PFF-Library

The repository for Pantetheine Force Field (PFF) library containing parameters of various pantetheine-containing ligands (PCLs) compatible with Amber force fields. Three charging methods (Gasteiger, AM1-BCC, or RESP) combined with gaff2 and ff14SB parameter sets were employed.

Tutorial

The tutorial for using PFF library for Phosphopantetheine adenylyltransferase-phosphopantetheine (PPAT-Ppant system) and 3-hydroxy-3-methylglutaryl synthase/acyl carrier protein complex-phosphopantetheinyl serine (HGMS/ACP-Ppant-Ser) can be found on:

• Tutorial on Github
• Tutorial on Amber

Parameter Files

PCL Name	PDB ID	Description	URL Links
Coenzyme A (CoA) Library
CoA	COA	“apo” coenzyme A	Link
Acetyl-CoA	ACO	2 Carbon Acyl-CoA	Link
Propionyl-CoA	1VU	3 Carbon Acyl-CoA	Link
Butyryl-CoA	BCO	4 Carbon Acyl-CoA	Link
Hexanoyl-CoA	HXC	6 Carbon Acyl-CoA	Link
Octanoyl-CoA	CO8	8 Carbon Acyl-CoA	Link
Decanoyl-CoA	MFK	10 Carbon Acyl-CoA	Link
Dodecanoyl-CoA	DCC	12 Carbon Acyl-CoA	Link
Tetradecanoyl-CoA	MYA	14 Carbon Acyl-CoA	Link
Hexadecanoyl-CoA	PKZ	16 Carbon Acyl-CoA	Link
Malonyl-CoA	MLC	CoA derivative of malonic acid	Link
Acetoacetyl-CoA	CAA	Precursor of HMG-CoA in mevalonate pathway	Link
Phosphopantetheine (Ppant) Library
Ppant	PNS	“apo” phosphopantetheine	Link
Acetyl-Ppant	6VG	2 Carbon Acyl-Ppant	Link
Butyryl-Ppant	PSR	4 Carbon Acyl-Ppant	Link
Hexanoyl-Ppant	SXH	6 Carbon Acyl-Ppant	Link
Octanoyl-Ppant	SXO	8 Carbon Acyl-Ppant	Link
Decanoyl-Ppant	PM8	10 Carbon Acyl-Ppant	Link
Dodecanoyl-Ppant	8Q1	12 Carbon Acyl-Ppant	Link
Tetradecanoyl-Ppant	ZMP	14 Carbon Acyl-Ppant	Link
Hexadecanoyl-Ppant	G9S	16 Carbon Acyl-Ppant	Link
Phosphopantetheinyl-Serine (Ppant-Ser) Library
Ppant	PNS	“apo” phosphopantetheinyl-serine	Link
Acetyl-Ppant	6VG	2 Carbon Acyl-Ppant	Link
Butyryl-Ppant	PSR	4 Carbon Acyl-Ppant	Link
Hexanoyl-Ppant	SXH	6 Carbon Acyl-Ppant	Link
Octanoyl-Ppant	SXO	8 Carbon Acyl-Ppant	Link
Decanoyl-Ppant	PM8	10 Carbon Acyl-Ppant	Link
Dodecanoyl-Ppant	8Q1	12 Carbon Acyl-Ppant	Link
Tetradecanoyl-Ppant	ZMP	14 Carbon Acyl-Ppant	Link
Hexadecanoyl-Ppant	G9S	16 Carbon Acyl-Ppant	Link

Citation

To cite PFF library, see the following publication:

Shiji Zhao, Andrew J. Schaub, Shiou-Chuan Tsai, and Ray Luo. "Development of a Pantetheine Force Field Library for Molecular Modeling." Journal of Chemical Information and Modeling 61, no. 2 (2021): 856-868.