FMO DATABASE

FMODB ID: LRVM9

Calculation Name: 6H8K-K-Xray547

Preferred Name:

Target Type:

Ligand Name: iron/sulfur cluster | fe2/s2 (inorganic) cluster

Ligand 3-letter code: SF4 | FES

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6H8K

Chain ID: K

ChEMBL ID:

UniProt ID: Q9B6E8

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	143
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1299012.224394
FMO2-HF: Nuclear repulsion	1240249.750303
FMO2-HF: Total energy	-58762.474091
FMO2-MP2: Total energy	-58924.633566

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:59:TYR)

Summations of interaction energy for fragment #1(A:59:TYR)

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.
36.052	43.81	6.123	-3.536	-10.345	0.009

Interaction energy analysis for fragmet #1(A:59:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.919 / q_NPA : 0.950

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	61	LEU	0	0.063	0.039	2.658	3.514	7.561	1.203	-1.829	-3.421	0.006
4	A	62	THR	0	-0.015	-0.024	2.323	0.383	3.385	2.874	-1.504	-4.372	0.000
5	A	63	THR	0	0.029	0.010	3.636	2.344	2.193	0.065	0.550	-0.464	0.001
6	A	64	LEU	0	0.021	0.014	2.143	1.146	1.825	1.982	-0.749	-1.912	0.002
7	A	65	ASP	-1	-0.884	-0.929	4.701	-22.842	-22.661	-0.001	-0.004	-0.176	0.000
8	A	66	ALA	0	0.029	0.003	6.402	2.164	2.164	0.000	0.000	0.000	0.000
9	A	67	VAL	0	-0.012	-0.004	8.848	1.800	1.800	0.000	0.000	0.000	0.000
10	A	68	ALA	0	0.042	0.024	9.683	1.495	1.495	0.000	0.000	0.000	0.000
11	A	69	ASN	0	-0.018	0.001	9.539	2.040	2.040	0.000	0.000	0.000	0.000
12	A	70	TRP	0	-0.022	-0.029	12.549	1.531	1.531	0.000	0.000	0.000	0.000
13	A	71	ALA	0	0.005	0.007	14.368	0.867	0.867	0.000	0.000	0.000	0.000
14	A	72	ARG	1	0.919	0.949	12.130	17.251	17.251	0.000	0.000	0.000	0.000
15	A	73	GLN	0	0.041	0.029	16.745	0.390	0.390	0.000	0.000	0.000	0.000
16	A	74	GLY	0	-0.002	-0.003	18.824	0.478	0.478	0.000	0.000	0.000	0.000
17	A	75	SER	0	0.027	0.018	20.231	0.376	0.376	0.000	0.000	0.000	0.000
18	A	76	PHE	0	-0.028	0.002	20.951	0.242	0.242	0.000	0.000	0.000	0.000
19	A	77	TRP	0	0.039	0.015	22.417	0.415	0.415	0.000	0.000	0.000	0.000
20	A	78	PRO	0	-0.005	-0.002	25.737	-0.080	-0.080	0.000	0.000	0.000	0.000
21	A	79	VAL	0	-0.029	-0.011	27.925	0.253	0.253	0.000	0.000	0.000	0.000
22	A	80	THR	0	0.050	0.004	30.907	-0.053	-0.053	0.000	0.000	0.000	0.000
23	A	81	PHE	0	-0.014	-0.002	33.763	0.236	0.236	0.000	0.000	0.000	0.000
24	A	82	GLY	0	0.001	-0.008	35.489	0.021	0.021	0.000	0.000	0.000	0.000
25	A	83	LEU	0	-0.080	-0.027	38.040	0.123	0.123	0.000	0.000	0.000	0.000
26	A	84	ALA	0	0.025	-0.008	41.281	0.173	0.173	0.000	0.000	0.000	0.000
27	A	85	CYS	0	-0.006	-0.002	42.850	-0.036	-0.036	0.000	0.000	0.000	0.000
28	A	86	CYS	0	-0.026	-0.006	38.128	0.023	0.023	0.000	0.000	0.000	0.000
29	A	87	ALA	0	0.054	0.040	38.680	-0.161	-0.161	0.000	0.000	0.000	0.000
30	A	88	VAL	0	-0.013	-0.003	39.650	-0.061	-0.061	0.000	0.000	0.000	0.000
31	A	89	GLU	-1	-0.806	-0.913	38.787	-7.191	-7.191	0.000	0.000	0.000	0.000
32	A	90	MET	0	-0.021	-0.012	32.056	-0.098	-0.098	0.000	0.000	0.000	0.000
33	A	91	MET	0	-0.022	-0.009	36.332	-0.159	-0.159	0.000	0.000	0.000	0.000
34	A	92	HIS	0	0.009	-0.002	38.659	-0.113	-0.113	0.000	0.000	0.000	0.000
35	A	93	VAL	0	-0.073	-0.025	32.741	-0.071	-0.071	0.000	0.000	0.000	0.000
36	A	94	SER	0	-0.049	-0.064	34.122	-0.136	-0.136	0.000	0.000	0.000	0.000
37	A	95	ALA	0	0.011	0.036	35.261	0.024	0.024	0.000	0.000	0.000	0.000
38	A	96	PRO	0	-0.025	0.002	36.186	-0.159	-0.159	0.000	0.000	0.000	0.000
39	A	97	ARG	1	0.841	0.920	35.250	7.930	7.930	0.000	0.000	0.000	0.000
40	A	98	TYR	0	-0.006	-0.022	25.840	-0.229	-0.229	0.000	0.000	0.000	0.000
41	A	99	ASP	-1	-0.858	-0.933	31.320	-8.479	-8.479	0.000	0.000	0.000	0.000
42	A	100	GLN	0	-0.073	-0.030	29.190	-0.094	-0.094	0.000	0.000	0.000	0.000
43	A	101	ASP	-1	-0.863	-0.951	24.270	-10.795	-10.795	0.000	0.000	0.000	0.000
44	A	102	ARG	0	0.010	0.053	25.052	-0.041	-0.041	0.000	0.000	0.000	0.000
45	A	103	LEU	0	0.025	0.002	27.063	-0.124	-0.124	0.000	0.000	0.000	0.000
46	A	104	GLY	0	-0.051	-0.016	28.409	0.163	0.163	0.000	0.000	0.000	0.000
47	A	105	ILE	0	0.040	0.004	29.316	0.166	0.166	0.000	0.000	0.000	0.000
48	A	106	ILE	0	0.035	0.007	32.029	-0.075	-0.075	0.000	0.000	0.000	0.000
49	A	107	PHE	0	0.025	0.023	28.804	0.110	0.110	0.000	0.000	0.000	0.000
50	A	108	ARG	1	0.931	0.954	32.355	7.602	7.602	0.000	0.000	0.000	0.000
51	A	109	ALA	0	-0.020	-0.004	34.596	0.119	0.119	0.000	0.000	0.000	0.000
52	A	110	SER	0	-0.035	0.021	30.321	0.005	0.005	0.000	0.000	0.000	0.000
53	A	111	PRO	0	-0.067	-0.034	29.973	0.220	0.220	0.000	0.000	0.000	0.000
54	A	112	ARG	1	0.926	0.952	26.331	9.317	9.317	0.000	0.000	0.000	0.000
55	A	113	GLN	0	-0.015	-0.001	25.872	-0.137	-0.137	0.000	0.000	0.000	0.000
56	A	114	SER	0	0.038	-0.009	24.890	0.190	0.190	0.000	0.000	0.000	0.000
57	A	115	ASP	-1	-0.877	-0.934	21.227	-11.668	-11.668	0.000	0.000	0.000	0.000
58	A	116	ILE	0	-0.010	0.007	21.553	-0.082	-0.082	0.000	0.000	0.000	0.000
59	A	117	MET	0	-0.028	-0.013	25.253	0.347	0.347	0.000	0.000	0.000	0.000
60	A	118	ILE	0	0.012	0.013	28.507	-0.045	-0.045	0.000	0.000	0.000	0.000
61	A	119	VAL	0	-0.005	-0.005	30.934	0.263	0.263	0.000	0.000	0.000	0.000
62	A	120	ALA	0	0.040	0.023	33.989	0.017	0.017	0.000	0.000	0.000	0.000
63	A	121	GLY	0	0.016	-0.010	36.550	0.198	0.198	0.000	0.000	0.000	0.000
64	A	122	THR	0	0.010	-0.024	39.686	-0.053	-0.053	0.000	0.000	0.000	0.000
65	A	123	LEU	0	0.044	0.016	37.816	-0.050	-0.050	0.000	0.000	0.000	0.000
66	A	124	THR	0	0.044	0.010	41.725	0.029	0.029	0.000	0.000	0.000	0.000
67	A	125	ASN	0	0.015	-0.010	43.197	-0.239	-0.239	0.000	0.000	0.000	0.000
68	A	126	LYS	1	0.951	0.976	44.005	5.897	5.897	0.000	0.000	0.000	0.000
69	A	127	MET	0	0.018	0.014	39.925	0.030	0.030	0.000	0.000	0.000	0.000
70	A	128	ALA	0	0.032	0.025	38.992	-0.166	-0.166	0.000	0.000	0.000	0.000
71	A	129	PRO	0	0.019	-0.004	37.889	-0.197	-0.197	0.000	0.000	0.000	0.000
72	A	130	VAL	0	-0.009	-0.005	37.760	-0.126	-0.126	0.000	0.000	0.000	0.000
73	A	131	LEU	0	0.011	0.010	34.482	-0.153	-0.153	0.000	0.000	0.000	0.000
74	A	132	ARG	1	0.930	0.960	32.979	8.086	8.086	0.000	0.000	0.000	0.000
75	A	133	CYS	0	-0.033	-0.013	32.808	-0.239	-0.239	0.000	0.000	0.000	0.000
76	A	134	VAL	0	0.001	-0.010	31.368	-0.120	-0.120	0.000	0.000	0.000	0.000
77	A	135	TYR	0	0.047	0.020	24.534	-0.204	-0.204	0.000	0.000	0.000	0.000
78	A	136	ASP	-1	-0.844	-0.921	28.179	-9.059	-9.059	0.000	0.000	0.000	0.000
79	A	137	GLN	0	-0.072	-0.049	29.459	-0.232	-0.232	0.000	0.000	0.000	0.000
80	A	138	MET	0	-0.012	0.014	25.776	-0.024	-0.024	0.000	0.000	0.000	0.000
81	A	139	PRO	0	-0.025	0.009	22.059	-0.051	-0.051	0.000	0.000	0.000	0.000
82	A	140	GLU	-1	-0.789	-0.876	19.507	-11.460	-11.460	0.000	0.000	0.000	0.000
83	A	141	PRO	0	-0.079	-0.023	16.755	-0.216	-0.216	0.000	0.000	0.000	0.000
84	A	142	ARG	1	0.792	0.867	18.701	11.000	11.000	0.000	0.000	0.000	0.000
85	A	143	TRP	0	0.015	0.002	16.152	-0.321	-0.321	0.000	0.000	0.000	0.000
86	A	144	VAL	0	-0.020	-0.012	22.935	0.403	0.403	0.000	0.000	0.000	0.000
87	A	145	ILE	0	-0.009	-0.006	26.025	-0.142	-0.142	0.000	0.000	0.000	0.000
88	A	146	SER	0	-0.002	0.002	28.764	0.314	0.314	0.000	0.000	0.000	0.000
89	A	147	MET	0	0.005	0.006	32.337	-0.072	-0.072	0.000	0.000	0.000	0.000
90	A	148	GLY	0	0.062	0.012	34.809	0.206	0.206	0.000	0.000	0.000	0.000
91	A	149	SER	0	-0.019	-0.018	38.050	-0.046	-0.046	0.000	0.000	0.000	0.000
92	A	150	CYS	-1	-0.828	-0.824	40.515	-6.765	-6.765	0.000	0.000	0.000	0.000
93	A	151	ALA	0	0.040	0.035	35.692	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	152	ASN	0	0.019	0.009	34.568	-0.314	-0.314	0.000	0.000	0.000	0.000
95	A	153	GLY	0	0.039	0.035	37.026	-0.058	-0.058	0.000	0.000	0.000	0.000
96	A	158	HIS	1	0.703	0.788	40.537	6.669	6.669	0.000	0.000	0.000	0.000
97	A	159	PHE	0	0.050	0.038	44.064	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	160	SER	0	-0.029	-0.021	46.466	0.163	0.163	0.000	0.000	0.000	0.000
99	A	161	TYR	0	0.033	0.018	48.116	-0.080	-0.080	0.000	0.000	0.000	0.000
100	A	162	SER	0	-0.002	-0.002	49.171	0.013	0.013	0.000	0.000	0.000	0.000
101	A	163	VAL	0	-0.026	-0.012	43.931	-0.039	-0.039	0.000	0.000	0.000	0.000
102	A	164	VAL	0	-0.021	-0.006	40.776	0.064	0.064	0.000	0.000	0.000	0.000
103	A	165	ARG	1	0.950	0.955	42.069	6.655	6.655	0.000	0.000	0.000	0.000
104	A	166	GLY	0	0.070	0.060	37.947	-0.050	-0.050	0.000	0.000	0.000	0.000
105	A	167	CYS	0	-0.049	-0.034	34.024	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	168	ASP	-1	-0.754	-0.851	32.346	-8.716	-8.716	0.000	0.000	0.000	0.000
107	A	169	ARG	1	0.886	0.949	32.846	7.244	7.244	0.000	0.000	0.000	0.000
108	A	170	ILE	0	-0.139	-0.063	34.811	0.145	0.145	0.000	0.000	0.000	0.000
109	A	171	VAL	0	0.013	-0.003	29.179	-0.072	-0.072	0.000	0.000	0.000	0.000
110	A	172	PRO	0	0.012	0.016	26.915	0.087	0.087	0.000	0.000	0.000	0.000
111	A	173	VAL	0	0.020	0.004	27.693	-0.125	-0.125	0.000	0.000	0.000	0.000
112	A	174	ASP	-1	-0.817	-0.895	22.255	-11.916	-11.916	0.000	0.000	0.000	0.000
113	A	175	VAL	0	-0.037	-0.029	24.375	-0.255	-0.255	0.000	0.000	0.000	0.000
114	A	176	TYR	0	-0.041	-0.039	27.052	0.078	0.078	0.000	0.000	0.000	0.000
115	A	177	VAL	0	0.004	-0.003	30.818	-0.065	-0.065	0.000	0.000	0.000	0.000
116	A	178	PRO	0	0.005	0.005	33.086	0.233	0.233	0.000	0.000	0.000	0.000
117	A	179	GLY	0	0.057	0.009	36.593	-0.028	-0.028	0.000	0.000	0.000	0.000
118	A	180	CYS	0	-0.085	-0.043	39.800	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	181	PRO	0	0.037	0.031	41.153	0.156	0.156	0.000	0.000	0.000	0.000
120	A	182	PRO	0	-0.028	-0.027	36.647	0.036	0.036	0.000	0.000	0.000	0.000
121	A	183	THR	0	0.061	0.034	38.609	-0.073	-0.073	0.000	0.000	0.000	0.000
122	A	184	SER	0	0.029	0.003	36.707	-0.240	-0.240	0.000	0.000	0.000	0.000
123	A	185	GLU	-1	-0.910	-0.963	34.667	-8.026	-8.026	0.000	0.000	0.000	0.000
124	A	186	ALA	0	-0.019	0.004	33.396	-0.287	-0.287	0.000	0.000	0.000	0.000
125	A	187	LEU	0	0.014	-0.010	31.413	-0.257	-0.257	0.000	0.000	0.000	0.000
126	A	188	MET	0	0.031	0.027	30.273	-0.203	-0.203	0.000	0.000	0.000	0.000
127	A	189	TYR	0	0.010	0.011	28.084	-0.479	-0.479	0.000	0.000	0.000	0.000
128	A	190	GLY	0	-0.037	-0.026	27.864	-0.348	-0.348	0.000	0.000	0.000	0.000
129	A	191	VAL	0	0.017	0.010	25.591	-0.345	-0.345	0.000	0.000	0.000	0.000
130	A	192	PHE	0	0.044	0.025	24.370	-0.456	-0.456	0.000	0.000	0.000	0.000
131	A	193	GLN	0	-0.012	-0.008	23.111	-0.685	-0.685	0.000	0.000	0.000	0.000
132	A	194	LEU	0	0.002	0.014	21.573	-0.519	-0.519	0.000	0.000	0.000	0.000
133	A	195	GLN	0	-0.001	-0.020	20.159	-0.351	-0.351	0.000	0.000	0.000	0.000
134	A	196	ARG	1	0.908	0.959	18.504	13.094	13.094	0.000	0.000	0.000	0.000
135	A	197	LYS	1	0.791	0.897	17.801	11.410	11.410	0.000	0.000	0.000	0.000
136	A	198	MET	0	0.000	0.007	16.432	-0.554	-0.554	0.000	0.000	0.000	0.000
137	A	199	ARG	1	0.817	0.914	13.859	14.255	14.255	0.000	0.000	0.000	0.000
138	A	200	ASN	0	0.019	0.016	9.832	0.082	0.082	0.000	0.000	0.000	0.000
139	A	201	THR	0	-0.052	-0.030	13.600	-0.351	-0.351	0.000	0.000	0.000	0.000
140	A	202	LYS	1	0.883	0.938	16.257	13.195	13.195	0.000	0.000	0.000	0.000
141	A	203	ILE	0	0.026	0.013	16.405	-0.017	-0.017	0.000	0.000	0.000	0.000
142	A	204	THR	0	-0.043	-0.020	20.219	0.417	0.417	0.000	0.000	0.000	0.000
143	A	205	ARG	0	0.016	0.018	23.878	-0.065	-0.065	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:59:TYR)