FMO DATABASE

FMODB ID: ZY49N

Calculation Name: 3TL8-B-Xray372

Preferred Name:

Target Type:

Ligand Name: phosphothreonine

ligand 3-letter code: TPO

PDB ID: 3TL8

Chain ID: B

ChEMBL ID:

UniProt ID: Q94F62

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-549451.230031
FMO2-HF: Nuclear repulsion	515878.528504
FMO2-HF: Total energy	-33572.701528
FMO2-MP2: Total energy	-33670.302554

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(B:267:ILE)

Summations of interaction energy for fragment #1(B:267:ILE)

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.
-2.753	0.401	0.554	-1.438	-2.271	-0.003

Interaction energy analysis for fragmet #1(B:267:ILE)

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 : 0.001

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	B	269	VAL	0	0.038	0.023	2.802	-3.504	-0.493	0.555	-1.426	-2.141	-0.003
4	B	270	ASP	-1	-0.856	-0.943	4.490	0.241	0.384	-0.001	-0.012	-0.130	0.000
5	B	271	ARG	1	0.980	0.977	7.416	0.257	0.257	0.000	0.000	0.000	0.000
6	B	272	ALA	0	-0.005	-0.015	10.628	0.022	0.022	0.000	0.000	0.000	0.000
7	B	273	ALA	0	0.055	0.037	8.600	0.010	0.010	0.000	0.000	0.000	0.000
8	B	274	MET	0	-0.046	-0.024	8.728	-0.046	-0.046	0.000	0.000	0.000	0.000
9	B	275	ARG	1	0.959	0.993	11.191	0.222	0.222	0.000	0.000	0.000	0.000
10	B	276	ASN	0	-0.019	-0.018	13.752	0.041	0.041	0.000	0.000	0.000	0.000
11	B	277	ARG	1	1.022	1.022	9.218	0.670	0.670	0.000	0.000	0.000	0.000
12	B	278	GLY	0	0.012	0.021	14.744	0.019	0.019	0.000	0.000	0.000	0.000
13	B	279	ASN	0	0.002	-0.019	17.050	0.022	0.022	0.000	0.000	0.000	0.000
14	B	280	ASP	-1	-0.907	-0.949	17.454	-0.178	-0.178	0.000	0.000	0.000	0.000
15	B	281	GLU	-1	-0.994	-1.010	16.527	-0.344	-0.344	0.000	0.000	0.000	0.000
16	B	282	ALA	0	-0.031	-0.006	19.848	0.015	0.015	0.000	0.000	0.000	0.000
17	B	283	ASP	-1	-0.889	-0.943	22.414	-0.106	-0.106	0.000	0.000	0.000	0.000
18	B	284	ALA	0	-0.024	-0.023	22.641	0.013	0.013	0.000	0.000	0.000	0.000
19	B	285	ALA	0	0.021	0.016	24.060	0.010	0.010	0.000	0.000	0.000	0.000
20	B	286	LEU	0	0.003	-0.021	25.775	0.010	0.010	0.000	0.000	0.000	0.000
21	B	287	ARG	1	0.909	0.951	23.756	0.140	0.140	0.000	0.000	0.000	0.000
22	B	288	GLY	0	0.045	0.029	28.558	0.008	0.008	0.000	0.000	0.000	0.000
23	B	289	LEU	0	-0.004	-0.008	29.241	0.007	0.007	0.000	0.000	0.000	0.000
24	B	290	VAL	0	-0.014	-0.008	31.988	0.007	0.007	0.000	0.000	0.000	0.000
25	B	291	GLN	0	-0.037	-0.008	31.902	0.000	0.000	0.000	0.000	0.000	0.000
26	B	292	GLN	0	-0.145	-0.101	32.427	0.007	0.007	0.000	0.000	0.000	0.000
27	B	293	GLY	0	-0.015	0.005	36.167	0.001	0.001	0.000	0.000	0.000	0.000
28	B	294	VAL	0	0.001	0.013	34.297	0.003	0.003	0.000	0.000	0.000	0.000
29	B	295	ASN	0	0.010	0.000	37.202	0.002	0.002	0.000	0.000	0.000	0.000
30	B	296	LEU	0	0.044	0.000	33.340	-0.004	-0.004	0.000	0.000	0.000	0.000
31	B	297	GLU	-1	-0.863	-0.947	36.168	-0.069	-0.069	0.000	0.000	0.000	0.000
32	B	298	HIS	0	-0.046	-0.005	38.517	0.002	0.002	0.000	0.000	0.000	0.000
33	B	299	LEU	0	-0.009	-0.002	31.862	-0.001	-0.001	0.000	0.000	0.000	0.000
34	B	300	ARG	1	0.908	0.948	33.783	0.069	0.069	0.000	0.000	0.000	0.000
35	B	301	THR	0	0.024	0.025	34.387	-0.003	-0.003	0.000	0.000	0.000	0.000
36	B	302	ALA	0	-0.029	-0.015	35.048	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	303	LEU	0	0.015	-0.007	28.683	-0.005	-0.005	0.000	0.000	0.000	0.000
38	B	304	GLU	-1	-0.930	-0.959	31.238	-0.087	-0.087	0.000	0.000	0.000	0.000
39	B	305	ARG	1	0.932	0.945	33.148	0.073	0.073	0.000	0.000	0.000	0.000
40	B	306	HIS	0	-0.055	-0.043	29.047	-0.009	-0.009	0.000	0.000	0.000	0.000
41	B	307	VAL	0	-0.005	-0.003	27.402	-0.005	-0.005	0.000	0.000	0.000	0.000
42	B	308	MET	0	-0.075	-0.016	29.573	-0.001	-0.001	0.000	0.000	0.000	0.000
43	B	309	GLN	0	-0.021	-0.011	32.124	-0.001	-0.001	0.000	0.000	0.000	0.000
44	B	310	ARG	1	0.923	0.961	27.031	0.150	0.150	0.000	0.000	0.000	0.000
45	B	311	LEU	0	-0.011	0.013	32.738	0.001	0.001	0.000	0.000	0.000	0.000
46	B	312	PRO	0	0.011	0.024	34.179	-0.007	-0.007	0.000	0.000	0.000	0.000
47	B	313	ILE	0	0.032	0.029	30.940	0.004	0.004	0.000	0.000	0.000	0.000
48	B	314	PRO	0	0.002	0.006	34.448	0.001	0.001	0.000	0.000	0.000	0.000
49	B	315	LEU	0	0.050	0.015	35.957	-0.005	-0.005	0.000	0.000	0.000	0.000
50	B	316	ASP	-1	-0.958	-0.957	37.182	-0.089	-0.089	0.000	0.000	0.000	0.000
51	B	317	ILE	0	0.092	0.018	33.340	-0.001	-0.001	0.000	0.000	0.000	0.000
52	B	318	GLY	0	-0.014	-0.014	32.465	-0.007	-0.007	0.000	0.000	0.000	0.000
53	B	319	SER	0	-0.002	0.000	31.937	-0.010	-0.010	0.000	0.000	0.000	0.000
54	B	320	ALA	0	0.072	0.032	32.675	-0.005	-0.005	0.000	0.000	0.000	0.000
55	B	321	LEU	0	-0.028	-0.023	28.698	-0.003	-0.003	0.000	0.000	0.000	0.000
56	B	322	GLN	0	0.053	0.028	27.609	-0.018	-0.018	0.000	0.000	0.000	0.000
57	B	323	ASN	0	-0.068	0.008	28.868	-0.008	-0.008	0.000	0.000	0.000	0.000
58	B	324	VAL	0	-0.013	-0.005	26.472	-0.003	-0.003	0.000	0.000	0.000	0.000
59	B	325	GLY	0	-0.013	0.003	24.898	-0.011	-0.011	0.000	0.000	0.000	0.000
60	B	326	ILE	0	-0.056	-0.029	24.157	-0.020	-0.020	0.000	0.000	0.000	0.000
61	B	327	ASN	0	-0.042	-0.045	23.430	-0.005	-0.005	0.000	0.000	0.000	0.000
62	B	328	PRO	0	-0.043	0.013	25.807	-0.006	-0.006	0.000	0.000	0.000	0.000
63	B	329	SER	0	0.037	-0.041	27.494	-0.001	-0.001	0.000	0.000	0.000	0.000
64	B	330	ILE	0	-0.088	-0.023	24.237	-0.011	-0.011	0.000	0.000	0.000	0.000
65	B	331	ASP	-1	-0.925	-0.959	26.250	-0.152	-0.152	0.000	0.000	0.000	0.000
66	B	332	LEU	0	0.030	0.041	21.500	0.008	0.008	0.000	0.000	0.000	0.000
67	B	333	GLY	0	-0.022	-0.033	25.836	0.007	0.007	0.000	0.000	0.000	0.000
68	B	334	GLU	-1	-0.958	-0.970	21.153	-0.252	-0.252	0.000	0.000	0.000	0.000
69	B	335	SER	0	-0.041	-0.026	18.955	0.004	0.004	0.000	0.000	0.000	0.000
70	B	336	LEU	0	0.027	0.016	18.724	-0.032	-0.032	0.000	0.000	0.000	0.000
71	B	337	VAL	0	-0.022	-0.009	12.365	0.009	0.009	0.000	0.000	0.000	0.000
72	B	338	GLN	0	-0.020	-0.030	13.127	-0.061	-0.061	0.000	0.000	0.000	0.000
73	B	339	HIS	0	0.087	0.041	17.151	-0.003	-0.003	0.000	0.000	0.000	0.000
74	B	340	PRO	0	0.046	0.029	19.429	0.013	0.013	0.000	0.000	0.000	0.000
75	B	341	LEU	0	0.057	0.023	21.535	0.015	0.015	0.000	0.000	0.000	0.000
76	B	342	LEU	0	-0.017	-0.001	21.479	0.014	0.014	0.000	0.000	0.000	0.000
77	B	343	ASN	0	-0.011	-0.009	17.951	0.021	0.021	0.000	0.000	0.000	0.000
78	B	344	LEU	0	0.029	0.019	22.310	0.014	0.014	0.000	0.000	0.000	0.000
79	B	345	ASN	0	0.028	0.011	25.368	0.019	0.019	0.000	0.000	0.000	0.000
80	B	346	VAL	0	-0.013	-0.007	23.999	0.014	0.014	0.000	0.000	0.000	0.000
81	B	347	ALA	0	-0.021	-0.017	24.814	0.012	0.012	0.000	0.000	0.000	0.000
82	B	348	LEU	0	0.024	0.014	26.643	0.009	0.009	0.000	0.000	0.000	0.000
83	B	349	ASN	0	-0.007	-0.014	30.046	0.015	0.015	0.000	0.000	0.000	0.000
84	B	350	ARG	1	0.922	0.973	25.931	0.106	0.106	0.000	0.000	0.000	0.000
85	B	351	MET	0	-0.032	0.000	30.192	0.006	0.006	0.000	0.000	0.000	0.000
86	B	352	LEU	0	-0.023	0.003	32.264	0.005	0.005	0.000	0.000	0.000	0.000
87	B	353	GLY	0	-0.008	0.010	34.018	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:267:ILE)