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