FMO DATABASE

FMODB ID: Z7L3N

Calculation Name: 1VJW-A-Xray547

Preferred Name:

Target Type:

Ligand Name: iron/sulfur cluster

Ligand 3-letter code: SF4

Ligand of Interest (LOI):

PDB ID: 1VJW

Chain ID: A

ChEMBL ID:

UniProt ID: P46797

Base Structure: X-ray

Registration Date: 2025-09-02

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	58
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-282988.587485
FMO2-HF: Nuclear repulsion	259930.504722
FMO2-HF: Total energy	-23058.082763
FMO2-MP2: Total energy	-23119.288287

3D Structure

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.
-369.894	-368.901	48.179	-22.937	-26.24	-0.232

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 : 0.674 / q_NPA : 0.836

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	VAL	0	0.024	0.018	3.691	3.833	5.390	0.007	-0.524	-1.040	0.001
20	A	20	CYS	0	-0.010	0.012	3.386	-1.383	-1.322	-0.005	0.186	-0.242	0.000
38	A	38	GLU	-1	-0.865	-0.928	1.724	-122.684	-127.106	14.816	-6.182	-4.213	-0.078
39	A	39	THR	0	0.011	-0.006	2.499	10.998	13.064	0.499	-0.793	-1.773	-0.004
40	A	40	ASP	-1	-0.919	-0.958	1.808	-89.239	-89.620	11.872	-6.299	-5.192	-0.081
41	A	41	LEU	0	0.044	0.018	2.636	2.680	3.742	1.856	-0.966	-1.952	-0.017
42	A	42	PRO	0	-0.011	-0.023	2.551	-4.442	-3.113	1.093	-0.906	-1.516	-0.010
43	A	44	ALA	0	0.021	0.004	3.117	1.685	2.152	0.119	-0.104	-0.483	0.000
44	A	45	LYS	1	0.912	0.959	2.542	31.654	27.925	8.944	-1.718	-3.498	0.018
57	A	58	VAL	0	-0.030	-0.038	2.345	-3.614	-3.411	2.112	-0.524	-1.791	-0.002
58	A	59	GLU	-2	-1.752	-1.860	2.137	-115.493	-112.713	6.866	-5.107	-4.540	-0.059
4	A	4	ARG	1	0.802	0.880	5.473	40.946	40.946	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.048	0.016	8.998	-0.283	-0.283	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.871	-0.917	12.120	-16.309	-16.309	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.027	-0.007	15.156	0.368	0.368	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.928	-0.954	18.032	-12.853	-12.853	0.000	0.000	0.000	0.000
9	A	9	ALA	0	-0.042	-0.013	16.781	0.553	0.553	0.000	0.000	0.000	0.000
10	A	10	CYS	-1	-0.831	-0.825	16.728	-16.131	-16.131	0.000	0.000	0.000	0.000
11	A	11	ILE	0	-0.025	-0.018	18.359	0.869	0.869	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.042	-0.006	19.832	0.498	0.498	0.000	0.000	0.000	0.000
13	A	13	CYS	0	-0.102	-0.046	19.004	0.004	0.004	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.072	0.041	18.003	0.323	0.323	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.026	-0.024	15.005	-0.419	-0.419	0.000	0.000	0.000	0.000
16	A	16	CYS	0	0.004	0.002	11.865	0.095	0.095	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.843	-0.909	12.160	-17.237	-17.237	0.000	0.000	0.000	0.000
18	A	18	ASN	0	-0.043	-0.040	14.368	0.042	0.042	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.038	-0.004	10.993	0.346	0.346	0.000	0.000	0.000	0.000
21	A	21	PRO	0	0.079	0.049	10.065	-1.411	-1.411	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.930	-0.959	9.819	-22.139	-22.139	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.059	-0.030	5.774	-1.873	-1.873	0.000	0.000	0.000	0.000
24	A	24	PHE	0	-0.013	-0.023	7.704	-0.857	-0.857	0.000	0.000	0.000	0.000
25	A	25	GLN	0	0.047	0.028	11.864	1.176	1.176	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.027	-0.012	15.634	-0.464	-0.464	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.022	-0.002	18.704	0.290	0.290	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.931	-0.979	21.016	-12.157	-12.157	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.962	-0.986	21.966	-13.868	-13.868	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.036	-0.007	23.335	0.292	0.292	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.828	0.886	18.917	13.980	13.980	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.014	-0.024	14.463	-0.166	-0.166	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.880	0.940	15.130	16.616	16.616	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.012	-0.011	8.671	-0.238	-0.238	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.052	-0.019	11.268	0.743	0.743	0.000	0.000	0.000	0.000
36	A	36	GLN	0	-0.023	-0.003	7.137	-3.899	-3.899	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.001	-0.005	6.684	-4.669	-4.669	0.000	0.000	0.000	0.000
45	A	46	ASP	-1	-0.831	-0.913	5.968	-22.217	-22.217	0.000	0.000	0.000	0.000
46	A	47	ALA	0	-0.029	-0.010	8.168	2.036	2.036	0.000	0.000	0.000	0.000
47	A	48	ALA	0	-0.022	-0.009	8.052	1.110	1.110	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.927	-0.966	9.484	-20.602	-20.602	0.000	0.000	0.000	0.000
49	A	50	SER	0	-0.080	-0.050	11.757	1.808	1.808	0.000	0.000	0.000	0.000
50	A	51	CYS	0	-0.059	-0.010	12.966	1.087	1.087	0.000	0.000	0.000	0.000
51	A	52	PRO	0	-0.020	-0.018	14.957	0.354	0.354	0.000	0.000	0.000	0.000
52	A	53	THR	0	-0.046	-0.047	17.507	0.516	0.516	0.000	0.000	0.000	0.000
53	A	54	GLY	0	-0.004	-0.003	14.201	0.091	0.091	0.000	0.000	0.000	0.000
54	A	55	ALA	0	0.001	0.003	13.572	-0.825	-0.825	0.000	0.000	0.000	0.000
55	A	56	ILE	0	-0.021	-0.001	8.126	-0.732	-0.732	0.000	0.000	0.000	0.000
56	A	57	SER	0	-0.003	0.005	8.290	1.317	1.317	0.000	0.000	0.000	0.000

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