FMO DATABASE

FMODB ID: 6NR8Z

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	OptHSide
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	-769655.88115
FMO2-HF: Nuclear repulsion	716173.867695
FMO2-HF: Total energy	-53482.013455
FMO2-MP2: Total energy	-53638.564105

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.
-2.95	0.02	2.408	-2.022	-3.355	0.007

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 : -0.033 / q_NPA : -0.033

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	0.001	-0.022	3.113	-0.726	1.799	-0.013	-1.187	-1.325	0.000
4	C	361	LEU	0	0.005	0.013	2.488	-1.122	-0.800	2.422	-0.821	-1.923	0.007
5	C	362	ILE	0	-0.030	-0.006	5.336	-0.605	-0.482	-0.001	-0.014	-0.107	0.000
6	C	363	ASN	0	0.028	0.004	7.541	-0.162	-0.162	0.000	0.000	0.000	0.000
7	C	364	LYS	1	0.802	0.900	9.089	-0.796	-0.796	0.000	0.000	0.000	0.000
8	C	365	TRP	0	0.038	0.014	6.749	-0.132	-0.132	0.000	0.000	0.000	0.000
9	C	366	SER	0	-0.036	-0.017	11.476	-0.090	-0.090	0.000	0.000	0.000	0.000
10	C	367	LEU	0	0.000	0.004	13.404	-0.041	-0.041	0.000	0.000	0.000	0.000
11	C	368	GLU	-1	-0.795	-0.887	13.366	0.534	0.534	0.000	0.000	0.000	0.000
12	C	369	LEU	0	0.057	0.018	15.209	-0.031	-0.031	0.000	0.000	0.000	0.000
13	C	370	GLU	-1	-0.970	-0.969	17.509	0.021	0.021	0.000	0.000	0.000	0.000
14	C	371	ASP	-1	-0.903	-0.963	19.152	0.201	0.201	0.000	0.000	0.000	0.000
15	C	372	GLN	0	-0.105	-0.060	19.299	-0.017	-0.017	0.000	0.000	0.000	0.000
16	C	373	GLU	-1	-0.953	-0.957	21.698	0.023	0.023	0.000	0.000	0.000	0.000
17	C	374	LYN	0	0.028	0.012	22.103	-0.011	-0.011	0.000	0.000	0.000	0.000
18	C	375	HIS	0	-0.051	-0.029	24.096	-0.008	-0.008	0.000	0.000	0.000	0.000
19	C	376	PHE	0	0.003	0.007	25.325	-0.009	-0.009	0.000	0.000	0.000	0.000
20	C	377	LEU	0	0.040	0.017	27.100	-0.007	-0.007	0.000	0.000	0.000	0.000
21	C	378	GLN	0	-0.027	0.005	29.546	-0.005	-0.005	0.000	0.000	0.000	0.000
22	C	379	GLN	0	-0.005	-0.009	27.712	-0.006	-0.006	0.000	0.000	0.000	0.000
23	C	380	ALA	0	0.032	0.009	31.183	-0.004	-0.004	0.000	0.000	0.000	0.000
24	C	381	THR	0	-0.047	-0.035	32.889	-0.006	-0.006	0.000	0.000	0.000	0.000
25	C	382	GLN	0	-0.030	-0.017	34.600	-0.001	-0.001	0.000	0.000	0.000	0.000
26	C	383	VAL	0	-0.018	-0.003	34.042	-0.001	-0.001	0.000	0.000	0.000	0.000
27	C	384	ASN	0	0.008	0.013	36.280	-0.002	-0.002	0.000	0.000	0.000	0.000
28	C	385	ALA	0	-0.018	0.012	38.983	-0.003	-0.003	0.000	0.000	0.000	0.000
29	C	386	TRP	0	-0.028	-0.043	37.617	0.000	0.000	0.000	0.000	0.000	0.000
30	C	387	ASP	-1	-0.898	-0.951	40.374	0.030	0.030	0.000	0.000	0.000	0.000
31	C	388	ARG	1	0.904	0.918	42.267	-0.025	-0.025	0.000	0.000	0.000	0.000
32	C	389	THR	0	-0.060	-0.023	44.653	-0.002	-0.002	0.000	0.000	0.000	0.000
33	C	390	LEU	0	-0.005	-0.007	43.571	-0.001	-0.001	0.000	0.000	0.000	0.000
34	C	391	MET	0	0.014	0.041	46.548	-0.001	-0.001	0.000	0.000	0.000	0.000
35	C	392	GLN	0	0.002	0.005	48.312	-0.002	-0.002	0.000	0.000	0.000	0.000
36	C	393	ASN	0	0.020	0.010	48.617	-0.002	-0.002	0.000	0.000	0.000	0.000
37	C	394	GLY	0	0.073	0.047	50.547	-0.001	-0.001	0.000	0.000	0.000	0.000
38	C	395	GLU	-1	-0.802	-0.888	51.674	0.019	0.019	0.000	0.000	0.000	0.000
39	C	396	ARG	1	0.864	0.915	53.744	-0.022	-0.022	0.000	0.000	0.000	0.000
40	C	397	ILE	0	-0.019	-0.010	53.538	0.000	0.000	0.000	0.000	0.000	0.000
41	C	398	THR	0	-0.026	-0.022	55.495	-0.001	-0.001	0.000	0.000	0.000	0.000
42	C	399	THR	0	-0.081	-0.053	58.011	-0.001	-0.001	0.000	0.000	0.000	0.000
43	C	400	LEU	0	0.006	0.002	59.172	-0.001	-0.001	0.000	0.000	0.000	0.000
44	C	401	HIS	0	-0.033	-0.009	60.095	0.000	0.000	0.000	0.000	0.000	0.000
45	C	402	ARG	1	0.981	0.988	60.106	-0.016	-0.016	0.000	0.000	0.000	0.000
46	C	403	GLU	-1	-0.806	-0.897	64.411	0.014	0.014	0.000	0.000	0.000	0.000
47	C	404	MET	0	-0.024	-0.011	64.662	0.000	0.000	0.000	0.000	0.000	0.000
48	C	405	GLU	-1	-0.825	-0.910	65.386	0.017	0.017	0.000	0.000	0.000	0.000
49	C	406	LYS	1	0.805	0.900	68.066	-0.014	-0.014	0.000	0.000	0.000	0.000
50	C	407	VAL	0	0.019	0.007	69.947	0.000	0.000	0.000	0.000	0.000	0.000
51	C	408	LYS	1	0.821	0.909	66.428	-0.018	-0.018	0.000	0.000	0.000	0.000
52	C	409	LEU	0	-0.033	-0.016	72.090	0.000	0.000	0.000	0.000	0.000	0.000
53	C	410	ASP	-1	-0.854	-0.930	74.334	0.012	0.012	0.000	0.000	0.000	0.000
54	C	411	GLN	0	-0.072	-0.036	75.060	0.000	0.000	0.000	0.000	0.000	0.000
55	C	412	LYS	1	0.968	0.977	74.983	-0.014	-0.014	0.000	0.000	0.000	0.000
56	C	413	ARG	1	0.819	0.907	78.139	-0.011	-0.011	0.000	0.000	0.000	0.000
57	C	414	LEU	0	-0.010	-0.016	79.636	0.000	0.000	0.000	0.000	0.000	0.000
58	C	415	ASP	-1	-0.835	-0.915	78.817	0.014	0.014	0.000	0.000	0.000	0.000
59	C	416	GLN	0	-0.027	-0.014	81.646	0.000	0.000	0.000	0.000	0.000	0.000
60	C	417	GLU	-1	-0.837	-0.903	84.345	0.010	0.010	0.000	0.000	0.000	0.000
61	C	418	LEU	0	-0.031	-0.015	84.519	0.000	0.000	0.000	0.000	0.000	0.000
62	C	419	ASP	-1	-0.891	-0.940	85.577	0.012	0.012	0.000	0.000	0.000	0.000
63	C	420	PHE	0	-0.071	-0.024	88.203	0.000	0.000	0.000	0.000	0.000	0.000
64	C	421	ILE	0	0.027	0.022	88.936	0.000	0.000	0.000	0.000	0.000	0.000
65	C	422	LEU	0	0.012	0.016	89.854	0.000	0.000	0.000	0.000	0.000	0.000
66	C	423	SER	0	-0.059	-0.047	92.461	0.000	0.000	0.000	0.000	0.000	0.000
67	C	424	GLN	0	-0.023	-0.017	94.408	0.000	0.000	0.000	0.000	0.000	0.000
68	C	425	GLN	0	-0.024	-0.019	94.313	0.000	0.000	0.000	0.000	0.000	0.000
69	C	426	LYS	1	0.758	0.871	96.420	-0.009	-0.009	0.000	0.000	0.000	0.000
70	C	427	GLU	-1	-0.901	-0.953	98.304	0.008	0.008	0.000	0.000	0.000	0.000
71	C	428	LEU	0	-0.053	-0.031	100.175	0.000	0.000	0.000	0.000	0.000	0.000
72	C	429	GLU	-1	-0.862	-0.922	100.961	0.009	0.009	0.000	0.000	0.000	0.000
73	C	430	ASP	-1	-0.856	-0.927	101.720	0.009	0.009	0.000	0.000	0.000	0.000
74	C	431	LEU	0	-0.071	-0.025	104.394	0.000	0.000	0.000	0.000	0.000	0.000
75	C	432	LEU	0	-0.014	-0.006	105.438	0.000	0.000	0.000	0.000	0.000	0.000
76	C	433	THR	0	0.053	0.022	106.164	0.000	0.000	0.000	0.000	0.000	0.000
77	C	434	PRO	0	-0.016	-0.003	108.416	0.000	0.000	0.000	0.000	0.000	0.000
78	C	435	LEU	0	-0.031	0.006	109.975	0.000	0.000	0.000	0.000	0.000	0.000
79	C	436	GLU	-1	-0.881	-0.949	108.600	0.008	0.008	0.000	0.000	0.000	0.000
80	C	437	GLU	-1	-0.897	-0.925	112.300	0.007	0.007	0.000	0.000	0.000	0.000
81	C	438	SER	0	-0.055	-0.041	114.783	0.000	0.000	0.000	0.000	0.000	0.000
82	C	439	VAL	0	-0.040	-0.026	115.846	0.000	0.000	0.000	0.000	0.000	0.000
83	C	440	LYS	1	0.796	0.879	113.311	-0.007	-0.007	0.000	0.000	0.000	0.000
84	C	441	GLU	-1	-0.962	-0.971	118.387	0.006	0.006	0.000	0.000	0.000	0.000
85	C	442	GLN	0	0.005	-0.003	121.688	0.000	0.000	0.000	0.000	0.000	0.000
86	C	443	SER	0	-0.023	-0.001	122.312	0.000	0.000	0.000	0.000	0.000	0.000
87	C	444	GLY	0	-0.054	-0.046	124.156	0.000	0.000	0.000	0.000	0.000	0.000
88	C	445	THR	0	-0.044	-0.003	125.827	0.000	0.000	0.000	0.000	0.000	0.000
89	C	446	ILE	0	-0.010	-0.019	128.107	0.000	0.000	0.000	0.000	0.000	0.000
90	C	447	TYR	0	0.003	0.014	131.783	0.000	0.000	0.000	0.000	0.000	0.000
91	C	448	LEU	0	-0.050	-0.016	130.872	0.000	0.000	0.000	0.000	0.000	0.000
92	C	449	GLN	0	0.056	0.008	129.477	0.000	0.000	0.000	0.000	0.000	0.000
93	C	450	HIS	0	0.037	0.036	130.488	0.000	0.000	0.000	0.000	0.000	0.000
94	C	451	ALA	0	-0.021	-0.021	129.466	0.000	0.000	0.000	0.000	0.000	0.000
95	C	452	ASP	-1	-0.798	-0.905	127.124	0.005	0.005	0.000	0.000	0.000	0.000
96	C	453	GLU	-1	-0.928	-0.954	126.003	0.006	0.006	0.000	0.000	0.000	0.000
97	C	454	GLU	-1	-0.873	-0.931	125.445	0.005	0.005	0.000	0.000	0.000	0.000
98	C	455	ARG	1	0.863	0.914	122.773	-0.005	-0.005	0.000	0.000	0.000	0.000
99	C	456	GLU	-1	-0.905	-0.951	121.005	0.006	0.006	0.000	0.000	0.000	0.000
100	C	457	LYS	1	0.878	0.930	120.423	-0.005	-0.005	0.000	0.000	0.000	0.000
101	C	458	THR	0	-0.066	-0.036	119.392	0.000	0.000	0.000	0.000	0.000	0.000
102	C	459	TYR	0	-0.002	-0.017	116.479	0.000	0.000	0.000	0.000	0.000	0.000
103	C	460	LYS	1	0.871	0.935	115.557	-0.007	-0.007	0.000	0.000	0.000	0.000
104	C	461	LEU	0	-0.046	-0.012	115.020	0.000	0.000	0.000	0.000	0.000	0.000
105	C	462	ALA	0	-0.013	-0.014	112.946	0.000	0.000	0.000	0.000	0.000	0.000
106	C	463	GLU	-1	-0.786	-0.872	111.247	0.007	0.007	0.000	0.000	0.000	0.000
107	C	464	ASN	0	0.002	-0.007	110.258	0.000	0.000	0.000	0.000	0.000	0.000
108	C	465	ILE	0	-0.002	0.002	108.998	0.000	0.000	0.000	0.000	0.000	0.000
109	C	466	ASP	-1	-0.827	-0.887	105.951	0.008	0.008	0.000	0.000	0.000	0.000
110	C	467	ALA	0	0.049	0.022	105.491	0.000	0.000	0.000	0.000	0.000	0.000
111	C	468	GLN	0	-0.081	-0.045	105.112	0.000	0.000	0.000	0.000	0.000	0.000
112	C	469	LEU	0	-0.004	-0.013	103.605	0.000	0.000	0.000	0.000	0.000	0.000
113	C	470	LYS	1	0.860	0.912	101.075	-0.008	-0.008	0.000	0.000	0.000	0.000
114	C	471	ARG	1	0.908	0.967	99.978	-0.009	-0.009	0.000	0.000	0.000	0.000
115	C	472	MET	0	-0.022	-0.015	99.519	0.000	0.000	0.000	0.000	0.000	0.000
116	C	473	ALA	0	-0.036	-0.013	97.417	0.000	0.000	0.000	0.000	0.000	0.000
117	C	474	GLN	0	0.016	0.001	93.483	0.000	0.000	0.000	0.000	0.000	0.000
118	C	475	ASP	-1	-0.832	-0.917	94.901	0.010	0.010	0.000	0.000	0.000	0.000
119	C	476	LEU	0	-0.053	-0.041	94.335	0.000	0.000	0.000	0.000	0.000	0.000
120	C	477	LYS	1	0.926	0.961	91.163	-0.010	-0.010	0.000	0.000	0.000	0.000
121	C	478	GLU	-1	-0.822	-0.893	89.993	0.012	0.012	0.000	0.000	0.000	0.000
122	C	479	VAL	0	-0.026	-0.009	89.765	0.000	0.000	0.000	0.000	0.000	0.000
123	C	480	ILE	0	-0.054	-0.043	86.772	0.000	0.000	0.000	0.000	0.000	0.000
124	C	481	GLU	-1	-0.963	-0.968	85.832	0.013	0.013	0.000	0.000	0.000	0.000
125	C	482	HIS	0	-0.057	-0.036	84.901	0.001	0.001	0.000	0.000	0.000	0.000
126	C	483	LEU	0	-0.081	-0.024	84.735	0.000	0.000	0.000	0.000	0.000	0.000
127	C	484	ASN	0	-0.074	-0.027	81.396	0.000	0.000	0.000	0.000	0.000	0.000
128	C	485	THR	0	-0.037	-0.012	77.462	0.000	0.000	0.000	0.000	0.000	0.000

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