FMO DATABASE

FMODB ID: 76J5K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1026035.606303
FMO2-HF: Nuclear repulsion	975301.471711
FMO2-HF: Total energy	-50734.134592
FMO2-MP2: Total energy	-50879.410393

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.
-18.267	-11.334	10.345	-6.528	-10.752	0.021

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 : 0.096 / q_NPA : 0.056

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	0.066	0.054	2.615	-1.467	1.702	0.346	-1.608	-1.908	0.006
4	D	553	HIS	0	0.006	0.007	2.038	-8.427	-8.140	6.278	-2.739	-3.826	0.026
5	D	554	THR	0	-0.010	-0.017	3.541	-2.490	-1.438	0.033	-0.391	-0.695	0.002
6	D	555	ARG	1	0.852	0.918	5.440	0.803	0.803	0.000	0.000	0.000	0.000
7	D	556	THR	0	-0.027	-0.024	6.318	-0.339	-0.339	0.000	0.000	0.000	0.000
8	D	557	LYS	1	0.842	0.906	7.537	0.062	0.062	0.000	0.000	0.000	0.000
9	D	558	ASP	-1	-0.827	-0.912	9.386	-0.502	-0.502	0.000	0.000	0.000	0.000
10	D	559	LEU	0	-0.006	0.003	11.297	-0.015	-0.015	0.000	0.000	0.000	0.000
11	D	560	LYS	1	0.931	0.960	10.681	-0.581	-0.581	0.000	0.000	0.000	0.000
12	D	561	ASP	-1	-0.788	-0.860	13.588	-0.145	-0.145	0.000	0.000	0.000	0.000
13	D	562	PHE	0	0.066	0.033	15.513	-0.003	-0.003	0.000	0.000	0.000	0.000
14	D	563	ILE	0	-0.002	-0.002	15.378	-0.010	-0.010	0.000	0.000	0.000	0.000
15	D	564	ARG	1	0.826	0.892	15.569	0.022	0.022	0.000	0.000	0.000	0.000
16	D	565	VAL	0	0.011	0.017	19.312	-0.010	-0.010	0.000	0.000	0.000	0.000
17	D	566	HIS	1	0.838	0.911	20.835	-0.014	-0.014	0.000	0.000	0.000	0.000
18	D	567	ARG	1	0.890	0.944	22.406	-0.036	-0.036	0.000	0.000	0.000	0.000
19	D	568	LEU	0	0.034	0.034	20.279	0.004	0.004	0.000	0.000	0.000	0.000
20	D	569	PRO	0	0.052	0.031	22.873	0.011	0.011	0.000	0.000	0.000	0.000
21	D	570	LYS	1	0.939	0.948	18.842	-0.232	-0.232	0.000	0.000	0.000	0.000
22	D	571	ALA	0	0.055	0.020	21.578	0.023	0.023	0.000	0.000	0.000	0.000
23	D	572	LEU	0	-0.023	-0.009	21.903	0.012	0.012	0.000	0.000	0.000	0.000
24	D	573	ALA	0	0.016	-0.006	18.589	0.018	0.018	0.000	0.000	0.000	0.000
25	D	574	GLN	0	-0.051	-0.018	16.608	0.018	0.018	0.000	0.000	0.000	0.000
26	D	575	ARG	1	1.044	1.024	17.361	-0.124	-0.124	0.000	0.000	0.000	0.000
27	D	576	MET	0	-0.031	-0.009	16.761	0.002	0.002	0.000	0.000	0.000	0.000
28	D	577	LEU	0	-0.006	-0.003	11.915	0.041	0.041	0.000	0.000	0.000	0.000
29	D	578	GLU	-1	-0.808	-0.903	13.373	0.450	0.450	0.000	0.000	0.000	0.000
30	D	579	CYS	0	-0.006	0.008	15.513	0.007	0.007	0.000	0.000	0.000	0.000
31	D	580	PHE	0	-0.020	0.012	7.874	-0.042	-0.042	0.000	0.000	0.000	0.000
32	D	581	GLN	0	-0.004	-0.008	8.566	-0.108	-0.108	0.000	0.000	0.000	0.000
33	D	582	THR	0	-0.036	-0.030	11.790	-0.040	-0.040	0.000	0.000	0.000	0.000
34	D	583	THR	0	-0.062	-0.058	14.196	-0.064	-0.064	0.000	0.000	0.000	0.000
35	D	584	TRP	0	-0.022	-0.002	5.311	0.035	0.035	0.000	0.000	0.000	0.000
36	D	585	SER	0	-0.001	-0.019	9.794	-0.089	-0.089	0.000	0.000	0.000	0.000
37	D	586	VAL	0	0.002	0.012	5.879	-0.046	-0.046	0.000	0.000	0.000	0.000
38	D	587	ASN	0	0.019	0.006	8.182	-0.193	-0.193	0.000	0.000	0.000	0.000
39	D	588	ASN	0	-0.099	-0.035	11.068	-0.020	-0.020	0.000	0.000	0.000	0.000
40	D	589	GLY	0	-0.003	-0.015	9.865	0.106	0.106	0.000	0.000	0.000	0.000
41	D	590	ILE	0	0.014	0.000	9.175	-0.084	-0.084	0.000	0.000	0.000	0.000
42	D	591	ASP	-1	-0.857	-0.911	9.588	-0.774	-0.774	0.000	0.000	0.000	0.000
43	D	592	VAL	0	0.007	-0.003	11.033	0.042	0.042	0.000	0.000	0.000	0.000
44	D	593	SER	0	-0.018	0.006	13.715	0.103	0.103	0.000	0.000	0.000	0.000
45	D	594	GLU	-1	-0.787	-0.889	15.280	-0.469	-0.469	0.000	0.000	0.000	0.000
46	D	595	LEU	0	-0.071	-0.024	15.680	0.066	0.066	0.000	0.000	0.000	0.000
47	D	609	MET	0	-0.005	-0.020	22.536	-0.003	-0.003	0.000	0.000	0.000	0.000
48	D	610	HIS	0	0.001	0.002	20.045	0.020	0.020	0.000	0.000	0.000	0.000
49	D	611	LEU	0	-0.007	-0.005	15.735	-0.017	-0.017	0.000	0.000	0.000	0.000
50	D	612	ASN	0	-0.044	-0.020	19.224	0.014	0.014	0.000	0.000	0.000	0.000
51	D	613	LYS	1	0.860	0.932	14.148	0.479	0.479	0.000	0.000	0.000	0.000
52	D	614	GLU	-1	-0.738	-0.851	14.695	-0.267	-0.267	0.000	0.000	0.000	0.000
53	D	615	LEU	0	0.041	0.033	15.516	0.020	0.020	0.000	0.000	0.000	0.000
54	D	616	LEU	0	-0.054	-0.041	18.315	0.020	0.020	0.000	0.000	0.000	0.000
55	D	617	GLN	0	-0.046	-0.010	21.119	0.024	0.024	0.000	0.000	0.000	0.000
56	D	618	LEU	0	-0.028	-0.001	21.383	0.012	0.012	0.000	0.000	0.000	0.000
57	D	629	LEU	0	0.060	0.022	25.000	0.002	0.002	0.000	0.000	0.000	0.000
58	D	630	ARG	1	0.983	0.980	24.024	0.157	0.157	0.000	0.000	0.000	0.000
59	D	631	SER	0	0.008	0.013	23.020	-0.025	-0.025	0.000	0.000	0.000	0.000
60	D	632	LEU	0	0.117	0.047	20.522	-0.017	-0.017	0.000	0.000	0.000	0.000
61	D	633	SER	0	-0.058	-0.031	19.025	-0.030	-0.030	0.000	0.000	0.000	0.000
62	D	634	LEU	0	-0.042	-0.032	18.392	-0.024	-0.024	0.000	0.000	0.000	0.000
63	D	635	ILE	0	0.027	0.027	16.956	-0.028	-0.028	0.000	0.000	0.000	0.000
64	D	636	ILE	0	-0.038	-0.008	14.273	-0.033	-0.033	0.000	0.000	0.000	0.000
65	D	637	LYS	1	0.813	0.914	10.638	0.505	0.505	0.000	0.000	0.000	0.000
66	D	638	THR	0	-0.019	-0.026	8.491	0.164	0.164	0.000	0.000	0.000	0.000
67	D	639	SER	0	-0.059	-0.030	4.062	-1.028	-0.879	0.000	-0.049	-0.100	0.000
68	D	640	PHE	0	0.027	0.027	2.531	-2.481	-0.637	3.690	-1.671	-3.863	-0.013
69	D	641	CYS	0	-0.084	-0.032	4.311	-1.044	-0.774	-0.001	-0.044	-0.225	0.000
70	D	642	ALA	0	0.017	-0.002	4.807	0.144	0.144	0.000	0.000	0.000	0.000
71	D	643	PRO	0	0.006	-0.006	6.648	-0.004	-0.004	0.000	0.000	0.000	0.000
72	D	644	GLY	0	0.001	0.005	10.353	0.114	0.114	0.000	0.000	0.000	0.000
73	D	645	GLU	-1	-0.806	-0.881	4.443	0.447	0.609	-0.001	-0.026	-0.135	0.000
74	D	646	PHE	0	0.047	0.005	8.802	-0.156	-0.156	0.000	0.000	0.000	0.000
75	D	647	LEU	0	0.032	0.032	9.675	-0.018	-0.018	0.000	0.000	0.000	0.000
76	D	648	ILE	0	0.010	-0.008	10.615	-0.049	-0.049	0.000	0.000	0.000	0.000
77	D	649	ARG	1	0.865	0.929	13.583	-0.212	-0.212	0.000	0.000	0.000	0.000
78	D	650	GLN	0	-0.008	-0.004	15.671	0.006	0.006	0.000	0.000	0.000	0.000
79	D	651	GLY	0	0.034	0.017	17.637	-0.012	-0.012	0.000	0.000	0.000	0.000
80	D	652	ASP	-1	-0.964	-0.971	20.126	-0.013	-0.013	0.000	0.000	0.000	0.000
81	D	653	ALA	0	0.028	0.021	16.885	-0.018	-0.018	0.000	0.000	0.000	0.000
82	D	654	LEU	0	-0.029	-0.024	17.139	0.011	0.011	0.000	0.000	0.000	0.000
83	D	655	GLN	0	-0.028	-0.009	14.837	0.015	0.015	0.000	0.000	0.000	0.000
84	D	656	ALA	0	0.013	0.017	14.340	-0.039	-0.039	0.000	0.000	0.000	0.000
85	D	657	ILE	0	-0.027	0.006	16.488	0.037	0.037	0.000	0.000	0.000	0.000
86	D	658	TYR	0	-0.004	-0.034	11.449	-0.073	-0.073	0.000	0.000	0.000	0.000
87	D	659	PHE	0	0.011	0.004	14.178	0.049	0.049	0.000	0.000	0.000	0.000
88	D	660	VAL	0	0.031	0.013	13.456	-0.066	-0.066	0.000	0.000	0.000	0.000
89	D	661	CYS	0	-0.075	-0.024	12.803	0.022	0.022	0.000	0.000	0.000	0.000
90	D	662	SER	0	-0.050	-0.067	12.007	0.045	0.045	0.000	0.000	0.000	0.000
91	D	663	GLY	0	0.046	0.019	13.216	-0.015	-0.015	0.000	0.000	0.000	0.000
92	D	664	SER	0	-0.053	-0.042	14.221	-0.011	-0.011	0.000	0.000	0.000	0.000
93	D	665	MET	0	-0.034	-0.007	11.006	0.006	0.006	0.000	0.000	0.000	0.000
94	D	666	GLU	-1	-0.804	-0.886	15.495	0.161	0.161	0.000	0.000	0.000	0.000
95	D	667	VAL	0	0.002	-0.005	16.796	-0.002	-0.002	0.000	0.000	0.000	0.000
96	D	668	LEU	0	0.006	0.025	18.083	-0.002	-0.002	0.000	0.000	0.000	0.000
97	D	669	LYS	1	0.993	0.985	20.530	-0.023	-0.023	0.000	0.000	0.000	0.000
98	D	670	ASP	-1	-0.862	-0.913	22.705	0.091	0.091	0.000	0.000	0.000	0.000
99	D	671	ASN	0	-0.041	-0.050	22.334	0.018	0.018	0.000	0.000	0.000	0.000
100	D	672	THR	0	-0.060	-0.019	24.513	-0.003	-0.003	0.000	0.000	0.000	0.000
101	D	673	VAL	0	0.012	-0.001	21.781	-0.002	-0.002	0.000	0.000	0.000	0.000
102	D	674	LEU	0	-0.042	-0.015	23.266	-0.007	-0.007	0.000	0.000	0.000	0.000
103	D	675	ALA	0	-0.003	-0.005	21.933	-0.009	-0.009	0.000	0.000	0.000	0.000
104	D	676	ILE	0	-0.007	-0.013	19.742	0.014	0.014	0.000	0.000	0.000	0.000
105	D	677	LEU	0	-0.029	0.006	17.753	-0.008	-0.008	0.000	0.000	0.000	0.000
106	D	678	GLY	0	0.013	-0.016	17.279	0.019	0.019	0.000	0.000	0.000	0.000
107	D	679	LYS	1	0.931	0.969	17.362	0.020	0.020	0.000	0.000	0.000	0.000
108	D	680	GLY	0	0.000	-0.002	17.932	0.013	0.013	0.000	0.000	0.000	0.000
109	D	681	ASP	-1	-0.817	-0.887	18.852	-0.062	-0.062	0.000	0.000	0.000	0.000
110	D	682	LEU	0	-0.031	-0.033	17.970	-0.031	-0.031	0.000	0.000	0.000	0.000
111	D	683	ILE	0	-0.005	0.004	15.727	0.008	0.008	0.000	0.000	0.000	0.000
112	D	698	ALA	0	-0.013	-0.012	21.164	0.000	0.000	0.000	0.000	0.000	0.000
113	D	699	ASN	0	-0.047	-0.025	16.438	0.003	0.003	0.000	0.000	0.000	0.000
114	D	700	VAL	0	-0.012	-0.012	14.117	-0.011	-0.011	0.000	0.000	0.000	0.000
115	D	701	LYS	1	0.852	0.919	12.248	-0.246	-0.246	0.000	0.000	0.000	0.000
116	D	702	ALA	0	0.039	0.021	9.703	-0.051	-0.051	0.000	0.000	0.000	0.000
117	D	703	LEU	0	-0.014	-0.007	11.642	0.071	0.071	0.000	0.000	0.000	0.000
118	D	704	THR	0	-0.015	-0.026	12.677	0.019	0.019	0.000	0.000	0.000	0.000
119	D	705	TYR	0	0.025	0.001	5.944	-0.001	-0.001	0.000	0.000	0.000	0.000
120	D	706	CYS	0	-0.045	0.007	8.590	0.004	0.004	0.000	0.000	0.000	0.000
121	D	707	ASP	-1	-0.850	-0.883	8.474	-0.298	-0.298	0.000	0.000	0.000	0.000
122	D	708	LEU	0	-0.012	-0.012	8.534	0.072	0.072	0.000	0.000	0.000	0.000
123	D	709	GLN	0	-0.046	-0.058	9.441	-0.146	-0.146	0.000	0.000	0.000	0.000
124	D	710	TYR	0	-0.016	-0.016	8.776	-0.009	-0.009	0.000	0.000	0.000	0.000
125	D	711	ILE	0	-0.004	0.005	13.711	-0.033	-0.033	0.000	0.000	0.000	0.000
126	D	712	SER	0	0.045	0.024	16.275	0.033	0.033	0.000	0.000	0.000	0.000

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