FMO DATABASE

FMODB ID: VRNJ1

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	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	57
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-262741.857201
FMO2-HF: Nuclear repulsion	240221.968511
FMO2-HF: Total energy	-22519.88869
FMO2-MP2: Total energy	-22585.21048

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.
-9.745	-7.515	9.741	-6.142	-5.83	-0.038

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 : 0.017 / 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	GLY	0	0.010	0.009	3.872	-1.151	0.502	-0.010	-0.801	-0.842	0.004
4	A	4	TYR	0	-0.034	-0.007	2.286	-0.430	1.456	1.684	-1.441	-2.130	0.003
5	A	5	PHE	0	0.027	0.008	1.919	-9.225	-10.608	8.068	-3.879	-2.806	-0.045
6	A	6	ASP	-1	-0.824	-0.919	4.054	0.693	0.767	-0.001	-0.021	-0.052	0.000
7	A	7	ALA	0	0.016	-0.003	6.135	0.210	0.210	0.000	0.000	0.000	0.000
8	A	8	HIS	0	-0.005	0.011	9.315	0.056	0.056	0.000	0.000	0.000	0.000
9	A	9	ALA	0	-0.003	-0.013	9.034	0.049	0.049	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.025	0.015	10.206	-0.010	-0.010	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.004	-0.006	12.024	0.014	0.014	0.000	0.000	0.000	0.000
12	A	12	MET	0	-0.069	-0.037	14.119	0.040	0.040	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.856	-0.917	13.511	0.059	0.059	0.000	0.000	0.000	0.000
14	A	14	TYR	0	0.011	0.003	15.959	0.018	0.018	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.933	0.978	18.907	-0.072	-0.072	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.026	-0.026	19.649	0.007	0.007	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.014	0.012	19.374	0.004	0.004	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.109	0.053	22.997	0.002	0.002	0.000	0.000	0.000	0.000
19	A	19	PHE	0	-0.034	-0.021	24.921	0.006	0.006	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.900	0.921	21.096	0.003	0.003	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.924	-0.944	27.191	-0.069	-0.069	0.000	0.000	0.000	0.000
22	A	22	CYS	0	-0.026	-0.010	29.023	0.003	0.003	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.021	-0.011	30.122	0.002	0.002	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.013	0.001	31.303	0.002	0.002	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.813	-0.890	33.059	-0.033	-0.033	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.013	-0.006	35.008	0.002	0.002	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.027	-0.025	36.005	0.002	0.002	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.838	0.905	37.238	0.036	0.036	0.000	0.000	0.000	0.000
29	A	29	TYR	0	-0.015	-0.037	39.000	0.000	0.000	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.004	-0.007	40.447	0.001	0.001	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.031	-0.004	41.741	0.001	0.001	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.083	-0.037	41.687	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.054	-0.016	43.827	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.870	-0.920	45.096	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	35	GLY	0	-0.023	0.004	47.099	0.001	0.001	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.023	0.003	45.122	0.001	0.001	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.764	-0.871	45.302	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.040	-0.035	43.143	0.001	0.001	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.043	-0.046	43.660	0.003	0.003	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.801	-0.894	45.632	0.007	0.007	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.006	-0.010	44.744	0.001	0.001	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.045	-0.018	43.762	0.003	0.003	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.881	0.931	40.081	0.008	0.008	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.019	0.017	40.078	0.001	0.001	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.934	0.992	39.412	-0.015	-0.015	0.000	0.000	0.000	0.000
46	A	46	LEU	0	0.008	0.017	37.264	0.004	0.004	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.046	0.013	35.051	0.002	0.002	0.000	0.000	0.000	0.000
48	A	48	SER	0	-0.026	-0.024	34.437	0.003	0.003	0.000	0.000	0.000	0.000
49	A	49	HIS	0	0.004	0.005	34.053	0.007	0.007	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.003	-0.005	32.075	0.006	0.006	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.019	-0.025	29.947	0.002	0.002	0.000	0.000	0.000	0.000
52	A	52	ASN	0	-0.002	0.012	29.210	0.008	0.008	0.000	0.000	0.000	0.000
53	A	53	TYR	0	0.064	0.033	28.860	0.009	0.009	0.000	0.000	0.000	0.000
54	A	54	ALA	0	-0.040	-0.005	25.913	0.005	0.005	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.056	-0.030	24.892	0.013	0.013	0.000	0.000	0.000	0.000
56	A	56	GLN	0	-0.012	-0.016	24.552	0.007	0.007	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.792	0.910	21.049	-0.030	-0.030	0.000	0.000	0.000	0.000

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