FMO DATABASE

FMODB ID: 39J5L

Calculation Name: 2VE8-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VE8

Chain ID: E

ChEMBL ID:

UniProt ID: Q9I0M3

Base Structure: X-ray

Registration Date: 2023-06-22

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	66
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-376273.374336
FMO2-HF: Nuclear repulsion	350131.4194
FMO2-HF: Total energy	-26141.954936
FMO2-MP2: Total energy	-26215.917586

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:744:SER)

Summations of interaction energy for fragment #1(E:744:SER)

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.
-7.62	0.611	1.251	-3.964	-5.515	-0.013

Interaction energy analysis for fragmet #1(E:744:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.016

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

Sort

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	746	ASP	-1	-0.885	-0.934	2.487	-3.324	0.825	0.349	-2.071	-2.427	-0.008
4	E	747	ASP	-1	-0.803	-0.855	2.580	-1.079	0.423	0.168	-0.515	-1.154	-0.001
5	E	748	PRO	0	0.015	-0.013	4.452	-0.569	-0.412	-0.001	-0.034	-0.122	0.000
6	E	749	LEU	0	-0.066	-0.034	7.019	0.223	0.223	0.000	0.000	0.000	0.000
7	E	750	TYR	0	0.024	0.024	4.892	-0.262	-0.262	0.000	0.000	0.000	0.000
8	E	751	ASP	-1	-0.807	-0.910	6.850	-1.311	-1.311	0.000	0.000	0.000	0.000
9	E	752	GLU	-1	-0.873	-0.912	10.379	-0.483	-0.483	0.000	0.000	0.000	0.000
10	E	753	ALA	0	-0.023	-0.021	8.242	0.219	0.219	0.000	0.000	0.000	0.000
11	E	754	VAL	0	0.045	0.020	8.718	0.231	0.231	0.000	0.000	0.000	0.000
12	E	755	ARG	1	0.885	0.967	11.215	0.903	0.903	0.000	0.000	0.000	0.000
13	E	756	PHE	0	0.008	-0.005	13.626	0.131	0.131	0.000	0.000	0.000	0.000
14	E	757	VAL	0	-0.008	0.014	11.488	0.125	0.125	0.000	0.000	0.000	0.000
15	E	758	THR	0	-0.034	-0.034	14.392	0.129	0.129	0.000	0.000	0.000	0.000
16	E	759	GLU	-1	-0.900	-0.958	16.548	-0.472	-0.472	0.000	0.000	0.000	0.000
17	E	760	SER	0	-0.103	-0.078	17.062	0.065	0.065	0.000	0.000	0.000	0.000
18	E	761	ARG	1	0.817	0.885	18.350	0.576	0.576	0.000	0.000	0.000	0.000
19	E	762	ARG	1	0.953	0.983	17.299	0.410	0.410	0.000	0.000	0.000	0.000
20	E	763	ALA	0	0.075	0.051	13.575	-0.077	-0.077	0.000	0.000	0.000	0.000
21	E	764	SER	0	-0.035	-0.025	13.886	0.064	0.064	0.000	0.000	0.000	0.000
22	E	765	ILE	0	0.095	0.039	10.086	-0.058	-0.058	0.000	0.000	0.000	0.000
23	E	766	SER	0	0.019	0.007	12.070	-0.006	-0.006	0.000	0.000	0.000	0.000
24	E	767	ALA	0	-0.022	-0.008	15.046	0.039	0.039	0.000	0.000	0.000	0.000
25	E	768	VAL	0	0.062	0.032	8.756	0.039	0.039	0.000	0.000	0.000	0.000
26	E	769	GLN	0	-0.034	-0.030	12.211	0.015	0.015	0.000	0.000	0.000	0.000
27	E	770	ARG	1	0.863	0.933	13.251	0.307	0.307	0.000	0.000	0.000	0.000
28	E	771	LYS	1	0.871	0.948	14.149	0.685	0.685	0.000	0.000	0.000	0.000
29	E	772	LEU	0	0.020	-0.004	10.078	0.074	0.074	0.000	0.000	0.000	0.000
30	E	773	LYS	1	0.858	0.952	13.220	0.371	0.371	0.000	0.000	0.000	0.000
31	E	774	ILE	0	0.022	0.027	8.436	0.075	0.075	0.000	0.000	0.000	0.000
32	E	775	GLY	0	0.040	0.013	11.878	0.013	0.013	0.000	0.000	0.000	0.000
33	E	776	TYR	0	0.034	0.009	10.573	-0.109	-0.109	0.000	0.000	0.000	0.000
34	E	777	ASN	0	0.046	0.006	9.465	-0.233	-0.233	0.000	0.000	0.000	0.000
35	E	778	ARG	1	0.830	0.891	5.616	1.310	1.310	0.000	0.000	0.000	0.000
36	E	779	ALA	0	0.042	0.010	5.513	-0.674	-0.674	0.000	0.000	0.000	0.000
37	E	780	ALA	0	-0.033	-0.012	7.491	-0.266	-0.266	0.000	0.000	0.000	0.000
38	E	781	ARG	1	0.961	0.990	2.666	-3.984	-3.142	0.295	-0.414	-0.723	0.003
39	E	782	MET	0	-0.026	0.004	3.150	-2.756	-1.643	0.074	-0.626	-0.561	-0.006
40	E	783	ILE	0	-0.001	-0.006	4.446	0.088	0.127	-0.001	-0.004	-0.033	0.000
41	E	784	GLU	-1	-0.898	-0.962	5.279	0.893	0.893	0.000	0.000	0.000	0.000
42	E	785	ALA	0	0.023	0.012	2.649	-0.238	0.138	0.368	-0.291	-0.453	-0.001
43	E	786	MET	0	-0.021	-0.007	4.708	0.572	0.625	-0.001	-0.009	-0.042	0.000
44	E	787	GLU	-1	-0.835	-0.899	8.258	-0.185	-0.185	0.000	0.000	0.000	0.000
45	E	788	MET	0	-0.054	-0.032	6.279	0.142	0.142	0.000	0.000	0.000	0.000
46	E	789	ALA	0	0.010	0.017	7.836	0.159	0.159	0.000	0.000	0.000	0.000
47	E	790	GLY	0	-0.009	0.004	9.512	0.136	0.136	0.000	0.000	0.000	0.000
48	E	791	VAL	0	-0.024	-0.016	10.686	0.114	0.114	0.000	0.000	0.000	0.000
49	E	792	VAL	0	-0.045	-0.037	11.080	0.113	0.113	0.000	0.000	0.000	0.000
50	E	793	THR	0	0.010	0.008	13.505	-0.007	-0.007	0.000	0.000	0.000	0.000
51	E	794	PRO	0	0.058	0.027	14.154	-0.053	-0.053	0.000	0.000	0.000	0.000
52	E	795	MET	0	-0.065	-0.017	14.082	-0.004	-0.004	0.000	0.000	0.000	0.000
53	E	796	ASN	0	0.045	0.024	16.805	0.053	0.053	0.000	0.000	0.000	0.000
54	E	797	THR	0	0.014	-0.013	20.546	0.007	0.007	0.000	0.000	0.000	0.000
55	E	798	ASN	0	-0.038	-0.016	22.964	0.006	0.006	0.000	0.000	0.000	0.000
56	E	799	GLY	0	0.011	0.011	19.181	0.009	0.009	0.000	0.000	0.000	0.000
57	E	800	SER	0	-0.082	-0.042	17.933	-0.035	-0.035	0.000	0.000	0.000	0.000
58	E	801	ARG	1	0.783	0.862	11.380	0.526	0.526	0.000	0.000	0.000	0.000
59	E	802	GLU	-1	-0.842	-0.901	17.011	-0.348	-0.348	0.000	0.000	0.000	0.000
60	E	803	VAL	0	-0.058	-0.032	15.238	-0.056	-0.056	0.000	0.000	0.000	0.000
61	E	804	ILE	0	-0.023	0.002	15.521	0.074	0.074	0.000	0.000	0.000	0.000
62	E	805	ALA	0	0.025	0.025	15.211	0.045	0.045	0.000	0.000	0.000	0.000
63	E	806	PRO	0	0.035	0.019	17.186	0.019	0.019	0.000	0.000	0.000	0.000
64	E	807	ALA	0	0.030	0.008	18.742	-0.059	-0.059	0.000	0.000	0.000	0.000
65	E	808	PRO	0	-0.024	-0.002	18.367	0.025	0.025	0.000	0.000	0.000	0.000
66	E	809	VAL	0	-0.011	-0.004	20.608	0.043	0.043	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:744:SER)