FMO DATABASE

FMODB ID: 76J2K

Calculation Name: 3F1I-S-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: 3F1I

Chain ID: S

ChEMBL ID:
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UniProt ID: O14964

Base Structure: X-ray

Registration Date: 2023-09-20

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	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-394991.033128
FMO2-HF: Nuclear repulsion	362093.306509
FMO2-HF: Total energy	-32897.726618
FMO2-MP2: Total energy	-32988.361767

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(S:301:PHE)

Summations of interaction energy for fragment #1(S:301:PHE)

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.
-12.339	-4.078	3.617	-2.943	-8.933	-0.001

Interaction energy analysis for fragmet #1(S:301:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.031

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	S	303	ASP	-1	-0.861	-0.939	3.824	-1.942	-0.251	0.000	-0.559	-1.131	0.001
4	S	304	GLU	-1	-0.862	-0.953	5.608	-0.361	-0.361	0.000	0.000	0.000	0.000
5	S	305	ASP	-1	-0.880	-0.924	8.834	-0.486	-0.486	0.000	0.000	0.000	0.000
6	S	306	LYS	1	0.811	0.888	4.674	0.732	0.849	-0.001	-0.004	-0.112	0.000
7	S	307	MET	0	-0.036	-0.023	6.913	0.132	0.132	0.000	0.000	0.000	0.000
8	S	308	ASP	-1	-0.888	-0.933	10.461	-0.393	-0.393	0.000	0.000	0.000	0.000
9	S	309	GLN	0	-0.083	-0.039	12.405	0.032	0.032	0.000	0.000	0.000	0.000
10	S	310	LEU	0	0.026	0.010	9.826	0.057	0.057	0.000	0.000	0.000	0.000
11	S	311	LEU	0	-0.007	0.004	13.217	0.066	0.066	0.000	0.000	0.000	0.000
12	S	312	GLN	0	-0.015	-0.023	15.435	0.053	0.053	0.000	0.000	0.000	0.000
13	S	313	MET	0	-0.009	0.022	15.439	0.022	0.022	0.000	0.000	0.000	0.000
14	S	314	LEU	0	0.003	0.015	14.225	0.035	0.035	0.000	0.000	0.000	0.000
15	S	315	GLN	0	-0.042	-0.026	18.288	0.039	0.039	0.000	0.000	0.000	0.000
16	S	316	SER	0	-0.115	-0.064	20.912	0.030	0.030	0.000	0.000	0.000	0.000
17	S	317	THR	0	-0.024	-0.014	20.564	0.021	0.021	0.000	0.000	0.000	0.000
18	S	318	ASP	-1	-0.851	-0.912	23.086	-0.157	-0.157	0.000	0.000	0.000	0.000
19	S	319	PRO	0	-0.043	-0.029	25.576	-0.001	-0.001	0.000	0.000	0.000	0.000
20	S	320	SER	0	-0.107	-0.082	26.524	0.006	0.006	0.000	0.000	0.000	0.000
21	S	321	ASP	-1	-0.887	-0.935	25.975	-0.174	-0.174	0.000	0.000	0.000	0.000
22	S	322	ASP	-1	-0.973	-0.977	28.203	-0.124	-0.124	0.000	0.000	0.000	0.000
23	S	323	GLN	0	-0.128	-0.059	24.798	0.011	0.011	0.000	0.000	0.000	0.000
24	S	324	PRO	0	-0.062	-0.023	21.423	-0.009	-0.009	0.000	0.000	0.000	0.000
25	S	325	ASP	-1	-0.847	-0.923	17.050	-0.319	-0.319	0.000	0.000	0.000	0.000
26	S	326	LEU	0	-0.008	-0.016	17.450	0.015	0.015	0.000	0.000	0.000	0.000
27	S	327	PRO	0	-0.003	-0.021	15.297	-0.033	-0.033	0.000	0.000	0.000	0.000
28	S	328	GLU	-1	-0.936	-0.971	13.229	-0.345	-0.345	0.000	0.000	0.000	0.000
29	S	329	LEU	0	0.033	0.021	12.172	-0.059	-0.059	0.000	0.000	0.000	0.000
30	S	330	LEU	0	0.057	0.024	11.900	-0.085	-0.085	0.000	0.000	0.000	0.000
31	S	331	HIS	0	-0.059	-0.025	7.109	-0.149	-0.149	0.000	0.000	0.000	0.000
32	S	332	LEU	0	0.010	-0.010	7.442	-0.159	-0.159	0.000	0.000	0.000	0.000
33	S	333	GLU	-1	-0.892	-0.931	7.727	-0.913	-0.913	0.000	0.000	0.000	0.000
34	S	334	ALA	0	-0.024	-0.014	6.921	-0.230	-0.230	0.000	0.000	0.000	0.000
35	S	335	MET	0	-0.077	-0.040	2.776	-2.240	-0.903	1.228	-0.538	-2.027	0.005
36	S	336	CYS	0	0.005	-0.008	3.198	-3.200	-2.167	0.073	-0.429	-0.677	-0.004
37	S	337	HIS	0	-0.003	0.007	5.532	-0.317	-0.317	0.000	0.000	0.000	0.000
38	S	338	GLN	0	-0.032	-0.025	2.546	-0.493	0.487	0.837	-0.453	-1.363	0.000
39	S	339	MET	0	-0.052	0.004	2.620	-2.222	-0.189	0.725	-0.610	-2.148	-0.003
40	S	340	GLY	0	0.023	0.028	3.727	1.039	1.181	0.009	-0.014	-0.138	0.000
41	S	341	PRO	0	0.056	0.014	6.170	0.322	0.322	0.000	0.000	0.000	0.000
42	S	342	LEU	0	-0.037	-0.009	2.545	-0.602	0.326	0.746	-0.336	-1.337	0.000
43	S	343	ILE	0	0.003	-0.004	6.322	0.440	0.440	0.000	0.000	0.000	0.000
44	S	344	ASP	-1	-0.876	-0.938	8.366	-0.257	-0.257	0.000	0.000	0.000	0.000
45	S	345	GLU	-1	-0.898	-0.925	9.188	1.001	1.001	0.000	0.000	0.000	0.000
46	S	346	LYS	1	0.816	0.888	7.044	-1.211	-1.211	0.000	0.000	0.000	0.000
47	S	347	LEU	0	-0.002	0.001	11.463	0.020	0.020	0.000	0.000	0.000	0.000
48	S	348	GLU	-1	-0.868	-0.925	14.176	0.186	0.186	0.000	0.000	0.000	0.000
49	S	349	ASP	-1	-0.863	-0.919	14.197	0.423	0.423	0.000	0.000	0.000	0.000
50	S	350	ILE	0	-0.045	-0.033	13.724	-0.007	-0.007	0.000	0.000	0.000	0.000
51	S	351	ASP	-1	-0.887	-0.944	17.210	-0.007	-0.007	0.000	0.000	0.000	0.000
52	S	352	ARG	1	0.825	0.919	17.230	-0.239	-0.239	0.000	0.000	0.000	0.000
53	S	353	LYS	1	0.881	0.939	15.817	-0.383	-0.383	0.000	0.000	0.000	0.000
54	S	354	HIS	0	-0.017	0.008	21.378	-0.012	-0.012	0.000	0.000	0.000	0.000
55	S	355	SER	0	-0.013	-0.023	23.165	-0.013	-0.013	0.000	0.000	0.000	0.000
56	S	356	GLU	-1	-0.911	-0.960	23.444	0.153	0.153	0.000	0.000	0.000	0.000
57	S	357	LEU	0	-0.038	-0.031	23.819	-0.007	-0.007	0.000	0.000	0.000	0.000
58	S	358	SER	0	-0.010	0.000	27.037	-0.011	-0.011	0.000	0.000	0.000	0.000
59	S	359	GLU	-1	-0.920	-0.971	28.869	0.038	0.038	0.000	0.000	0.000	0.000
60	S	360	LEU	0	-0.019	-0.006	30.280	-0.004	-0.004	0.000	0.000	0.000	0.000
61	S	361	ASN	0	-0.007	-0.010	31.182	-0.003	-0.003	0.000	0.000	0.000	0.000
62	S	362	VAL	0	0.012	0.006	32.917	-0.005	-0.005	0.000	0.000	0.000	0.000
63	S	363	LYS	1	0.842	0.920	34.907	-0.044	-0.044	0.000	0.000	0.000	0.000
64	S	364	VAL	0	-0.018	-0.011	34.881	-0.003	-0.003	0.000	0.000	0.000	0.000
65	S	365	MET	0	0.008	-0.003	36.521	-0.004	-0.004	0.000	0.000	0.000	0.000
66	S	366	GLU	-1	-0.847	-0.901	38.988	0.028	0.028	0.000	0.000	0.000	0.000
67	S	367	ALA	0	-0.006	0.004	40.504	-0.002	-0.002	0.000	0.000	0.000	0.000
68	S	368	LEU	0	-0.017	-0.007	39.505	-0.002	-0.002	0.000	0.000	0.000	0.000
69	S	369	SER	0	-0.033	-0.031	42.905	-0.004	-0.004	0.000	0.000	0.000	0.000
70	S	370	LEU	0	-0.041	-0.013	44.996	-0.002	-0.002	0.000	0.000	0.000	0.000
71	S	371	TYR	0	0.016	0.007	46.237	-0.001	-0.001	0.000	0.000	0.000	0.000
72	S	372	THR	0	-0.001	-0.009	46.840	-0.001	-0.001	0.000	0.000	0.000	0.000
73	S	373	LYS	1	0.911	0.947	47.392	-0.019	-0.019	0.000	0.000	0.000	0.000
74	S	374	LEU	0	0.007	0.012	49.777	-0.001	-0.001	0.000	0.000	0.000	0.000
75	S	375	MET	0	-0.061	-0.024	51.323	-0.001	-0.001	0.000	0.000	0.000	0.000
76	S	376	ASN	0	-0.089	-0.035	53.781	-0.001	-0.001	0.000	0.000	0.000	0.000
77	S	377	GLU	-1	-0.987	-0.978	55.278	0.017	0.017	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(S:301:PHE)