FMO DATABASE

FMODB ID: 538VZ

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	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	-111506.266275
FMO2-HF: Nuclear repulsion	98028.758918
FMO2-HF: Total energy	-13477.507357
FMO2-MP2: Total energy	-13514.696006

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.
-3.096	0.302	0.066	-1.324	-2.14	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 : 0.036 / q_NPA : 0.009

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	0.009	0.012	3.491	-2.142	0.034	-0.002	-0.963	-1.211	0.001
4	A	25	ARG	1	0.983	0.991	3.107	-2.275	-1.482	0.069	-0.212	-0.650	0.001
5	A	26	GLN	0	0.002	0.001	4.204	0.505	0.934	-0.001	-0.149	-0.279	0.000
6	A	27	ASN	0	0.016	-0.007	6.123	0.260	0.260	0.000	0.000	0.000	0.000
7	A	28	LEU	0	0.023	0.014	8.159	0.122	0.122	0.000	0.000	0.000	0.000
8	A	29	GLN	0	0.018	0.008	8.630	0.108	0.108	0.000	0.000	0.000	0.000
9	A	30	ASN	0	0.028	0.015	9.597	0.143	0.143	0.000	0.000	0.000	0.000
10	A	31	LEU	0	-0.016	-0.005	12.289	0.030	0.030	0.000	0.000	0.000	0.000
11	A	32	TYR	0	0.001	0.004	13.241	0.026	0.026	0.000	0.000	0.000	0.000
12	A	33	ILE	0	0.071	0.032	13.202	0.014	0.014	0.000	0.000	0.000	0.000
13	A	34	ASN	0	-0.052	-0.023	16.190	0.000	0.000	0.000	0.000	0.000	0.000
14	A	35	ARG	1	0.876	0.933	17.922	0.009	0.009	0.000	0.000	0.000	0.000
15	A	36	CYS	0	0.000	-0.007	18.137	0.008	0.008	0.000	0.000	0.000	0.000
16	A	37	LEU	0	0.021	0.012	19.337	0.000	0.000	0.000	0.000	0.000	0.000
17	A	38	ARG	1	0.930	0.967	22.173	0.034	0.034	0.000	0.000	0.000	0.000
18	A	39	GLU	-1	-0.853	-0.923	23.287	0.023	0.023	0.000	0.000	0.000	0.000
19	A	40	ILE	0	0.096	0.060	23.287	0.000	0.000	0.000	0.000	0.000	0.000
20	A	41	CYS	0	-0.091	-0.051	25.752	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	42	GLN	0	-0.099	-0.068	28.253	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	43	GLU	-1	-0.815	-0.905	28.392	0.057	0.057	0.000	0.000	0.000	0.000
23	A	44	LEU	0	-0.019	-0.017	29.306	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	45	LYS	1	0.800	0.892	30.201	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	46	GLU	-1	-0.827	-0.893	34.061	0.018	0.018	0.000	0.000	0.000	0.000
26	A	47	ILE	0	0.020	0.008	33.882	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	48	ARG	1	0.906	0.944	33.889	-0.016	-0.016	0.000	0.000	0.000	0.000
28	A	49	ALA	0	-0.035	-0.007	38.605	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	50	MET	0	-0.038	-0.022	38.148	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	51	LEU	0	-0.077	-0.009	39.621	0.000	0.000	0.000	0.000	0.000	0.000

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