FMO DATABASE

FMODB ID: 2JN9R

Calculation Name: 1WUD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WUD

Chain ID: A

ChEMBL ID:

UniProt ID: P15043

Base Structure: X-ray

Registration Date: 2023-06-22

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	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-506943.033283
FMO2-HF: Nuclear repulsion	475705.454887
FMO2-HF: Total energy	-31237.578396
FMO2-MP2: Total energy	-31326.395102

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(A:530:ASN)

Summations of interaction energy for fragment #1(A:530:ASN)

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.
-4.449	-2.008	-0.015	-0.964	-1.463	0.001

Interaction energy analysis for fragmet #1(A:530:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.024

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

Sort

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	A	532	ASP	-1	-0.779	-0.892	3.709	-2.861	-1.105	-0.016	-0.827	-0.914	0.001
4	A	533	ARG	1	0.978	0.967	4.074	-4.640	-4.285	0.001	-0.084	-0.272	0.000
5	A	534	LYS	1	0.929	0.980	7.715	0.887	0.887	0.000	0.000	0.000	0.000
6	A	535	LEU	0	0.008	0.018	9.882	0.201	0.201	0.000	0.000	0.000	0.000
7	A	536	PHE	0	0.052	0.021	8.897	0.214	0.214	0.000	0.000	0.000	0.000
8	A	537	ALA	0	-0.017	-0.014	10.949	0.086	0.086	0.000	0.000	0.000	0.000
9	A	538	LYS	1	0.862	0.934	13.576	0.379	0.379	0.000	0.000	0.000	0.000
10	A	539	LEU	0	0.058	0.031	11.913	0.026	0.026	0.000	0.000	0.000	0.000
11	A	540	ARG	1	0.936	0.975	14.682	-0.759	-0.759	0.000	0.000	0.000	0.000
12	A	541	LYS	1	0.923	0.952	16.403	-0.140	-0.140	0.000	0.000	0.000	0.000
13	A	542	LEU	0	0.016	0.026	18.867	-0.012	-0.012	0.000	0.000	0.000	0.000
14	A	543	ARG	1	0.807	0.889	16.638	-0.744	-0.744	0.000	0.000	0.000	0.000
15	A	544	LYS	1	0.895	0.955	20.372	-0.302	-0.302	0.000	0.000	0.000	0.000
16	A	545	SER	0	-0.004	0.010	22.424	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	546	ILE	0	0.068	0.033	22.563	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	547	ALA	0	-0.052	-0.034	23.724	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	548	ASP	-1	-0.897	-0.961	25.658	0.277	0.277	0.000	0.000	0.000	0.000
20	A	549	GLU	-1	-0.983	-0.984	28.113	0.113	0.113	0.000	0.000	0.000	0.000
21	A	550	SER	0	-0.103	-0.048	28.649	-0.014	-0.014	0.000	0.000	0.000	0.000
22	A	551	ASN	0	-0.037	-0.007	30.284	0.016	0.016	0.000	0.000	0.000	0.000
23	A	552	VAL	0	-0.025	-0.002	26.240	0.006	0.006	0.000	0.000	0.000	0.000
24	A	553	PRO	0	0.034	0.011	24.863	0.011	0.011	0.000	0.000	0.000	0.000
25	A	554	PRO	0	0.076	0.013	20.868	0.009	0.009	0.000	0.000	0.000	0.000
26	A	555	TYR	0	0.022	-0.003	20.050	0.000	0.000	0.000	0.000	0.000	0.000
27	A	556	VAL	0	-0.019	0.004	21.076	0.011	0.011	0.000	0.000	0.000	0.000
28	A	557	VAL	0	-0.042	0.010	20.994	-0.025	-0.025	0.000	0.000	0.000	0.000
29	A	558	PHE	0	0.071	0.018	17.004	-0.012	-0.012	0.000	0.000	0.000	0.000
30	A	559	ASN	0	0.042	0.023	15.805	0.069	0.069	0.000	0.000	0.000	0.000
31	A	560	ASP	-1	-0.790	-0.914	13.110	1.098	1.098	0.000	0.000	0.000	0.000
32	A	561	ALA	0	0.026	0.014	11.311	0.128	0.128	0.000	0.000	0.000	0.000
33	A	562	THR	0	0.011	0.005	11.201	0.145	0.145	0.000	0.000	0.000	0.000
34	A	563	LEU	0	-0.047	-0.026	12.316	-0.075	-0.075	0.000	0.000	0.000	0.000
35	A	564	ILE	0	-0.012	-0.006	6.285	-0.268	-0.268	0.000	0.000	0.000	0.000
36	A	565	GLU	-1	-0.787	-0.886	7.615	1.020	1.020	0.000	0.000	0.000	0.000
37	A	566	MET	0	-0.072	-0.041	9.388	-0.391	-0.391	0.000	0.000	0.000	0.000
38	A	567	ALA	0	-0.059	-0.039	7.802	-0.284	-0.284	0.000	0.000	0.000	0.000
39	A	568	GLU	-1	-0.948	-0.989	4.168	4.536	4.866	0.000	-0.053	-0.277	0.000
40	A	569	GLN	0	-0.011	-0.013	6.284	-1.010	-1.010	0.000	0.000	0.000	0.000
41	A	570	MET	0	-0.058	-0.013	8.300	-0.152	-0.152	0.000	0.000	0.000	0.000
42	A	571	PRO	0	-0.011	0.010	11.451	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	572	ILE	0	0.025	-0.004	14.570	0.034	0.034	0.000	0.000	0.000	0.000
44	A	573	THR	0	-0.038	-0.025	17.638	0.042	0.042	0.000	0.000	0.000	0.000
45	A	574	ALA	0	0.025	-0.011	19.514	0.033	0.033	0.000	0.000	0.000	0.000
46	A	575	SER	0	0.015	-0.005	20.704	0.044	0.044	0.000	0.000	0.000	0.000
47	A	576	GLU	-1	-0.785	-0.885	15.553	-0.248	-0.248	0.000	0.000	0.000	0.000
48	A	577	MET	0	-0.021	-0.015	16.126	0.075	0.075	0.000	0.000	0.000	0.000
49	A	578	LEU	0	-0.067	-0.036	17.854	0.076	0.076	0.000	0.000	0.000	0.000
50	A	579	SER	0	-0.039	-0.005	15.640	0.020	0.020	0.000	0.000	0.000	0.000
51	A	580	VAL	0	-0.029	0.014	13.140	0.082	0.082	0.000	0.000	0.000	0.000
52	A	581	ASN	0	0.062	0.023	14.687	-0.181	-0.181	0.000	0.000	0.000	0.000
53	A	582	GLY	0	-0.021	0.000	16.082	0.044	0.044	0.000	0.000	0.000	0.000
54	A	583	VAL	0	-0.057	-0.026	17.286	-0.056	-0.056	0.000	0.000	0.000	0.000
55	A	584	GLY	0	0.058	0.037	20.016	-0.015	-0.015	0.000	0.000	0.000	0.000
56	A	585	MET	0	0.039	-0.003	23.437	-0.018	-0.018	0.000	0.000	0.000	0.000
57	A	586	ARG	1	0.997	1.011	26.086	-0.215	-0.215	0.000	0.000	0.000	0.000
58	A	587	LYS	1	0.888	0.930	21.523	-0.455	-0.455	0.000	0.000	0.000	0.000
59	A	588	LEU	0	0.026	0.030	21.697	-0.012	-0.012	0.000	0.000	0.000	0.000
60	A	589	GLU	-1	-0.952	-0.982	24.034	0.112	0.112	0.000	0.000	0.000	0.000
61	A	590	ARG	1	0.854	0.941	26.512	-0.182	-0.182	0.000	0.000	0.000	0.000
62	A	591	PHE	0	0.040	-0.006	22.721	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	592	GLY	0	0.053	0.033	21.796	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	593	LYS	1	0.957	0.980	21.835	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	594	PRO	0	0.011	0.005	23.000	-0.034	-0.034	0.000	0.000	0.000	0.000
66	A	595	PHE	0	0.038	0.005	17.025	-0.017	-0.017	0.000	0.000	0.000	0.000
67	A	596	MET	0	0.051	0.037	18.236	-0.046	-0.046	0.000	0.000	0.000	0.000
68	A	597	ALA	0	-0.077	-0.035	19.426	-0.064	-0.064	0.000	0.000	0.000	0.000
69	A	598	LEU	0	-0.012	-0.003	16.924	-0.041	-0.041	0.000	0.000	0.000	0.000
70	A	599	ILE	0	-0.003	-0.009	13.767	-0.061	-0.061	0.000	0.000	0.000	0.000
71	A	600	ARG	1	0.958	0.970	16.072	0.087	0.087	0.000	0.000	0.000	0.000
72	A	601	ALA	0	0.062	0.047	18.431	-0.045	-0.045	0.000	0.000	0.000	0.000
73	A	602	HIS	0	-0.075	-0.040	10.783	0.196	0.196	0.000	0.000	0.000	0.000
74	A	603	VAL	0	-0.037	-0.028	12.928	-0.109	-0.109	0.000	0.000	0.000	0.000
75	A	604	ASP	-1	-0.891	-0.921	15.169	-0.641	-0.641	0.000	0.000	0.000	0.000
76	A	605	GLY	0	-0.107	-0.044	17.087	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	606	ASP	-1	-1.034	-1.018	17.996	-0.343	-0.343	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:530:ASN)