FMO DATABASE

FMODB ID: 1771Z

Calculation Name: 5GNA-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GNA

Chain ID: B

ChEMBL ID:

UniProt ID: P16328

Base Structure: X-ray

Registration Date: 2023-06-21

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	56
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-222295.27356
FMO2-HF: Nuclear repulsion	199549.497846
FMO2-HF: Total energy	-22745.775713
FMO2-MP2: Total energy	-22810.272556

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(B:412:ASN)

Summations of interaction energy for fragment #1(B:412:ASN)

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.
-3.309	-2.349	-0.001	-0.446	-0.512	0.002

Interaction energy analysis for fragmet #1(B:412:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : -0.003

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	B	414	THR	0	0.031	0.004	3.852	-2.000	-1.040	-0.001	-0.446	-0.512	0.002
4	B	415	LEU	0	0.108	0.049	6.393	0.649	0.649	0.000	0.000	0.000	0.000
5	B	416	LYS	1	0.958	0.986	8.257	-0.119	-0.119	0.000	0.000	0.000	0.000
6	B	417	SER	0	0.007	0.009	8.518	-0.037	-0.037	0.000	0.000	0.000	0.000
7	B	418	LEU	0	0.055	0.020	5.286	-0.158	-0.158	0.000	0.000	0.000	0.000
8	B	419	THR	0	-0.005	-0.010	9.730	-0.204	-0.204	0.000	0.000	0.000	0.000
9	B	420	LYS	1	0.931	0.960	12.956	-0.753	-0.753	0.000	0.000	0.000	0.000
10	B	421	GLN	0	-0.011	-0.002	8.649	0.041	0.041	0.000	0.000	0.000	0.000
11	B	422	TYR	0	0.033	0.020	13.409	-0.104	-0.104	0.000	0.000	0.000	0.000
12	B	423	LEU	0	0.011	-0.001	15.034	-0.111	-0.111	0.000	0.000	0.000	0.000
13	B	424	SER	0	0.004	0.011	17.220	-0.082	-0.082	0.000	0.000	0.000	0.000
14	B	425	VAL	0	-0.018	-0.001	15.806	-0.062	-0.062	0.000	0.000	0.000	0.000
15	B	426	SER	0	-0.019	-0.011	18.689	-0.064	-0.064	0.000	0.000	0.000	0.000
16	B	427	ASN	0	0.006	0.010	21.024	-0.044	-0.044	0.000	0.000	0.000	0.000
17	B	428	SER	0	0.029	0.009	21.271	-0.044	-0.044	0.000	0.000	0.000	0.000
18	B	429	ILE	0	-0.027	0.007	20.754	-0.043	-0.043	0.000	0.000	0.000	0.000
19	B	430	ASP	-1	-0.853	-0.929	24.527	0.441	0.441	0.000	0.000	0.000	0.000
20	B	431	GLU	-1	-0.928	-0.978	26.067	0.433	0.433	0.000	0.000	0.000	0.000
21	B	432	THR	0	-0.070	-0.049	26.503	-0.039	-0.039	0.000	0.000	0.000	0.000
22	B	433	VAL	0	0.006	-0.002	28.099	-0.033	-0.033	0.000	0.000	0.000	0.000
23	B	434	ALA	0	-0.025	-0.009	30.524	-0.029	-0.029	0.000	0.000	0.000	0.000
24	B	435	ARG	1	0.921	0.961	28.581	-0.427	-0.427	0.000	0.000	0.000	0.000
25	B	436	TYR	0	0.015	-0.004	29.684	-0.018	-0.018	0.000	0.000	0.000	0.000
26	B	437	LYS	1	0.963	0.989	32.797	-0.310	-0.310	0.000	0.000	0.000	0.000
27	B	438	ALA	0	0.006	0.025	36.647	-0.017	-0.017	0.000	0.000	0.000	0.000
28	B	439	GLN	0	0.026	0.007	37.292	-0.005	-0.005	0.000	0.000	0.000	0.000
29	B	440	PHE	0	0.011	0.002	38.689	-0.010	-0.010	0.000	0.000	0.000	0.000
30	B	441	THR	0	0.030	0.005	40.446	-0.013	-0.013	0.000	0.000	0.000	0.000
31	B	442	GLN	0	-0.044	-0.017	41.014	-0.004	-0.004	0.000	0.000	0.000	0.000
32	B	443	LEU	0	0.000	-0.001	41.244	-0.009	-0.009	0.000	0.000	0.000	0.000
33	B	444	ASP	-1	-0.900	-0.934	44.663	0.154	0.154	0.000	0.000	0.000	0.000
34	B	445	THR	0	-0.018	-0.023	46.586	-0.011	-0.011	0.000	0.000	0.000	0.000
35	B	446	MET	0	-0.049	-0.027	47.796	-0.006	-0.006	0.000	0.000	0.000	0.000
36	B	447	MET	0	0.018	0.004	47.436	-0.008	-0.008	0.000	0.000	0.000	0.000
37	B	448	SER	0	0.031	0.011	50.485	-0.009	-0.009	0.000	0.000	0.000	0.000
38	B	449	LYS	1	0.878	0.938	52.303	-0.130	-0.130	0.000	0.000	0.000	0.000
39	B	450	LEU	0	0.043	0.015	51.357	-0.006	-0.006	0.000	0.000	0.000	0.000
40	B	451	ASN	0	0.010	0.031	54.972	-0.005	-0.005	0.000	0.000	0.000	0.000
41	B	452	ASN	0	0.005	0.003	57.062	-0.005	-0.005	0.000	0.000	0.000	0.000
42	B	453	THR	0	0.015	-0.002	57.471	-0.003	-0.003	0.000	0.000	0.000	0.000
43	B	454	SER	0	-0.002	-0.006	57.841	-0.003	-0.003	0.000	0.000	0.000	0.000
44	B	455	SER	0	-0.003	0.017	60.495	-0.005	-0.005	0.000	0.000	0.000	0.000
45	B	456	TYR	0	0.014	0.002	62.813	-0.003	-0.003	0.000	0.000	0.000	0.000
46	B	457	LEU	0	0.023	-0.004	60.490	-0.003	-0.003	0.000	0.000	0.000	0.000
47	B	458	THR	0	-0.013	-0.009	63.954	-0.002	-0.002	0.000	0.000	0.000	0.000
48	B	459	GLN	0	-0.029	-0.010	66.294	-0.004	-0.004	0.000	0.000	0.000	0.000
49	B	460	GLN	0	-0.002	0.001	67.096	-0.004	-0.004	0.000	0.000	0.000	0.000
50	B	461	PHE	0	0.013	0.021	67.609	-0.002	-0.002	0.000	0.000	0.000	0.000
51	B	462	THR	0	-0.051	-0.038	69.552	-0.003	-0.003	0.000	0.000	0.000	0.000
52	B	463	ALA	0	-0.001	-0.003	72.116	-0.003	-0.003	0.000	0.000	0.000	0.000
53	B	464	MET	0	-0.031	-0.014	70.652	-0.003	-0.003	0.000	0.000	0.000	0.000
54	B	465	ASN	0	-0.026	-0.022	71.621	-0.002	-0.002	0.000	0.000	0.000	0.000
55	B	466	LYS	1	0.865	0.956	75.400	-0.068	-0.068	0.000	0.000	0.000	0.000
56	B	467	SER	0	0.009	0.006	78.534	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:412:ASN)