FMO DATABASE

FMODB ID: JQMK9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-385641.432102
FMO2-HF: Nuclear repulsion	358211.892809
FMO2-HF: Total energy	-27429.539293
FMO2-MP2: Total energy	-27505.773936

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.
-22.89	-6.939	26.195	-17.54	-24.603	-0.054

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 : -0.013 / q_NPA : 0.011

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	0.031	0.016	2.829	-1.426	1.774	0.132	-1.321	-2.011	0.003
4	B	11	THR	0	0.048	0.021	2.759	-3.706	-0.658	2.031	-2.006	-3.073	-0.021
5	B	12	CYS	0	-0.060	0.003	4.019	-0.233	0.127	-0.001	-0.040	-0.318	0.000
6	B	13	SER	0	0.048	0.018	6.015	0.339	0.339	0.000	0.000	0.000	0.000
7	B	14	LYS	1	0.914	0.954	9.448	-0.217	-0.217	0.000	0.000	0.000	0.000
8	B	15	MET	0	-0.029	0.003	8.584	-0.137	-0.137	0.000	0.000	0.000	0.000
9	B	16	THR	0	-0.027	-0.019	12.432	0.093	0.093	0.000	0.000	0.000	0.000
10	B	17	SER	0	0.022	0.008	14.690	-0.031	-0.031	0.000	0.000	0.000	0.000
11	B	18	LYS	1	0.965	0.970	18.075	0.258	0.258	0.000	0.000	0.000	0.000
12	B	19	ILE	0	0.038	0.035	15.965	0.030	0.030	0.000	0.000	0.000	0.000
13	B	20	PRO	0	-0.034	-0.031	20.085	-0.019	-0.019	0.000	0.000	0.000	0.000
14	B	21	VAL	0	0.089	0.048	21.151	-0.013	-0.013	0.000	0.000	0.000	0.000
15	B	22	ALA	0	0.033	0.019	22.202	-0.017	-0.017	0.000	0.000	0.000	0.000
16	B	23	LEU	0	-0.088	-0.057	21.079	0.009	0.009	0.000	0.000	0.000	0.000
17	B	24	LEU	0	-0.040	-0.015	16.712	-0.015	-0.015	0.000	0.000	0.000	0.000
18	B	25	ILE	0	-0.039	-0.025	17.355	0.037	0.037	0.000	0.000	0.000	0.000
19	B	26	HIS	0	0.042	0.035	14.438	-0.028	-0.028	0.000	0.000	0.000	0.000
20	B	27	TYR	0	-0.087	-0.077	12.238	-0.064	-0.064	0.000	0.000	0.000	0.000
21	B	28	GLN	0	0.030	0.015	7.518	0.216	0.216	0.000	0.000	0.000	0.000
22	B	29	GLN	0	0.009	0.009	7.950	-0.326	-0.326	0.000	0.000	0.000	0.000
23	B	30	ASN	0	0.001	0.005	1.995	-5.317	-4.338	5.597	-2.570	-4.006	-0.015
24	B	31	GLN	0	0.009	-0.005	1.763	-0.651	-0.117	12.615	-4.550	-8.598	-0.015
25	B	32	ALA	0	-0.013	-0.017	2.295	-4.463	-3.363	5.875	-2.911	-4.064	-0.033
28	B	36	LYS	1	0.918	0.977	3.797	-8.066	-1.336	-0.054	-4.142	-2.533	0.027
29	B	37	ARG	1	0.981	0.992	5.512	1.167	1.167	0.000	0.000	0.000	0.000
30	B	38	ALA	0	-0.011	-0.010	6.264	0.461	0.461	0.000	0.000	0.000	0.000
31	B	39	ILE	0	0.009	0.006	7.051	-0.565	-0.565	0.000	0.000	0.000	0.000
32	B	40	ILE	0	-0.019	-0.014	5.059	0.123	0.123	0.000	0.000	0.000	0.000
33	B	41	LEU	0	-0.022	-0.019	8.903	0.123	0.123	0.000	0.000	0.000	0.000
34	B	42	GLU	-1	-0.813	-0.925	12.329	-0.645	-0.645	0.000	0.000	0.000	0.000
35	B	43	THR	0	-0.012	-0.008	14.316	0.048	0.048	0.000	0.000	0.000	0.000
36	B	44	ARG	1	1.007	0.986	17.600	0.271	0.271	0.000	0.000	0.000	0.000
37	B	45	GLN	0	-0.116	-0.052	19.518	-0.006	-0.006	0.000	0.000	0.000	0.000
38	B	46	HIS	0	0.035	0.043	15.649	0.022	0.022	0.000	0.000	0.000	0.000
39	B	47	ARG	1	0.931	0.960	14.245	0.288	0.288	0.000	0.000	0.000	0.000
40	B	48	LEU	0	0.049	0.036	8.475	-0.049	-0.049	0.000	0.000	0.000	0.000
41	B	49	PHE	0	-0.008	-0.007	10.544	0.096	0.096	0.000	0.000	0.000	0.000
42	B	51	ALA	0	0.039	0.015	9.152	0.244	0.244	0.000	0.000	0.000	0.000
43	B	52	ASP	-1	-0.794	-0.934	10.687	-0.710	-0.710	0.000	0.000	0.000	0.000
44	B	53	PRO	0	0.001	-0.008	11.466	0.069	0.069	0.000	0.000	0.000	0.000
45	B	54	LYS	1	0.933	0.977	14.412	0.391	0.391	0.000	0.000	0.000	0.000
46	B	55	GLU	-1	-0.950	-0.977	16.954	-0.262	-0.262	0.000	0.000	0.000	0.000
47	B	56	GLN	0	0.012	-0.002	19.132	-0.045	-0.045	0.000	0.000	0.000	0.000
48	B	57	TRP	0	0.007	0.011	16.275	-0.026	-0.026	0.000	0.000	0.000	0.000
49	B	58	VAL	0	0.010	0.014	14.360	-0.014	-0.014	0.000	0.000	0.000	0.000
50	B	59	LYS	1	0.941	0.961	17.730	0.441	0.441	0.000	0.000	0.000	0.000
51	B	60	ASP	-1	-0.868	-0.940	19.157	-0.389	-0.389	0.000	0.000	0.000	0.000
52	B	61	ALA	0	-0.044	-0.031	17.962	0.012	0.012	0.000	0.000	0.000	0.000
53	B	62	MET	0	-0.030	0.002	14.909	-0.046	-0.046	0.000	0.000	0.000	0.000
54	B	63	GLN	0	0.077	0.043	18.119	-0.010	-0.010	0.000	0.000	0.000	0.000
55	B	64	HIS	0	-0.084	-0.035	21.535	0.033	0.033	0.000	0.000	0.000	0.000
56	B	65	LEU	0	-0.016	-0.008	16.815	0.017	0.017	0.000	0.000	0.000	0.000
57	B	66	ASP	-1	-0.825	-0.883	18.598	-0.672	-0.672	0.000	0.000	0.000	0.000
58	B	67	ARG	1	0.885	0.930	20.906	0.397	0.397	0.000	0.000	0.000	0.000
59	B	68	GLN	0	-0.040	-0.022	22.517	0.035	0.035	0.000	0.000	0.000	0.000
60	B	69	ALA	0	0.020	0.018	20.470	0.018	0.018	0.000	0.000	0.000	0.000
61	B	70	ALA	0	0.032	0.023	22.600	0.017	0.017	0.000	0.000	0.000	0.000
62	B	71	ALA	0	-0.017	-0.005	25.407	0.008	0.008	0.000	0.000	0.000	0.000
63	B	72	LEU	0	-0.093	-0.042	23.014	0.023	0.023	0.000	0.000	0.000	0.000
64	B	73	THR	0	-0.015	0.002	25.456	-0.008	-0.008	0.000	0.000	0.000	0.000

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