FMO DATABASE

FMODB ID: G5161

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	OptH
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	-1652968.306401
FMO2-HF: Nuclear repulsion	1586852.882188
FMO2-HF: Total energy	-66115.424214
FMO2-MP2: Total energy	-66308.196102

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.
-14.749	-7.556	3.586	-4.582	-6.196	-0.016

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 : -0.065 / q_NPA : -0.034

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	0.065	0.065	3.192	-0.738	2.011	0.000	-1.411	-1.337	-0.001
4	A	6	ARG	1	0.776	0.908	3.606	-1.415	-1.061	0.014	-0.216	-0.151	-0.001
5	A	7	PHE	0	0.011	-0.006	2.510	-1.148	-0.069	0.837	-0.695	-1.221	0.003
6	A	8	TYR	0	-0.062	-0.072	6.846	0.330	0.330	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.772	-0.866	10.421	-0.503	-0.503	0.000	0.000	0.000	0.000
8	A	10	ASN	0	-0.011	-0.014	13.305	-0.078	-0.078	0.000	0.000	0.000	0.000
9	A	11	LYS	1	0.965	0.966	11.612	0.513	0.513	0.000	0.000	0.000	0.000
10	A	12	TYR	0	0.019	-0.002	11.551	-0.101	-0.101	0.000	0.000	0.000	0.000
11	A	13	PRO	0	-0.008	0.022	12.245	0.002	0.002	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.917	-0.964	14.310	-0.212	-0.212	0.000	0.000	0.000	0.000
13	A	15	ILE	0	-0.071	-0.049	18.036	0.016	0.016	0.000	0.000	0.000	0.000
14	A	16	ASP	-1	-0.896	-0.956	20.465	-0.063	-0.063	0.000	0.000	0.000	0.000
15	A	17	ASP	-1	-0.895	-0.924	15.309	-0.173	-0.173	0.000	0.000	0.000	0.000
16	A	18	ILE	0	-0.023	-0.027	15.927	0.009	0.009	0.000	0.000	0.000	0.000
17	A	19	VAL	0	-0.045	-0.025	11.190	-0.017	-0.017	0.000	0.000	0.000	0.000
18	A	20	MET	0	0.013	-0.001	9.120	0.047	0.047	0.000	0.000	0.000	0.000
19	A	21	VAL	0	-0.045	-0.024	9.148	-0.033	-0.033	0.000	0.000	0.000	0.000
20	A	22	ASN	0	-0.023	-0.036	8.782	0.072	0.072	0.000	0.000	0.000	0.000
21	A	23	VAL	0	-0.011	-0.006	10.566	-0.067	-0.067	0.000	0.000	0.000	0.000
22	A	24	GLN	0	-0.030	-0.021	10.456	0.037	0.037	0.000	0.000	0.000	0.000
23	A	25	GLN	0	0.012	-0.005	14.167	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	26	ILE	0	-0.033	-0.006	17.915	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	27	ALA	0	0.007	0.009	20.903	0.000	0.000	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.940	-0.970	23.535	0.029	0.029	0.000	0.000	0.000	0.000
27	A	29	MET	0	0.007	-0.002	24.149	0.002	0.002	0.000	0.000	0.000	0.000
28	A	30	GLY	0	-0.012	-0.014	22.509	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	31	ALA	0	-0.036	-0.005	18.368	0.008	0.008	0.000	0.000	0.000	0.000
30	A	32	TYR	0	0.042	0.029	16.048	-0.015	-0.015	0.000	0.000	0.000	0.000
31	A	33	VAL	0	-0.021	-0.020	12.633	0.057	0.057	0.000	0.000	0.000	0.000
32	A	34	LYS	1	0.972	1.000	7.897	-0.425	-0.425	0.000	0.000	0.000	0.000
33	A	35	LEU	0	0.026	-0.004	8.815	0.154	0.154	0.000	0.000	0.000	0.000
34	A	36	LEU	0	-0.030	-0.013	4.849	-0.349	-0.349	0.000	0.000	0.000	0.000
35	A	37	GLU	-1	-0.805	-0.857	3.681	-0.815	-0.508	0.002	-0.091	-0.219	-0.001
36	A	38	TYR	0	-0.045	-0.041	5.721	-0.368	-0.368	0.000	0.000	0.000	0.000
37	A	39	ASP	-1	-0.869	-0.950	4.393	-2.888	-2.924	-0.001	-0.015	0.052	0.000
38	A	40	ASN	0	-0.074	-0.024	2.981	0.911	1.319	0.026	-0.093	-0.342	0.000
39	A	41	ILE	0	0.018	0.016	6.597	0.331	0.331	0.000	0.000	0.000	0.000
40	A	42	GLU	-1	-0.935	-0.979	10.226	0.013	0.013	0.000	0.000	0.000	0.000
41	A	43	GLY	0	0.012	0.010	12.714	-0.042	-0.042	0.000	0.000	0.000	0.000
42	A	44	MET	0	-0.017	0.005	15.152	0.043	0.043	0.000	0.000	0.000	0.000
43	A	45	ILE	0	-0.042	-0.020	16.159	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	46	LEU	0	0.015	0.004	19.456	0.009	0.009	0.000	0.000	0.000	0.000
45	A	47	LEU	0	0.023	0.015	22.850	0.012	0.012	0.000	0.000	0.000	0.000
46	A	48	SER	0	-0.005	0.007	25.671	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	61	LEU	0	0.013	-0.001	22.893	0.000	0.000	0.000	0.000	0.000	0.000
48	A	62	ILE	0	0.000	-0.001	18.273	0.015	0.015	0.000	0.000	0.000	0.000
49	A	63	ARG	1	0.932	0.958	18.999	-0.200	-0.200	0.000	0.000	0.000	0.000
50	A	64	VAL	0	0.048	0.023	16.451	0.022	0.022	0.000	0.000	0.000	0.000
51	A	65	GLY	0	0.039	0.028	13.273	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	66	LYS	1	0.899	0.972	12.128	-0.176	-0.176	0.000	0.000	0.000	0.000
53	A	67	ASN	0	0.045	0.001	8.788	-0.057	-0.057	0.000	0.000	0.000	0.000
54	A	68	ASP	-1	-0.818	-0.907	12.487	0.130	0.130	0.000	0.000	0.000	0.000
55	A	69	VAL	0	0.011	0.030	13.329	0.019	0.019	0.000	0.000	0.000	0.000
56	A	70	ALA	0	-0.042	-0.020	15.124	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	71	VAL	0	0.036	0.024	16.186	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	72	VAL	0	-0.011	0.003	15.465	0.005	0.005	0.000	0.000	0.000	0.000
59	A	73	LEU	0	-0.080	-0.044	18.199	0.010	0.010	0.000	0.000	0.000	0.000
60	A	74	ARG	1	0.901	0.929	20.376	0.065	0.065	0.000	0.000	0.000	0.000
61	A	75	VAL	0	0.002	0.012	16.974	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	76	ASP	-1	-0.878	-0.933	19.576	-0.139	-0.139	0.000	0.000	0.000	0.000
63	A	77	LYS	1	0.943	0.944	17.654	0.271	0.271	0.000	0.000	0.000	0.000
64	A	78	GLU	-1	-0.961	-0.963	19.803	-0.184	-0.184	0.000	0.000	0.000	0.000
65	A	79	LYS	1	0.912	0.950	21.762	0.105	0.105	0.000	0.000	0.000	0.000
66	A	80	GLY	0	-0.004	0.017	17.355	0.004	0.004	0.000	0.000	0.000	0.000
67	A	81	TYR	0	-0.035	-0.008	16.444	-0.019	-0.019	0.000	0.000	0.000	0.000
68	A	82	ILE	0	0.033	0.008	13.473	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	83	ASP	-1	-0.843	-0.897	17.569	-0.040	-0.040	0.000	0.000	0.000	0.000
70	A	84	LEU	0	0.021	-0.006	14.454	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	85	SER	0	-0.050	-0.081	18.872	0.019	0.019	0.000	0.000	0.000	0.000
72	A	86	LYS	1	0.914	0.948	19.151	-0.139	-0.139	0.000	0.000	0.000	0.000
73	A	87	ARG	1	0.876	0.976	21.197	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	88	ARG	1	0.930	0.950	23.690	0.019	0.019	0.000	0.000	0.000	0.000
75	A	89	VAL	0	0.035	0.049	18.876	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	90	SER	0	0.028	0.026	22.240	0.012	0.012	0.000	0.000	0.000	0.000
77	A	91	SER	0	0.009	-0.013	22.210	0.014	0.014	0.000	0.000	0.000	0.000
78	A	92	GLU	-1	-0.874	-0.954	22.589	0.058	0.058	0.000	0.000	0.000	0.000
79	A	93	ASP	-1	-0.858	-0.930	19.916	0.037	0.037	0.000	0.000	0.000	0.000
80	A	94	ILE	0	-0.055	-0.031	17.972	0.011	0.011	0.000	0.000	0.000	0.000
81	A	95	ILE	0	0.014	0.018	17.266	0.026	0.026	0.000	0.000	0.000	0.000
82	A	96	LYS	1	0.977	0.986	17.796	-0.014	-0.014	0.000	0.000	0.000	0.000
83	A	97	CYS	0	-0.038	0.005	13.628	0.023	0.023	0.000	0.000	0.000	0.000
84	A	98	GLU	-1	-0.898	-0.958	12.962	0.335	0.335	0.000	0.000	0.000	0.000
85	A	99	GLU	-1	-0.938	-0.963	13.267	0.228	0.228	0.000	0.000	0.000	0.000
86	A	100	LYS	1	0.931	0.975	11.847	0.117	0.117	0.000	0.000	0.000	0.000
87	A	101	TYR	0	0.060	0.019	5.288	-0.114	-0.114	0.000	0.000	0.000	0.000
88	A	102	GLN	0	-0.026	-0.022	9.163	0.296	0.296	0.000	0.000	0.000	0.000
89	A	103	LYS	1	0.864	0.917	10.896	-0.042	-0.042	0.000	0.000	0.000	0.000
90	A	104	SER	0	-0.002	-0.016	7.347	-0.105	-0.105	0.000	0.000	0.000	0.000
91	A	105	LYS	1	0.943	0.975	5.383	-1.210	-1.210	0.000	0.000	0.000	0.000
92	A	106	THR	0	-0.046	-0.013	7.288	-0.073	-0.073	0.000	0.000	0.000	0.000
93	A	107	VAL	0	-0.011	-0.001	9.099	-0.062	-0.062	0.000	0.000	0.000	0.000
94	A	108	HIS	0	-0.007	-0.016	2.572	-4.227	-2.067	1.407	-1.487	-2.079	-0.020
95	A	109	SER	0	-0.024	-0.019	6.424	-0.143	-0.143	0.000	0.000	0.000	0.000
96	A	110	ILE	0	-0.019	0.013	8.385	-0.087	-0.087	0.000	0.000	0.000	0.000
97	A	111	LEU	0	0.007	-0.002	8.553	-0.029	-0.029	0.000	0.000	0.000	0.000
98	A	112	ARG	1	0.952	0.979	2.117	-1.866	-1.694	1.301	-0.574	-0.899	0.004
99	A	113	TYR	0	-0.061	-0.023	8.569	0.032	0.032	0.000	0.000	0.000	0.000
100	A	114	CYS	0	-0.010	-0.016	11.473	0.003	0.003	0.000	0.000	0.000	0.000
101	A	115	ALA	0	0.022	0.007	10.665	0.008	0.008	0.000	0.000	0.000	0.000
102	A	116	GLU	-1	-0.926	-0.967	8.552	0.042	0.042	0.000	0.000	0.000	0.000
103	A	117	LYS	1	0.866	0.952	12.877	0.036	0.036	0.000	0.000	0.000	0.000
104	A	118	PHE	0	-0.019	-0.028	15.778	0.012	0.012	0.000	0.000	0.000	0.000
105	A	119	GLN	0	-0.017	0.019	15.774	-0.018	-0.018	0.000	0.000	0.000	0.000
106	A	120	ILE	0	-0.028	-0.010	14.674	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	121	PRO	0	0.026	0.010	13.008	-0.043	-0.043	0.000	0.000	0.000	0.000
108	A	122	LEU	0	0.063	0.027	5.500	-0.028	-0.028	0.000	0.000	0.000	0.000
109	A	123	GLU	-1	-0.885	-0.971	8.994	-1.345	-1.345	0.000	0.000	0.000	0.000
110	A	124	GLU	-1	-0.933	-0.964	10.535	-0.330	-0.330	0.000	0.000	0.000	0.000
111	A	125	LEU	0	0.006	0.013	11.408	0.057	0.057	0.000	0.000	0.000	0.000
112	A	126	TYR	0	0.018	0.015	6.137	-0.087	-0.087	0.000	0.000	0.000	0.000
113	A	127	LYS	1	0.912	0.952	11.520	0.537	0.537	0.000	0.000	0.000	0.000
114	A	128	THR	0	-0.014	0.000	14.713	0.060	0.060	0.000	0.000	0.000	0.000
115	A	129	ILE	0	0.032	0.019	14.336	0.049	0.049	0.000	0.000	0.000	0.000
116	A	130	ALA	0	0.006	-0.011	11.706	0.035	0.035	0.000	0.000	0.000	0.000
117	A	131	TRP	0	-0.039	-0.013	9.702	0.088	0.088	0.000	0.000	0.000	0.000
118	A	132	PRO	0	0.013	0.000	14.918	0.038	0.038	0.000	0.000	0.000	0.000
119	A	133	LEU	0	0.015	0.012	16.578	0.032	0.032	0.000	0.000	0.000	0.000
120	A	134	SER	0	-0.030	-0.015	14.485	0.036	0.036	0.000	0.000	0.000	0.000
121	A	135	ARG	1	0.833	0.912	17.086	0.320	0.320	0.000	0.000	0.000	0.000
122	A	136	LYS	1	0.957	0.987	20.066	0.134	0.134	0.000	0.000	0.000	0.000
123	A	137	PHE	0	0.017	0.005	19.143	0.018	0.018	0.000	0.000	0.000	0.000
124	A	138	GLY	0	-0.005	0.018	18.701	0.022	0.022	0.000	0.000	0.000	0.000
125	A	139	HIS	0	-0.025	-0.036	11.112	-0.066	-0.066	0.000	0.000	0.000	0.000
126	A	140	ALA	0	0.051	0.028	12.504	0.025	0.025	0.000	0.000	0.000	0.000
127	A	141	TYR	0	-0.005	-0.005	13.344	0.037	0.037	0.000	0.000	0.000	0.000
128	A	142	GLU	-1	-0.833	-0.918	14.882	0.058	0.058	0.000	0.000	0.000	0.000
129	A	143	ALA	0	0.037	0.043	17.580	0.003	0.003	0.000	0.000	0.000	0.000
130	A	144	PHE	0	0.031	-0.004	12.943	0.004	0.004	0.000	0.000	0.000	0.000
131	A	145	LYS	1	0.926	0.970	18.140	-0.022	-0.022	0.000	0.000	0.000	0.000
132	A	146	LEU	0	-0.022	-0.030	20.319	0.004	0.004	0.000	0.000	0.000	0.000
133	A	147	SER	0	-0.034	-0.018	20.808	0.000	0.000	0.000	0.000	0.000	0.000
134	A	148	ILE	0	-0.050	-0.019	21.187	0.002	0.002	0.000	0.000	0.000	0.000
135	A	149	ILE	0	-0.087	-0.040	24.323	0.002	0.002	0.000	0.000	0.000	0.000
136	A	150	ASP	-1	-0.834	-0.897	26.285	-0.042	-0.042	0.000	0.000	0.000	0.000
137	A	151	GLU	-1	-0.928	-0.977	25.951	-0.041	-0.041	0.000	0.000	0.000	0.000
138	A	152	THR	0	-0.034	-0.029	26.236	-0.011	-0.011	0.000	0.000	0.000	0.000
139	A	153	VAL	0	-0.060	-0.019	21.588	-0.009	-0.009	0.000	0.000	0.000	0.000
140	A	154	TRP	0	-0.046	-0.042	17.920	-0.023	-0.023	0.000	0.000	0.000	0.000
141	A	155	GLU	-1	-0.921	-0.946	23.736	-0.084	-0.084	0.000	0.000	0.000	0.000
142	A	156	GLY	0	-0.071	-0.038	25.153	-0.005	-0.005	0.000	0.000	0.000	0.000
143	A	157	ILE	0	-0.069	-0.030	19.027	-0.017	-0.017	0.000	0.000	0.000	0.000
144	A	158	GLU	-1	-0.908	-0.959	21.941	-0.135	-0.135	0.000	0.000	0.000	0.000
145	A	159	PRO	0	-0.064	-0.017	19.104	-0.025	-0.025	0.000	0.000	0.000	0.000
146	A	160	PRO	0	0.001	-0.001	16.771	0.013	0.013	0.000	0.000	0.000	0.000
147	A	161	SER	0	-0.011	-0.008	20.051	0.026	0.026	0.000	0.000	0.000	0.000
148	A	162	LYS	1	0.964	0.982	21.469	0.060	0.060	0.000	0.000	0.000	0.000
149	A	163	ASP	-1	-0.877	-0.945	23.023	-0.074	-0.074	0.000	0.000	0.000	0.000
150	A	164	VAL	0	-0.013	-0.009	16.340	0.006	0.006	0.000	0.000	0.000	0.000
151	A	165	LEU	0	-0.001	-0.001	18.424	-0.001	-0.001	0.000	0.000	0.000	0.000
152	A	166	ASP	-1	-0.852	-0.926	20.193	-0.056	-0.056	0.000	0.000	0.000	0.000
153	A	167	GLU	-1	-0.866	-0.926	17.724	-0.002	-0.002	0.000	0.000	0.000	0.000
154	A	168	LEU	0	0.008	0.007	14.465	0.019	0.019	0.000	0.000	0.000	0.000
155	A	169	LYS	1	0.935	0.961	17.638	0.069	0.069	0.000	0.000	0.000	0.000
156	A	170	ASN	0	-0.055	-0.043	20.861	0.020	0.020	0.000	0.000	0.000	0.000
157	A	171	TYR	0	-0.013	0.003	13.912	0.033	0.033	0.000	0.000	0.000	0.000
158	A	172	ILE	0	-0.041	-0.034	16.723	0.028	0.028	0.000	0.000	0.000	0.000
159	A	173	SER	0	-0.036	0.002	18.961	0.010	0.010	0.000	0.000	0.000	0.000
160	A	174	LYS	1	0.941	1.001	15.337	-0.146	-0.146	0.000	0.000	0.000	0.000
161	A	175	ARG	1	0.942	0.954	19.679	-0.061	-0.061	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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