FMO DATABASE

FMODB ID: 6686Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1010551.705575
FMO2-HF: Nuclear repulsion	963843.074016
FMO2-HF: Total energy	-46708.63156
FMO2-MP2: Total energy	-46846.287707

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.
-3.233	-2.807	17.422	-4.426	-13.422	-0.012

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 : -0.003 / 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	5	LEU	0	0.120	0.067	3.459	-2.545	-0.560	0.031	-0.967	-1.050	0.000
4	A	6	SER	0	0.071	0.027	5.400	0.144	0.144	0.000	0.000	0.000	0.000
5	A	7	ASP	-1	-0.885	-0.928	3.708	-0.651	-0.324	0.003	-0.044	-0.285	0.000
6	A	8	LEU	0	-0.048	-0.014	2.015	2.114	-2.988	12.563	-2.120	-5.342	0.003
7	A	9	HIS	0	0.005	-0.012	3.301	0.783	0.499	0.046	0.594	-0.357	0.000
8	A	10	ARG	1	0.919	0.931	6.852	0.817	0.817	0.000	0.000	0.000	0.000
9	A	11	GLN	0	-0.036	0.006	2.586	-0.359	0.220	0.955	-0.316	-1.217	-0.002
10	A	12	VAL	0	0.037	0.022	5.589	0.122	0.122	0.000	0.000	0.000	0.000
11	A	13	SER	0	-0.039	-0.033	7.812	0.126	0.126	0.000	0.000	0.000	0.000
12	A	14	ARG	1	0.924	0.967	7.498	0.465	0.465	0.000	0.000	0.000	0.000
13	A	15	LEU	0	-0.003	0.007	8.159	0.048	0.048	0.000	0.000	0.000	0.000
14	A	16	VAL	0	-0.023	-0.017	11.648	0.039	0.039	0.000	0.000	0.000	0.000
15	A	17	GLN	0	-0.041	-0.031	13.705	0.032	0.032	0.000	0.000	0.000	0.000
16	A	18	GLN	0	-0.060	-0.021	12.863	0.021	0.021	0.000	0.000	0.000	0.000
17	A	19	GLU	-1	-0.916	-0.944	16.408	-0.134	-0.134	0.000	0.000	0.000	0.000
18	A	20	SER	0	-0.012	-0.013	13.897	0.014	0.014	0.000	0.000	0.000	0.000
19	A	21	GLY	0	0.006	-0.005	14.546	-0.021	-0.021	0.000	0.000	0.000	0.000
20	A	22	ASP	-1	-0.899	-0.953	15.344	-0.219	-0.219	0.000	0.000	0.000	0.000
21	A	23	CYS	0	-0.046	-0.002	14.180	0.016	0.016	0.000	0.000	0.000	0.000
22	A	24	THR	0	-0.019	-0.046	13.320	-0.034	-0.034	0.000	0.000	0.000	0.000
23	A	25	GLY	0	0.011	0.014	8.956	0.009	0.009	0.000	0.000	0.000	0.000
24	A	26	LYS	1	0.912	0.956	8.546	0.212	0.212	0.000	0.000	0.000	0.000
25	A	27	LEU	0	0.016	-0.008	2.196	-0.924	-0.209	1.312	-0.373	-1.654	-0.001
26	A	28	ARG	1	0.963	0.965	5.626	0.052	0.052	0.000	0.000	0.000	0.000
27	A	29	GLY	0	-0.041	-0.004	4.405	0.168	0.296	-0.001	-0.029	-0.098	0.000
28	A	30	ASN	0	0.000	0.006	2.414	-1.887	-1.366	1.804	-0.728	-1.597	-0.011
29	A	31	VAL	0	-0.013	-0.021	2.767	-0.598	-0.079	0.225	-0.140	-0.604	0.000
30	A	32	ALA	0	-0.008	-0.001	4.968	0.056	0.092	-0.001	-0.003	-0.031	0.000
31	A	33	ALA	0	0.053	0.018	8.738	-0.041	-0.041	0.000	0.000	0.000	0.000
32	A	34	ASN	0	-0.087	-0.051	11.590	0.046	0.046	0.000	0.000	0.000	0.000
33	A	35	LYS	1	0.964	0.971	13.976	0.190	0.190	0.000	0.000	0.000	0.000
34	A	36	GLU	-1	-0.938	-0.947	17.129	-0.088	-0.088	0.000	0.000	0.000	0.000
35	A	37	THR	0	-0.002	0.007	17.951	0.006	0.006	0.000	0.000	0.000	0.000
36	A	38	THR	0	0.045	0.009	18.039	-0.015	-0.015	0.000	0.000	0.000	0.000
37	A	39	PHE	0	-0.004	-0.014	17.152	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	40	GLN	0	-0.045	-0.020	19.107	0.011	0.011	0.000	0.000	0.000	0.000
39	A	41	GLY	0	0.041	0.027	19.847	0.011	0.011	0.000	0.000	0.000	0.000
40	A	42	LEU	0	-0.067	-0.016	19.253	0.012	0.012	0.000	0.000	0.000	0.000
41	A	43	THR	0	0.068	0.017	18.502	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	44	ILE	0	-0.012	-0.004	15.540	0.002	0.002	0.000	0.000	0.000	0.000
43	A	45	ALA	0	-0.033	-0.008	19.302	0.006	0.006	0.000	0.000	0.000	0.000
44	A	46	SER	0	-0.017	-0.008	22.201	0.005	0.005	0.000	0.000	0.000	0.000
45	A	47	GLY	0	0.038	0.015	21.520	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	48	ALA	0	-0.054	-0.015	16.331	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	49	ARG	1	0.862	0.900	14.045	0.115	0.115	0.000	0.000	0.000	0.000
48	A	50	GLU	-1	-0.825	-0.932	13.950	-0.055	-0.055	0.000	0.000	0.000	0.000
49	A	51	SER	0	-0.004	-0.015	9.493	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.798	-0.832	9.244	-0.306	-0.306	0.000	0.000	0.000	0.000
51	A	53	LYS	1	1.021	1.031	10.916	0.007	0.007	0.000	0.000	0.000	0.000
52	A	54	VAL	0	-0.033	-0.008	6.442	-0.031	-0.031	0.000	0.000	0.000	0.000
53	A	55	PHE	0	-0.005	0.024	5.500	-0.195	-0.195	0.000	0.000	0.000	0.000
54	A	56	ALA	0	0.056	0.021	7.050	-0.115	-0.115	0.000	0.000	0.000	0.000
55	A	57	GLN	0	0.025	-0.011	9.453	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	58	THR	0	-0.033	-0.023	2.471	-0.531	-0.108	0.461	-0.167	-0.717	-0.001
57	A	59	VAL	0	-0.002	0.010	5.846	-0.127	-0.127	0.000	0.000	0.000	0.000
58	A	60	LEU	0	-0.003	-0.003	7.276	0.033	0.033	0.000	0.000	0.000	0.000
59	A	61	SER	0	-0.097	-0.057	6.973	0.053	0.053	0.000	0.000	0.000	0.000
60	A	62	HIS	0	0.010	-0.003	3.131	0.330	0.909	0.024	-0.133	-0.470	0.000
61	A	63	VAL	0	-0.016	-0.004	8.210	0.043	0.043	0.000	0.000	0.000	0.000
62	A	64	ALA	0	0.003	0.005	11.655	0.077	0.077	0.000	0.000	0.000	0.000
63	A	65	ASN	0	-0.086	-0.047	13.918	0.013	0.013	0.000	0.000	0.000	0.000
64	A	66	VAL	0	0.015	0.031	12.653	0.007	0.007	0.000	0.000	0.000	0.000
65	A	67	VAL	0	-0.083	-0.044	15.945	0.009	0.009	0.000	0.000	0.000	0.000
66	A	68	LEU	0	-0.022	-0.014	15.448	-0.023	-0.023	0.000	0.000	0.000	0.000
67	A	69	THR	0	0.047	0.004	19.299	0.029	0.029	0.000	0.000	0.000	0.000
68	A	70	GLN	0	0.055	0.008	21.974	0.001	0.001	0.000	0.000	0.000	0.000
69	A	71	GLU	-1	-0.935	-0.969	20.999	-0.200	-0.200	0.000	0.000	0.000	0.000
70	A	72	ASP	-1	-0.765	-0.845	18.024	-0.265	-0.265	0.000	0.000	0.000	0.000
71	A	73	THR	0	0.040	0.025	19.838	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	74	ALA	0	-0.027	-0.006	21.555	0.005	0.005	0.000	0.000	0.000	0.000
73	A	75	LYS	1	0.911	0.957	18.291	0.248	0.248	0.000	0.000	0.000	0.000
74	A	76	LEU	0	0.028	0.015	15.836	0.003	0.003	0.000	0.000	0.000	0.000
75	A	77	LEU	0	-0.016	-0.010	19.694	0.008	0.008	0.000	0.000	0.000	0.000
76	A	78	GLN	0	0.011	0.002	22.594	0.016	0.016	0.000	0.000	0.000	0.000
77	A	79	SER	0	-0.022	-0.003	18.288	0.016	0.016	0.000	0.000	0.000	0.000
78	A	80	THR	0	0.024	-0.007	21.091	0.010	0.010	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.039	-0.016	23.044	0.011	0.011	0.000	0.000	0.000	0.000
80	A	82	LYS	1	0.867	0.940	21.642	0.166	0.166	0.000	0.000	0.000	0.000
81	A	83	HIS	0	-0.033	-0.027	19.196	0.014	0.014	0.000	0.000	0.000	0.000
82	A	84	ASN	0	-0.062	-0.016	23.811	0.008	0.008	0.000	0.000	0.000	0.000
83	A	85	LEU	0	0.017	0.017	21.221	0.006	0.006	0.000	0.000	0.000	0.000
84	A	86	ASN	0	0.000	-0.002	22.454	-0.023	-0.023	0.000	0.000	0.000	0.000
85	A	87	ASN	0	0.032	0.017	15.539	0.027	0.027	0.000	0.000	0.000	0.000
86	A	88	TYR	0	-0.017	-0.043	14.678	-0.019	-0.019	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.828	-0.872	18.941	-0.098	-0.098	0.000	0.000	0.000	0.000
88	A	90	LEU	0	0.018	-0.002	18.679	-0.008	-0.008	0.000	0.000	0.000	0.000
89	A	91	ARG	1	0.964	0.981	21.160	0.114	0.114	0.000	0.000	0.000	0.000
90	A	92	SER	0	0.005	-0.016	23.710	-0.010	-0.010	0.000	0.000	0.000	0.000
91	A	93	VAL	0	-0.036	-0.012	23.217	0.009	0.009	0.000	0.000	0.000	0.000
92	A	94	GLY	0	0.026	0.023	25.993	0.005	0.005	0.000	0.000	0.000	0.000
93	A	95	ASN	0	-0.011	-0.024	27.622	0.000	0.000	0.000	0.000	0.000	0.000
94	A	96	GLY	0	0.007	0.012	27.938	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	97	ASN	0	0.055	0.027	23.473	-0.015	-0.015	0.000	0.000	0.000	0.000
96	A	98	SER	0	-0.095	-0.064	21.510	0.012	0.012	0.000	0.000	0.000	0.000
97	A	99	VAL	0	0.033	0.032	18.045	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	100	LEU	0	0.025	0.030	13.574	0.019	0.019	0.000	0.000	0.000	0.000
99	A	101	VAL	0	-0.065	-0.034	16.483	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	102	SER	0	-0.042	-0.058	16.266	0.013	0.013	0.000	0.000	0.000	0.000
101	A	103	LEU	0	-0.003	-0.005	12.137	-0.016	-0.016	0.000	0.000	0.000	0.000
102	A	104	ARG	1	0.859	0.937	16.744	0.137	0.137	0.000	0.000	0.000	0.000
103	A	105	SER	0	-0.037	-0.024	17.325	0.010	0.010	0.000	0.000	0.000	0.000
104	A	106	ASP	-1	-0.877	-0.937	14.672	-0.135	-0.135	0.000	0.000	0.000	0.000
105	A	107	GLN	0	-0.011	-0.028	13.930	-0.012	-0.012	0.000	0.000	0.000	0.000
106	A	108	MET	0	0.035	0.013	10.950	-0.021	-0.021	0.000	0.000	0.000	0.000
107	A	109	THR	0	0.012	0.020	12.218	-0.041	-0.041	0.000	0.000	0.000	0.000
108	A	110	LEU	0	0.034	0.008	8.848	-0.051	-0.051	0.000	0.000	0.000	0.000
109	A	111	GLN	0	-0.023	-0.023	11.597	-0.021	-0.021	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.761	-0.835	14.054	-0.276	-0.276	0.000	0.000	0.000	0.000
111	A	113	ALA	0	-0.021	-0.019	8.231	-0.018	-0.018	0.000	0.000	0.000	0.000
112	A	114	LYS	1	0.853	0.922	9.903	0.317	0.317	0.000	0.000	0.000	0.000
113	A	115	VAL	0	-0.001	0.005	11.162	-0.011	-0.011	0.000	0.000	0.000	0.000
114	A	116	LEU	0	-0.002	0.000	11.173	0.005	0.005	0.000	0.000	0.000	0.000
115	A	117	LEU	0	-0.001	-0.009	5.844	-0.039	-0.039	0.000	0.000	0.000	0.000
116	A	118	GLU	-1	-0.819	-0.881	9.671	-0.424	-0.424	0.000	0.000	0.000	0.000
117	A	119	ALA	0	-0.007	0.010	12.707	0.039	0.039	0.000	0.000	0.000	0.000
118	A	120	ALA	0	0.010	-0.006	10.174	0.038	0.038	0.000	0.000	0.000	0.000
119	A	121	LEU	0	-0.025	-0.010	9.596	0.007	0.007	0.000	0.000	0.000	0.000
120	A	122	ARG	1	0.842	0.891	12.483	0.315	0.315	0.000	0.000	0.000	0.000
121	A	123	GLN	0	-0.029	-0.009	15.107	0.037	0.037	0.000	0.000	0.000	0.000
122	A	124	GLU	-1	-0.943	-0.968	11.515	-0.479	-0.479	0.000	0.000	0.000	0.000
123	A	125	SER	0	-0.108	-0.039	15.037	0.057	0.057	0.000	0.000	0.000	0.000

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