FMO DATABASE

FMODB ID: J3J19

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	OptAll
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	-519460.973787
FMO2-HF: Nuclear repulsion	484328.569456
FMO2-HF: Total energy	-35132.404331
FMO2-MP2: Total energy	-35234.812582

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.
-3.891	-0.219	2.645	-2.507	-3.81	-0.008

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 : -0.036 / 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

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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	-0.824	-0.914	3.861	-2.720	-1.151	-0.008	-0.757	-0.804	0.003
4	B	331	TYR	0	0.012	0.008	6.826	-0.069	-0.069	0.000	0.000	0.000	0.000
5	B	332	PHE	0	0.032	0.012	2.578	-1.995	-0.259	2.652	-1.697	-2.692	-0.011
6	B	333	ARG	1	0.890	0.940	3.648	0.913	1.221	0.002	-0.051	-0.259	0.000
7	B	334	ILE	0	-0.009	-0.014	5.224	0.154	0.213	-0.001	-0.002	-0.055	0.000
8	B	335	LEU	0	0.018	0.018	8.242	0.060	0.060	0.000	0.000	0.000	0.000
9	B	336	VAL	0	-0.011	-0.005	5.799	0.036	0.036	0.000	0.000	0.000	0.000
10	B	337	GLN	0	-0.016	-0.015	8.635	-0.081	-0.081	0.000	0.000	0.000	0.000
11	B	338	GLN	0	-0.004	-0.009	10.276	0.082	0.082	0.000	0.000	0.000	0.000
12	B	339	PHE	0	-0.005	0.005	11.998	0.038	0.038	0.000	0.000	0.000	0.000
13	B	340	GLU	-1	-0.873	-0.926	12.022	-0.278	-0.278	0.000	0.000	0.000	0.000
14	B	341	VAL	0	0.037	0.025	13.783	0.030	0.030	0.000	0.000	0.000	0.000
15	B	342	GLN	0	0.030	0.013	16.377	0.021	0.021	0.000	0.000	0.000	0.000
16	B	343	LEU	0	-0.014	-0.001	15.828	0.019	0.019	0.000	0.000	0.000	0.000
17	B	344	GLN	0	0.000	-0.013	17.958	0.011	0.011	0.000	0.000	0.000	0.000
18	B	345	GLN	0	-0.046	-0.034	19.739	0.016	0.016	0.000	0.000	0.000	0.000
19	B	346	TYR	0	-0.003	-0.004	21.664	0.011	0.011	0.000	0.000	0.000	0.000
20	B	347	ARG	1	0.809	0.881	21.868	0.114	0.114	0.000	0.000	0.000	0.000
21	B	348	GLN	0	0.042	0.030	23.241	-0.003	-0.003	0.000	0.000	0.000	0.000
22	B	349	GLN	0	-0.040	-0.028	25.216	0.012	0.012	0.000	0.000	0.000	0.000
23	B	350	ILE	0	-0.010	0.000	26.566	0.006	0.006	0.000	0.000	0.000	0.000
24	B	351	GLU	-1	-0.788	-0.871	26.243	-0.087	-0.087	0.000	0.000	0.000	0.000
25	B	352	GLU	-1	-0.901	-0.932	29.694	-0.059	-0.059	0.000	0.000	0.000	0.000
26	B	353	LEU	0	-0.027	-0.018	31.776	0.004	0.004	0.000	0.000	0.000	0.000
27	B	354	GLU	-1	-0.927	-0.973	31.071	-0.046	-0.046	0.000	0.000	0.000	0.000
28	B	355	ASN	0	-0.007	-0.004	33.771	0.003	0.003	0.000	0.000	0.000	0.000
29	B	356	HIS	0	-0.060	-0.045	34.977	0.005	0.005	0.000	0.000	0.000	0.000
30	B	357	LEU	0	-0.031	-0.022	36.376	0.003	0.003	0.000	0.000	0.000	0.000
31	B	358	ALA	0	-0.006	0.016	37.265	0.002	0.002	0.000	0.000	0.000	0.000
32	B	359	THR	0	-0.069	-0.037	39.275	0.002	0.002	0.000	0.000	0.000	0.000
33	B	360	GLN	0	0.021	0.004	42.783	-0.001	-0.001	0.000	0.000	0.000	0.000
34	B	361	ALA	0	0.011	0.008	45.678	0.000	0.000	0.000	0.000	0.000	0.000
35	B	362	ASN	0	-0.009	-0.004	39.111	0.001	0.001	0.000	0.000	0.000	0.000
36	B	363	ASN	0	-0.015	-0.004	41.153	0.001	0.001	0.000	0.000	0.000	0.000
37	B	364	SER	0	-0.069	-0.047	42.974	0.001	0.001	0.000	0.000	0.000	0.000
38	B	365	HIS	0	-0.017	0.000	42.653	0.001	0.001	0.000	0.000	0.000	0.000
39	B	366	ILE	0	-0.040	-0.003	38.770	-0.002	-0.002	0.000	0.000	0.000	0.000
40	B	367	THR	0	-0.019	-0.037	42.285	0.003	0.003	0.000	0.000	0.000	0.000
41	B	368	PRO	0	0.031	-0.007	41.889	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	369	GLN	0	-0.004	-0.003	41.294	0.001	0.001	0.000	0.000	0.000	0.000
43	B	370	ASP	-1	-0.788	-0.863	38.367	-0.038	-0.038	0.000	0.000	0.000	0.000
44	B	371	LEU	0	0.020	0.014	37.005	-0.002	-0.002	0.000	0.000	0.000	0.000
45	B	372	SER	0	-0.017	-0.004	36.741	0.000	0.000	0.000	0.000	0.000	0.000
46	B	373	MET	0	-0.043	-0.021	33.825	-0.002	-0.002	0.000	0.000	0.000	0.000
47	B	374	ALA	0	0.025	0.010	32.669	-0.002	-0.002	0.000	0.000	0.000	0.000
48	B	375	MET	0	0.031	0.013	31.804	-0.003	-0.003	0.000	0.000	0.000	0.000
49	B	376	GLN	0	-0.002	0.002	31.909	0.001	0.001	0.000	0.000	0.000	0.000
50	B	377	LYS	1	0.892	0.951	28.955	0.054	0.054	0.000	0.000	0.000	0.000
51	B	378	ILE	0	0.081	0.058	27.577	-0.003	-0.003	0.000	0.000	0.000	0.000
52	B	379	TYR	0	-0.003	0.000	26.988	0.000	0.000	0.000	0.000	0.000	0.000
53	B	380	GLN	0	-0.016	-0.012	25.818	0.005	0.005	0.000	0.000	0.000	0.000
54	B	381	THR	0	-0.030	-0.019	22.369	-0.003	-0.003	0.000	0.000	0.000	0.000
55	B	382	PHE	0	-0.001	0.000	22.424	-0.002	-0.002	0.000	0.000	0.000	0.000
56	B	383	VAL	0	0.000	0.003	22.860	0.004	0.004	0.000	0.000	0.000	0.000
57	B	384	ALA	0	-0.028	-0.008	20.094	0.006	0.006	0.000	0.000	0.000	0.000
58	B	385	LEU	0	0.019	0.012	17.563	0.003	0.003	0.000	0.000	0.000	0.000
59	B	386	ALA	0	0.011	0.005	18.212	0.005	0.005	0.000	0.000	0.000	0.000
60	B	387	ALA	0	0.005	0.005	19.190	0.014	0.014	0.000	0.000	0.000	0.000
61	B	388	GLN	0	-0.013	-0.015	14.539	0.021	0.021	0.000	0.000	0.000	0.000
62	B	389	LEU	0	0.025	0.024	14.287	0.020	0.020	0.000	0.000	0.000	0.000
63	B	390	GLN	0	-0.015	0.003	15.430	0.014	0.014	0.000	0.000	0.000	0.000
64	B	391	SER	0	-0.041	-0.042	13.422	0.027	0.027	0.000	0.000	0.000	0.000
65	B	392	ILE	0	0.019	0.012	10.249	0.063	0.063	0.000	0.000	0.000	0.000
66	B	393	HIS	0	-0.024	-0.005	11.692	0.064	0.064	0.000	0.000	0.000	0.000
67	B	394	GLU	-1	-0.824	-0.930	14.202	0.213	0.213	0.000	0.000	0.000	0.000
68	B	395	ASN	0	-0.050	-0.037	8.662	0.185	0.185	0.000	0.000	0.000	0.000
69	B	396	VAL	0	0.011	0.003	10.367	0.127	0.127	0.000	0.000	0.000	0.000
70	B	397	LYS	1	0.831	0.923	11.520	-0.221	-0.221	0.000	0.000	0.000	0.000
71	B	398	VAL	0	0.044	0.007	11.298	0.011	0.011	0.000	0.000	0.000	0.000
72	B	399	LEU	0	-0.004	0.008	7.085	0.063	0.063	0.000	0.000	0.000	0.000
73	B	400	LYS	1	0.845	0.918	11.100	-0.269	-0.269	0.000	0.000	0.000	0.000
74	B	401	GLU	-1	-0.802	-0.889	14.097	0.261	0.261	0.000	0.000	0.000	0.000
75	B	402	GLN	0	-0.010	-0.004	10.774	0.060	0.060	0.000	0.000	0.000	0.000
76	B	403	TYR	0	0.003	0.013	12.241	-0.044	-0.044	0.000	0.000	0.000	0.000
77	B	404	LEU	0	-0.023	-0.024	13.938	-0.054	-0.054	0.000	0.000	0.000	0.000
78	B	405	GLY	0	0.010	0.014	17.102	-0.039	-0.039	0.000	0.000	0.000	0.000
79	B	406	TYR	0	0.055	0.005	11.942	-0.073	-0.073	0.000	0.000	0.000	0.000
80	B	407	ARG	1	0.908	0.960	16.688	-0.277	-0.277	0.000	0.000	0.000	0.000
81	B	408	LYS	1	0.949	0.967	18.847	-0.236	-0.236	0.000	0.000	0.000	0.000
82	B	409	MET	0	-0.050	-0.009	19.090	-0.006	-0.006	0.000	0.000	0.000	0.000
83	B	410	PHE	0	-0.016	-0.012	16.599	-0.012	-0.012	0.000	0.000	0.000	0.000
84	B	411	LEU	0	-0.052	-0.015	19.134	-0.013	-0.013	0.000	0.000	0.000	0.000
85	B	412	GLY	0	-0.022	0.004	22.745	-0.021	-0.021	0.000	0.000	0.000	0.000

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