FMO DATABASE

FMODB ID: 14G1Z

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	OptAll
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	-85216.234589
FMO2-HF: Nuclear repulsion	74181.388179
FMO2-HF: Total energy	-11034.84641
FMO2-MP2: Total energy	-11066.946005

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.
18.692	10.3	0.342	8.748	-0.698	0.002

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 : -0.981 / q_NPA : -0.998

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	-0.049	-0.011	2.677	-0.444	-8.836	0.342	8.748	-0.698	0.002
4	C	113	LYS	1	0.944	0.972	6.043	-32.652	-32.652	0.000	0.000	0.000	0.000
5	C	114	ASP	-1	-0.829	-0.918	8.490	27.387	27.387	0.000	0.000	0.000	0.000
6	C	115	CYS	0	-0.047	-0.021	10.939	-1.100	-1.100	0.000	0.000	0.000	0.000
7	C	116	VAL	0	0.033	0.020	10.745	-0.919	-0.919	0.000	0.000	0.000	0.000
8	C	117	PHE	0	-0.022	-0.005	10.257	-0.698	-0.698	0.000	0.000	0.000	0.000
9	C	118	LYS	1	0.839	0.893	12.122	-16.486	-16.486	0.000	0.000	0.000	0.000
10	C	119	ASP	-1	-0.890	-0.949	15.537	16.819	16.819	0.000	0.000	0.000	0.000
11	C	120	TRP	0	-0.067	-0.043	9.011	-0.112	-0.112	0.000	0.000	0.000	0.000
12	C	121	GLU	-1	-0.913	-0.951	15.427	15.852	15.852	0.000	0.000	0.000	0.000
13	C	122	GLU	-1	-0.834	-0.905	17.861	13.412	13.412	0.000	0.000	0.000	0.000
14	C	123	LEU	0	0.014	0.017	18.799	-0.729	-0.729	0.000	0.000	0.000	0.000
15	C	124	GLY	0	0.020	0.009	19.922	-0.600	-0.600	0.000	0.000	0.000	0.000
16	C	125	GLU	-1	-0.794	-0.878	21.221	10.970	10.970	0.000	0.000	0.000	0.000
17	C	126	GLU	-1	-0.980	-0.984	23.921	11.425	11.425	0.000	0.000	0.000	0.000
18	C	127	ILE	0	-0.040	-0.023	22.249	-0.575	-0.575	0.000	0.000	0.000	0.000
19	C	128	ARG	1	0.813	0.871	23.871	-11.963	-11.963	0.000	0.000	0.000	0.000
20	C	129	LEU	0	-0.035	-0.008	27.309	-0.519	-0.519	0.000	0.000	0.000	0.000
21	C	130	LYS	1	0.852	0.914	29.533	-9.893	-9.893	0.000	0.000	0.000	0.000
22	C	131	VAL	0	-0.005	0.010	28.781	-0.208	-0.208	0.000	0.000	0.000	0.000
23	C	132	PHE	0	-0.009	0.003	31.577	-0.252	-0.252	0.000	0.000	0.000	0.000
24	C	133	VAL	0	-0.001	-0.008	34.540	0.002	0.002	0.000	0.000	0.000	0.000
25	C	134	LEU	0	-0.025	-0.007	35.583	0.002	0.002	0.000	0.000	0.000	0.000
26	C	135	GLY	0	-0.029	-0.002	34.421	-0.027	-0.027	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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