FMO DATABASE

FMODB ID: N6JZQ

Calculation Name: 2V2K-A-Xray547

Preferred Name:

Target Type:

Ligand Name: fe3-s4 cluster | s-mercaptocysteine | acetate ion

Ligand 3-letter code: F3S | CSS | ACT

Ligand of Interest (LOI):

PDB ID: 2V2K

Chain ID: A

ChEMBL ID:

UniProt ID: P00215

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	104
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-766111.5342
FMO2-HF: Nuclear repulsion	724544.591123
FMO2-HF: Total energy	-41566.943077
FMO2-MP2: Total energy	-41681.46854

3D Structure

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:THR)

Summations of interaction energy for fragment #1(A:1: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.
-555.528	-553.424	46.286	-24.031	-24.357	-0.231

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.717 / q_NPA : 0.824

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	3	VAL	0	-0.016	-0.004	1.959	-12.886	-11.106	5.889	-3.828	-3.841	-0.038
4	A	4	ILE	0	-0.011	-0.001	4.705	3.110	3.175	-0.001	-0.016	-0.049	0.000
34	A	34	ILE	0	-0.003	-0.007	3.097	1.158	1.742	0.072	-0.207	-0.449	0.001
35	A	35	HIS	0	-0.006	-0.016	5.040	-3.420	-3.382	-0.001	-0.006	-0.030	0.000
36	A	36	PRO	0	-0.020	-0.009	2.503	-4.037	-2.215	1.647	-1.370	-2.099	0.013
37	A	37	ASP	-1	-0.909	-0.964	3.124	-40.316	-39.241	0.091	-0.099	-1.066	-0.005
39	A	39	CYS	0	-0.056	0.003	2.541	-4.395	-3.196	2.407	-1.435	-2.171	0.013
40	A	40	VAL	0	-0.026	-0.022	3.439	-10.395	-9.434	0.023	-0.366	-0.618	-0.003
41	A	41	ASP	-1	-0.819	-0.904	1.978	-122.504	-127.018	16.756	-6.641	-5.601	-0.094
42	A	42	CYS	0	-0.061	-0.035	4.512	5.159	5.238	-0.001	-0.040	-0.038	0.000
56	A	56	TYR	0	-0.043	-0.032	2.762	-8.804	-8.061	0.110	-0.258	-0.595	-0.001
57	A	57	GLU	-1	-0.852	-0.934	1.715	-116.542	-118.506	19.294	-9.733	-7.597	-0.117
58	A	58	ASP	-1	-0.914	-0.948	4.331	-37.120	-36.884	0.000	-0.032	-0.203	0.000
5	A	5	ALA	0	0.032	0.009	8.174	0.395	0.395	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.799	-0.897	11.001	-15.336	-15.336	0.000	0.000	0.000	0.000
7	A	7	PRO	0	-0.018	-0.001	13.847	0.817	0.817	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.032	0.005	13.022	0.535	0.535	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.009	-0.003	15.042	0.550	0.550	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.798	-0.868	17.165	-12.680	-12.680	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.052	-0.008	18.107	0.584	0.584	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.740	0.864	16.373	14.734	14.734	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.875	-0.947	17.486	-14.764	-14.764	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.818	0.888	15.470	14.854	14.854	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.052	0.043	16.324	-0.331	-0.331	0.000	0.000	0.000	0.000
16	A	16	CYS	0	-0.042	-0.020	11.382	0.070	0.070	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.007	-0.017	12.432	-1.295	-1.295	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.964	-0.970	13.809	-14.949	-14.949	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.934	-0.962	13.250	-17.513	-17.513	0.000	0.000	0.000	0.000
20	A	20	CYS	0	-0.048	-0.001	8.828	-1.927	-1.927	0.000	0.000	0.000	0.000
21	A	21	PRO	0	-0.037	-0.036	10.131	1.057	1.057	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.030	-0.029	8.105	1.116	1.116	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.852	-0.915	11.435	-18.204	-18.204	0.000	0.000	0.000	0.000
24	A	24	CYS	0	-0.006	0.009	6.902	-0.371	-0.371	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.030	0.001	7.769	-1.806	-1.806	0.000	0.000	0.000	0.000
26	A	26	TYR	0	-0.024	-0.037	9.534	2.801	2.801	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.787	-0.893	11.849	-15.174	-15.174	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.062	0.033	14.610	0.501	0.501	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.034	-0.011	16.245	0.262	0.262	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.687	0.797	17.051	13.576	13.576	0.000	0.000	0.000	0.000
31	A	31	MET	0	0.002	0.006	10.539	0.496	0.496	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.012	-0.009	11.338	0.588	0.588	0.000	0.000	0.000	0.000
33	A	33	TYR	0	-0.024	-0.045	8.480	-0.686	-0.686	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.793	-0.843	5.932	-21.617	-21.617	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.041	0.034	6.865	3.311	3.311	0.000	0.000	0.000	0.000
44	A	44	ALA	0	-0.029	-0.019	8.586	1.478	1.478	0.000	0.000	0.000	0.000
45	A	45	CYS	0	-0.015	-0.006	7.847	0.577	0.577	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.911	-0.954	9.502	-24.307	-24.307	0.000	0.000	0.000	0.000
47	A	47	PRO	0	-0.013	0.002	11.366	1.771	1.771	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.042	-0.015	14.346	1.537	1.537	0.000	0.000	0.000	0.000
49	A	49	CYS	0	-0.046	0.008	13.271	1.023	1.023	0.000	0.000	0.000	0.000
50	A	50	PRO	0	-0.015	-0.009	15.430	0.112	0.112	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.055	-0.040	16.209	0.831	0.831	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.941	-0.962	14.770	-18.396	-18.396	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.030	0.002	12.756	-0.569	-0.569	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.041	-0.023	7.463	-1.396	-1.396	0.000	0.000	0.000	0.000
55	A	55	TYR	0	0.024	0.012	7.594	2.085	2.085	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.931	-0.965	7.545	-27.861	-27.861	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.065	-0.024	6.070	3.078	3.078	0.000	0.000	0.000	0.000
61	A	61	PRO	0	-0.002	0.003	9.025	1.688	1.688	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.880	-0.946	12.739	-19.064	-19.064	0.000	0.000	0.000	0.000
63	A	63	GLN	0	-0.098	-0.039	14.520	0.880	0.880	0.000	0.000	0.000	0.000
64	A	64	TRP	0	-0.010	-0.013	12.194	0.388	0.388	0.000	0.000	0.000	0.000
65	A	65	SER	0	0.017	0.007	10.221	-1.408	-1.408	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.042	-0.022	9.692	-2.021	-2.021	0.000	0.000	0.000	0.000
67	A	67	TYR	0	-0.008	-0.050	9.399	-0.297	-0.297	0.000	0.000	0.000	0.000
68	A	68	ALA	0	0.020	0.023	5.552	-1.329	-1.329	0.000	0.000	0.000	0.000
69	A	69	GLN	0	-0.079	-0.045	5.853	-2.531	-2.531	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.010	0.004	8.397	0.333	0.333	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.025	-0.030	5.376	0.141	0.141	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.056	0.029	6.113	0.041	0.041	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.891	-0.943	7.503	-19.261	-19.261	0.000	0.000	0.000	0.000
74	A	74	PHE	0	-0.040	-0.006	10.536	1.468	1.468	0.000	0.000	0.000	0.000
75	A	75	PHE	0	0.010	-0.003	7.901	1.302	1.302	0.000	0.000	0.000	0.000
76	A	76	ALA	0	-0.054	-0.014	12.181	0.657	0.657	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.980	-0.993	14.559	-12.765	-12.765	0.000	0.000	0.000	0.000
78	A	78	LEU	0	-0.052	-0.014	13.445	0.588	0.588	0.000	0.000	0.000	0.000
79	A	79	GLY	0	-0.034	-0.009	14.327	0.308	0.308	0.000	0.000	0.000	0.000
80	A	80	SER	0	-0.056	-0.052	11.466	-1.465	-1.465	0.000	0.000	0.000	0.000
81	A	81	PRO	0	0.002	0.008	12.362	0.946	0.946	0.000	0.000	0.000	0.000
82	A	82	GLY	0	0.012	0.007	12.500	1.075	1.075	0.000	0.000	0.000	0.000
83	A	83	GLY	0	-0.057	-0.035	12.761	1.003	1.003	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.053	0.024	12.497	1.054	1.054	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.025	-0.020	14.418	1.313	1.313	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.732	0.868	16.663	17.031	17.031	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.050	-0.019	16.013	0.563	0.563	0.000	0.000	0.000	0.000
88	A	88	GLY	0	-0.003	0.006	17.986	0.578	0.578	0.000	0.000	0.000	0.000
89	A	89	GLN	0	-0.085	-0.037	17.246	-0.374	-0.374	0.000	0.000	0.000	0.000
90	A	90	THR	0	-0.048	-0.032	16.652	0.492	0.492	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.870	-0.927	17.505	-13.175	-13.175	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.021	-0.024	15.466	0.713	0.713	0.000	0.000	0.000	0.000
93	A	93	ASP	-1	-0.758	-0.853	15.285	-16.434	-16.434	0.000	0.000	0.000	0.000
94	A	94	PRO	0	0.050	0.026	12.617	1.028	1.028	0.000	0.000	0.000	0.000
95	A	95	GLN	0	-0.115	-0.092	15.841	0.211	0.211	0.000	0.000	0.000	0.000
96	A	96	ALA	0	0.012	-0.001	15.949	0.368	0.368	0.000	0.000	0.000	0.000
97	A	97	ILE	0	0.051	0.032	13.566	0.051	0.051	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.860	0.942	17.243	14.055	14.055	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.875	-0.933	20.355	-12.120	-12.120	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.016	0.021	17.364	0.530	0.530	0.000	0.000	0.000	0.000
101	A	101	PRO	0	-0.020	-0.014	21.963	0.331	0.331	0.000	0.000	0.000	0.000
102	A	102	PRO	0	-0.021	-0.009	23.424	-0.366	-0.366	0.000	0.000	0.000	0.000
103	A	103	GLN	0	-0.061	-0.028	19.410	0.191	0.191	0.000	0.000	0.000	0.000
104	A	104	GLY	-1	-0.932	-0.952	23.909	-10.810	-10.810	0.000	0.000	0.000	0.000

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