E002: Ser205 HG - H2O O¶
Probability density function¶
Hydrogen bonding¶
The following table presents the probability of the hydrogen bonding (within 2.5 Å).
| System | H bond |
|---|---|
| Reduced | 0.516 |
| Oxidized | 0.416 |
| Cu(I) | 0.517 |
| Na+ | 0.472 |
Quantitative¶
Reduced roGFP2
| Distance (Å) | Density |
|---|---|
| 1.32 | \(2.390 \times 10^{-09}\) |
| 1.82 | \(1.342 \times 10^{+00}\) |
| 2.92 | \(6.497 \times 10^{-03}\) |
| 3.14 | \(5.807 \times 10^{-03}\) |
| 3.24 | \(7.359 \times 10^{-03}\) |
| 3.31 | \(6.815 \times 10^{-03}\) |
| 5.11 | \(2.796 \times 10^{-01}\) |
| 6.35 | \(1.824 \times 10^{-02}\) |
| 6.43 | \(1.880 \times 10^{-02}\) |
| 6.61 | \(1.570 \times 10^{-02}\) |
| 7.05 | \(2.537 \times 10^{-02}\) |
| 7.13 | \(2.284 \times 10^{-02}\) |
| 7.19 | \(2.422 \times 10^{-02}\) |
| 7.23 | \(2.397 \times 10^{-02}\) |
| 7.37 | \(2.576 \times 10^{-02}\) |
| 7.90 | \(1.400 \times 10^{-02}\) |
| 7.96 | \(1.501 \times 10^{-02}\) |
| 8.32 | \(6.968 \times 10^{-03}\) |
| 8.38 | \(7.143 \times 10^{-03}\) |
| 8.82 | \(2.508 \times 10^{-03}\) |
| 8.88 | \(2.628 \times 10^{-03}\) |
| 8.96 | \(2.185 \times 10^{-03}\) |
| 9.06 | \(2.659 \times 10^{-03}\) |
| 9.14 | \(2.182 \times 10^{-03}\) |
| 9.20 | \(2.551 \times 10^{-03}\) |
| 9.30 | \(1.642 \times 10^{-03}\) |
| 9.44 | \(2.166 \times 10^{-03}\) |
| 9.70 | \(7.405 \times 10^{-04}\) |
| 9.78 | \(1.235 \times 10^{-03}\) |
| 9.96 | \(3.464 \times 10^{-04}\) |
Oxidized roGFP2
| Distance (Å) | Density |
|---|---|
| 1.40 | \(8.718 \times 10^{-08}\) |
| 1.86 | \(1.013 \times 10^{+00}\) |
| 3.33 | \(4.058 \times 10^{-03}\) |
| 3.47 | \(5.323 \times 10^{-03}\) |
| 3.53 | \(4.590 \times 10^{-03}\) |
| 3.67 | \(6.336 \times 10^{-03}\) |
| 3.71 | \(5.945 \times 10^{-03}\) |
| 3.85 | \(8.776 \times 10^{-03}\) |
| 3.95 | \(5.287 \times 10^{-03}\) |
| 4.23 | \(1.160 \times 10^{-02}\) |
| 4.29 | \(1.032 \times 10^{-02}\) |
| 5.27 | \(1.596 \times 10^{-01}\) |
| 6.53 | \(1.812 \times 10^{-02}\) |
| 6.59 | \(1.911 \times 10^{-02}\) |
| 6.77 | \(1.162 \times 10^{-02}\) |
| 6.85 | \(1.420 \times 10^{-02}\) |
| 6.93 | \(1.087 \times 10^{-02}\) |
| 6.99 | \(1.132 \times 10^{-02}\) |
| 7.07 | \(8.888 \times 10^{-03}\) |
| 7.11 | \(9.288 \times 10^{-03}\) |
| 7.19 | \(6.271 \times 10^{-03}\) |
| 7.27 | \(7.121 \times 10^{-03}\) |
| 7.33 | \(5.907 \times 10^{-03}\) |
| 7.37 | \(6.073 \times 10^{-03}\) |
| 7.43 | \(5.173 \times 10^{-03}\) |
| 7.49 | \(5.667 \times 10^{-03}\) |
| 7.65 | \(4.194 \times 10^{-03}\) |
| 7.71 | \(4.486 \times 10^{-03}\) |
| 7.78 | \(3.587 \times 10^{-03}\) |
| 7.84 | \(4.391 \times 10^{-03}\) |
| 7.92 | \(3.460 \times 10^{-03}\) |
| 7.96 | \(3.863 \times 10^{-03}\) |
| 8.28 | \(1.489 \times 10^{-03}\) |
| 8.34 | \(1.558 \times 10^{-03}\) |
| 8.56 | \(9.407 \times 10^{-04}\) |
| 8.62 | \(1.592 \times 10^{-03}\) |
| 8.70 | \(1.087 \times 10^{-03}\) |
| 8.78 | \(1.484 \times 10^{-03}\) |
| 8.82 | \(1.316 \times 10^{-03}\) |
| 8.96 | \(1.617 \times 10^{-03}\) |
| 9.08 | \(5.483 \times 10^{-04}\) |
| 9.28 | \(1.688 \times 10^{-03}\) |
| 9.42 | \(9.562 \times 10^{-04}\) |
| 9.52 | \(1.658 \times 10^{-03}\) |
| 9.68 | \(5.887 \times 10^{-04}\) |
| 9.76 | \(1.008 \times 10^{-03}\) |
| 9.82 | \(7.560 \times 10^{-04}\) |
| 9.94 | \(1.303 \times 10^{-03}\) |
roGFP2 and Cu(I)
| Distance (Å) | Density |
|---|---|
| 1.24 | \(2.503 \times 10^{-11}\) |
| 1.80 | \(1.381 \times 10^{+00}\) |
| 3.10 | \(9.027 \times 10^{-03}\) |
| 4.67 | \(1.526 \times 10^{-01}\) |
| 6.07 | \(3.128 \times 10^{-02}\) |
| 6.15 | \(3.150 \times 10^{-02}\) |
| 6.27 | \(2.900 \times 10^{-02}\) |
| 6.35 | \(3.083 \times 10^{-02}\) |
| 6.49 | \(2.918 \times 10^{-02}\) |
| 6.59 | \(3.020 \times 10^{-02}\) |
| 7.11 | \(1.694 \times 10^{-02}\) |
| 7.19 | \(1.748 \times 10^{-02}\) |
| 7.31 | \(1.668 \times 10^{-02}\) |
| 7.67 | \(2.695 \times 10^{-02}\) |
| 7.80 | \(2.579 \times 10^{-02}\) |
| 7.92 | \(2.859 \times 10^{-02}\) |
| 8.52 | \(1.554 \times 10^{-02}\) |
| 8.66 | \(1.706 \times 10^{-02}\) |
| 8.76 | \(1.646 \times 10^{-02}\) |
| 8.92 | \(1.948 \times 10^{-02}\) |
| 8.98 | \(1.880 \times 10^{-02}\) |
| 9.10 | \(2.090 \times 10^{-02}\) |
| 9.18 | \(2.030 \times 10^{-02}\) |
| 9.26 | \(2.067 \times 10^{-02}\) |
| 9.48 | \(1.712 \times 10^{-02}\) |
| 9.54 | \(1.785 \times 10^{-02}\) |
| 9.64 | \(1.603 \times 10^{-02}\) |
| 9.70 | \(1.614 \times 10^{-02}\) |
Potential of mean force¶
Quantitative¶
Reduced roGFP2
| Distance (Å) | PMF [kcal/mol] |
|---|---|
| 1.82 | -0.935 |
| 2.92 | 2.243 |
| 3.14 | 2.310 |
| 3.24 | 2.169 |
| 3.31 | 2.214 |
| 5.11 | -0.000 |
| 6.35 | 1.627 |
| 6.43 | 1.609 |
| 6.61 | 1.717 |
| 7.05 | 1.431 |
| 7.13 | 1.493 |
| 7.19 | 1.458 |
| 7.23 | 1.464 |
| 7.37 | 1.422 |
| 7.90 | 1.785 |
| 7.96 | 1.744 |
| 8.32 | 2.201 |
| 8.38 | 2.186 |
| 8.82 | 2.810 |
| 8.88 | 2.782 |
| 8.96 | 2.892 |
| 9.06 | 2.775 |
| 9.14 | 2.893 |
| 9.20 | 2.800 |
| 9.30 | 3.063 |
| 9.44 | 2.898 |
| 9.70 | 3.537 |
| 9.78 | 3.233 |
| 9.96 | 3.990 |
Oxidized roGFP2
| Distance (Å) | PMF [kcal/mol] |
|---|---|
| 1.86 | -1.155 |
| 3.33 | 2.135 |
| 3.47 | 1.974 |
| 3.53 | 2.062 |
| 3.67 | 1.870 |
| 3.71 | 1.908 |
| 3.85 | 1.676 |
| 3.95 | 1.978 |
| 4.23 | 1.509 |
| 4.29 | 1.579 |
| 5.27 | -0.054 |
| 6.53 | 1.243 |
| 6.59 | 1.212 |
| 6.77 | 1.508 |
| 6.85 | 1.389 |
| 6.93 | 1.548 |
| 6.99 | 1.524 |
| 7.07 | 1.668 |
| 7.11 | 1.642 |
| 7.19 | 1.876 |
| 7.27 | 1.800 |
| 7.33 | 1.912 |
| 7.37 | 1.895 |
| 7.43 | 1.991 |
| 7.49 | 1.936 |
| 7.65 | 2.116 |
| 7.71 | 2.076 |
| 7.78 | 2.209 |
| 7.84 | 2.088 |
| 7.92 | 2.231 |
| 7.96 | 2.165 |
| 8.28 | 2.733 |
| 8.34 | 2.706 |
| 8.56 | 3.007 |
| 8.62 | 2.693 |
| 8.70 | 2.921 |
| 8.78 | 2.735 |
| 8.82 | 2.807 |
| 8.96 | 2.684 |
| 9.08 | 3.329 |
| 9.28 | 2.658 |
| 9.42 | 2.997 |
| 9.52 | 2.669 |
| 9.68 | 3.286 |
| 9.76 | 2.966 |
| 9.82 | 3.137 |
| 9.94 | 2.813 |
roGFP2 and Cu(I)
| Distance (Å) | PMF [kcal/mol] |
|---|---|
| 1.80 | -1.478 |
| 3.10 | 1.521 |
| 4.67 | -0.165 |
| 6.07 | 0.780 |
| 6.15 | 0.776 |
| 6.27 | 0.825 |
| 6.35 | 0.788 |
| 6.49 | 0.821 |
| 6.59 | 0.801 |
| 7.11 | 1.145 |
| 7.19 | 1.127 |
| 7.31 | 1.154 |
| 7.67 | 0.869 |
| 7.80 | 0.895 |
| 7.92 | 0.833 |
| 8.52 | 1.197 |
| 8.66 | 1.141 |
| 8.76 | 1.162 |
| 8.92 | 1.062 |
| 8.98 | 1.083 |
| 9.10 | 1.020 |
| 9.18 | 1.037 |
| 9.26 | 1.027 |
| 9.48 | 1.139 |
| 9.54 | 1.114 |
| 9.64 | 1.178 |
| 9.70 | 1.174 |