FMO DATABASE

FMODB ID: K9KG3

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-137864.351177
FMO2-HF: Nuclear repulsion	120108.093358
FMO2-HF: Total energy	-17756.257819
FMO2-MP2: Total energy	-17806.821107

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.
-3.257	-0.694	-0.012	-0.939	-1.614	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 : -0.026 / 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	-0.065	-0.026	3.626	-1.113	0.894	-0.025	-0.815	-1.168	0.004
4	D	18	THR	0	0.028	0.017	3.218	-1.401	-0.918	0.014	-0.111	-0.387	0.000
5	D	19	GLY	0	0.012	0.001	4.472	0.515	0.588	-0.001	-0.013	-0.059	0.000
6	D	20	SER	0	-0.023	0.004	6.984	-0.127	-0.127	0.000	0.000	0.000	0.000
7	D	21	ILE	0	0.023	0.009	7.921	0.018	0.018	0.000	0.000	0.000	0.000
8	D	22	ILE	0	-0.039	-0.021	10.423	-0.082	-0.082	0.000	0.000	0.000	0.000
9	D	23	ASN	0	-0.001	0.003	10.035	-0.085	-0.085	0.000	0.000	0.000	0.000
10	D	24	ASN	0	0.024	0.002	9.610	0.188	0.188	0.000	0.000	0.000	0.000
11	D	25	TYR	0	-0.008	0.002	11.480	0.004	0.004	0.000	0.000	0.000	0.000
12	D	26	TYR	0	-0.010	0.005	13.214	0.028	0.028	0.000	0.000	0.000	0.000
13	D	27	MET	0	0.010	-0.004	12.715	-0.058	-0.058	0.000	0.000	0.000	0.000
14	D	28	GLN	0	0.061	0.013	8.331	-0.291	-0.291	0.000	0.000	0.000	0.000
15	D	29	GLN	0	0.016	-0.004	11.237	-0.136	-0.136	0.000	0.000	0.000	0.000
16	D	30	TYR	0	-0.053	-0.018	13.538	0.069	0.069	0.000	0.000	0.000	0.000
17	D	31	GLN	0	-0.022	0.002	8.321	0.151	0.151	0.000	0.000	0.000	0.000
18	D	32	ASN	0	-0.032	-0.021	6.124	-0.192	-0.192	0.000	0.000	0.000	0.000
19	D	33	SER	0	0.040	0.034	9.843	0.146	0.146	0.000	0.000	0.000	0.000
20	D	34	MET	0	-0.051	-0.030	10.781	-0.140	-0.140	0.000	0.000	0.000	0.000
21	D	35	ASP	-1	-0.895	-0.933	9.988	-1.062	-1.062	0.000	0.000	0.000	0.000
22	D	36	THR	0	-0.047	-0.025	13.291	0.041	0.041	0.000	0.000	0.000	0.000
23	D	37	GLN	0	0.001	-0.005	13.343	0.030	0.030	0.000	0.000	0.000	0.000
24	D	38	LEU	0	-0.010	0.002	17.947	0.033	0.033	0.000	0.000	0.000	0.000
25	D	65	ASN	0	-0.014	-0.031	14.377	0.060	0.060	0.000	0.000	0.000	0.000
26	D	66	ASP	-1	-0.850	-0.919	12.970	-0.117	-0.117	0.000	0.000	0.000	0.000
27	D	67	TRP	0	0.012	-0.003	15.199	0.037	0.037	0.000	0.000	0.000	0.000
28	D	68	PHE	0	0.067	0.012	17.259	0.020	0.020	0.000	0.000	0.000	0.000
29	D	69	SER	0	0.022	0.045	14.673	0.036	0.036	0.000	0.000	0.000	0.000
30	D	70	LYS	1	0.937	0.958	17.108	0.130	0.130	0.000	0.000	0.000	0.000
31	D	71	LEU	0	-0.012	-0.001	20.034	0.011	0.011	0.000	0.000	0.000	0.000
32	D	72	ALA	0	0.004	0.002	19.708	0.008	0.008	0.000	0.000	0.000	0.000
33	D	73	SER	0	-0.033	-0.024	19.285	0.016	0.016	0.000	0.000	0.000	0.000
34	D	74	SER	0	-0.110	-0.044	21.960	0.000	0.000	0.000	0.000	0.000	0.000
35	D	75	ALA	0	-0.009	0.006	24.930	-0.004	-0.004	0.000	0.000	0.000	0.000
36	D	76	PHE	0	0.007	0.006	26.952	0.003	0.003	0.000	0.000	0.000	0.000
37	D	77	SER	0	0.008	-0.015	28.508	0.009	0.009	0.000	0.000	0.000	0.000
38	D	78	GLY	0	-0.041	-0.008	31.040	-0.004	-0.004	0.000	0.000	0.000	0.000
39	D	79	LEU	0	-0.001	-0.004	34.192	0.000	0.000	0.000	0.000	0.000	0.000
40	D	80	PHE	0	0.036	0.026	37.632	-0.002	-0.002	0.000	0.000	0.000	0.000
41	D	81	GLY	0	-0.015	-0.015	39.481	0.000	0.000	0.000	0.000	0.000	0.000
42	D	82	ALA	0	-0.022	-0.012	42.380	0.002	0.002	0.000	0.000	0.000	0.000
43	D	83	LEU	0	0.028	0.018	40.589	0.001	0.001	0.000	0.000	0.000	0.000
44	D	84	LEU	0	-0.011	0.002	44.432	-0.001	-0.001	0.000	0.000	0.000	0.000
45	D	85	ALA	0	-0.004	-0.002	43.252	0.002	0.002	0.000	0.000	0.000	0.000

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