FMO DATABASE

FMODB ID: 76Y8K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-355724.304468
FMO2-HF: Nuclear repulsion	328778.347961
FMO2-HF: Total energy	-26945.956507
FMO2-MP2: Total energy	-27018.335765

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.
3.882	14.579	40.246	-20.717	-30.226	-0.187

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 : 0.880 / q_NPA : 0.936

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	A	3	CYS	0	-0.056	-0.016	2.778	-9.322	-5.842	5.037	-2.918	-5.599	0.001
4	A	4	LEU	0	0.022	0.009	4.489	3.388	3.433	-0.001	-0.016	-0.028	0.000
5	A	5	ILE	0	-0.069	-0.041	8.105	-0.507	-0.507	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.967	0.970	10.586	17.025	17.025	0.000	0.000	0.000	0.000
7	A	7	TYR	0	0.005	-0.010	12.446	-0.711	-0.711	0.000	0.000	0.000	0.000
8	A	8	SER	0	0.003	0.012	14.571	0.840	0.840	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.029	-0.002	17.093	-0.130	-0.130	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.019	0.019	19.276	0.153	0.153	0.000	0.000	0.000	0.000
11	A	11	ASN	0	0.006	0.006	18.534	0.007	0.007	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.845	-0.912	12.098	-24.045	-24.045	0.000	0.000	0.000	0.000
13	A	13	SER	0	0.011	0.011	12.755	0.866	0.866	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.004	-0.002	7.582	-1.653	-1.653	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.981	0.995	6.764	29.407	29.407	0.000	0.000	0.000	0.000
16	A	16	THR	0	0.045	0.012	3.758	-5.625	-5.392	0.001	-0.061	-0.173	0.000
17	A	17	CYS	0	-0.125	-0.036	2.531	0.569	2.333	1.814	-0.939	-2.639	0.000
18	A	18	PRO	0	0.020	0.029	4.371	0.368	0.496	-0.001	-0.026	-0.101	0.000
19	A	19	SER	0	0.071	0.010	5.547	-3.738	-3.738	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.044	0.024	6.608	1.545	1.545	0.000	0.000	0.000	0.000
21	A	21	GLN	0	-0.063	-0.033	5.138	-1.440	-1.440	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.074	0.028	2.510	-9.665	-5.599	1.646	-2.115	-3.597	-0.013
23	A	23	LEU	0	0.003	0.024	1.789	-37.448	-39.557	13.124	-5.511	-5.504	-0.075
24	A	25	LEU	0	0.015	0.010	4.773	2.684	2.736	-0.001	-0.010	-0.041	0.000
25	A	26	LYS	1	0.795	0.898	8.531	20.133	20.133	0.000	0.000	0.000	0.000
26	A	27	LYS	1	0.849	0.915	11.347	16.655	16.655	0.000	0.000	0.000	0.000
27	A	28	TRP	0	-0.005	-0.004	14.626	-0.429	-0.429	0.000	0.000	0.000	0.000
28	A	29	GLU	-1	-0.867	-0.920	18.306	-12.793	-12.793	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.046	-0.028	21.898	0.102	0.102	0.000	0.000	0.000	0.000
30	A	31	GLY	0	-0.012	-0.008	24.591	0.239	0.239	0.000	0.000	0.000	0.000
31	A	32	ASN	0	-0.013	-0.003	24.514	0.715	0.715	0.000	0.000	0.000	0.000
32	A	33	PRO	0	-0.001	0.002	27.506	-0.054	-0.054	0.000	0.000	0.000	0.000
33	A	34	SER	0	0.014	0.005	27.806	0.247	0.247	0.000	0.000	0.000	0.000
34	A	35	GLY	0	0.017	0.022	26.402	-0.068	-0.068	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.930	0.969	21.345	12.914	12.914	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.854	-0.942	20.476	-13.044	-13.044	0.000	0.000	0.000	0.000
37	A	38	VAL	0	-0.063	-0.024	14.603	-0.578	-0.578	0.000	0.000	0.000	0.000
38	A	39	LYS	1	0.966	0.990	13.266	18.026	18.026	0.000	0.000	0.000	0.000
39	A	40	ARG	1	0.872	0.931	9.964	20.291	20.291	0.000	0.000	0.000	0.000
40	A	41	GLY	0	-0.006	-0.013	7.889	1.457	1.457	0.000	0.000	0.000	0.000
41	A	43	VAL	0	0.024	0.011	5.332	4.426	4.426	0.000	0.000	0.000	0.000
42	A	44	ALA	0	0.037	0.012	5.941	-4.574	-4.574	0.000	0.000	0.000	0.000
43	A	45	THR	0	0.007	0.003	8.278	-1.605	-1.605	0.000	0.000	0.000	0.000
44	A	46	CYS	0	-0.034	-0.032	8.453	-0.660	-0.660	0.000	0.000	0.000	0.000
45	A	47	PRO	0	0.036	0.026	11.184	1.220	1.220	0.000	0.000	0.000	0.000
46	A	48	LYS	1	0.949	0.979	14.239	14.141	14.141	0.000	0.000	0.000	0.000
47	A	49	PRO	0	0.049	0.011	17.639	0.072	0.072	0.000	0.000	0.000	0.000
48	A	50	TRP	0	-0.016	-0.004	19.160	0.531	0.531	0.000	0.000	0.000	0.000
49	A	51	LYS	1	0.936	0.957	22.301	10.720	10.720	0.000	0.000	0.000	0.000
50	A	52	ASN	0	0.110	0.054	24.658	0.104	0.104	0.000	0.000	0.000	0.000
51	A	53	GLU	-1	-0.786	-0.879	18.795	-15.688	-15.688	0.000	0.000	0.000	0.000
52	A	54	ILE	0	0.009	0.018	16.700	-0.051	-0.051	0.000	0.000	0.000	0.000
53	A	55	ILE	0	-0.041	-0.029	13.251	-0.729	-0.729	0.000	0.000	0.000	0.000
54	A	56	GLN	0	0.077	0.037	10.906	1.346	1.346	0.000	0.000	0.000	0.000
55	A	58	CYS	0	0.021	0.047	4.657	4.899	5.097	-0.001	-0.012	-0.185	0.000
56	A	59	ALA	0	0.059	0.029	3.063	-4.793	-4.001	0.067	-0.223	-0.636	0.000
57	A	60	LYS	1	0.989	0.998	3.170	30.494	32.933	1.073	-1.119	-2.393	-0.004
58	A	61	ASP	-1	-0.750	-0.904	1.755	-101.880	-101.909	17.434	-8.459	-8.946	-0.095
59	A	62	LYS	1	0.795	0.871	3.111	35.401	35.039	0.054	0.692	-0.384	-0.001
60	A	64	ASN	0	-0.045	-0.016	6.247	1.370	1.370	0.000	0.000	0.000	0.000
61	A	65	ALA	0	0.038	0.020	7.978	2.757	2.757	0.000	0.000	0.000	0.000

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