FMO DATABASE

FMODB ID: 66MRZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-109534.777752
FMO2-HF: Nuclear repulsion	95027.133886
FMO2-HF: Total energy	-14507.643867
FMO2-MP2: Total energy	-14550.138278

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.
-4.26	-1.267	-0.018	-1.692	-1.281	0.005

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 : 0.002 / q_NPA : 0.000

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	-0.021	-0.003	3.872	-1.390	1.603	-0.018	-1.692	-1.281	0.005
4	B	15	ASN	0	-0.013	-0.009	6.288	-0.591	-0.591	0.000	0.000	0.000	0.000
5	B	16	ASP	-1	-0.904	-0.936	8.284	-1.514	-1.514	0.000	0.000	0.000	0.000
6	B	17	GLU	-1	-0.984	-1.000	10.257	-0.384	-0.384	0.000	0.000	0.000	0.000
7	B	18	LEU	0	-0.047	-0.029	13.865	-0.002	-0.002	0.000	0.000	0.000	0.000
8	B	19	ILE	0	0.011	0.009	17.410	0.022	0.022	0.000	0.000	0.000	0.000
9	B	20	SER	0	-0.018	-0.011	20.590	0.013	0.013	0.000	0.000	0.000	0.000
10	B	21	PHE	0	-0.004	0.013	22.446	0.008	0.008	0.000	0.000	0.000	0.000
11	B	22	LYS	1	0.767	0.859	26.525	0.134	0.134	0.000	0.000	0.000	0.000
12	B	23	ASP	-1	-0.823	-0.921	28.876	-0.115	-0.115	0.000	0.000	0.000	0.000
13	B	24	GLU	-1	-0.864	-0.949	27.656	-0.189	-0.189	0.000	0.000	0.000	0.000
14	B	25	GLY	0	-0.018	-0.005	30.861	0.006	0.006	0.000	0.000	0.000	0.000
15	B	26	GLU	-1	-0.800	-0.885	32.359	-0.106	-0.106	0.000	0.000	0.000	0.000
16	B	27	GLN	0	-0.053	-0.021	34.847	0.006	0.006	0.000	0.000	0.000	0.000
17	B	28	GLU	-1	-0.929	-0.953	36.752	-0.097	-0.097	0.000	0.000	0.000	0.000
18	B	29	GLU	-1	-0.918	-0.969	38.549	-0.083	-0.083	0.000	0.000	0.000	0.000
19	B	30	LYS	1	0.772	0.893	34.766	0.115	0.115	0.000	0.000	0.000	0.000
20	B	31	SER	0	-0.114	-0.064	40.478	0.003	0.003	0.000	0.000	0.000	0.000
21	B	32	SER	0	-0.045	-0.015	42.554	0.000	0.000	0.000	0.000	0.000	0.000
22	B	33	GLU	-1	-0.902	-0.938	44.329	-0.064	-0.064	0.000	0.000	0.000	0.000
23	B	34	ASN	0	0.017	0.000	44.923	-0.006	-0.006	0.000	0.000	0.000	0.000
24	B	35	SER	0	-0.002	0.004	45.205	0.004	0.004	0.000	0.000	0.000	0.000
25	B	36	SER	0	0.001	-0.006	47.013	0.001	0.001	0.000	0.000	0.000	0.000
26	B	37	ALA	0	0.062	0.020	47.681	-0.001	-0.001	0.000	0.000	0.000	0.000
27	B	38	GLU	-1	-0.789	-0.873	49.544	-0.049	-0.049	0.000	0.000	0.000	0.000
28	B	39	ARG	1	0.757	0.854	46.639	0.073	0.073	0.000	0.000	0.000	0.000
29	B	40	ASP	-1	-0.805	-0.868	48.537	-0.070	-0.070	0.000	0.000	0.000	0.000
30	B	41	LEU	0	-0.019	-0.027	49.453	0.001	0.001	0.000	0.000	0.000	0.000
31	B	42	ALA	0	-0.003	0.011	53.505	0.002	0.002	0.000	0.000	0.000	0.000
32	B	43	ASP	-1	-0.865	-0.924	56.514	-0.047	-0.047	0.000	0.000	0.000	0.000
33	B	44	VAL	0	-0.018	-0.004	52.278	0.002	0.002	0.000	0.000	0.000	0.000
34	B	45	LYS	1	0.810	0.874	54.994	0.050	0.050	0.000	0.000	0.000	0.000
35	B	46	SER	0	-0.033	-0.024	57.277	0.002	0.002	0.000	0.000	0.000	0.000
36	B	47	SER	0	-0.020	-0.011	58.103	0.002	0.002	0.000	0.000	0.000	0.000
37	B	48	LEU	0	-0.063	-0.011	55.116	0.001	0.001	0.000	0.000	0.000	0.000
38	B	49	VAL	0	-0.096	-0.049	58.745	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)