FMO DATABASE

FMODB ID: N9NMQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-375185.146352
FMO2-HF: Nuclear repulsion	349043.938599
FMO2-HF: Total energy	-26141.207753
FMO2-MP2: Total energy	-26215.345173

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.
-16.175	-10.042	7.176	-5.331	-7.977	0.02

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 : -0.003 / q_NPA : -0.006

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	-0.926	2.095	-9.643	-6.910	5.268	-3.596	-4.404	0.014
4	E	747	ASP	-1	-0.834	-0.879	2.235	-0.701	1.015	1.666	-1.136	-2.246	0.006
5	E	748	PRO	0	0.011	-0.012	3.904	-0.594	-0.381	0.004	-0.084	-0.133	0.000
6	E	749	LEU	0	-0.051	-0.031	6.473	0.065	0.065	0.000	0.000	0.000	0.000
7	E	750	TYR	0	0.021	0.011	4.103	-0.249	0.004	-0.001	-0.048	-0.203	0.000
8	E	751	ASP	-1	-0.830	-0.921	6.061	-0.629	-0.629	0.000	0.000	0.000	0.000
9	E	752	GLU	-1	-0.933	-0.967	9.573	-0.057	-0.057	0.000	0.000	0.000	0.000
10	E	753	ALA	0	-0.047	-0.029	7.721	0.124	0.124	0.000	0.000	0.000	0.000
11	E	754	VAL	0	0.067	0.033	8.585	0.122	0.122	0.000	0.000	0.000	0.000
12	E	755	ARG	1	0.984	1.012	10.941	0.313	0.313	0.000	0.000	0.000	0.000
13	E	756	PHE	0	0.011	-0.007	13.006	0.068	0.068	0.000	0.000	0.000	0.000
14	E	757	VAL	0	-0.025	-0.011	11.585	0.049	0.049	0.000	0.000	0.000	0.000
15	E	758	THR	0	-0.026	-0.013	14.314	0.032	0.032	0.000	0.000	0.000	0.000
16	E	759	GLU	-1	-0.925	-0.958	16.533	-0.095	-0.095	0.000	0.000	0.000	0.000
17	E	760	SER	0	-0.106	-0.070	16.793	0.030	0.030	0.000	0.000	0.000	0.000
18	E	761	ARG	1	0.832	0.894	18.301	0.110	0.110	0.000	0.000	0.000	0.000
19	E	762	ARG	1	0.931	0.982	17.115	-0.072	-0.072	0.000	0.000	0.000	0.000
20	E	763	ALA	0	0.079	0.048	14.178	-0.001	-0.001	0.000	0.000	0.000	0.000
21	E	764	SER	0	-0.001	-0.008	14.380	0.051	0.051	0.000	0.000	0.000	0.000
22	E	765	ILE	0	0.123	0.055	10.729	-0.042	-0.042	0.000	0.000	0.000	0.000
23	E	766	SER	0	-0.008	0.009	12.442	-0.011	-0.011	0.000	0.000	0.000	0.000
24	E	767	ALA	0	-0.031	-0.018	15.157	-0.013	-0.013	0.000	0.000	0.000	0.000
25	E	768	VAL	0	0.100	0.049	8.692	-0.028	-0.028	0.000	0.000	0.000	0.000
26	E	769	GLN	0	-0.017	-0.003	12.062	-0.010	-0.010	0.000	0.000	0.000	0.000
27	E	770	ARG	1	0.847	0.904	12.892	-0.253	-0.253	0.000	0.000	0.000	0.000
28	E	771	LYS	1	0.914	0.982	13.764	0.003	0.003	0.000	0.000	0.000	0.000
29	E	772	LEU	0	0.020	0.000	9.773	-0.013	-0.013	0.000	0.000	0.000	0.000
30	E	773	LYS	1	0.879	0.959	12.794	-0.149	-0.149	0.000	0.000	0.000	0.000
31	E	774	ILE	0	0.031	0.030	7.720	0.047	0.047	0.000	0.000	0.000	0.000
32	E	775	GLY	0	0.007	-0.012	11.086	-0.039	-0.039	0.000	0.000	0.000	0.000
33	E	776	TYR	0	0.029	0.007	10.245	0.149	0.149	0.000	0.000	0.000	0.000
34	E	777	ASN	0	0.062	0.020	9.571	-0.006	-0.006	0.000	0.000	0.000	0.000
35	E	778	ARG	1	0.827	0.893	5.331	-0.300	-0.300	0.000	0.000	0.000	0.000
36	E	779	ALA	0	0.018	0.007	5.440	0.408	0.408	0.000	0.000	0.000	0.000
37	E	780	ALA	0	-0.017	-0.023	7.568	-0.153	-0.153	0.000	0.000	0.000	0.000
38	E	781	ARG	1	0.981	1.004	3.918	-4.377	-4.011	0.009	-0.138	-0.237	0.001
39	E	782	MET	0	-0.023	0.000	3.448	-0.565	-0.093	0.006	-0.086	-0.392	0.000
40	E	783	ILE	0	-0.001	-0.008	4.660	-0.630	-0.611	-0.001	-0.004	-0.014	0.000
41	E	784	GLU	-1	-0.932	-0.974	6.128	1.750	1.750	0.000	0.000	0.000	0.000
42	E	785	ALA	0	0.016	0.010	2.727	-0.730	-0.379	0.226	-0.232	-0.346	-0.001
43	E	786	MET	0	-0.029	-0.009	4.844	-0.168	-0.158	-0.001	-0.007	-0.002	0.000
44	E	787	GLU	-1	-0.842	-0.915	8.116	0.217	0.217	0.000	0.000	0.000	0.000
45	E	788	MET	0	-0.047	-0.020	6.507	-0.133	-0.133	0.000	0.000	0.000	0.000
46	E	789	ALA	0	0.013	0.017	8.484	-0.037	-0.037	0.000	0.000	0.000	0.000
47	E	790	GLY	0	-0.016	0.001	10.090	0.034	0.034	0.000	0.000	0.000	0.000
48	E	791	VAL	0	-0.028	-0.005	10.738	0.040	0.040	0.000	0.000	0.000	0.000
49	E	792	VAL	0	-0.027	-0.031	11.111	0.057	0.057	0.000	0.000	0.000	0.000
50	E	793	THR	0	0.011	0.009	13.498	-0.013	-0.013	0.000	0.000	0.000	0.000
51	E	794	PRO	0	0.033	0.018	14.222	0.038	0.038	0.000	0.000	0.000	0.000
52	E	795	MET	0	-0.046	0.000	14.731	0.000	0.000	0.000	0.000	0.000	0.000
53	E	796	ASN	0	0.050	0.012	17.115	0.003	0.003	0.000	0.000	0.000	0.000
54	E	797	THR	0	0.024	-0.003	20.807	0.021	0.021	0.000	0.000	0.000	0.000
55	E	798	ASN	0	-0.071	-0.039	23.406	0.013	0.013	0.000	0.000	0.000	0.000
56	E	799	GLY	0	0.011	0.020	19.632	0.010	0.010	0.000	0.000	0.000	0.000
57	E	800	SER	0	-0.055	-0.010	18.987	0.032	0.032	0.000	0.000	0.000	0.000
58	E	801	ARG	1	0.821	0.881	11.843	-0.329	-0.329	0.000	0.000	0.000	0.000
59	E	802	GLU	-1	-0.884	-0.946	17.498	0.052	0.052	0.000	0.000	0.000	0.000
60	E	803	VAL	0	-0.076	-0.038	15.640	-0.009	-0.009	0.000	0.000	0.000	0.000
61	E	804	ILE	0	-0.027	-0.004	15.515	0.015	0.015	0.000	0.000	0.000	0.000
62	E	805	ALA	0	0.003	0.014	15.323	-0.004	-0.004	0.000	0.000	0.000	0.000
63	E	806	PRO	0	0.027	0.017	17.263	0.031	0.031	0.000	0.000	0.000	0.000
64	E	807	ALA	0	0.017	-0.001	18.815	-0.022	-0.022	0.000	0.000	0.000	0.000
65	E	808	PRO	0	-0.038	-0.012	17.917	-0.005	-0.005	0.000	0.000	0.000	0.000
66	E	809	VAL	0	0.005	0.003	20.468	0.021	0.021	0.000	0.000	0.000	0.000

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