Appendix¶
Atom Type |
R |
K |
IP |
POL |
Description |
---|---|---|---|---|---|
|
1.5 |
0.042 |
13.6 |
4 |
Non-polar hydrogen |
|
1.2 |
0.042 |
13.6 |
4 |
Polar hydrogen |
|
1.7 |
0.107 |
14.61 |
13.8 |
C sp3 (0 implicit H) |
|
1.8 |
0.107 |
14.61 |
16.38 |
C sp3 (1 implicit H) |
|
1.9 |
0.107 |
14.61 |
19.27 |
C sp3 (2 implicit H) |
|
2 |
0.107 |
14.61 |
22.47 |
C sp3 (3 implicit H) |
|
1.7 |
0.107 |
15.62 |
13.8 |
C sp2 (0 implicit H) |
|
1.7 |
0.107 |
15.62 |
13.8 |
C sp2 (guanidinium centre) |
|
1.8 |
0.107 |
15.62 |
16.38 |
C sp2 (1 implicit H) |
|
1.9 |
0.107 |
15.62 |
19.27 |
C sp2 (2 implicit H) |
|
1.7 |
0.107 |
15.62 |
13.8 |
C aromatic (0 implicit H) |
|
1.8 |
0.107 |
15.62 |
16.38 |
C aromatic (1 implicit H) |
|
1.7 |
0.107 |
17.47 |
13.8 |
C sp (0 implicit H) |
|
1.8 |
0.107 |
17.47 |
16.38 |
C sp (1 implicit H) |
|
1.55 |
0.095 |
33.29 |
8.4 |
N sp3+ (cationic) |
|
1.55 |
0.095 |
18.93 |
8.4 |
N sp3 |
|
1.55 |
0.095 |
19.72 |
8.4 |
N trigonal planar (non-amide) |
|
1.55 |
0.095 |
19.72 |
8.4 |
N trigonal planar (amide) |
|
1.55 |
0.095 |
22.1 |
8.4 |
N sp2 |
|
1.55 |
0.095 |
22.1 |
8.4 |
N aromatic |
|
1.55 |
0.095 |
23.91 |
8.4 |
N sp |
|
1.52 |
0.116 |
24.39 |
5.4 |
O sp3 |
|
1.52 |
0.116 |
26.65 |
5.4 |
O sp2 |
|
1.52 |
0.116 |
35.12 |
5.4 |
O carboxylate |
|
1.8 |
0.314 |
15.5 |
29.4 |
S sp3 |
|
1.7 |
0.314 |
15.5 |
29.4 |
sulfoxide |
|
1.7 |
0.314 |
15.5 |
29.4 |
sulfone |
|
1.8 |
0.314 |
17.78 |
29.4 |
S sp2 |
|
1.8 |
0.314 |
16.78 |
40.6 |
|
|
1.47 |
0.109 |
20.86 |
3.7 |
|
|
1.75 |
0.314 |
15.03 |
21.8 |
|
|
1.85 |
0.434 |
13.1 |
31.2 |
|
|
1.98 |
0.623 |
12.67 |
49 |
|
|
1.2 |
0.4 |
|||
|
1.2 |
0.4 |
|||
|
1.2 |
0.042 |
Term |
\(X\)a |
\(X_0\)b |
\(X_{\min}\)c |
\(X_{\max}\)d |
Description |
---|---|---|---|---|---|
\(S_{\text{polar}}\) |
\(R_{12}\) |
\(R\) + 0.05 Å |
0.25 Å |
0.6 Å |
Distance between interaction centres |
\(\alpha_{\text{DON}}\) |
180° |
30° |
80° |
Angle around donor H |
|
\(\alpha_{\text{ACC}}\) |
180° |
60° |
100° |
Angle around acceptor |
|
\(\alpha_{\text{C+}}\) |
180° |
60° |
100° |
Angle between C+ACC vector and normal to plane of guanidinium group |
|
\(\phi_{\text{ACC}\_\text{LP}}\) |
45° |
15° |
15° |
From [RiboDock2004] Figure 2. |
|
\(\theta_{\text{ACC}\_\text{LP}}\) |
0° |
20° |
60° |
From [RiboDock2004] Figure 2. |
|
\(\phi_{\text{ACC}\_\text{PLANE}}\) |
0° |
60° |
75° |
From [RiboDock2004] Figure 2. |
|
\(\theta_{\text{ACC}\_\text{PLANE}}\) |
0° |
20° |
60° |
From [RiboDock2004] Figure 2. |
|
\(S_{\text{repul}}\) |
\(R_{12}\) |
R + 1.1 Å |
0.25 Å |
0.6 Å |
Distance between interaction centres |
\(\alpha_{\text{DON}}\) |
180° |
30° |
60° |
Angle around donor H |
|
\(\alpha_{\text{ACC}}\) |
180° |
30° |
60° |
Angle around acceptor |
|
\(S_{\text{arom}}\) |
\(R_{\text{perp}}\) |
3.5 Å |
0.25 Å |
0.6 Å |
From [RiboDock2004] Figure 3. |
\(\alpha_{\text{slip}}\) |
0° |
20° |
60° |
From [RiboDock2004] Figure 3. |
\(\text{IC1}\)a |
\(\text{ANG}_{\text{IC1}}\)b |
\(\text{IC2}\)a |
\(\text{ANG}_{\text{IC2}}\)b |
---|---|---|---|
Attractive (\(S_{\text{polar}}\)) |
|||
DON |
\(f_1(|\Delta\alpha_{\text{DON}}|)\) |
ACC_LP |
\(f_1(|\Delta\phi_{\text{ACC}\_\text{LP}}|) \cdot f_1(|\Delta\theta_{\text{ACC}\_\text{LP}}|)\) |
DON |
\(f_1(|\Delta\alpha_{\text{DON}}|)\) |
ACC_PLANE |
\(f_1(|\Delta\phi_{\text{ACC}\_\text{PLANE}}|) \cdot f_1(|\Delta\theta_{\text{ACC}\_\text{PLANE}}|)\) |
DON |
\(f_1(|\Delta\alpha_{\text{DON}}|)\) |
ACC |
\(f_1(|\Delta\alpha_{\text{ACC}}|)\) |
M+ |
1 |
ACC_LP |
\(f_1(|\Delta\phi_{\text{ACC}\_\text{LP}}|) \cdot f_1(|\Delta\theta_{\text{ACC}\_\text{LP}}|)\) |
M+ |
1 |
ACC_PLANE |
\(f_1(|\Delta\phi_{\text{ACC}\_\text{PLANE}}|) \cdot f_1(|\Delta\theta_{\text{ACC}\_\text{PLANE}}|)\) |
M+ |
1 |
ACC |
\(f_1(|\Delta\alpha_{\text{ACC}}|)\) |
1 |
ACC_LP |
||
C+ |
\(f_1(|\Delta\alpha_{\text{C+}}|)\) |
ACC_PLANE |
\(f_1(|\Delta\alpha_{\text{ACC}}|)\) |
1 |
ACC |
||
Repulsive (\(S_{\text{repul}}\)) |
|||
DON |
\(f_1(|\Delta\alpha_{\text{DON}}|)\) |
DON |
\(f_1(|\Delta\alpha_{\text{DON}}|)\) |
DON |
\(f_1(|\Delta\alpha_{\text{DON}}|)\) |
M+ |
1 |
DON |
\(f_1(|\Delta\alpha_{\text{DON}}|)\) |
C+ |
1 |
M+ |
1 |
C+ |
1 |
C+ |
1 |
C+ |
1 |
ACC_LP |
ACC_LP |
||
ACC_PLANE |
\(f_1(|\Delta\alpha_{\text{ACC}}|)\) |
ACC_PLANE |
\(f_1(|\Delta\alpha_{\text{ACC}}|)\) |
ACC |
ACC |
Atom type |
Description |
\(N\)a |
\(r_i\) |
\(p_i\) |
\(w_i\) |
---|---|---|---|---|---|
|
Apolar carbon sp3 with 0 implicit H |
48 |
1.7 |
2.149 |
0.8438 |
|
Apolar carbon sp3 with 1 implicit H |
59 |
1.8 |
1.276 |
0.0114 |
|
Apolar carbon sp3 with 2 implicit H |
487 |
1.9 |
1.045 |
0.0046 |
|
Apolar carbon sp3 with 3 implicit H |
409 |
2 |
0.88 |
0.0064 |
|
Apolar carbon sp2 with 0 implicit H |
10 |
1.72 |
1.554 |
0.0789 |
|
Apolar carbon sp2 with 1 implicit H |
45 |
1.8 |
1.073 |
-0.0014 |
|
Apolar carbon sp2 with 2 implicit H |
26 |
1.8 |
0.961 |
0.0095 |
|
Positive charged carbon sp2 |
2 |
1.72 |
1.554 |
-0.7919 |
|
Apolar aromatic carbon with 0 implicit H |
116 |
1.72 |
1.554 |
0.017 |
|
Apolar aromatic carbon with 1 implicit H |
357 |
1.8 |
1.073 |
-0.0143 |
|
Carbon sp |
24 |
1.78 |
0.737 |
-0.0052 |
|
Polar carbon sp3 with 0 implicit H |
6 |
1.7 |
2.149 |
-0.0473 |
|
Polar carbon sp3 with 1 implicit H |
22 |
1.8 |
1.276 |
-0.0394 |
|
Polar carbon sp3 with 2 implicit H |
130 |
1.9 |
1.045 |
-0.0078 |
|
Polar carbon sp3 with 3 implicit H |
69 |
2 |
0.88 |
0.0033 |
|
Polar carbon sp2 with 0 implicit H |
57 |
1.72 |
1.554 |
-0.2609 |
|
Polar carbon sp2 with 1 implicit H |
30 |
1.8 |
0.961 |
-0.005 |
|
Polar carbon sp2 with 2 implicit H |
1 |
1.8 |
0.961 |
0.0095 |
|
Polar aromatic carbon with 0 implicit H |
53 |
1.72 |
1.554 |
-0.2609 |
|
Polar aromatic carbon with 1 implicit H |
34 |
1.8 |
1.073 |
-0.0015 |
|
Explicit apolar hydrogen (not used) |
0 |
1.2 |
1 |
0 |
|
Polar hydrogen bonded to O |
54 |
1 |
0.944 |
0.0499 |
|
Polar hydrogen bonded to N |
54 |
1.1 |
1.128 |
-0.0242 |
|
Positively charged polar hydrogen bonded to N |
23 |
1.2 |
1.049 |
-1.9513 |
|
Polar hydrogen bonded to S |
4 |
1.2 |
0.928 |
0.0487 |
|
Ether oxygen |
31 |
1.52 |
1.08 |
-0.138 |
|
Alcohol/phenol oxygen |
48 |
1.52 |
1.08 |
-0.272 |
|
Ester oxygen |
59 |
1.52 |
1.08 |
0.0965 |
|
Acid oxygen (neutral) |
6 |
1.52 |
1.08 |
-0.0985 |
|
Oxygen sp2 |
83 |
1.5 |
0.926 |
-0.1122 |
|
Nitro group oxygen |
18 |
1.5 |
0.926 |
-0.0055 |
|
Negatively charged oxygen (carboxylate etc.) |
7 |
1.7 |
0.922 |
-0.717 |
|
Nitrogen sp3 with 0 attached H |
8 |
1.6 |
1.215 |
-0.6249 |
|
Nitrogen sp3 with 1 attached H |
11 |
1.6 |
1.215 |
-0.396 |
|
Nitrogen sp3 with 2 attached H |
11 |
1.6 |
1.215 |
-0.215 |
|
Nitrogen sp3+ |
6 |
1.6 |
1.215 |
-0.1186 |
|
Amide nitrogen with 0 attached H |
15 |
1.55 |
1.028 |
-0.23 |
|
Amide nitrogen with 1 attached H |
8 |
1.55 |
1.028 |
-0.4149 |
|
Amide nitrogen with 2 attached H |
6 |
1.55 |
1.028 |
-0.1943 |
|
Nitrogen sp2 |
3 |
1.55 |
1.413 |
-0.0768 |
|
Nitrogen sp2+ |
5 |
1.55 |
1.413 |
-0.2744 |
|
Aromatic nitrogen |
26 |
1.55 |
1.413 |
-0.531 |
|
Nitrogen sp |
6 |
1.55 |
1 |
-0.1208 |
|
Sulphur sp3 |
15 |
1.8 |
1.121 |
-0.0685 |
|
Sulphur sp2 |
5 |
1.8 |
1.121 |
-0.0314 |
|
Phosphorous |
10 |
1.8 |
1.589 |
-1.275 |
|
Fluorine |
99 |
1.47 |
0.906 |
0.0043 |
|
Chlorine |
132 |
1.75 |
0.906 |
-0.0096 |
|
Bromine |
37 |
1.85 |
0.898 |
-0.0194 |
|
Iodine |
9 |
1.98 |
0.876 |
-0.0189 |
|
All metals |
0 |
0.7 |
1 |
-1.6667 |
|
Undefined types |
0 |
1.2 |
1 |
0 |