FMO DATABASE

FMODB ID: YY312

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

Total energy (hartree)

FMO2-HF: Electronic energy	-823139.909997
FMO2-HF: Nuclear repulsion	768795.369637
FMO2-HF: Total energy	-54344.54036
FMO2-MP2: Total energy	-54503.198961

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.
-2.426	0.053	2.697	-1.861	-3.314	-0.005

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 : 0.009 / q_NPA : -0.008

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	0.000	-0.004	3.854	-0.882	0.497	-0.015	-0.692	-0.671	-0.001
4	A	320	GLN	0	0.059	0.003	2.336	-1.031	-0.445	0.634	-0.341	-0.878	-0.001
5	A	321	ILE	0	0.049	0.044	2.279	-0.181	0.270	2.079	-0.811	-1.719	-0.003
6	A	322	LYS	1	1.015	0.989	4.547	1.667	1.730	-0.001	-0.017	-0.046	0.000
7	A	323	GLN	0	-0.067	-0.030	6.614	0.114	0.114	0.000	0.000	0.000	0.000
8	A	324	LEU	0	-0.007	0.008	5.343	0.247	0.247	0.000	0.000	0.000	0.000
9	A	325	ILE	0	-0.060	-0.012	7.761	-0.060	-0.060	0.000	0.000	0.000	0.000
10	A	326	GLN	0	0.034	0.022	10.209	-0.117	-0.117	0.000	0.000	0.000	0.000
11	A	327	ASN	0	-0.009	-0.012	12.431	0.044	0.044	0.000	0.000	0.000	0.000
12	A	328	PRO	0	0.045	0.025	14.474	-0.011	-0.011	0.000	0.000	0.000	0.000
13	A	329	LEU	0	0.038	0.016	12.441	0.034	0.034	0.000	0.000	0.000	0.000
14	A	330	SER	0	-0.049	-0.023	16.535	0.027	0.027	0.000	0.000	0.000	0.000
15	A	331	GLY	0	0.020	0.016	19.565	0.000	0.000	0.000	0.000	0.000	0.000
16	A	332	VAL	0	-0.079	-0.030	18.504	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	333	ASP	-1	-0.791	-0.901	21.082	-0.133	-0.133	0.000	0.000	0.000	0.000
18	A	334	PRO	0	0.013	-0.033	20.128	-0.027	-0.027	0.000	0.000	0.000	0.000
19	A	335	ILE	0	0.007	0.015	20.482	-0.027	-0.027	0.000	0.000	0.000	0.000
20	A	336	ILE	0	-0.013	-0.005	21.113	-0.021	-0.021	0.000	0.000	0.000	0.000
21	A	337	TRP	0	-0.038	-0.026	12.354	-0.028	-0.028	0.000	0.000	0.000	0.000
22	A	338	GLU	-1	-0.816	-0.915	16.607	-0.428	-0.428	0.000	0.000	0.000	0.000
23	A	339	GLN	0	-0.065	-0.038	18.150	-0.022	-0.022	0.000	0.000	0.000	0.000
24	A	340	ALA	0	0.000	0.000	16.291	-0.022	-0.022	0.000	0.000	0.000	0.000
25	A	341	LYS	1	0.723	0.852	12.858	0.380	0.380	0.000	0.000	0.000	0.000
26	A	342	VAL	0	-0.034	-0.008	14.625	-0.086	-0.086	0.000	0.000	0.000	0.000
27	A	343	ASP	-1	-0.866	-0.908	17.330	-0.367	-0.367	0.000	0.000	0.000	0.000
28	A	344	ASN	0	-0.069	-0.038	10.759	0.024	0.024	0.000	0.000	0.000	0.000
29	A	345	PRO	0	-0.018	-0.004	14.989	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	346	ASP	-1	-0.820	-0.934	11.663	-1.069	-1.069	0.000	0.000	0.000	0.000
31	A	347	PRO	0	-0.025	-0.018	10.294	-0.204	-0.204	0.000	0.000	0.000	0.000
32	A	348	GLU	-1	-0.918	-0.930	8.360	-1.379	-1.379	0.000	0.000	0.000	0.000
33	A	349	ARG	1	0.779	0.886	6.787	0.387	0.387	0.000	0.000	0.000	0.000
34	A	350	LEU	0	-0.027	-0.005	8.051	0.070	0.070	0.000	0.000	0.000	0.000
35	A	351	ILE	0	0.003	0.004	5.717	-0.104	-0.104	0.000	0.000	0.000	0.000
36	A	352	PRO	0	0.013	0.021	8.831	0.150	0.150	0.000	0.000	0.000	0.000
37	A	353	VAL	0	0.000	-0.012	10.647	0.053	0.053	0.000	0.000	0.000	0.000
38	A	354	PRO	0	-0.021	0.007	13.075	0.012	0.012	0.000	0.000	0.000	0.000
39	A	355	MET	0	-0.028	-0.022	16.601	0.011	0.011	0.000	0.000	0.000	0.000
40	A	356	ILE	0	0.040	0.021	19.275	0.001	0.001	0.000	0.000	0.000	0.000
41	A	357	GLY	0	0.038	0.014	22.466	0.012	0.012	0.000	0.000	0.000	0.000
42	A	358	PHE	0	0.047	-0.003	24.765	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	359	LYS	1	0.912	0.970	22.246	0.079	0.079	0.000	0.000	0.000	0.000
44	A	360	GLU	-1	-0.742	-0.867	19.131	-0.145	-0.145	0.000	0.000	0.000	0.000
45	A	361	LEU	0	-0.009	-0.002	21.679	-0.023	-0.023	0.000	0.000	0.000	0.000
46	A	362	LEU	0	0.028	0.024	23.860	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	363	ARG	1	0.864	0.930	15.957	0.213	0.213	0.000	0.000	0.000	0.000
48	A	364	ARG	1	0.924	0.944	14.830	0.397	0.397	0.000	0.000	0.000	0.000
49	A	365	LEU	0	0.014	0.016	20.935	-0.015	-0.015	0.000	0.000	0.000	0.000
50	A	366	GLU	-1	-0.887	-0.954	24.183	-0.107	-0.107	0.000	0.000	0.000	0.000
51	A	367	VAL	0	-0.039	-0.021	17.897	0.001	0.001	0.000	0.000	0.000	0.000
52	A	368	GLN	0	-0.002	-0.007	21.163	0.014	0.014	0.000	0.000	0.000	0.000
53	A	369	ASP	-1	-0.782	-0.846	22.564	-0.125	-0.125	0.000	0.000	0.000	0.000
54	A	370	GLN	0	0.006	0.007	20.277	0.020	0.020	0.000	0.000	0.000	0.000
55	A	371	MET	0	-0.015	-0.012	17.998	0.010	0.010	0.000	0.000	0.000	0.000
56	A	372	THR	0	0.007	-0.008	22.268	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	373	LYS	1	0.818	0.889	25.058	0.127	0.127	0.000	0.000	0.000	0.000
58	A	374	GLN	0	-0.034	-0.014	21.451	0.001	0.001	0.000	0.000	0.000	0.000
59	A	375	HIS	0	-0.064	-0.044	19.606	0.023	0.023	0.000	0.000	0.000	0.000
60	A	376	GLN	0	-0.025	-0.028	24.668	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	377	SER	0	0.001	0.016	27.327	0.010	0.010	0.000	0.000	0.000	0.000
62	A	378	ARG	1	0.960	0.963	19.492	0.190	0.190	0.000	0.000	0.000	0.000
63	A	379	LEU	0	-0.004	0.006	26.777	0.006	0.006	0.000	0.000	0.000	0.000
64	A	380	ASP	-1	-0.833	-0.891	29.198	-0.088	-0.088	0.000	0.000	0.000	0.000
65	A	381	ILE	0	-0.014	-0.007	28.480	0.007	0.007	0.000	0.000	0.000	0.000
66	A	382	ILE	0	-0.010	-0.018	25.989	0.002	0.002	0.000	0.000	0.000	0.000
67	A	383	SER	0	-0.008	-0.007	30.654	0.003	0.003	0.000	0.000	0.000	0.000
68	A	384	GLU	-1	-0.941	-0.965	33.756	-0.052	-0.052	0.000	0.000	0.000	0.000
69	A	385	ASP	-1	-0.943	-0.975	31.399	-0.056	-0.056	0.000	0.000	0.000	0.000
70	A	386	ILE	0	-0.064	-0.031	32.046	0.002	0.002	0.000	0.000	0.000	0.000
71	A	387	GLY	0	0.055	0.043	35.639	0.004	0.004	0.000	0.000	0.000	0.000
72	A	388	GLU	-1	-0.765	-0.857	37.340	-0.032	-0.032	0.000	0.000	0.000	0.000
73	A	389	LEU	0	0.035	0.027	34.178	0.004	0.004	0.000	0.000	0.000	0.000
74	A	390	GLN	0	0.031	0.007	38.050	0.004	0.004	0.000	0.000	0.000	0.000
75	A	391	LYS	1	0.847	0.910	40.550	0.037	0.037	0.000	0.000	0.000	0.000
76	A	392	ASN	0	-0.094	-0.067	40.065	0.006	0.006	0.000	0.000	0.000	0.000
77	A	393	GLN	0	-0.012	0.005	40.496	0.002	0.002	0.000	0.000	0.000	0.000
78	A	394	THR	0	-0.004	-0.013	42.414	0.002	0.002	0.000	0.000	0.000	0.000
79	A	395	THR	0	-0.034	-0.024	45.537	0.003	0.003	0.000	0.000	0.000	0.000
80	A	396	THR	0	-0.046	-0.028	43.110	0.003	0.003	0.000	0.000	0.000	0.000
81	A	397	MET	0	-0.010	-0.011	45.346	0.001	0.001	0.000	0.000	0.000	0.000
82	A	398	ALA	0	-0.002	0.015	47.663	0.001	0.001	0.000	0.000	0.000	0.000
83	A	399	LYS	1	0.962	0.975	47.036	0.023	0.023	0.000	0.000	0.000	0.000
84	A	400	ILE	0	0.005	0.011	45.808	0.002	0.002	0.000	0.000	0.000	0.000
85	A	401	GLY	0	0.014	0.009	50.326	0.001	0.001	0.000	0.000	0.000	0.000
86	A	402	GLN	0	-0.040	-0.027	53.490	0.000	0.000	0.000	0.000	0.000	0.000
87	A	403	TYR	0	0.026	0.009	49.695	0.001	0.001	0.000	0.000	0.000	0.000
88	A	404	LYS	1	0.984	0.998	50.930	0.028	0.028	0.000	0.000	0.000	0.000
89	A	405	ARG	1	0.986	0.998	55.327	0.024	0.024	0.000	0.000	0.000	0.000
90	A	406	LYS	1	0.841	0.893	57.645	0.014	0.014	0.000	0.000	0.000	0.000
91	A	407	LEU	0	0.021	0.022	55.001	0.001	0.001	0.000	0.000	0.000	0.000
92	A	408	MET	0	0.022	0.010	58.484	0.001	0.001	0.000	0.000	0.000	0.000
93	A	409	GLU	-1	-0.794	-0.864	60.879	-0.012	-0.012	0.000	0.000	0.000	0.000
94	A	410	LEU	0	-0.023	-0.033	59.526	0.001	0.001	0.000	0.000	0.000	0.000
95	A	411	SER	0	-0.007	0.004	60.940	0.001	0.001	0.000	0.000	0.000	0.000
96	A	412	HIS	0	0.059	0.032	62.890	0.001	0.001	0.000	0.000	0.000	0.000
97	A	413	ARG	1	0.871	0.917	65.660	0.011	0.011	0.000	0.000	0.000	0.000
98	A	414	VAL	0	0.015	0.005	63.699	0.001	0.001	0.000	0.000	0.000	0.000
99	A	415	LEU	0	0.036	0.027	66.854	0.001	0.001	0.000	0.000	0.000	0.000
100	A	416	GLN	0	-0.024	-0.023	68.567	0.001	0.001	0.000	0.000	0.000	0.000
101	A	417	VAL	0	-0.060	-0.021	69.796	0.000	0.000	0.000	0.000	0.000	0.000
102	A	418	LEU	0	0.037	0.021	66.875	0.000	0.000	0.000	0.000	0.000	0.000
103	A	419	ILE	0	0.034	0.023	71.425	0.000	0.000	0.000	0.000	0.000	0.000
104	A	420	LYS	1	0.915	0.962	74.183	0.009	0.009	0.000	0.000	0.000	0.000
105	A	421	GLN	0	-0.008	-0.016	71.603	0.000	0.000	0.000	0.000	0.000	0.000
106	A	422	GLU	-1	-0.790	-0.870	74.939	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	423	ILE	0	0.008	-0.011	76.769	0.000	0.000	0.000	0.000	0.000	0.000
108	A	424	GLN	0	-0.035	-0.012	78.888	0.000	0.000	0.000	0.000	0.000	0.000
109	A	425	ARG	1	0.824	0.909	75.457	0.005	0.005	0.000	0.000	0.000	0.000
110	A	426	LYS	1	0.815	0.909	77.966	0.007	0.007	0.000	0.000	0.000	0.000
111	A	427	SER	0	-0.047	-0.043	82.057	0.000	0.000	0.000	0.000	0.000	0.000
112	A	428	GLY	0	-0.037	-0.008	85.188	0.000	0.000	0.000	0.000	0.000	0.000
113	A	429	PHE	0	-0.023	-0.001	82.598	0.000	0.000	0.000	0.000	0.000	0.000
114	A	430	ALA	0	0.003	-0.003	86.553	0.000	0.000	0.000	0.000	0.000	0.000
115	A	431	ILE	0	0.038	0.004	83.585	0.000	0.000	0.000	0.000	0.000	0.000
116	A	432	GLN	0	0.000	0.001	81.588	0.000	0.000	0.000	0.000	0.000	0.000
117	A	433	ALA	0	0.012	0.005	81.438	0.000	0.000	0.000	0.000	0.000	0.000
118	A	434	GLU	-1	-0.909	-0.966	76.028	-0.008	-0.008	0.000	0.000	0.000	0.000
119	A	435	GLU	-1	-0.809	-0.897	76.961	-0.008	-0.008	0.000	0.000	0.000	0.000
120	A	436	GLU	-1	-0.919	-0.966	78.859	-0.010	-0.010	0.000	0.000	0.000	0.000
121	A	437	GLN	0	-0.050	-0.030	76.406	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	438	LEU	0	0.005	0.013	72.713	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	439	ARG	1	0.841	0.899	75.681	0.011	0.011	0.000	0.000	0.000	0.000
124	A	440	VAL	0	0.074	0.042	77.243	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	441	GLN	0	-0.009	0.005	72.091	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	442	LEU	0	-0.052	-0.021	72.081	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	443	ASP	-1	-0.835	-0.894	74.422	-0.013	-0.013	0.000	0.000	0.000	0.000
128	A	444	THR	0	-0.047	-0.043	74.477	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	445	ILE	0	-0.004	0.006	68.995	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	446	GLN	0	-0.014	-0.010	71.990	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	447	SER	0	0.002	-0.005	74.287	0.000	0.000	0.000	0.000	0.000	0.000
132	A	448	GLU	-1	-0.962	-0.963	70.087	-0.021	-0.021	0.000	0.000	0.000	0.000
133	A	449	LEU	0	-0.099	-0.038	69.492	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	450	ASN	0	-0.100	-0.045	71.524	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)