FMO DATABASE

FMODB ID: LZ499

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-649644.980614
FMO2-HF: Nuclear repulsion	614013.864744
FMO2-HF: Total energy	-35631.115869
FMO2-MP2: Total energy	-35738.275171

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.
-2.393	0.199	-0.024	-1.204	-1.364	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 : -0.016

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	-0.027	-0.004	3.806	-1.393	1.128	-0.023	-1.196	-1.302	0.001
4	A	371	ALA	0	0.041	0.014	4.942	0.200	0.271	-0.001	-0.008	-0.062	0.000
5	A	372	PRO	0	-0.020	-0.011	8.582	0.121	0.121	0.000	0.000	0.000	0.000
6	A	373	ALA	0	-0.001	0.006	11.423	0.025	0.025	0.000	0.000	0.000	0.000
7	A	374	LEU	0	-0.017	-0.014	14.300	0.016	0.016	0.000	0.000	0.000	0.000
8	A	375	ASP	-1	-0.904	-0.953	17.856	-0.162	-0.162	0.000	0.000	0.000	0.000
9	A	376	THR	0	-0.037	-0.014	19.912	0.021	0.021	0.000	0.000	0.000	0.000
10	A	377	LEU	0	0.009	-0.007	20.073	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	378	PRO	0	-0.077	-0.031	23.521	0.007	0.007	0.000	0.000	0.000	0.000
12	A	379	ALA	0	0.070	0.042	22.484	-0.008	-0.008	0.000	0.000	0.000	0.000
13	A	380	PRO	0	-0.029	-0.002	22.116	0.008	0.008	0.000	0.000	0.000	0.000
14	A	381	THR	0	0.009	-0.020	24.583	0.001	0.001	0.000	0.000	0.000	0.000
15	A	382	SER	0	0.018	0.000	26.832	0.003	0.003	0.000	0.000	0.000	0.000
16	A	383	LEU	0	0.031	0.025	21.371	0.001	0.001	0.000	0.000	0.000	0.000
17	A	384	VAL	0	-0.032	-0.026	25.560	0.006	0.006	0.000	0.000	0.000	0.000
18	A	385	LEU	0	-0.007	-0.004	21.899	0.000	0.000	0.000	0.000	0.000	0.000
19	A	386	SER	0	-0.008	-0.006	26.291	0.003	0.003	0.000	0.000	0.000	0.000
20	A	387	GLN	0	0.018	-0.002	28.194	0.003	0.003	0.000	0.000	0.000	0.000
21	A	388	VAL	0	0.008	0.025	26.747	0.002	0.002	0.000	0.000	0.000	0.000
22	A	389	THR	0	0.023	-0.007	27.709	0.002	0.002	0.000	0.000	0.000	0.000
23	A	390	SER	0	-0.013	-0.017	27.375	0.004	0.004	0.000	0.000	0.000	0.000
24	A	391	SER	0	0.000	-0.006	24.340	0.008	0.008	0.000	0.000	0.000	0.000
25	A	392	SER	0	0.024	0.041	23.656	0.004	0.004	0.000	0.000	0.000	0.000
26	A	393	ILE	0	0.036	0.025	21.294	0.002	0.002	0.000	0.000	0.000	0.000
27	A	394	ARG	1	0.864	0.920	24.810	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	395	LEU	0	0.003	0.015	20.130	0.002	0.002	0.000	0.000	0.000	0.000
29	A	396	SER	0	-0.014	-0.026	24.623	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	397	TRP	0	0.034	0.029	23.078	0.004	0.004	0.000	0.000	0.000	0.000
31	A	398	THR	0	0.010	0.000	26.674	0.001	0.001	0.000	0.000	0.000	0.000
32	A	399	PRO	0	-0.020	0.010	27.100	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	400	ALA	0	0.051	0.030	27.344	0.004	0.004	0.000	0.000	0.000	0.000
34	A	401	PRO	0	0.019	-0.011	29.082	0.000	0.000	0.000	0.000	0.000	0.000
35	A	402	ARG	1	0.943	0.994	27.735	0.103	0.103	0.000	0.000	0.000	0.000
36	A	403	HIS	0	-0.005	0.003	27.962	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	404	PRO	0	-0.019	0.006	22.838	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	405	LEU	0	0.021	0.017	22.290	0.010	0.010	0.000	0.000	0.000	0.000
39	A	406	LYS	1	0.834	0.887	19.372	0.102	0.102	0.000	0.000	0.000	0.000
40	A	407	TYR	0	0.033	0.025	19.487	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	408	LEU	0	-0.030	0.007	11.495	0.014	0.014	0.000	0.000	0.000	0.000
42	A	409	ILE	0	0.015	0.013	16.089	0.005	0.005	0.000	0.000	0.000	0.000
43	A	410	VAL	0	0.039	0.019	10.423	0.017	0.017	0.000	0.000	0.000	0.000
44	A	411	TRP	0	-0.005	0.004	13.633	0.014	0.014	0.000	0.000	0.000	0.000
45	A	412	ARG	1	0.902	0.944	7.921	-0.730	-0.730	0.000	0.000	0.000	0.000
46	A	413	ALA	0	0.025	0.019	13.661	-0.038	-0.038	0.000	0.000	0.000	0.000
47	A	414	SER	0	-0.044	-0.074	14.577	0.068	0.068	0.000	0.000	0.000	0.000
48	A	415	ARG	1	0.942	0.970	16.058	-0.201	-0.201	0.000	0.000	0.000	0.000
49	A	416	GLY	0	0.012	0.018	12.956	0.020	0.020	0.000	0.000	0.000	0.000
50	A	417	GLY	0	0.017	0.003	11.897	-0.049	-0.049	0.000	0.000	0.000	0.000
51	A	418	THR	0	-0.016	-0.007	6.774	0.162	0.162	0.000	0.000	0.000	0.000
52	A	419	PRO	0	-0.038	-0.013	6.879	-0.104	-0.104	0.000	0.000	0.000	0.000
53	A	420	ARG	1	0.920	0.969	9.244	-0.182	-0.182	0.000	0.000	0.000	0.000
54	A	421	GLU	-1	-0.884	-0.961	9.297	-0.275	-0.275	0.000	0.000	0.000	0.000
55	A	422	VAL	0	-0.029	-0.011	13.011	0.014	0.014	0.000	0.000	0.000	0.000
56	A	423	VAL	0	0.004	0.003	14.613	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	424	VAL	0	-0.002	0.000	17.250	0.013	0.013	0.000	0.000	0.000	0.000
58	A	425	GLU	-1	-0.834	-0.925	21.009	-0.080	-0.080	0.000	0.000	0.000	0.000
59	A	426	GLY	0	0.046	0.025	23.715	0.002	0.002	0.000	0.000	0.000	0.000
60	A	427	PRO	0	-0.042	-0.032	25.198	0.002	0.002	0.000	0.000	0.000	0.000
61	A	428	ALA	0	-0.019	0.017	24.879	0.007	0.007	0.000	0.000	0.000	0.000
62	A	429	ALA	0	0.036	0.000	26.708	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	430	SER	0	-0.019	-0.011	26.527	0.006	0.006	0.000	0.000	0.000	0.000
64	A	431	THR	0	-0.002	-0.005	21.594	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	432	GLU	-1	-0.881	-0.915	24.658	0.023	0.023	0.000	0.000	0.000	0.000
66	A	433	LEU	0	0.000	0.019	18.621	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	434	HIS	0	0.020	-0.019	21.103	0.003	0.003	0.000	0.000	0.000	0.000
68	A	435	ASN	0	-0.044	-0.025	20.402	0.009	0.009	0.000	0.000	0.000	0.000
69	A	436	LEU	0	-0.043	-0.017	19.021	0.020	0.020	0.000	0.000	0.000	0.000
70	A	437	ALA	0	0.013	0.006	20.199	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	438	SER	0	0.057	0.026	21.878	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	439	ARG	1	0.887	0.957	24.290	-0.098	-0.098	0.000	0.000	0.000	0.000
73	A	440	THR	0	-0.033	-0.020	19.348	0.017	0.017	0.000	0.000	0.000	0.000
74	A	441	GLU	-1	-0.836	-0.867	20.176	0.116	0.116	0.000	0.000	0.000	0.000
75	A	442	TYR	0	0.003	0.001	16.767	0.039	0.039	0.000	0.000	0.000	0.000
76	A	443	LEU	0	-0.015	0.000	13.365	-0.019	-0.019	0.000	0.000	0.000	0.000
77	A	444	VAL	0	-0.021	-0.021	15.520	0.010	0.010	0.000	0.000	0.000	0.000
78	A	445	SER	0	-0.008	-0.012	14.272	-0.013	-0.013	0.000	0.000	0.000	0.000
79	A	446	VAL	0	-0.012	-0.003	16.363	0.001	0.001	0.000	0.000	0.000	0.000
80	A	447	PHE	0	0.014	0.000	12.539	-0.010	-0.010	0.000	0.000	0.000	0.000
81	A	448	PRO	0	-0.012	0.015	16.953	0.006	0.006	0.000	0.000	0.000	0.000
82	A	449	ILE	0	0.006	-0.011	15.246	-0.025	-0.025	0.000	0.000	0.000	0.000
83	A	450	TYR	0	-0.024	-0.034	19.250	0.023	0.023	0.000	0.000	0.000	0.000
84	A	451	GLU	-1	-0.884	-0.954	20.482	-0.162	-0.162	0.000	0.000	0.000	0.000
85	A	452	GLY	0	-0.071	-0.030	21.683	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	453	GLY	0	0.028	0.022	17.961	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	454	VAL	0	-0.004	0.001	12.935	0.024	0.024	0.000	0.000	0.000	0.000
88	A	455	GLY	0	0.016	0.020	16.388	-0.012	-0.012	0.000	0.000	0.000	0.000
89	A	456	GLU	-1	-0.781	-0.905	16.252	-0.169	-0.169	0.000	0.000	0.000	0.000
90	A	457	GLY	0	-0.012	-0.012	17.278	0.015	0.015	0.000	0.000	0.000	0.000
91	A	458	LEU	0	-0.106	-0.026	18.806	0.012	0.012	0.000	0.000	0.000	0.000
92	A	459	ARG	1	0.901	0.909	14.501	0.086	0.086	0.000	0.000	0.000	0.000
93	A	460	GLY	0	-0.006	0.007	19.303	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	461	LEU	0	-0.023	-0.003	18.498	0.008	0.008	0.000	0.000	0.000	0.000
95	A	462	VAL	0	0.012	0.007	21.383	-0.009	-0.009	0.000	0.000	0.000	0.000
96	A	463	THR	0	0.016	-0.001	22.312	0.018	0.018	0.000	0.000	0.000	0.000
97	A	464	THR	0	-0.033	-0.019	23.153	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	465	ALA	0	0.020	0.013	25.724	0.003	0.003	0.000	0.000	0.000	0.000
99	A	466	PRO	0	0.011	-0.009	28.181	0.006	0.006	0.000	0.000	0.000	0.000

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