FMO DATABASE

FMODB ID: ZYK4N

Calculation Name: 3KF6-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KF6

Chain ID: B

ChEMBL ID:

UniProt ID: Q0E7J7

Base Structure: X-ray

Registration Date: 2023-06-19

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	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	105
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-798686.457292
FMO2-HF: Nuclear repulsion	757058.798299
FMO2-HF: Total energy	-41627.658993
FMO2-MP2: Total energy	-41747.36455

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:498:PRO)

Summations of interaction energy for fragment #1(B:498:PRO)

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.
-0.233	2.551	0.039	-1.27	-1.553	0.003

Interaction energy analysis for fragmet #1(B:498:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.080 / q_NPA : 0.022

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	B	500	GLY	0	0.023	0.025	2.659	-1.161	1.413	0.041	-1.244	-1.372	0.003
4	B	501	SER	0	0.012	-0.015	4.661	-0.085	-0.033	-0.001	-0.007	-0.043	0.000
5	B	502	ASP	-1	-0.779	-0.840	7.469	-0.460	-0.460	0.000	0.000	0.000	0.000
6	B	503	SER	0	0.042	0.023	9.459	-0.115	-0.115	0.000	0.000	0.000	0.000
7	B	504	ALA	0	-0.030	-0.014	11.851	-0.001	-0.001	0.000	0.000	0.000	0.000
8	B	505	LYS	1	0.864	0.914	13.222	0.184	0.184	0.000	0.000	0.000	0.000
9	B	506	LEU	0	-0.056	-0.020	16.889	-0.023	-0.023	0.000	0.000	0.000	0.000
10	B	507	ILE	0	-0.003	-0.009	18.510	0.022	0.022	0.000	0.000	0.000	0.000
11	B	508	PHE	0	0.007	0.010	20.595	-0.012	-0.012	0.000	0.000	0.000	0.000
12	B	509	ILE	0	0.058	0.018	20.220	-0.004	-0.004	0.000	0.000	0.000	0.000
13	B	510	ASN	0	-0.054	-0.039	22.138	0.002	0.002	0.000	0.000	0.000	0.000
14	B	511	GLN	0	0.120	0.065	22.921	-0.003	-0.003	0.000	0.000	0.000	0.000
15	B	512	ILE	0	-0.018	0.003	18.271	-0.002	-0.002	0.000	0.000	0.000	0.000
16	B	513	ASN	0	0.005	-0.012	20.926	-0.014	-0.014	0.000	0.000	0.000	0.000
17	B	514	ASP	-1	-0.858	-0.903	23.403	-0.088	-0.088	0.000	0.000	0.000	0.000
18	B	515	CYS	0	-0.131	-0.043	18.951	0.004	0.004	0.000	0.000	0.000	0.000
19	B	516	LYS	1	0.980	0.981	18.614	0.068	0.068	0.000	0.000	0.000	0.000
20	B	517	ASP	-1	-0.773	-0.884	16.786	-0.156	-0.156	0.000	0.000	0.000	0.000
21	B	518	GLY	0	-0.008	-0.009	12.615	0.026	0.026	0.000	0.000	0.000	0.000
22	B	519	GLN	0	0.004	0.005	12.045	-0.035	-0.035	0.000	0.000	0.000	0.000
23	B	520	LYS	1	0.825	0.907	6.615	0.808	0.808	0.000	0.000	0.000	0.000
24	B	521	LEU	0	-0.026	-0.018	12.005	0.069	0.069	0.000	0.000	0.000	0.000
25	B	522	ARG	1	0.920	0.941	12.976	0.183	0.183	0.000	0.000	0.000	0.000
26	B	523	PHE	0	0.016	0.005	14.941	0.041	0.041	0.000	0.000	0.000	0.000
27	B	524	LEU	0	-0.019	0.000	17.007	-0.021	-0.021	0.000	0.000	0.000	0.000
28	B	525	GLY	0	0.035	0.007	19.702	0.011	0.011	0.000	0.000	0.000	0.000
29	B	526	CYS	0	-0.057	-0.005	21.102	-0.004	-0.004	0.000	0.000	0.000	0.000
30	B	527	VAL	0	0.035	0.017	20.434	0.001	0.001	0.000	0.000	0.000	0.000
31	B	528	GLN	0	0.014	0.013	22.956	0.014	0.014	0.000	0.000	0.000	0.000
32	B	529	SER	0	-0.044	-0.051	23.524	0.015	0.015	0.000	0.000	0.000	0.000
33	B	530	TYR	0	0.041	0.015	17.208	-0.017	-0.017	0.000	0.000	0.000	0.000
34	B	531	LYS	1	0.995	1.000	21.517	0.120	0.120	0.000	0.000	0.000	0.000
35	B	532	ASN	0	0.004	0.000	21.208	-0.007	-0.007	0.000	0.000	0.000	0.000
36	B	533	GLY	0	0.082	0.054	17.076	0.000	0.000	0.000	0.000	0.000	0.000
37	B	534	ILE	0	-0.034	-0.011	16.312	-0.027	-0.027	0.000	0.000	0.000	0.000
38	B	535	LEU	0	0.010	-0.005	16.294	0.021	0.021	0.000	0.000	0.000	0.000
39	B	536	ARG	1	0.905	0.957	18.739	0.115	0.115	0.000	0.000	0.000	0.000
40	B	537	LEU	0	0.010	0.008	17.217	0.007	0.007	0.000	0.000	0.000	0.000
41	B	538	ILE	0	-0.017	-0.030	21.520	0.005	0.005	0.000	0.000	0.000	0.000
42	B	539	ASP	-1	-0.858	-0.935	24.216	-0.129	-0.129	0.000	0.000	0.000	0.000
43	B	540	GLY	0	0.014	0.024	26.079	0.005	0.005	0.000	0.000	0.000	0.000
44	B	541	SER	0	-0.014	-0.010	29.714	-0.002	-0.002	0.000	0.000	0.000	0.000
45	B	542	SER	0	-0.043	-0.011	25.940	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	543	SER	0	-0.025	-0.031	24.048	-0.001	-0.001	0.000	0.000	0.000	0.000
47	B	544	VAL	0	0.019	0.017	18.365	0.003	0.003	0.000	0.000	0.000	0.000
48	B	545	THR	0	-0.033	-0.005	19.025	0.002	0.002	0.000	0.000	0.000	0.000
49	B	546	CYS	0	-0.027	-0.016	14.747	-0.016	-0.016	0.000	0.000	0.000	0.000
50	B	547	ASP	-1	-0.762	-0.845	13.112	-0.277	-0.277	0.000	0.000	0.000	0.000
51	B	548	VAL	0	-0.005	-0.023	11.681	-0.065	-0.065	0.000	0.000	0.000	0.000
52	B	549	THR	0	-0.012	-0.023	12.448	0.003	0.003	0.000	0.000	0.000	0.000
53	B	550	VAL	0	-0.007	-0.008	7.248	0.023	0.023	0.000	0.000	0.000	0.000
54	B	551	VAL	0	-0.074	-0.029	7.743	-0.072	-0.072	0.000	0.000	0.000	0.000
55	B	552	LEU	0	0.009	0.001	9.647	0.038	0.038	0.000	0.000	0.000	0.000
56	B	553	PRO	0	-0.053	-0.021	13.326	-0.004	-0.004	0.000	0.000	0.000	0.000
57	B	554	ASP	-1	-0.919	-0.943	14.724	-0.227	-0.227	0.000	0.000	0.000	0.000
58	B	555	VAL	0	-0.013	-0.008	16.611	0.029	0.029	0.000	0.000	0.000	0.000
59	B	556	SER	0	-0.024	-0.022	19.094	-0.014	-0.014	0.000	0.000	0.000	0.000
60	B	557	ILE	0	-0.006	0.011	17.287	-0.002	-0.002	0.000	0.000	0.000	0.000
61	B	558	GLN	0	-0.024	-0.007	21.494	0.016	0.016	0.000	0.000	0.000	0.000
62	B	559	LYS	1	0.864	0.917	24.354	0.094	0.094	0.000	0.000	0.000	0.000
63	B	560	HIS	0	0.026	-0.006	25.800	0.011	0.011	0.000	0.000	0.000	0.000
64	B	561	GLU	-1	-0.831	-0.898	21.377	-0.170	-0.170	0.000	0.000	0.000	0.000
65	B	562	TRP	0	-0.005	-0.017	22.297	-0.009	-0.009	0.000	0.000	0.000	0.000
66	B	563	LEU	0	0.024	0.016	16.824	-0.006	-0.006	0.000	0.000	0.000	0.000
67	B	564	ASN	0	-0.003	-0.006	15.449	0.011	0.011	0.000	0.000	0.000	0.000
68	B	565	ILE	0	0.022	0.008	12.518	-0.031	-0.031	0.000	0.000	0.000	0.000
69	B	566	VAL	0	0.012	0.000	9.367	0.047	0.047	0.000	0.000	0.000	0.000
70	B	567	GLY	0	0.063	0.026	9.037	-0.116	-0.116	0.000	0.000	0.000	0.000
71	B	568	ARG	1	0.789	0.874	6.538	0.814	0.814	0.000	0.000	0.000	0.000
72	B	569	LYS	1	0.744	0.879	11.422	0.151	0.151	0.000	0.000	0.000	0.000
73	B	570	ARG	1	0.790	0.859	13.163	0.276	0.276	0.000	0.000	0.000	0.000
74	B	571	GLN	0	0.041	0.007	15.618	0.027	0.027	0.000	0.000	0.000	0.000
75	B	572	ASP	-1	-0.837	-0.908	19.340	-0.126	-0.126	0.000	0.000	0.000	0.000
76	B	573	GLY	0	-0.016	-0.009	21.572	0.002	0.002	0.000	0.000	0.000	0.000
77	B	574	ILE	0	-0.052	-0.020	15.608	-0.005	-0.005	0.000	0.000	0.000	0.000
78	B	575	VAL	0	0.008	-0.007	12.786	-0.003	-0.003	0.000	0.000	0.000	0.000
79	B	576	ASP	-1	-0.770	-0.841	9.861	-0.352	-0.352	0.000	0.000	0.000	0.000
80	B	577	VAL	0	-0.053	-0.032	9.727	-0.092	-0.092	0.000	0.000	0.000	0.000
81	B	578	LEU	0	-0.022	-0.008	4.182	-0.253	-0.095	-0.001	-0.019	-0.138	0.000
82	B	579	LEU	0	-0.033	-0.022	6.030	-0.057	-0.057	0.000	0.000	0.000	0.000
83	B	580	ILE	0	0.062	0.038	8.523	0.078	0.078	0.000	0.000	0.000	0.000
84	B	581	ARG	1	0.907	0.948	10.501	0.401	0.401	0.000	0.000	0.000	0.000
85	B	582	SER	0	0.059	0.044	14.917	0.012	0.012	0.000	0.000	0.000	0.000
86	B	583	ALA	0	-0.051	-0.028	18.641	0.001	0.001	0.000	0.000	0.000	0.000
87	B	584	VAL	0	0.044	0.016	20.899	0.015	0.015	0.000	0.000	0.000	0.000
88	B	585	GLY	0	0.017	0.009	23.993	0.002	0.002	0.000	0.000	0.000	0.000
89	B	586	ILE	0	-0.042	0.001	22.217	0.007	0.007	0.000	0.000	0.000	0.000
90	B	587	ASN	0	0.053	0.019	25.852	0.004	0.004	0.000	0.000	0.000	0.000
91	B	588	LEU	0	0.054	0.017	25.248	0.000	0.000	0.000	0.000	0.000	0.000
92	B	589	PRO	0	-0.014	-0.008	28.047	-0.001	-0.001	0.000	0.000	0.000	0.000
93	B	590	ARG	1	0.929	0.949	29.334	0.066	0.066	0.000	0.000	0.000	0.000
94	B	591	TYR	0	0.039	0.020	20.388	-0.004	-0.004	0.000	0.000	0.000	0.000
95	B	592	ARG	1	1.008	0.991	25.780	0.082	0.082	0.000	0.000	0.000	0.000
96	B	593	GLN	0	0.053	0.054	27.250	0.001	0.001	0.000	0.000	0.000	0.000
97	B	594	MET	0	0.031	0.003	25.873	0.004	0.004	0.000	0.000	0.000	0.000
98	B	595	VAL	0	-0.031	-0.004	22.339	0.000	0.000	0.000	0.000	0.000	0.000
99	B	596	SER	0	-0.024	-0.026	24.873	0.001	0.001	0.000	0.000	0.000	0.000
100	B	597	GLU	-1	-0.903	-0.961	27.967	-0.058	-0.058	0.000	0.000	0.000	0.000
101	B	598	ARG	1	0.910	0.951	19.491	0.114	0.114	0.000	0.000	0.000	0.000
102	B	599	GLN	0	-0.081	-0.028	22.872	0.009	0.009	0.000	0.000	0.000	0.000
103	B	600	LYS	1	0.911	0.959	25.944	0.068	0.068	0.000	0.000	0.000	0.000
104	B	601	CYS	0	-0.055	-0.006	28.496	0.006	0.006	0.000	0.000	0.000	0.000
105	B	602	ASP	-1	-0.949	-0.966	26.626	-0.043	-0.043	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:498:PRO)