FMO DATABASE

FMODB ID: M364Z

Calculation Name: 1T08-B-Xray319

Preferred Name: Adenomatous polyposis coli protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1T08

Chain ID: B

ChEMBL ID: CHEMBL3233

UniProt ID: P25054

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

Apendix: None

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	46
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-215599.563746
FMO2-HF: Nuclear repulsion	196807.592127
FMO2-HF: Total energy	-18791.971619
FMO2-MP2: Total energy	-18845.135219

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:8:GLY )

Summations of interaction energy for fragment #1(B:8: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.
0.619	2.063	9.111	-6.164	-4.392	-0.015

Interaction energy analysis for fragmet #1(B:8:GLY )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.026

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	B	10	SER	0	0.078	0.036	3.427	-0.120	1.871	-0.005	-0.995	-0.991	-0.001
4	B	11	PRO	0	0.048	0.013	4.601	-0.417	-0.258	0.000	-0.014	-0.145	0.000
5	B	12	GLU	-1	-0.916	-0.945	7.016	0.021	0.021	0.000	0.000	0.000	0.000
6	B	13	GLU	-1	-0.851	-0.937	2.503	0.327	1.539	1.057	-1.288	-0.982	-0.009
7	B	14	MET	0	-0.053	-0.019	2.456	0.569	-1.432	8.057	-3.819	-2.238	-0.005
8	B	15	TYR	0	0.005	0.007	4.167	0.131	0.145	0.002	-0.020	0.005	0.000
9	B	16	ILE	0	0.019	0.007	6.405	0.060	0.060	0.000	0.000	0.000	0.000
10	B	17	GLN	0	0.014	0.014	4.247	-0.243	-0.174	0.000	-0.028	-0.041	0.000
11	B	18	GLN	0	-0.024	-0.026	6.666	-0.070	-0.070	0.000	0.000	0.000	0.000
12	B	19	LYS	1	0.958	1.001	8.889	0.011	0.011	0.000	0.000	0.000	0.000
13	B	20	VAL	0	0.001	0.009	9.706	-0.001	-0.001	0.000	0.000	0.000	0.000
14	B	21	ARG	1	0.975	0.998	7.489	0.100	0.100	0.000	0.000	0.000	0.000
15	B	22	VAL	0	-0.030	-0.020	11.991	-0.003	-0.003	0.000	0.000	0.000	0.000
16	B	23	LEU	0	0.008	0.006	14.755	0.005	0.005	0.000	0.000	0.000	0.000
17	B	24	LEU	0	-0.003	0.001	13.327	0.001	0.001	0.000	0.000	0.000	0.000
18	B	25	MET	0	-0.009	-0.006	16.297	0.002	0.002	0.000	0.000	0.000	0.000
19	B	26	LEU	0	0.014	-0.008	18.089	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	27	ARG	1	0.995	1.004	19.129	-0.072	-0.072	0.000	0.000	0.000	0.000
21	B	28	LYS	1	0.903	0.965	20.084	-0.017	-0.017	0.000	0.000	0.000	0.000
22	B	29	MET	0	-0.094	-0.048	21.004	-0.005	-0.005	0.000	0.000	0.000	0.000
23	B	30	GLY	0	0.005	0.012	24.193	-0.003	-0.003	0.000	0.000	0.000	0.000
24	B	31	SER	0	-0.049	-0.005	24.217	-0.003	-0.003	0.000	0.000	0.000	0.000
25	B	32	ASN	0	-0.025	-0.024	24.520	0.009	0.009	0.000	0.000	0.000	0.000
26	B	33	LEU	0	-0.005	0.010	19.500	-0.005	-0.005	0.000	0.000	0.000	0.000
27	B	34	THR	0	-0.003	-0.008	21.866	0.003	0.003	0.000	0.000	0.000	0.000
28	B	35	ALA	0	0.074	0.023	22.701	0.008	0.008	0.000	0.000	0.000	0.000
29	B	36	SER	0	0.029	0.005	20.481	0.011	0.011	0.000	0.000	0.000	0.000
30	B	37	GLU	-1	-0.882	-0.934	18.165	0.015	0.015	0.000	0.000	0.000	0.000
31	B	38	GLU	-1	-0.906	-0.962	18.162	0.080	0.080	0.000	0.000	0.000	0.000
32	B	39	GLU	-1	-0.983	-0.996	19.154	0.093	0.093	0.000	0.000	0.000	0.000
33	B	40	PHE	0	-0.018	-0.013	10.793	0.021	0.021	0.000	0.000	0.000	0.000
34	B	41	LEU	0	0.027	-0.010	14.165	0.034	0.034	0.000	0.000	0.000	0.000
35	B	42	ARG	1	0.915	0.978	15.497	-0.071	-0.071	0.000	0.000	0.000	0.000
36	B	43	THR	0	-0.008	-0.003	13.664	0.027	0.027	0.000	0.000	0.000	0.000
37	B	44	TYR	0	-0.024	-0.015	10.107	0.058	0.058	0.000	0.000	0.000	0.000
38	B	45	ALA	0	0.079	0.033	11.938	0.025	0.025	0.000	0.000	0.000	0.000
39	B	46	GLY	0	-0.008	0.010	11.379	0.005	0.005	0.000	0.000	0.000	0.000
40	B	47	VAL	0	0.010	-0.004	6.985	0.044	0.044	0.000	0.000	0.000	0.000
41	B	48	VAL	0	-0.031	-0.018	8.949	-0.065	-0.065	0.000	0.000	0.000	0.000
42	B	49	ASN	0	0.011	-0.025	12.077	-0.048	-0.048	0.000	0.000	0.000	0.000
43	B	50	SER	0	-0.049	-0.013	8.221	0.071	0.071	0.000	0.000	0.000	0.000
44	B	51	GLN	0	-0.052	-0.027	7.627	-0.101	-0.101	0.000	0.000	0.000	0.000
45	B	52	LEU	0	-0.083	-0.026	10.426	-0.053	-0.053	0.000	0.000	0.000	0.000
46	B	53	SER	-1	-0.975	-0.973	13.084	0.187	0.187	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:8:GLY )