FMO DATABASE

FMODB ID: 53Y4Z

Calculation Name: 2DB7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DB7

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y5J3

Base Structure: X-ray

Registration Date: 2023-03-13

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	57
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-263042.964351
FMO2-HF: Nuclear repulsion	240523.371854
FMO2-HF: Total energy	-22519.592496
FMO2-MP2: Total energy	-22584.963714

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:SER)

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

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.
-8.254	-3.728	2.173	-3.034	-3.664	-0.011

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

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 : 0.017

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	GLY	0	-0.006	-0.006	3.791	-2.485	-0.364	-0.019	-1.079	-1.023	0.007
4	A	4	TYR	0	-0.025	-0.001	2.551	0.708	1.983	0.284	-0.490	-1.068	0.000
5	A	5	PHE	0	0.021	0.004	2.308	-7.679	-6.644	1.909	-1.457	-1.487	-0.018
6	A	6	ASP	-1	-0.816	-0.913	4.367	0.370	0.465	-0.001	-0.008	-0.086	0.000
7	A	7	ALA	0	0.003	-0.015	6.000	0.393	0.393	0.000	0.000	0.000	0.000
8	A	8	HIS	0	-0.011	0.001	9.243	0.136	0.136	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.000	-0.013	8.955	0.098	0.098	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.014	0.017	10.241	0.033	0.033	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.004	-0.002	11.924	0.055	0.055	0.000	0.000	0.000	0.000
12	A	12	MET	0	-0.046	-0.023	14.095	0.057	0.057	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.890	-0.934	13.372	-0.024	-0.024	0.000	0.000	0.000	0.000
14	A	14	TYR	0	0.003	-0.012	16.397	0.025	0.025	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.931	0.980	19.137	0.009	0.009	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.033	-0.025	19.510	0.009	0.009	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.007	0.007	19.411	0.010	0.010	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.084	0.048	22.919	0.003	0.003	0.000	0.000	0.000	0.000
19	A	19	PHE	0	-0.076	-0.042	24.780	0.008	0.008	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.936	0.937	21.333	0.042	0.042	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.915	-0.922	27.200	-0.092	-0.092	0.000	0.000	0.000	0.000
22	A	22	CYS	0	-0.005	-0.006	28.936	0.005	0.005	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.037	-0.008	30.003	0.004	0.004	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.001	-0.012	31.231	0.004	0.004	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.832	-0.920	32.955	-0.048	-0.048	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.037	-0.013	34.912	0.003	0.003	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.021	-0.018	36.040	0.003	0.003	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.918	0.964	37.217	0.050	0.050	0.000	0.000	0.000	0.000
29	A	29	TYR	0	-0.056	-0.035	39.007	0.000	0.000	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.016	-0.003	40.237	0.002	0.002	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.013	0.004	41.807	0.002	0.002	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.099	-0.057	41.448	0.000	0.000	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.054	-0.018	43.589	0.000	0.000	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.901	-0.937	45.179	-0.019	-0.019	0.000	0.000	0.000	0.000
35	A	35	GLY	0	-0.018	0.016	46.792	0.002	0.002	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.031	-0.008	44.478	0.002	0.002	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.787	-0.898	44.951	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.054	-0.062	42.981	0.001	0.001	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.046	-0.025	43.556	0.003	0.003	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.803	-0.892	45.475	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.009	-0.012	44.684	0.001	0.001	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.018	-0.004	43.045	0.002	0.002	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.912	0.958	39.798	0.018	0.018	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.017	0.015	39.984	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.939	0.972	39.121	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	46	LEU	0	0.003	0.014	37.137	0.003	0.003	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.034	0.009	34.654	0.001	0.001	0.000	0.000	0.000	0.000
48	A	48	SER	0	-0.044	-0.036	34.232	0.002	0.002	0.000	0.000	0.000	0.000
49	A	49	HIS	0	0.016	0.016	33.884	0.006	0.006	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.000	-0.007	31.834	0.004	0.004	0.000	0.000	0.000	0.000
51	A	51	ASN	0	0.019	0.001	29.894	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	52	ASN	0	0.016	0.001	28.992	0.006	0.006	0.000	0.000	0.000	0.000
53	A	53	TYR	0	0.000	0.019	27.846	0.007	0.007	0.000	0.000	0.000	0.000
54	A	54	ALA	0	-0.050	-0.041	25.648	0.006	0.006	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.077	-0.033	24.550	0.008	0.008	0.000	0.000	0.000	0.000
56	A	56	GLN	0	-0.026	-0.012	24.564	0.006	0.006	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.898	0.978	21.202	0.008	0.008	0.000	0.000	0.000	0.000

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