FMO DATABASE

FMODB ID: YZVM2

Calculation Name: 1TME-4-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TME

Chain ID: 4

ChEMBL ID:

UniProt ID: P13899

Base Structure: X-ray

Registration Date: 2023-06-22

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	25
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-64831.44272
FMO2-HF: Nuclear repulsion	55263.232906
FMO2-HF: Total energy	-9568.209814
FMO2-MP2: Total energy	-9596.340753

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(4:15:SER)

Summations of interaction energy for fragment #1(4:15: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.
0.025	1.607	-0.013	-0.987	-0.582	0

Interaction energy analysis for fragmet #1(4:15:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / 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].
3	4	17	ASN	0	-0.078	-0.048	3.812	-1.656	-0.074	-0.013	-0.987	-0.582
4	4	18	GLU	-1	-0.924	-0.950	4.976	1.006	1.006	0.000	0.000	0.000
5	4	19	GLY	0	0.017	0.004	5.390	-0.233	-0.233	0.000	0.000	0.000
6	4	20	VAL	0	-0.045	-0.022	7.959	0.062	0.062	0.000	0.000	0.000
7	4	21	ILE	0	0.099	0.039	10.224	0.085	0.085	0.000	0.000	0.000
8	4	22	ILE	0	-0.057	-0.016	11.997	0.058	0.058	0.000	0.000	0.000
9	4	23	ASN	0	-0.042	-0.030	8.060	-0.055	-0.055	0.000	0.000	0.000
10	4	24	ASN	0	-0.021	-0.017	11.748	0.061	0.061	0.000	0.000	0.000
11	4	25	PHE	0	-0.003	-0.002	14.468	0.007	0.007	0.000	0.000	0.000
12	4	26	TYR	0	0.011	0.038	16.675	-0.009	-0.009	0.000	0.000	0.000
13	4	27	SER	0	0.020	-0.007	16.034	0.044	0.044	0.000	0.000	0.000
14	4	28	ASN	0	0.041	-0.008	10.803	-0.009	-0.009	0.000	0.000	0.000
15	4	29	GLN	0	0.047	0.032	13.898	0.046	0.046	0.000	0.000	0.000
16	4	30	TYR	0	-0.059	-0.029	16.347	-0.017	-0.017	0.000	0.000	0.000
17	4	31	GLN	0	-0.064	-0.029	12.288	-0.056	-0.056	0.000	0.000	0.000
18	4	32	ASN	0	-0.014	0.006	10.207	-0.057	-0.057	0.000	0.000	0.000
19	4	33	SER	0	0.023	0.017	12.434	-0.041	-0.041	0.000	0.000	0.000
20	4	34	ILE	0	-0.014	-0.023	12.883	0.072	0.072	0.000	0.000	0.000
21	4	35	ASP	-1	-0.917	-0.926	10.328	0.746	0.746	0.000	0.000	0.000
22	4	36	LEU	0	-0.029	-0.020	13.887	-0.005	-0.005	0.000	0.000	0.000
23	4	37	SER	0	-0.017	-0.021	17.041	0.002	0.002	0.000	0.000	0.000
24	4	38	ALA	0	0.009	0.006	18.520	-0.023	-0.023	0.000	0.000	0.000
25	4	39	SER	0	0.022	0.028	21.915	-0.003	-0.003	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(4:15:SER)