FMO DATABASE

FMODB ID: LN3N9

Calculation Name: 2A28-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

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	-261514.194326
FMO2-HF: Nuclear repulsion	240654.343701
FMO2-HF: Total energy	-20859.850625
FMO2-MP2: Total energy	-20918.780207

3D Structure Molmil

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.
-5.479	-2.115	-0.003	-1.655	-1.707	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 : 0.016 / q_NPA : 0.005

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	-0.071	-0.026	3.734	0.299	2.432	-0.029	-1.123	-0.981	0.004
4	A	4	GLU	-1	-0.809	-0.889	7.090	-0.678	-0.678	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.044	0.017	10.498	0.158	0.158	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.053	-0.034	13.550	0.083	0.083	0.000	0.000	0.000	0.000
7	A	7	TYR	0	-0.073	-0.043	16.357	0.095	0.095	0.000	0.000	0.000	0.000
8	A	8	ALA	0	0.036	0.024	17.682	-0.058	-0.058	0.000	0.000	0.000	0.000
9	A	9	TYR	0	-0.103	-0.082	18.210	0.045	0.045	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.952	-0.971	20.167	-0.334	-0.334	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.021	-0.015	20.039	0.013	0.013	0.000	0.000	0.000	0.000
12	A	12	GLN	0	-0.092	-0.070	21.515	0.064	0.064	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.043	0.012	23.030	0.031	0.031	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.969	-0.981	21.896	-0.313	-0.313	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.967	-0.973	18.584	-0.395	-0.395	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.799	-0.865	17.250	-0.480	-0.480	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.060	-0.027	12.597	0.009	0.009	0.000	0.000	0.000	0.000
18	A	18	SER	0	-0.007	-0.010	17.267	0.002	0.002	0.000	0.000	0.000	0.000
19	A	19	ILE	0	-0.052	-0.011	13.774	-0.069	-0.069	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.871	-0.941	16.715	-0.379	-0.379	0.000	0.000	0.000	0.000
21	A	21	PRO	0	-0.066	-0.047	16.392	-0.073	-0.073	0.000	0.000	0.000	0.000
22	A	22	GLY	0	-0.035	-0.019	15.187	0.045	0.045	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.824	-0.894	13.078	-0.890	-0.890	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.071	-0.049	7.926	-0.082	-0.082	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.038	0.016	8.396	-0.023	-0.023	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.017	-0.013	3.757	-1.750	-1.575	0.001	-0.061	-0.115	0.000
27	A	27	VAL	0	-0.057	-0.035	3.114	1.502	2.242	0.022	-0.259	-0.504	-0.001
28	A	28	ILE	0	-0.052	-0.014	3.651	-0.856	-0.540	0.003	-0.212	-0.107	-0.001
29	A	29	ARG	1	0.749	0.855	6.414	1.131	1.131	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.031	0.018	8.001	-0.195	-0.195	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.785	-0.866	8.427	-0.245	-0.245	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.824	-0.881	11.565	-0.159	-0.159	0.000	0.000	0.000	0.000
33	A	33	GLY	0	-0.070	-0.043	14.270	0.061	0.061	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.091	-0.058	16.035	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.001	0.003	15.856	0.014	0.014	0.000	0.000	0.000	0.000
36	A	36	TRP	0	-0.004	0.011	14.663	-0.070	-0.070	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.030	-0.021	8.036	0.020	0.020	0.000	0.000	0.000	0.000
38	A	38	TYR	0	0.026	0.014	9.922	0.037	0.037	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.011	-0.027	8.073	-0.403	-0.403	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.866	-0.925	8.123	-1.501	-1.501	0.000	0.000	0.000	0.000
41	A	41	CYS	0	0.036	0.025	9.094	-0.488	-0.488	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.911	-0.938	11.572	-0.715	-0.715	0.000	0.000	0.000	0.000
43	A	43	GLY	0	-0.062	-0.042	12.342	0.160	0.160	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.038	-0.004	13.973	0.095	0.095	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.909	0.946	11.476	0.573	0.573	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.027	0.010	12.651	0.160	0.160	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.057	-0.038	12.580	-0.213	-0.213	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.062	0.035	8.864	0.017	0.017	0.000	0.000	0.000	0.000
49	A	49	PRO	0	0.045	0.022	13.929	-0.032	-0.032	0.000	0.000	0.000	0.000
50	A	50	THR	0	0.012	-0.030	10.210	-0.112	-0.112	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.045	-0.028	12.519	-0.028	-0.028	0.000	0.000	0.000	0.000
52	A	52	TYR	0	-0.045	-0.013	14.933	0.069	0.069	0.000	0.000	0.000	0.000
53	A	53	CYS	0	-0.010	0.016	10.606	-0.074	-0.074	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.804	0.918	8.260	0.463	0.463	0.000	0.000	0.000	0.000

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