FMO DATABASE

FMODB ID: JL599

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1441499.433555
FMO2-HF: Nuclear repulsion	1380707.462158
FMO2-HF: Total energy	-60791.971397
FMO2-MP2: Total energy	-60964.422277

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.
-38.093	-38.5	18.825	-9.807	-8.612	-0.093

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 : 0.011 / 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	7	ASN	0	-0.003	-0.021	3.282	-1.286	0.713	0.036	-0.921	-1.114	0.003
4	A	8	GLU	-1	-0.840	-0.896	1.700	-39.602	-42.510	18.787	-8.793	-7.087	-0.096
5	A	9	GLU	-1	-0.842	-0.925	3.873	1.252	1.754	0.002	-0.093	-0.411	0.000
6	A	10	VAL	0	-0.057	-0.016	5.799	0.724	0.724	0.000	0.000	0.000	0.000
7	A	11	LEU	0	-0.005	0.003	7.404	0.453	0.453	0.000	0.000	0.000	0.000
8	A	12	PHE	0	0.024	0.012	7.857	0.391	0.391	0.000	0.000	0.000	0.000
9	A	13	SER	0	-0.012	-0.018	9.587	0.399	0.399	0.000	0.000	0.000	0.000
10	A	14	ALA	0	-0.020	-0.010	11.660	0.163	0.163	0.000	0.000	0.000	0.000
11	A	15	VAL	0	-0.006	-0.004	12.621	0.134	0.134	0.000	0.000	0.000	0.000
12	A	16	ASN	0	0.029	-0.004	12.100	0.085	0.085	0.000	0.000	0.000	0.000
13	A	17	GLU	-1	-0.766	-0.866	15.406	-0.236	-0.236	0.000	0.000	0.000	0.000
14	A	18	ILE	0	-0.061	-0.033	16.550	0.062	0.062	0.000	0.000	0.000	0.000
15	A	19	PHE	0	-0.021	-0.028	17.753	0.039	0.039	0.000	0.000	0.000	0.000
16	A	20	GLU	-1	-0.818	-0.891	17.558	-0.424	-0.424	0.000	0.000	0.000	0.000
17	A	21	GLU	-1	-0.898	-0.939	20.314	-0.230	-0.230	0.000	0.000	0.000	0.000
18	A	22	LYS	1	0.751	0.857	21.590	0.326	0.326	0.000	0.000	0.000	0.000
19	A	23	ILE	0	0.002	0.029	22.585	0.023	0.023	0.000	0.000	0.000	0.000
20	A	24	PRO	0	0.014	-0.002	25.510	0.013	0.013	0.000	0.000	0.000	0.000
21	A	25	PHE	0	0.008	-0.019	28.476	0.018	0.018	0.000	0.000	0.000	0.000
22	A	26	ASN	0	0.086	0.054	23.726	0.011	0.011	0.000	0.000	0.000	0.000
23	A	27	LYS	1	0.920	0.960	27.777	0.162	0.162	0.000	0.000	0.000	0.000
24	A	28	ILE	0	-0.053	-0.021	31.157	0.014	0.014	0.000	0.000	0.000	0.000
25	A	29	ILE	0	-0.004	-0.013	28.387	0.007	0.007	0.000	0.000	0.000	0.000
26	A	30	GLY	0	-0.014	0.014	26.615	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	31	LEU	0	-0.007	-0.004	20.395	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	32	LYS	1	0.820	0.893	19.614	0.329	0.329	0.000	0.000	0.000	0.000
29	A	33	VAL	0	0.034	0.021	13.981	0.003	0.003	0.000	0.000	0.000	0.000
30	A	34	ARG	1	0.804	0.900	15.964	0.499	0.499	0.000	0.000	0.000	0.000
31	A	35	PHE	0	0.032	0.009	10.686	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	36	ILE	0	-0.005	-0.007	9.155	0.156	0.156	0.000	0.000	0.000	0.000
33	A	37	SER	0	0.036	0.016	10.070	-0.308	-0.308	0.000	0.000	0.000	0.000
34	A	38	PRO	0	-0.017	-0.012	9.450	0.251	0.251	0.000	0.000	0.000	0.000
35	A	39	GLU	-1	-0.880	-0.942	12.488	-1.145	-1.145	0.000	0.000	0.000	0.000
36	A	40	GLN	0	-0.051	-0.023	14.394	0.210	0.210	0.000	0.000	0.000	0.000
37	A	41	VAL	0	-0.009	0.018	14.313	-0.185	-0.185	0.000	0.000	0.000	0.000
38	A	42	LYS	1	0.937	0.967	16.039	0.564	0.564	0.000	0.000	0.000	0.000
39	A	43	LEU	0	0.013	0.021	17.183	-0.054	-0.054	0.000	0.000	0.000	0.000
40	A	44	SER	0	-0.030	-0.029	19.872	0.040	0.040	0.000	0.000	0.000	0.000
41	A	45	PHE	0	0.007	-0.003	22.469	-0.017	-0.017	0.000	0.000	0.000	0.000
42	A	46	GLU	-1	-0.760	-0.850	25.608	-0.172	-0.172	0.000	0.000	0.000	0.000
43	A	47	MET	0	-0.031	-0.008	28.555	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	48	ARG	1	0.796	0.888	27.039	0.207	0.207	0.000	0.000	0.000	0.000
45	A	49	ASP	-1	-0.816	-0.911	33.089	-0.113	-0.113	0.000	0.000	0.000	0.000
46	A	50	GLU	-1	-0.840	-0.908	35.431	-0.144	-0.144	0.000	0.000	0.000	0.000
47	A	51	LEU	0	-0.032	-0.012	37.259	0.000	0.000	0.000	0.000	0.000	0.000
48	A	52	ILE	0	0.039	0.007	39.909	0.003	0.003	0.000	0.000	0.000	0.000
49	A	53	GLY	0	-0.002	0.002	42.742	0.003	0.003	0.000	0.000	0.000	0.000
50	A	54	ASN	0	-0.005	0.006	43.335	0.004	0.004	0.000	0.000	0.000	0.000
51	A	55	ALA	0	0.034	0.008	45.380	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	56	ILE	0	0.005	0.006	43.880	0.000	0.000	0.000	0.000	0.000	0.000
53	A	57	ARG	1	0.858	0.927	37.831	0.127	0.127	0.000	0.000	0.000	0.000
54	A	58	ARG	1	0.963	0.966	40.092	0.108	0.108	0.000	0.000	0.000	0.000
55	A	59	MET	0	0.016	0.019	39.853	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	60	LEU	0	0.009	0.004	38.703	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	61	TYR	0	0.003	-0.009	35.179	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	62	GLY	0	0.032	0.030	34.904	-0.012	-0.012	0.000	0.000	0.000	0.000
59	A	63	GLY	0	0.040	0.034	35.013	-0.012	-0.012	0.000	0.000	0.000	0.000
60	A	64	VAL	0	0.002	0.010	31.119	-0.015	-0.015	0.000	0.000	0.000	0.000
61	A	65	ILE	0	0.033	0.010	30.656	-0.019	-0.019	0.000	0.000	0.000	0.000
62	A	66	SER	0	-0.039	-0.015	29.943	-0.019	-0.019	0.000	0.000	0.000	0.000
63	A	67	SER	0	0.005	-0.011	29.749	-0.016	-0.016	0.000	0.000	0.000	0.000
64	A	68	ALA	0	0.000	0.010	26.384	-0.024	-0.024	0.000	0.000	0.000	0.000
65	A	69	ILE	0	0.024	0.022	25.133	-0.044	-0.044	0.000	0.000	0.000	0.000
66	A	70	ASP	-1	-0.794	-0.872	25.243	-0.376	-0.376	0.000	0.000	0.000	0.000
67	A	71	MET	0	-0.006	0.000	22.576	-0.027	-0.027	0.000	0.000	0.000	0.000
68	A	72	THR	0	0.010	-0.017	20.493	-0.059	-0.059	0.000	0.000	0.000	0.000
69	A	73	ALA	0	-0.001	-0.010	20.502	-0.066	-0.066	0.000	0.000	0.000	0.000
70	A	74	GLY	0	0.043	0.021	21.348	-0.034	-0.034	0.000	0.000	0.000	0.000
71	A	75	LEU	0	-0.001	0.003	14.762	-0.048	-0.048	0.000	0.000	0.000	0.000
72	A	76	ALA	0	0.033	0.012	16.547	-0.113	-0.113	0.000	0.000	0.000	0.000
73	A	77	ALA	0	-0.020	-0.004	17.405	-0.045	-0.045	0.000	0.000	0.000	0.000
74	A	78	PHE	0	0.000	-0.012	12.737	-0.015	-0.015	0.000	0.000	0.000	0.000
75	A	79	MET	0	0.019	0.020	11.188	-0.141	-0.141	0.000	0.000	0.000	0.000
76	A	80	GLY	0	0.067	0.039	13.106	-0.101	-0.101	0.000	0.000	0.000	0.000
77	A	81	PHE	0	-0.051	-0.054	15.732	0.067	0.067	0.000	0.000	0.000	0.000
78	A	82	GLN	0	-0.003	-0.017	9.699	0.034	0.034	0.000	0.000	0.000	0.000
79	A	83	GLU	-1	-0.866	-0.915	9.643	-1.823	-1.823	0.000	0.000	0.000	0.000
80	A	84	LYS	1	0.840	0.918	12.259	0.658	0.658	0.000	0.000	0.000	0.000
81	A	85	MET	0	-0.085	-0.017	13.940	0.096	0.096	0.000	0.000	0.000	0.000
82	A	86	SER	0	0.006	0.002	11.256	-0.033	-0.033	0.000	0.000	0.000	0.000
83	A	87	GLY	0	0.010	0.007	10.795	-0.028	-0.028	0.000	0.000	0.000	0.000
84	A	88	LYS	1	0.770	0.871	12.927	0.383	0.383	0.000	0.000	0.000	0.000
85	A	89	PRO	0	0.018	0.000	11.973	-0.114	-0.114	0.000	0.000	0.000	0.000
86	A	90	MET	0	0.039	0.014	8.948	-0.037	-0.037	0.000	0.000	0.000	0.000
87	A	91	GLU	-1	-0.867	-0.925	11.680	-0.423	-0.423	0.000	0.000	0.000	0.000
88	A	92	GLU	-1	-0.810	-0.896	15.416	-0.316	-0.316	0.000	0.000	0.000	0.000
89	A	93	LYS	1	0.834	0.915	9.470	1.268	1.268	0.000	0.000	0.000	0.000
90	A	94	LEU	0	0.038	0.012	12.677	-0.021	-0.021	0.000	0.000	0.000	0.000
91	A	95	ALA	0	0.019	0.005	15.703	0.041	0.041	0.000	0.000	0.000	0.000
92	A	96	MET	0	-0.150	-0.060	15.874	0.072	0.072	0.000	0.000	0.000	0.000
93	A	97	ILE	0	0.051	0.023	16.903	0.034	0.034	0.000	0.000	0.000	0.000
94	A	98	GLY	0	-0.001	0.006	19.429	0.030	0.030	0.000	0.000	0.000	0.000
95	A	99	ARG	1	0.898	0.958	20.216	0.414	0.414	0.000	0.000	0.000	0.000
96	A	100	LEU	0	-0.040	-0.003	19.077	0.013	0.013	0.000	0.000	0.000	0.000
97	A	101	SER	0	0.000	0.006	23.617	0.021	0.021	0.000	0.000	0.000	0.000
98	A	102	THR	0	-0.020	-0.022	26.910	-0.014	-0.014	0.000	0.000	0.000	0.000
99	A	103	MET	0	-0.086	-0.037	28.275	0.014	0.014	0.000	0.000	0.000	0.000
100	A	104	SER	0	-0.011	-0.015	30.075	0.023	0.023	0.000	0.000	0.000	0.000
101	A	105	LEU	0	0.047	0.021	29.518	-0.026	-0.026	0.000	0.000	0.000	0.000
102	A	106	HIS	0	-0.071	-0.020	31.742	0.022	0.022	0.000	0.000	0.000	0.000
103	A	107	VAL	0	0.036	0.003	31.300	-0.022	-0.022	0.000	0.000	0.000	0.000
104	A	108	GLU	-1	-0.908	-0.945	33.378	-0.187	-0.187	0.000	0.000	0.000	0.000
105	A	109	TYR	0	-0.055	-0.056	34.424	-0.008	-0.008	0.000	0.000	0.000	0.000
106	A	110	LEU	0	-0.010	-0.004	34.006	0.010	0.010	0.000	0.000	0.000	0.000
107	A	111	ARG	1	0.818	0.894	35.137	0.180	0.180	0.000	0.000	0.000	0.000
108	A	112	PRO	0	-0.040	-0.015	36.667	-0.008	-0.008	0.000	0.000	0.000	0.000
109	A	113	GLY	0	0.059	0.002	34.461	0.004	0.004	0.000	0.000	0.000	0.000
110	A	114	LEU	0	-0.099	-0.048	35.298	0.003	0.003	0.000	0.000	0.000	0.000
111	A	115	GLY	0	0.051	0.046	34.302	0.011	0.011	0.000	0.000	0.000	0.000
112	A	116	ARG	1	0.776	0.880	31.723	0.148	0.148	0.000	0.000	0.000	0.000
113	A	117	GLU	-1	-0.950	-0.980	27.132	-0.211	-0.211	0.000	0.000	0.000	0.000
114	A	118	PHE	0	-0.023	-0.015	27.485	0.004	0.004	0.000	0.000	0.000	0.000
115	A	119	VAL	0	-0.006	-0.012	22.098	-0.027	-0.027	0.000	0.000	0.000	0.000
116	A	120	CYS	0	-0.051	-0.016	22.863	0.027	0.027	0.000	0.000	0.000	0.000
117	A	121	THR	0	0.006	0.007	19.375	-0.052	-0.052	0.000	0.000	0.000	0.000
118	A	122	GLY	0	0.044	0.012	19.825	0.057	0.057	0.000	0.000	0.000	0.000
119	A	123	TYR	0	-0.048	-0.047	19.079	-0.102	-0.102	0.000	0.000	0.000	0.000
120	A	124	ASN	0	-0.023	-0.014	17.892	0.132	0.132	0.000	0.000	0.000	0.000
121	A	125	VAL	0	-0.001	0.008	19.870	0.000	0.000	0.000	0.000	0.000	0.000
122	A	126	ARG	1	0.961	0.977	21.545	0.332	0.332	0.000	0.000	0.000	0.000
123	A	127	THR	0	0.022	0.014	18.906	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	128	GLY	0	-0.015	-0.003	21.125	0.004	0.004	0.000	0.000	0.000	0.000
125	A	129	ASN	0	0.010	-0.006	22.041	-0.034	-0.034	0.000	0.000	0.000	0.000
126	A	130	LYS	1	0.925	0.939	23.468	0.293	0.293	0.000	0.000	0.000	0.000
127	A	131	VAL	0	0.030	0.027	24.668	0.004	0.004	0.000	0.000	0.000	0.000
128	A	132	ALA	0	0.009	0.016	21.296	-0.015	-0.015	0.000	0.000	0.000	0.000
129	A	133	VAL	0	-0.031	-0.018	23.145	0.032	0.032	0.000	0.000	0.000	0.000
130	A	134	ILE	0	-0.025	-0.010	21.599	-0.029	-0.029	0.000	0.000	0.000	0.000
131	A	135	ARG	1	0.856	0.933	23.743	0.351	0.351	0.000	0.000	0.000	0.000
132	A	136	THR	0	0.005	-0.017	23.656	-0.039	-0.039	0.000	0.000	0.000	0.000
133	A	137	GLU	-1	-0.789	-0.855	24.920	-0.322	-0.322	0.000	0.000	0.000	0.000
134	A	138	LEU	0	0.021	0.008	25.259	-0.028	-0.028	0.000	0.000	0.000	0.000
135	A	139	MET	0	0.004	-0.001	24.431	0.028	0.028	0.000	0.000	0.000	0.000
136	A	140	ASN	0	-0.006	-0.012	28.245	-0.018	-0.018	0.000	0.000	0.000	0.000
137	A	141	ASP	-1	-0.766	-0.899	29.043	-0.192	-0.192	0.000	0.000	0.000	0.000
138	A	142	GLN	0	-0.133	-0.073	30.127	0.013	0.013	0.000	0.000	0.000	0.000
139	A	143	ASP	-1	-0.921	-0.953	26.164	-0.274	-0.274	0.000	0.000	0.000	0.000
140	A	144	GLU	-1	-0.812	-0.864	28.909	-0.158	-0.158	0.000	0.000	0.000	0.000
141	A	145	LEU	0	-0.022	-0.015	28.901	-0.005	-0.005	0.000	0.000	0.000	0.000
142	A	146	ILE	0	-0.043	-0.019	31.182	0.020	0.020	0.000	0.000	0.000	0.000
143	A	147	ALA	0	-0.005	0.000	31.375	0.013	0.013	0.000	0.000	0.000	0.000
144	A	148	VAL	0	0.008	0.014	29.488	-0.018	-0.018	0.000	0.000	0.000	0.000
145	A	149	GLY	0	0.040	0.016	28.952	0.017	0.017	0.000	0.000	0.000	0.000
146	A	150	SER	0	-0.062	-0.021	28.492	-0.019	-0.019	0.000	0.000	0.000	0.000
147	A	151	VAL	0	0.018	0.016	26.162	0.020	0.020	0.000	0.000	0.000	0.000
148	A	152	SER	0	-0.066	-0.038	26.455	-0.010	-0.010	0.000	0.000	0.000	0.000
149	A	153	TYR	0	0.027	-0.004	23.647	0.001	0.001	0.000	0.000	0.000	0.000
150	A	154	ILE	0	-0.018	-0.019	25.428	-0.001	-0.001	0.000	0.000	0.000	0.000
151	A	155	LEU	0	-0.039	-0.005	20.550	-0.010	-0.010	0.000	0.000	0.000	0.000
152	A	156	VAL	0	-0.010	-0.008	24.799	0.021	0.021	0.000	0.000	0.000	0.000

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