FMO DATABASE

FMODB ID: R5V28

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:

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	125
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1010591.599806
FMO2-HF: Nuclear repulsion	962190.544049
FMO2-HF: Total energy	-48401.055757
FMO2-MP2: Total energy	-48543.761392

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.
-37.881	-31.734	28.942	-12.384	-22.702	-0.053

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 : -0.060 / q_NPA : -0.053

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	0.035	0.018	2.418	-0.981	3.503	0.980	-1.887	-3.577	0.003
4	A	5	GLU	-1	-0.891	-0.943	4.251	0.382	0.596	0.004	-0.059	-0.159	0.000
5	A	6	PRO	0	-0.004	-0.007	7.884	0.024	0.024	0.000	0.000	0.000	0.000
6	A	7	ASN	0	0.036	0.040	9.115	0.244	0.244	0.000	0.000	0.000	0.000
7	A	8	THR	0	0.009	-0.006	11.254	-0.017	-0.017	0.000	0.000	0.000	0.000
8	A	9	ALA	0	-0.001	0.015	14.085	0.045	0.045	0.000	0.000	0.000	0.000
9	A	10	ILE	0	0.039	0.025	16.303	-0.030	-0.030	0.000	0.000	0.000	0.000
10	A	11	GLY	0	0.040	0.023	18.617	0.038	0.038	0.000	0.000	0.000	0.000
11	A	12	ALA	0	-0.017	-0.003	16.964	-0.047	-0.047	0.000	0.000	0.000	0.000
12	A	13	ASN	0	-0.008	-0.037	14.917	0.095	0.095	0.000	0.000	0.000	0.000
13	A	14	GLY	0	0.027	0.026	11.040	-0.087	-0.087	0.000	0.000	0.000	0.000
14	A	15	TYR	0	-0.052	-0.045	6.387	-0.185	-0.185	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.803	0.882	9.165	0.416	0.416	0.000	0.000	0.000	0.000
16	A	17	ILE	0	0.010	0.011	10.634	0.029	0.029	0.000	0.000	0.000	0.000
17	A	18	ILE	0	-0.015	-0.014	13.434	0.051	0.051	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.814	-0.902	16.992	-0.265	-0.265	0.000	0.000	0.000	0.000
19	A	20	ASN	0	-0.048	-0.018	16.191	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	21	LYS	1	0.835	0.921	14.768	0.272	0.272	0.000	0.000	0.000	0.000
21	A	22	ASN	0	-0.010	-0.013	9.541	-0.044	-0.044	0.000	0.000	0.000	0.000
22	A	23	PHE	0	0.025	0.012	11.922	0.128	0.128	0.000	0.000	0.000	0.000
23	A	24	TYR	0	0.034	0.011	7.963	-0.064	-0.064	0.000	0.000	0.000	0.000
24	A	25	PHE	0	-0.026	-0.011	11.528	0.078	0.078	0.000	0.000	0.000	0.000
25	A	26	ARG	1	0.957	0.981	11.824	-0.388	-0.388	0.000	0.000	0.000	0.000
26	A	27	ASN	0	-0.001	-0.003	16.176	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	28	GLY	0	0.020	0.021	18.595	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.019	-0.010	18.841	-0.025	-0.025	0.000	0.000	0.000	0.000
29	A	30	PRO	0	0.018	0.016	15.980	0.017	0.017	0.000	0.000	0.000	0.000
30	A	31	GLN	0	-0.057	-0.027	13.696	0.075	0.075	0.000	0.000	0.000	0.000
31	A	32	ILE	0	0.020	0.012	14.266	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	33	GLY	0	-0.026	-0.026	12.615	0.023	0.023	0.000	0.000	0.000	0.000
33	A	34	VAL	0	-0.020	0.006	7.026	-0.061	-0.061	0.000	0.000	0.000	0.000
34	A	35	PHE	0	-0.001	0.001	6.867	0.124	0.124	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.885	0.952	2.510	-8.124	-5.041	2.373	-1.723	-3.732	0.019
36	A	37	GLY	0	0.064	0.027	2.464	-2.862	-2.499	0.955	0.316	-1.634	0.002
37	A	38	PRO	0	-0.027	-0.009	1.637	-20.514	-28.093	18.401	-6.986	-3.836	-0.069
38	A	39	ASN	0	-0.023	-0.013	3.024	-3.296	-1.677	0.209	-0.802	-1.027	-0.008
39	A	40	GLY	0	0.033	0.019	2.561	0.786	2.816	3.593	-2.179	-3.443	0.012
40	A	41	PHE	0	-0.002	0.003	2.738	-3.694	-2.319	2.427	1.010	-4.812	-0.012
41	A	42	GLU	-1	-0.778	-0.873	4.445	-2.595	-2.415	0.001	-0.030	-0.151	0.000
42	A	43	TYR	0	0.035	0.004	7.412	0.170	0.170	0.000	0.000	0.000	0.000
43	A	44	PHE	0	-0.028	-0.009	7.342	-0.168	-0.168	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.039	0.012	12.493	0.063	0.063	0.000	0.000	0.000	0.000
45	A	46	PRO	0	0.066	0.026	15.892	-0.034	-0.034	0.000	0.000	0.000	0.000
46	A	47	ALA	0	0.002	0.018	19.573	-0.014	-0.014	0.000	0.000	0.000	0.000
47	A	48	ASN	0	-0.085	-0.050	21.736	0.002	0.002	0.000	0.000	0.000	0.000
48	A	49	THR	0	-0.036	-0.011	18.215	0.021	0.021	0.000	0.000	0.000	0.000
49	A	50	ASP	-1	-0.858	-0.929	18.583	-0.073	-0.073	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.017	-0.008	20.584	-0.017	-0.017	0.000	0.000	0.000	0.000
51	A	52	ASN	0	-0.022	-0.011	22.865	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	53	ASN	0	-0.008	0.015	18.271	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	54	ILE	0	0.044	0.018	19.195	0.022	0.022	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.822	-0.920	18.727	0.053	0.053	0.000	0.000	0.000	0.000
55	A	56	GLY	0	-0.027	-0.012	15.494	-0.019	-0.019	0.000	0.000	0.000	0.000
56	A	57	GLN	0	-0.011	-0.008	14.106	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	58	ALA	0	-0.032	-0.014	10.455	0.064	0.064	0.000	0.000	0.000	0.000
58	A	59	ILE	0	-0.052	-0.016	12.326	-0.060	-0.060	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.819	0.883	13.024	0.121	0.121	0.000	0.000	0.000	0.000
60	A	61	TYR	0	-0.050	-0.067	13.765	0.016	0.016	0.000	0.000	0.000	0.000
61	A	62	GLN	0	-0.048	-0.024	14.090	0.050	0.050	0.000	0.000	0.000	0.000
62	A	63	ASN	0	-0.011	-0.014	15.195	-0.044	-0.044	0.000	0.000	0.000	0.000
63	A	64	ARG	1	0.967	1.001	15.596	-0.121	-0.121	0.000	0.000	0.000	0.000
64	A	65	PHE	0	0.059	0.026	15.047	0.046	0.046	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.041	-0.002	12.792	-0.037	-0.037	0.000	0.000	0.000	0.000
66	A	67	HIS	0	0.034	0.026	15.375	0.053	0.053	0.000	0.000	0.000	0.000
67	A	68	LEU	0	0.007	-0.003	13.625	-0.034	-0.034	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.008	-0.014	16.026	0.044	0.044	0.000	0.000	0.000	0.000
69	A	70	GLY	0	0.020	0.020	18.298	0.013	0.013	0.000	0.000	0.000	0.000
70	A	71	ASN	0	-0.018	0.006	13.639	0.032	0.032	0.000	0.000	0.000	0.000
71	A	72	ILE	0	0.031	0.010	14.780	-0.037	-0.037	0.000	0.000	0.000	0.000
72	A	73	TYR	0	0.036	0.015	9.048	0.005	0.005	0.000	0.000	0.000	0.000
73	A	74	TYR	0	0.051	0.022	11.277	-0.118	-0.118	0.000	0.000	0.000	0.000
74	A	75	PHE	0	-0.010	0.016	8.964	0.120	0.120	0.000	0.000	0.000	0.000
75	A	76	GLY	0	0.078	0.042	10.998	-0.095	-0.095	0.000	0.000	0.000	0.000
76	A	77	ASN	0	-0.004	-0.019	12.769	-0.049	-0.049	0.000	0.000	0.000	0.000
77	A	78	ASN	0	0.055	0.028	8.426	0.061	0.061	0.000	0.000	0.000	0.000
78	A	79	SER	0	-0.008	0.001	10.915	-0.095	-0.095	0.000	0.000	0.000	0.000
79	A	80	LYS	1	0.837	0.929	5.772	0.297	0.297	0.000	0.000	0.000	0.000
80	A	81	ALA	0	-0.020	-0.004	6.395	-0.166	-0.166	0.000	0.000	0.000	0.000
81	A	82	VAL	0	-0.032	-0.014	6.323	0.314	0.314	0.000	0.000	0.000	0.000
82	A	83	THR	0	-0.018	-0.017	3.918	-0.149	0.067	0.000	-0.032	-0.183	0.000
83	A	84	GLY	0	0.025	0.017	7.027	-0.159	-0.159	0.000	0.000	0.000	0.000
84	A	85	TRP	0	0.013	0.002	9.565	-0.050	-0.050	0.000	0.000	0.000	0.000
85	A	86	GLN	0	-0.037	-0.017	9.647	-0.100	-0.100	0.000	0.000	0.000	0.000
86	A	87	THR	0	-0.006	-0.004	14.167	0.012	0.012	0.000	0.000	0.000	0.000
87	A	88	ILE	0	-0.028	-0.012	14.682	-0.026	-0.026	0.000	0.000	0.000	0.000
88	A	89	ASN	0	-0.009	-0.019	19.042	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	90	GLY	0	0.009	0.007	22.089	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	91	ASN	0	0.011	0.030	21.423	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	92	MET	0	0.052	0.044	17.739	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	93	TYR	0	0.033	0.023	15.095	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	94	TYR	0	0.066	0.019	11.072	0.039	0.039	0.000	0.000	0.000	0.000
94	A	95	PHE	0	-0.040	-0.007	9.307	-0.019	-0.019	0.000	0.000	0.000	0.000
95	A	96	MET	0	0.051	0.030	8.918	0.073	0.073	0.000	0.000	0.000	0.000
96	A	97	PRO	0	0.034	-0.004	5.374	0.065	0.065	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.892	-0.940	4.540	1.584	1.746	-0.001	-0.012	-0.148	0.000
98	A	99	THR	0	-0.033	-0.030	6.193	0.097	0.097	0.000	0.000	0.000	0.000
99	A	100	ALA	0	-0.032	-0.020	5.450	-0.033	-0.033	0.000	0.000	0.000	0.000
100	A	101	MET	0	-0.034	0.000	7.353	-0.155	-0.155	0.000	0.000	0.000	0.000
101	A	102	ALA	0	-0.022	-0.021	10.998	0.027	0.027	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.008	0.010	13.743	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	104	ALA	0	-0.005	-0.020	15.832	-0.043	-0.043	0.000	0.000	0.000	0.000
104	A	105	GLY	0	-0.045	-0.013	19.191	0.006	0.006	0.000	0.000	0.000	0.000
105	A	106	GLY	0	0.016	0.004	22.458	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	107	LEU	0	-0.038	-0.021	22.253	0.000	0.000	0.000	0.000	0.000	0.000
107	A	108	PHE	0	0.001	-0.002	16.631	0.025	0.025	0.000	0.000	0.000	0.000
108	A	109	GLU	-1	-0.908	-0.960	19.448	0.382	0.382	0.000	0.000	0.000	0.000
109	A	110	ILE	0	-0.070	-0.029	13.839	0.056	0.056	0.000	0.000	0.000	0.000
110	A	111	ASP	-1	-0.921	-0.976	13.187	0.718	0.718	0.000	0.000	0.000	0.000
111	A	112	GLY	0	0.005	0.011	16.093	-0.052	-0.052	0.000	0.000	0.000	0.000
112	A	113	VAL	0	-0.040	-0.013	19.195	-0.050	-0.050	0.000	0.000	0.000	0.000
113	A	114	ILE	0	0.004	0.006	20.114	0.030	0.030	0.000	0.000	0.000	0.000
114	A	115	TYR	0	-0.004	-0.004	18.405	-0.049	-0.049	0.000	0.000	0.000	0.000
115	A	116	PHE	0	-0.002	0.000	22.213	0.015	0.015	0.000	0.000	0.000	0.000
116	A	117	PHE	0	0.004	0.001	17.255	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	118	GLY	0	0.065	0.040	21.538	-0.005	-0.005	0.000	0.000	0.000	0.000
118	A	119	VAL	0	0.014	-0.013	21.655	0.025	0.025	0.000	0.000	0.000	0.000
119	A	120	ASP	-1	-0.894	-0.948	21.326	0.260	0.260	0.000	0.000	0.000	0.000
120	A	121	GLY	0	-0.002	-0.017	18.242	0.010	0.010	0.000	0.000	0.000	0.000
121	A	122	VAL	0	-0.061	-0.010	18.424	0.020	0.020	0.000	0.000	0.000	0.000
122	A	123	LYS	1	0.806	0.888	19.355	-0.260	-0.260	0.000	0.000	0.000	0.000
123	A	124	ALA	0	0.001	-0.005	21.220	-0.024	-0.024	0.000	0.000	0.000	0.000
124	A	125	PRO	0	-0.032	-0.027	24.751	0.009	0.009	0.000	0.000	0.000	0.000
125	A	126	GLY	0	0.010	0.020	26.411	-0.003	-0.003	0.000	0.000	0.000	0.000

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