FMO DATABASE

FMODB ID: 3JNGL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-385221.70874
FMO2-HF: Nuclear repulsion	357791.541726
FMO2-HF: Total energy	-27430.167014
FMO2-MP2: Total energy	-27506.313156

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.
-21.11	-7.988	21.907	-14.159	-20.87	-0.05

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 : -0.064 / q_NPA : -0.012

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	0.020	0.010	2.845	-1.299	1.681	0.039	-1.224	-1.795	0.003
4	B	11	THR	0	0.036	0.020	2.473	-7.552	-4.235	1.428	-2.033	-2.711	-0.024
5	B	12	CYS	0	-0.046	0.000	4.075	0.538	0.824	-0.002	-0.024	-0.260	0.000
6	B	13	SER	0	0.037	0.011	6.279	0.432	0.432	0.000	0.000	0.000	0.000
7	B	14	LYS	1	0.922	0.962	9.659	0.316	0.316	0.000	0.000	0.000	0.000
8	B	15	MET	0	-0.011	-0.002	9.333	-0.160	-0.160	0.000	0.000	0.000	0.000
9	B	16	THR	0	-0.025	-0.014	12.762	0.104	0.104	0.000	0.000	0.000	0.000
10	B	17	SER	0	0.020	0.011	14.958	-0.002	-0.002	0.000	0.000	0.000	0.000
11	B	18	LYS	1	0.950	0.958	18.340	0.294	0.294	0.000	0.000	0.000	0.000
12	B	19	ILE	0	0.037	0.032	16.149	0.027	0.027	0.000	0.000	0.000	0.000
13	B	20	PRO	0	-0.018	-0.022	20.304	-0.005	-0.005	0.000	0.000	0.000	0.000
14	B	21	VAL	0	0.072	0.042	21.226	-0.008	-0.008	0.000	0.000	0.000	0.000
15	B	22	ALA	0	0.043	0.024	22.283	-0.004	-0.004	0.000	0.000	0.000	0.000
16	B	23	LEU	0	-0.082	-0.050	21.286	0.018	0.018	0.000	0.000	0.000	0.000
17	B	24	LEU	0	-0.026	-0.012	16.650	-0.014	-0.014	0.000	0.000	0.000	0.000
18	B	25	ILE	0	-0.022	-0.021	17.471	0.031	0.031	0.000	0.000	0.000	0.000
19	B	26	HIS	0	0.046	0.040	14.588	0.005	0.005	0.000	0.000	0.000	0.000
20	B	27	TYR	0	-0.104	-0.091	12.377	-0.112	-0.112	0.000	0.000	0.000	0.000
21	B	28	GLN	0	0.025	0.016	6.860	0.223	0.223	0.000	0.000	0.000	0.000
22	B	29	GLN	0	0.009	0.008	8.146	-0.405	-0.405	0.000	0.000	0.000	0.000
23	B	30	ASN	0	0.014	0.011	2.518	-3.064	-1.542	2.545	-1.361	-2.706	-0.011
24	B	31	GLN	0	0.009	-0.011	1.942	-2.200	-3.234	13.133	-4.251	-7.848	-0.004
25	B	32	ALA	0	-0.019	-0.019	2.296	-5.392	-3.803	4.804	-2.586	-3.808	-0.029
28	B	36	LYS	1	0.928	0.981	3.797	-4.213	0.249	-0.040	-2.680	-1.742	0.015
29	B	37	ARG	1	0.990	0.998	5.430	1.013	1.013	0.000	0.000	0.000	0.000
30	B	38	ALA	0	-0.025	-0.016	6.208	0.549	0.549	0.000	0.000	0.000	0.000
31	B	39	ILE	0	0.012	0.002	7.009	-0.440	-0.440	0.000	0.000	0.000	0.000
32	B	40	ILE	0	-0.012	-0.007	5.071	-0.018	-0.018	0.000	0.000	0.000	0.000
33	B	41	LEU	0	-0.017	-0.014	8.933	0.212	0.212	0.000	0.000	0.000	0.000
34	B	42	GLU	-1	-0.790	-0.902	12.393	-0.329	-0.329	0.000	0.000	0.000	0.000
35	B	43	THR	0	-0.038	-0.036	14.337	0.040	0.040	0.000	0.000	0.000	0.000
36	B	44	ARG	1	0.979	0.975	17.610	0.224	0.224	0.000	0.000	0.000	0.000
37	B	45	GLN	0	-0.088	-0.029	19.499	-0.002	-0.002	0.000	0.000	0.000	0.000
38	B	46	HIS	0	-0.004	0.014	14.537	0.039	0.039	0.000	0.000	0.000	0.000
39	B	47	ARG	1	0.934	0.965	14.269	0.299	0.299	0.000	0.000	0.000	0.000
40	B	48	LEU	0	0.050	0.031	8.677	-0.019	-0.019	0.000	0.000	0.000	0.000
41	B	49	PHE	0	-0.005	-0.004	10.656	-0.026	-0.026	0.000	0.000	0.000	0.000
42	B	51	ALA	0	0.037	0.018	9.424	0.236	0.236	0.000	0.000	0.000	0.000
43	B	52	ASP	-1	-0.766	-0.896	10.785	-0.835	-0.835	0.000	0.000	0.000	0.000
44	B	53	PRO	0	0.013	-0.007	11.411	0.088	0.088	0.000	0.000	0.000	0.000
45	B	54	LYS	1	0.812	0.898	14.359	0.532	0.532	0.000	0.000	0.000	0.000
46	B	55	GLU	-1	-0.863	-0.920	17.179	-0.355	-0.355	0.000	0.000	0.000	0.000
47	B	56	GLN	0	0.071	0.031	19.051	-0.040	-0.040	0.000	0.000	0.000	0.000
48	B	57	TRP	0	0.005	0.009	16.614	-0.002	-0.002	0.000	0.000	0.000	0.000
49	B	58	VAL	0	0.001	0.009	14.240	0.003	0.003	0.000	0.000	0.000	0.000
50	B	59	LYS	1	0.893	0.937	17.629	0.441	0.441	0.000	0.000	0.000	0.000
51	B	60	ASP	-1	-0.898	-0.954	19.108	-0.333	-0.333	0.000	0.000	0.000	0.000
52	B	61	ALA	0	-0.036	-0.029	18.073	0.023	0.023	0.000	0.000	0.000	0.000
53	B	62	MET	0	-0.025	0.005	14.710	-0.028	-0.028	0.000	0.000	0.000	0.000
54	B	63	GLN	0	0.042	0.027	18.081	0.048	0.048	0.000	0.000	0.000	0.000
55	B	64	HIS	0	-0.060	-0.039	21.502	0.033	0.033	0.000	0.000	0.000	0.000
56	B	65	LEU	0	-0.024	-0.011	16.939	0.023	0.023	0.000	0.000	0.000	0.000
57	B	66	ASP	-1	-0.812	-0.879	18.539	-0.439	-0.439	0.000	0.000	0.000	0.000
58	B	67	ARG	1	0.870	0.932	20.914	0.303	0.303	0.000	0.000	0.000	0.000
59	B	68	GLN	0	-0.039	-0.013	22.360	0.026	0.026	0.000	0.000	0.000	0.000
60	B	69	ALA	0	0.019	0.021	20.469	0.022	0.022	0.000	0.000	0.000	0.000
61	B	70	ALA	0	0.035	0.017	22.610	0.023	0.023	0.000	0.000	0.000	0.000
62	B	71	ALA	0	0.008	0.003	25.441	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	72	LEU	0	-0.100	-0.041	23.447	0.017	0.017	0.000	0.000	0.000	0.000
64	B	73	THR	0	-0.025	-0.004	25.457	0.005	0.005	0.000	0.000	0.000	0.000

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