FMO DATABASE

FMODB ID: NN2JQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-675064.461205
FMO2-HF: Nuclear repulsion	634094.96869
FMO2-HF: Total energy	-40969.492515
FMO2-MP2: Total energy	-41088.206184

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.
-1.783	1.917	0.002	-1.779	-1.923	0.003

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 : -0.002 / q_NPA : -0.007

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	-0.073	-0.049	3.489	-0.474	3.009	0.003	-1.772	-1.714	0.003
4	B	70	ASP	-1	-0.916	-0.945	4.795	-1.628	-1.411	-0.001	-0.007	-0.209	0.000
5	B	71	HIS	0	-0.047	-0.041	6.662	0.607	0.607	0.000	0.000	0.000	0.000
6	B	72	GLU	-1	-0.960	-0.961	8.218	-0.501	-0.501	0.000	0.000	0.000	0.000
7	B	73	LEU	0	-0.076	-0.039	10.304	0.132	0.132	0.000	0.000	0.000	0.000
8	B	74	ASP	-1	-0.859	-0.926	9.633	0.100	0.100	0.000	0.000	0.000	0.000
9	B	75	ALA	0	-0.034	-0.006	11.037	-0.006	-0.006	0.000	0.000	0.000	0.000
10	B	76	VAL	0	-0.069	-0.041	14.587	-0.055	-0.055	0.000	0.000	0.000	0.000
11	B	90	TRP	0	0.007	-0.007	24.738	0.009	0.009	0.000	0.000	0.000	0.000
12	B	91	THR	0	0.003	-0.021	26.539	0.007	0.007	0.000	0.000	0.000	0.000
13	B	92	VAL	0	0.057	0.034	29.148	-0.006	-0.006	0.000	0.000	0.000	0.000
14	B	93	GLU	-1	-0.768	-0.849	31.045	-0.032	-0.032	0.000	0.000	0.000	0.000
15	B	94	LYS	1	0.881	0.921	25.132	-0.001	-0.001	0.000	0.000	0.000	0.000
16	B	95	GLN	0	0.010	0.036	25.406	-0.002	-0.002	0.000	0.000	0.000	0.000
17	B	96	ALA	0	0.048	0.035	27.652	-0.012	-0.012	0.000	0.000	0.000	0.000
18	B	97	ALA	0	-0.051	-0.013	27.134	-0.009	-0.009	0.000	0.000	0.000	0.000
19	B	98	ALA	0	0.019	0.007	23.236	-0.011	-0.011	0.000	0.000	0.000	0.000
20	B	99	THR	0	-0.022	-0.025	24.711	-0.020	-0.020	0.000	0.000	0.000	0.000
21	B	100	LEU	0	0.009	0.004	26.958	-0.009	-0.009	0.000	0.000	0.000	0.000
22	B	101	ASN	0	-0.029	-0.051	23.826	0.004	0.004	0.000	0.000	0.000	0.000
23	B	102	ALA	0	0.000	0.012	23.291	-0.016	-0.016	0.000	0.000	0.000	0.000
24	B	103	TRP	0	-0.002	-0.003	24.323	-0.006	-0.006	0.000	0.000	0.000	0.000
25	B	104	MET	0	-0.021	0.002	25.548	0.005	0.005	0.000	0.000	0.000	0.000
26	B	105	ARG	1	0.925	0.954	21.387	0.292	0.292	0.000	0.000	0.000	0.000
27	B	106	LYS	1	0.839	0.931	25.566	0.147	0.147	0.000	0.000	0.000	0.000
28	B	119	ALA	0	-0.013	-0.028	33.942	-0.002	-0.002	0.000	0.000	0.000	0.000
29	B	120	ALA	0	0.000	0.000	33.719	0.000	0.000	0.000	0.000	0.000	0.000
30	B	121	GLY	0	-0.002	-0.012	35.687	0.004	0.004	0.000	0.000	0.000	0.000
31	B	122	ILE	0	-0.041	-0.011	39.239	0.001	0.001	0.000	0.000	0.000	0.000
32	B	123	GLY	0	0.073	0.037	41.862	0.001	0.001	0.000	0.000	0.000	0.000
33	B	124	PRO	0	-0.023	0.002	40.283	0.002	0.002	0.000	0.000	0.000	0.000
34	B	125	ALA	0	0.062	0.019	39.106	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	126	THR	0	-0.022	-0.011	38.235	-0.002	-0.002	0.000	0.000	0.000	0.000
36	B	127	VAL	0	0.039	0.015	36.327	0.002	0.002	0.000	0.000	0.000	0.000
37	B	128	ASN	0	0.003	0.006	32.382	-0.004	-0.004	0.000	0.000	0.000	0.000
38	B	129	ARG	1	0.992	0.989	32.396	0.032	0.032	0.000	0.000	0.000	0.000
39	B	130	ILE	0	0.009	0.006	31.265	0.003	0.003	0.000	0.000	0.000	0.000
40	B	131	MET	0	0.002	0.019	27.059	-0.002	-0.002	0.000	0.000	0.000	0.000
41	B	132	LYS	1	0.906	0.971	26.684	0.008	0.008	0.000	0.000	0.000	0.000
42	B	133	ALA	0	-0.018	-0.019	28.248	0.009	0.009	0.000	0.000	0.000	0.000
43	B	134	GLU	-1	-0.938	-0.971	30.025	-0.010	-0.010	0.000	0.000	0.000	0.000
44	B	135	VAL	0	-0.035	-0.016	32.854	0.003	0.003	0.000	0.000	0.000	0.000
45	B	136	SER	0	-0.011	-0.026	34.352	-0.006	-0.006	0.000	0.000	0.000	0.000
46	B	137	THR	0	-0.040	-0.020	36.126	0.003	0.003	0.000	0.000	0.000	0.000
47	B	138	THR	0	0.038	0.020	38.104	-0.001	-0.001	0.000	0.000	0.000	0.000
48	B	139	ILE	0	0.112	0.034	39.227	-0.003	-0.003	0.000	0.000	0.000	0.000
49	B	140	GLY	0	0.041	0.035	40.821	-0.004	-0.004	0.000	0.000	0.000	0.000
50	B	141	VAL	0	-0.003	0.002	39.770	-0.003	-0.003	0.000	0.000	0.000	0.000
51	B	142	LEU	0	0.014	0.004	34.956	-0.004	-0.004	0.000	0.000	0.000	0.000
52	B	143	SER	0	0.023	0.012	37.853	-0.005	-0.005	0.000	0.000	0.000	0.000
53	B	144	SER	0	-0.062	-0.037	40.117	-0.003	-0.003	0.000	0.000	0.000	0.000
54	B	145	LEU	0	-0.043	-0.023	34.417	-0.003	-0.003	0.000	0.000	0.000	0.000
55	B	146	ALA	0	0.023	0.023	35.579	-0.006	-0.006	0.000	0.000	0.000	0.000
56	B	147	ARG	1	0.923	0.950	36.603	0.068	0.068	0.000	0.000	0.000	0.000
57	B	148	ALA	0	-0.039	-0.012	37.670	-0.002	-0.002	0.000	0.000	0.000	0.000
58	B	149	PHE	0	-0.040	-0.015	32.024	-0.004	-0.004	0.000	0.000	0.000	0.000
59	B	150	GLY	0	-0.029	-0.017	35.849	-0.007	-0.007	0.000	0.000	0.000	0.000
60	B	151	HIS	0	-0.047	-0.008	31.529	-0.010	-0.010	0.000	0.000	0.000	0.000
61	B	152	GLU	-1	-0.826	-0.930	36.237	-0.065	-0.065	0.000	0.000	0.000	0.000
62	B	153	ALA	0	-0.007	-0.015	36.027	-0.003	-0.003	0.000	0.000	0.000	0.000
63	B	154	TYR	0	-0.011	-0.023	34.536	0.001	0.001	0.000	0.000	0.000	0.000
64	B	155	GLU	-1	-0.735	-0.858	32.130	-0.110	-0.110	0.000	0.000	0.000	0.000
65	B	156	MET	0	-0.049	-0.020	30.682	-0.007	-0.007	0.000	0.000	0.000	0.000
66	B	157	ILE	0	-0.039	-0.022	30.555	0.003	0.003	0.000	0.000	0.000	0.000
67	B	158	ILE	0	0.037	0.030	28.725	0.008	0.008	0.000	0.000	0.000	0.000
68	B	159	PRO	0	-0.021	-0.006	27.488	-0.006	-0.006	0.000	0.000	0.000	0.000
69	B	160	VAL	0	0.017	-0.005	23.512	0.003	0.003	0.000	0.000	0.000	0.000
70	B	161	GLY	0	0.007	0.018	21.746	-0.010	-0.010	0.000	0.000	0.000	0.000
71	B	162	ALA	0	-0.036	-0.015	21.945	0.009	0.009	0.000	0.000	0.000	0.000
72	B	163	PRO	0	0.022	-0.012	21.656	-0.008	-0.008	0.000	0.000	0.000	0.000
73	B	164	GLY	0	-0.011	0.010	23.652	-0.005	-0.005	0.000	0.000	0.000	0.000
74	B	165	ILE	0	-0.077	-0.034	25.989	0.004	0.004	0.000	0.000	0.000	0.000
75	B	166	ILE	0	0.012	0.012	25.222	-0.009	-0.009	0.000	0.000	0.000	0.000
76	B	167	ASP	-1	-0.906	-0.956	22.784	-0.187	-0.187	0.000	0.000	0.000	0.000
77	B	168	TYR	0	-0.008	-0.010	25.329	-0.011	-0.011	0.000	0.000	0.000	0.000
78	B	169	ASP	-1	-0.774	-0.879	27.484	-0.138	-0.138	0.000	0.000	0.000	0.000
79	B	170	HIS	0	0.063	0.026	29.825	0.009	0.009	0.000	0.000	0.000	0.000
80	B	171	ARG	1	0.824	0.901	31.550	0.138	0.138	0.000	0.000	0.000	0.000
81	B	172	MET	0	-0.050	-0.029	30.706	0.000	0.000	0.000	0.000	0.000	0.000
82	B	173	TYR	0	0.032	0.012	32.782	0.005	0.005	0.000	0.000	0.000	0.000
83	B	174	ALA	0	-0.010	-0.015	34.592	0.006	0.006	0.000	0.000	0.000	0.000
84	B	175	ALA	0	-0.012	0.002	37.450	0.006	0.006	0.000	0.000	0.000	0.000
85	B	176	LEU	0	-0.019	0.019	33.900	0.001	0.001	0.000	0.000	0.000	0.000
86	B	177	PRO	0	0.034	0.007	38.369	0.007	0.007	0.000	0.000	0.000	0.000
87	B	178	GLN	0	0.003	-0.009	40.007	-0.003	-0.003	0.000	0.000	0.000	0.000
88	B	179	GLU	-1	-0.872	-0.918	41.032	-0.094	-0.094	0.000	0.000	0.000	0.000
89	B	180	GLU	-1	-0.798	-0.897	36.102	-0.118	-0.118	0.000	0.000	0.000	0.000
90	B	181	LYS	1	0.844	0.931	36.244	0.088	0.088	0.000	0.000	0.000	0.000
91	B	182	ASN	0	0.006	0.015	37.107	0.000	0.000	0.000	0.000	0.000	0.000
92	B	183	LYS	1	0.808	0.883	35.664	0.110	0.110	0.000	0.000	0.000	0.000
93	B	184	ILE	0	0.011	0.005	31.448	-0.003	-0.003	0.000	0.000	0.000	0.000
94	B	185	THR	0	-0.010	-0.018	33.141	-0.001	-0.001	0.000	0.000	0.000	0.000
95	B	186	SER	0	0.000	0.001	35.322	0.005	0.005	0.000	0.000	0.000	0.000
96	B	187	PHE	0	-0.025	-0.005	27.416	0.003	0.003	0.000	0.000	0.000	0.000
97	B	188	ILE	0	0.012	0.004	29.836	-0.002	-0.002	0.000	0.000	0.000	0.000
98	B	189	ASN	0	-0.028	-0.029	31.591	0.007	0.007	0.000	0.000	0.000	0.000
99	B	190	PHE	0	0.004	0.010	30.713	0.004	0.004	0.000	0.000	0.000	0.000
100	B	191	VAL	0	-0.009	-0.016	26.921	0.002	0.002	0.000	0.000	0.000	0.000
101	B	192	PHE	0	-0.035	-0.013	29.159	0.001	0.001	0.000	0.000	0.000	0.000
102	B	193	GLU	-1	-0.910	-0.924	31.649	-0.055	-0.055	0.000	0.000	0.000	0.000
103	B	194	GLN	0	-0.026	-0.012	29.621	0.009	0.009	0.000	0.000	0.000	0.000
104	B	195	ASN	0	-0.038	-0.020	26.277	-0.003	-0.003	0.000	0.000	0.000	0.000
105	B	196	LYS	1	0.849	0.919	28.904	0.058	0.058	0.000	0.000	0.000	0.000

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