FMO DATABASE

FMODB ID: YY1J2

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	OptHSide
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	-262756.599401
FMO2-HF: Nuclear repulsion	240236.811682
FMO2-HF: Total energy	-22519.787719
FMO2-MP2: Total energy	-22585.139345

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.
-8.671	-4.183	2.585	-3.25	-3.824	-0.015

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 : 0.022 / 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	-0.005	3.791	-2.287	-0.167	-0.019	-1.082	-1.020	0.006
4	A	4	TYR	0	-0.025	0.000	2.428	0.651	1.902	0.417	-0.543	-1.126	0.000
5	A	5	PHE	0	0.020	0.004	2.247	-8.187	-7.167	2.188	-1.617	-1.590	-0.021
6	A	6	ASP	-1	-0.830	-0.924	4.393	0.375	0.472	-0.001	-0.008	-0.088	0.000
7	A	7	ALA	0	0.011	-0.010	6.009	0.373	0.373	0.000	0.000	0.000	0.000
8	A	8	HIS	0	-0.003	0.007	9.256	0.126	0.126	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.001	-0.009	8.981	0.090	0.090	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.022	0.016	10.286	0.029	0.029	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.008	0.002	11.966	0.048	0.048	0.000	0.000	0.000	0.000
12	A	12	MET	0	-0.047	-0.026	14.132	0.053	0.053	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.890	-0.932	13.507	0.010	0.010	0.000	0.000	0.000	0.000
14	A	14	TYR	0	-0.007	-0.018	16.299	0.021	0.021	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.931	0.979	19.184	-0.016	-0.016	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.012	-0.006	19.706	0.007	0.007	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.015	0.013	19.374	0.008	0.008	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.088	0.050	22.977	0.002	0.002	0.000	0.000	0.000	0.000
19	A	19	PHE	0	-0.067	-0.044	24.833	0.008	0.008	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.913	0.921	21.184	0.031	0.031	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.919	-0.927	27.263	-0.085	-0.085	0.000	0.000	0.000	0.000
22	A	22	CYS	0	-0.018	-0.004	28.991	0.004	0.004	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.025	-0.012	29.992	0.004	0.004	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.004	-0.006	31.264	0.003	0.003	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.804	-0.888	33.019	-0.042	-0.042	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.015	-0.004	34.970	0.003	0.003	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.021	-0.016	36.105	0.002	0.002	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.858	0.913	37.283	0.045	0.045	0.000	0.000	0.000	0.000
29	A	29	TYR	0	-0.041	-0.038	39.065	0.000	0.000	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.015	-0.002	40.278	0.002	0.002	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.014	0.006	41.811	0.002	0.002	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.095	-0.057	41.602	0.000	0.000	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.043	-0.013	43.562	0.000	0.000	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.897	-0.923	45.097	-0.016	-0.016	0.000	0.000	0.000	0.000
35	A	35	GLY	0	-0.018	0.015	46.853	0.002	0.002	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.032	-0.011	44.750	0.002	0.002	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.790	-0.893	45.023	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.036	-0.037	43.094	0.001	0.001	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.032	-0.028	43.639	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.822	-0.898	45.651	0.000	0.000	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.004	-0.015	44.763	0.001	0.001	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.017	-0.007	43.345	0.002	0.002	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.885	0.933	39.844	0.015	0.015	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.019	0.015	40.060	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.941	0.987	39.201	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	46	LEU	0	0.004	0.012	37.413	0.003	0.003	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.048	0.013	34.799	0.001	0.001	0.000	0.000	0.000	0.000
48	A	48	SER	0	-0.021	-0.023	34.309	0.002	0.002	0.000	0.000	0.000	0.000
49	A	49	HIS	0	0.004	0.013	33.966	0.006	0.006	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.007	-0.006	31.924	0.005	0.005	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.033	-0.030	29.971	0.000	0.000	0.000	0.000	0.000	0.000
52	A	52	ASN	0	0.027	0.006	29.074	0.006	0.006	0.000	0.000	0.000	0.000
53	A	53	TYR	0	0.002	0.014	28.351	0.008	0.008	0.000	0.000	0.000	0.000
54	A	54	ALA	0	-0.048	-0.034	25.767	0.007	0.007	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.059	-0.019	24.629	0.009	0.009	0.000	0.000	0.000	0.000
56	A	56	GLN	0	-0.020	-0.007	24.649	0.006	0.006	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.859	0.955	21.428	0.002	0.002	0.000	0.000	0.000	0.000

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