FMO DATABASE

FMODB ID: NN49Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1662748.897233
FMO2-HF: Nuclear repulsion	1596631.243081
FMO2-HF: Total energy	-66117.654152
FMO2-MP2: Total energy	-66310.468342

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.
-27.268	-27.842	21.309	-9.237	-11.494	-0.004

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 : 0.005 / q_NPA : 0.000

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	0.002	0.013	2.985	-0.487	2.017	0.033	-1.232	-1.304	0.004
4	A	6	ARG	1	0.732	0.889	2.769	-3.048	-1.551	0.240	-0.922	-0.815	-0.011
5	A	7	PHE	0	0.014	0.006	2.409	-1.401	-0.609	1.362	-0.867	-1.287	0.002
6	A	8	TYR	0	-0.026	-0.021	6.380	0.309	0.309	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.748	-0.841	9.975	-0.444	-0.444	0.000	0.000	0.000	0.000
8	A	10	ASN	0	-0.021	-0.015	12.796	-0.090	-0.090	0.000	0.000	0.000	0.000
9	A	11	LYS	1	0.950	0.957	11.496	0.772	0.772	0.000	0.000	0.000	0.000
10	A	12	TYR	0	0.002	0.001	11.552	-0.179	-0.179	0.000	0.000	0.000	0.000
11	A	13	PRO	0	0.031	0.038	12.448	0.042	0.042	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.791	-0.882	14.603	-0.285	-0.285	0.000	0.000	0.000	0.000
13	A	15	ILE	0	-0.031	-0.034	18.379	0.017	0.017	0.000	0.000	0.000	0.000
14	A	16	ASP	-1	-0.857	-0.936	21.136	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	17	ASP	-1	-0.837	-0.894	14.524	0.028	0.028	0.000	0.000	0.000	0.000
16	A	18	ILE	0	-0.021	-0.014	16.256	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	19	VAL	0	-0.003	-0.006	12.039	0.046	0.046	0.000	0.000	0.000	0.000
18	A	20	MET	0	0.018	0.012	9.135	-0.025	-0.025	0.000	0.000	0.000	0.000
19	A	21	VAL	0	-0.048	-0.028	9.528	-0.104	-0.104	0.000	0.000	0.000	0.000
20	A	22	ASN	0	-0.015	-0.030	9.164	0.029	0.029	0.000	0.000	0.000	0.000
21	A	23	VAL	0	0.006	0.016	10.869	-0.159	-0.159	0.000	0.000	0.000	0.000
22	A	24	GLN	0	0.015	0.020	10.435	-0.140	-0.140	0.000	0.000	0.000	0.000
23	A	25	GLN	0	-0.003	-0.010	14.485	0.025	0.025	0.000	0.000	0.000	0.000
24	A	26	ILE	0	-0.043	-0.023	18.314	0.009	0.009	0.000	0.000	0.000	0.000
25	A	27	ALA	0	0.018	0.015	21.376	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.938	-0.971	24.119	-0.083	-0.083	0.000	0.000	0.000	0.000
27	A	29	MET	0	0.047	0.019	24.498	0.010	0.010	0.000	0.000	0.000	0.000
28	A	30	GLY	0	-0.014	-0.028	22.474	0.005	0.005	0.000	0.000	0.000	0.000
29	A	31	ALA	0	-0.025	-0.002	18.769	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	32	TYR	0	0.048	0.031	16.313	0.007	0.007	0.000	0.000	0.000	0.000
31	A	33	VAL	0	-0.036	-0.031	12.654	0.041	0.041	0.000	0.000	0.000	0.000
32	A	34	LYS	1	0.849	0.928	7.628	0.970	0.970	0.000	0.000	0.000	0.000
33	A	35	LEU	0	0.036	-0.002	8.897	0.270	0.270	0.000	0.000	0.000	0.000
34	A	36	LEU	0	-0.037	-0.019	5.041	-0.466	-0.466	0.000	0.000	0.000	0.000
35	A	37	GLU	-1	-0.762	-0.846	4.562	1.457	1.673	-0.001	-0.017	-0.197	0.000
36	A	38	TYR	0	-0.038	-0.042	6.281	-0.365	-0.365	0.000	0.000	0.000	0.000
37	A	39	ASP	-1	-0.778	-0.908	5.467	-2.718	-2.718	0.000	0.000	0.000	0.000
38	A	40	ASN	0	-0.086	-0.023	2.996	0.497	1.098	0.034	-0.180	-0.454	0.000
39	A	41	ILE	0	0.022	0.014	6.503	0.287	0.287	0.000	0.000	0.000	0.000
40	A	42	GLU	-1	-0.872	-0.938	10.208	-0.655	-0.655	0.000	0.000	0.000	0.000
41	A	43	GLY	0	0.020	0.011	12.845	0.035	0.035	0.000	0.000	0.000	0.000
42	A	44	MET	0	-0.058	-0.012	15.526	0.000	0.000	0.000	0.000	0.000	0.000
43	A	45	ILE	0	-0.033	-0.011	16.273	0.026	0.026	0.000	0.000	0.000	0.000
44	A	46	LEU	0	-0.001	0.002	19.578	0.005	0.005	0.000	0.000	0.000	0.000
45	A	47	LEU	0	0.000	0.008	23.307	0.028	0.028	0.000	0.000	0.000	0.000
46	A	48	SER	0	-0.012	-0.003	25.592	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	61	LEU	0	0.070	0.039	22.797	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	62	ILE	0	-0.031	-0.028	18.831	0.032	0.032	0.000	0.000	0.000	0.000
49	A	63	ARG	1	0.945	0.967	19.224	-0.207	-0.207	0.000	0.000	0.000	0.000
50	A	64	VAL	0	0.079	0.029	16.492	0.030	0.030	0.000	0.000	0.000	0.000
51	A	65	GLY	0	0.009	0.013	13.467	0.041	0.041	0.000	0.000	0.000	0.000
52	A	66	LYS	1	0.755	0.886	12.414	-0.158	-0.158	0.000	0.000	0.000	0.000
53	A	67	ASN	0	0.058	0.006	8.159	-0.249	-0.249	0.000	0.000	0.000	0.000
54	A	68	ASP	-1	-0.824	-0.885	12.327	0.150	0.150	0.000	0.000	0.000	0.000
55	A	69	VAL	0	0.044	0.026	13.249	0.060	0.060	0.000	0.000	0.000	0.000
56	A	70	ALA	0	-0.056	-0.028	15.507	-0.046	-0.046	0.000	0.000	0.000	0.000
57	A	71	VAL	0	0.036	0.031	16.784	0.016	0.016	0.000	0.000	0.000	0.000
58	A	72	VAL	0	-0.004	0.001	16.036	-0.029	-0.029	0.000	0.000	0.000	0.000
59	A	73	LEU	0	-0.054	-0.027	18.885	0.019	0.019	0.000	0.000	0.000	0.000
60	A	74	ARG	1	0.883	0.914	20.932	0.147	0.147	0.000	0.000	0.000	0.000
61	A	75	VAL	0	0.017	0.004	17.141	-0.018	-0.018	0.000	0.000	0.000	0.000
62	A	76	ASP	-1	-0.791	-0.873	19.886	-0.278	-0.278	0.000	0.000	0.000	0.000
63	A	77	LYS	1	0.800	0.868	18.008	0.268	0.268	0.000	0.000	0.000	0.000
64	A	78	GLU	-1	-0.911	-0.947	19.862	-0.357	-0.357	0.000	0.000	0.000	0.000
65	A	79	LYS	1	0.796	0.877	21.465	0.276	0.276	0.000	0.000	0.000	0.000
66	A	80	GLY	0	-0.034	-0.003	17.302	-0.033	-0.033	0.000	0.000	0.000	0.000
67	A	81	TYR	0	-0.013	0.006	16.432	-0.026	-0.026	0.000	0.000	0.000	0.000
68	A	82	ILE	0	0.034	0.002	13.838	0.021	0.021	0.000	0.000	0.000	0.000
69	A	83	ASP	-1	-0.830	-0.880	17.866	-0.174	-0.174	0.000	0.000	0.000	0.000
70	A	84	LEU	0	0.029	0.004	14.658	0.015	0.015	0.000	0.000	0.000	0.000
71	A	85	SER	0	-0.006	-0.027	19.132	0.009	0.009	0.000	0.000	0.000	0.000
72	A	86	LYS	1	0.946	0.948	19.060	-0.174	-0.174	0.000	0.000	0.000	0.000
73	A	87	ARG	1	0.876	0.953	21.096	0.039	0.039	0.000	0.000	0.000	0.000
74	A	88	ARG	1	0.881	0.934	23.535	0.010	0.010	0.000	0.000	0.000	0.000
75	A	89	VAL	0	-0.026	0.014	19.458	0.002	0.002	0.000	0.000	0.000	0.000
76	A	90	SER	0	-0.002	-0.020	22.545	0.006	0.006	0.000	0.000	0.000	0.000
77	A	91	SER	0	0.004	-0.030	23.027	0.019	0.019	0.000	0.000	0.000	0.000
78	A	92	GLU	-1	-0.832	-0.896	23.105	0.232	0.232	0.000	0.000	0.000	0.000
79	A	93	ASP	-1	-0.790	-0.864	20.241	0.225	0.225	0.000	0.000	0.000	0.000
80	A	94	ILE	0	-0.016	-0.005	17.771	0.033	0.033	0.000	0.000	0.000	0.000
81	A	95	ILE	0	0.048	0.030	17.184	0.068	0.068	0.000	0.000	0.000	0.000
82	A	96	LYS	1	0.819	0.893	17.650	-0.155	-0.155	0.000	0.000	0.000	0.000
83	A	97	CYS	0	-0.024	-0.004	12.882	0.037	0.037	0.000	0.000	0.000	0.000
84	A	98	GLU	-1	-0.939	-0.972	13.022	0.819	0.819	0.000	0.000	0.000	0.000
85	A	99	GLU	-1	-0.904	-0.966	13.060	0.753	0.753	0.000	0.000	0.000	0.000
86	A	100	LYS	1	0.812	0.907	11.582	-0.210	-0.210	0.000	0.000	0.000	0.000
87	A	101	TYR	0	0.041	0.018	4.765	-0.134	-0.050	-0.001	-0.011	-0.072	0.000
88	A	102	GLN	0	0.040	0.021	8.789	0.917	0.917	0.000	0.000	0.000	0.000
89	A	103	LYS	1	0.874	0.957	10.545	-0.383	-0.383	0.000	0.000	0.000	0.000
90	A	104	SER	0	0.025	-0.009	7.084	-0.103	-0.103	0.000	0.000	0.000	0.000
91	A	105	LYS	1	0.883	0.942	5.222	-2.661	-2.661	0.000	0.000	0.000	0.000
92	A	106	THR	0	-0.076	-0.035	6.695	0.146	0.146	0.000	0.000	0.000	0.000
93	A	107	VAL	0	0.003	0.000	8.741	-0.062	-0.062	0.000	0.000	0.000	0.000
94	A	108	HIS	0	0.025	0.016	2.002	-2.103	-5.888	11.969	-3.534	-4.650	-0.030
95	A	109	SER	0	-0.012	-0.021	5.653	0.331	0.331	0.000	0.000	0.000	0.000
96	A	110	ILE	0	-0.011	0.011	7.292	-0.411	-0.411	0.000	0.000	0.000	0.000
97	A	111	LEU	0	0.038	0.015	8.304	-0.196	-0.196	0.000	0.000	0.000	0.000
98	A	112	ARG	1	0.881	0.946	1.872	-16.256	-18.739	7.673	-2.474	-2.715	0.031
99	A	113	TYR	0	-0.062	-0.054	8.153	-0.223	-0.223	0.000	0.000	0.000	0.000
100	A	114	CYS	0	-0.031	-0.020	11.411	-0.169	-0.169	0.000	0.000	0.000	0.000
101	A	115	ALA	0	0.001	-0.001	10.141	-0.082	-0.082	0.000	0.000	0.000	0.000
102	A	116	GLU	-1	-0.854	-0.940	7.820	0.154	0.154	0.000	0.000	0.000	0.000
103	A	117	LYS	1	0.791	0.895	12.525	-0.307	-0.307	0.000	0.000	0.000	0.000
104	A	118	PHE	0	-0.030	-0.029	15.554	-0.022	-0.022	0.000	0.000	0.000	0.000
105	A	119	GLN	0	-0.053	-0.007	15.591	-0.083	-0.083	0.000	0.000	0.000	0.000
106	A	120	ILE	0	-0.012	0.006	14.766	-0.049	-0.049	0.000	0.000	0.000	0.000
107	A	121	PRO	0	0.017	-0.001	12.465	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	122	LEU	0	0.056	0.029	5.242	0.100	0.100	0.000	0.000	0.000	0.000
109	A	123	GLU	-1	-0.860	-0.952	8.795	-1.566	-1.566	0.000	0.000	0.000	0.000
110	A	124	GLU	-1	-0.797	-0.875	10.669	-0.333	-0.333	0.000	0.000	0.000	0.000
111	A	125	LEU	0	0.013	0.037	11.193	0.096	0.096	0.000	0.000	0.000	0.000
112	A	126	TYR	0	0.005	-0.007	5.989	0.087	0.087	0.000	0.000	0.000	0.000
113	A	127	LYS	1	0.800	0.876	11.294	0.542	0.542	0.000	0.000	0.000	0.000
114	A	128	THR	0	-0.034	-0.034	14.487	0.069	0.069	0.000	0.000	0.000	0.000
115	A	129	ILE	0	0.005	0.007	14.230	0.054	0.054	0.000	0.000	0.000	0.000
116	A	130	ALA	0	0.006	0.007	11.283	0.038	0.038	0.000	0.000	0.000	0.000
117	A	131	TRP	0	-0.027	-0.008	8.983	0.042	0.042	0.000	0.000	0.000	0.000
118	A	132	PRO	0	0.013	0.006	14.470	0.031	0.031	0.000	0.000	0.000	0.000
119	A	133	LEU	0	0.032	0.020	16.314	0.023	0.023	0.000	0.000	0.000	0.000
120	A	134	SER	0	-0.052	-0.049	14.009	0.050	0.050	0.000	0.000	0.000	0.000
121	A	135	ARG	1	0.793	0.858	16.427	0.159	0.159	0.000	0.000	0.000	0.000
122	A	136	LYS	1	0.844	0.938	19.474	-0.080	-0.080	0.000	0.000	0.000	0.000
123	A	137	PHE	0	0.003	-0.008	19.072	0.007	0.007	0.000	0.000	0.000	0.000
124	A	138	GLY	0	-0.001	0.017	18.307	0.038	0.038	0.000	0.000	0.000	0.000
125	A	139	HIS	0	-0.023	-0.034	10.802	-0.095	-0.095	0.000	0.000	0.000	0.000
126	A	140	ALA	0	0.052	0.033	12.187	0.007	0.007	0.000	0.000	0.000	0.000
127	A	141	TYR	0	-0.001	-0.002	12.818	0.008	0.008	0.000	0.000	0.000	0.000
128	A	142	GLU	-1	-0.806	-0.900	14.442	0.473	0.473	0.000	0.000	0.000	0.000
129	A	143	ALA	0	0.020	0.022	17.201	-0.031	-0.031	0.000	0.000	0.000	0.000
130	A	144	PHE	0	0.025	-0.005	12.073	-0.007	-0.007	0.000	0.000	0.000	0.000
131	A	145	LYS	1	0.864	0.933	17.707	-0.414	-0.414	0.000	0.000	0.000	0.000
132	A	146	LEU	0	0.005	-0.006	19.872	-0.020	-0.020	0.000	0.000	0.000	0.000
133	A	147	SER	0	-0.045	-0.032	20.101	-0.017	-0.017	0.000	0.000	0.000	0.000
134	A	148	ILE	0	-0.051	-0.016	20.208	-0.009	-0.009	0.000	0.000	0.000	0.000
135	A	149	ILE	0	-0.066	-0.034	23.669	-0.014	-0.014	0.000	0.000	0.000	0.000
136	A	150	ASP	-1	-0.827	-0.882	25.701	0.126	0.126	0.000	0.000	0.000	0.000
137	A	151	GLU	-1	-0.844	-0.925	25.229	0.173	0.173	0.000	0.000	0.000	0.000
138	A	152	THR	0	-0.031	-0.040	25.712	-0.011	-0.011	0.000	0.000	0.000	0.000
139	A	153	VAL	0	-0.025	-0.002	21.032	-0.014	-0.014	0.000	0.000	0.000	0.000
140	A	154	TRP	0	-0.017	-0.027	17.433	-0.012	-0.012	0.000	0.000	0.000	0.000
141	A	155	GLU	-1	-0.924	-0.950	23.114	0.036	0.036	0.000	0.000	0.000	0.000
142	A	156	GLY	0	-0.003	-0.005	25.157	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	157	ILE	0	-0.090	-0.031	19.281	-0.015	-0.015	0.000	0.000	0.000	0.000
144	A	158	GLU	-1	-0.916	-0.959	21.458	-0.051	-0.051	0.000	0.000	0.000	0.000
145	A	159	PRO	0	-0.039	-0.011	18.978	-0.027	-0.027	0.000	0.000	0.000	0.000
146	A	160	PRO	0	0.004	-0.006	16.516	-0.003	-0.003	0.000	0.000	0.000	0.000
147	A	161	SER	0	-0.020	-0.021	19.835	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	162	LYS	1	0.848	0.917	21.045	-0.076	-0.076	0.000	0.000	0.000	0.000
149	A	163	ASP	-1	-0.819	-0.919	22.415	0.088	0.088	0.000	0.000	0.000	0.000
150	A	164	VAL	0	0.004	0.016	15.865	0.035	0.035	0.000	0.000	0.000	0.000
151	A	165	LEU	0	0.026	0.015	17.536	0.047	0.047	0.000	0.000	0.000	0.000
152	A	166	ASP	-1	-0.803	-0.900	19.471	0.179	0.179	0.000	0.000	0.000	0.000
153	A	167	GLU	-1	-0.848	-0.867	16.933	0.350	0.350	0.000	0.000	0.000	0.000
154	A	168	LEU	0	0.013	0.004	13.853	0.069	0.069	0.000	0.000	0.000	0.000
155	A	169	LYS	1	0.857	0.928	16.852	-0.128	-0.128	0.000	0.000	0.000	0.000
156	A	170	ASN	0	-0.039	-0.035	20.120	0.012	0.012	0.000	0.000	0.000	0.000
157	A	171	TYR	0	-0.014	-0.010	13.649	0.103	0.103	0.000	0.000	0.000	0.000
158	A	172	ILE	0	-0.025	-0.019	16.225	0.086	0.086	0.000	0.000	0.000	0.000
159	A	173	SER	0	-0.043	0.002	17.976	0.007	0.007	0.000	0.000	0.000	0.000
160	A	174	LYS	1	0.913	0.959	14.556	-0.900	-0.900	0.000	0.000	0.000	0.000
161	A	175	ARG	1	0.936	0.972	19.010	-0.332	-0.332	0.000	0.000	0.000	0.000

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