FMO DATABASE

FMODB ID: VQL81

Calculation Name: 3EJ9-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3EJ9

Chain ID: C

ChEMBL ID:

UniProt ID: Q9EV84

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	63
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-317864.173216
FMO2-HF: Nuclear repulsion	292750.131114
FMO2-HF: Total energy	-25114.042102
FMO2-MP2: Total energy	-25186.033151

3D Structure Molmil

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:1:PRO)

Summations of interaction energy for fragment #1(C:1:PRO)

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.
-14.931	-7.705	11.769	-6.821	-12.174	-0.043

Interaction energy analysis for fragmet #1(C:1:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.001

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	C	3	ILE	0	0.000	0.007	2.889	-0.451	1.494	0.116	-0.788	-1.274	0.003
4	C	4	SER	0	0.005	-0.005	6.148	-0.189	-0.189	0.000	0.000	0.000	0.000
5	C	5	CYS	0	-0.066	-0.028	9.906	0.073	0.073	0.000	0.000	0.000	0.000
6	C	6	ASP	-1	-0.831	-0.896	12.824	0.051	0.051	0.000	0.000	0.000	0.000
7	C	7	MET	0	-0.052	-0.039	16.302	0.006	0.006	0.000	0.000	0.000	0.000
8	C	8	ARG	1	0.891	0.944	18.997	0.007	0.007	0.000	0.000	0.000	0.000
9	C	9	TYR	0	0.053	0.027	21.838	-0.011	-0.011	0.000	0.000	0.000	0.000
10	C	10	GLY	0	0.022	0.000	23.658	0.007	0.007	0.000	0.000	0.000	0.000
11	C	11	ARG	1	0.855	0.945	20.020	0.066	0.066	0.000	0.000	0.000	0.000
12	C	12	THR	0	0.045	0.019	22.501	-0.010	-0.010	0.000	0.000	0.000	0.000
13	C	13	ASP	-1	-0.859	-0.944	20.434	-0.199	-0.199	0.000	0.000	0.000	0.000
14	C	14	GLU	-1	-0.948	-0.978	19.451	-0.262	-0.262	0.000	0.000	0.000	0.000
15	C	15	GLN	0	0.010	0.000	19.495	-0.016	-0.016	0.000	0.000	0.000	0.000
16	C	16	LYS	1	0.882	0.939	16.313	0.149	0.149	0.000	0.000	0.000	0.000
17	C	17	ARG	1	0.985	0.994	14.865	0.259	0.259	0.000	0.000	0.000	0.000
18	C	18	ALA	0	0.027	0.021	15.001	-0.050	-0.050	0.000	0.000	0.000	0.000
19	C	19	LEU	0	-0.003	-0.003	12.630	-0.016	-0.016	0.000	0.000	0.000	0.000
20	C	20	SER	0	-0.031	-0.014	10.586	-0.035	-0.035	0.000	0.000	0.000	0.000
21	C	21	ALA	0	0.013	0.009	10.081	-0.111	-0.111	0.000	0.000	0.000	0.000
22	C	22	GLY	0	-0.033	-0.018	11.481	-0.051	-0.051	0.000	0.000	0.000	0.000
23	C	23	LEU	0	0.034	-0.003	7.878	0.016	0.016	0.000	0.000	0.000	0.000
24	C	24	LEU	0	0.001	-0.002	6.367	0.025	0.025	0.000	0.000	0.000	0.000
25	C	25	ARG	1	0.942	0.987	7.126	0.199	0.199	0.000	0.000	0.000	0.000
26	C	26	VAL	0	-0.024	-0.018	8.706	-0.014	-0.014	0.000	0.000	0.000	0.000
27	C	27	ILE	0	0.026	0.015	2.577	-0.707	0.010	0.787	-0.314	-1.189	0.001
28	C	28	SER	0	-0.059	-0.043	4.702	-0.091	0.052	-0.001	-0.011	-0.131	0.000
29	C	29	GLU	-1	-0.957	-0.972	5.800	-0.285	-0.285	0.000	0.000	0.000	0.000
30	C	30	ALA	0	-0.067	-0.026	6.690	0.089	0.089	0.000	0.000	0.000	0.000
31	C	31	THR	0	-0.063	-0.056	2.716	-1.593	-0.437	0.324	-0.493	-0.987	-0.002
32	C	32	GLY	0	0.021	0.025	5.461	0.033	0.033	0.000	0.000	0.000	0.000
33	C	33	GLU	-1	-0.878	-0.931	2.270	-3.059	-2.640	2.156	-0.662	-1.913	-0.004
34	C	34	PRO	0	0.024	0.046	4.777	0.111	0.181	-0.001	-0.008	-0.061	0.000
35	C	35	ARG	1	0.961	0.944	4.977	0.144	0.215	-0.001	-0.001	-0.068	0.000
36	C	36	GLU	-1	-0.982	-0.983	6.740	-1.186	-1.186	0.000	0.000	0.000	0.000
37	C	37	ASN	0	-0.051	-0.018	3.292	0.220	0.806	0.035	-0.214	-0.408	-0.001
38	C	38	ILE	0	-0.024	-0.002	2.043	-10.143	-8.625	8.349	-4.188	-5.680	-0.040
39	C	39	PHE	0	-0.009	0.003	3.509	1.980	2.581	0.005	-0.142	-0.463	0.000
40	C	40	PHE	0	-0.019	-0.034	5.330	0.099	0.099	0.000	0.000	0.000	0.000
41	C	41	VAL	0	-0.024	-0.002	7.782	0.100	0.100	0.000	0.000	0.000	0.000
42	C	42	ILE	0	0.001	-0.001	11.158	0.076	0.076	0.000	0.000	0.000	0.000
43	C	43	ARG	1	0.895	0.945	11.992	-0.114	-0.114	0.000	0.000	0.000	0.000
44	C	44	GLU	-1	-0.837	-0.919	16.739	-0.102	-0.102	0.000	0.000	0.000	0.000
45	C	45	GLY	0	0.031	0.016	20.155	0.010	0.010	0.000	0.000	0.000	0.000
46	C	46	SER	0	0.028	0.000	23.345	-0.009	-0.009	0.000	0.000	0.000	0.000
47	C	47	GLY	0	0.012	0.001	25.805	0.006	0.006	0.000	0.000	0.000	0.000
48	C	48	ILE	0	0.029	0.016	27.127	0.006	0.006	0.000	0.000	0.000	0.000
49	C	49	ASN	0	-0.017	-0.001	24.321	0.008	0.008	0.000	0.000	0.000	0.000
50	C	50	PHE	0	-0.057	-0.009	19.397	0.010	0.010	0.000	0.000	0.000	0.000
51	C	51	VAL	0	0.030	0.015	24.181	-0.007	-0.007	0.000	0.000	0.000	0.000
52	C	52	GLN	0	-0.039	-0.020	21.157	0.021	0.021	0.000	0.000	0.000	0.000
53	C	53	HIS	0	0.027	0.001	25.559	-0.002	-0.002	0.000	0.000	0.000	0.000
54	C	54	GLY	0	-0.008	0.010	27.914	-0.003	-0.003	0.000	0.000	0.000	0.000
55	C	55	GLU	-1	-0.941	-0.961	29.405	0.030	0.030	0.000	0.000	0.000	0.000
56	C	56	HIS	0	-0.059	-0.052	28.539	0.005	0.005	0.000	0.000	0.000	0.000
57	C	57	LEU	0	-0.043	-0.017	23.962	-0.006	-0.006	0.000	0.000	0.000	0.000
58	C	58	PRO	0	0.040	0.032	28.400	-0.001	-0.001	0.000	0.000	0.000	0.000
59	C	59	ASP	-1	-0.833	-0.935	28.536	-0.013	-0.013	0.000	0.000	0.000	0.000
60	C	60	TYR	0	-0.071	-0.047	24.904	-0.003	-0.003	0.000	0.000	0.000	0.000
61	C	61	VAL	0	0.027	0.013	27.505	-0.002	-0.002	0.000	0.000	0.000	0.000
62	C	62	PRO	0	-0.038	-0.012	27.508	-0.001	-0.001	0.000	0.000	0.000	0.000
63	C	63	GLY	0	0.013	0.018	27.766	0.005	0.005	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(C:1:PRO)