FMO DATABASE

FMODB ID: R5V58

Calculation Name: 1HUF-A-Xray372

Preferred Name: Secreted effector protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

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	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	123
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1011982.311789
FMO2-HF: Nuclear repulsion	965272.248085
FMO2-HF: Total energy	-46710.063704
FMO2-MP2: Total energy	-46847.547393

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.
-8.716	0.0090000000000004	7.56	-4.229	-12.057	-0.008

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 : 0.027 / q_NPA : 0.005

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

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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	0.073	0.040	3.079	-2.038	0.639	0.148	-1.410	-1.415	0.000
4	A	6	SER	0	0.027	-0.011	5.472	0.423	0.423	0.000	0.000	0.000	0.000
5	A	7	ASP	-1	-0.856	-0.893	3.470	-0.516	-0.179	0.010	-0.065	-0.283	0.000
6	A	8	LEU	0	0.014	0.015	2.284	-1.489	0.387	3.753	-1.557	-4.072	-0.001
7	A	9	HIS	0	0.005	0.000	3.221	0.704	0.528	0.057	0.467	-0.348	0.000
8	A	10	ARG	1	0.932	0.949	6.746	0.633	0.633	0.000	0.000	0.000	0.000
9	A	11	GLN	0	-0.048	-0.006	2.918	-0.683	0.100	0.543	-0.291	-1.035	-0.002
10	A	12	VAL	0	0.032	0.021	5.618	0.002	0.002	0.000	0.000	0.000	0.000
11	A	13	SER	0	-0.015	-0.017	7.622	-0.014	-0.014	0.000	0.000	0.000	0.000
12	A	14	ARG	1	0.912	0.938	6.819	-0.286	-0.286	0.000	0.000	0.000	0.000
13	A	15	LEU	0	-0.011	0.000	7.814	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	16	VAL	0	-0.027	-0.021	11.409	-0.021	-0.021	0.000	0.000	0.000	0.000
15	A	17	GLN	0	-0.027	-0.020	13.424	0.003	0.003	0.000	0.000	0.000	0.000
16	A	18	GLN	0	-0.046	-0.011	13.088	0.017	0.017	0.000	0.000	0.000	0.000
17	A	19	GLU	-1	-0.908	-0.944	16.039	0.086	0.086	0.000	0.000	0.000	0.000
18	A	20	SER	0	-0.010	-0.011	14.308	0.011	0.011	0.000	0.000	0.000	0.000
19	A	21	GLY	0	0.037	0.010	14.312	0.017	0.017	0.000	0.000	0.000	0.000
20	A	22	ASP	-1	-0.807	-0.885	15.383	0.030	0.030	0.000	0.000	0.000	0.000
21	A	23	CYS	0	-0.005	0.047	14.300	0.005	0.005	0.000	0.000	0.000	0.000
22	A	24	THR	0	-0.002	-0.031	13.116	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	25	GLY	0	0.010	0.006	9.101	0.034	0.034	0.000	0.000	0.000	0.000
24	A	26	LYS	1	0.801	0.898	8.780	-0.349	-0.349	0.000	0.000	0.000	0.000
25	A	27	LEU	0	-0.031	-0.014	2.390	-0.641	-0.620	2.392	-0.366	-2.047	0.000
26	A	28	ARG	1	0.941	0.962	5.805	-1.002	-1.002	0.000	0.000	0.000	0.000
27	A	29	GLY	0	0.008	0.004	4.762	-0.170	-0.088	-0.001	-0.013	-0.067	0.000
28	A	30	ASN	0	0.009	0.023	2.967	-0.777	0.691	0.335	-0.603	-1.200	-0.005
29	A	31	VAL	0	0.001	-0.014	2.832	-0.848	-0.141	0.222	-0.182	-0.747	0.000
30	A	32	ALA	0	-0.010	-0.006	4.866	-0.114	-0.078	-0.001	-0.003	-0.033	0.000
31	A	33	ALA	0	0.044	0.010	8.684	-0.029	-0.029	0.000	0.000	0.000	0.000
32	A	34	ASN	0	-0.030	-0.023	11.796	0.016	0.016	0.000	0.000	0.000	0.000
33	A	35	LYS	1	0.878	0.904	14.253	-0.243	-0.243	0.000	0.000	0.000	0.000
34	A	36	GLU	-1	-0.854	-0.885	17.287	0.233	0.233	0.000	0.000	0.000	0.000
35	A	37	THR	0	0.020	0.004	17.965	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	38	THR	0	0.018	0.008	18.089	0.011	0.011	0.000	0.000	0.000	0.000
37	A	39	PHE	0	-0.034	-0.015	16.380	0.008	0.008	0.000	0.000	0.000	0.000
38	A	40	GLN	0	-0.004	-0.012	18.810	0.000	0.000	0.000	0.000	0.000	0.000
39	A	41	GLY	0	0.048	0.032	19.515	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	42	LEU	0	-0.042	-0.003	18.753	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	43	THR	0	0.070	0.014	18.168	0.003	0.003	0.000	0.000	0.000	0.000
42	A	44	ILE	0	-0.009	0.002	15.217	0.004	0.004	0.000	0.000	0.000	0.000
43	A	45	ALA	0	-0.044	-0.022	19.157	0.003	0.003	0.000	0.000	0.000	0.000
44	A	46	SER	0	-0.024	-0.017	21.861	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	47	GLY	0	0.044	0.027	21.232	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	48	ALA	0	-0.046	0.000	15.771	0.017	0.017	0.000	0.000	0.000	0.000
47	A	49	ARG	1	0.823	0.873	14.140	-0.195	-0.195	0.000	0.000	0.000	0.000
48	A	50	GLU	-1	-0.792	-0.928	13.203	0.270	0.270	0.000	0.000	0.000	0.000
49	A	51	SER	0	-0.023	-0.008	9.584	0.025	0.025	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.789	-0.856	8.757	0.292	0.292	0.000	0.000	0.000	0.000
51	A	53	LYS	1	0.896	0.957	10.277	-0.142	-0.142	0.000	0.000	0.000	0.000
52	A	54	VAL	0	-0.006	-0.006	6.033	-0.060	-0.060	0.000	0.000	0.000	0.000
53	A	55	PHE	0	0.006	0.022	5.050	-0.050	-0.050	0.000	0.000	0.000	0.000
54	A	56	ALA	0	0.029	0.012	6.769	-0.174	-0.174	0.000	0.000	0.000	0.000
55	A	57	GLN	0	0.033	0.005	9.801	-0.168	-0.168	0.000	0.000	0.000	0.000
56	A	58	THR	0	-0.040	-0.019	2.983	-0.635	-0.180	0.100	-0.105	-0.450	0.000
57	A	59	VAL	0	-0.002	-0.008	6.334	-0.446	-0.446	0.000	0.000	0.000	0.000
58	A	60	LEU	0	-0.005	0.003	7.528	-0.096	-0.096	0.000	0.000	0.000	0.000
59	A	61	SER	0	-0.071	-0.046	7.485	-0.144	-0.144	0.000	0.000	0.000	0.000
60	A	62	HIS	0	-0.004	-0.016	3.342	0.578	1.037	0.002	-0.101	-0.360	0.000
61	A	63	VAL	0	-0.013	-0.002	8.653	0.078	0.078	0.000	0.000	0.000	0.000
62	A	64	ALA	0	0.017	0.016	12.067	0.134	0.134	0.000	0.000	0.000	0.000
63	A	65	ASN	0	-0.056	-0.033	14.055	0.023	0.023	0.000	0.000	0.000	0.000
64	A	66	VAL	0	0.038	0.040	13.214	0.006	0.006	0.000	0.000	0.000	0.000
65	A	67	VAL	0	-0.047	-0.023	16.452	0.047	0.047	0.000	0.000	0.000	0.000
66	A	68	LEU	0	-0.005	0.003	15.361	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	69	THR	0	0.013	-0.031	19.228	0.026	0.026	0.000	0.000	0.000	0.000
68	A	70	GLN	0	0.026	0.015	22.391	0.010	0.010	0.000	0.000	0.000	0.000
69	A	71	GLU	-1	-0.775	-0.847	21.689	-0.181	-0.181	0.000	0.000	0.000	0.000
70	A	72	ASP	-1	-0.727	-0.847	18.382	-0.249	-0.249	0.000	0.000	0.000	0.000
71	A	73	THR	0	-0.016	-0.018	20.220	0.010	0.010	0.000	0.000	0.000	0.000
72	A	74	ALA	0	-0.009	-0.001	22.182	0.015	0.015	0.000	0.000	0.000	0.000
73	A	75	LYS	1	0.803	0.879	19.090	0.198	0.198	0.000	0.000	0.000	0.000
74	A	76	LEU	0	0.025	0.009	16.060	0.015	0.015	0.000	0.000	0.000	0.000
75	A	77	LEU	0	-0.024	0.005	20.132	0.014	0.014	0.000	0.000	0.000	0.000
76	A	78	GLN	0	-0.025	-0.022	23.085	0.019	0.019	0.000	0.000	0.000	0.000
77	A	79	SER	0	-0.027	-0.035	18.565	0.009	0.009	0.000	0.000	0.000	0.000
78	A	80	THR	0	-0.030	-0.016	21.440	0.012	0.012	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.032	-0.020	23.211	0.009	0.009	0.000	0.000	0.000	0.000
80	A	82	LYS	1	0.787	0.881	21.023	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	83	HIS	0	-0.024	-0.023	18.507	0.014	0.014	0.000	0.000	0.000	0.000
82	A	84	ASN	0	-0.062	-0.023	23.767	0.002	0.002	0.000	0.000	0.000	0.000
83	A	85	LEU	0	0.006	0.011	21.251	0.001	0.001	0.000	0.000	0.000	0.000
84	A	86	ASN	0	0.029	0.023	22.524	-0.009	-0.009	0.000	0.000	0.000	0.000
85	A	87	ASN	0	0.045	0.021	15.827	0.014	0.014	0.000	0.000	0.000	0.000
86	A	88	TYR	0	-0.007	-0.037	15.045	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.800	-0.851	19.303	-0.096	-0.096	0.000	0.000	0.000	0.000
88	A	90	LEU	0	0.005	-0.008	18.983	-0.029	-0.029	0.000	0.000	0.000	0.000
89	A	91	ARG	1	0.944	0.975	21.011	0.266	0.266	0.000	0.000	0.000	0.000
90	A	92	SER	0	0.003	-0.003	23.561	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	93	VAL	0	-0.040	-0.024	23.500	0.002	0.002	0.000	0.000	0.000	0.000
92	A	94	GLY	0	0.050	0.034	26.260	0.003	0.003	0.000	0.000	0.000	0.000
93	A	95	ASN	0	-0.049	-0.044	27.825	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	96	GLY	0	0.044	0.025	28.313	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	97	ASN	0	-0.018	0.001	23.664	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	98	SER	0	0.004	-0.009	21.915	0.020	0.020	0.000	0.000	0.000	0.000
97	A	99	VAL	0	-0.022	0.003	18.187	-0.020	-0.020	0.000	0.000	0.000	0.000
98	A	100	LEU	0	-0.010	0.007	13.940	0.034	0.034	0.000	0.000	0.000	0.000
99	A	101	VAL	0	-0.050	-0.027	16.991	-0.039	-0.039	0.000	0.000	0.000	0.000
100	A	102	SER	0	-0.026	-0.035	16.910	-0.009	-0.009	0.000	0.000	0.000	0.000
101	A	103	LEU	0	0.003	-0.003	12.654	-0.007	-0.007	0.000	0.000	0.000	0.000
102	A	104	ARG	1	0.766	0.864	17.353	0.094	0.094	0.000	0.000	0.000	0.000
103	A	105	SER	0	-0.025	-0.023	17.381	0.022	0.022	0.000	0.000	0.000	0.000
104	A	106	ASP	-1	-0.826	-0.896	14.598	0.063	0.063	0.000	0.000	0.000	0.000
105	A	107	GLN	0	0.009	-0.009	13.569	0.026	0.026	0.000	0.000	0.000	0.000
106	A	108	MET	0	0.025	0.012	11.110	-0.044	-0.044	0.000	0.000	0.000	0.000
107	A	109	THR	0	-0.011	-0.018	12.377	0.052	0.052	0.000	0.000	0.000	0.000
108	A	110	LEU	0	-0.002	-0.003	8.901	-0.029	-0.029	0.000	0.000	0.000	0.000
109	A	111	GLN	0	-0.032	-0.022	12.116	-0.050	-0.050	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.741	-0.795	14.173	-0.082	-0.082	0.000	0.000	0.000	0.000
111	A	113	ALA	0	0.027	0.007	8.843	-0.050	-0.050	0.000	0.000	0.000	0.000
112	A	114	LYS	1	0.801	0.890	10.279	0.052	0.052	0.000	0.000	0.000	0.000
113	A	115	VAL	0	-0.008	0.003	11.744	-0.063	-0.063	0.000	0.000	0.000	0.000
114	A	116	LEU	0	-0.001	0.000	11.285	-0.039	-0.039	0.000	0.000	0.000	0.000
115	A	117	LEU	0	0.014	-0.001	6.290	-0.091	-0.091	0.000	0.000	0.000	0.000
116	A	118	GLU	-1	-0.777	-0.867	10.011	-0.295	-0.295	0.000	0.000	0.000	0.000
117	A	119	ALA	0	-0.005	0.001	13.130	0.001	0.001	0.000	0.000	0.000	0.000
118	A	120	ALA	0	0.010	0.002	10.718	0.013	0.013	0.000	0.000	0.000	0.000
119	A	121	LEU	0	-0.002	-0.009	9.243	-0.005	-0.005	0.000	0.000	0.000	0.000
120	A	122	ARG	1	0.816	0.915	12.559	0.355	0.355	0.000	0.000	0.000	0.000
121	A	123	GLN	0	-0.032	-0.012	15.543	0.073	0.073	0.000	0.000	0.000	0.000
122	A	124	GLU	-1	-0.971	-0.983	10.972	-1.130	-1.130	0.000	0.000	0.000	0.000
123	A	125	SER	0	-0.083	-0.043	15.006	0.065	0.065	0.000	0.000	0.000	0.000

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