FMO DATABASE

FMODB ID: 4YYGN

Calculation Name: 2PLS-A-Xray547

Preferred Name:

Target Type:

Ligand Name: acetate ion | 1,2-ethanediol | formic acid | magnesium ion

Ligand 3-letter code: ACT | EDO | FMT | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2PLS

Chain ID: A

ChEMBL ID:

UniProt ID: Q8KEZ1

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	86
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-609395.477146
FMO2-HF: Nuclear repulsion	575049.510813
FMO2-HF: Total energy	-34345.966334
FMO2-MP2: Total energy	-34446.136147

3D Structure Molmil

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:343:SER)

Summations of interaction energy for fragment #1(A:343:SER)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-214.734	-210.809	19.174	-11.775	-11.324	-0.133

Interaction energy analysis for fragmet #1(A:343:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.747 / q_NPA : 0.848

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	345	ALA	0	0.057	0.032	3.830	1.393	2.699	-0.015	-0.569	-0.722	-0.001
14	A	356	ASP	-1	-0.769	-0.870	1.708	-109.227	-111.745	15.459	-7.570	-5.371	-0.100
15	A	357	GLY	0	0.024	0.013	4.447	-0.060	0.068	-0.001	-0.017	-0.110	0.000
16	A	358	LEU	0	-0.062	-0.050	3.740	6.365	6.688	0.002	-0.065	-0.259	0.000
17	A	359	ILE	0	-0.038	-0.004	2.131	-10.302	-8.149	2.658	-2.353	-2.458	-0.008
18	A	360	ALA	0	0.024	0.005	2.977	12.139	11.636	0.083	0.822	-0.403	-0.001
19	A	361	VAL	0	0.035	0.011	5.026	0.598	0.616	-0.001	-0.001	-0.016	0.000
21	A	363	GLU	-1	-0.850	-0.924	2.631	-72.303	-69.285	0.989	-2.022	-1.985	-0.023
4	A	346	VAL	0	-0.016	-0.009	6.958	2.330	2.330	0.000	0.000	0.000	0.000
5	A	347	GLN	0	-0.005	0.011	10.470	1.131	1.131	0.000	0.000	0.000	0.000
6	A	348	ARG	1	0.871	0.930	13.769	19.283	19.283	0.000	0.000	0.000	0.000
7	A	349	GLU	-1	-0.909	-0.968	16.570	-15.762	-15.762	0.000	0.000	0.000	0.000
8	A	350	ASP	-1	-0.836	-0.879	18.958	-16.189	-16.189	0.000	0.000	0.000	0.000
9	A	351	GLY	0	-0.013	0.001	18.286	0.474	0.474	0.000	0.000	0.000	0.000
10	A	352	SER	0	-0.101	-0.068	16.376	-0.927	-0.927	0.000	0.000	0.000	0.000
11	A	353	TRP	0	0.037	-0.003	10.340	-1.333	-1.333	0.000	0.000	0.000	0.000
12	A	354	LEU	0	-0.025	-0.007	9.827	0.602	0.602	0.000	0.000	0.000	0.000
13	A	355	LEU	0	-0.002	-0.006	6.747	-2.314	-2.314	0.000	0.000	0.000	0.000
20	A	362	PRO	0	-0.003	-0.012	7.435	0.784	0.784	0.000	0.000	0.000	0.000
22	A	364	LEU	0	-0.011	0.003	6.414	0.917	0.917	0.000	0.000	0.000	0.000
23	A	365	LYS	1	0.783	0.882	7.890	20.833	20.833	0.000	0.000	0.000	0.000
24	A	366	ASP	-1	-0.916	-0.959	9.404	-22.693	-22.693	0.000	0.000	0.000	0.000
25	A	367	THR	0	-0.081	-0.052	7.613	0.682	0.682	0.000	0.000	0.000	0.000
26	A	368	LEU	0	-0.032	-0.021	10.298	1.350	1.350	0.000	0.000	0.000	0.000
27	A	369	GLY	0	0.003	0.017	12.975	1.701	1.701	0.000	0.000	0.000	0.000
28	A	370	LEU	0	-0.076	-0.023	12.372	1.210	1.210	0.000	0.000	0.000	0.000
29	A	371	ARG	1	0.902	0.940	15.531	13.521	13.521	0.000	0.000	0.000	0.000
30	A	372	ALA	0	-0.036	-0.020	17.073	0.097	0.097	0.000	0.000	0.000	0.000
31	A	373	VAL	0	0.025	0.021	12.405	-0.865	-0.865	0.000	0.000	0.000	0.000
32	A	374	PRO	0	0.011	0.014	15.445	0.959	0.959	0.000	0.000	0.000	0.000
33	A	375	GLU	-1	-0.850	-0.912	16.709	-14.676	-14.676	0.000	0.000	0.000	0.000
34	A	376	GLU	-1	-0.767	-0.861	15.455	-18.505	-18.505	0.000	0.000	0.000	0.000
35	A	377	GLU	-1	-0.951	-0.987	17.028	-14.046	-14.046	0.000	0.000	0.000	0.000
36	A	378	LYS	1	0.814	0.897	18.574	13.855	13.855	0.000	0.000	0.000	0.000
37	A	379	GLY	0	-0.039	-0.013	15.701	0.277	0.277	0.000	0.000	0.000	0.000
38	A	380	VAL	0	-0.012	-0.003	16.502	-0.212	-0.212	0.000	0.000	0.000	0.000
39	A	381	TYR	0	-0.069	-0.061	11.523	-0.727	-0.727	0.000	0.000	0.000	0.000
40	A	382	HIS	0	0.035	0.013	9.254	-0.527	-0.527	0.000	0.000	0.000	0.000
41	A	383	THR	0	-0.015	-0.002	5.852	-0.918	-0.918	0.000	0.000	0.000	0.000
42	A	384	LEU	0	0.061	0.039	6.812	3.965	3.965	0.000	0.000	0.000	0.000
43	A	385	SER	0	0.029	0.012	7.877	3.475	3.475	0.000	0.000	0.000	0.000
44	A	386	GLY	0	-0.052	-0.022	9.858	2.422	2.422	0.000	0.000	0.000	0.000
45	A	387	MET	0	0.011	0.019	11.382	1.709	1.709	0.000	0.000	0.000	0.000
46	A	388	ILE	0	0.029	0.004	11.385	1.676	1.676	0.000	0.000	0.000	0.000
47	A	389	MET	0	-0.028	-0.014	13.925	1.343	1.343	0.000	0.000	0.000	0.000
48	A	390	TRP	0	-0.028	-0.016	15.748	1.143	1.143	0.000	0.000	0.000	0.000
49	A	391	LEU	0	-0.014	-0.013	15.602	0.922	0.922	0.000	0.000	0.000	0.000
50	A	392	LEU	0	-0.057	-0.014	17.135	0.787	0.787	0.000	0.000	0.000	0.000
51	A	393	GLY	0	-0.022	0.004	20.089	0.750	0.750	0.000	0.000	0.000	0.000
52	A	394	ARG	1	0.729	0.817	20.128	15.087	15.087	0.000	0.000	0.000	0.000
53	A	395	LEU	0	-0.019	-0.018	17.161	-0.691	-0.691	0.000	0.000	0.000	0.000
54	A	396	PRO	0	0.016	0.012	14.120	0.801	0.801	0.000	0.000	0.000	0.000
55	A	397	GLN	0	-0.034	-0.015	17.139	0.366	0.366	0.000	0.000	0.000	0.000
56	A	398	THR	0	0.032	0.000	16.287	-0.522	-0.522	0.000	0.000	0.000	0.000
57	A	399	GLY	0	0.016	0.016	17.498	1.017	1.017	0.000	0.000	0.000	0.000
58	A	400	ASP	-1	-0.772	-0.838	17.438	-14.799	-14.799	0.000	0.000	0.000	0.000
59	A	401	ILE	0	-0.025	-0.012	17.510	-0.909	-0.909	0.000	0.000	0.000	0.000
60	A	402	THR	0	-0.009	-0.008	16.086	0.574	0.574	0.000	0.000	0.000	0.000
61	A	403	PHE	0	0.015	-0.007	18.296	-0.271	-0.271	0.000	0.000	0.000	0.000
62	A	404	TRP	0	-0.010	-0.015	15.897	0.410	0.410	0.000	0.000	0.000	0.000
63	A	405	GLU	-1	-0.802	-0.899	18.207	-16.450	-16.450	0.000	0.000	0.000	0.000
64	A	406	ASN	0	-0.012	0.000	19.661	0.631	0.631	0.000	0.000	0.000	0.000
65	A	407	TRP	0	0.006	0.000	15.722	-0.198	-0.198	0.000	0.000	0.000	0.000
66	A	408	ARG	1	0.962	0.988	18.207	15.465	15.465	0.000	0.000	0.000	0.000
67	A	409	LEU	0	-0.035	-0.020	12.308	-1.111	-1.111	0.000	0.000	0.000	0.000
68	A	410	GLU	-1	-0.907	-0.955	14.722	-15.619	-15.619	0.000	0.000	0.000	0.000
69	A	411	VAL	0	-0.029	-0.018	13.131	-1.911	-1.911	0.000	0.000	0.000	0.000
70	A	412	ILE	0	-0.008	-0.006	12.562	1.273	1.273	0.000	0.000	0.000	0.000
71	A	413	ASP	-1	-0.853	-0.930	11.233	-21.662	-21.662	0.000	0.000	0.000	0.000
72	A	414	MET	0	-0.058	-0.019	11.805	-2.154	-2.154	0.000	0.000	0.000	0.000
73	A	415	ASP	-1	-0.853	-0.910	10.221	-25.087	-25.087	0.000	0.000	0.000	0.000
74	A	416	SER	0	-0.020	-0.024	12.114	0.872	0.872	0.000	0.000	0.000	0.000
75	A	417	LYS	1	0.915	0.955	15.518	15.993	15.993	0.000	0.000	0.000	0.000
76	A	418	ARG	1	0.882	0.949	9.415	28.855	28.855	0.000	0.000	0.000	0.000
77	A	419	ILE	0	0.060	0.022	9.236	0.367	0.367	0.000	0.000	0.000	0.000
78	A	420	ASP	-1	-0.848	-0.914	6.961	-40.735	-40.735	0.000	0.000	0.000	0.000
79	A	421	LYS	1	0.793	0.876	6.020	34.776	34.776	0.000	0.000	0.000	0.000
80	A	422	VAL	0	0.002	0.005	8.935	3.052	3.052	0.000	0.000	0.000	0.000
81	A	423	LEU	0	-0.007	0.010	10.491	-1.725	-1.725	0.000	0.000	0.000	0.000
82	A	424	ALA	0	0.013	0.011	12.063	1.110	1.110	0.000	0.000	0.000	0.000
83	A	425	THR	0	-0.022	-0.032	13.803	0.388	0.388	0.000	0.000	0.000	0.000
84	A	426	LYS	1	0.856	0.927	17.492	14.940	14.940	0.000	0.000	0.000	0.000
85	A	427	ILE	0	-0.087	-0.054	19.560	0.387	0.387	0.000	0.000	0.000	0.000
86	A	428	ASP	-2	-1.759	-1.848	22.857	-24.361	-24.361	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:343:SER)