FMO DATABASE

FMODB ID: LNLR9

Calculation Name: 3ONA-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ONA

Chain ID: B

ChEMBL ID:

UniProt ID: P78423

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	64
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-384420.955683
FMO2-HF: Nuclear repulsion	356990.462911
FMO2-HF: Total energy	-27430.492772
FMO2-MP2: Total energy	-27506.563377

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(B:8:CYS)

Summations of interaction energy for fragment #1(B:8:CYS)

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.
-21.826	-8.716	15.281	-12.148	-16.241	-0.072

Interaction energy analysis for fragmet #1(B:8:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.044 / 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	B	10	ILE	0	0.000	0.005	3.084	-0.689	2.013	0.006	-1.198	-1.511	0.001
4	B	11	THR	0	0.041	0.018	2.534	-7.187	-4.252	0.998	-1.614	-2.318	-0.017
5	B	12	CYS	0	-0.061	-0.013	4.385	1.024	1.241	-0.003	-0.019	-0.196	0.000
6	B	13	SER	0	0.024	0.004	6.891	0.618	0.618	0.000	0.000	0.000	0.000
7	B	14	LYS	1	0.894	0.938	9.816	0.899	0.899	0.000	0.000	0.000	0.000
8	B	15	MET	0	-0.044	-0.005	9.574	-0.208	-0.208	0.000	0.000	0.000	0.000
9	B	16	THR	0	-0.026	-0.016	13.136	0.153	0.153	0.000	0.000	0.000	0.000
10	B	17	SER	0	0.040	0.020	15.624	0.000	0.000	0.000	0.000	0.000	0.000
11	B	18	LYS	1	0.946	0.961	18.780	0.421	0.421	0.000	0.000	0.000	0.000
12	B	19	ILE	0	0.047	0.038	16.444	0.044	0.044	0.000	0.000	0.000	0.000
13	B	20	PRO	0	-0.019	-0.021	20.554	0.005	0.005	0.000	0.000	0.000	0.000
14	B	21	VAL	0	0.065	0.033	21.342	-0.008	-0.008	0.000	0.000	0.000	0.000
15	B	22	ALA	0	0.045	0.031	22.424	-0.005	-0.005	0.000	0.000	0.000	0.000
16	B	23	LEU	0	-0.058	-0.030	21.955	0.028	0.028	0.000	0.000	0.000	0.000
17	B	24	LEU	0	-0.023	-0.012	16.807	-0.028	-0.028	0.000	0.000	0.000	0.000
18	B	25	ILE	0	-0.049	-0.022	17.305	0.052	0.052	0.000	0.000	0.000	0.000
19	B	26	HIS	0	0.038	0.037	14.903	0.015	0.015	0.000	0.000	0.000	0.000
20	B	27	TYR	0	-0.086	-0.091	12.859	-0.145	-0.145	0.000	0.000	0.000	0.000
21	B	28	GLN	0	0.010	0.011	7.045	0.350	0.350	0.000	0.000	0.000	0.000
22	B	29	GLN	0	0.009	0.007	8.690	-0.406	-0.406	0.000	0.000	0.000	0.000
23	B	30	ASN	0	0.011	-0.001	2.513	-2.357	-0.781	1.241	-0.957	-1.860	-0.011
24	B	31	GLN	0	0.022	0.008	2.659	-1.532	-0.249	6.284	-2.427	-5.139	-0.006
25	B	32	ALA	0	-0.015	-0.024	1.955	-12.836	-11.078	6.778	-4.388	-4.147	-0.046
28	B	36	LYS	1	0.931	0.975	3.862	-1.776	0.863	-0.023	-1.545	-1.070	0.007
29	B	37	ARG	1	1.002	1.010	5.674	1.168	1.168	0.000	0.000	0.000	0.000
30	B	38	ALA	0	-0.018	-0.008	6.607	0.805	0.805	0.000	0.000	0.000	0.000
31	B	39	ILE	0	0.020	0.012	7.752	-0.368	-0.368	0.000	0.000	0.000	0.000
32	B	40	ILE	0	-0.011	-0.007	5.234	-0.154	-0.154	0.000	0.000	0.000	0.000
33	B	41	LEU	0	-0.005	-0.010	9.140	0.279	0.279	0.000	0.000	0.000	0.000
34	B	42	GLU	-1	-0.797	-0.906	12.502	-0.557	-0.557	0.000	0.000	0.000	0.000
35	B	43	THR	0	-0.016	-0.030	14.664	0.052	0.052	0.000	0.000	0.000	0.000
36	B	44	ARG	1	0.935	0.944	17.949	0.321	0.321	0.000	0.000	0.000	0.000
37	B	45	GLN	0	-0.048	-0.008	19.647	0.001	0.001	0.000	0.000	0.000	0.000
38	B	46	HIS	0	-0.025	-0.003	13.720	0.039	0.039	0.000	0.000	0.000	0.000
39	B	47	ARG	1	0.947	0.978	14.086	0.461	0.461	0.000	0.000	0.000	0.000
40	B	48	LEU	0	0.039	0.027	8.404	-0.012	-0.012	0.000	0.000	0.000	0.000
41	B	49	PHE	0	0.001	-0.001	10.898	-0.073	-0.073	0.000	0.000	0.000	0.000
42	B	51	ALA	0	0.013	0.000	9.962	0.304	0.304	0.000	0.000	0.000	0.000
43	B	52	ASP	-1	-0.773	-0.884	11.435	-1.168	-1.168	0.000	0.000	0.000	0.000
44	B	53	PRO	0	0.034	0.005	11.874	0.117	0.117	0.000	0.000	0.000	0.000
45	B	54	LYS	1	0.815	0.889	14.792	0.800	0.800	0.000	0.000	0.000	0.000
46	B	55	GLU	-1	-0.828	-0.890	17.493	-0.537	-0.537	0.000	0.000	0.000	0.000
47	B	56	GLN	0	0.027	0.013	19.383	-0.038	-0.038	0.000	0.000	0.000	0.000
48	B	57	TRP	0	-0.004	-0.007	16.495	-0.006	-0.006	0.000	0.000	0.000	0.000
49	B	58	VAL	0	0.007	0.015	14.542	0.005	0.005	0.000	0.000	0.000	0.000
50	B	59	LYS	1	0.856	0.923	17.831	0.600	0.600	0.000	0.000	0.000	0.000
51	B	60	ASP	-1	-0.843	-0.935	19.403	-0.442	-0.442	0.000	0.000	0.000	0.000
52	B	61	ALA	0	-0.051	-0.028	18.629	0.035	0.035	0.000	0.000	0.000	0.000
53	B	62	MET	0	-0.022	0.001	15.026	-0.028	-0.028	0.000	0.000	0.000	0.000
54	B	63	GLN	0	0.020	0.013	18.214	0.078	0.078	0.000	0.000	0.000	0.000
55	B	64	HIS	0	-0.049	-0.030	21.662	0.049	0.049	0.000	0.000	0.000	0.000
56	B	65	LEU	0	-0.021	-0.017	17.093	0.031	0.031	0.000	0.000	0.000	0.000
57	B	66	ASP	-1	-0.783	-0.869	19.040	-0.521	-0.521	0.000	0.000	0.000	0.000
58	B	67	ARG	1	0.855	0.917	21.375	0.387	0.387	0.000	0.000	0.000	0.000
59	B	68	GLN	0	-0.027	0.003	22.681	0.035	0.035	0.000	0.000	0.000	0.000
60	B	69	ALA	0	0.035	0.032	20.749	0.021	0.021	0.000	0.000	0.000	0.000
61	B	70	ALA	0	0.027	0.020	22.886	0.033	0.033	0.000	0.000	0.000	0.000
62	B	71	ALA	0	-0.018	-0.010	26.102	-0.005	-0.005	0.000	0.000	0.000	0.000
63	B	72	LEU	0	-0.043	-0.021	23.846	0.018	0.018	0.000	0.000	0.000	0.000
64	B	73	THR	0	-0.063	-0.024	25.302	0.012	0.012	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:8:CYS)