FMO DATABASE

FMODB ID: YYK52

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	OptH
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	-85271.020273
FMO2-HF: Nuclear repulsion	74236.599293
FMO2-HF: Total energy	-11034.420979
FMO2-MP2: Total energy	-11066.514494

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.
36.037	14.503	0.43	21.837	-0.733	0.001

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 : -1.029 / q_NPA : -1.003

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	C	112	ILE	0	-0.066	-0.021	2.396	14.288	-7.246	0.430	21.837	-0.733	0.001
4	C	113	LYS	1	0.923	0.957	5.791	-27.183	-27.183	0.000	0.000	0.000	0.000
5	C	114	ASP	-1	-0.814	-0.896	8.117	24.470	24.470	0.000	0.000	0.000	0.000
6	C	115	CYS	0	-0.033	-0.038	10.537	-1.062	-1.062	0.000	0.000	0.000	0.000
7	C	116	VAL	0	0.005	0.013	10.218	-0.710	-0.710	0.000	0.000	0.000	0.000
8	C	117	PHE	0	0.006	0.004	10.082	-0.701	-0.701	0.000	0.000	0.000	0.000
9	C	118	LYS	1	0.881	0.936	11.948	-15.812	-15.812	0.000	0.000	0.000	0.000
10	C	119	ASP	-1	-0.869	-0.941	15.210	15.576	15.576	0.000	0.000	0.000	0.000
11	C	120	TRP	0	-0.052	-0.025	9.190	0.113	0.113	0.000	0.000	0.000	0.000
12	C	121	GLU	-1	-0.933	-0.964	15.574	14.971	14.971	0.000	0.000	0.000	0.000
13	C	122	GLU	-1	-0.923	-0.960	17.849	13.228	13.228	0.000	0.000	0.000	0.000
14	C	123	LEU	0	0.035	0.024	18.598	-0.582	-0.582	0.000	0.000	0.000	0.000
15	C	124	GLY	0	-0.009	-0.011	19.966	-0.628	-0.628	0.000	0.000	0.000	0.000
16	C	125	GLU	-1	-0.914	-0.970	21.376	10.882	10.882	0.000	0.000	0.000	0.000
17	C	126	GLU	-1	-0.924	-0.966	23.448	11.636	11.636	0.000	0.000	0.000	0.000
18	C	127	ILE	0	-0.049	-0.031	22.291	-0.567	-0.567	0.000	0.000	0.000	0.000
19	C	128	ARG	1	0.890	0.941	24.294	-11.553	-11.553	0.000	0.000	0.000	0.000
20	C	129	LEU	0	-0.042	-0.012	27.458	-0.484	-0.484	0.000	0.000	0.000	0.000
21	C	130	LYS	1	0.885	0.935	29.450	-9.494	-9.494	0.000	0.000	0.000	0.000
22	C	131	VAL	0	0.006	0.036	29.077	-0.185	-0.185	0.000	0.000	0.000	0.000
23	C	132	PHE	0	-0.040	-0.012	31.820	-0.253	-0.253	0.000	0.000	0.000	0.000
24	C	133	VAL	0	0.045	0.007	34.754	0.045	0.045	0.000	0.000	0.000	0.000
25	C	134	LEU	0	-0.052	-0.030	35.660	0.056	0.056	0.000	0.000	0.000	0.000
26	C	135	GLY	0	-0.025	0.003	34.850	-0.014	-0.014	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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