FMO DATABASE

FMODB ID: 823LY

Calculation Name: 4JO9-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JO9

Chain ID: B

ChEMBL ID:

UniProt ID: Q7Z3B4

Base Structure: X-ray

Registration Date: 2023-06-20

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	85
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-518589.514067
FMO2-HF: Nuclear repulsion	483457.821354
FMO2-HF: Total energy	-35131.692713
FMO2-MP2: Total energy	-35234.171407

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(B:328:PRO)

Summations of interaction energy for fragment #1(B:328: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.
-4.331	-1.105	5.698	-3.59	-5.334	-0.007

Interaction energy analysis for fragmet #1(B:328:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.049 / q_NPA : -0.030

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	B	330	ASP	-1	-0.797	-0.910	3.808	-3.008	-0.857	-0.015	-1.081	-1.054	0.007
4	B	331	TYR	0	-0.006	0.000	6.734	-0.071	-0.071	0.000	0.000	0.000	0.000
5	B	332	PHE	0	0.029	0.005	2.234	-1.607	-1.077	5.701	-2.418	-3.813	-0.014
6	B	333	ARG	1	0.962	0.983	3.544	0.150	0.632	0.013	-0.085	-0.410	0.000
7	B	334	ILE	0	-0.005	-0.018	4.854	0.070	0.133	-0.001	-0.006	-0.057	0.000
8	B	335	LEU	0	0.032	0.025	8.118	0.050	0.050	0.000	0.000	0.000	0.000
9	B	336	VAL	0	-0.007	0.002	5.282	0.041	0.041	0.000	0.000	0.000	0.000
10	B	337	GLN	0	-0.048	-0.012	8.042	0.020	0.020	0.000	0.000	0.000	0.000
11	B	338	GLN	0	-0.018	-0.025	9.844	0.028	0.028	0.000	0.000	0.000	0.000
12	B	339	PHE	0	-0.021	-0.004	11.217	0.022	0.022	0.000	0.000	0.000	0.000
13	B	340	GLU	-1	-0.916	-0.950	11.755	-0.132	-0.132	0.000	0.000	0.000	0.000
14	B	341	VAL	0	0.038	0.023	13.510	0.017	0.017	0.000	0.000	0.000	0.000
15	B	342	GLN	0	-0.020	-0.017	16.108	0.017	0.017	0.000	0.000	0.000	0.000
16	B	343	LEU	0	-0.018	-0.010	14.984	0.010	0.010	0.000	0.000	0.000	0.000
17	B	344	GLN	0	-0.003	0.009	17.672	0.003	0.003	0.000	0.000	0.000	0.000
18	B	345	GLN	0	-0.031	-0.024	19.426	0.014	0.014	0.000	0.000	0.000	0.000
19	B	346	TYR	0	0.010	0.002	21.420	0.007	0.007	0.000	0.000	0.000	0.000
20	B	347	ARG	1	0.908	0.963	20.504	0.088	0.088	0.000	0.000	0.000	0.000
21	B	348	GLN	0	0.044	0.023	23.101	0.001	0.001	0.000	0.000	0.000	0.000
22	B	349	GLN	0	0.026	0.014	25.639	0.003	0.003	0.000	0.000	0.000	0.000
23	B	350	ILE	0	0.012	0.007	26.246	0.004	0.004	0.000	0.000	0.000	0.000
24	B	351	GLU	-1	-0.868	-0.932	26.095	-0.062	-0.062	0.000	0.000	0.000	0.000
25	B	352	GLU	-1	-0.959	-0.983	29.695	-0.041	-0.041	0.000	0.000	0.000	0.000
26	B	353	LEU	0	-0.058	-0.019	31.473	0.003	0.003	0.000	0.000	0.000	0.000
27	B	354	GLU	-1	-0.943	-0.992	31.145	-0.046	-0.046	0.000	0.000	0.000	0.000
28	B	355	ASN	0	-0.008	-0.003	33.813	0.003	0.003	0.000	0.000	0.000	0.000
29	B	356	HIS	0	0.014	-0.002	35.672	0.003	0.003	0.000	0.000	0.000	0.000
30	B	357	LEU	0	-0.077	-0.048	36.550	0.002	0.002	0.000	0.000	0.000	0.000
31	B	358	ALA	0	-0.012	0.028	37.468	0.001	0.001	0.000	0.000	0.000	0.000
32	B	359	THR	0	-0.048	-0.016	39.313	0.002	0.002	0.000	0.000	0.000	0.000
33	B	360	GLN	0	0.039	-0.001	42.675	0.000	0.000	0.000	0.000	0.000	0.000
34	B	361	ALA	0	0.007	-0.009	45.619	0.000	0.000	0.000	0.000	0.000	0.000
35	B	362	ASN	0	-0.015	0.013	39.362	0.002	0.002	0.000	0.000	0.000	0.000
36	B	363	ASN	0	0.027	0.018	41.929	0.001	0.001	0.000	0.000	0.000	0.000
37	B	364	SER	0	-0.069	-0.048	42.915	0.001	0.001	0.000	0.000	0.000	0.000
38	B	365	HIS	0	-0.042	-0.017	42.430	0.001	0.001	0.000	0.000	0.000	0.000
39	B	366	ILE	0	-0.023	0.003	38.838	-0.001	-0.001	0.000	0.000	0.000	0.000
40	B	367	THR	0	-0.007	0.009	42.169	0.001	0.001	0.000	0.000	0.000	0.000
41	B	368	PRO	0	0.038	0.006	41.756	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	369	GLN	0	-0.022	-0.036	41.342	0.000	0.000	0.000	0.000	0.000	0.000
43	B	370	ASP	-1	-0.811	-0.892	38.152	-0.028	-0.028	0.000	0.000	0.000	0.000
44	B	371	LEU	0	0.017	0.007	36.723	-0.002	-0.002	0.000	0.000	0.000	0.000
45	B	372	SER	0	-0.041	-0.007	36.242	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	373	MET	0	0.003	0.002	34.378	-0.002	-0.002	0.000	0.000	0.000	0.000
47	B	374	ALA	0	0.044	0.017	32.313	-0.002	-0.002	0.000	0.000	0.000	0.000
48	B	375	MET	0	0.007	-0.001	31.484	-0.003	-0.003	0.000	0.000	0.000	0.000
49	B	376	GLN	0	-0.004	-0.007	31.688	-0.002	-0.002	0.000	0.000	0.000	0.000
50	B	377	LYS	1	0.861	0.933	28.891	0.039	0.039	0.000	0.000	0.000	0.000
51	B	378	ILE	0	0.054	0.030	27.184	-0.003	-0.003	0.000	0.000	0.000	0.000
52	B	379	TYR	0	0.002	0.004	26.716	-0.004	-0.004	0.000	0.000	0.000	0.000
53	B	380	GLN	0	0.021	0.009	25.686	-0.001	-0.001	0.000	0.000	0.000	0.000
54	B	381	THR	0	-0.038	-0.032	21.836	-0.003	-0.003	0.000	0.000	0.000	0.000
55	B	382	PHE	0	-0.004	0.007	22.293	-0.006	-0.006	0.000	0.000	0.000	0.000
56	B	383	VAL	0	-0.007	0.001	23.075	-0.003	-0.003	0.000	0.000	0.000	0.000
57	B	384	ALA	0	-0.017	-0.001	19.923	-0.002	-0.002	0.000	0.000	0.000	0.000
58	B	385	LEU	0	0.022	-0.007	18.057	-0.007	-0.007	0.000	0.000	0.000	0.000
59	B	386	ALA	0	-0.023	-0.004	18.476	-0.008	-0.008	0.000	0.000	0.000	0.000
60	B	387	ALA	0	0.000	0.005	19.387	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	388	GLN	0	-0.004	-0.019	14.491	-0.003	-0.003	0.000	0.000	0.000	0.000
62	B	389	LEU	0	0.031	0.017	14.549	-0.013	-0.013	0.000	0.000	0.000	0.000
63	B	390	GLN	0	0.004	0.021	15.970	-0.006	-0.006	0.000	0.000	0.000	0.000
64	B	391	SER	0	-0.051	-0.045	13.849	0.000	0.000	0.000	0.000	0.000	0.000
65	B	392	ILE	0	0.024	0.006	10.710	-0.007	-0.007	0.000	0.000	0.000	0.000
66	B	393	HIS	0	-0.030	-0.013	12.197	-0.015	-0.015	0.000	0.000	0.000	0.000
67	B	394	GLU	-1	-0.889	-0.952	14.507	-0.047	-0.047	0.000	0.000	0.000	0.000
68	B	395	ASN	0	-0.050	-0.024	9.030	-0.008	-0.008	0.000	0.000	0.000	0.000
69	B	396	VAL	0	0.022	-0.001	10.457	0.009	0.009	0.000	0.000	0.000	0.000
70	B	397	LYS	1	0.933	0.978	11.648	0.053	0.053	0.000	0.000	0.000	0.000
71	B	398	VAL	0	0.049	0.019	11.096	0.015	0.015	0.000	0.000	0.000	0.000
72	B	399	LEU	0	-0.039	-0.007	6.750	0.026	0.026	0.000	0.000	0.000	0.000
73	B	400	LYS	1	0.950	0.978	10.929	0.069	0.069	0.000	0.000	0.000	0.000
74	B	401	GLU	-1	-0.910	-0.959	14.131	0.010	0.010	0.000	0.000	0.000	0.000
75	B	402	GLN	0	0.023	0.010	10.337	0.037	0.037	0.000	0.000	0.000	0.000
76	B	403	TYR	0	-0.026	-0.004	12.003	0.018	0.018	0.000	0.000	0.000	0.000
77	B	404	LEU	0	-0.044	-0.038	13.567	0.005	0.005	0.000	0.000	0.000	0.000
78	B	405	GLY	0	0.012	0.009	16.581	0.002	0.002	0.000	0.000	0.000	0.000
79	B	406	TYR	0	0.048	0.001	11.349	0.012	0.012	0.000	0.000	0.000	0.000
80	B	407	ARG	1	0.915	0.970	16.566	-0.008	-0.008	0.000	0.000	0.000	0.000
81	B	408	LYS	1	0.954	0.972	18.654	-0.024	-0.024	0.000	0.000	0.000	0.000
82	B	409	MET	0	-0.061	-0.006	18.343	0.001	0.001	0.000	0.000	0.000	0.000
83	B	410	PHE	0	-0.014	-0.016	16.920	0.001	0.001	0.000	0.000	0.000	0.000
84	B	411	LEU	0	-0.055	-0.026	18.652	-0.005	-0.005	0.000	0.000	0.000	0.000
85	B	412	GLY	0	-0.018	0.018	22.417	-0.009	-0.009	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:328:PRO)