FMO DATABASE

FMODB ID: VRMJ1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-215708.96204
FMO2-HF: Nuclear repulsion	196916.419146
FMO2-HF: Total energy	-18792.542894
FMO2-MP2: Total energy	-18845.693603

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.
0.229	1.684	9.189	-6.206	-4.438	-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 : -0.004 / q_NPA : -0.029

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	0.081	0.039	3.427	-0.122	1.913	-0.014	-0.999	-1.022	-0.001
4	B	11	PRO	0	0.050	0.014	4.601	-0.440	-0.286	-0.001	-0.012	-0.141	0.000
5	B	12	GLU	-1	-0.914	-0.944	7.016	0.000	0.000	0.000	0.000	0.000	0.000
6	B	13	GLU	-1	-0.853	-0.938	2.503	0.233	1.443	1.067	-1.292	-0.985	-0.009
7	B	14	MET	0	-0.054	-0.020	2.435	0.599	-1.433	8.137	-3.856	-2.249	-0.005
8	B	15	TYR	0	0.007	0.008	4.167	0.150	0.163	0.001	-0.020	0.006	0.000
9	B	16	ILE	0	0.021	0.009	6.405	0.065	0.065	0.000	0.000	0.000	0.000
10	B	17	GLN	0	0.009	0.010	4.246	-0.253	-0.178	-0.001	-0.027	-0.047	0.000
11	B	18	GLN	0	-0.022	-0.025	6.667	-0.068	-0.068	0.000	0.000	0.000	0.000
12	B	19	LYS	1	0.964	1.005	8.889	0.004	0.004	0.000	0.000	0.000	0.000
13	B	20	VAL	0	0.001	0.009	9.706	-0.002	-0.002	0.000	0.000	0.000	0.000
14	B	21	ARG	1	0.965	0.992	7.487	0.058	0.058	0.000	0.000	0.000	0.000
15	B	22	VAL	0	-0.025	-0.017	11.991	-0.004	-0.004	0.000	0.000	0.000	0.000
16	B	23	LEU	0	0.009	0.008	14.756	0.003	0.003	0.000	0.000	0.000	0.000
17	B	24	LEU	0	-0.005	-0.002	13.328	0.000	0.000	0.000	0.000	0.000	0.000
18	B	25	MET	0	-0.013	-0.008	16.297	0.002	0.002	0.000	0.000	0.000	0.000
19	B	26	LEU	0	0.021	-0.005	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	-0.082	-0.082	0.000	0.000	0.000	0.000
21	B	28	LYS	1	0.898	0.961	20.084	-0.027	-0.027	0.000	0.000	0.000	0.000
22	B	29	MET	0	-0.094	-0.047	21.004	-0.005	-0.005	0.000	0.000	0.000	0.000
23	B	30	GLY	0	0.010	0.014	24.192	-0.004	-0.004	0.000	0.000	0.000	0.000
24	B	31	SER	0	-0.046	-0.002	24.218	-0.003	-0.003	0.000	0.000	0.000	0.000
25	B	32	ASN	0	-0.023	-0.023	24.521	0.009	0.009	0.000	0.000	0.000	0.000
26	B	33	LEU	0	-0.010	0.007	19.500	-0.005	-0.005	0.000	0.000	0.000	0.000
27	B	34	THR	0	0.004	-0.004	21.866	0.003	0.003	0.000	0.000	0.000	0.000
28	B	35	ALA	0	0.074	0.024	22.701	0.008	0.008	0.000	0.000	0.000	0.000
29	B	36	SER	0	0.030	0.005	20.481	0.011	0.011	0.000	0.000	0.000	0.000
30	B	37	GLU	-1	-0.883	-0.935	18.165	0.020	0.020	0.000	0.000	0.000	0.000
31	B	38	GLU	-1	-0.905	-0.962	18.162	0.087	0.087	0.000	0.000	0.000	0.000
32	B	39	GLU	-1	-0.982	-0.994	19.154	0.095	0.095	0.000	0.000	0.000	0.000
33	B	40	PHE	0	-0.022	-0.014	10.793	0.021	0.021	0.000	0.000	0.000	0.000
34	B	41	LEU	0	0.028	-0.011	14.166	0.036	0.036	0.000	0.000	0.000	0.000
35	B	42	ARG	1	0.915	0.978	15.498	-0.075	-0.075	0.000	0.000	0.000	0.000
36	B	43	THR	0	-0.002	0.000	13.664	0.027	0.027	0.000	0.000	0.000	0.000
37	B	44	TYR	0	-0.019	-0.011	10.107	0.058	0.058	0.000	0.000	0.000	0.000
38	B	45	ALA	0	0.078	0.033	11.939	0.029	0.029	0.000	0.000	0.000	0.000
39	B	46	GLY	0	-0.002	0.012	11.380	0.004	0.004	0.000	0.000	0.000	0.000
40	B	47	VAL	0	0.014	-0.001	6.986	0.047	0.047	0.000	0.000	0.000	0.000
41	B	48	VAL	0	-0.018	-0.010	8.951	-0.057	-0.057	0.000	0.000	0.000	0.000
42	B	49	ASN	0	0.020	-0.019	12.078	-0.048	-0.048	0.000	0.000	0.000	0.000
43	B	50	SER	0	-0.045	-0.013	8.221	0.063	0.063	0.000	0.000	0.000	0.000
44	B	51	GLN	0	-0.070	-0.040	7.626	-0.108	-0.108	0.000	0.000	0.000	0.000
45	B	52	LEU	0	-0.044	-0.001	10.426	-0.053	-0.053	0.000	0.000	0.000	0.000
46	B	53	SER	0	-0.052	-0.012	13.102	-0.045	-0.045	0.000	0.000	0.000	0.000

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