FMO DATABASE

FMODB ID: 89L5Y

Calculation Name: 2A1A-A-Xray372

Preferred Name: Interferon-induced, double-stranded RNA-activated protein kinase

Target Type: SINGLE PROTEIN

Ligand Name: phosphothreonine

ligand 3-letter code: TPO

PDB ID: 2A1A

Chain ID: A

ChEMBL ID: CHEMBL5785

UniProt ID: P19525

Base Structure: X-ray

Registration Date: 2023-09-24

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	161
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1655717.442714
FMO2-HF: Nuclear repulsion	1589600.492257
FMO2-HF: Total energy	-66116.950457
FMO2-MP2: Total energy	-66309.736222

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:3:SER)

Summations of interaction energy for fragment #1(A:3:SER)

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.
-27.492	-25.555	14.54	-7.254	-9.222	0.007

Interaction energy analysis for fragmet #1(A:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.006

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	5	CYS	0	0.049	0.043	3.522	-1.272	1.446	0.004	-1.380	-1.341	0.002
4	A	6	ARG	1	0.783	0.908	3.376	-1.114	-0.662	0.020	-0.298	-0.174	-0.002
5	A	7	PHE	0	-0.006	-0.015	2.404	-0.648	0.219	1.108	-0.731	-1.244	0.002
6	A	8	TYR	0	-0.037	-0.035	6.712	0.373	0.373	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.755	-0.843	10.299	-0.404	-0.404	0.000	0.000	0.000	0.000
8	A	10	ASN	0	-0.009	-0.002	13.134	-0.088	-0.088	0.000	0.000	0.000	0.000
9	A	11	LYS	1	0.958	0.961	11.496	0.801	0.801	0.000	0.000	0.000	0.000
10	A	12	TYR	0	0.026	0.000	11.493	-0.169	-0.169	0.000	0.000	0.000	0.000
11	A	13	PRO	0	-0.002	0.025	12.188	0.040	0.040	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.829	-0.922	14.362	-0.310	-0.310	0.000	0.000	0.000	0.000
13	A	15	ILE	0	-0.047	-0.038	18.095	0.016	0.016	0.000	0.000	0.000	0.000
14	A	16	ASP	-1	-0.914	-0.963	20.598	-0.049	-0.049	0.000	0.000	0.000	0.000
15	A	17	ASP	-1	-0.866	-0.909	15.321	-0.091	-0.091	0.000	0.000	0.000	0.000
16	A	18	ILE	0	-0.049	-0.038	15.876	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	19	VAL	0	-0.028	-0.021	11.509	0.018	0.018	0.000	0.000	0.000	0.000
18	A	20	MET	0	0.008	-0.002	9.395	0.006	0.006	0.000	0.000	0.000	0.000
19	A	21	VAL	0	-0.032	-0.022	9.428	-0.059	-0.059	0.000	0.000	0.000	0.000
20	A	22	ASN	0	-0.021	-0.033	8.753	0.009	0.009	0.000	0.000	0.000	0.000
21	A	23	VAL	0	-0.007	0.001	10.574	-0.169	-0.169	0.000	0.000	0.000	0.000
22	A	24	GLN	0	0.010	0.013	10.396	-0.147	-0.147	0.000	0.000	0.000	0.000
23	A	25	GLN	0	0.017	-0.002	14.194	0.048	0.048	0.000	0.000	0.000	0.000
24	A	26	ILE	0	-0.042	-0.013	17.937	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	27	ALA	0	0.005	0.008	20.916	0.003	0.003	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.937	-0.968	23.534	-0.095	-0.095	0.000	0.000	0.000	0.000
27	A	29	MET	0	0.014	0.003	24.095	0.008	0.008	0.000	0.000	0.000	0.000
28	A	30	GLY	0	-0.007	-0.018	22.463	0.006	0.006	0.000	0.000	0.000	0.000
29	A	31	ALA	0	-0.025	-0.001	18.452	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	32	TYR	0	0.050	0.032	16.024	0.001	0.001	0.000	0.000	0.000	0.000
31	A	33	VAL	0	-0.030	-0.027	12.645	0.033	0.033	0.000	0.000	0.000	0.000
32	A	34	LYS	1	0.911	0.968	7.716	1.069	1.069	0.000	0.000	0.000	0.000
33	A	35	LEU	0	0.029	-0.004	9.013	0.277	0.277	0.000	0.000	0.000	0.000
34	A	36	LEU	0	-0.029	-0.018	4.987	-0.463	-0.463	0.000	0.000	0.000	0.000
35	A	37	GLU	-1	-0.762	-0.833	3.924	0.542	0.774	0.000	-0.041	-0.191	0.000
36	A	38	TYR	0	-0.033	-0.031	5.860	-0.311	-0.311	0.000	0.000	0.000	0.000
37	A	39	ASP	-1	-0.809	-0.912	4.390	-3.917	-3.935	-0.001	-0.012	0.032	0.000
38	A	40	ASN	0	-0.100	-0.038	2.828	1.083	1.676	0.059	-0.177	-0.476	0.000
39	A	41	ILE	0	0.017	0.017	6.512	0.326	0.326	0.000	0.000	0.000	0.000
40	A	42	GLU	-1	-0.906	-0.968	10.126	-0.690	-0.690	0.000	0.000	0.000	0.000
41	A	43	GLY	0	0.015	0.011	12.639	0.038	0.038	0.000	0.000	0.000	0.000
42	A	44	MET	0	-0.039	-0.004	15.076	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	45	ILE	0	-0.046	-0.019	16.145	0.026	0.026	0.000	0.000	0.000	0.000
44	A	46	LEU	0	0.008	0.007	19.405	0.004	0.004	0.000	0.000	0.000	0.000
45	A	47	LEU	0	0.011	0.013	23.177	0.024	0.024	0.000	0.000	0.000	0.000
46	A	48	SER	0	-0.006	0.003	25.635	0.001	0.001	0.000	0.000	0.000	0.000
47	A	61	LEU	0	0.042	0.026	22.988	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	62	ILE	0	-0.040	-0.030	18.498	0.029	0.029	0.000	0.000	0.000	0.000
49	A	63	ARG	1	0.966	0.973	19.062	-0.164	-0.164	0.000	0.000	0.000	0.000
50	A	64	VAL	0	0.031	0.009	16.342	0.029	0.029	0.000	0.000	0.000	0.000
51	A	65	GLY	0	0.035	0.028	13.345	0.024	0.024	0.000	0.000	0.000	0.000
52	A	66	LYS	1	0.797	0.907	12.264	-0.134	-0.134	0.000	0.000	0.000	0.000
53	A	67	ASN	0	0.045	0.008	8.525	-0.234	-0.234	0.000	0.000	0.000	0.000
54	A	68	ASP	-1	-0.805	-0.882	12.512	0.101	0.101	0.000	0.000	0.000	0.000
55	A	69	VAL	0	0.037	0.039	13.479	0.027	0.027	0.000	0.000	0.000	0.000
56	A	70	ALA	0	-0.025	-0.014	15.395	-0.034	-0.034	0.000	0.000	0.000	0.000
57	A	71	VAL	0	0.015	0.015	16.420	0.009	0.009	0.000	0.000	0.000	0.000
58	A	72	VAL	0	0.005	0.012	15.708	-0.028	-0.028	0.000	0.000	0.000	0.000
59	A	73	LEU	0	-0.083	-0.037	18.372	0.027	0.027	0.000	0.000	0.000	0.000
60	A	74	ARG	1	0.904	0.917	20.520	0.176	0.176	0.000	0.000	0.000	0.000
61	A	75	VAL	0	0.006	0.011	17.132	-0.025	-0.025	0.000	0.000	0.000	0.000
62	A	76	ASP	-1	-0.831	-0.896	19.653	-0.291	-0.291	0.000	0.000	0.000	0.000
63	A	77	LYS	1	0.856	0.899	17.680	0.312	0.312	0.000	0.000	0.000	0.000
64	A	78	GLU	-1	-0.941	-0.953	19.791	-0.352	-0.352	0.000	0.000	0.000	0.000
65	A	79	LYS	1	0.843	0.902	21.773	0.278	0.278	0.000	0.000	0.000	0.000
66	A	80	GLY	0	-0.030	0.003	17.367	-0.028	-0.028	0.000	0.000	0.000	0.000
67	A	81	TYR	0	-0.034	-0.008	16.482	-0.043	-0.043	0.000	0.000	0.000	0.000
68	A	82	ILE	0	0.043	0.013	13.616	0.026	0.026	0.000	0.000	0.000	0.000
69	A	83	ASP	-1	-0.830	-0.885	17.700	-0.213	-0.213	0.000	0.000	0.000	0.000
70	A	84	LEU	0	0.017	-0.007	14.530	0.013	0.013	0.000	0.000	0.000	0.000
71	A	85	SER	0	-0.027	-0.048	19.090	0.016	0.016	0.000	0.000	0.000	0.000
72	A	86	LYS	1	0.931	0.935	18.969	-0.108	-0.108	0.000	0.000	0.000	0.000
73	A	87	ARG	1	0.891	0.965	21.418	0.070	0.070	0.000	0.000	0.000	0.000
74	A	88	ARG	1	0.946	0.964	23.822	0.058	0.058	0.000	0.000	0.000	0.000
75	A	89	VAL	0	0.000	0.035	19.542	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	90	SER	0	0.007	-0.012	22.497	0.012	0.012	0.000	0.000	0.000	0.000
77	A	91	SER	0	0.041	-0.005	22.478	0.014	0.014	0.000	0.000	0.000	0.000
78	A	92	GLU	-1	-0.848	-0.918	22.861	0.176	0.176	0.000	0.000	0.000	0.000
79	A	93	ASP	-1	-0.803	-0.878	20.210	0.150	0.150	0.000	0.000	0.000	0.000
80	A	94	ILE	0	-0.021	-0.010	18.202	0.028	0.028	0.000	0.000	0.000	0.000
81	A	95	ILE	0	0.014	0.013	17.529	0.052	0.052	0.000	0.000	0.000	0.000
82	A	96	LYS	1	0.859	0.917	18.027	-0.105	-0.105	0.000	0.000	0.000	0.000
83	A	97	CYS	0	-0.043	0.001	13.722	0.067	0.067	0.000	0.000	0.000	0.000
84	A	98	GLU	-1	-0.924	-0.966	13.186	0.649	0.649	0.000	0.000	0.000	0.000
85	A	99	GLU	-1	-0.930	-0.957	13.400	0.592	0.592	0.000	0.000	0.000	0.000
86	A	100	LYS	1	0.850	0.925	11.602	-0.121	-0.121	0.000	0.000	0.000	0.000
87	A	101	TYR	0	0.058	0.017	5.390	-0.129	-0.129	0.000	0.000	0.000	0.000
88	A	102	GLN	0	0.036	0.016	9.208	0.685	0.685	0.000	0.000	0.000	0.000
89	A	103	LYS	1	0.893	0.941	10.677	-0.283	-0.283	0.000	0.000	0.000	0.000
90	A	104	SER	0	0.004	-0.023	7.612	-0.045	-0.045	0.000	0.000	0.000	0.000
91	A	105	LYS	1	0.890	0.945	5.547	-2.344	-2.344	0.000	0.000	0.000	0.000
92	A	106	THR	0	-0.066	-0.033	7.053	0.180	0.180	0.000	0.000	0.000	0.000
93	A	107	VAL	0	0.000	0.002	9.131	0.000	0.000	0.000	0.000	0.000	0.000
94	A	108	HIS	0	0.000	-0.003	2.208	-2.382	-1.933	4.738	-2.063	-3.124	-0.028
95	A	109	SER	0	-0.005	-0.012	6.279	0.389	0.389	0.000	0.000	0.000	0.000
96	A	110	ILE	0	-0.035	0.003	8.126	-0.187	-0.187	0.000	0.000	0.000	0.000
97	A	111	LEU	0	0.026	0.011	8.532	-0.112	-0.112	0.000	0.000	0.000	0.000
98	A	112	ARG	1	0.902	0.945	1.850	-17.880	-21.236	8.612	-2.552	-2.704	0.033
99	A	113	TYR	0	-0.078	-0.062	8.665	-0.182	-0.182	0.000	0.000	0.000	0.000
100	A	114	CYS	0	-0.028	-0.026	11.658	-0.161	-0.161	0.000	0.000	0.000	0.000
101	A	115	ALA	0	0.025	0.012	10.832	-0.090	-0.090	0.000	0.000	0.000	0.000
102	A	116	GLU	-1	-0.899	-0.960	8.334	0.668	0.668	0.000	0.000	0.000	0.000
103	A	117	LYS	1	0.801	0.898	12.931	-0.407	-0.407	0.000	0.000	0.000	0.000
104	A	118	PHE	0	-0.033	-0.033	15.942	-0.049	-0.049	0.000	0.000	0.000	0.000
105	A	119	GLN	0	-0.042	0.006	15.694	-0.084	-0.084	0.000	0.000	0.000	0.000
106	A	120	ILE	0	-0.015	-0.001	14.849	-0.054	-0.054	0.000	0.000	0.000	0.000
107	A	121	PRO	0	0.018	0.004	13.144	0.018	0.018	0.000	0.000	0.000	0.000
108	A	122	LEU	0	0.056	0.029	5.777	0.064	0.064	0.000	0.000	0.000	0.000
109	A	123	GLU	-1	-0.863	-0.958	9.201	-1.263	-1.263	0.000	0.000	0.000	0.000
110	A	124	GLU	-1	-0.807	-0.885	10.772	-0.260	-0.260	0.000	0.000	0.000	0.000
111	A	125	LEU	0	0.018	0.031	11.671	0.057	0.057	0.000	0.000	0.000	0.000
112	A	126	TYR	0	0.006	0.004	6.148	0.037	0.037	0.000	0.000	0.000	0.000
113	A	127	LYS	1	0.797	0.875	11.693	0.410	0.410	0.000	0.000	0.000	0.000
114	A	128	THR	0	-0.025	-0.015	14.938	0.047	0.047	0.000	0.000	0.000	0.000
115	A	129	ILE	0	0.005	0.005	14.418	0.047	0.047	0.000	0.000	0.000	0.000
116	A	130	ALA	0	0.005	-0.003	11.880	0.021	0.021	0.000	0.000	0.000	0.000
117	A	131	TRP	0	-0.034	-0.009	9.303	0.038	0.038	0.000	0.000	0.000	0.000
118	A	132	PRO	0	0.027	0.011	15.063	0.016	0.016	0.000	0.000	0.000	0.000
119	A	133	LEU	0	0.016	0.013	16.645	0.019	0.019	0.000	0.000	0.000	0.000
120	A	134	SER	0	-0.049	-0.038	14.726	0.035	0.035	0.000	0.000	0.000	0.000
121	A	135	ARG	1	0.801	0.880	17.141	0.165	0.165	0.000	0.000	0.000	0.000
122	A	136	LYS	1	0.904	0.974	20.015	-0.053	-0.053	0.000	0.000	0.000	0.000
123	A	137	PHE	0	0.014	-0.003	19.226	0.012	0.012	0.000	0.000	0.000	0.000
124	A	138	GLY	0	0.000	0.022	18.656	0.035	0.035	0.000	0.000	0.000	0.000
125	A	139	HIS	0	-0.032	-0.044	11.254	-0.084	-0.084	0.000	0.000	0.000	0.000
126	A	140	ALA	0	0.057	0.030	12.492	0.024	0.024	0.000	0.000	0.000	0.000
127	A	141	TYR	0	-0.001	-0.006	13.121	0.008	0.008	0.000	0.000	0.000	0.000
128	A	142	GLU	-1	-0.795	-0.888	14.798	0.378	0.378	0.000	0.000	0.000	0.000
129	A	143	ALA	0	0.039	0.046	17.580	-0.021	-0.021	0.000	0.000	0.000	0.000
130	A	144	PHE	0	0.030	-0.009	12.508	0.003	0.003	0.000	0.000	0.000	0.000
131	A	145	LYS	1	0.855	0.929	18.048	-0.320	-0.320	0.000	0.000	0.000	0.000
132	A	146	LEU	0	-0.008	-0.024	20.190	-0.012	-0.012	0.000	0.000	0.000	0.000
133	A	147	SER	0	-0.037	-0.023	20.633	-0.012	-0.012	0.000	0.000	0.000	0.000
134	A	148	ILE	0	-0.058	-0.021	20.806	-0.008	-0.008	0.000	0.000	0.000	0.000
135	A	149	ILE	0	-0.074	-0.036	24.185	-0.012	-0.012	0.000	0.000	0.000	0.000
136	A	150	ASP	-1	-0.822	-0.882	26.192	0.108	0.108	0.000	0.000	0.000	0.000
137	A	151	GLU	-1	-0.848	-0.922	25.881	0.157	0.157	0.000	0.000	0.000	0.000
138	A	152	THR	0	-0.033	-0.043	26.209	-0.008	-0.008	0.000	0.000	0.000	0.000
139	A	153	VAL	0	-0.046	-0.014	21.661	-0.013	-0.013	0.000	0.000	0.000	0.000
140	A	154	TRP	0	-0.050	-0.045	17.860	-0.008	-0.008	0.000	0.000	0.000	0.000
141	A	155	GLU	-1	-0.916	-0.939	23.752	0.037	0.037	0.000	0.000	0.000	0.000
142	A	156	GLY	0	-0.041	-0.031	25.230	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	157	ILE	0	-0.082	-0.036	19.536	-0.018	-0.018	0.000	0.000	0.000	0.000
144	A	158	GLU	-1	-0.914	-0.954	22.048	-0.026	-0.026	0.000	0.000	0.000	0.000
145	A	159	PRO	0	-0.044	-0.014	19.204	-0.020	-0.020	0.000	0.000	0.000	0.000
146	A	160	PRO	0	0.001	-0.005	16.850	-0.006	-0.006	0.000	0.000	0.000	0.000
147	A	161	SER	0	-0.020	-0.014	20.158	0.000	0.000	0.000	0.000	0.000	0.000
148	A	162	LYS	1	0.900	0.935	21.495	-0.099	-0.099	0.000	0.000	0.000	0.000
149	A	163	ASP	-1	-0.858	-0.938	23.003	0.117	0.117	0.000	0.000	0.000	0.000
150	A	164	VAL	0	0.004	0.005	16.251	0.030	0.030	0.000	0.000	0.000	0.000
151	A	165	LEU	0	0.010	0.005	18.371	0.046	0.046	0.000	0.000	0.000	0.000
152	A	166	ASP	-1	-0.792	-0.891	20.166	0.180	0.180	0.000	0.000	0.000	0.000
153	A	167	GLU	-1	-0.827	-0.854	17.673	0.396	0.396	0.000	0.000	0.000	0.000
154	A	168	LEU	0	0.001	0.004	14.433	0.062	0.062	0.000	0.000	0.000	0.000
155	A	169	LYS	1	0.872	0.925	17.525	-0.142	-0.142	0.000	0.000	0.000	0.000
156	A	170	ASN	0	-0.049	-0.041	20.747	0.004	0.004	0.000	0.000	0.000	0.000
157	A	171	TYR	0	-0.019	-0.005	14.427	0.078	0.078	0.000	0.000	0.000	0.000
158	A	172	ILE	0	-0.038	-0.029	16.739	0.059	0.059	0.000	0.000	0.000	0.000
159	A	173	SER	0	-0.028	0.009	18.774	-0.010	-0.010	0.000	0.000	0.000	0.000
160	A	174	LYS	1	0.925	0.986	14.854	-0.782	-0.782	0.000	0.000	0.000	0.000
161	A	175	ARG	1	0.950	0.966	19.720	-0.336	-0.336	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:SER)