FMO DATABASE

FMODB ID: QNYRY

Calculation Name: 5TU9-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5TU9

Chain ID: B

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	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	137
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-849136.575486
FMO2-HF: Nuclear repulsion	797446.21842
FMO2-HF: Total energy	-51690.357066
FMO2-MP2: Total energy	-51844.199035

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(B:17:LYS)

Summations of interaction energy for fragment #1(B:17:LYS)

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.
-305.524	-306.46	37.078	-19.155	-16.985	-0.196

Interaction energy analysis for fragmet #1(B:17:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.800 / q_NPA : 0.875

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	B	19	GLU	-1	-0.817	-0.895	1.649	-146.683	-148.444	24.036	-12.743	-9.531	-0.132
4	B	20	PHE	0	0.057	0.035	3.905	7.585	7.789	0.005	-0.064	-0.144	0.000
5	B	21	ASN	0	-0.051	-0.042	7.464	-2.562	-2.562	0.000	0.000	0.000	0.000
6	B	22	PRO	0	0.019	0.009	9.279	1.845	1.845	0.000	0.000	0.000	0.000
7	B	23	ASP	-1	-0.876	-0.922	12.749	-23.510	-23.510	0.000	0.000	0.000	0.000
8	B	24	LEU	0	-0.025	0.013	10.418	0.671	0.671	0.000	0.000	0.000	0.000
9	B	25	LYS	1	0.893	0.917	14.307	15.727	15.727	0.000	0.000	0.000	0.000
10	B	26	PRO	0	-0.014	-0.013	15.773	-0.941	-0.941	0.000	0.000	0.000	0.000
11	B	27	GLY	0	-0.016	-0.008	15.618	1.078	1.078	0.000	0.000	0.000	0.000
12	B	28	GLU	-1	-0.908	-0.926	14.147	-19.670	-19.670	0.000	0.000	0.000	0.000
13	B	29	GLU	-1	-0.837	-0.919	8.755	-33.239	-33.239	0.000	0.000	0.000	0.000
14	B	30	ARG	1	0.731	0.832	9.515	31.406	31.406	0.000	0.000	0.000	0.000
15	B	31	VAL	0	-0.009	0.008	7.390	-4.193	-4.193	0.000	0.000	0.000	0.000
16	B	32	LYS	1	0.809	0.898	5.209	50.387	50.387	0.000	0.000	0.000	0.000
17	B	33	GLN	0	-0.078	-0.050	5.897	0.456	0.456	0.000	0.000	0.000	0.000
18	B	72	GLU	-1	-0.788	-0.874	2.810	-41.577	-40.823	0.125	-0.330	-0.550	0.000
19	B	73	ILE	0	-0.094	-0.040	1.837	-22.126	-22.952	12.911	-5.856	-6.230	-0.064
20	B	74	THR	0	0.035	-0.001	3.839	7.657	8.269	0.002	-0.149	-0.464	0.000
21	B	75	GLU	-1	-0.787	-0.866	4.935	-43.056	-42.975	-0.001	-0.013	-0.066	0.000
22	B	76	TYR	0	-0.054	-0.028	5.899	4.597	4.597	0.000	0.000	0.000	0.000
23	B	77	GLY	0	0.064	0.030	9.346	-0.623	-0.623	0.000	0.000	0.000	0.000
24	B	78	GLY	0	-0.013	-0.011	12.647	-0.662	-0.662	0.000	0.000	0.000	0.000
25	B	79	GLU	-1	-0.864	-0.936	14.664	-17.140	-17.140	0.000	0.000	0.000	0.000
26	B	80	GLU	-1	-0.844	-0.911	17.984	-14.090	-14.090	0.000	0.000	0.000	0.000
27	B	81	ILE	0	-0.033	-0.005	19.899	0.700	0.700	0.000	0.000	0.000	0.000
28	B	82	LYS	1	0.865	0.909	22.985	13.142	13.142	0.000	0.000	0.000	0.000
29	B	83	PRO	0	0.005	0.011	26.391	-0.064	-0.064	0.000	0.000	0.000	0.000
30	B	84	GLY	0	0.023	0.028	28.877	0.147	0.147	0.000	0.000	0.000	0.000
31	B	85	HIS	0	-0.062	-0.054	31.618	-0.085	-0.085	0.000	0.000	0.000	0.000
32	B	86	LYS	1	0.850	0.919	31.983	9.885	9.885	0.000	0.000	0.000	0.000
33	B	87	ASP	-1	-0.808	-0.874	37.299	-7.687	-7.687	0.000	0.000	0.000	0.000
34	B	88	GLU	-1	-0.946	-0.992	36.766	-8.859	-8.859	0.000	0.000	0.000	0.000
35	B	89	PHE	0	0.003	-0.022	41.534	0.201	0.201	0.000	0.000	0.000	0.000
36	B	90	ASP	-1	-0.794	-0.895	43.465	-7.468	-7.468	0.000	0.000	0.000	0.000
37	B	91	PRO	0	-0.040	-0.027	45.370	0.128	0.128	0.000	0.000	0.000	0.000
38	B	92	ASN	0	-0.089	-0.056	45.852	0.273	0.273	0.000	0.000	0.000	0.000
39	B	93	ALA	0	0.009	0.024	45.855	0.044	0.044	0.000	0.000	0.000	0.000
40	B	94	PRO	0	-0.014	-0.018	47.842	0.147	0.147	0.000	0.000	0.000	0.000
41	B	95	LYS	1	0.856	0.910	50.828	5.552	5.552	0.000	0.000	0.000	0.000
42	B	96	GLY	0	-0.048	-0.029	52.527	0.064	0.064	0.000	0.000	0.000	0.000
43	B	97	SER	0	-0.091	-0.047	48.136	-0.085	-0.085	0.000	0.000	0.000	0.000
44	B	98	GLN	0	-0.016	-0.031	43.923	0.156	0.156	0.000	0.000	0.000	0.000
45	B	99	GLU	-1	-0.870	-0.924	39.866	-8.006	-8.006	0.000	0.000	0.000	0.000
46	B	100	ASP	-1	-0.809	-0.865	39.469	-7.964	-7.964	0.000	0.000	0.000	0.000
47	B	101	VAL	0	-0.050	-0.028	34.219	-0.056	-0.056	0.000	0.000	0.000	0.000
48	B	102	PRO	0	-0.004	-0.001	32.713	-0.191	-0.191	0.000	0.000	0.000	0.000
49	B	103	GLY	0	0.069	0.039	30.335	-0.108	-0.108	0.000	0.000	0.000	0.000
50	B	104	LYS	1	0.758	0.856	24.970	10.989	10.989	0.000	0.000	0.000	0.000
51	B	105	PRO	0	-0.017	0.004	22.855	0.110	0.110	0.000	0.000	0.000	0.000
52	B	106	GLY	0	0.043	0.029	21.749	-0.260	-0.260	0.000	0.000	0.000	0.000
53	B	107	VAL	0	-0.062	-0.038	15.509	-0.149	-0.149	0.000	0.000	0.000	0.000
54	B	108	LYS	1	0.812	0.907	16.491	18.105	18.105	0.000	0.000	0.000	0.000
55	B	109	ASN	0	0.035	0.001	9.745	-1.262	-1.262	0.000	0.000	0.000	0.000
56	B	110	PRO	0	-0.028	-0.006	11.631	1.381	1.381	0.000	0.000	0.000	0.000
57	B	111	ASP	-1	-0.804	-0.876	8.218	-33.381	-33.381	0.000	0.000	0.000	0.000
58	B	112	THR	0	-0.024	-0.019	10.680	1.269	1.269	0.000	0.000	0.000	0.000
59	B	113	GLY	0	-0.030	-0.013	13.493	1.390	1.390	0.000	0.000	0.000	0.000
60	B	114	GLU	-1	-0.902	-0.945	12.399	-23.224	-23.224	0.000	0.000	0.000	0.000
61	B	115	VAL	0	-0.003	-0.010	16.085	-0.474	-0.474	0.000	0.000	0.000	0.000
62	B	116	VAL	0	0.026	0.026	13.005	0.536	0.536	0.000	0.000	0.000	0.000
63	B	117	THR	0	-0.069	-0.032	16.136	0.183	0.183	0.000	0.000	0.000	0.000
64	B	118	PRO	0	0.039	0.012	19.351	0.100	0.100	0.000	0.000	0.000	0.000
65	B	119	PRO	0	0.021	0.016	22.867	-0.242	-0.242	0.000	0.000	0.000	0.000
66	B	120	VAL	0	-0.058	-0.020	25.139	0.276	0.276	0.000	0.000	0.000	0.000
67	B	121	ASP	-1	-0.818	-0.902	27.962	-10.649	-10.649	0.000	0.000	0.000	0.000
68	B	122	ASP	-1	-0.827	-0.908	30.938	-10.040	-10.040	0.000	0.000	0.000	0.000
69	B	123	VAL	0	-0.058	-0.024	33.671	0.104	0.104	0.000	0.000	0.000	0.000
70	B	124	THR	0	-0.001	-0.001	36.693	-0.015	-0.015	0.000	0.000	0.000	0.000
71	B	125	LYS	1	0.823	0.909	39.942	8.143	8.143	0.000	0.000	0.000	0.000
72	B	126	TYR	0	-0.031	-0.046	42.147	0.180	0.180	0.000	0.000	0.000	0.000
73	B	127	GLY	0	0.034	0.027	46.000	-0.050	-0.050	0.000	0.000	0.000	0.000
74	B	128	PRO	0	-0.056	-0.021	48.710	0.058	0.058	0.000	0.000	0.000	0.000
75	B	129	VAL	0	0.017	0.013	51.946	0.046	0.046	0.000	0.000	0.000	0.000
76	B	130	ASP	-1	-0.832	-0.908	54.329	-5.522	-5.522	0.000	0.000	0.000	0.000
77	B	131	GLY	0	0.013	-0.003	57.803	-0.067	-0.067	0.000	0.000	0.000	0.000
78	B	132	ASP	-1	-0.865	-0.909	59.418	-5.368	-5.368	0.000	0.000	0.000	0.000
79	B	133	SER	0	-0.030	-0.013	62.533	0.006	0.006	0.000	0.000	0.000	0.000
80	B	134	ILE	0	0.021	0.022	63.537	0.041	0.041	0.000	0.000	0.000	0.000
81	B	135	THR	0	-0.026	-0.017	67.010	0.029	0.029	0.000	0.000	0.000	0.000
82	B	136	SER	0	-0.050	-0.029	70.799	-0.022	-0.022	0.000	0.000	0.000	0.000
83	B	137	THR	0	-0.018	-0.040	73.772	0.002	0.002	0.000	0.000	0.000	0.000
84	B	138	GLU	-1	-0.878	-0.910	76.201	-4.288	-4.288	0.000	0.000	0.000	0.000
85	B	139	GLU	-1	-0.882	-0.955	79.983	-3.841	-3.841	0.000	0.000	0.000	0.000
86	B	140	ILE	0	-0.078	-0.026	83.583	-0.022	-0.022	0.000	0.000	0.000	0.000
87	B	141	PRO	0	0.003	-0.002	85.798	0.040	0.040	0.000	0.000	0.000	0.000
88	B	142	PHE	0	-0.005	-0.007	88.917	0.003	0.003	0.000	0.000	0.000	0.000
89	B	143	ASP	-1	-0.819	-0.885	92.395	-3.418	-3.418	0.000	0.000	0.000	0.000
90	B	144	LYS	1	0.775	0.861	95.411	3.384	3.384	0.000	0.000	0.000	0.000
91	B	145	LYS	1	0.811	0.901	96.795	3.404	3.404	0.000	0.000	0.000	0.000
92	B	146	ARG	1	0.964	0.993	102.293	3.093	3.093	0.000	0.000	0.000	0.000
93	B	159	VAL	0	-0.063	-0.045	102.149	0.009	0.009	0.000	0.000	0.000	0.000
94	B	160	VAL	0	0.014	0.026	105.154	-0.012	-0.012	0.000	0.000	0.000	0.000
95	B	161	GLN	0	0.014	0.008	98.949	0.004	0.004	0.000	0.000	0.000	0.000
96	B	162	LYS	1	0.899	0.943	94.636	3.443	3.443	0.000	0.000	0.000	0.000
97	B	163	GLY	0	0.063	0.033	96.669	-0.016	-0.016	0.000	0.000	0.000	0.000
98	B	164	GLU	-1	-0.934	-0.965	92.139	-3.535	-3.535	0.000	0.000	0.000	0.000
99	B	165	PRO	0	0.066	0.040	87.962	0.007	0.007	0.000	0.000	0.000	0.000
100	B	166	GLY	0	0.004	0.011	87.377	0.023	0.023	0.000	0.000	0.000	0.000
101	B	167	THR	0	-0.010	-0.012	82.486	-0.002	-0.002	0.000	0.000	0.000	0.000
102	B	168	LYS	1	0.839	0.909	78.038	4.197	4.197	0.000	0.000	0.000	0.000
103	B	169	THR	0	-0.010	0.006	74.728	0.013	0.013	0.000	0.000	0.000	0.000
104	B	170	ILE	0	-0.015	-0.001	71.739	0.010	0.010	0.000	0.000	0.000	0.000
105	B	171	THR	0	0.008	-0.011	68.924	-0.028	-0.028	0.000	0.000	0.000	0.000
106	B	172	THR	0	0.011	-0.005	65.466	0.040	0.040	0.000	0.000	0.000	0.000
107	B	173	PRO	0	0.000	0.015	63.404	-0.043	-0.043	0.000	0.000	0.000	0.000
108	B	174	THR	0	-0.015	-0.026	60.407	-0.047	-0.047	0.000	0.000	0.000	0.000
109	B	175	THR	0	-0.004	0.001	55.716	0.002	0.002	0.000	0.000	0.000	0.000
110	B	176	LYS	1	0.859	0.912	54.850	5.694	5.694	0.000	0.000	0.000	0.000
111	B	177	ASN	0	0.057	0.031	47.621	-0.108	-0.108	0.000	0.000	0.000	0.000
112	B	178	PRO	0	-0.029	-0.018	48.464	0.079	0.079	0.000	0.000	0.000	0.000
113	B	179	LEU	0	0.002	0.016	44.048	0.037	0.037	0.000	0.000	0.000	0.000
114	B	180	THR	0	-0.036	-0.018	48.029	0.002	0.002	0.000	0.000	0.000	0.000
115	B	181	GLY	0	-0.040	-0.010	50.513	0.107	0.107	0.000	0.000	0.000	0.000
116	B	182	GLU	-1	-0.907	-0.952	50.333	-6.360	-6.360	0.000	0.000	0.000	0.000
117	B	183	LYS	1	0.854	0.911	54.080	5.321	5.321	0.000	0.000	0.000	0.000
118	B	184	VAL	0	-0.014	-0.011	51.558	-0.020	-0.020	0.000	0.000	0.000	0.000
119	B	185	GLY	0	-0.004	0.005	54.893	-0.026	-0.026	0.000	0.000	0.000	0.000
120	B	186	GLU	-1	-0.865	-0.923	57.756	-5.152	-5.152	0.000	0.000	0.000	0.000
121	B	187	GLY	0	-0.006	0.004	61.447	-0.039	-0.039	0.000	0.000	0.000	0.000
122	B	188	LYS	1	0.895	0.935	63.360	5.120	5.120	0.000	0.000	0.000	0.000
123	B	189	SER	0	0.053	0.027	66.815	-0.029	-0.029	0.000	0.000	0.000	0.000
124	B	190	THR	0	-0.055	-0.012	69.567	0.044	0.044	0.000	0.000	0.000	0.000
125	B	191	GLU	-1	-0.779	-0.883	72.348	-4.258	-4.258	0.000	0.000	0.000	0.000
126	B	192	LYS	1	0.942	0.974	75.855	4.208	4.208	0.000	0.000	0.000	0.000
127	B	193	VAL	0	0.012	0.009	78.493	-0.006	-0.006	0.000	0.000	0.000	0.000
128	B	194	THR	0	-0.046	-0.023	79.629	0.014	0.014	0.000	0.000	0.000	0.000
129	B	195	LYS	1	0.816	0.910	82.672	3.689	3.689	0.000	0.000	0.000	0.000
130	B	196	GLN	0	0.053	0.024	86.307	-0.016	-0.016	0.000	0.000	0.000	0.000
131	B	197	PRO	0	0.013	0.010	88.033	0.015	0.015	0.000	0.000	0.000	0.000
132	B	198	VAL	0	-0.061	-0.027	90.613	0.019	0.019	0.000	0.000	0.000	0.000
133	B	199	ASP	-1	-0.795	-0.907	94.356	-3.423	-3.423	0.000	0.000	0.000	0.000
134	B	200	GLU	-1	-0.827	-0.907	96.969	-3.310	-3.310	0.000	0.000	0.000	0.000
135	B	201	ILE	0	-0.026	-0.005	99.359	0.011	0.011	0.000	0.000	0.000	0.000
136	B	202	VAL	0	-0.022	-0.026	103.054	0.018	0.018	0.000	0.000	0.000	0.000
137	B	203	GLU	-1	-0.941	-0.970	105.686	-3.001	-3.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:17:LYS)