FMO DATABASE

FMODB ID: 2J58R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-768455.726012
FMO2-HF: Nuclear repulsion	714974.864861
FMO2-HF: Total energy	-53480.861151
FMO2-MP2: Total energy	-53637.391432

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.
-0.46	-0.584	5.33	-1.489	-3.717	0.002

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 : -0.042

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

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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	-0.007	-0.016	3.102	-0.589	1.934	-0.012	-1.181	-1.329	-0.001
4	C	361	LEU	0	0.021	0.032	2.521	1.080	-1.567	5.342	-0.308	-2.388	0.003
5	C	362	ILE	0	-0.009	-0.006	5.536	-0.488	-0.488	0.000	0.000	0.000	0.000
6	C	363	ASN	0	0.019	-0.009	7.541	-0.087	-0.087	0.000	0.000	0.000	0.000
7	C	364	LYS	1	0.890	0.958	9.085	-0.791	-0.791	0.000	0.000	0.000	0.000
8	C	365	TRP	0	0.010	0.011	6.571	-0.164	-0.164	0.000	0.000	0.000	0.000
9	C	366	SER	0	-0.031	-0.014	11.475	-0.092	-0.092	0.000	0.000	0.000	0.000
10	C	367	LEU	0	0.004	0.005	13.406	-0.042	-0.042	0.000	0.000	0.000	0.000
11	C	368	GLU	-1	-0.863	-0.932	14.175	0.504	0.504	0.000	0.000	0.000	0.000
12	C	369	LEU	0	0.047	0.013	15.315	-0.033	-0.033	0.000	0.000	0.000	0.000
13	C	370	GLU	-1	-0.965	-0.966	17.524	0.018	0.018	0.000	0.000	0.000	0.000
14	C	371	ASP	-1	-0.958	-1.013	19.127	0.209	0.209	0.000	0.000	0.000	0.000
15	C	372	GLN	0	-0.076	-0.040	19.119	-0.011	-0.011	0.000	0.000	0.000	0.000
16	C	373	GLU	-1	-0.936	-0.952	21.710	0.026	0.026	0.000	0.000	0.000	0.000
17	C	374	LYN	0	0.005	0.012	21.790	-0.012	-0.012	0.000	0.000	0.000	0.000
18	C	375	HIS	0	-0.014	-0.005	24.747	0.003	0.003	0.000	0.000	0.000	0.000
19	C	376	PHE	0	0.014	0.015	25.312	-0.009	-0.009	0.000	0.000	0.000	0.000
20	C	377	LEU	0	0.043	0.020	27.084	-0.006	-0.006	0.000	0.000	0.000	0.000
21	C	378	GLN	0	-0.031	0.028	29.548	-0.005	-0.005	0.000	0.000	0.000	0.000
22	C	379	GLN	0	-0.018	-0.014	28.226	-0.007	-0.007	0.000	0.000	0.000	0.000
23	C	380	ALA	0	0.035	0.011	31.189	-0.004	-0.004	0.000	0.000	0.000	0.000
24	C	381	THR	0	-0.060	-0.069	32.889	-0.006	-0.006	0.000	0.000	0.000	0.000
25	C	382	GLN	0	-0.008	-0.009	34.771	-0.004	-0.004	0.000	0.000	0.000	0.000
26	C	383	VAL	0	-0.030	-0.006	34.009	-0.001	-0.001	0.000	0.000	0.000	0.000
27	C	384	ASN	0	0.008	0.013	36.233	-0.003	-0.003	0.000	0.000	0.000	0.000
28	C	385	ALA	0	-0.026	0.010	38.983	-0.003	-0.003	0.000	0.000	0.000	0.000
29	C	386	TRP	0	-0.025	-0.039	38.058	-0.001	-0.001	0.000	0.000	0.000	0.000
30	C	387	ASP	-1	-0.880	-0.943	40.414	0.032	0.032	0.000	0.000	0.000	0.000
31	C	388	ARG	1	0.971	0.981	42.267	-0.026	-0.026	0.000	0.000	0.000	0.000
32	C	389	THR	0	-0.051	-0.016	44.652	-0.002	-0.002	0.000	0.000	0.000	0.000
33	C	390	LEU	0	-0.008	-0.012	43.674	-0.001	-0.001	0.000	0.000	0.000	0.000
34	C	391	MET	0	0.004	0.002	46.548	-0.001	-0.001	0.000	0.000	0.000	0.000
35	C	392	GLN	0	-0.016	-0.006	48.312	-0.002	-0.002	0.000	0.000	0.000	0.000
36	C	393	ASN	0	-0.003	0.000	48.851	-0.002	-0.002	0.000	0.000	0.000	0.000
37	C	394	GLY	0	0.050	0.035	50.549	-0.001	-0.001	0.000	0.000	0.000	0.000
38	C	395	GLU	-1	-0.898	-0.950	52.246	0.018	0.018	0.000	0.000	0.000	0.000
39	C	396	ARG	1	0.938	0.955	54.254	-0.023	-0.023	0.000	0.000	0.000	0.000
40	C	397	ILE	0	-0.017	-0.006	53.369	0.000	0.000	0.000	0.000	0.000	0.000
41	C	398	THR	0	-0.018	-0.001	55.609	-0.001	-0.001	0.000	0.000	0.000	0.000
42	C	399	THR	0	-0.078	-0.051	58.011	-0.001	-0.001	0.000	0.000	0.000	0.000
43	C	400	LEU	0	0.006	-0.003	59.089	-0.001	-0.001	0.000	0.000	0.000	0.000
44	C	401	HIS	0	0.002	0.008	60.068	-0.001	-0.001	0.000	0.000	0.000	0.000
45	C	402	ARG	1	0.984	0.991	60.578	-0.017	-0.017	0.000	0.000	0.000	0.000
46	C	403	GLU	-1	-0.905	-0.952	64.411	0.015	0.015	0.000	0.000	0.000	0.000
47	C	404	MET	0	-0.033	-0.016	64.632	0.000	0.000	0.000	0.000	0.000	0.000
48	C	405	GLU	-1	-0.925	-0.970	65.528	0.018	0.018	0.000	0.000	0.000	0.000
49	C	406	LYS	1	0.909	0.966	68.066	-0.014	-0.014	0.000	0.000	0.000	0.000
50	C	407	VAL	0	0.042	0.014	69.953	0.000	0.000	0.000	0.000	0.000	0.000
51	C	408	LYS	1	0.906	0.960	66.697	-0.019	-0.019	0.000	0.000	0.000	0.000
52	C	409	LEU	0	-0.024	-0.017	72.091	0.000	0.000	0.000	0.000	0.000	0.000
53	C	410	ASP	-1	-0.892	-0.945	74.408	0.013	0.013	0.000	0.000	0.000	0.000
54	C	411	GLN	0	-0.028	-0.005	75.043	0.000	0.000	0.000	0.000	0.000	0.000
55	C	412	LYS	1	0.965	0.974	75.128	-0.015	-0.015	0.000	0.000	0.000	0.000
56	C	413	ARG	1	0.893	0.962	78.140	-0.011	-0.011	0.000	0.000	0.000	0.000
57	C	414	LEU	0	0.004	-0.008	79.431	0.000	0.000	0.000	0.000	0.000	0.000
58	C	415	ASP	-1	-0.875	-0.939	78.972	0.014	0.014	0.000	0.000	0.000	0.000
59	C	416	GLN	0	-0.044	-0.021	81.190	0.000	0.000	0.000	0.000	0.000	0.000
60	C	417	GLU	-1	-0.926	-0.966	84.346	0.010	0.010	0.000	0.000	0.000	0.000
61	C	418	LEU	0	-0.016	-0.017	84.070	0.000	0.000	0.000	0.000	0.000	0.000
62	C	419	ASP	-1	-0.901	-0.943	85.443	0.012	0.012	0.000	0.000	0.000	0.000
63	C	420	PHE	0	-0.068	-0.025	88.205	0.000	0.000	0.000	0.000	0.000	0.000
64	C	421	ILE	0	0.019	0.000	89.025	0.000	0.000	0.000	0.000	0.000	0.000
65	C	422	LEU	0	0.012	0.013	90.306	0.000	0.000	0.000	0.000	0.000	0.000
66	C	423	SER	0	-0.047	-0.023	92.466	0.000	0.000	0.000	0.000	0.000	0.000
67	C	424	GLN	0	-0.016	-0.003	94.407	0.000	0.000	0.000	0.000	0.000	0.000
68	C	425	GLN	0	-0.018	-0.016	94.659	0.000	0.000	0.000	0.000	0.000	0.000
69	C	426	LYS	1	0.922	0.969	96.422	-0.010	-0.010	0.000	0.000	0.000	0.000
70	C	427	GLU	-1	-0.943	-0.973	98.306	0.008	0.008	0.000	0.000	0.000	0.000
71	C	428	LEU	0	-0.059	-0.034	100.179	0.000	0.000	0.000	0.000	0.000	0.000
72	C	429	GLU	-1	-0.917	-0.968	100.762	0.009	0.009	0.000	0.000	0.000	0.000
73	C	430	ASP	-1	-0.925	-0.960	101.803	0.009	0.009	0.000	0.000	0.000	0.000
74	C	431	LEU	0	-0.078	-0.032	104.396	0.000	0.000	0.000	0.000	0.000	0.000
75	C	432	LEU	0	-0.005	-0.003	105.405	0.000	0.000	0.000	0.000	0.000	0.000
76	C	433	THR	0	0.049	0.023	105.901	0.000	0.000	0.000	0.000	0.000	0.000
77	C	434	PRO	0	-0.018	-0.002	108.376	0.000	0.000	0.000	0.000	0.000	0.000
78	C	435	LEU	0	-0.039	-0.016	109.969	0.000	0.000	0.000	0.000	0.000	0.000
79	C	436	GLU	-1	-0.918	-0.965	108.789	0.008	0.008	0.000	0.000	0.000	0.000
80	C	437	GLU	-1	-0.934	-0.970	112.266	0.008	0.008	0.000	0.000	0.000	0.000
81	C	438	SER	0	-0.059	-0.027	114.786	0.000	0.000	0.000	0.000	0.000	0.000
82	C	439	VAL	0	-0.033	-0.021	115.687	0.000	0.000	0.000	0.000	0.000	0.000
83	C	440	LYS	1	0.844	0.927	114.250	-0.007	-0.007	0.000	0.000	0.000	0.000
84	C	441	GLU	-1	-0.941	-0.968	118.391	0.007	0.007	0.000	0.000	0.000	0.000
85	C	442	GLN	0	-0.014	-0.009	121.691	0.000	0.000	0.000	0.000	0.000	0.000
86	C	443	SER	0	-0.021	0.001	122.305	0.000	0.000	0.000	0.000	0.000	0.000
87	C	444	GLY	0	-0.049	-0.041	124.137	0.000	0.000	0.000	0.000	0.000	0.000
88	C	445	THR	0	-0.042	-0.006	126.196	0.000	0.000	0.000	0.000	0.000	0.000
89	C	446	ILE	0	-0.011	-0.020	128.110	0.000	0.000	0.000	0.000	0.000	0.000
90	C	447	TYR	0	0.010	0.019	132.051	0.000	0.000	0.000	0.000	0.000	0.000
91	C	448	LEU	0	-0.048	-0.005	131.186	0.000	0.000	0.000	0.000	0.000	0.000
92	C	449	GLN	0	0.023	-0.014	129.744	0.000	0.000	0.000	0.000	0.000	0.000
93	C	450	HIS	0	0.070	0.049	130.492	0.000	0.000	0.000	0.000	0.000	0.000
94	C	451	ALA	0	-0.013	-0.012	129.484	0.000	0.000	0.000	0.000	0.000	0.000
95	C	452	ASP	-1	-0.849	-0.952	127.158	0.005	0.005	0.000	0.000	0.000	0.000
96	C	453	GLU	-1	-0.918	-0.952	126.007	0.006	0.006	0.000	0.000	0.000	0.000
97	C	454	GLU	-1	-0.936	-0.968	125.450	0.006	0.006	0.000	0.000	0.000	0.000
98	C	455	ARG	1	0.895	0.952	122.580	-0.005	-0.005	0.000	0.000	0.000	0.000
99	C	456	GLU	-1	-0.914	-0.954	121.258	0.006	0.006	0.000	0.000	0.000	0.000
100	C	457	LYS	1	0.943	0.969	120.427	-0.006	-0.006	0.000	0.000	0.000	0.000
101	C	458	THR	0	-0.062	-0.038	119.353	0.000	0.000	0.000	0.000	0.000	0.000
102	C	459	TYR	0	-0.005	-0.023	116.646	0.000	0.000	0.000	0.000	0.000	0.000
103	C	460	LYS	1	0.915	0.973	115.777	-0.007	-0.007	0.000	0.000	0.000	0.000
104	C	461	LEU	0	-0.037	-0.005	115.025	0.000	0.000	0.000	0.000	0.000	0.000
105	C	462	ALA	0	-0.014	-0.016	112.927	0.000	0.000	0.000	0.000	0.000	0.000
106	C	463	GLU	-1	-0.824	-0.902	111.251	0.008	0.008	0.000	0.000	0.000	0.000
107	C	464	ASN	0	0.003	-0.009	110.263	0.000	0.000	0.000	0.000	0.000	0.000
108	C	465	ILE	0	-0.015	-0.005	108.865	0.000	0.000	0.000	0.000	0.000	0.000
109	C	466	ASP	-1	-0.813	-0.889	105.779	0.008	0.008	0.000	0.000	0.000	0.000
110	C	467	ALA	0	0.037	0.020	105.495	0.000	0.000	0.000	0.000	0.000	0.000
111	C	468	GLN	0	-0.099	-0.054	105.117	0.000	0.000	0.000	0.000	0.000	0.000
112	C	469	LEU	0	0.003	-0.010	103.533	0.000	0.000	0.000	0.000	0.000	0.000
113	C	470	LYS	1	0.881	0.928	101.084	-0.008	-0.008	0.000	0.000	0.000	0.000
114	C	471	ARG	1	0.983	1.010	99.984	-0.009	-0.009	0.000	0.000	0.000	0.000
115	C	472	MET	0	-0.038	-0.026	99.525	0.000	0.000	0.000	0.000	0.000	0.000
116	C	473	ALA	0	-0.037	-0.012	97.381	0.000	0.000	0.000	0.000	0.000	0.000
117	C	474	GLN	0	0.028	0.003	93.994	0.000	0.000	0.000	0.000	0.000	0.000
118	C	475	ASP	-1	-0.903	-0.956	94.907	0.011	0.011	0.000	0.000	0.000	0.000
119	C	476	LEU	0	-0.050	-0.034	94.274	0.000	0.000	0.000	0.000	0.000	0.000
120	C	477	LYS	1	0.910	0.951	91.210	-0.010	-0.010	0.000	0.000	0.000	0.000
121	C	478	GLU	-1	-0.855	-0.911	89.999	0.012	0.012	0.000	0.000	0.000	0.000
122	C	479	VAL	0	-0.039	-0.013	89.772	0.000	0.000	0.000	0.000	0.000	0.000
123	C	480	ILE	0	-0.062	-0.047	86.649	0.000	0.000	0.000	0.000	0.000	0.000
124	C	481	GLU	-1	-0.959	-0.963	85.679	0.013	0.013	0.000	0.000	0.000	0.000
125	C	482	HIS	0	-0.012	-0.016	84.908	0.001	0.001	0.000	0.000	0.000	0.000
126	C	483	LEU	0	-0.090	-0.027	84.860	0.000	0.000	0.000	0.000	0.000	0.000
127	C	484	ASN	0	-0.055	-0.023	81.339	0.000	0.000	0.000	0.000	0.000	0.000
128	C	485	THR	0	-0.041	-0.010	77.469	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)