FMO DATABASE

FMODB ID: MVMNZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-118366.668602
FMO2-HF: Nuclear repulsion	103641.269061
FMO2-HF: Total energy	-14725.399541
FMO2-MP2: Total energy	-14766.368812

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.
-18.45	-18.307	14.197	-8.052	-6.288	-0.063

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 : -0.043 / q_NPA : -0.032

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

Sort

Graph Options

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	0.040	0.011	3.292	-4.170	-1.818	0.081	-1.146	-1.287	0.006
4	A	17	ASP	-1	-0.867	-0.922	1.806	-17.725	-20.459	14.114	-6.748	-4.632	-0.069
5	A	18	GLU	-1	-0.957	-0.979	3.923	2.807	3.332	0.002	-0.158	-0.369	0.000
6	A	19	ILE	0	0.013	0.005	6.212	0.136	0.136	0.000	0.000	0.000	0.000
7	A	20	LEU	0	0.004	-0.003	6.612	0.049	0.049	0.000	0.000	0.000	0.000
8	A	21	LYS	1	0.938	1.000	8.117	0.152	0.152	0.000	0.000	0.000	0.000
9	A	22	GLU	-1	-0.984	-0.992	10.037	0.286	0.286	0.000	0.000	0.000	0.000
10	A	23	MET	0	-0.031	-0.021	11.704	0.022	0.022	0.000	0.000	0.000	0.000
11	A	24	THR	0	-0.086	-0.065	11.715	0.002	0.002	0.000	0.000	0.000	0.000
12	A	25	HIS	0	-0.024	0.002	14.194	-0.017	-0.017	0.000	0.000	0.000	0.000
13	A	26	SER	0	-0.033	-0.018	17.001	0.013	0.013	0.000	0.000	0.000	0.000
14	A	27	TRP	0	0.019	0.010	20.097	0.005	0.005	0.000	0.000	0.000	0.000
15	A	28	PRO	0	-0.043	-0.006	23.104	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	29	PRO	0	0.019	0.003	26.607	0.005	0.005	0.000	0.000	0.000	0.000
17	A	30	PRO	0	-0.007	0.000	29.044	0.002	0.002	0.000	0.000	0.000	0.000
18	A	31	LEU	0	0.015	0.000	31.251	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	32	THR	0	0.005	0.006	34.398	0.001	0.001	0.000	0.000	0.000	0.000
20	A	33	ALA	0	0.003	0.000	37.546	0.001	0.001	0.000	0.000	0.000	0.000
21	A	34	ILE	0	0.021	0.003	40.681	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	35	HIS	0	-0.039	-0.019	42.263	0.000	0.000	0.000	0.000	0.000	0.000
23	A	36	THR	0	-0.008	0.019	45.675	0.000	0.000	0.000	0.000	0.000	0.000
24	A	37	PRO	0	0.031	-0.004	48.753	0.000	0.000	0.000	0.000	0.000	0.000
25	A	38	CYS	0	0.002	-0.007	42.582	0.000	0.000	0.000	0.000	0.000	0.000
26	A	39	LYS	1	0.933	0.972	42.692	0.003	0.003	0.000	0.000	0.000	0.000
27	A	40	THR	0	-0.014	-0.011	36.974	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	41	GLU	-1	-0.940	-0.957	38.358	-0.014	-0.014	0.000	0.000	0.000	0.000
29	A	42	PRO	0	-0.026	-0.008	35.864	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	43	SER	0	0.066	0.015	31.902	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	44	LYS	1	0.936	0.977	29.584	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	45	PHE	0	0.035	0.010	23.172	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	46	PRO	0	-0.053	-0.022	24.582	0.008	0.008	0.000	0.000	0.000	0.000
34	A	47	PHE	0	0.015	0.002	22.752	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	48	PRO	0	0.017	0.021	17.649	0.003	0.003	0.000	0.000	0.000	0.000
36	A	49	THR	0	-0.014	-0.006	17.699	0.010	0.010	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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