FMO DATABASE

FMODB ID: YYL22

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	OptAll
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	-379583.343704
FMO2-HF: Nuclear repulsion	345334.937939
FMO2-HF: Total energy	-34248.405765
FMO2-MP2: Total energy	-34346.066325

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.
-153.741	-153.263	23.571	-11.374	-12.675	0.143

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 : -0.742 / q_NPA : -0.866

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	0.855	0.897	1.985	-95.353	-92.744	12.090	-7.175	-7.525	0.086
4	B	555	ASP	-1	-0.795	-0.896	1.775	29.346	26.393	11.466	-3.818	-4.695	0.054
5	B	556	GLN	0	-0.033	-0.006	3.783	-13.968	-13.146	0.015	-0.381	-0.455	0.003
6	B	557	VAL	0	0.020	0.007	5.663	-7.994	-7.994	0.000	0.000	0.000	0.000
7	B	558	LYS	1	0.927	0.964	6.414	-38.117	-38.117	0.000	0.000	0.000	0.000
8	B	559	LYS	1	0.966	0.985	7.680	-31.451	-31.451	0.000	0.000	0.000	0.000
9	B	560	LEU	0	0.001	-0.006	9.542	-3.212	-3.212	0.000	0.000	0.000	0.000
10	B	561	GLN	0	0.000	-0.009	11.002	-1.568	-1.568	0.000	0.000	0.000	0.000
11	B	562	LEU	0	-0.047	-0.007	12.371	-1.782	-1.782	0.000	0.000	0.000	0.000
12	B	563	MET	0	-0.023	-0.021	12.407	-0.719	-0.719	0.000	0.000	0.000	0.000
13	B	564	LEU	0	0.015	0.012	15.386	-1.101	-1.101	0.000	0.000	0.000	0.000
14	B	565	ARG	1	0.931	0.974	15.015	-19.248	-19.248	0.000	0.000	0.000	0.000
15	B	566	GLN	0	0.049	0.020	17.355	-1.033	-1.033	0.000	0.000	0.000	0.000
16	B	567	ALA	0	-0.029	-0.006	19.771	-0.757	-0.757	0.000	0.000	0.000	0.000
17	B	568	ASN	0	0.006	-0.005	21.069	-0.890	-0.890	0.000	0.000	0.000	0.000
18	B	569	ASP	-1	-0.852	-0.930	21.936	13.646	13.646	0.000	0.000	0.000	0.000
19	B	570	GLN	0	-0.017	-0.010	24.360	-0.907	-0.907	0.000	0.000	0.000	0.000
20	B	571	LEU	0	-0.005	0.014	25.730	-0.540	-0.540	0.000	0.000	0.000	0.000
21	B	572	GLU	-1	-0.923	-0.965	27.520	10.391	10.391	0.000	0.000	0.000	0.000
22	B	573	LYS	1	0.834	0.903	29.014	-10.168	-10.168	0.000	0.000	0.000	0.000
23	B	574	THR	0	-0.041	-0.039	29.056	-0.400	-0.400	0.000	0.000	0.000	0.000
24	B	575	MET	0	-0.049	-0.027	30.052	-0.390	-0.390	0.000	0.000	0.000	0.000
25	B	576	LYS	1	0.839	0.915	33.514	-9.224	-9.224	0.000	0.000	0.000	0.000
26	B	577	ASP	-1	-0.808	-0.883	34.550	8.974	8.974	0.000	0.000	0.000	0.000
27	B	578	LYS	1	0.767	0.863	35.779	-8.541	-8.541	0.000	0.000	0.000	0.000
28	B	579	GLN	0	-0.011	-0.001	37.573	-0.103	-0.103	0.000	0.000	0.000	0.000
29	B	580	GLU	-1	-0.800	-0.899	38.572	8.186	8.186	0.000	0.000	0.000	0.000
30	B	581	LEU	0	-0.039	-0.018	38.695	-0.238	-0.238	0.000	0.000	0.000	0.000
31	B	582	GLU	-1	-0.826	-0.898	40.501	7.748	7.748	0.000	0.000	0.000	0.000
32	B	583	ASP	-1	-0.862	-0.928	43.898	7.038	7.038	0.000	0.000	0.000	0.000
33	B	584	PHE	0	-0.053	-0.027	45.065	-0.210	-0.210	0.000	0.000	0.000	0.000
34	B	585	ILE	0	-0.011	-0.002	44.858	-0.180	-0.180	0.000	0.000	0.000	0.000
35	B	586	LYS	1	0.877	0.927	48.234	-6.355	-6.355	0.000	0.000	0.000	0.000
36	B	587	GLN	0	-0.012	-0.008	49.517	-0.088	-0.088	0.000	0.000	0.000	0.000
37	B	588	SER	0	-0.006	0.000	50.589	-0.136	-0.136	0.000	0.000	0.000	0.000
38	B	589	SER	0	-0.017	0.004	52.339	-0.151	-0.151	0.000	0.000	0.000	0.000
39	B	590	GLU	-1	-0.832	-0.904	53.452	5.934	5.934	0.000	0.000	0.000	0.000
40	B	591	ASP	-1	-0.864	-0.920	54.924	5.579	5.579	0.000	0.000	0.000	0.000
41	B	592	SER	0	-0.043	-0.030	56.494	-0.141	-0.141	0.000	0.000	0.000	0.000
42	B	593	SER	0	0.040	0.013	58.402	-0.121	-0.121	0.000	0.000	0.000	0.000
43	B	594	HIS	0	-0.013	0.009	59.901	-0.144	-0.144	0.000	0.000	0.000	0.000
44	B	595	GLN	0	-0.061	-0.051	57.519	-0.180	-0.180	0.000	0.000	0.000	0.000
45	B	596	ILE	0	-0.010	-0.010	61.895	-0.109	-0.109	0.000	0.000	0.000	0.000
46	B	597	SER	0	-0.019	-0.022	64.397	-0.111	-0.111	0.000	0.000	0.000	0.000
47	B	598	ALA	0	0.006	0.000	65.560	-0.095	-0.095	0.000	0.000	0.000	0.000
48	B	599	LEU	0	-0.070	-0.035	65.481	-0.089	-0.089	0.000	0.000	0.000	0.000
49	B	600	VAL	0	0.026	0.017	68.760	-0.081	-0.081	0.000	0.000	0.000	0.000
50	B	601	LEU	0	0.002	0.002	69.120	-0.077	-0.077	0.000	0.000	0.000	0.000
51	B	602	ARG	1	0.926	0.963	67.927	-4.692	-4.692	0.000	0.000	0.000	0.000
52	B	603	ALA	0	-0.017	0.016	72.981	-0.062	-0.062	0.000	0.000	0.000	0.000
53	B	604	GLN	0	0.017	-0.006	74.887	-0.067	-0.067	0.000	0.000	0.000	0.000
54	B	605	ALA	0	-0.022	-0.011	76.232	-0.063	-0.063	0.000	0.000	0.000	0.000
55	B	606	SER	0	-0.063	-0.041	76.447	-0.058	-0.058	0.000	0.000	0.000	0.000
56	B	607	GLU	-1	-0.905	-0.949	77.380	4.111	4.111	0.000	0.000	0.000	0.000
57	B	608	ILE	0	0.040	0.023	80.210	-0.058	-0.058	0.000	0.000	0.000	0.000
58	B	609	LEU	0	0.031	0.026	81.925	-0.055	-0.055	0.000	0.000	0.000	0.000
59	B	610	LEU	0	-0.045	-0.026	83.221	-0.058	-0.058	0.000	0.000	0.000	0.000
60	B	611	GLU	-1	-0.895	-0.949	85.062	3.692	3.692	0.000	0.000	0.000	0.000
61	B	612	GLU	-1	-0.936	-0.964	85.889	3.707	3.707	0.000	0.000	0.000	0.000
62	B	613	LEU	0	-0.039	-0.017	85.859	-0.062	-0.062	0.000	0.000	0.000	0.000
63	B	614	GLN	0	-0.048	-0.021	87.444	-0.058	-0.058	0.000	0.000	0.000	0.000
64	B	615	GLN	0	-0.007	0.005	89.794	-0.080	-0.080	0.000	0.000	0.000	0.000
65	B	616	GLY	0	0.048	0.025	92.471	-0.049	-0.049	0.000	0.000	0.000	0.000
66	B	617	LEU	0	-0.042	-0.026	93.380	-0.050	-0.050	0.000	0.000	0.000	0.000
67	B	618	SER	0	-0.062	-0.048	94.930	-0.050	-0.050	0.000	0.000	0.000	0.000
68	B	619	GLN	0	-0.020	-0.015	95.644	-0.021	-0.021	0.000	0.000	0.000	0.000
69	B	620	ALA	0	0.061	0.038	97.971	-0.040	-0.040	0.000	0.000	0.000	0.000
70	B	621	LYS	1	0.887	0.945	96.990	-3.361	-3.361	0.000	0.000	0.000	0.000
71	B	622	ARG	1	0.838	0.890	101.403	-3.164	-3.164	0.000	0.000	0.000	0.000
72	B	623	ASP	-1	-0.844	-0.921	101.253	3.169	3.169	0.000	0.000	0.000	0.000
73	B	624	VAL	0	-0.001	-0.003	103.102	-0.040	-0.040	0.000	0.000	0.000	0.000
74	B	625	GLN	0	-0.049	-0.024	104.228	-0.011	-0.011	0.000	0.000	0.000	0.000
75	B	626	GLU	-1	-0.832	-0.886	106.964	3.020	3.020	0.000	0.000	0.000	0.000
76	B	627	GLN	0	-0.019	-0.011	107.056	-0.020	-0.020	0.000	0.000	0.000	0.000
77	B	628	MET	0	-0.018	-0.020	109.429	-0.027	-0.027	0.000	0.000	0.000	0.000
78	B	629	ALA	0	-0.007	0.000	111.185	-0.032	-0.032	0.000	0.000	0.000	0.000
79	B	630	VAL	0	0.005	-0.002	112.867	-0.031	-0.031	0.000	0.000	0.000	0.000
80	B	631	LEU	0	-0.029	-0.015	113.064	-0.028	-0.028	0.000	0.000	0.000	0.000
81	B	632	MET	0	-0.038	-0.013	113.448	-0.036	-0.036	0.000	0.000	0.000	0.000
82	B	633	GLN	0	-0.041	0.002	116.952	-0.002	-0.002	0.000	0.000	0.000	0.000
83	B	634	SER	0	-0.081	-0.041	119.089	-0.035	-0.035	0.000	0.000	0.000	0.000

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