FMO DATABASE

FMODB ID: 949K2

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	OptAll
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	-647962.325463
FMO2-HF: Nuclear repulsion	612330.851889
FMO2-HF: Total energy	-35631.473574
FMO2-MP2: Total energy	-35738.637506

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.
-2.11	0.061999999999999	-0.015	-1.027	-1.13	0

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 : 0.016 / q_NPA : -0.009

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].
3	A	370	ALA	0	-0.020	0.000	3.864	-0.811	1.305	-0.014	-1.022	-1.081
4	A	371	ALA	0	0.032	0.015	5.022	0.106	0.162	-0.001	-0.005	-0.049
5	A	372	PRO	0	-0.013	-0.011	8.648	0.130	0.130	0.000	0.000	0.000
6	A	373	ALA	0	-0.022	-0.002	11.508	0.022	0.022	0.000	0.000	0.000
7	A	374	LEU	0	-0.021	-0.010	14.336	0.013	0.013	0.000	0.000	0.000
8	A	375	ASP	-1	-0.873	-0.938	18.102	-0.146	-0.146	0.000	0.000	0.000
9	A	376	THR	0	-0.033	-0.008	20.363	0.016	0.016	0.000	0.000	0.000
10	A	377	LEU	0	-0.031	-0.010	19.896	-0.003	-0.003	0.000	0.000	0.000
11	A	378	PRO	0	-0.054	-0.026	23.215	0.010	0.010	0.000	0.000	0.000
12	A	379	ALA	0	0.082	0.038	22.438	-0.008	-0.008	0.000	0.000	0.000
13	A	380	PRO	0	-0.038	-0.004	22.211	0.006	0.006	0.000	0.000	0.000
14	A	381	THR	0	0.006	-0.009	24.814	0.001	0.001	0.000	0.000	0.000
15	A	382	SER	0	0.009	-0.011	27.151	0.003	0.003	0.000	0.000	0.000
16	A	383	LEU	0	0.020	0.026	21.744	0.001	0.001	0.000	0.000	0.000
17	A	384	VAL	0	0.000	0.000	25.873	0.004	0.004	0.000	0.000	0.000
18	A	385	LEU	0	0.003	0.005	21.935	0.002	0.002	0.000	0.000	0.000
19	A	386	SER	0	-0.025	-0.018	26.285	-0.003	-0.003	0.000	0.000	0.000
20	A	387	GLN	0	0.025	-0.007	28.035	0.007	0.007	0.000	0.000	0.000
21	A	388	VAL	0	0.009	0.026	26.696	0.004	0.004	0.000	0.000	0.000
22	A	389	THR	0	0.034	0.006	27.779	-0.002	-0.002	0.000	0.000	0.000
23	A	390	SER	0	-0.015	-0.012	27.618	0.008	0.008	0.000	0.000	0.000
24	A	391	SER	0	-0.001	-0.006	24.656	0.011	0.011	0.000	0.000	0.000
25	A	392	SER	0	0.019	0.021	24.039	0.007	0.007	0.000	0.000	0.000
26	A	393	ILE	0	0.033	0.015	21.085	0.000	0.000	0.000	0.000	0.000
27	A	394	ARG	1	0.855	0.926	24.730	-0.040	-0.040	0.000	0.000	0.000
28	A	395	LEU	0	-0.014	0.001	20.059	0.002	0.002	0.000	0.000	0.000
29	A	396	SER	0	0.023	0.006	24.570	-0.006	-0.006	0.000	0.000	0.000
30	A	397	TRP	0	-0.017	-0.005	23.134	0.006	0.006	0.000	0.000	0.000
31	A	398	THR	0	0.031	0.019	27.026	0.000	0.000	0.000	0.000	0.000
32	A	399	PRO	0	-0.010	0.000	27.092	-0.005	-0.005	0.000	0.000	0.000
33	A	400	ALA	0	0.034	0.022	27.112	0.002	0.002	0.000	0.000	0.000
34	A	401	PRO	0	0.017	-0.004	28.818	0.000	0.000	0.000	0.000	0.000
35	A	402	ARG	1	0.946	0.993	27.911	0.092	0.092	0.000	0.000	0.000
36	A	403	HIS	0	-0.007	-0.005	27.880	-0.002	-0.002	0.000	0.000	0.000
37	A	404	PRO	0	-0.023	0.005	22.760	-0.004	-0.004	0.000	0.000	0.000
38	A	405	LEU	0	0.011	0.009	22.404	0.010	0.010	0.000	0.000	0.000
39	A	406	LYS	1	0.830	0.903	19.710	0.068	0.068	0.000	0.000	0.000
40	A	407	TYR	0	0.020	0.006	19.357	-0.012	-0.012	0.000	0.000	0.000
41	A	408	LEU	0	-0.006	0.012	11.355	0.011	0.011	0.000	0.000	0.000
42	A	409	ILE	0	-0.012	-0.008	15.941	0.003	0.003	0.000	0.000	0.000
43	A	410	VAL	0	0.035	0.015	10.502	0.025	0.025	0.000	0.000	0.000
44	A	411	TRP	0	-0.013	-0.013	13.464	-0.002	-0.002	0.000	0.000	0.000
45	A	412	ARG	1	0.905	0.946	7.770	-1.026	-1.026	0.000	0.000	0.000
46	A	413	ALA	0	0.024	0.021	13.765	-0.055	-0.055	0.000	0.000	0.000
47	A	414	SER	0	-0.048	-0.069	14.825	0.076	0.076	0.000	0.000	0.000
48	A	415	ARG	1	0.941	0.962	15.938	-0.236	-0.236	0.000	0.000	0.000
49	A	416	GLY	0	0.022	0.029	13.329	0.010	0.010	0.000	0.000	0.000
50	A	417	GLY	0	0.022	0.002	11.987	-0.081	-0.081	0.000	0.000	0.000
51	A	418	THR	0	-0.019	-0.009	7.331	0.207	0.207	0.000	0.000	0.000
52	A	419	PRO	0	-0.031	-0.004	7.059	-0.158	-0.158	0.000	0.000	0.000
53	A	420	ARG	1	0.879	0.931	9.797	-0.273	-0.273	0.000	0.000	0.000
54	A	421	GLU	-1	-0.889	-0.954	8.941	-0.038	-0.038	0.000	0.000	0.000
55	A	422	VAL	0	-0.031	-0.012	12.973	0.006	0.006	0.000	0.000	0.000
56	A	423	VAL	0	0.001	-0.003	15.233	-0.017	-0.017	0.000	0.000	0.000
57	A	424	VAL	0	0.002	0.016	17.924	0.009	0.009	0.000	0.000	0.000
58	A	425	GLU	-1	-0.820	-0.927	21.642	-0.043	-0.043	0.000	0.000	0.000
59	A	426	GLY	0	0.042	0.031	24.458	0.004	0.004	0.000	0.000	0.000
60	A	427	PRO	0	-0.009	-0.025	25.653	0.001	0.001	0.000	0.000	0.000
61	A	428	ALA	0	-0.040	0.003	24.906	0.006	0.006	0.000	0.000	0.000
62	A	429	ALA	0	0.051	0.013	26.619	-0.004	-0.004	0.000	0.000	0.000
63	A	430	SER	0	-0.023	-0.023	26.669	0.007	0.007	0.000	0.000	0.000
64	A	431	THR	0	-0.017	-0.015	21.653	-0.006	-0.006	0.000	0.000	0.000
65	A	432	GLU	-1	-0.853	-0.895	24.603	0.062	0.062	0.000	0.000	0.000
66	A	433	LEU	0	-0.003	0.013	18.744	0.000	0.000	0.000	0.000	0.000
67	A	434	HIS	0	0.027	-0.018	21.354	0.006	0.006	0.000	0.000	0.000
68	A	435	ASN	0	-0.020	-0.011	20.463	0.012	0.012	0.000	0.000	0.000
69	A	436	LEU	0	-0.035	0.011	19.406	0.030	0.030	0.000	0.000	0.000
70	A	437	ALA	0	0.036	0.024	20.555	-0.015	-0.015	0.000	0.000	0.000
71	A	438	SER	0	0.059	0.041	22.319	-0.005	-0.005	0.000	0.000	0.000
72	A	439	ARG	1	0.862	0.937	24.809	-0.134	-0.134	0.000	0.000	0.000
73	A	440	THR	0	-0.031	-0.014	19.826	0.015	0.015	0.000	0.000	0.000
74	A	441	GLU	-1	-0.833	-0.878	20.531	0.167	0.167	0.000	0.000	0.000
75	A	442	TYR	0	-0.034	-0.030	16.913	0.051	0.051	0.000	0.000	0.000
76	A	443	LEU	0	0.004	0.015	13.321	-0.029	-0.029	0.000	0.000	0.000
77	A	444	VAL	0	-0.022	-0.027	15.731	0.031	0.031	0.000	0.000	0.000
78	A	445	SER	0	-0.007	-0.012	14.596	-0.022	-0.022	0.000	0.000	0.000
79	A	446	VAL	0	-0.008	-0.002	16.704	0.008	0.008	0.000	0.000	0.000
80	A	447	PHE	0	0.007	0.011	12.763	-0.006	-0.006	0.000	0.000	0.000
81	A	448	PRO	0	-0.017	0.009	17.178	0.006	0.006	0.000	0.000	0.000
82	A	449	ILE	0	0.010	0.000	15.540	-0.028	-0.028	0.000	0.000	0.000
83	A	450	TYR	0	-0.025	-0.041	19.362	0.022	0.022	0.000	0.000	0.000
84	A	451	GLU	-1	-0.892	-0.954	20.768	-0.153	-0.153	0.000	0.000	0.000
85	A	452	GLY	0	-0.053	-0.018	22.090	-0.009	-0.009	0.000	0.000	0.000
86	A	453	GLY	0	0.013	0.010	18.030	-0.018	-0.018	0.000	0.000	0.000
87	A	454	VAL	0	-0.003	0.001	12.914	0.031	0.031	0.000	0.000	0.000
88	A	455	GLY	0	0.031	0.013	16.401	-0.020	-0.020	0.000	0.000	0.000
89	A	456	GLU	-1	-0.753	-0.879	15.933	-0.105	-0.105	0.000	0.000	0.000
90	A	457	GLY	0	-0.014	-0.021	17.322	0.011	0.011	0.000	0.000	0.000
91	A	458	LEU	0	-0.075	-0.009	18.466	0.012	0.012	0.000	0.000	0.000
92	A	459	ARG	1	0.840	0.876	15.592	0.041	0.041	0.000	0.000	0.000
93	A	460	GLY	0	-0.001	0.008	19.236	-0.009	-0.009	0.000	0.000	0.000
94	A	461	LEU	0	-0.018	0.002	18.788	0.019	0.019	0.000	0.000	0.000
95	A	462	VAL	0	0.015	0.008	21.436	-0.017	-0.017	0.000	0.000	0.000
96	A	463	THR	0	0.011	0.002	22.287	0.025	0.025	0.000	0.000	0.000
97	A	464	THR	0	-0.026	-0.023	23.339	-0.014	-0.014	0.000	0.000	0.000
98	A	465	ALA	0	0.015	0.009	25.795	0.000	0.000	0.000	0.000	0.000
99	A	466	PRO	0	0.015	-0.006	28.682	0.010	0.010	0.000	0.000	0.000

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