FMO DATABASE

FMODB ID: KVMJ3

Calculation Name: 3MB2-I-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion

Ligand 3-letter code: SO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3MB2

Chain ID: I

ChEMBL ID:

UniProt ID: A9W9U6

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	60
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-272680.119125
FMO2-HF: Nuclear repulsion	249845.956068
FMO2-HF: Total energy	-22834.163057
FMO2-MP2: Total energy	-22899.539562

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:1:MET)

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

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.
-116.221	-110.449	5.561	-5.255	-6.079	-0.073

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.808 / q_NPA : 0.897

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	A	3	LEU	0	-0.026	-0.008	2.580	3.066	5.059	0.536	-0.484	-2.045	-0.002
4	A	4	LEU	0	0.028	0.021	4.398	1.924	2.019	-0.001	-0.008	-0.086	0.000
34	A	34	VAL	0	-0.026	-0.005	4.176	-4.579	-4.449	-0.001	-0.022	-0.107	0.000
38	A	38	GLU	-1	-0.886	-0.958	1.931	-110.252	-106.821	5.028	-4.728	-3.732	-0.071
39	A	39	VAL	0	-0.049	0.004	4.508	-5.005	-4.882	-0.001	-0.013	-0.109	0.000
5	A	5	ARG	1	0.920	0.951	7.511	21.580	21.580	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.003	0.010	9.536	0.604	0.604	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.006	0.004	13.333	0.070	0.070	0.000	0.000	0.000	0.000
8	A	8	MET	0	-0.045	-0.023	15.862	0.302	0.302	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.037	0.024	19.145	0.181	0.181	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.881	-0.953	22.907	-11.076	-11.076	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.009	0.004	24.523	0.240	0.240	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.920	0.968	22.736	11.475	11.475	0.000	0.000	0.000	0.000
13	A	13	SER	0	0.036	0.013	25.091	-0.193	-0.193	0.000	0.000	0.000	0.000
14	A	14	THR	0	0.041	0.000	23.358	-0.432	-0.432	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.905	-0.947	22.824	-11.593	-11.593	0.000	0.000	0.000	0.000
16	A	16	GLN	0	0.003	0.003	23.236	-0.526	-0.526	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.816	0.889	19.335	12.191	12.191	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.011	0.013	18.387	-0.944	-0.944	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.757	-0.838	18.933	-15.880	-15.880	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.016	-0.005	17.220	-0.685	-0.685	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.025	0.004	14.841	-1.020	-1.020	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.814	0.874	14.586	14.413	14.413	0.000	0.000	0.000	0.000
23	A	23	ALA	0	-0.004	-0.004	15.590	-1.077	-1.077	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.001	-0.003	13.392	-0.662	-0.662	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.011	-0.023	11.080	-2.254	-2.254	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.023	-0.016	11.380	-1.977	-1.977	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.004	-0.001	13.417	-0.479	-0.479	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.006	-0.001	9.534	-0.240	-0.240	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.029	-0.023	8.625	-2.224	-2.224	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.026	-0.014	9.683	-0.536	-0.536	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.030	-0.001	12.488	0.904	0.904	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.061	-0.038	8.007	0.887	0.887	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.897	-0.931	7.953	-29.297	-29.297	0.000	0.000	0.000	0.000
35	A	35	PRO	0	0.007	-0.002	5.314	5.140	5.140	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.052	0.017	6.851	-3.783	-3.783	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.014	-0.004	9.114	-0.396	-0.396	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.840	0.918	5.054	44.748	44.748	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.019	0.020	7.282	-0.850	-0.850	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.024	-0.010	7.244	1.435	1.435	0.000	0.000	0.000	0.000
43	A	43	ILE	0	0.027	0.009	10.808	0.147	0.147	0.000	0.000	0.000	0.000
44	A	44	GLN	0	-0.038	-0.028	13.125	-0.371	-0.371	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.803	-0.887	16.095	-12.794	-12.794	0.000	0.000	0.000	0.000
46	A	46	VAL	0	0.003	0.002	19.608	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	47	PRO	0	0.053	0.044	22.235	0.033	0.033	0.000	0.000	0.000	0.000
48	A	48	PRO	0	0.006	-0.021	25.911	-0.127	-0.127	0.000	0.000	0.000	0.000
49	A	49	THR	0	0.027	0.001	28.161	0.082	0.082	0.000	0.000	0.000	0.000
50	A	50	HIS	0	-0.021	-0.004	23.799	0.174	0.174	0.000	0.000	0.000	0.000
51	A	51	TRP	0	-0.032	-0.004	19.025	-0.659	-0.659	0.000	0.000	0.000	0.000
52	A	52	THR	0	0.017	0.001	24.637	0.397	0.397	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.025	-0.012	25.402	-0.416	-0.416	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.003	0.002	27.718	0.285	0.285	0.000	0.000	0.000	0.000
55	A	55	GLY	0	-0.041	-0.020	29.310	0.247	0.247	0.000	0.000	0.000	0.000
56	A	56	ILE	0	-0.008	0.006	30.790	0.157	0.157	0.000	0.000	0.000	0.000
57	A	57	SER	0	0.013	0.006	29.390	-0.389	-0.389	0.000	0.000	0.000	0.000
58	A	58	MET	0	-0.007	-0.017	26.685	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.125	-0.054	29.905	0.059	0.059	0.000	0.000	0.000	0.000
60	A	60	GLU	-2	-1.850	-1.909	32.880	-16.234	-16.234	0.000	0.000	0.000	0.000

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