FMO DATABASE

FMODB ID: 3QLLL

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	OptH
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	-1320798.102019
FMO2-HF: Nuclear repulsion	1264758.792135
FMO2-HF: Total energy	-56039.309884
FMO2-MP2: Total energy	-56206.160998

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.
2.243	3.702	-0.016	-0.737	-0.706	0.002

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 : 0.043 / q_NPA : 0.012

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	0.950	0.983	3.769	1.530	2.989	-0.016	-0.737	-0.706	0.002
4	A	596	PHE	0	-0.022	-0.012	6.707	0.636	0.636	0.000	0.000	0.000	0.000
5	A	597	HIS	1	0.796	0.859	7.793	-0.091	-0.091	0.000	0.000	0.000	0.000
6	A	598	TYR	0	-0.003	-0.003	8.337	-0.054	-0.054	0.000	0.000	0.000	0.000
7	A	599	ASP	-1	-0.744	-0.875	12.220	-0.286	-0.286	0.000	0.000	0.000	0.000
8	A	600	ARG	1	0.962	0.973	15.076	0.153	0.153	0.000	0.000	0.000	0.000
9	A	601	ASN	0	-0.084	-0.050	17.451	0.019	0.019	0.000	0.000	0.000	0.000
10	A	602	ASN	0	-0.005	0.005	13.507	-0.049	-0.049	0.000	0.000	0.000	0.000
11	A	603	ILE	0	-0.018	-0.003	14.847	-0.066	-0.066	0.000	0.000	0.000	0.000
12	A	604	ALA	0	-0.010	0.000	12.970	0.006	0.006	0.000	0.000	0.000	0.000
13	A	605	VAL	0	-0.009	-0.006	13.871	0.068	0.068	0.000	0.000	0.000	0.000
14	A	606	GLY	0	0.026	0.009	13.433	0.089	0.089	0.000	0.000	0.000	0.000
15	A	607	ALA	0	0.005	-0.010	9.995	-0.170	-0.170	0.000	0.000	0.000	0.000
16	A	608	ASP	-1	-0.828	-0.881	7.284	0.552	0.552	0.000	0.000	0.000	0.000
17	A	609	GLU	-1	-0.890	-0.962	10.319	0.086	0.086	0.000	0.000	0.000	0.000
18	A	610	SER	0	-0.016	-0.005	9.881	-0.097	-0.097	0.000	0.000	0.000	0.000
19	A	611	VAL	0	0.017	0.009	8.618	-0.057	-0.057	0.000	0.000	0.000	0.000
20	A	612	VAL	0	0.012	0.002	11.828	-0.046	-0.046	0.000	0.000	0.000	0.000
21	A	613	LYS	1	0.891	0.957	15.021	-0.109	-0.109	0.000	0.000	0.000	0.000
22	A	614	GLU	-1	-0.840	-0.905	14.332	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	615	ALA	0	-0.062	-0.030	15.683	-0.020	-0.020	0.000	0.000	0.000	0.000
24	A	616	HIS	0	-0.030	-0.008	17.347	-0.016	-0.016	0.000	0.000	0.000	0.000
25	A	617	ARG	1	0.884	0.954	18.628	0.027	0.027	0.000	0.000	0.000	0.000
26	A	618	GLU	-1	-0.971	-0.980	21.429	-0.058	-0.058	0.000	0.000	0.000	0.000
27	A	619	VAL	0	-0.040	-0.026	24.014	-0.015	-0.015	0.000	0.000	0.000	0.000
28	A	620	ILE	0	-0.046	-0.023	27.167	0.004	0.004	0.000	0.000	0.000	0.000
29	A	621	ASN	0	-0.002	-0.013	29.984	0.010	0.010	0.000	0.000	0.000	0.000
30	A	622	SER	0	-0.070	-0.049	31.418	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	623	SER	0	0.064	0.086	32.832	0.004	0.004	0.000	0.000	0.000	0.000
32	A	624	THR	0	0.064	0.032	35.112	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	625	GLU	-1	-0.919	-0.976	37.305	-0.030	-0.030	0.000	0.000	0.000	0.000
34	A	626	GLY	0	0.028	-0.001	33.031	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	627	LEU	0	-0.059	-0.013	27.493	0.004	0.004	0.000	0.000	0.000	0.000
36	A	628	LEU	0	-0.029	0.000	30.089	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	629	LEU	0	0.032	0.005	23.674	0.007	0.007	0.000	0.000	0.000	0.000
38	A	630	ASN	0	0.009	0.011	23.736	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	631	ILE	0	0.036	0.017	19.881	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	632	ASP	-1	-0.797	-0.907	15.681	-0.483	-0.483	0.000	0.000	0.000	0.000
41	A	633	LYS	1	0.914	0.949	18.560	0.443	0.443	0.000	0.000	0.000	0.000
42	A	634	ASP	-1	-0.856	-0.955	15.082	-0.564	-0.564	0.000	0.000	0.000	0.000
43	A	635	ILE	0	-0.006	0.009	13.536	-0.029	-0.029	0.000	0.000	0.000	0.000
44	A	636	ARG	1	0.948	0.970	16.857	0.246	0.246	0.000	0.000	0.000	0.000
45	A	637	LYS	1	0.884	0.961	18.099	0.410	0.410	0.000	0.000	0.000	0.000
46	A	638	ILE	0	0.005	0.013	13.673	0.008	0.008	0.000	0.000	0.000	0.000
47	A	639	LEU	0	-0.044	-0.013	17.398	0.031	0.031	0.000	0.000	0.000	0.000
48	A	640	SER	0	-0.057	-0.056	20.131	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	641	GLY	0	-0.015	-0.005	22.966	0.006	0.006	0.000	0.000	0.000	0.000
50	A	642	TYR	0	-0.076	-0.073	22.014	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	643	ILE	0	0.055	0.042	25.774	0.000	0.000	0.000	0.000	0.000	0.000
52	A	644	VAL	0	-0.027	-0.026	27.572	0.004	0.004	0.000	0.000	0.000	0.000
53	A	645	GLU	-1	-0.773	-0.848	29.601	0.037	0.037	0.000	0.000	0.000	0.000
54	A	646	ILE	0	0.010	0.016	31.826	0.001	0.001	0.000	0.000	0.000	0.000
55	A	647	GLU	-1	-0.894	-0.949	30.817	0.062	0.062	0.000	0.000	0.000	0.000
56	A	648	ASP	-1	-0.807	-0.896	34.431	0.038	0.038	0.000	0.000	0.000	0.000
57	A	649	THR	0	-0.072	-0.079	36.176	0.003	0.003	0.000	0.000	0.000	0.000
58	A	650	GLU	-1	-0.935	-0.948	37.293	0.046	0.046	0.000	0.000	0.000	0.000
59	A	651	GLY	0	-0.029	0.005	34.183	0.004	0.004	0.000	0.000	0.000	0.000
60	A	652	LEU	0	-0.089	-0.047	34.315	0.001	0.001	0.000	0.000	0.000	0.000
61	A	653	LYS	1	0.888	0.951	28.849	-0.066	-0.066	0.000	0.000	0.000	0.000
62	A	654	GLU	-1	-0.903	-0.946	34.491	0.006	0.006	0.000	0.000	0.000	0.000
63	A	655	VAL	0	-0.056	-0.027	30.978	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	656	ILE	0	0.022	0.015	33.550	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	657	ASN	0	-0.057	-0.051	29.802	0.004	0.004	0.000	0.000	0.000	0.000
66	A	658	ASP	-1	-0.828	-0.930	31.991	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	659	ARG	1	0.857	0.891	32.737	0.032	0.032	0.000	0.000	0.000	0.000
68	A	660	TYR	0	-0.003	-0.012	29.760	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	661	ASP	-1	-0.860	-0.901	29.815	-0.051	-0.051	0.000	0.000	0.000	0.000
70	A	662	MET	0	-0.023	0.001	31.887	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	663	LEU	0	0.065	0.038	25.445	0.001	0.001	0.000	0.000	0.000	0.000
72	A	664	ASN	0	0.029	0.028	28.158	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	665	ILE	0	0.008	0.004	29.177	0.001	0.001	0.000	0.000	0.000	0.000
74	A	666	SER	0	-0.014	0.013	25.731	0.003	0.003	0.000	0.000	0.000	0.000
75	A	667	SER	0	-0.041	-0.016	28.853	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	668	LEU	0	0.018	0.003	26.234	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	669	ARG	1	0.867	0.905	30.109	0.085	0.085	0.000	0.000	0.000	0.000
78	A	670	GLN	0	0.003	-0.015	32.551	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	671	ASP	-1	-0.756	-0.846	32.319	-0.098	-0.098	0.000	0.000	0.000	0.000
80	A	672	GLY	0	-0.005	0.003	29.058	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	673	LYS	1	0.854	0.934	27.515	0.083	0.083	0.000	0.000	0.000	0.000
82	A	674	THR	0	-0.031	-0.014	25.523	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	675	PHE	0	-0.003	-0.010	27.938	0.007	0.007	0.000	0.000	0.000	0.000
84	A	676	ILE	0	-0.016	-0.008	25.298	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	677	ASP	-1	-0.878	-0.955	29.832	-0.042	-0.042	0.000	0.000	0.000	0.000
86	A	678	PHE	0	0.010	-0.005	30.248	0.000	0.000	0.000	0.000	0.000	0.000
87	A	679	LYS	1	0.978	1.006	34.598	0.037	0.037	0.000	0.000	0.000	0.000
88	A	680	LYS	1	0.810	0.935	33.434	0.071	0.071	0.000	0.000	0.000	0.000
89	A	681	TYR	0	-0.071	-0.070	33.053	0.000	0.000	0.000	0.000	0.000	0.000
90	A	682	ASN	0	0.043	0.024	37.290	0.005	0.005	0.000	0.000	0.000	0.000
91	A	683	ASP	-1	-0.893	-0.938	39.257	-0.016	-0.016	0.000	0.000	0.000	0.000
92	A	684	LYS	1	0.870	0.928	41.040	0.033	0.033	0.000	0.000	0.000	0.000
93	A	685	LEU	0	-0.004	0.004	41.578	0.000	0.000	0.000	0.000	0.000	0.000
94	A	686	PRO	0	-0.003	0.001	39.479	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	687	LEU	0	0.010	0.004	34.312	0.002	0.002	0.000	0.000	0.000	0.000
96	A	688	TYR	0	0.022	0.008	39.045	0.001	0.001	0.000	0.000	0.000	0.000
97	A	689	ILE	0	-0.021	-0.014	36.867	0.002	0.002	0.000	0.000	0.000	0.000
98	A	690	SER	0	0.016	0.012	40.542	0.000	0.000	0.000	0.000	0.000	0.000
99	A	691	ASN	0	0.044	0.021	41.679	0.001	0.001	0.000	0.000	0.000	0.000
100	A	692	PRO	0	0.043	0.011	40.410	0.001	0.001	0.000	0.000	0.000	0.000
101	A	693	ASN	0	-0.013	-0.013	38.267	0.002	0.002	0.000	0.000	0.000	0.000
102	A	694	TYR	0	0.025	0.023	36.948	0.004	0.004	0.000	0.000	0.000	0.000
103	A	695	LYS	1	0.902	0.942	29.314	-0.065	-0.065	0.000	0.000	0.000	0.000
104	A	696	VAL	0	0.043	0.034	31.083	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	697	ASN	0	-0.070	-0.034	27.460	0.004	0.004	0.000	0.000	0.000	0.000
106	A	698	VAL	0	0.010	-0.008	25.680	-0.008	-0.008	0.000	0.000	0.000	0.000
107	A	699	TYR	0	-0.095	-0.096	23.139	0.012	0.012	0.000	0.000	0.000	0.000
108	A	700	ALA	0	0.013	0.010	19.675	-0.013	-0.013	0.000	0.000	0.000	0.000
109	A	701	VAL	0	0.042	0.025	20.767	0.019	0.019	0.000	0.000	0.000	0.000
110	A	702	THR	0	0.011	0.000	15.444	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	703	LYS	1	0.905	0.939	18.519	0.262	0.262	0.000	0.000	0.000	0.000
112	A	704	GLU	-1	-0.881	-0.919	13.692	-0.162	-0.162	0.000	0.000	0.000	0.000
113	A	705	ASN	0	-0.042	-0.025	16.558	0.042	0.042	0.000	0.000	0.000	0.000
114	A	706	THR	0	-0.009	0.016	20.030	0.012	0.012	0.000	0.000	0.000	0.000
115	A	707	ILE	0	0.034	0.022	23.178	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	708	ILE	0	-0.037	-0.022	24.382	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	709	ASN	0	-0.040	-0.045	27.986	0.003	0.003	0.000	0.000	0.000	0.000
118	A	710	PRO	0	0.031	0.035	30.855	0.002	0.002	0.000	0.000	0.000	0.000
119	A	711	SER	0	0.024	0.024	32.239	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	712	GLU	-1	-0.822	-0.902	33.093	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	713	ASN	0	-0.110	-0.080	35.499	0.003	0.003	0.000	0.000	0.000	0.000
122	A	714	GLY	0	-0.022	-0.002	36.571	0.001	0.001	0.000	0.000	0.000	0.000
123	A	715	ASP	-1	-0.877	-0.924	33.824	0.000	0.000	0.000	0.000	0.000	0.000
124	A	716	THR	0	-0.054	-0.036	33.993	-0.004	-0.004	0.000	0.000	0.000	0.000
125	A	717	SER	0	-0.035	-0.020	33.080	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	718	THR	0	-0.046	-0.038	28.413	0.000	0.000	0.000	0.000	0.000	0.000
127	A	719	ASN	0	0.108	0.039	28.225	0.006	0.006	0.000	0.000	0.000	0.000
128	A	720	GLY	0	-0.061	-0.032	27.097	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	721	ILE	0	-0.020	0.037	23.468	0.002	0.002	0.000	0.000	0.000	0.000
130	A	722	LYS	1	0.908	0.966	15.532	-0.070	-0.070	0.000	0.000	0.000	0.000
131	A	723	LYS	1	0.930	0.969	20.781	-0.054	-0.054	0.000	0.000	0.000	0.000
132	A	724	ILE	0	0.013	0.009	15.525	0.022	0.022	0.000	0.000	0.000	0.000
133	A	725	LEU	0	0.000	0.016	19.639	-0.019	-0.019	0.000	0.000	0.000	0.000
134	A	726	ILE	0	-0.049	-0.062	19.251	0.015	0.015	0.000	0.000	0.000	0.000
135	A	727	PHE	0	0.008	0.010	21.749	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	728	SER	0	-0.003	-0.019	25.290	0.006	0.006	0.000	0.000	0.000	0.000
137	A	729	LYS	1	0.860	0.952	27.708	-0.022	-0.022	0.000	0.000	0.000	0.000
138	A	730	LYS	1	0.979	0.990	30.954	-0.055	-0.055	0.000	0.000	0.000	0.000
139	A	731	GLY	0	0.076	0.043	34.508	-0.004	-0.004	0.000	0.000	0.000	0.000
140	A	732	TYR	0	-0.064	-0.035	36.329	-0.002	-0.002	0.000	0.000	0.000	0.000
141	A	733	GLU	-1	-0.960	-0.978	32.582	0.041	0.041	0.000	0.000	0.000	0.000
142	A	734	ILE	0	-0.056	-0.009	33.375	-0.004	-0.004	0.000	0.000	0.000	0.000
143	A	735	GLY	0	0.059	0.000	35.568	0.000	0.000	0.000	0.000	0.000	0.000

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