FMO DATABASE

FMODB ID: 94ML2

Calculation Name: 3PZ8-A-Xray372

Preferred Name: Segment polarity protein dishevelled homolog DVL-1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3PZ8

Chain ID: A

ChEMBL ID: CHEMBL3813590

UniProt ID: P51141

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	82
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-561563.24021
FMO2-HF: Nuclear repulsion	528348.423084
FMO2-HF: Total energy	-33214.817126
FMO2-MP2: Total energy	-33311.740052

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:3:ASP)

Summations of interaction energy for fragment #1(A:3:ASP)

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.
8.583	2.976	27.795	-9.827	-12.363	-0.05

Interaction energy analysis for fragmet #1(A:3:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.939 / q_NPA : -0.962

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

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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	5	LYS	1	0.906	0.945	3.814	-38.370	-35.969	-0.037	-1.281	-1.083	0.003
4	A	6	ILE	0	0.011	0.021	7.037	-1.697	-1.697	0.000	0.000	0.000	0.000
5	A	7	ILE	0	-0.024	-0.020	10.053	-0.088	-0.088	0.000	0.000	0.000	0.000
6	A	8	TYR	0	-0.069	-0.080	13.477	-0.018	-0.018	0.000	0.000	0.000	0.000
7	A	9	HIS	0	-0.040	-0.024	16.136	-0.382	-0.382	0.000	0.000	0.000	0.000
8	A	10	MET	0	0.012	0.012	18.472	0.251	0.251	0.000	0.000	0.000	0.000
9	A	11	ASP	-1	-0.907	-0.961	22.462	11.156	11.156	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-1.006	-0.997	25.999	9.590	9.590	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.818	-0.911	22.064	13.377	13.377	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.957	-0.958	25.279	10.204	10.204	0.000	0.000	0.000	0.000
13	A	15	THR	0	-0.056	-0.038	21.425	0.003	0.003	0.000	0.000	0.000	0.000
14	A	16	PRO	0	-0.047	-0.011	17.873	0.081	0.081	0.000	0.000	0.000	0.000
15	A	17	ASP	-1	-0.733	-0.827	15.511	16.088	16.088	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.059	-0.056	10.472	1.000	1.000	0.000	0.000	0.000	0.000
17	A	19	VAL	0	-0.018	0.001	8.751	0.271	0.271	0.000	0.000	0.000	0.000
18	A	20	LYS	1	0.886	0.923	5.018	-25.886	-25.866	-0.001	-0.007	-0.013	0.000
19	A	21	LEU	0	0.018	0.015	4.398	-2.970	-2.588	-0.001	-0.122	-0.259	0.000
20	A	22	PRO	0	0.046	0.007	2.178	16.224	10.038	11.842	-2.613	-3.043	-0.016
21	A	23	VAL	0	-0.003	0.009	2.194	7.190	5.665	8.895	-3.356	-4.013	-0.024
22	A	24	ALA	0	0.051	0.027	2.098	1.063	1.352	6.267	-3.644	-2.913	-0.017
23	A	25	PRO	0	0.009	-0.005	2.327	-5.786	-6.774	0.830	1.196	-1.039	0.004
24	A	26	GLU	-1	-0.875	-0.931	5.439	32.762	32.762	0.000	0.000	0.000	0.000
25	A	27	ARG	1	0.856	0.919	6.789	-25.619	-25.619	0.000	0.000	0.000	0.000
26	A	28	VAL	0	0.015	0.023	6.427	-0.899	-0.899	0.000	0.000	0.000	0.000
27	A	29	THR	0	-0.067	-0.061	8.298	-2.361	-2.361	0.000	0.000	0.000	0.000
28	A	30	LEU	0	0.023	0.012	11.208	0.734	0.734	0.000	0.000	0.000	0.000
29	A	31	ALA	0	0.029	0.024	13.341	-0.171	-0.171	0.000	0.000	0.000	0.000
30	A	32	ASP	-1	-0.805	-0.886	8.030	26.225	26.225	0.000	0.000	0.000	0.000
31	A	33	PHE	0	-0.001	-0.002	10.175	-0.056	-0.056	0.000	0.000	0.000	0.000
32	A	34	LYS	1	0.905	0.929	11.119	-15.090	-15.090	0.000	0.000	0.000	0.000
33	A	35	ASN	0	-0.092	-0.047	10.168	-1.114	-1.114	0.000	0.000	0.000	0.000
34	A	36	VAL	0	-0.068	-0.031	9.456	-0.128	-0.128	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.043	-0.010	12.267	-0.414	-0.414	0.000	0.000	0.000	0.000
36	A	38	SER	0	0.026	0.006	15.725	-0.915	-0.915	0.000	0.000	0.000	0.000
37	A	39	ASN	0	-0.031	-0.013	18.005	-0.189	-0.189	0.000	0.000	0.000	0.000
38	A	40	ARG	1	0.807	0.896	18.184	-14.951	-14.951	0.000	0.000	0.000	0.000
39	A	41	PRO	0	0.032	0.029	21.170	0.200	0.200	0.000	0.000	0.000	0.000
40	A	42	VAL	0	0.014	-0.018	18.008	-0.364	-0.364	0.000	0.000	0.000	0.000
41	A	43	HIS	0	-0.015	-0.008	21.034	0.297	0.297	0.000	0.000	0.000	0.000
42	A	44	ALA	0	-0.033	-0.007	23.879	-0.321	-0.321	0.000	0.000	0.000	0.000
43	A	45	TYR	0	-0.001	-0.007	21.565	-0.166	-0.166	0.000	0.000	0.000	0.000
44	A	46	LYS	1	0.785	0.876	23.024	-10.960	-10.960	0.000	0.000	0.000	0.000
45	A	47	PHE	0	-0.029	-0.008	16.875	0.406	0.406	0.000	0.000	0.000	0.000
46	A	48	PHE	0	0.015	0.013	19.771	-0.088	-0.088	0.000	0.000	0.000	0.000
47	A	49	PHE	0	0.018	-0.010	13.748	0.827	0.827	0.000	0.000	0.000	0.000
48	A	50	LYS	1	0.861	0.956	17.627	-15.498	-15.498	0.000	0.000	0.000	0.000
49	A	51	SER	0	-0.031	-0.044	17.193	0.880	0.880	0.000	0.000	0.000	0.000
50	A	52	MET	0	-0.037	-0.029	18.763	-0.638	-0.638	0.000	0.000	0.000	0.000
51	A	53	ASP	-1	-0.757	-0.879	20.652	11.824	11.824	0.000	0.000	0.000	0.000
52	A	54	GLN	0	-0.147	-0.081	23.492	-0.010	-0.010	0.000	0.000	0.000	0.000
53	A	55	ASP	-1	-0.860	-0.907	25.015	10.114	10.114	0.000	0.000	0.000	0.000
54	A	56	PHE	0	-0.075	-0.041	27.299	-0.458	-0.458	0.000	0.000	0.000	0.000
55	A	57	GLY	0	-0.031	-0.008	24.933	-0.090	-0.090	0.000	0.000	0.000	0.000
56	A	58	VAL	0	-0.061	-0.049	21.877	0.440	0.440	0.000	0.000	0.000	0.000
57	A	59	VAL	0	0.025	0.024	22.626	-0.547	-0.547	0.000	0.000	0.000	0.000
58	A	60	LYS	1	0.888	0.940	21.758	-11.080	-11.080	0.000	0.000	0.000	0.000
59	A	61	GLU	-1	-0.836	-0.885	19.859	14.085	14.085	0.000	0.000	0.000	0.000
60	A	62	GLU	-1	-0.807	-0.899	20.398	11.886	11.886	0.000	0.000	0.000	0.000
61	A	63	ILE	0	-0.031	-0.020	16.750	0.119	0.119	0.000	0.000	0.000	0.000
62	A	64	PHE	0	0.023	0.006	19.932	0.117	0.117	0.000	0.000	0.000	0.000
63	A	65	ASP	-1	-0.892	-0.925	19.934	12.706	12.706	0.000	0.000	0.000	0.000
64	A	66	ASP	-1	-0.840	-0.918	16.924	15.584	15.584	0.000	0.000	0.000	0.000
65	A	67	ASN	0	-0.035	-0.023	15.347	0.626	0.626	0.000	0.000	0.000	0.000
66	A	68	ALA	0	-0.010	0.000	16.121	0.377	0.377	0.000	0.000	0.000	0.000
67	A	69	LYS	1	0.940	0.951	12.411	-19.166	-19.166	0.000	0.000	0.000	0.000
68	A	70	LEU	0	0.013	0.017	10.286	-1.044	-1.044	0.000	0.000	0.000	0.000
69	A	71	PRO	0	-0.002	0.014	12.422	1.227	1.227	0.000	0.000	0.000	0.000
70	A	72	CYS	0	-0.022	0.001	9.700	1.052	1.052	0.000	0.000	0.000	0.000
71	A	73	PHE	0	0.029	0.003	12.642	-1.117	-1.117	0.000	0.000	0.000	0.000
72	A	74	ASN	0	-0.021	-0.025	14.194	0.266	0.266	0.000	0.000	0.000	0.000
73	A	75	GLY	0	0.028	0.011	9.751	0.308	0.308	0.000	0.000	0.000	0.000
74	A	76	ARG	1	0.923	0.960	8.940	-19.914	-19.914	0.000	0.000	0.000	0.000
75	A	77	VAL	0	0.051	0.040	9.471	-1.464	-1.464	0.000	0.000	0.000	0.000
76	A	78	VAL	0	-0.032	-0.019	11.854	0.136	0.136	0.000	0.000	0.000	0.000
77	A	79	SER	0	0.017	0.006	14.884	-0.587	-0.587	0.000	0.000	0.000	0.000
78	A	80	TRP	0	0.001	-0.010	16.703	-0.089	-0.089	0.000	0.000	0.000	0.000
79	A	81	LEU	0	0.020	0.024	17.046	0.033	0.033	0.000	0.000	0.000	0.000
80	A	82	VAL	0	0.016	0.004	20.985	-0.320	-0.320	0.000	0.000	0.000	0.000
81	A	83	LEU	0	0.067	0.042	24.615	0.170	0.170	0.000	0.000	0.000	0.000
82	A	84	ALA	0	-0.046	-0.010	27.032	-0.291	-0.291	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ASP)