FMO DATABASE

FMODB ID: 6YYKZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-550037.353735
FMO2-HF: Nuclear repulsion	512372.118952
FMO2-HF: Total energy	-37665.234783
FMO2-MP2: Total energy	-37774.056032

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.
-1.188	1.865	-0.019	-1.529	-1.506	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	3.352	-1.781	1.072	-0.018	-1.492	-1.343
4	B	418	SER	0	0.000	-0.008	4.371	-0.988	-0.788	-0.001	-0.037	-0.163
5	B	419	VAL	0	0.027	-0.001	6.432	0.383	0.383	0.000	0.000	0.000
6	B	420	HIS	0	-0.005	0.000	8.511	0.287	0.287	0.000	0.000	0.000
7	B	421	THR	0	-0.024	0.008	8.700	-0.054	-0.054	0.000	0.000	0.000
8	B	422	ASP	-1	-0.791	-0.870	10.927	-0.378	-0.378	0.000	0.000	0.000
9	B	423	MET	0	0.064	-0.003	13.509	0.023	0.023	0.000	0.000	0.000
10	B	424	ALA	0	-0.003	0.012	15.181	0.058	0.058	0.000	0.000	0.000
11	B	425	SER	0	-0.046	-0.048	13.042	0.101	0.101	0.000	0.000	0.000
12	B	426	VAL	0	0.008	0.013	9.700	0.068	0.068	0.000	0.000	0.000
13	B	427	THR	0	-0.017	-0.017	11.829	0.109	0.109	0.000	0.000	0.000
14	B	428	LYS	1	0.928	0.954	15.070	0.193	0.193	0.000	0.000	0.000
15	B	429	ALA	0	-0.009	0.006	10.333	0.057	0.057	0.000	0.000	0.000
16	B	430	MET	0	-0.021	-0.010	12.439	0.092	0.092	0.000	0.000	0.000
17	B	431	ALA	0	-0.045	-0.018	13.485	0.034	0.034	0.000	0.000	0.000
18	B	432	ALA	0	-0.007	0.014	14.446	-0.008	-0.008	0.000	0.000	0.000
19	B	433	PRO	0	0.000	-0.021	16.349	0.018	0.018	0.000	0.000	0.000
20	B	434	GLU	-1	-0.946	-0.977	15.918	0.379	0.379	0.000	0.000	0.000
21	B	435	SER	0	-0.040	-0.004	12.470	0.100	0.100	0.000	0.000	0.000
22	B	436	GLY	0	0.019	0.010	11.785	0.096	0.096	0.000	0.000	0.000
23	B	437	LEU	0	-0.083	-0.035	14.151	-0.055	-0.055	0.000	0.000	0.000
24	B	438	GLU	-1	-0.912	-0.959	15.819	0.189	0.189	0.000	0.000	0.000
25	B	439	VAL	0	-0.025	-0.013	19.232	-0.033	-0.033	0.000	0.000	0.000
26	B	440	ARG	1	0.898	0.950	21.877	-0.068	-0.068	0.000	0.000	0.000
27	B	441	ASP	-1	-0.867	-0.934	25.675	0.061	0.061	0.000	0.000	0.000
28	B	442	ARG	1	0.909	0.956	28.827	-0.057	-0.057	0.000	0.000	0.000
29	B	443	MET	0	-0.007	-0.008	29.179	0.000	0.000	0.000	0.000	0.000
30	B	444	TRP	0	-0.002	-0.001	31.119	0.000	0.000	0.000	0.000	0.000
31	B	445	LEU	0	0.016	0.010	32.823	-0.003	-0.003	0.000	0.000	0.000
32	B	446	LYS	1	0.971	0.988	35.263	0.014	0.014	0.000	0.000	0.000
33	B	447	ILE	0	0.025	0.005	37.558	-0.003	-0.003	0.000	0.000	0.000
34	B	448	THR	0	-0.034	-0.020	40.791	0.002	0.002	0.000	0.000	0.000
35	B	449	ILE	0	0.017	0.013	43.354	-0.001	-0.001	0.000	0.000	0.000
36	B	450	PRO	0	-0.005	-0.007	46.714	0.001	0.001	0.000	0.000	0.000
37	B	451	ASN	0	-0.008	-0.002	49.694	0.001	0.001	0.000	0.000	0.000
38	B	452	ALA	0	0.012	0.014	47.110	0.001	0.001	0.000	0.000	0.000
39	B	453	PHE	0	0.004	0.000	48.597	0.000	0.000	0.000	0.000	0.000
40	B	454	LEU	0	0.036	0.027	43.772	0.000	0.000	0.000	0.000	0.000
41	B	455	GLY	0	0.004	-0.005	47.791	0.000	0.000	0.000	0.000	0.000
42	B	456	SER	0	0.040	-0.001	47.596	0.000	0.000	0.000	0.000	0.000
43	B	457	ASP	-1	-0.849	-0.914	48.327	0.012	0.012	0.000	0.000	0.000
44	B	458	VAL	0	-0.062	-0.018	51.066	-0.001	-0.001	0.000	0.000	0.000
45	B	459	VAL	0	-0.030	-0.028	52.903	0.000	0.000	0.000	0.000	0.000
46	B	460	ASP	-1	-0.851	-0.929	51.381	0.017	0.017	0.000	0.000	0.000
47	B	461	TRP	0	-0.025	-0.005	54.606	0.000	0.000	0.000	0.000	0.000
48	B	462	LEU	0	0.007	-0.007	57.022	0.000	0.000	0.000	0.000	0.000
49	B	463	TYR	0	-0.028	-0.021	57.368	0.000	0.000	0.000	0.000	0.000
50	B	464	HIS	0	-0.016	-0.015	55.504	0.000	0.000	0.000	0.000	0.000
51	B	465	HIS	0	-0.080	-0.025	58.298	-0.001	-0.001	0.000	0.000	0.000
52	B	466	VAL	0	-0.046	-0.015	62.676	-0.001	-0.001	0.000	0.000	0.000
53	B	467	GLU	-1	-0.917	-0.958	64.545	0.010	0.010	0.000	0.000	0.000
54	B	468	GLY	0	-0.011	-0.006	67.165	0.000	0.000	0.000	0.000	0.000
55	B	469	PHE	0	-0.046	-0.027	62.116	0.000	0.000	0.000	0.000	0.000
56	B	470	PRO	0	-0.035	-0.008	63.923	0.000	0.000	0.000	0.000	0.000
57	B	471	GLU	-1	-0.840	-0.927	59.420	0.020	0.020	0.000	0.000	0.000
58	B	472	ARG	1	0.838	0.911	51.099	-0.020	-0.020	0.000	0.000	0.000
59	B	473	ARG	1	0.910	0.956	55.886	-0.022	-0.022	0.000	0.000	0.000
60	B	474	GLU	-1	-0.892	-0.956	57.650	0.017	0.017	0.000	0.000	0.000
61	B	475	ALA	0	0.048	0.044	57.688	-0.001	-0.001	0.000	0.000	0.000
62	B	476	ARG	1	0.918	0.961	52.459	-0.023	-0.023	0.000	0.000	0.000
63	B	477	LYS	1	0.912	0.954	56.318	-0.016	-0.016	0.000	0.000	0.000
64	B	478	TYR	0	0.047	0.030	59.008	-0.001	-0.001	0.000	0.000	0.000
65	B	479	ALA	0	0.040	0.018	55.551	-0.001	-0.001	0.000	0.000	0.000
66	B	480	SER	0	-0.055	-0.031	55.919	-0.001	-0.001	0.000	0.000	0.000
67	B	481	GLY	0	0.013	0.001	57.136	-0.001	-0.001	0.000	0.000	0.000
68	B	482	LEU	0	0.020	0.012	58.403	-0.001	-0.001	0.000	0.000	0.000
69	B	483	LEU	0	-0.040	-0.010	53.351	-0.001	-0.001	0.000	0.000	0.000
70	B	484	LYS	1	0.914	0.959	57.256	-0.011	-0.011	0.000	0.000	0.000
71	B	485	ALA	0	-0.033	-0.020	59.645	-0.001	-0.001	0.000	0.000	0.000
72	B	486	GLY	0	0.002	0.013	58.890	-0.001	-0.001	0.000	0.000	0.000
73	B	487	LEU	0	0.014	0.007	59.772	-0.001	-0.001	0.000	0.000	0.000
74	B	488	ILE	0	-0.018	0.010	54.097	-0.001	-0.001	0.000	0.000	0.000
75	B	489	ARG	1	0.936	0.955	53.791	0.001	0.001	0.000	0.000	0.000
76	B	490	HIS	1	0.866	0.912	48.155	-0.012	-0.012	0.000	0.000	0.000
77	B	491	THR	0	-0.005	0.003	46.332	-0.001	-0.001	0.000	0.000	0.000
78	B	492	VAL	0	0.020	0.011	43.409	-0.001	-0.001	0.000	0.000	0.000
79	B	493	ASN	0	-0.036	-0.027	46.851	0.001	0.001	0.000	0.000	0.000
80	B	494	LYS	1	0.889	0.954	43.353	-0.016	-0.016	0.000	0.000	0.000
81	B	495	ILE	0	0.036	0.008	49.825	-0.001	-0.001	0.000	0.000	0.000
82	B	496	THR	0	-0.005	0.006	50.162	0.000	0.000	0.000	0.000	0.000
83	B	497	PHE	0	0.017	0.030	50.799	0.000	0.000	0.000	0.000	0.000
84	B	498	SER	0	-0.014	-0.028	45.805	0.002	0.002	0.000	0.000	0.000
85	B	499	GLU	-1	-0.750	-0.893	48.172	0.019	0.019	0.000	0.000	0.000
86	B	500	GLN	0	0.019	0.016	42.040	-0.002	-0.002	0.000	0.000	0.000
87	B	501	CYM	-1	-0.882	-0.910	43.608	0.017	0.017	0.000	0.000	0.000
88	B	502	TYR	0	0.023	0.003	41.697	0.000	0.000	0.000	0.000	0.000
89	B	503	TYR	0	-0.096	-0.056	46.683	0.000	0.000	0.000	0.000	0.000
90	B	504	VAL	0	0.059	0.027	50.165	-0.001	-0.001	0.000	0.000	0.000
91	B	505	PHE	0	0.057	0.022	52.617	0.001	0.001	0.000	0.000	0.000
92	B	506	GLY	0	-0.040	-0.022	56.398	-0.001	-0.001	0.000	0.000	0.000
93	B	507	ASP	-1	-0.869	-0.929	58.727	-0.003	-0.003	0.000	0.000	0.000
94	B	508	LEU	0	-0.043	-0.021	60.482	0.001	0.001	0.000	0.000	0.000
95	B	509	SER	0	-0.067	-0.028	63.770	0.000	0.000	0.000	0.000	0.000

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