FMO DATABASE

FMODB ID: 53KZZ

Calculation Name: 4N3Y-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4N3Y

Chain ID: B

ChEMBL ID:

UniProt ID: Q15276

Base Structure: X-ray

Registration Date: 2023-06-20

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	83
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-379842.885937
FMO2-HF: Nuclear repulsion	345594.765448
FMO2-HF: Total energy	-34248.120489
FMO2-MP2: Total energy	-34345.832896

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(B:552:GLU)

Summations of interaction energy for fragment #1(B:552:GLU)

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.
-156.038	-153.209	21.823	-11.312	-13.34	0.144

Interaction energy analysis for fragmet #1(B:552:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.814 / q_NPA : -0.914

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	B	554	ARG	1	0.908	0.923	1.917	-98.328	-95.128	12.226	-7.549	-7.876	0.089
4	B	555	ASP	-1	-0.834	-0.921	1.815	29.174	27.716	9.578	-3.298	-4.823	0.052
5	B	556	GLN	0	-0.052	-0.013	3.325	-12.836	-11.900	0.020	-0.456	-0.500	0.003
6	B	557	VAL	0	0.033	0.017	5.193	-8.171	-8.020	-0.001	-0.009	-0.141	0.000
7	B	558	LYS	1	0.935	0.967	6.760	-36.725	-36.725	0.000	0.000	0.000	0.000
8	B	559	LYS	1	0.973	0.994	7.323	-32.303	-32.303	0.000	0.000	0.000	0.000
9	B	560	LEU	0	0.007	-0.009	8.630	-3.103	-3.103	0.000	0.000	0.000	0.000
10	B	561	GLN	0	0.003	-0.002	10.908	-1.846	-1.846	0.000	0.000	0.000	0.000
11	B	562	LEU	0	-0.050	-0.010	12.612	-1.837	-1.837	0.000	0.000	0.000	0.000
12	B	563	MET	0	0.003	-0.011	11.906	-0.658	-0.658	0.000	0.000	0.000	0.000
13	B	564	LEU	0	0.007	0.022	15.011	-1.096	-1.096	0.000	0.000	0.000	0.000
14	B	565	ARG	1	0.947	0.975	14.734	-19.730	-19.730	0.000	0.000	0.000	0.000
15	B	566	GLN	0	0.018	0.008	17.244	-0.852	-0.852	0.000	0.000	0.000	0.000
16	B	567	ALA	0	-0.026	-0.009	18.990	-0.770	-0.770	0.000	0.000	0.000	0.000
17	B	568	ASN	0	0.024	-0.008	20.719	-0.827	-0.827	0.000	0.000	0.000	0.000
18	B	569	ASP	-1	-0.879	-0.929	22.646	13.413	13.413	0.000	0.000	0.000	0.000
19	B	570	GLN	0	-0.013	-0.012	23.703	-0.941	-0.941	0.000	0.000	0.000	0.000
20	B	571	LEU	0	-0.019	-0.007	24.957	-0.553	-0.553	0.000	0.000	0.000	0.000
21	B	572	GLU	-1	-0.926	-0.960	26.800	10.524	10.524	0.000	0.000	0.000	0.000
22	B	573	LYS	1	0.835	0.900	28.549	-10.201	-10.201	0.000	0.000	0.000	0.000
23	B	574	THR	0	-0.027	-0.026	28.505	-0.391	-0.391	0.000	0.000	0.000	0.000
24	B	575	MET	0	-0.051	-0.026	29.546	-0.403	-0.403	0.000	0.000	0.000	0.000
25	B	576	LYS	1	0.825	0.903	32.895	-9.272	-9.272	0.000	0.000	0.000	0.000
26	B	577	ASP	-1	-0.802	-0.883	33.911	9.011	9.011	0.000	0.000	0.000	0.000
27	B	578	LYS	1	0.782	0.873	35.112	-8.678	-8.678	0.000	0.000	0.000	0.000
28	B	579	GLN	0	-0.002	0.007	37.030	-0.099	-0.099	0.000	0.000	0.000	0.000
29	B	580	GLU	-1	-0.810	-0.890	37.973	8.224	8.224	0.000	0.000	0.000	0.000
30	B	581	LEU	0	-0.041	-0.020	38.012	-0.231	-0.231	0.000	0.000	0.000	0.000
31	B	582	GLU	-1	-0.839	-0.915	39.715	7.825	7.825	0.000	0.000	0.000	0.000
32	B	583	ASP	-1	-0.862	-0.934	43.201	7.046	7.046	0.000	0.000	0.000	0.000
33	B	584	PHE	0	-0.048	-0.023	44.378	-0.202	-0.202	0.000	0.000	0.000	0.000
34	B	585	ILE	0	-0.014	0.002	44.203	-0.183	-0.183	0.000	0.000	0.000	0.000
35	B	586	LYS	1	0.892	0.944	47.592	-6.354	-6.354	0.000	0.000	0.000	0.000
36	B	587	GLN	0	0.003	0.002	49.046	-0.106	-0.106	0.000	0.000	0.000	0.000
37	B	588	SER	0	-0.017	0.005	49.706	-0.134	-0.134	0.000	0.000	0.000	0.000
38	B	589	SER	0	-0.024	-0.005	51.529	-0.157	-0.157	0.000	0.000	0.000	0.000
39	B	590	GLU	-1	-0.882	-0.951	53.219	5.937	5.937	0.000	0.000	0.000	0.000
40	B	591	ASP	-1	-0.854	-0.919	54.203	5.609	5.609	0.000	0.000	0.000	0.000
41	B	592	SER	0	-0.030	-0.016	55.940	-0.135	-0.135	0.000	0.000	0.000	0.000
42	B	593	SER	0	-0.004	-0.010	57.779	-0.155	-0.155	0.000	0.000	0.000	0.000
43	B	594	HIS	0	0.037	0.012	59.433	-0.129	-0.129	0.000	0.000	0.000	0.000
44	B	595	GLN	0	-0.052	-0.044	57.153	-0.174	-0.174	0.000	0.000	0.000	0.000
45	B	596	ILE	0	-0.021	-0.010	61.492	-0.113	-0.113	0.000	0.000	0.000	0.000
46	B	597	SER	0	-0.005	0.002	64.069	-0.107	-0.107	0.000	0.000	0.000	0.000
47	B	598	ALA	0	0.001	0.000	65.092	-0.094	-0.094	0.000	0.000	0.000	0.000
48	B	599	LEU	0	-0.065	-0.036	65.021	-0.095	-0.095	0.000	0.000	0.000	0.000
49	B	600	VAL	0	0.020	0.011	68.222	-0.082	-0.082	0.000	0.000	0.000	0.000
50	B	601	LEU	0	0.011	0.007	68.742	-0.077	-0.077	0.000	0.000	0.000	0.000
51	B	602	ARG	1	0.918	0.959	67.729	-4.684	-4.684	0.000	0.000	0.000	0.000
52	B	603	ALA	0	-0.006	0.016	72.565	-0.066	-0.066	0.000	0.000	0.000	0.000
53	B	604	GLN	0	0.011	0.001	74.436	-0.070	-0.070	0.000	0.000	0.000	0.000
54	B	605	ALA	0	-0.014	-0.001	75.777	-0.064	-0.064	0.000	0.000	0.000	0.000
55	B	606	SER	0	-0.064	-0.048	76.090	-0.061	-0.061	0.000	0.000	0.000	0.000
56	B	607	GLU	-1	-0.890	-0.942	77.122	4.102	4.102	0.000	0.000	0.000	0.000
57	B	608	ILE	0	0.027	0.017	79.524	-0.057	-0.057	0.000	0.000	0.000	0.000
58	B	609	LEU	0	0.014	0.017	81.357	-0.052	-0.052	0.000	0.000	0.000	0.000
59	B	610	LEU	0	-0.037	-0.028	82.725	-0.060	-0.060	0.000	0.000	0.000	0.000
60	B	611	GLU	-1	-0.892	-0.947	84.514	3.694	3.694	0.000	0.000	0.000	0.000
61	B	612	GLU	-1	-0.951	-0.973	85.749	3.700	3.700	0.000	0.000	0.000	0.000
62	B	613	LEU	0	-0.036	-0.009	85.478	-0.060	-0.060	0.000	0.000	0.000	0.000
63	B	614	GLN	0	-0.059	-0.028	87.270	-0.053	-0.053	0.000	0.000	0.000	0.000
64	B	615	GLN	0	0.007	-0.002	89.312	-0.078	-0.078	0.000	0.000	0.000	0.000
65	B	616	GLY	0	0.038	0.020	91.988	-0.048	-0.048	0.000	0.000	0.000	0.000
66	B	617	LEU	0	-0.028	-0.018	93.106	-0.050	-0.050	0.000	0.000	0.000	0.000
67	B	618	SER	0	-0.086	-0.046	94.627	-0.051	-0.051	0.000	0.000	0.000	0.000
68	B	619	GLN	0	0.001	-0.016	95.471	-0.025	-0.025	0.000	0.000	0.000	0.000
69	B	620	ALA	0	0.046	0.042	97.532	-0.035	-0.035	0.000	0.000	0.000	0.000
70	B	621	LYS	1	0.913	0.949	96.907	-3.352	-3.352	0.000	0.000	0.000	0.000
71	B	622	ARG	1	0.904	0.954	100.715	-3.212	-3.212	0.000	0.000	0.000	0.000
72	B	623	ASP	-1	-0.826	-0.918	101.840	3.162	3.162	0.000	0.000	0.000	0.000
73	B	624	VAL	0	-0.008	0.005	102.666	-0.035	-0.035	0.000	0.000	0.000	0.000
74	B	625	GLN	0	-0.055	-0.031	104.154	-0.012	-0.012	0.000	0.000	0.000	0.000
75	B	626	GLU	-1	-0.919	-0.960	106.692	3.017	3.017	0.000	0.000	0.000	0.000
76	B	627	GLN	0	-0.014	-0.006	106.724	-0.021	-0.021	0.000	0.000	0.000	0.000
77	B	628	MET	0	-0.004	-0.010	108.919	-0.025	-0.025	0.000	0.000	0.000	0.000
78	B	629	ALA	0	0.002	0.008	110.799	-0.030	-0.030	0.000	0.000	0.000	0.000
79	B	630	VAL	0	0.018	0.004	112.623	-0.032	-0.032	0.000	0.000	0.000	0.000
80	B	631	LEU	0	-0.052	-0.038	112.325	-0.028	-0.028	0.000	0.000	0.000	0.000
81	B	632	MET	0	-0.037	-0.014	113.334	-0.031	-0.031	0.000	0.000	0.000	0.000
82	B	633	GLN	0	-0.064	-0.007	116.573	-0.003	-0.003	0.000	0.000	0.000	0.000
83	B	634	SER	0	-0.074	-0.028	118.752	-0.033	-0.033	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:552:GLU)