FMO DATABASE

FMODB ID: 534KZ

Calculation Name: 3LKX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LKX

Chain ID: A

ChEMBL ID:

UniProt ID: P20290

Base Structure: X-ray

Registration Date: 2023-06-19

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	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	66
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-329475.018238
FMO2-HF: Nuclear repulsion	304479.474655
FMO2-HF: Total energy	-24995.543583
FMO2-MP2: Total energy	-25068.054966

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:25:VAL)

Summations of interaction energy for fragment #1(A:25:VAL)

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.
-6.212	-1.3	3.461	-3.411	-4.963	-0.009

Interaction energy analysis for fragmet #1(A:25:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.020

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	27	ASN	0	-0.017	-0.010	3.817	-0.279	1.295	-0.022	-0.660	-0.892	0.002
4	A	28	ILE	0	0.025	0.016	5.898	0.134	0.134	0.000	0.000	0.000	0.000
5	A	29	SER	0	-0.051	-0.026	9.139	0.025	0.025	0.000	0.000	0.000	0.000
6	A	30	GLY	0	0.050	0.011	12.342	0.040	0.040	0.000	0.000	0.000	0.000
7	A	31	ILE	0	-0.021	0.003	11.689	0.031	0.031	0.000	0.000	0.000	0.000
8	A	32	GLU	-1	-0.877	-0.938	14.870	-0.063	-0.063	0.000	0.000	0.000	0.000
9	A	33	GLU	-1	-0.854	-0.936	17.637	0.019	0.019	0.000	0.000	0.000	0.000
10	A	34	VAL	0	-0.031	-0.011	13.007	0.014	0.014	0.000	0.000	0.000	0.000
11	A	35	ASN	0	0.018	0.023	16.413	-0.021	-0.021	0.000	0.000	0.000	0.000
12	A	36	MET	0	-0.030	-0.003	13.640	0.019	0.019	0.000	0.000	0.000	0.000
13	A	37	PHE	0	0.036	0.021	18.796	-0.015	-0.015	0.000	0.000	0.000	0.000
14	A	38	THR	0	-0.004	0.021	21.930	0.009	0.009	0.000	0.000	0.000	0.000
15	A	39	ASN	0	-0.008	-0.021	24.058	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	40	GLN	0	0.004	-0.003	27.164	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	41	GLY	0	0.057	0.031	28.762	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	42	THR	0	-0.015	-0.017	24.622	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	43	VAL	0	-0.007	-0.006	22.022	0.010	0.010	0.000	0.000	0.000	0.000
20	A	44	ILE	0	0.001	0.005	18.623	-0.010	-0.010	0.000	0.000	0.000	0.000
21	A	45	HIS	1	0.831	0.904	19.388	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	46	PHE	0	0.000	-0.009	15.033	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	47	ASN	0	0.064	0.015	18.149	0.017	0.017	0.000	0.000	0.000	0.000
24	A	48	ASN	0	-0.070	-0.034	16.740	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	49	PRO	0	-0.020	0.014	12.917	-0.020	-0.020	0.000	0.000	0.000	0.000
26	A	50	LYS	1	0.957	0.980	7.370	0.443	0.443	0.000	0.000	0.000	0.000
27	A	51	VAL	0	0.040	0.012	8.057	0.053	0.053	0.000	0.000	0.000	0.000
28	A	52	GLN	0	-0.057	-0.033	2.911	-1.342	-0.250	0.183	-0.280	-0.995	0.001
29	A	53	ALA	0	0.033	0.013	4.121	-0.160	0.232	0.001	-0.090	-0.303	0.000
30	A	54	SER	0	0.053	0.029	2.430	-3.934	-2.257	3.301	-2.359	-2.620	-0.012
31	A	55	LEU	0	0.056	0.048	4.451	-0.966	-0.899	-0.001	-0.017	-0.050	0.000
32	A	56	ALA	0	-0.003	-0.038	5.860	0.022	0.022	0.000	0.000	0.000	0.000
33	A	57	ALA	0	-0.016	-0.009	6.470	0.117	0.117	0.000	0.000	0.000	0.000
34	A	58	ASN	0	-0.066	-0.019	8.505	-0.242	-0.242	0.000	0.000	0.000	0.000
35	A	59	THR	0	0.009	0.018	5.163	-0.261	-0.261	0.000	0.000	0.000	0.000
36	A	60	PHE	0	0.017	-0.007	5.901	0.322	0.322	0.000	0.000	0.000	0.000
37	A	61	THR	0	-0.039	-0.015	4.552	-0.153	-0.043	-0.001	-0.005	-0.103	0.000
38	A	62	ILE	0	0.038	0.020	6.304	-0.089	-0.089	0.000	0.000	0.000	0.000
39	A	63	THR	0	-0.041	-0.025	8.596	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	64	GLY	0	0.030	0.004	11.369	-0.030	-0.030	0.000	0.000	0.000	0.000
41	A	65	HIS	0	-0.005	0.001	15.042	0.010	0.010	0.000	0.000	0.000	0.000
42	A	66	ALA	0	0.010	0.018	17.789	0.004	0.004	0.000	0.000	0.000	0.000
43	A	67	GLU	-1	-0.920	-0.962	19.495	-0.016	-0.016	0.000	0.000	0.000	0.000
44	A	68	THR	0	-0.075	-0.046	22.626	0.007	0.007	0.000	0.000	0.000	0.000
45	A	69	LYS	1	0.972	1.000	24.531	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	70	GLN	0	0.032	0.009	26.960	0.009	0.009	0.000	0.000	0.000	0.000
47	A	71	LEU	0	0.031	0.000	27.372	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	72	THR	0	-0.023	-0.025	28.974	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	73	GLU	-1	-0.883	-0.937	29.906	0.011	0.011	0.000	0.000	0.000	0.000
50	A	74	MET	0	-0.060	-0.021	23.756	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	75	LEU	0	-0.036	0.013	29.234	0.002	0.002	0.000	0.000	0.000	0.000
52	A	76	PRO	0	0.040	0.006	31.802	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	77	SER	0	0.034	0.003	28.471	0.003	0.003	0.000	0.000	0.000	0.000
54	A	78	ILE	0	0.004	0.002	23.487	0.004	0.004	0.000	0.000	0.000	0.000
55	A	79	LEU	0	0.017	-0.001	26.382	0.008	0.008	0.000	0.000	0.000	0.000
56	A	80	ASN	0	-0.061	-0.023	26.211	0.009	0.009	0.000	0.000	0.000	0.000
57	A	81	GLN	0	-0.072	-0.036	21.435	0.013	0.013	0.000	0.000	0.000	0.000
58	A	82	LEU	0	-0.055	-0.013	23.129	0.009	0.009	0.000	0.000	0.000	0.000
59	A	83	GLY	0	0.040	0.026	25.732	0.003	0.003	0.000	0.000	0.000	0.000
60	A	84	ALA	0	-0.019	-0.034	26.939	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	85	ASP	-1	-0.882	-0.937	27.861	0.099	0.099	0.000	0.000	0.000	0.000
62	A	86	SER	0	-0.023	-0.004	26.571	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	87	LEU	0	0.012	-0.018	28.334	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	88	THR	0	0.001	-0.002	31.604	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	89	SER	0	-0.073	-0.020	29.361	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	90	LEU	0	-0.056	0.005	26.940	-0.007	-0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:25:VAL)