FMO DATABASE

FMODB ID: 89N4Y

Calculation Name: 5D50-B-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: 5D50

Chain ID: B

ChEMBL ID:
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UniProt ID: T1S9Z0

Base Structure: X-ray

Registration Date: 2023-09-22

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	105
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-672979.367311
FMO2-HF: Nuclear repulsion	632010.399044
FMO2-HF: Total energy	-40968.968267
FMO2-MP2: Total energy	-41087.708329

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(B:67:LEU)

Summations of interaction energy for fragment #1(B:67: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.
-1.466	2.101	0.143	-1.535	-2.177	0.004

Interaction energy analysis for fragmet #1(B:67:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.016

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	B	69	VAL	0	-0.071	-0.043	2.763	-0.530	2.771	0.144	-1.510	-1.936	0.004
4	B	70	ASP	-1	-0.929	-0.956	4.339	-1.672	-1.406	-0.001	-0.025	-0.241	0.000
5	B	71	HIS	0	-0.055	-0.044	6.398	0.628	0.628	0.000	0.000	0.000	0.000
6	B	72	GLU	-1	-0.936	-0.955	7.889	-0.450	-0.450	0.000	0.000	0.000	0.000
7	B	73	LEU	0	-0.069	-0.048	9.794	0.088	0.088	0.000	0.000	0.000	0.000
8	B	74	ASP	-1	-0.948	-0.951	9.557	0.395	0.395	0.000	0.000	0.000	0.000
9	B	75	ALA	0	0.005	0.005	10.583	0.007	0.007	0.000	0.000	0.000	0.000
10	B	76	VAL	0	-0.033	-0.020	14.254	-0.036	-0.036	0.000	0.000	0.000	0.000
11	B	90	TRP	0	-0.028	-0.036	24.343	0.007	0.007	0.000	0.000	0.000	0.000
12	B	91	THR	0	0.007	-0.003	26.501	0.007	0.007	0.000	0.000	0.000	0.000
13	B	92	VAL	0	0.054	0.026	28.969	-0.008	-0.008	0.000	0.000	0.000	0.000
14	B	93	GLU	-1	-0.769	-0.869	30.885	-0.052	-0.052	0.000	0.000	0.000	0.000
15	B	94	LYS	1	0.919	0.953	25.048	0.031	0.031	0.000	0.000	0.000	0.000
16	B	95	GLN	0	0.012	0.030	24.893	-0.005	-0.005	0.000	0.000	0.000	0.000
17	B	96	ALA	0	0.023	0.019	27.345	-0.011	-0.011	0.000	0.000	0.000	0.000
18	B	97	ALA	0	-0.043	-0.016	27.254	-0.008	-0.008	0.000	0.000	0.000	0.000
19	B	98	ALA	0	0.005	0.005	23.313	-0.012	-0.012	0.000	0.000	0.000	0.000
20	B	99	THR	0	0.000	-0.011	24.776	-0.020	-0.020	0.000	0.000	0.000	0.000
21	B	100	LEU	0	-0.002	0.001	26.883	-0.008	-0.008	0.000	0.000	0.000	0.000
22	B	101	ASN	0	-0.046	-0.056	23.640	0.005	0.005	0.000	0.000	0.000	0.000
23	B	102	ALA	0	0.002	0.017	23.398	-0.019	-0.019	0.000	0.000	0.000	0.000
24	B	103	TRP	0	-0.011	-0.010	24.337	-0.007	-0.007	0.000	0.000	0.000	0.000
25	B	104	MET	0	-0.025	0.001	25.830	0.007	0.007	0.000	0.000	0.000	0.000
26	B	105	ARG	1	0.980	0.992	21.884	0.297	0.297	0.000	0.000	0.000	0.000
27	B	106	LYS	1	0.832	0.923	25.322	0.165	0.165	0.000	0.000	0.000	0.000
28	B	119	ALA	0	0.034	0.001	33.615	-0.001	-0.001	0.000	0.000	0.000	0.000
29	B	120	ALA	0	0.003	0.002	34.065	0.001	0.001	0.000	0.000	0.000	0.000
30	B	121	GLY	0	-0.068	-0.018	35.955	0.005	0.005	0.000	0.000	0.000	0.000
31	B	122	ILE	0	-0.037	-0.024	38.793	-0.001	-0.001	0.000	0.000	0.000	0.000
32	B	123	GLY	0	0.103	0.046	40.825	0.004	0.004	0.000	0.000	0.000	0.000
33	B	124	PRO	0	-0.041	-0.001	40.001	0.004	0.004	0.000	0.000	0.000	0.000
34	B	125	ALA	0	0.060	0.006	38.890	-0.005	-0.005	0.000	0.000	0.000	0.000
35	B	126	THR	0	-0.041	-0.017	38.493	-0.002	-0.002	0.000	0.000	0.000	0.000
36	B	127	VAL	0	0.083	0.031	36.385	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	128	ASN	0	-0.012	0.012	32.081	-0.002	-0.002	0.000	0.000	0.000	0.000
38	B	129	ARG	1	0.991	0.987	32.280	0.067	0.067	0.000	0.000	0.000	0.000
39	B	130	ILE	0	0.002	-0.012	30.735	0.001	0.001	0.000	0.000	0.000	0.000
40	B	131	MET	0	-0.003	0.015	26.826	0.000	0.000	0.000	0.000	0.000	0.000
41	B	132	LYS	1	0.943	0.988	26.165	0.064	0.064	0.000	0.000	0.000	0.000
42	B	133	ALA	0	-0.040	-0.026	28.151	0.007	0.007	0.000	0.000	0.000	0.000
43	B	134	GLU	-1	-0.949	-0.975	29.937	-0.048	-0.048	0.000	0.000	0.000	0.000
44	B	135	VAL	0	-0.038	-0.017	32.830	0.005	0.005	0.000	0.000	0.000	0.000
45	B	136	SER	0	-0.010	-0.027	34.330	-0.005	-0.005	0.000	0.000	0.000	0.000
46	B	137	THR	0	-0.048	-0.023	35.902	0.003	0.003	0.000	0.000	0.000	0.000
47	B	138	THR	0	0.049	0.034	38.083	0.001	0.001	0.000	0.000	0.000	0.000
48	B	139	ILE	0	0.099	0.023	39.278	-0.004	-0.004	0.000	0.000	0.000	0.000
49	B	140	GLY	0	0.029	0.027	40.862	-0.003	-0.003	0.000	0.000	0.000	0.000
50	B	141	VAL	0	0.009	-0.007	39.623	-0.002	-0.002	0.000	0.000	0.000	0.000
51	B	142	LEU	0	0.044	0.007	34.518	-0.004	-0.004	0.000	0.000	0.000	0.000
52	B	143	SER	0	0.031	0.016	37.736	-0.005	-0.005	0.000	0.000	0.000	0.000
53	B	144	SER	0	-0.055	-0.016	40.164	-0.003	-0.003	0.000	0.000	0.000	0.000
54	B	145	LEU	0	-0.071	-0.028	34.682	-0.002	-0.002	0.000	0.000	0.000	0.000
55	B	146	ALA	0	0.010	0.016	35.547	-0.007	-0.007	0.000	0.000	0.000	0.000
56	B	147	ARG	1	0.922	0.943	36.818	0.074	0.074	0.000	0.000	0.000	0.000
57	B	148	ALA	0	-0.048	-0.014	38.059	0.000	0.000	0.000	0.000	0.000	0.000
58	B	149	PHE	0	-0.058	-0.032	32.287	-0.003	-0.003	0.000	0.000	0.000	0.000
59	B	150	GLY	0	-0.035	-0.004	36.050	-0.006	-0.006	0.000	0.000	0.000	0.000
60	B	151	HIS	0	-0.065	-0.034	31.266	-0.008	-0.008	0.000	0.000	0.000	0.000
61	B	152	GLU	-1	-0.824	-0.925	36.154	-0.073	-0.073	0.000	0.000	0.000	0.000
62	B	153	ALA	0	0.000	-0.014	35.833	-0.004	-0.004	0.000	0.000	0.000	0.000
63	B	154	TYR	0	-0.004	-0.025	34.255	-0.001	-0.001	0.000	0.000	0.000	0.000
64	B	155	GLU	-1	-0.735	-0.857	31.990	-0.115	-0.115	0.000	0.000	0.000	0.000
65	B	156	MET	0	-0.042	-0.018	30.445	-0.008	-0.008	0.000	0.000	0.000	0.000
66	B	157	ILE	0	-0.040	-0.017	30.023	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	158	ILE	0	0.019	0.023	28.405	0.008	0.008	0.000	0.000	0.000	0.000
68	B	159	PRO	0	-0.014	-0.006	27.124	-0.008	-0.008	0.000	0.000	0.000	0.000
69	B	160	VAL	0	0.019	-0.004	23.260	0.005	0.005	0.000	0.000	0.000	0.000
70	B	161	GLY	0	-0.005	0.015	21.433	-0.007	-0.007	0.000	0.000	0.000	0.000
71	B	162	ALA	0	-0.042	-0.023	21.629	0.007	0.007	0.000	0.000	0.000	0.000
72	B	163	PRO	0	0.040	0.007	21.801	-0.007	-0.007	0.000	0.000	0.000	0.000
73	B	164	GLY	0	-0.010	0.003	23.266	-0.006	-0.006	0.000	0.000	0.000	0.000
74	B	165	ILE	0	-0.090	-0.035	25.616	0.004	0.004	0.000	0.000	0.000	0.000
75	B	166	ILE	0	0.020	0.014	24.945	-0.008	-0.008	0.000	0.000	0.000	0.000
76	B	167	ASP	-1	-0.909	-0.950	21.985	-0.199	-0.199	0.000	0.000	0.000	0.000
77	B	168	TYR	0	-0.025	-0.016	24.598	-0.011	-0.011	0.000	0.000	0.000	0.000
78	B	169	ASP	-1	-0.780	-0.885	27.060	-0.142	-0.142	0.000	0.000	0.000	0.000
79	B	170	HIS	0	0.075	0.020	29.381	0.010	0.010	0.000	0.000	0.000	0.000
80	B	171	ARG	1	0.860	0.931	31.397	0.146	0.146	0.000	0.000	0.000	0.000
81	B	172	MET	0	-0.072	-0.050	30.170	0.001	0.001	0.000	0.000	0.000	0.000
82	B	173	TYR	0	0.041	0.024	32.644	0.004	0.004	0.000	0.000	0.000	0.000
83	B	174	ALA	0	-0.005	-0.004	34.423	0.007	0.007	0.000	0.000	0.000	0.000
84	B	175	ALA	0	-0.010	-0.004	37.409	0.006	0.006	0.000	0.000	0.000	0.000
85	B	176	LEU	0	-0.014	0.025	33.764	0.002	0.002	0.000	0.000	0.000	0.000
86	B	177	PRO	0	0.050	0.020	38.265	0.006	0.006	0.000	0.000	0.000	0.000
87	B	178	GLN	0	0.054	0.013	39.923	-0.005	-0.005	0.000	0.000	0.000	0.000
88	B	179	GLU	-1	-0.884	-0.921	40.828	-0.082	-0.082	0.000	0.000	0.000	0.000
89	B	180	GLU	-1	-0.811	-0.902	36.150	-0.105	-0.105	0.000	0.000	0.000	0.000
90	B	181	LYS	1	0.846	0.927	36.010	0.082	0.082	0.000	0.000	0.000	0.000
91	B	182	ASN	0	-0.022	-0.014	36.675	0.000	0.000	0.000	0.000	0.000	0.000
92	B	183	LYS	1	0.812	0.880	35.202	0.096	0.096	0.000	0.000	0.000	0.000
93	B	184	ILE	0	-0.002	0.009	31.188	-0.003	-0.003	0.000	0.000	0.000	0.000
94	B	185	THR	0	-0.014	-0.023	32.829	0.000	0.000	0.000	0.000	0.000	0.000
95	B	186	SER	0	-0.026	-0.018	35.006	0.005	0.005	0.000	0.000	0.000	0.000
96	B	187	PHE	0	-0.006	0.000	27.063	0.004	0.004	0.000	0.000	0.000	0.000
97	B	188	ILE	0	0.012	0.016	29.516	0.000	0.000	0.000	0.000	0.000	0.000
98	B	189	ASN	0	-0.002	-0.012	31.157	0.006	0.006	0.000	0.000	0.000	0.000
99	B	190	PHE	0	-0.002	0.019	30.445	0.004	0.004	0.000	0.000	0.000	0.000
100	B	191	VAL	0	0.003	-0.009	26.472	0.004	0.004	0.000	0.000	0.000	0.000
101	B	192	PHE	0	-0.058	-0.040	28.584	0.003	0.003	0.000	0.000	0.000	0.000
102	B	193	GLU	-1	-0.927	-0.944	30.941	-0.034	-0.034	0.000	0.000	0.000	0.000
103	B	194	GLN	0	-0.085	-0.035	29.160	0.008	0.008	0.000	0.000	0.000	0.000
104	B	195	ASN	0	-0.071	-0.037	25.745	0.000	0.000	0.000	0.000	0.000	0.000
105	B	196	LYS	1	0.975	0.998	28.612	0.012	0.012	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:67:LEU)