FMO DATABASE

FMODB ID: M319Z

Calculation Name: 3T5X-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3T5X

Chain ID: B

ChEMBL ID:

UniProt ID: Q5JVF3

Base Structure: X-ray

Registration Date: 2023-06-19

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	30
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-107301.517856
FMO2-HF: Nuclear repulsion	94107.143866
FMO2-HF: Total energy	-13194.37399
FMO2-MP2: Total energy	-13232.395568

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(B:38:VAL)

Summations of interaction energy for fragment #1(B:38:VAL)

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.
-1.901	0.223	-0.023	-0.98	-1.12	-0.001

Interaction energy analysis for fragmet #1(B:38:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.054 / q_NPA : -0.045

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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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	B	40	GLU	-1	-0.882	-0.923	3.819	-1.264	0.860	-0.023	-0.980	-1.120	-0.001
4	B	41	ASP	-1	-0.907	-0.963	6.111	-0.032	-0.032	0.000	0.000	0.000	0.000
5	B	42	ASN	0	-0.084	-0.058	8.039	0.070	0.070	0.000	0.000	0.000	0.000
6	B	43	TRP	0	-0.059	-0.024	9.455	0.041	0.041	0.000	0.000	0.000	0.000
7	B	44	ASP	-1	-0.957	-0.972	12.234	-0.190	-0.190	0.000	0.000	0.000	0.000
8	B	45	ASP	-1	-0.881	-0.914	14.933	-0.102	-0.102	0.000	0.000	0.000	0.000
9	B	46	ASP	-1	-0.951	-0.977	16.540	-0.082	-0.082	0.000	0.000	0.000	0.000
10	B	47	ASN	0	-0.150	-0.078	17.074	0.028	0.028	0.000	0.000	0.000	0.000
11	B	48	VAL	0	0.000	-0.009	19.292	-0.017	-0.017	0.000	0.000	0.000	0.000
12	B	49	GLU	-1	-0.927	-0.977	17.364	-0.207	-0.207	0.000	0.000	0.000	0.000
13	B	50	ASP	-1	-0.766	-0.849	17.971	-0.251	-0.251	0.000	0.000	0.000	0.000
14	B	51	ASP	-1	-0.897	-0.961	19.879	-0.183	-0.183	0.000	0.000	0.000	0.000
15	B	52	PHE	0	0.025	0.014	20.802	0.022	0.022	0.000	0.000	0.000	0.000
16	B	53	SER	0	0.013	-0.027	20.841	0.027	0.027	0.000	0.000	0.000	0.000
17	B	54	ASN	0	-0.054	-0.015	23.440	0.032	0.032	0.000	0.000	0.000	0.000
18	B	55	GLN	0	-0.085	-0.046	24.879	0.020	0.020	0.000	0.000	0.000	0.000
19	B	56	LEU	0	0.025	0.018	25.657	0.013	0.013	0.000	0.000	0.000	0.000
20	B	57	ARG	1	0.852	0.920	24.912	0.135	0.135	0.000	0.000	0.000	0.000
21	B	58	ALA	0	-0.002	-0.003	29.397	0.011	0.011	0.000	0.000	0.000	0.000
22	B	59	GLU	-1	-0.797	-0.886	31.121	-0.095	-0.095	0.000	0.000	0.000	0.000
23	B	60	LEU	0	0.013	0.009	29.776	0.008	0.008	0.000	0.000	0.000	0.000
24	B	61	GLU	-1	-0.803	-0.884	33.447	-0.066	-0.066	0.000	0.000	0.000	0.000
25	B	62	LYS	1	0.735	0.857	34.476	0.102	0.102	0.000	0.000	0.000	0.000
26	B	63	HIS	0	-0.105	-0.060	35.867	0.006	0.006	0.000	0.000	0.000	0.000
27	B	64	GLY	0	-0.037	-0.007	38.336	0.004	0.004	0.000	0.000	0.000	0.000
28	B	65	TYR	0	-0.073	-0.030	34.889	0.004	0.004	0.000	0.000	0.000	0.000
29	B	66	LYS	1	0.846	0.906	34.259	0.062	0.062	0.000	0.000	0.000	0.000
30	B	67	MET	0	0.002	0.007	31.740	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:38:VAL)