FMO DATABASE

FMODB ID: R5748

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

Total energy (hartree)

FMO2-HF: Electronic energy	-550145.331628
FMO2-HF: Nuclear repulsion	516571.96261
FMO2-HF: Total energy	-33573.369018
FMO2-MP2: Total energy	-33670.875109

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.
-2.747	0.246	0.203	-1.329	-1.865	-0.001

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 : 0.007 / q_NPA : -0.003

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	0.046	0.026	3.013	-3.244	-0.370	0.204	-1.322	-1.755	-0.001
4	B	270	ASP	-1	-0.813	-0.923	4.777	0.236	0.355	-0.001	-0.007	-0.110	0.000
5	B	271	ARG	1	0.972	0.980	7.726	0.164	0.164	0.000	0.000	0.000	0.000
6	B	272	ALA	0	-0.024	-0.021	10.865	0.009	0.009	0.000	0.000	0.000	0.000
7	B	273	ALA	0	0.064	0.038	8.925	0.000	0.000	0.000	0.000	0.000	0.000
8	B	274	MET	0	-0.051	-0.023	8.978	-0.049	-0.049	0.000	0.000	0.000	0.000
9	B	275	ARG	1	0.950	0.984	11.649	0.157	0.157	0.000	0.000	0.000	0.000
10	B	276	ASN	0	-0.029	-0.027	14.113	0.032	0.032	0.000	0.000	0.000	0.000
11	B	277	ARG	1	0.955	0.977	10.517	0.522	0.522	0.000	0.000	0.000	0.000
12	B	278	GLY	0	0.018	0.026	15.084	0.016	0.016	0.000	0.000	0.000	0.000
13	B	279	ASN	0	-0.002	-0.024	17.475	0.023	0.023	0.000	0.000	0.000	0.000
14	B	280	ASP	-1	-0.912	-0.946	17.515	-0.157	-0.157	0.000	0.000	0.000	0.000
15	B	281	GLU	-1	-0.931	-0.974	15.884	-0.334	-0.334	0.000	0.000	0.000	0.000
16	B	282	ALA	0	-0.008	0.004	20.175	0.013	0.013	0.000	0.000	0.000	0.000
17	B	283	ASP	-1	-0.796	-0.890	22.753	-0.091	-0.091	0.000	0.000	0.000	0.000
18	B	284	ALA	0	-0.044	-0.025	22.870	0.012	0.012	0.000	0.000	0.000	0.000
19	B	285	ALA	0	0.031	0.022	24.386	0.008	0.008	0.000	0.000	0.000	0.000
20	B	286	LEU	0	-0.004	-0.015	26.101	0.009	0.009	0.000	0.000	0.000	0.000
21	B	287	ARG	1	0.898	0.933	23.657	0.126	0.126	0.000	0.000	0.000	0.000
22	B	288	GLY	0	0.056	0.034	28.840	0.007	0.007	0.000	0.000	0.000	0.000
23	B	289	LEU	0	-0.006	-0.009	29.908	0.006	0.006	0.000	0.000	0.000	0.000
24	B	290	VAL	0	-0.015	-0.007	32.387	0.006	0.006	0.000	0.000	0.000	0.000
25	B	291	GLN	0	-0.043	-0.013	32.192	0.001	0.001	0.000	0.000	0.000	0.000
26	B	292	GLN	0	-0.095	-0.063	32.429	0.007	0.007	0.000	0.000	0.000	0.000
27	B	293	GLY	0	-0.010	0.006	36.454	0.001	0.001	0.000	0.000	0.000	0.000
28	B	294	VAL	0	-0.013	0.005	34.717	0.002	0.002	0.000	0.000	0.000	0.000
29	B	295	ASN	0	0.002	-0.007	37.561	0.002	0.002	0.000	0.000	0.000	0.000
30	B	296	LEU	0	0.051	0.006	33.886	-0.003	-0.003	0.000	0.000	0.000	0.000
31	B	297	GLU	-1	-0.783	-0.893	36.525	-0.059	-0.059	0.000	0.000	0.000	0.000
32	B	298	HIS	0	-0.055	-0.012	38.894	0.002	0.002	0.000	0.000	0.000	0.000
33	B	299	LEU	0	0.013	0.009	31.893	-0.001	-0.001	0.000	0.000	0.000	0.000
34	B	300	ARG	1	0.821	0.892	33.948	0.056	0.056	0.000	0.000	0.000	0.000
35	B	301	THR	0	0.029	0.021	34.573	-0.002	-0.002	0.000	0.000	0.000	0.000
36	B	302	ALA	0	-0.024	-0.012	35.226	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	303	LEU	0	0.016	-0.008	28.535	-0.005	-0.005	0.000	0.000	0.000	0.000
38	B	304	GLU	-1	-0.946	-0.960	31.452	-0.070	-0.070	0.000	0.000	0.000	0.000
39	B	305	ARG	1	0.947	0.951	33.394	0.061	0.061	0.000	0.000	0.000	0.000
40	B	306	HIS	0	-0.018	0.009	29.450	-0.010	-0.010	0.000	0.000	0.000	0.000
41	B	307	VAL	0	-0.014	-0.008	27.647	-0.004	-0.004	0.000	0.000	0.000	0.000
42	B	308	MET	0	-0.055	-0.012	29.854	0.000	0.000	0.000	0.000	0.000	0.000
43	B	309	GLN	0	-0.010	-0.005	32.409	-0.001	-0.001	0.000	0.000	0.000	0.000
44	B	310	ARG	1	0.886	0.936	26.637	0.129	0.129	0.000	0.000	0.000	0.000
45	B	311	LEU	0	-0.016	0.006	33.003	0.001	0.001	0.000	0.000	0.000	0.000
46	B	312	PRO	0	0.003	0.003	34.398	-0.006	-0.006	0.000	0.000	0.000	0.000
47	B	313	ILE	0	0.016	0.009	30.916	0.005	0.005	0.000	0.000	0.000	0.000
48	B	314	PRO	0	0.018	0.004	34.617	0.000	0.000	0.000	0.000	0.000	0.000
49	B	315	LEU	0	0.040	0.016	36.074	-0.004	-0.004	0.000	0.000	0.000	0.000
50	B	316	ASP	-1	-0.953	-0.971	37.274	-0.079	-0.079	0.000	0.000	0.000	0.000
51	B	317	ILE	0	0.069	0.022	33.821	-0.002	-0.002	0.000	0.000	0.000	0.000
52	B	318	GLY	0	-0.012	-0.006	32.556	-0.006	-0.006	0.000	0.000	0.000	0.000
53	B	319	SER	0	0.001	0.000	32.045	-0.010	-0.010	0.000	0.000	0.000	0.000
54	B	320	ALA	0	0.064	0.028	32.919	-0.005	-0.005	0.000	0.000	0.000	0.000
55	B	321	LEU	0	-0.028	-0.024	28.852	-0.003	-0.003	0.000	0.000	0.000	0.000
56	B	322	GLN	0	0.055	0.022	27.814	-0.018	-0.018	0.000	0.000	0.000	0.000
57	B	323	ASN	0	-0.096	-0.020	29.085	-0.009	-0.009	0.000	0.000	0.000	0.000
58	B	324	VAL	0	-0.028	-0.010	27.037	-0.003	-0.003	0.000	0.000	0.000	0.000
59	B	325	GLY	0	-0.011	0.002	25.207	-0.010	-0.010	0.000	0.000	0.000	0.000
60	B	326	ILE	0	-0.065	-0.032	24.065	-0.017	-0.017	0.000	0.000	0.000	0.000
61	B	327	ASN	0	-0.019	-0.029	23.194	-0.004	-0.004	0.000	0.000	0.000	0.000
62	B	328	PRO	0	-0.045	0.014	25.924	-0.004	-0.004	0.000	0.000	0.000	0.000
63	B	329	SER	0	0.053	-0.032	27.617	-0.001	-0.001	0.000	0.000	0.000	0.000
64	B	330	ILE	0	-0.113	-0.033	24.429	-0.010	-0.010	0.000	0.000	0.000	0.000
65	B	331	ASP	-1	-0.940	-0.966	26.465	-0.132	-0.132	0.000	0.000	0.000	0.000
66	B	332	LEU	0	0.033	0.038	21.384	0.008	0.008	0.000	0.000	0.000	0.000
67	B	333	GLY	0	0.000	-0.006	25.697	0.006	0.006	0.000	0.000	0.000	0.000
68	B	334	GLU	-1	-0.949	-0.975	21.163	-0.212	-0.212	0.000	0.000	0.000	0.000
69	B	335	SER	0	-0.003	-0.008	18.846	0.015	0.015	0.000	0.000	0.000	0.000
70	B	336	LEU	0	-0.007	0.002	18.722	-0.029	-0.029	0.000	0.000	0.000	0.000
71	B	337	VAL	0	-0.040	-0.018	12.610	0.011	0.011	0.000	0.000	0.000	0.000
72	B	338	GLN	0	-0.007	-0.023	13.275	-0.046	-0.046	0.000	0.000	0.000	0.000
73	B	339	HIS	0	0.088	0.037	17.396	-0.003	-0.003	0.000	0.000	0.000	0.000
74	B	340	PRO	0	0.043	0.029	19.492	0.013	0.013	0.000	0.000	0.000	0.000
75	B	341	LEU	0	0.051	0.023	21.663	0.014	0.014	0.000	0.000	0.000	0.000
76	B	342	LEU	0	-0.011	0.002	21.561	0.013	0.013	0.000	0.000	0.000	0.000
77	B	343	ASN	0	-0.013	-0.010	18.072	0.019	0.019	0.000	0.000	0.000	0.000
78	B	344	LEU	0	0.030	0.019	22.471	0.012	0.012	0.000	0.000	0.000	0.000
79	B	345	ASN	0	0.027	0.011	25.653	0.017	0.017	0.000	0.000	0.000	0.000
80	B	346	VAL	0	-0.018	-0.006	24.264	0.012	0.012	0.000	0.000	0.000	0.000
81	B	347	ALA	0	-0.022	-0.015	25.184	0.010	0.010	0.000	0.000	0.000	0.000
82	B	348	LEU	0	0.036	0.017	27.064	0.008	0.008	0.000	0.000	0.000	0.000
83	B	349	ASN	0	0.035	0.013	30.392	0.013	0.013	0.000	0.000	0.000	0.000
84	B	350	ARG	1	0.831	0.970	25.469	0.100	0.100	0.000	0.000	0.000	0.000
85	B	351	MET	0	-0.039	-0.011	30.602	0.005	0.005	0.000	0.000	0.000	0.000
86	B	352	LEU	0	-0.033	0.002	32.643	0.004	0.004	0.000	0.000	0.000	0.000
87	B	353	GLY	0	-0.045	-0.055	33.815	0.004	0.004	0.000	0.000	0.000	0.000

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