FMO DATABASE

FMODB ID: GN1Z1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-216066.89779
FMO2-HF: Nuclear repulsion	197273.927236
FMO2-HF: Total energy	-18792.970554
FMO2-MP2: Total energy	-18846.076095

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.
0.744	4.111	3.484	-3.479	-3.373	-0.017

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 : -0.005 / q_NPA : -0.018

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	0.061	0.036	3.369	0.118	1.635	-0.002	-0.760	-0.756	0.001
4	B	11	PRO	0	0.056	0.008	4.403	-0.584	-0.397	0.000	-0.029	-0.157	0.000
5	B	12	GLU	-1	-0.917	-0.940	6.797	0.007	0.007	0.000	0.000	0.000	0.000
6	B	13	GLU	-1	-0.781	-0.875	2.335	1.735	2.644	2.387	-1.838	-1.458	-0.014
7	B	14	MET	0	-0.049	-0.016	3.233	-0.198	0.453	1.097	-0.802	-0.946	-0.004
8	B	15	TYR	0	0.061	0.024	4.096	0.190	0.207	0.002	-0.018	-0.002	0.000
9	B	16	ILE	0	0.001	0.008	6.515	0.082	0.082	0.000	0.000	0.000	0.000
10	B	17	GLN	0	0.040	0.027	3.794	-0.350	-0.264	0.000	-0.032	-0.054	0.000
11	B	18	GLN	0	-0.028	-0.024	6.577	-0.116	-0.116	0.000	0.000	0.000	0.000
12	B	19	LYS	1	0.966	0.993	8.731	0.004	0.004	0.000	0.000	0.000	0.000
13	B	20	VAL	0	0.012	0.004	10.120	-0.010	-0.010	0.000	0.000	0.000	0.000
14	B	21	ARG	1	0.893	0.953	7.410	-0.152	-0.152	0.000	0.000	0.000	0.000
15	B	22	VAL	0	-0.017	-0.008	12.193	-0.013	-0.013	0.000	0.000	0.000	0.000
16	B	23	LEU	0	-0.008	0.000	14.862	-0.002	-0.002	0.000	0.000	0.000	0.000
17	B	24	LEU	0	0.005	0.003	13.212	-0.002	-0.002	0.000	0.000	0.000	0.000
18	B	25	MET	0	-0.010	-0.007	16.284	-0.004	-0.004	0.000	0.000	0.000	0.000
19	B	26	LEU	0	-0.009	-0.003	18.057	-0.005	-0.005	0.000	0.000	0.000	0.000
20	B	27	ARG	1	0.874	0.890	19.546	-0.099	-0.099	0.000	0.000	0.000	0.000
21	B	28	LYS	1	0.905	0.958	19.828	-0.051	-0.051	0.000	0.000	0.000	0.000
22	B	29	MET	0	-0.083	-0.039	20.693	-0.007	-0.007	0.000	0.000	0.000	0.000
23	B	30	GLY	0	0.009	0.013	24.224	-0.005	-0.005	0.000	0.000	0.000	0.000
24	B	31	SER	0	-0.039	-0.004	24.326	-0.004	-0.004	0.000	0.000	0.000	0.000
25	B	32	ASN	0	-0.017	-0.022	24.402	0.011	0.011	0.000	0.000	0.000	0.000
26	B	33	LEU	0	0.000	0.009	19.390	-0.005	-0.005	0.000	0.000	0.000	0.000
27	B	34	THR	0	-0.013	-0.039	21.880	0.001	0.001	0.000	0.000	0.000	0.000
28	B	35	ALA	0	0.040	0.007	22.559	0.010	0.010	0.000	0.000	0.000	0.000
29	B	36	SER	0	0.032	0.007	20.912	0.013	0.013	0.000	0.000	0.000	0.000
30	B	37	GLU	-1	-0.857	-0.902	18.087	0.027	0.027	0.000	0.000	0.000	0.000
31	B	38	GLU	-1	-0.790	-0.857	18.008	0.123	0.123	0.000	0.000	0.000	0.000
32	B	39	GLU	-1	-0.820	-0.885	19.418	0.131	0.131	0.000	0.000	0.000	0.000
33	B	40	PHE	0	-0.032	-0.005	11.010	0.026	0.026	0.000	0.000	0.000	0.000
34	B	41	LEU	0	0.014	-0.015	14.619	0.042	0.042	0.000	0.000	0.000	0.000
35	B	42	ARG	1	0.813	0.892	15.946	-0.082	-0.082	0.000	0.000	0.000	0.000
36	B	43	THR	0	-0.030	-0.021	13.755	0.025	0.025	0.000	0.000	0.000	0.000
37	B	44	TYR	0	0.006	-0.005	10.274	0.041	0.041	0.000	0.000	0.000	0.000
38	B	45	ALA	0	0.071	0.041	12.190	0.058	0.058	0.000	0.000	0.000	0.000
39	B	46	GLY	0	0.016	0.011	11.923	0.000	0.000	0.000	0.000	0.000	0.000
40	B	47	VAL	0	-0.016	0.001	7.201	0.098	0.098	0.000	0.000	0.000	0.000
41	B	48	VAL	0	0.007	0.007	9.437	-0.048	-0.048	0.000	0.000	0.000	0.000
42	B	49	ASN	0	0.021	-0.006	12.576	-0.039	-0.039	0.000	0.000	0.000	0.000
43	B	50	SER	0	-0.032	-0.017	8.754	0.036	0.036	0.000	0.000	0.000	0.000
44	B	51	GLN	0	-0.080	-0.046	9.147	-0.133	-0.133	0.000	0.000	0.000	0.000
45	B	52	LEU	0	-0.035	-0.004	10.878	-0.059	-0.059	0.000	0.000	0.000	0.000
46	B	53	SER	0	-0.066	-0.024	12.985	-0.066	-0.066	0.000	0.000	0.000	0.000

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