FMO DATABASE

FMODB ID: M3LJZ

Calculation Name: 3K8A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K8A

Chain ID: A

ChEMBL ID:

UniProt ID: Q5F924

Base Structure: X-ray

Registration Date: 2023-03-14

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	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	100
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-717664.860461
FMO2-HF: Nuclear repulsion	677223.813843
FMO2-HF: Total energy	-40441.046619
FMO2-MP2: Total energy	-40557.4904

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:1:MET)

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

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.
-4.226	-1.66	1.36	-1.787	-2.138	-0.008

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.012

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	3	PHE	0	0.025	0.013	2.661	-5.529	-3.045	1.361	-1.783	-2.061	-0.008
4	A	4	THR	0	-0.005	-0.015	5.133	0.515	0.597	-0.001	-0.004	-0.077	0.000
5	A	5	ASN	0	-0.010	0.004	7.473	0.152	0.152	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.042	0.009	9.325	0.123	0.123	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.017	0.003	12.617	-0.030	-0.030	0.000	0.000	0.000	0.000
8	A	8	SER	0	0.049	0.015	16.410	0.044	0.044	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.042	-0.015	18.766	-0.020	-0.020	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.043	0.020	22.287	0.016	0.016	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.024	-0.018	25.626	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.051	0.027	28.130	0.010	0.010	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.060	-0.023	29.218	-0.008	-0.008	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.848	-0.915	31.277	-0.018	-0.018	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.933	0.957	32.841	0.010	0.010	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.024	0.002	32.025	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	17	PHE	0	-0.074	-0.037	31.453	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.015	0.011	32.951	0.004	0.004	0.000	0.000	0.000	0.000
19	A	19	ILE	0	0.048	0.030	30.139	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.822	0.911	27.179	0.015	0.015	0.000	0.000	0.000	0.000
21	A	21	TYR	0	0.042	0.007	28.663	0.005	0.005	0.000	0.000	0.000	0.000
22	A	22	THR	0	-0.080	-0.022	23.831	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	23	PRO	0	0.044	0.000	26.797	0.005	0.005	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.009	-0.003	25.180	0.002	0.002	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.030	0.025	27.327	0.008	0.008	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.059	-0.033	21.999	0.005	0.005	0.000	0.000	0.000	0.000
27	A	27	PRO	0	0.096	0.064	25.284	-0.012	-0.012	0.000	0.000	0.000	0.000
28	A	28	VAL	0	-0.084	-0.052	24.511	0.006	0.006	0.000	0.000	0.000	0.000
29	A	29	LEU	0	0.033	0.023	25.803	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.869	-0.914	26.434	-0.023	-0.023	0.000	0.000	0.000	0.000
31	A	31	ILE	0	0.007	-0.007	27.359	0.004	0.004	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.005	0.001	28.463	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.025	-0.004	24.599	0.008	0.008	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.985	1.013	28.631	0.015	0.015	0.000	0.000	0.000	0.000
35	A	35	HIS	0	-0.059	-0.048	26.608	0.003	0.003	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.924	-0.975	29.351	-0.026	-0.026	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.055	-0.022	27.864	0.007	0.007	0.000	0.000	0.000	0.000
38	A	38	TRP	0	0.052	0.016	30.406	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.050	-0.026	24.933	0.007	0.007	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.867	-0.942	26.326	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.984	-1.013	25.572	-0.088	-0.088	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.039	-0.015	26.747	0.002	0.002	0.000	0.000	0.000	0.000
43	A	43	GLY	0	-0.007	-0.001	28.502	0.002	0.002	0.000	0.000	0.000	0.000
44	A	44	GLN	0	-0.018	0.005	31.000	0.001	0.001	0.000	0.000	0.000	0.000
45	A	45	GLN	0	0.009	0.005	30.801	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	46	CYS	0	-0.021	-0.004	29.711	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.013	0.000	31.102	0.002	0.002	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.039	-0.016	26.832	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	49	GLN	0	0.023	0.015	30.219	0.007	0.007	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.044	-0.033	24.382	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.896	-0.944	28.939	-0.028	-0.028	0.000	0.000	0.000	0.000
52	A	52	ILE	0	-0.052	-0.020	22.358	-0.014	-0.014	0.000	0.000	0.000	0.000
53	A	53	PRO	0	0.017	0.018	25.760	0.012	0.012	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.011	-0.016	23.627	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.891	0.951	20.990	0.041	0.041	0.000	0.000	0.000	0.000
56	A	56	ILE	0	0.045	0.036	21.904	0.011	0.011	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.027	-0.033	19.206	-0.017	-0.017	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.012	-0.001	22.543	0.017	0.017	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.985	0.995	23.762	-0.150	-0.150	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.033	0.004	20.464	0.000	0.000	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.008	-0.007	25.124	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.904	-0.964	26.623	0.056	0.056	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.936	-0.975	27.111	0.121	0.121	0.000	0.000	0.000	0.000
64	A	64	TRP	0	0.047	0.000	26.926	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	65	GLN	0	-0.052	-0.029	29.953	-0.013	-0.013	0.000	0.000	0.000	0.000
66	A	66	TYR	0	-0.024	-0.020	31.962	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.785	0.897	31.570	-0.071	-0.071	0.000	0.000	0.000	0.000
68	A	68	GLN	0	-0.027	-0.019	33.632	0.001	0.001	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.000	0.003	35.026	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.822	-0.893	32.822	0.047	0.047	0.000	0.000	0.000	0.000
71	A	71	CYS	0	-0.036	-0.012	30.812	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.014	0.009	26.716	0.009	0.009	0.000	0.000	0.000	0.000
73	A	73	THR	0	0.001	-0.007	21.947	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	74	VAL	0	-0.019	-0.004	20.560	0.014	0.014	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.899	-0.945	15.426	0.275	0.275	0.000	0.000	0.000	0.000
76	A	76	GLY	0	-0.007	-0.021	15.632	0.028	0.028	0.000	0.000	0.000	0.000
77	A	77	PHE	0	-0.024	0.020	12.842	-0.034	-0.034	0.000	0.000	0.000	0.000
78	A	78	LEU	0	0.047	0.015	14.830	0.017	0.017	0.000	0.000	0.000	0.000
79	A	79	ALA	0	-0.036	-0.029	15.729	-0.061	-0.061	0.000	0.000	0.000	0.000
80	A	80	GLN	0	0.036	0.017	18.112	0.045	0.045	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.984	1.001	21.206	0.085	0.085	0.000	0.000	0.000	0.000
82	A	82	SER	0	0.006	0.005	22.818	0.006	0.006	0.000	0.000	0.000	0.000
83	A	83	ARG	1	1.012	0.996	21.420	0.264	0.264	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.880	0.930	23.418	0.176	0.176	0.000	0.000	0.000	0.000
85	A	85	SER	0	0.021	0.005	24.733	0.014	0.014	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.058	-0.022	24.709	0.009	0.009	0.000	0.000	0.000	0.000
87	A	87	MET	0	0.107	0.079	25.137	0.000	0.000	0.000	0.000	0.000	0.000
88	A	88	PRO	0	-0.007	-0.016	20.734	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	89	MET	0	-0.022	-0.018	20.582	0.024	0.024	0.000	0.000	0.000	0.000
90	A	90	LEU	0	0.030	0.019	18.424	-0.023	-0.023	0.000	0.000	0.000	0.000
91	A	91	ARG	1	0.846	0.924	16.342	0.095	0.095	0.000	0.000	0.000	0.000
92	A	92	ILE	0	0.014	0.021	17.487	0.019	0.019	0.000	0.000	0.000	0.000
93	A	93	GLN	0	0.027	0.007	13.951	-0.044	-0.044	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.056	-0.037	17.318	0.013	0.013	0.000	0.000	0.000	0.000
95	A	95	ILE	0	0.037	0.022	19.732	-0.019	-0.019	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.905	0.977	21.480	-0.217	-0.217	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.804	-0.894	25.668	0.072	0.072	0.000	0.000	0.000	0.000
98	A	98	TYR	0	-0.042	-0.021	26.717	0.010	0.010	0.000	0.000	0.000	0.000
99	A	99	LYS	1	0.968	0.975	28.108	-0.095	-0.095	0.000	0.000	0.000	0.000
100	A	100	GLY	0	-0.023	0.008	27.004	0.002	0.002	0.000	0.000	0.000	0.000

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