FMO DATABASE

FMODB ID: YMZV2

Calculation Name: 3D4U-B-Xray549

Preferred Name:

Target Type:

Ligand Name: acetate ion

Ligand 3-letter code: ACT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3D4U

Chain ID: B

ChEMBL ID:

UniProt ID: Q2KIG3

Base Structure: X-ray

Registration Date: 2025-10-12

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	68
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-380704.614495
FMO2-HF: Nuclear repulsion	350299.876501
FMO2-HF: Total energy	-30404.737994
FMO2-MP2: Total energy	-30482.554043

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(B:1:ASN)

Summations of interaction energy for fragment #1(B:1:ASN)

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.
12.23	15.529	18.988	-8.615	-13.672	0.014

Interaction energy analysis for fragmet #1(B:1:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.872 / q_NPA : 0.922

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

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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	B	3	CYS	0	-0.020	0.017	2.468	3.196	5.289	2.509	-1.586	-3.016	0.013
4	B	4	VAL	0	0.055	0.020	1.927	-5.744	-7.166	8.260	-2.447	-4.391	0.019
5	B	5	SER	0	-0.053	-0.036	3.467	1.663	2.613	0.015	-0.425	-0.540	0.001
10	B	10	CYS	0	-0.094	-0.030	2.472	-14.538	-13.691	5.502	-1.913	-4.436	-0.010
11	B	11	LEU	0	0.069	0.030	5.112	1.296	1.313	-0.001	-0.005	-0.011	0.000
25	B	25	GLY	0	0.063	0.030	5.364	0.273	0.305	-0.001	-0.012	-0.019	0.000
26	B	26	GLY	0	-0.035	-0.040	2.011	-7.867	-7.145	2.704	-2.206	-1.220	-0.009
27	B	28	SER	0	0.019	0.002	4.285	1.653	1.713	0.000	-0.021	-0.039	0.000
6	B	6	LYS	1	0.848	0.939	5.636	32.105	32.105	0.000	0.000	0.000	0.000
7	B	7	GLY	0	0.007	0.021	7.026	2.734	2.734	0.000	0.000	0.000	0.000
8	B	8	PHE	0	-0.020	-0.008	6.581	1.900	1.900	0.000	0.000	0.000	0.000
9	B	9	GLY	0	0.057	0.016	5.579	-2.419	-2.419	0.000	0.000	0.000	0.000
12	B	12	PRO	0	0.048	0.032	8.803	-0.734	-0.734	0.000	0.000	0.000	0.000
13	B	13	GLN	0	0.051	0.015	11.632	0.359	0.359	0.000	0.000	0.000	0.000
14	B	14	SER	0	-0.059	-0.042	13.761	0.466	0.466	0.000	0.000	0.000	0.000
15	B	15	ASP	-1	-0.806	-0.891	13.412	-15.205	-15.205	0.000	0.000	0.000	0.000
16	B	16	CYS	0	-0.025	0.007	7.009	2.489	2.489	0.000	0.000	0.000	0.000
17	B	17	PRO	0	0.067	0.030	13.883	-0.017	-0.017	0.000	0.000	0.000	0.000
18	B	18	GLN	0	0.005	-0.019	15.741	-1.027	-1.027	0.000	0.000	0.000	0.000
19	B	19	GLU	-1	-0.896	-0.945	17.222	-14.155	-14.155	0.000	0.000	0.000	0.000
20	B	20	ALA	0	0.034	0.032	14.316	-0.205	-0.205	0.000	0.000	0.000	0.000
21	B	21	ARG	1	0.810	0.903	11.909	15.477	15.477	0.000	0.000	0.000	0.000
22	B	22	LEU	0	-0.021	-0.004	9.023	0.591	0.591	0.000	0.000	0.000	0.000
23	B	23	SER	0	0.002	-0.011	9.767	-0.573	-0.573	0.000	0.000	0.000	0.000
24	B	24	TYR	0	-0.023	-0.006	5.917	-0.693	-0.693	0.000	0.000	0.000	0.000
28	B	29	THR	0	-0.050	-0.038	6.940	1.776	1.776	0.000	0.000	0.000	0.000
29	B	30	VAL	0	-0.014	-0.002	8.196	0.792	0.792	0.000	0.000	0.000	0.000
30	B	33	ASP	-1	-0.732	-0.851	9.337	-18.368	-18.368	0.000	0.000	0.000	0.000
31	B	34	LEU	0	0.005	-0.016	9.158	0.973	0.973	0.000	0.000	0.000	0.000
32	B	35	SER	0	-0.091	-0.056	12.906	1.190	1.190	0.000	0.000	0.000	0.000
33	B	36	LYS	1	0.876	0.928	15.771	16.089	16.089	0.000	0.000	0.000	0.000
34	B	37	LEU	0	-0.026	0.016	13.125	0.557	0.557	0.000	0.000	0.000	0.000
35	B	38	THR	0	-0.015	-0.013	17.516	0.422	0.422	0.000	0.000	0.000	0.000
36	B	39	GLY	0	0.051	0.024	20.440	-0.204	-0.204	0.000	0.000	0.000	0.000
37	B	40	CYS	0	-0.049	-0.020	20.777	-0.856	-0.856	0.000	0.000	0.000	0.000
38	B	41	LYS	1	0.900	0.949	16.293	14.428	14.428	0.000	0.000	0.000	0.000
39	B	42	GLY	0	-0.018	0.002	16.466	-0.795	-0.795	0.000	0.000	0.000	0.000
40	B	43	LYS	1	0.849	0.919	16.481	12.802	12.802	0.000	0.000	0.000	0.000
41	B	44	GLY	0	-0.001	0.006	16.368	-0.058	-0.058	0.000	0.000	0.000	0.000
42	B	45	GLY	0	-0.004	-0.005	17.069	0.149	0.149	0.000	0.000	0.000	0.000
43	B	46	GLU	-1	-0.841	-0.905	20.323	-11.956	-11.956	0.000	0.000	0.000	0.000
44	B	47	CYS	0	-0.062	-0.022	22.606	0.144	0.144	0.000	0.000	0.000	0.000
45	B	48	ASN	0	-0.006	-0.021	25.669	0.259	0.259	0.000	0.000	0.000	0.000
46	B	49	PRO	0	0.069	0.040	28.654	0.113	0.113	0.000	0.000	0.000	0.000
47	B	50	LEU	0	-0.002	-0.020	32.433	-0.075	-0.075	0.000	0.000	0.000	0.000
48	B	51	ASP	-1	-0.904	-0.944	34.636	-8.177	-8.177	0.000	0.000	0.000	0.000
49	B	52	ARG	1	0.894	0.956	28.588	9.735	9.735	0.000	0.000	0.000	0.000
50	B	53	GLN	0	0.016	0.012	32.585	0.010	0.010	0.000	0.000	0.000	0.000
51	B	54	CYS	0	-0.041	-0.011	25.933	0.023	0.023	0.000	0.000	0.000	0.000
52	B	55	LYS	1	0.936	0.978	26.403	10.023	10.023	0.000	0.000	0.000	0.000
53	B	56	GLU	-1	-0.763	-0.866	26.737	-9.407	-9.407	0.000	0.000	0.000	0.000
54	B	57	LEU	0	0.002	0.003	22.093	0.118	0.118	0.000	0.000	0.000	0.000
55	B	58	GLN	0	0.013	-0.005	26.199	-0.020	-0.020	0.000	0.000	0.000	0.000
56	B	59	ALA	0	-0.017	-0.003	26.821	0.160	0.160	0.000	0.000	0.000	0.000
57	B	60	GLU	-1	-0.809	-0.912	22.757	-11.597	-11.597	0.000	0.000	0.000	0.000
58	B	61	SER	0	-0.046	-0.043	26.054	-0.166	-0.166	0.000	0.000	0.000	0.000
59	B	62	ALA	0	0.008	0.013	28.639	0.107	0.107	0.000	0.000	0.000	0.000
60	B	63	SER	0	-0.059	-0.046	25.264	-0.016	-0.016	0.000	0.000	0.000	0.000
61	B	65	GLY	0	0.042	0.037	28.277	0.134	0.134	0.000	0.000	0.000	0.000
62	B	66	LYS	1	0.955	0.960	31.842	7.276	7.276	0.000	0.000	0.000	0.000
63	B	67	GLY	0	0.000	0.001	34.868	0.007	0.007	0.000	0.000	0.000	0.000
64	B	68	GLN	0	-0.069	-0.043	28.700	-0.095	-0.095	0.000	0.000	0.000	0.000
65	B	69	LYS	1	0.809	0.910	29.850	9.006	9.006	0.000	0.000	0.000	0.000
66	B	72	VAL	0	0.037	0.003	20.616	-0.387	-0.387	0.000	0.000	0.000	0.000
67	B	73	TRP	0	-0.105	-0.065	21.239	0.687	0.687	0.000	0.000	0.000	0.000
68	B	74	LEU	-1	-0.919	-0.948	20.465	-13.598	-13.598	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:ASN)