FMO DATABASE

FMODB ID: 3GL6L

Calculation Name: 1DEB-A-Xray549

Preferred Name: Adenomatous polyposis coli protein

Target Type: SINGLE PROTEIN

Ligand Name: sulfate ion

Ligand 3-letter code: SO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1DEB

Chain ID: A

ChEMBL ID: CHEMBL3233

UniProt ID: P25054

Base Structure: X-ray

Registration Date: 2025-10-11

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	54
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-211374.26995
FMO2-HF: Nuclear repulsion	189679.11743
FMO2-HF: Total energy	-21695.15252
FMO2-MP2: Total energy	-21757.443013

3D Structure Molmil

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(A:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
-27.077	-25.511	0.042	-0.808	-0.799	-0.002

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.847 / q_NPA : 0.915

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	A	4	ALA	0	0.018	0.021	3.415	-5.610	-4.044	0.042	-0.808	-0.799	-0.002
4	A	5	SER	0	0.008	-0.019	6.049	3.520	3.520	0.000	0.000	0.000	0.000
5	A	6	TYR	0	0.050	0.014	7.803	0.752	0.752	0.000	0.000	0.000	0.000
6	A	7	ASP	-1	-0.847	-0.931	11.546	-20.402	-20.402	0.000	0.000	0.000	0.000
7	A	8	GLN	0	-0.044	0.001	7.101	-1.805	-1.805	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.040	0.014	9.943	1.035	1.035	0.000	0.000	0.000	0.000
9	A	10	LEU	0	-0.019	0.007	12.351	1.310	1.310	0.000	0.000	0.000	0.000
10	A	11	LYS	1	1.006	0.996	14.144	20.658	20.658	0.000	0.000	0.000	0.000
11	A	12	GLN	0	-0.014	-0.004	10.770	-1.191	-1.191	0.000	0.000	0.000	0.000
12	A	13	VAL	0	0.008	0.001	15.355	1.200	1.200	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.964	-0.987	18.160	-14.963	-14.963	0.000	0.000	0.000	0.000
14	A	15	ALA	0	0.000	-0.001	17.968	0.798	0.798	0.000	0.000	0.000	0.000
15	A	16	LEU	0	0.032	0.014	16.753	0.629	0.629	0.000	0.000	0.000	0.000
16	A	17	LYS	1	0.915	0.966	20.607	14.932	14.932	0.000	0.000	0.000	0.000
17	A	18	MET	0	-0.023	0.018	23.255	0.816	0.816	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.878	-0.948	21.081	-14.649	-14.649	0.000	0.000	0.000	0.000
19	A	20	ASN	0	-0.021	-0.012	24.327	0.877	0.877	0.000	0.000	0.000	0.000
20	A	21	SER	0	-0.039	-0.035	26.089	0.575	0.575	0.000	0.000	0.000	0.000
21	A	22	ASN	0	-0.003	0.001	27.800	0.585	0.585	0.000	0.000	0.000	0.000
22	A	23	LEU	0	0.068	0.033	25.248	0.331	0.331	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.848	0.923	28.893	11.155	11.155	0.000	0.000	0.000	0.000
24	A	25	GLN	0	-0.018	-0.005	32.014	0.374	0.374	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.885	-0.949	30.173	-10.454	-10.454	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.028	-0.012	33.151	0.257	0.257	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.940	-0.955	35.112	-8.486	-8.486	0.000	0.000	0.000	0.000
28	A	29	ASP	-1	-0.921	-0.958	37.533	-7.902	-7.902	0.000	0.000	0.000	0.000
29	A	30	ASN	0	-0.008	-0.020	35.813	0.431	0.431	0.000	0.000	0.000	0.000
30	A	31	SER	0	-0.038	-0.026	38.454	0.191	0.191	0.000	0.000	0.000	0.000
31	A	32	ASN	0	-0.014	-0.005	40.923	0.397	0.397	0.000	0.000	0.000	0.000
32	A	33	HIS	0	0.011	0.000	41.962	0.283	0.283	0.000	0.000	0.000	0.000
33	A	34	LEU	0	0.001	0.009	42.420	0.163	0.163	0.000	0.000	0.000	0.000
34	A	35	THR	0	0.030	0.011	44.612	0.208	0.208	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.844	0.953	46.996	6.885	6.885	0.000	0.000	0.000	0.000
36	A	37	LEU	0	0.070	0.039	45.493	0.168	0.168	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.914	-0.966	47.368	-6.750	-6.750	0.000	0.000	0.000	0.000
38	A	39	THR	0	-0.059	-0.031	50.562	0.195	0.195	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.935	-0.975	50.947	-6.261	-6.261	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.000	-0.001	52.930	0.147	0.147	0.000	0.000	0.000	0.000
41	A	42	SER	0	-0.066	-0.046	54.170	0.147	0.147	0.000	0.000	0.000	0.000
42	A	43	ASN	0	0.008	-0.006	56.617	0.142	0.142	0.000	0.000	0.000	0.000
43	A	44	MET	0	-0.007	0.007	57.864	0.162	0.162	0.000	0.000	0.000	0.000
44	A	45	LYS	1	0.954	0.969	58.248	5.673	5.673	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.975	-0.983	60.556	-5.086	-5.086	0.000	0.000	0.000	0.000
46	A	47	VAL	0	0.032	0.015	62.374	0.108	0.108	0.000	0.000	0.000	0.000
47	A	48	LEU	0	0.003	0.000	61.477	0.100	0.100	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.952	0.970	64.381	5.087	5.087	0.000	0.000	0.000	0.000
49	A	50	GLN	0	-0.016	-0.009	66.747	0.023	0.023	0.000	0.000	0.000	0.000
50	A	51	LEU	0	-0.016	-0.004	66.748	0.079	0.079	0.000	0.000	0.000	0.000
51	A	52	GLN	0	-0.094	-0.056	67.834	0.088	0.088	0.000	0.000	0.000	0.000
52	A	53	GLY	0	-0.035	-0.005	70.858	0.052	0.052	0.000	0.000	0.000	0.000
53	A	54	SER	0	-0.054	-0.027	73.402	0.070	0.070	0.000	0.000	0.000	0.000
54	A	55	ILE	-1	-0.976	-0.967	75.215	-4.121	-4.121	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)