FMO DATABASE

FMODB ID: 5JN4Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-661711.391553
FMO2-HF: Nuclear repulsion	621232.948282
FMO2-HF: Total energy	-40478.443271
FMO2-MP2: Total energy	-40595.689552

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.
-3.86	-1.278	0.154	-1.236	-1.5	-0.002

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 : -0.020

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	-0.058	-0.039	3.044	-2.445	0.137	0.154	-1.236	-1.500	-0.002
4	J	70	ASP	-1	-0.886	-0.944	5.888	-0.853	-0.853	0.000	0.000	0.000	0.000
5	J	71	HIS	0	-0.003	-0.007	7.644	0.294	0.294	0.000	0.000	0.000	0.000
6	J	72	GLU	-1	-0.948	-0.972	12.132	-0.653	-0.653	0.000	0.000	0.000	0.000
7	J	73	LEU	0	-0.066	-0.030	15.022	0.109	0.109	0.000	0.000	0.000	0.000
8	J	74	ASP	-1	-0.948	-0.972	15.662	-0.581	-0.581	0.000	0.000	0.000	0.000
9	J	75	ALA	0	-0.026	-0.006	17.492	0.064	0.064	0.000	0.000	0.000	0.000
10	J	76	VAL	0	-0.088	-0.035	20.404	0.055	0.055	0.000	0.000	0.000	0.000
11	J	90	TRP	0	0.017	0.001	28.903	0.007	0.007	0.000	0.000	0.000	0.000
12	J	91	THR	0	-0.012	-0.035	31.053	0.005	0.005	0.000	0.000	0.000	0.000
13	J	92	VAL	0	0.080	0.036	32.836	-0.006	-0.006	0.000	0.000	0.000	0.000
14	J	93	GLU	-1	-0.787	-0.846	34.270	-0.097	-0.097	0.000	0.000	0.000	0.000
15	J	94	LYS	1	0.890	0.931	29.179	0.127	0.127	0.000	0.000	0.000	0.000
16	J	95	GLN	0	0.018	0.037	28.268	-0.011	-0.011	0.000	0.000	0.000	0.000
17	J	96	ALA	0	0.049	0.036	30.399	-0.004	-0.004	0.000	0.000	0.000	0.000
18	J	97	ALA	0	-0.013	0.000	29.669	0.000	0.000	0.000	0.000	0.000	0.000
19	J	98	ALA	0	-0.010	-0.006	25.886	-0.002	-0.002	0.000	0.000	0.000	0.000
20	J	99	THR	0	-0.005	-0.015	26.696	-0.010	-0.010	0.000	0.000	0.000	0.000
21	J	100	LEU	0	-0.005	0.003	29.074	0.002	0.002	0.000	0.000	0.000	0.000
22	J	101	ASN	0	0.024	-0.028	26.259	0.005	0.005	0.000	0.000	0.000	0.000
23	J	102	ALA	0	0.000	0.028	24.901	-0.005	-0.005	0.000	0.000	0.000	0.000
24	J	103	TRP	0	0.019	-0.010	25.859	0.007	0.007	0.000	0.000	0.000	0.000
25	J	104	MET	0	-0.049	-0.026	28.509	0.004	0.004	0.000	0.000	0.000	0.000
26	J	105	ARG	1	0.883	0.944	20.284	0.196	0.196	0.000	0.000	0.000	0.000
27	J	106	LYS	1	0.941	0.989	26.346	0.168	0.168	0.000	0.000	0.000	0.000
28	J	121	GLY	0	0.020	0.001	45.544	-0.001	-0.001	0.000	0.000	0.000	0.000
29	J	122	ILE	0	-0.015	-0.007	41.103	0.001	0.001	0.000	0.000	0.000	0.000
30	J	123	GLY	0	0.065	0.044	42.314	0.001	0.001	0.000	0.000	0.000	0.000
31	J	124	PRO	0	0.062	0.025	37.666	-0.004	-0.004	0.000	0.000	0.000	0.000
32	J	125	ALA	0	0.030	0.009	37.188	-0.003	-0.003	0.000	0.000	0.000	0.000
33	J	126	THR	0	-0.002	-0.022	38.045	-0.001	-0.001	0.000	0.000	0.000	0.000
34	J	127	VAL	0	0.033	0.013	34.524	-0.004	-0.004	0.000	0.000	0.000	0.000
35	J	128	ASN	0	-0.008	-0.009	32.111	-0.005	-0.005	0.000	0.000	0.000	0.000
36	J	129	ARG	1	0.858	0.934	33.498	0.051	0.051	0.000	0.000	0.000	0.000
37	J	130	ILE	0	0.001	0.011	34.078	-0.004	-0.004	0.000	0.000	0.000	0.000
38	J	131	MET	0	-0.036	-0.010	30.059	-0.007	-0.007	0.000	0.000	0.000	0.000
39	J	132	LYS	1	0.828	0.909	29.277	0.053	0.053	0.000	0.000	0.000	0.000
40	J	133	ALA	0	-0.024	-0.004	30.789	-0.001	-0.001	0.000	0.000	0.000	0.000
41	J	134	GLU	-1	-0.814	-0.882	32.927	-0.055	-0.055	0.000	0.000	0.000	0.000
42	J	135	VAL	0	-0.030	-0.034	35.135	0.008	0.008	0.000	0.000	0.000	0.000
43	J	136	SER	0	-0.025	-0.027	37.747	-0.004	-0.004	0.000	0.000	0.000	0.000
44	J	137	THR	0	-0.006	-0.001	37.570	0.004	0.004	0.000	0.000	0.000	0.000
45	J	138	THR	0	0.016	0.008	39.850	-0.001	-0.001	0.000	0.000	0.000	0.000
46	J	139	ILE	0	0.087	0.031	42.256	-0.001	-0.001	0.000	0.000	0.000	0.000
47	J	140	GLY	0	0.020	0.016	43.284	-0.001	-0.001	0.000	0.000	0.000	0.000
48	J	141	VAL	0	0.005	-0.002	40.286	0.000	0.000	0.000	0.000	0.000	0.000
49	J	142	LEU	0	0.022	0.009	36.448	0.000	0.000	0.000	0.000	0.000	0.000
50	J	143	SER	0	-0.011	0.002	39.551	-0.003	-0.003	0.000	0.000	0.000	0.000
51	J	144	SER	0	0.017	0.000	41.765	-0.001	-0.001	0.000	0.000	0.000	0.000
52	J	145	LEU	0	-0.025	-0.007	35.773	0.000	0.000	0.000	0.000	0.000	0.000
53	J	146	ALA	0	0.015	0.003	36.741	-0.002	-0.002	0.000	0.000	0.000	0.000
54	J	147	ARG	1	0.833	0.899	37.566	0.072	0.072	0.000	0.000	0.000	0.000
55	J	148	ALA	0	-0.009	0.008	37.800	0.000	0.000	0.000	0.000	0.000	0.000
56	J	149	PHE	0	-0.006	0.002	32.903	0.000	0.000	0.000	0.000	0.000	0.000
57	J	150	GLY	0	0.008	0.019	35.174	-0.007	-0.007	0.000	0.000	0.000	0.000
58	J	151	HIS	1	0.750	0.851	32.727	0.117	0.117	0.000	0.000	0.000	0.000
59	J	152	GLU	-1	-0.816	-0.903	37.311	-0.073	-0.073	0.000	0.000	0.000	0.000
60	J	153	ALA	0	-0.021	-0.018	39.826	-0.001	-0.001	0.000	0.000	0.000	0.000
61	J	154	TYR	0	-0.004	-0.012	37.695	0.000	0.000	0.000	0.000	0.000	0.000
62	J	155	GLU	-1	-0.810	-0.927	34.356	-0.124	-0.124	0.000	0.000	0.000	0.000
63	J	156	MET	0	-0.034	-0.010	33.255	-0.005	-0.005	0.000	0.000	0.000	0.000
64	J	157	ILE	0	-0.016	-0.012	33.135	-0.003	-0.003	0.000	0.000	0.000	0.000
65	J	158	ILE	0	0.006	0.011	32.940	0.002	0.002	0.000	0.000	0.000	0.000
66	J	159	PRO	0	0.002	0.000	31.159	-0.007	-0.007	0.000	0.000	0.000	0.000
67	J	160	VAL	0	-0.015	0.006	26.419	0.000	0.000	0.000	0.000	0.000	0.000
68	J	161	GLY	0	-0.011	-0.007	26.889	-0.019	-0.019	0.000	0.000	0.000	0.000
69	J	162	ALA	0	0.026	-0.007	27.571	0.004	0.004	0.000	0.000	0.000	0.000
70	J	163	PRO	0	-0.031	-0.015	28.653	0.000	0.000	0.000	0.000	0.000	0.000
71	J	164	GLY	0	-0.008	0.015	30.674	0.011	0.011	0.000	0.000	0.000	0.000
72	J	165	ILE	0	-0.009	-0.005	29.448	-0.014	-0.014	0.000	0.000	0.000	0.000
73	J	166	ILE	0	0.025	-0.004	23.318	0.011	0.011	0.000	0.000	0.000	0.000
74	J	167	ASP	-1	-0.955	-0.975	25.526	-0.211	-0.211	0.000	0.000	0.000	0.000
75	J	168	TYR	0	-0.009	0.016	27.473	0.004	0.004	0.000	0.000	0.000	0.000
76	J	169	ASP	-1	-0.745	-0.859	30.088	-0.127	-0.127	0.000	0.000	0.000	0.000
77	J	170	HIS	0	0.057	0.032	31.892	0.013	0.013	0.000	0.000	0.000	0.000
78	J	171	ARG	1	0.861	0.923	32.876	0.126	0.126	0.000	0.000	0.000	0.000
79	J	172	MET	0	-0.017	-0.013	31.309	0.003	0.003	0.000	0.000	0.000	0.000
80	J	173	TYR	0	0.039	0.019	35.380	0.004	0.004	0.000	0.000	0.000	0.000
81	J	174	ALA	0	-0.016	-0.018	36.904	0.005	0.005	0.000	0.000	0.000	0.000
82	J	175	ALA	0	0.000	0.002	38.613	0.005	0.005	0.000	0.000	0.000	0.000
83	J	176	LEU	0	-0.016	0.015	35.616	0.004	0.004	0.000	0.000	0.000	0.000
84	J	177	PRO	0	0.030	0.004	39.878	0.003	0.003	0.000	0.000	0.000	0.000
85	J	178	GLN	0	0.004	-0.005	42.127	-0.003	-0.003	0.000	0.000	0.000	0.000
86	J	179	GLU	-1	-0.833	-0.919	43.529	-0.102	-0.102	0.000	0.000	0.000	0.000
87	J	180	GLU	-1	-0.846	-0.909	38.401	-0.114	-0.114	0.000	0.000	0.000	0.000
88	J	181	LYS	1	0.796	0.904	38.624	0.095	0.095	0.000	0.000	0.000	0.000
89	J	182	ASN	0	-0.017	-0.014	39.765	-0.005	-0.005	0.000	0.000	0.000	0.000
90	J	183	LYS	1	0.849	0.914	38.188	0.105	0.105	0.000	0.000	0.000	0.000
91	J	184	ILE	0	0.005	0.008	34.424	-0.007	-0.007	0.000	0.000	0.000	0.000
92	J	185	THR	0	0.015	0.000	36.267	-0.006	-0.006	0.000	0.000	0.000	0.000
93	J	186	SER	0	-0.006	0.000	38.643	0.000	0.000	0.000	0.000	0.000	0.000
94	J	187	PHE	0	-0.030	-0.006	30.422	-0.001	-0.001	0.000	0.000	0.000	0.000
95	J	188	ILE	0	0.002	-0.003	33.443	-0.007	-0.007	0.000	0.000	0.000	0.000
96	J	189	ASN	0	-0.068	-0.042	35.361	-0.004	-0.004	0.000	0.000	0.000	0.000
97	J	190	PHE	0	0.033	0.028	34.743	-0.001	-0.001	0.000	0.000	0.000	0.000
98	J	191	VAL	0	0.010	0.001	31.138	-0.004	-0.004	0.000	0.000	0.000	0.000
99	J	192	PHE	0	-0.031	-0.020	33.502	-0.006	-0.006	0.000	0.000	0.000	0.000
100	J	193	GLU	-1	-0.883	-0.935	36.254	-0.128	-0.128	0.000	0.000	0.000	0.000
101	J	194	GLN	0	-0.066	-0.026	33.529	-0.004	-0.004	0.000	0.000	0.000	0.000
102	J	195	ASN	0	-0.108	-0.050	31.962	-0.013	-0.013	0.000	0.000	0.000	0.000
103	J	196	LYS	1	0.957	0.984	35.690	0.156	0.156	0.000	0.000	0.000	0.000

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