FMO DATABASE

FMODB ID: GQM61

Calculation Name: 3INO-A-Xray312

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	143
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1320539.430505
FMO2-HF: Nuclear repulsion	1264500.7797
FMO2-HF: Total energy	-56038.650805
FMO2-MP2: Total energy	-56205.493212

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.
2.198	3.349	-0.009	-0.548	-0.595	0

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 : 0.025 / 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].
3	A	595	ARG	1	0.952	0.984	3.769	1.523	2.674	-0.009	-0.548	-0.595
4	A	596	PHE	0	-0.019	-0.010	6.724	0.526	0.526	0.000	0.000	0.000
5	A	597	HIS	1	0.795	0.858	7.797	-0.216	-0.216	0.000	0.000	0.000
6	A	598	TYR	0	-0.001	-0.003	8.337	-0.035	-0.035	0.000	0.000	0.000
7	A	599	ASP	-1	-0.745	-0.876	12.216	-0.234	-0.234	0.000	0.000	0.000
8	A	600	ARG	1	0.961	0.973	15.071	0.124	0.124	0.000	0.000	0.000
9	A	601	ASN	0	-0.085	-0.051	17.448	0.009	0.009	0.000	0.000	0.000
10	A	602	ASN	0	-0.006	0.004	13.497	-0.046	-0.046	0.000	0.000	0.000
11	A	603	ILE	0	-0.016	-0.003	14.836	-0.051	-0.051	0.000	0.000	0.000
12	A	604	ALA	0	-0.012	0.000	12.970	0.003	0.003	0.000	0.000	0.000
13	A	605	VAL	0	-0.009	-0.005	13.874	0.062	0.062	0.000	0.000	0.000
14	A	606	GLY	0	0.026	0.009	13.439	0.072	0.072	0.000	0.000	0.000
15	A	607	ALA	0	0.000	-0.012	10.003	-0.136	-0.136	0.000	0.000	0.000
16	A	608	ASP	-1	-0.826	-0.881	7.291	0.689	0.689	0.000	0.000	0.000
17	A	609	GLU	-1	-0.887	-0.961	10.328	0.168	0.168	0.000	0.000	0.000
18	A	610	SER	0	-0.018	-0.005	9.896	-0.087	-0.087	0.000	0.000	0.000
19	A	611	VAL	0	0.014	0.008	8.636	-0.055	-0.055	0.000	0.000	0.000
20	A	612	VAL	0	0.017	0.003	11.847	-0.063	-0.063	0.000	0.000	0.000
21	A	613	LYS	1	0.886	0.957	15.037	-0.196	-0.196	0.000	0.000	0.000
22	A	614	GLU	-1	-0.841	-0.906	14.353	0.142	0.142	0.000	0.000	0.000
23	A	615	ALA	0	-0.066	-0.031	15.703	-0.030	-0.030	0.000	0.000	0.000
24	A	616	HIS	0	-0.028	-0.007	17.367	-0.036	-0.036	0.000	0.000	0.000
25	A	617	ARG	1	0.886	0.955	18.922	-0.101	-0.101	0.000	0.000	0.000
26	A	618	GLU	-1	-0.975	-0.982	21.450	0.019	0.019	0.000	0.000	0.000
27	A	619	VAL	0	-0.036	-0.024	24.178	-0.015	-0.015	0.000	0.000	0.000
28	A	620	ILE	0	-0.058	-0.030	27.188	0.001	0.001	0.000	0.000	0.000
29	A	621	ASN	0	-0.001	-0.014	30.184	0.005	0.005	0.000	0.000	0.000
30	A	622	SER	0	-0.124	-0.082	31.436	-0.002	-0.002	0.000	0.000	0.000
31	A	623	SER	0	0.070	0.104	32.851	0.002	0.002	0.000	0.000	0.000
32	A	624	THR	0	0.057	0.028	35.129	-0.001	-0.001	0.000	0.000	0.000
33	A	625	GLU	-1	-0.937	-0.985	37.322	-0.003	-0.003	0.000	0.000	0.000
34	A	626	GLY	0	0.017	-0.008	33.048	-0.004	-0.004	0.000	0.000	0.000
35	A	627	LEU	0	-0.054	-0.008	27.510	0.004	0.004	0.000	0.000	0.000
36	A	628	LEU	0	-0.031	-0.002	30.107	-0.009	-0.009	0.000	0.000	0.000
37	A	629	LEU	0	0.034	0.005	23.693	0.007	0.007	0.000	0.000	0.000
38	A	630	ASN	0	0.004	0.009	24.015	-0.017	-0.017	0.000	0.000	0.000
39	A	631	ILE	0	0.040	0.018	19.900	0.003	0.003	0.000	0.000	0.000
40	A	632	ASP	-1	-0.801	-0.910	15.903	-0.297	-0.297	0.000	0.000	0.000
41	A	633	LYS	1	0.916	0.950	18.659	0.311	0.311	0.000	0.000	0.000
42	A	634	ASP	-1	-0.859	-0.957	15.133	-0.408	-0.408	0.000	0.000	0.000
43	A	635	ILE	0	-0.005	0.009	13.555	-0.022	-0.022	0.000	0.000	0.000
44	A	636	ARG	1	0.951	0.973	16.873	0.146	0.146	0.000	0.000	0.000
45	A	637	LYS	1	0.882	0.961	18.099	0.294	0.294	0.000	0.000	0.000
46	A	638	ILE	0	-0.002	0.010	13.685	-0.001	-0.001	0.000	0.000	0.000
47	A	639	LEU	0	-0.039	-0.011	17.408	0.027	0.027	0.000	0.000	0.000
48	A	640	SER	0	-0.059	-0.058	20.142	-0.007	-0.007	0.000	0.000	0.000
49	A	641	GLY	0	-0.015	-0.004	22.976	0.001	0.001	0.000	0.000	0.000
50	A	642	TYR	0	-0.074	-0.073	22.030	-0.003	-0.003	0.000	0.000	0.000
51	A	643	ILE	0	0.051	0.040	25.782	-0.003	-0.003	0.000	0.000	0.000
52	A	644	VAL	0	-0.016	-0.020	27.584	0.008	0.008	0.000	0.000	0.000
53	A	645	GLU	-1	-0.782	-0.852	29.611	0.062	0.062	0.000	0.000	0.000
54	A	646	ILE	0	0.015	0.020	31.837	0.003	0.003	0.000	0.000	0.000
55	A	647	GLU	-1	-0.892	-0.950	30.827	0.083	0.083	0.000	0.000	0.000
56	A	648	ASP	-1	-0.808	-0.896	34.442	0.053	0.053	0.000	0.000	0.000
57	A	649	THR	0	-0.070	-0.077	36.187	0.004	0.004	0.000	0.000	0.000
58	A	650	GLU	-1	-0.940	-0.951	37.303	0.057	0.057	0.000	0.000	0.000
59	A	651	GLY	0	-0.030	0.004	34.192	0.003	0.003	0.000	0.000	0.000
60	A	652	LEU	0	-0.093	-0.049	34.323	0.001	0.001	0.000	0.000	0.000
61	A	653	LYS	1	0.890	0.953	28.857	-0.084	-0.084	0.000	0.000	0.000
62	A	654	GLU	-1	-0.906	-0.948	34.499	0.024	0.024	0.000	0.000	0.000
63	A	655	VAL	0	-0.055	-0.027	30.986	0.001	0.001	0.000	0.000	0.000
64	A	656	ILE	0	0.024	0.018	33.560	-0.003	-0.003	0.000	0.000	0.000
65	A	657	ASN	0	-0.056	-0.050	29.813	0.002	0.002	0.000	0.000	0.000
66	A	658	ASP	-1	-0.829	-0.931	32.000	0.018	0.018	0.000	0.000	0.000
67	A	659	ARG	1	0.853	0.888	32.743	0.011	0.011	0.000	0.000	0.000
68	A	660	TYR	0	-0.009	-0.015	29.765	-0.001	-0.001	0.000	0.000	0.000
69	A	661	ASP	-1	-0.859	-0.900	29.821	-0.025	-0.025	0.000	0.000	0.000
70	A	662	MET	0	-0.023	0.001	31.895	-0.001	-0.001	0.000	0.000	0.000
71	A	663	LEU	0	0.064	0.038	25.452	0.003	0.003	0.000	0.000	0.000
72	A	664	ASN	0	0.028	0.027	28.169	0.002	0.002	0.000	0.000	0.000
73	A	665	ILE	0	0.013	0.006	29.192	-0.001	-0.001	0.000	0.000	0.000
74	A	666	SER	0	-0.018	0.012	25.746	0.002	0.002	0.000	0.000	0.000
75	A	667	SER	0	-0.043	-0.018	28.867	-0.006	-0.006	0.000	0.000	0.000
76	A	668	LEU	0	0.014	0.002	26.268	0.000	0.000	0.000	0.000	0.000
77	A	669	ARG	1	0.877	0.909	30.127	0.035	0.035	0.000	0.000	0.000
78	A	670	GLN	0	-0.003	-0.018	32.773	-0.005	-0.005	0.000	0.000	0.000
79	A	671	ASP	-1	-0.760	-0.848	32.576	-0.046	-0.046	0.000	0.000	0.000
80	A	672	GLY	0	-0.009	0.000	29.274	-0.003	-0.003	0.000	0.000	0.000
81	A	673	LYS	1	0.857	0.935	27.751	0.033	0.033	0.000	0.000	0.000
82	A	674	THR	0	-0.026	-0.014	25.540	-0.008	-0.008	0.000	0.000	0.000
83	A	675	PHE	0	-0.006	-0.009	27.957	0.007	0.007	0.000	0.000	0.000
84	A	676	ILE	0	-0.020	-0.011	25.315	-0.007	-0.007	0.000	0.000	0.000
85	A	677	ASP	-1	-0.877	-0.953	29.848	-0.009	-0.009	0.000	0.000	0.000
86	A	678	PHE	0	0.010	-0.003	30.263	0.000	0.000	0.000	0.000	0.000
87	A	679	LYS	1	0.980	1.007	34.613	0.008	0.008	0.000	0.000	0.000
88	A	680	LYS	1	0.804	0.933	33.446	0.034	0.034	0.000	0.000	0.000
89	A	681	TYR	0	-0.076	-0.073	33.064	-0.002	-0.002	0.000	0.000	0.000
90	A	682	ASN	0	0.045	0.024	37.302	0.004	0.004	0.000	0.000	0.000
91	A	683	ASP	-1	-0.897	-0.941	39.270	0.003	0.003	0.000	0.000	0.000
92	A	684	LYS	1	0.863	0.925	41.052	0.011	0.011	0.000	0.000	0.000
93	A	685	LEU	0	-0.007	0.002	41.591	-0.001	-0.001	0.000	0.000	0.000
94	A	686	PRO	0	0.015	0.010	39.495	0.000	0.000	0.000	0.000	0.000
95	A	687	LEU	0	0.000	-0.001	34.326	0.001	0.001	0.000	0.000	0.000
96	A	688	TYR	0	0.021	0.010	39.059	0.001	0.001	0.000	0.000	0.000
97	A	689	ILE	0	-0.011	-0.010	36.883	0.002	0.002	0.000	0.000	0.000
98	A	690	SER	0	0.010	0.009	40.556	0.000	0.000	0.000	0.000	0.000
99	A	691	ASN	0	0.037	0.016	41.693	0.001	0.001	0.000	0.000	0.000
100	A	692	PRO	0	0.051	0.015	40.425	0.002	0.002	0.000	0.000	0.000
101	A	693	ASN	0	-0.017	-0.014	38.282	0.005	0.005	0.000	0.000	0.000
102	A	694	TYR	0	0.020	0.019	36.962	0.004	0.004	0.000	0.000	0.000
103	A	695	LYS	1	0.905	0.944	29.328	-0.092	-0.092	0.000	0.000	0.000
104	A	696	VAL	0	0.050	0.039	31.098	-0.004	-0.004	0.000	0.000	0.000
105	A	697	ASN	0	-0.067	-0.034	27.472	0.009	0.009	0.000	0.000	0.000
106	A	698	VAL	0	0.012	-0.006	25.694	-0.008	-0.008	0.000	0.000	0.000
107	A	699	TYR	0	-0.095	-0.096	23.149	0.018	0.018	0.000	0.000	0.000
108	A	700	ALA	0	0.008	0.008	19.688	-0.015	-0.015	0.000	0.000	0.000
109	A	701	VAL	0	0.048	0.027	20.775	0.017	0.017	0.000	0.000	0.000
110	A	702	THR	0	0.006	-0.003	15.451	-0.008	-0.008	0.000	0.000	0.000
111	A	703	LYS	1	0.904	0.939	18.526	0.174	0.174	0.000	0.000	0.000
112	A	704	GLU	-1	-0.885	-0.920	13.693	-0.086	-0.086	0.000	0.000	0.000
113	A	705	ASN	0	-0.037	-0.023	16.560	0.026	0.026	0.000	0.000	0.000
114	A	706	THR	0	-0.007	0.018	20.032	0.010	0.010	0.000	0.000	0.000
115	A	707	ILE	0	0.031	0.021	23.181	-0.003	-0.003	0.000	0.000	0.000
116	A	708	ILE	0	-0.038	-0.022	24.380	-0.002	-0.002	0.000	0.000	0.000
117	A	709	ASN	0	-0.042	-0.046	27.987	0.002	0.002	0.000	0.000	0.000
118	A	710	PRO	0	0.031	0.035	30.854	0.003	0.003	0.000	0.000	0.000
119	A	711	SER	0	0.025	0.025	32.237	-0.003	-0.003	0.000	0.000	0.000
120	A	712	GLU	-1	-0.824	-0.903	33.090	0.002	0.002	0.000	0.000	0.000
121	A	713	ASN	0	-0.111	-0.080	35.493	0.002	0.002	0.000	0.000	0.000
122	A	714	GLY	0	-0.022	-0.002	36.570	0.001	0.001	0.000	0.000	0.000
123	A	715	ASP	-1	-0.879	-0.925	33.824	0.015	0.015	0.000	0.000	0.000
124	A	716	THR	0	-0.055	-0.037	33.993	-0.003	-0.003	0.000	0.000	0.000
125	A	717	SER	0	-0.033	-0.018	33.083	-0.001	-0.001	0.000	0.000	0.000
126	A	718	THR	0	-0.047	-0.040	28.419	0.001	0.001	0.000	0.000	0.000
127	A	719	ASN	0	0.110	0.041	28.229	0.009	0.009	0.000	0.000	0.000
128	A	720	GLY	0	-0.062	-0.032	27.098	-0.002	-0.002	0.000	0.000	0.000
129	A	721	ILE	0	-0.023	0.036	23.472	0.002	0.002	0.000	0.000	0.000
130	A	722	LYS	1	0.907	0.965	15.532	-0.103	-0.103	0.000	0.000	0.000
131	A	723	LYS	1	0.930	0.970	20.788	-0.081	-0.081	0.000	0.000	0.000
132	A	724	ILE	0	0.011	0.007	15.536	0.022	0.022	0.000	0.000	0.000
133	A	725	LEU	0	-0.003	0.015	19.649	-0.015	-0.015	0.000	0.000	0.000
134	A	726	ILE	0	-0.052	-0.063	19.267	0.023	0.023	0.000	0.000	0.000
135	A	727	PHE	0	0.011	0.013	21.765	0.000	0.000	0.000	0.000	0.000
136	A	728	SER	0	-0.009	-0.022	25.306	0.002	0.002	0.000	0.000	0.000
137	A	729	LYS	1	0.865	0.953	27.724	-0.067	-0.067	0.000	0.000	0.000
138	A	730	LYS	1	0.972	0.984	30.970	-0.079	-0.079	0.000	0.000	0.000
139	A	731	GLY	0	0.082	0.047	34.524	-0.003	-0.003	0.000	0.000	0.000
140	A	732	TYR	0	-0.069	-0.036	36.345	-0.002	-0.002	0.000	0.000	0.000
141	A	733	GLU	-1	-0.980	-0.991	32.599	0.073	0.073	0.000	0.000	0.000
142	A	734	ILE	0	-0.095	-0.026	33.393	0.000	0.000	0.000	0.000	0.000
143	A	735	GLY	-1	-0.737	-0.909	35.586	0.018	0.018	0.000	0.000	0.000

Top

Graph

Manual

About

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