FMO DATABASE

FMODB ID: 2JKNR

Calculation Name: 5JW9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5JW9

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UHB7

Base Structure: X-ray

Registration Date: 2023-06-21

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	36
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-118590.661783
FMO2-HF: Nuclear repulsion	103865.124016
FMO2-HF: Total energy	-14725.537766
FMO2-MP2: Total energy	-14766.515315

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:14:SER)

Summations of interaction energy for fragment #1(A:14: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.
-34.882	-34.736	17.678	-9.798	-8.027	-0.105

Interaction energy analysis for fragmet #1(A:14:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.057 / q_NPA : -0.039

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	16	VAL	0	0.033	0.009	3.255	-1.110	0.681	0.013	-0.816	-0.988	0.002
4	A	17	ASP	-1	-0.840	-0.921	1.853	-14.843	-16.958	10.529	-4.648	-3.766	-0.050
5	A	18	GLU	-1	-0.926	-0.965	1.845	-22.582	-22.112	7.136	-4.334	-3.273	-0.057
6	A	19	ILE	0	0.048	0.020	5.797	1.278	1.278	0.000	0.000	0.000	0.000
7	A	20	LEU	0	-0.012	-0.007	6.928	0.605	0.605	0.000	0.000	0.000	0.000
8	A	21	LYS	1	0.922	0.976	8.128	1.727	1.727	0.000	0.000	0.000	0.000
9	A	22	GLU	-1	-0.968	-0.975	9.753	-0.898	-0.898	0.000	0.000	0.000	0.000
10	A	23	MET	0	-0.021	-0.022	11.877	0.270	0.270	0.000	0.000	0.000	0.000
11	A	24	THR	0	-0.079	-0.052	12.261	0.165	0.165	0.000	0.000	0.000	0.000
12	A	25	HIS	0	-0.056	-0.016	13.573	0.189	0.189	0.000	0.000	0.000	0.000
13	A	26	SER	0	-0.021	-0.018	17.073	0.051	0.051	0.000	0.000	0.000	0.000
14	A	27	TRP	0	0.013	0.006	19.549	0.056	0.056	0.000	0.000	0.000	0.000
15	A	28	PRO	0	-0.030	0.001	22.949	0.013	0.013	0.000	0.000	0.000	0.000
16	A	29	PRO	0	0.010	0.004	26.579	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	30	PRO	0	-0.009	-0.006	29.269	0.003	0.003	0.000	0.000	0.000	0.000
18	A	31	LEU	0	0.006	-0.003	31.618	0.009	0.009	0.000	0.000	0.000	0.000
19	A	32	THR	0	-0.008	-0.008	34.560	0.003	0.003	0.000	0.000	0.000	0.000
20	A	33	ALA	0	0.019	0.012	37.921	0.002	0.002	0.000	0.000	0.000	0.000
21	A	34	ILE	0	0.023	0.008	40.904	0.002	0.002	0.000	0.000	0.000	0.000
22	A	35	HIS	0	-0.019	0.003	42.699	0.007	0.007	0.000	0.000	0.000	0.000
23	A	36	THR	0	-0.002	0.015	45.829	0.000	0.000	0.000	0.000	0.000	0.000
24	A	37	PRO	0	0.032	0.000	48.490	0.003	0.003	0.000	0.000	0.000	0.000
25	A	38	CYS	0	-0.009	-0.018	41.917	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	39	LYS	1	0.895	0.945	43.045	0.109	0.109	0.000	0.000	0.000	0.000
27	A	40	THR	0	-0.024	-0.022	37.201	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	41	GLU	-1	-0.901	-0.929	37.851	-0.124	-0.124	0.000	0.000	0.000	0.000
29	A	42	PRO	0	-0.021	-0.001	35.675	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	43	SER	0	0.032	-0.001	32.730	0.004	0.004	0.000	0.000	0.000	0.000
31	A	44	LYS	1	0.940	0.973	28.662	0.183	0.183	0.000	0.000	0.000	0.000
32	A	45	PHE	0	0.060	0.025	22.629	0.008	0.008	0.000	0.000	0.000	0.000
33	A	46	PRO	0	-0.046	-0.018	24.166	0.004	0.004	0.000	0.000	0.000	0.000
34	A	47	PHE	0	0.008	-0.004	22.261	-0.021	-0.021	0.000	0.000	0.000	0.000
35	A	48	PRO	0	0.015	0.023	16.886	0.027	0.027	0.000	0.000	0.000	0.000
36	A	49	THR	0	-0.025	-0.010	16.794	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:14:SER)