Spectrally resolved three-pulse stimulated vibrational echo experiments are used as the basis for structural assignments of the A(1) and A(3) spectroscopic substates in the IR spectrum of the carbon monoxide (CO) stretch of carbonmonoxymyoglobin (MbCO). The measured dephasing dynamics of these substates is compared to the dephasing dynamics of MbCO predicted from molecular dynamics (MD) simulations. We assign the A(1) and A(3) substates to different protein conformations on the basis of the agreement between the measured and computed vibrational echoes. In the A(1) substate, the N-epsilon-H proton and N-delta of His64 are equidistant from the ligand, whereas in the A(3) substate, the N-epsilon-H of His64 is oriented toward the CO.