FMO DATABASE

FMODB ID: 4JQ4N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-359062.222481
FMO2-HF: Nuclear repulsion	327925.923171
FMO2-HF: Total energy	-31136.29931
FMO2-MP2: Total energy	-31226.661867

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.
-5.902	-9.232	13.555	-6.007	-4.219	-0.032

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 : 0.005 / q_NPA : -0.015

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	0.007	3.065	-2.521	0.009	0.210	-1.244	-1.497	0.008
4	C	641	GLY	0	0.027	0.027	3.323	0.003	0.748	0.038	-0.274	-0.509	-0.001
5	C	642	SER	0	0.024	0.008	1.777	-4.832	-11.517	13.308	-4.481	-2.142	-0.039
6	C	643	LYS	1	0.950	0.958	4.343	-0.209	-0.129	-0.001	-0.008	-0.071	0.000
7	C	644	LEU	0	0.012	-0.001	5.639	0.269	0.269	0.000	0.000	0.000	0.000
8	C	645	ASN	0	0.023	0.006	6.396	0.259	0.259	0.000	0.000	0.000	0.000
9	C	646	ASP	-1	-0.865	-0.918	5.194	1.016	1.016	0.000	0.000	0.000	0.000
10	C	647	ILE	0	-0.022	-0.020	7.083	0.151	0.151	0.000	0.000	0.000	0.000
11	C	648	LEU	0	-0.007	0.011	10.240	0.052	0.052	0.000	0.000	0.000	0.000
12	C	649	HIS	0	0.096	0.059	9.657	0.137	0.137	0.000	0.000	0.000	0.000
13	C	650	VAL	0	-0.007	-0.007	10.395	0.027	0.027	0.000	0.000	0.000	0.000
14	C	651	TYR	0	-0.006	0.004	12.923	0.004	0.004	0.000	0.000	0.000	0.000
15	C	652	GLU	-1	-0.867	-0.942	14.561	-0.193	-0.193	0.000	0.000	0.000	0.000
16	C	653	LYS	1	0.882	0.945	14.111	0.047	0.047	0.000	0.000	0.000	0.000
17	C	654	SER	0	-0.090	-0.040	17.033	0.005	0.005	0.000	0.000	0.000	0.000
18	C	655	LYS	1	0.887	0.927	19.098	-0.006	-0.006	0.000	0.000	0.000	0.000
19	C	656	GLU	-1	-0.847	-0.937	18.055	-0.051	-0.051	0.000	0.000	0.000	0.000
20	C	657	ARG	1	0.908	0.963	21.163	-0.074	-0.074	0.000	0.000	0.000	0.000
21	C	658	GLU	-1	-0.850	-0.917	22.995	0.017	0.017	0.000	0.000	0.000	0.000
22	C	659	LEU	0	0.029	0.014	24.665	-0.002	-0.002	0.000	0.000	0.000	0.000
23	C	660	GLN	0	-0.021	-0.029	22.934	0.001	0.001	0.000	0.000	0.000	0.000
24	C	661	SER	0	-0.031	-0.009	27.142	0.001	0.001	0.000	0.000	0.000	0.000
25	C	662	GLN	0	0.025	0.022	29.026	-0.001	-0.001	0.000	0.000	0.000	0.000
26	C	663	LEU	0	0.015	0.001	30.236	0.000	0.000	0.000	0.000	0.000	0.000
27	C	664	PHE	0	0.004	0.018	31.483	0.000	0.000	0.000	0.000	0.000	0.000
28	C	665	ASN	0	-0.030	-0.029	32.244	0.001	0.001	0.000	0.000	0.000	0.000
29	C	666	ALA	0	-0.011	0.007	34.966	0.000	0.000	0.000	0.000	0.000	0.000
30	C	667	TRP	0	-0.025	-0.012	34.201	-0.001	-0.001	0.000	0.000	0.000	0.000
31	C	668	ARG	1	0.979	0.979	37.043	-0.023	-0.023	0.000	0.000	0.000	0.000
32	C	669	ASN	0	0.018	-0.003	38.647	0.002	0.002	0.000	0.000	0.000	0.000
33	C	670	ARG	1	0.935	0.958	40.976	0.007	0.007	0.000	0.000	0.000	0.000
34	C	671	PHE	0	0.013	0.011	41.914	-0.001	-0.001	0.000	0.000	0.000	0.000
35	C	672	CYS	0	0.006	0.010	43.338	0.000	0.000	0.000	0.000	0.000	0.000
36	C	673	PHE	0	0.023	0.029	45.108	0.000	0.000	0.000	0.000	0.000	0.000
37	C	674	TYR	0	0.027	0.006	45.513	-0.001	-0.001	0.000	0.000	0.000	0.000
38	C	675	THR	0	-0.065	-0.039	46.693	0.000	0.000	0.000	0.000	0.000	0.000
39	C	676	GLU	-1	-0.929	-0.966	48.063	0.012	0.012	0.000	0.000	0.000	0.000
40	C	677	GLU	-1	-0.927	-0.957	49.114	0.007	0.007	0.000	0.000	0.000	0.000
41	C	678	CYS	0	-0.048	-0.037	50.569	-0.001	-0.001	0.000	0.000	0.000	0.000
42	C	679	ASN	0	0.009	0.009	52.608	-0.001	-0.001	0.000	0.000	0.000	0.000
43	C	680	ILE	0	0.072	0.045	53.120	0.000	0.000	0.000	0.000	0.000	0.000
44	C	681	GLN	0	-0.002	0.013	54.133	-0.001	-0.001	0.000	0.000	0.000	0.000
45	C	682	ALA	0	-0.018	-0.004	57.031	0.000	0.000	0.000	0.000	0.000	0.000
46	C	683	ILE	0	-0.006	-0.008	57.272	0.000	0.000	0.000	0.000	0.000	0.000
47	C	684	SER	0	-0.011	-0.013	59.677	0.000	0.000	0.000	0.000	0.000	0.000
48	C	685	LYS	1	0.904	0.931	61.615	0.000	0.000	0.000	0.000	0.000	0.000
49	C	686	ARG	1	0.914	0.971	63.032	-0.002	-0.002	0.000	0.000	0.000	0.000
50	C	687	ASN	0	0.043	-0.003	63.985	-0.001	-0.001	0.000	0.000	0.000	0.000
51	C	688	TYR	0	0.080	0.050	65.966	0.000	0.000	0.000	0.000	0.000	0.000
52	C	689	GLN	0	-0.021	-0.008	67.457	0.000	0.000	0.000	0.000	0.000	0.000
53	C	690	LEU	0	-0.022	-0.010	69.151	0.000	0.000	0.000	0.000	0.000	0.000
54	C	691	GLU	-1	-0.860	-0.927	69.149	0.005	0.005	0.000	0.000	0.000	0.000
55	C	692	LYS	1	0.903	0.953	71.572	-0.003	-0.003	0.000	0.000	0.000	0.000
56	C	693	MET	0	-0.057	-0.020	73.671	0.000	0.000	0.000	0.000	0.000	0.000
57	C	694	VAL	0	0.064	0.023	75.318	0.000	0.000	0.000	0.000	0.000	0.000
58	C	695	LEU	0	0.024	0.009	75.654	0.000	0.000	0.000	0.000	0.000	0.000
59	C	696	LYS	1	0.854	0.927	78.165	0.000	0.000	0.000	0.000	0.000	0.000
60	C	697	LYS	1	0.847	0.904	79.898	-0.001	-0.001	0.000	0.000	0.000	0.000
61	C	698	PHE	0	0.051	0.022	80.306	0.000	0.000	0.000	0.000	0.000	0.000
62	C	699	ARG	1	0.913	0.958	80.522	-0.003	-0.003	0.000	0.000	0.000	0.000
63	C	700	GLU	-1	-0.781	-0.866	83.118	0.001	0.001	0.000	0.000	0.000	0.000
64	C	701	ARG	1	0.868	0.924	84.976	-0.001	-0.001	0.000	0.000	0.000	0.000
65	C	702	LEU	0	-0.006	-0.002	85.470	0.000	0.000	0.000	0.000	0.000	0.000
66	C	703	LEU	0	-0.007	-0.005	88.314	0.000	0.000	0.000	0.000	0.000	0.000
67	C	704	GLU	-1	-0.850	-0.907	88.942	0.001	0.001	0.000	0.000	0.000	0.000
68	C	705	ILE	0	-0.003	-0.005	90.017	0.000	0.000	0.000	0.000	0.000	0.000
69	C	706	VAL	0	0.020	0.017	92.999	0.000	0.000	0.000	0.000	0.000	0.000
70	C	707	LYS	1	0.829	0.905	94.802	-0.001	-0.001	0.000	0.000	0.000	0.000
71	C	708	SER	0	-0.032	-0.015	95.904	0.000	0.000	0.000	0.000	0.000	0.000
72	C	709	GLU	-1	-0.982	-0.974	97.732	0.002	0.002	0.000	0.000	0.000	0.000
73	C	710	GLU	-1	-0.978	-0.976	100.020	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)