FMO DATABASE

FMODB ID: Z6VKN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-509241.171808
FMO2-HF: Nuclear repulsion	478002.825518
FMO2-HF: Total energy	-31238.346291
FMO2-MP2: Total energy	-31327.175304

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.
-60.911	-59.739	18.068	-9.983	-9.257	0.025

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 : 0.018

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	-0.734	-0.849	3.869	4.486	6.749	-0.019	-1.135	-1.109	0.006
4	A	533	ARG	1	0.901	0.922	1.879	-41.982	-44.022	11.924	-5.024	-4.860	0.073
5	A	534	LYS	1	0.942	0.984	7.973	-1.146	-1.146	0.000	0.000	0.000	0.000
6	A	535	LEU	0	0.010	0.015	9.989	-0.163	-0.163	0.000	0.000	0.000	0.000
7	A	536	PHE	0	0.030	0.004	8.920	-0.036	-0.036	0.000	0.000	0.000	0.000
8	A	537	ALA	0	-0.037	-0.020	10.970	-0.192	-0.192	0.000	0.000	0.000	0.000
9	A	538	LYS	1	0.859	0.930	13.759	-0.422	-0.422	0.000	0.000	0.000	0.000
10	A	539	LEU	0	0.035	0.018	11.686	-0.059	-0.059	0.000	0.000	0.000	0.000
11	A	540	ARG	1	0.835	0.908	14.113	-1.127	-1.127	0.000	0.000	0.000	0.000
12	A	541	LYS	1	0.931	0.965	16.281	-0.807	-0.807	0.000	0.000	0.000	0.000
13	A	542	LEU	0	0.026	0.028	18.928	-0.044	-0.044	0.000	0.000	0.000	0.000
14	A	543	ARG	1	0.794	0.864	16.877	-0.541	-0.541	0.000	0.000	0.000	0.000
15	A	544	LYS	1	0.755	0.857	20.213	-0.386	-0.386	0.000	0.000	0.000	0.000
16	A	545	SER	0	-0.020	-0.017	22.280	-0.019	-0.019	0.000	0.000	0.000	0.000
17	A	546	ILE	0	0.060	0.022	22.699	-0.024	-0.024	0.000	0.000	0.000	0.000
18	A	547	ALA	0	-0.042	-0.018	23.392	-0.025	-0.025	0.000	0.000	0.000	0.000
19	A	548	ASP	-1	-0.775	-0.862	25.383	0.301	0.301	0.000	0.000	0.000	0.000
20	A	549	GLU	-1	-0.908	-0.938	27.505	0.136	0.136	0.000	0.000	0.000	0.000
21	A	550	SER	0	-0.086	-0.052	27.816	-0.027	-0.027	0.000	0.000	0.000	0.000
22	A	551	ASN	0	-0.039	-0.007	30.054	0.000	0.000	0.000	0.000	0.000	0.000
23	A	552	VAL	0	-0.033	-0.012	25.681	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	553	PRO	0	0.026	0.021	24.800	0.029	0.029	0.000	0.000	0.000	0.000
25	A	554	PRO	0	0.058	-0.002	20.484	-0.020	-0.020	0.000	0.000	0.000	0.000
26	A	555	TYR	0	0.035	0.007	19.789	-0.027	-0.027	0.000	0.000	0.000	0.000
27	A	556	VAL	0	-0.018	-0.005	20.811	-0.049	-0.049	0.000	0.000	0.000	0.000
28	A	557	VAL	0	-0.014	0.021	20.608	-0.038	-0.038	0.000	0.000	0.000	0.000
29	A	558	PHE	0	0.058	0.025	16.355	-0.064	-0.064	0.000	0.000	0.000	0.000
30	A	559	ASN	0	0.042	0.034	14.824	0.135	0.135	0.000	0.000	0.000	0.000
31	A	560	ASP	-1	-0.729	-0.848	13.164	0.763	0.763	0.000	0.000	0.000	0.000
32	A	561	ALA	0	0.060	0.036	10.728	0.128	0.128	0.000	0.000	0.000	0.000
33	A	562	THR	0	0.011	-0.005	10.177	-0.149	-0.149	0.000	0.000	0.000	0.000
34	A	563	LEU	0	-0.038	-0.019	11.545	-0.142	-0.142	0.000	0.000	0.000	0.000
35	A	564	ILE	0	-0.009	-0.008	5.864	0.023	0.023	0.000	0.000	0.000	0.000
36	A	565	GLU	-1	-0.789	-0.890	6.937	-1.512	-1.512	0.000	0.000	0.000	0.000
37	A	566	MET	0	-0.039	-0.028	8.078	-0.387	-0.387	0.000	0.000	0.000	0.000
38	A	567	ALA	0	-0.034	-0.018	7.829	-0.041	-0.041	0.000	0.000	0.000	0.000
39	A	568	GLU	-1	-0.930	-0.959	1.957	-18.407	-17.458	6.163	-3.824	-3.288	-0.054
40	A	569	GLN	0	-0.012	-0.017	5.585	0.307	0.307	0.000	0.000	0.000	0.000
41	A	570	MET	0	-0.052	-0.009	8.446	0.515	0.515	0.000	0.000	0.000	0.000
42	A	571	PRO	0	-0.009	-0.006	10.936	0.142	0.142	0.000	0.000	0.000	0.000
43	A	572	ILE	0	0.054	0.032	14.222	0.154	0.154	0.000	0.000	0.000	0.000
44	A	573	THR	0	-0.074	-0.064	17.248	0.117	0.117	0.000	0.000	0.000	0.000
45	A	574	ALA	0	0.030	-0.011	18.866	-0.026	-0.026	0.000	0.000	0.000	0.000
46	A	575	SER	0	0.022	0.007	19.999	0.015	0.015	0.000	0.000	0.000	0.000
47	A	576	GLU	-1	-0.744	-0.827	14.809	-0.769	-0.769	0.000	0.000	0.000	0.000
48	A	577	MET	0	-0.025	-0.012	15.232	-0.055	-0.055	0.000	0.000	0.000	0.000
49	A	578	LEU	0	-0.061	-0.034	16.661	0.015	0.015	0.000	0.000	0.000	0.000
50	A	579	SER	0	-0.039	-0.015	14.917	0.025	0.025	0.000	0.000	0.000	0.000
51	A	580	VAL	0	-0.036	-0.001	11.727	-0.092	-0.092	0.000	0.000	0.000	0.000
52	A	581	ASN	0	0.020	-0.002	12.798	0.216	0.216	0.000	0.000	0.000	0.000
53	A	582	GLY	0	-0.002	0.005	14.453	0.064	0.064	0.000	0.000	0.000	0.000
54	A	583	VAL	0	-0.069	-0.036	15.693	0.090	0.090	0.000	0.000	0.000	0.000
55	A	584	GLY	0	0.068	0.042	18.400	-0.032	-0.032	0.000	0.000	0.000	0.000
56	A	585	MET	0	0.034	-0.001	21.903	0.011	0.011	0.000	0.000	0.000	0.000
57	A	586	ARG	1	0.937	0.964	24.521	0.055	0.055	0.000	0.000	0.000	0.000
58	A	587	LYS	1	0.815	0.905	20.106	0.014	0.014	0.000	0.000	0.000	0.000
59	A	588	LEU	0	0.020	0.011	20.784	0.017	0.017	0.000	0.000	0.000	0.000
60	A	589	GLU	-1	-0.874	-0.939	22.695	-0.086	-0.086	0.000	0.000	0.000	0.000
61	A	590	ARG	1	0.875	0.948	25.933	-0.020	-0.020	0.000	0.000	0.000	0.000
62	A	591	PHE	0	0.039	0.001	22.143	0.030	0.030	0.000	0.000	0.000	0.000
63	A	592	GLY	0	0.037	0.026	20.568	0.008	0.008	0.000	0.000	0.000	0.000
64	A	593	LYS	1	0.971	0.990	21.024	0.043	0.043	0.000	0.000	0.000	0.000
65	A	594	PRO	0	0.004	-0.002	22.767	-0.017	-0.017	0.000	0.000	0.000	0.000
66	A	595	PHE	0	0.038	0.005	16.385	0.023	0.023	0.000	0.000	0.000	0.000
67	A	596	MET	0	0.039	0.024	17.899	-0.023	-0.023	0.000	0.000	0.000	0.000
68	A	597	ALA	0	-0.063	-0.023	19.020	-0.027	-0.027	0.000	0.000	0.000	0.000
69	A	598	LEU	0	-0.007	0.002	17.038	0.010	0.010	0.000	0.000	0.000	0.000
70	A	599	ILE	0	-0.007	-0.006	13.325	0.059	0.059	0.000	0.000	0.000	0.000
71	A	600	ARG	1	0.908	0.950	15.705	0.228	0.228	0.000	0.000	0.000	0.000
72	A	601	ALA	0	0.094	0.051	18.037	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	602	HIS	0	-0.089	-0.041	10.947	0.139	0.139	0.000	0.000	0.000	0.000
74	A	603	VAL	0	-0.022	-0.016	12.519	0.015	0.015	0.000	0.000	0.000	0.000
75	A	604	ASP	-1	-0.904	-0.944	14.919	-0.341	-0.341	0.000	0.000	0.000	0.000
76	A	605	GLY	0	-0.064	-0.019	17.271	0.025	0.025	0.000	0.000	0.000	0.000
77	A	606	ASP	-1	-1.072	-1.052	18.216	0.098	0.098	0.000	0.000	0.000	0.000

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