FMO DATABASE

FMODB ID: RY9Z8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-848026.715719
FMO2-HF: Nuclear repulsion	796336.734337
FMO2-HF: Total energy	-51689.981382
FMO2-MP2: Total energy	-51843.783479

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.
-283.142	-284.579	33.729	-18.013	-14.281	-0.175

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 : 0.826 / q_NPA : 0.897

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	-0.854	-0.912	1.635	-136.976	-137.619	21.127	-12.358	-8.126	-0.121
4	B	20	PHE	0	0.041	0.026	3.813	7.133	7.347	0.005	-0.078	-0.141	-0.001
5	B	21	ASN	0	-0.051	-0.055	7.534	-1.592	-1.592	0.000	0.000	0.000	0.000
6	B	22	PRO	0	-0.006	-0.014	9.494	1.942	1.942	0.000	0.000	0.000	0.000
7	B	23	ASP	-1	-0.874	-0.921	12.751	-21.989	-21.989	0.000	0.000	0.000	0.000
8	B	24	LEU	0	-0.096	-0.016	10.934	1.055	1.055	0.000	0.000	0.000	0.000
9	B	25	LYS	1	0.894	0.926	14.656	16.027	16.027	0.000	0.000	0.000	0.000
10	B	26	PRO	0	0.004	-0.008	15.965	-0.774	-0.774	0.000	0.000	0.000	0.000
11	B	27	GLY	0	-0.050	-0.017	15.983	0.962	0.962	0.000	0.000	0.000	0.000
12	B	28	GLU	-1	-0.920	-0.938	14.882	-19.578	-19.578	0.000	0.000	0.000	0.000
13	B	29	GLU	-1	-0.872	-0.945	9.568	-30.296	-30.296	0.000	0.000	0.000	0.000
14	B	30	ARG	1	0.842	0.898	9.802	30.265	30.265	0.000	0.000	0.000	0.000
15	B	31	VAL	0	0.008	0.029	7.385	-3.767	-3.767	0.000	0.000	0.000	0.000
16	B	32	LYS	1	0.802	0.896	5.389	48.436	48.436	0.000	0.000	0.000	0.000
17	B	33	GLN	0	-0.042	-0.015	5.828	0.303	0.303	0.000	0.000	0.000	0.000
18	B	72	GLU	-1	-0.867	-0.921	3.470	-37.741	-37.247	0.002	-0.251	-0.246	0.000
19	B	73	ILE	0	-0.052	-0.026	1.821	-18.824	-20.818	12.593	-5.203	-5.397	-0.053
20	B	74	THR	0	0.028	-0.017	3.949	7.169	7.661	0.002	-0.123	-0.371	0.000
21	B	75	GLU	-1	-0.855	-0.910	5.705	-42.306	-42.306	0.000	0.000	0.000	0.000
22	B	76	TYR	0	-0.007	-0.019	6.016	4.110	4.110	0.000	0.000	0.000	0.000
23	B	77	GLY	0	0.057	0.038	9.823	-1.414	-1.414	0.000	0.000	0.000	0.000
24	B	78	GLY	0	-0.014	-0.019	12.629	-0.027	-0.027	0.000	0.000	0.000	0.000
25	B	79	GLU	-1	-0.871	-0.935	14.410	-16.801	-16.801	0.000	0.000	0.000	0.000
26	B	80	GLU	-1	-0.853	-0.915	17.884	-13.921	-13.921	0.000	0.000	0.000	0.000
27	B	81	ILE	0	-0.049	-0.003	20.009	0.416	0.416	0.000	0.000	0.000	0.000
28	B	82	LYS	1	0.875	0.915	23.119	12.691	12.691	0.000	0.000	0.000	0.000
29	B	83	PRO	0	0.011	0.011	26.594	-0.084	-0.084	0.000	0.000	0.000	0.000
30	B	84	GLY	0	0.019	0.021	28.883	0.171	0.171	0.000	0.000	0.000	0.000
31	B	85	HIS	0	-0.052	-0.049	31.710	-0.085	-0.085	0.000	0.000	0.000	0.000
32	B	86	LYS	1	0.844	0.911	31.966	9.969	9.969	0.000	0.000	0.000	0.000
33	B	87	ASP	-1	-0.814	-0.899	37.191	-7.717	-7.717	0.000	0.000	0.000	0.000
34	B	88	GLU	-1	-0.952	-0.990	36.744	-8.863	-8.863	0.000	0.000	0.000	0.000
35	B	89	PHE	0	0.002	-0.014	41.561	0.182	0.182	0.000	0.000	0.000	0.000
36	B	90	ASP	-1	-0.796	-0.912	43.402	-7.501	-7.501	0.000	0.000	0.000	0.000
37	B	91	PRO	0	-0.044	-0.030	45.222	0.145	0.145	0.000	0.000	0.000	0.000
38	B	92	ASN	0	-0.086	-0.050	45.829	0.288	0.288	0.000	0.000	0.000	0.000
39	B	93	ALA	0	0.005	0.022	45.822	0.017	0.017	0.000	0.000	0.000	0.000
40	B	94	PRO	0	-0.012	-0.016	47.764	0.157	0.157	0.000	0.000	0.000	0.000
41	B	95	LYS	1	0.850	0.903	50.645	5.557	5.557	0.000	0.000	0.000	0.000
42	B	96	GLY	0	-0.047	-0.031	52.576	0.052	0.052	0.000	0.000	0.000	0.000
43	B	97	SER	0	-0.085	-0.042	47.931	-0.086	-0.086	0.000	0.000	0.000	0.000
44	B	98	GLN	0	-0.002	-0.024	44.122	0.142	0.142	0.000	0.000	0.000	0.000
45	B	99	GLU	-1	-0.895	-0.925	39.950	-8.053	-8.053	0.000	0.000	0.000	0.000
46	B	100	ASP	-1	-0.824	-0.881	39.429	-7.965	-7.965	0.000	0.000	0.000	0.000
47	B	101	VAL	0	-0.049	-0.025	34.200	-0.032	-0.032	0.000	0.000	0.000	0.000
48	B	102	PRO	0	-0.025	-0.017	32.660	-0.149	-0.149	0.000	0.000	0.000	0.000
49	B	103	GLY	0	0.032	0.023	30.558	-0.093	-0.093	0.000	0.000	0.000	0.000
50	B	104	LYS	1	0.854	0.906	25.333	11.161	11.161	0.000	0.000	0.000	0.000
51	B	105	PRO	0	-0.001	0.006	22.890	0.079	0.079	0.000	0.000	0.000	0.000
52	B	106	GLY	0	0.028	0.015	21.744	-0.232	-0.232	0.000	0.000	0.000	0.000
53	B	107	VAL	0	-0.039	-0.032	15.443	-0.194	-0.194	0.000	0.000	0.000	0.000
54	B	108	LYS	1	0.864	0.927	16.860	17.681	17.681	0.000	0.000	0.000	0.000
55	B	109	ASN	0	0.073	0.032	9.474	-0.374	-0.374	0.000	0.000	0.000	0.000
56	B	110	PRO	0	-0.032	-0.012	12.279	1.029	1.029	0.000	0.000	0.000	0.000
57	B	111	ASP	-1	-0.789	-0.856	8.267	-31.789	-31.789	0.000	0.000	0.000	0.000
58	B	112	THR	0	-0.013	-0.018	10.652	1.335	1.335	0.000	0.000	0.000	0.000
59	B	113	GLY	0	-0.029	-0.015	13.312	1.402	1.402	0.000	0.000	0.000	0.000
60	B	114	GLU	-1	-0.971	-0.975	12.945	-22.346	-22.346	0.000	0.000	0.000	0.000
61	B	115	VAL	0	0.000	-0.012	16.175	-0.370	-0.370	0.000	0.000	0.000	0.000
62	B	116	VAL	0	0.001	0.014	13.083	0.159	0.159	0.000	0.000	0.000	0.000
63	B	117	THR	0	-0.045	-0.019	16.325	0.159	0.159	0.000	0.000	0.000	0.000
64	B	118	PRO	0	0.026	0.007	19.385	0.119	0.119	0.000	0.000	0.000	0.000
65	B	119	PRO	0	0.013	0.010	22.778	-0.127	-0.127	0.000	0.000	0.000	0.000
66	B	120	VAL	0	-0.067	-0.030	25.088	0.245	0.245	0.000	0.000	0.000	0.000
67	B	121	ASP	-1	-0.816	-0.891	28.020	-10.552	-10.552	0.000	0.000	0.000	0.000
68	B	122	ASP	-1	-0.822	-0.906	31.121	-9.944	-9.944	0.000	0.000	0.000	0.000
69	B	123	VAL	0	-0.050	-0.014	33.763	0.097	0.097	0.000	0.000	0.000	0.000
70	B	124	THR	0	-0.010	0.002	36.758	0.001	0.001	0.000	0.000	0.000	0.000
71	B	125	LYS	1	0.829	0.896	39.162	8.214	8.214	0.000	0.000	0.000	0.000
72	B	126	TYR	0	-0.019	-0.021	42.257	0.214	0.214	0.000	0.000	0.000	0.000
73	B	127	GLY	0	0.023	0.026	46.036	-0.041	-0.041	0.000	0.000	0.000	0.000
74	B	128	PRO	0	-0.051	-0.017	48.643	0.069	0.069	0.000	0.000	0.000	0.000
75	B	129	VAL	0	0.014	0.009	51.849	0.035	0.035	0.000	0.000	0.000	0.000
76	B	130	ASP	-1	-0.838	-0.898	54.514	-5.523	-5.523	0.000	0.000	0.000	0.000
77	B	131	GLY	0	-0.001	-0.022	57.795	-0.073	-0.073	0.000	0.000	0.000	0.000
78	B	132	ASP	-1	-0.897	-0.938	59.229	-5.320	-5.320	0.000	0.000	0.000	0.000
79	B	133	SER	0	-0.017	-0.006	62.675	-0.008	-0.008	0.000	0.000	0.000	0.000
80	B	134	ILE	0	0.005	0.010	63.630	0.024	0.024	0.000	0.000	0.000	0.000
81	B	135	THR	0	-0.020	-0.007	67.159	0.033	0.033	0.000	0.000	0.000	0.000
82	B	136	SER	0	0.004	0.008	70.909	-0.013	-0.013	0.000	0.000	0.000	0.000
83	B	137	THR	0	-0.011	-0.015	73.632	0.003	0.003	0.000	0.000	0.000	0.000
84	B	138	GLU	-1	-0.934	-0.957	76.429	-4.265	-4.265	0.000	0.000	0.000	0.000
85	B	139	GLU	-1	-0.894	-0.958	79.768	-3.857	-3.857	0.000	0.000	0.000	0.000
86	B	140	ILE	0	-0.069	-0.027	83.363	-0.019	-0.019	0.000	0.000	0.000	0.000
87	B	141	PRO	0	-0.003	0.002	85.704	0.039	0.039	0.000	0.000	0.000	0.000
88	B	142	PHE	0	0.006	0.002	88.871	0.006	0.006	0.000	0.000	0.000	0.000
89	B	143	ASP	-1	-0.814	-0.883	92.275	-3.479	-3.479	0.000	0.000	0.000	0.000
90	B	144	LYS	1	0.803	0.876	95.078	3.391	3.391	0.000	0.000	0.000	0.000
91	B	145	LYS	1	0.838	0.922	96.821	3.402	3.402	0.000	0.000	0.000	0.000
92	B	146	ARG	1	0.968	0.987	101.675	3.110	3.110	0.000	0.000	0.000	0.000
93	B	159	VAL	0	-0.073	-0.050	102.003	0.009	0.009	0.000	0.000	0.000	0.000
94	B	160	VAL	0	0.032	0.033	105.048	-0.005	-0.005	0.000	0.000	0.000	0.000
95	B	161	GLN	0	0.005	0.000	99.474	-0.019	-0.019	0.000	0.000	0.000	0.000
96	B	162	LYS	1	0.914	0.959	94.692	3.450	3.450	0.000	0.000	0.000	0.000
97	B	163	GLY	0	0.054	0.031	96.246	-0.015	-0.015	0.000	0.000	0.000	0.000
98	B	164	GLU	-1	-0.941	-0.959	92.012	-3.551	-3.551	0.000	0.000	0.000	0.000
99	B	165	PRO	0	0.040	0.019	87.842	0.007	0.007	0.000	0.000	0.000	0.000
100	B	166	GLY	0	0.014	-0.002	87.083	0.006	0.006	0.000	0.000	0.000	0.000
101	B	167	THR	0	-0.006	-0.006	82.346	-0.007	-0.007	0.000	0.000	0.000	0.000
102	B	168	LYS	1	0.820	0.895	78.022	4.199	4.199	0.000	0.000	0.000	0.000
103	B	169	THR	0	-0.004	0.004	74.347	0.004	0.004	0.000	0.000	0.000	0.000
104	B	170	ILE	0	-0.005	-0.004	71.756	0.010	0.010	0.000	0.000	0.000	0.000
105	B	171	THR	0	0.020	0.002	68.695	-0.033	-0.033	0.000	0.000	0.000	0.000
106	B	172	THR	0	-0.009	-0.018	65.219	0.035	0.035	0.000	0.000	0.000	0.000
107	B	173	PRO	0	-0.007	0.011	63.190	-0.044	-0.044	0.000	0.000	0.000	0.000
108	B	174	THR	0	-0.001	-0.020	60.252	-0.048	-0.048	0.000	0.000	0.000	0.000
109	B	175	THR	0	-0.002	0.010	55.634	0.006	0.006	0.000	0.000	0.000	0.000
110	B	176	LYS	1	0.908	0.958	54.760	5.728	5.728	0.000	0.000	0.000	0.000
111	B	177	ASN	0	0.101	0.051	47.353	-0.084	-0.084	0.000	0.000	0.000	0.000
112	B	178	PRO	0	-0.037	-0.017	48.827	0.084	0.084	0.000	0.000	0.000	0.000
113	B	179	LEU	0	0.005	0.014	44.244	0.052	0.052	0.000	0.000	0.000	0.000
114	B	180	THR	0	-0.006	-0.006	47.740	0.014	0.014	0.000	0.000	0.000	0.000
115	B	181	GLY	0	-0.033	-0.010	50.176	0.102	0.102	0.000	0.000	0.000	0.000
116	B	182	GLU	-1	-0.981	-0.981	50.586	-6.281	-6.281	0.000	0.000	0.000	0.000
117	B	183	LYS	1	0.837	0.895	53.853	5.345	5.345	0.000	0.000	0.000	0.000
118	B	184	VAL	0	-0.001	-0.006	51.448	-0.049	-0.049	0.000	0.000	0.000	0.000
119	B	185	GLY	0	-0.008	0.002	54.731	-0.018	-0.018	0.000	0.000	0.000	0.000
120	B	186	GLU	-1	-0.856	-0.912	57.743	-5.162	-5.162	0.000	0.000	0.000	0.000
121	B	187	GLY	0	-0.026	-0.014	61.430	-0.028	-0.028	0.000	0.000	0.000	0.000
122	B	188	LYS	1	0.910	0.942	63.185	5.117	5.117	0.000	0.000	0.000	0.000
123	B	189	SER	0	0.062	0.030	66.660	-0.031	-0.031	0.000	0.000	0.000	0.000
124	B	190	THR	0	-0.046	-0.008	69.475	0.047	0.047	0.000	0.000	0.000	0.000
125	B	191	GLU	-1	-0.787	-0.877	72.352	-4.266	-4.266	0.000	0.000	0.000	0.000
126	B	192	LYS	1	0.934	0.964	75.812	4.237	4.237	0.000	0.000	0.000	0.000
127	B	193	VAL	0	0.010	0.002	78.272	-0.005	-0.005	0.000	0.000	0.000	0.000
128	B	194	THR	0	-0.038	-0.016	79.861	0.021	0.021	0.000	0.000	0.000	0.000
129	B	195	LYS	1	0.828	0.919	82.704	3.707	3.707	0.000	0.000	0.000	0.000
130	B	196	GLN	0	0.037	0.018	86.172	-0.014	-0.014	0.000	0.000	0.000	0.000
131	B	197	PRO	0	0.000	0.003	88.004	0.017	0.017	0.000	0.000	0.000	0.000
132	B	198	VAL	0	-0.035	-0.013	90.563	0.019	0.019	0.000	0.000	0.000	0.000
133	B	199	ASP	-1	-0.839	-0.930	94.264	-3.425	-3.425	0.000	0.000	0.000	0.000
134	B	200	GLU	-1	-0.849	-0.921	96.689	-3.319	-3.319	0.000	0.000	0.000	0.000
135	B	201	ILE	0	-0.019	-0.011	99.034	0.011	0.011	0.000	0.000	0.000	0.000
136	B	202	VAL	0	-0.027	-0.022	102.681	0.014	0.014	0.000	0.000	0.000	0.000
137	B	203	GLU	-1	-0.935	-0.968	105.457	-3.015	-3.015	0.000	0.000	0.000	0.000

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