FMO DATABASE

FMODB ID: YY4L2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-329950.40531
FMO2-HF: Nuclear repulsion	304954.44016
FMO2-HF: Total energy	-24995.96515
FMO2-MP2: Total energy	-25068.469892

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.
-10.77	-4.353	4.198	-4.611	-6.003	-0.013

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 : 0.002 / q_NPA : 0.004

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	-0.004	-0.006	3.817	-0.363	1.891	-0.025	-1.078	-1.151	0.005
4	A	28	ILE	0	0.027	0.017	5.915	-0.056	-0.056	0.000	0.000	0.000	0.000
5	A	29	SER	0	-0.044	-0.023	9.115	0.143	0.143	0.000	0.000	0.000	0.000
6	A	30	GLY	0	0.043	0.007	12.324	0.010	0.010	0.000	0.000	0.000	0.000
7	A	31	ILE	0	-0.028	-0.002	11.418	0.030	0.030	0.000	0.000	0.000	0.000
8	A	32	GLU	-1	-0.840	-0.922	14.753	-0.118	-0.118	0.000	0.000	0.000	0.000
9	A	33	GLU	-1	-0.854	-0.922	17.507	0.004	0.004	0.000	0.000	0.000	0.000
10	A	34	VAL	0	-0.045	-0.018	13.030	-0.009	-0.009	0.000	0.000	0.000	0.000
11	A	35	ASN	0	0.011	0.005	16.438	0.015	0.015	0.000	0.000	0.000	0.000
12	A	36	MET	0	-0.031	-0.006	13.370	0.014	0.014	0.000	0.000	0.000	0.000
13	A	37	PHE	0	0.041	0.021	18.740	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	38	THR	0	0.001	0.009	21.825	0.019	0.019	0.000	0.000	0.000	0.000
15	A	39	ASN	0	-0.002	-0.019	23.969	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	40	GLN	0	0.011	0.003	27.049	0.000	0.000	0.000	0.000	0.000	0.000
17	A	41	GLY	0	0.056	0.034	28.673	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	42	THR	0	-0.062	-0.029	24.758	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	43	VAL	0	-0.003	-0.009	21.895	0.005	0.005	0.000	0.000	0.000	0.000
20	A	44	ILE	0	0.000	0.007	18.664	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	45	HIS	1	0.844	0.912	19.398	-0.012	-0.012	0.000	0.000	0.000	0.000
22	A	46	PHE	0	-0.014	-0.018	15.178	0.010	0.010	0.000	0.000	0.000	0.000
23	A	47	ASN	0	0.050	0.017	18.245	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	48	ASN	0	-0.059	-0.029	16.609	0.026	0.026	0.000	0.000	0.000	0.000
25	A	49	PRO	0	-0.020	0.016	12.903	0.002	0.002	0.000	0.000	0.000	0.000
26	A	50	LYS	1	0.915	0.953	7.222	-0.118	-0.118	0.000	0.000	0.000	0.000
27	A	51	VAL	0	0.036	0.012	8.162	0.130	0.130	0.000	0.000	0.000	0.000
28	A	52	GLN	0	-0.032	-0.015	2.521	-1.864	-0.673	0.406	-0.399	-1.197	0.001
29	A	53	ALA	0	0.036	0.014	4.148	0.255	0.675	0.001	-0.092	-0.328	0.000
30	A	54	SER	0	0.050	0.029	2.274	-9.602	-7.300	3.818	-3.008	-3.113	-0.019
31	A	55	LEU	0	0.064	0.053	4.383	0.276	0.376	-0.001	-0.021	-0.078	0.000
32	A	56	ALA	0	-0.011	-0.041	4.985	0.044	0.044	0.000	0.000	0.000	0.000
33	A	57	ALA	0	0.011	0.003	6.387	0.426	0.426	0.000	0.000	0.000	0.000
34	A	58	ASN	0	-0.079	-0.028	8.267	-0.058	-0.058	0.000	0.000	0.000	0.000
35	A	59	THR	0	0.011	0.019	4.922	0.041	0.041	0.000	0.000	0.000	0.000
36	A	60	PHE	0	0.016	-0.005	5.725	-0.041	-0.041	0.000	0.000	0.000	0.000
37	A	61	THR	0	-0.038	-0.014	4.168	0.135	0.285	-0.001	-0.013	-0.136	0.000
38	A	62	ILE	0	0.031	0.017	6.332	-0.183	-0.183	0.000	0.000	0.000	0.000
39	A	63	THR	0	-0.038	-0.032	8.592	0.051	0.051	0.000	0.000	0.000	0.000
40	A	64	GLY	0	0.035	0.013	11.460	-0.067	-0.067	0.000	0.000	0.000	0.000
41	A	65	HIS	0	-0.005	0.000	15.079	0.031	0.031	0.000	0.000	0.000	0.000
42	A	66	ALA	0	0.014	0.021	17.869	-0.011	-0.011	0.000	0.000	0.000	0.000
43	A	67	GLU	-1	-0.880	-0.936	19.604	0.030	0.030	0.000	0.000	0.000	0.000
44	A	68	THR	0	-0.033	-0.032	22.687	0.005	0.005	0.000	0.000	0.000	0.000
45	A	69	LYS	1	0.852	0.942	24.577	-0.033	-0.033	0.000	0.000	0.000	0.000
46	A	70	GLN	0	0.006	-0.013	26.964	0.006	0.006	0.000	0.000	0.000	0.000
47	A	71	LEU	0	0.038	0.009	26.680	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	72	THR	0	0.012	-0.020	28.947	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	73	GLU	-1	-0.837	-0.905	29.828	0.031	0.031	0.000	0.000	0.000	0.000
50	A	74	MET	0	-0.045	-0.017	23.585	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	75	LEU	0	-0.039	0.015	29.243	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	76	PRO	0	0.029	-0.001	31.786	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	77	SER	0	0.041	0.004	28.506	0.000	0.000	0.000	0.000	0.000	0.000
54	A	78	ILE	0	0.002	0.004	23.522	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	79	LEU	0	0.018	0.004	26.321	0.004	0.004	0.000	0.000	0.000	0.000
56	A	80	ASN	0	-0.070	-0.027	25.595	0.004	0.004	0.000	0.000	0.000	0.000
57	A	81	GLN	0	-0.068	-0.042	21.673	0.003	0.003	0.000	0.000	0.000	0.000
58	A	82	LEU	0	-0.052	-0.008	23.089	0.012	0.012	0.000	0.000	0.000	0.000
59	A	83	GLY	0	0.041	0.027	25.653	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	84	ALA	0	-0.024	-0.038	26.915	0.001	0.001	0.000	0.000	0.000	0.000
61	A	85	ASP	-1	-0.874	-0.934	27.361	0.058	0.058	0.000	0.000	0.000	0.000
62	A	86	SER	0	-0.019	-0.005	26.303	0.006	0.006	0.000	0.000	0.000	0.000
63	A	87	LEU	0	0.012	-0.003	28.194	0.004	0.004	0.000	0.000	0.000	0.000
64	A	88	THR	0	0.016	0.004	31.483	0.000	0.000	0.000	0.000	0.000	0.000
65	A	89	SER	0	-0.070	-0.021	29.204	0.003	0.003	0.000	0.000	0.000	0.000
66	A	90	LEU	0	-0.094	-0.017	26.594	-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:25:VAL)