FMO DATABASE

FMODB ID: 9G9Q2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-717589.376464
FMO2-HF: Nuclear repulsion	675971.353245
FMO2-HF: Total energy	-41618.023219
FMO2-MP2: Total energy	-41734.83043

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.
-37.332	-29.643	2.251	-4.228	-5.711	0.041

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 : -0.881 / 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	-0.003	0.007	3.413	-14.481	-11.860	0.059	-1.238	-1.442	0.010
4	A	32	THR	0	-0.001	-0.009	5.458	-3.865	-3.791	-0.001	-0.002	-0.070	0.000
5	A	33	SER	0	0.097	0.032	9.098	0.625	0.625	0.000	0.000	0.000	0.000
6	A	34	SER	0	-0.005	-0.001	11.771	-0.381	-0.381	0.000	0.000	0.000	0.000
7	A	35	GLN	0	0.045	0.020	7.460	1.927	1.927	0.000	0.000	0.000	0.000
8	A	36	LEU	0	0.027	0.025	9.099	-0.754	-0.754	0.000	0.000	0.000	0.000
9	A	37	LEU	0	0.015	0.001	11.382	-1.311	-1.311	0.000	0.000	0.000	0.000
10	A	38	SER	0	-0.017	-0.010	13.193	-1.484	-1.484	0.000	0.000	0.000	0.000
11	A	39	VAL	0	-0.030	-0.023	10.245	-0.925	-0.925	0.000	0.000	0.000	0.000
12	A	40	ARG	1	0.828	0.873	13.580	-17.042	-17.042	0.000	0.000	0.000	0.000
13	A	41	HIS	0	0.011	-0.016	16.038	-0.857	-0.857	0.000	0.000	0.000	0.000
14	A	42	GLN	0	0.010	0.025	14.489	0.261	0.261	0.000	0.000	0.000	0.000
15	A	43	LEU	0	0.016	0.022	16.654	-0.726	-0.726	0.000	0.000	0.000	0.000
16	A	44	ALA	0	-0.038	-0.026	18.537	-0.777	-0.777	0.000	0.000	0.000	0.000
17	A	45	GLU	-1	-0.930	-0.952	21.526	12.000	12.000	0.000	0.000	0.000	0.000
18	A	46	SER	0	-0.071	-0.052	20.238	-0.434	-0.434	0.000	0.000	0.000	0.000
19	A	47	ALA	0	-0.016	0.009	22.146	-0.276	-0.276	0.000	0.000	0.000	0.000
20	A	48	GLY	0	0.014	-0.014	23.811	-0.415	-0.415	0.000	0.000	0.000	0.000
21	A	49	LEU	0	-0.095	-0.024	27.401	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	50	PRO	0	0.041	0.024	29.436	-0.152	-0.152	0.000	0.000	0.000	0.000
23	A	51	ARG	1	0.988	0.967	32.428	-8.323	-8.323	0.000	0.000	0.000	0.000
24	A	52	ASP	-1	-0.879	-0.932	35.906	8.780	8.780	0.000	0.000	0.000	0.000
25	A	53	GLN	0	0.034	-0.011	31.393	0.138	0.138	0.000	0.000	0.000	0.000
26	A	54	HIS	0	0.002	0.000	32.547	0.148	0.148	0.000	0.000	0.000	0.000
27	A	55	GLU	-1	-0.941	-0.964	35.264	7.629	7.629	0.000	0.000	0.000	0.000
28	A	56	PHE	0	-0.024	-0.012	38.068	-0.249	-0.249	0.000	0.000	0.000	0.000
29	A	57	VAL	0	-0.020	-0.010	33.562	0.081	0.081	0.000	0.000	0.000	0.000
30	A	58	SER	0	-0.067	-0.036	36.848	0.034	0.034	0.000	0.000	0.000	0.000
31	A	59	SER	0	-0.022	-0.019	39.261	-0.234	-0.234	0.000	0.000	0.000	0.000
32	A	60	GLN	0	-0.012	-0.006	40.606	-0.156	-0.156	0.000	0.000	0.000	0.000
33	A	61	ALA	0	0.014	0.015	37.733	0.143	0.143	0.000	0.000	0.000	0.000
34	A	62	PRO	0	0.023	0.021	35.555	-0.066	-0.066	0.000	0.000	0.000	0.000
35	A	63	GLN	0	0.011	-0.019	36.929	0.077	0.077	0.000	0.000	0.000	0.000
36	A	64	SER	0	0.024	0.029	37.016	0.079	0.079	0.000	0.000	0.000	0.000
37	A	65	LEU	0	0.022	-0.008	32.860	0.218	0.218	0.000	0.000	0.000	0.000
38	A	66	ARG	1	0.904	0.964	31.642	-8.932	-8.932	0.000	0.000	0.000	0.000
39	A	67	ASN	0	0.067	0.034	31.758	-0.029	-0.029	0.000	0.000	0.000	0.000
40	A	68	ARG	1	0.920	0.956	24.835	-11.731	-11.731	0.000	0.000	0.000	0.000
41	A	69	TYR	0	0.033	0.023	26.857	0.599	0.599	0.000	0.000	0.000	0.000
42	A	70	ASN	0	0.062	0.022	27.500	0.479	0.479	0.000	0.000	0.000	0.000
43	A	71	ASN	0	-0.032	-0.024	26.412	0.021	0.021	0.000	0.000	0.000	0.000
44	A	72	LEU	0	0.032	0.039	21.095	0.373	0.373	0.000	0.000	0.000	0.000
45	A	73	TYR	0	0.014	0.011	23.250	0.589	0.589	0.000	0.000	0.000	0.000
46	A	74	SER	0	0.018	0.003	24.384	0.502	0.502	0.000	0.000	0.000	0.000
47	A	75	HIS	0	0.058	0.026	17.245	-0.518	-0.518	0.000	0.000	0.000	0.000
48	A	76	THR	0	0.041	0.018	19.847	1.019	1.019	0.000	0.000	0.000	0.000
49	A	77	GLN	0	-0.010	0.003	20.277	0.835	0.835	0.000	0.000	0.000	0.000
50	A	78	ARG	1	0.888	0.945	20.077	-14.154	-14.154	0.000	0.000	0.000	0.000
51	A	79	THR	0	-0.001	-0.008	14.965	0.835	0.835	0.000	0.000	0.000	0.000
52	A	80	LEU	0	-0.016	-0.016	16.394	1.249	1.249	0.000	0.000	0.000	0.000
53	A	81	ASP	-1	-0.889	-0.933	18.478	14.793	14.793	0.000	0.000	0.000	0.000
54	A	82	MET	0	-0.019	0.000	14.856	0.212	0.212	0.000	0.000	0.000	0.000
55	A	83	ALA	0	0.001	0.004	13.880	1.373	1.373	0.000	0.000	0.000	0.000
56	A	84	ASP	-1	-0.774	-0.861	14.877	17.320	17.320	0.000	0.000	0.000	0.000
57	A	85	MET	0	-0.108	-0.045	16.943	-0.240	-0.240	0.000	0.000	0.000	0.000
58	A	86	GLN	0	0.014	-0.009	10.402	-0.031	-0.031	0.000	0.000	0.000	0.000
59	A	87	HIS	0	0.042	0.032	13.411	1.531	1.531	0.000	0.000	0.000	0.000
60	A	88	ARG	1	0.863	0.909	14.673	-16.122	-16.122	0.000	0.000	0.000	0.000
61	A	89	TYR	0	0.011	0.014	12.289	-1.115	-1.115	0.000	0.000	0.000	0.000
62	A	90	MET	0	-0.046	-0.003	8.794	0.137	0.137	0.000	0.000	0.000	0.000
63	A	91	THR	0	-0.095	-0.059	13.503	-0.571	-0.571	0.000	0.000	0.000	0.000
64	A	92	GLY	0	0.032	0.032	16.565	-0.786	-0.786	0.000	0.000	0.000	0.000
65	A	93	ALA	0	-0.078	-0.028	18.741	-0.929	-0.929	0.000	0.000	0.000	0.000
66	A	94	SER	0	-0.023	-0.024	19.446	-0.881	-0.881	0.000	0.000	0.000	0.000
67	A	95	GLY	0	0.048	0.024	18.974	0.803	0.803	0.000	0.000	0.000	0.000
68	A	96	ILE	0	-0.050	-0.023	19.199	-0.097	-0.097	0.000	0.000	0.000	0.000
69	A	97	ASN	0	0.026	0.007	13.715	1.627	1.627	0.000	0.000	0.000	0.000
70	A	98	PRO	0	-0.024	-0.021	13.170	-0.843	-0.843	0.000	0.000	0.000	0.000
71	A	99	GLY	0	0.002	0.001	14.254	-0.892	-0.892	0.000	0.000	0.000	0.000
72	A	100	MET	0	-0.015	0.017	10.673	-0.514	-0.514	0.000	0.000	0.000	0.000
73	A	101	LEU	0	-0.008	-0.020	5.533	0.279	0.279	0.000	0.000	0.000	0.000
74	A	102	PRO	0	0.058	0.014	5.830	0.124	0.124	0.000	0.000	0.000	0.000
75	A	103	HIS	1	0.864	0.914	2.867	-83.559	-78.802	2.195	-2.973	-3.980	0.031
76	A	104	GLU	-1	-0.833	-0.912	4.774	33.726	33.845	-0.001	-0.015	-0.103	0.000
77	A	105	ASN	0	0.041	0.020	7.436	-2.657	-2.657	0.000	0.000	0.000	0.000
78	A	106	VAL	0	-0.045	-0.026	6.249	-3.113	-3.113	0.000	0.000	0.000	0.000
79	A	107	ASP	-1	-0.842	-0.919	5.496	48.006	48.124	-0.001	0.000	-0.116	0.000
80	A	108	ASP	-1	-0.891	-0.929	8.610	21.760	21.760	0.000	0.000	0.000	0.000
81	A	109	MET	0	-0.077	-0.035	11.677	-3.002	-3.002	0.000	0.000	0.000	0.000
82	A	110	ARG	1	0.902	0.945	7.873	-30.908	-30.908	0.000	0.000	0.000	0.000
83	A	111	SER	0	0.032	0.027	12.693	-1.285	-1.285	0.000	0.000	0.000	0.000
84	A	112	ALA	0	0.014	0.019	14.369	-1.352	-1.352	0.000	0.000	0.000	0.000
85	A	113	ILE	0	-0.035	-0.018	15.288	-1.205	-1.205	0.000	0.000	0.000	0.000
86	A	114	THR	0	0.011	-0.006	16.863	-0.694	-0.694	0.000	0.000	0.000	0.000
87	A	115	ASP	-1	-0.865	-0.928	18.662	15.353	15.353	0.000	0.000	0.000	0.000
88	A	116	TRP	0	-0.041	-0.035	20.731	-1.505	-1.505	0.000	0.000	0.000	0.000
89	A	117	SER	0	-0.061	-0.040	21.846	-0.549	-0.549	0.000	0.000	0.000	0.000
90	A	118	ASP	-1	-0.848	-0.901	22.706	13.340	13.340	0.000	0.000	0.000	0.000
91	A	119	MET	0	-0.096	-0.039	24.982	-0.765	-0.765	0.000	0.000	0.000	0.000
92	A	120	ARG	1	0.895	0.948	23.019	-13.308	-13.308	0.000	0.000	0.000	0.000
93	A	121	GLU	-1	-0.895	-0.931	27.722	10.799	10.799	0.000	0.000	0.000	0.000
94	A	122	ALA	0	-0.062	-0.050	28.831	-0.428	-0.428	0.000	0.000	0.000	0.000
95	A	123	LEU	0	-0.057	-0.032	30.563	-0.393	-0.393	0.000	0.000	0.000	0.000
96	A	124	GLN	0	0.060	0.034	32.448	-0.135	-0.135	0.000	0.000	0.000	0.000
97	A	125	HIS	0	-0.022	-0.005	33.318	-0.247	-0.247	0.000	0.000	0.000	0.000
98	A	126	ALA	0	-0.051	-0.033	34.648	-0.251	-0.251	0.000	0.000	0.000	0.000
99	A	127	MET	0	-0.044	-0.011	36.566	-0.158	-0.158	0.000	0.000	0.000	0.000
100	A	128	GLY	0	-0.020	0.017	38.137	-0.254	-0.254	0.000	0.000	0.000	0.000
101	A	129	ILE	0	-0.069	-0.031	39.988	-0.093	-0.093	0.000	0.000	0.000	0.000

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