FMO DATABASE

FMODB ID: Y9YZ2

Calculation Name: 4BD2-C-Xray540

Preferred Name: Apoptosis regulator BAX

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4BD2

Chain ID: C

ChEMBL ID: CHEMBL5318

UniProt ID: Q07812

Base Structure: X-ray

Registration Date: 2025-07-11

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	56
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-93289.580509
FMO2-HF: Nuclear repulsion	81549.127111
FMO2-HF: Total energy	-11740.453399
FMO2-MP2: Total energy	-11774.121096

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(C:76:SER)

Summations of interaction energy for fragment #1(C:76:SER)

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.
0.207	4.952	0.352	-2.151	-2.949	-0.001

Interaction energy analysis for fragmet #1(C:76:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.096 / q_NPA : 0.042

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].
4	C	77	GLU	-1	-0.868	-0.793	3.387	-3.895	-2.086	0.096	-0.957	-0.949	-0.006
5	C	78	SER	0	0.015	-0.065	3.084	0.137	1.916	-0.011	-0.818	-0.951	0.006
6	C	78	SER	0	-0.008	0.074	3.882	0.365	0.424	0.002	0.001	-0.062	0.000
7	C	79	GLN	0	0.029	-0.121	3.447	1.504	1.707	0.008	0.053	-0.264	-0.001
8	C	79	GLN	0	-0.064	0.103	2.495	-0.198	0.519	0.259	-0.394	-0.582	0.000
9	C	80	GLU	0	0.180	-0.060	4.124	1.190	1.368	-0.002	-0.036	-0.141	0.000
10	C	80	GLU	-1	-0.945	-0.813	4.836	-1.466	-1.466	0.000	0.000	0.000	0.000
11	C	81	ASP	0	0.089	-0.134	5.955	0.699	0.699	0.000	0.000	0.000	0.000
12	C	81	ASP	-1	-0.942	-0.789	8.270	-1.880	-1.880	0.000	0.000	0.000	0.000
13	C	82	ILE	0	0.018	-0.112	7.738	0.410	0.410	0.000	0.000	0.000	0.000
14	C	82	ILE	0	-0.081	0.096	7.408	0.048	0.048	0.000	0.000	0.000	0.000
15	C	83	ILE	0	0.081	-0.105	8.110	0.303	0.303	0.000	0.000	0.000	0.000
16	C	83	ILE	0	-0.054	0.126	6.328	0.059	0.059	0.000	0.000	0.000	0.000
17	C	84	ARG	0	0.113	-0.090	9.760	0.224	0.224	0.000	0.000	0.000	0.000
18	C	84	ARG	1	0.704	0.976	8.359	1.602	1.602	0.000	0.000	0.000	0.000
19	C	85	ASN	0	0.033	-0.093	11.717	0.151	0.151	0.000	0.000	0.000	0.000
20	C	85	ASN	0	-0.083	0.078	12.500	0.069	0.069	0.000	0.000	0.000	0.000
21	C	86	ILE	0	0.123	-0.076	12.786	0.085	0.085	0.000	0.000	0.000	0.000
22	C	86	ILE	0	-0.095	0.095	11.458	0.012	0.012	0.000	0.000	0.000	0.000
23	C	87	ALA	0	0.123	-0.088	13.984	0.083	0.083	0.000	0.000	0.000	0.000
24	C	87	ALA	0	-0.082	0.106	14.499	-0.002	-0.002	0.000	0.000	0.000	0.000
25	C	88	ARG	0	0.111	-0.070	15.839	0.066	0.066	0.000	0.000	0.000	0.000
26	C	88	ARG	1	0.777	1.007	15.057	0.578	0.578	0.000	0.000	0.000	0.000
27	C	89	HIS	0	0.075	-0.078	17.368	0.040	0.040	0.000	0.000	0.000	0.000
28	C	89	HIS	0	-0.082	0.074	18.169	-0.016	-0.016	0.000	0.000	0.000	0.000
29	C	90	LEU	0	0.038	-0.111	18.503	0.030	0.030	0.000	0.000	0.000	0.000
30	C	90	LEU	0	-0.070	0.092	17.266	0.005	0.005	0.000	0.000	0.000	0.000
31	C	91	ALA	0	0.149	-0.068	19.955	0.036	0.036	0.000	0.000	0.000	0.000
32	C	91	ALA	0	-0.083	0.098	20.668	-0.004	-0.004	0.000	0.000	0.000	0.000
33	C	92	GLN	0	0.139	-0.066	21.695	0.025	0.025	0.000	0.000	0.000	0.000
34	C	92	GLN	0	-0.153	0.073	22.612	0.009	0.009	0.000	0.000	0.000	0.000
35	C	93	VAL	0	0.056	-0.100	23.055	0.018	0.018	0.000	0.000	0.000	0.000
36	C	93	VAL	0	-0.104	0.084	23.120	0.002	0.002	0.000	0.000	0.000	0.000
37	C	94	GLY	0	-0.001	-0.117	24.340	0.017	0.017	0.000	0.000	0.000	0.000
38	C	95	ASP	0	0.112	-0.010	25.987	0.019	0.019	0.000	0.000	0.000	0.000
39	C	95	ASP	-1	-0.996	-0.853	25.691	-0.195	-0.195	0.000	0.000	0.000	0.000
40	C	96	SER	0	-0.016	-0.089	27.701	0.013	0.013	0.000	0.000	0.000	0.000
41	C	96	SER	0	-0.127	0.020	27.239	0.000	0.000	0.000	0.000	0.000	0.000
42	C	97	MET	0	0.087	-0.094	29.262	0.005	0.005	0.000	0.000	0.000	0.000
43	C	97	MET	0	-0.106	0.084	28.626	0.000	0.000	0.000	0.000	0.000	0.000
44	C	98	ASP	0	0.145	-0.112	30.965	0.010	0.010	0.000	0.000	0.000	0.000
45	C	98	ASP	-1	-1.010	-0.829	32.843	-0.106	-0.106	0.000	0.000	0.000	0.000
46	C	99	ARG	0	-0.031	-0.099	33.273	0.009	0.009	0.000	0.000	0.000	0.000
47	C	99	ARG	1	0.813	1.037	31.058	0.142	0.142	0.000	0.000	0.000	0.000
48	C	100	SER	0	-0.005	-0.106	35.194	0.001	0.001	0.000	0.000	0.000	0.000
49	C	100	SER	0	-0.032	0.080	34.364	0.000	0.000	0.000	0.000	0.000	0.000
50	C	101	ILE	0	0.080	-0.078	36.782	0.000	0.000	0.000	0.000	0.000	0.000
51	C	101	ILE	0	-0.106	0.105	39.898	0.001	0.001	0.000	0.000	0.000	0.000
52	C	102	PRO	0	-0.033	-0.138	37.790	0.003	0.003	0.000	0.000	0.000	0.000
53	C	103	PRO	0	0.053	0.021	33.441	-0.002	-0.002	0.000	0.000	0.000	0.000
54	C	104	GLY	0	-0.016	-0.014	31.615	0.006	0.006	0.000	0.000	0.000	0.000
55	C	105	LEU	0	-0.069	-0.025	29.787	-0.004	-0.004	0.000	0.000	0.000	0.000
56	C	105	LEU	0	0.061	0.036	26.345	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:76:SER)