
H71 |
H73 |
240.0 |
240.0 |
| H72 |
C7 |
H71 |
H73 |
120.0 |
119.9 |
| C5 |
C7 |
H72 |
H71 |
240.0 |
239.9 |
| C5 |
C7 |
H72 |
H73 |
120.0 |
120.0 |
| H71 |
C7 |
H72 |
H73 |
240.0 |
240.1 |
| C5 |
C7 |
H73 |
H71 |
120.0 |
120.1 |
| C5 |
C7 |
H73 |
H72 |
240.0 |
240.0 |
| H71 |
C7 |
H73 |
H72 |
120.0 |
119.9 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
179.6 |
| CB' |
CA' |
HCA2 |
HCA1 |
119.3 |
240.0 |
| CB' |
CA' |
HCA1 |
HCA2 |
240.7 |
119.9 |
| HCD1 |
CD' |
OC' |
CB' |
180.0 |
300.0 |
| OC' |
CD' |
HCD1 |
HCD2 |
120.0 |
120.0 |
| OC' |
CD' |
HCD1 |
HCD3 |
240.0 |
240.0 |
| HCD2 |
CD' |
HCD1 |
HCD3 |
120.0 |
120.0 |
| HCD2 |
CD' |
OC' |
CB' |
300.0 |
59.9 |
| OC' |
CD' |
HCD2 |
HCD1 |
239.9 |
240.0 |
| OC' |
CD' |
HCD2 |
HCD3 |
120.0 |
120.1 |
| HCD1 |
CD' |
HCD2 |
HCD3 |
240.1 |
240.1 |
| HCD3 |
CD' |
OC' |
CB' |
60.0 |
180.0 |
| OC' |
CD' |
HCD3 |
HCD1 |
120.0 |
120.0 |
| OC' |
CD' |
HCD3 |
HCD2 |
240.0 |
239.9 |
| HCD1 |
CD' |
HCD3 |
HCD2 |
120.0 |
119.9 |
| OC' |
CB' |
HCB1 |
HCB2 |
118.7 |
240.1 |
| HCB1 |
CB' |
CA' |
HCA2 |
326.2 |
65.0 |
| HCB1 |
CB' |
CA' |
HCA1 |
85.7 |
305.0 |
| OC' |
CB' |
HCB2 |
HCB1 |
241.3 |
119.9 |
| HCB2 |
CB' |
CA' |
HCA2 |
207.0 |
185.0 |
| HCB2 |
CB' |
CA' |
HCA1 |
326.5 |
65.0 |