FMO DATABASE

FMODB ID: 536GZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-811137.30641
FMO2-HF: Nuclear repulsion	769974.584617
FMO2-HF: Total energy	-41162.721793
FMO2-MP2: Total energy	-41284.944592

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.
-89.829	-90.324	27.947	-14.668	-12.781	0.075

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 : -0.922 / q_NPA : -0.953

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	-0.006	-0.014	3.882	-7.608	-5.069	-0.012	-1.468	-1.059	0.004
4	A	8	GLU	-1	-0.939	-0.947	6.855	30.022	30.022	0.000	0.000	0.000	0.000
5	A	9	GLU	-1	-0.920	-0.970	10.170	18.196	18.196	0.000	0.000	0.000	0.000
6	A	10	VAL	0	-0.013	-0.005	13.710	-0.308	-0.308	0.000	0.000	0.000	0.000
7	A	11	VAL	0	0.014	0.007	16.442	-0.535	-0.535	0.000	0.000	0.000	0.000
8	A	12	GLY	0	0.023	0.002	20.103	0.093	0.093	0.000	0.000	0.000	0.000
9	A	13	VAL	0	-0.069	-0.033	22.533	-0.332	-0.332	0.000	0.000	0.000	0.000
10	A	14	SER	0	0.003	-0.032	26.207	0.118	0.118	0.000	0.000	0.000	0.000
11	A	15	GLY	0	-0.002	0.008	28.002	-0.321	-0.321	0.000	0.000	0.000	0.000
12	A	16	LYS	1	0.909	0.957	27.280	-10.788	-10.788	0.000	0.000	0.000	0.000
13	A	17	PRO	0	0.010	0.019	24.105	0.252	0.252	0.000	0.000	0.000	0.000
14	A	18	VAL	0	-0.025	-0.006	19.177	0.043	0.043	0.000	0.000	0.000	0.000
15	A	19	GLN	0	-0.014	-0.023	16.342	-0.874	-0.874	0.000	0.000	0.000	0.000
16	A	20	LEU	0	0.008	0.028	12.819	0.289	0.289	0.000	0.000	0.000	0.000
17	A	21	ARG	1	0.858	0.905	11.285	-24.615	-24.615	0.000	0.000	0.000	0.000
18	A	22	PRO	0	0.063	0.053	7.859	1.325	1.325	0.000	0.000	0.000	0.000
19	A	23	SER	0	0.026	0.011	7.349	-1.840	-1.840	0.000	0.000	0.000	0.000
20	A	24	ASN	0	-0.034	-0.031	5.932	4.132	4.132	0.000	0.000	0.000	0.000
21	A	25	ILE	0	0.037	0.024	5.258	11.438	11.565	-0.001	-0.003	-0.123	0.000
22	A	26	GLN	0	-0.023	-0.001	7.312	-1.987	-1.987	0.000	0.000	0.000	0.000
23	A	27	THR	0	0.030	0.009	10.182	-0.055	-0.055	0.000	0.000	0.000	0.000
24	A	28	LYS	1	0.939	0.954	13.056	-19.007	-19.007	0.000	0.000	0.000	0.000
25	A	29	ASP	-1	-0.857	-0.913	14.939	18.701	18.701	0.000	0.000	0.000	0.000
26	A	30	VAL	0	-0.046	-0.021	11.409	1.125	1.125	0.000	0.000	0.000	0.000
27	A	31	SER	0	0.007	0.029	13.328	-1.292	-1.292	0.000	0.000	0.000	0.000
28	A	32	VAL	0	-0.010	-0.019	11.114	2.340	2.340	0.000	0.000	0.000	0.000
29	A	33	GLN	0	0.026	0.020	11.322	-1.085	-1.085	0.000	0.000	0.000	0.000
30	A	34	TRP	0	-0.008	-0.008	11.113	2.562	2.562	0.000	0.000	0.000	0.000
31	A	35	LYS	1	0.795	0.885	11.680	-22.595	-22.595	0.000	0.000	0.000	0.000
32	A	36	LYS	1	0.859	0.948	12.726	-13.997	-13.997	0.000	0.000	0.000	0.000
33	A	37	THR	0	-0.042	-0.040	12.194	-0.615	-0.615	0.000	0.000	0.000	0.000
34	A	38	GLU	-1	-0.859	-0.905	14.860	12.354	12.354	0.000	0.000	0.000	0.000
35	A	39	GLN	0	-0.036	-0.036	17.871	-0.128	-0.128	0.000	0.000	0.000	0.000
36	A	40	GLY	0	0.020	0.016	19.531	-0.633	-0.633	0.000	0.000	0.000	0.000
37	A	41	SER	0	-0.060	-0.045	20.119	-0.475	-0.475	0.000	0.000	0.000	0.000
38	A	42	HIS	0	-0.006	-0.005	17.893	0.875	0.875	0.000	0.000	0.000	0.000
39	A	43	ARG	1	0.805	0.892	16.405	-13.698	-13.698	0.000	0.000	0.000	0.000
40	A	44	LYS	1	0.886	0.937	8.933	-23.919	-23.919	0.000	0.000	0.000	0.000
41	A	45	ILE	0	0.041	0.030	15.410	-0.371	-0.371	0.000	0.000	0.000	0.000
42	A	46	GLU	-1	-0.808	-0.884	15.397	17.146	17.146	0.000	0.000	0.000	0.000
43	A	47	ILE	0	-0.037	-0.008	16.225	-0.914	-0.914	0.000	0.000	0.000	0.000
44	A	48	LEU	0	-0.005	0.001	15.759	-0.766	-0.766	0.000	0.000	0.000	0.000
45	A	49	ASN	0	0.019	0.009	15.829	2.197	2.197	0.000	0.000	0.000	0.000
46	A	50	TRP	0	-0.005	0.002	15.959	-0.664	-0.664	0.000	0.000	0.000	0.000
47	A	51	TYR	0	0.043	0.015	14.779	0.994	0.994	0.000	0.000	0.000	0.000
48	A	52	ASN	0	-0.046	-0.030	19.140	0.371	0.371	0.000	0.000	0.000	0.000
49	A	53	ASP	-1	-0.880	-0.932	22.600	11.791	11.791	0.000	0.000	0.000	0.000
50	A	54	GLY	0	-0.013	0.009	21.731	-0.330	-0.330	0.000	0.000	0.000	0.000
51	A	55	PRO	0	-0.049	-0.033	18.837	0.332	0.332	0.000	0.000	0.000	0.000
52	A	56	SER	0	-0.007	-0.009	20.054	-0.803	-0.803	0.000	0.000	0.000	0.000
53	A	57	TRP	0	0.026	-0.002	19.455	0.749	0.749	0.000	0.000	0.000	0.000
54	A	58	SER	0	-0.050	-0.048	19.410	-0.394	-0.394	0.000	0.000	0.000	0.000
55	A	59	ASN	0	-0.018	-0.011	22.281	-0.806	-0.806	0.000	0.000	0.000	0.000
56	A	60	VAL	0	0.028	0.007	25.455	0.196	0.196	0.000	0.000	0.000	0.000
57	A	61	SER	0	0.050	0.037	27.428	-0.020	-0.020	0.000	0.000	0.000	0.000
58	A	62	PHE	0	-0.041	-0.026	20.847	0.114	0.114	0.000	0.000	0.000	0.000
59	A	63	SER	0	0.034	0.008	23.813	0.440	0.440	0.000	0.000	0.000	0.000
60	A	64	ASP	-1	-0.940	-0.964	25.671	10.585	10.585	0.000	0.000	0.000	0.000
61	A	65	ILE	0	-0.048	-0.015	23.302	-0.125	-0.125	0.000	0.000	0.000	0.000
62	A	66	TYR	0	-0.005	-0.008	20.074	0.257	0.257	0.000	0.000	0.000	0.000
63	A	67	GLY	0	-0.005	-0.003	21.063	-0.756	-0.756	0.000	0.000	0.000	0.000
64	A	68	PHE	0	0.012	-0.006	14.246	0.687	0.687	0.000	0.000	0.000	0.000
65	A	69	ASP	-1	-0.846	-0.888	16.842	16.091	16.091	0.000	0.000	0.000	0.000
66	A	70	TYR	0	0.001	-0.018	16.910	1.011	1.011	0.000	0.000	0.000	0.000
67	A	71	GLY	0	-0.032	-0.021	17.264	0.111	0.111	0.000	0.000	0.000	0.000
68	A	72	ASP	-1	-0.889	-0.957	13.728	21.647	21.647	0.000	0.000	0.000	0.000
69	A	73	PHE	0	0.001	-0.006	11.212	2.449	2.449	0.000	0.000	0.000	0.000
70	A	74	ALA	0	0.013	0.010	13.075	1.078	1.078	0.000	0.000	0.000	0.000
71	A	75	LEU	0	-0.016	0.012	14.396	-1.230	-1.230	0.000	0.000	0.000	0.000
72	A	76	SER	0	0.007	-0.011	16.138	0.193	0.193	0.000	0.000	0.000	0.000
73	A	77	ILE	0	-0.006	-0.002	18.913	-0.321	-0.321	0.000	0.000	0.000	0.000
74	A	78	LYS	1	0.874	0.945	22.051	-12.139	-12.139	0.000	0.000	0.000	0.000
75	A	79	SER	0	-0.058	-0.040	25.671	-0.358	-0.358	0.000	0.000	0.000	0.000
76	A	80	ALA	0	0.005	0.025	23.150	-0.041	-0.041	0.000	0.000	0.000	0.000
77	A	81	LYS	1	0.941	0.960	24.707	-11.680	-11.680	0.000	0.000	0.000	0.000
78	A	82	LEU	0	0.072	0.037	24.392	0.470	0.470	0.000	0.000	0.000	0.000
79	A	83	GLN	0	0.022	0.010	23.667	0.296	0.296	0.000	0.000	0.000	0.000
80	A	84	ASP	-1	-0.834	-0.924	20.862	13.332	13.332	0.000	0.000	0.000	0.000
81	A	85	SER	0	0.008	0.009	19.194	0.956	0.956	0.000	0.000	0.000	0.000
82	A	86	GLY	0	-0.012	-0.004	16.948	-0.451	-0.451	0.000	0.000	0.000	0.000
83	A	87	HIS	0	0.029	0.037	8.133	-1.329	-1.329	0.000	0.000	0.000	0.000
84	A	88	TYR	0	-0.011	-0.038	11.756	-1.371	-1.371	0.000	0.000	0.000	0.000
85	A	89	LEU	0	-0.092	-0.035	5.437	1.833	1.833	0.000	0.000	0.000	0.000
86	A	90	LEU	0	0.029	0.036	7.123	-1.860	-1.860	0.000	0.000	0.000	0.000
87	A	91	GLU	-1	-0.782	-0.901	6.464	29.864	29.864	0.000	0.000	0.000	0.000
88	A	92	ILE	0	0.017	0.022	6.920	-2.812	-2.812	0.000	0.000	0.000	0.000
89	A	93	THR	0	-0.033	-0.020	7.795	2.161	2.161	0.000	0.000	0.000	0.000
90	A	94	ASN	0	0.034	0.010	10.313	-2.398	-2.398	0.000	0.000	0.000	0.000
91	A	95	THR	0	0.025	-0.005	12.341	-0.107	-0.107	0.000	0.000	0.000	0.000
92	A	96	GLY	0	-0.049	-0.007	13.735	-1.099	-1.099	0.000	0.000	0.000	0.000
93	A	97	GLY	0	-0.017	-0.011	13.278	-0.048	-0.048	0.000	0.000	0.000	0.000
94	A	98	LYS	1	0.899	0.958	8.121	-24.620	-24.620	0.000	0.000	0.000	0.000
95	A	99	VAL	0	0.031	0.007	5.592	-0.547	-0.547	0.000	0.000	0.000	0.000
96	A	100	CYS	0	-0.025	-0.012	3.435	8.029	8.741	0.054	-0.197	-0.569	0.000
97	A	101	ASN	0	-0.046	-0.020	2.399	-4.990	-3.384	1.151	-0.856	-1.899	0.003
98	A	102	LYS	1	0.863	0.923	1.656	-117.347	-123.134	26.755	-12.102	-8.866	0.068
99	A	103	ASN	0	0.027	-0.002	3.852	-11.235	-10.927	0.000	-0.042	-0.265	0.000
100	A	104	PHE	0	0.018	-0.001	6.505	1.552	1.552	0.000	0.000	0.000	0.000
101	A	105	GLN	0	0.027	0.026	10.172	-0.682	-0.682	0.000	0.000	0.000	0.000
102	A	106	LEU	0	-0.021	-0.008	13.140	-0.022	-0.022	0.000	0.000	0.000	0.000
103	A	107	LEU	0	-0.010	-0.010	16.398	-0.815	-0.815	0.000	0.000	0.000	0.000
104	A	108	ILE	0	-0.035	-0.011	19.783	-0.102	-0.102	0.000	0.000	0.000	0.000
105	A	109	LEU	0	0.020	0.008	22.979	-0.402	-0.402	0.000	0.000	0.000	0.000
106	A	110	ASP	-1	-0.883	-0.925	26.064	10.036	10.036	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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