FMO DATABASE

FMODB ID: R8868

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

Total energy (hartree)

FMO2-HF: Electronic energy	-554511.808888
FMO2-HF: Nuclear repulsion	516845.947423
FMO2-HF: Total energy	-37665.861464
FMO2-MP2: Total energy	-37774.800903

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.
-0.755	1.842	0.006	-1.233	-1.369	0.001

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 : 0.018 / q_NPA : -0.006

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	B	417	LEU	0	-0.012	0.000	3.227	-1.280	1.062	0.004	-1.158	-1.187	0.001
4	B	418	SER	0	-0.007	-0.008	3.977	-1.231	-0.976	0.002	-0.075	-0.182	0.000
5	B	419	VAL	0	0.036	-0.002	6.609	0.384	0.384	0.000	0.000	0.000	0.000
6	B	420	HIS	0	0.016	0.019	7.907	0.327	0.327	0.000	0.000	0.000	0.000
7	B	421	THR	0	-0.037	-0.004	8.347	-0.107	-0.107	0.000	0.000	0.000	0.000
8	B	422	ASP	-1	-0.767	-0.853	10.691	-0.227	-0.227	0.000	0.000	0.000	0.000
9	B	423	MET	0	0.090	0.021	13.173	0.059	0.059	0.000	0.000	0.000	0.000
10	B	424	ALA	0	0.049	0.048	14.606	0.074	0.074	0.000	0.000	0.000	0.000
11	B	425	SER	0	-0.096	-0.084	13.046	0.113	0.113	0.000	0.000	0.000	0.000
12	B	426	VAL	0	0.015	0.014	9.280	0.088	0.088	0.000	0.000	0.000	0.000
13	B	427	THR	0	-0.034	-0.025	11.481	0.136	0.136	0.000	0.000	0.000	0.000
14	B	428	LYS	1	0.861	0.912	14.850	0.167	0.167	0.000	0.000	0.000	0.000
15	B	429	ALA	0	-0.002	0.007	10.365	0.051	0.051	0.000	0.000	0.000	0.000
16	B	430	MET	0	-0.003	-0.002	12.442	0.095	0.095	0.000	0.000	0.000	0.000
17	B	431	ALA	0	-0.038	-0.013	13.457	0.020	0.020	0.000	0.000	0.000	0.000
18	B	432	ALA	0	-0.007	0.016	14.442	-0.027	-0.027	0.000	0.000	0.000	0.000
19	B	433	PRO	0	-0.005	-0.013	16.470	0.011	0.011	0.000	0.000	0.000	0.000
20	B	434	GLU	-1	-0.931	-0.979	15.676	0.460	0.460	0.000	0.000	0.000	0.000
21	B	435	SER	0	-0.061	-0.022	12.691	0.115	0.115	0.000	0.000	0.000	0.000
22	B	436	GLY	0	0.010	0.007	12.181	0.110	0.110	0.000	0.000	0.000	0.000
23	B	437	LEU	0	-0.047	-0.016	14.374	-0.063	-0.063	0.000	0.000	0.000	0.000
24	B	438	GLU	-1	-0.806	-0.883	16.255	0.222	0.222	0.000	0.000	0.000	0.000
25	B	439	VAL	0	-0.026	-0.008	19.602	-0.041	-0.041	0.000	0.000	0.000	0.000
26	B	440	ARG	1	0.763	0.853	21.919	-0.168	-0.168	0.000	0.000	0.000	0.000
27	B	441	ASP	-1	-0.796	-0.873	25.738	0.103	0.103	0.000	0.000	0.000	0.000
28	B	442	ARG	1	0.817	0.885	28.971	-0.102	-0.102	0.000	0.000	0.000	0.000
29	B	443	MET	0	0.004	0.003	29.078	0.004	0.004	0.000	0.000	0.000	0.000
30	B	444	TRP	0	0.001	-0.003	31.033	-0.003	-0.003	0.000	0.000	0.000	0.000
31	B	445	LEU	0	0.016	0.005	32.845	-0.002	-0.002	0.000	0.000	0.000	0.000
32	B	446	LYS	1	0.972	0.992	35.447	-0.008	-0.008	0.000	0.000	0.000	0.000
33	B	447	ILE	0	0.037	0.011	37.643	-0.003	-0.003	0.000	0.000	0.000	0.000
34	B	448	THR	0	-0.038	-0.024	40.847	0.002	0.002	0.000	0.000	0.000	0.000
35	B	449	ILE	0	0.016	0.014	43.354	-0.002	-0.002	0.000	0.000	0.000	0.000
36	B	450	PRO	0	0.009	-0.008	46.619	0.001	0.001	0.000	0.000	0.000	0.000
37	B	451	ASN	0	-0.025	-0.015	49.573	0.001	0.001	0.000	0.000	0.000	0.000
38	B	452	ALA	0	0.014	0.025	47.290	0.001	0.001	0.000	0.000	0.000	0.000
39	B	453	PHE	0	-0.008	0.000	48.530	0.000	0.000	0.000	0.000	0.000	0.000
40	B	454	LEU	0	0.017	0.015	43.603	0.001	0.001	0.000	0.000	0.000	0.000
41	B	455	GLY	0	0.015	-0.005	47.792	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	456	SER	0	-0.010	-0.038	47.721	0.000	0.000	0.000	0.000	0.000	0.000
43	B	457	ASP	-1	-0.841	-0.907	48.565	0.026	0.026	0.000	0.000	0.000	0.000
44	B	458	VAL	0	-0.025	-0.002	51.339	-0.001	-0.001	0.000	0.000	0.000	0.000
45	B	459	VAL	0	-0.020	-0.012	53.103	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	460	ASP	-1	-0.784	-0.878	52.620	0.029	0.029	0.000	0.000	0.000	0.000
47	B	461	TRP	0	-0.024	0.002	54.822	-0.001	-0.001	0.000	0.000	0.000	0.000
48	B	462	LEU	0	0.006	-0.010	56.995	-0.001	-0.001	0.000	0.000	0.000	0.000
49	B	463	TYR	0	-0.029	-0.027	57.465	0.000	0.000	0.000	0.000	0.000	0.000
50	B	464	HIS	0	-0.048	-0.026	54.868	-0.001	-0.001	0.000	0.000	0.000	0.000
51	B	465	HIS	0	-0.079	-0.035	58.134	-0.001	-0.001	0.000	0.000	0.000	0.000
52	B	466	VAL	0	-0.048	-0.018	62.667	-0.001	-0.001	0.000	0.000	0.000	0.000
53	B	467	GLU	-1	-0.919	-0.948	64.610	0.017	0.017	0.000	0.000	0.000	0.000
54	B	468	GLY	0	0.011	-0.003	67.115	0.000	0.000	0.000	0.000	0.000	0.000
55	B	469	PHE	0	-0.048	-0.028	62.077	0.001	0.001	0.000	0.000	0.000	0.000
56	B	470	PRO	0	0.014	0.011	64.242	0.000	0.000	0.000	0.000	0.000	0.000
57	B	471	GLU	-1	-0.904	-0.959	59.618	0.031	0.031	0.000	0.000	0.000	0.000
58	B	472	ARG	1	0.818	0.864	51.013	-0.033	-0.033	0.000	0.000	0.000	0.000
59	B	473	ARG	1	0.815	0.899	56.687	-0.031	-0.031	0.000	0.000	0.000	0.000
60	B	474	GLU	-1	-0.812	-0.909	57.720	0.028	0.028	0.000	0.000	0.000	0.000
61	B	475	ALA	0	0.044	0.045	57.898	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	476	ARG	1	0.861	0.914	51.314	-0.037	-0.037	0.000	0.000	0.000	0.000
63	B	477	LYS	1	0.909	0.967	56.323	-0.025	-0.025	0.000	0.000	0.000	0.000
64	B	478	TYR	0	0.035	0.014	59.123	-0.001	-0.001	0.000	0.000	0.000	0.000
65	B	479	ALA	0	0.043	0.023	55.439	-0.001	-0.001	0.000	0.000	0.000	0.000
66	B	480	SER	0	-0.028	-0.022	56.090	0.000	0.000	0.000	0.000	0.000	0.000
67	B	481	GLY	0	-0.027	-0.010	57.089	-0.001	-0.001	0.000	0.000	0.000	0.000
68	B	482	LEU	0	0.024	0.006	58.394	-0.001	-0.001	0.000	0.000	0.000	0.000
69	B	483	LEU	0	-0.023	-0.004	53.331	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	484	LYS	1	0.899	0.952	57.196	-0.020	-0.020	0.000	0.000	0.000	0.000
71	B	485	ALA	0	-0.027	-0.014	59.756	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	486	GLY	0	-0.007	0.007	58.666	-0.001	-0.001	0.000	0.000	0.000	0.000
73	B	487	LEU	0	0.014	0.005	59.311	-0.001	-0.001	0.000	0.000	0.000	0.000
74	B	488	ILE	0	-0.023	0.001	54.162	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	489	ARG	1	0.895	0.931	53.849	-0.011	-0.011	0.000	0.000	0.000	0.000
76	B	490	HIS	1	0.865	0.911	48.403	-0.028	-0.028	0.000	0.000	0.000	0.000
77	B	491	THR	0	-0.015	-0.022	46.124	-0.001	-0.001	0.000	0.000	0.000	0.000
78	B	492	VAL	0	0.007	0.007	43.719	-0.001	-0.001	0.000	0.000	0.000	0.000
79	B	493	ASN	0	-0.025	-0.021	47.037	0.001	0.001	0.000	0.000	0.000	0.000
80	B	494	LYS	1	0.853	0.886	43.670	-0.035	-0.035	0.000	0.000	0.000	0.000
81	B	495	ILE	0	0.011	0.005	49.855	-0.001	-0.001	0.000	0.000	0.000	0.000
82	B	496	THR	0	0.012	0.007	50.455	-0.001	-0.001	0.000	0.000	0.000	0.000
83	B	497	PHE	0	0.023	0.033	51.171	0.000	0.000	0.000	0.000	0.000	0.000
84	B	498	SER	0	-0.037	-0.095	46.775	0.003	0.003	0.000	0.000	0.000	0.000
85	B	499	GLU	-1	-0.669	-0.808	48.046	0.033	0.033	0.000	0.000	0.000	0.000
86	B	500	GLN	0	0.042	0.022	42.673	-0.003	-0.003	0.000	0.000	0.000	0.000
87	B	501	CYM	-1	-0.844	-0.771	43.697	0.034	0.034	0.000	0.000	0.000	0.000
88	B	502	TYR	0	0.058	0.033	41.422	0.000	0.000	0.000	0.000	0.000	0.000
89	B	503	TYR	0	-0.090	-0.052	46.510	0.000	0.000	0.000	0.000	0.000	0.000
90	B	504	VAL	0	0.046	0.026	50.103	-0.001	-0.001	0.000	0.000	0.000	0.000
91	B	505	PHE	0	0.080	0.031	52.597	0.001	0.001	0.000	0.000	0.000	0.000
92	B	506	GLY	0	0.019	0.017	56.291	0.000	0.000	0.000	0.000	0.000	0.000
93	B	507	ASP	-1	-0.888	-0.905	58.878	0.006	0.006	0.000	0.000	0.000	0.000
94	B	508	LEU	0	-0.042	-0.029	60.373	0.001	0.001	0.000	0.000	0.000	0.000
95	B	509	SER	0	-0.093	-0.062	63.703	-0.001	-0.001	0.000	0.000	0.000	0.000

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