FMO DATABASE

FMODB ID: 8GQLY

Calculation Name: 1CLF-A-Other547

Preferred Name:

Target Type:

Ligand Name: iron/sulfur cluster

Ligand 3-letter code: SF4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1CLF

Chain ID: A

ChEMBL ID:

UniProt ID: P00195

Base Structure: SolutionNMR

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
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	55
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-241052.479381
FMO2-HF: Nuclear repulsion	219647.766425
FMO2-HF: Total energy	-21404.712956
FMO2-MP2: Total energy	-21459.787314

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:ALA)

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

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.
-291.203	-290.982	26.612	-14.137	-12.696	-0.147

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.753 / q_NPA : 0.876

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	0.819	0.912	3.860	25.154	26.675	-0.016	-0.814	-0.691	0.001
32	A	32	ILE	0	0.022	-0.007	3.667	-0.087	0.098	0.002	-0.041	-0.146	0.000
34	A	34	ALA	0	-0.043	-0.046	2.541	-2.771	-2.342	0.613	-0.358	-0.684	-0.001
35	A	35	ASP	-1	-0.927	-0.945	2.878	-41.343	-39.958	1.271	-1.020	-1.636	-0.016
37	A	37	CYS	0	-0.113	-0.036	2.355	-2.896	-2.347	1.910	-1.001	-1.458	-0.003
38	A	38	ILE	0	0.051	0.024	2.548	-12.911	-11.197	0.882	-1.021	-1.575	-0.013
39	A	39	ASP	-1	-0.790	-0.887	1.868	-132.722	-138.328	21.951	-9.847	-6.498	-0.115
40	A	40	CYS	0	-0.074	-0.044	4.512	8.792	8.836	-0.001	-0.035	-0.008	0.000
4	A	4	ILE	0	-0.011	-0.021	6.828	-0.700	-0.700	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.042	0.013	9.800	1.545	1.545	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.884	-0.964	12.239	-15.736	-15.736	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.030	-0.008	15.007	0.992	0.992	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.069	-0.022	14.145	0.398	0.398	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.041	0.026	16.229	0.774	0.774	0.000	0.000	0.000	0.000
10	A	10	SER	0	0.003	-0.011	17.912	-0.879	-0.879	0.000	0.000	0.000	0.000
11	A	11	CYS	0	-0.058	-0.034	18.183	0.426	0.426	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.037	0.025	17.103	0.471	0.471	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.012	-0.008	16.616	-0.649	-0.649	0.000	0.000	0.000	0.000
14	A	14	CYS	0	-0.051	-0.054	11.755	-0.764	-0.764	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.027	0.014	12.385	-1.201	-1.201	0.000	0.000	0.000	0.000
16	A	16	SER	0	0.000	-0.023	13.066	-0.811	-0.811	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.909	-0.918	13.491	-16.957	-16.957	0.000	0.000	0.000	0.000
18	A	18	CYS	0	-0.043	0.010	8.080	-1.350	-1.350	0.000	0.000	0.000	0.000
19	A	19	PRO	0	-0.029	-0.027	9.717	0.986	0.986	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.006	-0.006	7.987	1.352	1.352	0.000	0.000	0.000	0.000
21	A	21	ASN	0	-0.041	-0.028	11.319	0.771	0.771	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.013	0.021	6.660	0.925	0.925	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.015	-0.001	7.317	-2.792	-2.792	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.008	0.010	9.871	2.314	2.314	0.000	0.000	0.000	0.000
25	A	25	GLN	0	-0.002	-0.004	12.605	-0.580	-0.580	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.006	-0.001	13.295	0.392	0.392	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.817	-0.893	13.708	-19.608	-19.608	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.093	-0.067	15.617	1.544	1.544	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.010	0.034	13.751	0.839	0.839	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.006	-0.033	12.433	0.297	0.297	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.003	0.004	9.353	-0.577	-0.577	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.875	-0.931	6.383	-26.335	-26.335	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.006	-0.015	5.351	0.004	0.004	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.032	0.024	6.946	4.204	4.204	0.000	0.000	0.000	0.000
42	A	42	ASN	0	0.002	-0.006	8.789	2.513	2.513	0.000	0.000	0.000	0.000
43	A	43	CYS	0	-0.017	-0.006	7.161	-4.114	-4.114	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.034	-0.003	7.986	1.936	1.936	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.068	-0.037	9.901	2.678	2.678	0.000	0.000	0.000	0.000
46	A	46	VAL	0	0.005	0.013	12.858	1.269	1.269	0.000	0.000	0.000	0.000
47	A	47	CYS	0	-0.028	0.024	12.784	1.431	1.431	0.000	0.000	0.000	0.000
48	A	48	PRO	0	-0.013	-0.017	14.719	-0.028	-0.028	0.000	0.000	0.000	0.000
49	A	49	VAL	0	-0.017	-0.010	16.193	0.673	0.673	0.000	0.000	0.000	0.000
50	A	50	GLY	0	-0.006	0.001	13.472	-0.187	-0.187	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.034	0.005	12.322	-1.322	-1.322	0.000	0.000	0.000	0.000
52	A	52	PRO	0	-0.051	-0.015	7.658	-0.922	-0.922	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.011	-0.005	7.617	-3.117	-3.117	0.000	0.000	0.000	0.000
54	A	54	GLN	0	-0.060	-0.045	5.413	-3.403	-3.403	0.000	0.000	0.000	0.000
55	A	55	GLU	-2	-1.731	-1.840	7.294	-59.121	-59.121	0.000	0.000	0.000	0.000

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