FMO DATABASE

FMODB ID: ZY8ZN

Calculation Name: 2OKU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2OKU

Chain ID: A

ChEMBL ID:

UniProt ID: Q7MW70

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	OptAll
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	122
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1046874.18565
FMO2-HF: Nuclear repulsion	997198.568893
FMO2-HF: Total energy	-49675.616757
FMO2-MP2: Total energy	-49820.40615

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:443:GLN)

Summations of interaction energy for fragment #1(A:443:GLN)

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.
-15.393	-9.883	2.61	-3.443	-4.677	-0.002

Interaction energy analysis for fragmet #1(A:443:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.005

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	445	VAL	0	0.030	0.001	2.186	1.935	3.399	1.884	-1.281	-2.067	0.001
4	A	446	ALA	0	-0.053	-0.024	2.654	-3.291	-1.643	0.677	-0.783	-1.542	0.006
5	A	447	ALA	0	-0.022	-0.014	4.010	-2.252	-1.704	0.001	-0.194	-0.355	0.001
6	A	448	ILE	0	-0.006	0.009	5.970	-0.986	-0.986	0.000	0.000	0.000	0.000
7	A	449	ARG	1	1.007	1.017	7.763	-2.911	-2.911	0.000	0.000	0.000	0.000
8	A	450	HIS	0	0.027	0.025	9.310	-0.260	-0.260	0.000	0.000	0.000	0.000
9	A	451	ILE	0	0.006	0.018	11.810	-0.263	-0.263	0.000	0.000	0.000	0.000
10	A	452	THR	0	0.038	0.007	9.389	-0.056	-0.056	0.000	0.000	0.000	0.000
11	A	453	THR	0	-0.105	-0.061	12.444	-0.136	-0.136	0.000	0.000	0.000	0.000
12	A	454	GLY	0	0.051	0.033	14.840	-0.095	-0.095	0.000	0.000	0.000	0.000
13	A	455	THR	0	-0.063	-0.057	15.704	-0.076	-0.076	0.000	0.000	0.000	0.000
14	A	456	TYR	0	0.005	-0.008	15.216	-0.027	-0.027	0.000	0.000	0.000	0.000
15	A	457	ILE	0	0.002	0.011	19.041	-0.058	-0.058	0.000	0.000	0.000	0.000
16	A	458	ALA	0	0.032	0.028	21.183	-0.051	-0.051	0.000	0.000	0.000	0.000
17	A	459	ARG	1	0.838	0.882	22.325	-0.559	-0.559	0.000	0.000	0.000	0.000
18	A	460	ILE	0	-0.030	-0.016	22.789	-0.041	-0.041	0.000	0.000	0.000	0.000
19	A	461	ARG	1	0.779	0.842	23.718	-0.410	-0.410	0.000	0.000	0.000	0.000
20	A	462	GLU	-1	-0.925	-0.964	25.330	0.467	0.467	0.000	0.000	0.000	0.000
21	A	463	GLU	-1	-0.824	-0.872	27.329	0.421	0.421	0.000	0.000	0.000	0.000
22	A	464	TYR	0	-0.029	-0.016	24.385	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	465	GLN	0	-0.019	-0.034	29.450	-0.039	-0.039	0.000	0.000	0.000	0.000
24	A	466	GLN	0	-0.062	-0.030	31.550	-0.037	-0.037	0.000	0.000	0.000	0.000
25	A	467	THR	0	-0.062	-0.031	32.430	-0.010	-0.010	0.000	0.000	0.000	0.000
26	A	468	GLU	-1	-0.944	-0.955	35.029	0.164	0.164	0.000	0.000	0.000	0.000
27	A	469	VAL	0	-0.001	-0.003	36.179	0.003	0.003	0.000	0.000	0.000	0.000
28	A	470	LYS	1	0.902	0.949	39.425	-0.136	-0.136	0.000	0.000	0.000	0.000
29	A	471	PRO	0	0.009	-0.010	41.462	0.003	0.003	0.000	0.000	0.000	0.000
30	A	472	GLU	-1	-0.828	-0.908	42.374	0.126	0.126	0.000	0.000	0.000	0.000
31	A	473	LEU	0	-0.011	-0.006	35.911	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	474	GLN	0	-0.029	-0.020	37.322	0.015	0.015	0.000	0.000	0.000	0.000
33	A	475	PRO	0	0.037	0.010	37.046	0.007	0.007	0.000	0.000	0.000	0.000
34	A	476	MET	0	-0.062	-0.011	31.608	0.001	0.001	0.000	0.000	0.000	0.000
35	A	477	LYS	1	0.916	0.952	32.975	-0.212	-0.212	0.000	0.000	0.000	0.000
36	A	478	GLU	-1	-0.870	-0.911	32.319	0.169	0.169	0.000	0.000	0.000	0.000
37	A	479	ALA	0	-0.068	-0.037	32.398	0.004	0.004	0.000	0.000	0.000	0.000
38	A	480	LEU	0	0.015	0.010	28.122	0.004	0.004	0.000	0.000	0.000	0.000
39	A	481	ALA	0	0.031	0.033	27.693	0.025	0.025	0.000	0.000	0.000	0.000
40	A	482	ARG	1	0.960	0.979	27.602	-0.140	-0.140	0.000	0.000	0.000	0.000
41	A	483	MET	0	-0.029	0.002	25.437	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	484	THR	0	0.006	-0.003	23.226	0.029	0.029	0.000	0.000	0.000	0.000
43	A	485	ASP	-1	-0.859	-0.923	22.900	0.302	0.302	0.000	0.000	0.000	0.000
44	A	486	ARG	1	0.698	0.807	23.606	-0.120	-0.120	0.000	0.000	0.000	0.000
45	A	487	ALA	0	0.030	0.006	19.462	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	488	GLU	-1	-0.807	-0.873	18.880	0.434	0.434	0.000	0.000	0.000	0.000
47	A	489	ALA	0	0.023	0.012	19.300	0.008	0.008	0.000	0.000	0.000	0.000
48	A	490	LEU	0	-0.061	-0.013	17.403	-0.042	-0.042	0.000	0.000	0.000	0.000
49	A	491	ILE	0	0.005	-0.005	13.798	-0.017	-0.017	0.000	0.000	0.000	0.000
50	A	492	ALA	0	0.009	0.028	15.073	0.018	0.018	0.000	0.000	0.000	0.000
51	A	493	PHE	0	0.011	0.011	17.113	-0.015	-0.015	0.000	0.000	0.000	0.000
52	A	494	VAL	0	0.008	0.018	12.046	-0.051	-0.051	0.000	0.000	0.000	0.000
53	A	495	THR	0	-0.036	-0.040	11.294	-0.019	-0.019	0.000	0.000	0.000	0.000
54	A	496	GLU	-1	-0.921	-0.965	13.570	0.241	0.241	0.000	0.000	0.000	0.000
55	A	497	GLN	0	-0.055	-0.038	15.241	-0.071	-0.071	0.000	0.000	0.000	0.000
56	A	498	LYS	1	0.813	0.902	12.909	-0.235	-0.235	0.000	0.000	0.000	0.000
57	A	499	ASP	-1	-0.805	-0.889	11.946	-0.504	-0.504	0.000	0.000	0.000	0.000
58	A	500	GLN	0	-0.013	-0.037	4.825	0.603	0.603	0.000	0.000	0.000	0.000
59	A	501	GLU	-1	-0.852	-0.901	7.399	-1.813	-1.813	0.000	0.000	0.000	0.000
60	A	502	LEU	0	-0.010	-0.008	9.349	-0.092	-0.092	0.000	0.000	0.000	0.000
61	A	503	LEU	0	-0.027	-0.010	7.145	0.090	0.090	0.000	0.000	0.000	0.000
62	A	504	ASP	-1	-0.806	-0.911	3.179	-6.256	-4.406	0.048	-1.185	-0.713	-0.010
63	A	505	PHE	0	-0.024	-0.001	6.347	0.047	0.047	0.000	0.000	0.000	0.000
64	A	506	GLN	0	0.048	0.017	9.920	0.110	0.110	0.000	0.000	0.000	0.000
65	A	507	ALA	0	0.002	0.012	7.377	0.188	0.188	0.000	0.000	0.000	0.000
66	A	508	ARG	1	0.936	0.959	9.463	0.389	0.389	0.000	0.000	0.000	0.000
67	A	509	ARG	1	0.934	0.980	11.315	0.409	0.409	0.000	0.000	0.000	0.000
68	A	510	LEU	0	0.055	0.033	11.372	0.050	0.050	0.000	0.000	0.000	0.000
69	A	511	VAL	0	-0.028	-0.001	10.908	0.086	0.086	0.000	0.000	0.000	0.000
70	A	512	GLU	-1	-0.919	-0.972	14.159	0.074	0.074	0.000	0.000	0.000	0.000
71	A	513	MET	0	-0.034	0.014	16.868	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	514	THR	0	0.007	-0.003	16.286	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	515	ALA	0	-0.024	-0.011	17.463	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	516	HIS	0	0.010	0.005	19.384	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	517	ALA	0	0.021	0.024	22.302	-0.021	-0.021	0.000	0.000	0.000	0.000
76	A	518	VAL	0	-0.003	0.003	20.083	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	519	PHE	0	-0.011	-0.024	19.208	-0.012	-0.012	0.000	0.000	0.000	0.000
78	A	520	GLY	0	0.045	0.022	24.530	-0.022	-0.022	0.000	0.000	0.000	0.000
79	A	521	HIS	0	0.033	0.002	26.101	-0.031	-0.031	0.000	0.000	0.000	0.000
80	A	522	LEU	0	-0.028	-0.007	23.933	-0.010	-0.010	0.000	0.000	0.000	0.000
81	A	523	LEU	0	-0.017	-0.012	28.219	-0.019	-0.019	0.000	0.000	0.000	0.000
82	A	524	MET	0	-0.015	-0.006	30.589	-0.019	-0.019	0.000	0.000	0.000	0.000
83	A	525	LEU	0	-0.018	-0.010	29.453	-0.010	-0.010	0.000	0.000	0.000	0.000
84	A	526	ALA	0	0.047	0.026	32.503	-0.013	-0.013	0.000	0.000	0.000	0.000
85	A	527	ALA	0	-0.042	-0.023	34.316	-0.014	-0.014	0.000	0.000	0.000	0.000
86	A	528	ASN	0	-0.024	-0.026	36.212	-0.020	-0.020	0.000	0.000	0.000	0.000
87	A	529	ASP	-1	-0.962	-0.964	35.613	0.212	0.212	0.000	0.000	0.000	0.000
88	A	530	ASP	-1	-0.868	-0.920	38.610	0.126	0.126	0.000	0.000	0.000	0.000
89	A	531	ASP	-1	-0.762	-0.850	39.351	0.132	0.132	0.000	0.000	0.000	0.000
90	A	532	SER	0	-0.071	-0.053	41.056	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	533	PHE	0	-0.050	-0.022	35.901	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	534	ARG	1	0.791	0.862	36.609	-0.122	-0.122	0.000	0.000	0.000	0.000
93	A	535	GLN	0	0.003	0.005	37.051	0.001	0.001	0.000	0.000	0.000	0.000
94	A	536	SER	0	0.012	-0.010	35.131	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	537	ALA	0	0.032	0.017	32.693	0.002	0.002	0.000	0.000	0.000	0.000
96	A	538	GLU	-1	-0.832	-0.919	32.586	0.130	0.130	0.000	0.000	0.000	0.000
97	A	539	VAL	0	-0.042	-0.013	33.394	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	540	TYR	0	-0.015	-0.014	27.697	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	541	LEU	0	-0.012	0.012	29.052	0.007	0.007	0.000	0.000	0.000	0.000
100	A	542	ARG	1	0.844	0.916	30.000	-0.126	-0.126	0.000	0.000	0.000	0.000
101	A	543	TYR	0	-0.008	0.004	24.092	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	544	GLY	0	0.059	0.024	25.585	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	545	GLN	0	0.027	-0.010	25.825	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	546	ALA	0	0.008	0.012	27.571	-0.008	-0.008	0.000	0.000	0.000	0.000
105	A	547	GLU	-1	-0.838	-0.909	22.982	0.039	0.039	0.000	0.000	0.000	0.000
106	A	548	GLN	0	-0.020	-0.045	22.023	-0.029	-0.029	0.000	0.000	0.000	0.000
107	A	549	GLU	-1	-0.839	-0.866	23.284	0.074	0.074	0.000	0.000	0.000	0.000
108	A	550	LYS	1	0.789	0.873	23.824	-0.050	-0.050	0.000	0.000	0.000	0.000
109	A	551	ILE	0	-0.009	-0.002	18.193	-0.028	-0.028	0.000	0.000	0.000	0.000
110	A	552	ASP	-1	-0.740	-0.855	20.045	0.113	0.113	0.000	0.000	0.000	0.000
111	A	553	SER	0	-0.001	0.005	21.757	-0.022	-0.022	0.000	0.000	0.000	0.000
112	A	554	TYR	0	-0.022	-0.014	16.962	-0.033	-0.033	0.000	0.000	0.000	0.000
113	A	555	VAL	0	-0.038	-0.035	16.151	-0.033	-0.033	0.000	0.000	0.000	0.000
114	A	556	ARG	1	0.767	0.847	18.548	-0.148	-0.148	0.000	0.000	0.000	0.000
115	A	557	ALA	0	-0.032	-0.004	21.210	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	558	PHE	0	-0.061	-0.029	15.637	-0.018	-0.018	0.000	0.000	0.000	0.000
117	A	559	ARG	1	0.812	0.890	19.182	0.260	0.260	0.000	0.000	0.000	0.000
118	A	560	PRO	0	0.021	0.004	15.878	-0.046	-0.046	0.000	0.000	0.000	0.000
119	A	561	GLU	-1	-0.837	-0.920	16.572	-0.297	-0.297	0.000	0.000	0.000	0.000
120	A	562	GLU	-1	-0.906	-0.923	18.389	-0.304	-0.304	0.000	0.000	0.000	0.000
121	A	563	LEU	0	-0.086	-0.033	12.191	-0.061	-0.061	0.000	0.000	0.000	0.000
122	A	564	THR	0	-0.087	-0.057	12.316	-0.008	-0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:443:GLN)