FMO DATABASE

FMODB ID: JLVL9

Calculation Name: 4J4F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4J4F

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	99
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-568168.548203
FMO2-HF: Nuclear repulsion	528943.908416
FMO2-HF: Total energy	-39224.639787
FMO2-MP2: Total energy	-39336.754595

3D Structure Molmil

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.
-9.104	-5.828	0.662	-1.691	-2.247	0.007

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 : 0.008 / q_NPA : 0.000

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	0.926	0.950	2.633	-9.667	-6.569	0.662	-1.672	-2.088	0.007
4	A	4	PHE	0	0.067	0.035	6.417	0.089	0.089	0.000	0.000	0.000	0.000
5	A	5	SER	0	0.016	0.008	9.062	0.032	0.032	0.000	0.000	0.000	0.000
6	A	6	GLN	0	-0.042	-0.023	8.563	0.189	0.189	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.036	0.026	11.411	0.012	0.012	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.111	-0.060	12.804	-0.039	-0.039	0.000	0.000	0.000	0.000
9	A	9	TYR	0	0.026	0.012	14.859	0.003	0.003	0.000	0.000	0.000	0.000
10	A	10	ASN	0	0.002	-0.014	18.123	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.052	-0.032	16.184	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.005	0.012	18.279	0.000	0.000	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.008	-0.003	15.676	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	14	GLN	0	0.027	0.022	19.592	0.010	0.010	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.009	0.001	21.602	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.021	-0.030	18.429	0.004	0.004	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.013	-0.006	17.293	-0.019	-0.019	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.013	0.012	12.270	0.017	0.017	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.024	0.007	16.362	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	20	SER	0	0.035	0.020	14.744	0.016	0.016	0.000	0.000	0.000	0.000
21	A	21	THR	0	0.027	0.029	17.172	-0.016	-0.016	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.836	-0.890	14.901	0.291	0.291	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.906	0.951	14.497	-0.089	-0.089	0.000	0.000	0.000	0.000
24	A	25	THR	0	0.035	0.000	13.369	0.008	0.008	0.000	0.000	0.000	0.000
25	A	26	ASN	0	-0.065	-0.025	15.918	0.024	0.024	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.059	0.047	18.786	-0.017	-0.017	0.000	0.000	0.000	0.000
27	A	28	GLY	0	-0.005	0.001	20.503	-0.020	-0.020	0.000	0.000	0.000	0.000
28	A	29	TYR	0	-0.049	-0.061	17.569	0.003	0.003	0.000	0.000	0.000	0.000
29	A	30	ASN	0	-0.033	-0.021	17.677	-0.023	-0.023	0.000	0.000	0.000	0.000
30	A	31	THR	0	-0.007	0.007	17.919	0.013	0.013	0.000	0.000	0.000	0.000
31	A	32	SER	0	-0.077	-0.029	15.753	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	33	SER	0	0.032	-0.015	17.024	0.011	0.011	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.028	-0.011	10.642	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.798	-0.882	14.932	-0.128	-0.128	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.032	-0.028	11.673	-0.034	-0.034	0.000	0.000	0.000	0.000
36	A	37	ASN	0	-0.016	-0.017	14.427	-0.022	-0.022	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.005	0.012	14.805	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	39	VAL	0	-0.013	-0.007	9.972	-0.028	-0.028	0.000	0.000	0.000	0.000
39	A	40	ILE	0	-0.039	-0.013	11.175	-0.046	-0.046	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.836	-0.909	13.598	-0.209	-0.209	0.000	0.000	0.000	0.000
41	A	42	ASN	0	-0.025	-0.022	16.649	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	43	VAL	0	0.026	0.009	16.776	0.002	0.002	0.000	0.000	0.000	0.000
43	A	44	ASP	-1	-0.896	-0.954	19.668	-0.118	-0.118	0.000	0.000	0.000	0.000
44	A	45	GLY	0	-0.016	-0.001	22.402	0.009	0.009	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.076	-0.037	17.671	0.005	0.005	0.000	0.000	0.000	0.000
46	A	47	LEU	0	0.007	0.004	15.771	-0.011	-0.011	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.906	0.958	13.218	0.176	0.176	0.000	0.000	0.000	0.000
48	A	49	TRP	0	-0.052	-0.029	8.179	-0.038	-0.038	0.000	0.000	0.000	0.000
49	A	50	GLN	0	-0.034	-0.010	10.628	0.001	0.001	0.000	0.000	0.000	0.000
50	A	51	GLY	0	-0.026	-0.002	10.428	-0.068	-0.068	0.000	0.000	0.000	0.000
51	A	52	SER	0	-0.024	-0.030	11.921	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	53	ASN	0	0.007	-0.006	13.549	0.023	0.023	0.000	0.000	0.000	0.000
53	A	54	PHE	0	0.044	0.005	17.085	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	55	ILE	0	0.010	-0.005	18.672	0.000	0.000	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.886	-0.919	17.032	-0.226	-0.226	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.059	-0.033	13.352	-0.018	-0.018	0.000	0.000	0.000	0.000
57	A	58	CYS	0	-0.060	-0.023	15.788	-0.018	-0.018	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.858	0.921	18.723	0.176	0.176	0.000	0.000	0.000	0.000
59	A	60	ASN	0	-0.046	-0.053	21.939	0.001	0.001	0.000	0.000	0.000	0.000
60	A	61	THR	0	0.005	0.022	23.456	0.001	0.001	0.000	0.000	0.000	0.000
61	A	62	GLN	0	-0.050	-0.032	25.691	0.013	0.013	0.000	0.000	0.000	0.000
62	A	63	LEU	0	0.021	0.020	28.333	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	64	ALA	0	-0.025	-0.018	29.559	0.002	0.002	0.000	0.000	0.000	0.000
64	A	65	GLY	0	-0.001	-0.003	31.398	0.000	0.000	0.000	0.000	0.000	0.000
65	A	66	SER	0	0.006	-0.010	34.574	0.000	0.000	0.000	0.000	0.000	0.000
66	A	67	SER	0	0.004	-0.004	32.587	0.000	0.000	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.811	-0.871	28.181	-0.101	-0.101	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.032	0.001	24.327	0.002	0.002	0.000	0.000	0.000	0.000
69	A	70	ALA	0	-0.007	-0.014	25.031	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	71	ALA	0	0.017	-0.004	21.438	0.001	0.001	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.795	-0.862	20.211	-0.149	-0.149	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.867	0.944	11.826	0.345	0.345	0.000	0.000	0.000	0.000
73	A	75	THR	0	0.031	0.023	10.556	-0.045	-0.045	0.000	0.000	0.000	0.000
74	A	76	ARG	1	0.982	0.971	4.001	0.626	0.804	0.000	-0.019	-0.159	0.000
75	A	77	ALA	0	-0.001	0.001	6.678	-0.153	-0.153	0.000	0.000	0.000	0.000
76	A	78	GLN	0	0.001	0.000	8.207	0.153	0.153	0.000	0.000	0.000	0.000
77	A	79	GLN	0	0.032	0.022	11.326	0.066	0.066	0.000	0.000	0.000	0.000
78	A	80	PHE	0	0.000	-0.011	14.073	-0.026	-0.026	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.001	0.003	15.429	0.013	0.013	0.000	0.000	0.000	0.000
80	A	82	SER	0	0.018	0.014	17.888	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	83	THR	0	-0.044	-0.020	18.775	0.000	0.000	0.000	0.000	0.000	0.000
82	A	84	LYS	1	0.852	0.898	21.102	0.106	0.106	0.000	0.000	0.000	0.000
83	A	85	ILE	0	0.019	0.020	21.998	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	86	ASN	0	0.030	0.003	24.623	0.006	0.006	0.000	0.000	0.000	0.000
85	A	87	LEU	0	-0.006	-0.013	27.274	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	88	ASP	-1	-0.833	-0.923	29.438	-0.072	-0.072	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.935	-0.935	26.666	-0.096	-0.096	0.000	0.000	0.000	0.000
88	A	90	HIS	1	0.846	0.905	26.263	0.100	0.100	0.000	0.000	0.000	0.000
89	A	91	ILE	0	-0.030	0.003	28.637	0.000	0.000	0.000	0.000	0.000	0.000
90	A	92	ALA	0	0.052	0.039	31.958	0.003	0.003	0.000	0.000	0.000	0.000
91	A	93	ASN	0	-0.008	-0.013	35.536	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	94	ILE	0	-0.009	-0.015	37.783	0.002	0.002	0.000	0.000	0.000	0.000
93	A	95	ASP	-1	-0.934	-0.968	40.515	-0.043	-0.043	0.000	0.000	0.000	0.000
94	A	96	GLY	0	-0.004	0.002	42.791	0.001	0.001	0.000	0.000	0.000	0.000
95	A	97	THR	0	-0.052	-0.017	38.119	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	98	LEU	0	-0.031	-0.011	34.600	0.000	0.000	0.000	0.000	0.000	0.000
97	A	99	LYS	1	0.842	0.902	34.149	0.066	0.066	0.000	0.000	0.000	0.000
98	A	100	TYR	0	0.005	0.012	26.165	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-0.863	-0.921	30.637	-0.064	-0.064	0.000	0.000	0.000	0.000

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