FMO DATABASE

FMODB ID: R4Y78

Calculation Name: 7NHM-X-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: X

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	99
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-629478.269262
FMO2-HF: Nuclear repulsion	591925.205408
FMO2-HF: Total energy	-37553.063854
FMO2-MP2: Total energy	-37663.75526

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.
137.782	149.97	8.394	-6.476	-14.106	-0.056

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 : 0.837 / q_NPA : 0.916

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	ILE	0	0.022	0.030	3.121	7.073	10.393	0.138	-1.316	-2.141	-0.003
4	A	4	LYS	1	0.933	0.963	2.455	19.134	21.340	1.645	-1.670	-2.182	-0.024
5	A	5	LYS	1	0.942	0.959	4.788	24.356	24.470	-0.001	-0.005	-0.108	0.000
26	A	26	THR	0	0.004	-0.002	2.429	-0.427	0.571	0.848	-0.354	-1.493	-0.001
27	A	27	LEU	0	0.003	-0.001	3.292	1.907	2.294	0.023	-0.120	-0.291	0.000
28	A	28	PRO	0	0.042	0.007	2.442	-2.390	-1.050	1.328	-0.784	-1.884	0.001
29	A	29	LYS	1	0.973	0.983	3.388	24.207	23.675	0.048	0.763	-0.279	0.000
31	A	31	ASP	-1	-0.880	-0.930	2.983	-62.837	-60.892	0.183	-0.922	-1.205	-0.007
32	A	32	ARG	1	0.888	0.947	3.269	27.388	28.003	0.048	-0.195	-0.468	-0.002
33	A	33	VAL	0	0.009	0.001	2.697	-7.863	-6.059	0.507	-0.980	-1.330	-0.013
34	A	34	VAL	0	0.010	0.017	4.873	1.790	1.807	-0.001	-0.007	-0.009	0.000
65	A	65	VAL	0	0.018	-0.008	2.317	-0.138	-0.164	3.628	-0.886	-2.716	-0.007
6	A	6	GLY	0	-0.002	-0.001	7.423	0.481	0.481	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.744	-0.820	7.321	-29.413	-29.413	0.000	0.000	0.000	0.000
8	A	8	ASN	0	0.031	0.003	10.232	0.396	0.396	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.020	-0.017	8.516	-1.419	-1.419	0.000	0.000	0.000	0.000
10	A	10	LYS	1	1.010	1.011	11.716	17.550	17.550	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.038	-0.010	11.761	-1.982	-1.982	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.048	-0.016	10.923	1.232	1.232	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.008	-0.015	13.965	1.344	1.344	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.034	0.012	14.241	-0.821	-0.821	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.950	0.960	16.371	13.550	13.550	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.776	-0.864	15.965	-14.357	-14.357	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.919	0.959	17.096	13.404	13.404	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.005	-0.008	17.091	0.836	0.836	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.895	0.943	16.325	14.207	14.207	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.909	-0.952	15.083	-15.801	-15.801	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.031	0.022	14.304	0.845	0.845	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.915	0.949	12.522	14.282	14.282	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.063	-0.016	6.334	-0.100	-0.100	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.052	0.027	9.673	-0.021	-0.021	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.019	-0.028	8.080	0.288	0.288	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.942	0.971	5.622	24.908	24.908	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.008	0.000	8.639	-0.990	-0.990	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.800	-0.891	11.178	-15.622	-15.622	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.066	0.031	14.884	-0.025	-0.025	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.065	-0.040	12.734	0.303	0.303	0.000	0.000	0.000	0.000
39	A	39	ASN	0	-0.065	-0.044	12.233	0.466	0.466	0.000	0.000	0.000	0.000
40	A	40	ILE	0	0.028	0.025	15.288	-0.291	-0.291	0.000	0.000	0.000	0.000
41	A	41	MET	0	-0.070	-0.014	15.886	0.406	0.406	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.901	0.926	18.999	10.850	10.850	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.891	0.956	19.542	12.711	12.711	0.000	0.000	0.000	0.000
44	A	44	HIS	0	0.047	0.022	22.571	0.278	0.278	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.001	-0.001	23.154	-0.707	-0.707	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.975	0.984	26.789	9.702	9.702	0.000	0.000	0.000	0.000
47	A	47	PRO	0	0.038	0.010	29.494	-0.191	-0.191	0.000	0.000	0.000	0.000
48	A	48	THR	0	-0.068	-0.018	28.189	0.181	0.181	0.000	0.000	0.000	0.000
49	A	49	GLN	0	0.031	0.001	27.052	-0.153	-0.153	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.015	0.003	24.102	-0.113	-0.113	0.000	0.000	0.000	0.000
51	A	51	ASN	0	0.027	0.022	28.611	-0.016	-0.016	0.000	0.000	0.000	0.000
52	A	52	PRO	0	-0.004	-0.025	30.381	-0.233	-0.233	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.886	-0.939	32.414	-8.270	-8.270	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.001	0.014	28.481	-0.067	-0.067	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.001	-0.012	28.500	-0.101	-0.101	0.000	0.000	0.000	0.000
56	A	56	ILE	0	-0.051	-0.025	25.724	-0.243	-0.243	0.000	0.000	0.000	0.000
57	A	57	LEU	0	0.022	0.014	22.635	-0.035	-0.035	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.860	-0.922	21.947	-11.225	-11.225	0.000	0.000	0.000	0.000
59	A	59	THR	0	-0.017	-0.014	17.495	-0.159	-0.159	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.871	-0.933	13.462	-14.919	-14.919	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.025	-0.001	13.112	-0.303	-0.303	0.000	0.000	0.000	0.000
62	A	62	ALA	0	-0.053	-0.037	7.846	-0.958	-0.958	0.000	0.000	0.000	0.000
63	A	63	ILE	0	-0.004	-0.003	8.147	0.909	0.909	0.000	0.000	0.000	0.000
64	A	64	HIS	0	0.019	0.028	6.410	-1.149	-1.149	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.014	-0.030	5.513	0.462	0.462	0.000	0.000	0.000	0.000
67	A	67	ASN	0	-0.006	0.004	8.488	1.712	1.712	0.000	0.000	0.000	0.000
68	A	68	VAL	0	0.003	0.003	7.023	1.865	1.865	0.000	0.000	0.000	0.000
69	A	69	GLN	0	-0.023	-0.024	8.305	-2.321	-2.321	0.000	0.000	0.000	0.000
70	A	70	LEU	0	0.022	0.013	8.596	0.393	0.393	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.017	0.010	10.800	0.710	0.710	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.783	-0.870	14.239	-16.858	-16.858	0.000	0.000	0.000	0.000
73	A	73	PRO	0	-0.016	0.002	15.779	0.507	0.507	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.980	1.003	17.886	12.783	12.783	0.000	0.000	0.000	0.000
75	A	75	THR	0	-0.054	-0.064	20.617	0.472	0.472	0.000	0.000	0.000	0.000
76	A	76	ASN	0	0.001	0.003	18.566	-0.396	-0.396	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.810	-0.877	19.140	-14.369	-14.369	0.000	0.000	0.000	0.000
78	A	78	PRO	0	-0.036	-0.018	15.085	-0.931	-0.931	0.000	0.000	0.000	0.000
79	A	79	THR	0	-0.020	-0.013	13.070	0.202	0.202	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.943	0.965	11.164	20.144	20.144	0.000	0.000	0.000	0.000
81	A	81	VAL	0	0.032	0.015	7.770	1.154	1.154	0.000	0.000	0.000	0.000
82	A	82	GLY	0	-0.015	-0.004	10.005	-0.162	-0.162	0.000	0.000	0.000	0.000
83	A	83	TYR	0	-0.028	-0.026	6.127	-3.475	-3.475	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.971	0.996	12.239	17.451	17.451	0.000	0.000	0.000	0.000
85	A	85	PHE	0	-0.012	-0.013	13.874	-1.359	-1.359	0.000	0.000	0.000	0.000
86	A	86	VAL	0	0.052	0.028	17.198	0.759	0.759	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.841	-0.913	19.553	-14.015	-14.015	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.016	0.012	19.020	0.102	0.102	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.867	0.929	16.062	14.148	14.148	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.917	0.959	8.497	31.691	31.691	0.000	0.000	0.000	0.000
91	A	91	VAL	0	0.050	0.033	13.572	-0.272	-0.272	0.000	0.000	0.000	0.000
92	A	92	ARG	1	0.741	0.820	6.705	30.396	30.396	0.000	0.000	0.000	0.000
93	A	93	ILE	0	0.008	0.016	11.886	1.260	1.260	0.000	0.000	0.000	0.000
94	A	94	ALA	0	0.047	0.025	13.181	-2.122	-2.122	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.879	0.929	13.252	21.215	21.215	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.791	0.871	15.297	16.740	16.740	0.000	0.000	0.000	0.000
97	A	97	SER	0	-0.017	-0.017	18.408	0.609	0.609	0.000	0.000	0.000	0.000
98	A	98	GLY	0	-0.028	-0.022	18.712	0.699	0.699	0.000	0.000	0.000	0.000
99	A	99	GLU	-2	-1.789	-1.881	16.605	-33.057	-33.057	0.000	0.000	0.000	0.000

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