FMO DATABASE

FMODB ID: 4GQZN

Calculation Name: 7NHM-2-Other547

Preferred Name:

Target Type:

Ligand Name: n-formylmethionine | potassium ion

Ligand 3-letter code: FME | K

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7NHM

Chain ID: 2

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

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	64
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-363338.629873
FMO2-HF: Nuclear repulsion	337494.415638
FMO2-HF: Total energy	-25844.214234
FMO2-MP2: Total energy	-25921.432238

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:2:LYS)

Summations of interaction energy for fragment #1(A:2:LYS)

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.
-58.449	-48.721	21.727	-15.133	-16.322	-0.17

Interaction energy analysis for fragmet #1(A:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.699 / q_NPA : 1.835

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	4	LYS	1	1.017	1.027	3.851	72.906	77.533	-0.033	-2.335	-2.259	-0.013
4	A	5	GLU	-1	-0.705	-0.847	1.838	-212.586	-209.839	18.624	-11.626	-9.744	-0.148
5	A	6	ILE	0	-0.026	-0.007	2.401	-0.879	-0.519	2.309	-0.593	-2.075	-0.005
48	A	49	THR	0	-0.059	-0.033	2.475	-5.735	-4.894	0.796	-0.288	-1.350	-0.003
49	A	50	ILE	0	0.071	0.046	4.973	-1.005	-0.972	-0.001	-0.002	-0.030	0.000
51	A	52	ARG	1	0.924	0.973	3.553	91.990	92.936	0.033	-0.279	-0.701	-0.001
52	A	53	LEU	0	0.023	0.023	4.467	1.379	1.553	-0.001	-0.010	-0.163	0.000
6	A	7	ARG	1	0.788	0.870	6.028	64.781	64.781	0.000	0.000	0.000	0.000
7	A	8	ASP	-1	-0.878	-0.944	7.877	-61.571	-61.571	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.046	-0.002	5.145	1.645	1.645	0.000	0.000	0.000	0.000
9	A	10	THR	0	0.011	-0.015	8.805	3.431	3.431	0.000	0.000	0.000	0.000
10	A	11	THR	0	-0.002	-0.015	11.016	-3.132	-3.132	0.000	0.000	0.000	0.000
11	A	12	SER	0	0.046	0.035	12.539	-1.187	-1.187	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.772	-0.877	9.228	-50.830	-50.830	0.000	0.000	0.000	0.000
13	A	14	ILE	0	-0.020	-0.018	7.757	-5.253	-5.253	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.927	-0.968	8.999	-38.310	-38.310	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-0.848	-0.938	11.494	-36.859	-36.859	0.000	0.000	0.000	0.000
16	A	17	GLN	0	-0.029	0.014	5.403	-8.577	-8.577	0.000	0.000	0.000	0.000
17	A	18	ILE	0	-0.064	-0.029	7.910	-0.309	-0.309	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.903	0.955	9.451	35.630	35.630	0.000	0.000	0.000	0.000
19	A	20	SER	0	0.078	0.029	9.311	-0.319	-0.319	0.000	0.000	0.000	0.000
20	A	21	SER	0	-0.009	-0.019	6.909	-1.209	-1.209	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.878	0.925	9.098	40.053	40.053	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.886	-0.931	12.749	-33.024	-33.024	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.862	-0.902	8.307	-52.382	-52.382	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.065	-0.043	11.608	1.923	1.923	0.000	0.000	0.000	0.000
25	A	26	PHE	0	-0.005	-0.003	13.184	1.845	1.845	0.000	0.000	0.000	0.000
26	A	27	ASN	0	0.003	-0.013	15.455	2.962	2.962	0.000	0.000	0.000	0.000
27	A	28	LEU	0	0.011	0.014	11.933	1.113	1.113	0.000	0.000	0.000	0.000
28	A	29	ARG	1	0.880	0.932	16.228	33.502	33.502	0.000	0.000	0.000	0.000
29	A	30	PHE	0	0.051	0.033	18.526	1.178	1.178	0.000	0.000	0.000	0.000
30	A	31	GLN	0	0.046	0.026	17.538	0.309	0.309	0.000	0.000	0.000	0.000
31	A	32	LEU	0	-0.040	-0.023	18.641	0.769	0.769	0.000	0.000	0.000	0.000
32	A	33	ALA	0	-0.046	-0.026	21.225	0.868	0.868	0.000	0.000	0.000	0.000
33	A	34	THR	0	-0.029	-0.017	24.006	1.171	1.171	0.000	0.000	0.000	0.000
34	A	35	GLY	0	-0.016	0.006	24.517	0.861	0.861	0.000	0.000	0.000	0.000
35	A	36	GLN	0	-0.072	-0.046	23.080	-0.267	-0.267	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.027	-0.018	16.339	-1.132	-1.132	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.826	-0.903	19.142	-27.468	-27.468	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.848	-0.904	14.357	-38.670	-38.670	0.000	0.000	0.000	0.000
39	A	40	THR	0	-0.005	-0.017	14.448	-3.063	-3.063	0.000	0.000	0.000	0.000
40	A	41	ALA	0	-0.012	-0.011	12.194	-1.327	-1.327	0.000	0.000	0.000	0.000
41	A	42	ARG	1	0.863	0.909	9.931	40.364	40.364	0.000	0.000	0.000	0.000
42	A	43	ILE	0	0.040	0.026	10.187	-2.650	-2.650	0.000	0.000	0.000	0.000
43	A	44	ARG	1	0.895	0.936	10.550	40.953	40.953	0.000	0.000	0.000	0.000
44	A	45	THR	0	0.015	-0.004	5.935	-1.157	-1.157	0.000	0.000	0.000	0.000
45	A	46	VAL	0	0.101	0.068	6.083	-7.435	-7.435	0.000	0.000	0.000	0.000
46	A	47	ARG	1	0.933	0.975	7.580	38.313	38.313	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.913	0.944	6.486	52.431	52.431	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.021	-0.007	8.095	1.986	1.986	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.958	0.970	7.274	44.552	44.552	0.000	0.000	0.000	0.000
54	A	55	THR	0	-0.043	-0.020	9.339	3.725	3.725	0.000	0.000	0.000	0.000
55	A	56	VAL	0	-0.010	-0.006	7.769	2.133	2.133	0.000	0.000	0.000	0.000
56	A	57	ALA	0	-0.011	0.002	10.464	2.484	2.484	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.860	0.921	12.770	32.880	32.880	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.822	-0.909	11.918	-49.152	-49.152	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.889	0.940	10.246	51.251	51.251	0.000	0.000	0.000	0.000
60	A	61	GLU	-1	-0.842	-0.904	16.362	-29.165	-29.165	0.000	0.000	0.000	0.000
61	A	62	ILE	0	-0.041	-0.020	18.410	1.604	1.604	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.994	-0.980	17.819	-33.900	-33.900	0.000	0.000	0.000	0.000
63	A	64	GLN	0	-0.112	-0.048	19.564	1.313	1.313	0.000	0.000	0.000	0.000
64	A	65	SER	-1	-0.958	-0.971	23.348	-22.201	-22.201	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LYS)