FMO DATABASE

FMODB ID: 22Y5R

Calculation Name: 1JDH-B-Xray372

Preferred Name: Catenin beta-1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1JDH

Chain ID: B

ChEMBL ID: CHEMBL5866

UniProt ID: P35222

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	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	38
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-109642.775767
FMO2-HF: Nuclear repulsion	95135.272548
FMO2-HF: Total energy	-14507.503219
FMO2-MP2: Total energy	-14550.013746

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:12:LEU)

Summations of interaction energy for fragment #1(B:12:LEU)

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.
-5.979	-2.266	-0.024	-2.049	-1.639	0.008

Interaction energy analysis for fragmet #1(B:12:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.003

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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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	14	ALA	0	-0.038	-0.015	3.788	-2.801	0.912	-0.024	-2.049	-1.639	0.008
4	B	15	ASN	0	0.003	0.002	6.341	-0.757	-0.757	0.000	0.000	0.000	0.000
5	B	16	ASP	-1	-0.910	-0.944	7.987	-1.526	-1.526	0.000	0.000	0.000	0.000
6	B	17	GLU	-1	-0.982	-1.001	10.355	-0.461	-0.461	0.000	0.000	0.000	0.000
7	B	18	LEU	0	-0.057	-0.025	13.915	0.012	0.012	0.000	0.000	0.000	0.000
8	B	19	ILE	0	0.021	0.012	17.307	0.011	0.011	0.000	0.000	0.000	0.000
9	B	20	SER	0	-0.054	-0.019	20.411	0.016	0.016	0.000	0.000	0.000	0.000
10	B	21	PHE	0	0.017	0.002	22.661	-0.002	-0.002	0.000	0.000	0.000	0.000
11	B	22	LYS	1	0.785	0.886	26.853	0.152	0.152	0.000	0.000	0.000	0.000
12	B	23	ASP	-1	-0.845	-0.932	29.161	-0.135	-0.135	0.000	0.000	0.000	0.000
13	B	24	GLU	-1	-0.873	-0.952	27.691	-0.207	-0.207	0.000	0.000	0.000	0.000
14	B	25	GLY	0	-0.030	-0.015	30.978	0.008	0.008	0.000	0.000	0.000	0.000
15	B	26	GLU	-1	-0.803	-0.889	32.614	-0.121	-0.121	0.000	0.000	0.000	0.000
16	B	27	GLN	0	-0.025	-0.011	34.849	0.006	0.006	0.000	0.000	0.000	0.000
17	B	28	GLU	-1	-0.919	-0.953	36.741	-0.104	-0.104	0.000	0.000	0.000	0.000
18	B	29	GLU	-1	-0.928	-0.967	38.087	-0.098	-0.098	0.000	0.000	0.000	0.000
19	B	30	LYS	1	0.802	0.919	35.088	0.125	0.125	0.000	0.000	0.000	0.000
20	B	31	SER	0	-0.112	-0.068	40.350	0.004	0.004	0.000	0.000	0.000	0.000
21	B	32	SER	0	-0.063	-0.026	42.395	0.003	0.003	0.000	0.000	0.000	0.000
22	B	33	GLU	-1	-0.898	-0.933	44.189	-0.071	-0.071	0.000	0.000	0.000	0.000
23	B	34	ASN	0	0.007	-0.010	44.987	-0.006	-0.006	0.000	0.000	0.000	0.000
24	B	35	SER	0	0.000	0.003	45.512	0.005	0.005	0.000	0.000	0.000	0.000
25	B	36	SER	0	0.009	0.004	47.257	0.001	0.001	0.000	0.000	0.000	0.000
26	B	37	ALA	0	0.035	0.002	47.969	-0.001	-0.001	0.000	0.000	0.000	0.000
27	B	38	GLU	-1	-0.785	-0.877	50.010	-0.053	-0.053	0.000	0.000	0.000	0.000
28	B	39	ARG	1	0.778	0.870	46.925	0.078	0.078	0.000	0.000	0.000	0.000
29	B	40	ASP	-1	-0.806	-0.883	49.253	-0.073	-0.073	0.000	0.000	0.000	0.000
30	B	41	LEU	0	-0.006	-0.013	49.453	0.001	0.001	0.000	0.000	0.000	0.000
31	B	42	ALA	0	-0.018	0.006	53.458	0.002	0.002	0.000	0.000	0.000	0.000
32	B	43	ASP	-1	-0.865	-0.944	56.663	-0.050	-0.050	0.000	0.000	0.000	0.000
33	B	44	VAL	0	-0.025	-0.010	52.366	0.001	0.001	0.000	0.000	0.000	0.000
34	B	45	LYS	1	0.799	0.873	55.376	0.054	0.054	0.000	0.000	0.000	0.000
35	B	46	SER	0	-0.021	-0.006	57.565	0.002	0.002	0.000	0.000	0.000	0.000
36	B	47	SER	0	-0.009	-0.008	58.106	0.002	0.002	0.000	0.000	0.000	0.000
37	B	48	LEU	0	-0.082	-0.026	55.352	0.001	0.001	0.000	0.000	0.000	0.000
38	B	49	VAL	0	-0.077	-0.025	58.866	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:12:LEU)