FMO DATABASE

FMODB ID: N1LJQ

Calculation Name: 3LE4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LE4

Chain ID: A

ChEMBL ID:

UniProt ID: Q8WYQ5

Base Structure: X-ray

Registration Date: 2023-03-14

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

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
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	55
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-267294.439372
FMO2-HF: Nuclear repulsion	245499.093693
FMO2-HF: Total energy	-21795.345679
FMO2-MP2: Total energy	-21858.957521

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:298:PRO)

Summations of interaction energy for fragment #1(A:298:PRO)

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.
-6.562	-1.43	2.768	-2.634	-5.265	-0.012

Interaction energy analysis for fragmet #1(A:298:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.013

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	300	THR	0	-0.046	-0.030	3.000	-3.008	-0.750	0.157	-1.171	-1.244	-0.002
4	A	301	GLU	-1	-0.856	-0.922	5.367	-0.384	-0.260	-0.001	-0.005	-0.117	0.000
5	A	302	PRO	0	-0.011	-0.011	7.907	0.032	0.032	0.000	0.000	0.000	0.000
6	A	303	LEU	0	-0.015	0.000	10.876	-0.044	-0.044	0.000	0.000	0.000	0.000
7	A	304	PRO	0	0.008	0.010	13.090	0.029	0.029	0.000	0.000	0.000	0.000
8	A	305	ASP	-1	-0.858	-0.931	16.022	-0.108	-0.108	0.000	0.000	0.000	0.000
9	A	306	GLY	0	-0.033	-0.022	19.493	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	307	TRP	0	-0.048	-0.028	15.677	0.001	0.001	0.000	0.000	0.000	0.000
11	A	308	ILE	0	-0.024	-0.009	15.892	0.009	0.009	0.000	0.000	0.000	0.000
12	A	309	MET	0	-0.011	0.007	9.890	-0.034	-0.034	0.000	0.000	0.000	0.000
13	A	310	THR	0	-0.023	-0.020	13.768	0.042	0.042	0.000	0.000	0.000	0.000
14	A	311	PHE	0	0.045	0.026	15.301	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	312	HIS	0	0.068	0.056	16.537	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	313	ASN	0	0.030	-0.005	18.084	0.018	0.018	0.000	0.000	0.000	0.000
17	A	314	SER	0	-0.047	-0.036	17.529	0.008	0.008	0.000	0.000	0.000	0.000
18	A	315	GLY	0	-0.009	-0.003	16.394	0.003	0.003	0.000	0.000	0.000	0.000
19	A	316	VAL	0	-0.048	-0.007	11.519	0.037	0.037	0.000	0.000	0.000	0.000
20	A	317	PRO	0	-0.003	-0.006	9.639	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	318	VAL	0	-0.013	-0.001	12.537	-0.051	-0.051	0.000	0.000	0.000	0.000
22	A	319	TYR	0	0.010	-0.007	8.289	0.007	0.007	0.000	0.000	0.000	0.000
23	A	320	LEU	0	-0.005	-0.004	14.734	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	321	HIS	0	0.082	0.063	18.353	0.006	0.006	0.000	0.000	0.000	0.000
25	A	322	ARG	1	0.836	0.877	20.330	0.057	0.057	0.000	0.000	0.000	0.000
26	A	323	GLU	-1	-0.829	-0.903	23.050	-0.053	-0.053	0.000	0.000	0.000	0.000
27	A	324	SER	0	-0.020	-0.022	23.368	0.002	0.002	0.000	0.000	0.000	0.000
28	A	325	ARG	1	0.896	0.953	24.023	0.041	0.041	0.000	0.000	0.000	0.000
29	A	326	VAL	0	0.042	0.041	20.225	0.001	0.001	0.000	0.000	0.000	0.000
30	A	327	VAL	0	-0.008	-0.014	17.717	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	328	THR	0	-0.004	0.002	14.145	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	329	TRP	0	0.038	0.001	13.855	0.013	0.013	0.000	0.000	0.000	0.000
33	A	330	SER	0	-0.037	-0.005	9.941	-0.020	-0.020	0.000	0.000	0.000	0.000
34	A	331	ARG	1	0.896	0.951	6.585	0.566	0.566	0.000	0.000	0.000	0.000
35	A	332	PRO	0	0.006	0.019	9.714	-0.090	-0.090	0.000	0.000	0.000	0.000
36	A	333	TYR	0	-0.008	-0.041	10.356	-0.040	-0.040	0.000	0.000	0.000	0.000
37	A	334	PHE	0	0.021	0.014	12.486	0.049	0.049	0.000	0.000	0.000	0.000
38	A	335	LEU	0	0.005	0.017	14.403	-0.020	-0.020	0.000	0.000	0.000	0.000
39	A	336	GLY	0	0.033	0.011	16.226	0.011	0.011	0.000	0.000	0.000	0.000
40	A	337	THR	0	-0.038	-0.030	19.207	0.001	0.001	0.000	0.000	0.000	0.000
41	A	338	GLY	0	0.033	0.032	17.686	0.008	0.008	0.000	0.000	0.000	0.000
42	A	339	SER	0	-0.032	-0.020	18.762	0.008	0.008	0.000	0.000	0.000	0.000
43	A	340	ILE	0	0.084	0.022	17.403	-0.018	-0.018	0.000	0.000	0.000	0.000
44	A	341	ARG	1	0.921	0.943	17.711	0.129	0.129	0.000	0.000	0.000	0.000
45	A	342	LYS	1	0.946	0.964	18.297	0.145	0.145	0.000	0.000	0.000	0.000
46	A	343	HIS	0	-0.032	0.037	12.874	-0.036	-0.036	0.000	0.000	0.000	0.000
47	A	344	ASP	-1	-0.848	-0.915	10.781	-0.343	-0.343	0.000	0.000	0.000	0.000
48	A	345	PRO	0	-0.048	-0.023	8.626	0.000	0.000	0.000	0.000	0.000	0.000
49	A	346	PRO	0	0.070	0.036	6.660	-0.076	-0.076	0.000	0.000	0.000	0.000
50	A	347	LEU	0	0.061	0.015	2.588	-1.289	-0.294	1.239	-0.602	-1.632	0.000
51	A	348	SER	0	-0.051	-0.019	2.549	-3.073	-1.212	1.349	-1.148	-2.063	-0.010
52	A	349	SER	0	-0.066	-0.062	3.322	0.780	0.674	0.024	0.292	-0.209	0.000
53	A	350	ILE	0	-0.054	0.000	5.052	0.357	0.357	0.000	0.000	0.000	0.000
54	A	351	PRO	0	-0.004	0.003	6.092	-0.158	-0.158	0.000	0.000	0.000	0.000
55	A	352	CYS	0	-0.007	0.001	8.860	-0.030	-0.030	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:298:PRO)