FMO DATABASE

FMODB ID: 2M7GR

Calculation Name: 1H98-A-Xray547

Preferred Name:

Target Type:

Ligand Name: iron/sulfur cluster | fe3-s4 cluster

Ligand 3-letter code: SF4 | F3S

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1H98

Chain ID: A

ChEMBL ID:

UniProt ID: P03942

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	77
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-498884.513945
FMO2-HF: Nuclear repulsion	466900.444864
FMO2-HF: Total energy	-31984.069081
FMO2-MP2: Total energy	-32070.48637

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:PRO)

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

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.
-382.766	-374.689	21.099	-13.539	-15.638	-0.159

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.790 / q_NPA : 0.874

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	0.009	0.007	3.705	0.909	2.784	0.002	-0.798	-1.079	0.001
34	A	34	ILE	0	0.034	0.011	4.257	1.585	1.687	-0.001	-0.012	-0.089	0.000
36	A	36	PRO	0	-0.025	-0.030	2.267	-4.502	-3.742	1.296	-0.781	-1.275	-0.001
37	A	37	GLU	-1	-0.929	-0.968	2.759	-48.977	-46.738	0.549	-0.938	-1.851	-0.018
38	A	38	GLU	-1	-0.881	-0.917	5.317	-24.090	-24.098	-0.001	-0.004	0.013	0.000
39	A	39	CYS	0	-0.066	-0.007	2.699	-0.013	0.853	0.348	-0.378	-0.837	-0.001
40	A	40	ILE	0	0.003	-0.004	3.869	-7.156	-6.684	0.001	-0.136	-0.337	-0.001
41	A	41	ASP	-1	-0.792	-0.870	1.803	-120.117	-122.684	17.577	-8.198	-6.812	-0.111
42	A	42	CYS	0	-0.061	-0.023	4.630	4.061	4.090	-0.001	-0.019	-0.009	0.000
57	A	57	GLU	-1	-0.912	-0.966	2.447	-62.312	-58.540	1.326	-2.013	-3.085	-0.026
58	A	58	GLU	-1	-0.967	-0.997	3.596	-56.993	-56.456	0.003	-0.262	-0.277	-0.002
4	A	4	ILE	0	-0.024	-0.005	5.619	3.171	3.171	0.000	0.000	0.000	0.000
5	A	5	CYS	0	-0.008	-0.004	9.299	0.597	0.597	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.803	-0.890	11.630	-15.566	-15.566	0.000	0.000	0.000	0.000
7	A	7	PRO	0	-0.012	-0.002	14.663	0.778	0.778	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.013	0.021	14.273	0.609	0.609	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.018	0.008	16.250	0.679	0.679	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.053	-0.020	18.339	0.494	0.494	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.073	-0.025	19.338	0.601	0.601	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.748	0.840	17.781	15.296	15.296	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.831	-0.904	18.568	-15.114	-15.114	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.034	-0.021	16.716	0.499	0.499	0.000	0.000	0.000	0.000
15	A	15	SER	0	0.025	0.013	17.340	-0.170	-0.170	0.000	0.000	0.000	0.000
16	A	16	CYS	0	-0.084	-0.042	12.373	-0.058	-0.058	0.000	0.000	0.000	0.000
17	A	17	VAL	0	0.006	-0.004	13.022	-1.360	-1.360	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.947	-0.970	14.747	-15.006	-15.006	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.037	-0.008	13.188	0.260	0.260	0.000	0.000	0.000	0.000
20	A	20	CYS	0	-0.033	0.003	9.268	-1.915	-1.915	0.000	0.000	0.000	0.000
21	A	21	PRO	0	-0.025	-0.022	10.645	0.718	0.718	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.024	-0.031	8.517	0.834	0.834	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.950	-0.970	11.677	-17.634	-17.634	0.000	0.000	0.000	0.000
24	A	24	CYS	0	-0.024	0.016	7.540	-0.986	-0.986	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.029	-0.032	8.340	-2.421	-2.421	0.000	0.000	0.000	0.000
26	A	26	TYR	0	-0.051	-0.040	9.938	2.753	2.753	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.827	-0.898	13.120	-16.103	-16.103	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.034	0.010	14.545	-0.193	-0.193	0.000	0.000	0.000	0.000
29	A	29	GLY	0	-0.040	-0.016	15.419	0.432	0.432	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.847	-0.916	16.825	-16.315	-16.315	0.000	0.000	0.000	0.000
31	A	31	GLN	0	0.002	-0.014	11.347	1.220	1.220	0.000	0.000	0.000	0.000
32	A	32	PHE	0	0.052	0.009	13.121	0.481	0.481	0.000	0.000	0.000	0.000
33	A	33	TYR	0	-0.038	-0.020	8.513	-0.574	-0.574	0.000	0.000	0.000	0.000
35	A	35	HIS	0	0.068	0.030	6.024	-4.393	-4.393	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.063	0.035	7.218	3.390	3.390	0.000	0.000	0.000	0.000
44	A	44	ALA	0	-0.025	-0.018	8.995	1.673	1.673	0.000	0.000	0.000	0.000
45	A	45	CYS	0	-0.009	-0.002	7.951	1.036	1.036	0.000	0.000	0.000	0.000
46	A	46	VAL	0	0.027	0.018	9.343	1.057	1.057	0.000	0.000	0.000	0.000
47	A	47	PRO	0	-0.050	-0.025	11.930	1.480	1.480	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.000	0.007	14.658	1.231	1.231	0.000	0.000	0.000	0.000
49	A	49	CYS	0	-0.030	0.015	14.156	0.810	0.810	0.000	0.000	0.000	0.000
50	A	50	PRO	0	0.018	0.016	16.220	0.043	0.043	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.034	-0.026	17.144	0.615	0.615	0.000	0.000	0.000	0.000
52	A	52	ASN	0	-0.051	-0.035	15.869	-0.388	-0.388	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.025	0.004	13.730	-0.700	-0.700	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.018	-0.015	8.569	-1.280	-1.280	0.000	0.000	0.000	0.000
55	A	55	TYR	0	0.018	0.007	8.531	2.855	2.855	0.000	0.000	0.000	0.000
56	A	56	PRO	0	0.053	0.030	4.879	-4.513	-4.513	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.919	-0.960	6.704	-25.712	-25.712	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.058	-0.020	7.309	3.325	3.325	0.000	0.000	0.000	0.000
61	A	61	PRO	0	-0.009	-0.001	9.891	1.490	1.490	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.847	-0.916	13.489	-21.352	-21.352	0.000	0.000	0.000	0.000
63	A	63	GLN	0	-0.036	-0.028	15.386	-0.423	-0.423	0.000	0.000	0.000	0.000
64	A	64	TRP	0	-0.026	-0.027	12.583	0.226	0.226	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.908	0.951	10.401	23.208	23.208	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.017	-0.009	10.402	-1.763	-1.763	0.000	0.000	0.000	0.000
67	A	67	TYR	0	-0.035	-0.047	10.008	0.027	0.027	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.026	0.037	5.077	-0.317	-0.317	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.841	-0.937	6.974	-25.557	-25.557	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.759	0.866	9.532	19.723	19.723	0.000	0.000	0.000	0.000
71	A	71	ASN	0	0.004	-0.022	6.184	0.412	0.412	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.927	0.967	5.960	31.951	31.951	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.900	0.955	8.183	20.751	20.751	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.080	-0.028	10.955	1.465	1.465	0.000	0.000	0.000	0.000
75	A	75	ALA	0	0.015	0.014	8.340	1.004	1.004	0.000	0.000	0.000	0.000
76	A	76	GLY	0	-0.083	-0.029	10.338	0.484	0.484	0.000	0.000	0.000	0.000
77	A	77	LEU	-1	-0.961	-0.968	6.813	-23.026	-23.026	0.000	0.000	0.000	0.000

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