FMO DATABASE

FMODB ID: YYLV2

Calculation Name: 3OKQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3OKQ

Chain ID: A

ChEMBL ID:

UniProt ID: P41697

Base Structure: X-ray

Registration Date: 2023-06-20

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-810811.495566
FMO2-HF: Nuclear repulsion	759019.07124
FMO2-HF: Total energy	-51792.424326
FMO2-MP2: Total energy	-51940.855267

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:553:SER)

Summations of interaction energy for fragment #1(A:553:SER)

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.
-11.374	-5.298	0.485	-2.899	-3.662	-0.004

Interaction energy analysis for fragmet #1(A:553:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.014

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	555	ASN	0	0.073	0.018	2.806	-6.567	-3.790	0.144	-1.554	-1.367	-0.004
4	A	556	ARG	1	0.853	0.915	5.373	0.557	0.639	-0.001	-0.003	-0.078	0.000
5	A	557	MET	0	0.002	0.002	3.142	0.048	1.573	0.206	-0.694	-1.036	0.003
6	A	558	TYR	0	-0.078	-0.072	2.609	-0.115	1.259	0.130	-0.559	-0.946	-0.003
7	A	559	MET	0	-0.002	0.032	3.714	0.780	0.929	0.007	-0.058	-0.098	0.000
8	A	560	GLU	-1	-0.883	-0.944	7.111	0.630	0.630	0.000	0.000	0.000	0.000
9	A	561	LYS	1	0.920	0.955	4.207	-5.511	-5.342	-0.001	-0.031	-0.137	0.000
10	A	562	SER	0	0.048	0.030	7.437	-0.120	-0.120	0.000	0.000	0.000	0.000
11	A	563	GLN	0	-0.021	-0.021	9.110	0.004	0.004	0.000	0.000	0.000	0.000
12	A	564	THR	0	-0.038	-0.019	11.145	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	565	GLU	-1	-0.920	-0.952	11.239	0.164	0.164	0.000	0.000	0.000	0.000
14	A	566	LEU	0	-0.036	-0.016	13.153	-0.053	-0.053	0.000	0.000	0.000	0.000
15	A	567	GLY	0	0.014	-0.001	15.363	-0.017	-0.017	0.000	0.000	0.000	0.000
16	A	568	ASP	-1	-0.832	-0.915	15.564	0.324	0.324	0.000	0.000	0.000	0.000
17	A	569	LEU	0	-0.064	-0.024	16.127	-0.025	-0.025	0.000	0.000	0.000	0.000
18	A	570	SER	0	-0.079	-0.043	19.181	-0.019	-0.019	0.000	0.000	0.000	0.000
19	A	571	ASP	-1	-0.896	-0.949	20.900	0.100	0.100	0.000	0.000	0.000	0.000
20	A	572	THR	0	-0.038	-0.022	21.174	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	573	LEU	0	-0.061	-0.031	23.527	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	574	LEU	0	0.016	0.005	25.228	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	575	SER	0	-0.007	0.012	26.754	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	576	LYS	1	0.934	0.970	25.304	-0.055	-0.055	0.000	0.000	0.000	0.000
25	A	577	VAL	0	-0.042	-0.024	29.421	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	578	ASP	-1	-0.856	-0.928	31.196	0.030	0.030	0.000	0.000	0.000	0.000
27	A	579	ASP	-1	-0.923	-0.957	32.445	0.052	0.052	0.000	0.000	0.000	0.000
28	A	580	LEU	0	-0.092	-0.057	32.744	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	581	GLN	0	-0.045	-0.032	35.025	0.000	0.000	0.000	0.000	0.000	0.000
30	A	582	ASP	-1	-0.903	-0.937	37.266	0.029	0.029	0.000	0.000	0.000	0.000
31	A	583	VAL	0	-0.037	-0.024	38.422	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	584	ILE	0	-0.009	-0.022	38.311	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	585	GLU	-1	-0.809	-0.886	41.554	0.002	0.002	0.000	0.000	0.000	0.000
34	A	586	ILE	0	-0.008	0.004	42.696	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	587	MET	0	-0.079	-0.034	43.236	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	588	ARG	1	0.848	0.911	42.935	0.001	0.001	0.000	0.000	0.000	0.000
37	A	589	LYS	1	0.949	0.982	47.409	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	590	ASP	-1	-0.813	-0.908	49.325	0.013	0.013	0.000	0.000	0.000	0.000
39	A	591	VAL	0	-0.058	-0.038	50.041	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	592	ALA	0	-0.050	-0.031	51.192	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	593	GLU	-1	-0.933	-0.960	53.016	0.008	0.008	0.000	0.000	0.000	0.000
42	A	594	ARG	1	0.840	0.927	52.999	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	595	ARG	1	0.890	0.955	55.503	0.002	0.002	0.000	0.000	0.000	0.000
44	A	596	SER	0	-0.021	-0.001	53.322	0.000	0.000	0.000	0.000	0.000	0.000
45	A	597	GLN	0	-0.029	-0.025	51.845	0.000	0.000	0.000	0.000	0.000	0.000
46	A	598	PRO	0	0.077	0.042	46.960	0.002	0.002	0.000	0.000	0.000	0.000
47	A	599	ALA	0	-0.003	-0.007	47.662	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	600	LYS	1	1.007	0.984	47.279	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	601	LYS	1	1.007	1.019	41.489	-0.024	-0.024	0.000	0.000	0.000	0.000
50	A	602	LYS	1	0.898	0.943	42.256	-0.024	-0.024	0.000	0.000	0.000	0.000
51	A	603	LEU	0	0.034	0.017	42.320	0.000	0.000	0.000	0.000	0.000	0.000
52	A	604	GLU	-1	-0.895	-0.944	42.271	0.005	0.005	0.000	0.000	0.000	0.000
53	A	605	THR	0	-0.074	-0.071	38.604	0.000	0.000	0.000	0.000	0.000	0.000
54	A	606	VAL	0	0.076	0.050	37.615	0.001	0.001	0.000	0.000	0.000	0.000
55	A	607	SER	0	0.013	0.014	37.571	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	608	LYS	1	0.945	0.979	35.666	-0.020	-0.020	0.000	0.000	0.000	0.000
57	A	609	ASP	-1	-0.909	-0.949	33.382	0.022	0.022	0.000	0.000	0.000	0.000
58	A	610	LEU	0	-0.036	-0.024	32.720	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	611	GLU	-1	-0.952	-0.967	33.111	-0.026	-0.026	0.000	0.000	0.000	0.000
60	A	612	ASN	0	-0.033	-0.033	29.544	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	613	ALA	0	0.043	0.033	28.467	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	614	GLN	0	-0.018	-0.012	28.385	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	615	ALA	0	-0.007	-0.004	27.350	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	616	ASP	-1	-0.911	-0.963	24.329	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	617	VAL	0	0.001	-0.003	23.607	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	618	LEU	0	-0.055	-0.024	24.396	-0.014	-0.014	0.000	0.000	0.000	0.000
67	A	619	LYS	1	0.999	0.997	20.729	0.028	0.028	0.000	0.000	0.000	0.000
68	A	620	LEU	0	0.003	0.016	19.098	-0.018	-0.018	0.000	0.000	0.000	0.000
69	A	621	GLN	0	-0.055	-0.032	19.639	0.000	0.000	0.000	0.000	0.000	0.000
70	A	622	GLU	-1	-0.934	-0.972	19.756	-0.204	-0.204	0.000	0.000	0.000	0.000
71	A	623	PHE	0	0.010	0.016	11.702	-0.072	-0.072	0.000	0.000	0.000	0.000
72	A	624	ILE	0	-0.008	-0.010	15.483	-0.066	-0.066	0.000	0.000	0.000	0.000
73	A	625	ASP	-1	-0.925	-0.968	16.938	-0.302	-0.302	0.000	0.000	0.000	0.000
74	A	626	THR	0	-0.102	-0.051	14.986	-0.065	-0.065	0.000	0.000	0.000	0.000
75	A	627	GLU	-1	-0.788	-0.855	10.194	-0.920	-0.920	0.000	0.000	0.000	0.000
76	A	628	LYS	1	0.950	0.983	12.714	0.187	0.187	0.000	0.000	0.000	0.000
77	A	629	PRO	0	-0.062	-0.045	15.121	-0.030	-0.030	0.000	0.000	0.000	0.000
78	A	630	HIS	0	0.022	0.009	6.767	0.362	0.362	0.000	0.000	0.000	0.000
79	A	631	TRP	0	0.025	-0.002	9.423	-0.060	-0.060	0.000	0.000	0.000	0.000
80	A	632	LYS	1	0.935	0.954	12.100	0.434	0.434	0.000	0.000	0.000	0.000
81	A	633	LYS	1	0.996	1.007	13.137	0.795	0.795	0.000	0.000	0.000	0.000
82	A	634	THR	0	-0.038	-0.008	8.883	-0.173	-0.173	0.000	0.000	0.000	0.000
83	A	635	TRP	0	-0.014	-0.023	11.582	0.068	0.068	0.000	0.000	0.000	0.000
84	A	636	GLU	-1	-0.933	-0.966	14.431	-0.467	-0.467	0.000	0.000	0.000	0.000
85	A	637	ALA	0	0.012	0.018	13.158	0.046	0.046	0.000	0.000	0.000	0.000
86	A	638	GLU	-1	-0.887	-0.931	11.087	-0.620	-0.620	0.000	0.000	0.000	0.000
87	A	639	LEU	0	-0.016	-0.024	15.209	0.084	0.084	0.000	0.000	0.000	0.000
88	A	640	ASP	-1	-0.878	-0.929	18.528	-0.347	-0.347	0.000	0.000	0.000	0.000
89	A	641	LYS	1	0.845	0.923	17.293	0.299	0.299	0.000	0.000	0.000	0.000
90	A	642	VAL	0	0.002	-0.002	18.302	0.047	0.047	0.000	0.000	0.000	0.000
91	A	643	CYS	0	-0.013	-0.004	20.787	0.039	0.039	0.000	0.000	0.000	0.000
92	A	644	GLU	-1	-0.947	-0.973	22.689	-0.239	-0.239	0.000	0.000	0.000	0.000
93	A	645	GLU	-1	-0.929	-0.958	20.357	-0.153	-0.153	0.000	0.000	0.000	0.000
94	A	646	GLN	0	-0.025	-0.020	24.457	0.014	0.014	0.000	0.000	0.000	0.000
95	A	647	GLN	0	0.030	0.008	26.789	0.007	0.007	0.000	0.000	0.000	0.000
96	A	648	PHE	0	-0.022	0.000	27.268	0.012	0.012	0.000	0.000	0.000	0.000
97	A	649	LEU	0	-0.019	-0.012	28.543	0.011	0.011	0.000	0.000	0.000	0.000
98	A	650	THR	0	0.026	0.015	30.341	0.008	0.008	0.000	0.000	0.000	0.000
99	A	651	LEU	0	0.002	-0.001	31.403	0.005	0.005	0.000	0.000	0.000	0.000
100	A	652	GLN	0	-0.071	-0.032	31.504	0.013	0.013	0.000	0.000	0.000	0.000
101	A	653	GLU	-1	-0.964	-0.989	34.235	-0.035	-0.035	0.000	0.000	0.000	0.000
102	A	654	GLU	-1	-0.927	-0.971	36.459	-0.065	-0.065	0.000	0.000	0.000	0.000
103	A	655	LEU	0	0.019	0.024	36.587	0.003	0.003	0.000	0.000	0.000	0.000
104	A	656	ILE	0	-0.053	-0.033	38.482	0.006	0.006	0.000	0.000	0.000	0.000
105	A	657	LEU	0	-0.051	-0.031	40.203	0.005	0.005	0.000	0.000	0.000	0.000
106	A	658	ASP	-1	-0.811	-0.897	42.380	-0.045	-0.045	0.000	0.000	0.000	0.000
107	A	659	LEU	0	-0.044	-0.021	40.135	0.003	0.003	0.000	0.000	0.000	0.000
108	A	660	LYS	1	0.873	0.935	42.462	0.017	0.017	0.000	0.000	0.000	0.000
109	A	661	GLU	-1	-0.941	-0.956	46.136	-0.030	-0.030	0.000	0.000	0.000	0.000
110	A	662	ASP	-1	-0.892	-0.953	47.021	-0.034	-0.034	0.000	0.000	0.000	0.000
111	A	663	LEU	0	-0.086	-0.049	46.926	0.002	0.002	0.000	0.000	0.000	0.000
112	A	664	GLY	0	0.009	0.001	49.420	0.002	0.002	0.000	0.000	0.000	0.000
113	A	665	LYS	1	0.987	0.987	51.878	0.027	0.027	0.000	0.000	0.000	0.000
114	A	666	ALA	0	-0.013	0.006	52.152	0.001	0.001	0.000	0.000	0.000	0.000
115	A	667	LEU	0	-0.026	-0.023	52.250	0.001	0.001	0.000	0.000	0.000	0.000
116	A	668	GLU	-1	-0.912	-0.941	55.215	-0.015	-0.015	0.000	0.000	0.000	0.000
117	A	669	THR	0	-0.036	-0.020	57.313	0.000	0.000	0.000	0.000	0.000	0.000
118	A	670	PHE	0	-0.039	-0.032	57.179	0.001	0.001	0.000	0.000	0.000	0.000
119	A	671	ASP	-1	-0.895	-0.954	59.113	-0.007	-0.007	0.000	0.000	0.000	0.000
120	A	672	LEU	0	-0.006	-0.009	61.258	0.001	0.001	0.000	0.000	0.000	0.000
121	A	673	ILE	0	-0.024	-0.004	60.200	0.000	0.000	0.000	0.000	0.000	0.000
122	A	674	LYS	1	0.918	0.948	60.518	0.007	0.007	0.000	0.000	0.000	0.000
123	A	675	LEU	0	-0.043	-0.004	64.703	0.001	0.001	0.000	0.000	0.000	0.000
124	A	676	CYS	0	-0.086	-0.038	67.007	0.000	0.000	0.000	0.000	0.000	0.000
125	A	677	CYS	0	-0.092	-0.025	66.621	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:553:SER)