Table 1 Description of datasets used in parameterization case study
From: NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges
Dataset | |||||
|---|---|---|---|---|---|
Denotation | DTP_small | DTP_large | CCD_gen | CCD_exp | |
Source database | DTP NCI | wwPDB CCD | |||
Number of molecules | 1956 | 4475 | 4443 | ||
Atomic types (elements and bond orders) | C1, C2, O1,O2, N1, N2,H, S1 | H1, C1, C2,C3, N1, N2,N3, O1, O2,F1, P1, P2,S1, S2, Cl1,Br1, I1 | H1, C1, C2, C3, N1,N2, N3, O1, O2, F1,P2, S1, S2, Cl1, Br1 | ||
Size of molecules | 6-176 atoms | 5-124 atoms | 3-305 atoms | ||
Type of molecules | Small organic molecules | Small organic molecules | Small organic and inorganic molecules, organometals, peptides | ||
Source of 3D structures | Generated by CORINA | Experimental structures | |||
Characterization of a dataset | Variability of atomic types | Low | High | ||
Variability of molecules | Low | High | |||
Variability of structure sources | Low | High | |||
Reference to publication | [35] (set beg2) | [40] | – | – | |