FMO DATABASE

FMODB ID: 438VN

Calculation Name: 1YOD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YOD

Chain ID: A

ChEMBL ID:

UniProt ID:

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	-111357.597425
FMO2-HF: Nuclear repulsion	97880.398267
FMO2-HF: Total energy	-13477.199159
FMO2-MP2: Total energy	-13514.427588

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:22:GLN)

Summations of interaction energy for fragment #1(A:22:GLN)

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.
-4.353	-0.749	0.059	-1.507	-2.156	0.002

Interaction energy analysis for fragmet #1(A:22:GLN)

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 : 0.016

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	A	24	ALA	0	0.024	0.016	3.549	-2.449	-0.136	-0.015	-1.110	-1.188	0.002
4	A	25	ARG	1	0.978	0.993	3.153	-2.806	-1.958	0.075	-0.249	-0.674	0.000
5	A	26	GLN	0	0.012	0.007	4.201	0.709	1.152	-0.001	-0.148	-0.294	0.000
6	A	27	ASN	0	0.013	-0.009	6.104	0.209	0.209	0.000	0.000	0.000	0.000
7	A	28	LEU	0	0.020	0.014	8.171	0.047	0.047	0.000	0.000	0.000	0.000
8	A	29	GLN	0	0.007	-0.001	8.627	0.103	0.103	0.000	0.000	0.000	0.000
9	A	30	ASN	0	0.031	0.017	9.678	0.106	0.106	0.000	0.000	0.000	0.000
10	A	31	LEU	0	-0.024	-0.009	12.232	-0.025	-0.025	0.000	0.000	0.000	0.000
11	A	32	TYR	0	-0.005	0.001	13.270	-0.024	-0.024	0.000	0.000	0.000	0.000
12	A	33	ILE	0	0.063	0.023	13.432	-0.020	-0.020	0.000	0.000	0.000	0.000
13	A	34	ASN	0	-0.052	-0.020	16.176	-0.045	-0.045	0.000	0.000	0.000	0.000
14	A	35	ARG	1	0.948	0.974	17.918	-0.146	-0.146	0.000	0.000	0.000	0.000
15	A	36	CYS	0	0.002	0.002	18.201	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	37	LEU	0	0.011	0.007	19.340	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	38	ARG	1	0.921	0.961	22.162	-0.119	-0.119	0.000	0.000	0.000	0.000
18	A	39	GLU	-1	-0.902	-0.958	23.628	0.148	0.148	0.000	0.000	0.000	0.000
19	A	40	ILE	0	0.101	0.063	23.387	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	41	CYS	0	-0.103	-0.058	25.799	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	42	GLN	0	-0.108	-0.057	28.243	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	43	GLU	-1	-0.830	-0.917	28.077	0.159	0.159	0.000	0.000	0.000	0.000
23	A	44	LEU	0	-0.018	-0.018	29.382	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	45	LYS	1	0.848	0.918	30.568	-0.111	-0.111	0.000	0.000	0.000	0.000
25	A	46	GLU	-1	-0.832	-0.906	33.977	0.093	0.093	0.000	0.000	0.000	0.000
26	A	47	ILE	0	0.014	0.005	34.013	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	48	ARG	1	0.893	0.936	33.872	-0.107	-0.107	0.000	0.000	0.000	0.000
28	A	49	ALA	0	-0.044	-0.007	38.547	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	50	MET	0	-0.047	-0.023	38.224	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	51	LEU	0	-0.044	0.006	39.633	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:22:GLN)