FMO DATABASE

FMODB ID: QNYGY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-945223.891664
FMO2-HF: Nuclear repulsion	898471.78598
FMO2-HF: Total energy	-46752.105684
FMO2-MP2: Total energy	-46889.365476

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.
-3.44	-0.596	0.269	-1.295	-1.814	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 : 0.018 / 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

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	D	255	MET	0	-0.042	0.008	2.644	-1.480	1.166	0.272	-1.261	-1.656	0.002
4	D	256	ILE	0	0.017	0.012	4.627	-1.206	-1.214	-0.001	-0.008	0.018	0.000
5	D	257	LYS	1	0.982	0.969	7.692	0.314	0.314	0.000	0.000	0.000	0.000
6	D	258	PRO	0	0.023	0.030	9.778	0.019	0.019	0.000	0.000	0.000	0.000
7	D	259	ILE	0	-0.017	-0.010	12.476	-0.061	-0.061	0.000	0.000	0.000	0.000
8	D	260	THR	0	0.004	-0.004	15.145	0.024	0.024	0.000	0.000	0.000	0.000
9	D	261	ILE	0	-0.007	-0.001	17.904	-0.018	-0.018	0.000	0.000	0.000	0.000
10	D	262	GLN	0	0.001	0.000	21.227	0.002	0.002	0.000	0.000	0.000	0.000
11	D	263	ALA	0	0.049	0.012	23.359	0.001	0.001	0.000	0.000	0.000	0.000
12	D	264	GLU	-1	-0.839	-0.912	25.340	0.039	0.039	0.000	0.000	0.000	0.000
13	D	265	ALA	0	-0.039	0.006	26.594	-0.004	-0.004	0.000	0.000	0.000	0.000
14	D	266	THR	0	-0.016	-0.048	28.502	0.005	0.005	0.000	0.000	0.000	0.000
15	D	267	LEU	0	0.047	0.014	28.624	0.001	0.001	0.000	0.000	0.000	0.000
16	D	268	ASN	0	-0.014	-0.011	29.275	0.002	0.002	0.000	0.000	0.000	0.000
17	D	269	ASP	-1	-0.823	-0.884	27.694	0.018	0.018	0.000	0.000	0.000	0.000
18	D	270	ALA	0	0.030	0.018	24.913	-0.002	-0.002	0.000	0.000	0.000	0.000
19	D	271	VAL	0	0.048	0.031	25.191	0.001	0.001	0.000	0.000	0.000	0.000
20	D	272	HIS	0	-0.001	0.000	27.107	-0.003	-0.003	0.000	0.000	0.000	0.000
21	D	273	ILE	0	-0.039	-0.020	21.482	-0.008	-0.008	0.000	0.000	0.000	0.000
22	D	274	MET	0	-0.010	0.010	22.420	-0.007	-0.007	0.000	0.000	0.000	0.000
23	D	275	ARG	1	0.935	0.957	23.387	-0.002	-0.002	0.000	0.000	0.000	0.000
24	D	276	GLN	0	-0.043	-0.023	23.785	-0.006	-0.006	0.000	0.000	0.000	0.000
25	D	277	LYS	1	0.887	0.951	18.868	0.001	0.001	0.000	0.000	0.000	0.000
26	D	278	ARG	1	0.912	0.960	20.413	-0.015	-0.015	0.000	0.000	0.000	0.000
27	D	279	VAL	0	-0.016	0.004	17.450	0.002	0.002	0.000	0.000	0.000	0.000
28	D	280	ASP	-1	-0.881	-0.921	19.934	0.136	0.136	0.000	0.000	0.000	0.000
29	D	281	THR	0	-0.023	-0.052	18.040	0.007	0.007	0.000	0.000	0.000	0.000
30	D	282	ILE	0	-0.090	-0.025	18.065	-0.004	-0.004	0.000	0.000	0.000	0.000
31	D	283	PHE	0	-0.010	-0.021	14.689	0.026	0.026	0.000	0.000	0.000	0.000
32	D	284	VAL	0	-0.011	0.000	17.892	-0.024	-0.024	0.000	0.000	0.000	0.000
33	D	285	VAL	0	0.014	0.006	16.237	0.019	0.019	0.000	0.000	0.000	0.000
34	D	286	ASP	-1	-0.709	-0.851	19.612	0.027	0.027	0.000	0.000	0.000	0.000
35	D	287	SER	0	0.010	0.022	20.710	-0.005	-0.005	0.000	0.000	0.000	0.000
36	D	288	ASN	0	-0.125	-0.076	20.389	-0.020	-0.020	0.000	0.000	0.000	0.000
37	D	289	ASN	0	-0.045	-0.032	15.720	-0.003	-0.003	0.000	0.000	0.000	0.000
38	D	290	HIS	0	0.008	0.013	16.068	0.021	0.021	0.000	0.000	0.000	0.000
39	D	291	LEU	0	-0.035	-0.028	14.525	-0.002	-0.002	0.000	0.000	0.000	0.000
40	D	292	LEU	0	-0.036	-0.021	17.275	-0.004	-0.004	0.000	0.000	0.000	0.000
41	D	293	GLY	0	0.030	0.001	19.664	-0.005	-0.005	0.000	0.000	0.000	0.000
42	D	294	PHE	0	-0.066	-0.023	17.866	0.020	0.020	0.000	0.000	0.000	0.000
43	D	295	LEU	0	0.017	0.016	20.486	-0.016	-0.016	0.000	0.000	0.000	0.000
44	D	296	ASP	-1	-0.819	-0.909	21.886	0.125	0.125	0.000	0.000	0.000	0.000
45	D	297	ILE	0	-0.002	-0.021	23.617	-0.012	-0.012	0.000	0.000	0.000	0.000
46	D	298	GLU	-1	-0.857	-0.918	26.674	0.057	0.057	0.000	0.000	0.000	0.000
47	D	299	ASP	-1	-0.808	-0.883	24.763	0.115	0.115	0.000	0.000	0.000	0.000
48	D	300	ILE	0	-0.013	-0.017	25.502	-0.008	-0.008	0.000	0.000	0.000	0.000
49	D	301	ASN	0	-0.070	-0.046	29.284	-0.010	-0.010	0.000	0.000	0.000	0.000
50	D	302	GLN	0	-0.068	-0.049	29.672	-0.006	-0.006	0.000	0.000	0.000	0.000
51	D	303	GLY	0	0.022	0.014	31.746	-0.003	-0.003	0.000	0.000	0.000	0.000
52	D	304	ILE	0	-0.016	-0.016	32.847	-0.005	-0.005	0.000	0.000	0.000	0.000
53	D	305	ARG	1	0.901	0.957	35.199	-0.048	-0.048	0.000	0.000	0.000	0.000
54	D	306	GLY	0	0.015	-0.007	37.702	0.002	0.002	0.000	0.000	0.000	0.000
55	D	307	HIS	0	-0.094	-0.037	37.126	0.000	0.000	0.000	0.000	0.000	0.000
56	D	308	LYS	1	0.831	0.922	33.240	-0.062	-0.062	0.000	0.000	0.000	0.000
57	D	309	SER	0	-0.015	-0.035	32.235	0.000	0.000	0.000	0.000	0.000	0.000
58	D	310	LEU	0	0.016	0.015	24.788	0.005	0.005	0.000	0.000	0.000	0.000
59	D	311	ARG	1	0.898	0.901	27.361	-0.043	-0.043	0.000	0.000	0.000	0.000
60	D	312	ASP	-1	-0.852	-0.875	28.610	0.059	0.059	0.000	0.000	0.000	0.000
61	D	313	THR	0	-0.023	-0.014	28.556	-0.001	-0.001	0.000	0.000	0.000	0.000
62	D	314	MET	0	-0.065	-0.005	23.730	0.005	0.005	0.000	0.000	0.000	0.000
63	D	315	GLN	0	0.003	-0.006	22.798	0.002	0.002	0.000	0.000	0.000	0.000
64	D	316	GLN	0	-0.011	-0.024	22.524	0.008	0.008	0.000	0.000	0.000	0.000
65	D	317	HIS	0	-0.015	0.006	22.207	0.014	0.014	0.000	0.000	0.000	0.000
66	D	318	ILE	0	-0.011	-0.003	16.341	0.007	0.007	0.000	0.000	0.000	0.000
67	D	319	TYR	0	-0.032	-0.016	13.207	-0.020	-0.020	0.000	0.000	0.000	0.000
68	D	320	THR	0	0.011	-0.005	12.642	0.021	0.021	0.000	0.000	0.000	0.000
69	D	321	VAL	0	-0.039	-0.025	7.592	-0.005	-0.005	0.000	0.000	0.000	0.000
70	D	322	GLN	0	0.062	0.021	8.872	0.028	0.028	0.000	0.000	0.000	0.000
71	D	323	ILE	0	-0.002	-0.008	3.998	0.280	0.375	-0.001	-0.012	-0.081	0.000
72	D	324	ASP	-1	-0.925	-0.953	4.404	-0.239	-0.128	-0.001	-0.014	-0.095	0.000
73	D	325	SER	0	-0.051	-0.010	6.773	-0.032	-0.032	0.000	0.000	0.000	0.000
74	D	326	LYS	1	0.899	0.920	6.130	0.037	0.037	0.000	0.000	0.000	0.000
75	D	327	LEU	0	0.078	0.038	5.664	-0.187	-0.187	0.000	0.000	0.000	0.000
76	D	328	GLN	0	0.079	0.023	7.639	-0.076	-0.076	0.000	0.000	0.000	0.000
77	D	329	ASP	-1	-0.880	-0.910	11.058	0.315	0.315	0.000	0.000	0.000	0.000
78	D	330	SER	0	-0.074	-0.038	10.015	0.012	0.012	0.000	0.000	0.000	0.000
79	D	331	VAL	0	0.032	0.015	10.801	-0.061	-0.061	0.000	0.000	0.000	0.000
80	D	332	ARG	1	0.961	0.975	12.343	-0.383	-0.383	0.000	0.000	0.000	0.000
81	D	333	THR	0	-0.010	-0.002	15.274	-0.066	-0.066	0.000	0.000	0.000	0.000
82	D	334	ILE	0	0.034	0.017	11.085	-0.064	-0.064	0.000	0.000	0.000	0.000
83	D	335	LEU	0	0.015	0.014	15.071	-0.056	-0.056	0.000	0.000	0.000	0.000
84	D	336	LYS	1	0.922	0.969	17.392	-0.249	-0.249	0.000	0.000	0.000	0.000
85	D	337	ARG	1	0.920	0.975	18.457	-0.272	-0.272	0.000	0.000	0.000	0.000
86	D	338	ASN	0	0.021	-0.003	19.993	0.008	0.008	0.000	0.000	0.000	0.000
87	D	339	VAL	0	-0.002	0.007	16.048	-0.022	-0.022	0.000	0.000	0.000	0.000
88	D	340	ARG	1	0.998	0.992	16.457	-0.117	-0.117	0.000	0.000	0.000	0.000
89	D	341	ASN	0	0.022	0.020	13.857	0.048	0.048	0.000	0.000	0.000	0.000
90	D	342	VAL	0	-0.011	-0.006	10.925	-0.064	-0.064	0.000	0.000	0.000	0.000
91	D	343	PRO	0	0.008	0.009	10.233	0.197	0.197	0.000	0.000	0.000	0.000
92	D	344	VAL	0	-0.024	-0.009	5.098	0.111	0.111	0.000	0.000	0.000	0.000
93	D	345	VAL	0	0.017	0.003	8.447	-0.211	-0.211	0.000	0.000	0.000	0.000
94	D	346	ASP	-1	-0.755	-0.881	8.987	0.105	0.105	0.000	0.000	0.000	0.000
95	D	347	ASP	-1	-0.911	-0.942	10.973	0.157	0.157	0.000	0.000	0.000	0.000
96	D	348	GLN	0	-0.049	-0.007	13.957	0.002	0.002	0.000	0.000	0.000	0.000
97	D	349	GLN	0	-0.046	-0.038	14.596	-0.013	-0.013	0.000	0.000	0.000	0.000
98	D	350	ARG	0	-0.039	-0.022	13.626	0.012	0.012	0.000	0.000	0.000	0.000
99	D	351	LEU	0	-0.059	-0.032	11.193	0.040	0.040	0.000	0.000	0.000	0.000
100	D	352	VAL	0	-0.011	-0.006	7.018	-0.077	-0.077	0.000	0.000	0.000	0.000
101	D	353	GLY	0	-0.024	-0.034	6.423	-0.192	-0.192	0.000	0.000	0.000	0.000
102	D	354	LEU	0	-0.038	-0.003	7.301	0.038	0.038	0.000	0.000	0.000	0.000
103	D	355	ILE	0	0.027	0.028	6.073	0.139	0.139	0.000	0.000	0.000	0.000
104	D	356	THR	0	0.033	0.002	8.746	-0.179	-0.179	0.000	0.000	0.000	0.000
105	D	357	ARG	1	0.885	0.925	12.114	-0.229	-0.229	0.000	0.000	0.000	0.000
106	D	358	ALA	0	-0.025	-0.003	14.580	-0.021	-0.021	0.000	0.000	0.000	0.000
107	D	359	ASN	0	0.047	0.022	10.738	0.023	0.023	0.000	0.000	0.000	0.000
108	D	360	VAL	0	-0.028	-0.009	10.060	-0.011	-0.011	0.000	0.000	0.000	0.000
109	D	361	VAL	0	-0.032	-0.023	11.921	-0.050	-0.050	0.000	0.000	0.000	0.000
110	D	362	ASP	-1	-0.835	-0.914	13.351	0.084	0.084	0.000	0.000	0.000	0.000
111	D	363	ILE	0	0.012	0.004	7.664	-0.032	-0.032	0.000	0.000	0.000	0.000
112	D	364	VAL	0	-0.059	-0.022	11.800	-0.032	-0.032	0.000	0.000	0.000	0.000
113	D	365	TYR	0	-0.069	-0.035	13.772	-0.020	-0.020	0.000	0.000	0.000	0.000
114	D	366	ASP	-1	-0.844	-0.935	14.612	-0.049	-0.049	0.000	0.000	0.000	0.000
115	D	367	THR	0	-0.126	-0.061	12.218	-0.039	-0.039	0.000	0.000	0.000	0.000
116	D	368	ILE	0	-0.073	-0.020	14.557	-0.004	-0.004	0.000	0.000	0.000	0.000
117	D	369	TRP	0	-0.041	-0.017	18.073	-0.016	-0.016	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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