FMO DATABASE

FMODB ID: MNRKZ

Calculation Name: 2H8U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2H8U

Chain ID: A

ChEMBL ID:

UniProt ID: P83346

Base Structure: X-ray

Registration Date: 2023-09-22

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	61
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-355747.134284
FMO2-HF: Nuclear repulsion	328801.909366
FMO2-HF: Total energy	-26945.224917
FMO2-MP2: Total energy	-27017.662867

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(A:1:ARG)

Summations of interaction energy for fragment #1(A:1:ARG)

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.
12.374	27.074	32.453	-19.175	-27.977	-0.166

Interaction energy analysis for fragmet #1(A:1:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.902 / q_NPA : 0.941

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

Sort

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	A	3	CYS	0	-0.049	-0.008	2.995	-10.186	-6.038	3.469	-2.537	-5.080	0.003
4	A	4	LEU	0	0.020	0.004	4.357	3.128	3.179	-0.001	-0.020	-0.030	0.000
5	A	5	ILE	0	-0.050	-0.030	8.100	-0.580	-0.580	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.973	0.974	10.537	16.872	16.872	0.000	0.000	0.000	0.000
7	A	7	TYR	0	-0.002	-0.014	12.579	-0.777	-0.777	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.029	-0.002	14.560	0.912	0.912	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.044	0.006	17.280	-0.202	-0.202	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.020	0.019	19.526	0.138	0.138	0.000	0.000	0.000	0.000
11	A	11	ASN	0	0.037	0.029	18.210	0.026	0.026	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.940	-0.982	12.254	-23.110	-23.110	0.000	0.000	0.000	0.000
13	A	13	SER	0	0.003	0.012	12.622	0.854	0.854	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.002	-0.008	7.472	-1.484	-1.484	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.948	0.985	6.817	29.308	29.308	0.000	0.000	0.000	0.000
16	A	16	THR	0	0.029	0.010	3.707	-5.933	-5.688	0.002	-0.071	-0.176	0.000
17	A	17	CYS	0	-0.119	-0.033	2.620	0.083	2.040	1.180	-0.773	-2.364	0.000
18	A	18	PRO	0	0.024	0.029	4.370	0.234	0.352	-0.001	-0.025	-0.093	0.000
19	A	19	SER	0	0.056	0.007	5.549	-3.607	-3.607	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.057	0.027	6.618	1.534	1.534	0.000	0.000	0.000	0.000
21	A	21	GLN	0	-0.053	-0.027	5.074	-1.626	-1.626	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.061	0.021	2.505	-9.762	-5.577	1.430	-2.052	-3.563	-0.013
23	A	23	LEU	0	0.012	0.033	1.733	-34.473	-37.732	14.395	-6.041	-5.095	-0.073
24	A	25	LEU	0	0.019	0.009	4.853	2.756	2.801	-0.001	-0.007	-0.036	0.000
25	A	26	LYS	1	0.852	0.914	8.589	19.517	19.517	0.000	0.000	0.000	0.000
26	A	27	LYS	1	0.940	0.979	11.474	17.120	17.120	0.000	0.000	0.000	0.000
27	A	28	TRP	0	-0.017	-0.015	14.636	-0.463	-0.463	0.000	0.000	0.000	0.000
28	A	29	GLU	-1	-0.847	-0.909	18.425	-12.672	-12.672	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.067	-0.035	21.998	0.088	0.088	0.000	0.000	0.000	0.000
30	A	31	GLY	0	-0.013	-0.008	24.665	0.230	0.230	0.000	0.000	0.000	0.000
31	A	32	ASN	0	0.014	0.007	25.203	0.605	0.605	0.000	0.000	0.000	0.000
32	A	33	PRO	0	-0.024	-0.003	27.638	-0.037	-0.037	0.000	0.000	0.000	0.000
33	A	34	SER	0	0.013	-0.005	28.103	0.203	0.203	0.000	0.000	0.000	0.000
34	A	35	GLY	0	0.034	0.038	26.417	-0.070	-0.070	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.942	0.977	21.552	12.886	12.886	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.892	-0.961	20.517	-12.945	-12.945	0.000	0.000	0.000	0.000
37	A	38	VAL	0	-0.068	-0.030	14.896	-0.599	-0.599	0.000	0.000	0.000	0.000
38	A	39	LYS	1	0.976	0.991	13.154	17.917	17.917	0.000	0.000	0.000	0.000
39	A	40	ARG	1	0.822	0.911	9.831	20.556	20.556	0.000	0.000	0.000	0.000
40	A	41	GLY	0	-0.012	-0.017	7.948	1.453	1.453	0.000	0.000	0.000	0.000
41	A	43	VAL	0	0.036	0.017	5.330	4.457	4.457	0.000	0.000	0.000	0.000
42	A	44	ALA	0	0.029	0.006	6.037	-4.546	-4.546	0.000	0.000	0.000	0.000
43	A	45	THR	0	0.011	0.012	8.412	-1.632	-1.632	0.000	0.000	0.000	0.000
44	A	46	CYS	0	-0.038	-0.039	8.474	-0.699	-0.699	0.000	0.000	0.000	0.000
45	A	47	PRO	0	0.043	0.027	11.268	1.234	1.234	0.000	0.000	0.000	0.000
46	A	48	LYS	1	0.940	0.980	14.269	14.246	14.246	0.000	0.000	0.000	0.000
47	A	49	PRO	0	0.042	0.010	17.664	0.030	0.030	0.000	0.000	0.000	0.000
48	A	50	TRP	0	-0.024	-0.009	19.141	0.533	0.533	0.000	0.000	0.000	0.000
49	A	51	LYS	1	0.913	0.941	22.275	10.856	10.856	0.000	0.000	0.000	0.000
50	A	52	ASN	0	0.137	0.065	24.667	0.044	0.044	0.000	0.000	0.000	0.000
51	A	53	GLU	-1	-0.850	-0.921	18.865	-15.546	-15.546	0.000	0.000	0.000	0.000
52	A	54	ILE	0	0.007	0.015	16.716	-0.041	-0.041	0.000	0.000	0.000	0.000
53	A	55	ILE	0	-0.028	-0.023	13.153	-0.733	-0.733	0.000	0.000	0.000	0.000
54	A	56	GLN	0	0.041	0.019	11.029	1.214	1.214	0.000	0.000	0.000	0.000
55	A	58	CYS	0	0.016	0.042	4.762	4.532	4.744	-0.001	-0.017	-0.194	0.000
56	A	59	ALA	0	0.061	0.028	3.432	-4.282	-3.666	0.019	-0.129	-0.505	0.000
57	A	60	LYS	1	0.992	0.999	3.320	30.486	32.879	0.494	-1.032	-1.855	-0.002
58	A	61	ASP	-1	-0.772	-0.905	1.929	-98.908	-94.557	11.399	-7.178	-8.572	-0.080
59	A	62	LYS	1	0.881	0.922	3.082	38.612	38.250	0.069	0.707	-0.414	-0.001
60	A	64	ASN	0	-0.021	0.007	6.429	1.596	1.596	0.000	0.000	0.000	0.000
61	A	65	ALA	0	0.048	0.018	8.130	3.027	3.027	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:1:ARG)