FMO DATABASE

FMODB ID: LJYY9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1321974.743559
FMO2-HF: Nuclear repulsion	1265934.047815
FMO2-HF: Total energy	-56040.695744
FMO2-MP2: Total energy	-56207.565722

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.
1.946	3.903	-0.018	-1.061	-0.877	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 : 0.053 / q_NPA : 0.028

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	0.867	0.930	3.769	1.116	3.073	-0.018	-1.061	-0.877	0.004
4	A	596	PHE	0	-0.018	-0.009	6.722	0.643	0.643	0.000	0.000	0.000	0.000
5	A	597	HIS	1	0.799	0.867	7.794	0.198	0.198	0.000	0.000	0.000	0.000
6	A	598	TYR	0	0.002	-0.009	8.282	0.135	0.135	0.000	0.000	0.000	0.000
7	A	599	ASP	-1	-0.728	-0.883	12.222	-0.237	-0.237	0.000	0.000	0.000	0.000
8	A	600	ARG	1	0.923	0.977	15.078	0.165	0.165	0.000	0.000	0.000	0.000
9	A	601	ASN	0	-0.087	-0.059	17.454	0.036	0.036	0.000	0.000	0.000	0.000
10	A	602	ASN	0	-0.011	0.001	13.373	-0.055	-0.055	0.000	0.000	0.000	0.000
11	A	603	ILE	0	0.001	0.011	14.844	-0.074	-0.074	0.000	0.000	0.000	0.000
12	A	604	ALA	0	-0.010	-0.001	12.966	0.010	0.010	0.000	0.000	0.000	0.000
13	A	605	VAL	0	-0.017	-0.011	13.853	0.071	0.071	0.000	0.000	0.000	0.000
14	A	606	GLY	0	0.038	0.016	13.438	0.097	0.097	0.000	0.000	0.000	0.000
15	A	607	ALA	0	0.012	-0.004	9.990	-0.181	-0.181	0.000	0.000	0.000	0.000
16	A	608	ASP	-1	-0.827	-0.878	7.152	-0.113	-0.113	0.000	0.000	0.000	0.000
17	A	609	GLU	-1	-0.808	-0.920	10.326	-0.158	-0.158	0.000	0.000	0.000	0.000
18	A	610	SER	0	-0.012	-0.001	9.865	-0.060	-0.060	0.000	0.000	0.000	0.000
19	A	611	VAL	0	0.012	0.005	8.637	-0.024	-0.024	0.000	0.000	0.000	0.000
20	A	612	VAL	0	0.008	0.001	11.845	0.010	0.010	0.000	0.000	0.000	0.000
21	A	613	LYS	1	0.848	0.937	15.035	0.160	0.160	0.000	0.000	0.000	0.000
22	A	614	GLU	-1	-0.821	-0.880	14.041	-0.313	-0.313	0.000	0.000	0.000	0.000
23	A	615	ALA	0	-0.060	-0.026	15.617	0.009	0.009	0.000	0.000	0.000	0.000
24	A	616	HIS	0	-0.046	-0.033	17.219	0.036	0.036	0.000	0.000	0.000	0.000
25	A	617	ARG	1	0.811	0.895	18.284	0.304	0.304	0.000	0.000	0.000	0.000
26	A	618	GLU	-1	-0.905	-0.940	21.213	-0.203	-0.203	0.000	0.000	0.000	0.000
27	A	619	VAL	0	-0.037	-0.023	23.714	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	620	ILE	0	-0.045	-0.027	26.912	0.008	0.008	0.000	0.000	0.000	0.000
29	A	621	ASN	0	-0.010	-0.017	29.765	0.015	0.015	0.000	0.000	0.000	0.000
30	A	622	SER	0	0.044	0.035	31.028	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	623	SER	0	0.025	-0.006	32.849	0.007	0.007	0.000	0.000	0.000	0.000
32	A	624	THR	0	0.071	0.035	35.127	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	625	GLU	-1	-0.806	-0.892	37.319	-0.081	-0.081	0.000	0.000	0.000	0.000
34	A	626	GLY	0	0.038	0.011	33.080	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	627	LEU	0	-0.057	-0.008	27.608	0.002	0.002	0.000	0.000	0.000	0.000
36	A	628	LEU	0	-0.032	-0.002	30.105	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	629	LEU	0	0.033	0.009	23.675	0.003	0.003	0.000	0.000	0.000	0.000
38	A	630	ASN	0	0.011	0.012	23.676	0.002	0.002	0.000	0.000	0.000	0.000
39	A	631	ILE	0	0.050	0.024	19.906	-0.014	-0.014	0.000	0.000	0.000	0.000
40	A	632	ASP	-1	-0.729	-0.850	15.703	-0.697	-0.697	0.000	0.000	0.000	0.000
41	A	633	LYS	1	0.884	0.915	18.303	0.581	0.581	0.000	0.000	0.000	0.000
42	A	634	ASP	-1	-0.868	-0.944	15.269	-0.653	-0.653	0.000	0.000	0.000	0.000
43	A	635	ILE	0	0.018	0.021	13.558	-0.036	-0.036	0.000	0.000	0.000	0.000
44	A	636	ARG	1	0.923	0.954	16.870	0.367	0.367	0.000	0.000	0.000	0.000
45	A	637	LYS	1	0.913	0.968	18.090	0.525	0.525	0.000	0.000	0.000	0.000
46	A	638	ILE	0	-0.002	0.021	13.487	0.021	0.021	0.000	0.000	0.000	0.000
47	A	639	LEU	0	-0.040	-0.015	17.405	0.027	0.027	0.000	0.000	0.000	0.000
48	A	640	SER	0	-0.049	-0.050	20.139	0.003	0.003	0.000	0.000	0.000	0.000
49	A	641	GLY	0	-0.018	-0.004	22.970	0.015	0.015	0.000	0.000	0.000	0.000
50	A	642	TYR	0	-0.071	-0.064	21.979	-0.015	-0.015	0.000	0.000	0.000	0.000
51	A	643	ILE	0	0.053	0.042	25.651	0.007	0.007	0.000	0.000	0.000	0.000
52	A	644	VAL	0	-0.026	-0.022	27.581	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	645	GLU	-1	-0.751	-0.856	29.343	-0.050	-0.050	0.000	0.000	0.000	0.000
54	A	646	ILE	0	0.020	0.017	31.835	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	647	GLU	-1	-0.828	-0.894	30.821	-0.025	-0.025	0.000	0.000	0.000	0.000
56	A	648	ASP	-1	-0.808	-0.901	34.441	-0.020	-0.020	0.000	0.000	0.000	0.000
57	A	649	THR	0	-0.058	-0.078	36.185	0.000	0.000	0.000	0.000	0.000	0.000
58	A	650	GLU	-1	-0.914	-0.923	37.302	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	651	GLY	0	-0.033	0.000	34.180	0.004	0.004	0.000	0.000	0.000	0.000
60	A	652	LEU	0	-0.050	-0.030	34.321	0.000	0.000	0.000	0.000	0.000	0.000
61	A	653	LYS	1	0.807	0.893	29.347	0.016	0.016	0.000	0.000	0.000	0.000
62	A	654	GLU	-1	-0.909	-0.949	34.498	-0.040	-0.040	0.000	0.000	0.000	0.000
63	A	655	VAL	0	-0.056	-0.029	31.025	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	656	ILE	0	0.003	0.005	33.553	0.002	0.002	0.000	0.000	0.000	0.000
65	A	657	ASN	0	-0.054	-0.046	29.809	0.005	0.005	0.000	0.000	0.000	0.000
66	A	658	ASP	-1	-0.793	-0.907	31.997	-0.061	-0.061	0.000	0.000	0.000	0.000
67	A	659	ARG	1	0.846	0.876	32.740	0.071	0.071	0.000	0.000	0.000	0.000
68	A	660	TYR	0	-0.002	-0.014	29.762	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	661	ASP	-1	-0.849	-0.883	29.818	-0.093	-0.093	0.000	0.000	0.000	0.000
70	A	662	MET	0	-0.034	-0.005	31.889	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	663	LEU	0	0.068	0.045	25.472	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	664	ASN	0	0.020	0.029	28.166	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	665	ILE	0	0.015	0.014	29.230	0.005	0.005	0.000	0.000	0.000	0.000
74	A	666	SER	0	-0.007	0.018	25.792	0.004	0.004	0.000	0.000	0.000	0.000
75	A	667	SER	0	-0.039	-0.016	28.865	0.001	0.001	0.000	0.000	0.000	0.000
76	A	668	LEU	0	0.011	0.001	26.167	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	669	ARG	1	0.871	0.903	30.124	0.159	0.159	0.000	0.000	0.000	0.000
78	A	670	GLN	0	0.002	-0.008	32.677	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	671	ASP	-1	-0.753	-0.845	32.375	-0.170	-0.170	0.000	0.000	0.000	0.000
80	A	672	GLY	0	-0.002	0.007	29.214	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	673	LYS	1	0.842	0.923	27.616	0.163	0.163	0.000	0.000	0.000	0.000
82	A	674	THR	0	-0.032	-0.017	25.523	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	675	PHE	0	-0.003	-0.009	27.954	0.004	0.004	0.000	0.000	0.000	0.000
84	A	676	ILE	0	-0.020	-0.012	25.328	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	677	ASP	-1	-0.866	-0.938	29.845	-0.100	-0.100	0.000	0.000	0.000	0.000
86	A	678	PHE	0	0.024	-0.020	30.241	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	679	LYS	1	0.875	0.935	34.610	0.088	0.088	0.000	0.000	0.000	0.000
88	A	680	LYS	1	0.806	0.926	33.426	0.128	0.128	0.000	0.000	0.000	0.000
89	A	681	TYR	0	-0.069	-0.078	33.014	0.004	0.004	0.000	0.000	0.000	0.000
90	A	682	ASN	0	0.032	0.015	37.299	0.005	0.005	0.000	0.000	0.000	0.000
91	A	683	ASP	-1	-0.895	-0.942	39.267	-0.055	-0.055	0.000	0.000	0.000	0.000
92	A	684	LYS	1	0.870	0.930	41.051	0.071	0.071	0.000	0.000	0.000	0.000
93	A	685	LEU	0	-0.008	0.005	41.569	0.001	0.001	0.000	0.000	0.000	0.000
94	A	686	PRO	0	-0.014	0.000	39.493	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	687	LEU	0	0.012	0.001	34.354	0.004	0.004	0.000	0.000	0.000	0.000
96	A	688	TYR	0	0.018	0.008	39.057	0.002	0.002	0.000	0.000	0.000	0.000
97	A	689	ILE	0	-0.019	-0.015	36.942	0.001	0.001	0.000	0.000	0.000	0.000
98	A	690	SER	0	0.007	0.010	40.554	0.001	0.001	0.000	0.000	0.000	0.000
99	A	691	ASN	0	0.069	0.032	41.690	0.001	0.001	0.000	0.000	0.000	0.000
100	A	692	PRO	0	0.033	0.006	40.422	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	693	ASN	0	-0.046	-0.033	38.278	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	694	TYR	0	0.035	0.028	36.960	0.001	0.001	0.000	0.000	0.000	0.000
103	A	695	LYS	1	0.882	0.932	28.749	0.035	0.035	0.000	0.000	0.000	0.000
104	A	696	VAL	0	0.023	0.020	31.213	0.000	0.000	0.000	0.000	0.000	0.000
105	A	697	ASN	0	-0.077	-0.039	27.559	-0.008	-0.008	0.000	0.000	0.000	0.000
106	A	698	VAL	0	0.013	-0.007	25.850	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	699	TYR	0	-0.067	-0.068	23.009	-0.008	-0.008	0.000	0.000	0.000	0.000
108	A	700	ALA	0	0.014	0.011	19.690	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	701	VAL	0	0.054	0.031	20.764	0.011	0.011	0.000	0.000	0.000	0.000
110	A	702	THR	0	0.014	0.014	15.301	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	703	LYS	1	0.884	0.934	18.523	0.363	0.363	0.000	0.000	0.000	0.000
112	A	704	GLU	-1	-0.856	-0.913	13.737	-0.308	-0.308	0.000	0.000	0.000	0.000
113	A	705	ASN	0	-0.040	-0.025	16.095	0.067	0.067	0.000	0.000	0.000	0.000
114	A	706	THR	0	0.006	0.012	20.029	0.013	0.013	0.000	0.000	0.000	0.000
115	A	707	ILE	0	0.046	0.029	23.178	0.003	0.003	0.000	0.000	0.000	0.000
116	A	708	ILE	0	-0.015	-0.018	24.158	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	709	ASN	0	-0.076	-0.053	27.984	0.005	0.005	0.000	0.000	0.000	0.000
118	A	710	PRO	0	0.044	0.039	30.851	0.001	0.001	0.000	0.000	0.000	0.000
119	A	711	SER	0	0.021	0.022	32.013	0.000	0.000	0.000	0.000	0.000	0.000
120	A	712	GLU	-1	-0.825	-0.905	33.088	-0.025	-0.025	0.000	0.000	0.000	0.000
121	A	713	ASN	0	-0.106	-0.075	35.498	0.004	0.004	0.000	0.000	0.000	0.000
122	A	714	GLY	0	-0.023	-0.002	36.574	0.001	0.001	0.000	0.000	0.000	0.000
123	A	715	ASP	-1	-0.858	-0.905	33.977	-0.040	-0.040	0.000	0.000	0.000	0.000
124	A	716	THR	0	-0.055	-0.038	33.991	-0.005	-0.005	0.000	0.000	0.000	0.000
125	A	717	SER	0	-0.056	-0.034	33.081	-0.007	-0.007	0.000	0.000	0.000	0.000
126	A	718	THR	0	-0.032	-0.028	28.331	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	719	ASN	0	0.035	0.016	28.226	0.000	0.000	0.000	0.000	0.000	0.000
128	A	720	GLY	0	-0.035	-0.014	27.095	0.001	0.001	0.000	0.000	0.000	0.000
129	A	721	ILE	0	-0.012	0.007	23.672	0.000	0.000	0.000	0.000	0.000	0.000
130	A	722	LYS	1	0.852	0.930	15.230	0.097	0.097	0.000	0.000	0.000	0.000
131	A	723	LYS	1	0.859	0.939	20.822	0.048	0.048	0.000	0.000	0.000	0.000
132	A	724	ILE	0	-0.011	-0.006	15.566	0.012	0.012	0.000	0.000	0.000	0.000
133	A	725	LEU	0	-0.009	0.008	19.647	-0.016	-0.016	0.000	0.000	0.000	0.000
134	A	726	ILE	0	-0.039	-0.052	19.227	-0.011	-0.011	0.000	0.000	0.000	0.000
135	A	727	PHE	0	0.029	0.022	21.763	-0.006	-0.006	0.000	0.000	0.000	0.000
136	A	728	SER	0	0.016	-0.009	25.304	0.012	0.012	0.000	0.000	0.000	0.000
137	A	729	LYS	1	0.771	0.895	27.745	0.080	0.080	0.000	0.000	0.000	0.000
138	A	730	LYS	1	0.937	0.959	30.969	0.038	0.038	0.000	0.000	0.000	0.000
139	A	731	GLY	0	0.070	0.034	34.522	-0.005	-0.005	0.000	0.000	0.000	0.000
140	A	732	TYR	0	-0.050	-0.020	36.442	-0.002	-0.002	0.000	0.000	0.000	0.000
141	A	733	GLU	-1	-0.868	-0.914	31.896	-0.056	-0.056	0.000	0.000	0.000	0.000
142	A	734	ILE	0	-0.052	-0.008	32.999	-0.009	-0.009	0.000	0.000	0.000	0.000
143	A	735	GLY	0	-0.011	0.008	35.585	0.006	0.006	0.000	0.000	0.000	0.000

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