FMO DATABASE

FMODB ID: KGK63

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

Total energy (hartree)

FMO2-HF: Electronic energy	-358601.243395
FMO2-HF: Nuclear repulsion	327465.684754
FMO2-HF: Total energy	-31135.55864
FMO2-MP2: Total energy	-31225.932635

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.
-4.957	-8.361	13.148	-5.737	-4.007	-0.034

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 : -0.004 / q_NPA : -0.020

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	0.009	0.011	3.036	-2.293	-0.018	0.098	-1.082	-1.291	0.005
4	C	641	GLY	0	0.013	0.026	3.299	-0.073	0.695	0.040	-0.279	-0.530	-0.001
5	C	642	SER	0	0.027	0.009	1.785	-4.837	-11.353	13.011	-4.368	-2.126	-0.038
6	C	643	LYS	1	1.044	1.009	4.357	0.095	0.164	-0.001	-0.008	-0.060	0.000
7	C	644	LEU	0	0.003	-0.013	5.644	0.260	0.260	0.000	0.000	0.000	0.000
8	C	645	ASN	0	0.021	0.007	6.409	0.382	0.382	0.000	0.000	0.000	0.000
9	C	646	ASP	-1	-0.878	-0.935	5.050	1.356	1.356	0.000	0.000	0.000	0.000
10	C	647	ILE	0	-0.045	-0.032	7.070	0.167	0.167	0.000	0.000	0.000	0.000
11	C	648	LEU	0	-0.019	0.006	10.230	0.061	0.061	0.000	0.000	0.000	0.000
12	C	649	HIS	0	0.087	0.049	9.324	0.127	0.127	0.000	0.000	0.000	0.000
13	C	650	VAL	0	-0.003	-0.005	10.346	0.035	0.035	0.000	0.000	0.000	0.000
14	C	651	TYR	0	-0.005	0.004	12.903	0.012	0.012	0.000	0.000	0.000	0.000
15	C	652	GLU	-1	-0.862	-0.944	14.358	-0.213	-0.213	0.000	0.000	0.000	0.000
16	C	653	LYS	1	0.946	0.975	14.287	0.057	0.057	0.000	0.000	0.000	0.000
17	C	654	SER	0	-0.096	-0.040	17.012	0.008	0.008	0.000	0.000	0.000	0.000
18	C	655	LYS	1	0.967	0.979	19.079	0.018	0.018	0.000	0.000	0.000	0.000
19	C	656	GLU	-1	-0.905	-0.956	18.428	-0.081	-0.081	0.000	0.000	0.000	0.000
20	C	657	ARG	1	0.899	0.955	21.142	-0.060	-0.060	0.000	0.000	0.000	0.000
21	C	658	GLU	-1	-0.939	-0.977	22.972	0.005	0.005	0.000	0.000	0.000	0.000
22	C	659	LEU	0	0.037	0.019	24.645	-0.001	-0.001	0.000	0.000	0.000	0.000
23	C	660	GLN	0	-0.029	-0.023	23.230	0.002	0.002	0.000	0.000	0.000	0.000
24	C	661	SER	0	-0.039	-0.014	27.120	0.002	0.002	0.000	0.000	0.000	0.000
25	C	662	GLN	0	0.034	0.021	29.005	0.001	0.001	0.000	0.000	0.000	0.000
26	C	663	LEU	0	0.010	-0.007	30.432	0.001	0.001	0.000	0.000	0.000	0.000
27	C	664	PHE	0	-0.004	0.017	31.462	0.000	0.000	0.000	0.000	0.000	0.000
28	C	665	ASN	0	0.012	-0.003	32.459	0.001	0.001	0.000	0.000	0.000	0.000
29	C	666	ALA	0	-0.030	-0.001	34.944	0.000	0.000	0.000	0.000	0.000	0.000
30	C	667	TRP	0	-0.021	-0.007	34.359	0.000	0.000	0.000	0.000	0.000	0.000
31	C	668	ARG	1	0.979	0.975	37.011	-0.017	-0.017	0.000	0.000	0.000	0.000
32	C	669	ASN	0	0.030	0.005	38.447	0.002	0.002	0.000	0.000	0.000	0.000
33	C	670	ARG	1	0.938	0.963	40.955	0.012	0.012	0.000	0.000	0.000	0.000
34	C	671	PHE	0	-0.001	0.006	41.838	-0.001	-0.001	0.000	0.000	0.000	0.000
35	C	672	CYS	0	0.002	-0.003	42.719	0.001	0.001	0.000	0.000	0.000	0.000
36	C	673	PHE	0	0.021	0.027	45.084	0.000	0.000	0.000	0.000	0.000	0.000
37	C	674	TYR	0	0.012	-0.005	45.804	-0.001	-0.001	0.000	0.000	0.000	0.000
38	C	675	THR	0	-0.078	-0.032	46.703	0.000	0.000	0.000	0.000	0.000	0.000
39	C	676	GLU	-1	-0.910	-0.959	48.110	0.009	0.009	0.000	0.000	0.000	0.000
40	C	677	GLU	-1	-0.912	-0.947	48.895	0.004	0.004	0.000	0.000	0.000	0.000
41	C	678	CYS	0	-0.048	-0.040	50.633	-0.001	-0.001	0.000	0.000	0.000	0.000
42	C	679	ASN	0	0.021	0.017	52.588	-0.001	-0.001	0.000	0.000	0.000	0.000
43	C	680	ILE	0	0.049	0.033	52.921	0.000	0.000	0.000	0.000	0.000	0.000
44	C	681	GLN	0	-0.010	-0.006	54.089	0.000	0.000	0.000	0.000	0.000	0.000
45	C	682	ALA	0	-0.023	-0.007	57.007	0.000	0.000	0.000	0.000	0.000	0.000
46	C	683	ILE	0	-0.008	-0.010	57.172	0.000	0.000	0.000	0.000	0.000	0.000
47	C	684	SER	0	0.007	0.010	59.956	0.000	0.000	0.000	0.000	0.000	0.000
48	C	685	LYS	1	0.924	0.958	61.593	0.002	0.002	0.000	0.000	0.000	0.000
49	C	686	ARG	1	0.914	0.971	63.011	0.001	0.001	0.000	0.000	0.000	0.000
50	C	687	ASN	0	0.042	-0.001	63.596	-0.001	-0.001	0.000	0.000	0.000	0.000
51	C	688	TYR	0	0.080	0.056	65.940	0.000	0.000	0.000	0.000	0.000	0.000
52	C	689	GLN	0	-0.065	-0.045	67.617	-0.001	-0.001	0.000	0.000	0.000	0.000
53	C	690	LEU	0	0.000	-0.004	68.632	0.000	0.000	0.000	0.000	0.000	0.000
54	C	691	GLU	-1	-0.861	-0.928	69.492	0.003	0.003	0.000	0.000	0.000	0.000
55	C	692	LYS	1	0.902	0.949	71.638	-0.001	-0.001	0.000	0.000	0.000	0.000
56	C	693	MET	0	-0.065	-0.022	73.656	0.000	0.000	0.000	0.000	0.000	0.000
57	C	694	VAL	0	0.069	0.024	75.294	0.000	0.000	0.000	0.000	0.000	0.000
58	C	695	LEU	0	0.031	0.011	75.769	0.000	0.000	0.000	0.000	0.000	0.000
59	C	696	LYS	1	0.907	0.961	78.150	0.001	0.001	0.000	0.000	0.000	0.000
60	C	697	LYS	1	0.954	0.979	79.872	0.001	0.001	0.000	0.000	0.000	0.000
61	C	698	PHE	0	0.039	0.014	79.866	0.000	0.000	0.000	0.000	0.000	0.000
62	C	699	ARG	1	0.905	0.953	80.083	-0.002	-0.002	0.000	0.000	0.000	0.000
63	C	700	GLU	-1	-0.913	-0.962	83.110	-0.001	-0.001	0.000	0.000	0.000	0.000
64	C	701	ARG	1	0.899	0.945	84.598	0.000	0.000	0.000	0.000	0.000	0.000
65	C	702	LEU	0	-0.003	-0.003	85.392	0.000	0.000	0.000	0.000	0.000	0.000
66	C	703	LEU	0	-0.005	-0.002	88.070	0.000	0.000	0.000	0.000	0.000	0.000
67	C	704	GLU	-1	-0.892	-0.933	89.295	0.000	0.000	0.000	0.000	0.000	0.000
68	C	705	ILE	0	-0.010	-0.009	89.857	0.000	0.000	0.000	0.000	0.000	0.000
69	C	706	VAL	0	0.027	0.024	92.896	0.000	0.000	0.000	0.000	0.000	0.000
70	C	707	LYS	1	0.873	0.928	94.780	0.000	0.000	0.000	0.000	0.000	0.000
71	C	708	SER	0	-0.047	-0.020	95.787	0.000	0.000	0.000	0.000	0.000	0.000
72	C	709	GLU	-1	-0.987	-0.980	97.709	0.001	0.001	0.000	0.000	0.000	0.000
73	C	710	GLU	-1	-1.002	-0.990	99.997	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)