FMO DATABASE

FMODB ID: 9QL32

Calculation Name: 7NHM-k-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: k

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	102
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-685740.43381
FMO2-HF: Nuclear repulsion	645674.359796
FMO2-HF: Total energy	-40066.074014
FMO2-MP2: Total energy	-40184.25781

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:MET)

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

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.
80.671	83.533	0.351	-1.107	-2.105	0

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.867 / q_NPA : 0.925

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].
3	A	3	LYS	1	0.959	0.988	3.452	34.005	36.867	0.351	-1.107	-2.105
4	A	4	GLN	0	0.044	0.021	5.650	0.381	0.381	0.000	0.000	0.000
5	A	5	LYS	1	0.811	0.888	5.549	32.573	32.573	0.000	0.000	0.000
6	A	6	ILE	0	0.069	0.056	10.000	0.633	0.633	0.000	0.000	0.000
7	A	7	ARG	1	0.887	0.961	10.348	24.157	24.157	0.000	0.000	0.000
8	A	8	ILE	0	0.040	0.015	13.219	0.723	0.723	0.000	0.000	0.000
9	A	9	ARG	1	0.864	0.931	16.451	15.348	15.348	0.000	0.000	0.000
10	A	10	LEU	0	0.053	0.033	18.917	0.462	0.462	0.000	0.000	0.000
11	A	11	LYS	1	0.873	0.932	22.159	12.816	12.816	0.000	0.000	0.000
12	A	12	ALA	0	0.079	0.046	25.090	0.296	0.296	0.000	0.000	0.000
13	A	13	TYR	0	-0.003	-0.008	28.532	-0.172	-0.172	0.000	0.000	0.000
14	A	14	ASP	-1	-0.825	-0.899	30.551	-8.895	-8.895	0.000	0.000	0.000
15	A	15	HIS	0	-0.026	-0.025	27.020	-0.311	-0.311	0.000	0.000	0.000
16	A	16	ARG	1	0.897	0.940	27.539	8.524	8.524	0.000	0.000	0.000
17	A	17	VAL	0	0.050	0.034	29.092	0.177	0.177	0.000	0.000	0.000
18	A	18	ILE	0	-0.020	0.007	23.269	-0.233	-0.233	0.000	0.000	0.000
19	A	19	ASP	-1	-0.874	-0.935	23.810	-11.143	-11.143	0.000	0.000	0.000
20	A	20	GLN	0	0.000	-0.005	24.435	-0.146	-0.146	0.000	0.000	0.000
21	A	21	SER	0	0.033	0.008	25.485	0.278	0.278	0.000	0.000	0.000
22	A	22	ALA	0	-0.019	-0.025	20.435	-0.275	-0.275	0.000	0.000	0.000
23	A	23	GLU	-1	-0.959	-0.979	20.803	-11.863	-11.863	0.000	0.000	0.000
24	A	24	LYS	1	0.945	0.974	22.357	10.307	10.307	0.000	0.000	0.000
25	A	25	ILE	0	0.034	0.029	19.799	-0.150	-0.150	0.000	0.000	0.000
26	A	26	VAL	0	0.004	0.001	16.904	-0.489	-0.489	0.000	0.000	0.000
27	A	27	GLU	-1	-0.991	-0.991	18.849	-11.283	-11.283	0.000	0.000	0.000
28	A	28	THR	0	-0.035	-0.033	21.164	0.041	0.041	0.000	0.000	0.000
29	A	29	ALA	0	0.021	0.026	16.129	-0.016	-0.016	0.000	0.000	0.000
30	A	30	LYS	1	0.916	0.954	17.307	12.745	12.745	0.000	0.000	0.000
31	A	31	ARG	1	0.968	1.006	18.204	10.904	10.904	0.000	0.000	0.000
32	A	32	SER	0	-0.059	-0.050	20.151	0.117	0.117	0.000	0.000	0.000
33	A	33	GLY	0	0.016	-0.003	16.651	0.102	0.102	0.000	0.000	0.000
34	A	34	ALA	0	0.025	0.010	14.329	0.525	0.525	0.000	0.000	0.000
35	A	35	ASP	-1	-0.910	-0.962	9.442	-20.326	-20.326	0.000	0.000	0.000
36	A	36	VAL	0	-0.038	-0.010	9.733	-1.572	-1.572	0.000	0.000	0.000
37	A	37	SER	0	-0.029	-0.008	8.888	-0.638	-0.638	0.000	0.000	0.000
38	A	38	GLY	0	0.014	0.005	10.653	1.076	1.076	0.000	0.000	0.000
39	A	39	PRO	0	-0.019	-0.015	13.278	-0.808	-0.808	0.000	0.000	0.000
40	A	40	ILE	0	0.025	0.010	11.567	0.242	0.242	0.000	0.000	0.000
41	A	41	PRO	0	-0.019	-0.009	15.443	0.390	0.390	0.000	0.000	0.000
42	A	42	LEU	0	-0.008	-0.009	16.080	-0.731	-0.731	0.000	0.000	0.000
43	A	43	PRO	0	0.016	-0.010	19.651	0.557	0.557	0.000	0.000	0.000
44	A	44	THR	0	-0.066	-0.008	22.582	0.564	0.564	0.000	0.000	0.000
45	A	45	GLU	-1	-0.804	-0.886	23.200	-12.767	-12.767	0.000	0.000	0.000
46	A	46	LYS	1	0.856	0.914	27.314	9.329	9.329	0.000	0.000	0.000
47	A	47	SER	0	-0.014	0.006	31.052	-0.031	-0.031	0.000	0.000	0.000
48	A	48	VAL	0	-0.006	-0.009	33.861	0.134	0.134	0.000	0.000	0.000
49	A	49	TYR	0	0.020	0.009	36.451	-0.020	-0.020	0.000	0.000	0.000
50	A	50	THR	0	-0.009	-0.009	40.515	0.097	0.097	0.000	0.000	0.000
51	A	51	ILE	0	0.006	0.011	43.668	0.030	0.030	0.000	0.000	0.000
52	A	52	ILE	0	-0.028	-0.020	47.099	0.007	0.007	0.000	0.000	0.000
53	A	53	ARG	1	0.895	0.930	47.996	6.465	6.465	0.000	0.000	0.000
54	A	54	ALA	0	-0.030	0.002	52.423	0.078	0.078	0.000	0.000	0.000
55	A	55	VAL	0	0.045	0.012	54.553	-0.076	-0.076	0.000	0.000	0.000
56	A	56	HIS	0	-0.017	0.000	56.688	-0.022	-0.022	0.000	0.000	0.000
57	A	57	LYS	1	0.981	0.992	58.458	5.047	5.047	0.000	0.000	0.000
58	A	58	TYR	0	0.021	-0.009	57.413	-0.021	-0.021	0.000	0.000	0.000
59	A	59	LYS	1	1.023	1.014	51.335	6.141	6.141	0.000	0.000	0.000
60	A	60	ASP	-1	-0.872	-0.931	52.451	-6.070	-6.070	0.000	0.000	0.000
61	A	61	SER	0	-0.022	-0.001	52.317	-0.049	-0.049	0.000	0.000	0.000
62	A	62	ARG	1	0.860	0.923	47.527	6.577	6.577	0.000	0.000	0.000
63	A	63	GLU	-1	-0.859	-0.920	46.120	-6.549	-6.549	0.000	0.000	0.000
64	A	64	GLN	0	-0.052	-0.037	41.546	-0.083	-0.083	0.000	0.000	0.000
65	A	65	PHE	0	0.060	0.043	40.829	-0.006	-0.006	0.000	0.000	0.000
66	A	66	GLU	-1	-0.844	-0.934	35.429	-8.995	-8.995	0.000	0.000	0.000
67	A	67	GLN	0	0.017	0.032	33.319	-0.160	-0.160	0.000	0.000	0.000
68	A	68	ARG	1	0.967	0.967	30.452	9.293	9.293	0.000	0.000	0.000
69	A	69	THR	0	0.022	0.021	26.568	0.020	0.020	0.000	0.000	0.000
70	A	70	HIS	0	0.051	0.031	23.616	-0.923	-0.923	0.000	0.000	0.000
71	A	71	LYS	1	0.820	0.901	21.340	12.583	12.583	0.000	0.000	0.000
72	A	72	ARG	1	0.897	0.939	19.083	13.158	13.158	0.000	0.000	0.000
73	A	73	LEU	0	-0.015	-0.005	12.433	-0.051	-0.051	0.000	0.000	0.000
74	A	74	ILE	0	0.045	0.020	14.201	0.019	0.019	0.000	0.000	0.000
75	A	75	ASP	-1	-0.815	-0.899	8.381	-28.152	-28.152	0.000	0.000	0.000
76	A	76	ILE	0	0.061	0.033	10.817	-0.508	-0.508	0.000	0.000	0.000
77	A	77	VAL	0	-0.027	-0.020	6.898	-1.035	-1.035	0.000	0.000	0.000
78	A	78	ASN	0	-0.013	-0.002	9.538	-0.019	-0.019	0.000	0.000	0.000
79	A	79	PRO	0	0.035	0.035	11.530	0.954	0.954	0.000	0.000	0.000
80	A	80	THR	0	-0.005	-0.030	14.330	0.700	0.700	0.000	0.000	0.000
81	A	81	PRO	0	0.050	0.024	18.118	0.015	0.015	0.000	0.000	0.000
82	A	82	LYS	1	0.983	0.994	20.959	12.891	12.891	0.000	0.000	0.000
83	A	83	THR	0	0.011	0.005	16.360	0.171	0.171	0.000	0.000	0.000
84	A	84	VAL	0	-0.027	-0.007	18.301	-0.167	-0.167	0.000	0.000	0.000
85	A	85	ASP	-1	-0.877	-0.949	20.426	-11.513	-11.513	0.000	0.000	0.000
86	A	86	ALA	0	-0.047	-0.029	22.217	0.356	0.356	0.000	0.000	0.000
87	A	87	LEU	0	-0.067	-0.030	17.702	0.131	0.131	0.000	0.000	0.000
88	A	88	MET	0	-0.041	-0.014	22.040	-0.017	-0.017	0.000	0.000	0.000
89	A	89	GLY	0	-0.019	-0.001	24.423	0.381	0.381	0.000	0.000	0.000
90	A	90	LEU	0	-0.046	-0.022	25.317	0.398	0.398	0.000	0.000	0.000
91	A	91	ASN	0	-0.007	-0.002	26.013	-0.286	-0.286	0.000	0.000	0.000
92	A	92	LEU	0	0.006	0.016	27.997	0.369	0.369	0.000	0.000	0.000
93	A	93	PRO	0	-0.015	-0.026	28.271	-0.267	-0.267	0.000	0.000	0.000
94	A	94	SER	0	0.058	0.019	30.582	-0.131	-0.131	0.000	0.000	0.000
95	A	95	GLY	0	-0.035	-0.003	32.375	0.064	0.064	0.000	0.000	0.000
96	A	96	VAL	0	-0.071	-0.048	25.797	-0.165	-0.165	0.000	0.000	0.000
97	A	97	ASP	-1	-0.860	-0.899	26.919	-10.303	-10.303	0.000	0.000	0.000
98	A	98	ILE	0	-0.036	-0.040	22.439	-0.536	-0.536	0.000	0.000	0.000
99	A	99	GLU	-1	-0.917	-0.965	20.206	-14.197	-14.197	0.000	0.000	0.000
100	A	100	ILE	0	0.028	0.005	18.146	-0.843	-0.843	0.000	0.000	0.000
101	A	101	LYS	1	0.873	0.926	14.617	19.194	19.194	0.000	0.000	0.000
102	A	102	LEU	-1	-0.878	-0.924	14.789	-18.861	-18.861	0.000	0.000	0.000

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