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, non-clashing: 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, non-clashing: 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