FMO DATABASE

FMODB ID: 9GYZ2

Calculation Name: 5FCG-C-Xray323

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	26
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-85211.526526
FMO2-HF: Nuclear repulsion	74177.748321
FMO2-HF: Total energy	-11033.778205
FMO2-MP2: Total energy	-11065.877184

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.
43.716	22.313	0.718	21.404	-0.719	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 : -1.031 / 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

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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	-0.064	-0.017	2.396	13.923	-7.480	0.718	21.404	-0.719
4	C	113	LYS	1	0.925	0.958	5.792	-27.287	-27.287	0.000	0.000	0.000
5	C	114	ASP	-1	-0.816	-0.897	8.117	24.396	24.396	0.000	0.000	0.000
6	C	115	CYS	0	-0.036	-0.039	10.537	-1.107	-1.107	0.000	0.000	0.000
7	C	116	VAL	0	0.005	0.013	10.219	-0.702	-0.702	0.000	0.000	0.000
8	C	117	PHE	0	0.003	0.003	10.081	-0.691	-0.691	0.000	0.000	0.000
9	C	118	LYS	1	0.885	0.937	11.948	-15.864	-15.864	0.000	0.000	0.000
10	C	119	ASP	-1	-0.874	-0.942	15.210	15.564	15.564	0.000	0.000	0.000
11	C	120	TRP	0	-0.048	-0.025	9.190	0.165	0.165	0.000	0.000	0.000
12	C	121	GLU	-1	-0.937	-0.966	15.574	14.962	14.962	0.000	0.000	0.000
13	C	122	GLU	-1	-0.921	-0.960	17.849	13.211	13.211	0.000	0.000	0.000
14	C	123	LEU	0	0.034	0.024	18.598	-0.577	-0.577	0.000	0.000	0.000
15	C	124	GLY	0	-0.009	-0.010	19.966	-0.630	-0.630	0.000	0.000	0.000
16	C	125	GLU	-1	-0.916	-0.971	21.376	10.875	10.875	0.000	0.000	0.000
17	C	126	GLU	-1	-0.930	-0.969	23.448	11.634	11.634	0.000	0.000	0.000
18	C	127	ILE	0	-0.047	-0.030	22.292	-0.550	-0.550	0.000	0.000	0.000
19	C	128	ARG	1	0.892	0.944	24.293	-11.550	-11.550	0.000	0.000	0.000
20	C	129	LEU	0	-0.050	-0.017	27.458	-0.488	-0.488	0.000	0.000	0.000
21	C	130	LYS	1	0.873	0.927	29.450	-9.492	-9.492	0.000	0.000	0.000
22	C	131	VAL	0	0.009	0.038	29.076	-0.161	-0.161	0.000	0.000	0.000
23	C	132	PHE	0	-0.039	-0.009	31.820	-0.258	-0.258	0.000	0.000	0.000
24	C	133	VAL	0	0.008	-0.009	34.754	0.040	0.040	0.000	0.000	0.000
25	C	134	LEU	0	-0.096	-0.057	35.660	0.030	0.030	0.000	0.000	0.000
26	C	135	GLY	-1	-0.922	-0.942	34.850	8.273	8.273	0.000	0.000	0.000

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