FMO DATABASE

FMODB ID: ZY1YN

Calculation Name: 1HUF-A-Xray372

Preferred Name: Secreted effector protein

Target Type: SINGLE PROTEIN

Ligand Name:
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ligand 3-letter code:
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PDB ID: 1HUF

Chain ID: A

ChEMBL ID: CHEMBL3646

UniProt ID: O68720

Base Structure: X-ray

Registration Date: 2023-06-19

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	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	123
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1011645.563899
FMO2-HF: Nuclear repulsion	964936.020597
FMO2-HF: Total energy	-46709.543303
FMO2-MP2: Total energy	-46847.144709

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:3:LEU)

Summations of interaction energy for fragment #1(A:3:LEU)

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.
-6.695	-1.188	11.2	-4.018	-12.688	-0.011

Interaction energy analysis for fragmet #1(A:3:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.019

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	5	LEU	0	0.112	0.056	3.417	-2.559	0.303	0.011	-1.470	-1.402	0.006
4	A	6	SER	0	0.053	0.021	6.061	0.294	0.294	0.000	0.000	0.000	0.000
5	A	7	ASP	-1	-0.869	-0.935	3.662	-0.438	-0.157	0.003	-0.045	-0.240	0.000
6	A	8	LEU	0	-0.018	0.000	2.072	-0.328	-0.864	5.646	-1.197	-3.914	0.000
7	A	9	HIS	0	0.005	-0.003	3.193	0.893	0.568	0.045	0.624	-0.344	-0.001
8	A	10	ARG	1	0.915	0.940	6.763	0.702	0.702	0.000	0.000	0.000	0.000
9	A	11	GLN	0	-0.040	-0.003	2.592	-0.460	0.032	1.171	-0.317	-1.345	-0.002
10	A	12	VAL	0	0.029	0.018	5.633	0.080	0.080	0.000	0.000	0.000	0.000
11	A	13	SER	0	-0.022	-0.027	7.912	0.064	0.064	0.000	0.000	0.000	0.000
12	A	14	ARG	1	0.916	0.961	6.757	0.041	0.041	0.000	0.000	0.000	0.000
13	A	15	LEU	0	0.000	0.007	8.034	0.018	0.018	0.000	0.000	0.000	0.000
14	A	16	VAL	0	-0.036	-0.026	11.669	0.008	0.008	0.000	0.000	0.000	0.000
15	A	17	GLN	0	-0.023	-0.018	13.694	0.021	0.021	0.000	0.000	0.000	0.000
16	A	18	GLN	0	-0.063	-0.024	12.808	0.016	0.016	0.000	0.000	0.000	0.000
17	A	19	GLU	-1	-0.899	-0.933	16.374	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	20	SER	0	-0.007	-0.012	13.879	0.020	0.020	0.000	0.000	0.000	0.000
19	A	21	GLY	0	0.019	0.005	14.607	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	22	ASP	-1	-0.800	-0.888	15.464	-0.077	-0.077	0.000	0.000	0.000	0.000
21	A	23	CYS	0	-0.033	0.012	14.220	0.014	0.014	0.000	0.000	0.000	0.000
22	A	24	THR	0	-0.009	-0.033	13.187	-0.021	-0.021	0.000	0.000	0.000	0.000
23	A	25	GLY	0	0.002	0.011	9.078	0.029	0.029	0.000	0.000	0.000	0.000
24	A	26	LYS	1	0.822	0.909	8.785	-0.143	-0.143	0.000	0.000	0.000	0.000
25	A	27	LEU	0	-0.019	-0.016	2.359	-1.067	-0.506	1.834	-0.365	-2.031	-0.002
26	A	28	ARG	1	0.966	0.968	5.661	-0.809	-0.809	0.000	0.000	0.000	0.000
27	A	29	GLY	0	-0.002	0.003	4.381	0.048	0.179	-0.001	-0.027	-0.102	0.000
28	A	30	ASN	0	0.006	0.014	2.555	-0.837	-0.302	2.218	-0.872	-1.880	-0.012
29	A	31	VAL	0	-0.020	-0.015	2.828	-0.781	-0.161	0.170	-0.163	-0.628	0.000
30	A	32	ALA	0	-0.007	0.000	4.818	-0.005	0.035	-0.001	-0.004	-0.034	0.000
31	A	33	ALA	0	0.049	0.013	8.609	-0.042	-0.042	0.000	0.000	0.000	0.000
32	A	34	ASN	0	-0.043	-0.039	11.608	0.051	0.051	0.000	0.000	0.000	0.000
33	A	35	LYS	1	0.903	0.930	14.109	-0.072	-0.072	0.000	0.000	0.000	0.000
34	A	36	GLU	-1	-0.879	-0.903	17.183	0.119	0.119	0.000	0.000	0.000	0.000
35	A	37	THR	0	0.035	0.030	18.157	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	38	THR	0	0.040	0.016	18.300	0.000	0.000	0.000	0.000	0.000	0.000
37	A	39	PHE	0	-0.029	-0.029	16.793	0.004	0.004	0.000	0.000	0.000	0.000
38	A	40	GLN	0	-0.033	-0.026	18.994	0.005	0.005	0.000	0.000	0.000	0.000
39	A	41	GLY	0	0.045	0.035	19.574	0.000	0.000	0.000	0.000	0.000	0.000
40	A	42	LEU	0	-0.048	-0.005	18.828	0.002	0.002	0.000	0.000	0.000	0.000
41	A	43	THR	0	0.064	0.015	18.204	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	44	ILE	0	0.015	0.016	15.130	0.004	0.004	0.000	0.000	0.000	0.000
43	A	45	ALA	0	-0.040	-0.016	18.957	0.006	0.006	0.000	0.000	0.000	0.000
44	A	46	SER	0	-0.027	-0.011	21.802	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	47	GLY	0	0.053	0.023	21.278	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	48	ALA	0	-0.056	-0.016	15.905	0.011	0.011	0.000	0.000	0.000	0.000
47	A	49	ARG	1	0.820	0.869	14.187	-0.088	-0.088	0.000	0.000	0.000	0.000
48	A	50	GLU	-1	-0.817	-0.929	13.541	0.177	0.177	0.000	0.000	0.000	0.000
49	A	51	SER	0	-0.016	-0.014	9.819	0.012	0.012	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.781	-0.847	9.047	0.037	0.037	0.000	0.000	0.000	0.000
51	A	53	LYS	1	0.907	0.959	10.481	-0.076	-0.076	0.000	0.000	0.000	0.000
52	A	54	VAL	0	-0.017	-0.001	6.020	-0.064	-0.064	0.000	0.000	0.000	0.000
53	A	55	PHE	0	-0.007	0.020	5.310	-0.163	-0.163	0.000	0.000	0.000	0.000
54	A	56	ALA	0	0.041	0.014	6.900	-0.167	-0.167	0.000	0.000	0.000	0.000
55	A	57	GLN	0	0.034	-0.005	9.675	-0.130	-0.130	0.000	0.000	0.000	0.000
56	A	58	THR	0	-0.041	-0.025	3.113	-0.525	-0.098	0.099	-0.098	-0.429	0.000
57	A	59	VAL	0	-0.010	0.002	6.450	-0.367	-0.367	0.000	0.000	0.000	0.000
58	A	60	LEU	0	0.007	0.001	7.733	-0.064	-0.064	0.000	0.000	0.000	0.000
59	A	61	SER	0	-0.091	-0.049	7.284	-0.111	-0.111	0.000	0.000	0.000	0.000
60	A	62	HIS	0	0.009	-0.004	3.370	0.687	1.106	0.005	-0.084	-0.339	0.000
61	A	63	VAL	0	-0.022	-0.007	8.543	0.086	0.086	0.000	0.000	0.000	0.000
62	A	64	ALA	0	0.003	0.003	12.001	0.134	0.134	0.000	0.000	0.000	0.000
63	A	65	ASN	0	-0.077	-0.046	14.168	0.022	0.022	0.000	0.000	0.000	0.000
64	A	66	VAL	0	0.027	0.040	13.222	0.005	0.005	0.000	0.000	0.000	0.000
65	A	67	VAL	0	-0.071	-0.032	16.461	0.036	0.036	0.000	0.000	0.000	0.000
66	A	68	LEU	0	-0.025	-0.014	15.809	-0.017	-0.017	0.000	0.000	0.000	0.000
67	A	69	THR	0	0.062	0.013	19.684	0.035	0.035	0.000	0.000	0.000	0.000
68	A	70	GLN	0	0.026	0.004	22.273	0.004	0.004	0.000	0.000	0.000	0.000
69	A	71	GLU	-1	-0.805	-0.893	21.066	-0.218	-0.218	0.000	0.000	0.000	0.000
70	A	72	ASP	-1	-0.734	-0.833	18.249	-0.291	-0.291	0.000	0.000	0.000	0.000
71	A	73	THR	0	0.027	0.006	20.108	0.005	0.005	0.000	0.000	0.000	0.000
72	A	74	ALA	0	-0.027	0.000	21.869	0.012	0.012	0.000	0.000	0.000	0.000
73	A	75	LYS	1	0.797	0.877	18.819	0.249	0.249	0.000	0.000	0.000	0.000
74	A	76	LEU	0	0.003	0.002	16.215	0.011	0.011	0.000	0.000	0.000	0.000
75	A	77	LEU	0	-0.027	-0.009	19.992	0.015	0.015	0.000	0.000	0.000	0.000
76	A	78	GLN	0	0.008	-0.008	22.818	0.021	0.021	0.000	0.000	0.000	0.000
77	A	79	SER	0	-0.019	-0.018	18.536	0.018	0.018	0.000	0.000	0.000	0.000
78	A	80	THR	0	0.006	-0.016	21.351	0.012	0.012	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.034	-0.016	23.267	0.012	0.012	0.000	0.000	0.000	0.000
80	A	82	LYS	1	0.766	0.877	20.776	0.084	0.084	0.000	0.000	0.000	0.000
81	A	83	HIS	0	-0.022	-0.027	18.952	0.019	0.019	0.000	0.000	0.000	0.000
82	A	84	ASN	0	-0.063	-0.014	23.852	0.006	0.006	0.000	0.000	0.000	0.000
83	A	85	LEU	0	0.005	0.008	21.058	0.002	0.002	0.000	0.000	0.000	0.000
84	A	86	ASN	0	0.010	0.012	22.479	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	87	ASN	0	0.040	0.019	15.433	0.017	0.017	0.000	0.000	0.000	0.000
86	A	88	TYR	0	-0.018	-0.036	14.985	-0.018	-0.018	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.827	-0.871	19.426	-0.121	-0.121	0.000	0.000	0.000	0.000
88	A	90	LEU	0	0.016	-0.005	19.099	-0.024	-0.024	0.000	0.000	0.000	0.000
89	A	91	ARG	1	0.948	0.978	21.384	0.250	0.250	0.000	0.000	0.000	0.000
90	A	92	SER	0	0.026	-0.008	23.969	-0.010	-0.010	0.000	0.000	0.000	0.000
91	A	93	VAL	0	-0.032	-0.010	23.493	0.006	0.006	0.000	0.000	0.000	0.000
92	A	94	GLY	0	0.024	0.021	26.337	0.003	0.003	0.000	0.000	0.000	0.000
93	A	95	ASN	0	-0.028	-0.034	28.086	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	96	GLY	0	0.016	0.014	28.266	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	97	ASN	0	0.018	0.010	23.941	-0.008	-0.008	0.000	0.000	0.000	0.000
96	A	98	SER	0	-0.047	-0.038	21.923	0.021	0.021	0.000	0.000	0.000	0.000
97	A	99	VAL	0	0.011	0.023	18.275	-0.019	-0.019	0.000	0.000	0.000	0.000
98	A	100	LEU	0	0.013	0.027	14.033	0.035	0.035	0.000	0.000	0.000	0.000
99	A	101	VAL	0	-0.062	-0.033	16.809	-0.033	-0.033	0.000	0.000	0.000	0.000
100	A	102	SER	0	-0.018	-0.035	16.784	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	103	LEU	0	-0.016	-0.008	12.401	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	104	ARG	1	0.857	0.931	17.096	0.139	0.139	0.000	0.000	0.000	0.000
103	A	105	SER	0	-0.047	-0.040	17.362	0.024	0.024	0.000	0.000	0.000	0.000
104	A	106	ASP	-1	-0.828	-0.900	14.576	-0.035	-0.035	0.000	0.000	0.000	0.000
105	A	107	GLN	0	0.012	-0.007	13.523	0.013	0.013	0.000	0.000	0.000	0.000
106	A	108	MET	0	0.036	0.015	11.017	-0.040	-0.040	0.000	0.000	0.000	0.000
107	A	109	THR	0	-0.017	-0.005	12.016	0.016	0.016	0.000	0.000	0.000	0.000
108	A	110	LEU	0	0.023	0.002	8.880	-0.045	-0.045	0.000	0.000	0.000	0.000
109	A	111	GLN	0	-0.025	-0.025	11.749	-0.040	-0.040	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.755	-0.817	14.210	-0.194	-0.194	0.000	0.000	0.000	0.000
111	A	113	ALA	0	0.010	0.000	8.507	-0.039	-0.039	0.000	0.000	0.000	0.000
112	A	114	LYS	1	0.803	0.896	10.153	0.186	0.186	0.000	0.000	0.000	0.000
113	A	115	VAL	0	0.014	0.010	11.326	-0.042	-0.042	0.000	0.000	0.000	0.000
114	A	116	LEU	0	-0.016	-0.006	11.526	-0.025	-0.025	0.000	0.000	0.000	0.000
115	A	117	LEU	0	0.011	-0.004	6.331	-0.072	-0.072	0.000	0.000	0.000	0.000
116	A	118	GLU	-1	-0.782	-0.870	9.915	-0.374	-0.374	0.000	0.000	0.000	0.000
117	A	119	ALA	0	-0.013	0.005	12.876	0.016	0.016	0.000	0.000	0.000	0.000
118	A	120	ALA	0	0.017	-0.003	10.799	0.020	0.020	0.000	0.000	0.000	0.000
119	A	121	LEU	0	-0.014	-0.002	9.732	-0.022	-0.022	0.000	0.000	0.000	0.000
120	A	122	ARG	1	0.842	0.903	13.099	0.366	0.366	0.000	0.000	0.000	0.000
121	A	123	GLN	0	-0.041	-0.019	15.860	0.061	0.061	0.000	0.000	0.000	0.000
122	A	124	GLU	-1	-0.947	-0.966	11.769	-0.949	-0.949	0.000	0.000	0.000	0.000
123	A	125	SER	0	-0.096	-0.040	15.809	0.070	0.070	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LEU)