FMO DATABASE

FMODB ID: Z6Q7N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-270727.610708
FMO2-HF: Nuclear repulsion	244407.857483
FMO2-HF: Total energy	-26319.753225
FMO2-MP2: Total energy	-26394.670619

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.
-6.063	-2.104	3.978	-4.247	-3.689	-0.024

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 : 0.031 / q_NPA : 0.023

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	-0.866	-0.943	2.319	-6.507	-2.623	3.979	-4.242	-3.621	-0.024
4	D	590	MET	0	0.021	0.003	5.314	0.948	1.023	-0.001	-0.005	-0.068	0.000
5	D	591	GLU	-1	-0.901	-0.946	7.089	-1.560	-1.560	0.000	0.000	0.000	0.000
6	D	592	LEU	0	-0.007	-0.004	6.382	0.581	0.581	0.000	0.000	0.000	0.000
7	D	593	GLU	-1	-0.901	-0.941	9.384	-0.475	-0.475	0.000	0.000	0.000	0.000
8	D	594	ILE	0	0.003	0.001	11.329	0.259	0.259	0.000	0.000	0.000	0.000
9	D	595	ASP	-1	-0.891	-0.944	12.548	-0.783	-0.783	0.000	0.000	0.000	0.000
10	D	596	ARG	1	0.784	0.874	12.644	0.820	0.820	0.000	0.000	0.000	0.000
11	D	597	ASN	0	-0.022	-0.026	15.035	0.161	0.161	0.000	0.000	0.000	0.000
12	D	598	LEU	0	-0.007	-0.004	16.613	0.099	0.099	0.000	0.000	0.000	0.000
13	D	599	ASP	-1	-0.823	-0.883	17.617	-0.415	-0.415	0.000	0.000	0.000	0.000
14	D	600	GLN	0	-0.054	-0.031	19.531	0.081	0.081	0.000	0.000	0.000	0.000
15	D	601	ILE	0	0.002	-0.005	20.314	0.048	0.048	0.000	0.000	0.000	0.000
16	D	602	GLN	0	-0.009	-0.005	22.730	0.030	0.030	0.000	0.000	0.000	0.000
17	D	603	GLN	0	-0.015	-0.010	22.845	0.051	0.051	0.000	0.000	0.000	0.000
18	D	604	VAL	0	-0.020	-0.016	25.760	0.028	0.028	0.000	0.000	0.000	0.000
19	D	605	SER	0	0.016	0.014	27.117	0.027	0.027	0.000	0.000	0.000	0.000
20	D	606	ASN	0	-0.026	-0.013	28.770	0.023	0.023	0.000	0.000	0.000	0.000
21	D	607	ARG	1	0.962	0.971	27.291	0.200	0.200	0.000	0.000	0.000	0.000
22	D	608	LEU	0	0.029	0.020	30.023	0.013	0.013	0.000	0.000	0.000	0.000
23	D	609	LYS	1	0.980	0.997	33.097	0.185	0.185	0.000	0.000	0.000	0.000
24	D	610	LYS	1	0.952	0.971	34.986	0.143	0.143	0.000	0.000	0.000	0.000
25	D	611	MET	0	0.033	0.027	34.110	0.011	0.011	0.000	0.000	0.000	0.000
26	D	612	ALA	0	0.016	0.034	37.473	0.008	0.008	0.000	0.000	0.000	0.000
27	D	613	LEU	0	-0.031	-0.020	38.478	0.006	0.006	0.000	0.000	0.000	0.000
28	D	614	THR	0	-0.040	-0.034	40.593	0.007	0.007	0.000	0.000	0.000	0.000
29	D	615	THR	0	-0.006	-0.018	41.152	0.006	0.006	0.000	0.000	0.000	0.000
30	D	616	GLY	0	0.012	0.012	43.425	0.004	0.004	0.000	0.000	0.000	0.000
31	D	617	LYS	1	0.963	0.986	45.362	0.083	0.083	0.000	0.000	0.000	0.000
32	D	618	GLU	-1	-0.754	-0.855	46.680	-0.065	-0.065	0.000	0.000	0.000	0.000
33	D	619	LEU	0	-0.002	0.002	46.153	0.004	0.004	0.000	0.000	0.000	0.000
34	D	620	ASP	-1	-0.912	-0.948	49.478	-0.077	-0.077	0.000	0.000	0.000	0.000
35	D	621	SER	0	-0.127	-0.086	51.311	0.005	0.005	0.000	0.000	0.000	0.000
36	D	622	GLN	0	-0.049	-0.056	50.307	0.004	0.004	0.000	0.000	0.000	0.000
37	D	623	GLN	0	0.007	0.020	53.595	0.001	0.001	0.000	0.000	0.000	0.000
38	D	624	LYS	1	0.938	0.965	55.308	0.063	0.063	0.000	0.000	0.000	0.000
39	D	625	ARG	1	0.854	0.922	52.846	0.062	0.062	0.000	0.000	0.000	0.000
40	D	626	LEU	0	0.017	0.005	55.046	0.002	0.002	0.000	0.000	0.000	0.000
41	D	627	ASN	0	0.022	0.016	59.111	0.000	0.000	0.000	0.000	0.000	0.000
42	D	628	ASN	0	0.040	0.019	61.384	0.001	0.001	0.000	0.000	0.000	0.000
43	D	629	ILE	0	-0.034	-0.005	59.818	0.002	0.002	0.000	0.000	0.000	0.000
44	D	630	GLU	-1	-0.953	-0.956	62.901	-0.047	-0.047	0.000	0.000	0.000	0.000
45	D	631	GLU	-1	-0.919	-0.955	64.689	-0.042	-0.042	0.000	0.000	0.000	0.000
46	D	632	SER	0	-0.014	-0.022	66.854	0.002	0.002	0.000	0.000	0.000	0.000
47	D	633	THR	0	-0.100	-0.068	66.028	0.002	0.002	0.000	0.000	0.000	0.000
48	D	634	ASP	-1	-0.911	-0.952	68.661	-0.037	-0.037	0.000	0.000	0.000	0.000
49	D	635	ASP	-1	-0.872	-0.934	70.753	-0.035	-0.035	0.000	0.000	0.000	0.000
50	D	636	LEU	0	-0.121	-0.069	70.277	0.002	0.002	0.000	0.000	0.000	0.000
51	D	637	ASP	-1	-0.857	-0.924	72.307	-0.032	-0.032	0.000	0.000	0.000	0.000
52	D	638	ILE	0	0.031	0.016	74.269	0.002	0.002	0.000	0.000	0.000	0.000
53	D	639	ASN	0	-0.028	-0.022	76.721	0.002	0.002	0.000	0.000	0.000	0.000
54	D	640	LEU	0	-0.004	-0.003	74.866	0.001	0.001	0.000	0.000	0.000	0.000
55	D	641	HIS	0	0.006	0.020	75.694	0.002	0.002	0.000	0.000	0.000	0.000
56	D	642	MET	0	-0.067	-0.010	80.300	0.001	0.001	0.000	0.000	0.000	0.000
57	D	643	ASN	0	-0.029	-0.048	81.311	0.002	0.002	0.000	0.000	0.000	0.000
58	D	644	THR	0	-0.020	-0.009	81.318	0.001	0.001	0.000	0.000	0.000	0.000
59	D	645	ASN	0	-0.010	-0.015	83.470	0.001	0.001	0.000	0.000	0.000	0.000
60	D	646	ARG	1	0.889	0.945	86.298	0.024	0.024	0.000	0.000	0.000	0.000
61	D	647	LEU	0	-0.016	-0.013	85.076	0.001	0.001	0.000	0.000	0.000	0.000
62	D	648	ALA	0	-0.002	0.013	87.972	0.001	0.001	0.000	0.000	0.000	0.000
63	D	649	GLY	0	-0.041	-0.006	89.756	0.001	0.001	0.000	0.000	0.000	0.000
64	D	650	ILE	0	-0.090	-0.036	91.003	0.001	0.001	0.000	0.000	0.000	0.000

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