FMO DATABASE

FMODB ID: 3JV1L

Calculation Name: 2W6A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2W6A

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Z272

Base Structure: X-ray

Registration Date: 2023-09-23

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	63
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-257807.630509
FMO2-HF: Nuclear repulsion	233375.261117
FMO2-HF: Total energy	-24432.369392
FMO2-MP2: Total energy	-24504.337323

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:421:GLY)

Summations of interaction energy for fragment #1(A:421:GLY)

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.
-9.833	-5.92	2.342	-2.924	-3.331	0.002

Interaction energy analysis for fragmet #1(A:421:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : 0.004

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	423	LEU	0	0.026	0.014	3.830	-0.510	0.672	-0.006	-0.726	-0.450	0.003
4	A	424	GLY	0	0.030	0.015	6.799	0.419	0.419	0.000	0.000	0.000	0.000
5	A	425	SER	0	-0.052	-0.034	9.000	0.328	0.328	0.000	0.000	0.000	0.000
6	A	426	SER	0	-0.063	-0.069	8.123	-0.187	-0.187	0.000	0.000	0.000	0.000
7	A	427	ASP	-1	-0.912	-0.944	10.538	-0.631	-0.631	0.000	0.000	0.000	0.000
8	A	428	GLY	0	0.030	0.034	9.975	0.095	0.095	0.000	0.000	0.000	0.000
9	A	429	ALA	0	-0.037	-0.025	10.594	0.083	0.083	0.000	0.000	0.000	0.000
10	A	430	VAL	0	-0.016	0.004	6.152	0.216	0.216	0.000	0.000	0.000	0.000
11	A	431	THR	0	0.014	-0.025	7.252	-0.539	-0.539	0.000	0.000	0.000	0.000
12	A	432	LEU	0	-0.032	-0.025	3.931	0.266	0.435	0.001	-0.032	-0.138	0.000
13	A	433	GLN	0	-0.005	-0.024	5.712	0.566	0.566	0.000	0.000	0.000	0.000
14	A	434	GLU	-1	-0.752	-0.843	8.331	0.079	0.079	0.000	0.000	0.000	0.000
15	A	435	TYR	0	0.012	0.010	2.848	-4.640	-2.078	2.347	-2.166	-2.743	-0.001
16	A	436	LEU	0	-0.030	-0.029	5.547	0.659	0.659	0.000	0.000	0.000	0.000
17	A	437	GLU	-1	-0.872	-0.921	7.141	0.290	0.290	0.000	0.000	0.000	0.000
18	A	438	LEU	0	0.006	0.014	8.276	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	439	LYS	1	0.903	0.946	5.857	-5.039	-5.039	0.000	0.000	0.000	0.000
20	A	440	LYS	1	0.985	1.000	9.244	-0.601	-0.601	0.000	0.000	0.000	0.000
21	A	441	ALA	0	0.008	0.019	12.206	-0.119	-0.119	0.000	0.000	0.000	0.000
22	A	442	LEU	0	0.008	0.005	11.657	-0.094	-0.094	0.000	0.000	0.000	0.000
23	A	443	ALA	0	0.038	0.021	13.276	-0.106	-0.106	0.000	0.000	0.000	0.000
24	A	444	THR	0	-0.060	-0.046	14.999	-0.133	-0.133	0.000	0.000	0.000	0.000
25	A	445	SER	0	-0.021	-0.010	17.163	-0.090	-0.090	0.000	0.000	0.000	0.000
26	A	446	GLU	-1	-0.913	-0.967	15.654	0.874	0.874	0.000	0.000	0.000	0.000
27	A	447	ALA	0	-0.002	0.000	19.067	-0.061	-0.061	0.000	0.000	0.000	0.000
28	A	448	LYS	1	0.946	0.974	21.012	-0.343	-0.343	0.000	0.000	0.000	0.000
29	A	449	VAL	0	0.012	0.007	22.366	-0.042	-0.042	0.000	0.000	0.000	0.000
30	A	450	GLN	0	0.013	0.007	22.403	-0.064	-0.064	0.000	0.000	0.000	0.000
31	A	451	GLN	0	0.021	0.008	25.059	-0.026	-0.026	0.000	0.000	0.000	0.000
32	A	452	LEU	0	-0.030	-0.027	26.334	-0.028	-0.028	0.000	0.000	0.000	0.000
33	A	453	MET	0	0.014	0.010	27.656	-0.025	-0.025	0.000	0.000	0.000	0.000
34	A	454	LYS	1	0.959	0.995	29.357	-0.222	-0.222	0.000	0.000	0.000	0.000
35	A	455	VAL	0	-0.030	-0.021	31.199	-0.017	-0.017	0.000	0.000	0.000	0.000
36	A	456	ASN	0	0.032	0.009	31.709	-0.023	-0.023	0.000	0.000	0.000	0.000
37	A	457	SER	0	0.020	0.029	33.835	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	458	SER	0	-0.016	-0.010	35.568	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	459	LEU	0	-0.001	-0.002	36.164	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	460	SER	0	-0.033	-0.025	37.566	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	461	ASP	-1	-0.922	-0.960	39.695	0.137	0.137	0.000	0.000	0.000	0.000
42	A	462	GLU	-1	-0.828	-0.914	41.657	0.097	0.097	0.000	0.000	0.000	0.000
43	A	463	LEU	0	-0.021	-0.002	42.852	-0.008	-0.008	0.000	0.000	0.000	0.000
44	A	464	ARG	1	0.945	0.965	44.318	-0.115	-0.115	0.000	0.000	0.000	0.000
45	A	465	LYS	1	0.810	0.916	46.400	-0.101	-0.101	0.000	0.000	0.000	0.000
46	A	466	LEU	0	0.052	0.015	46.132	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	467	GLN	0	0.008	0.007	47.052	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	468	ARG	1	0.923	0.943	47.299	-0.101	-0.101	0.000	0.000	0.000	0.000
49	A	469	GLU	-1	-0.886	-0.910	52.339	0.074	0.074	0.000	0.000	0.000	0.000
50	A	470	ILE	0	0.032	0.008	53.006	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	471	HIS	0	-0.015	-0.010	52.728	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	472	LYS	1	0.878	0.935	56.257	-0.072	-0.072	0.000	0.000	0.000	0.000
53	A	473	LEU	0	0.034	0.008	56.844	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	474	GLN	0	-0.028	-0.002	58.890	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	475	ALA	0	-0.003	-0.007	60.984	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	476	GLU	-1	-0.907	-0.948	62.909	0.053	0.053	0.000	0.000	0.000	0.000
57	A	477	ASN	0	-0.016	-0.013	63.491	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	478	LEU	0	-0.026	-0.028	63.835	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	479	GLN	0	-0.028	-0.011	67.039	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	480	LEU	0	-0.016	-0.010	67.000	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	481	ARG	1	0.855	0.925	65.325	-0.052	-0.052	0.000	0.000	0.000	0.000
62	A	482	GLN	0	-0.041	0.013	71.179	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	483	PRO	0	0.013	0.009	73.374	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:421:GLY)