FMO DATABASE

FMODB ID: 3G28L

Calculation Name: 2FD4-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2FD4

Chain ID: A

ChEMBL ID:

UniProt ID: Q8RSY1

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	120
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230712

Total energy (hartree)

FMO2-HF: Electronic energy	-948234.349564
FMO2-HF: Nuclear repulsion	901876.756468
FMO2-HF: Total energy	-46357.593096
FMO2-MP2: Total energy	-46492.050372

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:435:LYS)

Summations of interaction energy for fragment #1(A:435: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.
-225.14	-222.562	0.217	-1.382	-1.414	-0.008

Interaction energy analysis for fragmet #1(A:435:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.816 / q_NPA : 1.895

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	436	ALA	0	0.020	0.003	3.105	-13.482	-10.904	0.217	-1.382	-1.414	-0.008
4	A	437	ALA	0	0.010	0.014	5.786	4.055	4.055	0.000	0.000	0.000	0.000
5	A	438	LEU	0	0.006	0.005	9.571	-0.384	-0.384	0.000	0.000	0.000	0.000
6	A	439	ASP	-1	-0.811	-0.901	12.227	-33.503	-33.503	0.000	0.000	0.000	0.000
7	A	440	PRO	0	0.023	0.023	14.770	0.679	0.679	0.000	0.000	0.000	0.000
8	A	441	ILE	0	0.032	0.021	18.336	1.701	1.701	0.000	0.000	0.000	0.000
9	A	442	ALA	0	0.022	-0.008	16.171	0.564	0.564	0.000	0.000	0.000	0.000
10	A	443	SER	0	-0.104	-0.064	15.863	0.308	0.308	0.000	0.000	0.000	0.000
11	A	444	GLN	0	-0.022	-0.029	17.360	1.263	1.263	0.000	0.000	0.000	0.000
12	A	445	PHE	0	0.047	0.028	19.286	0.908	0.908	0.000	0.000	0.000	0.000
13	A	446	SER	0	-0.024	-0.032	18.732	0.983	0.983	0.000	0.000	0.000	0.000
14	A	447	GLN	0	-0.057	-0.036	21.566	0.233	0.233	0.000	0.000	0.000	0.000
15	A	448	LEU	0	-0.038	0.005	24.032	0.845	0.845	0.000	0.000	0.000	0.000
16	A	449	ARG	1	0.809	0.915	26.256	18.897	18.897	0.000	0.000	0.000	0.000
17	A	450	THR	0	-0.023	-0.012	27.355	-0.513	-0.513	0.000	0.000	0.000	0.000
18	A	451	ILE	0	0.028	0.027	29.718	0.603	0.603	0.000	0.000	0.000	0.000
19	A	452	SER	0	0.011	-0.018	30.721	-0.823	-0.823	0.000	0.000	0.000	0.000
20	A	453	LYS	1	0.865	0.914	30.965	20.427	20.427	0.000	0.000	0.000	0.000
21	A	454	ALA	0	-0.070	-0.037	33.709	0.408	0.408	0.000	0.000	0.000	0.000
22	A	455	ASP	-1	-1.016	-0.997	35.694	-16.527	-16.527	0.000	0.000	0.000	0.000
23	A	456	ALA	0	-0.001	0.007	35.938	0.366	0.366	0.000	0.000	0.000	0.000
24	A	457	GLU	-1	-0.916	-0.975	37.843	-15.879	-15.879	0.000	0.000	0.000	0.000
25	A	458	SER	-1	-0.902	-0.935	39.473	-14.745	-14.745	0.000	0.000	0.000	0.000
26	A	459	GLU	0	-0.115	-0.094	41.599	0.004	0.004	0.000	0.000	0.000	0.000
27	A	460	GLU	-1	-0.743	-0.855	37.808	-15.842	-15.842	0.000	0.000	0.000	0.000
28	A	461	LEU	0	-0.011	0.027	34.591	-0.705	-0.705	0.000	0.000	0.000	0.000
29	A	462	GLY	0	-0.031	-0.012	36.778	0.045	0.045	0.000	0.000	0.000	0.000
30	A	463	PHE	0	-0.095	-0.049	27.979	-0.373	-0.373	0.000	0.000	0.000	0.000
31	A	464	LYS	1	0.810	0.890	33.307	16.951	16.951	0.000	0.000	0.000	0.000
32	A	465	ASP	-1	-0.737	-0.893	28.636	-22.281	-22.281	0.000	0.000	0.000	0.000
33	A	466	ALA	0	0.014	0.017	27.355	0.501	0.501	0.000	0.000	0.000	0.000
34	A	467	ALA	0	-0.043	-0.023	29.412	-0.073	-0.073	0.000	0.000	0.000	0.000
35	A	468	ASP	-1	-0.878	-0.940	28.890	-21.772	-21.772	0.000	0.000	0.000	0.000
36	A	469	HIS	0	-0.088	-0.040	29.808	0.546	0.546	0.000	0.000	0.000	0.000
37	A	470	HIS	0	-0.121	-0.075	31.479	0.451	0.451	0.000	0.000	0.000	0.000
38	A	471	THR	0	0.026	0.014	29.326	-0.383	-0.383	0.000	0.000	0.000	0.000
39	A	472	ASP	-1	-0.922	-0.957	31.888	-17.307	-17.307	0.000	0.000	0.000	0.000
40	A	473	ASP	-1	-0.890	-0.932	35.546	-16.566	-16.566	0.000	0.000	0.000	0.000
41	A	474	VAL	0	0.020	0.032	29.387	-0.033	-0.033	0.000	0.000	0.000	0.000
42	A	475	THR	0	0.001	0.012	30.236	-0.056	-0.056	0.000	0.000	0.000	0.000
43	A	476	HIS	0	-0.070	-0.047	27.965	-1.083	-1.083	0.000	0.000	0.000	0.000
44	A	477	CYS	-1	-0.852	-0.816	24.299	-25.331	-25.331	0.000	0.000	0.000	0.000
45	A	478	LEU	0	0.022	0.016	26.496	0.421	0.421	0.000	0.000	0.000	0.000
46	A	479	PHE	0	-0.061	-0.091	23.091	0.148	0.148	0.000	0.000	0.000	0.000
47	A	480	GLY	0	-0.042	-0.017	23.515	-0.821	-0.821	0.000	0.000	0.000	0.000
48	A	481	GLY	0	-0.039	-0.024	23.338	-1.239	-1.239	0.000	0.000	0.000	0.000
49	A	482	GLU	-1	-0.853	-0.929	24.666	-21.736	-21.736	0.000	0.000	0.000	0.000
50	A	483	LEU	0	-0.011	0.011	23.853	-1.404	-1.404	0.000	0.000	0.000	0.000
51	A	484	SER	0	0.030	0.007	24.331	0.717	0.717	0.000	0.000	0.000	0.000
52	A	485	LEU	0	-0.026	-0.011	23.766	-1.288	-1.288	0.000	0.000	0.000	0.000
53	A	486	SER	0	-0.048	-0.019	23.573	-0.443	-0.443	0.000	0.000	0.000	0.000
54	A	487	ASN	0	-0.023	-0.009	19.367	-2.046	-2.046	0.000	0.000	0.000	0.000
55	A	488	PRO	0	-0.024	-0.012	16.041	-0.237	-0.237	0.000	0.000	0.000	0.000
56	A	489	ASP	-1	-0.957	-0.980	13.196	-45.065	-45.065	0.000	0.000	0.000	0.000
57	A	490	GLN	0	-0.083	-0.048	16.010	0.503	0.503	0.000	0.000	0.000	0.000
58	A	491	GLN	0	-0.044	-0.038	17.229	-0.061	-0.061	0.000	0.000	0.000	0.000
59	A	492	VAL	0	0.032	0.016	20.055	0.555	0.555	0.000	0.000	0.000	0.000
60	A	493	ILE	0	-0.020	-0.020	23.442	0.270	0.270	0.000	0.000	0.000	0.000
61	A	494	GLY	0	0.068	0.043	25.930	0.238	0.238	0.000	0.000	0.000	0.000
62	A	495	LEU	0	-0.086	-0.055	27.389	-0.358	-0.358	0.000	0.000	0.000	0.000
63	A	496	ALA	0	0.092	0.057	29.942	0.352	0.352	0.000	0.000	0.000	0.000
64	A	497	GLY	0	0.045	0.031	33.165	-0.394	-0.394	0.000	0.000	0.000	0.000
65	A	498	ASN	0	-0.051	-0.041	35.766	-0.050	-0.050	0.000	0.000	0.000	0.000
66	A	499	PRO	0	-0.051	-0.012	33.982	-0.218	-0.218	0.000	0.000	0.000	0.000
67	A	500	THR	0	0.040	0.017	35.016	0.742	0.742	0.000	0.000	0.000	0.000
68	A	501	ASP	-1	-0.929	-0.971	34.683	-17.155	-17.155	0.000	0.000	0.000	0.000
69	A	502	THR	0	-0.019	-0.023	30.141	-0.135	-0.135	0.000	0.000	0.000	0.000
70	A	503	SER	0	-0.025	-0.023	32.951	-0.145	-0.145	0.000	0.000	0.000	0.000
71	A	504	GLN	0	0.013	0.038	34.639	0.469	0.469	0.000	0.000	0.000	0.000
72	A	505	PRO	0	0.008	-0.014	35.914	-0.611	-0.611	0.000	0.000	0.000	0.000
73	A	506	TYR	0	-0.052	-0.045	34.974	-0.154	-0.154	0.000	0.000	0.000	0.000
74	A	507	SER	0	0.033	0.015	36.889	0.467	0.467	0.000	0.000	0.000	0.000
75	A	508	GLN	0	0.036	0.005	40.458	0.029	0.029	0.000	0.000	0.000	0.000
76	A	509	GLU	-1	-0.923	-0.955	40.635	-15.171	-15.171	0.000	0.000	0.000	0.000
77	A	510	GLY	0	0.034	0.007	38.159	-0.021	-0.021	0.000	0.000	0.000	0.000
78	A	511	ASN	0	-0.096	-0.057	35.948	-1.052	-1.052	0.000	0.000	0.000	0.000
79	A	512	LYS	0	-0.043	0.009	37.840	0.335	0.335	0.000	0.000	0.000	0.000
80	A	513	ASP	-1	-0.916	-0.971	36.365	-17.109	-17.109	0.000	0.000	0.000	0.000
81	A	514	LEU	0	-0.048	-0.010	31.881	-0.550	-0.550	0.000	0.000	0.000	0.000
82	A	515	ALA	0	0.022	0.022	31.021	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	516	PHE	0	0.023	-0.001	29.100	-0.799	-0.799	0.000	0.000	0.000	0.000
84	A	517	MET	0	-0.011	-0.026	24.904	-0.358	-0.358	0.000	0.000	0.000	0.000
85	A	518	ASP	-1	-0.755	-0.912	19.033	-32.503	-32.503	0.000	0.000	0.000	0.000
86	A	519	MET	0	-0.035	-0.009	20.056	-0.361	-0.361	0.000	0.000	0.000	0.000
87	A	520	LYS	1	0.915	0.954	13.245	39.551	39.551	0.000	0.000	0.000	0.000
88	A	521	LYS	1	0.926	0.974	17.503	29.625	29.625	0.000	0.000	0.000	0.000
89	A	522	LEU	0	0.041	0.022	19.927	0.236	0.236	0.000	0.000	0.000	0.000
90	A	523	ALA	0	-0.022	-0.011	17.796	0.507	0.507	0.000	0.000	0.000	0.000
91	A	524	GLN	0	-0.032	-0.013	16.755	-0.456	-0.456	0.000	0.000	0.000	0.000
92	A	525	PHE	0	-0.035	-0.012	18.413	0.409	0.409	0.000	0.000	0.000	0.000
93	A	526	LEU	0	-0.007	-0.008	22.208	0.444	0.444	0.000	0.000	0.000	0.000
94	A	527	ALA	0	-0.048	-0.024	18.637	0.560	0.560	0.000	0.000	0.000	0.000
95	A	528	GLY	0	-0.050	-0.015	20.653	-0.035	-0.035	0.000	0.000	0.000	0.000
96	A	529	LYS	1	0.822	0.897	22.552	21.875	21.875	0.000	0.000	0.000	0.000
97	A	530	PRO	0	0.023	0.035	25.397	0.169	0.169	0.000	0.000	0.000	0.000
98	A	531	GLU	-1	-0.779	-0.854	26.721	-18.834	-18.834	0.000	0.000	0.000	0.000
99	A	532	HIS	0	0.054	0.003	28.538	-0.958	-0.958	0.000	0.000	0.000	0.000
100	A	533	PRO	0	-0.034	-0.018	27.542	0.478	0.478	0.000	0.000	0.000	0.000
101	A	534	MET	0	-0.030	-0.012	29.955	0.056	0.056	0.000	0.000	0.000	0.000
102	A	535	THR	0	0.027	0.006	33.581	0.340	0.340	0.000	0.000	0.000	0.000
103	A	536	ARG	1	0.751	0.845	32.905	18.782	18.782	0.000	0.000	0.000	0.000
104	A	537	GLU	-1	-0.863	-0.918	33.969	-16.783	-16.783	0.000	0.000	0.000	0.000
105	A	538	THR	0	-0.051	-0.030	30.414	-0.587	-0.587	0.000	0.000	0.000	0.000
106	A	539	LEU	0	-0.033	0.009	26.946	0.201	0.201	0.000	0.000	0.000	0.000
107	A	540	ASN	0	0.036	-0.001	25.142	-0.479	-0.479	0.000	0.000	0.000	0.000
108	A	541	ALA	0	0.023	0.017	22.101	0.064	0.064	0.000	0.000	0.000	0.000
109	A	542	GLU	-1	-0.894	-0.946	23.978	-23.722	-23.722	0.000	0.000	0.000	0.000
110	A	543	ASN	0	-0.079	-0.059	27.413	0.213	0.213	0.000	0.000	0.000	0.000
111	A	544	ILE	0	0.069	0.056	23.535	0.492	0.492	0.000	0.000	0.000	0.000
112	A	545	ALA	0	0.037	0.014	26.537	0.433	0.433	0.000	0.000	0.000	0.000
113	A	546	LYS	1	0.900	0.950	27.988	19.488	19.488	0.000	0.000	0.000	0.000
114	A	547	TYR	0	0.031	0.019	29.764	0.746	0.746	0.000	0.000	0.000	0.000
115	A	548	ALA	0	-0.026	-0.005	26.280	0.167	0.167	0.000	0.000	0.000	0.000
116	A	549	PHE	0	0.029	0.013	28.371	0.119	0.119	0.000	0.000	0.000	0.000
117	A	550	ARG	1	0.884	0.953	22.817	24.422	24.422	0.000	0.000	0.000	0.000
118	A	551	ILE	0	0.010	0.013	26.283	0.708	0.708	0.000	0.000	0.000	0.000
119	A	552	VAL	0	-0.080	-0.044	25.950	-1.244	-1.244	0.000	0.000	0.000	0.000
120	A	553	PRO	-1	-0.847	-0.910	26.933	-18.958	-18.958	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:435:LYS)