FMO DATABASE

FMODB ID: 434RN

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	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	83
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-379315.08597
FMO2-HF: Nuclear repulsion	345067.924403
FMO2-HF: Total energy	-34247.161566
FMO2-MP2: Total energy	-34344.935936

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.
-125.392	-115.553	10.411	-9.161	-11.089	0.103

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 : -0.835 / q_NPA : -0.930

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	1.001	0.989	2.634	-81.581	-74.015	2.584	-4.957	-5.194	0.057
4	B	555	ASP	-1	-0.884	-0.936	1.908	42.570	43.875	7.810	-3.827	-5.288	0.044
5	B	556	GLN	0	-0.067	-0.029	3.247	-12.898	-12.049	0.018	-0.371	-0.496	0.002
6	B	557	VAL	0	0.031	0.016	5.131	-7.211	-7.092	-0.001	-0.006	-0.111	0.000
7	B	558	LYS	1	0.930	0.966	6.896	-36.125	-36.125	0.000	0.000	0.000	0.000
8	B	559	LYS	1	0.969	0.997	6.350	-32.912	-32.912	0.000	0.000	0.000	0.000
9	B	560	LEU	0	-0.004	-0.015	8.510	-2.889	-2.889	0.000	0.000	0.000	0.000
10	B	561	GLN	0	0.023	0.004	10.844	-1.393	-1.393	0.000	0.000	0.000	0.000
11	B	562	LEU	0	-0.045	-0.008	12.684	-1.654	-1.654	0.000	0.000	0.000	0.000
12	B	563	MET	0	0.011	-0.012	11.987	-0.722	-0.722	0.000	0.000	0.000	0.000
13	B	564	LEU	0	0.009	0.020	14.969	-1.089	-1.089	0.000	0.000	0.000	0.000
14	B	565	ARG	1	0.953	0.981	14.409	-19.829	-19.829	0.000	0.000	0.000	0.000
15	B	566	GLN	0	0.011	0.003	17.843	-0.517	-0.517	0.000	0.000	0.000	0.000
16	B	567	ALA	0	-0.016	-0.007	18.941	-0.730	-0.730	0.000	0.000	0.000	0.000
17	B	568	ASN	0	0.010	-0.012	20.667	-0.993	-0.993	0.000	0.000	0.000	0.000
18	B	569	ASP	-1	-0.871	-0.918	22.736	13.007	13.007	0.000	0.000	0.000	0.000
19	B	570	GLN	0	-0.035	-0.025	23.509	-0.947	-0.947	0.000	0.000	0.000	0.000
20	B	571	LEU	0	-0.028	-0.012	24.906	-0.540	-0.540	0.000	0.000	0.000	0.000
21	B	572	GLU	-1	-0.922	-0.955	26.744	10.624	10.624	0.000	0.000	0.000	0.000
22	B	573	LYS	1	0.799	0.880	28.501	-10.026	-10.026	0.000	0.000	0.000	0.000
23	B	574	THR	0	-0.011	-0.015	28.524	-0.383	-0.383	0.000	0.000	0.000	0.000
24	B	575	MET	0	-0.056	-0.033	29.337	-0.407	-0.407	0.000	0.000	0.000	0.000
25	B	576	LYS	1	0.968	0.988	32.844	-9.573	-9.573	0.000	0.000	0.000	0.000
26	B	577	ASP	-1	-0.769	-0.865	33.474	8.952	8.952	0.000	0.000	0.000	0.000
27	B	578	LYS	1	0.892	0.947	34.414	-8.858	-8.858	0.000	0.000	0.000	0.000
28	B	579	GLN	0	0.023	0.024	36.977	-0.117	-0.117	0.000	0.000	0.000	0.000
29	B	580	GLU	-1	-0.896	-0.949	38.498	7.984	7.984	0.000	0.000	0.000	0.000
30	B	581	LEU	0	-0.057	-0.029	37.932	-0.227	-0.227	0.000	0.000	0.000	0.000
31	B	582	GLU	-1	-0.961	-0.989	39.642	7.666	7.666	0.000	0.000	0.000	0.000
32	B	583	ASP	-1	-0.905	-0.961	43.146	7.022	7.022	0.000	0.000	0.000	0.000
33	B	584	PHE	0	-0.034	-0.021	44.330	-0.201	-0.201	0.000	0.000	0.000	0.000
34	B	585	ILE	0	-0.016	0.003	44.214	-0.182	-0.182	0.000	0.000	0.000	0.000
35	B	586	LYS	1	0.933	0.967	47.542	-6.334	-6.334	0.000	0.000	0.000	0.000
36	B	587	GLN	0	0.004	-0.009	48.513	-0.145	-0.145	0.000	0.000	0.000	0.000
37	B	588	SER	0	-0.006	0.021	49.603	-0.112	-0.112	0.000	0.000	0.000	0.000
38	B	589	SER	0	-0.032	-0.005	51.486	-0.148	-0.148	0.000	0.000	0.000	0.000
39	B	590	GLU	-1	-0.961	-0.986	53.736	5.753	5.753	0.000	0.000	0.000	0.000
40	B	591	ASP	-1	-0.808	-0.912	54.122	5.584	5.584	0.000	0.000	0.000	0.000
41	B	592	SER	0	-0.067	-0.037	55.866	-0.137	-0.137	0.000	0.000	0.000	0.000
42	B	593	SER	0	-0.022	-0.017	57.737	-0.159	-0.159	0.000	0.000	0.000	0.000
43	B	594	HIS	0	0.040	0.012	59.426	-0.118	-0.118	0.000	0.000	0.000	0.000
44	B	595	GLN	0	-0.031	-0.025	57.369	-0.166	-0.166	0.000	0.000	0.000	0.000
45	B	596	ILE	0	-0.025	-0.010	61.817	-0.111	-0.111	0.000	0.000	0.000	0.000
46	B	597	SER	0	0.000	0.000	64.027	-0.111	-0.111	0.000	0.000	0.000	0.000
47	B	598	ALA	0	-0.001	0.002	65.053	-0.092	-0.092	0.000	0.000	0.000	0.000
48	B	599	LEU	0	-0.063	-0.037	64.907	-0.095	-0.095	0.000	0.000	0.000	0.000
49	B	600	VAL	0	0.015	0.011	68.184	-0.082	-0.082	0.000	0.000	0.000	0.000
50	B	601	LEU	0	0.002	0.001	68.677	-0.076	-0.076	0.000	0.000	0.000	0.000
51	B	602	ARG	1	0.914	0.957	67.853	-4.646	-4.646	0.000	0.000	0.000	0.000
52	B	603	ALA	0	0.000	0.006	72.521	-0.061	-0.061	0.000	0.000	0.000	0.000
53	B	604	GLN	0	0.074	0.035	74.395	-0.102	-0.102	0.000	0.000	0.000	0.000
54	B	605	ALA	0	-0.014	0.003	75.742	-0.060	-0.060	0.000	0.000	0.000	0.000
55	B	606	SER	0	-0.052	-0.036	76.388	-0.063	-0.063	0.000	0.000	0.000	0.000
56	B	607	GLU	-1	-0.945	-0.972	77.558	4.061	4.061	0.000	0.000	0.000	0.000
57	B	608	ILE	0	0.018	0.017	79.421	-0.056	-0.056	0.000	0.000	0.000	0.000
58	B	609	LEU	0	0.003	0.014	81.403	-0.051	-0.051	0.000	0.000	0.000	0.000
59	B	610	LEU	0	-0.038	-0.031	82.695	-0.060	-0.060	0.000	0.000	0.000	0.000
60	B	611	GLU	-1	-0.898	-0.941	84.478	3.692	3.692	0.000	0.000	0.000	0.000
61	B	612	GLU	-1	-0.939	-0.980	85.671	3.692	3.692	0.000	0.000	0.000	0.000
62	B	613	LEU	0	-0.046	-0.015	85.530	-0.061	-0.061	0.000	0.000	0.000	0.000
63	B	614	GLN	0	-0.056	-0.025	87.247	-0.051	-0.051	0.000	0.000	0.000	0.000
64	B	615	GLN	0	0.007	-0.002	90.294	-0.036	-0.036	0.000	0.000	0.000	0.000
65	B	616	GLY	0	0.023	0.011	91.953	-0.049	-0.049	0.000	0.000	0.000	0.000
66	B	617	LEU	0	-0.012	-0.010	93.074	-0.049	-0.049	0.000	0.000	0.000	0.000
67	B	618	SER	0	-0.064	-0.029	94.869	-0.054	-0.054	0.000	0.000	0.000	0.000
68	B	619	GLN	0	-0.028	-0.040	95.445	-0.030	-0.030	0.000	0.000	0.000	0.000
69	B	620	ALA	0	0.076	0.055	97.521	-0.033	-0.033	0.000	0.000	0.000	0.000
70	B	621	LYS	1	0.920	0.952	97.250	-3.320	-3.320	0.000	0.000	0.000	0.000
71	B	622	ARG	1	0.930	0.985	100.029	-3.205	-3.205	0.000	0.000	0.000	0.000
72	B	623	ASP	-1	-0.899	-0.959	101.559	3.135	3.135	0.000	0.000	0.000	0.000
73	B	624	VAL	0	0.051	0.032	102.899	-0.034	-0.034	0.000	0.000	0.000	0.000
74	B	625	GLN	0	-0.067	-0.037	104.964	-0.022	-0.022	0.000	0.000	0.000	0.000
75	B	626	GLU	-1	-0.936	-0.967	106.939	2.996	2.996	0.000	0.000	0.000	0.000
76	B	627	GLN	0	-0.001	-0.006	106.455	-0.020	-0.020	0.000	0.000	0.000	0.000
77	B	628	MET	0	-0.009	-0.017	108.839	-0.022	-0.022	0.000	0.000	0.000	0.000
78	B	629	ALA	0	-0.007	0.012	110.769	-0.030	-0.030	0.000	0.000	0.000	0.000
79	B	630	VAL	0	0.021	0.005	112.648	-0.032	-0.032	0.000	0.000	0.000	0.000
80	B	631	LEU	0	-0.055	-0.042	111.648	-0.028	-0.028	0.000	0.000	0.000	0.000
81	B	632	MET	0	-0.026	-0.003	113.473	-0.031	-0.031	0.000	0.000	0.000	0.000
82	B	633	GLN	0	-0.071	-0.005	116.542	0.000	0.000	0.000	0.000	0.000	0.000
83	B	634	SER	0	-0.086	-0.039	118.636	-0.034	-0.034	0.000	0.000	0.000	0.000

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