FMO DATABASE

FMODB ID: 2NJ2R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-244869.861796
FMO2-HF: Nuclear repulsion	220286.746074
FMO2-HF: Total energy	-24583.115723
FMO2-MP2: Total energy	-24654.627075

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.
41.781	45.176	6.053	-4.43	-5.017	-0.048

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 : 0.963 / q_NPA : 0.983

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	-0.013	-0.033	2.171	-38.247	-35.084	6.053	-4.363	-4.852	-0.048
4	J	15	LEU	0	0.005	0.019	3.921	5.354	5.586	0.000	-0.067	-0.165	0.000
5	J	16	LYS	1	0.966	0.975	7.612	28.024	28.024	0.000	0.000	0.000	0.000
6	J	17	ASN	0	0.043	0.038	8.834	0.467	0.467	0.000	0.000	0.000	0.000
7	J	44	LYS	1	1.014	1.007	8.995	30.150	30.150	0.000	0.000	0.000	0.000
8	J	45	SER	0	-0.037	-0.040	15.403	0.779	0.779	0.000	0.000	0.000	0.000
9	J	46	GLN	0	-0.021	-0.008	16.100	-0.201	-0.201	0.000	0.000	0.000	0.000
10	J	47	LYS	1	0.939	0.965	17.048	16.386	16.386	0.000	0.000	0.000	0.000
11	J	48	TRP	0	0.039	0.028	17.842	-1.226	-1.226	0.000	0.000	0.000	0.000
12	J	49	ASP	-1	-0.831	-0.912	18.875	-14.873	-14.873	0.000	0.000	0.000	0.000
13	J	50	GLU	-1	-0.862	-0.956	20.701	-12.440	-12.440	0.000	0.000	0.000	0.000
14	J	51	MET	0	-0.006	0.010	23.585	0.692	0.692	0.000	0.000	0.000	0.000
15	J	52	ASN	0	-0.041	-0.016	20.195	0.566	0.566	0.000	0.000	0.000	0.000
16	J	53	ILE	0	-0.005	0.006	22.772	0.271	0.271	0.000	0.000	0.000	0.000
17	J	54	LEU	0	-0.037	-0.021	25.330	0.404	0.404	0.000	0.000	0.000	0.000
18	J	55	ALA	0	-0.035	-0.005	25.475	0.353	0.353	0.000	0.000	0.000	0.000
19	J	56	THR	0	-0.118	-0.058	23.689	0.578	0.578	0.000	0.000	0.000	0.000
20	J	130	LEU	0	0.011	0.010	40.559	-0.051	-0.051	0.000	0.000	0.000	0.000
21	J	131	SER	0	0.007	0.003	43.343	0.271	0.271	0.000	0.000	0.000	0.000
22	J	132	PRO	0	0.018	-0.012	45.211	-0.105	-0.105	0.000	0.000	0.000	0.000
23	J	133	GLU	-1	-0.841	-0.900	44.840	-7.197	-7.197	0.000	0.000	0.000	0.000
24	J	134	GLU	-1	-0.828	-0.924	40.784	-7.776	-7.776	0.000	0.000	0.000	0.000
25	J	135	ARG	1	0.922	0.966	41.816	7.251	7.251	0.000	0.000	0.000	0.000
26	J	136	GLU	-1	-0.745	-0.836	43.739	-6.901	-6.901	0.000	0.000	0.000	0.000
27	J	137	LYS	1	0.895	0.926	40.618	7.556	7.556	0.000	0.000	0.000	0.000
28	J	138	LYS	1	0.865	0.930	36.196	8.581	8.581	0.000	0.000	0.000	0.000
29	J	139	ARG	1	0.861	0.915	40.238	6.702	6.702	0.000	0.000	0.000	0.000
30	J	140	GLN	0	-0.013	-0.026	42.891	-0.087	-0.087	0.000	0.000	0.000	0.000
31	J	141	PHE	0	-0.015	-0.004	33.139	-0.056	-0.056	0.000	0.000	0.000	0.000
32	J	142	GLU	-1	-0.777	-0.885	37.246	-8.801	-8.801	0.000	0.000	0.000	0.000
33	J	143	MET	0	-0.029	-0.004	39.583	-0.035	-0.035	0.000	0.000	0.000	0.000
34	J	144	LYS	1	0.963	0.972	39.867	8.002	8.002	0.000	0.000	0.000	0.000
35	J	145	ARG	1	0.859	0.928	33.438	9.085	9.085	0.000	0.000	0.000	0.000
36	J	146	LYS	1	0.952	0.967	37.714	7.240	7.240	0.000	0.000	0.000	0.000
37	J	147	LEU	0	-0.019	-0.003	40.002	0.036	0.036	0.000	0.000	0.000	0.000
38	J	148	HIS	0	-0.032	-0.008	33.938	0.054	0.054	0.000	0.000	0.000	0.000
39	J	149	TYR	0	-0.052	-0.016	31.061	-0.065	-0.065	0.000	0.000	0.000	0.000
40	J	150	ASN	0	-0.017	-0.007	37.162	0.136	0.136	0.000	0.000	0.000	0.000
41	J	151	GLU	-1	-0.788	-0.909	34.181	-9.019	-9.019	0.000	0.000	0.000	0.000
42	J	152	GLY	0	-0.025	-0.020	38.185	0.079	0.079	0.000	0.000	0.000	0.000
43	J	153	LEU	0	-0.044	-0.015	39.126	0.152	0.152	0.000	0.000	0.000	0.000
44	J	154	ASN	0	0.028	-0.001	40.855	0.280	0.280	0.000	0.000	0.000	0.000
45	J	155	ILE	0	-0.006	0.009	36.816	0.020	0.020	0.000	0.000	0.000	0.000
46	J	156	LYS	1	0.909	0.955	40.027	7.249	7.249	0.000	0.000	0.000	0.000
47	J	157	LEU	0	0.095	0.054	43.445	0.025	0.025	0.000	0.000	0.000	0.000
48	J	158	ALA	0	0.020	0.009	39.180	0.037	0.037	0.000	0.000	0.000	0.000
49	J	159	ARG	1	0.957	0.970	36.579	8.347	8.347	0.000	0.000	0.000	0.000
50	J	160	GLN	0	-0.010	-0.008	41.748	-0.007	-0.007	0.000	0.000	0.000	0.000
51	J	161	LEU	0	0.011	0.007	43.126	0.108	0.108	0.000	0.000	0.000	0.000
52	J	162	ILE	0	0.047	0.018	37.944	0.024	0.024	0.000	0.000	0.000	0.000
53	J	163	SER	0	-0.049	-0.015	42.096	0.047	0.047	0.000	0.000	0.000	0.000
54	J	164	LYS	1	0.875	0.911	44.798	6.736	6.736	0.000	0.000	0.000	0.000
55	J	165	ASP	-1	-0.864	-0.907	43.713	-6.941	-6.941	0.000	0.000	0.000	0.000
56	J	166	LEU	0	-0.030	-0.011	41.339	-0.021	-0.021	0.000	0.000	0.000	0.000
57	J	167	HIS	0	-0.108	-0.065	44.241	0.171	0.171	0.000	0.000	0.000	0.000
58	J	168	ASP	-1	-1.002	-0.974	46.574	-6.383	-6.383	0.000	0.000	0.000	0.000

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