FMO DATABASE

FMODB ID: K9233

Calculation Name: 3F27-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F27

Chain ID: D

ChEMBL ID:

UniProt ID: Q61473

Base Structure: X-ray

Registration Date: 2023-06-22

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	74
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-469444.328555
FMO2-HF: Nuclear repulsion	437595.654186
FMO2-HF: Total energy	-31848.674369
FMO2-MP2: Total energy	-31940.561662

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(D:68:ILE)

Summations of interaction energy for fragment #1(D:68:ILE)

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.
-12.65	-3.536	7.03	-4.733	-11.409	-0.024

Interaction energy analysis for fragmet #1(D:68:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / 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	D	70	ARG	1	0.967	0.980	3.322	-2.575	0.111	0.046	-1.288	-1.444	0.000
4	D	71	PRO	0	0.043	0.047	4.964	0.097	0.189	-0.001	-0.003	-0.087	0.000
5	D	72	MET	0	-0.031	-0.011	7.097	0.120	0.120	0.000	0.000	0.000	0.000
6	D	73	ASN	0	0.054	0.028	10.584	-0.021	-0.021	0.000	0.000	0.000	0.000
7	D	74	ALA	0	0.109	0.022	13.335	0.020	0.020	0.000	0.000	0.000	0.000
8	D	75	PHE	0	0.000	0.023	16.865	0.015	0.015	0.000	0.000	0.000	0.000
9	D	76	MET	0	-0.043	-0.030	12.808	0.015	0.015	0.000	0.000	0.000	0.000
10	D	77	VAL	0	0.033	0.012	14.028	0.026	0.026	0.000	0.000	0.000	0.000
11	D	78	TRP	0	0.032	0.030	16.125	0.014	0.014	0.000	0.000	0.000	0.000
12	D	79	ALA	0	-0.037	-0.032	18.020	0.012	0.012	0.000	0.000	0.000	0.000
13	D	80	LYS	1	0.787	0.889	15.784	-0.034	-0.034	0.000	0.000	0.000	0.000
14	D	81	ASP	-1	-0.823	-0.890	17.895	0.056	0.056	0.000	0.000	0.000	0.000
15	D	82	GLU	-1	-0.716	-0.836	21.178	0.047	0.047	0.000	0.000	0.000	0.000
16	D	83	ARG	1	0.860	0.928	19.581	-0.140	-0.140	0.000	0.000	0.000	0.000
17	D	84	LYS	1	0.950	0.982	21.941	-0.086	-0.086	0.000	0.000	0.000	0.000
18	D	85	ARG	1	0.807	0.875	23.798	-0.038	-0.038	0.000	0.000	0.000	0.000
19	D	86	LEU	0	0.007	-0.027	26.061	0.001	0.001	0.000	0.000	0.000	0.000
20	D	87	ALA	0	0.010	0.005	25.558	-0.001	-0.001	0.000	0.000	0.000	0.000
21	D	88	GLN	0	-0.043	-0.017	26.889	0.006	0.006	0.000	0.000	0.000	0.000
22	D	89	GLN	0	-0.061	-0.037	29.799	-0.008	-0.008	0.000	0.000	0.000	0.000
23	D	90	ASN	0	-0.046	-0.030	30.722	-0.007	-0.007	0.000	0.000	0.000	0.000
24	D	91	PRO	0	-0.013	0.005	30.124	0.007	0.007	0.000	0.000	0.000	0.000
25	D	92	ASP	-1	-0.890	-0.941	31.002	0.081	0.081	0.000	0.000	0.000	0.000
26	D	93	LEU	0	-0.006	0.007	30.487	0.006	0.006	0.000	0.000	0.000	0.000
27	D	94	HIS	0	0.078	0.040	25.575	0.005	0.005	0.000	0.000	0.000	0.000
28	D	95	ASN	0	0.077	0.027	20.656	-0.020	-0.020	0.000	0.000	0.000	0.000
29	D	96	ALA	0	0.016	0.006	24.750	-0.006	-0.006	0.000	0.000	0.000	0.000
30	D	97	GLU	-1	-0.792	-0.893	25.715	0.071	0.071	0.000	0.000	0.000	0.000
31	D	98	LEU	0	0.066	0.032	24.707	-0.009	-0.009	0.000	0.000	0.000	0.000
32	D	99	SER	0	-0.034	-0.027	21.401	-0.007	-0.007	0.000	0.000	0.000	0.000
33	D	100	LYS	1	0.812	0.913	23.883	-0.092	-0.092	0.000	0.000	0.000	0.000
34	D	101	MET	0	-0.011	0.005	26.961	-0.013	-0.013	0.000	0.000	0.000	0.000
35	D	102	LEU	0	0.018	0.027	21.637	-0.009	-0.009	0.000	0.000	0.000	0.000
36	D	103	GLY	0	0.004	-0.003	24.120	-0.011	-0.011	0.000	0.000	0.000	0.000
37	D	104	LYS	1	0.927	0.948	24.996	-0.054	-0.054	0.000	0.000	0.000	0.000
38	D	105	SER	0	0.016	-0.009	27.717	-0.007	-0.007	0.000	0.000	0.000	0.000
39	D	106	TRP	0	0.046	0.036	20.355	-0.007	-0.007	0.000	0.000	0.000	0.000
40	D	107	LYS	1	0.927	0.958	25.563	-0.017	-0.017	0.000	0.000	0.000	0.000
41	D	108	ALA	0	-0.021	-0.006	27.788	-0.003	-0.003	0.000	0.000	0.000	0.000
42	D	109	LEU	0	0.011	0.035	25.717	-0.003	-0.003	0.000	0.000	0.000	0.000
43	D	110	THR	0	0.028	0.005	28.265	-0.004	-0.004	0.000	0.000	0.000	0.000
44	D	111	LEU	0	-0.019	-0.020	25.676	-0.003	-0.003	0.000	0.000	0.000	0.000
45	D	112	ALA	0	0.027	0.007	26.562	-0.006	-0.006	0.000	0.000	0.000	0.000
46	D	113	GLU	-1	-0.819	-0.897	27.672	-0.021	-0.021	0.000	0.000	0.000	0.000
47	D	114	LYS	1	0.801	0.882	23.072	0.022	0.022	0.000	0.000	0.000	0.000
48	D	115	ARG	1	0.904	0.945	22.674	0.070	0.070	0.000	0.000	0.000	0.000
49	D	116	PRO	0	0.030	0.022	22.208	-0.014	-0.014	0.000	0.000	0.000	0.000
50	D	117	PHE	0	0.023	0.010	19.465	-0.009	-0.009	0.000	0.000	0.000	0.000
51	D	118	VAL	0	-0.036	-0.009	18.052	-0.019	-0.019	0.000	0.000	0.000	0.000
52	D	119	GLU	-1	-0.816	-0.904	17.575	-0.129	-0.129	0.000	0.000	0.000	0.000
53	D	120	GLU	-1	-0.852	-0.910	16.250	-0.130	-0.130	0.000	0.000	0.000	0.000
54	D	121	ALA	0	-0.048	-0.045	13.795	-0.032	-0.032	0.000	0.000	0.000	0.000
55	D	122	GLU	-1	-0.803	-0.863	12.801	-0.360	-0.360	0.000	0.000	0.000	0.000
56	D	123	ARG	1	0.865	0.933	13.737	0.105	0.105	0.000	0.000	0.000	0.000
57	D	124	LEU	0	0.010	0.006	10.475	-0.056	-0.056	0.000	0.000	0.000	0.000
58	D	125	ARG	1	0.756	0.842	9.296	0.257	0.257	0.000	0.000	0.000	0.000
59	D	126	VAL	0	0.019	-0.011	9.595	-0.120	-0.120	0.000	0.000	0.000	0.000
60	D	127	GLN	0	-0.034	-0.026	9.530	0.006	0.006	0.000	0.000	0.000	0.000
61	D	128	HIS	0	-0.017	-0.020	2.438	-0.763	-0.036	0.822	-0.396	-1.153	-0.001
62	D	129	MET	0	-0.058	-0.018	6.302	-0.291	-0.291	0.000	0.000	0.000	0.000
63	D	130	GLN	0	-0.026	0.003	8.293	-0.046	-0.046	0.000	0.000	0.000	0.000
64	D	131	ASP	-1	-0.864	-0.915	6.086	-1.016	-1.016	0.000	0.000	0.000	0.000
65	D	132	HIS	0	-0.094	-0.057	2.589	-5.630	-1.864	1.273	-1.721	-3.317	-0.021
66	D	133	PRO	0	0.065	0.043	4.734	0.076	0.130	-0.001	-0.002	-0.050	0.000
67	D	134	ASN	0	-0.013	-0.016	5.658	0.119	0.119	0.000	0.000	0.000	0.000
68	D	135	TYR	0	-0.014	0.003	2.280	-2.396	-0.748	4.889	-1.307	-5.231	-0.002
69	D	136	LYS	1	0.977	0.989	4.093	0.190	0.331	0.002	-0.016	-0.127	0.000
70	D	137	TYR	0	0.018	-0.005	5.578	0.097	0.097	0.000	0.000	0.000	0.000
71	D	138	ARG	1	0.964	0.978	6.157	0.261	0.261	0.000	0.000	0.000	0.000
72	D	139	PRO	0	0.011	0.019	7.662	0.072	0.072	0.000	0.000	0.000	0.000
73	D	140	ARG	1	0.939	0.955	8.716	-0.224	-0.224	0.000	0.000	0.000	0.000
74	D	141	ARG	1	1.032	1.033	12.481	-0.087	-0.087	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:68:ILE)