FMO DATABASE

FMODB ID: VKJV1

Calculation Name: 3L4F-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L4F

Chain ID: A

ChEMBL ID:

UniProt ID: O55043

Base Structure: X-ray

Registration Date: 2025-07-08

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	121
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-271191.024974
FMO2-HF: Nuclear repulsion	245185.837847
FMO2-HF: Total energy	-26005.187127
FMO2-MP2: Total energy	-26079.432607

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:586:MET)

Summations of interaction energy for fragment #1(A:586: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.
-16.65	-25.094	0.738	10.441	-2.737	-0.001

Interaction energy analysis for fragmet #1(A:586:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.102

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].
4	A	587	GLU	-1	-1.008	-0.849	3.944	-0.177	0.587	0.009	-0.374	-0.399	-0.001
5	A	588	LYS	0	0.071	-0.095	3.671	-0.869	1.382	-0.017	-1.323	-0.911	-0.001
6	A	588	LYS	1	0.831	1.036	3.230	-11.849	-11.077	0.121	-0.411	-0.482	0.003
7	A	589	SER	0	0.165	-0.024	5.381	-0.678	-0.678	0.000	0.000	0.000	0.000
8	A	589	SER	0	-0.022	0.079	9.597	-0.034	-0.034	0.000	0.000	0.000	0.000
9	A	590	LEU	0	0.117	-0.041	7.870	-0.369	-0.369	0.000	0.000	0.000	0.000
10	A	590	LEU	0	-0.086	0.110	8.076	0.054	0.054	0.000	0.000	0.000	0.000
11	A	591	VAL	0	0.072	-0.102	3.753	-1.046	-0.958	0.014	-0.031	-0.072	0.000
12	A	591	VAL	0	-0.042	0.089	2.758	0.114	0.507	0.307	-0.266	-0.434	0.001
13	A	592	ASP	0	0.086	-0.120	4.681	-0.080	-0.064	-0.002	-0.016	0.001	0.000
14	A	592	ASP	-1	-0.919	-0.790	2.775	-1.454	-14.173	0.308	12.863	-0.452	-0.003
15	A	593	THR	0	0.070	-0.064	5.240	0.035	0.026	-0.002	-0.001	0.012	0.000
16	A	593	THR	0	-0.102	-0.009	9.240	0.066	0.066	0.000	0.000	0.000	0.000
17	A	594	VAL	0	0.011	-0.070	8.221	-0.066	-0.066	0.000	0.000	0.000	0.000
18	A	594	VAL	0	-0.099	0.066	7.995	0.082	0.082	0.000	0.000	0.000	0.000
19	A	595	TYR	0	0.057	-0.090	6.306	0.505	0.505	0.000	0.000	0.000	0.000
20	A	595	TYR	0	-0.031	0.083	5.454	0.055	0.055	0.000	0.000	0.000	0.000
21	A	596	ALA	0	0.144	-0.074	7.615	-0.066	-0.066	0.000	0.000	0.000	0.000
22	A	596	ALA	0	-0.058	0.121	8.979	0.002	0.002	0.000	0.000	0.000	0.000
23	A	597	LEU	0	0.184	-0.053	9.677	0.119	0.119	0.000	0.000	0.000	0.000
24	A	597	LEU	0	-0.125	0.103	12.443	0.039	0.039	0.000	0.000	0.000	0.000
25	A	598	LYS	0	0.105	-0.080	11.268	0.138	0.138	0.000	0.000	0.000	0.000
26	A	598	LYS	1	0.788	1.035	9.677	0.308	0.308	0.000	0.000	0.000	0.000
27	A	599	ASP	0	0.061	-0.140	11.341	0.219	0.219	0.000	0.000	0.000	0.000
28	A	599	ASP	-1	-1.002	-0.850	10.012	-1.630	-1.630	0.000	0.000	0.000	0.000
29	A	600	GLU	0	0.040	-0.132	12.858	0.111	0.111	0.000	0.000	0.000	0.000
30	A	600	GLU	-1	-1.014	-0.859	13.546	-0.815	-0.815	0.000	0.000	0.000	0.000
31	A	601	VAL	0	0.057	-0.105	15.284	0.072	0.072	0.000	0.000	0.000	0.000
32	A	601	VAL	0	-0.112	0.089	15.925	0.025	0.025	0.000	0.000	0.000	0.000
33	A	602	GLN	0	0.057	-0.136	16.128	0.093	0.093	0.000	0.000	0.000	0.000
34	A	602	GLN	0	-0.099	0.094	16.300	0.084	0.084	0.000	0.000	0.000	0.000
35	A	603	GLU	0	0.049	-0.141	17.503	0.071	0.071	0.000	0.000	0.000	0.000
36	A	603	GLU	-1	-0.969	-0.810	17.315	-0.543	-0.543	0.000	0.000	0.000	0.000
37	A	604	LEU	0	0.167	-0.083	19.298	0.046	0.046	0.000	0.000	0.000	0.000
38	A	604	LEU	0	-0.084	0.129	20.467	0.005	0.005	0.000	0.000	0.000	0.000
39	A	605	ARG	0	0.132	-0.101	20.899	0.047	0.047	0.000	0.000	0.000	0.000
40	A	605	ARG	1	0.795	1.044	18.520	0.252	0.252	0.000	0.000	0.000	0.000
41	A	606	GLN	0	-0.030	-0.152	22.087	0.051	0.051	0.000	0.000	0.000	0.000
42	A	606	GLN	0	-0.097	0.105	20.776	0.006	0.006	0.000	0.000	0.000	0.000
43	A	607	ASP	0	0.089	-0.140	23.552	0.034	0.034	0.000	0.000	0.000	0.000
44	A	607	ASP	-1	-0.914	-0.790	23.452	-0.360	-0.360	0.000	0.000	0.000	0.000
45	A	608	ASN	0	0.119	-0.064	25.364	0.021	0.021	0.000	0.000	0.000	0.000
46	A	608	ASN	0	-0.121	0.078	25.869	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	609	LYS	0	0.102	-0.076	26.725	0.023	0.023	0.000	0.000	0.000	0.000
48	A	609	LYS	1	0.839	1.048	23.903	0.194	0.194	0.000	0.000	0.000	0.000
49	A	610	LYS	0	0.057	-0.106	28.071	0.022	0.022	0.000	0.000	0.000	0.000
50	A	610	LYS	1	0.884	1.076	26.042	0.295	0.295	0.000	0.000	0.000	0.000
51	A	611	MET	0	0.108	-0.094	29.444	0.012	0.012	0.000	0.000	0.000	0.000
52	A	611	MET	0	-0.108	0.102	29.131	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	612	LYS	0	0.072	-0.089	31.120	0.010	0.010	0.000	0.000	0.000	0.000
54	A	612	LYS	1	0.877	1.053	31.805	0.100	0.100	0.000	0.000	0.000	0.000
55	A	613	LYS	0	0.073	-0.109	32.619	0.014	0.014	0.000	0.000	0.000	0.000
56	A	613	LYS	1	0.860	1.086	31.395	0.146	0.146	0.000	0.000	0.000	0.000
57	A	614	SER	0	0.116	-0.055	34.003	0.011	0.011	0.000	0.000	0.000	0.000
58	A	614	SER	0	-0.012	0.087	34.516	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	615	LEU	0	0.085	-0.084	35.779	0.005	0.005	0.000	0.000	0.000	0.000
60	A	615	LEU	0	-0.088	0.104	34.993	0.001	0.001	0.000	0.000	0.000	0.000
61	A	616	GLU	0	0.100	-0.101	37.273	0.008	0.008	0.000	0.000	0.000	0.000
62	A	616	GLU	-1	-1.043	-0.868	36.135	-0.104	-0.104	0.000	0.000	0.000	0.000
63	A	617	GLU	0	0.052	-0.152	38.615	0.011	0.011	0.000	0.000	0.000	0.000
64	A	617	GLU	-1	-0.987	-0.835	36.713	-0.141	-0.141	0.000	0.000	0.000	0.000
65	A	618	GLU	0	0.138	-0.105	39.855	0.007	0.007	0.000	0.000	0.000	0.000
66	A	618	GLU	-1	-1.025	-0.844	39.981	-0.114	-0.114	0.000	0.000	0.000	0.000
67	A	619	GLN	0	0.019	-0.111	41.562	0.005	0.005	0.000	0.000	0.000	0.000
68	A	619	GLN	0	-0.157	0.047	40.152	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	620	ARG	0	0.023	-0.134	43.211	0.006	0.006	0.000	0.000	0.000	0.000
70	A	620	ARG	1	0.878	1.078	42.849	0.087	0.087	0.000	0.000	0.000	0.000
71	A	621	ALA	0	0.031	-0.121	44.592	0.006	0.006	0.000	0.000	0.000	0.000
72	A	621	ALA	0	-0.013	0.153	44.753	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	622	ARG	0	0.110	-0.098	45.838	0.003	0.003	0.000	0.000	0.000	0.000
74	A	622	ARG	1	0.793	1.032	45.513	0.075	0.075	0.000	0.000	0.000	0.000
75	A	623	LYS	0	0.064	-0.093	47.602	0.003	0.003	0.000	0.000	0.000	0.000
76	A	623	LYS	1	0.852	1.044	46.414	0.064	0.064	0.000	0.000	0.000	0.000
77	A	624	ASP	0	0.085	-0.143	49.271	0.006	0.006	0.000	0.000	0.000	0.000
78	A	624	ASP	-1	-0.942	-0.808	49.732	-0.072	-0.072	0.000	0.000	0.000	0.000
79	A	625	LEU	0	0.073	-0.141	50.606	0.003	0.003	0.000	0.000	0.000	0.000
80	A	625	LEU	0	-0.035	0.159	50.639	0.000	0.000	0.000	0.000	0.000	0.000
81	A	626	GLU	0	0.096	-0.122	52.079	0.002	0.002	0.000	0.000	0.000	0.000
82	A	626	GLU	-1	-0.962	-0.784	50.909	-0.063	-0.063	0.000	0.000	0.000	0.000
83	A	627	LYS	0	0.071	-0.098	53.821	0.004	0.004	0.000	0.000	0.000	0.000
84	A	627	LYS	1	0.836	1.055	51.419	0.059	0.059	0.000	0.000	0.000	0.000
85	A	628	LEU	0	0.030	-0.124	55.308	0.004	0.004	0.000	0.000	0.000	0.000
86	A	628	LEU	0	-0.068	0.123	54.652	0.000	0.000	0.000	0.000	0.000	0.000
87	A	629	VAL	0	0.119	-0.083	56.499	0.003	0.003	0.000	0.000	0.000	0.000
88	A	629	VAL	0	-0.038	0.117	55.582	0.000	0.000	0.000	0.000	0.000	0.000
89	A	630	ARG	0	0.128	-0.067	57.804	0.002	0.002	0.000	0.000	0.000	0.000
90	A	630	ARG	1	0.840	1.039	54.651	0.049	0.049	0.000	0.000	0.000	0.000
91	A	631	LYS	0	0.010	-0.096	59.632	0.003	0.003	0.000	0.000	0.000	0.000
92	A	631	LYS	1	0.814	1.042	60.061	0.047	0.047	0.000	0.000	0.000	0.000
93	A	632	VAL	0	0.123	-0.113	60.969	0.002	0.002	0.000	0.000	0.000	0.000
94	A	632	VAL	0	-0.061	0.110	60.385	0.000	0.000	0.000	0.000	0.000	0.000
95	A	633	LEU	0	0.030	-0.123	62.395	0.001	0.001	0.000	0.000	0.000	0.000
96	A	633	LEU	0	-0.082	0.102	61.043	0.000	0.000	0.000	0.000	0.000	0.000
97	A	634	LYS	0	0.128	-0.063	63.970	0.002	0.002	0.000	0.000	0.000	0.000
98	A	634	LYS	1	0.838	1.038	64.499	0.037	0.037	0.000	0.000	0.000	0.000
99	A	635	ASN	0	0.094	-0.056	65.798	0.002	0.002	0.000	0.000	0.000	0.000
100	A	635	ASN	0	-0.095	0.054	65.411	0.001	0.001	0.000	0.000	0.000	0.000
101	A	636	MET	0	0.094	-0.061	66.997	0.001	0.001	0.000	0.000	0.000	0.000
102	A	636	MET	0	-0.110	0.057	65.595	0.000	0.000	0.000	0.000	0.000	0.000
103	A	637	ASN	0	0.091	-0.016	68.600	0.001	0.001	0.000	0.000	0.000	0.000
104	A	637	ASN	0	-0.188	-0.002	69.113	0.001	0.001	0.000	0.000	0.000	0.000
105	A	638	ASP	0	0.119	-0.091	70.146	0.001	0.001	0.000	0.000	0.000	0.000
106	A	638	ASP	-1	-1.059	-0.869	71.250	-0.031	-0.031	0.000	0.000	0.000	0.000
107	A	639	PRO	0	0.003	-0.105	70.817	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	640	ALA	0	0.110	0.007	70.752	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	640	ALA	0	-0.119	0.091	70.558	0.000	0.000	0.000	0.000	0.000	0.000
110	A	641	TRP	0	0.015	-0.144	72.569	0.001	0.001	0.000	0.000	0.000	0.000
111	A	641	TRP	0	-0.133	0.076	71.080	0.000	0.000	0.000	0.000	0.000	0.000
112	A	642	ASP	0	0.091	-0.099	73.907	0.000	0.000	0.000	0.000	0.000	0.000
113	A	642	ASP	-1	-0.965	-0.813	77.739	-0.030	-0.030	0.000	0.000	0.000	0.000
114	A	643	GLU	0	0.034	-0.175	77.645	0.000	0.000	0.000	0.000	0.000	0.000
115	A	643	GLU	-1	-1.016	-0.823	77.449	-0.035	-0.035	0.000	0.000	0.000	0.000
116	A	644	THR	0	-0.019	-0.091	80.375	0.001	0.001	0.000	0.000	0.000	0.000
117	A	644	THR	0	0.005	0.062	83.162	0.000	0.000	0.000	0.000	0.000	0.000
118	A	645	ASN	0	0.089	-0.076	84.142	0.000	0.000	0.000	0.000	0.000	0.000
119	A	645	ASN	0	-0.121	0.075	85.638	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	646	LEU	0	-0.076	-0.124	87.017	0.001	0.001	0.000	0.000	0.000	0.000
121	A	646	LEU	0	0.045	0.028	86.121	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:586:MET)