FMO DATABASE

FMODB ID: Q1J6Y

Calculation Name: 2F6E-A-Xray372

Preferred Name: Toxin A

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2F6E

Chain ID: A

ChEMBL ID: CHEMBL3580504

UniProt ID: P16154

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:

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1010667.028261
FMO2-HF: Nuclear repulsion	962265.848916
FMO2-HF: Total energy	-48401.179345
FMO2-MP2: Total energy	-48543.851778

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:2:TYR)

Summations of interaction energy for fragment #1(A:2:TYR)

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.
-36.008	-29.621	29.166	-11.516	-24.037	-0.048

Interaction energy analysis for fragmet #1(A:2:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.046 / q_NPA : -0.042

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

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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	4	PHE	0	0.048	0.021	2.507	-1.381	3.142	0.995	-1.840	-3.678	0.006
4	A	5	GLU	-1	-0.770	-0.862	4.378	0.926	1.146	0.003	-0.059	-0.164	0.000
5	A	6	PRO	0	-0.016	-0.011	7.538	0.027	0.027	0.000	0.000	0.000	0.000
6	A	7	ASN	0	0.039	0.045	8.784	0.222	0.222	0.000	0.000	0.000	0.000
7	A	8	THR	0	0.006	-0.016	10.953	-0.012	-0.012	0.000	0.000	0.000	0.000
8	A	9	ALA	0	-0.004	0.015	13.744	0.033	0.033	0.000	0.000	0.000	0.000
9	A	10	ILE	0	0.023	0.015	16.203	-0.016	-0.016	0.000	0.000	0.000	0.000
10	A	11	GLY	0	0.048	0.018	18.153	0.035	0.035	0.000	0.000	0.000	0.000
11	A	12	ALA	0	-0.015	0.006	16.941	-0.035	-0.035	0.000	0.000	0.000	0.000
12	A	13	ASN	0	-0.021	-0.039	14.943	0.080	0.080	0.000	0.000	0.000	0.000
13	A	14	GLY	0	0.032	0.028	10.940	-0.068	-0.068	0.000	0.000	0.000	0.000
14	A	15	TYR	0	-0.034	-0.030	6.572	-0.281	-0.281	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.792	0.883	9.011	0.274	0.274	0.000	0.000	0.000	0.000
16	A	17	ILE	0	0.010	0.006	10.369	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	18	ILE	0	-0.017	-0.008	13.463	0.036	0.036	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.795	-0.894	17.132	-0.225	-0.225	0.000	0.000	0.000	0.000
19	A	20	ASN	0	-0.071	-0.035	16.644	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	21	LYS	1	0.863	0.940	14.949	0.223	0.223	0.000	0.000	0.000	0.000
21	A	22	ASN	0	0.007	-0.011	9.248	0.017	0.017	0.000	0.000	0.000	0.000
22	A	23	PHE	0	0.017	0.007	11.487	0.112	0.112	0.000	0.000	0.000	0.000
23	A	24	TYR	0	0.028	0.010	7.884	-0.080	-0.080	0.000	0.000	0.000	0.000
24	A	25	PHE	0	-0.024	-0.007	11.424	0.037	0.037	0.000	0.000	0.000	0.000
25	A	26	ARG	1	0.915	0.951	11.957	-0.353	-0.353	0.000	0.000	0.000	0.000
26	A	27	ASN	0	-0.010	-0.006	16.225	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	28	GLY	0	0.034	0.031	18.786	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.014	-0.007	19.032	-0.025	-0.025	0.000	0.000	0.000	0.000
29	A	30	PRO	0	0.041	0.024	16.091	0.017	0.017	0.000	0.000	0.000	0.000
30	A	31	GLN	0	-0.045	-0.023	13.461	0.078	0.078	0.000	0.000	0.000	0.000
31	A	32	ILE	0	0.016	0.017	14.081	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	33	GLY	0	-0.024	-0.024	12.663	0.021	0.021	0.000	0.000	0.000	0.000
33	A	34	VAL	0	-0.014	0.006	7.176	-0.055	-0.055	0.000	0.000	0.000	0.000
34	A	35	PHE	0	-0.005	0.003	6.817	0.054	0.054	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.829	0.902	2.532	-7.322	-4.233	2.119	-1.661	-3.546	0.018
36	A	37	GLY	0	0.057	0.021	2.336	-2.214	-1.470	0.844	-0.014	-1.575	0.004
37	A	38	PRO	0	-0.035	-0.007	1.648	-18.829	-25.948	17.145	-6.434	-3.593	-0.064
38	A	39	ASN	0	-0.017	-0.004	3.028	-3.049	-1.522	0.179	-0.770	-0.936	-0.008
39	A	40	GLY	0	0.037	0.017	2.533	0.541	2.110	4.661	-2.435	-3.795	0.012
40	A	41	PHE	0	0.003	0.005	2.648	-4.199	-3.127	3.219	1.832	-6.122	-0.016
41	A	42	GLU	-1	-0.793	-0.880	4.358	-1.994	-1.812	0.001	-0.030	-0.153	0.000
42	A	43	TYR	0	0.028	0.001	7.592	0.140	0.140	0.000	0.000	0.000	0.000
43	A	44	PHE	0	-0.021	-0.009	7.529	-0.137	-0.137	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.048	0.016	12.667	0.053	0.053	0.000	0.000	0.000	0.000
45	A	46	PRO	0	0.065	0.021	16.189	-0.021	-0.021	0.000	0.000	0.000	0.000
46	A	47	ALA	0	-0.002	0.025	19.851	-0.013	-0.013	0.000	0.000	0.000	0.000
47	A	48	ASN	0	-0.083	-0.049	21.969	0.001	0.001	0.000	0.000	0.000	0.000
48	A	49	THR	0	-0.039	-0.010	18.400	0.013	0.013	0.000	0.000	0.000	0.000
49	A	50	ASP	-1	-0.830	-0.917	18.689	-0.086	-0.086	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.036	-0.011	20.769	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	52	ASN	0	-0.016	-0.001	22.800	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	53	ASN	0	-0.022	-0.011	18.422	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	54	ILE	0	0.035	0.015	19.334	0.018	0.018	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.810	-0.920	18.746	0.034	0.034	0.000	0.000	0.000	0.000
55	A	56	GLY	0	-0.036	-0.014	15.526	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	57	GLN	0	-0.019	-0.016	14.250	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	58	ALA	0	-0.023	-0.006	10.683	0.053	0.053	0.000	0.000	0.000	0.000
58	A	59	ILE	0	-0.045	-0.014	12.504	-0.040	-0.040	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.826	0.895	13.213	0.121	0.121	0.000	0.000	0.000	0.000
60	A	61	TYR	0	-0.038	-0.057	13.896	0.013	0.013	0.000	0.000	0.000	0.000
61	A	62	GLN	0	-0.030	-0.015	14.170	0.043	0.043	0.000	0.000	0.000	0.000
62	A	63	ASN	0	-0.012	-0.011	15.536	-0.024	-0.024	0.000	0.000	0.000	0.000
63	A	64	ARG	1	0.961	1.001	16.176	-0.052	-0.052	0.000	0.000	0.000	0.000
64	A	65	PHE	0	0.071	0.024	15.346	0.027	0.027	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.043	-0.004	12.986	-0.024	-0.024	0.000	0.000	0.000	0.000
66	A	67	HIS	0	0.043	0.024	15.770	0.031	0.031	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.003	-0.002	13.828	-0.026	-0.026	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.008	-0.011	16.141	0.034	0.034	0.000	0.000	0.000	0.000
69	A	70	GLY	0	0.025	0.023	18.513	0.010	0.010	0.000	0.000	0.000	0.000
70	A	71	ASN	0	-0.023	-0.001	13.567	0.024	0.024	0.000	0.000	0.000	0.000
71	A	72	ILE	0	0.022	0.014	14.896	-0.026	-0.026	0.000	0.000	0.000	0.000
72	A	73	TYR	0	0.031	0.009	9.157	0.007	0.007	0.000	0.000	0.000	0.000
73	A	74	TYR	0	0.025	0.007	11.637	-0.074	-0.074	0.000	0.000	0.000	0.000
74	A	75	PHE	0	0.004	0.020	9.334	0.092	0.092	0.000	0.000	0.000	0.000
75	A	76	GLY	0	0.064	0.037	10.940	-0.072	-0.072	0.000	0.000	0.000	0.000
76	A	77	ASN	0	-0.013	-0.027	12.231	-0.029	-0.029	0.000	0.000	0.000	0.000
77	A	78	ASN	0	0.047	0.017	8.422	0.065	0.065	0.000	0.000	0.000	0.000
78	A	79	SER	0	-0.022	-0.004	11.126	-0.066	-0.066	0.000	0.000	0.000	0.000
79	A	80	LYS	1	0.799	0.909	5.957	0.297	0.297	0.000	0.000	0.000	0.000
80	A	81	ALA	0	0.001	0.011	6.566	-0.140	-0.140	0.000	0.000	0.000	0.000
81	A	82	VAL	0	-0.035	-0.017	6.280	0.221	0.221	0.000	0.000	0.000	0.000
82	A	83	THR	0	-0.016	-0.016	3.766	-0.425	-0.159	0.000	-0.041	-0.225	0.000
83	A	84	GLY	0	0.033	0.029	6.998	-0.111	-0.111	0.000	0.000	0.000	0.000
84	A	85	TRP	0	-0.017	-0.012	8.687	-0.050	-0.050	0.000	0.000	0.000	0.000
85	A	86	GLN	0	-0.040	-0.023	9.334	-0.072	-0.072	0.000	0.000	0.000	0.000
86	A	87	THR	0	-0.018	-0.016	13.745	0.017	0.017	0.000	0.000	0.000	0.000
87	A	88	ILE	0	-0.029	-0.005	14.806	-0.023	-0.023	0.000	0.000	0.000	0.000
88	A	89	ASN	0	-0.020	-0.025	18.791	0.003	0.003	0.000	0.000	0.000	0.000
89	A	90	GLY	0	0.021	0.022	21.751	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	91	ASN	0	0.007	0.022	21.449	0.001	0.001	0.000	0.000	0.000	0.000
91	A	92	MET	0	0.082	0.067	17.476	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	93	TYR	0	0.028	0.009	15.204	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	94	TYR	0	0.048	0.014	10.494	0.025	0.025	0.000	0.000	0.000	0.000
94	A	95	PHE	0	-0.033	0.000	9.247	-0.016	-0.016	0.000	0.000	0.000	0.000
95	A	96	MET	0	0.039	0.020	8.591	0.032	0.032	0.000	0.000	0.000	0.000
96	A	97	PRO	0	0.023	-0.015	4.891	-0.029	-0.029	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.880	-0.917	4.059	0.836	1.150	0.000	-0.064	-0.250	0.000
98	A	99	THR	0	-0.045	-0.053	5.789	0.038	0.038	0.000	0.000	0.000	0.000
99	A	100	ALA	0	-0.029	-0.011	5.714	-0.026	-0.026	0.000	0.000	0.000	0.000
100	A	101	MET	0	-0.022	0.002	7.353	-0.084	-0.084	0.000	0.000	0.000	0.000
101	A	102	ALA	0	-0.015	-0.017	10.918	0.021	0.021	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.004	0.013	13.493	0.011	0.011	0.000	0.000	0.000	0.000
103	A	104	ALA	0	-0.012	-0.026	15.553	-0.038	-0.038	0.000	0.000	0.000	0.000
104	A	105	GLY	0	-0.032	-0.016	18.868	0.010	0.010	0.000	0.000	0.000	0.000
105	A	106	GLY	0	0.009	0.003	22.209	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	107	LEU	0	-0.032	-0.019	22.275	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	108	PHE	0	-0.001	-0.004	16.594	0.021	0.021	0.000	0.000	0.000	0.000
108	A	109	GLU	-1	-0.941	-0.966	19.223	0.337	0.337	0.000	0.000	0.000	0.000
109	A	110	ILE	0	-0.053	-0.029	13.454	0.052	0.052	0.000	0.000	0.000	0.000
110	A	111	ASP	-1	-0.885	-0.957	12.672	0.583	0.583	0.000	0.000	0.000	0.000
111	A	112	GLY	0	0.010	0.021	15.502	-0.038	-0.038	0.000	0.000	0.000	0.000
112	A	113	VAL	0	-0.042	-0.019	18.825	-0.044	-0.044	0.000	0.000	0.000	0.000
113	A	114	ILE	0	0.011	0.008	19.680	0.025	0.025	0.000	0.000	0.000	0.000
114	A	115	TYR	0	0.001	0.000	18.021	-0.044	-0.044	0.000	0.000	0.000	0.000
115	A	116	PHE	0	-0.001	-0.005	21.978	0.010	0.010	0.000	0.000	0.000	0.000
116	A	117	PHE	0	0.006	0.001	16.813	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	118	GLY	0	0.047	0.031	21.297	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	119	VAL	0	-0.003	-0.017	21.360	0.020	0.020	0.000	0.000	0.000	0.000
119	A	120	ASP	-1	-0.867	-0.935	21.313	0.185	0.185	0.000	0.000	0.000	0.000
120	A	121	GLY	0	0.006	-0.006	17.817	0.006	0.006	0.000	0.000	0.000	0.000
121	A	122	VAL	0	-0.067	-0.023	18.262	0.009	0.009	0.000	0.000	0.000	0.000
122	A	123	LYS	1	0.810	0.892	18.852	-0.189	-0.189	0.000	0.000	0.000	0.000
123	A	124	ALA	0	-0.005	-0.008	20.908	-0.020	-0.020	0.000	0.000	0.000	0.000
124	A	125	PRO	0	-0.024	-0.026	24.019	0.006	0.006	0.000	0.000	0.000	0.000
125	A	126	GLY	0	0.003	0.018	26.049	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:TYR)