FMO DATABASE

FMODB ID: 9RRR2

Calculation Name: 2PIJ-B-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion | 2,3-dihydroxy-1,4-dithiobutane | bicarbonate ion

Ligand 3-letter code: SO4 | DTT | BCT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2PIJ

Chain ID: B

ChEMBL ID:

UniProt ID: J3IU59

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	-300856.213051
FMO2-HF: Nuclear repulsion	277903.25753
FMO2-HF: Total energy	-22952.955521
FMO2-MP2: Total energy	-23019.525866

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.
-162.851	-150.199	14.2	-12.384	-14.468	-0.136

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 : 0.800 / q_NPA : 0.909

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	LYS	1	0.916	0.962	3.239	31.778	34.760	0.286	-0.914	-2.354	-0.001
4	A	4	ILE	0	-0.005	-0.005	5.173	0.926	0.942	-0.001	-0.004	-0.011	0.000
43	A	43	THR	0	-0.013	-0.013	2.856	-3.279	-2.831	1.186	-0.303	-1.331	-0.002
44	A	44	LEU	0	-0.012	-0.005	3.717	3.368	3.830	0.002	-0.132	-0.333	0.000
45	A	45	TYR	0	-0.025	-0.055	2.267	-33.303	-28.082	5.433	-4.921	-5.733	-0.058
46	A	46	GLU	-1	-0.893	-0.960	2.060	-108.529	-105.043	7.295	-6.103	-4.678	-0.075
47	A	47	ASP	-1	-0.859	-0.927	5.041	-30.403	-30.366	-0.001	-0.007	-0.028	0.000
5	A	5	PRO	0	0.029	0.021	8.853	0.604	0.604	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.057	0.026	12.137	-0.040	-0.040	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.026	-0.001	14.123	-0.188	-0.188	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.883	0.937	12.457	21.793	21.793	0.000	0.000	0.000	0.000
9	A	9	TYR	0	0.018	-0.004	10.350	0.168	0.168	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.044	-0.038	13.372	0.279	0.279	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.941	-0.958	17.062	-13.598	-13.598	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.887	-0.910	14.594	-20.912	-20.912	0.000	0.000	0.000	0.000
13	A	13	HIS	0	-0.119	-0.055	11.733	-1.663	-1.663	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.035	0.016	14.110	0.129	0.129	0.000	0.000	0.000	0.000
15	A	15	THR	0	0.017	0.004	15.555	0.422	0.422	0.000	0.000	0.000	0.000
16	A	16	GLN	0	0.081	0.031	17.419	-0.418	-0.418	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.021	-0.002	18.695	-0.245	-0.245	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.042	0.021	15.901	-0.049	-0.049	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.026	0.016	11.865	-0.596	-0.596	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.023	-0.020	14.816	-0.286	-0.286	0.000	0.000	0.000	0.000
21	A	21	ALA	0	-0.014	-0.001	17.361	0.113	0.113	0.000	0.000	0.000	0.000
22	A	22	ALA	0	-0.022	-0.014	11.949	-0.058	-0.058	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.030	-0.010	10.982	-0.918	-0.918	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.012	0.030	13.941	0.484	0.484	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.051	-0.022	16.744	0.855	0.855	0.000	0.000	0.000	0.000
26	A	26	ASN	0	0.054	0.031	19.247	0.076	0.076	0.000	0.000	0.000	0.000
27	A	27	GLN	0	0.062	0.010	21.070	-0.360	-0.360	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.013	-0.022	22.182	-0.053	-0.053	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.013	-0.010	20.300	0.168	0.168	0.000	0.000	0.000	0.000
30	A	30	ILE	0	0.030	0.005	16.444	-0.013	-0.013	0.000	0.000	0.000	0.000
31	A	31	SER	0	0.051	0.016	20.199	0.040	0.040	0.000	0.000	0.000	0.000
32	A	32	GLN	0	-0.063	-0.014	23.152	-0.092	-0.092	0.000	0.000	0.000	0.000
33	A	33	MET	0	0.001	-0.002	16.685	0.097	0.097	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.007	0.017	19.680	-0.018	-0.018	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.910	0.955	21.637	11.138	11.138	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.041	-0.019	23.703	0.344	0.344	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.018	0.025	21.835	0.067	0.067	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.825	0.894	19.398	13.269	13.269	0.000	0.000	0.000	0.000
39	A	39	SER	0	0.042	0.022	16.045	-0.480	-0.480	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.037	-0.021	13.112	-0.465	-0.465	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.862	-0.923	7.370	-28.604	-28.604	0.000	0.000	0.000	0.000
42	A	42	ILE	0	0.007	0.000	8.090	0.539	0.539	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.001	0.004	6.982	4.147	4.147	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.784	0.893	7.325	31.759	31.759	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.001	-0.014	6.544	-4.857	-4.857	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.799	-0.857	6.872	-25.606	-25.606	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.001	-0.014	8.353	-1.322	-1.322	0.000	0.000	0.000	0.000
53	A	53	ASN	0	-0.014	0.003	8.432	2.139	2.139	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.816	-0.888	11.979	-13.906	-13.906	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.015	-0.009	10.766	0.307	0.307	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.892	0.934	14.815	13.242	13.242	0.000	0.000	0.000	0.000
57	A	57	PRO	0	-0.004	0.013	18.064	-0.317	-0.317	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.011	0.003	19.871	0.346	0.346	0.000	0.000	0.000	0.000
59	A	59	PRO	0	-0.044	-0.036	22.185	-0.040	-0.040	0.000	0.000	0.000	0.000
60	A	60	ALA	-1	-0.908	-0.951	23.691	-10.830	-10.830	0.000	0.000	0.000	0.000

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