FMO DATABASE

FMODB ID: QYN1Y

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:

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. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	74
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-469342.254413
FMO2-HF: Nuclear repulsion	437494.452212
FMO2-HF: Total energy	-31847.802201
FMO2-MP2: Total energy	-31939.7392

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.
-8.816	-2.806	7.837	-3.964	-9.882	-0.01

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 : 0.041 / q_NPA : 0.014

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	0.951	0.971	3.381	-2.323	0.287	0.010	-1.330	-1.290	0.000
4	D	71	PRO	0	0.053	0.048	5.428	0.204	0.204	0.000	0.000	0.000	0.000
5	D	72	MET	0	-0.036	-0.011	7.223	0.107	0.107	0.000	0.000	0.000	0.000
6	D	73	ASN	0	0.047	0.035	10.680	-0.010	-0.010	0.000	0.000	0.000	0.000
7	D	74	ALA	0	0.113	0.019	13.571	0.024	0.024	0.000	0.000	0.000	0.000
8	D	75	PHE	0	-0.009	0.017	17.020	0.018	0.018	0.000	0.000	0.000	0.000
9	D	76	MET	0	-0.054	-0.037	13.184	0.019	0.019	0.000	0.000	0.000	0.000
10	D	77	VAL	0	0.046	0.019	13.937	0.030	0.030	0.000	0.000	0.000	0.000
11	D	78	TRP	0	0.046	0.044	16.068	0.017	0.017	0.000	0.000	0.000	0.000
12	D	79	ALA	0	-0.042	-0.038	17.984	0.014	0.014	0.000	0.000	0.000	0.000
13	D	80	LYS	1	0.903	0.957	14.140	-0.120	-0.120	0.000	0.000	0.000	0.000
14	D	81	ASP	-1	-0.908	-0.940	17.769	0.054	0.054	0.000	0.000	0.000	0.000
15	D	82	GLU	-1	-0.780	-0.904	20.977	0.040	0.040	0.000	0.000	0.000	0.000
16	D	83	ARG	1	0.926	0.979	18.928	-0.118	-0.118	0.000	0.000	0.000	0.000
17	D	84	LYS	1	0.943	0.982	21.630	-0.095	-0.095	0.000	0.000	0.000	0.000
18	D	85	ARG	1	0.857	0.923	23.728	-0.033	-0.033	0.000	0.000	0.000	0.000
19	D	86	LEU	0	-0.010	-0.029	26.261	0.001	0.001	0.000	0.000	0.000	0.000
20	D	87	ALA	0	0.013	0.017	25.608	-0.001	-0.001	0.000	0.000	0.000	0.000
21	D	88	GLN	0	-0.064	-0.023	26.799	0.009	0.009	0.000	0.000	0.000	0.000
22	D	89	GLN	0	-0.040	-0.028	29.815	-0.003	-0.003	0.000	0.000	0.000	0.000
23	D	90	ASN	0	-0.068	-0.048	30.539	-0.008	-0.008	0.000	0.000	0.000	0.000
24	D	91	PRO	0	-0.016	0.004	30.151	0.006	0.006	0.000	0.000	0.000	0.000
25	D	92	ASP	-1	-0.870	-0.937	31.026	0.074	0.074	0.000	0.000	0.000	0.000
26	D	93	LEU	0	-0.010	0.004	30.435	0.004	0.004	0.000	0.000	0.000	0.000
27	D	94	HIS	0	0.081	0.044	25.341	0.002	0.002	0.000	0.000	0.000	0.000
28	D	95	ASN	0	0.039	-0.001	20.774	-0.013	-0.013	0.000	0.000	0.000	0.000
29	D	96	ALA	0	0.002	-0.006	24.789	-0.007	-0.007	0.000	0.000	0.000	0.000
30	D	97	GLU	-1	-0.876	-0.947	25.716	0.051	0.051	0.000	0.000	0.000	0.000
31	D	98	LEU	0	0.045	0.025	24.967	-0.009	-0.009	0.000	0.000	0.000	0.000
32	D	99	SER	0	-0.070	-0.052	22.112	-0.007	-0.007	0.000	0.000	0.000	0.000
33	D	100	LYS	1	0.928	0.975	24.081	-0.068	-0.068	0.000	0.000	0.000	0.000
34	D	101	MET	0	0.012	0.012	27.220	-0.012	-0.012	0.000	0.000	0.000	0.000
35	D	102	LEU	0	0.009	0.017	21.666	-0.008	-0.008	0.000	0.000	0.000	0.000
36	D	103	GLY	0	0.002	-0.001	24.399	-0.011	-0.011	0.000	0.000	0.000	0.000
37	D	104	LYS	1	0.909	0.941	25.270	-0.035	-0.035	0.000	0.000	0.000	0.000
38	D	105	SER	0	0.010	-0.003	27.828	-0.006	-0.006	0.000	0.000	0.000	0.000
39	D	106	TRP	0	0.052	0.040	21.000	-0.006	-0.006	0.000	0.000	0.000	0.000
40	D	107	LYS	1	0.906	0.937	25.769	-0.003	-0.003	0.000	0.000	0.000	0.000
41	D	108	ALA	0	-0.022	-0.008	28.081	-0.003	-0.003	0.000	0.000	0.000	0.000
42	D	109	LEU	0	-0.002	0.033	25.293	-0.002	-0.002	0.000	0.000	0.000	0.000
43	D	110	THR	0	0.015	0.017	28.477	-0.006	-0.006	0.000	0.000	0.000	0.000
44	D	111	LEU	0	-0.002	-0.016	25.589	-0.003	-0.003	0.000	0.000	0.000	0.000
45	D	112	ALA	0	0.006	0.002	26.706	-0.006	-0.006	0.000	0.000	0.000	0.000
46	D	113	GLU	-1	-0.842	-0.938	27.719	-0.026	-0.026	0.000	0.000	0.000	0.000
47	D	114	LYS	1	0.897	0.943	23.216	0.040	0.040	0.000	0.000	0.000	0.000
48	D	115	ARG	1	0.987	1.005	22.735	0.064	0.064	0.000	0.000	0.000	0.000
49	D	116	PRO	0	0.022	0.017	22.224	-0.014	-0.014	0.000	0.000	0.000	0.000
50	D	117	PHE	0	0.038	0.013	19.500	-0.008	-0.008	0.000	0.000	0.000	0.000
51	D	118	VAL	0	-0.040	-0.004	18.039	-0.019	-0.019	0.000	0.000	0.000	0.000
52	D	119	GLU	-1	-0.912	-0.970	17.620	-0.134	-0.134	0.000	0.000	0.000	0.000
53	D	120	GLU	-1	-0.948	-0.981	15.739	-0.109	-0.109	0.000	0.000	0.000	0.000
54	D	121	ALA	0	-0.038	-0.040	13.762	-0.030	-0.030	0.000	0.000	0.000	0.000
55	D	122	GLU	-1	-0.834	-0.886	12.814	-0.371	-0.371	0.000	0.000	0.000	0.000
56	D	123	ARG	1	0.979	1.011	13.661	0.101	0.101	0.000	0.000	0.000	0.000
57	D	124	LEU	0	0.014	0.011	10.339	-0.051	-0.051	0.000	0.000	0.000	0.000
58	D	125	ARG	1	0.811	0.888	9.312	0.281	0.281	0.000	0.000	0.000	0.000
59	D	126	VAL	0	0.031	-0.002	9.544	-0.121	-0.121	0.000	0.000	0.000	0.000
60	D	127	GLN	0	-0.012	-0.003	9.905	-0.005	-0.005	0.000	0.000	0.000	0.000
61	D	128	HIS	0	-0.044	-0.037	2.682	-0.640	0.172	0.320	-0.296	-0.836	-0.001
62	D	129	MET	0	-0.094	-0.050	6.219	-0.274	-0.274	0.000	0.000	0.000	0.000
63	D	130	GLN	0	-0.019	0.008	8.242	-0.053	-0.053	0.000	0.000	0.000	0.000
64	D	131	ASP	-1	-0.890	-0.939	5.996	-0.799	-0.799	0.000	0.000	0.000	0.000
65	D	132	HIS	0	-0.099	-0.065	3.007	-3.663	-1.153	0.687	-0.891	-2.306	-0.010
66	D	133	PRO	0	0.076	0.054	5.102	-0.001	0.053	-0.001	0.000	-0.053	0.000
67	D	134	ASN	0	-0.006	-0.018	5.716	0.109	0.109	0.000	0.000	0.000	0.000
68	D	135	TYR	0	-0.024	0.001	2.027	-1.389	-1.565	6.816	-1.497	-5.143	0.001
69	D	136	LYS	1	0.989	0.993	3.754	0.137	0.254	0.006	0.056	-0.179	0.000
70	D	137	TYR	0	0.003	-0.010	4.876	-0.011	0.072	-0.001	-0.006	-0.075	0.000
71	D	138	ARG	1	0.957	0.975	5.597	0.424	0.424	0.000	0.000	0.000	0.000
72	D	139	PRO	0	0.022	0.023	7.652	0.017	0.017	0.000	0.000	0.000	0.000
73	D	140	ARG	1	0.941	0.955	9.211	-0.026	-0.026	0.000	0.000	0.000	0.000
74	D	141	ARG	1	1.024	1.031	12.457	-0.003	-0.003	0.000	0.000	0.000	0.000

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