FMO DATABASE

FMODB ID: V2481

Calculation Name: 3F1I-H-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F1I

Chain ID: H

ChEMBL ID:

UniProt ID: O14964

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

Apendix: None

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	98
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-554395.793725
FMO2-HF: Nuclear repulsion	514456.047096
FMO2-HF: Total energy	-39939.746629
FMO2-MP2: Total energy	-40056.199616

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(H:404:SER )

Summations of interaction energy for fragment #1(H:404: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.
-19.379	-14.992	6.244	-4.441	-6.192	0.027

Interaction energy analysis for fragmet #1(H:404:SER )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.013

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	H	406	GLU	-1	-0.921	-0.958	2.503	-0.836	1.882	1.165	-1.454	-2.430	0.007
4	H	407	GLN	0	-0.068	-0.025	2.222	-9.621	-8.951	5.058	-2.458	-3.270	0.017
5	H	408	PHE	0	0.034	-0.001	3.453	-2.996	-1.997	0.021	-0.529	-0.492	0.003
6	H	409	LEU	0	0.035	0.014	5.459	-0.708	-0.708	0.000	0.000	0.000	0.000
7	H	410	LYS	1	0.967	0.983	5.937	-3.299	-3.299	0.000	0.000	0.000	0.000
8	H	411	ALA	0	-0.016	0.010	7.863	-0.460	-0.460	0.000	0.000	0.000	0.000
9	H	412	LEU	0	0.059	0.023	9.457	-0.325	-0.325	0.000	0.000	0.000	0.000
10	H	413	GLN	0	0.009	-0.002	11.445	-0.151	-0.151	0.000	0.000	0.000	0.000
11	H	414	ASN	0	0.019	0.006	12.038	-0.216	-0.216	0.000	0.000	0.000	0.000
12	H	415	ALA	0	0.013	0.022	13.584	-0.144	-0.144	0.000	0.000	0.000	0.000
13	H	416	VAL	0	0.044	0.017	15.444	-0.113	-0.113	0.000	0.000	0.000	0.000
14	H	417	THR	0	-0.023	-0.018	17.001	-0.096	-0.096	0.000	0.000	0.000	0.000
15	H	418	THR	0	-0.045	-0.039	17.473	-0.077	-0.077	0.000	0.000	0.000	0.000
16	H	419	PHE	0	-0.010	-0.001	19.422	-0.057	-0.057	0.000	0.000	0.000	0.000
17	H	420	VAL	0	0.038	0.014	21.238	-0.049	-0.049	0.000	0.000	0.000	0.000
18	H	421	ASN	0	-0.007	-0.014	22.790	-0.052	-0.052	0.000	0.000	0.000	0.000
19	H	422	ARG	1	0.892	0.939	23.802	-0.320	-0.320	0.000	0.000	0.000	0.000
20	H	423	MET	0	-0.022	-0.007	24.133	-0.034	-0.034	0.000	0.000	0.000	0.000
21	H	424	LYS	1	0.958	0.988	26.274	-0.295	-0.295	0.000	0.000	0.000	0.000
22	H	425	SER	0	0.034	0.015	28.204	-0.020	-0.020	0.000	0.000	0.000	0.000
23	H	426	ASN	0	-0.076	-0.052	28.493	-0.030	-0.030	0.000	0.000	0.000	0.000
24	H	427	HIS	0	0.083	0.052	31.553	-0.009	-0.009	0.000	0.000	0.000	0.000
25	H	428	MET	0	-0.032	-0.025	32.854	-0.006	-0.006	0.000	0.000	0.000	0.000
26	H	429	ARG	1	0.882	0.961	29.959	-0.202	-0.202	0.000	0.000	0.000	0.000
27	H	430	GLY	0	0.004	0.018	36.045	-0.008	-0.008	0.000	0.000	0.000	0.000
28	H	431	ARG	1	0.838	0.912	31.434	-0.180	-0.180	0.000	0.000	0.000	0.000
29	H	432	SER	0	0.047	0.020	34.446	0.009	0.009	0.000	0.000	0.000	0.000
30	H	433	ILE	0	0.048	-0.004	28.453	0.004	0.004	0.000	0.000	0.000	0.000
31	H	434	THR	0	0.013	0.015	29.739	0.010	0.010	0.000	0.000	0.000	0.000
32	H	435	ASN	0	-0.022	-0.008	31.752	-0.006	-0.006	0.000	0.000	0.000	0.000
33	H	436	ASP	-1	-0.860	-0.910	27.080	0.254	0.254	0.000	0.000	0.000	0.000
34	H	437	SER	0	0.044	0.021	27.011	0.016	0.016	0.000	0.000	0.000	0.000
35	H	438	ALA	0	0.039	0.009	22.926	0.015	0.015	0.000	0.000	0.000	0.000
36	H	439	VAL	0	-0.019	-0.008	22.376	0.034	0.034	0.000	0.000	0.000	0.000
37	H	440	LEU	0	0.031	0.024	23.180	0.021	0.021	0.000	0.000	0.000	0.000
38	H	441	SER	0	0.014	0.013	20.340	0.025	0.025	0.000	0.000	0.000	0.000
39	H	442	LEU	0	0.011	-0.002	17.440	0.035	0.035	0.000	0.000	0.000	0.000
40	H	443	PHE	0	0.000	-0.002	18.709	0.038	0.038	0.000	0.000	0.000	0.000
41	H	444	GLN	0	-0.006	-0.003	19.890	0.001	0.001	0.000	0.000	0.000	0.000
42	H	445	SER	0	-0.005	-0.010	14.935	0.034	0.034	0.000	0.000	0.000	0.000
43	H	446	ILE	0	-0.031	-0.011	14.981	0.073	0.073	0.000	0.000	0.000	0.000
44	H	447	ASN	0	-0.014	-0.009	16.096	0.022	0.022	0.000	0.000	0.000	0.000
45	H	448	GLY	0	-0.017	0.003	15.823	-0.023	-0.023	0.000	0.000	0.000	0.000
46	H	449	MET	0	-0.023	-0.023	11.000	0.094	0.094	0.000	0.000	0.000	0.000
47	H	450	HIS	0	-0.001	0.007	12.693	0.074	0.074	0.000	0.000	0.000	0.000
48	H	451	PRO	0	0.053	0.020	14.450	-0.008	-0.008	0.000	0.000	0.000	0.000
49	H	452	GLN	0	0.060	0.047	5.761	0.002	0.002	0.000	0.000	0.000	0.000
50	H	453	LEU	0	-0.050	-0.037	11.064	0.011	0.011	0.000	0.000	0.000	0.000
51	H	454	LEU	0	-0.016	-0.008	12.477	-0.068	-0.068	0.000	0.000	0.000	0.000
52	H	455	GLU	-1	-0.895	-0.943	11.924	0.199	0.199	0.000	0.000	0.000	0.000
53	H	456	LEU	0	-0.057	-0.034	7.404	-0.091	-0.091	0.000	0.000	0.000	0.000
54	H	457	LEU	0	-0.035	-0.020	11.440	-0.063	-0.063	0.000	0.000	0.000	0.000
55	H	458	ASN	0	0.064	0.044	14.736	-0.035	-0.035	0.000	0.000	0.000	0.000
56	H	459	GLN	0	-0.002	-0.008	11.418	-0.110	-0.110	0.000	0.000	0.000	0.000
57	H	460	LEU	0	-0.039	-0.020	12.055	-0.058	-0.058	0.000	0.000	0.000	0.000
58	H	461	ASP	-1	-0.863	-0.928	14.806	0.067	0.067	0.000	0.000	0.000	0.000
59	H	462	GLU	-1	-0.942	-0.975	16.563	-0.163	-0.163	0.000	0.000	0.000	0.000
60	H	463	ARG	1	0.865	0.933	11.889	0.381	0.381	0.000	0.000	0.000	0.000
61	H	464	ARG	1	0.848	0.930	17.253	-0.026	-0.026	0.000	0.000	0.000	0.000
62	H	465	LEU	0	0.033	0.014	19.841	-0.001	-0.001	0.000	0.000	0.000	0.000
63	H	466	TYR	0	-0.051	-0.018	19.903	-0.004	-0.004	0.000	0.000	0.000	0.000
64	H	467	TYR	0	-0.005	-0.023	17.464	-0.002	-0.002	0.000	0.000	0.000	0.000
65	H	468	GLU	-1	-0.872	-0.928	22.702	-0.003	-0.003	0.000	0.000	0.000	0.000
66	H	469	GLY	0	0.076	0.056	25.221	0.003	0.003	0.000	0.000	0.000	0.000
67	H	470	LEU	0	-0.080	-0.044	23.769	0.001	0.001	0.000	0.000	0.000	0.000
68	H	471	GLN	0	-0.002	-0.019	26.849	0.004	0.004	0.000	0.000	0.000	0.000
69	H	472	ASP	-1	-0.865	-0.927	28.657	-0.034	-0.034	0.000	0.000	0.000	0.000
70	H	473	LYS	1	0.926	0.962	29.837	0.101	0.101	0.000	0.000	0.000	0.000
71	H	474	LEU	0	-0.016	-0.016	29.293	0.002	0.002	0.000	0.000	0.000	0.000
72	H	475	ALA	0	-0.018	0.009	32.778	0.004	0.004	0.000	0.000	0.000	0.000
73	H	476	GLN	0	0.040	0.011	34.902	-0.002	-0.002	0.000	0.000	0.000	0.000
74	H	477	ILE	0	-0.016	-0.001	33.773	0.001	0.001	0.000	0.000	0.000	0.000
75	H	478	ARG	1	0.922	0.966	35.845	0.030	0.030	0.000	0.000	0.000	0.000
76	H	479	ASP	-1	-0.879	-0.945	38.695	-0.028	-0.028	0.000	0.000	0.000	0.000
77	H	480	ALA	0	-0.010	0.007	40.550	0.002	0.002	0.000	0.000	0.000	0.000
78	H	481	ARG	1	0.914	0.951	41.349	0.049	0.049	0.000	0.000	0.000	0.000
79	H	482	GLY	0	0.026	0.002	42.859	0.002	0.002	0.000	0.000	0.000	0.000
80	H	483	ALA	0	0.024	0.015	44.731	0.002	0.002	0.000	0.000	0.000	0.000
81	H	484	LEU	0	0.004	0.000	45.837	0.001	0.001	0.000	0.000	0.000	0.000
82	H	485	SER	0	-0.072	-0.047	46.481	0.000	0.000	0.000	0.000	0.000	0.000
83	H	486	ALA	0	0.007	0.010	48.925	0.001	0.001	0.000	0.000	0.000	0.000
84	H	487	LEU	0	0.053	0.032	49.799	0.001	0.001	0.000	0.000	0.000	0.000
85	H	488	ARG	1	0.882	0.939	48.177	0.039	0.039	0.000	0.000	0.000	0.000
86	H	489	GLU	-1	-0.872	-0.935	53.188	-0.020	-0.020	0.000	0.000	0.000	0.000
87	H	490	GLU	-1	-0.807	-0.878	54.955	-0.019	-0.019	0.000	0.000	0.000	0.000
88	H	491	HIS	0	-0.040	-0.028	56.420	0.001	0.001	0.000	0.000	0.000	0.000
89	H	492	ARG	1	0.904	0.938	53.222	0.027	0.027	0.000	0.000	0.000	0.000
90	H	493	GLU	-1	-0.940	-0.968	57.917	-0.016	-0.016	0.000	0.000	0.000	0.000
91	H	494	LYS	1	0.837	0.893	59.411	0.020	0.020	0.000	0.000	0.000	0.000
92	H	495	LEU	0	-0.038	-0.016	61.196	0.000	0.000	0.000	0.000	0.000	0.000
93	H	496	ARG	1	0.890	0.956	59.388	0.018	0.018	0.000	0.000	0.000	0.000
94	H	497	ARG	1	1.008	1.004	63.902	0.015	0.015	0.000	0.000	0.000	0.000
95	H	498	ALA	0	-0.041	-0.022	67.051	0.001	0.001	0.000	0.000	0.000	0.000
96	H	499	ALA	0	-0.039	-0.012	68.437	0.000	0.000	0.000	0.000	0.000	0.000
97	H	500	GLU	-1	-1.032	-1.022	67.959	-0.013	-0.013	0.000	0.000	0.000	0.000
98	H	501	GLU	-2	-1.947	-1.944	71.782	-0.026	-0.026	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(H:404:SER )