Dataset

Raw data supporting the manuscript “Computational reflections on mirror life: can chiral selectivity be a built-in containment mechanism for mirror organisms?” README.md # Mirror MBP–maltose: computational data Data supporting the manuscript *“Computational reflections on mirror life: can chiral selectivity be a built-in containment mechanism for mirror organisms?”*, submitted to Heliyon. ## Software and dependencies - **GOLD 2022:** molecular docking. - **GROMACS 2022.6:** molecular dynamics simulations using CHARMM36 (`charmm36_ljpme-jul2022.ff`). - **SwissParam:** ligand parametrization. - **gmx_MMPBSA 1.6.4 / AmberTools:** binding free-energy calculations. - **Python:** mirror-image structure generation. - **PyMOL 2.5.0 / Open Babel:** structural preparation and editing. Simulation parameters and settings are provided in the corresponding input files. ## Repository structure ```text 01_Structures/ Starting protein–ligand structures 02_GOLD_Docking/ Docking inputs, scores, logs, and poses 03_GROMACS_MD/ MD inputs, topologies, logs, and trajectories 04_MMPBSA/ MM/PBSA inputs, topologies, and results mirror.py Script for mirror-image transformation README.md Repository documentation ``` Five protein–ligand systems were investigated using two independent 250-ns MD replicas per system. The D-MBP–L-maltose complex was obtained by mirror transformation without separate docking. MM/PBSA was not performed for the unstable D-MBP–D-maltose complex. ## Commands and expected outputs Representative commands, to be executed within the corresponding directories: ```bash gold_auto gold.conf gmx mdrun -s md_0.tpr -deffnm md_0 ``` GOLD generates ranked docking poses, scores, and logs. GROMACS generates trajectories (`.xtc`), final coordinates (`.gro`), energies (`.edr`), and simulation logs (`.log`). MM/PBSA calculations use the parameters provided in `mmpbsa.in`, with outputs including `FINAL_RESULTS_MMPBSA.dat` and per-frame energy results. The command used to run each MM/PBSA calculation can be found inside the `gmx_MMPBSA.log` files. The `mirror.py` script generates mirror-image molecular structures. **Trajectory note:** Cleaned MD trajectories were subsampled by retaining one frame every ten saved frames to reduce repository size. Following the hierarchy of the directories found in the ZIP archive. MBP_Heliyon_Repository└── MirrorMBP_Heliyon_data ├── 01_Structures │ ├── S01_Native_MBP_D_maltose │ │ ├── Replica_01 │ │ └── Replica_02 │ ├── S02_Mirror_D_MBP_L_maltose │ │ ├── Replica_01 │ │ └── Replica_02 │ ├── S03_Mirror_D_MBP_D_maltose │ │ ├── Replica_01 │ │ └── Replica_02 │ ├── S04_D_Trp88_L_Trp_D_maltose │ │ ├── Replica_01 │ │ └── Replica_02 │ └── S05_D_Ala89_D_Ser_D_maltose │ ├── Replica_01 │ └── Replica_02 ├── 02_GOLD_Docking │ ├── S01_Native_MBP_D_maltose │ │ └── Run │ │ └── maltose_m1 │ ├── S03_Mirror_D_MBP_D_maltose │ │ └── Run │ │ └── maltose_m1 │ ├── S04_D_Trp88_L_Trp_D_maltose │ │ └── Run │ │ └── maltose_m1 │ └── S05_D_Ala89_D_Ser_D_maltose │ └── Run │ └── maltose_m1 ├── 03_GROMACS_MD │ ├── charmm36_ljpme-jul2022.ff │ ├── S01_Native_MBP_D_maltose │ │ ├── Replica_01 │ │ │ ├── 01_Parameters │ │ │ ├── 02_Coordinates │ │ │ ├── 03_Run_inputs │ │ │ ├── 04_Logs │ │ │ └── 05_Trajectories │ │ └── Replica_02 │ │ ├── 01_Parameters │ │ ├── 02_Coordinates │ │ ├── 03_Run_inputs │ │ ├── 04_Logs │ │ └── 05_Trajectories │ ├── S02_Mirror_D_MBP_L_maltose │ │ ├── Replica_01 │ │ │ ├── 01_Parameters │ │ │ ├── 02_Coordinates │ │ │ ├── 03_Run_inputs │ │ │ ├── 04_Logs │ │ │ └── 05_Trajectories │ │ └── Replica_02 │ │ ├── 01_Parameters │ │ ├── 02_Coordinates │ │ ├── 03_Run_inputs │ │ ├── 04_Logs │ │ └── 05_Trajectories │ ├── S03_Mirror_D_MBP_D_maltose │ │ ├── Replica_01 │ │ │ ├── 01_Parameters │ │ │ ├── 02_Coordinates │ │ │ ├── 03_Run_inputs │ │ │ ├── 04_Logs │ │ │ └── 05_Trajectories │ │ └── Replica_02 │ │ ├── 01_Parameters │ │ ├── 02_Coordinates │ │ ├── 03_Run_inputs │ │ ├── 04_Logs │ │ └── 05_Trajectories │ ├── S04_D_Trp88_L_Trp_D_maltose │ │ ├── Replica_01 │ │ │ ├── 01_Parameters │ │ │ ├── 02_Coordinates │ │ │ ├── 03_Run_inputs │ │ │ ├── 04_Logs │ │ │ └── 05_Trajectories │ │ └── Replica_02 │ │ ├── 01_Parameters │ │ ├── 02_Coordinates │ │ ├── 03_Run_inputs │ │ ├── 04_Logs │ │ └── 05_Trajectories │ └── S05_D_Ala89_D_Ser_D_maltose │ ├── Replica_01 │ │ ├── 01_Parameters │ │ ├── 02_Coordinates │ │ ├── 03_Run_inputs │ │ ├── 04_Logs │ │ └── 05_Trajectories │ └── Replica_02 │ ├── 01_Parameters │ ├── 02_Coordinates │ ├── 03_Run_inputs │ ├── 04_Logs │ └── 05_Trajectories └── 04_MMPBSA ├── S01_Native_MBP_D_maltose │ ├── Replica_01 │ └── Replica_02 ├── S02_Mirror_D_MBP_L_maltose │ ├── Replica_01 │ └── Replica_02 ├── S04_D_Trp88_L_Trp_D_maltose │ ├── Replica_01 │ └── Replica_02 └── S05_D_Ala89_D_Ser_D_maltose ├── Replica_01 └── Replica_02 110 directories