1. A design system of a binding structure for polymer molecule which is executed by a parallel and distributed computer system, the parallel and distributed computer system comprising: a plurality of computing units including a CPU that executes computing, a memory system that holds necessary program and data, an input/output interface, and a bus that connects the CPU, the memory system, and the input/output interface; a personal computer including an input system that inputs necessary data by a user, an output system that outputs data for the user, a memory system that holds necessary program and data, an input/output interface, and a bus that connects the input system, the output system, the memory system, and the input/output interface, and executing a transaction for distributing computation to the plurality of computing units and integrating the computation result of the plurality of computing units; and a network that executes data transfer between the personal computer and the computing units through the input/output interface, a transaction procedure of distributing computation to the respective computing units by the personal computer and integrating the computation results of the respective computing units with respect to the number of operable computing units that are designated by the user, and the search region of polymer molecule, comprising the steps of: (1) determining a decomposition width that decomposes a search region and the number of searches that compute a binding energy; (2) determining the number of decomposed search regions (decomposed regions) and a range of the decomposed regions by using the decomposition width of the search region; (3) determining the number of computing units in the parallel and distributed environment for allocation of the decomposed regions within the number of operable computing units by using the number of decomposed regions; (4) determining the number of decomposed regions that are allocated to the respective computing units and the decomposed regions by using the number of decomposed regions, the number of searches, and the number of computing units to which the decomposed regions are allocated; (5) determining the search points within the decomposed regions where the binding energy is computed in the decomposed regions that are allocated to the respective computing units; (6) transmitting data at the respective search points which are allocated in order to compute the binding energy to the respective computing units that are determined in the steps (4) and (5), and receiving the binding energies and the energy gradient vector at the respective search points which are computed by the respective computing units for communication control; (7) determining the minimum value in the local minimum values of the binding energies that are computed by the respective computing units which are received in the step (6), and the local minimum value that is computed by all of the computing units; (8) determining whether iterative calculation is executed, or not, on the basis of the convergence of the local minimum value of the binding energy within the decomposed region, or denies the iterative calculation when the number of searches exceeds a given value; and (9) returning the control to the step (5) in the case where the iterative calculation is executed, and outputting data of the atomic coordinates with respect to the minimum value of the binding energy of polymer molecule and the binding structure of polymer molecule to the output system in the case where the iterative calculation is completed, wherein the transaction in the respective computing units includes a step of receiving data at the search points from the step (6), and computing the binding energy of polymer molecule and the energy gradient vector at the designated search point.