FMO DATABASE

FMODB ID: 5JRKZ

Calculation Name: 2GV5-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GV5

Chain ID: C

ChEMBL ID:

UniProt ID: P06704

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	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	73
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-359211.21923
FMO2-HF: Nuclear repulsion	328074.689094
FMO2-HF: Total energy	-31136.530136
FMO2-MP2: Total energy	-31226.834344

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(C:638:GLY)

Summations of interaction energy for fragment #1(C:638: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.
-4.775	-4.228	7.315	-4.037	-3.824	-0.025

Interaction energy analysis for fragmet #1(C:638:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : -0.002

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	C	640	LEU	0	0.011	0.014	2.913	-1.095	1.217	0.342	-1.154	-1.500	0.006
4	C	641	GLY	0	0.027	0.023	3.395	0.524	1.128	0.009	-0.227	-0.386	0.000
5	C	642	SER	0	0.017	0.000	1.935	-5.530	-7.942	6.965	-2.652	-1.901	-0.031
6	C	643	LYS	1	0.912	0.933	4.373	-0.156	-0.113	-0.001	-0.004	-0.037	0.000
7	C	644	LEU	0	0.022	0.007	5.800	0.241	0.241	0.000	0.000	0.000	0.000
8	C	645	ASN	0	-0.001	0.008	6.296	0.276	0.276	0.000	0.000	0.000	0.000
9	C	646	ASP	-1	-0.812	-0.901	5.387	0.703	0.703	0.000	0.000	0.000	0.000
10	C	647	ILE	0	-0.017	-0.011	7.271	0.148	0.148	0.000	0.000	0.000	0.000
11	C	648	LEU	0	-0.002	0.014	10.525	0.057	0.057	0.000	0.000	0.000	0.000
12	C	649	HIS	0	0.093	0.054	9.911	0.146	0.146	0.000	0.000	0.000	0.000
13	C	650	VAL	0	-0.009	-0.012	10.622	0.056	0.056	0.000	0.000	0.000	0.000
14	C	651	TYR	0	-0.002	0.007	13.087	0.023	0.023	0.000	0.000	0.000	0.000
15	C	652	GLU	-1	-0.874	-0.939	14.377	-0.268	-0.268	0.000	0.000	0.000	0.000
16	C	653	LYS	1	0.860	0.928	14.081	0.159	0.159	0.000	0.000	0.000	0.000
17	C	654	SER	0	-0.108	-0.057	17.184	0.020	0.020	0.000	0.000	0.000	0.000
18	C	655	LYS	1	0.882	0.910	19.355	0.034	0.034	0.000	0.000	0.000	0.000
19	C	656	GLU	-1	-0.847	-0.931	18.283	-0.106	-0.106	0.000	0.000	0.000	0.000
20	C	657	ARG	1	0.940	0.982	21.449	-0.035	-0.035	0.000	0.000	0.000	0.000
21	C	658	GLU	-1	-0.860	-0.910	23.282	-0.013	-0.013	0.000	0.000	0.000	0.000
22	C	659	LEU	0	0.040	0.026	25.027	0.002	0.002	0.000	0.000	0.000	0.000
23	C	660	GLN	0	-0.017	-0.027	23.386	0.004	0.004	0.000	0.000	0.000	0.000
24	C	661	SER	0	-0.022	-0.003	27.433	0.003	0.003	0.000	0.000	0.000	0.000
25	C	662	GLN	0	0.008	0.008	29.308	-0.001	-0.001	0.000	0.000	0.000	0.000
26	C	663	LEU	0	0.013	0.000	30.380	0.002	0.002	0.000	0.000	0.000	0.000
27	C	664	PHE	0	0.005	0.013	31.774	0.002	0.002	0.000	0.000	0.000	0.000
28	C	665	ASN	0	-0.027	-0.032	32.463	0.003	0.003	0.000	0.000	0.000	0.000
29	C	666	ALA	0	0.000	0.012	35.189	0.001	0.001	0.000	0.000	0.000	0.000
30	C	667	TRP	0	-0.030	-0.011	34.427	0.000	0.000	0.000	0.000	0.000	0.000
31	C	668	ARG	1	0.980	0.987	37.192	-0.008	-0.008	0.000	0.000	0.000	0.000
32	C	669	ASN	0	0.018	0.001	38.815	0.002	0.002	0.000	0.000	0.000	0.000
33	C	670	ARG	1	0.932	0.959	41.143	0.019	0.019	0.000	0.000	0.000	0.000
34	C	671	PHE	0	0.024	0.013	42.101	0.000	0.000	0.000	0.000	0.000	0.000
35	C	672	CYS	0	0.005	0.017	43.473	0.001	0.001	0.000	0.000	0.000	0.000
36	C	673	PHE	0	0.013	0.019	45.254	0.000	0.000	0.000	0.000	0.000	0.000
37	C	674	TYR	0	0.014	0.000	45.418	-0.001	-0.001	0.000	0.000	0.000	0.000
38	C	675	THR	0	-0.044	-0.044	46.771	0.001	0.001	0.000	0.000	0.000	0.000
39	C	676	GLU	-1	-0.910	-0.947	48.366	0.003	0.003	0.000	0.000	0.000	0.000
40	C	677	GLU	-1	-0.918	-0.961	49.590	-0.002	-0.002	0.000	0.000	0.000	0.000
41	C	678	CYS	0	-0.029	-0.021	50.739	0.000	0.000	0.000	0.000	0.000	0.000
42	C	679	ASN	0	-0.018	0.001	52.826	-0.001	-0.001	0.000	0.000	0.000	0.000
43	C	680	ILE	0	0.062	0.030	53.214	0.000	0.000	0.000	0.000	0.000	0.000
44	C	681	GLN	0	-0.022	0.009	53.561	-0.001	-0.001	0.000	0.000	0.000	0.000
45	C	682	ALA	0	-0.007	-0.003	57.224	0.000	0.000	0.000	0.000	0.000	0.000
46	C	683	ILE	0	-0.004	-0.002	57.369	0.000	0.000	0.000	0.000	0.000	0.000
47	C	684	SER	0	-0.013	-0.016	59.777	0.000	0.000	0.000	0.000	0.000	0.000
48	C	685	LYS	1	0.883	0.922	61.749	0.005	0.005	0.000	0.000	0.000	0.000
49	C	686	ARG	1	0.916	0.963	63.136	0.003	0.003	0.000	0.000	0.000	0.000
50	C	687	ASN	0	0.022	0.007	64.451	-0.001	-0.001	0.000	0.000	0.000	0.000
51	C	688	TYR	0	0.104	0.054	66.268	0.000	0.000	0.000	0.000	0.000	0.000
52	C	689	GLN	0	-0.013	-0.011	67.427	0.000	0.000	0.000	0.000	0.000	0.000
53	C	690	LEU	0	-0.014	0.002	69.461	0.000	0.000	0.000	0.000	0.000	0.000
54	C	691	GLU	-1	-0.857	-0.938	68.905	0.000	0.000	0.000	0.000	0.000	0.000
55	C	692	LYS	1	0.894	0.955	71.541	0.002	0.002	0.000	0.000	0.000	0.000
56	C	693	MET	0	-0.041	-0.003	73.891	0.000	0.000	0.000	0.000	0.000	0.000
57	C	694	VAL	0	0.058	0.019	75.320	0.000	0.000	0.000	0.000	0.000	0.000
58	C	695	LEU	0	0.023	0.000	75.489	0.000	0.000	0.000	0.000	0.000	0.000
59	C	696	LYS	1	0.859	0.926	78.187	0.003	0.003	0.000	0.000	0.000	0.000
60	C	697	LYS	1	0.801	0.885	79.767	0.003	0.003	0.000	0.000	0.000	0.000
61	C	698	PHE	0	0.049	0.022	79.961	0.000	0.000	0.000	0.000	0.000	0.000
62	C	699	ARG	1	0.916	0.958	80.785	0.000	0.000	0.000	0.000	0.000	0.000
63	C	700	GLU	-1	-0.770	-0.850	83.198	-0.003	-0.003	0.000	0.000	0.000	0.000
64	C	701	ARG	1	0.886	0.917	85.089	0.002	0.002	0.000	0.000	0.000	0.000
65	C	702	LEU	0	-0.009	0.001	85.404	0.000	0.000	0.000	0.000	0.000	0.000
66	C	703	LEU	0	-0.020	-0.008	88.139	0.000	0.000	0.000	0.000	0.000	0.000
67	C	704	GLU	-1	-0.850	-0.920	88.666	-0.002	-0.002	0.000	0.000	0.000	0.000
68	C	705	ILE	0	0.005	0.004	90.063	0.000	0.000	0.000	0.000	0.000	0.000
69	C	706	VAL	0	-0.013	-0.006	92.928	0.000	0.000	0.000	0.000	0.000	0.000
70	C	707	LYS	1	0.801	0.910	94.858	0.001	0.001	0.000	0.000	0.000	0.000
71	C	708	SER	0	-0.061	-0.036	96.398	0.000	0.000	0.000	0.000	0.000	0.000
72	C	709	GLU	-1	-0.897	-0.936	98.074	0.000	0.000	0.000	0.000	0.000	0.000
73	C	710	GLU	-1	-0.962	-0.968	100.126	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:638:GLY)