FMO DATABASE

FMODB ID: ZY3NN

Calculation Name: 3OUX-B-Xray372

Preferred Name: Catenin beta-1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3OUX

Chain ID: B

ChEMBL ID: CHEMBL4105846

UniProt ID: Q02248

Base Structure: X-ray

Registration Date: 2023-06-20

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	50
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-163798.218119
FMO2-HF: Nuclear repulsion	143926.345438
FMO2-HF: Total energy	-19871.872681
FMO2-MP2: Total energy	-19928.365297

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:11:GLY)

Summations of interaction energy for fragment #1(B:11:GLY)

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.
-0.165	1.322	-0.01	-0.693	-0.785	0.003

Interaction energy analysis for fragmet #1(B:11:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.008

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	13	PRO	0	-0.048	-0.037	3.795	0.738	2.225	-0.010	-0.693	-0.785	0.003
4	B	14	GLU	-1	-0.921	-0.957	6.009	-0.581	-0.581	0.000	0.000	0.000	0.000
5	B	15	LEU	0	-0.042	-0.020	5.608	0.390	0.390	0.000	0.000	0.000	0.000
6	B	16	CYS	0	-0.060	-0.033	9.051	0.281	0.281	0.000	0.000	0.000	0.000
7	B	17	ALA	0	-0.029	0.000	12.060	0.127	0.127	0.000	0.000	0.000	0.000
8	B	18	THR	0	-0.016	-0.001	13.920	0.026	0.026	0.000	0.000	0.000	0.000
9	B	19	ASP	-1	-0.926	-0.955	15.465	-0.565	-0.565	0.000	0.000	0.000	0.000
10	B	20	GLU	-1	-1.002	-1.005	17.717	-0.321	-0.321	0.000	0.000	0.000	0.000
11	B	21	MET	0	-0.048	-0.031	21.216	0.012	0.012	0.000	0.000	0.000	0.000
12	B	22	ILE	0	0.034	0.025	24.211	-0.005	-0.005	0.000	0.000	0.000	0.000
13	B	23	PRO	0	-0.062	-0.036	26.967	0.012	0.012	0.000	0.000	0.000	0.000
14	B	24	PHE	0	0.024	0.010	28.084	0.005	0.005	0.000	0.000	0.000	0.000
15	B	25	LYS	1	0.900	0.937	32.564	0.130	0.130	0.000	0.000	0.000	0.000
16	B	26	ASP	-1	-0.856	-0.901	36.298	-0.087	-0.087	0.000	0.000	0.000	0.000
17	B	27	GLU	-1	-0.997	-1.005	34.559	-0.137	-0.137	0.000	0.000	0.000	0.000
18	B	28	GLY	0	-0.033	-0.011	38.995	0.000	0.000	0.000	0.000	0.000	0.000
19	B	29	ASP	-1	-0.892	-0.967	39.846	-0.078	-0.078	0.000	0.000	0.000	0.000
20	B	30	PRO	0	0.078	0.030	41.429	-0.001	-0.001	0.000	0.000	0.000	0.000
21	B	31	GLN	0	0.005	-0.002	43.653	0.004	0.004	0.000	0.000	0.000	0.000
22	B	32	LYS	1	0.848	0.927	38.326	0.104	0.104	0.000	0.000	0.000	0.000
23	B	33	GLU	-1	-0.869	-0.926	37.238	-0.108	-0.108	0.000	0.000	0.000	0.000
24	B	34	LYS	1	0.845	0.934	39.662	0.067	0.067	0.000	0.000	0.000	0.000
25	B	35	ILE	0	-0.026	-0.012	40.417	-0.004	-0.004	0.000	0.000	0.000	0.000
26	B	36	PHE	0	-0.026	-0.014	41.051	0.002	0.002	0.000	0.000	0.000	0.000
27	B	37	ALA	0	-0.036	-0.022	42.802	0.002	0.002	0.000	0.000	0.000	0.000
28	B	38	GLU	-1	-0.902	-0.953	45.208	-0.044	-0.044	0.000	0.000	0.000	0.000
29	B	39	ILE	0	-0.049	-0.036	45.151	0.002	0.002	0.000	0.000	0.000	0.000
30	B	40	SER	0	-0.012	-0.012	49.653	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	41	HIS	0	-0.021	0.000	48.982	0.003	0.003	0.000	0.000	0.000	0.000
32	B	42	PRO	0	-0.002	0.023	52.959	0.001	0.001	0.000	0.000	0.000	0.000
33	B	43	GLU	-1	-0.971	-0.994	54.791	-0.032	-0.032	0.000	0.000	0.000	0.000
34	B	44	GLU	-1	-0.889	-0.954	54.286	-0.037	-0.037	0.000	0.000	0.000	0.000
35	B	45	GLU	-1	-0.971	-0.982	57.235	-0.030	-0.030	0.000	0.000	0.000	0.000
36	B	46	GLY	0	-0.038	-0.029	59.418	0.000	0.000	0.000	0.000	0.000	0.000
37	B	47	ASP	-1	-0.836	-0.918	54.301	-0.030	-0.030	0.000	0.000	0.000	0.000
38	B	48	LEU	0	-0.006	-0.024	54.743	0.002	0.002	0.000	0.000	0.000	0.000
39	B	49	ALA	0	-0.029	-0.016	58.443	0.001	0.001	0.000	0.000	0.000	0.000
40	B	50	ASP	-1	-0.882	-0.942	60.708	-0.020	-0.020	0.000	0.000	0.000	0.000
41	B	51	ILE	0	-0.015	-0.005	56.745	0.001	0.001	0.000	0.000	0.000	0.000
42	B	52	LYS	1	0.868	0.932	60.596	0.027	0.027	0.000	0.000	0.000	0.000
43	B	53	SER	0	-0.020	-0.007	62.583	0.001	0.001	0.000	0.000	0.000	0.000
44	B	54	SER	0	-0.003	0.002	62.404	0.001	0.001	0.000	0.000	0.000	0.000
45	B	55	LEU	0	-0.027	-0.024	59.870	0.001	0.001	0.000	0.000	0.000	0.000
46	B	56	VAL	0	-0.042	-0.012	64.074	0.000	0.000	0.000	0.000	0.000	0.000
47	B	57	ASN	0	-0.009	0.000	67.488	0.000	0.000	0.000	0.000	0.000	0.000
48	B	58	GLU	-1	-0.946	-0.971	62.971	-0.012	-0.012	0.000	0.000	0.000	0.000
49	B	59	SER	0	-0.096	-0.011	67.499	0.001	0.001	0.000	0.000	0.000	0.000
50	B	60	GLU	-1	-1.033	-1.025	69.233	-0.013	-0.013	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:11:GLY)