FMO DATABASE

FMODB ID: KR6J3

Calculation Name: 1YOD-A-Xray310

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	30
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-111294.213386
FMO2-HF: Nuclear repulsion	97817.626209
FMO2-HF: Total energy	-13476.587178
FMO2-MP2: Total energy	-13513.834727

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.
-4.331	-0.762	0.067	-1.495	-2.142	0.001

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	0.025	0.017	3.549	-2.450	-0.163	-0.008	-1.106	-1.173	0.001
4	A	25	ARG	1	0.976	0.993	3.153	-2.824	-1.983	0.075	-0.246	-0.671	0.000
5	A	26	GLN	0	0.012	0.008	4.201	0.698	1.139	0.000	-0.143	-0.298	0.000
6	A	27	ASN	0	0.013	-0.009	6.104	0.195	0.195	0.000	0.000	0.000	0.000
7	A	28	LEU	0	0.020	0.014	8.171	0.043	0.043	0.000	0.000	0.000	0.000
8	A	29	GLN	0	0.008	-0.001	8.627	0.104	0.104	0.000	0.000	0.000	0.000
9	A	30	ASN	0	0.030	0.017	9.677	0.103	0.103	0.000	0.000	0.000	0.000
10	A	31	LEU	0	-0.023	-0.009	12.232	-0.029	-0.029	0.000	0.000	0.000	0.000
11	A	32	TYR	0	-0.006	0.001	13.270	-0.023	-0.023	0.000	0.000	0.000	0.000
12	A	33	ILE	0	0.062	0.022	13.431	-0.020	-0.020	0.000	0.000	0.000	0.000
13	A	34	ASN	0	-0.050	-0.019	16.176	-0.047	-0.047	0.000	0.000	0.000	0.000
14	A	35	ARG	1	0.945	0.972	17.918	-0.150	-0.150	0.000	0.000	0.000	0.000
15	A	36	CYS	0	-0.002	0.000	18.201	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	37	LEU	0	0.014	0.007	19.339	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	38	ARG	1	0.922	0.961	22.162	-0.122	-0.122	0.000	0.000	0.000	0.000
18	A	39	GLU	-1	-0.906	-0.960	23.628	0.150	0.150	0.000	0.000	0.000	0.000
19	A	40	ILE	0	0.101	0.062	23.385	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	41	CYS	0	-0.104	-0.058	25.799	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	42	GLN	0	-0.111	-0.058	28.243	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	43	GLU	-1	-0.837	-0.920	28.077	0.160	0.160	0.000	0.000	0.000	0.000
23	A	44	LEU	0	-0.020	-0.019	29.382	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	45	LYS	1	0.847	0.918	30.568	-0.112	-0.112	0.000	0.000	0.000	0.000
25	A	46	GLU	-1	-0.843	-0.913	33.977	0.094	0.094	0.000	0.000	0.000	0.000
26	A	47	ILE	0	0.005	-0.001	34.013	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	48	ARG	1	0.887	0.935	33.871	-0.107	-0.107	0.000	0.000	0.000	0.000
28	A	49	ALA	0	-0.037	-0.001	38.547	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	50	MET	0	-0.092	-0.045	38.322	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	51	LEU	-1	-0.959	-0.954	39.640	0.082	0.082	0.000	0.000	0.000	0.000

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