FMO DATABASE

FMODB ID: 3JVJL

Calculation Name: 2A28-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2A28

Chain ID: A

ChEMBL ID:

UniProt ID: P38822

Base Structure: X-ray

Registration Date: 2023-09-23

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	54
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-261569.733577
FMO2-HF: Nuclear repulsion	240710.069527
FMO2-HF: Total energy	-20859.66405
FMO2-MP2: Total energy	-20918.565669

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(A:1:GLY)

Summations of interaction energy for fragment #1(A:1:GLY)

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.
-5.314	-1.914	0.005	-1.671	-1.733	0.002

Interaction energy analysis for fragmet #1(A:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : 0.006

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	3	MET	0	-0.070	-0.025	3.734	0.326	2.446	-0.029	-1.116	-0.974	0.004
4	A	4	GLU	-1	-0.893	-0.951	7.090	-0.731	-0.731	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.036	0.015	10.498	0.159	0.159	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.064	-0.040	13.550	0.085	0.085	0.000	0.000	0.000	0.000
7	A	7	TYR	0	-0.070	-0.038	16.356	0.097	0.097	0.000	0.000	0.000	0.000
8	A	8	ALA	0	0.035	0.023	17.682	-0.059	-0.059	0.000	0.000	0.000	0.000
9	A	9	TYR	0	-0.098	-0.079	18.216	0.045	0.045	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.961	-0.975	20.166	-0.328	-0.328	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.026	-0.023	20.096	0.013	0.013	0.000	0.000	0.000	0.000
12	A	12	GLN	0	-0.078	-0.050	21.513	0.062	0.062	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.041	0.011	22.995	0.032	0.032	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.958	-0.979	21.895	-0.315	-0.315	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.968	-0.971	18.527	-0.397	-0.397	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.832	-0.890	17.249	-0.479	-0.479	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.054	-0.028	12.795	0.007	0.007	0.000	0.000	0.000	0.000
18	A	18	SER	0	-0.005	-0.005	17.265	0.004	0.004	0.000	0.000	0.000	0.000
19	A	19	ILE	0	-0.046	-0.006	13.898	-0.070	-0.070	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.881	-0.942	16.756	-0.412	-0.412	0.000	0.000	0.000	0.000
21	A	21	PRO	0	-0.074	-0.054	16.392	-0.072	-0.072	0.000	0.000	0.000	0.000
22	A	22	GLY	0	-0.016	-0.006	15.186	0.046	0.046	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.833	-0.903	13.199	-0.884	-0.884	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.056	-0.037	7.892	-0.099	-0.099	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.038	0.016	8.264	-0.025	-0.025	0.000	0.000	0.000	0.000
26	A	26	THR	0	0.011	0.007	3.494	-1.762	-1.555	0.004	-0.079	-0.132	0.000
27	A	27	VAL	0	-0.053	-0.031	3.065	1.536	2.296	0.027	-0.267	-0.520	-0.001
28	A	28	ILE	0	-0.052	-0.016	3.651	-0.847	-0.534	0.003	-0.209	-0.107	-0.001
29	A	29	ARG	1	0.830	0.900	6.414	1.114	1.114	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.041	0.022	8.003	-0.199	-0.199	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.793	-0.870	8.427	-0.225	-0.225	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.876	-0.934	11.565	-0.142	-0.142	0.000	0.000	0.000	0.000
33	A	33	GLY	0	-0.080	-0.050	14.270	0.061	0.061	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.079	-0.030	15.929	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.010	0.006	15.857	0.013	0.013	0.000	0.000	0.000	0.000
36	A	36	TRP	0	-0.015	0.006	14.657	-0.075	-0.075	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.038	-0.032	8.064	0.026	0.026	0.000	0.000	0.000	0.000
38	A	38	TYR	0	0.003	0.007	9.910	0.043	0.043	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.014	-0.025	8.072	-0.401	-0.401	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.913	-0.943	8.118	-1.330	-1.330	0.000	0.000	0.000	0.000
41	A	41	CYS	0	0.018	0.008	9.091	-0.432	-0.432	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.892	-0.936	11.602	-0.726	-0.726	0.000	0.000	0.000	0.000
43	A	43	GLY	0	-0.057	-0.038	12.342	0.161	0.161	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.045	-0.007	13.971	0.098	0.098	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.907	0.946	11.699	0.584	0.584	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.030	0.005	12.649	0.158	0.158	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.057	-0.038	12.578	-0.211	-0.211	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.059	0.036	8.893	0.018	0.018	0.000	0.000	0.000	0.000
49	A	49	PRO	0	0.039	0.017	13.929	-0.033	-0.033	0.000	0.000	0.000	0.000
50	A	50	THR	0	0.020	-0.014	10.352	-0.109	-0.109	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.066	-0.039	12.519	-0.027	-0.027	0.000	0.000	0.000	0.000
52	A	52	TYR	0	-0.038	-0.010	14.915	0.069	0.069	0.000	0.000	0.000	0.000
53	A	53	CYS	0	0.003	0.019	10.571	-0.078	-0.078	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.914	0.984	8.257	0.407	0.407	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:GLY)