FMO DATABASE

FMODB ID: LZK39

Calculation Name: 3H6X-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: 3H6X

Chain ID: A

ChEMBL ID:
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UniProt ID: Q8DVY3

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	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	129
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1069317.002144
FMO2-HF: Nuclear repulsion	1019332.843143
FMO2-HF: Total energy	-49984.159001
FMO2-MP2: Total energy	-50129.938202

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:4:THR)

Summations of interaction energy for fragment #1(A:4:THR)

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.
-6.885	-3.053	3.749	-2.757	-4.825	-0.012

Interaction energy analysis for fragmet #1(A:4:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.049 / q_NPA : -0.032

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	6	GLY	0	-0.031	-0.002	3.811	1.090	2.939	-0.025	-0.993	-0.832	0.000
4	A	7	PHE	0	0.001	-0.011	6.791	-0.380	-0.380	0.000	0.000	0.000	0.000
5	A	8	GLU	-1	-0.811	-0.879	8.505	-0.469	-0.469	0.000	0.000	0.000	0.000
6	A	9	LEU	0	-0.002	-0.001	11.187	-0.040	-0.040	0.000	0.000	0.000	0.000
7	A	10	ILE	0	-0.055	-0.017	14.517	-0.036	-0.036	0.000	0.000	0.000	0.000
8	A	11	THR	0	-0.028	-0.050	16.490	0.043	0.043	0.000	0.000	0.000	0.000
9	A	12	ASP	-1	-0.942	-0.960	18.778	-0.158	-0.158	0.000	0.000	0.000	0.000
10	A	13	TYR	0	-0.117	-0.090	19.689	0.013	0.013	0.000	0.000	0.000	0.000
11	A	14	THR	0	0.011	-0.011	19.306	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	15	ASP	-1	-0.852	-0.924	20.604	-0.011	-0.011	0.000	0.000	0.000	0.000
13	A	16	GLU	-1	-0.881	-0.954	16.415	0.032	0.032	0.000	0.000	0.000	0.000
14	A	17	ASN	0	-0.064	-0.019	17.885	0.023	0.023	0.000	0.000	0.000	0.000
15	A	18	LEU	0	-0.021	-0.013	18.580	0.005	0.005	0.000	0.000	0.000	0.000
16	A	19	LEU	0	-0.006	0.015	12.547	-0.033	-0.033	0.000	0.000	0.000	0.000
17	A	20	PRO	0	-0.016	0.004	13.220	0.040	0.040	0.000	0.000	0.000	0.000
18	A	21	LYS	1	0.971	0.983	13.167	-0.036	-0.036	0.000	0.000	0.000	0.000
19	A	22	ARG	1	0.841	0.910	11.990	-0.224	-0.224	0.000	0.000	0.000	0.000
20	A	23	GLU	-1	-0.855	-0.897	15.539	0.033	0.033	0.000	0.000	0.000	0.000
21	A	24	THR	0	0.009	-0.011	18.358	0.015	0.015	0.000	0.000	0.000	0.000
22	A	25	ALA	0	0.042	0.009	16.285	0.000	0.000	0.000	0.000	0.000	0.000
23	A	26	HIS	0	0.009	0.006	15.653	0.036	0.036	0.000	0.000	0.000	0.000
24	A	27	ALA	0	-0.023	0.016	16.864	-0.020	-0.020	0.000	0.000	0.000	0.000
25	A	28	ALA	0	0.060	0.026	14.527	0.023	0.023	0.000	0.000	0.000	0.000
26	A	29	GLY	0	-0.009	0.006	13.614	-0.038	-0.038	0.000	0.000	0.000	0.000
27	A	30	TYR	0	-0.035	-0.029	8.866	0.091	0.091	0.000	0.000	0.000	0.000
28	A	31	ASP	-1	-0.775	-0.868	14.474	-0.079	-0.079	0.000	0.000	0.000	0.000
29	A	32	LEU	0	0.001	0.009	14.777	0.013	0.013	0.000	0.000	0.000	0.000
30	A	33	LYS	1	0.842	0.907	18.212	0.032	0.032	0.000	0.000	0.000	0.000
31	A	34	VAL	0	-0.005	0.018	21.377	-0.021	-0.021	0.000	0.000	0.000	0.000
32	A	35	ALA	0	0.026	0.011	21.853	0.015	0.015	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.845	-0.903	23.425	-0.102	-0.102	0.000	0.000	0.000	0.000
34	A	37	ARG	1	0.792	0.867	27.109	0.046	0.046	0.000	0.000	0.000	0.000
35	A	38	THR	0	-0.004	-0.008	28.462	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	39	GLU	-1	-0.939	-0.965	30.931	-0.056	-0.056	0.000	0.000	0.000	0.000
37	A	40	ILE	0	-0.014	-0.012	30.505	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	41	SER	0	0.040	0.015	34.880	0.004	0.004	0.000	0.000	0.000	0.000
39	A	42	ALA	0	0.043	0.023	37.872	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	43	GLY	0	-0.002	0.006	38.591	0.000	0.000	0.000	0.000	0.000	0.000
41	A	44	ALA	0	-0.043	-0.016	36.424	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	45	ILE	0	-0.019	-0.025	30.813	0.000	0.000	0.000	0.000	0.000	0.000
43	A	46	VAL	0	0.022	0.009	29.696	0.000	0.000	0.000	0.000	0.000	0.000
44	A	47	LEU	0	-0.033	-0.012	25.139	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	48	VAL	0	-0.011	-0.013	25.204	0.005	0.005	0.000	0.000	0.000	0.000
46	A	49	PRO	0	0.055	0.049	22.719	-0.019	-0.019	0.000	0.000	0.000	0.000
47	A	50	THR	0	-0.032	-0.031	17.714	0.014	0.014	0.000	0.000	0.000	0.000
48	A	51	GLY	0	0.022	0.012	19.137	0.013	0.013	0.000	0.000	0.000	0.000
49	A	52	VAL	0	-0.047	-0.013	13.700	0.001	0.001	0.000	0.000	0.000	0.000
50	A	53	LYS	1	0.819	0.914	11.370	0.471	0.471	0.000	0.000	0.000	0.000
51	A	54	ALA	0	-0.016	-0.029	9.570	0.056	0.056	0.000	0.000	0.000	0.000
52	A	55	TYR	0	0.029	0.045	2.457	-2.470	-1.331	0.564	-0.583	-1.121	0.001
53	A	56	MET	0	-0.043	-0.031	4.973	-0.205	-0.205	0.000	0.000	0.000	0.000
54	A	57	GLN	0	-0.008	-0.003	2.533	-0.613	0.028	3.210	-1.117	-2.733	-0.013
55	A	58	VAL	0	0.033	0.006	5.408	0.428	0.428	0.000	0.000	0.000	0.000
56	A	59	GLY	0	0.009	0.008	8.095	0.040	0.040	0.000	0.000	0.000	0.000
57	A	60	GLU	-1	-0.811	-0.869	4.275	-3.151	-2.948	0.000	-0.064	-0.139	0.000
58	A	61	VAL	0	0.025	0.009	8.551	-0.025	-0.025	0.000	0.000	0.000	0.000
59	A	62	LEU	0	-0.021	0.001	10.455	0.014	0.014	0.000	0.000	0.000	0.000
60	A	63	TYR	0	0.020	0.009	11.937	0.052	0.052	0.000	0.000	0.000	0.000
61	A	64	LEU	0	-0.014	-0.002	15.382	0.020	0.020	0.000	0.000	0.000	0.000
62	A	65	PHE	0	0.030	0.003	16.530	0.017	0.017	0.000	0.000	0.000	0.000
63	A	66	ASP	-1	-0.683	-0.847	20.605	-0.100	-0.100	0.000	0.000	0.000	0.000
64	A	67	ARG	1	0.816	0.918	21.569	0.061	0.061	0.000	0.000	0.000	0.000
65	A	68	SER	0	-0.008	-0.009	24.585	0.005	0.005	0.000	0.000	0.000	0.000
66	A	69	SER	0	-0.030	-0.034	27.273	0.002	0.002	0.000	0.000	0.000	0.000
67	A	70	ASN	0	-0.050	-0.031	25.618	0.015	0.015	0.000	0.000	0.000	0.000
68	A	71	PRO	0	0.083	0.047	29.126	0.004	0.004	0.000	0.000	0.000	0.000
69	A	72	ARG	1	0.938	0.956	31.316	0.032	0.032	0.000	0.000	0.000	0.000
70	A	73	LYS	1	0.872	0.934	32.298	0.027	0.027	0.000	0.000	0.000	0.000
71	A	74	LYS	1	0.825	0.904	29.249	0.057	0.057	0.000	0.000	0.000	0.000
72	A	75	GLY	0	0.049	0.051	33.724	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	76	LEU	0	-0.026	-0.013	30.231	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	77	VAL	0	0.004	-0.011	29.287	0.003	0.003	0.000	0.000	0.000	0.000
75	A	78	LEU	0	0.009	0.001	22.193	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	79	ILE	0	-0.032	-0.016	26.791	0.002	0.002	0.000	0.000	0.000	0.000
77	A	80	ASN	0	0.011	0.000	22.761	0.013	0.013	0.000	0.000	0.000	0.000
78	A	81	SER	0	-0.056	-0.017	25.189	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	82	VAL	0	-0.023	-0.030	19.265	0.006	0.006	0.000	0.000	0.000	0.000
80	A	83	GLY	0	-0.048	-0.007	19.749	0.000	0.000	0.000	0.000	0.000	0.000
81	A	84	VAL	0	0.014	-0.007	16.608	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	85	ILE	0	-0.012	-0.003	13.477	0.017	0.017	0.000	0.000	0.000	0.000
83	A	86	ASP	-1	-0.840	-0.920	13.122	-0.610	-0.610	0.000	0.000	0.000	0.000
84	A	87	GLY	0	-0.002	-0.023	10.597	-0.052	-0.052	0.000	0.000	0.000	0.000
85	A	88	ASP	-1	-0.956	-0.980	11.091	-0.732	-0.732	0.000	0.000	0.000	0.000
86	A	89	TYR	0	-0.026	-0.009	13.590	0.102	0.102	0.000	0.000	0.000	0.000
87	A	90	TYR	0	-0.074	-0.074	8.786	-0.013	-0.013	0.000	0.000	0.000	0.000
88	A	91	ASN	0	0.011	0.010	11.054	0.058	0.058	0.000	0.000	0.000	0.000
89	A	92	ASN	0	-0.023	0.003	14.150	0.090	0.090	0.000	0.000	0.000	0.000
90	A	93	PRO	0	0.018	-0.017	17.222	0.022	0.022	0.000	0.000	0.000	0.000
91	A	94	ASN	0	-0.052	-0.014	20.305	0.034	0.034	0.000	0.000	0.000	0.000
92	A	95	ASN	0	0.022	-0.007	19.409	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	96	GLU	-1	-0.728	-0.826	15.401	-0.326	-0.326	0.000	0.000	0.000	0.000
94	A	97	GLY	0	0.032	0.016	14.839	-0.069	-0.069	0.000	0.000	0.000	0.000
95	A	98	HIS	0	-0.010	-0.001	15.453	-0.016	-0.016	0.000	0.000	0.000	0.000
96	A	99	ILE	0	-0.014	0.006	13.669	0.009	0.009	0.000	0.000	0.000	0.000
97	A	100	PHE	0	0.004	-0.001	18.033	0.036	0.036	0.000	0.000	0.000	0.000
98	A	101	ALA	0	-0.014	-0.004	21.642	-0.016	-0.016	0.000	0.000	0.000	0.000
99	A	102	GLN	0	0.008	0.007	23.499	0.026	0.026	0.000	0.000	0.000	0.000
100	A	103	MET	0	0.009	0.019	26.294	0.000	0.000	0.000	0.000	0.000	0.000
101	A	104	LYS	1	0.933	0.967	28.855	0.086	0.086	0.000	0.000	0.000	0.000
102	A	105	ASN	0	-0.016	0.000	32.419	0.005	0.005	0.000	0.000	0.000	0.000
103	A	106	MET	0	-0.088	-0.044	33.944	0.001	0.001	0.000	0.000	0.000	0.000
104	A	107	THR	0	-0.044	-0.023	37.098	0.005	0.005	0.000	0.000	0.000	0.000
105	A	108	ASP	-1	-0.866	-0.938	39.871	-0.044	-0.044	0.000	0.000	0.000	0.000
106	A	109	GLN	0	-0.056	-0.032	41.280	0.002	0.002	0.000	0.000	0.000	0.000
107	A	110	THR	0	-0.010	-0.008	38.061	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	111	VAL	0	-0.017	0.009	33.556	0.004	0.004	0.000	0.000	0.000	0.000
109	A	112	VAL	0	-0.003	-0.007	33.786	-0.005	-0.005	0.000	0.000	0.000	0.000
110	A	113	LEU	0	-0.038	-0.010	27.780	0.004	0.004	0.000	0.000	0.000	0.000
111	A	114	GLU	-1	-0.785	-0.867	30.504	-0.050	-0.050	0.000	0.000	0.000	0.000
112	A	115	ALA	0	0.045	0.017	26.713	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	116	GLY	0	-0.006	-0.005	24.107	0.010	0.010	0.000	0.000	0.000	0.000
114	A	117	GLU	-1	-0.843	-0.910	24.468	-0.042	-0.042	0.000	0.000	0.000	0.000
115	A	118	ARG	1	0.723	0.832	21.395	0.001	0.001	0.000	0.000	0.000	0.000
116	A	119	VAL	0	0.026	0.008	22.238	0.005	0.005	0.000	0.000	0.000	0.000
117	A	120	VAL	0	0.009	0.009	19.152	0.002	0.002	0.000	0.000	0.000	0.000
118	A	121	GLN	0	-0.079	-0.043	17.908	0.022	0.022	0.000	0.000	0.000	0.000
119	A	122	GLY	0	0.035	0.017	14.504	-0.017	-0.017	0.000	0.000	0.000	0.000
120	A	123	VAL	0	-0.014	-0.018	12.620	0.046	0.046	0.000	0.000	0.000	0.000
121	A	124	PHE	0	0.039	0.024	7.509	-0.033	-0.033	0.000	0.000	0.000	0.000
122	A	125	MET	0	-0.058	-0.028	9.631	0.151	0.151	0.000	0.000	0.000	0.000
123	A	126	PRO	0	0.025	0.020	9.693	-0.127	-0.127	0.000	0.000	0.000	0.000
124	A	127	PHE	0	-0.039	-0.016	10.549	0.087	0.087	0.000	0.000	0.000	0.000
125	A	128	LEU	0	-0.019	-0.014	13.229	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	129	LEU	0	-0.002	-0.003	15.523	-0.011	-0.011	0.000	0.000	0.000	0.000
127	A	130	ILE	0	-0.011	-0.004	18.234	0.025	0.025	0.000	0.000	0.000	0.000
128	A	131	ASP	-1	-0.920	-0.952	21.841	-0.116	-0.116	0.000	0.000	0.000	0.000
129	A	132	GLY	0	-0.038	-0.018	22.752	-0.008	-0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:THR)