FMO DATABASE

FMODB ID: M3YZZ

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	OptAll
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	-721008.515521
FMO2-HF: Nuclear repulsion	679390.047177
FMO2-HF: Total energy	-41618.468344
FMO2-MP2: Total energy	-41735.243551

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.
-46.029	-38.174	4.969	-5.346	-7.479	0.058

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 : -0.868 / q_NPA : -0.950

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	-0.018	0.004	3.006	-19.775	-15.986	0.110	-1.922	-1.978	0.017
4	A	32	THR	0	0.024	0.006	5.091	-2.305	-2.195	-0.001	-0.005	-0.104	0.000
5	A	33	SER	0	0.067	0.019	8.499	0.129	0.129	0.000	0.000	0.000	0.000
6	A	34	SER	0	0.006	0.001	11.123	-0.253	-0.253	0.000	0.000	0.000	0.000
7	A	35	GLN	0	0.041	0.023	7.661	1.213	1.213	0.000	0.000	0.000	0.000
8	A	36	LEU	0	0.021	0.021	8.398	-0.786	-0.786	0.000	0.000	0.000	0.000
9	A	37	LEU	0	0.015	0.007	10.793	-1.499	-1.499	0.000	0.000	0.000	0.000
10	A	38	SER	0	-0.014	-0.010	13.172	-1.534	-1.534	0.000	0.000	0.000	0.000
11	A	39	VAL	0	-0.039	-0.022	10.267	-1.156	-1.156	0.000	0.000	0.000	0.000
12	A	40	ARG	1	0.852	0.886	13.539	-17.353	-17.353	0.000	0.000	0.000	0.000
13	A	41	HIS	0	0.015	-0.011	15.983	-1.090	-1.090	0.000	0.000	0.000	0.000
14	A	42	GLN	0	0.011	0.022	14.175	0.436	0.436	0.000	0.000	0.000	0.000
15	A	43	LEU	0	0.014	0.020	16.825	-0.697	-0.697	0.000	0.000	0.000	0.000
16	A	44	ALA	0	-0.033	-0.025	18.584	-0.872	-0.872	0.000	0.000	0.000	0.000
17	A	45	GLU	-1	-0.931	-0.960	21.346	12.124	12.124	0.000	0.000	0.000	0.000
18	A	46	SER	0	-0.068	-0.051	20.114	-0.456	-0.456	0.000	0.000	0.000	0.000
19	A	47	ALA	0	-0.015	0.016	22.259	-0.261	-0.261	0.000	0.000	0.000	0.000
20	A	48	GLY	0	-0.003	-0.008	23.840	-0.489	-0.489	0.000	0.000	0.000	0.000
21	A	49	LEU	0	-0.049	-0.013	27.106	0.275	0.275	0.000	0.000	0.000	0.000
22	A	50	PRO	0	0.020	0.020	29.887	-0.144	-0.144	0.000	0.000	0.000	0.000
23	A	51	ARG	1	0.878	0.911	32.784	-8.207	-8.207	0.000	0.000	0.000	0.000
24	A	52	ASP	-1	-0.803	-0.902	36.172	8.839	8.839	0.000	0.000	0.000	0.000
25	A	53	GLN	0	0.060	0.002	31.408	0.129	0.129	0.000	0.000	0.000	0.000
26	A	54	HIS	0	0.006	0.006	32.941	0.144	0.144	0.000	0.000	0.000	0.000
27	A	55	GLU	-1	-0.875	-0.925	35.482	7.678	7.678	0.000	0.000	0.000	0.000
28	A	56	PHE	0	0.017	0.009	38.581	-0.238	-0.238	0.000	0.000	0.000	0.000
29	A	57	VAL	0	-0.002	0.002	33.563	-0.076	-0.076	0.000	0.000	0.000	0.000
30	A	58	SER	0	-0.065	-0.035	36.938	0.010	0.010	0.000	0.000	0.000	0.000
31	A	59	SER	0	-0.049	-0.029	39.378	-0.232	-0.232	0.000	0.000	0.000	0.000
32	A	60	GLN	0	-0.055	-0.030	41.009	-0.181	-0.181	0.000	0.000	0.000	0.000
33	A	61	ALA	0	0.031	0.025	38.133	0.148	0.148	0.000	0.000	0.000	0.000
34	A	62	PRO	0	0.010	0.023	36.389	-0.083	-0.083	0.000	0.000	0.000	0.000
35	A	63	GLN	0	0.024	-0.015	36.666	0.109	0.109	0.000	0.000	0.000	0.000
36	A	64	SER	0	0.035	0.021	36.636	0.270	0.270	0.000	0.000	0.000	0.000
37	A	65	LEU	0	0.036	0.010	33.023	0.228	0.228	0.000	0.000	0.000	0.000
38	A	66	ARG	1	0.914	0.964	31.765	-9.007	-9.007	0.000	0.000	0.000	0.000
39	A	67	ASN	0	0.009	0.005	31.801	0.232	0.232	0.000	0.000	0.000	0.000
40	A	68	ARG	1	0.874	0.937	24.601	-11.845	-11.845	0.000	0.000	0.000	0.000
41	A	69	TYR	0	0.034	0.017	26.943	0.612	0.612	0.000	0.000	0.000	0.000
42	A	70	ASN	0	0.037	0.012	27.661	0.406	0.406	0.000	0.000	0.000	0.000
43	A	71	ASN	0	-0.017	-0.010	26.209	0.091	0.091	0.000	0.000	0.000	0.000
44	A	72	LEU	0	0.032	0.035	21.030	0.452	0.452	0.000	0.000	0.000	0.000
45	A	73	TYR	0	0.024	0.023	23.111	0.614	0.614	0.000	0.000	0.000	0.000
46	A	74	SER	0	-0.015	-0.022	24.406	0.464	0.464	0.000	0.000	0.000	0.000
47	A	75	HIS	0	0.072	0.034	16.931	-0.583	-0.583	0.000	0.000	0.000	0.000
48	A	76	THR	0	0.023	0.018	19.843	1.080	1.080	0.000	0.000	0.000	0.000
49	A	77	GLN	0	0.006	0.002	20.156	0.933	0.933	0.000	0.000	0.000	0.000
50	A	78	ARG	1	0.852	0.921	19.742	-14.442	-14.442	0.000	0.000	0.000	0.000
51	A	79	THR	0	-0.003	0.000	14.770	0.923	0.923	0.000	0.000	0.000	0.000
52	A	80	LEU	0	-0.006	-0.006	16.209	1.231	1.231	0.000	0.000	0.000	0.000
53	A	81	ASP	-1	-0.843	-0.911	17.852	15.536	15.536	0.000	0.000	0.000	0.000
54	A	82	MET	0	0.012	0.009	14.577	0.302	0.302	0.000	0.000	0.000	0.000
55	A	83	ALA	0	0.002	0.005	13.311	1.452	1.452	0.000	0.000	0.000	0.000
56	A	84	ASP	-1	-0.776	-0.870	14.211	17.750	17.750	0.000	0.000	0.000	0.000
57	A	85	MET	0	-0.100	-0.018	16.293	-0.337	-0.337	0.000	0.000	0.000	0.000
58	A	86	GLN	0	0.049	0.011	10.017	-0.540	-0.540	0.000	0.000	0.000	0.000
59	A	87	HIS	0	0.028	0.019	12.989	1.239	1.239	0.000	0.000	0.000	0.000
60	A	88	ARG	1	0.806	0.875	14.225	-16.818	-16.818	0.000	0.000	0.000	0.000
61	A	89	TYR	0	-0.010	0.009	11.904	-1.070	-1.070	0.000	0.000	0.000	0.000
62	A	90	MET	0	-0.039	-0.017	8.062	-0.047	-0.047	0.000	0.000	0.000	0.000
63	A	91	THR	0	-0.095	-0.054	13.046	-0.351	-0.351	0.000	0.000	0.000	0.000
64	A	92	GLY	0	0.001	0.009	16.267	-0.986	-0.986	0.000	0.000	0.000	0.000
65	A	93	ALA	0	-0.056	-0.021	18.242	-0.974	-0.974	0.000	0.000	0.000	0.000
66	A	94	SER	0	-0.002	-0.013	19.172	-0.847	-0.847	0.000	0.000	0.000	0.000
67	A	95	GLY	0	0.034	0.021	18.515	0.823	0.823	0.000	0.000	0.000	0.000
68	A	96	ILE	0	-0.049	-0.031	18.815	0.203	0.203	0.000	0.000	0.000	0.000
69	A	97	ASN	0	0.023	0.014	13.119	1.469	1.469	0.000	0.000	0.000	0.000
70	A	98	PRO	0	-0.010	-0.015	12.665	-0.977	-0.977	0.000	0.000	0.000	0.000
71	A	99	GLY	0	-0.009	-0.002	13.948	-0.809	-0.809	0.000	0.000	0.000	0.000
72	A	100	MET	0	-0.011	0.021	10.434	-0.498	-0.498	0.000	0.000	0.000	0.000
73	A	101	LEU	0	0.002	-0.010	5.240	0.347	0.347	0.000	0.000	0.000	0.000
74	A	102	PRO	0	0.031	-0.002	5.251	0.693	0.693	0.000	0.000	0.000	0.000
75	A	103	HIS	1	0.870	0.915	2.698	-84.644	-80.821	4.860	-3.381	-5.303	0.041
76	A	104	GLU	-1	-0.846	-0.909	4.647	32.542	32.675	0.000	-0.038	-0.094	0.000
77	A	105	ASN	0	0.038	0.005	7.226	-2.680	-2.680	0.000	0.000	0.000	0.000
78	A	106	VAL	0	-0.027	-0.023	6.654	-3.287	-3.287	0.000	0.000	0.000	0.000
79	A	107	ASP	-1	-0.836	-0.908	5.908	45.085	45.085	0.000	0.000	0.000	0.000
80	A	108	ASP	-1	-0.892	-0.937	9.110	21.763	21.763	0.000	0.000	0.000	0.000
81	A	109	MET	0	-0.059	-0.019	11.866	-2.950	-2.950	0.000	0.000	0.000	0.000
82	A	110	ARG	1	0.880	0.952	8.375	-29.358	-29.358	0.000	0.000	0.000	0.000
83	A	111	SER	0	0.001	0.012	13.165	-1.306	-1.306	0.000	0.000	0.000	0.000
84	A	112	ALA	0	0.024	0.013	15.063	-1.282	-1.282	0.000	0.000	0.000	0.000
85	A	113	ILE	0	-0.040	-0.028	15.051	-1.133	-1.133	0.000	0.000	0.000	0.000
86	A	114	THR	0	-0.021	-0.003	16.637	-0.946	-0.946	0.000	0.000	0.000	0.000
87	A	115	ASP	-1	-0.875	-0.934	18.521	15.532	15.532	0.000	0.000	0.000	0.000
88	A	116	TRP	0	-0.015	-0.038	21.014	-1.431	-1.431	0.000	0.000	0.000	0.000
89	A	117	SER	0	-0.040	-0.026	22.164	-0.521	-0.521	0.000	0.000	0.000	0.000
90	A	118	ASP	-1	-0.822	-0.909	22.938	13.125	13.125	0.000	0.000	0.000	0.000
91	A	119	MET	0	-0.096	-0.036	25.100	-0.621	-0.621	0.000	0.000	0.000	0.000
92	A	120	ARG	1	0.853	0.920	22.997	-13.364	-13.364	0.000	0.000	0.000	0.000
93	A	121	GLU	-1	-0.923	-0.951	28.043	10.549	10.549	0.000	0.000	0.000	0.000
94	A	122	ALA	0	-0.015	-0.013	29.095	-0.431	-0.431	0.000	0.000	0.000	0.000
95	A	123	LEU	0	-0.038	-0.020	30.873	-0.387	-0.387	0.000	0.000	0.000	0.000
96	A	124	GLN	0	0.030	0.010	32.753	-0.109	-0.109	0.000	0.000	0.000	0.000
97	A	125	HIS	0	-0.017	-0.004	33.731	-0.203	-0.203	0.000	0.000	0.000	0.000
98	A	126	ALA	0	-0.058	-0.029	34.966	-0.252	-0.252	0.000	0.000	0.000	0.000
99	A	127	MET	0	-0.032	-0.006	36.809	-0.129	-0.129	0.000	0.000	0.000	0.000
100	A	128	GLY	0	-0.017	0.013	38.469	-0.224	-0.224	0.000	0.000	0.000	0.000
101	A	129	ILE	0	-0.067	-0.031	40.119	-0.133	-0.133	0.000	0.000	0.000	0.000

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