FMO DATABASE

FMODB ID: 72MZK

Calculation Name: 4BD2-C-Xray372

Preferred Name: Apoptosis regulator BAX

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4BD2

Chain ID: C

ChEMBL ID: CHEMBL5318

UniProt ID: Q07812

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	30
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-93295.051233
FMO2-HF: Nuclear repulsion	81549.127111
FMO2-HF: Total energy	-11745.924123
FMO2-MP2: Total energy	-11779.739035

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(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.
-10.288	-2.766	1.73	-3.822	-5.43	0.024

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 : 0.027 / q_NPA : 0.013

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	C	78	SER	0	-0.021	-0.003	2.611	-2.931	0.846	0.489	-2.049	-2.217	0.010
4	C	79	GLN	0	-0.007	-0.019	2.444	-6.309	-2.970	1.240	-1.678	-2.901	0.014
5	C	80	GLU	-1	-0.810	-0.888	4.124	-2.308	-1.902	0.001	-0.095	-0.312	0.000
6	C	81	ASP	-1	-0.825	-0.898	5.955	0.089	0.089	0.000	0.000	0.000	0.000
7	C	82	ILE	0	-0.067	-0.027	6.364	-0.053	-0.053	0.000	0.000	0.000	0.000
8	C	83	ILE	0	0.031	0.017	6.328	0.027	0.027	0.000	0.000	0.000	0.000
9	C	84	ARG	1	0.803	0.874	8.359	1.119	1.119	0.000	0.000	0.000	0.000
10	C	85	ASN	0	-0.016	-0.006	11.717	-0.029	-0.029	0.000	0.000	0.000	0.000
11	C	86	ILE	0	0.007	0.014	11.458	0.022	0.022	0.000	0.000	0.000	0.000
12	C	87	ALA	0	0.007	0.009	13.984	0.017	0.017	0.000	0.000	0.000	0.000
13	C	88	ARG	1	0.910	0.947	14.931	0.096	0.096	0.000	0.000	0.000	0.000
14	C	89	HIS	0	-0.003	-0.005	17.368	0.012	0.012	0.000	0.000	0.000	0.000
15	C	90	LEU	0	0.000	-0.002	17.266	0.010	0.010	0.000	0.000	0.000	0.000
16	C	91	ALA	0	0.006	0.009	19.955	0.005	0.005	0.000	0.000	0.000	0.000
17	C	92	GLN	0	-0.002	0.011	21.695	0.020	0.020	0.000	0.000	0.000	0.000
18	C	93	VAL	0	-0.012	-0.012	23.055	0.010	0.010	0.000	0.000	0.000	0.000
19	C	94	GLY	0	-0.006	-0.006	24.340	0.005	0.005	0.000	0.000	0.000	0.000
20	C	95	ASP	-1	-0.896	-0.946	25.691	-0.094	-0.094	0.000	0.000	0.000	0.000
21	C	96	SER	0	-0.127	-0.089	27.239	0.010	0.010	0.000	0.000	0.000	0.000
22	C	97	MET	0	-0.029	-0.010	28.626	0.007	0.007	0.000	0.000	0.000	0.000
23	C	98	ASP	-1	-0.861	-0.930	30.965	-0.049	-0.049	0.000	0.000	0.000	0.000
24	C	99	ARG	1	0.803	0.911	31.058	0.023	0.023	0.000	0.000	0.000	0.000
25	C	100	SER	0	-0.040	0.003	34.364	0.007	0.007	0.000	0.000	0.000	0.000
26	C	101	ILE	0	-0.018	0.019	36.782	-0.004	-0.004	0.000	0.000	0.000	0.000
27	C	102	PRO	0	-0.021	-0.034	37.790	0.003	0.003	0.000	0.000	0.000	0.000
28	C	103	PRO	0	0.051	0.013	33.441	0.003	0.003	0.000	0.000	0.000	0.000
29	C	104	GLY	0	-0.011	-0.005	31.615	0.003	0.003	0.000	0.000	0.000	0.000
30	C	105	LEU	0	-0.007	0.003	26.247	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)