This dataset contains 3D structures, MD trajectories and powder X-ray diffractograms (simulated and experimental) of tetrameric carboxynaphthalene disulfide. The MD simulations were performed in water with periodic boundary conditions. Either AMBER or GROMACS packages were used. For detailed description of the simulations see the linked paper (the link will appear upon acceptance).  PDB files are snapshots from the MD simulations; they can be viewed using any 3D structure viewer (e.g. Avogadro). The trajectories (*.xtc - GROMACS, *.mdcrd - AMBER/NetCDF) can be visualized using e.g. VMD.Partial charges for the naphthalene building blocks are provided within *.mol2 files (N-0 for the neutral and N-1 for the deprotonated subunit). The parameter/topology files have .top (GROMACS) and .prmtop (AMBER) extensions. Files labeled "sheet1" contain results of simulations of 16 repeats of tetramer IV showed in Figure 4 and S13 of the paper. The suffix "-exp_box" refers to structures which were constrained to the box determined experimentally ("min" - after energy minimization, "equil" - after equilibration).Files labeled "sheet2" contain results of simulations of 12 repeats of tetramer IV showed in Figure S14 of the paper. Files labeled "sheet3" contain results of simulations of 16 repeats of tetramer IV showed in Figure S15 of the paper. The assembly was unstable, the initial structure started dissociating from the very beginning of the simulation. The trajectory is in NetCDF format.Files labeled "tetramerIV-2" contain results of simulations of isolated, partially deprotonated tetramer IV in water (solvent was removed from the trajectory).Link to the article will be added upon its acceptance.

This dataset contains 3D structures, MD trajectories and powder X-ray diffractograms (simulated and experimental) of tetrameric carboxynaphthalene disulfide. The MD simulations were performed in water with periodic boundary conditions. Either AMBER or GROMACS packages were used. For detailed description of the simulations see the linked paper (the link will appear upon acceptance).  PDB files are snapshots from the MD simulations; they can be viewed using any 3D structure viewer (e.g. Avogadro). The trajectories (*.xtc - GROMACS, *.mdcrd - AMBER/NetCDF) can be visualized using e.g. VMD.Partial charges for the naphthalene building blocks are provided within *.mol2 files (N-0 for the neutral and N-1 for the deprotonated subunit). The parameter/topology files have .top (GROMACS) and .prmtop (AMBER) extensions. Files labeled "sheet1" contain results of simulations of 16 repeats of tetramer IV showed in Figure 4 and S13 of the paper. The suffix "-exp_box" refers to structures which were constrained to the box determined experimentally ("min" - after energy minimization, "equil" - after equilibration).Files labeled "sheet2" contain results of simulations of 12 repeats of tetramer IV showed in Figure S14 of the paper. Files labeled "sheet3" contain results of simulations of 16 repeats of tetramer IV showed in Figure S15 of the paper. The assembly was unstable, the initial structure started dissociating from the very beginning of the simulation. The trajectory is in NetCDF format.Files labeled "tetramerIV-2" contain results of simulations of isolated, partially deprotonated tetramer IV in water (solvent was removed from the trajectory).Link to the article will be added upon its acceptance.

Raw results of the molecular dynamics simulations performed for the paper:Catenanes from Catenanes: Quantitative Assessment of Cooperativity in Dynamic Combinatorial Catenation, J. Li, P. Nowak, H. Fanlo-Virgos and S. Otto, Chemical Science, 2014, DOI: 10.1039/C4SC01998AThis fileset contains results of MD simulations on the self-assembled tetrameric azobenzene macrocycle (4AB), beta-cyclodextrin (BCD), gamma-cyclodextrin (GCD) and [2]- and [3]catenanes formed by them. In case of [3]catenanes there are two possible orientations of the cyclodextrins - parallel and antiparallel. They are denoted by "p" and "ap" suffixes. Example: filenames containing "4AB-2BCDap" correspond to the [3]catenane composed of a single tetrameric azobenzene macrocycle and two beta-cyclodextrins oriented in an antiparallel fashion.Files with the "-structure_" prefix are snaphots from MD simulations at the time indicated in the filename.Files with the ".traj" extension are 40 ns trajectory files (without water box) which can be loaded into a trajectory visualisation program (e.g. VMD, http://www.ks.uiuc.edu/Research/vmd/). The corresponding topology/parameter files have the ".prmtop" extension.Files with the "distCD_" prefix contain the distance between the center of a cyclodextrin (CD1 and CD2 for the first and the second, respectively) and the 4AB macrocycle in the function of time.Files with the "distSS_" prefix contain the distance between the centers of the opposite disulfide bonds in the 4AB macrocycle in the function of time.Files with the "sasa_" prefix contain the solvent accessible surface areas in the function of time. The surface was partitioned between different molecules (4AB, CD1, and CD2 suffixes) and with respect to the hydrophobicity/hydrophilicity (denoted by the suffix). Files with the "hbond_" prefix contain the number of hydrogen bonds between the 4AB macrocycle and cyclodextrins in the function of time.File "AB2.mol2" is the azobenzene fragment used to construct the 4AB macrocycle with the leap program. It was generated using restrained electrostatic fit (RESP) with RED.III.5 program.

Raw results of the molecular dynamics simulations performed for the paper:An Allosteric Receptor by Simultaneous Casting and Molding in a Dynamic Combinatorial Library, J. Li, P. Nowak and S. Otto.This fileset contains results of MD simulations on the macrocyclic isomer III (isoIII), gamma-cyclodextrin (CD), quaternary ammonium template (2) and complexes formed by them (CD-isoIII, isoIII-2, CD-isoIII-2). Files with the "structure_" prefix are snaphots from MD simulations at the time indicated in the filename.Files with the ".traj" extension are Amber trajectory files (without water box) which can be loaded into a trajectory visualisation program (e.g. VMD, http://www.ks.uiuc.edu/Research/vmd/). The corresponding topology/parameter files have the ".prmtop" extension. The structures were saved every 10000 steps and the timestep was 2 fs. Therefore, in order to convert the frame number into simulation time, the former has to be multiplied by 1/50 ns. Files with the "distGAX-Y_" prefix contain the distances between the mass centers of glucopyranose residues X and Y of either free or complexed gamma-cyclodextrin as a function of simulation time.Files with the "rmsfit" extension contain RMSD errors as a function of simulation time.File "1BB.mol2" is the naphtalene fragment (from building block 1) used to construct the isomer III macrocycle with the leap program. It was generated using restrained electrostatic fit (RESP) with RED.III.5 program. File "2TM" corresponds to the template 2 and was obtained the same way.

Raw results of the molecular dynamics simulations performed for the paper:Catenanes from Catenanes: Quantitative Assessment of Cooperativity in Dynamic Combinatorial Catenation, J. Li, P. Nowak, H. Fanlo-Virgos and S. Otto, Chemical Science, 2014, DOI: 10.1039/C4SC01998AThis fileset contains results of MD simulations on the self-assembled tetrameric azobenzene macrocycle (4AB), beta-cyclodextrin (BCD), gamma-cyclodextrin (GCD) and [2]- and [3]catenanes formed by them. In case of [3]catenanes there are two possible orientations of the cyclodextrins - parallel and antiparallel. They are denoted by "p" and "ap" suffixes. Example: filenames containing "4AB-2BCDap" correspond to the [3]catenane composed of a single tetrameric azobenzene macrocycle and two beta-cyclodextrins oriented in an antiparallel fashion.Files with the "-structure_" prefix are snaphots from MD simulations at the time indicated in the filename.Files with the ".traj" extension are 40 ns trajectory files (without water box) which can be loaded into a trajectory visualisation program (e.g. VMD, http://www.ks.uiuc.edu/Research/vmd/). The corresponding topology/parameter files have the ".prmtop" extension.Files with the "distCD_" prefix contain the distance between the center of a cyclodextrin (CD1 and CD2 for the first and the second, respectively) and the 4AB macrocycle in the function of time.Files with the "distSS_" prefix contain the distance between the centers of the opposite disulfide bonds in the 4AB macrocycle in the function of time.Files with the "sasa_" prefix contain the solvent accessible surface areas in the function of time. The surface was partitioned between different molecules (4AB, CD1, and CD2 suffixes) and with respect to the hydrophobicity/hydrophilicity (denoted by the suffix). Files with the "hbond_" prefix contain the number of hydrogen bonds between the 4AB macrocycle and cyclodextrins in the function of time.File "AB2.mol2" is the azobenzene fragment used to construct the 4AB macrocycle with the leap program. It was generated using restrained electrostatic fit (RESP) with RED.III.5 program.

Raw results of the molecular dynamics simulations performed for the paper:An Allosteric Receptor by Simultaneous Casting and Molding in a Dynamic Combinatorial Library, J. Li, P. Nowak and S. Otto.This fileset contains results of MD simulations on the macrocyclic isomer III (isoIII), gamma-cyclodextrin (CD), quaternary ammonium template (2) and complexes formed by them (CD-isoIII, isoIII-2, CD-isoIII-2). Files with the "structure_" prefix are snaphots from MD simulations at the time indicated in the filename.Files with the ".traj" extension are Amber trajectory files (without water box) which can be loaded into a trajectory visualisation program (e.g. VMD, http://www.ks.uiuc.edu/Research/vmd/). The corresponding topology/parameter files have the ".prmtop" extension. The structures were saved every 10000 steps and the timestep was 2 fs. Therefore, in order to convert the frame number into simulation time, the former has to be multiplied by 1/50 ns. Files with the "distGAX-Y_" prefix contain the distances between the mass centers of glucopyranose residues X and Y of either free or complexed gamma-cyclodextrin as a function of simulation time.Files with the "rmsfit" extension contain RMSD errors as a function of simulation time.File "1BB.mol2" is the naphtalene fragment (from building block 1) used to construct the isomer III macrocycle with the leap program. It was generated using restrained electrostatic fit (RESP) with RED.III.5 program. File "2TM" corresponds to the template 2 and was obtained the same way.