FMO DATABASE

FMODB ID: MNV3Z

Calculation Name: 2O8A-J-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2O8A

Chain ID: J

ChEMBL ID:

UniProt ID: Q9DCL8

Base Structure: X-ray

Registration Date: 2023-09-21

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	58
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-243379.482122
FMO2-HF: Nuclear repulsion	218797.295048
FMO2-HF: Total energy	-24582.187075
FMO2-MP2: Total energy	-24653.682592

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(J:12:LYS)

Summations of interaction energy for fragment #1(J:12:LYS)

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.
66.718	68.534	-0.003	-0.877	-0.937	0.002

Interaction energy analysis for fragmet #1(J:12:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.992 / q_NPA : 0.988

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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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	J	14	ILE	0	-0.008	-0.015	3.568	-9.399	-7.583	-0.003	-0.877	-0.937	0.002
4	J	15	LEU	0	-0.008	0.006	5.580	2.978	2.978	0.000	0.000	0.000	0.000
5	J	16	LYS	1	0.947	0.971	9.107	27.243	27.243	0.000	0.000	0.000	0.000
6	J	17	ASN	0	0.052	0.038	10.484	-0.044	-0.044	0.000	0.000	0.000	0.000
7	J	44	LYS	1	1.007	1.002	8.604	30.957	30.957	0.000	0.000	0.000	0.000
8	J	45	SER	0	-0.033	-0.031	15.515	0.546	0.546	0.000	0.000	0.000	0.000
9	J	46	GLN	0	-0.019	0.000	15.910	-0.375	-0.375	0.000	0.000	0.000	0.000
10	J	47	LYS	1	0.957	0.967	16.599	16.454	16.454	0.000	0.000	0.000	0.000
11	J	48	TRP	0	0.044	0.024	17.525	-1.165	-1.165	0.000	0.000	0.000	0.000
12	J	49	ASP	-1	-0.874	-0.935	17.842	-16.104	-16.104	0.000	0.000	0.000	0.000
13	J	50	GLU	-1	-0.878	-0.963	19.800	-12.368	-12.368	0.000	0.000	0.000	0.000
14	J	51	MET	0	-0.001	0.010	22.695	0.718	0.718	0.000	0.000	0.000	0.000
15	J	52	ASN	0	-0.047	-0.025	20.165	0.488	0.488	0.000	0.000	0.000	0.000
16	J	53	ILE	0	-0.005	-0.012	21.482	0.276	0.276	0.000	0.000	0.000	0.000
17	J	54	LEU	0	-0.034	-0.010	24.408	0.428	0.428	0.000	0.000	0.000	0.000
18	J	55	ALA	0	-0.036	-0.005	24.627	0.358	0.358	0.000	0.000	0.000	0.000
19	J	56	THR	0	-0.082	-0.021	23.209	0.352	0.352	0.000	0.000	0.000	0.000
20	J	130	LEU	0	-0.030	-0.025	40.000	0.027	0.027	0.000	0.000	0.000	0.000
21	J	131	SER	0	0.000	0.022	42.849	0.253	0.253	0.000	0.000	0.000	0.000
22	J	132	PRO	0	0.025	-0.004	44.936	-0.049	-0.049	0.000	0.000	0.000	0.000
23	J	133	GLU	-1	-0.898	-0.933	45.071	-6.972	-6.972	0.000	0.000	0.000	0.000
24	J	134	GLU	-1	-0.845	-0.964	40.369	-7.829	-7.829	0.000	0.000	0.000	0.000
25	J	135	ARG	1	0.910	0.961	41.507	7.251	7.251	0.000	0.000	0.000	0.000
26	J	136	GLU	-1	-0.815	-0.902	43.632	-6.830	-6.830	0.000	0.000	0.000	0.000
27	J	137	LYS	1	0.986	0.990	38.073	8.156	8.156	0.000	0.000	0.000	0.000
28	J	138	LYS	1	0.939	0.963	36.055	8.510	8.510	0.000	0.000	0.000	0.000
29	J	139	ARG	1	0.931	0.973	40.106	6.713	6.713	0.000	0.000	0.000	0.000
30	J	140	GLN	0	-0.013	-0.010	42.579	0.041	0.041	0.000	0.000	0.000	0.000
31	J	141	PHE	0	-0.013	-0.008	33.379	-0.034	-0.034	0.000	0.000	0.000	0.000
32	J	142	GLU	-1	-0.940	-0.979	37.872	-8.440	-8.440	0.000	0.000	0.000	0.000
33	J	143	MET	0	-0.013	0.001	39.419	-0.021	-0.021	0.000	0.000	0.000	0.000
34	J	144	LYS	1	0.972	0.977	39.019	8.132	8.132	0.000	0.000	0.000	0.000
35	J	145	ARG	1	0.947	0.982	32.740	9.297	9.297	0.000	0.000	0.000	0.000
36	J	146	LYS	1	0.943	0.971	37.902	7.189	7.189	0.000	0.000	0.000	0.000
37	J	147	LEU	0	-0.034	-0.014	40.196	0.027	0.027	0.000	0.000	0.000	0.000
38	J	148	HIS	0	-0.036	-0.011	34.688	0.101	0.101	0.000	0.000	0.000	0.000
39	J	149	TYR	0	-0.047	-0.005	31.415	-0.117	-0.117	0.000	0.000	0.000	0.000
40	J	150	ASN	0	0.022	0.008	37.680	-0.053	-0.053	0.000	0.000	0.000	0.000
41	J	151	GLU	-1	-0.791	-0.910	34.833	-8.867	-8.867	0.000	0.000	0.000	0.000
42	J	152	GLY	0	-0.046	-0.027	38.701	0.064	0.064	0.000	0.000	0.000	0.000
43	J	153	LEU	0	-0.032	-0.021	40.179	0.146	0.146	0.000	0.000	0.000	0.000
44	J	154	ASN	0	-0.005	-0.005	41.670	0.142	0.142	0.000	0.000	0.000	0.000
45	J	155	ILE	0	0.009	0.026	38.353	0.019	0.019	0.000	0.000	0.000	0.000
46	J	156	LYS	1	0.964	0.968	41.427	6.987	6.987	0.000	0.000	0.000	0.000
47	J	157	LEU	0	0.045	0.033	44.803	0.032	0.032	0.000	0.000	0.000	0.000
48	J	158	ALA	0	0.040	0.020	40.029	0.043	0.043	0.000	0.000	0.000	0.000
49	J	159	ARG	1	0.967	0.972	37.971	8.018	8.018	0.000	0.000	0.000	0.000
50	J	160	GLN	0	-0.023	-0.020	42.775	0.028	0.028	0.000	0.000	0.000	0.000
51	J	161	LEU	0	-0.001	-0.011	43.540	0.121	0.121	0.000	0.000	0.000	0.000
52	J	162	ILE	0	0.019	0.028	38.445	-0.020	-0.020	0.000	0.000	0.000	0.000
53	J	163	SER	0	-0.058	-0.033	42.270	0.033	0.033	0.000	0.000	0.000	0.000
54	J	164	LYS	1	0.961	0.968	45.116	6.303	6.303	0.000	0.000	0.000	0.000
55	J	165	ASP	-1	-0.876	-0.918	43.325	-6.863	-6.863	0.000	0.000	0.000	0.000
56	J	166	LEU	0	-0.060	-0.015	41.925	-0.048	-0.048	0.000	0.000	0.000	0.000
57	J	167	HIS	0	-0.142	-0.086	44.329	0.166	0.166	0.000	0.000	0.000	0.000
58	J	168	ASP	-1	-0.962	-0.959	46.498	-6.281	-6.281	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(J:12:LYS)