FMO DATABASE

FMODB ID: K35Q3

Calculation Name: 2PTU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PTU

Chain ID: A

ChEMBL ID:

UniProt ID: Q07763

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	106
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-809168.026942
FMO2-HF: Nuclear repulsion	768006.318557
FMO2-HF: Total energy	-41161.708385
FMO2-MP2: Total energy	-41283.929421

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:5:ASP)

Summations of interaction energy for fragment #1(A:5: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.
-27.525	-22.755	4.737	-4.334	-5.174	-0.026

Interaction energy analysis for fragmet #1(A:5:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.961 / q_NPA : -0.986

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	7	SER	0	-0.071	-0.034	3.848	-3.968	-1.796	-0.027	-1.253	-0.892	0.002
4	A	8	GLU	-1	-0.883	-0.943	7.165	23.878	23.878	0.000	0.000	0.000	0.000
5	A	9	GLU	-1	-0.933	-0.943	10.427	17.174	17.174	0.000	0.000	0.000	0.000
6	A	10	VAL	0	0.016	0.015	13.924	-0.355	-0.355	0.000	0.000	0.000	0.000
7	A	11	VAL	0	0.007	0.003	16.341	-0.376	-0.376	0.000	0.000	0.000	0.000
8	A	12	GLY	0	0.005	-0.008	19.968	-0.032	-0.032	0.000	0.000	0.000	0.000
9	A	13	VAL	0	-0.036	-0.005	22.781	-0.185	-0.185	0.000	0.000	0.000	0.000
10	A	14	SER	0	0.014	-0.001	26.332	0.133	0.133	0.000	0.000	0.000	0.000
11	A	15	GLY	0	-0.013	-0.006	27.807	-0.240	-0.240	0.000	0.000	0.000	0.000
12	A	16	LYS	1	0.925	0.959	27.101	-10.509	-10.509	0.000	0.000	0.000	0.000
13	A	17	PRO	0	-0.014	0.015	24.263	0.252	0.252	0.000	0.000	0.000	0.000
14	A	18	VAL	0	0.000	0.003	18.809	0.037	0.037	0.000	0.000	0.000	0.000
15	A	19	GLN	0	-0.025	-0.035	17.286	-0.415	-0.415	0.000	0.000	0.000	0.000
16	A	20	LEU	0	0.007	0.012	12.830	0.303	0.303	0.000	0.000	0.000	0.000
17	A	21	ARG	1	0.959	0.979	13.660	-19.677	-19.677	0.000	0.000	0.000	0.000
18	A	22	PRO	0	0.044	0.047	8.936	1.139	1.139	0.000	0.000	0.000	0.000
19	A	23	SER	0	0.000	-0.015	8.797	-1.167	-1.167	0.000	0.000	0.000	0.000
20	A	24	ASN	0	-0.047	-0.038	7.804	2.095	2.095	0.000	0.000	0.000	0.000
21	A	25	ILE	0	0.019	0.028	6.628	6.053	6.053	0.000	0.000	0.000	0.000
22	A	26	GLN	0	-0.057	-0.037	8.614	-0.888	-0.888	0.000	0.000	0.000	0.000
23	A	27	THR	0	0.028	0.010	10.720	0.264	0.264	0.000	0.000	0.000	0.000
24	A	28	LYS	1	0.937	0.957	13.769	-16.903	-16.903	0.000	0.000	0.000	0.000
25	A	29	ASP	-1	-0.892	-0.936	15.349	17.038	17.038	0.000	0.000	0.000	0.000
26	A	30	VAL	0	-0.044	-0.017	11.803	0.962	0.962	0.000	0.000	0.000	0.000
27	A	31	SER	0	0.006	0.023	13.916	-0.795	-0.795	0.000	0.000	0.000	0.000
28	A	32	VAL	0	-0.012	-0.013	12.295	1.872	1.872	0.000	0.000	0.000	0.000
29	A	33	GLN	0	-0.006	-0.004	11.782	-0.740	-0.740	0.000	0.000	0.000	0.000
30	A	34	TRP	0	-0.009	0.011	11.157	2.102	2.102	0.000	0.000	0.000	0.000
31	A	35	LYS	1	0.834	0.904	11.467	-21.572	-21.572	0.000	0.000	0.000	0.000
32	A	36	LYS	1	0.929	0.982	12.534	-13.337	-13.337	0.000	0.000	0.000	0.000
33	A	37	THR	0	-0.055	-0.034	12.314	-0.536	-0.536	0.000	0.000	0.000	0.000
34	A	38	GLU	-1	-0.927	-0.958	14.899	12.047	12.047	0.000	0.000	0.000	0.000
35	A	39	GLN	0	0.001	-0.019	18.245	-0.260	-0.260	0.000	0.000	0.000	0.000
36	A	40	GLY	0	-0.029	0.003	19.537	-0.592	-0.592	0.000	0.000	0.000	0.000
37	A	41	SER	0	0.002	0.004	20.698	-0.421	-0.421	0.000	0.000	0.000	0.000
38	A	42	HIS	0	0.009	0.005	18.269	0.906	0.906	0.000	0.000	0.000	0.000
39	A	43	ARG	1	0.884	0.946	16.826	-13.185	-13.185	0.000	0.000	0.000	0.000
40	A	44	LYS	1	0.967	0.989	10.091	-22.179	-22.179	0.000	0.000	0.000	0.000
41	A	45	ILE	0	0.056	0.031	15.992	-0.451	-0.451	0.000	0.000	0.000	0.000
42	A	46	GLU	-1	-0.905	-0.960	15.957	16.095	16.095	0.000	0.000	0.000	0.000
43	A	47	ILE	0	-0.046	-0.027	15.579	-0.763	-0.763	0.000	0.000	0.000	0.000
44	A	48	LEU	0	0.006	0.002	16.361	-0.761	-0.761	0.000	0.000	0.000	0.000
45	A	49	ASN	0	0.002	0.003	15.961	1.898	1.898	0.000	0.000	0.000	0.000
46	A	50	TRP	0	0.027	0.014	16.633	-0.656	-0.656	0.000	0.000	0.000	0.000
47	A	51	TYR	0	0.024	0.003	15.193	1.021	1.021	0.000	0.000	0.000	0.000
48	A	52	ASN	0	-0.015	-0.016	19.681	0.267	0.267	0.000	0.000	0.000	0.000
49	A	53	ASP	-1	-0.921	-0.941	23.129	11.157	11.157	0.000	0.000	0.000	0.000
50	A	54	GLY	0	-0.026	-0.007	22.646	-0.271	-0.271	0.000	0.000	0.000	0.000
51	A	55	PRO	0	-0.043	-0.028	19.686	0.215	0.215	0.000	0.000	0.000	0.000
52	A	56	SER	0	0.035	0.000	20.568	-0.526	-0.526	0.000	0.000	0.000	0.000
53	A	57	TRP	0	-0.025	-0.014	19.330	0.652	0.652	0.000	0.000	0.000	0.000
54	A	58	SER	0	-0.007	-0.008	19.559	-0.348	-0.348	0.000	0.000	0.000	0.000
55	A	59	ASN	0	-0.033	-0.009	22.429	-0.729	-0.729	0.000	0.000	0.000	0.000
56	A	60	VAL	0	0.069	0.019	25.512	0.175	0.175	0.000	0.000	0.000	0.000
57	A	61	SER	0	0.022	0.012	27.760	0.053	0.053	0.000	0.000	0.000	0.000
58	A	62	PHE	0	-0.042	-0.025	20.594	0.044	0.044	0.000	0.000	0.000	0.000
59	A	63	SER	0	-0.006	0.014	23.839	0.244	0.244	0.000	0.000	0.000	0.000
60	A	64	ASP	-1	-0.876	-0.935	25.742	9.712	9.712	0.000	0.000	0.000	0.000
61	A	65	ILE	0	-0.089	-0.034	23.049	-0.114	-0.114	0.000	0.000	0.000	0.000
62	A	66	TYR	0	0.032	0.006	19.101	0.421	0.421	0.000	0.000	0.000	0.000
63	A	67	GLY	0	-0.035	-0.002	20.853	-0.695	-0.695	0.000	0.000	0.000	0.000
64	A	68	PHE	0	0.003	-0.002	15.240	0.573	0.573	0.000	0.000	0.000	0.000
65	A	69	ASP	-1	-0.825	-0.879	17.821	14.656	14.656	0.000	0.000	0.000	0.000
66	A	70	TYR	0	-0.012	-0.021	17.499	0.919	0.919	0.000	0.000	0.000	0.000
67	A	71	GLY	0	-0.023	-0.005	18.040	0.414	0.414	0.000	0.000	0.000	0.000
68	A	72	ASP	-1	-0.903	-0.974	14.854	18.370	18.370	0.000	0.000	0.000	0.000
69	A	73	PHE	0	-0.013	-0.027	11.472	1.920	1.920	0.000	0.000	0.000	0.000
70	A	74	ALA	0	0.013	0.006	14.152	0.613	0.613	0.000	0.000	0.000	0.000
71	A	75	LEU	0	-0.014	0.022	14.938	-1.024	-1.024	0.000	0.000	0.000	0.000
72	A	76	SER	0	-0.037	-0.025	16.482	0.136	0.136	0.000	0.000	0.000	0.000
73	A	77	ILE	0	0.029	0.018	18.452	-0.267	-0.267	0.000	0.000	0.000	0.000
74	A	78	LYS	1	0.879	0.906	21.646	-11.838	-11.838	0.000	0.000	0.000	0.000
75	A	79	SER	0	-0.017	-0.015	25.239	-0.266	-0.266	0.000	0.000	0.000	0.000
76	A	80	ALA	0	0.007	0.022	23.257	-0.075	-0.075	0.000	0.000	0.000	0.000
77	A	81	LYS	1	1.006	0.992	24.628	-10.611	-10.611	0.000	0.000	0.000	0.000
78	A	82	LEU	0	0.057	0.026	24.083	0.453	0.453	0.000	0.000	0.000	0.000
79	A	83	GLN	0	-0.041	-0.020	23.393	0.438	0.438	0.000	0.000	0.000	0.000
80	A	84	ASP	-1	-0.827	-0.901	20.600	12.676	12.676	0.000	0.000	0.000	0.000
81	A	85	SER	0	0.007	0.018	18.881	0.924	0.924	0.000	0.000	0.000	0.000
82	A	86	GLY	0	-0.050	-0.028	16.790	-0.435	-0.435	0.000	0.000	0.000	0.000
83	A	87	HIS	0	0.012	0.022	8.085	-1.361	-1.361	0.000	0.000	0.000	0.000
84	A	88	TYR	0	-0.038	-0.062	11.566	-1.084	-1.084	0.000	0.000	0.000	0.000
85	A	89	LEU	0	-0.059	-0.034	5.667	1.694	1.694	0.000	0.000	0.000	0.000
86	A	90	LEU	0	0.030	0.020	7.542	-1.649	-1.649	0.000	0.000	0.000	0.000
87	A	91	GLU	-1	-0.866	-0.934	6.618	28.949	28.949	0.000	0.000	0.000	0.000
88	A	92	ILE	0	0.040	0.023	7.459	-2.561	-2.561	0.000	0.000	0.000	0.000
89	A	93	THR	0	-0.040	-0.009	8.312	2.703	2.703	0.000	0.000	0.000	0.000
90	A	94	ASN	0	0.077	0.033	10.585	-2.130	-2.130	0.000	0.000	0.000	0.000
91	A	95	THR	0	0.051	0.016	12.593	-0.066	-0.066	0.000	0.000	0.000	0.000
92	A	96	GLY	0	-0.049	-0.013	14.127	-0.892	-0.892	0.000	0.000	0.000	0.000
93	A	97	GLY	0	0.015	0.011	13.156	-0.563	-0.563	0.000	0.000	0.000	0.000
94	A	98	LYS	1	0.879	0.937	8.259	-26.909	-26.909	0.000	0.000	0.000	0.000
95	A	99	VAL	0	0.034	0.014	6.407	-0.219	-0.219	0.000	0.000	0.000	0.000
96	A	100	CYS	0	-0.008	0.002	3.647	6.296	6.756	0.020	-0.101	-0.379	0.000
97	A	101	ASN	0	-0.050	-0.024	2.501	-4.228	-2.832	0.432	-0.490	-1.337	0.003
98	A	102	LYS	1	0.937	0.967	2.112	-46.810	-46.529	4.308	-2.350	-2.240	-0.032
99	A	103	ASN	0	-0.025	-0.025	3.767	-9.540	-9.079	0.004	-0.140	-0.326	0.001
100	A	104	PHE	0	0.039	0.019	6.444	0.594	0.594	0.000	0.000	0.000	0.000
101	A	105	GLN	0	-0.009	-0.017	10.080	0.087	0.087	0.000	0.000	0.000	0.000
102	A	106	LEU	0	-0.015	0.000	13.158	-0.283	-0.283	0.000	0.000	0.000	0.000
103	A	107	LEU	0	-0.024	-0.015	16.283	-0.733	-0.733	0.000	0.000	0.000	0.000
104	A	108	ILE	0	-0.015	-0.009	19.533	-0.150	-0.150	0.000	0.000	0.000	0.000
105	A	109	LEU	0	-0.006	-0.009	22.782	-0.290	-0.290	0.000	0.000	0.000	0.000
106	A	110	ASP	-1	-0.931	-0.974	25.908	9.481	9.481	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ASP)