FMO DATABASE

FMODB ID: KZ3G3

Calculation Name: 3B2E-G-Xray549

Preferred Name:

Target Type:

Ligand Name: adenosine-5'-diphosphate

Ligand 3-letter code: ADP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3B2E

Chain ID: G

ChEMBL ID:

UniProt ID: P53192

Base Structure: X-ray

Registration Date: 2025-10-12

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	67
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230712

Total energy (hartree)

FMO2-HF: Electronic energy	-371990.500211
FMO2-HF: Nuclear repulsion	345052.715015
FMO2-HF: Total energy	-26937.785196
FMO2-MP2: Total energy	-27018.258325

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(G:29:ILE)

Summations of interaction energy for fragment #1(G:29:ILE)

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.
40.146	46.392	1.404	-2.927	-4.722	-0.024

Interaction energy analysis for fragmet #1(G:29:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.909 / q_NPA : 0.942

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	G	31	LYS	1	1.034	1.012	3.884	45.098	47.546	-0.015	-1.059	-1.375	-0.003
4	G	32	PHE	0	-0.040	-0.014	2.222	0.658	3.508	1.334	-1.601	-2.582	-0.021
5	G	33	ALA	0	0.109	0.050	2.948	6.065	6.773	0.084	-0.217	-0.575	0.000
6	G	34	PRO	0	0.032	0.032	3.860	2.717	2.957	0.001	-0.050	-0.190	0.000
7	G	35	GLY	0	0.005	-0.012	7.022	-0.146	-0.146	0.000	0.000	0.000	0.000
8	G	36	ASN	0	-0.095	-0.038	7.586	6.774	6.774	0.000	0.000	0.000	0.000
9	G	37	GLU	-1	-0.891	-0.943	7.639	-24.120	-24.120	0.000	0.000	0.000	0.000
10	G	38	LEU	0	0.022	0.012	8.042	2.951	2.951	0.000	0.000	0.000	0.000
11	G	39	SER	0	-0.013	0.001	10.962	2.434	2.434	0.000	0.000	0.000	0.000
12	G	40	LYS	1	0.903	0.941	11.765	25.307	25.307	0.000	0.000	0.000	0.000
13	G	41	LYS	1	0.858	0.940	12.643	20.341	20.341	0.000	0.000	0.000	0.000
14	G	42	TYR	0	0.087	0.038	14.622	1.287	1.287	0.000	0.000	0.000	0.000
15	G	43	LEU	0	0.004	-0.005	16.527	1.056	1.056	0.000	0.000	0.000	0.000
16	G	44	ALA	0	-0.026	-0.009	18.160	0.860	0.860	0.000	0.000	0.000	0.000
17	G	45	LYS	1	0.899	0.939	19.014	15.159	15.159	0.000	0.000	0.000	0.000
18	G	46	VAL	0	0.012	0.012	20.575	0.751	0.751	0.000	0.000	0.000	0.000
19	G	47	LYS	1	0.825	0.914	22.423	12.516	12.516	0.000	0.000	0.000	0.000
20	G	48	GLU	-1	-0.901	-0.949	23.656	-11.848	-11.848	0.000	0.000	0.000	0.000
21	G	49	ARG	1	0.816	0.879	24.894	11.496	11.496	0.000	0.000	0.000	0.000
22	G	50	HIS	0	-0.118	-0.050	26.627	0.435	0.435	0.000	0.000	0.000	0.000
23	G	51	GLU	-1	-0.775	-0.888	27.156	-10.993	-10.993	0.000	0.000	0.000	0.000
24	G	52	LEU	0	-0.041	-0.021	29.338	0.435	0.435	0.000	0.000	0.000	0.000
25	G	53	LYS	1	0.945	0.966	30.713	9.812	9.812	0.000	0.000	0.000	0.000
26	G	54	GLU	-1	-0.875	-0.933	32.143	-9.297	-9.297	0.000	0.000	0.000	0.000
27	G	55	PHE	0	0.006	0.008	34.029	0.289	0.289	0.000	0.000	0.000	0.000
28	G	56	ASN	0	0.016	-0.005	34.880	0.409	0.409	0.000	0.000	0.000	0.000
29	G	57	ASN	0	-0.046	-0.022	36.749	0.222	0.222	0.000	0.000	0.000	0.000
30	G	58	SER	0	-0.050	-0.031	38.927	0.195	0.195	0.000	0.000	0.000	0.000
31	G	59	ILE	0	-0.061	-0.015	39.069	0.169	0.169	0.000	0.000	0.000	0.000
32	G	60	SER	0	0.025	-0.009	42.407	-0.040	-0.040	0.000	0.000	0.000	0.000
33	G	61	ALA	0	-0.012	-0.015	42.682	-0.008	-0.008	0.000	0.000	0.000	0.000
34	G	62	GLN	0	0.026	0.017	43.943	-0.029	-0.029	0.000	0.000	0.000	0.000
35	G	63	ASP	-1	-0.830	-0.901	47.505	-6.350	-6.350	0.000	0.000	0.000	0.000
36	G	64	ASN	0	-0.060	-0.043	43.071	-0.078	-0.078	0.000	0.000	0.000	0.000
37	G	65	TYR	0	0.070	0.060	42.565	-0.228	-0.228	0.000	0.000	0.000	0.000
38	G	66	ALA	0	-0.011	-0.006	41.701	-0.192	-0.192	0.000	0.000	0.000	0.000
39	G	67	LYS	1	0.912	0.941	38.958	7.237	7.237	0.000	0.000	0.000	0.000
40	G	68	TRP	0	0.124	0.065	37.710	-0.231	-0.231	0.000	0.000	0.000	0.000
41	G	69	THR	0	0.016	0.006	37.413	-0.228	-0.228	0.000	0.000	0.000	0.000
42	G	70	LYS	1	0.856	0.928	35.222	7.876	7.876	0.000	0.000	0.000	0.000
43	G	71	ASN	0	-0.002	-0.004	33.323	-0.440	-0.440	0.000	0.000	0.000	0.000
44	G	72	ASN	0	-0.006	-0.002	32.432	-0.400	-0.400	0.000	0.000	0.000	0.000
45	G	73	ARG	1	0.986	1.001	32.080	8.147	8.147	0.000	0.000	0.000	0.000
46	G	74	LYS	1	0.949	0.993	27.827	9.939	9.939	0.000	0.000	0.000	0.000
47	G	75	LEU	0	0.018	0.018	27.880	-0.456	-0.456	0.000	0.000	0.000	0.000
48	G	76	ASP	-1	-0.850	-0.931	27.882	-9.666	-9.666	0.000	0.000	0.000	0.000
49	G	77	SER	0	-0.134	-0.074	25.732	-0.308	-0.308	0.000	0.000	0.000	0.000
50	G	78	LEU	0	0.031	-0.001	23.016	-0.445	-0.445	0.000	0.000	0.000	0.000
51	G	79	ASP	-1	-0.793	-0.887	23.081	-11.330	-11.330	0.000	0.000	0.000	0.000
52	G	80	LYS	1	0.924	0.973	23.545	10.372	10.372	0.000	0.000	0.000	0.000
53	G	81	GLU	-1	-0.819	-0.894	19.285	-14.721	-14.721	0.000	0.000	0.000	0.000
54	G	82	ILE	0	-0.020	-0.008	18.442	-0.851	-0.851	0.000	0.000	0.000	0.000
55	G	83	ASN	0	-0.048	-0.028	18.984	-0.154	-0.154	0.000	0.000	0.000	0.000
56	G	84	ASN	0	-0.005	-0.003	17.145	0.030	0.030	0.000	0.000	0.000	0.000
57	G	85	LEU	0	0.031	0.012	13.136	-0.919	-0.919	0.000	0.000	0.000	0.000
58	G	86	LYS	1	0.914	0.965	14.437	13.029	13.029	0.000	0.000	0.000	0.000
59	G	87	ASP	-1	-0.860	-0.936	16.128	-14.912	-14.912	0.000	0.000	0.000	0.000
60	G	88	GLU	-1	-0.975	-0.968	10.081	-22.914	-22.914	0.000	0.000	0.000	0.000
61	G	89	ILE	0	-0.045	-0.017	10.928	-1.450	-1.450	0.000	0.000	0.000	0.000
62	G	90	GLN	0	-0.055	-0.030	12.162	0.664	0.664	0.000	0.000	0.000	0.000
63	G	91	SER	0	-0.064	-0.051	13.194	-0.132	-0.132	0.000	0.000	0.000	0.000
64	G	92	GLU	-1	-0.807	-0.901	5.607	-36.072	-36.072	0.000	0.000	0.000	0.000
65	G	93	ASN	0	-0.111	-0.063	10.225	-1.167	-1.167	0.000	0.000	0.000	0.000
66	G	94	LYS	1	0.855	0.892	12.533	17.926	17.926	0.000	0.000	0.000	0.000
67	G	95	ALA	-1	-0.907	-0.909	11.378	-22.385	-22.385	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:29:ILE)