FMO DATABASE

FMODB ID: 39R8L

Calculation Name: 5KF4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5KF4

Chain ID: A

ChEMBL ID:

UniProt ID: Q9P218

Base Structure: X-ray

Registration Date: 2023-09-19

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	99
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-649537.360602
FMO2-HF: Nuclear repulsion	613906.662774
FMO2-HF: Total energy	-35630.697828
FMO2-MP2: Total energy	-35737.886508

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:368:PRO)

Summations of interaction energy for fragment #1(A:368:PRO)

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.
-2.222	0.209	-0.022	-1.042	-1.366	0.001

Interaction energy analysis for fragmet #1(A:368:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / 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	A	370	ALA	0	-0.029	-0.005	3.605	-1.256	1.102	-0.021	-1.034	-1.302	0.001
4	A	371	ALA	0	0.033	0.008	5.006	0.189	0.262	-0.001	-0.008	-0.064	0.000
5	A	372	PRO	0	-0.019	-0.008	8.665	0.104	0.104	0.000	0.000	0.000	0.000
6	A	373	ALA	0	0.008	0.007	11.475	0.025	0.025	0.000	0.000	0.000	0.000
7	A	374	LEU	0	-0.028	-0.021	14.347	0.017	0.017	0.000	0.000	0.000	0.000
8	A	375	ASP	-1	-0.880	-0.950	17.907	-0.172	-0.172	0.000	0.000	0.000	0.000
9	A	376	THR	0	-0.040	-0.013	19.940	0.021	0.021	0.000	0.000	0.000	0.000
10	A	377	LEU	0	-0.009	-0.023	20.745	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	378	PRO	0	-0.076	-0.026	23.576	0.007	0.007	0.000	0.000	0.000	0.000
12	A	379	ALA	0	0.077	0.043	22.512	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	380	PRO	0	-0.030	-0.004	22.124	0.009	0.009	0.000	0.000	0.000	0.000
14	A	381	THR	0	0.008	-0.013	24.601	0.001	0.001	0.000	0.000	0.000	0.000
15	A	382	SER	0	0.012	-0.016	26.843	0.003	0.003	0.000	0.000	0.000	0.000
16	A	383	LEU	0	0.027	0.040	21.412	0.001	0.001	0.000	0.000	0.000	0.000
17	A	384	VAL	0	-0.033	-0.022	25.550	0.006	0.006	0.000	0.000	0.000	0.000
18	A	385	LEU	0	-0.007	-0.008	21.984	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	386	SER	0	-0.006	-0.001	26.263	0.004	0.004	0.000	0.000	0.000	0.000
20	A	387	GLN	0	0.010	-0.008	28.168	0.003	0.003	0.000	0.000	0.000	0.000
21	A	388	VAL	0	0.004	0.026	26.563	0.002	0.002	0.000	0.000	0.000	0.000
22	A	389	THR	0	0.022	-0.002	27.670	0.003	0.003	0.000	0.000	0.000	0.000
23	A	390	SER	0	0.007	-0.016	27.327	0.003	0.003	0.000	0.000	0.000	0.000
24	A	391	SER	0	-0.018	-0.010	24.295	0.008	0.008	0.000	0.000	0.000	0.000
25	A	392	SER	0	0.007	0.036	23.617	0.003	0.003	0.000	0.000	0.000	0.000
26	A	393	ILE	0	0.058	0.029	21.670	0.003	0.003	0.000	0.000	0.000	0.000
27	A	394	ARG	1	0.930	0.970	24.786	0.003	0.003	0.000	0.000	0.000	0.000
28	A	395	LEU	0	0.007	0.012	20.212	0.002	0.002	0.000	0.000	0.000	0.000
29	A	396	SER	0	-0.004	-0.016	24.620	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	397	TRP	0	0.010	0.017	23.490	0.003	0.003	0.000	0.000	0.000	0.000
31	A	398	THR	0	0.023	-0.002	26.686	0.002	0.002	0.000	0.000	0.000	0.000
32	A	399	PRO	0	-0.017	0.014	27.134	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	400	ALA	0	0.052	0.025	27.395	0.004	0.004	0.000	0.000	0.000	0.000
34	A	401	PRO	0	0.014	-0.014	29.129	0.000	0.000	0.000	0.000	0.000	0.000
35	A	402	ARG	1	0.952	0.996	26.957	0.107	0.107	0.000	0.000	0.000	0.000
36	A	403	HIS	0	-0.011	0.014	27.750	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	404	PRO	0	-0.020	0.016	22.591	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	405	LEU	0	0.034	0.015	22.265	0.010	0.010	0.000	0.000	0.000	0.000
39	A	406	LYS	1	0.872	0.915	19.204	0.113	0.113	0.000	0.000	0.000	0.000
40	A	407	TYR	0	0.042	0.025	19.246	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	408	LEU	0	-0.019	0.017	11.324	0.014	0.014	0.000	0.000	0.000	0.000
42	A	409	ILE	0	0.014	0.010	15.832	0.005	0.005	0.000	0.000	0.000	0.000
43	A	410	VAL	0	0.044	0.016	10.516	0.012	0.012	0.000	0.000	0.000	0.000
44	A	411	TRP	0	-0.006	0.005	13.637	0.016	0.016	0.000	0.000	0.000	0.000
45	A	412	ARG	1	0.897	0.938	7.696	-0.574	-0.574	0.000	0.000	0.000	0.000
46	A	413	ALA	0	0.020	0.014	13.599	-0.032	-0.032	0.000	0.000	0.000	0.000
47	A	414	SER	0	-0.056	-0.052	14.477	0.062	0.062	0.000	0.000	0.000	0.000
48	A	415	ARG	1	0.962	0.980	15.942	-0.189	-0.189	0.000	0.000	0.000	0.000
49	A	416	GLY	0	0.006	0.016	12.833	0.023	0.023	0.000	0.000	0.000	0.000
50	A	417	GLY	0	0.003	-0.005	11.835	-0.037	-0.037	0.000	0.000	0.000	0.000
51	A	418	THR	0	0.012	0.005	6.686	0.142	0.142	0.000	0.000	0.000	0.000
52	A	419	PRO	0	-0.040	-0.010	6.837	-0.099	-0.099	0.000	0.000	0.000	0.000
53	A	420	ARG	1	0.955	0.981	9.212	-0.168	-0.168	0.000	0.000	0.000	0.000
54	A	421	GLU	-1	-0.877	-0.954	8.780	-0.332	-0.332	0.000	0.000	0.000	0.000
55	A	422	VAL	0	-0.021	-0.003	12.887	0.017	0.017	0.000	0.000	0.000	0.000
56	A	423	VAL	0	0.010	0.003	14.390	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	424	VAL	0	-0.028	-0.005	17.011	0.016	0.016	0.000	0.000	0.000	0.000
58	A	425	GLU	-1	-0.870	-0.952	20.767	-0.083	-0.083	0.000	0.000	0.000	0.000
59	A	426	GLY	0	0.029	0.008	23.493	0.001	0.001	0.000	0.000	0.000	0.000
60	A	427	PRO	0	-0.043	-0.026	24.978	0.002	0.002	0.000	0.000	0.000	0.000
61	A	428	ALA	0	-0.021	0.011	24.636	0.007	0.007	0.000	0.000	0.000	0.000
62	A	429	ALA	0	0.027	0.000	26.469	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	430	SER	0	-0.032	-0.032	26.457	0.005	0.005	0.000	0.000	0.000	0.000
64	A	431	THR	0	0.023	0.007	21.177	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	432	GLU	-1	-0.943	-0.964	24.553	0.014	0.014	0.000	0.000	0.000	0.000
66	A	433	LEU	0	-0.016	0.010	18.649	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	434	HIS	0	0.037	-0.003	21.094	0.004	0.004	0.000	0.000	0.000	0.000
68	A	435	ASN	0	-0.071	-0.039	20.269	0.009	0.009	0.000	0.000	0.000	0.000
69	A	436	LEU	0	-0.057	-0.020	18.831	0.017	0.017	0.000	0.000	0.000	0.000
70	A	437	ALA	0	0.018	0.007	20.203	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	438	SER	0	0.042	0.025	21.819	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	439	ARG	1	0.893	0.969	24.223	-0.088	-0.088	0.000	0.000	0.000	0.000
73	A	440	THR	0	-0.026	-0.025	19.318	0.016	0.016	0.000	0.000	0.000	0.000
74	A	441	GLU	-1	-0.835	-0.893	19.956	0.090	0.090	0.000	0.000	0.000	0.000
75	A	442	TYR	0	0.008	-0.002	16.491	0.028	0.028	0.000	0.000	0.000	0.000
76	A	443	LEU	0	-0.025	-0.002	13.389	-0.019	-0.019	0.000	0.000	0.000	0.000
77	A	444	VAL	0	-0.008	-0.015	15.471	0.005	0.005	0.000	0.000	0.000	0.000
78	A	445	SER	0	-0.027	-0.022	14.243	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	446	VAL	0	0.000	0.001	16.352	0.000	0.000	0.000	0.000	0.000	0.000
80	A	447	PHE	0	0.032	0.011	12.650	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	448	PRO	0	-0.011	0.008	16.994	0.008	0.008	0.000	0.000	0.000	0.000
82	A	449	ILE	0	-0.005	-0.007	15.220	-0.024	-0.024	0.000	0.000	0.000	0.000
83	A	450	TYR	0	-0.024	-0.045	19.061	0.024	0.024	0.000	0.000	0.000	0.000
84	A	451	GLU	-1	-0.887	-0.955	20.351	-0.168	-0.168	0.000	0.000	0.000	0.000
85	A	452	GLY	0	-0.074	-0.029	21.600	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	453	GLY	0	0.031	0.022	17.862	-0.010	-0.010	0.000	0.000	0.000	0.000
87	A	454	VAL	0	-0.014	0.003	13.095	0.024	0.024	0.000	0.000	0.000	0.000
88	A	455	GLY	0	0.011	0.019	16.415	-0.011	-0.011	0.000	0.000	0.000	0.000
89	A	456	GLU	-1	-0.889	-0.963	15.646	-0.212	-0.212	0.000	0.000	0.000	0.000
90	A	457	GLY	0	0.002	-0.001	17.381	0.016	0.016	0.000	0.000	0.000	0.000
91	A	458	LEU	0	-0.098	-0.025	18.820	0.012	0.012	0.000	0.000	0.000	0.000
92	A	459	ARG	1	0.985	0.969	13.901	0.086	0.086	0.000	0.000	0.000	0.000
93	A	460	GLY	0	-0.004	0.004	19.273	0.001	0.001	0.000	0.000	0.000	0.000
94	A	461	LEU	0	-0.029	-0.009	18.453	0.005	0.005	0.000	0.000	0.000	0.000
95	A	462	VAL	0	0.017	0.014	21.318	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	463	THR	0	0.009	-0.005	22.243	0.016	0.016	0.000	0.000	0.000	0.000
97	A	464	THR	0	-0.040	-0.024	23.005	-0.008	-0.008	0.000	0.000	0.000	0.000
98	A	465	ALA	0	0.024	0.013	25.670	0.003	0.003	0.000	0.000	0.000	0.000
99	A	466	PRO	0	0.015	-0.008	28.122	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:368:PRO)