FMO DATABASE

FMODB ID: 98YK2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1024220.736457
FMO2-HF: Nuclear repulsion	973487.777599
FMO2-HF: Total energy	-50732.958858
FMO2-MP2: Total energy	-50878.293923

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.
-15.081	-13.007	17.178	-7.633	-11.618	0.019

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 : 0.068 / q_NPA : 0.043

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	0.078	0.045	3.178	-1.276	1.728	0.076	-1.497	-1.583	0.007
4	D	553	HIS	0	0.000	-0.009	1.964	-7.225	-8.533	8.512	-3.184	-4.020	0.029
5	D	554	THR	0	0.025	0.009	3.383	-2.467	-1.669	0.042	-0.103	-0.737	0.003
6	D	555	ARG	1	0.936	0.982	5.575	0.608	0.608	0.000	0.000	0.000	0.000
7	D	556	THR	0	0.006	0.007	6.549	-0.421	-0.421	0.000	0.000	0.000	0.000
8	D	557	LYS	1	0.810	0.885	7.417	0.184	0.184	0.000	0.000	0.000	0.000
9	D	558	ASP	-1	-0.840	-0.913	9.239	-0.511	-0.511	0.000	0.000	0.000	0.000
10	D	559	LEU	0	-0.018	-0.011	11.164	-0.006	-0.006	0.000	0.000	0.000	0.000
11	D	560	LYS	1	0.934	0.959	10.585	-0.511	-0.511	0.000	0.000	0.000	0.000
12	D	561	ASP	-1	-0.850	-0.907	13.112	-0.244	-0.244	0.000	0.000	0.000	0.000
13	D	562	PHE	0	0.043	0.012	15.210	0.001	0.001	0.000	0.000	0.000	0.000
14	D	563	ILE	0	0.018	0.011	15.543	-0.009	-0.009	0.000	0.000	0.000	0.000
15	D	564	ARG	1	0.892	0.965	16.362	0.060	0.060	0.000	0.000	0.000	0.000
16	D	565	VAL	0	0.051	0.014	19.364	-0.013	-0.013	0.000	0.000	0.000	0.000
17	D	566	HIS	1	0.807	0.913	20.898	0.010	0.010	0.000	0.000	0.000	0.000
18	D	567	ARG	1	0.887	0.943	21.441	-0.009	-0.009	0.000	0.000	0.000	0.000
19	D	568	LEU	0	0.026	0.021	20.161	0.004	0.004	0.000	0.000	0.000	0.000
20	D	569	PRO	0	0.045	0.023	22.421	0.012	0.012	0.000	0.000	0.000	0.000
21	D	570	LYS	1	0.941	0.959	18.954	-0.213	-0.213	0.000	0.000	0.000	0.000
22	D	571	ALA	0	0.064	0.022	21.534	0.022	0.022	0.000	0.000	0.000	0.000
23	D	572	LEU	0	-0.002	-0.002	21.941	0.015	0.015	0.000	0.000	0.000	0.000
24	D	573	ALA	0	-0.007	-0.019	18.246	0.018	0.018	0.000	0.000	0.000	0.000
25	D	574	GLN	0	-0.017	0.004	17.115	0.019	0.019	0.000	0.000	0.000	0.000
26	D	575	ARG	1	1.048	1.031	17.791	-0.112	-0.112	0.000	0.000	0.000	0.000
27	D	576	MET	0	-0.069	-0.025	16.898	0.000	0.000	0.000	0.000	0.000	0.000
28	D	577	LEU	0	-0.001	-0.004	12.281	0.038	0.038	0.000	0.000	0.000	0.000
29	D	578	GLU	-1	-0.842	-0.928	13.655	0.411	0.411	0.000	0.000	0.000	0.000
30	D	579	CYS	0	-0.006	-0.022	15.526	0.018	0.018	0.000	0.000	0.000	0.000
31	D	580	PHE	0	-0.027	0.014	8.051	-0.057	-0.057	0.000	0.000	0.000	0.000
32	D	581	GLN	0	0.010	0.013	8.796	-0.094	-0.094	0.000	0.000	0.000	0.000
33	D	582	THR	0	-0.015	0.007	12.150	-0.056	-0.056	0.000	0.000	0.000	0.000
34	D	583	THR	0	-0.058	-0.056	14.667	-0.051	-0.051	0.000	0.000	0.000	0.000
35	D	584	TRP	0	-0.027	-0.016	6.065	0.081	0.081	0.000	0.000	0.000	0.000
36	D	585	SER	0	-0.036	-0.022	10.691	-0.055	-0.055	0.000	0.000	0.000	0.000
37	D	586	VAL	0	0.021	0.019	6.514	-0.036	-0.036	0.000	0.000	0.000	0.000
38	D	587	ASN	0	0.024	0.024	9.082	-0.176	-0.176	0.000	0.000	0.000	0.000
39	D	588	ASN	0	-0.089	-0.005	12.053	-0.028	-0.028	0.000	0.000	0.000	0.000
40	D	589	GLY	0	0.018	-0.026	10.965	0.089	0.089	0.000	0.000	0.000	0.000
41	D	590	ILE	0	-0.039	-0.020	9.521	-0.087	-0.087	0.000	0.000	0.000	0.000
42	D	591	ASP	-1	-0.986	-1.003	9.283	-0.938	-0.938	0.000	0.000	0.000	0.000
43	D	592	VAL	0	0.019	0.005	11.180	0.036	0.036	0.000	0.000	0.000	0.000
44	D	593	SER	0	-0.031	0.000	13.727	0.091	0.091	0.000	0.000	0.000	0.000
45	D	594	GLU	-1	-0.771	-0.888	15.266	-0.459	-0.459	0.000	0.000	0.000	0.000
46	D	595	LEU	0	-0.051	-0.007	15.182	0.042	0.042	0.000	0.000	0.000	0.000
47	D	609	MET	0	0.007	-0.011	22.002	-0.005	-0.005	0.000	0.000	0.000	0.000
48	D	610	HIS	0	-0.014	-0.007	19.664	0.017	0.017	0.000	0.000	0.000	0.000
49	D	611	LEU	0	0.001	-0.003	15.080	-0.015	-0.015	0.000	0.000	0.000	0.000
50	D	612	ASN	0	-0.043	-0.017	18.669	0.014	0.014	0.000	0.000	0.000	0.000
51	D	613	LYS	1	0.861	0.930	13.706	0.465	0.465	0.000	0.000	0.000	0.000
52	D	614	GLU	-1	-0.869	-0.930	16.100	-0.145	-0.145	0.000	0.000	0.000	0.000
53	D	615	LEU	0	0.033	0.024	15.671	0.017	0.017	0.000	0.000	0.000	0.000
54	D	616	LEU	0	-0.080	-0.047	18.652	0.013	0.013	0.000	0.000	0.000	0.000
55	D	617	GLN	0	-0.036	-0.001	21.477	0.019	0.019	0.000	0.000	0.000	0.000
56	D	618	LEU	0	0.002	0.005	21.760	0.006	0.006	0.000	0.000	0.000	0.000
57	D	629	LEU	0	0.062	0.018	25.391	0.000	0.000	0.000	0.000	0.000	0.000
58	D	630	ARG	1	0.958	0.961	23.744	0.166	0.166	0.000	0.000	0.000	0.000
59	D	631	SER	0	-0.019	-0.002	22.844	-0.023	-0.023	0.000	0.000	0.000	0.000
60	D	632	LEU	0	0.152	0.059	20.289	-0.017	-0.017	0.000	0.000	0.000	0.000
61	D	633	SER	0	0.018	0.017	18.854	-0.026	-0.026	0.000	0.000	0.000	0.000
62	D	634	LEU	0	-0.084	-0.051	17.793	-0.026	-0.026	0.000	0.000	0.000	0.000
63	D	635	ILE	0	0.017	0.020	16.636	-0.022	-0.022	0.000	0.000	0.000	0.000
64	D	636	ILE	0	-0.050	-0.003	14.301	-0.021	-0.021	0.000	0.000	0.000	0.000
65	D	637	LYS	1	0.845	0.926	10.745	0.517	0.517	0.000	0.000	0.000	0.000
66	D	638	THR	0	-0.025	-0.012	8.482	0.053	0.053	0.000	0.000	0.000	0.000
67	D	639	SER	0	-0.026	-0.012	4.648	-0.781	-0.744	-0.001	-0.008	-0.027	0.000
68	D	640	PHE	0	0.038	0.024	1.942	-1.221	-1.964	8.551	-2.814	-4.995	-0.020
69	D	641	CYS	0	-0.056	-0.025	4.499	-0.693	-0.508	-0.001	-0.023	-0.161	0.000
70	D	642	ALA	0	0.026	0.020	5.588	0.112	0.112	0.000	0.000	0.000	0.000
71	D	643	PRO	0	0.016	0.005	7.065	-0.041	-0.041	0.000	0.000	0.000	0.000
72	D	644	GLY	0	-0.027	-0.002	10.182	0.113	0.113	0.000	0.000	0.000	0.000
73	D	645	GLU	-1	-0.884	-0.944	4.909	0.419	0.520	-0.001	-0.004	-0.095	0.000
74	D	646	PHE	0	0.018	-0.005	9.156	-0.126	-0.126	0.000	0.000	0.000	0.000
75	D	647	LEU	0	0.043	0.029	10.214	-0.005	-0.005	0.000	0.000	0.000	0.000
76	D	648	ILE	0	-0.007	-0.016	11.386	-0.035	-0.035	0.000	0.000	0.000	0.000
77	D	649	ARG	1	0.916	0.952	14.317	-0.172	-0.172	0.000	0.000	0.000	0.000
78	D	650	GLN	0	-0.021	-0.024	16.611	0.000	0.000	0.000	0.000	0.000	0.000
79	D	651	GLY	0	0.021	0.022	18.615	-0.005	-0.005	0.000	0.000	0.000	0.000
80	D	652	ASP	-1	-0.961	-0.966	20.771	-0.020	-0.020	0.000	0.000	0.000	0.000
81	D	653	ALA	0	0.028	0.015	17.639	-0.019	-0.019	0.000	0.000	0.000	0.000
82	D	654	LEU	0	-0.082	-0.052	17.728	0.012	0.012	0.000	0.000	0.000	0.000
83	D	655	GLN	0	0.000	-0.009	14.955	0.014	0.014	0.000	0.000	0.000	0.000
84	D	656	ALA	0	0.010	0.022	14.404	-0.026	-0.026	0.000	0.000	0.000	0.000
85	D	657	ILE	0	-0.014	0.007	16.544	0.034	0.034	0.000	0.000	0.000	0.000
86	D	658	TYR	0	-0.030	-0.046	11.441	-0.064	-0.064	0.000	0.000	0.000	0.000
87	D	659	PHE	0	0.022	0.025	14.637	0.044	0.044	0.000	0.000	0.000	0.000
88	D	660	VAL	0	0.005	-0.005	13.707	-0.050	-0.050	0.000	0.000	0.000	0.000
89	D	661	CYS	0	-0.019	0.006	12.769	0.018	0.018	0.000	0.000	0.000	0.000
90	D	662	SER	0	0.008	-0.008	12.857	0.026	0.026	0.000	0.000	0.000	0.000
91	D	663	GLY	0	0.026	-0.004	13.449	-0.011	-0.011	0.000	0.000	0.000	0.000
92	D	664	SER	0	-0.024	-0.014	14.635	-0.020	-0.020	0.000	0.000	0.000	0.000
93	D	665	MET	0	-0.014	-0.021	11.970	0.005	0.005	0.000	0.000	0.000	0.000
94	D	666	GLU	-1	-0.886	-0.930	15.954	0.157	0.157	0.000	0.000	0.000	0.000
95	D	667	VAL	0	-0.007	-0.022	17.548	-0.002	-0.002	0.000	0.000	0.000	0.000
96	D	668	LEU	0	0.012	0.029	19.061	-0.007	-0.007	0.000	0.000	0.000	0.000
97	D	669	LYS	1	0.968	0.958	21.512	-0.035	-0.035	0.000	0.000	0.000	0.000
98	D	670	ASP	-1	-0.904	-0.958	23.415	0.090	0.090	0.000	0.000	0.000	0.000
99	D	671	ASN	0	-0.022	-0.012	22.820	0.024	0.024	0.000	0.000	0.000	0.000
100	D	672	THR	0	-0.026	-0.016	24.906	0.000	0.000	0.000	0.000	0.000	0.000
101	D	673	VAL	0	0.024	0.016	22.280	-0.003	-0.003	0.000	0.000	0.000	0.000
102	D	674	LEU	0	-0.053	-0.013	24.027	-0.006	-0.006	0.000	0.000	0.000	0.000
103	D	675	ALA	0	-0.011	-0.016	22.761	-0.009	-0.009	0.000	0.000	0.000	0.000
104	D	676	ILE	0	0.009	-0.015	20.232	0.015	0.015	0.000	0.000	0.000	0.000
105	D	677	LEU	0	-0.022	0.022	18.058	-0.007	-0.007	0.000	0.000	0.000	0.000
106	D	678	GLY	0	0.006	-0.016	17.885	0.022	0.022	0.000	0.000	0.000	0.000
107	D	679	LYS	1	0.992	0.985	17.526	-0.012	-0.012	0.000	0.000	0.000	0.000
108	D	680	GLY	0	-0.058	-0.025	18.353	0.007	0.007	0.000	0.000	0.000	0.000
109	D	681	ASP	-1	-0.829	-0.883	19.332	-0.032	-0.032	0.000	0.000	0.000	0.000
110	D	682	LEU	0	-0.035	-0.039	18.287	-0.023	-0.023	0.000	0.000	0.000	0.000
111	D	683	ILE	0	-0.024	-0.026	15.656	0.009	0.009	0.000	0.000	0.000	0.000
112	D	698	ALA	0	-0.025	-0.035	22.023	0.002	0.002	0.000	0.000	0.000	0.000
113	D	699	ASN	0	-0.013	0.010	17.639	0.003	0.003	0.000	0.000	0.000	0.000
114	D	700	VAL	0	0.007	0.003	14.579	-0.009	-0.009	0.000	0.000	0.000	0.000
115	D	701	LYS	1	0.950	0.988	13.194	-0.279	-0.279	0.000	0.000	0.000	0.000
116	D	702	ALA	0	0.029	0.028	10.387	-0.046	-0.046	0.000	0.000	0.000	0.000
117	D	703	LEU	0	0.004	-0.001	12.295	0.048	0.048	0.000	0.000	0.000	0.000
118	D	704	THR	0	-0.020	-0.021	13.317	0.021	0.021	0.000	0.000	0.000	0.000
119	D	705	TYR	0	-0.012	-0.015	6.346	-0.025	-0.025	0.000	0.000	0.000	0.000
120	D	706	CYS	0	-0.038	0.002	9.039	-0.031	-0.031	0.000	0.000	0.000	0.000
121	D	707	ASP	-1	-0.870	-0.916	8.443	-0.148	-0.148	0.000	0.000	0.000	0.000
122	D	708	LEU	0	-0.021	-0.009	8.704	0.029	0.029	0.000	0.000	0.000	0.000
123	D	709	GLN	0	0.021	-0.020	9.696	-0.122	-0.122	0.000	0.000	0.000	0.000
124	D	710	TYR	0	0.019	0.015	8.373	0.110	0.110	0.000	0.000	0.000	0.000
125	D	711	ILE	0	0.005	0.006	13.869	-0.044	-0.044	0.000	0.000	0.000	0.000
126	D	712	SER	0	0.041	0.020	16.393	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)