FMO DATABASE

FMODB ID: 6NYKZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-507943.337762
FMO2-HF: Nuclear repulsion	476705.199623
FMO2-HF: Total energy	-31238.138139
FMO2-MP2: Total energy	-31326.970387

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.
-37.581	-34.267	5.837	-4.462	-4.687	0.041

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 : 0.037 / q_NPA : 0.013

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	-0.764	-0.859	3.685	0.281	3.376	-0.020	-1.610	-1.464	0.007
4	A	533	ARG	1	0.950	0.948	1.930	-28.851	-29.271	5.854	-2.583	-2.850	0.036
5	A	534	LYS	1	0.950	0.986	7.779	-0.330	-0.330	0.000	0.000	0.000	0.000
6	A	535	LEU	0	0.001	0.007	9.699	0.014	0.014	0.000	0.000	0.000	0.000
7	A	536	PHE	0	0.048	0.014	8.916	0.084	0.084	0.000	0.000	0.000	0.000
8	A	537	ALA	0	-0.020	-0.014	10.974	-0.067	-0.067	0.000	0.000	0.000	0.000
9	A	538	LYS	1	0.848	0.921	13.657	-0.051	-0.051	0.000	0.000	0.000	0.000
10	A	539	LEU	0	0.040	0.022	11.877	-0.019	-0.019	0.000	0.000	0.000	0.000
11	A	540	ARG	1	0.868	0.927	14.618	-0.985	-0.985	0.000	0.000	0.000	0.000
12	A	541	LYS	1	0.924	0.955	16.426	-0.576	-0.576	0.000	0.000	0.000	0.000
13	A	542	LEU	0	0.018	0.028	18.890	-0.028	-0.028	0.000	0.000	0.000	0.000
14	A	543	ARG	1	0.791	0.861	16.820	-0.490	-0.490	0.000	0.000	0.000	0.000
15	A	544	LYS	1	0.780	0.872	20.395	-0.335	-0.335	0.000	0.000	0.000	0.000
16	A	545	SER	0	0.031	0.021	22.447	-0.016	-0.016	0.000	0.000	0.000	0.000
17	A	546	ILE	0	0.035	0.019	22.791	-0.019	-0.019	0.000	0.000	0.000	0.000
18	A	547	ALA	0	-0.041	-0.023	23.716	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	548	ASP	-1	-0.803	-0.887	25.680	0.267	0.267	0.000	0.000	0.000	0.000
20	A	549	GLU	-1	-0.970	-0.976	28.136	0.066	0.066	0.000	0.000	0.000	0.000
21	A	550	SER	0	-0.100	-0.052	28.436	-0.020	-0.020	0.000	0.000	0.000	0.000
22	A	551	ASN	0	-0.039	-0.011	30.334	0.007	0.007	0.000	0.000	0.000	0.000
23	A	552	VAL	0	-0.028	-0.002	26.118	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	553	PRO	0	0.030	0.011	24.901	0.022	0.022	0.000	0.000	0.000	0.000
25	A	554	PRO	0	0.073	0.012	20.878	-0.019	-0.019	0.000	0.000	0.000	0.000
26	A	555	TYR	0	0.026	0.000	20.074	-0.033	-0.033	0.000	0.000	0.000	0.000
27	A	556	VAL	0	-0.020	-0.001	21.094	-0.041	-0.041	0.000	0.000	0.000	0.000
28	A	557	VAL	0	-0.030	0.006	20.948	-0.039	-0.039	0.000	0.000	0.000	0.000
29	A	558	PHE	0	0.061	0.030	17.054	-0.058	-0.058	0.000	0.000	0.000	0.000
30	A	559	ASN	0	0.059	0.036	15.660	0.111	0.111	0.000	0.000	0.000	0.000
31	A	560	ASP	-1	-0.737	-0.859	13.193	0.774	0.774	0.000	0.000	0.000	0.000
32	A	561	ALA	0	0.048	0.029	11.324	0.081	0.081	0.000	0.000	0.000	0.000
33	A	562	THR	0	0.005	0.005	11.182	-0.116	-0.116	0.000	0.000	0.000	0.000
34	A	563	LEU	0	-0.033	-0.018	12.214	-0.164	-0.164	0.000	0.000	0.000	0.000
35	A	564	ILE	0	-0.009	-0.006	6.313	-0.084	-0.084	0.000	0.000	0.000	0.000
36	A	565	GLU	-1	-0.775	-0.878	7.635	-1.276	-1.276	0.000	0.000	0.000	0.000
37	A	566	MET	0	-0.042	-0.027	8.888	-0.410	-0.410	0.000	0.000	0.000	0.000
38	A	567	ALA	0	-0.054	-0.034	7.835	-0.069	-0.069	0.000	0.000	0.000	0.000
39	A	568	GLU	-1	-0.975	-0.993	3.755	-4.860	-4.221	0.003	-0.269	-0.373	-0.002
40	A	569	GLN	0	-0.032	-0.022	6.135	-0.293	-0.293	0.000	0.000	0.000	0.000
41	A	570	MET	0	-0.047	-0.012	8.604	0.372	0.372	0.000	0.000	0.000	0.000
42	A	571	PRO	0	-0.005	0.007	11.479	0.133	0.133	0.000	0.000	0.000	0.000
43	A	572	ILE	0	0.022	0.007	14.618	0.152	0.152	0.000	0.000	0.000	0.000
44	A	573	THR	0	-0.070	-0.060	17.676	0.122	0.122	0.000	0.000	0.000	0.000
45	A	574	ALA	0	0.015	-0.015	19.488	-0.019	-0.019	0.000	0.000	0.000	0.000
46	A	575	SER	0	0.023	-0.001	20.731	0.018	0.018	0.000	0.000	0.000	0.000
47	A	576	GLU	-1	-0.736	-0.839	15.590	-0.877	-0.877	0.000	0.000	0.000	0.000
48	A	577	MET	0	-0.026	-0.017	15.862	-0.056	-0.056	0.000	0.000	0.000	0.000
49	A	578	LEU	0	-0.065	-0.034	17.355	0.036	0.036	0.000	0.000	0.000	0.000
50	A	579	SER	0	-0.045	-0.011	15.234	0.027	0.027	0.000	0.000	0.000	0.000
51	A	580	VAL	0	-0.032	0.004	12.547	-0.050	-0.050	0.000	0.000	0.000	0.000
52	A	581	ASN	0	0.033	0.008	13.786	0.172	0.172	0.000	0.000	0.000	0.000
53	A	582	GLY	0	-0.011	0.000	15.491	0.044	0.044	0.000	0.000	0.000	0.000
54	A	583	VAL	0	-0.052	-0.030	16.651	0.074	0.074	0.000	0.000	0.000	0.000
55	A	584	GLY	0	0.061	0.040	19.364	-0.033	-0.033	0.000	0.000	0.000	0.000
56	A	585	MET	0	0.023	-0.009	22.676	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	586	ARG	1	0.946	0.984	25.482	0.060	0.060	0.000	0.000	0.000	0.000
58	A	587	LYS	1	0.853	0.917	21.294	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	588	LEU	0	0.021	0.027	21.225	0.011	0.011	0.000	0.000	0.000	0.000
60	A	589	GLU	-1	-0.877	-0.947	23.541	-0.109	-0.109	0.000	0.000	0.000	0.000
61	A	590	ARG	1	0.872	0.947	26.455	0.015	0.015	0.000	0.000	0.000	0.000
62	A	591	PHE	0	0.030	-0.011	22.736	0.022	0.022	0.000	0.000	0.000	0.000
63	A	592	GLY	0	0.051	0.032	21.538	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	593	LYS	1	0.958	0.978	21.702	0.105	0.105	0.000	0.000	0.000	0.000
65	A	594	PRO	0	0.014	0.007	23.000	-0.025	-0.025	0.000	0.000	0.000	0.000
66	A	595	PHE	0	0.049	0.010	16.894	0.016	0.016	0.000	0.000	0.000	0.000
67	A	596	MET	0	0.043	0.027	18.236	-0.042	-0.042	0.000	0.000	0.000	0.000
68	A	597	ALA	0	-0.067	-0.029	19.550	-0.041	-0.041	0.000	0.000	0.000	0.000
69	A	598	LEU	0	-0.009	0.003	16.756	0.003	0.003	0.000	0.000	0.000	0.000
70	A	599	ILE	0	-0.007	-0.012	13.728	0.019	0.019	0.000	0.000	0.000	0.000
71	A	600	ARG	1	0.944	0.966	15.900	0.318	0.318	0.000	0.000	0.000	0.000
72	A	601	ALA	0	0.066	0.051	18.442	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	602	HIS	0	-0.077	-0.051	10.574	0.214	0.214	0.000	0.000	0.000	0.000
74	A	603	VAL	0	-0.025	-0.019	12.793	-0.022	-0.022	0.000	0.000	0.000	0.000
75	A	604	ASP	-1	-0.895	-0.926	14.873	-0.583	-0.583	0.000	0.000	0.000	0.000
76	A	605	GLY	0	-0.098	-0.042	16.776	0.043	0.043	0.000	0.000	0.000	0.000
77	A	606	ASP	-1	-1.053	-1.023	17.717	-0.106	-0.106	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

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