FMO DATABASE

FMODB ID: 391VL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1068829.040286
FMO2-HF: Nuclear repulsion	1018845.432713
FMO2-HF: Total energy	-49983.607573
FMO2-MP2: Total energy	-50129.393407

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.
-7.368	-6.322	9.138	-3.826	-6.358	-0.019

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 : -0.026

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	6	GLY	0	-0.033	-0.003	3.811	0.885	2.862	-0.024	-1.085	-0.869	0.002
4	A	7	PHE	0	0.000	-0.010	6.892	-0.513	-0.513	0.000	0.000	0.000	0.000
5	A	8	GLU	-1	-0.825	-0.888	8.176	1.074	1.074	0.000	0.000	0.000	0.000
6	A	9	LEU	0	-0.005	0.000	11.429	-0.125	-0.125	0.000	0.000	0.000	0.000
7	A	10	ILE	0	-0.054	-0.024	14.732	0.019	0.019	0.000	0.000	0.000	0.000
8	A	11	THR	0	-0.038	-0.057	16.711	0.011	0.011	0.000	0.000	0.000	0.000
9	A	12	ASP	-1	-0.920	-0.949	18.969	0.090	0.090	0.000	0.000	0.000	0.000
10	A	13	TYR	0	-0.092	-0.045	19.898	-0.014	-0.014	0.000	0.000	0.000	0.000
11	A	14	THR	0	0.011	-0.012	19.524	0.021	0.021	0.000	0.000	0.000	0.000
12	A	15	ASP	-1	-0.857	-0.922	20.816	0.205	0.205	0.000	0.000	0.000	0.000
13	A	16	GLU	-1	-0.885	-0.959	16.645	0.465	0.465	0.000	0.000	0.000	0.000
14	A	17	ASN	0	-0.087	-0.034	17.988	0.028	0.028	0.000	0.000	0.000	0.000
15	A	18	LEU	0	-0.053	-0.037	18.792	-0.022	-0.022	0.000	0.000	0.000	0.000
16	A	19	LEU	0	-0.011	0.012	12.562	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	20	PRO	0	-0.015	0.004	13.281	-0.015	-0.015	0.000	0.000	0.000	0.000
18	A	21	LYS	1	0.966	0.981	13.233	-0.096	-0.096	0.000	0.000	0.000	0.000
19	A	22	ARG	1	0.870	0.932	11.956	0.065	0.065	0.000	0.000	0.000	0.000
20	A	23	GLU	-1	-0.907	-0.938	15.648	0.019	0.019	0.000	0.000	0.000	0.000
21	A	24	THR	0	-0.003	-0.011	18.211	0.004	0.004	0.000	0.000	0.000	0.000
22	A	25	ALA	0	0.029	-0.001	16.219	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	26	HIS	0	-0.003	-0.007	15.296	-0.047	-0.047	0.000	0.000	0.000	0.000
24	A	27	ALA	0	-0.024	0.016	16.551	-0.030	-0.030	0.000	0.000	0.000	0.000
25	A	28	ALA	0	0.051	0.018	13.708	-0.017	-0.017	0.000	0.000	0.000	0.000
26	A	29	GLY	0	-0.017	0.003	12.900	-0.054	-0.054	0.000	0.000	0.000	0.000
27	A	30	TYR	0	-0.025	-0.019	8.830	0.125	0.125	0.000	0.000	0.000	0.000
28	A	31	ASP	-1	-0.879	-0.955	14.437	-0.047	-0.047	0.000	0.000	0.000	0.000
29	A	32	LEU	0	0.012	0.009	15.018	0.039	0.039	0.000	0.000	0.000	0.000
30	A	33	LYS	1	0.879	0.933	18.356	-0.155	-0.155	0.000	0.000	0.000	0.000
31	A	34	VAL	0	-0.007	0.014	21.494	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	35	ALA	0	0.024	0.006	22.044	0.014	0.014	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.890	-0.955	23.692	0.059	0.059	0.000	0.000	0.000	0.000
34	A	37	ARG	1	0.865	0.940	27.374	-0.047	-0.047	0.000	0.000	0.000	0.000
35	A	38	THR	0	0.003	-0.004	28.766	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	39	GLU	-1	-0.944	-0.966	31.203	0.006	0.006	0.000	0.000	0.000	0.000
37	A	40	ILE	0	-0.022	-0.014	30.628	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	41	SER	0	0.042	0.013	35.135	0.001	0.001	0.000	0.000	0.000	0.000
39	A	42	ALA	0	0.043	0.026	37.830	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	43	GLY	0	-0.009	0.002	38.552	0.000	0.000	0.000	0.000	0.000	0.000
41	A	44	ALA	0	-0.041	-0.013	36.443	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	45	ILE	0	-0.017	-0.024	30.660	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	46	VAL	0	0.027	0.010	29.848	0.002	0.002	0.000	0.000	0.000	0.000
44	A	47	LEU	0	-0.041	-0.017	25.419	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	48	VAL	0	-0.008	-0.012	25.299	0.009	0.009	0.000	0.000	0.000	0.000
46	A	49	PRO	0	0.046	0.042	22.985	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	50	THR	0	-0.024	-0.014	18.056	0.002	0.002	0.000	0.000	0.000	0.000
48	A	51	GLY	0	0.019	0.006	19.408	0.023	0.023	0.000	0.000	0.000	0.000
49	A	52	VAL	0	-0.048	-0.007	14.020	0.039	0.039	0.000	0.000	0.000	0.000
50	A	53	LYS	1	0.847	0.924	11.528	-0.295	-0.295	0.000	0.000	0.000	0.000
51	A	54	ALA	0	-0.018	-0.029	9.838	0.132	0.132	0.000	0.000	0.000	0.000
52	A	55	TYR	0	0.034	0.046	2.675	-3.404	-2.216	0.540	-0.596	-1.132	0.003
53	A	56	MET	0	-0.042	-0.032	4.685	-0.183	-0.111	-0.001	-0.017	-0.054	0.000
54	A	57	GLN	0	0.001	0.003	2.259	-1.102	-3.556	8.624	-2.066	-4.104	-0.024
55	A	58	VAL	0	0.033	0.009	5.009	0.386	0.441	-0.001	-0.007	-0.047	0.000
56	A	59	GLY	0	0.006	0.003	7.867	-0.115	-0.115	0.000	0.000	0.000	0.000
57	A	60	GLU	-1	-0.808	-0.875	4.236	-4.339	-4.131	0.000	-0.055	-0.152	0.000
58	A	61	VAL	0	0.030	0.011	8.433	0.097	0.097	0.000	0.000	0.000	0.000
59	A	62	LEU	0	-0.017	0.003	10.451	-0.059	-0.059	0.000	0.000	0.000	0.000
60	A	63	TYR	0	0.011	0.000	11.896	0.079	0.079	0.000	0.000	0.000	0.000
61	A	64	LEU	0	-0.018	-0.002	15.296	0.019	0.019	0.000	0.000	0.000	0.000
62	A	65	PHE	0	0.038	0.008	16.417	0.005	0.005	0.000	0.000	0.000	0.000
63	A	66	ASP	-1	-0.679	-0.846	20.384	-0.066	-0.066	0.000	0.000	0.000	0.000
64	A	67	ARG	1	0.909	0.972	22.349	0.021	0.021	0.000	0.000	0.000	0.000
65	A	68	SER	0	0.000	-0.002	24.187	0.007	0.007	0.000	0.000	0.000	0.000
66	A	69	SER	0	-0.056	-0.050	26.739	0.003	0.003	0.000	0.000	0.000	0.000
67	A	70	ASN	0	-0.018	-0.010	25.525	0.017	0.017	0.000	0.000	0.000	0.000
68	A	71	PRO	0	0.092	0.048	28.766	0.007	0.007	0.000	0.000	0.000	0.000
69	A	72	ARG	1	0.943	0.961	31.844	0.050	0.050	0.000	0.000	0.000	0.000
70	A	73	LYS	1	0.833	0.910	32.042	0.020	0.020	0.000	0.000	0.000	0.000
71	A	74	LYS	1	0.972	0.992	28.914	0.012	0.012	0.000	0.000	0.000	0.000
72	A	75	GLY	0	0.055	0.056	33.602	0.003	0.003	0.000	0.000	0.000	0.000
73	A	76	LEU	0	-0.019	-0.011	30.130	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	77	VAL	0	-0.006	-0.014	29.061	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	78	LEU	0	0.013	0.000	22.236	0.007	0.007	0.000	0.000	0.000	0.000
76	A	79	ILE	0	-0.034	-0.014	26.727	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	80	ASN	0	0.028	0.004	22.919	0.013	0.013	0.000	0.000	0.000	0.000
78	A	81	SER	0	-0.050	-0.013	25.144	-0.015	-0.015	0.000	0.000	0.000	0.000
79	A	82	VAL	0	-0.022	-0.029	19.340	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	83	GLY	0	-0.057	-0.009	19.678	0.006	0.006	0.000	0.000	0.000	0.000
81	A	84	VAL	0	0.009	-0.010	16.474	-0.028	-0.028	0.000	0.000	0.000	0.000
82	A	85	ILE	0	-0.020	-0.005	13.303	0.036	0.036	0.000	0.000	0.000	0.000
83	A	86	ASP	-1	-0.836	-0.920	12.931	-0.496	-0.496	0.000	0.000	0.000	0.000
84	A	87	GLY	0	0.000	-0.022	10.278	0.012	0.012	0.000	0.000	0.000	0.000
85	A	88	ASP	-1	-0.943	-0.974	10.929	-0.397	-0.397	0.000	0.000	0.000	0.000
86	A	89	TYR	0	-0.025	0.005	13.585	0.092	0.092	0.000	0.000	0.000	0.000
87	A	90	TYR	0	-0.077	-0.075	8.623	0.006	0.006	0.000	0.000	0.000	0.000
88	A	91	ASN	0	0.022	0.015	11.358	0.021	0.021	0.000	0.000	0.000	0.000
89	A	92	ASN	0	-0.022	0.008	14.299	0.037	0.037	0.000	0.000	0.000	0.000
90	A	93	PRO	0	0.024	-0.013	17.362	0.026	0.026	0.000	0.000	0.000	0.000
91	A	94	ASN	0	-0.054	-0.016	20.433	0.021	0.021	0.000	0.000	0.000	0.000
92	A	95	ASN	0	0.016	-0.009	19.552	0.005	0.005	0.000	0.000	0.000	0.000
93	A	96	GLU	-1	-0.730	-0.829	15.562	0.164	0.164	0.000	0.000	0.000	0.000
94	A	97	GLY	0	0.019	0.006	15.044	0.005	0.005	0.000	0.000	0.000	0.000
95	A	98	HIS	0	-0.012	0.002	15.686	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	99	ILE	0	-0.013	-0.003	13.938	-0.034	-0.034	0.000	0.000	0.000	0.000
97	A	100	PHE	0	0.024	0.005	18.288	0.029	0.029	0.000	0.000	0.000	0.000
98	A	101	ALA	0	-0.026	-0.008	21.605	-0.026	-0.026	0.000	0.000	0.000	0.000
99	A	102	GLN	0	0.004	0.003	23.417	0.020	0.020	0.000	0.000	0.000	0.000
100	A	103	MET	0	0.005	0.016	26.212	-0.011	-0.011	0.000	0.000	0.000	0.000
101	A	104	LYS	1	0.946	0.974	28.818	0.060	0.060	0.000	0.000	0.000	0.000
102	A	105	ASN	0	-0.020	0.002	32.382	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	106	MET	0	-0.091	-0.049	33.780	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	107	THR	0	-0.043	-0.023	36.959	0.001	0.001	0.000	0.000	0.000	0.000
105	A	108	ASP	-1	-0.898	-0.958	39.661	-0.020	-0.020	0.000	0.000	0.000	0.000
106	A	109	GLN	0	-0.020	-0.013	41.185	0.005	0.005	0.000	0.000	0.000	0.000
107	A	110	THR	0	-0.004	-0.005	38.207	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	111	VAL	0	-0.021	0.006	33.688	0.002	0.002	0.000	0.000	0.000	0.000
109	A	112	VAL	0	-0.005	-0.006	33.972	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	113	LEU	0	-0.049	-0.012	27.939	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	114	GLU	-1	-0.834	-0.926	30.625	0.038	0.038	0.000	0.000	0.000	0.000
112	A	115	ALA	0	0.034	0.014	26.936	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	116	GLY	0	-0.012	-0.008	24.178	0.004	0.004	0.000	0.000	0.000	0.000
114	A	117	GLU	-1	-0.955	-0.984	24.554	0.018	0.018	0.000	0.000	0.000	0.000
115	A	118	ARG	1	0.786	0.889	21.625	-0.021	-0.021	0.000	0.000	0.000	0.000
116	A	119	VAL	0	0.018	0.006	22.374	-0.009	-0.009	0.000	0.000	0.000	0.000
117	A	120	VAL	0	0.003	0.008	18.986	-0.013	-0.013	0.000	0.000	0.000	0.000
118	A	121	GLN	0	-0.062	-0.028	17.451	0.019	0.019	0.000	0.000	0.000	0.000
119	A	122	GLY	0	0.030	0.010	14.211	-0.022	-0.022	0.000	0.000	0.000	0.000
120	A	123	VAL	0	-0.011	-0.014	12.163	0.024	0.024	0.000	0.000	0.000	0.000
121	A	124	PHE	0	0.027	0.019	7.409	-0.027	-0.027	0.000	0.000	0.000	0.000
122	A	125	MET	0	-0.057	-0.027	9.456	0.047	0.047	0.000	0.000	0.000	0.000
123	A	126	PRO	0	0.029	0.026	9.805	-0.100	-0.100	0.000	0.000	0.000	0.000
124	A	127	PHE	0	-0.037	-0.017	10.631	0.139	0.139	0.000	0.000	0.000	0.000
125	A	128	LEU	0	-0.023	-0.018	13.177	-0.038	-0.038	0.000	0.000	0.000	0.000
126	A	129	LEU	0	0.004	0.000	15.511	0.018	0.018	0.000	0.000	0.000	0.000
127	A	130	ILE	0	-0.017	-0.008	18.090	0.013	0.013	0.000	0.000	0.000	0.000
128	A	131	ASP	-1	-0.912	-0.945	21.663	-0.226	-0.226	0.000	0.000	0.000	0.000
129	A	132	GLY	0	-0.043	-0.023	22.513	0.003	0.003	0.000	0.000	0.000	0.000

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