FMO DATABASE

FMODB ID: MNMJZ

Calculation Name: 3UKV-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3UKV

Chain ID: D

ChEMBL ID:

UniProt ID: A8WHX9

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1023651.317436
FMO2-HF: Nuclear repulsion	972917.691075
FMO2-HF: Total energy	-50733.626362
FMO2-MP2: Total energy	-50878.92816

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(D:550:SER)

Summations of interaction energy for fragment #1(D:550: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.
-16	-8.078	7.365	-5.854	-9.432	0.017

Interaction energy analysis for fragmet #1(D:550:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.086 / q_NPA : 0.050

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	D	552	TYR	0	0.072	0.049	3.042	-1.347	1.636	0.066	-1.481	-1.568	0.007
4	D	553	HIS	0	0.007	0.009	2.266	-7.337	-5.528	3.571	-2.147	-3.233	0.023
5	D	554	THR	0	0.008	-0.018	3.492	-2.658	-1.633	0.021	-0.420	-0.625	0.002
6	D	555	ARG	1	0.887	0.960	5.706	0.578	0.578	0.000	0.000	0.000	0.000
7	D	556	THR	0	-0.016	-0.015	6.687	-0.361	-0.361	0.000	0.000	0.000	0.000
8	D	557	LYS	1	0.825	0.892	7.877	0.149	0.149	0.000	0.000	0.000	0.000
9	D	558	ASP	-1	-0.812	-0.899	9.737	-0.506	-0.506	0.000	0.000	0.000	0.000
10	D	559	LEU	0	0.002	-0.003	11.463	-0.008	-0.008	0.000	0.000	0.000	0.000
11	D	560	LYS	1	0.933	0.966	10.938	-0.426	-0.426	0.000	0.000	0.000	0.000
12	D	561	ASP	-1	-0.783	-0.866	13.753	-0.210	-0.210	0.000	0.000	0.000	0.000
13	D	562	PHE	0	0.052	0.023	15.726	0.001	0.001	0.000	0.000	0.000	0.000
14	D	563	ILE	0	0.014	0.007	15.632	-0.008	-0.008	0.000	0.000	0.000	0.000
15	D	564	ARG	1	0.797	0.903	16.087	0.079	0.079	0.000	0.000	0.000	0.000
16	D	565	VAL	0	0.025	0.013	19.729	-0.012	-0.012	0.000	0.000	0.000	0.000
17	D	566	HIS	1	0.828	0.916	21.162	0.015	0.015	0.000	0.000	0.000	0.000
18	D	567	ARG	1	0.889	0.944	21.914	0.002	0.002	0.000	0.000	0.000	0.000
19	D	568	LEU	0	0.034	0.028	20.389	0.003	0.003	0.000	0.000	0.000	0.000
20	D	569	PRO	0	0.045	0.019	22.705	0.010	0.010	0.000	0.000	0.000	0.000
21	D	570	LYS	1	0.931	0.951	18.999	-0.175	-0.175	0.000	0.000	0.000	0.000
22	D	571	ALA	0	0.060	0.022	21.663	0.018	0.018	0.000	0.000	0.000	0.000
23	D	572	LEU	0	0.004	0.000	22.127	0.013	0.013	0.000	0.000	0.000	0.000
24	D	573	ALA	0	-0.010	-0.020	18.505	0.017	0.017	0.000	0.000	0.000	0.000
25	D	574	GLN	0	-0.035	-0.007	16.792	0.017	0.017	0.000	0.000	0.000	0.000
26	D	575	ARG	1	1.051	1.033	17.882	-0.092	-0.092	0.000	0.000	0.000	0.000
27	D	576	MET	0	-0.060	-0.020	17.080	0.003	0.003	0.000	0.000	0.000	0.000
28	D	577	LEU	0	0.011	-0.002	12.168	0.035	0.035	0.000	0.000	0.000	0.000
29	D	578	GLU	-1	-0.828	-0.916	13.728	0.356	0.356	0.000	0.000	0.000	0.000
30	D	579	CYS	0	-0.018	-0.012	15.555	0.019	0.019	0.000	0.000	0.000	0.000
31	D	580	PHE	0	-0.022	0.009	8.065	-0.048	-0.048	0.000	0.000	0.000	0.000
32	D	581	GLN	0	0.016	0.016	8.652	-0.091	-0.091	0.000	0.000	0.000	0.000
33	D	582	THR	0	-0.024	-0.011	12.156	-0.048	-0.048	0.000	0.000	0.000	0.000
34	D	583	THR	0	-0.054	-0.050	14.571	-0.048	-0.048	0.000	0.000	0.000	0.000
35	D	584	TRP	0	-0.027	-0.023	5.830	0.025	0.025	0.000	0.000	0.000	0.000
36	D	585	SER	0	-0.036	-0.031	10.542	-0.047	-0.047	0.000	0.000	0.000	0.000
37	D	586	VAL	0	0.017	0.016	6.367	-0.045	-0.045	0.000	0.000	0.000	0.000
38	D	587	ASN	0	0.015	0.004	8.876	-0.162	-0.162	0.000	0.000	0.000	0.000
39	D	588	ASN	0	-0.089	-0.008	11.837	-0.022	-0.022	0.000	0.000	0.000	0.000
40	D	589	GLY	0	0.017	-0.024	10.766	0.081	0.081	0.000	0.000	0.000	0.000
41	D	590	ILE	0	-0.035	-0.015	9.506	-0.091	-0.091	0.000	0.000	0.000	0.000
42	D	591	ASP	-1	-0.942	-0.978	9.418	-0.788	-0.788	0.000	0.000	0.000	0.000
43	D	592	VAL	0	-0.004	-0.013	11.125	0.043	0.043	0.000	0.000	0.000	0.000
44	D	593	SER	0	-0.023	0.007	13.622	0.085	0.085	0.000	0.000	0.000	0.000
45	D	594	GLU	-1	-0.755	-0.879	15.205	-0.390	-0.390	0.000	0.000	0.000	0.000
46	D	595	LEU	0	-0.075	-0.020	15.121	0.052	0.052	0.000	0.000	0.000	0.000
47	D	609	MET	0	-0.003	-0.019	21.970	-0.004	-0.004	0.000	0.000	0.000	0.000
48	D	610	HIS	0	0.003	0.004	19.674	0.015	0.015	0.000	0.000	0.000	0.000
49	D	611	LEU	0	-0.006	-0.006	15.219	-0.008	-0.008	0.000	0.000	0.000	0.000
50	D	612	ASN	0	-0.051	-0.023	18.765	0.009	0.009	0.000	0.000	0.000	0.000
51	D	613	LYS	1	0.868	0.934	13.687	0.356	0.356	0.000	0.000	0.000	0.000
52	D	614	GLU	-1	-0.750	-0.858	15.233	-0.122	-0.122	0.000	0.000	0.000	0.000
53	D	615	LEU	0	0.030	0.028	15.622	0.013	0.013	0.000	0.000	0.000	0.000
54	D	616	LEU	0	-0.073	-0.048	18.621	0.008	0.008	0.000	0.000	0.000	0.000
55	D	617	GLN	0	-0.052	-0.009	21.370	0.015	0.015	0.000	0.000	0.000	0.000
56	D	618	LEU	0	0.012	0.011	21.716	0.003	0.003	0.000	0.000	0.000	0.000
57	D	629	LEU	0	0.058	0.012	25.326	0.000	0.000	0.000	0.000	0.000	0.000
58	D	630	ARG	1	0.952	0.966	23.779	0.128	0.128	0.000	0.000	0.000	0.000
59	D	631	SER	0	-0.013	-0.002	22.889	-0.019	-0.019	0.000	0.000	0.000	0.000
60	D	632	LEU	0	0.140	0.056	20.202	-0.014	-0.014	0.000	0.000	0.000	0.000
61	D	633	SER	0	0.038	0.021	18.858	-0.021	-0.021	0.000	0.000	0.000	0.000
62	D	634	LEU	0	-0.091	-0.049	17.856	-0.019	-0.019	0.000	0.000	0.000	0.000
63	D	635	ILE	0	0.006	0.018	16.620	-0.019	-0.019	0.000	0.000	0.000	0.000
64	D	636	ILE	0	-0.027	0.005	14.205	-0.021	-0.021	0.000	0.000	0.000	0.000
65	D	637	LYS	1	0.822	0.909	10.643	0.436	0.436	0.000	0.000	0.000	0.000
66	D	638	THR	0	-0.006	-0.002	8.186	0.114	0.114	0.000	0.000	0.000	0.000
67	D	639	SER	0	-0.049	-0.022	4.560	-0.718	-0.667	-0.001	-0.010	-0.040	0.000
68	D	640	PHE	0	0.023	0.013	2.258	-2.247	-0.498	3.710	-1.766	-3.694	-0.015
69	D	641	CYS	0	-0.058	-0.019	4.556	-0.700	-0.507	-0.001	-0.023	-0.169	0.000
70	D	642	ALA	0	0.005	0.006	5.516	0.088	0.088	0.000	0.000	0.000	0.000
71	D	643	PRO	0	0.026	0.005	7.050	-0.029	-0.029	0.000	0.000	0.000	0.000
72	D	644	GLY	0	-0.032	-0.006	10.185	0.101	0.101	0.000	0.000	0.000	0.000
73	D	645	GLU	-1	-0.854	-0.923	4.800	0.498	0.610	-0.001	-0.007	-0.103	0.000
74	D	646	PHE	0	0.031	0.002	9.065	-0.118	-0.118	0.000	0.000	0.000	0.000
75	D	647	LEU	0	0.059	0.037	10.044	-0.007	-0.007	0.000	0.000	0.000	0.000
76	D	648	ILE	0	-0.020	-0.016	11.200	-0.034	-0.034	0.000	0.000	0.000	0.000
77	D	649	ARG	1	0.901	0.944	14.095	-0.164	-0.164	0.000	0.000	0.000	0.000
78	D	650	GLN	0	-0.013	-0.016	16.444	0.001	0.001	0.000	0.000	0.000	0.000
79	D	651	GLY	0	0.033	0.026	18.506	-0.006	-0.006	0.000	0.000	0.000	0.000
80	D	652	ASP	-1	-0.964	-0.968	20.924	-0.016	-0.016	0.000	0.000	0.000	0.000
81	D	653	ALA	0	0.028	0.018	17.492	-0.016	-0.016	0.000	0.000	0.000	0.000
82	D	654	LEU	0	-0.063	-0.037	17.735	0.012	0.012	0.000	0.000	0.000	0.000
83	D	655	GLN	0	-0.014	-0.007	14.989	0.012	0.012	0.000	0.000	0.000	0.000
84	D	656	ALA	0	0.011	0.023	14.359	-0.022	-0.022	0.000	0.000	0.000	0.000
85	D	657	ILE	0	-0.009	0.007	16.533	0.030	0.030	0.000	0.000	0.000	0.000
86	D	658	TYR	0	-0.031	-0.042	11.508	-0.053	-0.053	0.000	0.000	0.000	0.000
87	D	659	PHE	0	0.021	0.021	14.631	0.037	0.037	0.000	0.000	0.000	0.000
88	D	660	VAL	0	0.013	-0.002	13.728	-0.036	-0.036	0.000	0.000	0.000	0.000
89	D	661	CYS	0	-0.061	-0.020	12.860	0.009	0.009	0.000	0.000	0.000	0.000
90	D	662	SER	0	-0.052	-0.059	12.479	0.023	0.023	0.000	0.000	0.000	0.000
91	D	663	GLY	0	0.048	0.013	13.487	-0.008	-0.008	0.000	0.000	0.000	0.000
92	D	664	SER	0	-0.035	-0.019	14.580	-0.019	-0.019	0.000	0.000	0.000	0.000
93	D	665	MET	0	-0.020	-0.014	11.475	0.008	0.008	0.000	0.000	0.000	0.000
94	D	666	GLU	-1	-0.832	-0.893	15.837	0.157	0.157	0.000	0.000	0.000	0.000
95	D	667	VAL	0	-0.006	-0.020	17.410	0.000	0.000	0.000	0.000	0.000	0.000
96	D	668	LEU	0	0.008	0.025	19.027	-0.007	-0.007	0.000	0.000	0.000	0.000
97	D	669	LYS	1	0.978	0.962	21.377	-0.035	-0.035	0.000	0.000	0.000	0.000
98	D	670	ASP	-1	-0.900	-0.948	23.125	0.083	0.083	0.000	0.000	0.000	0.000
99	D	671	ASN	0	-0.045	-0.034	22.710	0.019	0.019	0.000	0.000	0.000	0.000
100	D	672	THR	0	-0.013	-0.007	24.794	0.000	0.000	0.000	0.000	0.000	0.000
101	D	673	VAL	0	0.013	0.013	21.963	-0.002	-0.002	0.000	0.000	0.000	0.000
102	D	674	LEU	0	-0.044	-0.008	23.879	-0.005	-0.005	0.000	0.000	0.000	0.000
103	D	675	ALA	0	-0.014	-0.013	22.489	-0.008	-0.008	0.000	0.000	0.000	0.000
104	D	676	ILE	0	0.005	-0.021	20.018	0.013	0.013	0.000	0.000	0.000	0.000
105	D	677	LEU	0	-0.019	0.023	18.014	-0.006	-0.006	0.000	0.000	0.000	0.000
106	D	678	GLY	0	0.012	-0.011	17.874	0.019	0.019	0.000	0.000	0.000	0.000
107	D	679	LYS	1	0.992	0.984	17.550	-0.027	-0.027	0.000	0.000	0.000	0.000
108	D	680	GLY	0	-0.058	-0.018	18.377	0.004	0.004	0.000	0.000	0.000	0.000
109	D	681	ASP	-1	-0.818	-0.881	19.351	-0.014	-0.014	0.000	0.000	0.000	0.000
110	D	682	LEU	0	-0.044	-0.043	18.304	-0.017	-0.017	0.000	0.000	0.000	0.000
111	D	683	ILE	0	-0.020	-0.021	15.895	0.006	0.006	0.000	0.000	0.000	0.000
112	D	698	ALA	0	-0.011	-0.009	21.863	-0.001	-0.001	0.000	0.000	0.000	0.000
113	D	699	ASN	0	-0.033	-0.016	17.514	-0.003	-0.003	0.000	0.000	0.000	0.000
114	D	700	VAL	0	0.001	-0.001	14.785	-0.008	-0.008	0.000	0.000	0.000	0.000
115	D	701	LYS	1	0.875	0.936	13.054	-0.238	-0.238	0.000	0.000	0.000	0.000
116	D	702	ALA	0	0.034	0.023	10.267	-0.041	-0.041	0.000	0.000	0.000	0.000
117	D	703	LEU	0	-0.014	-0.007	12.195	0.041	0.041	0.000	0.000	0.000	0.000
118	D	704	THR	0	-0.004	-0.012	13.295	0.014	0.014	0.000	0.000	0.000	0.000
119	D	705	TYR	0	0.003	-0.008	6.234	-0.005	-0.005	0.000	0.000	0.000	0.000
120	D	706	CYS	0	-0.029	0.001	8.974	-0.028	-0.028	0.000	0.000	0.000	0.000
121	D	707	ASP	-1	-0.859	-0.882	8.486	0.054	0.054	0.000	0.000	0.000	0.000
122	D	708	LEU	0	-0.006	-0.007	8.712	0.006	0.006	0.000	0.000	0.000	0.000
123	D	709	GLN	0	-0.031	-0.056	9.679	-0.109	-0.109	0.000	0.000	0.000	0.000
124	D	710	TYR	0	0.014	0.013	8.738	-0.004	-0.004	0.000	0.000	0.000	0.000
125	D	711	ILE	0	0.009	0.007	13.840	-0.037	-0.037	0.000	0.000	0.000	0.000
126	D	712	SER	0	0.042	0.019	16.348	0.022	0.022	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:550:SER)