FMO DATABASE

FMODB ID: NNVYQ

Calculation Name: 2Q8R-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Q8R

Chain ID: E

ChEMBL ID:

UniProt ID: Q16627

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

Total energy (hartree)

FMO2-HF: Electronic energy	-393590.057993
FMO2-HF: Nuclear repulsion	365081.30682
FMO2-HF: Total energy	-28508.751173
FMO2-MP2: Total energy	-28587.811274

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(E:1:GLY)

Summations of interaction energy for fragment #1(E:1:GLY)

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.
4.555	7.425	0.001	-1.426	-1.444	0.003

Interaction energy analysis for fragmet #1(E:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.076 / q_NPA : 0.037

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	E	3	TYR	0	0.016	0.005	3.603	-0.498	1.787	-0.010	-1.183	-1.092	0.002
4	E	4	HIS	1	0.849	0.936	3.209	5.342	5.904	0.012	-0.240	-0.334	0.001
5	E	5	PRO	0	0.084	0.045	5.398	0.115	0.138	-0.001	-0.003	-0.018	0.000
6	E	6	SER	0	-0.022	-0.012	8.338	-0.288	-0.288	0.000	0.000	0.000	0.000
7	E	7	GLU	-1	-0.899	-0.936	10.862	-0.474	-0.474	0.000	0.000	0.000	0.000
8	E	8	CYS	0	-0.072	-0.027	13.880	-0.019	-0.019	0.000	0.000	0.000	0.000
9	E	9	CYS	0	0.026	0.024	17.130	0.026	0.026	0.000	0.000	0.000	0.000
10	E	10	PHE	0	0.057	0.024	19.381	0.006	0.006	0.000	0.000	0.000	0.000
11	E	11	THR	0	-0.024	-0.025	23.554	0.020	0.020	0.000	0.000	0.000	0.000
12	E	12	TYR	0	-0.076	-0.060	23.856	0.002	0.002	0.000	0.000	0.000	0.000
13	E	13	THR	0	-0.003	0.002	27.030	0.018	0.018	0.000	0.000	0.000	0.000
14	E	14	THR	0	0.052	0.020	29.266	-0.005	-0.005	0.000	0.000	0.000	0.000
15	E	15	TYR	0	-0.076	-0.028	32.068	0.008	0.008	0.000	0.000	0.000	0.000
16	E	16	LYS	1	0.978	0.987	31.283	0.097	0.097	0.000	0.000	0.000	0.000
17	E	17	ILE	0	-0.001	0.012	26.295	0.010	0.010	0.000	0.000	0.000	0.000
18	E	18	PRO	0	0.001	0.003	30.600	0.002	0.002	0.000	0.000	0.000	0.000
19	E	19	ARG	1	1.052	1.019	30.456	0.084	0.084	0.000	0.000	0.000	0.000
20	E	20	GLN	0	0.047	0.024	30.035	-0.005	-0.005	0.000	0.000	0.000	0.000
21	E	21	ARG	1	0.861	0.924	28.221	0.097	0.097	0.000	0.000	0.000	0.000
22	E	22	ILE	0	-0.012	-0.004	24.706	-0.002	-0.002	0.000	0.000	0.000	0.000
23	E	23	MET	0	-0.057	-0.027	22.288	0.020	0.020	0.000	0.000	0.000	0.000
24	E	24	ASP	-1	-0.803	-0.893	18.315	-0.200	-0.200	0.000	0.000	0.000	0.000
25	E	25	TYR	0	-0.059	-0.044	20.125	0.008	0.008	0.000	0.000	0.000	0.000
26	E	26	TYR	0	0.036	0.022	14.884	-0.002	-0.002	0.000	0.000	0.000	0.000
27	E	27	GLU	-1	-0.939	-0.958	17.065	-0.369	-0.369	0.000	0.000	0.000	0.000
28	E	28	THR	0	-0.044	-0.031	15.568	-0.055	-0.055	0.000	0.000	0.000	0.000
29	E	29	ASN	0	0.014	-0.006	11.741	0.145	0.145	0.000	0.000	0.000	0.000
30	E	30	SER	0	0.022	0.014	14.852	0.070	0.070	0.000	0.000	0.000	0.000
31	E	31	GLN	0	-0.005	-0.017	13.185	-0.083	-0.083	0.000	0.000	0.000	0.000
32	E	33	SER	0	0.044	0.014	18.137	0.027	0.027	0.000	0.000	0.000	0.000
33	E	34	LYS	1	0.841	0.937	21.316	0.299	0.299	0.000	0.000	0.000	0.000
34	E	35	PRO	0	0.065	0.043	21.072	-0.035	-0.035	0.000	0.000	0.000	0.000
35	E	36	GLY	0	0.035	0.030	20.789	0.031	0.031	0.000	0.000	0.000	0.000
36	E	37	ILE	0	0.023	0.037	20.249	-0.031	-0.031	0.000	0.000	0.000	0.000
37	E	38	VAL	0	0.005	0.005	17.683	0.035	0.035	0.000	0.000	0.000	0.000
38	E	39	PHE	0	0.007	-0.006	20.154	0.002	0.002	0.000	0.000	0.000	0.000
39	E	40	ILE	0	0.056	0.030	16.489	0.001	0.001	0.000	0.000	0.000	0.000
40	E	41	THR	0	-0.023	-0.023	20.939	0.029	0.029	0.000	0.000	0.000	0.000
41	E	42	LYS	1	0.952	0.962	23.040	0.055	0.055	0.000	0.000	0.000	0.000
42	E	43	ARG	1	0.862	0.928	24.923	0.061	0.061	0.000	0.000	0.000	0.000
43	E	44	GLY	0	0.067	0.043	20.891	0.009	0.009	0.000	0.000	0.000	0.000
44	E	45	HIS	0	-0.021	0.003	19.912	-0.024	-0.024	0.000	0.000	0.000	0.000
45	E	46	SER	0	0.056	0.029	18.098	-0.011	-0.011	0.000	0.000	0.000	0.000
46	E	47	VAL	0	-0.044	-0.020	20.473	0.006	0.006	0.000	0.000	0.000	0.000
47	E	49	THR	0	-0.035	-0.033	23.019	0.034	0.034	0.000	0.000	0.000	0.000
48	E	50	ASN	0	0.112	0.056	24.371	-0.039	-0.039	0.000	0.000	0.000	0.000
49	E	51	PRO	0	0.043	0.020	23.450	0.019	0.019	0.000	0.000	0.000	0.000
50	E	52	SER	0	-0.056	-0.035	26.240	0.016	0.016	0.000	0.000	0.000	0.000
51	E	53	ASP	-1	-0.872	-0.928	29.632	-0.154	-0.154	0.000	0.000	0.000	0.000
52	E	54	LYS	1	0.961	0.974	30.783	0.103	0.103	0.000	0.000	0.000	0.000
53	E	55	TRP	0	-0.001	-0.015	28.432	0.003	0.003	0.000	0.000	0.000	0.000
54	E	56	VAL	0	0.015	0.026	26.014	0.004	0.004	0.000	0.000	0.000	0.000
55	E	57	GLN	0	0.007	-0.006	27.866	0.007	0.007	0.000	0.000	0.000	0.000
56	E	58	ASP	-1	-0.905	-0.965	29.255	-0.118	-0.118	0.000	0.000	0.000	0.000
57	E	59	TYR	0	-0.102	-0.086	27.850	0.011	0.011	0.000	0.000	0.000	0.000
58	E	60	ILE	0	0.042	0.024	23.860	0.005	0.005	0.000	0.000	0.000	0.000
59	E	61	LYS	1	0.905	0.955	26.464	0.113	0.113	0.000	0.000	0.000	0.000
60	E	62	ASP	-1	-0.946	-0.972	29.104	-0.094	-0.094	0.000	0.000	0.000	0.000
61	E	63	MET	0	-0.108	-0.038	23.600	0.004	0.004	0.000	0.000	0.000	0.000
62	E	64	LYS	1	0.925	0.987	23.146	0.188	0.188	0.000	0.000	0.000	0.000
63	E	65	GLU	-1	-0.885	-0.930	25.132	-0.061	-0.061	0.000	0.000	0.000	0.000
64	E	66	ASN	0	-0.068	-0.043	25.968	-0.010	-0.010	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:1:GLY)