FMO DATABASE

FMODB ID: 3Z5ML

Calculation Name: 7ML4-F-Other547

Preferred Name:

Target Type:

Ligand Name: iron/sulfur cluster

Ligand 3-letter code: SF4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7ML4

Chain ID: F

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

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	85
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-564657.735643
FMO2-HF: Nuclear repulsion	530377.920623
FMO2-HF: Total energy	-34279.815019
FMO2-MP2: Total energy	-34379.686163

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:71:GLU)

Summations of interaction energy for fragment #1(A:71:GLU)

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.
-33.054	-39.512	7.291	3.956	-4.789	-0.076

Interaction energy analysis for fragmet #1(A:71:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.144 / q_NPA : -0.064

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	73	ALA	0	0.015	0.004	2.589	4.430	-2.911	-0.001	8.937	-1.596	-0.007
4	A	74	ILE	0	0.005	0.005	1.905	-35.015	-34.163	7.293	-4.975	-3.170	-0.069
5	A	75	PRO	0	-0.009	0.004	4.727	1.688	1.719	-0.001	-0.006	-0.023	0.000
6	A	76	LYS	1	0.981	0.993	7.472	5.161	5.161	0.000	0.000	0.000	0.000
7	A	77	ASP	-1	-0.872	-0.920	10.987	-5.594	-5.594	0.000	0.000	0.000	0.000
8	A	78	GLN	0	-0.051	-0.071	9.418	-2.111	-2.111	0.000	0.000	0.000	0.000
9	A	79	ARG	1	0.751	0.876	9.949	4.355	4.355	0.000	0.000	0.000	0.000
10	A	80	ALA	0	-0.010	-0.015	11.353	0.656	0.656	0.000	0.000	0.000	0.000
11	A	81	THR	0	-0.103	-0.065	12.785	0.787	0.787	0.000	0.000	0.000	0.000
12	A	82	THR	0	-0.018	-0.015	15.159	0.006	0.006	0.000	0.000	0.000	0.000
13	A	83	PRO	0	0.034	0.028	18.169	-0.084	-0.084	0.000	0.000	0.000	0.000
14	A	84	TYR	0	0.029	0.022	19.585	0.043	0.043	0.000	0.000	0.000	0.000
15	A	85	MET	0	0.002	0.023	20.649	-0.128	-0.128	0.000	0.000	0.000	0.000
16	A	86	THR	0	-0.004	-0.034	20.986	0.214	0.214	0.000	0.000	0.000	0.000
17	A	87	LYS	1	1.007	0.988	23.505	0.576	0.576	0.000	0.000	0.000	0.000
18	A	88	TYR	0	0.000	-0.007	23.166	0.053	0.053	0.000	0.000	0.000	0.000
19	A	89	GLU	-1	-0.760	-0.824	18.275	-1.675	-1.675	0.000	0.000	0.000	0.000
20	A	90	ARG	1	1.043	1.021	22.524	0.773	0.773	0.000	0.000	0.000	0.000
21	A	91	ALA	0	-0.009	-0.002	25.768	0.043	0.043	0.000	0.000	0.000	0.000
22	A	92	ARG	1	0.939	0.975	20.552	0.602	0.602	0.000	0.000	0.000	0.000
23	A	93	ILE	0	0.023	0.031	21.213	0.056	0.056	0.000	0.000	0.000	0.000
24	A	94	LEU	0	0.020	0.017	25.004	0.043	0.043	0.000	0.000	0.000	0.000
25	A	95	GLY	0	0.013	0.012	28.375	0.044	0.044	0.000	0.000	0.000	0.000
26	A	96	THR	0	-0.060	-0.071	23.879	0.018	0.018	0.000	0.000	0.000	0.000
27	A	97	ARG	1	0.760	0.842	27.073	0.781	0.781	0.000	0.000	0.000	0.000
28	A	98	ALA	0	0.042	0.021	28.525	0.029	0.029	0.000	0.000	0.000	0.000
29	A	99	LEU	0	-0.014	0.000	28.679	0.034	0.034	0.000	0.000	0.000	0.000
30	A	100	GLN	0	0.035	0.017	24.785	0.001	0.001	0.000	0.000	0.000	0.000
31	A	101	ILE	0	0.013	0.013	30.403	0.029	0.029	0.000	0.000	0.000	0.000
32	A	102	SER	0	-0.082	-0.055	33.436	0.041	0.041	0.000	0.000	0.000	0.000
33	A	103	MET	0	-0.078	-0.039	32.352	0.038	0.038	0.000	0.000	0.000	0.000
34	A	104	ASN	0	-0.032	-0.018	34.140	0.017	0.017	0.000	0.000	0.000	0.000
35	A	105	ALA	0	0.006	0.018	30.327	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	106	PRO	0	-0.016	-0.013	30.686	0.003	0.003	0.000	0.000	0.000	0.000
37	A	107	VAL	0	0.011	0.023	31.474	-0.041	-0.041	0.000	0.000	0.000	0.000
38	A	108	PHE	0	-0.079	-0.046	27.682	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	109	VAL	0	-0.041	-0.013	32.200	-0.039	-0.039	0.000	0.000	0.000	0.000
40	A	110	ASP	-1	-0.825	-0.906	35.130	-0.559	-0.559	0.000	0.000	0.000	0.000
41	A	111	LEU	0	-0.004	-0.001	37.605	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	112	GLU	-1	-0.807	-0.897	40.487	-0.488	-0.488	0.000	0.000	0.000	0.000
43	A	113	GLY	0	-0.043	-0.022	43.423	0.019	0.019	0.000	0.000	0.000	0.000
44	A	114	GLU	-1	-0.859	-0.910	39.905	-0.399	-0.399	0.000	0.000	0.000	0.000
45	A	115	THR	0	0.001	-0.012	41.274	0.003	0.003	0.000	0.000	0.000	0.000
46	A	116	ASP	-1	-0.848	-0.929	38.455	-0.363	-0.363	0.000	0.000	0.000	0.000
47	A	117	PRO	0	0.030	0.008	34.979	-0.031	-0.031	0.000	0.000	0.000	0.000
48	A	118	LEU	0	-0.001	0.001	33.320	-0.050	-0.050	0.000	0.000	0.000	0.000
49	A	119	ARG	1	0.808	0.882	34.461	0.390	0.390	0.000	0.000	0.000	0.000
50	A	120	ILE	0	0.013	0.021	34.294	-0.035	-0.035	0.000	0.000	0.000	0.000
51	A	121	ALA	0	0.010	0.008	30.430	-0.050	-0.050	0.000	0.000	0.000	0.000
52	A	122	MET	0	-0.073	-0.059	30.925	-0.065	-0.065	0.000	0.000	0.000	0.000
53	A	123	LYS	1	0.741	0.885	32.967	0.564	0.564	0.000	0.000	0.000	0.000
54	A	124	GLU	-1	-0.650	-0.802	29.700	-0.815	-0.815	0.000	0.000	0.000	0.000
55	A	125	LEU	0	-0.064	-0.037	26.605	-0.088	-0.088	0.000	0.000	0.000	0.000
56	A	126	ALA	0	-0.041	-0.007	28.903	-0.073	-0.073	0.000	0.000	0.000	0.000
57	A	127	GLU	-1	-0.861	-0.951	31.391	-0.806	-0.806	0.000	0.000	0.000	0.000
58	A	128	LYS	1	0.743	0.864	24.397	1.421	1.421	0.000	0.000	0.000	0.000
59	A	129	LYS	1	0.942	0.973	27.459	0.991	0.991	0.000	0.000	0.000	0.000
60	A	130	ILE	0	0.008	0.002	24.392	0.070	0.070	0.000	0.000	0.000	0.000
61	A	131	PRO	0	0.024	0.019	22.071	-0.129	-0.129	0.000	0.000	0.000	0.000
62	A	132	LEU	0	-0.027	-0.021	21.109	0.095	0.095	0.000	0.000	0.000	0.000
63	A	133	VAL	0	-0.004	-0.001	16.208	-0.233	-0.233	0.000	0.000	0.000	0.000
64	A	134	ILE	0	-0.060	-0.038	16.661	0.346	0.346	0.000	0.000	0.000	0.000
65	A	135	ARG	1	0.863	0.935	9.701	2.947	2.947	0.000	0.000	0.000	0.000
66	A	136	ARG	1	0.816	0.887	12.370	2.988	2.988	0.000	0.000	0.000	0.000
67	A	137	TYR	0	-0.013	-0.029	10.188	-0.414	-0.414	0.000	0.000	0.000	0.000
68	A	138	LEU	0	0.016	0.023	8.790	0.289	0.289	0.000	0.000	0.000	0.000
69	A	139	PRO	0	0.005	-0.017	11.448	0.611	0.611	0.000	0.000	0.000	0.000
70	A	140	ASP	-1	-0.826	-0.882	7.263	0.606	0.606	0.000	0.000	0.000	0.000
71	A	141	GLY	0	0.002	0.001	9.195	1.912	1.912	0.000	0.000	0.000	0.000
72	A	142	SER	0	-0.071	-0.047	5.142	-0.134	-0.134	0.000	0.000	0.000	0.000
73	A	143	PHE	0	0.000	-0.013	5.793	1.055	1.055	0.000	0.000	0.000	0.000
74	A	144	GLU	-1	-0.729	-0.823	6.543	-8.064	-8.064	0.000	0.000	0.000	0.000
75	A	145	ASP	-1	-0.815	-0.903	9.246	-4.137	-4.137	0.000	0.000	0.000	0.000
76	A	146	TRP	0	-0.034	-0.025	11.444	-0.109	-0.109	0.000	0.000	0.000	0.000
77	A	147	SER	0	-0.024	-0.021	14.977	0.310	0.310	0.000	0.000	0.000	0.000
78	A	148	VAL	0	0.014	-0.002	18.158	0.018	0.018	0.000	0.000	0.000	0.000
79	A	149	GLU	-1	-0.879	-0.941	21.492	-1.617	-1.617	0.000	0.000	0.000	0.000
80	A	150	GLU	-1	-0.796	-0.861	16.452	-3.424	-3.424	0.000	0.000	0.000	0.000
81	A	151	LEU	0	-0.005	0.010	17.909	0.018	0.018	0.000	0.000	0.000	0.000
82	A	152	ILE	0	-0.013	-0.009	21.192	0.166	0.166	0.000	0.000	0.000	0.000
83	A	153	VAL	0	-0.042	-0.038	24.481	0.001	0.001	0.000	0.000	0.000	0.000
84	A	154	ASP	-1	-0.924	-0.965	26.914	-0.916	-0.916	0.000	0.000	0.000	0.000
85	A	155	LEU	-1	-1.000	-0.983	26.557	-0.688	-0.688	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:71:GLU)