FMO DATABASE

FMODB ID: 72K2K

Calculation Name: 4J4E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J4E

Chain ID: A

ChEMBL ID:

UniProt ID: P81180

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	99
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-532582.07041
FMO2-HF: Nuclear repulsion	493358.131686
FMO2-HF: Total energy	-39223.938724
FMO2-MP2: Total energy	-39335.841516

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:1:LEU)

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

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.
-11.555	-6.403	1.831	-2.282	-4.701	0.011

Interaction energy analysis for fragmet #1(A:1:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : -0.006

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	3	LYS	1	0.915	0.947	2.940	-8.227	-5.123	0.555	-1.401	-2.258	0.012
4	A	4	PHE	0	0.083	0.035	5.524	0.051	0.051	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.004	-0.003	8.721	0.090	0.090	0.000	0.000	0.000	0.000
6	A	6	GLN	0	0.000	-0.003	7.315	-0.007	-0.007	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.013	0.018	9.431	-0.003	-0.003	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.070	-0.016	11.880	-0.041	-0.041	0.000	0.000	0.000	0.000
9	A	9	TYR	0	0.036	0.016	14.118	0.044	0.044	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.036	-0.029	17.480	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	11	SER	0	0.026	0.023	16.089	-0.026	-0.026	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.000	0.013	18.552	0.021	0.021	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.023	0.005	15.807	-0.022	-0.022	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.005	0.003	19.766	0.011	0.011	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.008	0.002	22.274	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	16	SER	0	0.004	-0.001	18.637	0.007	0.007	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.002	0.011	17.914	-0.022	-0.022	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.012	0.008	12.923	0.020	0.020	0.000	0.000	0.000	0.000
19	A	19	THR	0	-0.012	-0.017	16.899	-0.022	-0.022	0.000	0.000	0.000	0.000
20	A	20	SER	0	0.000	-0.027	15.462	0.014	0.014	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.003	0.005	17.564	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.884	-0.938	13.100	-0.162	-0.162	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.911	0.956	14.261	0.155	0.155	0.000	0.000	0.000	0.000
24	A	25	THR	0	-0.005	-0.020	13.364	0.010	0.010	0.000	0.000	0.000	0.000
25	A	26	ASN	0	-0.020	-0.008	15.194	0.018	0.018	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.048	0.046	18.030	0.018	0.018	0.000	0.000	0.000	0.000
27	A	28	GLY	0	-0.006	-0.005	19.881	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	29	TYR	0	-0.005	-0.020	16.789	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	30	ASN	0	-0.035	-0.022	17.580	0.028	0.028	0.000	0.000	0.000	0.000
30	A	31	THR	0	0.008	0.016	18.066	-0.017	-0.017	0.000	0.000	0.000	0.000
31	A	32	SER	0	-0.067	-0.024	16.271	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	33	SER	0	0.043	-0.001	17.528	0.007	0.007	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.016	-0.003	11.326	-0.022	-0.022	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.835	-0.929	15.593	-0.138	-0.138	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.020	-0.023	11.704	-0.023	-0.023	0.000	0.000	0.000	0.000
36	A	37	ASN	0	0.003	-0.003	14.751	0.007	0.007	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.015	0.012	15.868	0.001	0.001	0.000	0.000	0.000	0.000
38	A	39	VAL	0	-0.043	-0.021	10.349	-0.018	-0.018	0.000	0.000	0.000	0.000
39	A	40	ILE	0	-0.052	-0.020	11.420	0.000	0.000	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.858	-0.922	13.668	-0.042	-0.042	0.000	0.000	0.000	0.000
41	A	42	ASN	0	-0.052	-0.043	16.360	0.016	0.016	0.000	0.000	0.000	0.000
42	A	43	VAL	0	0.008	-0.002	16.398	0.001	0.001	0.000	0.000	0.000	0.000
43	A	44	ASP	-1	-0.938	-0.981	19.148	0.039	0.039	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.014	0.027	22.013	0.005	0.005	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.035	-0.019	17.149	0.010	0.010	0.000	0.000	0.000	0.000
46	A	47	LEU	0	-0.026	-0.008	15.098	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.936	0.965	12.346	-0.047	-0.047	0.000	0.000	0.000	0.000
48	A	49	TRP	0	-0.014	-0.003	7.728	-0.075	-0.075	0.000	0.000	0.000	0.000
49	A	50	GLN	0	0.015	0.027	10.215	0.036	0.036	0.000	0.000	0.000	0.000
50	A	51	GLY	0	-0.023	-0.013	10.704	-0.019	-0.019	0.000	0.000	0.000	0.000
51	A	52	SER	0	-0.045	-0.026	11.888	-0.030	-0.030	0.000	0.000	0.000	0.000
52	A	53	ASN	0	0.090	0.050	14.130	0.022	0.022	0.000	0.000	0.000	0.000
53	A	54	PHE	0	0.043	-0.005	17.627	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	55	ILE	0	-0.007	-0.007	18.960	0.005	0.005	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.933	-0.954	18.284	-0.099	-0.099	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.097	-0.058	14.302	0.000	0.000	0.000	0.000	0.000	0.000
57	A	58	CYS	0	-0.066	-0.026	16.421	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.863	0.931	19.703	0.009	0.009	0.000	0.000	0.000	0.000
59	A	60	ASN	0	-0.043	-0.037	23.131	0.002	0.002	0.000	0.000	0.000	0.000
60	A	61	THR	0	0.011	0.021	24.082	0.002	0.002	0.000	0.000	0.000	0.000
61	A	62	GLN	0	-0.035	-0.023	26.378	0.002	0.002	0.000	0.000	0.000	0.000
62	A	63	LEU	0	0.012	0.019	28.650	0.001	0.001	0.000	0.000	0.000	0.000
63	A	64	ALA	0	-0.016	-0.003	29.795	0.000	0.000	0.000	0.000	0.000	0.000
64	A	65	GLY	0	0.020	0.007	31.628	0.001	0.001	0.000	0.000	0.000	0.000
65	A	66	SER	0	-0.032	-0.027	34.554	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	67	SER	0	-0.031	-0.020	32.240	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.858	-0.921	28.337	0.016	0.016	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.046	-0.006	23.940	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	70	ALA	0	0.001	-0.001	24.931	0.004	0.004	0.000	0.000	0.000	0.000
70	A	71	ALA	0	0.027	-0.013	21.758	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.832	-0.895	21.054	0.003	0.003	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.953	0.977	14.163	0.082	0.082	0.000	0.000	0.000	0.000
73	A	75	THR	0	0.006	0.009	10.402	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	76	ARG	1	0.968	0.968	2.702	-1.630	-0.931	0.256	-0.237	-0.718	0.002
75	A	77	ALA	0	0.033	0.026	8.345	0.009	0.009	0.000	0.000	0.000	0.000
76	A	78	GLN	0	-0.025	-0.005	6.977	-0.023	-0.023	0.000	0.000	0.000	0.000
77	A	79	GLN	0	0.002	0.000	4.512	-0.171	-0.056	-0.001	-0.018	-0.096	0.000
78	A	80	PHE	0	0.009	0.003	6.638	-0.018	-0.018	0.000	0.000	0.000	0.000
79	A	81	VAL	0	0.007	0.000	2.450	-1.383	-0.292	1.022	-0.605	-1.508	-0.003
80	A	82	SER	0	-0.012	-0.002	5.669	0.138	0.138	0.000	0.000	0.000	0.000
81	A	83	THR	0	-0.032	-0.023	4.387	-0.675	-0.532	-0.001	-0.021	-0.121	0.000
82	A	84	LYS	1	0.976	0.974	5.763	0.251	0.251	0.000	0.000	0.000	0.000
83	A	85	ILE	0	0.014	0.013	8.139	0.194	0.194	0.000	0.000	0.000	0.000
84	A	86	ASN	0	0.034	0.017	10.908	-0.091	-0.091	0.000	0.000	0.000	0.000
85	A	87	LEU	0	0.007	-0.004	14.175	0.016	0.016	0.000	0.000	0.000	0.000
86	A	88	ASP	-1	-0.845	-0.922	17.102	0.081	0.081	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.995	-0.983	14.960	0.280	0.280	0.000	0.000	0.000	0.000
88	A	90	HIS	1	0.827	0.898	17.331	-0.203	-0.203	0.000	0.000	0.000	0.000
89	A	91	ILE	0	-0.033	0.006	19.797	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	92	ALA	0	0.072	0.048	22.253	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	93	ASN	0	-0.023	-0.023	25.721	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	94	ILE	0	-0.017	-0.018	28.766	0.002	0.002	0.000	0.000	0.000	0.000
93	A	95	ASP	-1	-0.920	-0.964	31.727	0.027	0.027	0.000	0.000	0.000	0.000
94	A	96	GLY	0	-0.001	0.013	33.051	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	97	THR	0	-0.050	-0.030	31.208	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	98	LEU	0	-0.005	0.002	24.792	0.005	0.005	0.000	0.000	0.000	0.000
97	A	99	LYS	1	0.911	0.953	26.300	-0.053	-0.053	0.000	0.000	0.000	0.000
98	A	100	TYR	0	0.010	0.014	19.222	0.010	0.010	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-0.928	-0.964	23.011	0.089	0.089	0.000	0.000	0.000	0.000

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