FMO DATABASE

FMODB ID: 14R8Z

Calculation Name: 1T08-B-Xray372

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: 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:

Apendix: None

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	46
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-215802.722466
FMO2-HF: Nuclear repulsion	197009.84456
FMO2-HF: Total energy	-18792.877906
FMO2-MP2: Total energy	-18846.013592

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.
1.178	4.655	4.868	-4.311	-4.035	-0.02

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 : -0.008 / q_NPA : -0.019

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	10	SER	0	0.071	0.035	3.440	0.041	1.963	-0.013	-0.949	-0.960	0.000
4	B	11	PRO	0	0.060	0.017	4.600	-0.422	-0.262	-0.001	-0.013	-0.146	0.000
5	B	12	GLU	-1	-0.920	-0.947	7.011	0.043	0.043	0.000	0.000	0.000	0.000
6	B	13	GLU	-1	-0.789	-0.883	2.319	2.169	3.072	2.738	-2.048	-1.593	-0.016
7	B	14	MET	0	-0.043	-0.020	3.000	-0.389	0.024	2.144	-1.258	-1.299	-0.004
8	B	15	TYR	0	0.031	0.015	4.164	0.152	0.158	0.001	-0.016	0.009	0.000
9	B	16	ILE	0	0.011	0.004	6.422	0.066	0.066	0.000	0.000	0.000	0.000
10	B	17	GLN	0	0.045	0.031	4.076	-0.283	-0.210	-0.001	-0.027	-0.046	0.000
11	B	18	GLN	0	-0.012	-0.017	6.670	-0.074	-0.074	0.000	0.000	0.000	0.000
12	B	19	LYS	1	0.968	1.005	8.891	-0.029	-0.029	0.000	0.000	0.000	0.000
13	B	20	VAL	0	0.005	0.007	9.753	-0.009	-0.009	0.000	0.000	0.000	0.000
14	B	21	ARG	1	0.900	0.954	7.269	-0.037	-0.037	0.000	0.000	0.000	0.000
15	B	22	VAL	0	-0.019	-0.012	11.983	-0.010	-0.010	0.000	0.000	0.000	0.000
16	B	23	LEU	0	-0.004	0.001	14.754	0.000	0.000	0.000	0.000	0.000	0.000
17	B	24	LEU	0	0.009	0.004	13.081	-0.002	-0.002	0.000	0.000	0.000	0.000
18	B	25	MET	0	-0.009	-0.005	16.294	-0.002	-0.002	0.000	0.000	0.000	0.000
19	B	26	LEU	0	0.000	0.002	18.079	-0.004	-0.004	0.000	0.000	0.000	0.000
20	B	27	ARG	1	0.900	0.919	19.384	-0.093	-0.093	0.000	0.000	0.000	0.000
21	B	28	LYS	1	0.905	0.963	20.024	-0.036	-0.036	0.000	0.000	0.000	0.000
22	B	29	MET	0	-0.092	-0.051	20.732	-0.006	-0.006	0.000	0.000	0.000	0.000
23	B	30	GLY	0	0.011	0.014	24.182	-0.004	-0.004	0.000	0.000	0.000	0.000
24	B	31	SER	0	-0.041	-0.002	24.207	-0.004	-0.004	0.000	0.000	0.000	0.000
25	B	32	ASN	0	-0.021	-0.021	24.520	0.010	0.010	0.000	0.000	0.000	0.000
26	B	33	LEU	0	-0.010	0.007	19.340	-0.005	-0.005	0.000	0.000	0.000	0.000
27	B	34	THR	0	-0.017	-0.043	21.912	0.002	0.002	0.000	0.000	0.000	0.000
28	B	35	ALA	0	0.055	0.014	22.694	0.009	0.009	0.000	0.000	0.000	0.000
29	B	36	SER	0	0.018	0.004	20.521	0.008	0.008	0.000	0.000	0.000	0.000
30	B	37	GLU	-1	-0.834	-0.891	18.161	0.037	0.037	0.000	0.000	0.000	0.000
31	B	38	GLU	-1	-0.829	-0.891	18.156	0.115	0.115	0.000	0.000	0.000	0.000
32	B	39	GLU	-1	-0.846	-0.921	19.341	0.129	0.129	0.000	0.000	0.000	0.000
33	B	40	PHE	0	-0.055	-0.026	10.821	0.026	0.026	0.000	0.000	0.000	0.000
34	B	41	LEU	0	0.027	-0.010	14.632	0.041	0.041	0.000	0.000	0.000	0.000
35	B	42	ARG	1	0.849	0.938	15.520	-0.089	-0.089	0.000	0.000	0.000	0.000
36	B	43	THR	0	-0.019	-0.015	13.862	0.028	0.028	0.000	0.000	0.000	0.000
37	B	44	TYR	0	-0.020	-0.011	9.878	0.043	0.043	0.000	0.000	0.000	0.000
38	B	45	ALA	0	0.090	0.040	11.963	0.035	0.035	0.000	0.000	0.000	0.000
39	B	46	GLY	0	-0.005	0.011	11.410	0.004	0.004	0.000	0.000	0.000	0.000
40	B	47	VAL	0	0.009	0.000	6.846	0.045	0.045	0.000	0.000	0.000	0.000
41	B	48	VAL	0	-0.014	-0.008	8.972	-0.060	-0.060	0.000	0.000	0.000	0.000
42	B	49	ASN	0	0.032	-0.008	12.092	-0.058	-0.058	0.000	0.000	0.000	0.000
43	B	50	SER	0	-0.042	-0.017	8.288	0.056	0.056	0.000	0.000	0.000	0.000
44	B	51	GLN	0	-0.067	-0.031	8.576	-0.138	-0.138	0.000	0.000	0.000	0.000
45	B	52	LEU	0	-0.030	0.005	10.423	-0.057	-0.057	0.000	0.000	0.000	0.000
46	B	53	SER	0	-0.077	-0.031	12.716	-0.070	-0.070	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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