FMO DATABASE

FMODB ID: 2NNZR

Calculation Name: 3KJK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KJK

Chain ID: A

ChEMBL ID:

UniProt ID: Q9JZJ4

Base Structure: X-ray

Registration Date: 2023-09-21

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	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	116
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-914708.820531
FMO2-HF: Nuclear repulsion	868940.053354
FMO2-HF: Total energy	-45768.767177
FMO2-MP2: Total energy	-45899.751048

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:MET)

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

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.
-4.051	-1.466	2.806	-1.799	-3.592	0.005

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.033

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	ILE	0	-0.043	-0.028	3.861	0.779	1.864	-0.003	-0.398	-0.684	0.002
4	A	4	ARG	1	0.887	0.955	6.192	-0.441	-0.441	0.000	0.000	0.000	0.000
5	A	5	TYR	0	0.028	0.008	9.297	-0.049	-0.049	0.000	0.000	0.000	0.000
6	A	6	PHE	0	0.013	0.003	11.244	0.103	0.103	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.073	0.025	15.481	-0.029	-0.029	0.000	0.000	0.000	0.000
8	A	8	THR	0	-0.060	-0.035	15.874	-0.010	-0.010	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.027	0.025	18.371	0.017	0.017	0.000	0.000	0.000	0.000
10	A	10	PRO	0	-0.018	-0.034	19.737	-0.034	-0.034	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.912	0.968	21.071	0.149	0.149	0.000	0.000	0.000	0.000
12	A	12	TYR	0	-0.027	-0.003	17.332	-0.050	-0.050	0.000	0.000	0.000	0.000
13	A	13	SER	0	0.026	0.013	14.286	0.005	0.005	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.854	-0.913	16.131	-0.062	-0.062	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.031	0.016	14.190	0.033	0.033	0.000	0.000	0.000	0.000
16	A	16	VAL	0	-0.029	-0.008	8.330	-0.061	-0.061	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.013	0.009	8.264	0.102	0.102	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.020	-0.002	3.107	-1.016	-0.588	0.078	-0.127	-0.378	0.000
19	A	19	ASN	0	0.000	-0.001	2.841	-1.815	-0.959	2.728	-1.187	-2.397	0.003
20	A	20	GLY	0	-0.004	0.002	4.301	-1.433	-1.217	0.003	-0.087	-0.133	0.000
21	A	21	LEU	0	0.014	0.021	5.360	-0.579	-0.579	0.000	0.000	0.000	0.000
22	A	22	ILE	0	-0.022	-0.017	7.986	-0.080	-0.080	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.021	-0.006	6.665	-0.066	-0.066	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.018	0.007	11.597	-0.040	-0.040	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.049	-0.034	15.278	-0.048	-0.048	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.062	-0.018	17.449	0.035	0.035	0.000	0.000	0.000	0.000
27	A	27	MET	0	-0.013	0.001	19.470	0.000	0.000	0.000	0.000	0.000	0.000
28	A	28	VAL	0	0.025	0.000	22.853	0.005	0.005	0.000	0.000	0.000	0.000
29	A	29	PRO	0	-0.015	-0.004	26.409	0.005	0.005	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.999	-0.987	27.668	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.109	-0.056	31.234	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.008	0.001	33.623	0.003	0.003	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-1.000	-1.009	36.242	0.004	0.004	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.014	-0.011	37.475	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	35	ALA	0	0.047	0.021	34.197	0.001	0.001	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.006	0.006	33.388	0.005	0.005	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.848	-0.917	33.896	0.033	0.033	0.000	0.000	0.000	0.000
38	A	38	GLN	0	0.008	0.002	31.691	0.002	0.002	0.000	0.000	0.000	0.000
39	A	39	THR	0	-0.001	-0.019	28.702	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	ALA	0	-0.004	-0.005	28.893	0.009	0.009	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.784	-0.881	29.716	0.044	0.044	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.028	0.011	24.641	0.007	0.007	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.019	-0.025	24.605	0.009	0.009	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.020	0.022	25.252	0.019	0.019	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.088	-0.058	24.118	0.009	0.009	0.000	0.000	0.000	0.000
46	A	46	ILE	0	0.003	-0.006	19.954	0.014	0.014	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.863	-0.936	21.013	0.210	0.210	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.908	0.953	22.283	-0.045	-0.045	0.000	0.000	0.000	0.000
49	A	49	TRP	0	0.042	0.011	18.364	0.015	0.015	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.002	0.002	16.578	0.042	0.042	0.000	0.000	0.000	0.000
51	A	51	ALA	0	-0.014	-0.003	17.430	0.067	0.067	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.952	-0.970	17.643	0.198	0.198	0.000	0.000	0.000	0.000
53	A	53	CYS	0	-0.095	-0.028	13.259	0.013	0.013	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.049	-0.027	13.569	0.162	0.162	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.031	-0.045	15.013	0.052	0.052	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.773	-0.877	16.979	0.360	0.360	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.959	0.970	19.296	-0.156	-0.156	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.052	-0.003	21.357	-0.010	-0.010	0.000	0.000	0.000	0.000
59	A	59	HIS	0	-0.086	-0.060	16.395	0.056	0.056	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.038	0.026	15.860	0.060	0.060	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.051	-0.026	11.512	0.005	0.005	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.919	-0.969	14.990	0.102	0.102	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.021	0.012	16.739	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.014	0.007	18.346	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	65	ILE	0	0.006	-0.019	20.882	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	66	TYR	0	0.001	-0.004	20.640	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	67	LEU	0	0.041	0.009	26.161	0.003	0.003	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.929	0.976	29.886	0.021	0.021	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.873	-0.939	32.288	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	70	MET	0	-0.016	-0.010	30.138	0.009	0.009	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.046	-0.029	34.432	0.006	0.006	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.811	-0.896	34.491	0.018	0.018	0.000	0.000	0.000	0.000
73	A	73	TYR	0	-0.037	-0.021	29.988	0.009	0.009	0.000	0.000	0.000	0.000
74	A	74	ALA	0	-0.012	-0.019	33.513	0.007	0.007	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.826	-0.911	35.689	0.038	0.038	0.000	0.000	0.000	0.000
76	A	76	MET	0	-0.013	0.012	29.201	0.009	0.009	0.000	0.000	0.000	0.000
77	A	77	ASN	0	0.043	-0.001	30.648	0.013	0.013	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.016	0.023	32.137	0.009	0.009	0.000	0.000	0.000	0.000
79	A	79	VAL	0	-0.044	-0.014	30.823	0.007	0.007	0.000	0.000	0.000	0.000
80	A	80	TRP	0	0.015	-0.005	22.278	0.010	0.010	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.907	-0.973	28.727	0.117	0.117	0.000	0.000	0.000	0.000
82	A	82	ALA	0	-0.072	-0.026	30.929	0.010	0.010	0.000	0.000	0.000	0.000
83	A	83	TRP	0	-0.064	-0.018	22.039	0.010	0.010	0.000	0.000	0.000	0.000
84	A	84	VAL	0	0.010	0.010	24.806	0.021	0.021	0.000	0.000	0.000	0.000
85	A	85	ALA	0	0.001	0.005	24.348	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.053	0.019	26.107	0.006	0.006	0.000	0.000	0.000	0.000
87	A	87	GLY	0	-0.048	-0.028	27.376	0.012	0.012	0.000	0.000	0.000	0.000
88	A	88	ARG	1	0.803	0.886	19.857	-0.407	-0.407	0.000	0.000	0.000	0.000
89	A	89	THR	0	0.009	0.018	22.502	0.006	0.006	0.000	0.000	0.000	0.000
90	A	90	PRO	0	-0.002	0.012	19.340	0.014	0.014	0.000	0.000	0.000	0.000
91	A	91	ALA	0	-0.011	-0.004	18.157	-0.026	-0.026	0.000	0.000	0.000	0.000
92	A	92	ARG	1	0.885	0.934	20.052	-0.100	-0.100	0.000	0.000	0.000	0.000
93	A	93	ALA	0	-0.004	0.006	21.784	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	94	CYS	0	-0.068	-0.016	23.403	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	95	VAL	0	0.002	0.003	25.246	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.857	-0.921	27.556	-0.011	-0.011	0.000	0.000	0.000	0.000
97	A	97	ALA	0	-0.013	-0.008	27.095	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.907	0.950	29.186	0.041	0.041	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.037	0.029	26.457	-0.008	-0.008	0.000	0.000	0.000	0.000
100	A	100	ALA	0	-0.049	-0.024	27.545	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	101	ARG	1	0.945	0.988	29.546	0.048	0.048	0.000	0.000	0.000	0.000
102	A	102	PRO	0	-0.053	-0.038	32.758	0.004	0.004	0.000	0.000	0.000	0.000
103	A	103	GLU	-1	-0.874	-0.949	35.460	-0.028	-0.028	0.000	0.000	0.000	0.000
104	A	104	TRP	0	-0.012	0.008	27.530	0.001	0.001	0.000	0.000	0.000	0.000
105	A	105	ARG	1	0.880	0.899	32.422	-0.008	-0.008	0.000	0.000	0.000	0.000
106	A	106	VAL	0	-0.021	-0.006	27.441	0.001	0.001	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.853	-0.931	22.824	-0.068	-0.068	0.000	0.000	0.000	0.000
108	A	108	ILE	0	-0.021	-0.004	21.367	0.005	0.005	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.975	0.989	13.666	0.096	0.096	0.000	0.000	0.000	0.000
110	A	110	ILE	0	0.018	0.007	15.903	0.016	0.016	0.000	0.000	0.000	0.000
111	A	111	THR	0	-0.017	0.002	10.744	-0.058	-0.058	0.000	0.000	0.000	0.000
112	A	112	ALA	0	-0.002	-0.015	12.302	0.013	0.013	0.000	0.000	0.000	0.000
113	A	113	VAL	0	0.006	0.013	10.815	0.092	0.092	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.894	0.964	10.033	-1.490	-1.490	0.000	0.000	0.000	0.000
115	A	115	ARG	1	0.870	0.933	12.965	-0.448	-0.448	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.973	-0.979	13.285	1.282	1.282	0.000	0.000	0.000	0.000

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