FMO DATABASE

FMODB ID: VR131

Calculation Name: 5FCG-C-Xray372

Preferred Name: Apoptosis regulator Bcl-2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5FCG

Chain ID: C

ChEMBL ID: CHEMBL4860

UniProt ID: P10415

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:

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	26
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-85297.343079
FMO2-HF: Nuclear repulsion	74262.672528
FMO2-HF: Total energy	-11034.670551
FMO2-MP2: Total energy	-11066.781183

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:110:GLU)

Summations of interaction energy for fragment #1(C:110:GLU)

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.
34.755	14.199	0.43	20.829	-0.703	0

Interaction energy analysis for fragmet #1(C:110:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -1.010 / q_NPA : -0.995

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].
3	C	112	ILE	0	-0.073	-0.021	2.424	13.059	-7.497	0.430	20.829	-0.703
4	C	113	LYS	1	0.934	0.961	5.813	-28.511	-28.511	0.000	0.000	0.000
5	C	114	ASP	-1	-0.814	-0.899	8.138	25.726	25.726	0.000	0.000	0.000
6	C	115	CYS	0	-0.024	-0.029	10.551	-0.931	-0.931	0.000	0.000	0.000
7	C	116	VAL	0	0.000	0.009	10.231	-0.811	-0.811	0.000	0.000	0.000
8	C	117	PHE	0	-0.005	-0.001	10.070	-0.808	-0.808	0.000	0.000	0.000
9	C	118	LYS	1	0.844	0.888	11.963	-16.099	-16.099	0.000	0.000	0.000
10	C	119	ASP	-1	-0.866	-0.938	15.228	16.099	16.099	0.000	0.000	0.000
11	C	120	TRP	0	-0.067	-0.034	9.228	0.004	0.004	0.000	0.000	0.000
12	C	121	GLU	-1	-0.916	-0.955	15.464	15.354	15.354	0.000	0.000	0.000
13	C	122	GLU	-1	-0.863	-0.901	17.861	13.494	13.494	0.000	0.000	0.000
14	C	123	LEU	0	0.004	0.004	18.606	-0.644	-0.644	0.000	0.000	0.000
15	C	124	GLY	0	0.011	0.001	19.955	-0.642	-0.642	0.000	0.000	0.000
16	C	125	GLU	-1	-0.804	-0.890	21.376	10.861	10.861	0.000	0.000	0.000
17	C	126	GLU	-1	-0.947	-0.968	23.904	11.484	11.484	0.000	0.000	0.000
18	C	127	ILE	0	-0.047	-0.035	22.214	-0.579	-0.579	0.000	0.000	0.000
19	C	128	ARG	1	0.785	0.863	24.073	-11.811	-11.811	0.000	0.000	0.000
20	C	129	LEU	0	-0.042	-0.012	27.458	-0.475	-0.475	0.000	0.000	0.000
21	C	130	LYS	1	0.875	0.933	29.450	-9.642	-9.642	0.000	0.000	0.000
22	C	131	VAL	0	0.010	0.033	29.009	-0.189	-0.189	0.000	0.000	0.000
23	C	132	PHE	0	-0.039	-0.012	31.820	-0.258	-0.258	0.000	0.000	0.000
24	C	133	VAL	0	0.038	0.008	34.746	0.039	0.039	0.000	0.000	0.000
25	C	134	LEU	0	-0.045	-0.025	35.660	0.047	0.047	0.000	0.000	0.000
26	C	135	GLY	0	-0.019	0.003	34.850	-0.012	-0.012	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:110:GLU)