Appendix 2: SZMAP Atom Properties

SZMAP calculations at a list of coordinates attach one or more of the following properties to the atoms that specify the coordinates. Key properties are in bold.

Complex, Apo or Ligand

Property Name (cplx, lig, or apo)	Description
szmap_neut_diff_free_energy	water - neutral probe free energy difference
szmap_neut_diff_enthalpy	water - neutral probe enthalpy difference
szmap_neut_diff_entropy	water - neutral probe entropy difference
szmap_vdw	van der Waals energy
szmap_order	fractional entropy loss from electrostatics
szmap_clash	if point clashes, property = “CLASH”
szmap_mask	clashing: 0, nonclashing: 1
szmap_vac_diff_free_energy	water - vacuum probe free energy difference
szmap_vac_diff_enthalpy	water - vacuum probe enthalpy difference
szmap_vac_diff_entropy	water - vacuum probe entropy difference
szmap_free_energy	free energy of probe water vs continuum
szmap_enthalpy	enthalpy of probe water vs continuum
szmap_entropy	entropy of probe water vs continuum
szmap_neutral_free_energy	free energy of neutral probe vs continuum
szmap_neutral_enthalpy	enthalpy of neutral probe vs continuum
szmap_neutral_entropy	entropy of neutral probe vs continuum
szmap_interaction	Poisson Boltzmann electrostatic interaction
szmap_psolv	protein desolvation penalty
szmap_wsolv	water probe desolvation penalty
szmap_intvdw	interaction + van der Waals (for masking)
szmap_probe_burial	fractional amount water probe is buried

(Complex - Protein - Ligand) Stabilization

Property Name (cplx - prot - lig)	Description
szmap_neut_diff_stbl_free_energy	neutral free energy difference stabilization
szmap_neut_diff_stbl_enthalpy	neutral enthalpy difference stabilization
szmap_neut_diff_stbl_entropy	neutral entropy difference stabilization
szmap_stbl_vdw	van der Waals energy stabilization
szmap_stbl_order	fractional entropy loss (ES) stabilization
szmap_stbl_clash	if point clashes, property = “CLASH”
szmap_stbl_mask	clashing: 0, nonclashing: 1
szmap_vac_diff_stbl_free_energy	vacuum free energy difference stabilization
szmap_vac_diff_stbl_enthalpy	vacuum enthalpy difference stabilization
szmap_vac_diff_stbl_entropy	vacuum entropy difference stabilization
szmap_stbl_free_energy	probe water free energy stabilization
szmap_stbl_enthalpy	probe water enthalpy stabilization
szmap_stbl_entropy	probe water entropy stabilization
szmap_stbl_neutral_free_energy	neutral probe free energy stabilization
szmap_stbl_neutral_enthalpy	neutral probe enthalpy stabilization
szmap_stbl_neutral_entropy	neutral probe enthalpy stabilization
szmap_stbl_interaction	Poisson Boltzmann electrostatic interaction
szmap_stbl_psolv	protein desolvation stabilization
szmap_stbl_wsolv	water probe desolvation stabilization
szmap_stbl_intvdw	interaction + van der Waals stabilization
szmap_stbl_probe_burial	fractional probe burial stabilization