FMO DATABASE

FMODB ID: 98V82

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	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	54
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-260981.517334
FMO2-HF: Nuclear repulsion	240121.577324
FMO2-HF: Total energy	-20859.94001
FMO2-MP2: Total energy	-20918.874187

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.
-6.088	-2.692	0.051	-1.781	-1.668	0

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 : 0.020 / q_NPA : 0.007

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	-0.064	-0.021	3.850	0.291	2.196	-0.014	-1.087	-0.805	0.002
4	A	4	GLU	-1	-0.784	-0.869	7.208	-0.627	-0.627	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.062	0.026	10.841	0.142	0.142	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.066	-0.041	13.653	0.077	0.077	0.000	0.000	0.000	0.000
7	A	7	TYR	0	-0.073	-0.042	16.665	0.080	0.080	0.000	0.000	0.000	0.000
8	A	8	ALA	0	0.043	0.031	18.137	-0.047	-0.047	0.000	0.000	0.000	0.000
9	A	9	TYR	0	-0.093	-0.078	18.303	0.047	0.047	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.952	-0.975	20.354	-0.318	-0.318	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.017	-0.014	20.236	0.012	0.012	0.000	0.000	0.000	0.000
12	A	12	GLN	0	-0.077	-0.058	21.664	0.060	0.060	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.008	0.001	22.606	0.034	0.034	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.964	-0.982	21.733	-0.303	-0.303	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.957	-0.971	18.334	-0.378	-0.378	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.812	-0.869	16.988	-0.455	-0.455	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.055	-0.026	12.617	0.001	0.001	0.000	0.000	0.000	0.000
18	A	18	SER	0	0.002	-0.001	17.244	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	19	ILE	0	-0.044	-0.006	14.020	-0.070	-0.070	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.871	-0.950	17.015	-0.354	-0.354	0.000	0.000	0.000	0.000
21	A	21	PRO	0	-0.108	-0.064	16.650	-0.071	-0.071	0.000	0.000	0.000	0.000
22	A	22	GLY	0	-0.023	-0.009	15.602	0.056	0.056	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.829	-0.900	13.224	-0.861	-0.861	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.055	-0.043	8.243	-0.078	-0.078	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.029	0.024	8.582	-0.173	-0.173	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.028	-0.031	4.084	-1.407	-1.293	-0.001	-0.039	-0.074	0.000
27	A	27	VAL	0	-0.046	-0.021	3.045	1.134	1.969	0.056	-0.303	-0.589	0.000
28	A	28	ILE	0	-0.069	-0.034	3.465	-1.510	-0.968	0.010	-0.352	-0.200	-0.002
29	A	29	ARG	1	0.705	0.827	6.150	1.062	1.062	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.044	0.027	7.343	-0.168	-0.168	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.754	-0.857	8.149	-0.210	-0.210	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.816	-0.881	11.470	-0.073	-0.073	0.000	0.000	0.000	0.000
33	A	33	GLY	0	-0.065	-0.028	14.287	0.050	0.050	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.085	-0.064	15.755	-0.023	-0.023	0.000	0.000	0.000	0.000
35	A	35	GLY	0	-0.006	0.000	15.970	0.005	0.005	0.000	0.000	0.000	0.000
36	A	36	TRP	0	-0.008	0.006	14.442	-0.060	-0.060	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.017	-0.001	7.849	0.039	0.039	0.000	0.000	0.000	0.000
38	A	38	TYR	0	0.011	0.007	10.053	0.003	0.003	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.028	-0.013	7.907	-0.385	-0.385	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.873	-0.926	8.266	-1.518	-1.518	0.000	0.000	0.000	0.000
41	A	41	CYS	0	0.014	0.012	9.277	-0.475	-0.475	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.880	-0.924	11.811	-0.710	-0.710	0.000	0.000	0.000	0.000
43	A	43	GLY	0	-0.069	-0.037	12.670	0.156	0.156	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.045	-0.015	14.189	0.065	0.065	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.928	0.952	11.146	0.609	0.609	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.015	0.004	12.644	0.154	0.154	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.037	-0.026	12.510	-0.191	-0.191	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.060	0.021	8.702	0.005	0.005	0.000	0.000	0.000	0.000
49	A	49	PRO	0	0.036	0.023	13.738	-0.023	-0.023	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.002	-0.033	10.226	-0.108	-0.108	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.047	-0.031	12.741	-0.025	-0.025	0.000	0.000	0.000	0.000
52	A	52	TYR	0	-0.028	-0.002	15.119	0.063	0.063	0.000	0.000	0.000	0.000
53	A	53	CYS	0	0.000	0.028	10.925	-0.074	-0.074	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.752	0.874	8.717	0.467	0.467	0.000	0.000	0.000	0.000

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