FMO DATABASE

FMODB ID: V5V31

Calculation Name: 1JFI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JFI

Chain ID: A

ChEMBL ID:

UniProt ID: Q14919

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	-331336.573598
FMO2-HF: Nuclear repulsion	305182.484607
FMO2-HF: Total energy	-26154.08899
FMO2-MP2: Total energy	-26228.674568

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(A:10:ALA)

Summations of interaction energy for fragment #1(A:10:ALA)

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.
-11.715	-6.183	2.638	-3.947	-4.221	-0.022

Interaction energy analysis for fragmet #1(A:10:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.025

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	A	12	PHE	0	0.018	-0.003	3.183	-1.558	1.602	0.094	-1.621	-1.633	0.006
4	A	13	PRO	0	0.017	-0.008	6.067	0.169	0.169	0.000	0.000	0.000	0.000
5	A	14	PRO	0	0.080	0.043	9.298	0.067	0.067	0.000	0.000	0.000	0.000
6	A	15	ALA	0	0.034	0.021	12.151	0.057	0.057	0.000	0.000	0.000	0.000
7	A	16	ARG	1	0.893	0.947	11.431	0.350	0.350	0.000	0.000	0.000	0.000
8	A	17	ILE	0	0.079	0.041	9.259	0.044	0.044	0.000	0.000	0.000	0.000
9	A	18	LYS	1	0.948	0.979	13.345	0.351	0.351	0.000	0.000	0.000	0.000
10	A	19	LYS	1	0.934	0.951	16.532	0.277	0.277	0.000	0.000	0.000	0.000
11	A	20	ILE	0	-0.017	-0.006	12.876	0.022	0.022	0.000	0.000	0.000	0.000
12	A	21	MET	0	-0.041	-0.026	16.380	0.003	0.003	0.000	0.000	0.000	0.000
13	A	22	GLN	0	-0.037	-0.030	18.575	0.020	0.020	0.000	0.000	0.000	0.000
14	A	23	THR	0	-0.039	0.020	20.428	0.026	0.026	0.000	0.000	0.000	0.000
15	A	24	ASP	-1	-0.900	-0.960	22.260	-0.229	-0.229	0.000	0.000	0.000	0.000
16	A	25	GLU	-1	-0.885	-0.955	24.128	-0.175	-0.175	0.000	0.000	0.000	0.000
17	A	26	GLU	-1	-0.960	-0.963	27.000	-0.164	-0.164	0.000	0.000	0.000	0.000
18	A	27	ILE	0	-0.124	-0.038	22.071	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	28	GLY	0	0.061	0.039	25.311	0.010	0.010	0.000	0.000	0.000	0.000
20	A	29	LYS	1	0.894	0.930	25.104	0.161	0.161	0.000	0.000	0.000	0.000
21	A	30	VAL	0	0.066	0.021	19.646	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	31	ALA	0	-0.002	-0.005	21.418	0.004	0.004	0.000	0.000	0.000	0.000
23	A	32	ALA	0	0.035	0.007	19.441	-0.046	-0.046	0.000	0.000	0.000	0.000
24	A	33	ALA	0	0.047	0.017	16.832	-0.044	-0.044	0.000	0.000	0.000	0.000
25	A	34	VAL	0	0.035	0.012	15.626	-0.088	-0.088	0.000	0.000	0.000	0.000
26	A	35	PRO	0	0.024	0.000	14.368	-0.103	-0.103	0.000	0.000	0.000	0.000
27	A	36	VAL	0	0.006	0.001	11.324	-0.173	-0.173	0.000	0.000	0.000	0.000
28	A	37	ILE	0	0.014	0.018	10.561	-0.283	-0.283	0.000	0.000	0.000	0.000
29	A	38	ILE	0	0.022	0.017	11.276	-0.179	-0.179	0.000	0.000	0.000	0.000
30	A	39	SER	0	0.019	0.016	6.807	-0.118	-0.118	0.000	0.000	0.000	0.000
31	A	40	ARG	1	0.903	0.958	5.430	2.092	2.092	0.000	0.000	0.000	0.000
32	A	41	ALA	0	0.020	0.006	7.846	-0.167	-0.167	0.000	0.000	0.000	0.000
33	A	42	LEU	0	-0.016	-0.016	7.198	0.079	0.079	0.000	0.000	0.000	0.000
34	A	43	GLU	-1	-0.882	-0.954	2.270	-13.550	-11.258	2.545	-2.324	-2.512	-0.028
35	A	44	LEU	0	-0.010	-0.011	5.285	0.398	0.478	-0.001	-0.002	-0.076	0.000
36	A	45	PHE	0	-0.018	-0.003	8.041	0.356	0.356	0.000	0.000	0.000	0.000
37	A	46	LEU	0	0.014	0.002	5.250	0.291	0.291	0.000	0.000	0.000	0.000
38	A	47	GLU	-1	-0.903	-0.937	6.258	-0.084	-0.084	0.000	0.000	0.000	0.000
39	A	48	SER	0	-0.022	-0.017	7.803	0.298	0.298	0.000	0.000	0.000	0.000
40	A	49	LEU	0	0.009	0.006	10.930	0.125	0.125	0.000	0.000	0.000	0.000
41	A	50	LEU	0	-0.009	-0.020	7.515	0.123	0.123	0.000	0.000	0.000	0.000
42	A	51	LYS	1	0.934	0.969	10.001	-0.060	-0.060	0.000	0.000	0.000	0.000
43	A	52	LYS	1	0.953	1.005	13.015	0.183	0.183	0.000	0.000	0.000	0.000
44	A	53	ALA	0	0.080	0.020	14.697	0.030	0.030	0.000	0.000	0.000	0.000
45	A	54	CYS	0	0.003	-0.001	14.415	0.043	0.043	0.000	0.000	0.000	0.000
46	A	55	GLN	0	-0.017	0.025	16.374	0.002	0.002	0.000	0.000	0.000	0.000
47	A	56	VAL	0	0.007	0.008	19.219	0.009	0.009	0.000	0.000	0.000	0.000
48	A	57	THR	0	-0.128	-0.076	17.578	0.018	0.018	0.000	0.000	0.000	0.000
49	A	58	GLN	0	-0.013	-0.031	18.877	0.020	0.020	0.000	0.000	0.000	0.000
50	A	59	SER	0	0.002	0.022	22.263	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	60	ARG	1	0.913	0.968	24.418	-0.034	-0.034	0.000	0.000	0.000	0.000
52	A	61	ASN	0	0.024	0.009	26.371	0.021	0.021	0.000	0.000	0.000	0.000
53	A	62	ALA	0	0.086	0.053	22.610	0.000	0.000	0.000	0.000	0.000	0.000
54	A	63	LYS	1	0.850	0.920	22.373	-0.126	-0.126	0.000	0.000	0.000	0.000
55	A	64	THR	0	-0.023	-0.025	18.504	0.029	0.029	0.000	0.000	0.000	0.000
56	A	65	MET	0	0.021	0.041	12.460	-0.031	-0.031	0.000	0.000	0.000	0.000
57	A	66	THR	0	0.007	-0.006	17.729	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	67	THR	0	0.036	0.004	18.250	-0.018	-0.018	0.000	0.000	0.000	0.000
59	A	68	SER	0	-0.020	-0.026	19.288	-0.022	-0.022	0.000	0.000	0.000	0.000
60	A	69	HIS	0	0.075	0.031	18.651	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	70	LEU	0	0.061	0.018	13.508	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	71	LYS	1	0.982	0.979	17.369	0.029	0.029	0.000	0.000	0.000	0.000
63	A	72	GLN	0	-0.056	-0.017	19.872	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	73	CYS	0	-0.009	0.018	17.010	0.009	0.009	0.000	0.000	0.000	0.000
65	A	74	ILE	0	-0.102	-0.044	16.140	-0.039	-0.039	0.000	0.000	0.000	0.000
66	A	75	GLU	-1	-0.942	-0.960	19.379	-0.096	-0.096	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:10:ALA)