FMO DATABASE

FMODB ID: KG2J3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-658105.408775
FMO2-HF: Nuclear repulsion	617627.87105
FMO2-HF: Total energy	-40477.537724
FMO2-MP2: Total energy	-40594.78017

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.
-0.687	1.002	-0.011	-0.768	-0.91	0

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 : -0.063 / q_NPA : -0.051

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	J	69	VAL	0	-0.073	-0.048	3.838	-0.073	1.616	-0.011	-0.768	-0.910
4	J	70	ASP	-1	-0.880	-0.917	6.170	-0.625	-0.625	0.000	0.000	0.000
5	J	71	HIS	0	0.012	-0.013	7.895	0.286	0.286	0.000	0.000	0.000
6	J	72	GLU	-1	-0.949	-0.986	12.239	-0.418	-0.418	0.000	0.000	0.000
7	J	73	LEU	0	-0.074	-0.038	15.073	0.055	0.055	0.000	0.000	0.000
8	J	74	ASP	-1	-0.970	-0.977	15.876	-0.218	-0.218	0.000	0.000	0.000
9	J	75	ALA	0	-0.019	-0.004	17.600	0.029	0.029	0.000	0.000	0.000
10	J	76	VAL	0	-0.079	-0.032	20.520	0.029	0.029	0.000	0.000	0.000
11	J	90	TRP	0	-0.020	-0.042	29.353	0.002	0.002	0.000	0.000	0.000
12	J	91	THR	0	-0.002	-0.010	31.393	0.005	0.005	0.000	0.000	0.000
13	J	92	VAL	0	0.100	0.042	32.730	-0.007	-0.007	0.000	0.000	0.000
14	J	93	GLU	-1	-0.815	-0.846	34.556	-0.099	-0.099	0.000	0.000	0.000
15	J	94	LYS	1	0.928	0.958	29.289	0.135	0.135	0.000	0.000	0.000
16	J	95	GLN	0	0.001	0.040	28.698	-0.008	-0.008	0.000	0.000	0.000
17	J	96	ALA	0	0.075	0.031	30.533	-0.004	-0.004	0.000	0.000	0.000
18	J	97	ALA	0	-0.003	0.021	29.687	-0.001	-0.001	0.000	0.000	0.000
19	J	98	ALA	0	-0.009	-0.006	25.828	-0.003	-0.003	0.000	0.000	0.000
20	J	99	THR	0	0.002	0.003	26.802	-0.009	-0.009	0.000	0.000	0.000
21	J	100	LEU	0	-0.021	-0.011	29.289	0.004	0.004	0.000	0.000	0.000
22	J	101	ASN	0	0.019	-0.030	26.148	0.009	0.009	0.000	0.000	0.000
23	J	102	ALA	0	-0.037	-0.011	24.782	-0.003	-0.003	0.000	0.000	0.000
24	J	103	TRP	0	0.045	0.015	25.744	0.004	0.004	0.000	0.000	0.000
25	J	104	MET	0	-0.047	-0.025	28.736	0.005	0.005	0.000	0.000	0.000
26	J	105	ARG	1	0.927	0.975	19.673	0.230	0.230	0.000	0.000	0.000
27	J	106	LYS	1	0.938	0.986	26.640	0.128	0.128	0.000	0.000	0.000
28	J	121	GLY	0	0.015	-0.003	45.417	-0.001	-0.001	0.000	0.000	0.000
29	J	122	ILE	0	-0.008	-0.008	41.089	0.001	0.001	0.000	0.000	0.000
30	J	123	GLY	0	0.049	0.041	42.554	0.000	0.000	0.000	0.000	0.000
31	J	124	PRO	0	0.086	0.054	38.199	-0.003	-0.003	0.000	0.000	0.000
32	J	125	ALA	0	0.038	0.010	37.364	-0.005	-0.005	0.000	0.000	0.000
33	J	126	THR	0	-0.073	-0.069	38.263	-0.002	-0.002	0.000	0.000	0.000
34	J	127	VAL	0	0.073	0.032	34.539	-0.002	-0.002	0.000	0.000	0.000
35	J	128	ASN	0	-0.023	-0.017	31.931	-0.002	-0.002	0.000	0.000	0.000
36	J	129	ARG	1	0.903	0.962	33.461	0.078	0.078	0.000	0.000	0.000
37	J	130	ILE	0	-0.006	-0.003	34.291	-0.004	-0.004	0.000	0.000	0.000
38	J	131	MET	0	-0.028	-0.008	29.891	-0.006	-0.006	0.000	0.000	0.000
39	J	132	LYS	1	0.895	0.960	29.425	0.097	0.097	0.000	0.000	0.000
40	J	133	ALA	0	-0.012	0.008	30.907	-0.004	-0.004	0.000	0.000	0.000
41	J	134	GLU	-1	-0.893	-0.950	32.975	-0.093	-0.093	0.000	0.000	0.000
42	J	135	VAL	0	-0.047	-0.029	35.360	0.006	0.006	0.000	0.000	0.000
43	J	136	SER	0	-0.042	-0.088	37.485	-0.004	-0.004	0.000	0.000	0.000
44	J	137	THR	0	-0.022	-0.011	37.653	0.002	0.002	0.000	0.000	0.000
45	J	138	THR	0	0.027	0.021	40.015	0.001	0.001	0.000	0.000	0.000
46	J	139	ILE	0	0.119	0.041	41.794	-0.003	-0.003	0.000	0.000	0.000
47	J	140	GLY	0	0.023	0.019	43.097	-0.001	-0.001	0.000	0.000	0.000
48	J	141	VAL	0	-0.005	-0.007	39.849	0.001	0.001	0.000	0.000	0.000
49	J	142	LEU	0	0.052	0.018	36.652	-0.002	-0.002	0.000	0.000	0.000
50	J	143	SER	0	-0.084	-0.039	39.638	-0.002	-0.002	0.000	0.000	0.000
51	J	144	SER	0	-0.022	-0.033	41.514	0.000	0.000	0.000	0.000	0.000
52	J	145	LEU	0	-0.036	0.003	35.749	0.001	0.001	0.000	0.000	0.000
53	J	146	ALA	0	0.030	0.014	36.861	-0.002	-0.002	0.000	0.000	0.000
54	J	147	ARG	1	0.992	0.990	37.667	0.064	0.064	0.000	0.000	0.000
55	J	148	ALA	0	-0.005	0.016	38.082	0.001	0.001	0.000	0.000	0.000
56	J	149	PHE	0	-0.017	0.004	32.519	-0.001	-0.001	0.000	0.000	0.000
57	J	150	GLY	0	-0.028	-0.011	35.442	-0.003	-0.003	0.000	0.000	0.000
58	J	151	HIS	1	0.858	0.931	32.082	0.105	0.105	0.000	0.000	0.000
59	J	152	GLU	-1	-0.927	-0.973	37.137	-0.069	-0.069	0.000	0.000	0.000
60	J	153	ALA	0	-0.015	-0.012	39.727	-0.001	-0.001	0.000	0.000	0.000
61	J	154	TYR	0	-0.019	-0.027	37.849	-0.001	-0.001	0.000	0.000	0.000
62	J	155	GLU	-1	-0.878	-0.953	34.753	-0.100	-0.100	0.000	0.000	0.000
63	J	156	MET	0	-0.027	-0.001	32.982	-0.005	-0.005	0.000	0.000	0.000
64	J	157	ILE	0	-0.022	-0.019	33.294	-0.006	-0.006	0.000	0.000	0.000
65	J	158	ILE	0	-0.002	0.007	33.386	0.003	0.003	0.000	0.000	0.000
66	J	159	PRO	0	-0.007	0.003	31.507	-0.008	-0.008	0.000	0.000	0.000
67	J	160	VAL	0	-0.004	-0.005	26.639	0.005	0.005	0.000	0.000	0.000
68	J	161	GLY	0	-0.022	-0.007	27.491	-0.012	-0.012	0.000	0.000	0.000
69	J	162	ALA	0	0.014	-0.005	28.413	0.002	0.002	0.000	0.000	0.000
70	J	163	PRO	0	-0.031	-0.016	29.327	0.003	0.003	0.000	0.000	0.000
71	J	164	GLY	0	0.013	0.022	31.777	0.005	0.005	0.000	0.000	0.000
72	J	165	ILE	0	0.022	0.007	30.042	-0.009	-0.009	0.000	0.000	0.000
73	J	166	ILE	0	0.012	-0.010	23.922	0.002	0.002	0.000	0.000	0.000
74	J	167	ASP	-1	-0.954	-0.967	25.881	-0.172	-0.172	0.000	0.000	0.000
75	J	168	TYR	0	-0.018	0.010	27.893	0.002	0.002	0.000	0.000	0.000
76	J	169	ASP	-1	-0.870	-0.960	30.345	-0.106	-0.106	0.000	0.000	0.000
77	J	170	HIS	0	0.085	0.050	32.120	0.011	0.011	0.000	0.000	0.000
78	J	171	ARG	1	0.960	0.993	33.149	0.098	0.098	0.000	0.000	0.000
79	J	172	MET	0	-0.060	-0.044	31.198	0.004	0.004	0.000	0.000	0.000
80	J	173	TYR	0	0.081	0.042	35.949	0.005	0.005	0.000	0.000	0.000
81	J	174	ALA	0	-0.004	-0.012	37.398	0.005	0.005	0.000	0.000	0.000
82	J	175	ALA	0	-0.030	-0.016	38.926	0.004	0.004	0.000	0.000	0.000
83	J	176	LEU	0	-0.013	0.014	36.379	0.003	0.003	0.000	0.000	0.000
84	J	177	PRO	0	0.016	0.009	40.400	0.002	0.002	0.000	0.000	0.000
85	J	178	GLN	0	0.027	0.012	42.692	-0.002	-0.002	0.000	0.000	0.000
86	J	179	GLU	-1	-0.859	-0.947	44.133	-0.050	-0.050	0.000	0.000	0.000
87	J	180	GLU	-1	-0.880	-0.925	38.967	-0.061	-0.061	0.000	0.000	0.000
88	J	181	LYS	1	0.797	0.909	39.257	0.060	0.060	0.000	0.000	0.000
89	J	182	ASN	0	-0.022	-0.025	40.130	-0.002	-0.002	0.000	0.000	0.000
90	J	183	LYS	1	0.890	0.935	38.396	0.055	0.055	0.000	0.000	0.000
91	J	184	ILE	0	0.023	0.021	34.955	-0.002	-0.002	0.000	0.000	0.000
92	J	185	THR	0	-0.035	-0.004	36.943	-0.002	-0.002	0.000	0.000	0.000
93	J	186	SER	0	0.017	0.012	39.231	-0.001	-0.001	0.000	0.000	0.000
94	J	187	PHE	0	0.017	0.012	31.157	0.001	0.001	0.000	0.000	0.000
95	J	188	ILE	0	0.006	-0.004	34.070	-0.002	-0.002	0.000	0.000	0.000
96	J	189	ASN	0	-0.001	-0.005	35.893	-0.004	-0.004	0.000	0.000	0.000
97	J	190	PHE	0	0.018	0.026	35.309	0.001	0.001	0.000	0.000	0.000
98	J	191	VAL	0	-0.007	-0.008	31.807	0.000	0.000	0.000	0.000	0.000
99	J	192	PHE	0	-0.037	-0.027	34.131	-0.002	-0.002	0.000	0.000	0.000
100	J	193	GLU	-1	-0.904	-0.962	36.700	-0.057	-0.057	0.000	0.000	0.000
101	J	194	GLN	0	-0.104	-0.035	34.078	0.000	0.000	0.000	0.000	0.000
102	J	195	ASN	0	-0.100	-0.043	33.117	-0.007	-0.007	0.000	0.000	0.000
103	J	196	LYS	1	0.965	0.987	36.302	0.053	0.053	0.000	0.000	0.000

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