FMO DATABASE

FMODB ID: LZ7Q9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-561957.969678
FMO2-HF: Nuclear repulsion	528743.887564
FMO2-HF: Total energy	-33214.082114
FMO2-MP2: Total energy	-33311.073611

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.
19.885	7.778	37.391	-10.819	-14.467	-0.051

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 : -0.941 / q_NPA : -0.960

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	0.918	0.949	3.814	-34.385	-31.967	-0.038	-1.301	-1.080	0.002
4	A	6	ILE	0	0.018	0.020	7.012	-1.717	-1.717	0.000	0.000	0.000	0.000
5	A	7	ILE	0	-0.019	-0.013	9.926	-0.063	-0.063	0.000	0.000	0.000	0.000
6	A	8	TYR	0	-0.028	-0.029	13.347	-0.289	-0.289	0.000	0.000	0.000	0.000
7	A	9	HIS	0	-0.018	-0.003	16.010	-0.282	-0.282	0.000	0.000	0.000	0.000
8	A	10	MET	0	0.017	0.007	19.121	0.282	0.282	0.000	0.000	0.000	0.000
9	A	11	ASP	-1	-0.894	-0.958	22.339	11.386	11.386	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-1.016	-1.001	25.865	9.685	9.685	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.888	-0.952	21.551	13.365	13.365	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.974	-0.972	25.153	10.139	10.139	0.000	0.000	0.000	0.000
13	A	15	THR	0	-0.072	-0.045	21.491	-0.020	-0.020	0.000	0.000	0.000	0.000
14	A	16	PRO	0	-0.031	-0.008	17.804	0.089	0.089	0.000	0.000	0.000	0.000
15	A	17	ASP	-1	-0.832	-0.901	15.625	15.873	15.873	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.064	-0.054	10.223	1.088	1.088	0.000	0.000	0.000	0.000
17	A	19	VAL	0	-0.034	-0.004	8.862	0.239	0.239	0.000	0.000	0.000	0.000
18	A	20	LYS	1	0.901	0.926	4.926	-26.801	-26.786	-0.001	-0.008	-0.006	0.000
19	A	21	LEU	0	0.004	0.009	4.343	-2.913	-2.505	-0.001	-0.145	-0.262	0.000
20	A	22	PRO	0	0.043	0.009	2.087	15.328	8.564	12.919	-2.925	-3.231	-0.019
21	A	23	VAL	0	0.017	0.028	2.132	17.537	12.187	14.151	-3.611	-5.189	-0.019
22	A	24	ALA	0	0.043	0.022	1.876	0.472	-0.100	9.332	-5.309	-3.452	-0.016
23	A	25	PRO	0	0.020	-0.007	2.403	-5.175	-7.604	1.030	2.486	-1.087	0.001
24	A	26	GLU	-1	-0.865	-0.923	5.295	31.804	31.971	-0.001	-0.006	-0.160	0.000
25	A	27	ARG	1	0.841	0.920	6.554	-26.814	-26.814	0.000	0.000	0.000	0.000
26	A	28	VAL	0	0.037	0.009	6.257	-0.853	-0.853	0.000	0.000	0.000	0.000
27	A	29	THR	0	-0.068	-0.036	8.124	-2.674	-2.674	0.000	0.000	0.000	0.000
28	A	30	LEU	0	0.041	0.017	11.159	0.822	0.822	0.000	0.000	0.000	0.000
29	A	31	ALA	0	0.033	0.023	13.301	-0.204	-0.204	0.000	0.000	0.000	0.000
30	A	32	ASP	-1	-0.810	-0.898	8.012	27.705	27.705	0.000	0.000	0.000	0.000
31	A	33	PHE	0	0.000	-0.002	10.135	-0.136	-0.136	0.000	0.000	0.000	0.000
32	A	34	LYS	1	0.948	0.970	11.039	-15.299	-15.299	0.000	0.000	0.000	0.000
33	A	35	ASN	0	-0.098	-0.048	10.206	-1.152	-1.152	0.000	0.000	0.000	0.000
34	A	36	VAL	0	-0.034	-0.022	9.215	-0.151	-0.151	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.066	-0.021	12.195	-0.565	-0.565	0.000	0.000	0.000	0.000
36	A	38	SER	0	0.046	0.015	15.641	-0.915	-0.915	0.000	0.000	0.000	0.000
37	A	39	ASN	0	-0.042	-0.013	17.939	-0.118	-0.118	0.000	0.000	0.000	0.000
38	A	40	ARG	1	0.923	0.967	18.028	-15.007	-15.007	0.000	0.000	0.000	0.000
39	A	41	PRO	0	0.033	0.030	21.082	0.232	0.232	0.000	0.000	0.000	0.000
40	A	42	VAL	0	0.028	-0.011	17.898	-0.379	-0.379	0.000	0.000	0.000	0.000
41	A	43	HIS	0	-0.033	-0.018	20.955	0.313	0.313	0.000	0.000	0.000	0.000
42	A	44	ALA	0	-0.025	-0.003	23.807	-0.317	-0.317	0.000	0.000	0.000	0.000
43	A	45	TYR	0	0.004	-0.008	21.484	-0.190	-0.190	0.000	0.000	0.000	0.000
44	A	46	LYS	1	0.876	0.932	22.931	-10.859	-10.859	0.000	0.000	0.000	0.000
45	A	47	PHE	0	-0.032	-0.005	16.445	0.461	0.461	0.000	0.000	0.000	0.000
46	A	48	PHE	0	0.011	0.012	19.673	-0.067	-0.067	0.000	0.000	0.000	0.000
47	A	49	PHE	0	0.031	-0.015	13.385	0.798	0.798	0.000	0.000	0.000	0.000
48	A	50	LYS	1	0.877	0.958	17.550	-15.428	-15.428	0.000	0.000	0.000	0.000
49	A	51	SER	0	-0.013	-0.013	17.059	0.870	0.870	0.000	0.000	0.000	0.000
50	A	52	MET	0	-0.032	-0.024	18.783	-0.668	-0.668	0.000	0.000	0.000	0.000
51	A	53	ASP	-1	-0.768	-0.889	20.744	11.836	11.836	0.000	0.000	0.000	0.000
52	A	54	GLN	0	-0.097	-0.039	23.527	-0.440	-0.440	0.000	0.000	0.000	0.000
53	A	55	ASP	-1	-0.890	-0.930	25.104	10.247	10.247	0.000	0.000	0.000	0.000
54	A	56	PHE	0	-0.087	-0.049	27.402	-0.472	-0.472	0.000	0.000	0.000	0.000
55	A	57	GLY	0	-0.030	-0.008	25.009	-0.093	-0.093	0.000	0.000	0.000	0.000
56	A	58	VAL	0	-0.056	-0.043	22.246	0.437	0.437	0.000	0.000	0.000	0.000
57	A	59	VAL	0	0.029	0.022	22.550	-0.535	-0.535	0.000	0.000	0.000	0.000
58	A	60	LYS	1	0.894	0.937	21.658	-10.973	-10.973	0.000	0.000	0.000	0.000
59	A	61	GLU	-1	-0.854	-0.917	19.608	14.004	14.004	0.000	0.000	0.000	0.000
60	A	62	GLU	-1	-0.871	-0.944	20.309	12.145	12.145	0.000	0.000	0.000	0.000
61	A	63	ILE	0	-0.032	-0.023	16.680	0.136	0.136	0.000	0.000	0.000	0.000
62	A	64	PHE	0	0.000	-0.009	19.858	0.134	0.134	0.000	0.000	0.000	0.000
63	A	65	ASP	-1	-0.896	-0.921	19.836	12.975	12.975	0.000	0.000	0.000	0.000
64	A	66	ASP	-1	-0.888	-0.959	16.897	15.909	15.909	0.000	0.000	0.000	0.000
65	A	67	ASN	0	-0.041	-0.030	15.319	0.786	0.786	0.000	0.000	0.000	0.000
66	A	68	ALA	0	-0.014	0.000	15.942	0.420	0.420	0.000	0.000	0.000	0.000
67	A	69	LYS	1	0.927	0.945	11.825	-19.487	-19.487	0.000	0.000	0.000	0.000
68	A	70	LEU	0	0.020	0.017	10.356	-1.136	-1.136	0.000	0.000	0.000	0.000
69	A	71	PRO	0	-0.008	0.017	12.012	1.172	1.172	0.000	0.000	0.000	0.000
70	A	72	CYS	0	0.002	0.000	9.222	0.904	0.904	0.000	0.000	0.000	0.000
71	A	73	PHE	0	-0.004	-0.004	12.674	-1.074	-1.074	0.000	0.000	0.000	0.000
72	A	74	ASN	0	-0.019	-0.021	14.209	0.253	0.253	0.000	0.000	0.000	0.000
73	A	75	GLY	0	0.012	0.008	9.774	0.256	0.256	0.000	0.000	0.000	0.000
74	A	76	ARG	1	0.926	0.960	8.964	-20.140	-20.140	0.000	0.000	0.000	0.000
75	A	77	VAL	0	0.067	0.048	9.562	-1.481	-1.481	0.000	0.000	0.000	0.000
76	A	78	VAL	0	-0.049	-0.026	11.752	0.115	0.115	0.000	0.000	0.000	0.000
77	A	79	SER	0	0.008	0.004	14.935	-0.602	-0.602	0.000	0.000	0.000	0.000
78	A	80	TRP	0	-0.019	-0.017	16.586	-0.069	-0.069	0.000	0.000	0.000	0.000
79	A	81	LEU	0	0.012	0.014	16.941	0.060	0.060	0.000	0.000	0.000	0.000
80	A	82	VAL	0	0.036	0.019	20.873	-0.328	-0.328	0.000	0.000	0.000	0.000
81	A	83	LEU	0	0.050	0.032	24.507	0.192	0.192	0.000	0.000	0.000	0.000
82	A	84	ALA	0	-0.051	-0.012	26.930	-0.313	-0.313	0.000	0.000	0.000	0.000

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