FMO DATABASE

FMODB ID: 9GVM2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-107264.89186
FMO2-HF: Nuclear repulsion	94070.792457
FMO2-HF: Total energy	-13194.099402
FMO2-MP2: Total energy	-13232.102952

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.
-2.455	-0.289	-0.022	-0.989	-1.155	-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 : -0.050 / q_NPA : -0.042

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	B	40	GLU	-1	-0.956	-0.967	3.819	-1.493	0.673	-0.022	-0.989	-1.155	-0.001
4	B	41	ASP	-1	-0.889	-0.956	6.100	-0.146	-0.146	0.000	0.000	0.000	0.000
5	B	42	ASN	0	-0.066	-0.050	8.980	-0.077	-0.077	0.000	0.000	0.000	0.000
6	B	43	TRP	0	-0.020	0.011	9.737	0.045	0.045	0.000	0.000	0.000	0.000
7	B	44	ASP	-1	-0.976	-0.989	12.225	-0.187	-0.187	0.000	0.000	0.000	0.000
8	B	45	ASP	-1	-0.864	-0.887	14.923	-0.134	-0.134	0.000	0.000	0.000	0.000
9	B	46	ASP	-1	-0.931	-0.977	16.531	-0.098	-0.098	0.000	0.000	0.000	0.000
10	B	47	ASN	0	-0.185	-0.101	16.960	0.034	0.034	0.000	0.000	0.000	0.000
11	B	48	VAL	0	-0.012	-0.010	19.285	-0.017	-0.017	0.000	0.000	0.000	0.000
12	B	49	GLU	-1	-0.923	-0.981	17.236	-0.211	-0.211	0.000	0.000	0.000	0.000
13	B	50	ASP	-1	-0.788	-0.842	17.887	-0.262	-0.262	0.000	0.000	0.000	0.000
14	B	51	ASP	-1	-0.902	-0.973	19.875	-0.187	-0.187	0.000	0.000	0.000	0.000
15	B	52	PHE	0	0.014	0.010	20.813	0.022	0.022	0.000	0.000	0.000	0.000
16	B	53	SER	0	0.009	-0.047	20.665	0.024	0.024	0.000	0.000	0.000	0.000
17	B	54	ASN	0	-0.040	-0.024	23.434	0.031	0.031	0.000	0.000	0.000	0.000
18	B	55	GLN	0	-0.080	-0.033	24.779	0.019	0.019	0.000	0.000	0.000	0.000
19	B	56	LEU	0	0.034	0.023	25.735	0.013	0.013	0.000	0.000	0.000	0.000
20	B	57	ARG	1	0.878	0.947	25.473	0.137	0.137	0.000	0.000	0.000	0.000
21	B	58	ALA	0	0.004	-0.002	29.391	0.011	0.011	0.000	0.000	0.000	0.000
22	B	59	GLU	-1	-0.932	-0.968	31.116	-0.101	-0.101	0.000	0.000	0.000	0.000
23	B	60	LEU	0	0.008	-0.005	29.780	0.009	0.009	0.000	0.000	0.000	0.000
24	B	61	GLU	-1	-0.928	-0.962	33.440	-0.072	-0.072	0.000	0.000	0.000	0.000
25	B	62	LYS	1	0.845	0.934	34.953	0.104	0.104	0.000	0.000	0.000	0.000
26	B	63	HIS	0	-0.088	-0.046	36.301	0.006	0.006	0.000	0.000	0.000	0.000
27	B	64	GLY	0	-0.037	-0.005	38.343	0.004	0.004	0.000	0.000	0.000	0.000
28	B	65	TYR	0	-0.065	-0.026	34.829	0.005	0.005	0.000	0.000	0.000	0.000
29	B	66	LYS	1	0.984	0.985	34.249	0.062	0.062	0.000	0.000	0.000	0.000
30	B	67	MET	0	-0.006	0.007	31.746	0.004	0.004	0.000	0.000	0.000	0.000

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