FMO DATABASE

FMODB ID: 49QJN

Calculation Name: 5D8A-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D8A

Chain ID: D

ChEMBL ID:

UniProt ID: Q6PN23

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:

Apendix: None

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	45
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-137780.948991
FMO2-HF: Nuclear repulsion	120024.460478
FMO2-HF: Total energy	-17756.488513
FMO2-MP2: Total energy	-17807.011736

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(D:15:SER)

Summations of interaction energy for fragment #1(D: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.
-1.166	1.672	-0.009	-1.343	-1.487	0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / 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	D	17	ASN	0	-0.067	-0.027	3.821	0.078	2.323	-0.024	-1.197	-1.025	0.004
4	D	18	THR	0	0.023	0.016	3.231	-0.386	0.161	0.016	-0.135	-0.428	0.000
5	D	19	GLY	0	0.013	0.001	4.539	-0.329	-0.283	-0.001	-0.011	-0.034	0.000
6	D	20	SER	0	-0.024	0.007	6.999	-0.209	-0.209	0.000	0.000	0.000	0.000
7	D	21	ILE	0	0.017	0.001	7.903	0.251	0.251	0.000	0.000	0.000	0.000
8	D	22	ILE	0	-0.047	-0.023	10.411	0.039	0.039	0.000	0.000	0.000	0.000
9	D	23	ASN	0	0.005	0.006	10.214	0.214	0.214	0.000	0.000	0.000	0.000
10	D	24	ASN	0	0.023	0.000	8.920	-0.037	-0.037	0.000	0.000	0.000	0.000
11	D	25	TYR	0	-0.011	-0.001	10.971	-0.025	-0.025	0.000	0.000	0.000	0.000
12	D	26	TYR	0	-0.007	0.005	12.659	-0.035	-0.035	0.000	0.000	0.000	0.000
13	D	27	MET	0	0.006	0.000	12.124	0.027	0.027	0.000	0.000	0.000	0.000
14	D	28	GLN	0	0.061	0.016	8.176	-0.186	-0.186	0.000	0.000	0.000	0.000
15	D	29	GLN	0	0.022	-0.006	10.779	-0.095	-0.095	0.000	0.000	0.000	0.000
16	D	30	TYR	0	-0.041	-0.013	13.083	0.000	0.000	0.000	0.000	0.000	0.000
17	D	31	GLN	0	-0.035	0.004	7.918	0.110	0.110	0.000	0.000	0.000	0.000
18	D	32	ASN	0	-0.033	-0.025	6.005	-0.108	-0.108	0.000	0.000	0.000	0.000
19	D	33	SER	0	0.048	0.040	9.673	0.105	0.105	0.000	0.000	0.000	0.000
20	D	34	MET	0	-0.044	-0.029	10.677	-0.062	-0.062	0.000	0.000	0.000	0.000
21	D	35	ASP	-1	-0.894	-0.932	10.055	-0.590	-0.590	0.000	0.000	0.000	0.000
22	D	36	THR	0	-0.047	-0.027	13.379	0.058	0.058	0.000	0.000	0.000	0.000
23	D	37	GLN	0	-0.017	-0.014	13.716	-0.009	-0.009	0.000	0.000	0.000	0.000
24	D	38	LEU	0	0.000	0.009	18.081	0.017	0.017	0.000	0.000	0.000	0.000
25	D	65	ASN	0	-0.018	-0.030	14.482	0.041	0.041	0.000	0.000	0.000	0.000
26	D	66	ASP	-1	-0.833	-0.912	13.196	-0.423	-0.423	0.000	0.000	0.000	0.000
27	D	67	TRP	0	0.008	-0.004	15.217	0.031	0.031	0.000	0.000	0.000	0.000
28	D	68	PHE	0	0.069	0.014	17.217	0.026	0.026	0.000	0.000	0.000	0.000
29	D	69	SER	0	0.010	0.037	14.947	0.036	0.036	0.000	0.000	0.000	0.000
30	D	70	LYS	1	0.942	0.969	17.112	0.215	0.215	0.000	0.000	0.000	0.000
31	D	71	LEU	0	-0.005	0.005	20.039	0.017	0.017	0.000	0.000	0.000	0.000
32	D	72	ALA	0	0.000	0.005	19.675	0.017	0.017	0.000	0.000	0.000	0.000
33	D	73	SER	0	-0.038	-0.036	19.319	0.014	0.014	0.000	0.000	0.000	0.000
34	D	74	SER	0	-0.104	-0.049	21.955	0.016	0.016	0.000	0.000	0.000	0.000
35	D	75	ALA	0	-0.015	0.003	24.926	0.010	0.010	0.000	0.000	0.000	0.000
36	D	76	PHE	0	0.009	0.006	26.947	0.005	0.005	0.000	0.000	0.000	0.000
37	D	77	SER	0	-0.005	-0.015	28.597	-0.005	-0.005	0.000	0.000	0.000	0.000
38	D	78	GLY	0	-0.028	-0.006	31.027	0.004	0.004	0.000	0.000	0.000	0.000
39	D	79	LEU	0	0.005	0.000	34.176	-0.001	-0.001	0.000	0.000	0.000	0.000
40	D	80	PHE	0	0.022	0.021	37.618	0.000	0.000	0.000	0.000	0.000	0.000
41	D	81	GLY	0	-0.009	-0.015	39.471	0.001	0.001	0.000	0.000	0.000	0.000
42	D	82	ALA	0	-0.023	-0.015	42.366	0.000	0.000	0.000	0.000	0.000	0.000
43	D	83	LEU	0	0.031	0.022	40.615	-0.001	-0.001	0.000	0.000	0.000	0.000
44	D	84	LEU	0	0.004	0.008	44.414	0.002	0.002	0.000	0.000	0.000	0.000
45	D	85	ALA	0	-0.021	-0.010	43.275	0.001	0.001	0.000	0.000	0.000	0.000

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