FMO DATABASE

FMODB ID: 85YVY

Calculation Name: 3HDU-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: 3HDU

Chain ID: A

ChEMBL ID:
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UniProt ID: Q2LUI2

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	152
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1434232.984577
FMO2-HF: Nuclear repulsion	1373442.036187
FMO2-HF: Total energy	-60790.94839
FMO2-MP2: Total energy	-60963.285059

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:SER)

Summations of interaction energy for fragment #1(A:5:SER)

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.
-32.56	-26.011	9.062	-7.696	-7.914	-0.069

Interaction energy analysis for fragmet #1(A:5:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : -0.010

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	ASN	0	-0.005	-0.031	3.050	-1.882	0.015	0.043	-0.880	-1.060	0.003
4	A	8	GLU	-1	-0.848	-0.918	1.995	-31.615	-27.500	9.005	-6.770	-6.349	-0.071
5	A	9	GLU	-1	-0.862	-0.922	3.360	-1.586	-1.049	0.014	-0.046	-0.505	-0.001
6	A	10	VAL	0	-0.065	-0.021	5.690	1.140	1.140	0.000	0.000	0.000	0.000
7	A	11	LEU	0	-0.026	-0.005	6.962	0.543	0.543	0.000	0.000	0.000	0.000
8	A	12	PHE	0	0.044	0.012	7.669	0.498	0.498	0.000	0.000	0.000	0.000
9	A	13	SER	0	-0.003	-0.013	9.365	0.495	0.495	0.000	0.000	0.000	0.000
10	A	14	ALA	0	-0.030	-0.009	11.394	0.241	0.241	0.000	0.000	0.000	0.000
11	A	15	VAL	0	-0.015	-0.010	12.206	0.187	0.187	0.000	0.000	0.000	0.000
12	A	16	ASN	0	0.030	-0.003	12.714	0.117	0.117	0.000	0.000	0.000	0.000
13	A	17	GLU	-1	-0.892	-0.945	15.482	-0.408	-0.408	0.000	0.000	0.000	0.000
14	A	18	ILE	0	-0.058	-0.024	16.740	0.095	0.095	0.000	0.000	0.000	0.000
15	A	19	PHE	0	-0.005	-0.026	17.286	0.064	0.064	0.000	0.000	0.000	0.000
16	A	20	GLU	-1	-0.835	-0.906	17.028	-0.735	-0.735	0.000	0.000	0.000	0.000
17	A	21	GLU	-1	-0.937	-0.954	20.243	-0.402	-0.402	0.000	0.000	0.000	0.000
18	A	22	LYS	1	0.868	0.923	21.568	0.438	0.438	0.000	0.000	0.000	0.000
19	A	23	ILE	0	0.000	0.031	22.726	0.040	0.040	0.000	0.000	0.000	0.000
20	A	24	PRO	0	0.019	0.002	25.568	0.011	0.011	0.000	0.000	0.000	0.000
21	A	25	PHE	0	-0.006	-0.020	28.684	0.020	0.020	0.000	0.000	0.000	0.000
22	A	26	ASN	0	0.070	0.054	24.011	0.006	0.006	0.000	0.000	0.000	0.000
23	A	27	LYS	1	0.924	0.953	28.096	0.226	0.226	0.000	0.000	0.000	0.000
24	A	28	ILE	0	-0.040	-0.011	31.358	0.017	0.017	0.000	0.000	0.000	0.000
25	A	29	ILE	0	-0.012	-0.013	28.285	0.010	0.010	0.000	0.000	0.000	0.000
26	A	30	GLY	0	-0.018	-0.004	26.706	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	31	LEU	0	0.030	0.014	20.679	0.001	0.001	0.000	0.000	0.000	0.000
28	A	32	LYS	1	0.854	0.918	19.464	0.546	0.546	0.000	0.000	0.000	0.000
29	A	33	VAL	0	0.032	0.007	14.343	0.035	0.035	0.000	0.000	0.000	0.000
30	A	34	ARG	1	0.850	0.934	15.426	0.595	0.595	0.000	0.000	0.000	0.000
31	A	35	PHE	0	0.015	-0.002	11.243	-0.070	-0.070	0.000	0.000	0.000	0.000
32	A	36	ILE	0	0.000	-0.004	9.283	0.212	0.212	0.000	0.000	0.000	0.000
33	A	37	SER	0	0.022	0.007	9.638	-0.347	-0.347	0.000	0.000	0.000	0.000
34	A	38	PRO	0	0.021	0.005	8.863	0.219	0.219	0.000	0.000	0.000	0.000
35	A	39	GLU	-1	-0.909	-0.948	11.978	-1.034	-1.034	0.000	0.000	0.000	0.000
36	A	40	GLN	0	-0.061	-0.037	13.979	0.185	0.185	0.000	0.000	0.000	0.000
37	A	41	VAL	0	-0.011	0.021	14.065	-0.202	-0.202	0.000	0.000	0.000	0.000
38	A	42	LYS	1	0.967	0.982	16.141	0.784	0.784	0.000	0.000	0.000	0.000
39	A	43	LEU	0	0.007	0.021	17.819	-0.080	-0.080	0.000	0.000	0.000	0.000
40	A	44	SER	0	-0.005	-0.008	20.398	0.034	0.034	0.000	0.000	0.000	0.000
41	A	45	PHE	0	-0.025	-0.023	22.827	-0.021	-0.021	0.000	0.000	0.000	0.000
42	A	46	GLU	-1	-0.854	-0.926	25.931	-0.295	-0.295	0.000	0.000	0.000	0.000
43	A	47	MET	0	-0.048	-0.015	28.645	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	48	ARG	1	0.883	0.938	26.667	0.323	0.323	0.000	0.000	0.000	0.000
45	A	49	ASP	-1	-0.853	-0.926	33.373	-0.165	-0.165	0.000	0.000	0.000	0.000
46	A	50	GLU	-1	-0.889	-0.962	35.905	-0.205	-0.205	0.000	0.000	0.000	0.000
47	A	51	LEU	0	-0.036	0.000	37.614	0.004	0.004	0.000	0.000	0.000	0.000
48	A	52	ILE	0	0.010	-0.004	40.120	0.006	0.006	0.000	0.000	0.000	0.000
49	A	53	GLY	0	0.009	0.002	43.247	0.004	0.004	0.000	0.000	0.000	0.000
50	A	54	ASN	0	-0.015	0.003	43.997	0.006	0.006	0.000	0.000	0.000	0.000
51	A	55	ALA	0	0.034	0.000	46.013	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	56	ILE	0	-0.006	0.001	44.426	0.002	0.002	0.000	0.000	0.000	0.000
53	A	57	ARG	1	0.953	0.996	38.943	0.169	0.169	0.000	0.000	0.000	0.000
54	A	58	ARG	1	0.976	0.967	40.802	0.142	0.142	0.000	0.000	0.000	0.000
55	A	59	MET	0	0.012	0.015	40.219	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	60	LEU	0	0.024	0.010	39.040	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	61	TYR	0	-0.019	-0.034	35.535	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	62	GLY	0	0.022	0.029	35.226	-0.014	-0.014	0.000	0.000	0.000	0.000
59	A	63	GLY	0	0.052	0.029	35.062	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	64	VAL	0	0.000	0.009	31.413	-0.015	-0.015	0.000	0.000	0.000	0.000
61	A	65	ILE	0	0.027	0.001	30.864	-0.022	-0.022	0.000	0.000	0.000	0.000
62	A	66	SER	0	-0.061	-0.026	30.094	-0.018	-0.018	0.000	0.000	0.000	0.000
63	A	67	SER	0	0.029	0.007	29.469	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	68	ALA	0	0.007	0.015	26.448	-0.026	-0.026	0.000	0.000	0.000	0.000
65	A	69	ILE	0	0.015	0.011	25.131	-0.047	-0.047	0.000	0.000	0.000	0.000
66	A	70	ASP	-1	-0.827	-0.890	25.134	-0.393	-0.393	0.000	0.000	0.000	0.000
67	A	71	MET	0	0.001	0.000	22.692	-0.021	-0.021	0.000	0.000	0.000	0.000
68	A	72	THR	0	0.012	-0.017	20.477	-0.068	-0.068	0.000	0.000	0.000	0.000
69	A	73	ALA	0	-0.001	-0.014	20.157	-0.065	-0.065	0.000	0.000	0.000	0.000
70	A	74	GLY	0	0.043	0.019	20.941	-0.023	-0.023	0.000	0.000	0.000	0.000
71	A	75	LEU	0	0.002	0.005	14.612	-0.031	-0.031	0.000	0.000	0.000	0.000
72	A	76	ALA	0	0.024	0.000	16.153	-0.099	-0.099	0.000	0.000	0.000	0.000
73	A	77	ALA	0	-0.027	-0.010	16.904	-0.024	-0.024	0.000	0.000	0.000	0.000
74	A	78	PHE	0	-0.008	-0.019	12.175	0.025	0.025	0.000	0.000	0.000	0.000
75	A	79	MET	0	0.001	0.011	11.140	-0.096	-0.096	0.000	0.000	0.000	0.000
76	A	80	GLY	0	0.066	0.041	12.872	-0.052	-0.052	0.000	0.000	0.000	0.000
77	A	81	PHE	0	-0.042	-0.055	15.342	0.063	0.063	0.000	0.000	0.000	0.000
78	A	82	GLN	0	-0.041	-0.027	9.162	0.096	0.096	0.000	0.000	0.000	0.000
79	A	83	GLU	-1	-0.896	-0.933	9.784	-1.059	-1.059	0.000	0.000	0.000	0.000
80	A	84	LYS	1	0.875	0.940	12.135	0.513	0.513	0.000	0.000	0.000	0.000
81	A	85	MET	0	-0.110	-0.032	13.805	0.092	0.092	0.000	0.000	0.000	0.000
82	A	86	SER	0	0.027	0.011	11.218	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	87	GLY	0	-0.007	-0.009	10.736	0.036	0.036	0.000	0.000	0.000	0.000
84	A	88	LYS	1	0.900	0.969	13.038	0.157	0.157	0.000	0.000	0.000	0.000
85	A	89	PRO	0	0.047	0.018	11.838	-0.039	-0.039	0.000	0.000	0.000	0.000
86	A	90	MET	0	0.011	-0.007	9.095	-0.065	-0.065	0.000	0.000	0.000	0.000
87	A	91	GLU	-1	-0.879	-0.932	11.956	-0.432	-0.432	0.000	0.000	0.000	0.000
88	A	92	GLU	-1	-0.912	-0.977	15.736	-0.200	-0.200	0.000	0.000	0.000	0.000
89	A	93	LYS	1	0.901	0.962	8.649	0.821	0.821	0.000	0.000	0.000	0.000
90	A	94	LEU	0	0.035	0.005	12.295	-0.031	-0.031	0.000	0.000	0.000	0.000
91	A	95	ALA	0	0.015	0.015	15.779	0.030	0.030	0.000	0.000	0.000	0.000
92	A	96	MET	0	-0.136	-0.054	15.921	0.058	0.058	0.000	0.000	0.000	0.000
93	A	97	ILE	0	0.037	0.016	16.526	0.033	0.033	0.000	0.000	0.000	0.000
94	A	98	GLY	0	0.016	0.016	19.267	0.017	0.017	0.000	0.000	0.000	0.000
95	A	99	ARG	1	0.903	0.959	20.786	0.353	0.353	0.000	0.000	0.000	0.000
96	A	100	LEU	0	-0.040	0.003	18.843	0.024	0.024	0.000	0.000	0.000	0.000
97	A	101	SER	0	0.029	0.018	23.405	0.008	0.008	0.000	0.000	0.000	0.000
98	A	102	THR	0	-0.017	-0.026	26.827	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	103	MET	0	-0.083	-0.041	28.221	0.018	0.018	0.000	0.000	0.000	0.000
100	A	104	SER	0	-0.019	-0.024	29.994	0.021	0.021	0.000	0.000	0.000	0.000
101	A	105	LEU	0	0.053	0.030	29.187	-0.023	-0.023	0.000	0.000	0.000	0.000
102	A	106	HIS	0	-0.051	-0.009	31.347	0.026	0.026	0.000	0.000	0.000	0.000
103	A	107	VAL	0	0.016	-0.008	31.038	-0.022	-0.022	0.000	0.000	0.000	0.000
104	A	108	GLU	-1	-0.902	-0.934	33.373	-0.192	-0.192	0.000	0.000	0.000	0.000
105	A	109	TYR	0	-0.066	-0.056	34.351	-0.015	-0.015	0.000	0.000	0.000	0.000
106	A	110	LEU	0	-0.015	-0.008	34.221	0.014	0.014	0.000	0.000	0.000	0.000
107	A	111	ARG	1	0.891	0.957	36.131	0.219	0.219	0.000	0.000	0.000	0.000
108	A	112	PRO	0	-0.053	-0.021	37.380	-0.009	-0.009	0.000	0.000	0.000	0.000
109	A	113	GLY	0	0.045	0.000	35.313	0.002	0.002	0.000	0.000	0.000	0.000
110	A	114	LEU	0	-0.110	-0.060	35.964	0.002	0.002	0.000	0.000	0.000	0.000
111	A	115	GLY	0	0.084	0.062	34.331	0.010	0.010	0.000	0.000	0.000	0.000
112	A	116	ARG	1	0.891	0.962	31.976	0.231	0.231	0.000	0.000	0.000	0.000
113	A	117	GLU	-1	-0.933	-0.954	27.154	-0.339	-0.339	0.000	0.000	0.000	0.000
114	A	118	PHE	0	-0.018	-0.015	28.037	0.012	0.012	0.000	0.000	0.000	0.000
115	A	119	VAL	0	-0.020	-0.012	22.314	-0.038	-0.038	0.000	0.000	0.000	0.000
116	A	120	CYS	0	-0.047	-0.009	23.494	0.046	0.046	0.000	0.000	0.000	0.000
117	A	121	THR	0	0.011	0.013	19.356	-0.070	-0.070	0.000	0.000	0.000	0.000
118	A	122	GLY	0	0.005	-0.006	19.835	0.067	0.067	0.000	0.000	0.000	0.000
119	A	123	TYR	0	0.010	0.000	18.792	-0.101	-0.101	0.000	0.000	0.000	0.000
120	A	124	ASN	0	-0.019	-0.014	17.476	0.135	0.135	0.000	0.000	0.000	0.000
121	A	125	VAL	0	-0.012	0.011	19.411	0.009	0.009	0.000	0.000	0.000	0.000
122	A	126	ARG	1	0.974	0.981	21.364	0.291	0.291	0.000	0.000	0.000	0.000
123	A	127	THR	0	0.021	0.013	18.369	-0.025	-0.025	0.000	0.000	0.000	0.000
124	A	128	GLY	0	-0.037	-0.022	20.980	0.026	0.026	0.000	0.000	0.000	0.000
125	A	129	ASN	0	-0.013	-0.028	22.046	-0.029	-0.029	0.000	0.000	0.000	0.000
126	A	130	LYS	1	0.977	0.973	23.026	0.210	0.210	0.000	0.000	0.000	0.000
127	A	131	VAL	0	0.013	0.023	25.024	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	132	ALA	0	0.026	0.024	21.049	0.000	0.000	0.000	0.000	0.000	0.000
129	A	133	VAL	0	-0.036	-0.015	22.836	0.016	0.016	0.000	0.000	0.000	0.000
130	A	134	ILE	0	-0.002	-0.001	20.996	-0.026	-0.026	0.000	0.000	0.000	0.000
131	A	135	ARG	1	0.862	0.925	23.247	0.381	0.381	0.000	0.000	0.000	0.000
132	A	136	THR	0	-0.015	-0.028	23.268	-0.039	-0.039	0.000	0.000	0.000	0.000
133	A	137	GLU	-1	-0.848	-0.901	24.774	-0.339	-0.339	0.000	0.000	0.000	0.000
134	A	138	LEU	0	0.019	0.011	25.525	-0.035	-0.035	0.000	0.000	0.000	0.000
135	A	139	MET	0	0.023	-0.006	24.719	0.038	0.038	0.000	0.000	0.000	0.000
136	A	140	ASN	0	-0.027	-0.016	28.561	-0.025	-0.025	0.000	0.000	0.000	0.000
137	A	141	ASP	-1	-0.824	-0.927	29.266	-0.285	-0.285	0.000	0.000	0.000	0.000
138	A	142	GLN	0	-0.124	-0.058	29.797	0.003	0.003	0.000	0.000	0.000	0.000
139	A	143	ASP	-1	-0.934	-0.948	27.231	-0.328	-0.328	0.000	0.000	0.000	0.000
140	A	144	GLU	-1	-0.882	-0.941	29.778	-0.195	-0.195	0.000	0.000	0.000	0.000
141	A	145	LEU	0	-0.007	-0.011	29.282	-0.009	-0.009	0.000	0.000	0.000	0.000
142	A	146	ILE	0	-0.042	-0.027	31.735	0.022	0.022	0.000	0.000	0.000	0.000
143	A	147	ALA	0	-0.006	-0.003	31.665	0.016	0.016	0.000	0.000	0.000	0.000
144	A	148	VAL	0	0.006	0.017	29.549	-0.023	-0.023	0.000	0.000	0.000	0.000
145	A	149	GLY	0	0.027	0.014	28.649	0.020	0.020	0.000	0.000	0.000	0.000
146	A	150	SER	0	-0.048	-0.011	27.911	-0.020	-0.020	0.000	0.000	0.000	0.000
147	A	151	VAL	0	0.005	0.002	25.640	0.019	0.019	0.000	0.000	0.000	0.000
148	A	152	SER	0	-0.031	-0.013	25.933	-0.023	-0.023	0.000	0.000	0.000	0.000
149	A	153	TYR	0	0.022	0.017	23.188	0.004	0.004	0.000	0.000	0.000	0.000
150	A	154	ILE	0	-0.016	-0.023	24.901	0.006	0.006	0.000	0.000	0.000	0.000
151	A	155	LEU	0	-0.044	-0.005	20.658	-0.005	-0.005	0.000	0.000	0.000	0.000
152	A	156	VAL	0	-0.027	-0.019	24.762	0.023	0.023	0.000	0.000	0.000	0.000

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