FMO DATABASE

FMODB ID: 4G99N

Calculation Name: 7C3F-L-Xray547

Preferred Name:

Target Type:

Ligand Name: iron/sulfur cluster

Ligand 3-letter code: SF4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7C3F

Chain ID: L

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2025-10-06

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	107
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-817043.482918
FMO2-HF: Nuclear repulsion	776066.774049
FMO2-HF: Total energy	-40976.708869
FMO2-MP2: Total energy	-41096.823421

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:7:THR)

Summations of interaction energy for fragment #1(A:7:THR)

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.
-59.502	-56.69	0.053	-1.106	-1.758	-0.007

Interaction energy analysis for fragmet #1(A:7:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.853 / q_NPA : 0.908

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

Sort

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	9	ASP	-1	-0.855	-0.915	3.282	-41.859	-39.505	0.056	-1.059	-1.351	-0.007
4	A	10	ILE	0	-0.047	-0.009	4.951	1.333	1.361	-0.001	-0.001	-0.025	0.000
43	A	49	ASN	0	0.020	0.000	4.548	-0.801	-0.748	-0.001	-0.003	-0.049	0.000
47	A	53	GLN	0	-0.052	-0.025	4.203	-8.524	-8.147	-0.001	-0.043	-0.333	0.000
5	A	11	GLN	0	0.015	0.023	7.553	0.690	0.690	0.000	0.000	0.000	0.000
6	A	12	VAL	0	0.032	0.013	10.631	0.825	0.825	0.000	0.000	0.000	0.000
7	A	13	VAL	0	-0.043	-0.011	13.617	0.307	0.307	0.000	0.000	0.000	0.000
8	A	14	ASN	0	0.010	-0.011	17.014	-0.371	-0.371	0.000	0.000	0.000	0.000
9	A	15	ASP	-1	-0.701	-0.837	20.300	-11.851	-11.851	0.000	0.000	0.000	0.000
10	A	16	SER	0	-0.046	-0.016	23.154	0.166	0.166	0.000	0.000	0.000	0.000
11	A	17	THR	0	0.041	0.015	19.078	0.197	0.197	0.000	0.000	0.000	0.000
12	A	18	TRP	0	0.083	0.036	19.606	-0.592	-0.592	0.000	0.000	0.000	0.000
13	A	19	ASP	-1	-0.808	-0.897	22.355	-11.547	-11.547	0.000	0.000	0.000	0.000
14	A	20	SER	0	-0.033	-0.028	22.076	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	21	LEU	0	-0.033	-0.013	16.549	-0.319	-0.319	0.000	0.000	0.000	0.000
16	A	22	VAL	0	0.005	0.004	18.361	-0.756	-0.756	0.000	0.000	0.000	0.000
17	A	23	LEU	0	-0.081	-0.028	20.625	0.266	0.266	0.000	0.000	0.000	0.000
18	A	24	LYS	1	0.852	0.900	24.037	11.458	11.458	0.000	0.000	0.000	0.000
19	A	25	ALA	0	-0.023	0.014	19.714	-0.053	-0.053	0.000	0.000	0.000	0.000
20	A	26	THR	0	-0.024	-0.016	20.463	0.529	0.529	0.000	0.000	0.000	0.000
21	A	27	GLY	0	0.014	0.008	20.087	-0.656	-0.656	0.000	0.000	0.000	0.000
22	A	28	PRO	0	0.004	0.003	17.834	0.272	0.272	0.000	0.000	0.000	0.000
23	A	29	VAL	0	-0.021	-0.006	16.292	-1.104	-1.104	0.000	0.000	0.000	0.000
24	A	30	VAL	0	0.001	0.007	13.811	0.963	0.963	0.000	0.000	0.000	0.000
25	A	31	VAL	0	-0.010	-0.014	14.939	-0.881	-0.881	0.000	0.000	0.000	0.000
26	A	32	ASP	-1	-0.871	-0.936	13.703	-17.664	-17.664	0.000	0.000	0.000	0.000
27	A	33	PHE	0	-0.003	-0.006	15.794	-0.218	-0.218	0.000	0.000	0.000	0.000
28	A	34	TRP	0	0.034	0.010	14.785	0.294	0.294	0.000	0.000	0.000	0.000
29	A	35	ALA	0	0.081	0.041	17.671	0.607	0.607	0.000	0.000	0.000	0.000
30	A	36	PRO	0	-0.010	0.012	17.806	-0.552	-0.552	0.000	0.000	0.000	0.000
31	A	37	TRP	0	0.022	-0.003	18.734	-0.597	-0.597	0.000	0.000	0.000	0.000
32	A	38	CYS	0	-0.022	0.010	19.731	0.454	0.454	0.000	0.000	0.000	0.000
33	A	39	GLY	0	0.032	0.011	18.757	-0.742	-0.742	0.000	0.000	0.000	0.000
34	A	40	PRO	0	0.028	-0.022	18.140	-0.725	-0.725	0.000	0.000	0.000	0.000
35	A	41	SER	0	0.020	0.017	15.917	-0.388	-0.388	0.000	0.000	0.000	0.000
36	A	42	LYS	1	0.951	0.965	13.929	16.050	16.050	0.000	0.000	0.000	0.000
37	A	43	MET	0	-0.058	-0.019	13.293	-0.817	-0.817	0.000	0.000	0.000	0.000
38	A	44	ILE	0	0.008	0.008	13.791	-0.223	-0.223	0.000	0.000	0.000	0.000
39	A	45	ASP	-1	-0.787	-0.862	9.731	-23.699	-23.699	0.000	0.000	0.000	0.000
40	A	46	PRO	0	-0.044	-0.024	7.662	-2.473	-2.473	0.000	0.000	0.000	0.000
41	A	47	LEU	0	-0.003	0.009	8.014	-1.785	-1.785	0.000	0.000	0.000	0.000
42	A	48	VAL	0	0.026	0.002	10.086	-0.354	-0.354	0.000	0.000	0.000	0.000
44	A	50	ASP	-1	-0.872	-0.905	5.612	-27.615	-27.615	0.000	0.000	0.000	0.000
45	A	51	LEU	0	0.019	-0.009	7.494	-0.115	-0.115	0.000	0.000	0.000	0.000
46	A	52	ALA	0	0.011	0.014	6.394	0.665	0.665	0.000	0.000	0.000	0.000
48	A	54	HIS	0	-0.068	-0.024	6.264	1.536	1.536	0.000	0.000	0.000	0.000
49	A	55	TYR	0	-0.024	-0.048	9.935	0.971	0.971	0.000	0.000	0.000	0.000
50	A	56	THR	0	0.007	-0.003	6.974	0.992	0.992	0.000	0.000	0.000	0.000
51	A	57	GLY	0	-0.056	-0.029	10.261	1.277	1.277	0.000	0.000	0.000	0.000
52	A	58	LYS	1	0.911	0.962	13.217	19.052	19.052	0.000	0.000	0.000	0.000
53	A	59	ILE	0	0.025	0.017	13.623	1.106	1.106	0.000	0.000	0.000	0.000
54	A	60	LYS	1	0.860	0.949	10.848	22.594	22.594	0.000	0.000	0.000	0.000
55	A	61	PHE	0	0.037	0.009	9.725	0.948	0.948	0.000	0.000	0.000	0.000
56	A	62	TYR	0	-0.035	-0.036	11.562	-1.507	-1.507	0.000	0.000	0.000	0.000
57	A	63	LYS	1	0.857	0.913	10.181	22.598	22.598	0.000	0.000	0.000	0.000
58	A	64	LEU	0	-0.004	-0.001	13.564	0.077	0.077	0.000	0.000	0.000	0.000
59	A	65	ASN	0	-0.039	-0.026	17.021	0.533	0.533	0.000	0.000	0.000	0.000
60	A	66	THR	0	-0.010	-0.043	18.374	0.678	0.678	0.000	0.000	0.000	0.000
61	A	67	ASP	-1	-0.894	-0.946	21.624	-11.894	-11.894	0.000	0.000	0.000	0.000
62	A	68	GLU	-1	-0.934	-0.956	18.743	-14.912	-14.912	0.000	0.000	0.000	0.000
63	A	69	SER	0	-0.078	-0.039	21.363	-0.128	-0.128	0.000	0.000	0.000	0.000
64	A	70	PRO	0	0.077	0.043	23.371	-0.184	-0.184	0.000	0.000	0.000	0.000
65	A	71	ASN	0	-0.078	-0.054	26.219	0.575	0.575	0.000	0.000	0.000	0.000
66	A	72	THR	0	0.013	-0.019	22.371	0.222	0.222	0.000	0.000	0.000	0.000
67	A	73	PRO	0	-0.034	-0.018	23.272	0.114	0.114	0.000	0.000	0.000	0.000
68	A	74	GLY	0	-0.020	-0.006	25.195	0.271	0.271	0.000	0.000	0.000	0.000
69	A	75	GLN	0	-0.032	-0.009	27.718	0.090	0.090	0.000	0.000	0.000	0.000
70	A	76	TYR	0	0.016	0.002	25.212	0.152	0.152	0.000	0.000	0.000	0.000
71	A	77	GLY	0	-0.006	0.004	27.936	0.038	0.038	0.000	0.000	0.000	0.000
72	A	78	VAL	0	-0.017	-0.001	23.001	0.086	0.086	0.000	0.000	0.000	0.000
73	A	79	ARG	1	0.901	0.943	26.277	9.932	9.932	0.000	0.000	0.000	0.000
74	A	80	SER	0	0.009	0.013	25.715	-0.064	-0.064	0.000	0.000	0.000	0.000
75	A	81	ILE	0	0.025	0.041	20.091	-0.329	-0.329	0.000	0.000	0.000	0.000
76	A	82	PRO	0	0.007	-0.010	17.790	0.259	0.259	0.000	0.000	0.000	0.000
77	A	83	THR	0	-0.023	-0.023	19.577	0.785	0.785	0.000	0.000	0.000	0.000
78	A	84	ILE	0	0.002	0.014	15.266	-0.523	-0.523	0.000	0.000	0.000	0.000
79	A	85	MET	0	-0.069	-0.023	18.626	0.771	0.771	0.000	0.000	0.000	0.000
80	A	86	ILE	0	0.015	0.017	18.076	-0.877	-0.877	0.000	0.000	0.000	0.000
81	A	87	PHE	0	0.008	-0.012	20.108	0.886	0.886	0.000	0.000	0.000	0.000
82	A	88	VAL	0	0.028	0.003	20.993	-0.579	-0.579	0.000	0.000	0.000	0.000
83	A	89	GLY	0	0.019	0.022	23.492	0.484	0.484	0.000	0.000	0.000	0.000
84	A	90	GLY	0	0.025	0.024	24.659	0.425	0.425	0.000	0.000	0.000	0.000
85	A	91	GLU	-1	-0.920	-0.952	26.300	-9.792	-9.792	0.000	0.000	0.000	0.000
86	A	92	LYS	1	0.891	0.950	24.666	10.421	10.421	0.000	0.000	0.000	0.000
87	A	93	LYS	1	0.813	0.896	24.064	11.069	11.069	0.000	0.000	0.000	0.000
88	A	94	ASP	-1	-0.812	-0.901	22.639	-12.046	-12.046	0.000	0.000	0.000	0.000
89	A	95	THR	0	-0.109	-0.081	22.681	-0.196	-0.196	0.000	0.000	0.000	0.000
90	A	96	ILE	0	0.035	0.037	19.433	0.406	0.406	0.000	0.000	0.000	0.000
91	A	97	ILE	0	0.005	-0.006	21.457	-0.328	-0.328	0.000	0.000	0.000	0.000
92	A	98	GLY	0	-0.004	0.007	22.003	0.301	0.301	0.000	0.000	0.000	0.000
93	A	99	ALA	0	-0.019	-0.014	18.835	-0.532	-0.532	0.000	0.000	0.000	0.000
94	A	100	VAL	0	0.027	0.013	18.214	0.659	0.659	0.000	0.000	0.000	0.000
95	A	101	PRO	0	0.003	0.004	17.844	-0.830	-0.830	0.000	0.000	0.000	0.000
96	A	102	LYS	1	0.913	0.922	11.736	22.167	22.167	0.000	0.000	0.000	0.000
97	A	103	THR	0	0.010	0.016	16.502	-0.262	-0.262	0.000	0.000	0.000	0.000
98	A	104	THR	0	0.021	0.017	19.434	0.398	0.398	0.000	0.000	0.000	0.000
99	A	105	LEU	0	0.028	0.029	14.580	0.274	0.274	0.000	0.000	0.000	0.000
100	A	106	THR	0	-0.012	-0.024	15.721	-0.409	-0.409	0.000	0.000	0.000	0.000
101	A	107	SER	0	0.018	0.019	17.025	0.402	0.402	0.000	0.000	0.000	0.000
102	A	108	SER	0	-0.065	-0.038	19.789	0.781	0.781	0.000	0.000	0.000	0.000
103	A	109	LEU	0	0.010	-0.001	14.174	0.233	0.233	0.000	0.000	0.000	0.000
104	A	110	ASP	-1	-0.805	-0.901	17.960	-15.724	-15.724	0.000	0.000	0.000	0.000
105	A	111	LYS	1	0.805	0.901	19.786	12.585	12.585	0.000	0.000	0.000	0.000
106	A	112	PHE	0	-0.066	-0.031	19.676	0.590	0.590	0.000	0.000	0.000	0.000
107	A	113	LEU	-1	-0.945	-0.951	17.104	-13.906	-13.906	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:7:THR)