FMO DATABASE

FMODB ID: Z7JQN

Calculation Name: 2B1X-B-Xray547

Preferred Name:

Target Type:

Ligand Name: (4s)-2-methyl-2,4-pentanediol | fe2/s2 (inorganic) cluster | fe (iii) ion

Ligand 3-letter code: MPD | FES | FE

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2B1X

Chain ID: B

ChEMBL ID:

UniProt ID: Q9X3R9

Base Structure: X-ray

Registration Date: 2025-10-03

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	167
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1725185.557995
FMO2-HF: Nuclear repulsion	1656691.195426
FMO2-HF: Total energy	-68494.362569
FMO2-MP2: Total energy	-68690.867972

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:513:ARG)

Summations of interaction energy for fragment #1(A:513:ARG)

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.
-359.651	-355.406	1.748	-2.749	-3.24	-0.031

Interaction energy analysis for fragmet #1(A:513:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.811 / q_NPA : 1.896

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	515	SER	0	0.043	0.007	3.554	-1.473	-0.461	0.018	-0.435	-0.594	0.000
100	A	612	ALA	0	-0.062	-0.027	4.537	-9.405	-9.331	-0.001	-0.007	-0.065	0.000
101	A	613	THR	0	0.019	0.000	2.407	-20.597	-17.567	1.732	-2.263	-2.498	-0.031
102	A	614	GLY	0	0.026	0.010	4.260	1.355	1.484	-0.001	-0.044	-0.083	0.000
4	A	516	ASP	-1	-0.925	-0.952	6.967	-45.741	-45.741	0.000	0.000	0.000	0.000
5	A	517	THR	0	0.071	0.038	9.758	1.719	1.719	0.000	0.000	0.000	0.000
6	A	518	THR	0	0.026	0.015	8.789	2.230	2.230	0.000	0.000	0.000	0.000
7	A	519	VAL	0	-0.010	-0.003	8.444	-0.083	-0.083	0.000	0.000	0.000	0.000
8	A	520	ARG	1	0.814	0.905	10.905	33.640	33.640	0.000	0.000	0.000	0.000
9	A	521	GLU	-1	-0.846	-0.916	13.645	-37.207	-37.207	0.000	0.000	0.000	0.000
10	A	522	ILE	0	0.036	0.022	9.910	1.635	1.635	0.000	0.000	0.000	0.000
11	A	523	THR	0	-0.052	-0.042	13.564	1.491	1.491	0.000	0.000	0.000	0.000
12	A	524	GLU	-1	-0.835	-0.906	15.810	-28.196	-28.196	0.000	0.000	0.000	0.000
13	A	525	TRP	0	0.002	0.009	16.796	1.141	1.141	0.000	0.000	0.000	0.000
14	A	526	LEU	0	0.018	-0.005	15.108	1.382	1.382	0.000	0.000	0.000	0.000
15	A	527	TYR	0	-0.079	-0.036	18.965	0.909	0.909	0.000	0.000	0.000	0.000
16	A	528	MET	0	0.016	0.027	21.356	1.541	1.541	0.000	0.000	0.000	0.000
17	A	529	GLU	-1	-0.713	-0.822	21.203	-25.572	-25.572	0.000	0.000	0.000	0.000
18	A	530	ALA	0	0.005	-0.010	23.089	0.978	0.978	0.000	0.000	0.000	0.000
19	A	531	GLU	-1	-1.004	-0.993	24.860	-20.383	-20.383	0.000	0.000	0.000	0.000
20	A	532	LEU	0	-0.010	-0.013	25.854	1.003	1.003	0.000	0.000	0.000	0.000
21	A	533	LEU	0	-0.008	0.003	25.474	0.926	0.926	0.000	0.000	0.000	0.000
22	A	534	ASP	-1	-0.801	-0.863	28.937	-20.066	-20.066	0.000	0.000	0.000	0.000
23	A	535	ALA	0	-0.054	-0.017	30.971	0.652	0.652	0.000	0.000	0.000	0.000
24	A	536	GLY	0	-0.009	-0.002	32.630	0.542	0.542	0.000	0.000	0.000	0.000
25	A	537	LYS	1	0.826	0.913	30.963	19.117	19.117	0.000	0.000	0.000	0.000
26	A	538	TYR	0	0.026	-0.010	30.736	-0.670	-0.670	0.000	0.000	0.000	0.000
27	A	539	ARG	1	0.802	0.871	30.520	16.894	16.894	0.000	0.000	0.000	0.000
28	A	540	GLU	-1	-0.861	-0.917	29.183	-19.217	-19.217	0.000	0.000	0.000	0.000
29	A	541	TRP	0	-0.006	-0.034	24.044	-0.264	-0.264	0.000	0.000	0.000	0.000
30	A	542	LEU	0	0.016	0.006	25.747	-0.702	-0.702	0.000	0.000	0.000	0.000
31	A	543	ALA	0	-0.033	-0.010	26.631	-0.231	-0.231	0.000	0.000	0.000	0.000
32	A	544	LEU	0	-0.022	-0.008	21.784	-0.658	-0.658	0.000	0.000	0.000	0.000
33	A	545	VAL	0	-0.044	-0.013	21.177	-1.498	-1.498	0.000	0.000	0.000	0.000
34	A	546	THR	0	-0.046	-0.030	19.552	-0.037	-0.037	0.000	0.000	0.000	0.000
35	A	547	GLU	-1	-0.863	-0.928	22.007	-24.173	-24.173	0.000	0.000	0.000	0.000
36	A	548	ASP	-1	-0.847	-0.896	19.783	-26.844	-26.844	0.000	0.000	0.000	0.000
37	A	549	LEU	0	-0.040	-0.004	21.525	-0.911	-0.911	0.000	0.000	0.000	0.000
38	A	550	SER	0	-0.022	-0.006	21.048	0.442	0.442	0.000	0.000	0.000	0.000
39	A	551	TYR	0	0.012	-0.040	21.383	-1.108	-1.108	0.000	0.000	0.000	0.000
40	A	552	VAL	0	-0.002	-0.005	23.113	0.951	0.951	0.000	0.000	0.000	0.000
41	A	553	VAL	0	-0.017	-0.007	24.090	-0.852	-0.852	0.000	0.000	0.000	0.000
42	A	554	PRO	0	0.027	0.010	24.191	0.895	0.895	0.000	0.000	0.000	0.000
43	A	555	ILE	0	-0.001	0.018	27.386	0.173	0.173	0.000	0.000	0.000	0.000
44	A	556	ARG	1	0.803	0.863	25.315	22.824	22.824	0.000	0.000	0.000	0.000
45	A	557	VAL	0	-0.006	-0.015	30.323	0.760	0.760	0.000	0.000	0.000	0.000
46	A	558	THR	0	-0.010	-0.018	32.230	-0.549	-0.549	0.000	0.000	0.000	0.000
47	A	559	ARG	1	0.848	0.928	31.801	19.490	19.490	0.000	0.000	0.000	0.000
48	A	560	GLU	-1	-0.815	-0.896	32.976	-18.275	-18.275	0.000	0.000	0.000	0.000
49	A	561	ARG	1	0.925	0.943	25.980	22.018	22.018	0.000	0.000	0.000	0.000
50	A	562	GLU	-1	-0.946	-0.967	29.234	-19.159	-19.159	0.000	0.000	0.000	0.000
51	A	563	ALA	0	-0.058	-0.014	30.501	-0.146	-0.146	0.000	0.000	0.000	0.000
52	A	564	VAL	0	-0.003	-0.009	25.438	-0.596	-0.596	0.000	0.000	0.000	0.000
53	A	565	THR	0	0.028	0.012	25.535	-1.200	-1.200	0.000	0.000	0.000	0.000
54	A	566	ASP	-1	-0.818	-0.874	27.078	-21.966	-21.966	0.000	0.000	0.000	0.000
55	A	567	VAL	0	0.001	0.001	24.503	0.610	0.610	0.000	0.000	0.000	0.000
56	A	568	VAL	0	-0.054	-0.028	27.946	0.284	0.284	0.000	0.000	0.000	0.000
57	A	569	GLU	-1	-0.917	-0.955	28.146	-21.333	-21.333	0.000	0.000	0.000	0.000
58	A	570	GLY	0	-0.033	-0.022	29.853	0.644	0.644	0.000	0.000	0.000	0.000
59	A	571	MET	0	-0.053	-0.023	31.526	0.542	0.542	0.000	0.000	0.000	0.000
60	A	572	THR	0	0.004	-0.009	28.498	-0.676	-0.676	0.000	0.000	0.000	0.000
61	A	573	HIS	0	-0.008	-0.008	30.234	0.965	0.965	0.000	0.000	0.000	0.000
62	A	574	MET	0	-0.047	-0.024	28.546	0.410	0.410	0.000	0.000	0.000	0.000
63	A	575	ASP	-1	-0.936	-0.977	26.827	-22.361	-22.361	0.000	0.000	0.000	0.000
64	A	576	ASP	-1	-0.794	-0.830	26.992	-18.814	-18.814	0.000	0.000	0.000	0.000
65	A	577	ASP	-1	-0.795	-0.893	26.045	-20.498	-20.498	0.000	0.000	0.000	0.000
66	A	578	ALA	0	0.028	-0.002	26.319	0.184	0.184	0.000	0.000	0.000	0.000
67	A	579	ASP	-1	-0.887	-0.927	27.856	-17.884	-17.884	0.000	0.000	0.000	0.000
68	A	580	SER	0	-0.075	-0.069	30.703	0.385	0.385	0.000	0.000	0.000	0.000
69	A	581	MET	0	-0.011	0.005	26.490	0.548	0.548	0.000	0.000	0.000	0.000
70	A	582	GLU	-1	-0.862	-0.937	30.083	-17.268	-17.268	0.000	0.000	0.000	0.000
71	A	583	MET	0	-0.062	-0.024	32.218	0.644	0.644	0.000	0.000	0.000	0.000
72	A	584	ARG	1	0.800	0.860	30.745	19.317	19.317	0.000	0.000	0.000	0.000
73	A	585	VAL	0	-0.011	-0.006	30.818	0.315	0.315	0.000	0.000	0.000	0.000
74	A	586	LEU	0	0.017	0.004	34.015	0.444	0.444	0.000	0.000	0.000	0.000
75	A	587	ARG	1	0.892	0.953	37.262	15.657	15.657	0.000	0.000	0.000	0.000
76	A	588	LEU	0	-0.046	-0.023	34.214	0.454	0.454	0.000	0.000	0.000	0.000
77	A	589	GLU	-1	-0.792	-0.850	36.197	-16.424	-16.424	0.000	0.000	0.000	0.000
78	A	590	THR	0	-0.084	-0.041	39.552	0.508	0.508	0.000	0.000	0.000	0.000
79	A	591	GLU	-1	-0.901	-0.946	43.001	-12.727	-12.727	0.000	0.000	0.000	0.000
80	A	592	TYR	0	-0.037	-0.038	44.802	0.336	0.336	0.000	0.000	0.000	0.000
81	A	593	ALA	0	-0.011	0.006	40.563	-0.053	-0.053	0.000	0.000	0.000	0.000
82	A	594	TRP	0	0.031	-0.003	41.892	-0.319	-0.319	0.000	0.000	0.000	0.000
83	A	595	ALA	0	-0.084	-0.040	40.109	-0.009	-0.009	0.000	0.000	0.000	0.000
84	A	596	GLU	-1	-0.772	-0.857	36.550	-16.685	-16.685	0.000	0.000	0.000	0.000
85	A	597	ASP	-1	-0.891	-0.914	39.977	-14.002	-14.002	0.000	0.000	0.000	0.000
86	A	598	PRO	0	0.015	-0.018	43.175	0.301	0.301	0.000	0.000	0.000	0.000
87	A	599	PRO	0	0.032	0.037	38.671	-0.114	-0.114	0.000	0.000	0.000	0.000
88	A	600	SER	0	-0.065	-0.073	36.562	0.356	0.356	0.000	0.000	0.000	0.000
89	A	601	ARG	1	0.787	0.895	36.786	14.792	14.792	0.000	0.000	0.000	0.000
90	A	602	SER	0	-0.010	-0.022	31.471	0.208	0.208	0.000	0.000	0.000	0.000
91	A	603	ARG	1	0.849	0.923	29.125	19.847	19.847	0.000	0.000	0.000	0.000
92	A	604	HIS	1	0.844	0.884	25.097	21.836	21.836	0.000	0.000	0.000	0.000
93	A	605	PHE	0	-0.023	-0.018	25.280	-0.301	-0.301	0.000	0.000	0.000	0.000
94	A	606	VAL	0	0.046	0.030	18.940	-0.279	-0.279	0.000	0.000	0.000	0.000
95	A	607	THR	0	-0.009	-0.026	19.552	-0.161	-0.161	0.000	0.000	0.000	0.000
96	A	608	ASN	0	-0.035	-0.017	16.517	0.355	0.355	0.000	0.000	0.000	0.000
97	A	609	VAL	0	0.074	0.048	12.715	-1.082	-1.082	0.000	0.000	0.000	0.000
98	A	610	ARG	1	0.707	0.842	9.661	37.551	37.551	0.000	0.000	0.000	0.000
99	A	611	VAL	0	0.057	0.028	7.140	2.237	2.237	0.000	0.000	0.000	0.000
103	A	615	ASP	-1	-0.890	-0.932	7.053	-52.104	-52.104	0.000	0.000	0.000	0.000
104	A	616	SER	0	-0.048	-0.016	9.831	1.831	1.831	0.000	0.000	0.000	0.000
105	A	617	GLU	-1	-0.954	-0.986	7.676	-62.931	-62.931	0.000	0.000	0.000	0.000
106	A	618	ASP	-1	-0.886	-0.959	9.539	-34.494	-34.494	0.000	0.000	0.000	0.000
107	A	619	GLU	-1	-0.841	-0.907	10.179	-38.116	-38.116	0.000	0.000	0.000	0.000
108	A	620	PHE	0	-0.061	-0.042	5.966	-8.804	-8.804	0.000	0.000	0.000	0.000
109	A	621	LYS	1	0.840	0.917	7.797	56.904	56.904	0.000	0.000	0.000	0.000
110	A	622	VAL	0	-0.001	-0.011	8.932	-5.016	-5.016	0.000	0.000	0.000	0.000
111	A	623	THR	0	-0.005	0.012	11.637	1.302	1.302	0.000	0.000	0.000	0.000
112	A	624	SER	0	-0.004	-0.006	13.622	-0.377	-0.377	0.000	0.000	0.000	0.000
113	A	625	ASN	0	0.009	0.007	16.619	-0.082	-0.082	0.000	0.000	0.000	0.000
114	A	626	LEU	0	-0.002	0.003	19.779	0.046	0.046	0.000	0.000	0.000	0.000
115	A	627	LEU	0	-0.022	0.004	23.066	0.638	0.638	0.000	0.000	0.000	0.000
116	A	628	LEU	0	0.020	0.004	26.443	-0.006	-0.006	0.000	0.000	0.000	0.000
117	A	629	TYR	0	-0.008	-0.007	28.823	0.561	0.561	0.000	0.000	0.000	0.000
118	A	630	ARG	1	0.817	0.874	32.255	16.756	16.756	0.000	0.000	0.000	0.000
119	A	631	THR	0	-0.005	0.010	35.313	0.444	0.444	0.000	0.000	0.000	0.000
120	A	632	ARG	1	0.865	0.927	39.046	14.982	14.982	0.000	0.000	0.000	0.000
121	A	633	GLY	0	0.013	0.011	41.881	0.179	0.179	0.000	0.000	0.000	0.000
122	A	634	ASP	-1	-0.890	-0.949	44.897	-12.931	-12.931	0.000	0.000	0.000	0.000
123	A	635	VAL	0	-0.005	0.008	44.813	0.107	0.107	0.000	0.000	0.000	0.000
124	A	636	ALA	0	-0.005	0.000	44.793	-0.317	-0.317	0.000	0.000	0.000	0.000
125	A	637	THR	0	-0.046	-0.032	42.420	-0.061	-0.061	0.000	0.000	0.000	0.000
126	A	638	TYR	0	-0.035	-0.022	36.011	0.090	0.090	0.000	0.000	0.000	0.000
127	A	639	ASP	-1	-0.782	-0.840	35.716	-16.227	-16.227	0.000	0.000	0.000	0.000
128	A	640	VAL	0	-0.037	-0.041	30.977	-0.314	-0.314	0.000	0.000	0.000	0.000
129	A	641	LEU	0	-0.032	0.002	29.167	0.136	0.136	0.000	0.000	0.000	0.000
130	A	642	SER	0	-0.035	-0.040	25.715	-0.333	-0.333	0.000	0.000	0.000	0.000
131	A	643	GLY	0	0.066	0.034	23.899	0.696	0.696	0.000	0.000	0.000	0.000
132	A	644	GLU	-1	-0.869	-0.904	16.793	-35.570	-35.570	0.000	0.000	0.000	0.000
133	A	645	ARG	1	0.803	0.901	18.726	29.363	29.363	0.000	0.000	0.000	0.000
134	A	646	THR	0	-0.028	-0.016	14.170	-2.701	-2.701	0.000	0.000	0.000	0.000
135	A	647	ASP	-1	-0.762	-0.871	14.846	-30.058	-30.058	0.000	0.000	0.000	0.000
136	A	648	VAL	0	-0.053	-0.035	12.085	-3.388	-3.388	0.000	0.000	0.000	0.000
137	A	649	LEU	0	-0.014	-0.001	12.418	2.440	2.440	0.000	0.000	0.000	0.000
138	A	650	ARG	1	0.834	0.893	12.106	27.170	27.170	0.000	0.000	0.000	0.000
139	A	651	ARG	1	0.846	0.915	10.103	44.165	44.165	0.000	0.000	0.000	0.000
140	A	652	ALA	0	0.020	0.008	15.034	1.096	1.096	0.000	0.000	0.000	0.000
141	A	653	GLY	0	-0.042	-0.020	18.831	0.786	0.786	0.000	0.000	0.000	0.000
142	A	654	ASP	-1	-0.964	-0.983	18.082	-27.656	-27.656	0.000	0.000	0.000	0.000
143	A	655	SER	0	0.007	0.008	17.905	-1.335	-1.335	0.000	0.000	0.000	0.000
144	A	656	PHE	0	-0.028	-0.033	11.461	-2.173	-2.173	0.000	0.000	0.000	0.000
145	A	657	LEU	0	0.026	0.027	16.627	1.531	1.531	0.000	0.000	0.000	0.000
146	A	658	MET	0	-0.046	-0.012	16.833	-2.055	-2.055	0.000	0.000	0.000	0.000
147	A	659	ALA	0	0.048	0.022	16.238	1.460	1.460	0.000	0.000	0.000	0.000
148	A	660	LYS	1	0.888	0.944	16.593	29.789	29.789	0.000	0.000	0.000	0.000
149	A	661	ARG	1	0.740	0.799	17.499	26.800	26.800	0.000	0.000	0.000	0.000
150	A	662	VAL	0	-0.034	-0.004	19.029	1.286	1.286	0.000	0.000	0.000	0.000
151	A	663	VAL	0	0.019	0.003	20.191	-1.184	-1.184	0.000	0.000	0.000	0.000
152	A	664	LEU	0	-0.004	0.000	21.680	1.241	1.241	0.000	0.000	0.000	0.000
153	A	665	LEU	0	0.033	0.014	23.365	-0.420	-0.420	0.000	0.000	0.000	0.000
154	A	666	ASP	-1	-0.884	-0.925	24.794	-24.546	-24.546	0.000	0.000	0.000	0.000
155	A	667	GLN	0	-0.040	-0.034	27.289	1.026	1.026	0.000	0.000	0.000	0.000
156	A	668	THR	0	0.001	0.012	30.248	-0.181	-0.181	0.000	0.000	0.000	0.000
157	A	669	THR	0	-0.023	-0.015	32.803	0.333	0.333	0.000	0.000	0.000	0.000
158	A	670	ILE	0	0.000	-0.001	31.186	-0.216	-0.216	0.000	0.000	0.000	0.000
159	A	671	MET	0	-0.053	-0.030	33.841	0.715	0.715	0.000	0.000	0.000	0.000
160	A	672	THR	0	-0.026	-0.047	33.842	-0.129	-0.129	0.000	0.000	0.000	0.000
161	A	673	HIS	0	-0.024	-0.001	36.562	-0.050	-0.050	0.000	0.000	0.000	0.000
162	A	674	ASN	0	0.019	-0.006	37.380	0.051	0.051	0.000	0.000	0.000	0.000
163	A	675	LEU	0	0.050	0.031	30.590	-0.150	-0.150	0.000	0.000	0.000	0.000
164	A	676	ALA	0	-0.022	-0.007	33.468	-0.097	-0.097	0.000	0.000	0.000	0.000
165	A	677	LEU	0	-0.032	-0.004	31.714	-0.015	-0.015	0.000	0.000	0.000	0.000
166	A	678	ILE	0	0.023	0.025	26.425	-0.179	-0.179	0.000	0.000	0.000	0.000
167	A	679	MET	-1	-0.740	-0.805	23.984	-25.028	-25.028	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:513:ARG)