FMO DATABASE

FMODB ID: 5375Z

Calculation Name: 5C3L-A-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: A

ChEMBL ID:
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UniProt ID: Q91349

Base Structure: X-ray

Registration Date: 2023-06-20

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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-823131.706273
FMO2-HF: Nuclear repulsion	768788.07732
FMO2-HF: Total energy	-54343.628953
FMO2-MP2: Total energy	-54502.372195

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(A:317:SER)

Summations of interaction energy for fragment #1(A:317:SER)

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.
-1.446	0.961	3.113	-1.955	-3.564	-0.003

Interaction energy analysis for fragmet #1(A:317:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.011

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	A	319	VAL	0	0.005	-0.005	3.854	-0.675	1.248	-0.016	-1.061	-0.845	0.003
4	A	320	GLN	0	0.051	-0.002	2.299	-0.233	0.230	0.719	-0.309	-0.873	-0.001
5	A	321	ILE	0	0.065	0.058	2.307	0.356	0.313	2.411	-0.566	-1.802	-0.005
6	A	322	LYS	1	0.998	0.981	4.534	2.111	2.175	-0.001	-0.019	-0.044	0.000
7	A	323	GLN	0	-0.074	-0.032	6.896	-0.116	-0.116	0.000	0.000	0.000	0.000
8	A	324	LEU	0	-0.004	0.011	4.994	0.298	0.298	0.000	0.000	0.000	0.000
9	A	325	ILE	0	-0.062	-0.018	7.780	0.047	0.047	0.000	0.000	0.000	0.000
10	A	326	GLN	0	-0.009	-0.009	10.067	-0.235	-0.235	0.000	0.000	0.000	0.000
11	A	327	ASN	0	0.013	0.000	12.625	0.055	0.055	0.000	0.000	0.000	0.000
12	A	328	PRO	0	0.025	0.018	14.485	0.061	0.061	0.000	0.000	0.000	0.000
13	A	329	LEU	0	0.049	0.022	12.449	0.033	0.033	0.000	0.000	0.000	0.000
14	A	330	SER	0	-0.051	-0.027	16.475	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	331	GLY	0	0.017	0.016	19.548	-0.025	-0.025	0.000	0.000	0.000	0.000
16	A	332	VAL	0	-0.076	-0.026	18.462	-0.023	-0.023	0.000	0.000	0.000	0.000
17	A	333	ASP	-1	-0.814	-0.929	21.043	0.087	0.087	0.000	0.000	0.000	0.000
18	A	334	PRO	0	0.011	-0.026	20.001	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	335	ILE	0	0.029	0.037	20.351	-0.024	-0.024	0.000	0.000	0.000	0.000
20	A	336	ILE	0	-0.009	-0.005	20.914	-0.022	-0.022	0.000	0.000	0.000	0.000
21	A	337	TRP	0	-0.045	-0.030	12.275	0.014	0.014	0.000	0.000	0.000	0.000
22	A	338	GLU	-1	-0.861	-0.956	16.539	-0.066	-0.066	0.000	0.000	0.000	0.000
23	A	339	GLN	0	-0.017	0.009	18.055	-0.054	-0.054	0.000	0.000	0.000	0.000
24	A	340	ALA	0	0.008	0.007	16.273	-0.024	-0.024	0.000	0.000	0.000	0.000
25	A	341	LYS	1	0.800	0.902	12.781	0.130	0.130	0.000	0.000	0.000	0.000
26	A	342	VAL	0	-0.022	-0.003	14.580	-0.102	-0.102	0.000	0.000	0.000	0.000
27	A	343	ASP	-1	-0.906	-0.942	17.274	-0.182	-0.182	0.000	0.000	0.000	0.000
28	A	344	ASN	0	-0.079	-0.040	12.136	-0.089	-0.089	0.000	0.000	0.000	0.000
29	A	345	PRO	0	-0.015	-0.002	14.757	-0.061	-0.061	0.000	0.000	0.000	0.000
30	A	346	ASP	-1	-0.829	-0.945	12.051	-0.960	-0.960	0.000	0.000	0.000	0.000
31	A	347	PRO	0	0.000	-0.002	10.354	-0.070	-0.070	0.000	0.000	0.000	0.000
32	A	348	GLU	-1	-1.007	-0.982	8.353	-1.746	-1.746	0.000	0.000	0.000	0.000
33	A	349	ARG	1	0.864	0.933	6.804	0.262	0.262	0.000	0.000	0.000	0.000
34	A	350	LEU	0	-0.038	-0.017	8.045	0.523	0.523	0.000	0.000	0.000	0.000
35	A	351	ILE	0	0.008	0.015	5.771	-0.195	-0.195	0.000	0.000	0.000	0.000
36	A	352	PRO	0	-0.008	0.008	8.928	0.117	0.117	0.000	0.000	0.000	0.000
37	A	353	VAL	0	0.002	-0.013	10.797	0.170	0.170	0.000	0.000	0.000	0.000
38	A	354	PRO	0	-0.022	0.005	13.176	-0.103	-0.103	0.000	0.000	0.000	0.000
39	A	355	MET	0	-0.019	-0.014	16.676	0.071	0.071	0.000	0.000	0.000	0.000
40	A	356	ILE	0	0.036	0.020	19.402	-0.048	-0.048	0.000	0.000	0.000	0.000
41	A	357	GLY	0	0.037	0.010	22.567	0.016	0.016	0.000	0.000	0.000	0.000
42	A	358	PHE	0	0.053	-0.002	24.921	0.012	0.012	0.000	0.000	0.000	0.000
43	A	359	LYS	1	0.964	1.002	23.236	-0.366	-0.366	0.000	0.000	0.000	0.000
44	A	360	GLU	-1	-0.784	-0.890	19.387	0.495	0.495	0.000	0.000	0.000	0.000
45	A	361	LEU	0	-0.002	-0.011	21.912	0.004	0.004	0.000	0.000	0.000	0.000
46	A	362	LEU	0	0.031	0.025	24.061	-0.017	-0.017	0.000	0.000	0.000	0.000
47	A	363	ARG	1	0.859	0.930	16.515	-0.539	-0.539	0.000	0.000	0.000	0.000
48	A	364	ARG	1	0.922	0.944	14.673	-0.388	-0.388	0.000	0.000	0.000	0.000
49	A	365	LEU	0	0.022	0.015	21.125	-0.017	-0.017	0.000	0.000	0.000	0.000
50	A	366	GLU	-1	-0.906	-0.957	24.426	0.221	0.221	0.000	0.000	0.000	0.000
51	A	367	VAL	0	-0.041	-0.016	18.006	0.004	0.004	0.000	0.000	0.000	0.000
52	A	368	GLN	0	-0.023	-0.017	21.340	-0.025	-0.025	0.000	0.000	0.000	0.000
53	A	369	ASP	-1	-0.817	-0.887	22.542	0.102	0.102	0.000	0.000	0.000	0.000
54	A	370	GLN	0	0.009	0.009	20.572	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	371	MET	0	-0.021	-0.017	18.313	0.006	0.006	0.000	0.000	0.000	0.000
56	A	372	THR	0	0.021	0.018	22.193	-0.034	-0.034	0.000	0.000	0.000	0.000
57	A	373	LYS	1	0.860	0.917	25.054	-0.134	-0.134	0.000	0.000	0.000	0.000
58	A	374	GLN	0	-0.036	-0.020	21.597	-0.016	-0.016	0.000	0.000	0.000	0.000
59	A	375	HIS	0	-0.055	-0.036	19.852	-0.012	-0.012	0.000	0.000	0.000	0.000
60	A	376	GLN	0	0.000	-0.008	24.773	-0.018	-0.018	0.000	0.000	0.000	0.000
61	A	377	SER	0	-0.002	0.008	27.548	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	378	ARG	1	0.950	0.968	19.550	-0.010	-0.010	0.000	0.000	0.000	0.000
63	A	379	LEU	0	-0.010	0.000	26.813	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	380	ASP	-1	-0.844	-0.906	29.213	0.008	0.008	0.000	0.000	0.000	0.000
65	A	381	ILE	0	0.001	0.003	28.779	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	382	ILE	0	-0.024	-0.023	26.090	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	383	SER	0	-0.010	-0.009	30.684	-0.010	-0.010	0.000	0.000	0.000	0.000
68	A	384	GLU	-1	-0.945	-0.966	33.782	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	385	ASP	-1	-0.935	-0.973	31.677	-0.029	-0.029	0.000	0.000	0.000	0.000
70	A	386	ILE	0	-0.063	-0.027	32.005	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	387	GLY	0	0.053	0.038	35.679	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	388	GLU	-1	-0.843	-0.917	37.287	-0.026	-0.026	0.000	0.000	0.000	0.000
73	A	389	LEU	0	0.043	0.021	34.325	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	390	GLN	0	0.005	-0.004	38.064	0.002	0.002	0.000	0.000	0.000	0.000
75	A	391	LYS	1	0.922	0.967	40.597	0.020	0.020	0.000	0.000	0.000	0.000
76	A	392	ASN	0	-0.105	-0.067	39.433	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	393	GLN	0	-0.006	0.002	40.671	0.001	0.001	0.000	0.000	0.000	0.000
78	A	394	THR	0	0.017	0.004	42.394	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	395	THR	0	-0.023	-0.014	45.374	0.002	0.002	0.000	0.000	0.000	0.000
80	A	396	THR	0	-0.042	-0.026	42.967	0.001	0.001	0.000	0.000	0.000	0.000
81	A	397	MET	0	-0.008	-0.013	45.346	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	398	ALA	0	0.008	0.021	47.596	0.001	0.001	0.000	0.000	0.000	0.000
83	A	399	LYS	1	0.949	0.964	47.141	0.038	0.038	0.000	0.000	0.000	0.000
84	A	400	ILE	0	0.017	0.020	45.734	0.000	0.000	0.000	0.000	0.000	0.000
85	A	401	GLY	0	0.008	0.005	50.135	0.000	0.000	0.000	0.000	0.000	0.000
86	A	402	GLN	0	-0.055	-0.035	53.360	0.001	0.001	0.000	0.000	0.000	0.000
87	A	403	TYR	0	0.021	0.007	49.752	0.001	0.001	0.000	0.000	0.000	0.000
88	A	404	LYS	1	0.989	0.998	50.808	0.062	0.062	0.000	0.000	0.000	0.000
89	A	405	ARG	1	0.987	1.000	55.086	0.039	0.039	0.000	0.000	0.000	0.000
90	A	406	LYS	1	0.837	0.901	57.300	0.032	0.032	0.000	0.000	0.000	0.000
91	A	407	LEU	0	0.021	0.020	54.620	0.001	0.001	0.000	0.000	0.000	0.000
92	A	408	MET	0	0.019	0.009	58.137	0.001	0.001	0.000	0.000	0.000	0.000
93	A	409	GLU	-1	-0.794	-0.884	60.596	-0.030	-0.030	0.000	0.000	0.000	0.000
94	A	410	LEU	0	-0.054	-0.048	58.936	0.001	0.001	0.000	0.000	0.000	0.000
95	A	411	SER	0	-0.012	0.003	60.603	0.001	0.001	0.000	0.000	0.000	0.000
96	A	412	HIS	0	0.057	0.029	62.496	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	413	ARG	1	0.910	0.952	64.910	0.030	0.030	0.000	0.000	0.000	0.000
98	A	414	VAL	0	0.008	0.004	63.224	0.001	0.001	0.000	0.000	0.000	0.000
99	A	415	LEU	0	0.036	0.024	66.378	0.001	0.001	0.000	0.000	0.000	0.000
100	A	416	GLN	0	-0.012	-0.016	68.131	0.001	0.001	0.000	0.000	0.000	0.000
101	A	417	VAL	0	-0.051	-0.018	69.311	0.001	0.001	0.000	0.000	0.000	0.000
102	A	418	LEU	0	0.030	0.016	66.341	0.001	0.001	0.000	0.000	0.000	0.000
103	A	419	ILE	0	0.039	0.027	70.897	0.001	0.001	0.000	0.000	0.000	0.000
104	A	420	LYS	1	0.922	0.959	73.745	0.027	0.027	0.000	0.000	0.000	0.000
105	A	421	GLN	0	-0.014	-0.017	70.812	0.000	0.000	0.000	0.000	0.000	0.000
106	A	422	GLU	-1	-0.824	-0.897	74.247	-0.032	-0.032	0.000	0.000	0.000	0.000
107	A	423	ILE	0	0.012	-0.008	76.218	0.001	0.001	0.000	0.000	0.000	0.000
108	A	424	GLN	0	-0.048	-0.019	77.931	0.001	0.001	0.000	0.000	0.000	0.000
109	A	425	ARG	1	0.844	0.926	74.558	0.032	0.032	0.000	0.000	0.000	0.000
110	A	426	LYS	1	0.923	0.985	77.785	0.031	0.031	0.000	0.000	0.000	0.000
111	A	427	SER	0	-0.041	-0.038	81.465	0.000	0.000	0.000	0.000	0.000	0.000
112	A	428	GLY	0	-0.031	-0.005	84.608	0.000	0.000	0.000	0.000	0.000	0.000
113	A	429	PHE	0	-0.035	-0.011	82.430	0.000	0.000	0.000	0.000	0.000	0.000
114	A	430	ALA	0	-0.006	-0.012	86.017	0.000	0.000	0.000	0.000	0.000	0.000
115	A	431	ILE	0	0.036	0.001	83.078	0.000	0.000	0.000	0.000	0.000	0.000
116	A	432	GLN	0	0.030	0.019	80.696	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	433	ALA	0	0.012	0.004	80.861	0.000	0.000	0.000	0.000	0.000	0.000
118	A	434	GLU	-1	-0.941	-0.979	75.054	-0.036	-0.036	0.000	0.000	0.000	0.000
119	A	435	GLU	-1	-0.888	-0.950	76.507	-0.032	-0.032	0.000	0.000	0.000	0.000
120	A	436	GLU	-1	-0.945	-0.974	78.400	-0.031	-0.031	0.000	0.000	0.000	0.000
121	A	437	GLN	0	-0.033	-0.028	75.817	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	438	LEU	0	0.012	0.019	72.113	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	439	ARG	1	0.976	1.002	75.329	0.030	0.030	0.000	0.000	0.000	0.000
124	A	440	VAL	0	0.073	0.047	76.875	0.000	0.000	0.000	0.000	0.000	0.000
125	A	441	GLN	0	0.001	-0.006	71.493	0.000	0.000	0.000	0.000	0.000	0.000
126	A	442	LEU	0	-0.070	-0.030	71.793	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	443	ASP	-1	-0.928	-0.973	74.152	-0.033	-0.033	0.000	0.000	0.000	0.000
128	A	444	THR	0	-0.067	-0.047	74.054	0.000	0.000	0.000	0.000	0.000	0.000
129	A	445	ILE	0	0.015	0.023	68.977	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	446	GLN	0	-0.018	-0.016	71.856	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	447	SER	0	-0.091	-0.052	74.140	0.000	0.000	0.000	0.000	0.000	0.000
132	A	448	GLU	-1	-0.929	-0.957	70.063	-0.044	-0.044	0.000	0.000	0.000	0.000
133	A	449	LEU	0	-0.105	-0.034	69.669	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	450	ASN	0	-0.060	-0.025	71.480	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:317:SER)