Considering the high importance and widespread use of Fsp3 and FCstereo indicators in medicinal chemistry and their link to biologically relevant compound features, we propose a new scoring system that combines the benefits of both Fsp3 and FCstereo, but also overcomes shortcomings caused by their simplistic nature. SPS and its sizenormalised version nSPS provide a more granular evaluation for a diverse range of structures than Fsp3 and FCstereo, retaining strong correlation to both indicators, but also explicitly accounting for such topological features as ring sizes and skeletal branching. Thus, the normalised spacial score appears to reflect more the chemist's intuitive assessment of complexity regarding spacial arrangements in molecules. Furthermore, the nSPS is applicable in a biological context. Analysis of ChEMBL compounds showing activities in assays revealed trends of generally increasing selectivity and potency with increasing nSPS values. At very high nSPS values above 40, the impact on activity strength became unfavourable. The average nSPS of the FDA-approved drugs over the last seven decades was over 20 units and does not have a general rising or falling trend. Based on the observed results, in the case of biological assays and the absence of any known contradictions, we recommend to select for compounds with nSPS in the range of 20 to 40, which could potentially maximise the chance of reaching high potency and target selectivity. In addition, SPS can be used in the context of synthesis planning and analysis by directly comparing different chemical transformations and their impact on spacial arrangements and molecular complexity in the resulting products' molecular structures.