FMO DATABASE

FMODB ID: 7JR7K

Calculation Name: 2F6E-A-Xray311

Preferred Name: Toxin A

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2F6E

Chain ID: A

ChEMBL ID: CHEMBL3580504

UniProt ID: P16154

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:

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. 1.20200116
Remarks	Structural optimization was performed under the unconstrained condition of hydrogen and heavy atoms fixed using MOE with Auto-FMO protocol as OptH.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	126
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1011603.070414
FMO2-HF: Nuclear repulsion	963183.129157
FMO2-HF: Total energy	-48419.941257
FMO2-MP2: Total energy	-48562.716728

3D Structure Molmil

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.
-38.256	-31.246	27.78	-11.623	-23.168	-0.05

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 : -0.050 / q_NPA : -0.045

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	0.029	0.008	2.437	-0.409	3.724	0.871	-1.682	-3.322	0.003
4	A	5	GLU	-1	-0.886	-0.946	4.254	0.226	0.439	0.005	-0.052	-0.165	0.000
5	A	6	PRO	0	-0.007	-0.006	7.922	0.026	0.026	0.000	0.000	0.000	0.000
6	A	7	ASN	0	0.030	0.038	9.169	0.283	0.283	0.000	0.000	0.000	0.000
7	A	8	THR	0	-0.007	-0.025	11.303	-0.016	-0.016	0.000	0.000	0.000	0.000
8	A	9	ALA	0	-0.004	0.011	14.136	0.052	0.052	0.000	0.000	0.000	0.000
9	A	10	ILE	0	0.027	0.010	16.349	-0.026	-0.026	0.000	0.000	0.000	0.000
10	A	11	GLY	0	0.039	0.021	18.673	0.040	0.040	0.000	0.000	0.000	0.000
11	A	12	ALA	0	-0.019	-0.002	17.001	-0.046	-0.046	0.000	0.000	0.000	0.000
12	A	13	ASN	0	-0.007	-0.039	14.554	0.113	0.113	0.000	0.000	0.000	0.000
13	A	14	GLY	0	0.006	0.013	11.070	-0.093	-0.093	0.000	0.000	0.000	0.000
14	A	15	TYR	0	-0.024	-0.018	6.779	-0.176	-0.176	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.865	0.933	9.195	0.403	0.403	0.000	0.000	0.000	0.000
16	A	17	ILE	0	0.015	0.016	10.687	0.034	0.034	0.000	0.000	0.000	0.000
17	A	18	ILE	0	-0.018	-0.016	13.458	0.051	0.051	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.828	-0.911	17.012	-0.250	-0.250	0.000	0.000	0.000	0.000
19	A	20	ASN	0	-0.047	-0.025	16.203	-0.023	-0.023	0.000	0.000	0.000	0.000
20	A	21	LYS	1	0.846	0.937	14.775	0.252	0.252	0.000	0.000	0.000	0.000
21	A	22	ASN	0	-0.022	-0.020	9.436	-0.062	-0.062	0.000	0.000	0.000	0.000
22	A	23	PHE	0	0.026	0.010	11.929	0.133	0.133	0.000	0.000	0.000	0.000
23	A	24	TYR	0	0.027	0.010	7.832	-0.054	-0.054	0.000	0.000	0.000	0.000
24	A	25	PHE	0	-0.022	-0.004	11.540	0.077	0.077	0.000	0.000	0.000	0.000
25	A	26	ARG	1	0.983	0.984	12.037	-0.467	-0.467	0.000	0.000	0.000	0.000
26	A	27	ASN	0	-0.007	-0.002	16.194	-0.012	-0.012	0.000	0.000	0.000	0.000
27	A	28	GLY	0	0.023	0.022	18.627	-0.012	-0.012	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.014	-0.014	18.879	-0.027	-0.027	0.000	0.000	0.000	0.000
29	A	30	PRO	0	0.013	0.015	15.988	0.022	0.022	0.000	0.000	0.000	0.000
30	A	31	GLN	0	-0.064	-0.029	13.768	0.072	0.072	0.000	0.000	0.000	0.000
31	A	32	ILE	0	0.021	0.014	14.260	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	33	GLY	0	-0.039	-0.030	12.591	0.027	0.027	0.000	0.000	0.000	0.000
33	A	34	VAL	0	-0.024	0.006	6.978	-0.055	-0.055	0.000	0.000	0.000	0.000
34	A	35	PHE	0	0.004	0.002	6.865	0.163	0.163	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.895	0.961	2.428	-9.424	-6.115	2.907	-1.885	-4.331	0.021
36	A	37	GLY	0	0.054	0.035	2.446	-3.348	-2.901	0.937	0.228	-1.611	0.002
37	A	38	PRO	0	-0.019	-0.008	1.668	-20.619	-26.674	16.335	-6.429	-3.853	-0.068
38	A	39	ASN	0	-0.022	-0.012	3.049	-3.360	-1.765	0.192	-0.775	-1.013	-0.007
39	A	40	GLY	0	0.031	0.015	2.540	0.860	2.709	4.064	-2.344	-3.568	0.013
40	A	41	PHE	0	-0.007	0.002	2.743	-2.958	-2.024	2.466	1.390	-4.791	-0.014
41	A	42	GLU	-1	-0.791	-0.891	4.402	-2.739	-2.530	0.002	-0.034	-0.178	0.000
42	A	43	TYR	0	0.032	0.000	7.364	0.178	0.178	0.000	0.000	0.000	0.000
43	A	44	PHE	0	-0.023	-0.006	7.337	-0.191	-0.191	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.042	0.014	12.474	0.063	0.063	0.000	0.000	0.000	0.000
45	A	46	PRO	0	0.061	0.022	15.861	-0.040	-0.040	0.000	0.000	0.000	0.000
46	A	47	ALA	0	0.008	0.014	19.544	-0.015	-0.015	0.000	0.000	0.000	0.000
47	A	48	ASN	0	-0.065	-0.036	21.716	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	49	THR	0	-0.053	-0.021	18.295	0.021	0.021	0.000	0.000	0.000	0.000
49	A	50	ASP	-1	-0.920	-0.988	18.562	-0.049	-0.049	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.023	-0.009	20.560	-0.018	-0.018	0.000	0.000	0.000	0.000
51	A	52	ASN	0	-0.032	-0.016	22.845	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	53	ASN	0	-0.017	0.011	18.257	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	54	ILE	0	0.044	0.016	19.069	0.022	0.022	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.821	-0.920	18.714	0.091	0.091	0.000	0.000	0.000	0.000
55	A	56	GLY	0	-0.022	-0.007	15.484	-0.021	-0.021	0.000	0.000	0.000	0.000
56	A	57	GLN	0	-0.002	-0.001	14.100	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	58	ALA	0	-0.032	-0.018	10.393	0.067	0.067	0.000	0.000	0.000	0.000
58	A	59	ILE	0	-0.058	-0.015	12.310	-0.072	-0.072	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.904	0.944	12.992	0.112	0.112	0.000	0.000	0.000	0.000
60	A	61	TYR	0	-0.064	-0.070	13.664	0.014	0.014	0.000	0.000	0.000	0.000
61	A	62	GLN	0	-0.046	-0.028	14.005	0.058	0.058	0.000	0.000	0.000	0.000
62	A	63	ASN	0	-0.008	-0.001	15.090	-0.046	-0.046	0.000	0.000	0.000	0.000
63	A	64	ARG	1	0.977	1.006	15.504	-0.169	-0.169	0.000	0.000	0.000	0.000
64	A	65	PHE	0	0.056	0.024	14.966	0.054	0.054	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.051	-0.002	12.641	-0.043	-0.043	0.000	0.000	0.000	0.000
66	A	67	HIS	0	0.037	0.028	15.337	0.063	0.063	0.000	0.000	0.000	0.000
67	A	68	LEU	0	0.005	-0.006	13.664	-0.038	-0.038	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.017	-0.018	15.885	0.048	0.048	0.000	0.000	0.000	0.000
69	A	70	GLY	0	0.015	0.019	18.323	0.013	0.013	0.000	0.000	0.000	0.000
70	A	71	ASN	0	0.003	0.019	13.631	0.011	0.011	0.000	0.000	0.000	0.000
71	A	72	ILE	0	0.034	0.011	14.769	-0.041	-0.041	0.000	0.000	0.000	0.000
72	A	73	TYR	0	0.035	0.014	9.010	0.010	0.010	0.000	0.000	0.000	0.000
73	A	74	TYR	0	0.046	0.012	11.198	-0.139	-0.139	0.000	0.000	0.000	0.000
74	A	75	PHE	0	-0.010	0.016	8.984	0.138	0.138	0.000	0.000	0.000	0.000
75	A	76	GLY	0	0.075	0.041	10.892	-0.112	-0.112	0.000	0.000	0.000	0.000
76	A	77	ASN	0	-0.002	-0.021	12.732	-0.054	-0.054	0.000	0.000	0.000	0.000
77	A	78	ASN	0	0.045	0.024	8.412	0.083	0.083	0.000	0.000	0.000	0.000
78	A	79	SER	0	-0.010	-0.001	10.878	-0.096	-0.096	0.000	0.000	0.000	0.000
79	A	80	LYS	1	0.865	0.945	5.863	0.417	0.417	0.000	0.000	0.000	0.000
80	A	81	ALA	0	-0.017	-0.002	6.311	-0.188	-0.188	0.000	0.000	0.000	0.000
81	A	82	VAL	0	-0.041	-0.017	6.220	0.312	0.312	0.000	0.000	0.000	0.000
82	A	83	THR	0	-0.024	-0.022	3.841	-0.128	0.089	0.001	-0.029	-0.188	0.000
83	A	84	GLY	0	0.026	0.015	7.030	-0.192	-0.192	0.000	0.000	0.000	0.000
84	A	85	TRP	0	0.018	0.004	9.644	-0.070	-0.070	0.000	0.000	0.000	0.000
85	A	86	GLN	0	-0.037	-0.018	9.700	-0.123	-0.123	0.000	0.000	0.000	0.000
86	A	87	THR	0	0.001	0.001	14.199	0.010	0.010	0.000	0.000	0.000	0.000
87	A	88	ILE	0	-0.026	-0.012	14.639	-0.030	-0.030	0.000	0.000	0.000	0.000
88	A	89	ASN	0	-0.015	-0.019	19.027	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	90	GLY	0	0.008	0.007	22.125	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	91	ASN	0	0.006	0.024	21.254	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	92	MET	0	0.010	0.006	17.473	0.001	0.001	0.000	0.000	0.000	0.000
92	A	93	TYR	0	0.045	0.031	15.021	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	94	TYR	0	0.063	0.017	10.759	0.047	0.047	0.000	0.000	0.000	0.000
94	A	95	PHE	0	-0.042	-0.008	9.364	-0.023	-0.023	0.000	0.000	0.000	0.000
95	A	96	MET	0	0.045	0.026	8.947	0.115	0.115	0.000	0.000	0.000	0.000
96	A	97	PRO	0	0.043	0.005	5.528	0.095	0.095	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.922	-0.956	4.603	1.954	2.113	0.000	-0.011	-0.148	0.000
98	A	99	THR	0	-0.011	-0.018	6.266	0.112	0.112	0.000	0.000	0.000	0.000
99	A	100	ALA	0	-0.028	-0.018	5.446	-0.041	-0.041	0.000	0.000	0.000	0.000
100	A	101	MET	0	-0.039	-0.004	7.327	-0.210	-0.210	0.000	0.000	0.000	0.000
101	A	102	ALA	0	-0.012	-0.022	10.987	0.028	0.028	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.019	0.011	13.777	-0.007	-0.007	0.000	0.000	0.000	0.000
103	A	104	ALA	0	0.000	-0.019	15.874	-0.051	-0.051	0.000	0.000	0.000	0.000
104	A	105	GLY	0	-0.044	-0.013	19.232	0.005	0.005	0.000	0.000	0.000	0.000
105	A	106	GLY	0	0.015	0.005	22.510	-0.005	-0.005	0.000	0.000	0.000	0.000
106	A	107	LEU	0	-0.039	-0.021	22.295	0.001	0.001	0.000	0.000	0.000	0.000
107	A	108	PHE	0	0.002	0.000	16.682	0.030	0.030	0.000	0.000	0.000	0.000
108	A	109	GLU	-1	-0.901	-0.956	19.477	0.407	0.407	0.000	0.000	0.000	0.000
109	A	110	ILE	0	-0.075	-0.032	13.906	0.064	0.064	0.000	0.000	0.000	0.000
110	A	111	ASP	-1	-0.934	-0.978	13.376	0.799	0.799	0.000	0.000	0.000	0.000
111	A	112	GLY	0	-0.005	0.004	16.214	-0.061	-0.061	0.000	0.000	0.000	0.000
112	A	113	VAL	0	-0.022	-0.002	19.314	-0.056	-0.056	0.000	0.000	0.000	0.000
113	A	114	ILE	0	0.005	0.006	20.235	0.036	0.036	0.000	0.000	0.000	0.000
114	A	115	TYR	0	-0.003	-0.007	18.473	-0.054	-0.054	0.000	0.000	0.000	0.000
115	A	116	PHE	0	0.003	-0.001	22.250	0.017	0.017	0.000	0.000	0.000	0.000
116	A	117	PHE	0	0.000	0.001	17.374	0.000	0.000	0.000	0.000	0.000	0.000
117	A	118	GLY	0	0.066	0.037	21.571	-0.007	-0.007	0.000	0.000	0.000	0.000
118	A	119	VAL	0	0.016	-0.010	21.688	0.030	0.030	0.000	0.000	0.000	0.000
119	A	120	ASP	-1	-0.908	-0.952	21.299	0.302	0.302	0.000	0.000	0.000	0.000
120	A	121	GLY	0	-0.004	-0.018	18.268	0.015	0.015	0.000	0.000	0.000	0.000
121	A	122	VAL	0	-0.046	-0.006	18.446	0.022	0.022	0.000	0.000	0.000	0.000
122	A	123	LYS	1	0.859	0.929	19.407	-0.302	-0.302	0.000	0.000	0.000	0.000
123	A	124	ALA	0	-0.012	-0.009	21.239	-0.029	-0.029	0.000	0.000	0.000	0.000
124	A	125	PRO	0	-0.041	-0.033	24.769	0.008	0.008	0.000	0.000	0.000	0.000
125	A	126	GLY	0	0.036	0.013	26.482	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	1	NME	0	-0.020	0.010	25.842	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:2:TYR )