FMO DATABASE

FMODB ID: RY9G8

Calculation Name: 5IIP-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5IIP

Chain ID: D

ChEMBL ID:

UniProt ID: A0A160

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	117
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-944847.590968
FMO2-HF: Nuclear repulsion	898096.135315
FMO2-HF: Total energy	-46751.455654
FMO2-MP2: Total energy	-46888.311697

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:253:GLY)

Summations of interaction energy for fragment #1(D:253:GLY)

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.
-3.806	-0.874	0.192	-1.274	-1.85	-0.002

Interaction energy analysis for fragmet #1(D:253:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : -0.001

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	255	MET	0	-0.063	0.003	2.787	-2.023	0.745	0.195	-1.247	-1.716	-0.002
4	D	256	ILE	0	0.022	0.018	4.583	-0.668	-0.672	-0.001	-0.009	0.014	0.000
5	D	257	LYS	1	1.002	0.980	7.682	0.447	0.447	0.000	0.000	0.000	0.000
6	D	258	PRO	0	-0.013	0.016	9.673	0.054	0.054	0.000	0.000	0.000	0.000
7	D	259	ILE	0	-0.010	-0.007	12.369	-0.021	-0.021	0.000	0.000	0.000	0.000
8	D	260	THR	0	-0.007	-0.013	15.255	0.021	0.021	0.000	0.000	0.000	0.000
9	D	261	ILE	0	-0.001	0.001	17.957	-0.004	-0.004	0.000	0.000	0.000	0.000
10	D	262	GLN	0	-0.008	0.003	20.812	0.005	0.005	0.000	0.000	0.000	0.000
11	D	263	ALA	0	0.043	0.003	23.162	0.006	0.006	0.000	0.000	0.000	0.000
12	D	264	GLU	-1	-0.850	-0.920	25.093	-0.024	-0.024	0.000	0.000	0.000	0.000
13	D	265	ALA	0	-0.054	0.005	26.272	0.001	0.001	0.000	0.000	0.000	0.000
14	D	266	THR	0	-0.012	-0.047	28.221	0.006	0.006	0.000	0.000	0.000	0.000
15	D	267	LEU	0	0.048	0.020	28.141	-0.003	-0.003	0.000	0.000	0.000	0.000
16	D	268	ASN	0	-0.001	-0.008	29.090	0.000	0.000	0.000	0.000	0.000	0.000
17	D	269	ASP	-1	-0.827	-0.888	27.746	-0.033	-0.033	0.000	0.000	0.000	0.000
18	D	270	ALA	0	0.014	-0.001	25.017	-0.006	-0.006	0.000	0.000	0.000	0.000
19	D	271	VAL	0	0.035	0.020	25.197	-0.002	-0.002	0.000	0.000	0.000	0.000
20	D	272	HIS	0	-0.019	-0.008	27.162	-0.004	-0.004	0.000	0.000	0.000	0.000
21	D	273	ILE	0	-0.025	-0.016	21.574	-0.007	-0.007	0.000	0.000	0.000	0.000
22	D	274	MET	0	0.007	0.029	22.274	-0.009	-0.009	0.000	0.000	0.000	0.000
23	D	275	ARG	1	0.944	0.999	23.269	0.045	0.045	0.000	0.000	0.000	0.000
24	D	276	GLN	0	-0.050	-0.025	23.912	-0.011	-0.011	0.000	0.000	0.000	0.000
25	D	277	LYS	1	0.911	0.952	18.857	0.093	0.093	0.000	0.000	0.000	0.000
26	D	278	ARG	1	0.915	0.949	20.313	0.030	0.030	0.000	0.000	0.000	0.000
27	D	279	VAL	0	-0.036	-0.017	17.023	0.001	0.001	0.000	0.000	0.000	0.000
28	D	280	ASP	-1	-0.898	-0.956	19.277	0.049	0.049	0.000	0.000	0.000	0.000
29	D	281	THR	0	0.005	-0.019	17.368	0.006	0.006	0.000	0.000	0.000	0.000
30	D	282	ILE	0	-0.108	-0.042	17.835	-0.013	-0.013	0.000	0.000	0.000	0.000
31	D	283	PHE	0	0.025	-0.002	14.354	0.019	0.019	0.000	0.000	0.000	0.000
32	D	284	VAL	0	-0.005	0.006	17.543	-0.019	-0.019	0.000	0.000	0.000	0.000
33	D	285	VAL	0	0.013	0.001	15.902	0.007	0.007	0.000	0.000	0.000	0.000
34	D	286	ASP	-1	-0.749	-0.878	19.276	-0.047	-0.047	0.000	0.000	0.000	0.000
35	D	287	SER	0	-0.005	0.010	20.818	-0.010	-0.010	0.000	0.000	0.000	0.000
36	D	288	ASN	0	-0.105	-0.058	20.586	-0.014	-0.014	0.000	0.000	0.000	0.000
37	D	289	ASN	0	-0.036	-0.025	15.598	-0.020	-0.020	0.000	0.000	0.000	0.000
38	D	290	HIS	0	0.027	0.015	15.980	-0.005	-0.005	0.000	0.000	0.000	0.000
39	D	291	LEU	0	-0.045	-0.027	13.954	0.000	0.000	0.000	0.000	0.000	0.000
40	D	292	LEU	0	-0.025	-0.012	17.103	0.010	0.010	0.000	0.000	0.000	0.000
41	D	293	GLY	0	0.014	-0.015	19.435	0.008	0.008	0.000	0.000	0.000	0.000
42	D	294	PHE	0	-0.064	-0.019	16.930	-0.002	-0.002	0.000	0.000	0.000	0.000
43	D	295	LEU	0	0.033	0.017	19.936	-0.002	-0.002	0.000	0.000	0.000	0.000
44	D	296	ASP	-1	-0.811	-0.895	21.067	0.052	0.052	0.000	0.000	0.000	0.000
45	D	297	ILE	0	0.019	-0.011	22.990	-0.005	-0.005	0.000	0.000	0.000	0.000
46	D	298	GLU	-1	-0.878	-0.931	26.132	0.024	0.024	0.000	0.000	0.000	0.000
47	D	299	ASP	-1	-0.846	-0.924	24.660	0.046	0.046	0.000	0.000	0.000	0.000
48	D	300	ILE	0	-0.012	-0.024	24.860	-0.005	-0.005	0.000	0.000	0.000	0.000
49	D	301	ASN	0	-0.070	-0.031	28.746	-0.007	-0.007	0.000	0.000	0.000	0.000
50	D	302	GLN	0	-0.075	-0.042	29.119	-0.002	-0.002	0.000	0.000	0.000	0.000
51	D	303	GLY	0	0.042	0.026	31.422	-0.001	-0.001	0.000	0.000	0.000	0.000
52	D	304	ILE	0	-0.025	-0.011	32.310	-0.003	-0.003	0.000	0.000	0.000	0.000
53	D	305	ARG	1	0.902	0.968	34.852	-0.014	-0.014	0.000	0.000	0.000	0.000
54	D	306	GLY	0	0.021	0.013	36.291	0.002	0.002	0.000	0.000	0.000	0.000
55	D	307	HIS	0	-0.068	-0.041	36.802	0.000	0.000	0.000	0.000	0.000	0.000
56	D	308	LYS	1	0.936	0.980	33.030	-0.019	-0.019	0.000	0.000	0.000	0.000
57	D	309	SER	0	-0.038	-0.040	31.928	-0.003	-0.003	0.000	0.000	0.000	0.000
58	D	310	LEU	0	0.039	0.020	24.713	0.004	0.004	0.000	0.000	0.000	0.000
59	D	311	ARG	1	0.906	0.920	26.816	0.014	0.014	0.000	0.000	0.000	0.000
60	D	312	ASP	-1	-0.912	-0.927	28.121	0.017	0.017	0.000	0.000	0.000	0.000
61	D	313	THR	0	-0.048	-0.046	27.977	0.003	0.003	0.000	0.000	0.000	0.000
62	D	314	MET	0	-0.066	0.006	23.405	0.002	0.002	0.000	0.000	0.000	0.000
63	D	315	GLN	0	-0.031	-0.013	22.422	0.006	0.006	0.000	0.000	0.000	0.000
64	D	316	GLN	0	-0.009	-0.026	21.843	0.003	0.003	0.000	0.000	0.000	0.000
65	D	317	HIS	0	-0.031	0.005	21.556	0.011	0.011	0.000	0.000	0.000	0.000
66	D	318	ILE	0	0.011	0.001	15.743	0.010	0.010	0.000	0.000	0.000	0.000
67	D	319	TYR	0	-0.049	-0.013	13.067	-0.007	-0.007	0.000	0.000	0.000	0.000
68	D	320	THR	0	0.036	0.005	12.218	0.000	0.000	0.000	0.000	0.000	0.000
69	D	321	VAL	0	-0.047	-0.035	7.581	0.032	0.032	0.000	0.000	0.000	0.000
70	D	322	GLN	0	0.065	0.027	8.944	-0.051	-0.051	0.000	0.000	0.000	0.000
71	D	323	ILE	0	-0.005	-0.011	4.025	0.157	0.257	-0.001	-0.016	-0.083	0.000
72	D	324	ASP	-1	-0.943	-0.958	4.864	-0.210	-0.142	-0.001	-0.002	-0.065	0.000
73	D	325	SER	0	-0.026	0.001	6.773	0.063	0.063	0.000	0.000	0.000	0.000
74	D	326	LYS	1	0.893	0.937	5.731	-0.177	-0.177	0.000	0.000	0.000	0.000
75	D	327	LEU	0	0.064	0.021	5.988	-0.123	-0.123	0.000	0.000	0.000	0.000
76	D	328	GLN	0	0.043	0.000	7.689	-0.217	-0.217	0.000	0.000	0.000	0.000
77	D	329	ASP	-1	-0.872	-0.922	10.666	0.325	0.325	0.000	0.000	0.000	0.000
78	D	330	SER	0	-0.043	-0.022	9.471	-0.034	-0.034	0.000	0.000	0.000	0.000
79	D	331	VAL	0	0.029	0.019	11.237	-0.096	-0.096	0.000	0.000	0.000	0.000
80	D	332	ARG	1	0.983	0.984	12.553	-0.436	-0.436	0.000	0.000	0.000	0.000
81	D	333	THR	0	-0.030	-0.016	15.155	-0.068	-0.068	0.000	0.000	0.000	0.000
82	D	334	ILE	0	0.034	0.016	10.615	-0.069	-0.069	0.000	0.000	0.000	0.000
83	D	335	LEU	0	0.014	0.018	14.837	-0.059	-0.059	0.000	0.000	0.000	0.000
84	D	336	LYS	1	0.929	0.974	17.013	-0.280	-0.280	0.000	0.000	0.000	0.000
85	D	337	ARG	1	0.922	0.983	18.269	-0.252	-0.252	0.000	0.000	0.000	0.000
86	D	338	ASN	0	0.021	-0.005	19.403	0.015	0.015	0.000	0.000	0.000	0.000
87	D	339	VAL	0	-0.019	0.002	15.641	-0.018	-0.018	0.000	0.000	0.000	0.000
88	D	340	ARG	1	1.034	1.002	16.000	-0.065	-0.065	0.000	0.000	0.000	0.000
89	D	341	ASN	0	0.008	0.010	13.196	0.027	0.027	0.000	0.000	0.000	0.000
90	D	342	VAL	0	0.015	0.005	10.352	-0.029	-0.029	0.000	0.000	0.000	0.000
91	D	343	PRO	0	-0.002	0.003	9.526	0.089	0.089	0.000	0.000	0.000	0.000
92	D	344	VAL	0	-0.020	-0.018	4.804	0.097	0.097	0.000	0.000	0.000	0.000
93	D	345	VAL	0	-0.002	-0.016	8.046	-0.153	-0.153	0.000	0.000	0.000	0.000
94	D	346	ASP	-1	-0.736	-0.861	9.515	-0.089	-0.089	0.000	0.000	0.000	0.000
95	D	347	ASP	-1	-0.901	-0.944	11.137	0.076	0.076	0.000	0.000	0.000	0.000
96	D	348	GLN	0	-0.066	-0.025	13.947	0.028	0.028	0.000	0.000	0.000	0.000
97	D	349	GLN	0	-0.066	-0.029	14.629	0.001	0.001	0.000	0.000	0.000	0.000
98	D	350	ARG	0	-0.027	-0.026	13.461	0.006	0.006	0.000	0.000	0.000	0.000
99	D	351	LEU	0	-0.063	-0.022	10.716	-0.011	-0.011	0.000	0.000	0.000	0.000
100	D	352	VAL	0	0.014	0.002	6.817	-0.053	-0.053	0.000	0.000	0.000	0.000
101	D	353	GLY	0	-0.047	-0.042	6.242	-0.198	-0.198	0.000	0.000	0.000	0.000
102	D	354	LEU	0	-0.033	0.003	7.270	0.193	0.193	0.000	0.000	0.000	0.000
103	D	355	ILE	0	0.025	0.017	5.422	-0.024	-0.024	0.000	0.000	0.000	0.000
104	D	356	THR	0	0.009	-0.012	8.172	-0.054	-0.054	0.000	0.000	0.000	0.000
105	D	357	ARG	1	0.891	0.921	11.442	-0.168	-0.168	0.000	0.000	0.000	0.000
106	D	358	ALA	0	-0.029	-0.014	13.936	0.013	0.013	0.000	0.000	0.000	0.000
107	D	359	ASN	0	0.092	0.057	10.043	-0.009	-0.009	0.000	0.000	0.000	0.000
108	D	360	VAL	0	-0.006	0.004	9.597	0.024	0.024	0.000	0.000	0.000	0.000
109	D	361	VAL	0	-0.024	-0.021	11.677	-0.015	-0.015	0.000	0.000	0.000	0.000
110	D	362	ASP	-1	-0.866	-0.925	13.605	0.084	0.084	0.000	0.000	0.000	0.000
111	D	363	ILE	0	0.008	0.011	7.982	-0.001	-0.001	0.000	0.000	0.000	0.000
112	D	364	VAL	0	-0.044	-0.006	12.253	-0.014	-0.014	0.000	0.000	0.000	0.000
113	D	365	TYR	0	-0.078	-0.045	14.059	-0.026	-0.026	0.000	0.000	0.000	0.000
114	D	366	ASP	-1	-0.826	-0.920	14.777	0.018	0.018	0.000	0.000	0.000	0.000
115	D	367	THR	0	-0.149	-0.070	12.791	-0.015	-0.015	0.000	0.000	0.000	0.000
116	D	368	ILE	0	-0.105	-0.043	15.088	-0.017	-0.017	0.000	0.000	0.000	0.000
117	D	369	TRP	0	-0.013	-0.003	18.421	-0.012	-0.012	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:253:GLY)