FMO DATABASE

FMODB ID: Z6G1N

Calculation Name: 5C3L-C-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: 5C3L

Chain ID: C

ChEMBL ID:
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UniProt ID: Q91349

Base Structure: X-ray

Registration Date: 2023-06-26

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	128
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-769938.266297
FMO2-HF: Nuclear repulsion	716455.796262
FMO2-HF: Total energy	-53482.470035
FMO2-MP2: Total energy	-53638.941084

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(C:358:LEU)

Summations of interaction energy for fragment #1(C:358: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.
-2.901	0.191	1.014	-1.515	-2.59	0.004

Interaction energy analysis for fragmet #1(C:358:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.027

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	C	360	ASN	0	0.021	-0.021	3.340	-0.427	1.496	-0.015	-0.873	-1.035	0.000
4	C	361	LEU	0	-0.006	0.002	2.685	-1.434	-0.407	1.030	-0.625	-1.432	0.004
5	C	362	ILE	0	-0.010	0.001	5.367	-0.631	-0.489	-0.001	-0.017	-0.123	0.000
6	C	363	ASN	0	-0.013	-0.002	7.603	-0.083	-0.083	0.000	0.000	0.000	0.000
7	C	364	LYS	1	0.807	0.903	8.843	-0.891	-0.891	0.000	0.000	0.000	0.000
8	C	365	TRP	0	0.019	-0.007	6.993	-0.075	-0.075	0.000	0.000	0.000	0.000
9	C	366	SER	0	0.003	0.002	11.481	-0.088	-0.088	0.000	0.000	0.000	0.000
10	C	367	LEU	0	0.009	0.013	13.317	-0.023	-0.023	0.000	0.000	0.000	0.000
11	C	368	GLU	-1	-0.797	-0.889	13.038	0.589	0.589	0.000	0.000	0.000	0.000
12	C	369	LEU	0	-0.010	-0.014	15.031	-0.031	-0.031	0.000	0.000	0.000	0.000
13	C	370	GLU	-1	-0.973	-0.976	17.464	0.025	0.025	0.000	0.000	0.000	0.000
14	C	371	ASP	-1	-0.881	-0.928	19.087	0.192	0.192	0.000	0.000	0.000	0.000
15	C	372	GLN	0	-0.076	-0.058	19.587	-0.023	-0.023	0.000	0.000	0.000	0.000
16	C	373	GLU	-1	-0.956	-0.959	21.727	0.008	0.008	0.000	0.000	0.000	0.000
17	C	374	LYN	0	0.031	0.010	22.544	-0.012	-0.012	0.000	0.000	0.000	0.000
18	C	375	HIS	0	-0.045	-0.025	23.820	-0.009	-0.009	0.000	0.000	0.000	0.000
19	C	376	PHE	0	0.002	0.007	25.429	-0.007	-0.007	0.000	0.000	0.000	0.000
20	C	377	LEU	0	0.028	0.008	27.130	-0.007	-0.007	0.000	0.000	0.000	0.000
21	C	378	GLN	0	-0.030	-0.002	29.561	-0.006	-0.006	0.000	0.000	0.000	0.000
22	C	379	GLN	0	-0.004	-0.005	27.195	-0.007	-0.007	0.000	0.000	0.000	0.000
23	C	380	ALA	0	0.013	0.001	31.219	-0.004	-0.004	0.000	0.000	0.000	0.000
24	C	381	THR	0	-0.051	-0.040	33.013	-0.006	-0.006	0.000	0.000	0.000	0.000
25	C	382	GLN	0	-0.038	-0.013	34.524	0.000	0.000	0.000	0.000	0.000	0.000
26	C	383	VAL	0	0.020	0.008	34.241	-0.002	-0.002	0.000	0.000	0.000	0.000
27	C	384	ASN	0	-0.025	-0.004	36.075	-0.001	-0.001	0.000	0.000	0.000	0.000
28	C	385	ALA	0	0.004	0.010	39.116	-0.003	-0.003	0.000	0.000	0.000	0.000
29	C	386	TRP	0	-0.032	-0.017	37.490	0.000	0.000	0.000	0.000	0.000	0.000
30	C	387	ASP	-1	-0.833	-0.908	40.592	0.027	0.027	0.000	0.000	0.000	0.000
31	C	388	ARG	1	0.842	0.876	42.520	-0.022	-0.022	0.000	0.000	0.000	0.000
32	C	389	THR	0	-0.051	-0.028	44.727	-0.001	-0.001	0.000	0.000	0.000	0.000
33	C	390	LEU	0	-0.008	-0.004	43.902	-0.001	-0.001	0.000	0.000	0.000	0.000
34	C	391	MET	0	0.006	0.023	46.556	-0.001	-0.001	0.000	0.000	0.000	0.000
35	C	392	GLN	0	-0.003	0.002	48.429	-0.003	-0.003	0.000	0.000	0.000	0.000
36	C	393	ASN	0	0.032	0.018	48.669	-0.002	-0.002	0.000	0.000	0.000	0.000
37	C	394	GLY	0	0.041	0.030	50.690	-0.001	-0.001	0.000	0.000	0.000	0.000
38	C	395	GLU	-1	-0.788	-0.875	51.607	0.018	0.018	0.000	0.000	0.000	0.000
39	C	396	ARG	1	0.823	0.903	53.602	-0.021	-0.021	0.000	0.000	0.000	0.000
40	C	397	ILE	0	0.032	0.020	54.084	-0.001	-0.001	0.000	0.000	0.000	0.000
41	C	398	THR	0	-0.023	-0.030	55.519	-0.001	-0.001	0.000	0.000	0.000	0.000
42	C	399	THR	0	-0.076	-0.058	58.134	-0.001	-0.001	0.000	0.000	0.000	0.000
43	C	400	LEU	0	0.000	0.005	59.671	-0.001	-0.001	0.000	0.000	0.000	0.000
44	C	401	HIS	0	-0.038	-0.021	60.431	-0.001	-0.001	0.000	0.000	0.000	0.000
45	C	402	ARG	1	0.959	0.976	59.918	-0.015	-0.015	0.000	0.000	0.000	0.000
46	C	403	GLU	-1	-0.808	-0.891	64.673	0.013	0.013	0.000	0.000	0.000	0.000
47	C	404	MET	0	-0.018	0.001	65.011	0.000	0.000	0.000	0.000	0.000	0.000
48	C	405	GLU	-1	-0.810	-0.903	65.548	0.017	0.017	0.000	0.000	0.000	0.000
49	C	406	LYS	1	0.817	0.909	68.284	-0.014	-0.014	0.000	0.000	0.000	0.000
50	C	407	VAL	0	0.032	0.015	70.082	0.000	0.000	0.000	0.000	0.000	0.000
51	C	408	LYS	1	0.802	0.890	66.572	-0.018	-0.018	0.000	0.000	0.000	0.000
52	C	409	LEU	0	-0.040	-0.013	72.363	0.000	0.000	0.000	0.000	0.000	0.000
53	C	410	ASP	-1	-0.856	-0.934	73.935	0.012	0.012	0.000	0.000	0.000	0.000
54	C	411	GLN	0	-0.063	-0.041	75.366	0.000	0.000	0.000	0.000	0.000	0.000
55	C	412	LYS	1	0.960	0.972	75.102	-0.014	-0.014	0.000	0.000	0.000	0.000
56	C	413	ARG	1	0.814	0.902	78.235	-0.010	-0.010	0.000	0.000	0.000	0.000
57	C	414	LEU	0	-0.005	-0.022	79.675	0.000	0.000	0.000	0.000	0.000	0.000
58	C	415	ASP	-1	-0.845	-0.908	78.989	0.014	0.014	0.000	0.000	0.000	0.000
59	C	416	GLN	0	-0.015	-0.010	82.242	0.000	0.000	0.000	0.000	0.000	0.000
60	C	417	GLU	-1	-0.833	-0.893	84.639	0.009	0.009	0.000	0.000	0.000	0.000
61	C	418	LEU	0	-0.023	-0.004	84.913	0.000	0.000	0.000	0.000	0.000	0.000
62	C	419	ASP	-1	-0.896	-0.947	85.634	0.012	0.012	0.000	0.000	0.000	0.000
63	C	420	PHE	0	-0.061	-0.020	88.359	0.000	0.000	0.000	0.000	0.000	0.000
64	C	421	ILE	0	0.019	0.015	89.029	0.000	0.000	0.000	0.000	0.000	0.000
65	C	422	LEU	0	0.004	0.009	89.845	0.000	0.000	0.000	0.000	0.000	0.000
66	C	423	SER	0	-0.085	-0.060	92.547	0.000	0.000	0.000	0.000	0.000	0.000
67	C	424	GLN	0	-0.006	-0.024	94.480	0.000	0.000	0.000	0.000	0.000	0.000
68	C	425	GLN	0	-0.036	-0.019	93.928	0.000	0.000	0.000	0.000	0.000	0.000
69	C	426	LYS	1	0.759	0.863	96.698	-0.009	-0.009	0.000	0.000	0.000	0.000
70	C	427	GLU	-1	-0.884	-0.934	98.508	0.008	0.008	0.000	0.000	0.000	0.000
71	C	428	LEU	0	-0.025	-0.017	100.409	0.000	0.000	0.000	0.000	0.000	0.000
72	C	429	GLU	-1	-0.864	-0.921	101.015	0.009	0.009	0.000	0.000	0.000	0.000
73	C	430	ASP	-1	-0.843	-0.911	102.064	0.009	0.009	0.000	0.000	0.000	0.000
74	C	431	LEU	0	-0.068	-0.024	104.628	0.000	0.000	0.000	0.000	0.000	0.000
75	C	432	LEU	0	-0.029	-0.010	105.861	0.000	0.000	0.000	0.000	0.000	0.000
76	C	433	THR	0	0.046	0.013	106.414	0.000	0.000	0.000	0.000	0.000	0.000
77	C	434	PRO	0	-0.029	-0.014	108.546	0.000	0.000	0.000	0.000	0.000	0.000
78	C	435	LEU	0	-0.026	0.008	110.325	0.000	0.000	0.000	0.000	0.000	0.000
79	C	436	GLU	-1	-0.888	-0.951	108.499	0.008	0.008	0.000	0.000	0.000	0.000
80	C	437	GLU	-1	-0.886	-0.913	112.557	0.008	0.008	0.000	0.000	0.000	0.000
81	C	438	SER	0	-0.034	-0.039	115.025	0.000	0.000	0.000	0.000	0.000	0.000
82	C	439	VAL	0	-0.042	-0.024	116.039	0.000	0.000	0.000	0.000	0.000	0.000
83	C	440	LYS	1	0.798	0.876	113.301	-0.008	-0.008	0.000	0.000	0.000	0.000
84	C	441	GLU	-1	-0.969	-0.968	118.519	0.007	0.007	0.000	0.000	0.000	0.000
85	C	442	GLN	0	-0.021	-0.032	121.495	0.000	0.000	0.000	0.000	0.000	0.000
86	C	443	SER	0	-0.014	0.014	122.413	0.000	0.000	0.000	0.000	0.000	0.000
87	C	444	GLY	0	-0.051	-0.042	124.260	0.000	0.000	0.000	0.000	0.000	0.000
88	C	445	THR	0	-0.041	-0.006	126.163	0.000	0.000	0.000	0.000	0.000	0.000
89	C	446	ILE	0	-0.015	-0.020	128.268	0.000	0.000	0.000	0.000	0.000	0.000
90	C	447	TYR	0	0.006	0.017	132.056	0.000	0.000	0.000	0.000	0.000	0.000
91	C	448	LEU	0	-0.064	-0.007	130.990	0.000	0.000	0.000	0.000	0.000	0.000
92	C	449	GLN	0	0.079	0.013	129.579	0.000	0.000	0.000	0.000	0.000	0.000
93	C	450	HIS	0	-0.020	-0.004	130.514	0.000	0.000	0.000	0.000	0.000	0.000
94	C	451	ALA	0	0.000	-0.020	129.524	0.000	0.000	0.000	0.000	0.000	0.000
95	C	452	ASP	-1	-0.788	-0.889	127.039	0.005	0.005	0.000	0.000	0.000	0.000
96	C	453	GLU	-1	-0.853	-0.923	125.801	0.006	0.006	0.000	0.000	0.000	0.000
97	C	454	GLU	-1	-0.830	-0.910	125.248	0.005	0.005	0.000	0.000	0.000	0.000
98	C	455	ARG	1	0.838	0.930	122.860	-0.005	-0.005	0.000	0.000	0.000	0.000
99	C	456	GLU	-1	-0.886	-0.949	120.700	0.006	0.006	0.000	0.000	0.000	0.000
100	C	457	LYS	1	0.810	0.890	120.373	-0.006	-0.006	0.000	0.000	0.000	0.000
101	C	458	THR	0	-0.045	-0.027	119.312	0.000	0.000	0.000	0.000	0.000	0.000
102	C	459	TYR	0	-0.016	-0.019	116.486	0.000	0.000	0.000	0.000	0.000	0.000
103	C	460	LYS	1	0.856	0.922	115.762	-0.007	-0.007	0.000	0.000	0.000	0.000
104	C	461	LEU	0	-0.014	0.015	115.303	0.000	0.000	0.000	0.000	0.000	0.000
105	C	462	ALA	0	-0.014	-0.012	113.014	0.000	0.000	0.000	0.000	0.000	0.000
106	C	463	GLU	-1	-0.810	-0.891	111.401	0.007	0.007	0.000	0.000	0.000	0.000
107	C	464	ASN	0	-0.044	-0.032	110.534	0.000	0.000	0.000	0.000	0.000	0.000
108	C	465	ILE	0	0.004	0.000	109.148	0.000	0.000	0.000	0.000	0.000	0.000
109	C	466	ASP	-1	-0.817	-0.885	106.380	0.008	0.008	0.000	0.000	0.000	0.000
110	C	467	ALA	0	0.050	0.026	105.592	0.000	0.000	0.000	0.000	0.000	0.000
111	C	468	GLN	0	-0.065	-0.037	105.045	0.000	0.000	0.000	0.000	0.000	0.000
112	C	469	LEU	0	-0.005	-0.007	103.726	0.000	0.000	0.000	0.000	0.000	0.000
113	C	470	LYS	1	0.844	0.901	101.202	-0.008	-0.008	0.000	0.000	0.000	0.000
114	C	471	ARG	1	0.890	0.945	100.148	-0.009	-0.009	0.000	0.000	0.000	0.000
115	C	472	MET	0	-0.027	-0.011	99.597	0.000	0.000	0.000	0.000	0.000	0.000
116	C	473	ALA	0	-0.032	-0.017	97.602	0.000	0.000	0.000	0.000	0.000	0.000
117	C	474	GLN	0	0.028	0.012	93.262	0.000	0.000	0.000	0.000	0.000	0.000
118	C	475	ASP	-1	-0.816	-0.907	94.841	0.010	0.010	0.000	0.000	0.000	0.000
119	C	476	LEU	0	-0.045	-0.032	94.420	0.000	0.000	0.000	0.000	0.000	0.000
120	C	477	LYS	1	0.929	0.970	91.353	-0.010	-0.010	0.000	0.000	0.000	0.000
121	C	478	GLU	-1	-0.818	-0.895	90.215	0.012	0.012	0.000	0.000	0.000	0.000
122	C	479	VAL	0	-0.028	-0.007	89.683	0.000	0.000	0.000	0.000	0.000	0.000
123	C	480	ILE	0	-0.045	-0.030	87.184	0.000	0.000	0.000	0.000	0.000	0.000
124	C	481	GLU	-1	-0.954	-0.965	85.867	0.013	0.013	0.000	0.000	0.000	0.000
125	C	482	HIS	0	-0.043	-0.044	84.893	0.001	0.001	0.000	0.000	0.000	0.000
126	C	483	LEU	0	-0.077	-0.021	84.785	0.000	0.000	0.000	0.000	0.000	0.000
127	C	484	ASN	0	-0.111	-0.053	81.743	0.000	0.000	0.000	0.000	0.000	0.000
128	C	485	THR	0	-0.051	-0.019	77.781	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:358:LEU)