FMO DATABASE

FMODB ID: 6YYJZ

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	OptHSide
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	-916417.833103
FMO2-HF: Nuclear repulsion	870648.698474
FMO2-HF: Total energy	-45769.134629
FMO2-MP2: Total energy	-45900.178767

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.
-5.219	-2.596	3.568	-2.141	-4.049	0.003

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 : -0.031 / q_NPA : -0.037

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	A	3	ILE	0	-0.043	-0.027	3.866	1.060	2.136	-0.001	-0.390	-0.685	0.002
4	A	4	ARG	1	0.896	0.959	6.166	-0.522	-0.522	0.000	0.000	0.000	0.000
5	A	5	TYR	0	0.015	-0.003	9.250	-0.012	-0.012	0.000	0.000	0.000	0.000
6	A	6	PHE	0	0.013	0.008	11.093	0.088	0.088	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.072	0.028	15.415	-0.028	-0.028	0.000	0.000	0.000	0.000
8	A	8	THR	0	-0.032	-0.021	15.785	-0.006	-0.006	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.025	0.026	18.344	0.016	0.016	0.000	0.000	0.000	0.000
10	A	10	PRO	0	-0.019	-0.035	19.711	-0.033	-0.033	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.903	0.961	20.999	0.138	0.138	0.000	0.000	0.000	0.000
12	A	12	TYR	0	-0.056	-0.032	17.299	-0.051	-0.051	0.000	0.000	0.000	0.000
13	A	13	SER	0	0.043	0.013	14.308	-0.021	-0.021	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.833	-0.876	16.177	-0.018	-0.018	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.039	0.019	14.168	0.038	0.038	0.000	0.000	0.000	0.000
16	A	16	VAL	0	-0.018	-0.003	9.145	-0.074	-0.074	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.012	0.011	8.172	0.110	0.110	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.022	0.000	3.096	-1.096	-0.687	0.066	-0.120	-0.355	0.000
19	A	19	ASN	0	-0.005	-0.008	2.654	-2.988	-2.124	3.497	-1.500	-2.860	0.001
20	A	20	GLY	0	-0.007	0.002	4.211	-1.563	-1.289	0.006	-0.131	-0.149	0.000
21	A	21	LEU	0	0.010	0.022	5.367	-0.690	-0.690	0.000	0.000	0.000	0.000
22	A	22	ILE	0	-0.015	-0.016	8.187	-0.072	-0.072	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.017	-0.005	6.312	-0.069	-0.069	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.021	0.013	11.625	-0.048	-0.048	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.049	-0.039	15.296	-0.050	-0.050	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.039	-0.012	17.408	0.037	0.037	0.000	0.000	0.000	0.000
27	A	27	MET	0	-0.043	-0.003	19.352	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	28	VAL	0	0.028	0.001	22.852	0.004	0.004	0.000	0.000	0.000	0.000
29	A	29	PRO	0	0.000	0.007	26.386	0.005	0.005	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.977	-0.989	28.206	0.024	0.024	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.105	-0.063	31.286	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.021	0.007	33.644	0.004	0.004	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.999	-0.999	36.243	0.012	0.012	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.048	-0.051	37.469	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	35	ALA	0	0.035	0.014	34.164	0.002	0.002	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.007	-0.002	33.419	0.006	0.006	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.824	-0.890	33.954	0.047	0.047	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.005	-0.007	31.736	0.003	0.003	0.000	0.000	0.000	0.000
39	A	39	THR	0	0.003	-0.015	28.795	0.004	0.004	0.000	0.000	0.000	0.000
40	A	40	ALA	0	-0.006	-0.005	28.955	0.011	0.011	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.764	-0.862	29.800	0.063	0.063	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.043	0.018	24.700	0.008	0.008	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.019	-0.022	24.647	0.012	0.012	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.012	0.015	25.357	0.021	0.021	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.086	-0.062	24.188	0.012	0.012	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.002	-0.008	20.176	0.018	0.018	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.846	-0.926	21.085	0.256	0.256	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.877	0.953	22.183	-0.059	-0.059	0.000	0.000	0.000	0.000
49	A	49	TRP	0	0.001	-0.014	18.283	0.021	0.021	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.007	0.007	16.509	0.048	0.048	0.000	0.000	0.000	0.000
51	A	51	ALA	0	-0.017	-0.003	17.332	0.072	0.072	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.935	-0.969	17.552	0.227	0.227	0.000	0.000	0.000	0.000
53	A	53	CYS	0	-0.102	-0.038	13.186	0.013	0.013	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.044	-0.019	13.479	0.167	0.167	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.034	-0.050	14.886	0.053	0.053	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.768	-0.868	16.878	0.404	0.404	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.936	0.965	19.489	-0.174	-0.174	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.044	-0.003	21.538	-0.009	-0.009	0.000	0.000	0.000	0.000
59	A	59	HIS	0	-0.091	-0.058	16.679	0.059	0.059	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.042	0.028	16.061	0.074	0.074	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.047	-0.022	11.735	0.003	0.003	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.889	-0.944	14.720	0.156	0.156	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.017	0.023	16.822	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.010	0.004	18.247	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	65	ILE	0	0.016	-0.013	20.880	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	66	TYR	0	0.011	0.002	20.303	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	67	LEU	0	0.043	0.013	26.117	0.003	0.003	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.910	0.968	29.848	0.009	0.009	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.847	-0.924	32.224	0.009	0.009	0.000	0.000	0.000	0.000
70	A	70	MET	0	-0.001	0.000	30.027	0.009	0.009	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.031	-0.015	34.378	0.006	0.006	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.804	-0.874	34.198	0.030	0.030	0.000	0.000	0.000	0.000
73	A	73	TYR	0	-0.006	-0.011	29.812	0.010	0.010	0.000	0.000	0.000	0.000
74	A	74	ALA	0	-0.016	-0.021	33.549	0.007	0.007	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.820	-0.906	35.748	0.052	0.052	0.000	0.000	0.000	0.000
76	A	76	MET	0	-0.007	0.016	29.199	0.010	0.010	0.000	0.000	0.000	0.000
77	A	77	ASN	0	0.031	0.000	30.763	0.016	0.016	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.031	0.029	32.226	0.009	0.009	0.000	0.000	0.000	0.000
79	A	79	VAL	0	-0.052	-0.015	30.996	0.007	0.007	0.000	0.000	0.000	0.000
80	A	80	TRP	0	0.018	-0.005	22.395	0.012	0.012	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.902	-0.972	28.846	0.141	0.141	0.000	0.000	0.000	0.000
82	A	82	ALA	0	-0.071	-0.023	31.050	0.010	0.010	0.000	0.000	0.000	0.000
83	A	83	TRP	0	-0.066	-0.031	22.168	0.011	0.011	0.000	0.000	0.000	0.000
84	A	84	VAL	0	0.018	0.011	24.851	0.023	0.023	0.000	0.000	0.000	0.000
85	A	85	ALA	0	0.006	0.012	24.516	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.053	0.019	26.297	0.007	0.007	0.000	0.000	0.000	0.000
87	A	87	GLY	0	-0.047	-0.027	27.581	0.012	0.012	0.000	0.000	0.000	0.000
88	A	88	ARG	1	0.789	0.876	20.234	-0.456	-0.456	0.000	0.000	0.000	0.000
89	A	89	THR	0	0.013	0.023	22.688	0.009	0.009	0.000	0.000	0.000	0.000
90	A	90	PRO	0	-0.006	0.011	19.427	0.014	0.014	0.000	0.000	0.000	0.000
91	A	91	ALA	0	-0.009	-0.008	18.217	-0.032	-0.032	0.000	0.000	0.000	0.000
92	A	92	ARG	1	0.861	0.917	20.130	-0.127	-0.127	0.000	0.000	0.000	0.000
93	A	93	ALA	0	-0.006	0.007	21.710	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	94	CYS	0	-0.081	-0.026	23.409	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	95	VAL	0	0.027	0.011	25.166	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.881	-0.932	27.506	0.004	0.004	0.000	0.000	0.000	0.000
97	A	97	ALA	0	-0.022	-0.013	27.001	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.925	0.961	29.088	0.026	0.026	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.037	0.030	26.450	-0.008	-0.008	0.000	0.000	0.000	0.000
100	A	100	ALA	0	-0.044	-0.022	27.417	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	101	ARG	1	0.882	0.940	29.432	0.025	0.025	0.000	0.000	0.000	0.000
102	A	102	PRO	0	-0.044	-0.040	32.662	0.005	0.005	0.000	0.000	0.000	0.000
103	A	103	GLU	-1	-0.797	-0.898	35.371	-0.017	-0.017	0.000	0.000	0.000	0.000
104	A	104	TRP	0	-0.049	-0.002	27.600	0.001	0.001	0.000	0.000	0.000	0.000
105	A	105	ARG	1	0.818	0.851	32.373	-0.023	-0.023	0.000	0.000	0.000	0.000
106	A	106	VAL	0	-0.026	-0.008	27.508	0.002	0.002	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.866	-0.938	22.536	-0.042	-0.042	0.000	0.000	0.000	0.000
108	A	108	ILE	0	-0.019	-0.002	21.402	0.005	0.005	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.970	0.988	13.345	0.005	0.005	0.000	0.000	0.000	0.000
110	A	110	ILE	0	0.007	0.003	16.082	0.018	0.018	0.000	0.000	0.000	0.000
111	A	111	THR	0	-0.052	-0.034	10.870	-0.048	-0.048	0.000	0.000	0.000	0.000
112	A	112	ALA	0	-0.001	-0.015	12.417	0.002	0.002	0.000	0.000	0.000	0.000
113	A	113	VAL	0	0.001	0.013	10.892	0.136	0.136	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.838	0.931	10.385	-1.743	-1.743	0.000	0.000	0.000	0.000
115	A	115	ARG	1	0.871	0.929	12.868	-0.490	-0.490	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.912	-0.950	12.787	1.482	1.482	0.000	0.000	0.000	0.000

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