FMO DATABASE

FMODB ID: YNZ52

Calculation Name: 5TU8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5TU8

Chain ID: A

ChEMBL ID:

UniProt ID: Q5HKE8

Base Structure: X-ray

Registration Date: 2023-09-26

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	132
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-801293.328261
FMO2-HF: Nuclear repulsion	751733.701883
FMO2-HF: Total energy	-49559.626378
FMO2-MP2: Total energy	-49706.825556

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:14:PHE)

Summations of interaction energy for fragment #1(A:14:PHE)

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.
-23.848	-9.844	11.884	-8.822	-17.065	0.005

Interaction energy analysis for fragmet #1(A:14:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.010

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

Sort

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	16	LYS	1	0.889	0.940	2.413	-4.916	1.191	2.328	-3.644	-4.791	-0.018
4	A	17	LYS	1	0.943	0.971	4.234	3.315	3.474	0.000	-0.035	-0.123	0.000
5	A	18	ARG	1	0.844	0.903	7.527	0.993	0.993	0.000	0.000	0.000	0.000
6	A	19	GLU	-1	-0.827	-0.908	10.677	-0.583	-0.583	0.000	0.000	0.000	0.000
7	A	20	PHE	0	0.011	0.011	13.691	0.059	0.059	0.000	0.000	0.000	0.000
8	A	21	ASN	0	-0.008	-0.021	16.661	0.029	0.029	0.000	0.000	0.000	0.000
9	A	22	PRO	0	-0.021	-0.008	18.359	0.014	0.014	0.000	0.000	0.000	0.000
10	A	23	ASP	-1	-0.930	-0.957	20.657	-0.094	-0.094	0.000	0.000	0.000	0.000
11	A	24	LEU	0	-0.124	-0.045	15.505	0.028	0.028	0.000	0.000	0.000	0.000
12	A	25	LYS	1	0.943	0.960	20.230	0.042	0.042	0.000	0.000	0.000	0.000
13	A	26	PRO	0	0.012	-0.010	20.737	-0.021	-0.021	0.000	0.000	0.000	0.000
14	A	27	GLY	0	-0.021	0.000	19.722	0.020	0.020	0.000	0.000	0.000	0.000
15	A	28	GLU	-1	-0.943	-0.948	17.496	-0.060	-0.060	0.000	0.000	0.000	0.000
16	A	29	GLU	-1	-0.842	-0.931	11.656	-0.560	-0.560	0.000	0.000	0.000	0.000
17	A	30	ARG	1	0.857	0.932	12.793	0.139	0.139	0.000	0.000	0.000	0.000
18	A	31	VAL	0	-0.017	-0.001	7.201	-0.058	-0.058	0.000	0.000	0.000	0.000
19	A	32	LYS	1	0.858	0.949	9.711	0.500	0.500	0.000	0.000	0.000	0.000
20	A	33	GLN	0	-0.018	-0.018	6.449	0.225	0.225	0.000	0.000	0.000	0.000
21	A	34	LYS	1	0.928	0.969	2.496	-12.837	-11.584	3.174	-1.698	-2.729	0.026
22	A	35	GLY	0	0.014	0.011	2.716	-2.634	0.451	3.237	-1.473	-4.849	0.006
23	A	71	ASP	-1	-0.966	-0.999	2.337	-2.739	-2.077	0.868	-0.644	-0.886	-0.002
24	A	72	GLU	-1	-0.943	-0.970	2.643	-2.607	-0.002	2.274	-1.310	-3.569	-0.007
25	A	73	ILE	0	0.018	0.024	4.088	-1.357	-1.224	0.003	-0.018	-0.118	0.000
26	A	74	THR	0	-0.015	-0.011	6.565	0.571	0.571	0.000	0.000	0.000	0.000
27	A	75	GLU	-1	-0.813	-0.902	9.077	-0.287	-0.287	0.000	0.000	0.000	0.000
28	A	76	TYR	0	-0.056	-0.069	12.904	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	77	GLY	0	0.062	0.041	15.406	0.003	0.003	0.000	0.000	0.000	0.000
30	A	78	GLY	0	0.000	-0.021	19.198	-0.036	-0.036	0.000	0.000	0.000	0.000
31	A	79	GLU	-1	-0.865	-0.926	21.988	-0.291	-0.291	0.000	0.000	0.000	0.000
32	A	80	GLU	-1	-0.915	-0.975	24.290	-0.108	-0.108	0.000	0.000	0.000	0.000
33	A	81	ILE	0	-0.082	-0.015	27.574	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	82	LYS	1	0.929	0.952	29.888	0.137	0.137	0.000	0.000	0.000	0.000
35	A	83	PRO	0	0.021	0.016	33.584	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	84	GLY	0	0.022	0.029	36.804	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	85	HIS	0	-0.048	-0.042	39.979	0.000	0.000	0.000	0.000	0.000	0.000
38	A	86	LYS	1	0.926	0.977	43.384	0.059	0.059	0.000	0.000	0.000	0.000
39	A	87	ASP	-1	-0.810	-0.911	46.508	-0.049	-0.049	0.000	0.000	0.000	0.000
40	A	88	GLU	-1	-0.931	-1.000	48.095	-0.048	-0.048	0.000	0.000	0.000	0.000
41	A	89	PHE	0	-0.019	-0.017	51.613	0.002	0.002	0.000	0.000	0.000	0.000
42	A	90	ASP	-1	-0.863	-0.944	53.786	-0.030	-0.030	0.000	0.000	0.000	0.000
43	A	91	PRO	0	-0.039	-0.028	55.740	0.001	0.001	0.000	0.000	0.000	0.000
44	A	92	ASN	0	-0.055	-0.031	57.936	0.002	0.002	0.000	0.000	0.000	0.000
45	A	93	ALA	0	0.026	0.042	55.507	0.002	0.002	0.000	0.000	0.000	0.000
46	A	94	PRO	0	-0.002	-0.017	56.672	0.000	0.000	0.000	0.000	0.000	0.000
47	A	95	LYS	1	0.876	0.923	59.230	0.019	0.019	0.000	0.000	0.000	0.000
48	A	96	GLY	0	-0.061	-0.029	60.464	0.001	0.001	0.000	0.000	0.000	0.000
49	A	97	SER	0	-0.097	-0.045	55.916	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	98	GLN	0	0.059	0.006	51.450	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	99	GLU	-1	-0.963	-0.978	48.378	-0.029	-0.029	0.000	0.000	0.000	0.000
52	A	100	ASP	-1	-0.924	-0.956	44.584	-0.050	-0.050	0.000	0.000	0.000	0.000
53	A	101	VAL	0	-0.036	-0.025	42.815	0.003	0.003	0.000	0.000	0.000	0.000
54	A	102	PRO	0	0.005	0.004	39.321	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	103	GLY	0	0.011	0.008	38.710	0.003	0.003	0.000	0.000	0.000	0.000
56	A	104	LYS	1	0.847	0.911	33.835	0.055	0.055	0.000	0.000	0.000	0.000
57	A	105	PRO	0	0.028	0.017	30.330	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	106	GLY	0	0.022	0.009	30.894	0.005	0.005	0.000	0.000	0.000	0.000
59	A	107	VAL	0	-0.041	-0.033	24.499	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	108	LYS	1	0.831	0.930	25.165	0.272	0.272	0.000	0.000	0.000	0.000
61	A	109	ASN	0	0.084	0.027	22.160	-0.036	-0.036	0.000	0.000	0.000	0.000
62	A	110	PRO	0	-0.041	-0.026	19.393	0.014	0.014	0.000	0.000	0.000	0.000
63	A	111	ASP	-1	-0.851	-0.882	18.389	-0.547	-0.547	0.000	0.000	0.000	0.000
64	A	112	THR	0	-0.025	-0.029	21.301	0.008	0.008	0.000	0.000	0.000	0.000
65	A	113	GLY	0	-0.039	-0.017	24.527	0.019	0.019	0.000	0.000	0.000	0.000
66	A	114	GLU	-1	-0.933	-0.968	26.668	-0.207	-0.207	0.000	0.000	0.000	0.000
67	A	115	VAL	0	-0.047	-0.014	27.419	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	116	VAL	0	-0.018	0.006	24.700	0.000	0.000	0.000	0.000	0.000	0.000
69	A	117	THR	0	-0.026	-0.025	28.128	0.011	0.011	0.000	0.000	0.000	0.000
70	A	118	PRO	0	0.029	0.016	30.540	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	119	PRO	0	0.008	0.009	33.591	0.004	0.004	0.000	0.000	0.000	0.000
72	A	120	VAL	0	-0.090	-0.038	34.778	0.004	0.004	0.000	0.000	0.000	0.000
73	A	121	ASP	-1	-0.872	-0.955	37.881	-0.085	-0.085	0.000	0.000	0.000	0.000
74	A	122	ASP	-1	-0.831	-0.899	39.657	-0.065	-0.065	0.000	0.000	0.000	0.000
75	A	123	VAL	0	-0.092	-0.054	41.817	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	124	THR	0	0.018	0.039	45.422	0.001	0.001	0.000	0.000	0.000	0.000
77	A	125	LYS	1	0.879	0.957	47.562	0.039	0.039	0.000	0.000	0.000	0.000
78	A	126	TYR	0	0.007	0.006	51.262	0.002	0.002	0.000	0.000	0.000	0.000
79	A	127	GLY	0	0.046	0.041	54.923	0.000	0.000	0.000	0.000	0.000	0.000
80	A	128	PRO	0	-0.043	-0.015	57.931	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	129	VAL	0	0.002	-0.006	60.712	0.001	0.001	0.000	0.000	0.000	0.000
82	A	130	ASP	-1	-0.832	-0.908	63.407	-0.022	-0.022	0.000	0.000	0.000	0.000
83	A	131	GLY	0	-0.026	-0.024	66.582	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	132	ASP	-1	-0.918	-0.946	68.605	-0.026	-0.026	0.000	0.000	0.000	0.000
85	A	133	SER	0	-0.035	-0.016	72.015	0.001	0.001	0.000	0.000	0.000	0.000
86	A	134	ILE	0	0.001	0.009	74.636	0.000	0.000	0.000	0.000	0.000	0.000
87	A	135	THR	0	-0.054	-0.040	77.456	0.001	0.001	0.000	0.000	0.000	0.000
88	A	136	SER	0	0.027	0.019	80.992	0.000	0.000	0.000	0.000	0.000	0.000
89	A	137	THR	0	0.002	0.004	84.468	0.000	0.000	0.000	0.000	0.000	0.000
90	A	138	GLU	-1	-0.881	-0.945	87.892	-0.015	-0.015	0.000	0.000	0.000	0.000
91	A	139	GLU	-1	-0.920	-0.968	91.001	-0.015	-0.015	0.000	0.000	0.000	0.000
92	A	140	ILE	0	-0.091	-0.039	93.125	0.000	0.000	0.000	0.000	0.000	0.000
93	A	141	PRO	0	-0.009	-0.009	96.340	0.000	0.000	0.000	0.000	0.000	0.000
94	A	142	PHE	0	0.015	0.009	100.016	0.000	0.000	0.000	0.000	0.000	0.000
95	A	143	ASP	-1	-1.000	-0.989	102.530	-0.010	-0.010	0.000	0.000	0.000	0.000
96	A	163	GLY	0	-0.006	-0.017	105.464	0.000	0.000	0.000	0.000	0.000	0.000
97	A	164	GLU	-1	-0.975	-0.981	100.972	-0.013	-0.013	0.000	0.000	0.000	0.000
98	A	165	PRO	0	0.020	0.011	98.658	0.000	0.000	0.000	0.000	0.000	0.000
99	A	166	GLY	0	0.032	0.017	96.411	0.000	0.000	0.000	0.000	0.000	0.000
100	A	167	THR	0	-0.037	-0.028	91.360	0.000	0.000	0.000	0.000	0.000	0.000
101	A	168	LYS	1	0.870	0.956	88.765	0.014	0.014	0.000	0.000	0.000	0.000
102	A	169	THR	0	0.000	-0.011	83.662	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	170	ILE	0	0.014	0.025	82.485	0.000	0.000	0.000	0.000	0.000	0.000
104	A	171	THR	0	-0.043	-0.041	78.120	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	172	THR	0	0.064	0.043	75.680	0.001	0.001	0.000	0.000	0.000	0.000
106	A	173	PRO	0	0.003	0.039	72.680	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	174	THR	0	0.010	-0.023	70.456	0.000	0.000	0.000	0.000	0.000	0.000
108	A	175	THR	0	-0.007	0.008	65.535	0.000	0.000	0.000	0.000	0.000	0.000
109	A	176	LYS	1	0.968	0.979	63.840	0.031	0.031	0.000	0.000	0.000	0.000
110	A	177	ASN	0	0.087	0.045	57.783	0.000	0.000	0.000	0.000	0.000	0.000
111	A	178	PRO	0	-0.055	-0.034	57.829	0.000	0.000	0.000	0.000	0.000	0.000
112	A	179	LEU	0	0.021	0.020	53.847	0.000	0.000	0.000	0.000	0.000	0.000
113	A	180	THR	0	-0.015	-0.008	57.678	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	181	GLY	0	-0.001	0.004	60.320	0.000	0.000	0.000	0.000	0.000	0.000
115	A	182	GLU	-1	-0.986	-0.996	62.637	-0.034	-0.034	0.000	0.000	0.000	0.000
116	A	183	LYS	1	0.881	0.951	64.497	0.025	0.025	0.000	0.000	0.000	0.000
117	A	184	VAL	0	-0.022	-0.007	62.267	0.000	0.000	0.000	0.000	0.000	0.000
118	A	185	GLY	0	-0.004	0.001	65.704	0.001	0.001	0.000	0.000	0.000	0.000
119	A	186	GLU	-1	-0.896	-0.951	68.716	-0.022	-0.022	0.000	0.000	0.000	0.000
120	A	187	GLY	0	-0.001	-0.006	72.271	0.000	0.000	0.000	0.000	0.000	0.000
121	A	188	LYS	1	0.894	0.934	73.290	0.014	0.014	0.000	0.000	0.000	0.000
122	A	189	SER	0	0.023	-0.011	76.737	0.000	0.000	0.000	0.000	0.000	0.000
123	A	190	THR	0	-0.071	-0.036	79.677	0.001	0.001	0.000	0.000	0.000	0.000
124	A	191	GLU	-1	-0.863	-0.933	82.222	-0.015	-0.015	0.000	0.000	0.000	0.000
125	A	192	LYS	1	0.877	0.926	80.800	0.017	0.017	0.000	0.000	0.000	0.000
126	A	193	VAL	0	0.021	0.008	86.688	0.000	0.000	0.000	0.000	0.000	0.000
127	A	194	THR	0	-0.046	-0.010	87.959	0.000	0.000	0.000	0.000	0.000	0.000
128	A	195	LYS	1	0.960	0.980	89.786	0.014	0.014	0.000	0.000	0.000	0.000
129	A	196	GLN	0	0.009	-0.004	93.628	0.000	0.000	0.000	0.000	0.000	0.000
130	A	197	PRO	0	0.008	0.007	95.998	0.000	0.000	0.000	0.000	0.000	0.000
131	A	198	VAL	0	-0.041	-0.004	98.898	0.000	0.000	0.000	0.000	0.000	0.000
132	A	199	ASP	-1	-0.901	-0.949	102.384	-0.010	-0.010	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:14:PHE)