FMO DATABASE

FMODB ID: MRZ3Z

Calculation Name: 1DOI-A-Xray547

Preferred Name:

Target Type:

Ligand Name: fe2/s2 (inorganic) cluster | potassium ion

Ligand 3-letter code: FES | K

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1DOI

Chain ID: A

ChEMBL ID:

UniProt ID: P00217

Base Structure: X-ray

Registration Date: 2025-09-02

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	128
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1134803.154745
FMO2-HF: Nuclear repulsion	1082414.259886
FMO2-HF: Total energy	-52388.894859
FMO2-MP2: Total energy	-52536.288488

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.
-665.526	-650.291	15.268	-13.257	-17.247	-0.151

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 : 0.737 / q_NPA : 0.867

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	-0.007	-0.006	3.597	3.960	5.317	-0.010	-0.425	-0.922	0.000
41	A	41	GLU	-1	-0.899	-0.938	2.453	-96.243	-93.178	0.910	-2.091	-1.885	-0.026
42	A	42	VAL	0	-0.018	-0.002	2.711	11.100	12.426	0.033	-0.482	-0.878	-0.001
43	A	43	ASN	0	-0.103	-0.077	1.910	-37.106	-36.084	7.667	-4.648	-4.041	-0.060
44	A	44	GLU	-1	-0.882	-0.949	2.889	-43.079	-41.690	0.534	-0.397	-1.526	-0.003
45	A	45	GLY	0	-0.053	-0.031	4.035	3.888	3.930	0.002	-0.016	-0.028	0.000
106	A	106	PRO	0	-0.014	-0.011	2.530	2.573	3.537	1.190	-0.490	-1.664	-0.001
107	A	107	ASP	-1	-0.920	-0.970	4.622	-29.711	-29.545	-0.001	-0.014	-0.150	0.000
108	A	108	ALA	0	-0.057	-0.027	4.333	4.800	4.908	-0.001	-0.040	-0.067	0.000
109	A	109	ASP	-1	-0.974	-0.992	2.461	-75.910	-71.963	2.096	-2.632	-3.412	-0.030
110	A	110	GLU	-1	-0.930	-0.963	2.492	-55.690	-54.089	2.846	-1.993	-2.454	-0.030
111	A	111	VAL	0	-0.030	-0.025	3.647	3.748	3.996	0.002	-0.029	-0.220	0.000
4	A	4	GLU	-1	-0.780	-0.870	5.680	-21.628	-21.628	0.000	0.000	0.000	0.000
5	A	5	TYR	0	-0.068	-0.060	9.371	-0.414	-0.414	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.040	0.019	11.919	0.763	0.763	0.000	0.000	0.000	0.000
7	A	7	ASN	0	-0.026	-0.015	15.714	-0.039	-0.039	0.000	0.000	0.000	0.000
8	A	8	TYR	0	-0.040	-0.048	18.244	0.408	0.408	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.918	-0.955	20.390	-12.373	-12.373	0.000	0.000	0.000	0.000
10	A	10	VAL	0	0.021	0.016	21.052	0.562	0.562	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.013	-0.002	19.983	0.198	0.198	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.902	-0.945	23.036	-10.820	-10.820	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.960	-0.983	26.110	-10.499	-10.499	0.000	0.000	0.000	0.000
14	A	14	ASN	0	-0.150	-0.080	25.011	0.785	0.785	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.095	-0.040	27.811	0.310	0.310	0.000	0.000	0.000	0.000
16	A	16	TRP	0	-0.036	-0.014	21.799	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.877	-0.950	23.599	-12.738	-12.738	0.000	0.000	0.000	0.000
18	A	18	MET	0	-0.053	-0.038	18.766	-0.560	-0.560	0.000	0.000	0.000	0.000
19	A	19	TYR	0	-0.058	-0.028	17.602	-1.079	-1.079	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.991	-0.985	20.967	-11.625	-11.625	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.888	-0.935	23.269	-11.653	-11.653	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.940	-0.961	19.546	-16.180	-16.180	0.000	0.000	0.000	0.000
23	A	23	VAL	0	0.022	-0.006	17.543	-0.137	-0.137	0.000	0.000	0.000	0.000
24	A	24	PHE	0	-0.001	-0.002	13.434	-0.392	-0.392	0.000	0.000	0.000	0.000
25	A	25	GLY	0	-0.001	0.003	17.365	-0.131	-0.131	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.927	-0.982	19.701	-12.152	-12.152	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.002	-0.004	18.626	0.431	0.431	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.034	-0.014	17.533	0.061	0.061	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-1.000	-0.990	19.610	-13.069	-13.069	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.130	-0.052	22.618	0.797	0.797	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-1.022	-1.014	22.898	-12.957	-12.957	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.027	-0.015	20.108	0.467	0.467	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.902	-0.949	20.874	-13.951	-13.951	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.897	-0.950	16.323	-18.188	-18.188	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.914	-0.942	15.681	-17.826	-17.826	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.825	-0.910	16.020	-16.110	-16.110	0.000	0.000	0.000	0.000
37	A	37	TYR	0	-0.048	-0.061	14.399	0.236	0.236	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.032	0.038	13.624	0.478	0.478	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.056	-0.040	8.379	-1.424	-1.424	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.049	-0.003	7.153	1.732	1.732	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.900	-0.930	6.072	-37.016	-37.016	0.000	0.000	0.000	0.000
47	A	47	TYR	0	-0.092	-0.064	7.191	-1.985	-1.985	0.000	0.000	0.000	0.000
48	A	48	ILE	0	0.051	0.010	6.142	0.166	0.166	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.044	-0.002	8.698	0.542	0.542	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.913	-0.966	12.144	-19.989	-19.989	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.015	0.008	7.773	0.924	0.924	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.043	0.025	9.820	0.228	0.228	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.761	-0.852	12.062	-16.872	-16.872	0.000	0.000	0.000	0.000
54	A	54	ALA	0	-0.110	-0.050	11.584	1.396	1.396	0.000	0.000	0.000	0.000
55	A	55	GLN	0	-0.082	-0.035	10.529	1.107	1.107	0.000	0.000	0.000	0.000
56	A	56	GLY	0	-0.101	-0.049	14.095	1.108	1.108	0.000	0.000	0.000	0.000
57	A	57	TYR	0	-0.003	0.006	12.721	1.154	1.154	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.985	-0.988	17.082	-14.682	-14.682	0.000	0.000	0.000	0.000
59	A	59	TRP	0	-0.002	-0.003	10.547	-0.402	-0.402	0.000	0.000	0.000	0.000
60	A	60	PRO	0	-0.021	0.004	17.222	0.432	0.432	0.000	0.000	0.000	0.000
61	A	61	PHE	0	0.038	0.002	18.342	-0.280	-0.280	0.000	0.000	0.000	0.000
62	A	62	SER	0	-0.016	-0.031	20.097	0.774	0.774	0.000	0.000	0.000	0.000
63	A	63	CYS	0	-0.078	-0.003	22.773	-0.288	-0.288	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.773	0.851	16.913	17.342	17.342	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.021	0.009	18.876	-0.466	-0.466	0.000	0.000	0.000	0.000
66	A	66	GLY	0	0.075	0.037	19.182	0.384	0.384	0.000	0.000	0.000	0.000
67	A	67	ALA	0	-0.049	-0.039	20.001	0.392	0.392	0.000	0.000	0.000	0.000
68	A	68	CYS	0	-0.090	-0.069	21.956	0.448	0.448	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.089	0.035	20.974	-0.605	-0.605	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.063	-0.060	20.690	-0.200	-0.200	0.000	0.000	0.000	0.000
71	A	71	CYS	0	0.003	0.048	16.039	-0.129	-0.129	0.000	0.000	0.000	0.000
72	A	72	ALA	0	-0.003	0.012	15.624	-1.201	-1.201	0.000	0.000	0.000	0.000
73	A	73	ALA	0	0.001	0.006	12.898	0.215	0.215	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.040	-0.015	14.966	0.474	0.474	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.016	-0.003	9.723	-0.761	-0.761	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.014	-0.011	12.135	1.284	1.284	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.921	-0.974	10.007	-22.786	-22.786	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.012	0.009	7.132	-2.329	-2.329	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.819	-0.893	7.100	-20.077	-20.077	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.073	-0.044	6.914	-4.364	-4.364	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.847	-0.902	8.517	-20.295	-20.295	0.000	0.000	0.000	0.000
82	A	82	MET	0	-0.047	-0.026	10.348	-0.500	-0.500	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.841	-0.878	13.081	-18.348	-18.348	0.000	0.000	0.000	0.000
84	A	84	MET	0	-0.107	-0.071	15.670	0.724	0.724	0.000	0.000	0.000	0.000
85	A	85	GLN	0	0.097	0.060	18.279	0.626	0.626	0.000	0.000	0.000	0.000
86	A	86	GLN	0	-0.082	-0.050	20.704	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	87	ILE	0	-0.056	-0.010	21.853	0.660	0.660	0.000	0.000	0.000	0.000
88	A	88	LEU	0	0.021	0.018	18.401	0.434	0.434	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.063	-0.056	22.474	-0.050	-0.050	0.000	0.000	0.000	0.000
90	A	90	ASP	-1	-0.854	-0.931	22.330	-12.764	-12.764	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.841	-0.907	21.757	-11.785	-11.785	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.843	-0.894	21.554	-12.472	-12.472	0.000	0.000	0.000	0.000
93	A	93	VAL	0	0.006	0.013	16.498	-0.617	-0.617	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.974	-0.980	17.372	-14.485	-14.485	0.000	0.000	0.000	0.000
95	A	95	ASP	-1	-0.931	-0.966	19.138	-12.741	-12.741	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.785	0.898	20.652	12.039	12.039	0.000	0.000	0.000	0.000
97	A	97	ASN	0	0.007	0.024	15.179	-0.440	-0.440	0.000	0.000	0.000	0.000
98	A	98	VAL	0	-0.003	-0.003	15.335	-0.906	-0.906	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.795	0.869	11.727	20.592	20.592	0.000	0.000	0.000	0.000
100	A	100	LEU	0	0.002	-0.031	14.305	0.481	0.481	0.000	0.000	0.000	0.000
101	A	101	THR	0	0.055	0.000	11.187	-0.378	-0.378	0.000	0.000	0.000	0.000
102	A	102	CYS	0	-0.102	-0.074	12.257	-0.526	-0.526	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.021	-0.003	14.024	0.479	0.479	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.037	0.023	10.990	0.467	0.467	0.000	0.000	0.000	0.000
105	A	105	SER	0	-0.052	-0.006	6.312	-1.453	-1.453	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.844	0.942	6.062	27.337	27.337	0.000	0.000	0.000	0.000
113	A	113	ILE	0	-0.033	-0.020	9.092	1.576	1.576	0.000	0.000	0.000	0.000
114	A	114	VAL	0	0.043	0.034	11.738	0.391	0.391	0.000	0.000	0.000	0.000
115	A	115	TYR	0	0.017	-0.017	13.357	0.206	0.206	0.000	0.000	0.000	0.000
116	A	116	ASN	0	0.026	-0.004	15.184	1.192	1.192	0.000	0.000	0.000	0.000
117	A	117	ALA	0	0.041	0.028	17.907	0.963	0.963	0.000	0.000	0.000	0.000
118	A	118	LYS	1	0.902	0.970	19.635	13.280	13.280	0.000	0.000	0.000	0.000
119	A	119	HIS	0	-0.049	-0.018	22.002	1.086	1.086	0.000	0.000	0.000	0.000
120	A	120	LEU	0	0.032	0.040	20.960	0.571	0.571	0.000	0.000	0.000	0.000
121	A	121	ASP	-1	-0.905	-0.960	24.795	-9.829	-9.829	0.000	0.000	0.000	0.000
122	A	122	TYR	0	-0.033	-0.034	21.257	0.363	0.363	0.000	0.000	0.000	0.000
123	A	123	LEU	0	0.030	0.019	20.778	-0.024	-0.024	0.000	0.000	0.000	0.000
124	A	124	GLN	0	0.005	0.003	25.091	0.355	0.355	0.000	0.000	0.000	0.000
125	A	125	ASN	0	-0.076	-0.030	27.676	-0.074	-0.074	0.000	0.000	0.000	0.000
126	A	126	ARG	1	0.667	0.768	24.745	12.132	12.132	0.000	0.000	0.000	0.000
127	A	127	VAL	0	-0.031	0.002	24.184	-0.488	-0.488	0.000	0.000	0.000	0.000
128	A	128	ILE	-1	-0.946	-0.953	25.477	-10.848	-10.848	0.000	0.000	0.000	0.000

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