FMO DATABASE

FMODB ID: M36MZ

Calculation Name: 3L4F-A-Xray317

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	61
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-271137.218988
FMO2-HF: Nuclear repulsion	245118.813455
FMO2-HF: Total energy	-26018.405533
FMO2-MP2: Total energy	-26092.987284

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.
-17.503	-15.555	16.262	-7.746	-10.463	-0.058

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 : -0.065 / q_NPA : -0.036

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	588	LYS	1	0.924	0.968	3.229	-7.409	-3.830	0.070	-1.814	-1.834	0.000
4	A	589	SER	0	0.080	0.040	4.929	-0.482	-0.385	0.000	-0.003	-0.095	0.000
5	A	590	LEU	0	0.026	0.067	7.506	0.099	0.099	0.000	0.000	0.000	0.000
6	A	591	VAL	0	-0.007	-0.024	2.444	-0.782	0.188	0.712	-0.349	-1.333	0.000
7	A	592	ASP	-1	-0.790	-0.908	2.038	-5.394	-9.510	14.934	-5.157	-5.661	-0.058
8	A	593	THR	0	-0.027	-0.058	4.444	0.312	0.510	0.001	-0.026	-0.172	0.000
9	A	594	VAL	0	-0.046	-0.029	6.666	0.073	0.073	0.000	0.000	0.000	0.000
10	A	595	TYR	0	-0.008	-0.031	3.429	-1.325	-0.133	0.545	-0.382	-1.355	0.000
11	A	596	ALA	0	0.074	0.074	5.492	-0.356	-0.328	0.000	-0.015	-0.013	0.000
12	A	597	LEU	0	0.083	0.042	7.564	-0.101	-0.101	0.000	0.000	0.000	0.000
13	A	598	LYS	1	0.830	0.943	7.739	-1.507	-1.507	0.000	0.000	0.000	0.000
14	A	599	ASP	-1	-0.889	-0.953	6.713	-0.026	-0.026	0.000	0.000	0.000	0.000
15	A	600	GLU	-1	-0.952	-0.991	10.032	-0.041	-0.041	0.000	0.000	0.000	0.000
16	A	601	VAL	0	-0.061	-0.035	12.870	-0.039	-0.039	0.000	0.000	0.000	0.000
17	A	602	GLN	0	-0.094	-0.058	12.639	0.020	0.020	0.000	0.000	0.000	0.000
18	A	603	GLU	-1	-0.861	-0.934	13.906	-0.130	-0.130	0.000	0.000	0.000	0.000
19	A	604	LEU	0	0.059	0.034	16.119	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	605	ARG	1	0.886	0.951	15.992	-0.212	-0.212	0.000	0.000	0.000	0.000
21	A	606	GLN	0	-0.078	-0.051	17.017	0.004	0.004	0.000	0.000	0.000	0.000
22	A	607	ASP	-1	-0.848	-0.918	20.184	-0.053	-0.053	0.000	0.000	0.000	0.000
23	A	608	ASN	0	0.031	0.010	22.342	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	609	LYS	1	0.887	0.950	20.775	-0.091	-0.091	0.000	0.000	0.000	0.000
25	A	610	LYS	1	0.949	0.981	22.191	0.066	0.066	0.000	0.000	0.000	0.000
26	A	611	MET	0	0.049	0.026	26.223	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	612	LYS	1	0.908	0.943	28.060	-0.050	-0.050	0.000	0.000	0.000	0.000
28	A	613	LYS	1	0.966	0.981	27.816	-0.011	-0.011	0.000	0.000	0.000	0.000
29	A	614	SER	0	0.072	0.036	30.653	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	615	LEU	0	0.002	0.017	32.083	0.000	0.000	0.000	0.000	0.000	0.000
31	A	616	GLU	-1	-0.947	-0.963	32.974	0.023	0.023	0.000	0.000	0.000	0.000
32	A	617	GLU	-1	-0.953	-0.988	33.062	-0.020	-0.020	0.000	0.000	0.000	0.000
33	A	618	GLU	-1	-0.884	-0.950	36.502	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	619	GLN	0	-0.088	-0.056	37.227	0.002	0.002	0.000	0.000	0.000	0.000
35	A	620	ARG	1	0.870	0.939	39.364	0.007	0.007	0.000	0.000	0.000	0.000
36	A	621	ALA	0	0.023	0.027	41.197	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	622	ARG	1	0.909	0.937	42.545	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	623	LYS	1	0.928	0.936	43.455	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	624	ASP	-1	-0.885	-0.943	45.894	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	625	LEU	0	0.044	0.021	47.228	0.000	0.000	0.000	0.000	0.000	0.000
41	A	626	GLU	-1	-0.869	-0.910	47.938	0.004	0.004	0.000	0.000	0.000	0.000
42	A	627	LYS	1	0.886	0.952	48.018	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	628	LEU	0	0.021	0.018	51.098	0.000	0.000	0.000	0.000	0.000	0.000
44	A	629	VAL	0	0.054	0.028	52.388	0.000	0.000	0.000	0.000	0.000	0.000
45	A	630	ARG	1	0.950	0.960	51.550	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	631	LYS	1	0.894	0.941	56.324	0.004	0.004	0.000	0.000	0.000	0.000
47	A	632	VAL	0	-0.008	0.006	56.967	0.000	0.000	0.000	0.000	0.000	0.000
48	A	633	LEU	0	-0.001	-0.008	57.953	0.000	0.000	0.000	0.000	0.000	0.000
49	A	634	LYS	1	0.904	0.951	60.708	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	635	ASN	0	0.054	0.013	61.873	0.001	0.001	0.000	0.000	0.000	0.000
51	A	636	MET	0	-0.041	0.000	62.388	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	637	ASN	0	-0.047	-0.025	65.345	0.000	0.000	0.000	0.000	0.000	0.000
53	A	638	ASP	-1	-0.944	-0.951	66.876	0.000	0.000	0.000	0.000	0.000	0.000
54	A	639	PRO	0	-0.002	-0.003	67.391	0.000	0.000	0.000	0.000	0.000	0.000
55	A	640	ALA	0	-0.049	-0.017	67.036	0.000	0.000	0.000	0.000	0.000	0.000
56	A	641	TRP	0	-0.077	-0.040	67.263	0.000	0.000	0.000	0.000	0.000	0.000
57	A	642	ASP	-1	-0.879	-0.933	70.281	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	643	GLU	-1	-0.992	-0.998	73.828	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	644	THR	0	-0.035	-0.033	76.739	0.001	0.001	0.000	0.000	0.000	0.000
60	A	645	ASN	0	-0.065	-0.022	80.493	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	646	LEU	-1	-0.955	-0.969	82.357	-0.006	-0.006	0.000	0.000	0.000	0.000

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