FMO DATABASE

FMODB ID: R51Y8

Calculation Name: 4JO9-B-Xray322

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	86
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-521895.514486
FMO2-HF: Nuclear repulsion	486612.572525
FMO2-HF: Total energy	-35282.941961
FMO2-MP2: Total energy	-35385.854897

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:327:ACE )

Summations of interaction energy for fragment #1(B:327:ACE )

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.
1.888	2.632	0.001	-0.265	-0.48	0

Interaction energy analysis for fragmet #1(B:327:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.003

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].
3	B	329	ALA	0	0.039	0.035	3.867	1.150	1.826	0.001	-0.260	-0.417
4	B	330	ASP	-1	-0.806	-0.914	5.823	-0.606	-0.538	0.000	-0.005	-0.063
5	B	331	TYR	0	-0.007	-0.001	9.543	0.075	0.075	0.000	0.000	0.000
6	B	332	PHE	0	0.035	0.010	6.571	-0.014	-0.014	0.000	0.000	0.000
7	B	333	ARG	1	0.959	0.981	8.350	0.853	0.853	0.000	0.000	0.000
8	B	334	ILE	0	-0.008	-0.020	9.673	0.190	0.190	0.000	0.000	0.000
9	B	335	LEU	0	0.035	0.026	12.213	0.097	0.097	0.000	0.000	0.000
10	B	336	VAL	0	-0.013	0.000	9.732	0.094	0.094	0.000	0.000	0.000
11	B	337	GLN	0	-0.047	-0.012	12.929	0.066	0.066	0.000	0.000	0.000
12	B	338	GLN	0	-0.018	-0.026	15.329	0.049	0.049	0.000	0.000	0.000
13	B	339	PHE	0	-0.018	-0.002	15.665	0.042	0.042	0.000	0.000	0.000
14	B	340	GLU	-1	-0.919	-0.951	16.914	-0.154	-0.154	0.000	0.000	0.000
15	B	341	VAL	0	0.040	0.023	18.660	0.029	0.029	0.000	0.000	0.000
16	B	342	GLN	0	-0.020	-0.017	21.278	0.033	0.033	0.000	0.000	0.000
17	B	343	LEU	0	-0.014	-0.008	19.318	0.020	0.020	0.000	0.000	0.000
18	B	344	GLN	0	-0.008	0.008	22.726	0.014	0.014	0.000	0.000	0.000
19	B	345	GLN	0	-0.032	-0.025	24.580	0.023	0.023	0.000	0.000	0.000
20	B	346	TYR	0	0.013	0.003	26.235	0.010	0.010	0.000	0.000	0.000
21	B	347	ARG	1	0.908	0.964	25.038	0.080	0.080	0.000	0.000	0.000
22	B	348	GLN	0	0.043	0.022	28.197	0.004	0.004	0.000	0.000	0.000
23	B	349	GLN	0	0.024	0.014	30.692	0.004	0.004	0.000	0.000	0.000
24	B	350	ILE	0	0.013	0.008	30.764	0.005	0.005	0.000	0.000	0.000
25	B	351	GLU	-1	-0.869	-0.932	30.645	-0.058	-0.058	0.000	0.000	0.000
26	B	352	GLU	-1	-0.959	-0.983	34.424	-0.048	-0.048	0.000	0.000	0.000
27	B	353	LEU	0	-0.059	-0.019	36.302	0.003	0.003	0.000	0.000	0.000
28	B	354	GLU	-1	-0.944	-0.992	35.221	-0.043	-0.043	0.000	0.000	0.000
29	B	355	ASN	0	-0.009	-0.003	38.505	0.005	0.005	0.000	0.000	0.000
30	B	356	HIS	0	0.015	-0.002	40.403	0.004	0.004	0.000	0.000	0.000
31	B	357	LEU	0	-0.078	-0.049	40.943	0.002	0.002	0.000	0.000	0.000
32	B	358	ALA	0	-0.012	0.027	41.906	0.002	0.002	0.000	0.000	0.000
33	B	359	THR	0	-0.049	-0.017	43.729	0.003	0.003	0.000	0.000	0.000
34	B	360	GLN	0	0.041	-0.001	47.196	-0.002	-0.002	0.000	0.000	0.000
35	B	361	ALA	0	0.004	-0.010	50.211	-0.001	-0.001	0.000	0.000	0.000
36	B	362	ASN	0	-0.015	0.013	44.135	0.001	0.001	0.000	0.000	0.000
37	B	363	ASN	0	0.027	0.019	46.553	-0.001	-0.001	0.000	0.000	0.000
38	B	364	SER	0	-0.066	-0.046	47.769	0.000	0.000	0.000	0.000	0.000
39	B	365	HIS	0	-0.045	-0.018	47.571	0.000	0.000	0.000	0.000	0.000
40	B	366	ILE	0	-0.028	0.001	43.861	-0.002	-0.002	0.000	0.000	0.000
41	B	367	THR	0	-0.003	0.009	47.327	0.001	0.001	0.000	0.000	0.000
42	B	368	PRO	0	0.040	0.007	46.775	-0.002	-0.002	0.000	0.000	0.000
43	B	369	GLN	0	-0.022	-0.036	46.250	0.000	0.000	0.000	0.000	0.000
44	B	370	ASP	-1	-0.812	-0.892	43.313	-0.045	-0.045	0.000	0.000	0.000
45	B	371	LEU	0	0.018	0.007	41.749	-0.003	-0.003	0.000	0.000	0.000
46	B	372	SER	0	-0.041	-0.006	41.019	-0.004	-0.004	0.000	0.000	0.000
47	B	373	MET	0	0.002	0.001	39.382	-0.005	-0.005	0.000	0.000	0.000
48	B	374	ALA	0	0.047	0.018	37.308	-0.004	-0.004	0.000	0.000	0.000
49	B	375	MET	0	0.004	-0.002	36.271	-0.004	-0.004	0.000	0.000	0.000
50	B	376	GLN	0	-0.002	-0.005	36.187	-0.003	-0.003	0.000	0.000	0.000
51	B	377	LYS	1	0.857	0.931	33.941	0.068	0.068	0.000	0.000	0.000
52	B	378	ILE	0	0.057	0.030	31.676	-0.007	-0.007	0.000	0.000	0.000
53	B	379	TYR	0	0.000	0.004	31.144	-0.006	-0.006	0.000	0.000	0.000
54	B	380	GLN	0	0.022	0.010	30.287	-0.003	-0.003	0.000	0.000	0.000
55	B	381	THR	0	-0.037	-0.031	26.649	-0.010	-0.010	0.000	0.000	0.000
56	B	382	PHE	0	-0.003	0.007	26.634	-0.011	-0.011	0.000	0.000	0.000
57	B	383	VAL	0	-0.011	0.000	26.863	-0.006	-0.006	0.000	0.000	0.000
58	B	384	ALA	0	-0.018	-0.002	24.357	-0.010	-0.010	0.000	0.000	0.000
59	B	385	LEU	0	0.024	-0.006	22.369	-0.017	-0.017	0.000	0.000	0.000
60	B	386	ALA	0	-0.023	-0.003	21.996	-0.013	-0.013	0.000	0.000	0.000
61	B	387	ALA	0	0.000	0.005	22.899	-0.005	-0.005	0.000	0.000	0.000
62	B	388	GLN	0	-0.004	-0.019	18.284	-0.007	-0.007	0.000	0.000	0.000
63	B	389	LEU	0	0.030	0.017	17.852	-0.028	-0.028	0.000	0.000	0.000
64	B	390	GLN	0	0.003	0.020	18.652	0.004	0.004	0.000	0.000	0.000
65	B	391	SER	0	-0.052	-0.046	17.054	-0.012	-0.012	0.000	0.000	0.000
66	B	392	ILE	0	0.023	0.006	13.417	-0.037	-0.037	0.000	0.000	0.000
67	B	393	HIS	0	-0.030	-0.013	14.280	-0.009	-0.009	0.000	0.000	0.000
68	B	394	GLU	-1	-0.889	-0.952	16.410	-0.152	-0.152	0.000	0.000	0.000
69	B	395	ASN	0	-0.051	-0.025	11.078	-0.020	-0.020	0.000	0.000	0.000
70	B	396	VAL	0	0.023	0.000	11.474	0.005	0.005	0.000	0.000	0.000
71	B	397	LYS	1	0.929	0.977	12.534	0.173	0.173	0.000	0.000	0.000
72	B	398	VAL	0	0.049	0.019	11.036	0.033	0.033	0.000	0.000	0.000
73	B	399	LEU	0	-0.041	-0.008	6.902	0.043	0.043	0.000	0.000	0.000
74	B	400	LYS	1	0.949	0.977	10.630	0.118	0.118	0.000	0.000	0.000
75	B	401	GLU	-1	-0.912	-0.959	13.629	-0.063	-0.063	0.000	0.000	0.000
76	B	402	GLN	0	0.019	0.008	9.120	0.044	0.044	0.000	0.000	0.000
77	B	403	TYR	0	-0.031	-0.007	10.844	0.059	0.059	0.000	0.000	0.000
78	B	404	LEU	0	-0.043	-0.038	12.138	0.026	0.026	0.000	0.000	0.000
79	B	405	GLY	0	0.014	0.012	15.089	0.003	0.003	0.000	0.000	0.000
80	B	406	TYR	0	0.032	-0.008	9.229	0.012	0.012	0.000	0.000	0.000
81	B	407	ARG	1	0.902	0.960	14.540	-0.177	-0.177	0.000	0.000	0.000
82	B	408	LYS	1	0.977	0.990	16.698	-0.049	-0.049	0.000	0.000	0.000
83	B	409	MET	0	-0.084	-0.013	15.891	-0.010	-0.010	0.000	0.000	0.000
84	B	410	PHE	0	-0.045	-0.035	14.390	0.002	0.002	0.000	0.000	0.000
85	B	411	LEU	0	-0.101	-0.054	16.727	0.011	0.011	0.000	0.000	0.000
86	B	412	GLY	-1	-0.898	-0.921	20.240	0.079	0.079	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:327:ACE )