FMO DATABASE

FMODB ID: 85JVY

Calculation Name: 1PQ1-B-Xray372

Preferred Name: Bcl-2-like protein 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1PQ1

Chain ID: B

ChEMBL ID: CHEMBL3309112

UniProt ID: Q64373

Base Structure: X-ray

Registration Date: 2023-06-21

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	33
LigandResidueName
LigandFragmentNumber	0
LigandCharge	DAS=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-126943.503886
FMO2-HF: Nuclear repulsion	112778.560381
FMO2-HF: Total energy	-14164.943504
FMO2-MP2: Total energy	-14207.261629

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(B:83:DAS)

Summations of interaction energy for fragment #1(B:83:DAS)

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.
-166.359	-173.978	32.516	-14.281	-10.616	0.152

Interaction energy analysis for fragmet #1(B:83:DAS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.735 / q_NPA : -0.829

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	B	85	ARG	1	0.884	0.922	3.850	-25.927	-22.687	-0.010	-1.589	-1.641	0.008
4	B	86	PRO	0	0.024	0.004	6.151	3.934	3.934	0.000	0.000	0.000	0.000
5	B	87	GLU	-1	-0.750	-0.869	7.092	32.036	32.036	0.000	0.000	0.000	0.000
6	B	88	ILE	0	0.001	0.004	6.819	-1.986	-1.986	0.000	0.000	0.000	0.000
7	B	89	ARG	1	0.834	0.882	1.653	-139.258	-150.184	32.527	-12.691	-8.910	0.144
8	B	90	ILE	0	0.019	0.011	5.068	-3.921	-3.854	-0.001	-0.001	-0.065	0.000
9	B	91	ALA	0	0.016	0.009	8.499	-2.645	-2.645	0.000	0.000	0.000	0.000
10	B	92	GLN	0	0.001	-0.004	6.816	-6.065	-6.065	0.000	0.000	0.000	0.000
11	B	93	GLU	-1	-0.824	-0.880	7.841	30.239	30.239	0.000	0.000	0.000	0.000
12	B	94	LEU	0	-0.014	-0.018	9.481	-2.694	-2.694	0.000	0.000	0.000	0.000
13	B	95	ARG	1	0.872	0.943	10.848	-25.746	-25.746	0.000	0.000	0.000	0.000
14	B	96	ARG	1	0.861	0.918	6.032	-38.488	-38.488	0.000	0.000	0.000	0.000
15	B	97	ILE	0	0.051	0.022	13.064	-1.598	-1.598	0.000	0.000	0.000	0.000
16	B	98	GLY	0	-0.003	0.007	15.383	-1.379	-1.379	0.000	0.000	0.000	0.000
17	B	99	ASP	-1	-0.903	-0.965	15.952	17.309	17.309	0.000	0.000	0.000	0.000
18	B	100	GLU	-1	-0.937	-0.967	17.331	16.291	16.291	0.000	0.000	0.000	0.000
19	B	101	PHE	0	-0.017	0.005	19.174	-1.129	-1.129	0.000	0.000	0.000	0.000
20	B	102	ASN	0	0.009	-0.004	21.153	-1.156	-1.156	0.000	0.000	0.000	0.000
21	B	103	GLU	-1	-0.816	-0.876	21.819	11.720	11.720	0.000	0.000	0.000	0.000
22	B	104	THR	0	-0.021	-0.024	22.497	-0.786	-0.786	0.000	0.000	0.000	0.000
23	B	105	TYR	0	-0.058	-0.044	25.004	-0.815	-0.815	0.000	0.000	0.000	0.000
24	B	106	THR	0	-0.004	-0.010	26.370	-0.568	-0.568	0.000	0.000	0.000	0.000
25	B	107	ARG	1	0.823	0.891	23.691	-12.941	-12.941	0.000	0.000	0.000	0.000
26	B	108	ARG	1	0.881	0.945	28.907	-10.879	-10.879	0.000	0.000	0.000	0.000
27	B	109	VAL	0	-0.027	0.009	31.554	-0.352	-0.352	0.000	0.000	0.000	0.000
28	B	110	PHE	0	0.025	0.004	30.561	-0.202	-0.202	0.000	0.000	0.000	0.000
29	B	111	ALA	0	-0.005	0.022	33.510	-0.153	-0.153	0.000	0.000	0.000	0.000
30	B	112	ASN	0	-0.101	-0.078	34.896	-0.374	-0.374	0.000	0.000	0.000	0.000
31	B	113	ASP	-1	-0.877	-0.933	37.115	8.381	8.381	0.000	0.000	0.000	0.000
32	B	114	TYR	0	-0.030	-0.008	38.526	-0.229	-0.229	0.000	0.000	0.000	0.000
33	B	115	ARG	1	0.914	0.966	42.510	-6.978	-6.978	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:83:DAS)