FMO DATABASE

FMODB ID: 9GZZ2

Calculation Name: 3INO-A-Xray372

Preferred Name: Protective antigen

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3INO

Chain ID: A

ChEMBL ID: CHEMBL5352

UniProt ID: P13423

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	143
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1322431.733589
FMO2-HF: Nuclear repulsion	1266390.357869
FMO2-HF: Total energy	-56041.375721
FMO2-MP2: Total energy	-56208.279795

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:593:GLY)

Summations of interaction energy for fragment #1(A:593: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.
1.889	3.657	-0.012	-0.984	-0.773	0.004

Interaction energy analysis for fragmet #1(A:593:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.062 / q_NPA : 0.033

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	595	ARG	1	0.845	0.917	3.869	1.073	2.841	-0.012	-0.984	-0.773	0.004
4	A	596	PHE	0	-0.019	-0.016	6.799	0.583	0.583	0.000	0.000	0.000	0.000
5	A	597	HIS	1	0.792	0.877	7.758	0.033	0.033	0.000	0.000	0.000	0.000
6	A	598	TYR	0	0.020	-0.004	8.125	0.162	0.162	0.000	0.000	0.000	0.000
7	A	599	ASP	-1	-0.711	-0.840	12.310	-0.230	-0.230	0.000	0.000	0.000	0.000
8	A	600	ARG	1	0.901	0.934	15.319	0.173	0.173	0.000	0.000	0.000	0.000
9	A	601	ASN	0	-0.094	-0.049	17.519	0.017	0.017	0.000	0.000	0.000	0.000
10	A	602	ASN	0	-0.021	-0.014	13.955	-0.067	-0.067	0.000	0.000	0.000	0.000
11	A	603	ILE	0	0.002	0.015	14.727	-0.083	-0.083	0.000	0.000	0.000	0.000
12	A	604	ALA	0	-0.003	0.000	13.195	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	605	VAL	0	-0.020	-0.020	13.948	0.073	0.073	0.000	0.000	0.000	0.000
14	A	606	GLY	0	0.042	0.016	13.543	0.093	0.093	0.000	0.000	0.000	0.000
15	A	607	ALA	0	0.015	0.006	9.995	-0.182	-0.182	0.000	0.000	0.000	0.000
16	A	608	ASP	-1	-0.815	-0.884	7.460	0.076	0.076	0.000	0.000	0.000	0.000
17	A	609	GLU	-1	-0.795	-0.912	10.369	-0.015	-0.015	0.000	0.000	0.000	0.000
18	A	610	SER	0	-0.011	0.004	9.512	-0.064	-0.064	0.000	0.000	0.000	0.000
19	A	611	VAL	0	0.006	0.002	8.049	-0.036	-0.036	0.000	0.000	0.000	0.000
20	A	612	VAL	0	-0.014	-0.008	11.297	-0.032	-0.032	0.000	0.000	0.000	0.000
21	A	613	LYS	1	0.842	0.916	14.555	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	614	GLU	-1	-0.808	-0.872	13.992	-0.139	-0.139	0.000	0.000	0.000	0.000
23	A	615	ALA	0	-0.069	-0.036	15.427	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	616	HIS	0	-0.012	-0.016	17.123	0.000	0.000	0.000	0.000	0.000	0.000
25	A	617	ARG	1	0.775	0.864	18.549	0.141	0.141	0.000	0.000	0.000	0.000
26	A	618	GLU	-1	-0.890	-0.923	21.108	-0.119	-0.119	0.000	0.000	0.000	0.000
27	A	619	VAL	0	-0.028	-0.021	23.596	-0.012	-0.012	0.000	0.000	0.000	0.000
28	A	620	ILE	0	-0.022	-0.005	26.473	0.008	0.008	0.000	0.000	0.000	0.000
29	A	621	ASN	0	-0.008	-0.015	29.320	0.012	0.012	0.000	0.000	0.000	0.000
30	A	622	SER	0	0.014	0.016	30.173	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	623	SER	0	0.006	0.004	32.124	0.005	0.005	0.000	0.000	0.000	0.000
32	A	624	THR	0	0.070	0.027	34.626	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	625	GLU	-1	-0.774	-0.869	37.024	-0.051	-0.051	0.000	0.000	0.000	0.000
34	A	626	GLY	0	0.037	0.009	32.778	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	627	LEU	0	-0.042	0.003	26.885	0.004	0.004	0.000	0.000	0.000	0.000
36	A	628	LEU	0	-0.037	-0.018	29.601	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	629	LEU	0	0.016	0.008	22.969	0.005	0.005	0.000	0.000	0.000	0.000
38	A	630	ASN	0	0.032	0.016	23.673	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	631	ILE	0	0.061	0.032	19.714	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	632	ASP	-1	-0.734	-0.855	15.684	-0.565	-0.565	0.000	0.000	0.000	0.000
41	A	633	LYS	1	0.894	0.938	17.925	0.545	0.545	0.000	0.000	0.000	0.000
42	A	634	ASP	-1	-0.861	-0.939	15.199	-0.595	-0.595	0.000	0.000	0.000	0.000
43	A	635	ILE	0	0.015	0.011	13.320	-0.020	-0.020	0.000	0.000	0.000	0.000
44	A	636	ARG	1	0.918	0.948	16.551	0.293	0.293	0.000	0.000	0.000	0.000
45	A	637	LYS	1	0.891	0.959	17.809	0.498	0.498	0.000	0.000	0.000	0.000
46	A	638	ILE	0	-0.007	0.026	13.256	0.019	0.019	0.000	0.000	0.000	0.000
47	A	639	LEU	0	-0.012	0.012	17.132	0.032	0.032	0.000	0.000	0.000	0.000
48	A	640	SER	0	-0.058	-0.026	19.899	0.001	0.001	0.000	0.000	0.000	0.000
49	A	641	GLY	0	0.013	0.009	23.053	0.010	0.010	0.000	0.000	0.000	0.000
50	A	642	TYR	0	-0.070	-0.068	21.657	-0.013	-0.013	0.000	0.000	0.000	0.000
51	A	643	ILE	0	0.040	0.026	25.529	0.004	0.004	0.000	0.000	0.000	0.000
52	A	644	VAL	0	-0.011	-0.005	27.340	0.001	0.001	0.000	0.000	0.000	0.000
53	A	645	GLU	-1	-0.760	-0.856	29.239	0.001	0.001	0.000	0.000	0.000	0.000
54	A	646	ILE	0	0.027	0.021	31.569	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	647	GLU	-1	-0.783	-0.863	30.294	0.029	0.029	0.000	0.000	0.000	0.000
56	A	648	ASP	-1	-0.784	-0.891	33.954	0.015	0.015	0.000	0.000	0.000	0.000
57	A	649	THR	0	-0.092	-0.099	35.742	0.002	0.002	0.000	0.000	0.000	0.000
58	A	650	GLU	-1	-0.853	-0.880	37.483	0.024	0.024	0.000	0.000	0.000	0.000
59	A	651	GLY	0	-0.018	0.005	34.168	0.004	0.004	0.000	0.000	0.000	0.000
60	A	652	LEU	0	-0.048	-0.021	33.883	0.001	0.001	0.000	0.000	0.000	0.000
61	A	653	LYS	1	0.804	0.875	29.333	-0.029	-0.029	0.000	0.000	0.000	0.000
62	A	654	GLU	-1	-0.914	-0.938	34.620	-0.013	-0.013	0.000	0.000	0.000	0.000
63	A	655	VAL	0	-0.038	-0.025	31.024	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	656	ILE	0	0.013	0.001	33.322	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	657	ASN	0	-0.042	-0.041	29.535	0.004	0.004	0.000	0.000	0.000	0.000
66	A	658	ASP	-1	-0.755	-0.835	32.059	-0.032	-0.032	0.000	0.000	0.000	0.000
67	A	659	ARG	1	0.847	0.872	32.599	0.053	0.053	0.000	0.000	0.000	0.000
68	A	660	TYR	0	0.011	0.004	29.620	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	661	ASP	-1	-0.844	-0.887	29.885	-0.074	-0.074	0.000	0.000	0.000	0.000
70	A	662	MET	0	-0.020	-0.005	32.228	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	663	LEU	0	0.059	0.046	25.705	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	664	ASN	0	0.001	0.025	28.075	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	665	ILE	0	0.022	0.005	28.792	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	666	SER	0	-0.056	-0.003	26.517	0.000	0.000	0.000	0.000	0.000	0.000
75	A	667	SER	0	-0.023	-0.011	28.471	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	668	LEU	0	-0.003	-0.009	25.881	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	669	ARG	1	0.858	0.902	29.917	0.116	0.116	0.000	0.000	0.000	0.000
78	A	670	GLN	0	0.020	0.000	32.261	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	671	ASP	-1	-0.747	-0.829	32.509	-0.125	-0.125	0.000	0.000	0.000	0.000
80	A	672	GLY	0	0.001	-0.002	29.063	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	673	LYS	1	0.815	0.915	27.491	0.121	0.121	0.000	0.000	0.000	0.000
82	A	674	THR	0	-0.008	-0.016	24.991	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	675	PHE	0	-0.005	-0.005	27.457	0.006	0.006	0.000	0.000	0.000	0.000
84	A	676	ILE	0	-0.016	-0.016	25.024	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	677	ASP	-1	-0.847	-0.922	29.589	-0.066	-0.066	0.000	0.000	0.000	0.000
86	A	678	PHE	0	0.018	-0.007	29.992	0.000	0.000	0.000	0.000	0.000	0.000
87	A	679	LYS	1	0.840	0.912	34.363	0.057	0.057	0.000	0.000	0.000	0.000
88	A	680	LYS	1	0.771	0.896	33.120	0.098	0.098	0.000	0.000	0.000	0.000
89	A	681	TYR	0	0.004	-0.030	33.107	0.001	0.001	0.000	0.000	0.000	0.000
90	A	682	ASN	0	0.013	0.023	37.282	0.007	0.007	0.000	0.000	0.000	0.000
91	A	683	ASP	-1	-0.848	-0.930	38.837	-0.037	-0.037	0.000	0.000	0.000	0.000
92	A	684	LYS	1	0.799	0.896	40.594	0.046	0.046	0.000	0.000	0.000	0.000
93	A	685	LEU	0	-0.018	-0.003	41.522	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	686	PRO	0	0.002	0.008	39.246	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	687	LEU	0	-0.001	-0.006	34.024	0.003	0.003	0.000	0.000	0.000	0.000
96	A	688	TYR	0	0.019	0.002	38.741	0.002	0.002	0.000	0.000	0.000	0.000
97	A	689	ILE	0	0.005	-0.004	36.369	0.002	0.002	0.000	0.000	0.000	0.000
98	A	690	SER	0	-0.019	-0.002	39.953	0.001	0.001	0.000	0.000	0.000	0.000
99	A	691	ASN	0	0.076	0.044	41.305	0.001	0.001	0.000	0.000	0.000	0.000
100	A	692	PRO	0	0.017	0.002	40.045	0.000	0.000	0.000	0.000	0.000	0.000
101	A	693	ASN	0	-0.036	-0.028	37.977	0.001	0.001	0.000	0.000	0.000	0.000
102	A	694	TYR	0	-0.022	-0.008	36.796	0.002	0.002	0.000	0.000	0.000	0.000
103	A	695	LYS	1	0.801	0.884	28.639	-0.027	-0.027	0.000	0.000	0.000	0.000
104	A	696	VAL	0	0.006	0.015	30.924	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	697	ASN	0	-0.050	-0.029	27.509	0.001	0.001	0.000	0.000	0.000	0.000
106	A	698	VAL	0	0.000	-0.010	25.734	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	699	TYR	0	-0.038	-0.051	22.842	0.005	0.005	0.000	0.000	0.000	0.000
108	A	700	ALA	0	0.029	0.020	19.469	-0.009	-0.009	0.000	0.000	0.000	0.000
109	A	701	VAL	0	0.051	0.023	20.749	0.016	0.016	0.000	0.000	0.000	0.000
110	A	702	THR	0	0.003	0.006	15.016	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	703	LYS	1	0.863	0.899	18.291	0.311	0.311	0.000	0.000	0.000	0.000
112	A	704	GLU	-1	-0.807	-0.883	13.713	-0.212	-0.212	0.000	0.000	0.000	0.000
113	A	705	ASN	0	-0.050	-0.022	16.583	0.053	0.053	0.000	0.000	0.000	0.000
114	A	706	THR	0	0.002	-0.005	20.418	0.010	0.010	0.000	0.000	0.000	0.000
115	A	707	ILE	0	0.059	0.035	23.558	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	708	ILE	0	-0.017	-0.020	23.943	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	709	ASN	0	-0.089	-0.055	27.879	0.004	0.004	0.000	0.000	0.000	0.000
118	A	710	PRO	0	0.039	0.026	30.910	0.001	0.001	0.000	0.000	0.000	0.000
119	A	711	SER	0	-0.003	0.021	32.299	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	712	GLU	-1	-0.832	-0.907	32.978	-0.020	-0.020	0.000	0.000	0.000	0.000
121	A	713	ASN	0	-0.101	-0.075	35.526	0.004	0.004	0.000	0.000	0.000	0.000
122	A	714	GLY	0	-0.012	0.004	36.843	0.002	0.002	0.000	0.000	0.000	0.000
123	A	715	ASP	-1	-0.810	-0.881	33.852	-0.024	-0.024	0.000	0.000	0.000	0.000
124	A	716	THR	0	-0.074	-0.057	33.866	-0.006	-0.006	0.000	0.000	0.000	0.000
125	A	717	SER	0	-0.045	-0.020	33.269	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	718	THR	0	-0.047	-0.064	28.266	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	719	ASN	0	-0.054	-0.037	28.189	0.005	0.005	0.000	0.000	0.000	0.000
128	A	720	GLY	0	0.035	0.013	27.155	0.006	0.006	0.000	0.000	0.000	0.000
129	A	721	ILE	0	-0.059	-0.016	23.271	0.000	0.000	0.000	0.000	0.000	0.000
130	A	722	LYS	1	0.835	0.918	15.404	0.052	0.052	0.000	0.000	0.000	0.000
131	A	723	LYS	1	0.841	0.929	19.893	-0.006	-0.006	0.000	0.000	0.000	0.000
132	A	724	ILE	0	-0.012	-0.007	15.364	0.017	0.017	0.000	0.000	0.000	0.000
133	A	725	LEU	0	-0.006	0.004	19.397	-0.017	-0.017	0.000	0.000	0.000	0.000
134	A	726	ILE	0	-0.057	-0.047	18.854	0.004	0.004	0.000	0.000	0.000	0.000
135	A	727	PHE	0	0.027	0.016	21.388	-0.004	-0.004	0.000	0.000	0.000	0.000
136	A	728	SER	0	0.014	-0.014	24.930	0.009	0.009	0.000	0.000	0.000	0.000
137	A	729	LYS	1	0.777	0.894	27.480	0.010	0.010	0.000	0.000	0.000	0.000
138	A	730	LYS	1	0.927	0.951	30.731	-0.016	-0.016	0.000	0.000	0.000	0.000
139	A	731	GLY	0	0.055	0.032	34.372	-0.004	-0.004	0.000	0.000	0.000	0.000
140	A	732	TYR	0	-0.042	-0.026	36.220	-0.002	-0.002	0.000	0.000	0.000	0.000
141	A	733	GLU	-1	-0.856	-0.896	31.499	0.005	0.005	0.000	0.000	0.000	0.000
142	A	734	ILE	0	-0.038	-0.006	32.744	-0.006	-0.006	0.000	0.000	0.000	0.000
143	A	735	GLY	0	-0.002	0.001	35.213	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:593:GLY)