FMO DATABASE

FMODB ID: 6NQZZ

Calculation Name: 3B5N-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B5N

Chain ID: D

ChEMBL ID:

UniProt ID: P40357

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	64
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-270417.766784
FMO2-HF: Nuclear repulsion	244098.239324
FMO2-HF: Total energy	-26319.527459
FMO2-MP2: Total energy	-26394.455304

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(D:587:GLY)

Summations of interaction energy for fragment #1(D:587: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.
-4.644	-0.977	1.666	-2.614	-2.719	-0.02

Interaction energy analysis for fragmet #1(D:587: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 : -0.002

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	D	589	GLU	-1	-0.882	-0.948	2.529	-5.467	-1.877	1.667	-2.609	-2.648	-0.020
4	D	590	MET	0	0.012	-0.002	5.281	0.886	0.963	-0.001	-0.005	-0.071	0.000
5	D	591	GLU	-1	-0.897	-0.943	7.069	-0.727	-0.727	0.000	0.000	0.000	0.000
6	D	592	LEU	0	-0.008	-0.004	6.400	0.481	0.481	0.000	0.000	0.000	0.000
7	D	593	GLU	-1	-0.902	-0.946	9.350	-0.556	-0.556	0.000	0.000	0.000	0.000
8	D	594	ILE	0	-0.005	-0.004	11.290	0.210	0.210	0.000	0.000	0.000	0.000
9	D	595	ASP	-1	-0.897	-0.945	12.510	-0.419	-0.419	0.000	0.000	0.000	0.000
10	D	596	ARG	1	0.845	0.919	12.299	0.492	0.492	0.000	0.000	0.000	0.000
11	D	597	ASN	0	-0.004	-0.010	15.225	0.108	0.108	0.000	0.000	0.000	0.000
12	D	598	LEU	0	-0.013	-0.006	16.793	0.074	0.074	0.000	0.000	0.000	0.000
13	D	599	ASP	-1	-0.857	-0.916	17.612	-0.227	-0.227	0.000	0.000	0.000	0.000
14	D	600	GLN	0	-0.056	-0.037	19.425	0.058	0.058	0.000	0.000	0.000	0.000
15	D	601	ILE	0	0.000	-0.003	20.184	0.036	0.036	0.000	0.000	0.000	0.000
16	D	602	GLN	0	-0.009	-0.002	22.725	0.020	0.020	0.000	0.000	0.000	0.000
17	D	603	GLN	0	-0.029	-0.017	22.728	0.031	0.031	0.000	0.000	0.000	0.000
18	D	604	VAL	0	-0.017	-0.015	25.679	0.020	0.020	0.000	0.000	0.000	0.000
19	D	605	SER	0	0.009	0.011	27.083	0.020	0.020	0.000	0.000	0.000	0.000
20	D	606	ASN	0	-0.006	-0.002	28.760	0.016	0.016	0.000	0.000	0.000	0.000
21	D	607	ARG	1	0.951	0.962	27.842	0.146	0.146	0.000	0.000	0.000	0.000
22	D	608	LEU	0	0.021	0.018	30.155	0.009	0.009	0.000	0.000	0.000	0.000
23	D	609	LYS	1	0.983	1.000	33.061	0.108	0.108	0.000	0.000	0.000	0.000
24	D	610	LYS	1	0.946	0.964	34.968	0.082	0.082	0.000	0.000	0.000	0.000
25	D	611	MET	0	0.042	0.020	34.296	0.007	0.007	0.000	0.000	0.000	0.000
26	D	612	ALA	0	0.013	0.031	37.434	0.005	0.005	0.000	0.000	0.000	0.000
27	D	613	LEU	0	-0.036	-0.023	38.712	0.005	0.005	0.000	0.000	0.000	0.000
28	D	614	THR	0	-0.035	-0.019	40.762	0.005	0.005	0.000	0.000	0.000	0.000
29	D	615	THR	0	-0.005	-0.016	41.099	0.003	0.003	0.000	0.000	0.000	0.000
30	D	616	GLY	0	0.020	0.013	43.391	0.002	0.002	0.000	0.000	0.000	0.000
31	D	617	LYS	1	0.960	0.985	45.327	0.052	0.052	0.000	0.000	0.000	0.000
32	D	618	GLU	-1	-0.869	-0.928	46.647	-0.049	-0.049	0.000	0.000	0.000	0.000
33	D	619	LEU	0	-0.001	-0.006	46.022	0.002	0.002	0.000	0.000	0.000	0.000
34	D	620	ASP	-1	-0.908	-0.944	49.438	-0.051	-0.051	0.000	0.000	0.000	0.000
35	D	621	SER	0	-0.100	-0.053	51.278	0.003	0.003	0.000	0.000	0.000	0.000
36	D	622	GLN	0	-0.068	-0.067	50.557	0.002	0.002	0.000	0.000	0.000	0.000
37	D	623	GLN	0	0.052	0.045	53.549	0.000	0.000	0.000	0.000	0.000	0.000
38	D	624	LYS	1	0.929	0.962	55.272	0.041	0.041	0.000	0.000	0.000	0.000
39	D	625	ARG	1	0.944	0.972	54.477	0.043	0.043	0.000	0.000	0.000	0.000
40	D	626	LEU	0	0.009	0.002	54.967	0.001	0.001	0.000	0.000	0.000	0.000
41	D	627	ASN	0	0.014	0.007	59.066	0.000	0.000	0.000	0.000	0.000	0.000
42	D	628	ASN	0	0.021	0.010	61.348	0.001	0.001	0.000	0.000	0.000	0.000
43	D	629	ILE	0	-0.044	-0.017	59.843	0.001	0.001	0.000	0.000	0.000	0.000
44	D	630	GLU	-1	-0.952	-0.964	62.901	-0.037	-0.037	0.000	0.000	0.000	0.000
45	D	631	GLU	-1	-0.914	-0.949	64.653	-0.029	-0.029	0.000	0.000	0.000	0.000
46	D	632	SER	0	-0.012	-0.012	66.924	0.001	0.001	0.000	0.000	0.000	0.000
47	D	633	THR	0	-0.099	-0.061	65.983	0.001	0.001	0.000	0.000	0.000	0.000
48	D	634	ASP	-1	-0.905	-0.951	68.626	-0.029	-0.029	0.000	0.000	0.000	0.000
49	D	635	ASP	-1	-0.856	-0.925	70.718	-0.026	-0.026	0.000	0.000	0.000	0.000
50	D	636	LEU	0	-0.125	-0.074	70.186	0.001	0.001	0.000	0.000	0.000	0.000
51	D	637	ASP	-1	-0.912	-0.949	72.267	-0.027	-0.027	0.000	0.000	0.000	0.000
52	D	638	ILE	0	0.034	0.017	74.234	0.001	0.001	0.000	0.000	0.000	0.000
53	D	639	ASN	0	-0.063	-0.035	76.683	0.001	0.001	0.000	0.000	0.000	0.000
54	D	640	LEU	0	0.003	-0.009	74.884	0.001	0.001	0.000	0.000	0.000	0.000
55	D	641	HIS	0	0.044	0.034	76.275	0.001	0.001	0.000	0.000	0.000	0.000
56	D	642	MET	0	-0.067	0.002	80.265	0.001	0.001	0.000	0.000	0.000	0.000
57	D	643	ASN	0	0.027	-0.029	81.535	0.001	0.001	0.000	0.000	0.000	0.000
58	D	644	THR	0	-0.033	-0.009	81.274	0.001	0.001	0.000	0.000	0.000	0.000
59	D	645	ASN	0	-0.004	-0.013	83.467	0.000	0.000	0.000	0.000	0.000	0.000
60	D	646	ARG	1	0.881	0.940	86.262	0.019	0.019	0.000	0.000	0.000	0.000
61	D	647	LEU	0	-0.021	-0.016	84.975	0.001	0.001	0.000	0.000	0.000	0.000
62	D	648	ALA	0	-0.001	0.015	87.976	0.000	0.000	0.000	0.000	0.000	0.000
63	D	649	GLY	0	-0.044	-0.008	89.721	0.000	0.000	0.000	0.000	0.000	0.000
64	D	650	ILE	0	-0.089	-0.034	90.904	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:587:GLY)