E003: H2O O - Cro66 OH¶
Water detection¶
The following table presents the probability of either a water molecule was (a) near or (hydrogen bonding) to the chromophore.
| System | H bond |
|---|---|
| Reduced | 0.560 |
| Oxidized | 0.601 |
| Cu(I) | 0.538 |
| Na+ | 0.404 |
Probability density function¶
Quantitative¶
Reduced roGFP2
| Distance (Å) | Density |
|---|---|
| 0.11 | \(3.934 \times 10^{-06}\) |
| 0.71 | \(3.528 \times 10^{-245}\) |
| 1.30 | \(1.084 \times 10^{-11}\) |
| 1.73 | \(1.521 \times 10^{+00}\) |
| 2.27 | \(8.669 \times 10^{-02}\) |
| 2.53 | \(2.012 \times 10^{-01}\) |
| 2.87 | \(7.741 \times 10^{-02}\) |
| 3.11 | \(1.250 \times 10^{-01}\) |
| 3.15 | \(1.210 \times 10^{-01}\) |
| 3.18 | \(1.228 \times 10^{-01}\) |
| 3.24 | \(1.171 \times 10^{-01}\) |
| 3.54 | \(2.501 \times 10^{-01}\) |
| 4.02 | \(5.208 \times 10^{-02}\) |
| 4.05 | \(5.261 \times 10^{-02}\) |
| 4.13 | \(5.102 \times 10^{-02}\) |
| 4.31 | \(7.662 \times 10^{-02}\) |
| 4.33 | \(7.637 \times 10^{-02}\) |
| 4.38 | \(7.987 \times 10^{-02}\) |
| 4.88 | \(1.980 \times 10^{-02}\) |
| 4.93 | \(2.190 \times 10^{-02}\) |
| 4.95 | \(2.168 \times 10^{-02}\) |
| 4.98 | \(2.206 \times 10^{-02}\) |
| 5.05 | \(1.958 \times 10^{-02}\) |
| 5.11 | \(2.185 \times 10^{-02}\) |
| 5.20 | \(1.827 \times 10^{-02}\) |
| 5.23 | \(1.889 \times 10^{-02}\) |
| 5.96 | \(8.430 \times 10^{-04}\) |
| 6.01 | \(9.955 \times 10^{-04}\) |
| 6.04 | \(9.763 \times 10^{-04}\) |
| 6.08 | \(1.242 \times 10^{-03}\) |
| 6.16 | \(6.613 \times 10^{-04}\) |
| 6.19 | \(7.239 \times 10^{-04}\) |
| 6.21 | \(6.813 \times 10^{-04}\) |
| 6.25 | \(8.198 \times 10^{-04}\) |
| 6.34 | \(2.815 \times 10^{-05}\) |
| 6.38 | \(1.179 \times 10^{-04}\) |
| 6.44 | \(1.143 \times 10^{-05}\) |
| 6.49 | \(1.247 \times 10^{-04}\) |
| 6.53 | \(3.234 \times 10^{-05}\) |
| 6.58 | \(1.249 \times 10^{-04}\) |
| 6.67 | \(2.974 \times 10^{-08}\) |
| 6.76 | \(1.234 \times 10^{-04}\) |
| 6.88 | \(3.663 \times 10^{-11}\) |
Oxidized roGFP2
| Distance (Å) | Density |
|---|---|
| 0.03 | \(4.148 \times 10^{-02}\) |
| 1.36 | \(1.324 \times 10^{-08}\) |
| 1.75 | \(1.721 \times 10^{+00}\) |
| 2.56 | \(2.096 \times 10^{-02}\) |
| 2.59 | \(2.429 \times 10^{-02}\) |
| 2.62 | \(1.181 \times 10^{-02}\) |
| 2.65 | \(1.847 \times 10^{-02}\) |
| 2.67 | \(1.721 \times 10^{-02}\) |
| 2.69 | \(1.860 \times 10^{-02}\) |
| 2.82 | \(1.133 \times 10^{-02}\) |
| 2.91 | \(2.159 \times 10^{-02}\) |
| 2.94 | \(1.580 \times 10^{-02}\) |
| 2.99 | \(2.360 \times 10^{-02}\) |
| 3.01 | \(2.175 \times 10^{-02}\) |
| 3.10 | \(2.862 \times 10^{-02}\) |
| 3.13 | \(2.485 \times 10^{-02}\) |
| 3.16 | \(2.759 \times 10^{-02}\) |
| 3.18 | \(2.282 \times 10^{-02}\) |
| 3.20 | \(2.592 \times 10^{-02}\) |
| 3.28 | \(1.725 \times 10^{-02}\) |
| 3.34 | \(1.931 \times 10^{-02}\) |
| 3.41 | \(1.332 \times 10^{-02}\) |
| 3.43 | \(1.367 \times 10^{-02}\) |
| 3.46 | \(1.013 \times 10^{-02}\) |
| 3.49 | \(1.336 \times 10^{-02}\) |
| 3.52 | \(9.466 \times 10^{-03}\) |
| 3.58 | \(9.592 \times 10^{-03}\) |
| 3.60 | \(1.225 \times 10^{-02}\) |
| 3.67 | \(9.868 \times 10^{-03}\) |
| 3.71 | \(7.400 \times 10^{-03}\) |
| 3.73 | \(8.684 \times 10^{-03}\) |
| 3.82 | \(5.649 \times 10^{-03}\) |
| 3.85 | \(6.139 \times 10^{-03}\) |
| 3.88 | \(3.801 \times 10^{-03}\) |
| 3.91 | \(6.530 \times 10^{-03}\) |
| 3.94 | \(3.339 \times 10^{-03}\) |
| 3.99 | \(3.440 \times 10^{-03}\) |
| 4.01 | \(5.192 \times 10^{-03}\) |
| 4.04 | \(3.910 \times 10^{-03}\) |
| 4.06 | \(4.685 \times 10^{-03}\) |
| 4.10 | \(3.020 \times 10^{-03}\) |
| 4.12 | \(4.014 \times 10^{-03}\) |
| 4.15 | \(2.760 \times 10^{-03}\) |
| 4.18 | \(5.568 \times 10^{-03}\) |
| 4.27 | \(2.823 \times 10^{-03}\) |
| 4.30 | \(4.368 \times 10^{-03}\) |
| 4.33 | \(3.857 \times 10^{-03}\) |
| 4.36 | \(5.771 \times 10^{-03}\) |
| 4.38 | \(4.324 \times 10^{-03}\) |
| 4.41 | \(6.006 \times 10^{-03}\) |
| 4.44 | \(4.305 \times 10^{-03}\) |
| 4.50 | \(6.980 \times 10^{-03}\) |
| 4.54 | \(3.547 \times 10^{-03}\) |
| 4.59 | \(6.525 \times 10^{-03}\) |
| 4.62 | \(2.821 \times 10^{-03}\) |
| 4.65 | \(5.687 \times 10^{-03}\) |
| 4.68 | \(5.273 \times 10^{-03}\) |
| 4.70 | \(5.483 \times 10^{-03}\) |
| 4.72 | \(5.411 \times 10^{-03}\) |
| 4.75 | \(6.746 \times 10^{-03}\) |
| 4.78 | \(3.683 \times 10^{-03}\) |
| 4.81 | \(5.190 \times 10^{-03}\) |
| 4.85 | \(3.556 \times 10^{-03}\) |
| 4.87 | \(4.162 \times 10^{-03}\) |
| 4.90 | \(3.288 \times 10^{-03}\) |
| 4.92 | \(3.604 \times 10^{-03}\) |
| 4.95 | \(2.200 \times 10^{-03}\) |
| 5.06 | \(3.407 \times 10^{-03}\) |
| 5.08 | \(2.666 \times 10^{-03}\) |
| 5.10 | \(2.897 \times 10^{-03}\) |
| 5.13 | \(1.744 \times 10^{-03}\) |
| 5.16 | \(2.603 \times 10^{-03}\) |
| 5.18 | \(1.605 \times 10^{-03}\) |
| 5.21 | \(2.063 \times 10^{-03}\) |
| 5.26 | \(5.971 \times 10^{-04}\) |
| 5.29 | \(8.855 \times 10^{-04}\) |
| 5.31 | \(8.098 \times 10^{-04}\) |
| 5.36 | \(1.276 \times 10^{-03}\) |
| 5.43 | \(3.117 \times 10^{-04}\) |
| 5.47 | \(9.359 \times 10^{-04}\) |
| 5.53 | \(6.653 \times 10^{-05}\) |
| 5.57 | \(8.493 \times 10^{-04}\) |
| 5.60 | \(2.222 \times 10^{-04}\) |
| 5.62 | \(3.656 \times 10^{-04}\) |
| 5.66 | \(3.689 \times 10^{-06}\) |
| 5.69 | \(6.603 \times 10^{-04}\) |
| 5.73 | \(5.300 \times 10^{-05}\) |
| 5.76 | \(1.282 \times 10^{-03}\) |
| 5.82 | \(2.763 \times 10^{-07}\) |
| 5.88 | \(8.114 \times 10^{-04}\) |
| 5.91 | \(1.607 \times 10^{-05}\) |
| 5.96 | \(3.130 \times 10^{-19}\) |
| 6.01 | \(6.861 \times 10^{-08}\) |
| 6.04 | \(2.516 \times 10^{-04}\) |
| 6.07 | \(5.497 \times 10^{-06}\) |
| 6.14 | \(3.516 \times 10^{-30}\) |
| 6.21 | \(4.474 \times 10^{-08}\) |
| 6.25 | \(4.745 \times 10^{-04}\) |
| 6.29 | \(3.763 \times 10^{-07}\) |
| 7.10 | \(2.125 \times 10^{-07}\) |
| 7.13 | \(2.893 \times 10^{-04}\) |
| 7.16 | \(2.347 \times 10^{-06}\) |
roGFP2 and Cu(I)
| Distance (Å) | Density |
|---|---|
| 0.15 | \(2.581 \times 10^{-08}\) |
| 0.69 | \(1.175 \times 10^{-168}\) |
| 1.21 | \(3.316 \times 10^{-14}\) |
| 1.73 | \(1.494 \times 10^{+00}\) |
| 2.53 | \(4.433 \times 10^{-02}\) |
| 3.13 | \(2.391 \times 10^{-01}\) |
| 3.57 | \(9.003 \times 10^{-02}\) |
| 3.60 | \(9.014 \times 10^{-02}\) |
| 3.69 | \(7.925 \times 10^{-02}\) |
| 3.75 | \(8.158 \times 10^{-02}\) |
| 3.92 | \(6.893 \times 10^{-02}\) |
| 3.96 | \(6.949 \times 10^{-02}\) |
| 4.02 | \(6.581 \times 10^{-02}\) |
| 4.07 | \(6.827 \times 10^{-02}\) |
| 4.12 | \(6.589 \times 10^{-02}\) |
| 4.21 | \(7.558 \times 10^{-02}\) |
| 4.25 | \(7.348 \times 10^{-02}\) |
| 4.35 | \(7.834 \times 10^{-02}\) |
| 4.39 | \(7.739 \times 10^{-02}\) |
| 4.42 | \(7.770 \times 10^{-02}\) |
| 4.45 | \(7.722 \times 10^{-02}\) |
| 4.53 | \(8.196 \times 10^{-02}\) |
| 4.56 | \(8.157 \times 10^{-02}\) |
| 4.62 | \(8.566 \times 10^{-02}\) |
| 4.80 | \(7.394 \times 10^{-02}\) |
| 4.84 | \(7.512 \times 10^{-02}\) |
| 5.27 | \(4.658 \times 10^{-02}\) |
| 5.31 | \(4.950 \times 10^{-02}\) |
| 5.50 | \(3.781 \times 10^{-02}\) |
| 5.54 | \(3.873 \times 10^{-02}\) |
| 5.60 | \(3.687 \times 10^{-02}\) |
| 5.65 | \(3.987 \times 10^{-02}\) |
| 5.73 | \(3.602 \times 10^{-02}\) |
| 5.78 | \(3.748 \times 10^{-02}\) |
| 5.84 | \(3.336 \times 10^{-02}\) |
| 5.89 | \(3.518 \times 10^{-02}\) |
| 5.99 | \(2.851 \times 10^{-02}\) |
| 6.14 | \(2.362 \times 10^{-02}\) |
| 6.23 | \(1.935 \times 10^{-02}\) |
| 6.27 | \(1.988 \times 10^{-02}\) |
| 6.43 | \(1.431 \times 10^{-02}\) |
| 6.46 | \(1.442 \times 10^{-02}\) |
| 6.57 | \(9.219 \times 10^{-03}\) |
| 6.61 | \(1.031 \times 10^{-02}\) |
| 6.87 | \(5.185 \times 10^{-03}\) |
| 6.95 | \(6.284 \times 10^{-03}\) |
| 7.02 | \(4.811 \times 10^{-03}\) |
| 7.08 | \(4.941 \times 10^{-03}\) |
| 7.24 | \(1.993 \times 10^{-03}\) |
| 7.29 | \(2.272 \times 10^{-03}\) |
| 7.38 | \(1.075 \times 10^{-03}\) |
| 7.43 | \(1.618 \times 10^{-03}\) |
| 7.49 | \(1.148 \times 10^{-03}\) |
| 7.54 | \(1.264 \times 10^{-03}\) |
| 7.65 | \(5.581 \times 10^{-04}\) |
| 7.70 | \(7.944 \times 10^{-04}\) |
| 7.75 | \(4.506 \times 10^{-04}\) |
| 7.80 | \(5.470 \times 10^{-04}\) |
| 7.86 | \(3.215 \times 10^{-04}\) |
| 7.90 | \(4.106 \times 10^{-04}\) |
| 7.96 | \(8.748 \times 10^{-05}\) |
| 8.02 | \(2.381 \times 10^{-04}\) |
| 8.08 | \(7.335 \times 10^{-05}\) |
| 8.15 | \(2.795 \times 10^{-04}\) |
| 8.22 | \(2.273 \times 10^{-05}\) |
| 8.27 | \(1.072 \times 10^{-04}\) |
| 8.30 | \(7.110 \times 10^{-05}\) |
| 8.40 | \(2.894 \times 10^{-04}\) |
| 8.62 | \(4.436 \times 10^{-13}\) |
Potential of mean force¶
Quantitative¶
Reduced roGFP2
| Distance (Å) | PMF [kcal/mol] |
|---|---|
| 0.71 | 334.736 |
| 1.73 | -1.077 |
| 2.27 | 0.631 |
| 2.53 | 0.129 |
| 2.87 | 0.698 |
| 3.11 | 0.413 |
| 3.15 | 0.432 |
| 3.18 | 0.423 |
| 3.24 | 0.452 |
| 3.54 | -0.001 |
| 4.02 | 0.935 |
| 4.05 | 0.929 |
| 4.13 | 0.947 |
| 4.31 | 0.705 |
| 4.33 | 0.707 |
| 4.38 | 0.680 |
| 4.88 | 1.511 |
| 4.93 | 1.451 |
| 4.95 | 1.457 |
| 4.98 | 1.447 |
| 5.05 | 1.518 |
| 5.11 | 1.453 |
| 5.20 | 1.559 |
| 5.23 | 1.539 |
| 5.96 | 3.393 |
| 6.01 | 3.294 |
| 6.04 | 3.306 |
| 6.08 | 3.162 |
| 6.16 | 3.538 |
| 6.19 | 3.484 |
| 6.21 | 3.520 |
| 6.25 | 3.410 |
| 6.34 | 5.420 |
| 6.38 | 4.566 |
| 6.44 | 5.957 |
| 6.49 | 4.533 |
| 6.53 | 5.337 |
| 6.58 | 4.531 |
| 6.67 | 9.505 |
| 6.76 | 4.538 |
| 7.56 | 427.100 |
| 7.58 | 67.809 |
| 9.99 | 67.809 |
Oxidized roGFP2
| Distance (Å) | PMF [kcal/mol] |
|---|---|
| 0.32 | 403.579 |
| 0.34 | 65.876 |
| 1.05 | 65.876 |
| 1.07 | 432.789 |
| 1.75 | -3.084 |
| 2.56 | -0.456 |
| 2.59 | -0.544 |
| 2.62 | -0.113 |
| 2.65 | -0.380 |
| 2.67 | -0.338 |
| 2.69 | -0.384 |
| 2.82 | -0.089 |
| 2.91 | -0.473 |
| 2.94 | -0.287 |
| 2.99 | -0.526 |
| 3.01 | -0.478 |
| 3.10 | -0.641 |
| 3.13 | -0.557 |
| 3.16 | -0.620 |
| 3.18 | -0.506 |
| 3.20 | -0.582 |
| 3.28 | -0.339 |
| 3.34 | -0.407 |
| 3.41 | -0.185 |
| 3.43 | -0.201 |
| 3.46 | -0.022 |
| 3.49 | -0.187 |
| 3.52 | 0.018 |
| 3.58 | 0.010 |
| 3.60 | -0.135 |
| 3.67 | -0.007 |
| 3.71 | 0.165 |
| 3.73 | 0.070 |
| 3.83 | 0.340 |
| 3.85 | 0.276 |
| 3.88 | 0.562 |
| 3.91 | 0.240 |
| 3.94 | 0.640 |
| 3.99 | 0.622 |
| 4.01 | 0.376 |
| 4.04 | 0.545 |
| 4.06 | 0.438 |
| 4.10 | 0.699 |
| 4.12 | 0.530 |
| 4.15 | 0.753 |
| 4.18 | 0.335 |
| 4.27 | 0.740 |
| 4.30 | 0.479 |
| 4.33 | 0.553 |
| 4.36 | 0.313 |
| 4.38 | 0.485 |
| 4.41 | 0.289 |
| 4.44 | 0.488 |
| 4.50 | 0.200 |
| 4.54 | 0.603 |
| 4.59 | 0.240 |
| 4.62 | 0.740 |
| 4.65 | 0.322 |
| 4.68 | 0.367 |
| 4.70 | 0.344 |
| 4.72 | 0.352 |
| 4.75 | 0.220 |
| 4.78 | 0.581 |
| 4.81 | 0.377 |
| 4.85 | 0.602 |
| 4.87 | 0.508 |
| 4.90 | 0.649 |
| 4.92 | 0.594 |
| 4.95 | 0.888 |
| 5.06 | 0.627 |
| 5.08 | 0.774 |
| 5.10 | 0.724 |
| 5.13 | 1.027 |
| 5.16 | 0.788 |
| 5.18 | 1.076 |
| 5.21 | 0.927 |
| 5.26 | 1.666 |
| 5.29 | 1.431 |
| 5.31 | 1.484 |
| 5.36 | 1.213 |
| 5.43 | 2.053 |
| 5.47 | 1.398 |
| 5.53 | 2.974 |
| 5.57 | 1.456 |
| 5.60 | 2.255 |
| 5.62 | 1.958 |
| 5.65 | 3.314 |
| 5.69 | 1.606 |
| 5.73 | 3.109 |
| 5.76 | 1.210 |
| 5.82 | 6.243 |
| 5.88 | 1.483 |
| 5.96 | 22.641 |
| 6.04 | 2.181 |
| 6.14 | 37.672 |
| 6.25 | 1.803 |
| 6.58 | 414.380 |
| 6.60 | 65.876 |
| 6.79 | 65.876 |
| 6.81 | 417.763 |
| 7.13 | 2.098 |
| 7.45 | 402.488 |
| 7.47 | 65.876 |
roGFP2 and Cu(I)
| Distance (Å) | PMF [kcal/mol] |
|---|---|
| 0.69 | 229.101 |
| 1.73 | -1.658 |
| 2.53 | 0.440 |
| 3.13 | -0.565 |
| 3.57 | 0.017 |
| 3.60 | 0.016 |
| 3.69 | 0.093 |
| 3.75 | 0.076 |
| 3.92 | 0.176 |
| 3.96 | 0.171 |
| 4.02 | 0.204 |
| 4.07 | 0.182 |
| 4.12 | 0.203 |
| 4.21 | 0.121 |
| 4.25 | 0.138 |
| 4.35 | 0.100 |
| 4.39 | 0.107 |
| 4.42 | 0.105 |
| 4.45 | 0.109 |
| 4.53 | 0.073 |
| 4.56 | 0.076 |
| 4.62 | 0.047 |
| 4.80 | 0.135 |
| 4.84 | 0.125 |
| 5.27 | 0.410 |
| 5.31 | 0.374 |
| 5.50 | 0.534 |
| 5.54 | 0.520 |
| 5.60 | 0.549 |
| 5.65 | 0.503 |
| 5.73 | 0.563 |
| 5.78 | 0.540 |
| 5.84 | 0.609 |
| 5.89 | 0.577 |
| 5.99 | 0.703 |
| 6.14 | 0.815 |
| 6.23 | 0.934 |
| 6.27 | 0.918 |
| 6.43 | 1.113 |
| 6.46 | 1.109 |
| 6.57 | 1.376 |
| 6.61 | 1.309 |
| 6.87 | 1.719 |
| 6.95 | 1.604 |
| 7.02 | 1.763 |
| 7.08 | 1.747 |
| 7.24 | 2.289 |
| 7.29 | 2.211 |
| 7.38 | 2.657 |
| 7.43 | 2.413 |
| 7.49 | 2.618 |
| 7.54 | 2.560 |
| 7.65 | 3.048 |
| 7.70 | 2.837 |
| 7.75 | 3.175 |
| 7.80 | 3.060 |
| 7.86 | 3.377 |
| 7.90 | 3.231 |
| 7.96 | 4.152 |
| 8.02 | 3.556 |
| 8.08 | 4.257 |
| 8.15 | 3.460 |
| 8.22 | 4.956 |
| 8.27 | 4.031 |
| 8.30 | 4.276 |
| 8.40 | 3.439 |
| 9.40 | 427.399 |
| 9.42 | 67.217 |