FMO DATABASE

FMODB ID: ZYJ9N

Calculation Name: 1F39-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 1F39

Chain ID: A

ChEMBL ID:
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UniProt ID: P03034

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	-691413.041681
FMO2-HF: Nuclear repulsion	652222.236777
FMO2-HF: Total energy	-39190.804905
FMO2-MP2: Total energy	-39301.965365

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:136:ALA)

Summations of interaction energy for fragment #1(A:136:ALA)

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.
-8.848	-3.04	4.016	-4.374	-5.451	-0.018

Interaction energy analysis for fragmet #1(A:136:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.013

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	138	ALA	0	-0.010	-0.017	3.869	-1.195	0.621	-0.012	-1.057	-0.748	0.004
4	A	139	SER	0	-0.045	-0.041	6.679	0.582	0.582	0.000	0.000	0.000	0.000
5	A	140	ALA	0	-0.063	-0.020	2.705	0.083	0.575	0.441	-0.296	-0.637	-0.002
6	A	141	PHE	0	-0.038	-0.020	4.650	0.090	0.115	-0.001	-0.005	-0.019	0.000
7	A	142	TRP	0	0.016	0.000	6.911	0.373	0.373	0.000	0.000	0.000	0.000
8	A	143	LEU	0	-0.031	-0.014	8.897	-0.128	-0.128	0.000	0.000	0.000	0.000
9	A	144	GLU	-1	-0.875	-0.945	12.327	0.298	0.298	0.000	0.000	0.000	0.000
10	A	145	VAL	0	-0.100	-0.049	15.247	-0.015	-0.015	0.000	0.000	0.000	0.000
11	A	146	GLU	-1	-0.894	-0.929	17.399	0.109	0.109	0.000	0.000	0.000	0.000
12	A	147	GLY	0	0.012	-0.002	20.817	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	148	ASN	0	-0.003	-0.020	22.196	0.030	0.030	0.000	0.000	0.000	0.000
14	A	149	SER	0	-0.025	-0.004	22.088	0.009	0.009	0.000	0.000	0.000	0.000
15	A	150	MET	0	-0.003	0.023	17.076	-0.016	-0.016	0.000	0.000	0.000	0.000
16	A	151	THR	0	-0.014	-0.004	20.383	0.025	0.025	0.000	0.000	0.000	0.000
17	A	152	ALA	0	0.017	0.012	22.261	-0.026	-0.026	0.000	0.000	0.000	0.000
18	A	153	PRO	0	0.001	-0.004	24.076	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	154	THR	0	0.019	0.002	26.984	0.017	0.017	0.000	0.000	0.000	0.000
20	A	155	GLY	0	0.013	0.015	26.840	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	156	SER	0	-0.057	-0.025	24.731	0.003	0.003	0.000	0.000	0.000	0.000
22	A	157	LYS	1	0.923	0.968	20.603	-0.353	-0.353	0.000	0.000	0.000	0.000
23	A	158	PRO	0	0.001	-0.001	16.656	-0.017	-0.017	0.000	0.000	0.000	0.000
24	A	159	SER	0	-0.033	-0.030	18.614	-0.044	-0.044	0.000	0.000	0.000	0.000
25	A	160	PHE	0	0.046	0.007	13.862	0.036	0.036	0.000	0.000	0.000	0.000
26	A	161	PRO	0	-0.028	-0.015	18.471	-0.030	-0.030	0.000	0.000	0.000	0.000
27	A	162	ASP	-1	-0.849	-0.911	19.412	0.217	0.217	0.000	0.000	0.000	0.000
28	A	163	GLY	0	0.053	0.036	19.600	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	164	MET	0	-0.106	-0.025	14.740	0.011	0.011	0.000	0.000	0.000	0.000
30	A	165	LEU	0	0.041	0.027	11.750	-0.019	-0.019	0.000	0.000	0.000	0.000
31	A	166	ILE	0	-0.042	-0.029	10.190	0.117	0.117	0.000	0.000	0.000	0.000
32	A	167	LEU	0	-0.005	0.008	2.540	-0.520	-0.164	0.498	-0.222	-0.632	0.000
33	A	168	VAL	0	0.013	-0.004	6.794	0.368	0.368	0.000	0.000	0.000	0.000
34	A	169	ASP	-1	-0.724	-0.836	2.516	-5.174	-3.602	1.725	-1.766	-1.531	-0.019
35	A	170	PRO	0	0.022	-0.002	5.289	0.125	0.140	-0.001	-0.001	-0.012	0.000
36	A	171	GLU	-1	-0.896	-0.915	6.080	-1.923	-1.923	0.000	0.000	0.000	0.000
37	A	172	GLN	0	-0.103	-0.058	2.837	-1.113	-0.315	0.176	-0.366	-0.608	-0.001
38	A	173	ALA	0	0.019	0.008	7.562	0.104	0.104	0.000	0.000	0.000	0.000
39	A	174	VAL	0	-0.026	-0.021	10.494	0.175	0.175	0.000	0.000	0.000	0.000
40	A	175	GLU	-1	-0.899	-0.948	12.908	0.086	0.086	0.000	0.000	0.000	0.000
41	A	176	PRO	0	-0.074	-0.059	15.777	0.042	0.042	0.000	0.000	0.000	0.000
42	A	177	GLY	0	-0.025	-0.011	17.911	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	178	ASP	-1	-0.793	-0.872	12.356	0.772	0.772	0.000	0.000	0.000	0.000
44	A	179	PHE	0	-0.005	-0.017	12.308	-0.119	-0.119	0.000	0.000	0.000	0.000
45	A	180	CYS	0	-0.048	-0.016	11.503	0.074	0.074	0.000	0.000	0.000	0.000
46	A	181	ILE	0	0.053	0.036	11.495	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	182	ALA	0	0.013	0.003	13.643	-0.036	-0.036	0.000	0.000	0.000	0.000
48	A	183	ARG	1	0.822	0.899	16.610	0.050	0.050	0.000	0.000	0.000	0.000
49	A	184	LEU	0	-0.004	-0.009	19.354	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	185	GLY	0	0.046	0.013	23.091	-0.013	-0.013	0.000	0.000	0.000	0.000
51	A	186	GLY	0	-0.042	-0.013	26.060	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	187	ASP	-1	-0.878	-0.916	22.853	-0.036	-0.036	0.000	0.000	0.000	0.000
53	A	188	GLU	-1	-0.862	-0.922	21.702	0.045	0.045	0.000	0.000	0.000	0.000
54	A	189	PHE	0	0.021	-0.010	14.899	0.002	0.002	0.000	0.000	0.000	0.000
55	A	190	THR	0	-0.012	-0.007	18.069	0.021	0.021	0.000	0.000	0.000	0.000
56	A	191	PHE	0	0.071	0.042	13.606	0.006	0.006	0.000	0.000	0.000	0.000
57	A	192	LYS	1	0.834	0.887	16.080	-0.263	-0.263	0.000	0.000	0.000	0.000
58	A	193	LYS	1	0.908	0.971	15.861	-0.294	-0.294	0.000	0.000	0.000	0.000
59	A	194	LEU	0	0.027	0.033	16.510	-0.055	-0.055	0.000	0.000	0.000	0.000
60	A	195	ILE	0	-0.023	-0.023	18.168	0.029	0.029	0.000	0.000	0.000	0.000
61	A	196	ARG	1	0.884	0.919	21.202	-0.126	-0.126	0.000	0.000	0.000	0.000
62	A	197	ASP	-1	-0.837	-0.892	24.070	0.128	0.128	0.000	0.000	0.000	0.000
63	A	198	SER	0	-0.027	-0.035	27.776	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	199	GLY	0	-0.033	-0.011	28.330	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	200	GLN	0	-0.010	0.014	27.329	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	201	VAL	0	0.034	0.004	21.128	0.012	0.012	0.000	0.000	0.000	0.000
67	A	202	PHE	0	-0.020	-0.004	22.876	-0.015	-0.015	0.000	0.000	0.000	0.000
68	A	203	LEU	0	0.036	0.024	18.402	0.027	0.027	0.000	0.000	0.000	0.000
69	A	204	GLN	0	0.025	-0.005	21.035	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	205	PRO	0	0.055	0.028	20.772	0.034	0.034	0.000	0.000	0.000	0.000
71	A	206	LEU	0	-0.036	-0.027	18.498	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	207	ASN	0	-0.014	0.008	22.687	-0.018	-0.018	0.000	0.000	0.000	0.000
73	A	208	PRO	0	0.010	-0.023	25.758	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	209	GLN	0	-0.044	-0.010	29.040	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	210	TYR	0	-0.006	0.006	26.452	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	211	PRO	0	0.005	0.008	28.232	0.006	0.006	0.000	0.000	0.000	0.000
77	A	212	MET	0	-0.010	-0.013	25.518	0.016	0.016	0.000	0.000	0.000	0.000
78	A	213	ILE	0	0.003	0.007	23.912	-0.015	-0.015	0.000	0.000	0.000	0.000
79	A	214	PRO	0	-0.013	-0.012	24.339	0.011	0.011	0.000	0.000	0.000	0.000
80	A	215	CYS	0	-0.012	-0.011	20.764	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	216	ASN	0	-0.027	-0.012	23.394	0.000	0.000	0.000	0.000	0.000	0.000
82	A	217	GLU	-1	-0.870	-0.949	24.508	-0.013	-0.013	0.000	0.000	0.000	0.000
83	A	218	SER	0	-0.065	-0.020	25.302	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	219	CYS	0	-0.044	-0.013	20.675	0.011	0.011	0.000	0.000	0.000	0.000
85	A	220	SER	0	-0.007	0.006	18.389	-0.014	-0.014	0.000	0.000	0.000	0.000
86	A	221	VAL	0	0.010	-0.006	12.754	0.027	0.027	0.000	0.000	0.000	0.000
87	A	222	VAL	0	-0.033	-0.015	12.091	-0.050	-0.050	0.000	0.000	0.000	0.000
88	A	223	GLY	0	0.046	0.012	9.172	-0.125	-0.125	0.000	0.000	0.000	0.000
89	A	224	LYS	1	0.822	0.925	7.072	-0.912	-0.912	0.000	0.000	0.000	0.000
90	A	225	VAL	0	-0.037	-0.019	7.332	0.090	0.090	0.000	0.000	0.000	0.000
91	A	226	ILE	0	-0.047	-0.030	2.623	-0.871	-0.137	1.190	-0.661	-1.264	0.000
92	A	227	ALA	0	-0.017	-0.005	5.871	0.331	0.331	0.000	0.000	0.000	0.000
93	A	228	SER	0	-0.044	-0.038	7.471	-0.296	-0.296	0.000	0.000	0.000	0.000
94	A	229	GLN	0	-0.029	-0.006	10.197	0.150	0.150	0.000	0.000	0.000	0.000
95	A	230	TRP	0	0.033	0.016	13.019	-0.033	-0.033	0.000	0.000	0.000	0.000
96	A	231	PRO	0	0.078	0.045	14.878	0.044	0.044	0.000	0.000	0.000	0.000
97	A	232	GLU	-1	-0.920	-0.942	15.446	0.234	0.234	0.000	0.000	0.000	0.000
98	A	233	GLU	-1	-0.864	-0.951	17.877	0.179	0.179	0.000	0.000	0.000	0.000
99	A	234	THR	0	-0.077	-0.050	19.027	-0.019	-0.019	0.000	0.000	0.000	0.000
100	A	235	PHE	0	-0.055	-0.021	17.704	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	236	GLY	0	-0.096	-0.040	22.875	-0.025	-0.025	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:136:ALA)