FMO DATABASE

FMODB ID: 4JL5N

Calculation Name: 5D50-J-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: J

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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-658473.946338
FMO2-HF: Nuclear repulsion	617995.851182
FMO2-HF: Total energy	-40478.095156
FMO2-MP2: Total energy	-40595.350149

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(J:67:LEU)

Summations of interaction energy for fragment #1(J: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.
-2.361	-0.114	-0.008	-1.046	-1.194	0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.017

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	J	69	VAL	0	-0.064	-0.046	3.691	-1.015	1.232	-0.008	-1.046	-1.194	0.003
4	J	70	ASP	-1	-0.882	-0.933	6.306	-0.922	-0.922	0.000	0.000	0.000	0.000
5	J	71	HIS	0	-0.007	-0.014	7.763	0.390	0.390	0.000	0.000	0.000	0.000
6	J	72	GLU	-1	-0.934	-0.972	12.130	-0.652	-0.652	0.000	0.000	0.000	0.000
7	J	73	LEU	0	-0.081	-0.038	15.020	0.107	0.107	0.000	0.000	0.000	0.000
8	J	74	ASP	-1	-0.971	-0.976	15.710	-0.564	-0.564	0.000	0.000	0.000	0.000
9	J	75	ALA	0	-0.005	-0.001	17.399	0.057	0.057	0.000	0.000	0.000	0.000
10	J	76	VAL	0	-0.083	-0.032	20.294	0.049	0.049	0.000	0.000	0.000	0.000
11	J	90	TRP	0	-0.010	-0.029	28.935	0.005	0.005	0.000	0.000	0.000	0.000
12	J	91	THR	0	-0.032	-0.048	31.150	0.006	0.006	0.000	0.000	0.000	0.000
13	J	92	VAL	0	0.095	0.043	32.526	-0.008	-0.008	0.000	0.000	0.000	0.000
14	J	93	GLU	-1	-0.797	-0.861	34.384	-0.112	-0.112	0.000	0.000	0.000	0.000
15	J	94	LYS	1	0.915	0.951	29.146	0.153	0.153	0.000	0.000	0.000	0.000
16	J	95	GLN	0	-0.006	0.030	28.311	-0.012	-0.012	0.000	0.000	0.000	0.000
17	J	96	ALA	0	0.075	0.045	30.367	-0.005	-0.005	0.000	0.000	0.000	0.000
18	J	97	ALA	0	0.000	0.023	29.656	0.001	0.001	0.000	0.000	0.000	0.000
19	J	98	ALA	0	-0.003	-0.002	25.709	0.000	0.000	0.000	0.000	0.000	0.000
20	J	99	THR	0	-0.011	-0.022	26.685	-0.010	-0.010	0.000	0.000	0.000	0.000
21	J	100	LEU	0	-0.026	-0.008	29.153	0.005	0.005	0.000	0.000	0.000	0.000
22	J	101	ASN	0	0.003	-0.038	26.156	0.008	0.008	0.000	0.000	0.000	0.000
23	J	102	ALA	0	-0.019	-0.003	24.684	0.001	0.001	0.000	0.000	0.000	0.000
24	J	103	TRP	0	0.024	0.005	25.670	0.006	0.006	0.000	0.000	0.000	0.000
25	J	104	MET	0	-0.048	-0.018	28.737	0.005	0.005	0.000	0.000	0.000	0.000
26	J	105	ARG	1	0.929	0.976	19.905	0.227	0.227	0.000	0.000	0.000	0.000
27	J	106	LYS	1	0.941	0.987	26.662	0.161	0.161	0.000	0.000	0.000	0.000
28	J	121	GLY	0	0.015	-0.002	45.433	-0.001	-0.001	0.000	0.000	0.000	0.000
29	J	122	ILE	0	-0.019	-0.013	41.139	0.001	0.001	0.000	0.000	0.000	0.000
30	J	123	GLY	0	0.059	0.043	42.616	0.001	0.001	0.000	0.000	0.000	0.000
31	J	124	PRO	0	0.073	0.027	38.094	-0.004	-0.004	0.000	0.000	0.000	0.000
32	J	125	ALA	0	0.028	0.007	37.366	-0.004	-0.004	0.000	0.000	0.000	0.000
33	J	126	THR	0	-0.011	-0.024	38.143	-0.002	-0.002	0.000	0.000	0.000	0.000
34	J	127	VAL	0	0.037	0.021	34.612	-0.004	-0.004	0.000	0.000	0.000	0.000
35	J	128	ASN	0	0.003	-0.006	31.859	-0.005	-0.005	0.000	0.000	0.000	0.000
36	J	129	ARG	1	0.879	0.945	33.352	0.066	0.066	0.000	0.000	0.000	0.000
37	J	130	ILE	0	-0.007	-0.006	34.207	-0.005	-0.005	0.000	0.000	0.000	0.000
38	J	131	MET	0	-0.020	0.000	29.898	-0.008	-0.008	0.000	0.000	0.000	0.000
39	J	132	LYS	1	0.822	0.910	29.403	0.074	0.074	0.000	0.000	0.000	0.000
40	J	133	ALA	0	-0.018	0.006	30.767	-0.005	-0.005	0.000	0.000	0.000	0.000
41	J	134	GLU	-1	-0.824	-0.895	32.904	-0.078	-0.078	0.000	0.000	0.000	0.000
42	J	135	VAL	0	-0.054	-0.031	35.125	0.006	0.006	0.000	0.000	0.000	0.000
43	J	136	SER	0	-0.014	-0.029	37.411	-0.004	-0.004	0.000	0.000	0.000	0.000
44	J	137	THR	0	-0.019	-0.011	37.551	0.003	0.003	0.000	0.000	0.000	0.000
45	J	138	THR	0	0.026	0.018	39.920	0.001	0.001	0.000	0.000	0.000	0.000
46	J	139	ILE	0	0.106	0.038	41.685	-0.003	-0.003	0.000	0.000	0.000	0.000
47	J	140	GLY	0	0.029	0.021	42.972	-0.001	-0.001	0.000	0.000	0.000	0.000
48	J	141	VAL	0	-0.003	-0.007	39.895	0.001	0.001	0.000	0.000	0.000	0.000
49	J	142	LEU	0	0.045	0.020	36.508	-0.001	-0.001	0.000	0.000	0.000	0.000
50	J	143	SER	0	-0.033	-0.015	39.528	-0.003	-0.003	0.000	0.000	0.000	0.000
51	J	144	SER	0	-0.027	-0.039	41.417	-0.002	-0.002	0.000	0.000	0.000	0.000
52	J	145	LEU	0	-0.025	0.007	35.788	0.001	0.001	0.000	0.000	0.000	0.000
53	J	146	ALA	0	0.013	0.009	36.777	-0.001	-0.001	0.000	0.000	0.000	0.000
54	J	147	ARG	1	0.886	0.926	37.587	0.074	0.074	0.000	0.000	0.000	0.000
55	J	148	ALA	0	-0.019	0.007	38.106	0.001	0.001	0.000	0.000	0.000	0.000
56	J	149	PHE	0	-0.019	-0.008	32.893	0.000	0.000	0.000	0.000	0.000	0.000
57	J	150	GLY	0	-0.010	-0.001	35.369	-0.005	-0.005	0.000	0.000	0.000	0.000
58	J	151	HIS	1	0.749	0.877	32.447	0.124	0.124	0.000	0.000	0.000	0.000
59	J	152	GLU	-1	-0.856	-0.935	37.008	-0.075	-0.075	0.000	0.000	0.000	0.000
60	J	153	ALA	0	-0.019	-0.016	39.548	-0.003	-0.003	0.000	0.000	0.000	0.000
61	J	154	TYR	0	-0.006	-0.012	37.572	0.001	0.001	0.000	0.000	0.000	0.000
62	J	155	GLU	-1	-0.810	-0.916	34.563	-0.128	-0.128	0.000	0.000	0.000	0.000
63	J	156	MET	0	-0.012	-0.002	33.213	-0.005	-0.005	0.000	0.000	0.000	0.000
64	J	157	ILE	0	-0.020	-0.013	33.110	-0.006	-0.006	0.000	0.000	0.000	0.000
65	J	158	ILE	0	0.002	0.008	33.065	0.002	0.002	0.000	0.000	0.000	0.000
66	J	159	PRO	0	-0.008	-0.001	31.220	-0.008	-0.008	0.000	0.000	0.000	0.000
67	J	160	VAL	0	-0.006	-0.004	26.496	0.003	0.003	0.000	0.000	0.000	0.000
68	J	161	GLY	0	-0.019	-0.004	27.156	-0.017	-0.017	0.000	0.000	0.000	0.000
69	J	162	ALA	0	0.015	-0.004	28.011	0.001	0.001	0.000	0.000	0.000	0.000
70	J	163	PRO	0	-0.028	-0.014	28.923	0.001	0.001	0.000	0.000	0.000	0.000
71	J	164	GLY	0	0.008	0.021	31.415	0.005	0.005	0.000	0.000	0.000	0.000
72	J	165	ILE	0	0.015	0.003	29.673	-0.013	-0.013	0.000	0.000	0.000	0.000
73	J	166	ILE	0	0.025	-0.004	23.575	0.008	0.008	0.000	0.000	0.000	0.000
74	J	167	ASP	-1	-0.951	-0.965	25.596	-0.216	-0.216	0.000	0.000	0.000	0.000
75	J	168	TYR	0	-0.019	0.012	27.614	0.003	0.003	0.000	0.000	0.000	0.000
76	J	169	ASP	-1	-0.775	-0.897	30.064	-0.129	-0.129	0.000	0.000	0.000	0.000
77	J	170	HIS	0	0.085	0.036	31.891	0.014	0.014	0.000	0.000	0.000	0.000
78	J	171	ARG	1	0.871	0.943	32.884	0.123	0.123	0.000	0.000	0.000	0.000
79	J	172	MET	0	-0.027	-0.024	31.046	0.004	0.004	0.000	0.000	0.000	0.000
80	J	173	TYR	0	0.069	0.038	35.629	0.005	0.005	0.000	0.000	0.000	0.000
81	J	174	ALA	0	-0.001	-0.013	37.148	0.005	0.005	0.000	0.000	0.000	0.000
82	J	175	ALA	0	-0.019	-0.009	38.702	0.005	0.005	0.000	0.000	0.000	0.000
83	J	176	LEU	0	-0.020	0.013	36.122	0.004	0.004	0.000	0.000	0.000	0.000
84	J	177	PRO	0	0.026	0.007	40.168	0.003	0.003	0.000	0.000	0.000	0.000
85	J	178	GLN	0	0.009	0.000	42.424	-0.003	-0.003	0.000	0.000	0.000	0.000
86	J	179	GLU	-1	-0.854	-0.952	43.831	-0.092	-0.092	0.000	0.000	0.000	0.000
87	J	180	GLU	-1	-0.844	-0.910	38.984	-0.101	-0.101	0.000	0.000	0.000	0.000
88	J	181	LYS	1	0.789	0.907	38.954	0.089	0.089	0.000	0.000	0.000	0.000
89	J	182	ASN	0	-0.006	-0.013	39.799	-0.004	-0.004	0.000	0.000	0.000	0.000
90	J	183	LYS	1	0.862	0.933	38.217	0.094	0.094	0.000	0.000	0.000	0.000
91	J	184	ILE	0	0.010	0.011	34.406	-0.006	-0.006	0.000	0.000	0.000	0.000
92	J	185	THR	0	-0.025	0.005	36.567	-0.004	-0.004	0.000	0.000	0.000	0.000
93	J	186	SER	0	0.041	0.018	38.834	-0.001	-0.001	0.000	0.000	0.000	0.000
94	J	187	PHE	0	-0.018	-0.003	30.742	-0.001	-0.001	0.000	0.000	0.000	0.000
95	J	188	ILE	0	0.006	-0.003	33.541	-0.006	-0.006	0.000	0.000	0.000	0.000
96	J	189	ASN	0	-0.061	-0.043	35.482	-0.006	-0.006	0.000	0.000	0.000	0.000
97	J	190	PHE	0	0.015	0.023	35.091	-0.001	-0.001	0.000	0.000	0.000	0.000
98	J	191	VAL	0	0.004	-0.003	31.326	-0.004	-0.004	0.000	0.000	0.000	0.000
99	J	192	PHE	0	-0.040	-0.030	33.647	-0.006	-0.006	0.000	0.000	0.000	0.000
100	J	193	GLU	-1	-0.870	-0.932	36.233	-0.120	-0.120	0.000	0.000	0.000	0.000
101	J	194	GLN	0	-0.081	-0.026	33.953	-0.002	-0.002	0.000	0.000	0.000	0.000
102	J	195	ASN	0	-0.101	-0.044	32.455	-0.017	-0.017	0.000	0.000	0.000	0.000
103	J	196	LYS	1	0.967	0.988	36.021	0.145	0.145	0.000	0.000	0.000	0.000

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