FMO DATABASE

FMODB ID: LJ4R9

Calculation Name: 2QKW-A-Xray372

Preferred Name:

Target Type:

Ligand Name: phosphothreonine

ligand 3-letter code: TPO

PDB ID: 2QKW

Chain ID: A

ChEMBL ID:

UniProt ID: Q40234

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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-717510.09068
FMO2-HF: Nuclear repulsion	675892.615377
FMO2-HF: Total energy	-41617.475303
FMO2-MP2: Total energy	-41734.34454

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:29:ASP)

Summations of interaction energy for fragment #1(A:29:ASP)

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.
-41.842	-33.845	1.868	-4.399	-5.466	0.044

Interaction energy analysis for fragmet #1(A:29:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.872 / q_NPA : -0.944

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	A	31	VAL	0	0.010	0.014	2.908	-14.848	-11.511	0.277	-1.695	-1.919	0.017
4	A	32	THR	0	-0.031	-0.014	5.226	-4.725	-4.658	-0.001	-0.002	-0.063	0.000
5	A	33	SER	0	0.106	0.039	8.918	0.772	0.772	0.000	0.000	0.000	0.000
6	A	34	SER	0	-0.004	-0.002	11.573	-0.375	-0.375	0.000	0.000	0.000	0.000
7	A	35	GLN	0	0.044	0.012	7.056	2.243	2.243	0.000	0.000	0.000	0.000
8	A	36	LEU	0	0.027	0.023	8.758	-0.674	-0.674	0.000	0.000	0.000	0.000
9	A	37	LEU	0	0.008	-0.002	11.061	-1.293	-1.293	0.000	0.000	0.000	0.000
10	A	38	SER	0	-0.043	-0.019	13.193	-1.559	-1.559	0.000	0.000	0.000	0.000
11	A	39	VAL	0	0.022	0.005	10.171	-0.834	-0.834	0.000	0.000	0.000	0.000
12	A	40	ARG	1	0.864	0.932	13.584	-16.975	-16.975	0.000	0.000	0.000	0.000
13	A	41	HIS	0	0.005	-0.025	15.950	-0.821	-0.821	0.000	0.000	0.000	0.000
14	A	42	GLN	0	0.006	0.024	14.753	0.072	0.072	0.000	0.000	0.000	0.000
15	A	43	LEU	0	0.000	0.006	17.055	-0.711	-0.711	0.000	0.000	0.000	0.000
16	A	44	ALA	0	-0.037	-0.028	18.746	-0.770	-0.770	0.000	0.000	0.000	0.000
17	A	45	GLU	-1	-0.940	-0.960	21.533	11.985	11.985	0.000	0.000	0.000	0.000
18	A	46	SER	0	-0.075	-0.037	20.306	-0.478	-0.478	0.000	0.000	0.000	0.000
19	A	47	ALA	0	-0.013	-0.001	22.638	-0.251	-0.251	0.000	0.000	0.000	0.000
20	A	48	GLY	0	0.008	-0.016	24.253	-0.426	-0.426	0.000	0.000	0.000	0.000
21	A	49	LEU	0	-0.085	-0.025	27.719	0.005	0.005	0.000	0.000	0.000	0.000
22	A	50	PRO	0	0.039	0.020	29.776	-0.162	-0.162	0.000	0.000	0.000	0.000
23	A	51	ARG	1	0.978	0.960	32.537	-8.356	-8.356	0.000	0.000	0.000	0.000
24	A	52	ASP	-1	-0.895	-0.938	36.087	8.708	8.708	0.000	0.000	0.000	0.000
25	A	53	GLN	0	0.051	-0.014	31.821	0.166	0.166	0.000	0.000	0.000	0.000
26	A	54	HIS	0	-0.019	-0.016	32.585	0.140	0.140	0.000	0.000	0.000	0.000
27	A	55	GLU	-1	-0.958	-0.980	35.657	7.600	7.600	0.000	0.000	0.000	0.000
28	A	56	PHE	0	-0.020	-0.018	38.459	-0.229	-0.229	0.000	0.000	0.000	0.000
29	A	57	VAL	0	-0.025	-0.015	33.987	0.090	0.090	0.000	0.000	0.000	0.000
30	A	58	SER	0	-0.063	-0.032	37.183	0.043	0.043	0.000	0.000	0.000	0.000
31	A	59	SER	0	-0.016	-0.009	39.605	-0.237	-0.237	0.000	0.000	0.000	0.000
32	A	60	GLN	0	-0.006	0.000	40.936	-0.169	-0.169	0.000	0.000	0.000	0.000
33	A	61	ALA	0	0.017	0.013	37.896	0.144	0.144	0.000	0.000	0.000	0.000
34	A	62	PRO	0	0.014	0.024	35.795	-0.077	-0.077	0.000	0.000	0.000	0.000
35	A	63	GLN	0	-0.001	-0.027	37.117	0.055	0.055	0.000	0.000	0.000	0.000
36	A	64	SER	0	0.032	0.027	37.204	0.062	0.062	0.000	0.000	0.000	0.000
37	A	65	LEU	0	0.008	-0.012	32.668	0.229	0.229	0.000	0.000	0.000	0.000
38	A	66	ARG	1	0.913	0.967	31.827	-8.953	-8.953	0.000	0.000	0.000	0.000
39	A	67	ASN	0	0.097	0.053	31.947	-0.137	-0.137	0.000	0.000	0.000	0.000
40	A	68	ARG	1	0.892	0.941	25.733	-11.539	-11.539	0.000	0.000	0.000	0.000
41	A	69	TYR	0	0.078	0.054	27.117	0.547	0.547	0.000	0.000	0.000	0.000
42	A	70	ASN	0	0.065	0.017	27.804	0.505	0.505	0.000	0.000	0.000	0.000
43	A	71	ASN	0	-0.050	-0.029	26.537	0.099	0.099	0.000	0.000	0.000	0.000
44	A	72	LEU	0	0.049	0.045	21.677	0.337	0.337	0.000	0.000	0.000	0.000
45	A	73	TYR	0	0.012	0.030	23.563	0.668	0.668	0.000	0.000	0.000	0.000
46	A	74	SER	0	0.013	0.002	24.726	0.516	0.516	0.000	0.000	0.000	0.000
47	A	75	HIS	0	0.002	0.005	17.498	-0.497	-0.497	0.000	0.000	0.000	0.000
48	A	76	THR	0	0.036	-0.008	20.192	0.969	0.969	0.000	0.000	0.000	0.000
49	A	77	GLN	0	-0.013	0.004	20.605	0.827	0.827	0.000	0.000	0.000	0.000
50	A	78	ARG	1	0.951	0.968	20.188	-13.951	-13.951	0.000	0.000	0.000	0.000
51	A	79	THR	0	-0.024	-0.013	15.253	0.832	0.832	0.000	0.000	0.000	0.000
52	A	80	LEU	0	0.001	-0.017	16.452	1.240	1.240	0.000	0.000	0.000	0.000
53	A	81	ASP	-1	-0.880	-0.923	18.231	14.809	14.809	0.000	0.000	0.000	0.000
54	A	82	MET	0	-0.018	-0.007	14.881	0.113	0.113	0.000	0.000	0.000	0.000
55	A	83	ALA	0	-0.016	-0.006	13.636	1.401	1.401	0.000	0.000	0.000	0.000
56	A	84	ASP	-1	-0.862	-0.930	14.649	17.262	17.262	0.000	0.000	0.000	0.000
57	A	85	MET	0	-0.111	-0.071	16.722	-0.306	-0.306	0.000	0.000	0.000	0.000
58	A	86	GLN	0	-0.015	-0.025	10.356	-0.312	-0.312	0.000	0.000	0.000	0.000
59	A	87	HIS	0	0.047	0.036	13.303	1.532	1.532	0.000	0.000	0.000	0.000
60	A	88	ARG	1	0.929	0.961	14.504	-16.000	-16.000	0.000	0.000	0.000	0.000
61	A	89	TYR	0	0.005	0.014	12.550	-1.206	-1.206	0.000	0.000	0.000	0.000
62	A	90	MET	0	-0.043	-0.005	8.632	0.155	0.155	0.000	0.000	0.000	0.000
63	A	91	THR	0	-0.091	-0.058	13.467	-0.555	-0.555	0.000	0.000	0.000	0.000
64	A	92	GLY	0	0.030	0.031	16.496	-0.793	-0.793	0.000	0.000	0.000	0.000
65	A	93	ALA	0	-0.076	-0.027	18.737	-0.924	-0.924	0.000	0.000	0.000	0.000
66	A	94	SER	0	-0.031	-0.032	19.412	-0.794	-0.794	0.000	0.000	0.000	0.000
67	A	95	GLY	0	0.053	0.030	18.977	0.779	0.779	0.000	0.000	0.000	0.000
68	A	96	ILE	0	-0.048	-0.021	19.184	-0.096	-0.096	0.000	0.000	0.000	0.000
69	A	97	ASN	0	0.032	0.003	13.510	1.967	1.967	0.000	0.000	0.000	0.000
70	A	98	PRO	0	-0.027	-0.018	13.100	-0.861	-0.861	0.000	0.000	0.000	0.000
71	A	99	GLY	0	-0.009	-0.002	14.270	-0.873	-0.873	0.000	0.000	0.000	0.000
72	A	100	MET	0	-0.005	0.032	10.574	-0.636	-0.636	0.000	0.000	0.000	0.000
73	A	101	LEU	0	-0.030	-0.036	5.585	0.700	0.700	0.000	0.000	0.000	0.000
74	A	102	PRO	0	0.076	0.025	5.690	0.251	0.251	0.000	0.000	0.000	0.000
75	A	103	HIS	1	0.938	0.952	2.608	-85.532	-81.052	1.593	-2.686	-3.387	0.027
76	A	104	GLU	-1	-0.834	-0.913	4.760	33.010	33.123	-0.001	-0.016	-0.097	0.000
77	A	105	ASN	0	0.071	0.037	7.630	-1.586	-1.586	0.000	0.000	0.000	0.000
78	A	106	VAL	0	-0.051	-0.028	6.397	-3.157	-3.157	0.000	0.000	0.000	0.000
79	A	107	ASP	-1	-0.892	-0.950	6.103	44.123	44.123	0.000	0.000	0.000	0.000
80	A	108	ASP	-1	-0.903	-0.934	8.920	22.896	22.896	0.000	0.000	0.000	0.000
81	A	109	MET	0	-0.089	-0.050	11.694	-2.983	-2.983	0.000	0.000	0.000	0.000
82	A	110	ARG	1	0.922	0.946	7.714	-31.325	-31.325	0.000	0.000	0.000	0.000
83	A	111	SER	0	0.011	0.016	13.020	-1.324	-1.324	0.000	0.000	0.000	0.000
84	A	112	ALA	0	0.001	0.006	14.662	-1.281	-1.281	0.000	0.000	0.000	0.000
85	A	113	ILE	0	-0.039	-0.019	15.308	-1.206	-1.206	0.000	0.000	0.000	0.000
86	A	114	THR	0	0.005	0.004	16.769	-0.818	-0.818	0.000	0.000	0.000	0.000
87	A	115	ASP	-1	-0.824	-0.907	18.925	15.666	15.666	0.000	0.000	0.000	0.000
88	A	116	TRP	0	-0.051	-0.031	21.184	-1.503	-1.503	0.000	0.000	0.000	0.000
89	A	117	SER	0	-0.073	-0.047	22.093	-0.560	-0.560	0.000	0.000	0.000	0.000
90	A	118	ASP	-1	-0.818	-0.886	22.515	13.402	13.402	0.000	0.000	0.000	0.000
91	A	119	MET	0	-0.115	-0.043	25.274	-0.788	-0.788	0.000	0.000	0.000	0.000
92	A	120	ARG	1	0.932	0.970	23.430	-13.148	-13.148	0.000	0.000	0.000	0.000
93	A	121	GLU	-1	-0.888	-0.917	27.337	10.940	10.940	0.000	0.000	0.000	0.000
94	A	122	ALA	0	-0.064	-0.054	29.114	-0.435	-0.435	0.000	0.000	0.000	0.000
95	A	123	LEU	0	-0.075	-0.043	30.831	-0.388	-0.388	0.000	0.000	0.000	0.000
96	A	124	GLN	0	0.077	0.046	32.775	-0.196	-0.196	0.000	0.000	0.000	0.000
97	A	125	HIS	0	-0.040	-0.012	33.493	-0.296	-0.296	0.000	0.000	0.000	0.000
98	A	126	ALA	0	-0.045	-0.033	34.918	-0.253	-0.253	0.000	0.000	0.000	0.000
99	A	127	MET	0	-0.047	-0.004	36.824	-0.160	-0.160	0.000	0.000	0.000	0.000
100	A	128	GLY	0	-0.014	0.021	38.439	-0.255	-0.255	0.000	0.000	0.000	0.000
101	A	129	ILE	0	-0.075	-0.035	40.288	-0.105	-0.105	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:29:ASP)