FMO DATABASE

FMODB ID: G5YZ1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-673172.37707
FMO2-HF: Nuclear repulsion	632204.05056
FMO2-HF: Total energy	-40968.32651
FMO2-MP2: Total energy	-41087.100916

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.
-1.639	1.045	0.155	-1.008	-1.83	0

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 : -0.042 / q_NPA : -0.050

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].
3	B	69	VAL	0	-0.081	-0.046	2.752	0.192	2.610	0.156	-0.981	-1.592
4	B	70	ASP	-1	-0.940	-0.973	4.296	-2.055	-1.789	-0.001	-0.027	-0.238
5	B	71	HIS	0	-0.039	-0.026	6.387	0.680	0.680	0.000	0.000	0.000
6	B	72	GLU	-1	-0.940	-0.958	7.812	-0.731	-0.731	0.000	0.000	0.000
7	B	73	LEU	0	-0.071	-0.044	10.113	0.095	0.095	0.000	0.000	0.000
8	B	74	ASP	-1	-0.953	-0.950	9.809	0.033	0.033	0.000	0.000	0.000
9	B	75	ALA	0	0.012	0.006	10.850	0.060	0.060	0.000	0.000	0.000
10	B	76	VAL	0	-0.037	-0.026	14.503	-0.035	-0.035	0.000	0.000	0.000
11	B	90	TRP	0	-0.017	-0.027	23.983	0.005	0.005	0.000	0.000	0.000
12	B	91	THR	0	0.008	0.002	26.202	0.012	0.012	0.000	0.000	0.000
13	B	92	VAL	0	0.051	0.030	28.624	-0.011	-0.011	0.000	0.000	0.000
14	B	93	GLU	-1	-0.792	-0.890	30.511	-0.120	-0.120	0.000	0.000	0.000
15	B	94	LYS	1	0.943	0.963	24.454	0.156	0.156	0.000	0.000	0.000
16	B	95	GLN	0	0.000	0.019	24.581	-0.015	-0.015	0.000	0.000	0.000
17	B	96	ALA	0	0.026	0.020	26.959	-0.008	-0.008	0.000	0.000	0.000
18	B	97	ALA	0	-0.050	-0.021	26.908	-0.003	-0.003	0.000	0.000	0.000
19	B	98	ALA	0	0.014	0.012	22.914	-0.009	-0.009	0.000	0.000	0.000
20	B	99	THR	0	0.000	-0.008	24.351	-0.020	-0.020	0.000	0.000	0.000
21	B	100	LEU	0	-0.006	-0.003	26.449	-0.001	-0.001	0.000	0.000	0.000
22	B	101	ASN	0	-0.061	-0.055	23.292	0.003	0.003	0.000	0.000	0.000
23	B	102	ALA	0	0.007	0.018	23.091	-0.016	-0.016	0.000	0.000	0.000
24	B	103	TRP	0	-0.034	-0.016	24.139	0.001	0.001	0.000	0.000	0.000
25	B	104	MET	0	-0.031	-0.006	25.802	0.015	0.015	0.000	0.000	0.000
26	B	105	ARG	1	0.992	1.001	21.838	0.294	0.294	0.000	0.000	0.000
27	B	106	LYS	1	0.912	0.966	25.161	0.202	0.202	0.000	0.000	0.000
28	B	119	ALA	0	0.040	0.010	33.550	0.000	0.000	0.000	0.000	0.000
29	B	120	ALA	0	0.002	-0.004	33.988	0.002	0.002	0.000	0.000	0.000
30	B	121	GLY	0	-0.054	-0.017	35.827	0.004	0.004	0.000	0.000	0.000
31	B	122	ILE	0	-0.031	-0.017	38.615	0.000	0.000	0.000	0.000	0.000
32	B	123	GLY	0	0.085	0.037	40.692	0.004	0.004	0.000	0.000	0.000
33	B	124	PRO	0	-0.040	0.000	39.604	0.004	0.004	0.000	0.000	0.000
34	B	125	ALA	0	0.063	0.007	38.671	-0.005	-0.005	0.000	0.000	0.000
35	B	126	THR	0	-0.052	-0.018	38.195	-0.004	-0.004	0.000	0.000	0.000
36	B	127	VAL	0	0.095	0.033	36.073	-0.003	-0.003	0.000	0.000	0.000
37	B	128	ASN	0	-0.020	0.008	31.589	-0.004	-0.004	0.000	0.000	0.000
38	B	129	ARG	1	0.994	0.990	31.942	0.105	0.105	0.000	0.000	0.000
39	B	130	ILE	0	0.002	-0.011	30.604	-0.003	-0.003	0.000	0.000	0.000
40	B	131	MET	0	-0.015	-0.002	26.442	-0.005	-0.005	0.000	0.000	0.000
41	B	132	LYS	1	0.944	0.991	26.061	0.143	0.143	0.000	0.000	0.000
42	B	133	ALA	0	-0.037	-0.021	27.738	0.001	0.001	0.000	0.000	0.000
43	B	134	GLU	-1	-0.949	-0.977	29.613	-0.113	-0.113	0.000	0.000	0.000
44	B	135	VAL	0	-0.033	-0.014	32.534	0.008	0.008	0.000	0.000	0.000
45	B	136	SER	0	-0.020	-0.027	33.993	-0.006	-0.006	0.000	0.000	0.000
46	B	137	THR	0	-0.044	-0.025	35.439	0.006	0.006	0.000	0.000	0.000
47	B	138	THR	0	0.038	0.033	37.712	0.000	0.000	0.000	0.000	0.000
48	B	139	ILE	0	0.097	0.022	38.961	-0.003	-0.003	0.000	0.000	0.000
49	B	140	GLY	0	0.026	0.020	40.460	-0.002	-0.002	0.000	0.000	0.000
50	B	141	VAL	0	0.006	-0.007	39.161	-0.001	-0.001	0.000	0.000	0.000
51	B	142	LEU	0	0.050	0.002	34.062	-0.003	-0.003	0.000	0.000	0.000
52	B	143	SER	0	0.000	0.009	37.305	-0.006	-0.006	0.000	0.000	0.000
53	B	144	SER	0	-0.005	0.001	39.721	-0.001	-0.001	0.000	0.000	0.000
54	B	145	LEU	0	-0.080	-0.027	34.194	-0.001	-0.001	0.000	0.000	0.000
55	B	146	ALA	0	0.017	0.018	35.180	-0.009	-0.009	0.000	0.000	0.000
56	B	147	ARG	1	0.972	0.987	36.441	0.094	0.094	0.000	0.000	0.000
57	B	148	ALA	0	-0.050	-0.021	37.875	0.002	0.002	0.000	0.000	0.000
58	B	149	PHE	0	-0.060	-0.028	32.122	-0.001	-0.001	0.000	0.000	0.000
59	B	150	GLY	0	-0.044	-0.014	35.885	-0.004	-0.004	0.000	0.000	0.000
60	B	151	HIS	0	-0.115	-0.070	31.452	-0.004	-0.004	0.000	0.000	0.000
61	B	152	GLU	-1	-0.841	-0.943	35.877	-0.099	-0.099	0.000	0.000	0.000
62	B	153	ALA	0	-0.015	-0.024	35.384	-0.006	-0.006	0.000	0.000	0.000
63	B	154	TYR	0	-0.008	-0.025	34.229	-0.004	-0.004	0.000	0.000	0.000
64	B	155	GLU	-1	-0.748	-0.864	31.628	-0.154	-0.154	0.000	0.000	0.000
65	B	156	MET	0	-0.044	-0.016	30.012	-0.012	-0.012	0.000	0.000	0.000
66	B	157	ILE	0	-0.035	-0.010	29.605	-0.006	-0.006	0.000	0.000	0.000
67	B	158	ILE	0	0.017	0.021	28.174	0.006	0.006	0.000	0.000	0.000
68	B	159	PRO	0	-0.012	-0.007	26.871	-0.011	-0.011	0.000	0.000	0.000
69	B	160	VAL	0	0.021	0.000	22.844	0.001	0.001	0.000	0.000	0.000
70	B	161	GLY	0	-0.009	0.012	21.251	-0.011	-0.011	0.000	0.000	0.000
71	B	162	ALA	0	-0.044	-0.024	21.551	-0.003	-0.003	0.000	0.000	0.000
72	B	163	PRO	0	0.035	0.006	21.976	-0.003	-0.003	0.000	0.000	0.000
73	B	164	GLY	0	-0.007	0.001	23.188	-0.003	-0.003	0.000	0.000	0.000
74	B	165	ILE	0	-0.089	-0.032	25.521	0.014	0.014	0.000	0.000	0.000
75	B	166	ILE	0	0.023	0.017	24.852	-0.014	-0.014	0.000	0.000	0.000
76	B	167	ASP	-1	-0.912	-0.953	21.854	-0.281	-0.281	0.000	0.000	0.000
77	B	168	TYR	0	-0.028	-0.019	24.491	-0.006	-0.006	0.000	0.000	0.000
78	B	169	ASP	-1	-0.829	-0.919	27.008	-0.172	-0.172	0.000	0.000	0.000
79	B	170	HIS	0	0.067	0.016	29.424	0.019	0.019	0.000	0.000	0.000
80	B	171	ARG	1	0.938	0.988	31.900	0.166	0.166	0.000	0.000	0.000
81	B	172	MET	0	-0.092	-0.070	29.943	0.005	0.005	0.000	0.000	0.000
82	B	173	TYR	0	0.054	0.029	32.702	0.005	0.005	0.000	0.000	0.000
83	B	174	ALA	0	-0.042	-0.021	34.458	0.008	0.008	0.000	0.000	0.000
84	B	175	ALA	0	-0.032	-0.023	37.454	0.006	0.006	0.000	0.000	0.000
85	B	176	LEU	0	-0.017	0.016	33.865	0.004	0.004	0.000	0.000	0.000
86	B	177	PRO	0	0.033	0.012	38.294	0.005	0.005	0.000	0.000	0.000
87	B	178	GLN	0	0.025	-0.002	39.947	-0.007	-0.007	0.000	0.000	0.000
88	B	179	GLU	-1	-0.948	-0.966	40.847	-0.087	-0.087	0.000	0.000	0.000
89	B	180	GLU	-1	-0.841	-0.943	36.181	-0.114	-0.114	0.000	0.000	0.000
90	B	181	LYS	1	0.926	0.979	36.028	0.098	0.098	0.000	0.000	0.000
91	B	182	ASN	0	-0.009	-0.008	36.689	-0.004	-0.004	0.000	0.000	0.000
92	B	183	LYS	1	0.896	0.958	35.199	0.101	0.101	0.000	0.000	0.000
93	B	184	ILE	0	0.007	0.014	31.398	-0.004	-0.004	0.000	0.000	0.000
94	B	185	THR	0	-0.015	-0.019	32.741	-0.004	-0.004	0.000	0.000	0.000
95	B	186	SER	0	-0.071	-0.034	34.906	0.001	0.001	0.000	0.000	0.000
96	B	187	PHE	0	0.033	0.015	27.130	0.003	0.003	0.000	0.000	0.000
97	B	188	ILE	0	0.017	0.019	29.547	-0.002	-0.002	0.000	0.000	0.000
98	B	189	ASN	0	0.029	0.001	31.064	-0.002	-0.002	0.000	0.000	0.000
99	B	190	PHE	0	-0.003	0.018	30.390	0.004	0.004	0.000	0.000	0.000
100	B	191	VAL	0	-0.001	-0.011	26.373	0.002	0.002	0.000	0.000	0.000
101	B	192	PHE	0	-0.060	-0.039	28.511	-0.002	-0.002	0.000	0.000	0.000
102	B	193	GLU	-1	-0.942	-0.957	30.856	-0.075	-0.075	0.000	0.000	0.000
103	B	194	GLN	0	-0.074	-0.029	28.963	0.009	0.009	0.000	0.000	0.000
104	B	195	ASN	0	-0.066	-0.031	25.919	-0.005	-0.005	0.000	0.000	0.000
105	B	196	LYS	1	0.965	0.993	28.542	0.076	0.076	0.000	0.000	0.000

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