FMO DATABASE

FMODB ID: ZVVKN

Calculation Name: 5SUZ-B-Xray372

Preferred Name: Segment polarity protein dishevelled homolog DVL-2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5SUZ

Chain ID: B

ChEMBL ID: CHEMBL1255125

UniProt ID: O14641

Base Structure: X-ray

Registration Date: 2023-09-21

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	95
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-551084.749297
FMO2-HF: Nuclear repulsion	513419.031878
FMO2-HF: Total energy	-37665.717419
FMO2-MP2: Total energy	-37774.606175

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:415:SER)

Summations of interaction energy for fragment #1(B:415:SER)

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.
-1.216	1.837	-0.019	-1.528	-1.505	0

Interaction energy analysis for fragmet #1(B:415:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.015

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].
3	B	417	LEU	0	-0.023	0.001	3.364	-1.859	0.995	-0.018	-1.492	-1.343
4	B	418	SER	0	0.000	-0.010	4.395	-0.963	-0.764	-0.001	-0.036	-0.162
5	B	419	VAL	0	0.023	-0.006	6.436	0.372	0.372	0.000	0.000	0.000
6	B	420	HIS	0	0.007	0.012	8.214	0.301	0.301	0.000	0.000	0.000
7	B	421	THR	0	-0.033	0.003	8.718	-0.062	-0.062	0.000	0.000	0.000
8	B	422	ASP	-1	-0.760	-0.841	10.927	-0.334	-0.334	0.000	0.000	0.000
9	B	423	MET	0	0.080	0.005	13.520	0.024	0.024	0.000	0.000	0.000
10	B	424	ALA	0	0.028	0.026	15.173	0.060	0.060	0.000	0.000	0.000
11	B	425	SER	0	-0.090	-0.083	12.950	0.111	0.111	0.000	0.000	0.000
12	B	426	VAL	0	0.013	0.016	9.683	0.069	0.069	0.000	0.000	0.000
13	B	427	THR	0	-0.016	-0.012	11.832	0.110	0.110	0.000	0.000	0.000
14	B	428	LYS	1	0.880	0.927	15.070	0.224	0.224	0.000	0.000	0.000
15	B	429	ALA	0	-0.006	0.005	10.305	0.056	0.056	0.000	0.000	0.000
16	B	430	MET	0	-0.012	-0.005	12.427	0.092	0.092	0.000	0.000	0.000
17	B	431	ALA	0	-0.044	-0.014	13.478	0.034	0.034	0.000	0.000	0.000
18	B	432	ALA	0	-0.011	0.016	14.395	-0.008	-0.008	0.000	0.000	0.000
19	B	433	PRO	0	0.003	-0.013	16.327	0.016	0.016	0.000	0.000	0.000
20	B	434	GLU	-1	-0.935	-0.977	15.898	0.379	0.379	0.000	0.000	0.000
21	B	435	SER	0	-0.047	-0.016	12.452	0.105	0.105	0.000	0.000	0.000
22	B	436	GLY	0	0.014	0.009	11.762	0.098	0.098	0.000	0.000	0.000
23	B	437	LEU	0	-0.074	-0.030	14.129	-0.054	-0.054	0.000	0.000	0.000
24	B	438	GLU	-1	-0.810	-0.893	15.804	0.164	0.164	0.000	0.000	0.000
25	B	439	VAL	0	-0.006	-0.001	19.217	-0.032	-0.032	0.000	0.000	0.000
26	B	440	ARG	1	0.755	0.859	21.861	-0.100	-0.100	0.000	0.000	0.000
27	B	441	ASP	-1	-0.799	-0.893	25.661	0.067	0.067	0.000	0.000	0.000
28	B	442	ARG	1	0.847	0.923	28.811	-0.067	-0.067	0.000	0.000	0.000
29	B	443	MET	0	-0.005	-0.010	29.168	0.001	0.001	0.000	0.000	0.000
30	B	444	TRP	0	0.001	-0.001	31.118	-0.001	-0.001	0.000	0.000	0.000
31	B	445	LEU	0	0.013	0.012	32.820	-0.003	-0.003	0.000	0.000	0.000
32	B	446	LYS	1	0.976	0.990	35.260	0.010	0.010	0.000	0.000	0.000
33	B	447	ILE	0	0.024	0.002	37.558	-0.003	-0.003	0.000	0.000	0.000
34	B	448	THR	0	-0.036	-0.021	40.792	0.002	0.002	0.000	0.000	0.000
35	B	449	ILE	0	0.014	0.010	43.357	-0.001	-0.001	0.000	0.000	0.000
36	B	450	PRO	0	0.001	-0.005	46.716	0.001	0.001	0.000	0.000	0.000
37	B	451	ASN	0	-0.014	-0.006	49.696	0.001	0.001	0.000	0.000	0.000
38	B	452	ALA	0	0.017	0.020	47.110	0.001	0.001	0.000	0.000	0.000
39	B	453	PHE	0	0.014	0.004	48.615	0.000	0.000	0.000	0.000	0.000
40	B	454	LEU	0	0.039	0.030	43.615	0.000	0.000	0.000	0.000	0.000
41	B	455	GLY	0	0.013	-0.003	47.784	-0.001	-0.001	0.000	0.000	0.000
42	B	456	SER	0	0.017	-0.006	47.554	0.000	0.000	0.000	0.000	0.000
43	B	457	ASP	-1	-0.861	-0.934	48.415	0.015	0.015	0.000	0.000	0.000
44	B	458	VAL	0	-0.054	-0.009	51.059	-0.001	-0.001	0.000	0.000	0.000
45	B	459	VAL	0	-0.019	-0.020	52.972	0.000	0.000	0.000	0.000	0.000
46	B	460	ASP	-1	-0.793	-0.900	52.582	0.020	0.020	0.000	0.000	0.000
47	B	461	TRP	0	-0.020	0.007	54.597	0.000	0.000	0.000	0.000	0.000
48	B	462	LEU	0	0.006	-0.008	57.016	-0.001	-0.001	0.000	0.000	0.000
49	B	463	TYR	0	-0.021	-0.021	57.073	0.000	0.000	0.000	0.000	0.000
50	B	464	HIS	0	-0.031	-0.017	54.968	0.000	0.000	0.000	0.000	0.000
51	B	465	HIS	0	-0.080	-0.029	58.275	-0.001	-0.001	0.000	0.000	0.000
52	B	466	VAL	0	-0.044	-0.015	62.670	-0.001	-0.001	0.000	0.000	0.000
53	B	467	GLU	-1	-0.923	-0.954	64.536	0.011	0.011	0.000	0.000	0.000
54	B	468	GLY	0	0.000	-0.005	67.145	0.000	0.000	0.000	0.000	0.000
55	B	469	PHE	0	-0.032	-0.019	62.044	0.000	0.000	0.000	0.000	0.000
56	B	470	PRO	0	-0.024	-0.008	63.911	0.000	0.000	0.000	0.000	0.000
57	B	471	GLU	-1	-0.897	-0.952	59.432	0.022	0.022	0.000	0.000	0.000
58	B	472	ARG	1	0.816	0.878	51.213	-0.022	-0.022	0.000	0.000	0.000
59	B	473	ARG	1	0.896	0.954	56.643	-0.024	-0.024	0.000	0.000	0.000
60	B	474	GLU	-1	-0.868	-0.955	57.635	0.019	0.019	0.000	0.000	0.000
61	B	475	ALA	0	0.050	0.048	57.745	-0.001	-0.001	0.000	0.000	0.000
62	B	476	ARG	1	0.843	0.905	51.429	-0.026	-0.026	0.000	0.000	0.000
63	B	477	LYS	1	0.912	0.959	56.305	-0.018	-0.018	0.000	0.000	0.000
64	B	478	TYR	0	0.041	0.025	58.994	-0.001	-0.001	0.000	0.000	0.000
65	B	479	ALA	0	0.035	0.016	55.563	-0.001	-0.001	0.000	0.000	0.000
66	B	480	SER	0	-0.020	-0.015	56.198	0.000	0.000	0.000	0.000	0.000
67	B	481	GLY	0	-0.031	-0.019	57.124	-0.001	-0.001	0.000	0.000	0.000
68	B	482	LEU	0	0.026	0.016	58.378	-0.001	-0.001	0.000	0.000	0.000
69	B	483	LEU	0	-0.043	-0.013	53.304	-0.001	-0.001	0.000	0.000	0.000
70	B	484	LYS	1	0.919	0.961	57.246	-0.012	-0.012	0.000	0.000	0.000
71	B	485	ALA	0	-0.035	-0.018	59.634	-0.001	-0.001	0.000	0.000	0.000
72	B	486	GLY	0	0.004	0.013	58.883	-0.001	-0.001	0.000	0.000	0.000
73	B	487	LEU	0	0.013	0.009	59.766	-0.001	-0.001	0.000	0.000	0.000
74	B	488	ILE	0	-0.021	0.006	54.212	-0.001	-0.001	0.000	0.000	0.000
75	B	489	ARG	1	0.905	0.935	53.922	-0.001	-0.001	0.000	0.000	0.000
76	B	490	HIS	1	0.862	0.896	48.287	-0.015	-0.015	0.000	0.000	0.000
77	B	491	THR	0	-0.002	0.000	46.414	-0.001	-0.001	0.000	0.000	0.000
78	B	492	VAL	0	0.006	0.005	43.482	-0.001	-0.001	0.000	0.000	0.000
79	B	493	ASN	0	-0.030	-0.022	46.844	0.001	0.001	0.000	0.000	0.000
80	B	494	LYS	1	0.844	0.886	43.539	-0.019	-0.019	0.000	0.000	0.000
81	B	495	ILE	0	0.026	0.005	49.813	-0.001	-0.001	0.000	0.000	0.000
82	B	496	THR	0	-0.005	-0.001	49.993	-0.001	-0.001	0.000	0.000	0.000
83	B	497	PHE	0	0.031	0.041	50.786	0.000	0.000	0.000	0.000	0.000
84	B	498	SER	0	-0.010	-0.088	46.216	0.002	0.002	0.000	0.000	0.000
85	B	499	GLU	-1	-0.685	-0.830	48.219	0.022	0.022	0.000	0.000	0.000
86	B	500	GLN	0	0.031	0.023	42.366	-0.002	-0.002	0.000	0.000	0.000
87	B	501	CYM	-1	-0.846	-0.767	43.599	0.020	0.020	0.000	0.000	0.000
88	B	502	TYR	0	0.032	0.006	41.542	0.000	0.000	0.000	0.000	0.000
89	B	503	TYR	0	-0.094	-0.055	46.677	0.000	0.000	0.000	0.000	0.000
90	B	504	VAL	0	0.054	0.025	50.134	-0.001	-0.001	0.000	0.000	0.000
91	B	505	PHE	0	0.071	0.030	52.614	0.001	0.001	0.000	0.000	0.000
92	B	506	GLY	0	-0.022	-0.009	56.395	-0.001	-0.001	0.000	0.000	0.000
93	B	507	ASP	-1	-0.863	-0.911	58.723	-0.001	-0.001	0.000	0.000	0.000
94	B	508	LEU	0	-0.033	-0.019	60.636	0.001	0.001	0.000	0.000	0.000
95	B	509	SER	0	-0.090	-0.051	63.768	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:415:SER)