FMO DATABASE

FMODB ID: 43ZGN

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:

Apendix: None

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	106
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-810660.962782
FMO2-HF: Nuclear repulsion	769498.593761
FMO2-HF: Total energy	-41162.369022
FMO2-MP2: Total energy	-41284.585496

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.
-86.388	-83.967	19.421	-11.358	-10.481	0.048

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 : -0.925 / q_NPA : -0.961

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

Sort

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	-0.028	-0.012	3.848	-4.739	-2.387	-0.029	-1.333	-0.990	0.002
4	A	8	GLU	-1	-0.921	-0.954	7.068	27.364	27.364	0.000	0.000	0.000	0.000
5	A	9	GLU	-1	-0.922	-0.944	10.334	17.793	17.793	0.000	0.000	0.000	0.000
6	A	10	VAL	0	0.010	0.008	13.681	-0.232	-0.232	0.000	0.000	0.000	0.000
7	A	11	VAL	0	0.011	0.003	16.252	-0.460	-0.460	0.000	0.000	0.000	0.000
8	A	12	GLY	0	0.011	-0.003	19.878	0.016	0.016	0.000	0.000	0.000	0.000
9	A	13	VAL	0	-0.039	-0.009	22.696	-0.220	-0.220	0.000	0.000	0.000	0.000
10	A	14	SER	0	-0.003	-0.013	26.248	0.143	0.143	0.000	0.000	0.000	0.000
11	A	15	GLY	0	-0.006	-0.003	27.727	-0.249	-0.249	0.000	0.000	0.000	0.000
12	A	16	LYS	1	0.907	0.952	27.045	-10.697	-10.697	0.000	0.000	0.000	0.000
13	A	17	PRO	0	-0.009	0.013	24.177	0.252	0.252	0.000	0.000	0.000	0.000
14	A	18	VAL	0	-0.012	-0.002	18.844	0.046	0.046	0.000	0.000	0.000	0.000
15	A	19	GLN	0	-0.023	-0.030	17.157	-0.716	-0.716	0.000	0.000	0.000	0.000
16	A	20	LEU	0	-0.003	0.013	12.783	0.340	0.340	0.000	0.000	0.000	0.000
17	A	21	ARG	1	0.892	0.925	12.653	-22.082	-22.082	0.000	0.000	0.000	0.000
18	A	22	PRO	0	0.063	0.057	8.594	1.326	1.326	0.000	0.000	0.000	0.000
19	A	23	SER	0	-0.001	-0.008	8.194	-2.136	-2.136	0.000	0.000	0.000	0.000
20	A	24	ASN	0	-0.045	-0.031	6.778	2.502	2.502	0.000	0.000	0.000	0.000
21	A	25	ILE	0	0.024	0.027	5.977	8.000	8.000	0.000	0.000	0.000	0.000
22	A	26	GLN	0	-0.045	-0.022	7.782	-1.725	-1.725	0.000	0.000	0.000	0.000
23	A	27	THR	0	0.025	0.003	10.303	0.312	0.312	0.000	0.000	0.000	0.000
24	A	28	LYS	1	0.927	0.955	13.335	-18.032	-18.032	0.000	0.000	0.000	0.000
25	A	29	ASP	-1	-0.905	-0.949	15.252	17.604	17.604	0.000	0.000	0.000	0.000
26	A	30	VAL	0	-0.033	-0.015	11.700	0.938	0.938	0.000	0.000	0.000	0.000
27	A	31	SER	0	0.008	0.030	13.637	-0.749	-0.749	0.000	0.000	0.000	0.000
28	A	32	VAL	0	-0.011	-0.012	11.709	2.094	2.094	0.000	0.000	0.000	0.000
29	A	33	GLN	0	0.019	0.007	11.807	-0.979	-0.979	0.000	0.000	0.000	0.000
30	A	34	TRP	0	-0.011	0.010	11.161	2.345	2.345	0.000	0.000	0.000	0.000
31	A	35	LYS	1	0.783	0.869	11.643	-22.211	-22.211	0.000	0.000	0.000	0.000
32	A	36	LYS	1	0.877	0.967	12.498	-13.707	-13.707	0.000	0.000	0.000	0.000
33	A	37	THR	0	-0.047	-0.045	12.193	-0.720	-0.720	0.000	0.000	0.000	0.000
34	A	38	GLU	-1	-0.855	-0.903	14.856	12.131	12.131	0.000	0.000	0.000	0.000
35	A	39	GLN	0	-0.004	-0.018	18.112	-0.250	-0.250	0.000	0.000	0.000	0.000
36	A	40	GLY	0	-0.027	0.000	19.489	-0.583	-0.583	0.000	0.000	0.000	0.000
37	A	41	SER	0	-0.043	-0.040	20.445	-0.452	-0.452	0.000	0.000	0.000	0.000
38	A	42	HIS	0	-0.006	-0.002	18.353	0.924	0.924	0.000	0.000	0.000	0.000
39	A	43	ARG	1	0.834	0.908	16.825	-13.486	-13.486	0.000	0.000	0.000	0.000
40	A	44	LYS	1	0.936	0.977	9.541	-23.008	-23.008	0.000	0.000	0.000	0.000
41	A	45	ILE	0	0.053	0.029	15.976	-0.466	-0.466	0.000	0.000	0.000	0.000
42	A	46	GLU	-1	-0.821	-0.895	15.886	16.580	16.580	0.000	0.000	0.000	0.000
43	A	47	ILE	0	-0.054	-0.011	15.899	-0.839	-0.839	0.000	0.000	0.000	0.000
44	A	48	LEU	0	0.012	0.002	16.350	-0.768	-0.768	0.000	0.000	0.000	0.000
45	A	49	ASN	0	0.022	0.015	15.966	2.080	2.080	0.000	0.000	0.000	0.000
46	A	50	TRP	0	0.030	0.014	16.452	-0.691	-0.691	0.000	0.000	0.000	0.000
47	A	51	TYR	0	0.025	0.004	15.146	1.004	1.004	0.000	0.000	0.000	0.000
48	A	52	ASN	0	-0.050	-0.024	19.319	0.456	0.456	0.000	0.000	0.000	0.000
49	A	53	ASP	-1	-0.896	-0.941	22.786	11.446	11.446	0.000	0.000	0.000	0.000
50	A	54	GLY	0	-0.018	0.001	22.364	-0.280	-0.280	0.000	0.000	0.000	0.000
51	A	55	PRO	0	-0.050	-0.031	19.323	0.197	0.197	0.000	0.000	0.000	0.000
52	A	56	SER	0	0.029	0.003	20.547	-0.598	-0.598	0.000	0.000	0.000	0.000
53	A	57	TRP	0	-0.020	-0.016	19.336	0.678	0.678	0.000	0.000	0.000	0.000
54	A	58	SER	0	-0.036	-0.040	19.601	-0.340	-0.340	0.000	0.000	0.000	0.000
55	A	59	ASN	0	-0.046	-0.017	22.427	-0.791	-0.791	0.000	0.000	0.000	0.000
56	A	60	VAL	0	0.062	0.014	25.501	0.196	0.196	0.000	0.000	0.000	0.000
57	A	61	SER	0	0.031	0.023	27.521	0.062	0.062	0.000	0.000	0.000	0.000
58	A	62	PHE	0	-0.029	-0.022	20.647	0.055	0.055	0.000	0.000	0.000	0.000
59	A	63	SER	0	0.056	0.048	23.809	0.387	0.387	0.000	0.000	0.000	0.000
60	A	64	ASP	-1	-0.914	-0.960	25.717	10.141	10.141	0.000	0.000	0.000	0.000
61	A	65	ILE	0	-0.090	-0.033	23.081	-0.127	-0.127	0.000	0.000	0.000	0.000
62	A	66	TYR	0	0.013	-0.002	19.535	0.342	0.342	0.000	0.000	0.000	0.000
63	A	67	GLY	0	-0.005	0.014	20.818	-0.731	-0.731	0.000	0.000	0.000	0.000
64	A	68	PHE	0	0.010	-0.009	14.902	0.653	0.653	0.000	0.000	0.000	0.000
65	A	69	ASP	-1	-0.847	-0.896	17.788	15.295	15.295	0.000	0.000	0.000	0.000
66	A	70	TYR	0	-0.011	-0.019	17.433	1.104	1.104	0.000	0.000	0.000	0.000
67	A	71	GLY	0	-0.018	-0.007	17.859	0.467	0.467	0.000	0.000	0.000	0.000
68	A	72	ASP	-1	-0.877	-0.955	14.390	20.425	20.425	0.000	0.000	0.000	0.000
69	A	73	PHE	0	0.004	-0.018	11.394	2.277	2.277	0.000	0.000	0.000	0.000
70	A	74	ALA	0	0.009	0.004	14.021	0.612	0.612	0.000	0.000	0.000	0.000
71	A	75	LEU	0	-0.008	0.025	14.782	-1.197	-1.197	0.000	0.000	0.000	0.000
72	A	76	SER	0	-0.004	-0.013	16.442	0.139	0.139	0.000	0.000	0.000	0.000
73	A	77	ILE	0	-0.007	0.000	18.424	-0.320	-0.320	0.000	0.000	0.000	0.000
74	A	78	LYS	1	0.859	0.912	21.589	-11.997	-11.997	0.000	0.000	0.000	0.000
75	A	79	SER	0	-0.025	-0.023	25.183	-0.341	-0.341	0.000	0.000	0.000	0.000
76	A	80	ALA	0	-0.005	0.020	23.176	-0.086	-0.086	0.000	0.000	0.000	0.000
77	A	81	LYS	1	0.967	0.975	24.579	-11.293	-11.293	0.000	0.000	0.000	0.000
78	A	82	LEU	0	0.070	0.031	24.009	0.459	0.459	0.000	0.000	0.000	0.000
79	A	83	GLN	0	0.026	0.011	23.316	0.356	0.356	0.000	0.000	0.000	0.000
80	A	84	ASP	-1	-0.839	-0.913	20.510	13.166	13.166	0.000	0.000	0.000	0.000
81	A	85	SER	0	0.016	0.003	18.809	0.956	0.956	0.000	0.000	0.000	0.000
82	A	86	GLY	0	-0.035	-0.015	16.716	-0.498	-0.498	0.000	0.000	0.000	0.000
83	A	87	HIS	0	0.030	0.040	7.943	-1.565	-1.565	0.000	0.000	0.000	0.000
84	A	88	TYR	0	-0.036	-0.053	11.513	-1.215	-1.215	0.000	0.000	0.000	0.000
85	A	89	LEU	0	-0.057	-0.032	5.726	1.729	1.729	0.000	0.000	0.000	0.000
86	A	90	LEU	0	0.026	0.024	7.516	-1.521	-1.521	0.000	0.000	0.000	0.000
87	A	91	GLU	-1	-0.852	-0.929	6.620	29.817	29.817	0.000	0.000	0.000	0.000
88	A	92	ILE	0	0.041	0.028	7.353	-2.720	-2.720	0.000	0.000	0.000	0.000
89	A	93	THR	0	-0.055	-0.018	8.122	2.597	2.597	0.000	0.000	0.000	0.000
90	A	94	ASN	0	0.070	0.024	10.623	-2.451	-2.451	0.000	0.000	0.000	0.000
91	A	95	THR	0	0.069	0.025	12.704	-0.169	-0.169	0.000	0.000	0.000	0.000
92	A	96	GLY	0	-0.059	-0.014	14.140	-0.975	-0.975	0.000	0.000	0.000	0.000
93	A	97	GLY	0	0.011	0.009	13.214	-0.634	-0.634	0.000	0.000	0.000	0.000
94	A	98	LYS	1	0.880	0.940	8.219	-25.739	-25.739	0.000	0.000	0.000	0.000
95	A	99	VAL	0	0.037	0.012	6.266	0.051	0.051	0.000	0.000	0.000	0.000
96	A	100	CYS	0	-0.022	-0.002	3.784	8.118	8.802	0.049	-0.216	-0.517	0.000
97	A	101	ASN	0	-0.052	-0.030	2.494	-5.475	-4.085	0.589	-0.572	-1.406	0.002
98	A	102	LYS	1	0.896	0.930	1.715	-109.611	-112.083	18.805	-9.102	-7.230	0.043
99	A	103	ASN	0	-0.005	-0.008	3.733	-10.540	-10.073	0.007	-0.135	-0.338	0.001
100	A	104	PHE	0	0.023	0.007	6.364	1.018	1.018	0.000	0.000	0.000	0.000
101	A	105	GLN	0	-0.005	-0.007	9.996	-0.230	-0.230	0.000	0.000	0.000	0.000
102	A	106	LEU	0	-0.009	-0.003	13.069	-0.274	-0.274	0.000	0.000	0.000	0.000
103	A	107	LEU	0	-0.022	-0.016	16.198	-0.824	-0.824	0.000	0.000	0.000	0.000
104	A	108	ILE	0	-0.017	-0.009	19.444	-0.114	-0.114	0.000	0.000	0.000	0.000
105	A	109	LEU	0	-0.008	-0.008	22.696	-0.335	-0.335	0.000	0.000	0.000	0.000
106	A	110	ASP	-1	-0.907	-0.952	25.818	9.807	9.807	0.000	0.000	0.000	0.000

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