FMO DATABASE

FMODB ID: JLQZ9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-375639.604278
FMO2-HF: Nuclear repulsion	349497.90044
FMO2-HF: Total energy	-26141.703838
FMO2-MP2: Total energy	-26215.760276

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.
-5.94	2.11	3.374	-4.774	-6.648	0.001

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 : -0.027 / q_NPA : -0.012

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	-0.886	-0.925	2.703	-2.984	2.082	0.457	-2.410	-3.114	0.004
4	E	747	ASP	-1	-0.830	-0.870	1.920	-4.275	-2.955	2.621	-1.758	-2.183	-0.001
5	E	748	PRO	0	0.014	-0.013	3.674	0.553	0.834	0.009	-0.103	-0.187	-0.001
6	E	749	LEU	0	-0.055	-0.032	6.393	0.445	0.445	0.000	0.000	0.000	0.000
7	E	750	TYR	0	0.022	0.019	4.425	-0.241	-0.037	-0.001	-0.039	-0.163	0.000
8	E	751	ASP	-1	-0.821	-0.913	6.313	-0.795	-0.795	0.000	0.000	0.000	0.000
9	E	752	GLU	-1	-0.863	-0.915	9.837	-0.422	-0.422	0.000	0.000	0.000	0.000
10	E	753	ALA	0	-0.054	-0.030	7.769	0.222	0.222	0.000	0.000	0.000	0.000
11	E	754	VAL	0	0.077	0.034	8.598	0.222	0.222	0.000	0.000	0.000	0.000
12	E	755	ARG	1	0.928	0.992	11.033	0.731	0.731	0.000	0.000	0.000	0.000
13	E	756	PHE	0	-0.006	-0.019	13.149	0.136	0.136	0.000	0.000	0.000	0.000
14	E	757	VAL	0	-0.015	0.003	11.526	0.109	0.109	0.000	0.000	0.000	0.000
15	E	758	THR	0	-0.020	-0.017	14.392	0.104	0.104	0.000	0.000	0.000	0.000
16	E	759	GLU	-1	-0.904	-0.955	16.561	-0.355	-0.355	0.000	0.000	0.000	0.000
17	E	760	SER	0	-0.113	-0.084	16.757	0.057	0.057	0.000	0.000	0.000	0.000
18	E	761	ARG	1	0.813	0.883	18.302	0.381	0.381	0.000	0.000	0.000	0.000
19	E	762	ARG	1	0.934	0.976	17.189	0.311	0.311	0.000	0.000	0.000	0.000
20	E	763	ALA	0	0.075	0.048	14.030	-0.068	-0.068	0.000	0.000	0.000	0.000
21	E	764	SER	0	-0.009	-0.016	14.237	0.063	0.063	0.000	0.000	0.000	0.000
22	E	765	ILE	0	0.126	0.057	10.432	-0.079	-0.079	0.000	0.000	0.000	0.000
23	E	766	SER	0	-0.012	0.004	12.215	-0.037	-0.037	0.000	0.000	0.000	0.000
24	E	767	ALA	0	-0.007	-0.005	15.147	-0.001	-0.001	0.000	0.000	0.000	0.000
25	E	768	VAL	0	0.083	0.040	8.587	0.002	0.002	0.000	0.000	0.000	0.000
26	E	769	GLN	0	-0.034	-0.019	11.726	0.005	0.005	0.000	0.000	0.000	0.000
27	E	770	ARG	1	0.861	0.918	12.808	0.197	0.197	0.000	0.000	0.000	0.000
28	E	771	LYS	1	0.872	0.946	13.949	0.563	0.563	0.000	0.000	0.000	0.000
29	E	772	LEU	0	0.015	-0.007	9.776	0.048	0.048	0.000	0.000	0.000	0.000
30	E	773	LYS	1	0.866	0.958	12.880	0.318	0.318	0.000	0.000	0.000	0.000
31	E	774	ILE	0	0.035	0.034	7.620	0.038	0.038	0.000	0.000	0.000	0.000
32	E	775	GLY	0	0.021	-0.002	11.021	0.044	0.044	0.000	0.000	0.000	0.000
33	E	776	TYR	0	0.032	0.012	10.093	-0.073	-0.073	0.000	0.000	0.000	0.000
34	E	777	ASN	0	0.047	0.009	9.495	-0.114	-0.114	0.000	0.000	0.000	0.000
35	E	778	ARG	1	0.842	0.890	5.309	1.793	1.793	0.000	0.000	0.000	0.000
36	E	779	ALA	0	0.017	0.004	5.222	-0.288	-0.288	0.000	0.000	0.000	0.000
37	E	780	ALA	0	-0.022	-0.022	7.318	-0.207	-0.207	0.000	0.000	0.000	0.000
38	E	781	ARG	1	0.976	1.000	3.755	-2.888	-2.569	0.006	-0.088	-0.237	0.000
39	E	782	MET	0	-0.035	0.000	3.628	-0.644	-0.182	0.004	-0.097	-0.369	0.000
40	E	783	ILE	0	-0.002	-0.010	4.442	-0.037	-0.008	-0.001	-0.007	-0.021	0.000
41	E	784	GLU	-1	-0.904	-0.961	5.888	0.952	0.952	0.000	0.000	0.000	0.000
42	E	785	ALA	0	0.009	0.005	2.680	-0.407	-0.057	0.280	-0.265	-0.365	-0.001
43	E	786	MET	0	-0.025	-0.008	4.832	0.272	0.291	-0.001	-0.007	-0.009	0.000
44	E	787	GLU	-1	-0.843	-0.903	8.093	0.020	0.020	0.000	0.000	0.000	0.000
45	E	788	MET	0	-0.047	-0.024	6.868	0.063	0.063	0.000	0.000	0.000	0.000
46	E	789	ALA	0	0.009	0.014	8.405	0.100	0.100	0.000	0.000	0.000	0.000
47	E	790	GLY	0	-0.013	0.003	10.097	0.067	0.067	0.000	0.000	0.000	0.000
48	E	791	VAL	0	-0.027	-0.009	10.809	0.048	0.048	0.000	0.000	0.000	0.000
49	E	792	VAL	0	-0.026	-0.033	11.082	0.052	0.052	0.000	0.000	0.000	0.000
50	E	793	THR	0	0.018	0.014	13.481	0.007	0.007	0.000	0.000	0.000	0.000
51	E	794	PRO	0	0.037	0.015	14.202	-0.026	-0.026	0.000	0.000	0.000	0.000
52	E	795	MET	0	-0.048	-0.006	14.542	-0.009	-0.009	0.000	0.000	0.000	0.000
53	E	796	ASN	0	0.045	0.018	17.091	0.030	0.030	0.000	0.000	0.000	0.000
54	E	797	THR	0	0.026	0.001	20.785	0.006	0.006	0.000	0.000	0.000	0.000
55	E	798	ASN	0	-0.060	-0.033	23.409	0.003	0.003	0.000	0.000	0.000	0.000
56	E	799	GLY	0	0.004	0.016	19.602	0.002	0.002	0.000	0.000	0.000	0.000
57	E	800	SER	0	-0.058	-0.020	18.951	-0.016	-0.016	0.000	0.000	0.000	0.000
58	E	801	ARG	1	0.785	0.866	11.685	0.220	0.220	0.000	0.000	0.000	0.000
59	E	802	GLU	-1	-0.866	-0.930	17.464	-0.204	-0.204	0.000	0.000	0.000	0.000
60	E	803	VAL	0	-0.065	-0.036	15.507	-0.034	-0.034	0.000	0.000	0.000	0.000
61	E	804	ILE	0	-0.026	-0.007	15.509	0.049	0.049	0.000	0.000	0.000	0.000
62	E	805	ALA	0	0.015	0.024	15.320	0.025	0.025	0.000	0.000	0.000	0.000
63	E	806	PRO	0	0.039	0.023	17.242	0.006	0.006	0.000	0.000	0.000	0.000
64	E	807	ALA	0	0.016	0.000	18.787	-0.044	-0.044	0.000	0.000	0.000	0.000
65	E	808	PRO	0	-0.039	-0.008	18.076	0.025	0.025	0.000	0.000	0.000	0.000
66	E	809	VAL	0	0.010	0.006	20.606	0.019	0.019	0.000	0.000	0.000	0.000

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