FMO DATABASE

FMODB ID: 52RJZ

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	OptAll
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	-137622.231727
FMO2-HF: Nuclear repulsion	119865.632171
FMO2-HF: Total energy	-17756.599556
FMO2-MP2: Total energy	-17807.12756

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.
0.618	3.513	-0.006	-1.476	-1.412	0.005

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 : 0.042 / q_NPA : 0.024

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	-0.054	-0.020	3.875	1.243	3.609	-0.015	-1.345	-1.005	0.005
4	D	18	THR	0	0.021	0.011	3.489	0.092	0.615	0.010	-0.128	-0.405	0.000
5	D	19	GLY	0	0.022	0.005	4.975	-0.950	-0.944	-0.001	-0.003	-0.002	0.000
6	D	20	SER	0	-0.045	-0.016	7.334	0.048	0.048	0.000	0.000	0.000	0.000
7	D	21	ILE	0	0.022	0.012	8.221	-0.005	-0.005	0.000	0.000	0.000	0.000
8	D	22	ILE	0	-0.046	-0.009	10.532	0.035	0.035	0.000	0.000	0.000	0.000
9	D	23	ASN	0	0.005	-0.007	9.580	0.075	0.075	0.000	0.000	0.000	0.000
10	D	24	ASN	0	-0.017	-0.024	8.518	-0.053	-0.053	0.000	0.000	0.000	0.000
11	D	25	TYR	0	-0.006	0.007	10.465	-0.027	-0.027	0.000	0.000	0.000	0.000
12	D	26	TYR	0	-0.002	0.008	12.611	-0.046	-0.046	0.000	0.000	0.000	0.000
13	D	27	MET	0	0.027	0.007	11.866	0.048	0.048	0.000	0.000	0.000	0.000
14	D	28	GLN	0	0.059	0.024	8.308	-0.004	-0.004	0.000	0.000	0.000	0.000
15	D	29	GLN	0	0.039	-0.013	10.961	0.074	0.074	0.000	0.000	0.000	0.000
16	D	30	TYR	0	-0.036	-0.009	13.560	-0.047	-0.047	0.000	0.000	0.000	0.000
17	D	31	GLN	0	-0.048	-0.004	8.657	-0.095	-0.095	0.000	0.000	0.000	0.000
18	D	32	ASN	0	-0.025	-0.019	6.739	0.090	0.090	0.000	0.000	0.000	0.000
19	D	33	SER	0	0.043	0.031	10.571	-0.085	-0.085	0.000	0.000	0.000	0.000
20	D	34	MET	0	-0.048	-0.021	10.791	0.054	0.054	0.000	0.000	0.000	0.000
21	D	35	ASP	-1	-0.899	-0.933	10.197	0.264	0.264	0.000	0.000	0.000	0.000
22	D	36	THR	0	-0.046	-0.028	13.314	-0.011	-0.011	0.000	0.000	0.000	0.000
23	D	37	GLN	0	-0.017	-0.016	14.208	-0.034	-0.034	0.000	0.000	0.000	0.000
24	D	38	LEU	0	0.006	0.014	18.158	-0.002	-0.002	0.000	0.000	0.000	0.000
25	D	65	ASN	0	0.029	-0.001	14.328	0.006	0.006	0.000	0.000	0.000	0.000
26	D	66	ASP	-1	-0.814	-0.901	12.957	-0.377	-0.377	0.000	0.000	0.000	0.000
27	D	67	TRP	0	0.028	0.016	14.944	0.015	0.015	0.000	0.000	0.000	0.000
28	D	68	PHE	0	0.056	0.016	16.885	0.015	0.015	0.000	0.000	0.000	0.000
29	D	69	SER	0	0.002	0.017	14.776	0.020	0.020	0.000	0.000	0.000	0.000
30	D	70	LYS	1	0.861	0.924	16.870	0.218	0.218	0.000	0.000	0.000	0.000
31	D	71	LEU	0	0.011	0.015	19.793	0.012	0.012	0.000	0.000	0.000	0.000
32	D	72	ALA	0	0.005	0.008	19.605	0.014	0.014	0.000	0.000	0.000	0.000
33	D	73	SER	0	-0.049	-0.042	19.312	0.004	0.004	0.000	0.000	0.000	0.000
34	D	74	SER	0	-0.095	-0.051	21.974	0.017	0.017	0.000	0.000	0.000	0.000
35	D	75	ALA	0	-0.013	0.005	24.966	0.014	0.014	0.000	0.000	0.000	0.000
36	D	76	PHE	0	0.013	0.003	26.891	0.000	0.000	0.000	0.000	0.000	0.000
37	D	77	SER	0	-0.011	-0.018	28.887	-0.010	-0.010	0.000	0.000	0.000	0.000
38	D	78	GLY	0	-0.018	0.009	31.157	0.005	0.005	0.000	0.000	0.000	0.000
39	D	79	LEU	0	-0.008	-0.013	34.261	0.001	0.001	0.000	0.000	0.000	0.000
40	D	80	PHE	0	0.008	0.007	37.591	0.000	0.000	0.000	0.000	0.000	0.000
41	D	81	GLY	0	0.015	0.011	39.721	0.002	0.002	0.000	0.000	0.000	0.000
42	D	82	ALA	0	-0.022	-0.011	42.688	-0.002	-0.002	0.000	0.000	0.000	0.000
43	D	83	LEU	0	0.028	0.005	40.735	-0.001	-0.001	0.000	0.000	0.000	0.000
44	D	84	LEU	0	0.008	0.018	44.642	0.001	0.001	0.000	0.000	0.000	0.000
45	D	85	ALA	0	-0.034	-0.017	43.499	0.000	0.000	0.000	0.000	0.000	0.000

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