FMO DATABASE

FMODB ID: 5J88Z

Calculation Name: 3KXE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KXE

Chain ID: A

ChEMBL ID:

UniProt ID: P58091

Base Structure: X-ray

Registration Date: 2023-09-23

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	94
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-681596.209714
FMO2-HF: Nuclear repulsion	643175.369684
FMO2-HF: Total energy	-38420.84003
FMO2-MP2: Total energy	-38532.051396

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:2:LYS)

Summations of interaction energy for fragment #1(A:2:LYS)

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.
-138.231	-133.692	18.31	-12.452	-10.394	-0.146

Interaction energy analysis for fragmet #1(A:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.895 / q_NPA : 0.923

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

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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	4	TYR	0	0.019	0.008	3.846	4.255	5.915	-0.019	-0.729	-0.912	0.003
4	A	5	ARG	1	0.862	0.920	6.708	20.054	20.054	0.000	0.000	0.000	0.000
5	A	6	LEU	0	0.039	0.007	10.436	-0.704	-0.704	0.000	0.000	0.000	0.000
6	A	7	SER	0	-0.060	-0.011	12.861	1.307	1.307	0.000	0.000	0.000	0.000
7	A	8	ARG	1	1.044	1.001	16.516	14.456	14.456	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.834	0.930	18.813	13.233	13.233	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.048	0.024	15.964	0.221	0.221	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.814	0.875	15.578	16.259	16.259	0.000	0.000	0.000	0.000
11	A	12	ALA	0	-0.001	-0.012	17.225	0.213	0.213	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.724	-0.830	18.964	-14.546	-14.546	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.020	0.012	14.115	0.180	0.180	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.773	-0.848	18.360	-15.255	-15.255	0.000	0.000	0.000	0.000
15	A	16	ASP	-1	-0.841	-0.907	21.028	-12.225	-12.225	0.000	0.000	0.000	0.000
16	A	17	ILE	0	-0.057	-0.043	19.044	0.406	0.406	0.000	0.000	0.000	0.000
17	A	18	TRP	0	-0.026	-0.013	17.714	-0.215	-0.215	0.000	0.000	0.000	0.000
18	A	19	THR	0	-0.012	-0.012	21.908	0.566	0.566	0.000	0.000	0.000	0.000
19	A	20	TYR	0	-0.028	-0.015	25.551	0.572	0.572	0.000	0.000	0.000	0.000
20	A	21	SER	0	-0.013	-0.029	22.794	0.342	0.342	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.843	-0.904	24.656	-12.109	-12.109	0.000	0.000	0.000	0.000
22	A	23	GLN	0	-0.071	-0.023	26.024	0.309	0.309	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.848	0.924	28.184	10.700	10.700	0.000	0.000	0.000	0.000
24	A	25	TRP	0	-0.078	-0.062	25.355	0.218	0.218	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.074	0.066	27.506	0.014	0.014	0.000	0.000	0.000	0.000
26	A	27	VAL	0	0.029	-0.007	23.702	-0.400	-0.400	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.895	-0.937	22.364	-13.386	-13.386	0.000	0.000	0.000	0.000
28	A	29	GLN	0	0.055	0.021	21.319	-0.930	-0.930	0.000	0.000	0.000	0.000
29	A	30	ALA	0	-0.020	0.002	21.093	-0.661	-0.661	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.015	-0.014	18.289	-0.895	-0.895	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.851	-0.919	16.783	-17.558	-17.558	0.000	0.000	0.000	0.000
32	A	33	TYR	0	-0.029	-0.026	16.502	-1.075	-1.075	0.000	0.000	0.000	0.000
33	A	34	ALA	0	0.011	0.001	15.624	-0.883	-0.883	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.869	0.922	12.281	17.539	17.539	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.877	-0.918	11.573	-23.882	-23.882	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.027	-0.004	12.646	-1.318	-1.318	0.000	0.000	0.000	0.000
37	A	38	GLN	0	-0.089	-0.055	7.174	1.991	1.991	0.000	0.000	0.000	0.000
38	A	39	ALA	0	0.033	0.023	8.017	-4.422	-4.422	0.000	0.000	0.000	0.000
39	A	40	THR	0	-0.012	-0.027	8.404	-2.256	-2.256	0.000	0.000	0.000	0.000
40	A	41	ILE	0	-0.039	-0.020	8.091	-0.435	-0.435	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.899	-0.955	4.001	-54.942	-54.694	-0.001	-0.022	-0.224	0.000
42	A	43	MET	0	0.005	0.003	4.786	-8.714	-8.641	-0.001	-0.003	-0.068	0.000
43	A	44	ILE	0	-0.068	-0.023	7.227	1.806	1.806	0.000	0.000	0.000	0.000
44	A	45	ALA	0	-0.059	-0.041	3.378	2.102	2.366	0.006	-0.075	-0.195	0.000
45	A	46	GLU	-1	-0.847	-0.906	1.749	-145.202	-142.993	18.326	-11.617	-8.917	-0.149
46	A	47	HIS	0	0.030	0.015	4.424	7.761	7.846	-0.001	-0.006	-0.078	0.000
47	A	48	PRO	0	0.017	0.023	6.313	3.499	3.499	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.039	-0.031	8.801	2.064	2.064	0.000	0.000	0.000	0.000
49	A	50	MET	0	0.003	0.004	11.467	1.398	1.398	0.000	0.000	0.000	0.000
50	A	51	GLY	0	0.028	0.038	12.609	0.895	0.895	0.000	0.000	0.000	0.000
51	A	52	GLN	0	0.023	0.021	14.325	0.576	0.576	0.000	0.000	0.000	0.000
52	A	53	PRO	0	-0.024	-0.025	17.910	-0.200	-0.200	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.867	-0.947	18.892	-12.038	-12.038	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.807	-0.910	20.903	-13.111	-13.111	0.000	0.000	0.000	0.000
55	A	56	ASN	0	0.007	0.006	22.836	0.383	0.383	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.066	-0.003	22.246	0.270	0.270	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.915	0.939	21.883	12.710	12.710	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.052	0.032	21.596	-0.449	-0.449	0.000	0.000	0.000	0.000
59	A	60	GLY	0	-0.024	-0.017	18.216	-0.323	-0.323	0.000	0.000	0.000	0.000
60	A	61	TYR	0	-0.062	-0.044	16.389	-0.894	-0.894	0.000	0.000	0.000	0.000
61	A	62	ARG	1	0.882	0.946	13.255	18.878	18.878	0.000	0.000	0.000	0.000
62	A	63	ARG	1	0.824	0.912	15.879	13.342	13.342	0.000	0.000	0.000	0.000
63	A	64	CYS	0	-0.018	-0.016	12.697	0.246	0.246	0.000	0.000	0.000	0.000
64	A	65	ALA	0	-0.011	0.002	15.782	-0.243	-0.243	0.000	0.000	0.000	0.000
65	A	66	SER	0	0.041	0.014	14.738	-0.617	-0.617	0.000	0.000	0.000	0.000
66	A	67	GLY	0	0.052	0.029	17.154	0.578	0.578	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.041	-0.015	20.134	0.829	0.829	0.000	0.000	0.000	0.000
68	A	69	HIS	0	0.013	0.007	19.310	0.518	0.518	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.001	0.003	18.979	-0.442	-0.442	0.000	0.000	0.000	0.000
70	A	71	VAL	0	0.005	0.011	12.828	0.378	0.378	0.000	0.000	0.000	0.000
71	A	72	PHE	0	0.005	0.000	15.857	0.004	0.004	0.000	0.000	0.000	0.000
72	A	73	TYR	0	-0.049	-0.053	10.702	-0.412	-0.412	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.901	0.952	13.209	16.862	16.862	0.000	0.000	0.000	0.000
74	A	75	VAL	0	-0.007	-0.006	9.663	-1.495	-1.495	0.000	0.000	0.000	0.000
75	A	76	GLY	0	0.030	0.035	11.862	1.315	1.315	0.000	0.000	0.000	0.000
76	A	77	VAL	0	0.005	-0.012	11.892	-0.593	-0.593	0.000	0.000	0.000	0.000
77	A	78	ARG	1	0.939	0.961	7.064	24.013	24.013	0.000	0.000	0.000	0.000
78	A	79	VAL	0	0.058	0.036	6.177	2.164	2.164	0.000	0.000	0.000	0.000
79	A	80	GLU	-1	-0.822	-0.894	8.380	-18.573	-18.573	0.000	0.000	0.000	0.000
80	A	81	ILE	0	0.054	0.029	9.390	1.344	1.344	0.000	0.000	0.000	0.000
81	A	82	ILE	0	-0.053	-0.026	12.589	0.991	0.991	0.000	0.000	0.000	0.000
82	A	83	ARG	1	0.819	0.875	16.289	14.715	14.715	0.000	0.000	0.000	0.000
83	A	84	VAL	0	0.018	0.021	15.661	-0.761	-0.761	0.000	0.000	0.000	0.000
84	A	85	LEU	0	-0.014	-0.004	18.587	0.756	0.756	0.000	0.000	0.000	0.000
85	A	86	HIS	0	0.082	0.051	21.898	-0.226	-0.226	0.000	0.000	0.000	0.000
86	A	87	GLN	0	0.041	0.014	23.944	-0.084	-0.084	0.000	0.000	0.000	0.000
87	A	88	SER	0	-0.025	-0.030	25.191	0.352	0.352	0.000	0.000	0.000	0.000
88	A	89	MET	0	-0.052	-0.029	25.543	0.430	0.430	0.000	0.000	0.000	0.000
89	A	90	ASN	0	-0.039	-0.006	23.922	-0.458	-0.458	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.038	0.015	26.579	0.434	0.434	0.000	0.000	0.000	0.000
91	A	92	ARG	1	0.925	0.968	27.531	9.881	9.881	0.000	0.000	0.000	0.000
92	A	93	ALA	0	0.037	0.026	26.832	0.288	0.288	0.000	0.000	0.000	0.000
93	A	94	HIS	0	-0.013	-0.010	28.812	0.014	0.014	0.000	0.000	0.000	0.000
94	A	95	LEU	0	-0.010	0.007	29.749	0.070	0.070	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LYS)