FMO DATABASE

FMODB ID: 8J3MY

Calculation Name: 2A1A-A-Xray307

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

Target Type: SINGLE PROTEIN

Ligand Name: phosphothreonine

Ligand 3-letter code: TPO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2A1A

Chain ID: A

ChEMBL ID: CHEMBL5785

UniProt ID: P19525

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	164
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-1667982.508901
FMO2-HF: Nuclear repulsion	1601544.889058
FMO2-HF: Total energy	-66437.619843
FMO2-MP2: Total energy	-66631.401203

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:ACE )

Summations of interaction energy for fragment #1(A:2:ACE )

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.
8.194	-7.179	27.708	-5.874	-6.46	-0.029

Interaction energy analysis for fragmet #1(A:2:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.106

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	4	HIS	0	0.049	0.026	3.433	0.767	0.874	-0.007	0.924	-1.023	-0.005
4	A	5	CYS	0	0.063	0.066	5.348	0.289	0.289	0.000	0.000	0.000	0.000
5	A	6	ARG	1	0.780	0.910	5.272	-0.172	-0.172	0.000	0.000	0.000	0.000
6	A	7	PHE	0	-0.010	0.041	2.100	9.035	-3.035	15.640	-1.498	-2.071	-0.005
7	A	8	TYR	0	-0.061	-0.071	6.830	0.217	0.217	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.773	-0.866	10.611	-0.083	-0.083	0.000	0.000	0.000	0.000
9	A	10	ASN	0	-0.012	-0.014	13.867	-0.011	-0.011	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.964	0.966	13.120	0.223	0.223	0.000	0.000	0.000	0.000
11	A	12	TYR	0	0.018	-0.002	13.733	-0.064	-0.064	0.000	0.000	0.000	0.000
12	A	13	PRO	0	-0.006	0.023	14.270	0.026	0.026	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.918	-0.965	15.871	-0.111	-0.111	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.072	-0.050	19.385	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	16	ASP	-1	-0.897	-0.957	21.647	-0.075	-0.075	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.894	-0.924	16.065	-0.136	-0.136	0.000	0.000	0.000	0.000
17	A	18	ILE	0	-0.024	-0.027	15.562	-0.021	-0.021	0.000	0.000	0.000	0.000
18	A	19	VAL	0	-0.045	-0.025	12.108	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	20	MET	0	0.014	-0.001	8.138	0.041	0.041	0.000	0.000	0.000	0.000
20	A	21	VAL	0	-0.043	-0.023	9.596	-0.172	-0.172	0.000	0.000	0.000	0.000
21	A	22	ASN	0	-0.020	-0.034	9.845	0.072	0.072	0.000	0.000	0.000	0.000
22	A	23	VAL	0	-0.012	-0.006	11.740	-0.015	-0.015	0.000	0.000	0.000	0.000
23	A	24	GLN	0	-0.030	-0.021	13.196	0.022	0.022	0.000	0.000	0.000	0.000
24	A	25	GLN	0	0.010	-0.006	16.815	0.047	0.047	0.000	0.000	0.000	0.000
25	A	26	ILE	0	-0.032	-0.006	20.544	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	27	ALA	0	0.006	0.008	23.087	0.010	0.010	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.941	-0.971	26.033	-0.085	-0.085	0.000	0.000	0.000	0.000
28	A	29	MET	0	0.005	0.000	26.503	0.001	0.001	0.000	0.000	0.000	0.000
29	A	30	GLY	0	-0.012	-0.017	24.466	0.000	0.000	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.036	-0.004	20.086	0.000	0.000	0.000	0.000	0.000	0.000
31	A	32	TYR	0	0.040	0.028	19.027	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.021	-0.020	14.296	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.971	1.000	10.748	0.642	0.642	0.000	0.000	0.000	0.000
34	A	35	LEU	0	0.021	-0.007	10.722	-0.011	-0.011	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.011	-0.005	5.350	-0.063	-0.063	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.802	-0.853	5.307	-1.074	-1.183	-0.001	-0.016	0.125	0.000
37	A	38	TYR	0	-0.051	-0.045	6.991	0.210	0.210	0.000	0.000	0.000	0.000
38	A	39	ASP	-1	-0.866	-0.948	7.263	-0.895	-0.895	0.000	0.000	0.000	0.000
39	A	40	ASN	0	-0.073	-0.023	6.865	0.041	0.041	0.000	0.000	0.000	0.000
40	A	41	ILE	0	0.014	0.015	9.703	0.180	0.180	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.936	-0.979	12.990	-0.397	-0.397	0.000	0.000	0.000	0.000
42	A	43	GLY	0	0.012	0.010	15.629	0.024	0.024	0.000	0.000	0.000	0.000
43	A	44	MET	0	-0.018	0.004	17.512	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	45	ILE	0	-0.040	-0.019	16.983	0.012	0.012	0.000	0.000	0.000	0.000
45	A	46	LEU	0	0.017	0.005	20.873	0.010	0.010	0.000	0.000	0.000	0.000
46	A	47	LEU	0	0.025	0.016	24.165	0.002	0.002	0.000	0.000	0.000	0.000
47	A	48	SER	0	-0.002	0.005	26.884	0.009	0.009	0.000	0.000	0.000	0.000
48	A	49	NME	0	0.016	0.012	28.549	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	60	ACE	0	0.015	-0.002	24.694	0.002	0.002	0.000	0.000	0.000	0.000
50	A	61	LEU	0	-0.012	-0.003	23.094	0.000	0.000	0.000	0.000	0.000	0.000
51	A	62	ILE	0	0.009	0.002	18.970	0.000	0.000	0.000	0.000	0.000	0.000
52	A	63	ARG	1	0.934	0.960	19.449	0.091	0.091	0.000	0.000	0.000	0.000
53	A	64	VAL	0	0.047	0.022	17.862	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	65	GLY	0	0.038	0.027	15.301	0.027	0.027	0.000	0.000	0.000	0.000
55	A	66	LYS	1	0.897	0.972	13.403	0.106	0.106	0.000	0.000	0.000	0.000
56	A	67	ASN	0	0.044	0.001	8.006	-0.097	-0.097	0.000	0.000	0.000	0.000
57	A	68	ASP	-1	-0.820	-0.908	12.098	-0.098	-0.098	0.000	0.000	0.000	0.000
58	A	69	VAL	0	0.013	0.031	12.929	-0.052	-0.052	0.000	0.000	0.000	0.000
59	A	70	ALA	0	-0.043	-0.020	14.973	0.023	0.023	0.000	0.000	0.000	0.000
60	A	71	VAL	0	0.037	0.025	16.558	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	72	VAL	0	-0.010	0.003	16.980	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	73	LEU	0	-0.076	-0.036	19.512	0.025	0.025	0.000	0.000	0.000	0.000
63	A	74	ARG	1	0.899	0.929	22.228	0.132	0.132	0.000	0.000	0.000	0.000
64	A	75	VAL	0	0.003	0.013	19.314	-0.020	-0.020	0.000	0.000	0.000	0.000
65	A	76	ASP	-1	-0.879	-0.934	21.866	-0.126	-0.126	0.000	0.000	0.000	0.000
66	A	77	LYS	1	0.944	0.944	19.732	0.144	0.144	0.000	0.000	0.000	0.000
67	A	78	GLU	-1	-0.963	-0.964	22.387	-0.125	-0.125	0.000	0.000	0.000	0.000
68	A	79	LYS	1	0.911	0.949	24.692	0.121	0.121	0.000	0.000	0.000	0.000
69	A	80	GLY	0	-0.003	0.017	20.267	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	81	TYR	0	-0.036	-0.008	19.257	-0.031	-0.031	0.000	0.000	0.000	0.000
71	A	82	ILE	0	0.034	0.009	15.934	0.012	0.012	0.000	0.000	0.000	0.000
72	A	83	ASP	-1	-0.842	-0.898	19.965	-0.165	-0.165	0.000	0.000	0.000	0.000
73	A	84	LEU	0	0.020	-0.009	16.154	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	85	SER	0	-0.052	-0.085	20.237	0.017	0.017	0.000	0.000	0.000	0.000
75	A	86	LYS	1	0.911	0.945	18.946	0.128	0.128	0.000	0.000	0.000	0.000
76	A	87	ARG	1	0.857	0.965	21.364	0.106	0.106	0.000	0.000	0.000	0.000
77	A	88	ARG	1	0.928	0.949	24.031	0.092	0.092	0.000	0.000	0.000	0.000
78	A	89	VAL	0	0.035	0.049	18.616	0.006	0.006	0.000	0.000	0.000	0.000
79	A	90	SER	0	0.027	0.025	21.902	0.006	0.006	0.000	0.000	0.000	0.000
80	A	91	SER	0	0.007	-0.014	21.128	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	92	GLU	-1	-0.874	-0.954	20.896	0.012	0.012	0.000	0.000	0.000	0.000
82	A	93	ASP	-1	-0.858	-0.930	19.109	-0.033	-0.033	0.000	0.000	0.000	0.000
83	A	94	ILE	0	-0.057	-0.032	16.458	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	95	ILE	0	0.014	0.018	15.529	0.002	0.002	0.000	0.000	0.000	0.000
85	A	96	LYS	1	0.978	0.987	15.569	0.009	0.009	0.000	0.000	0.000	0.000
86	A	97	CYS	0	-0.038	0.005	12.770	0.012	0.012	0.000	0.000	0.000	0.000
87	A	98	GLU	-1	-0.900	-0.959	11.141	0.010	0.010	0.000	0.000	0.000	0.000
88	A	99	GLU	-1	-0.934	-0.961	10.650	0.204	0.204	0.000	0.000	0.000	0.000
89	A	100	LYS	1	0.930	0.975	10.716	0.138	0.138	0.000	0.000	0.000	0.000
90	A	101	TYR	0	0.062	0.020	4.288	-0.127	-0.030	-0.001	-0.024	-0.072	0.000
91	A	102	GLN	0	-0.025	-0.021	6.439	0.485	0.485	0.000	0.000	0.000	0.000
92	A	103	LYS	1	0.871	0.921	7.820	0.035	0.035	0.000	0.000	0.000	0.000
93	A	104	SER	0	-0.008	-0.019	5.784	0.119	0.119	0.000	0.000	0.000	0.000
94	A	105	LYS	1	0.937	0.970	2.500	-1.258	-0.874	0.484	-0.368	-0.500	0.000
95	A	106	THR	0	-0.036	-0.007	4.448	0.464	0.554	-0.001	-0.012	-0.077	0.000
96	A	107	VAL	0	-0.010	0.000	7.246	0.004	0.004	0.000	0.000	0.000	0.000
97	A	108	HIS	0	-0.011	-0.001	2.264	2.090	-2.057	11.559	-4.708	-2.705	-0.019
98	A	109	SER	0	-0.023	-0.019	4.833	-0.070	-0.099	-0.001	-0.008	0.039	0.000
99	A	110	ILE	0	-0.012	0.018	6.718	-0.308	-0.308	0.000	0.000	0.000	0.000
100	A	111	LEU	0	0.004	-0.004	7.785	-0.135	-0.135	0.000	0.000	0.000	0.000
101	A	112	ARG	1	0.952	0.978	3.178	-1.970	-1.666	0.036	-0.164	-0.176	0.000
102	A	113	TYR	0	-0.058	-0.022	8.495	-0.160	-0.160	0.000	0.000	0.000	0.000
103	A	114	CYS	0	-0.008	-0.015	11.262	-0.101	-0.101	0.000	0.000	0.000	0.000
104	A	115	ALA	0	0.019	0.006	11.307	-0.057	-0.057	0.000	0.000	0.000	0.000
105	A	116	GLU	-1	-0.927	-0.967	10.011	0.233	0.233	0.000	0.000	0.000	0.000
106	A	117	LYS	1	0.866	0.953	13.882	-0.236	-0.236	0.000	0.000	0.000	0.000
107	A	118	PHE	0	-0.019	-0.028	16.350	-0.026	-0.026	0.000	0.000	0.000	0.000
108	A	119	GLN	0	-0.019	0.017	16.869	-0.017	-0.017	0.000	0.000	0.000	0.000
109	A	120	ILE	0	-0.029	-0.010	15.355	-0.023	-0.023	0.000	0.000	0.000	0.000
110	A	121	PRO	0	0.025	0.009	14.297	0.019	0.019	0.000	0.000	0.000	0.000
111	A	122	LEU	0	0.065	0.028	6.233	0.016	0.016	0.000	0.000	0.000	0.000
112	A	123	GLU	-1	-0.886	-0.972	10.501	-0.185	-0.185	0.000	0.000	0.000	0.000
113	A	124	GLU	-1	-0.934	-0.964	11.665	0.018	0.018	0.000	0.000	0.000	0.000
114	A	125	LEU	0	0.007	0.014	11.377	0.004	0.004	0.000	0.000	0.000	0.000
115	A	126	TYR	0	0.020	0.016	5.385	0.092	0.092	0.000	0.000	0.000	0.000
116	A	127	LYS	1	0.910	0.951	11.640	0.019	0.019	0.000	0.000	0.000	0.000
117	A	128	THR	0	-0.016	-0.001	15.143	0.002	0.002	0.000	0.000	0.000	0.000
118	A	129	ILE	0	0.034	0.021	13.803	0.008	0.008	0.000	0.000	0.000	0.000
119	A	130	ALA	0	0.009	-0.009	11.105	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	131	TRP	0	-0.040	-0.013	10.186	-0.012	-0.012	0.000	0.000	0.000	0.000
121	A	132	PRO	0	0.010	-0.001	14.584	-0.011	-0.011	0.000	0.000	0.000	0.000
122	A	133	LEU	0	0.016	0.013	15.568	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	134	SER	0	-0.029	-0.014	13.537	0.002	0.002	0.000	0.000	0.000	0.000
124	A	135	ARG	1	0.830	0.910	16.089	-0.014	-0.014	0.000	0.000	0.000	0.000
125	A	136	LYS	1	0.955	0.986	19.330	-0.071	-0.071	0.000	0.000	0.000	0.000
126	A	137	PHE	0	0.018	0.007	17.700	0.000	0.000	0.000	0.000	0.000	0.000
127	A	138	GLY	0	-0.006	0.017	17.475	0.013	0.013	0.000	0.000	0.000	0.000
128	A	139	HIS	0	-0.026	-0.036	9.253	-0.024	-0.024	0.000	0.000	0.000	0.000
129	A	140	ALA	0	0.047	0.026	11.048	0.015	0.015	0.000	0.000	0.000	0.000
130	A	141	TYR	0	0.002	-0.002	11.050	0.026	0.026	0.000	0.000	0.000	0.000
131	A	142	GLU	-1	-0.832	-0.917	12.879	0.205	0.205	0.000	0.000	0.000	0.000
132	A	143	ALA	0	0.032	0.041	15.975	-0.017	-0.017	0.000	0.000	0.000	0.000
133	A	144	PHE	0	0.031	-0.004	11.323	0.003	0.003	0.000	0.000	0.000	0.000
134	A	145	LYS	1	0.936	0.976	16.303	-0.186	-0.186	0.000	0.000	0.000	0.000
135	A	146	LEU	0	-0.025	-0.031	18.214	-0.013	-0.013	0.000	0.000	0.000	0.000
136	A	147	SER	0	-0.039	-0.021	18.998	-0.010	-0.010	0.000	0.000	0.000	0.000
137	A	148	ILE	0	-0.039	-0.013	19.026	-0.008	-0.008	0.000	0.000	0.000	0.000
138	A	149	ILE	0	-0.086	-0.039	22.368	-0.010	-0.010	0.000	0.000	0.000	0.000
139	A	150	ASP	-1	-0.838	-0.899	24.449	0.082	0.082	0.000	0.000	0.000	0.000
140	A	151	GLU	-1	-0.927	-0.977	24.325	0.115	0.115	0.000	0.000	0.000	0.000
141	A	152	THR	0	-0.038	-0.031	24.892	0.001	0.001	0.000	0.000	0.000	0.000
142	A	153	VAL	0	-0.059	-0.018	20.045	-0.005	-0.005	0.000	0.000	0.000	0.000
143	A	154	TRP	0	-0.044	-0.041	16.627	0.006	0.006	0.000	0.000	0.000	0.000
144	A	155	GLU	-1	-0.923	-0.947	22.628	0.062	0.062	0.000	0.000	0.000	0.000
145	A	156	GLY	0	-0.073	-0.039	24.300	0.000	0.000	0.000	0.000	0.000	0.000
146	A	157	ILE	0	-0.067	-0.029	18.404	-0.004	-0.004	0.000	0.000	0.000	0.000
147	A	158	GLU	-1	-0.910	-0.960	21.706	0.050	0.050	0.000	0.000	0.000	0.000
148	A	159	PRO	0	-0.062	-0.016	18.994	-0.001	-0.001	0.000	0.000	0.000	0.000
149	A	160	PRO	0	0.000	-0.002	17.118	-0.008	-0.008	0.000	0.000	0.000	0.000
150	A	161	SER	0	-0.013	-0.009	20.166	-0.010	-0.010	0.000	0.000	0.000	0.000
151	A	162	LYS	1	0.963	0.981	21.228	-0.087	-0.087	0.000	0.000	0.000	0.000
152	A	163	ASP	-1	-0.878	-0.945	22.651	0.113	0.113	0.000	0.000	0.000	0.000
153	A	164	VAL	0	-0.013	-0.010	16.098	0.015	0.015	0.000	0.000	0.000	0.000
154	A	165	LEU	0	-0.001	-0.001	17.770	0.031	0.031	0.000	0.000	0.000	0.000
155	A	166	ASP	-1	-0.853	-0.926	19.492	0.144	0.144	0.000	0.000	0.000	0.000
156	A	167	GLU	-1	-0.867	-0.927	16.859	0.256	0.256	0.000	0.000	0.000	0.000
157	A	168	LEU	0	0.007	0.006	13.263	0.035	0.035	0.000	0.000	0.000	0.000
158	A	169	LYS	1	0.934	0.960	16.457	-0.123	-0.123	0.000	0.000	0.000	0.000
159	A	170	ASN	0	-0.057	-0.045	19.478	-0.010	-0.010	0.000	0.000	0.000	0.000
160	A	171	TYR	0	-0.014	0.002	12.493	0.052	0.052	0.000	0.000	0.000	0.000
161	A	172	ILE	0	-0.042	-0.034	15.127	0.031	0.031	0.000	0.000	0.000	0.000
162	A	173	SER	0	-0.043	-0.002	17.093	-0.014	-0.014	0.000	0.000	0.000	0.000
163	A	174	LYS	1	0.906	0.981	13.168	-0.495	-0.495	0.000	0.000	0.000	0.000
164	A	175	ARG	0	0.003	-0.011	17.381	0.074	0.074	0.000	0.000	0.000	0.000

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