FMO DATABASE

FMODB ID: VR971

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	OptAll
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	-329869.998467
FMO2-HF: Nuclear repulsion	304873.565809
FMO2-HF: Total energy	-24996.432658
FMO2-MP2: Total energy	-25068.880369

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.
-14.531	-9.187	8.28	-6.439	-7.189	-0.005

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 : 0.012 / q_NPA : 0.007

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	27	ASN	0	-0.013	-0.011	3.860	-0.289	1.773	-0.016	-1.007	-1.039	0.005
4	A	28	ILE	0	0.011	0.011	5.961	0.052	0.052	0.000	0.000	0.000	0.000
5	A	29	SER	0	-0.025	-0.014	9.000	0.101	0.101	0.000	0.000	0.000	0.000
6	A	30	GLY	0	0.041	0.008	12.386	0.022	0.022	0.000	0.000	0.000	0.000
7	A	31	ILE	0	-0.020	-0.001	11.436	0.032	0.032	0.000	0.000	0.000	0.000
8	A	32	GLU	-1	-0.833	-0.919	14.819	-0.147	-0.147	0.000	0.000	0.000	0.000
9	A	33	GLU	-1	-0.855	-0.917	17.524	0.006	0.006	0.000	0.000	0.000	0.000
10	A	34	VAL	0	-0.033	-0.017	13.017	-0.007	-0.007	0.000	0.000	0.000	0.000
11	A	35	ASN	0	0.003	-0.002	16.385	0.005	0.005	0.000	0.000	0.000	0.000
12	A	36	MET	0	-0.037	-0.010	13.355	0.024	0.024	0.000	0.000	0.000	0.000
13	A	37	PHE	0	0.040	0.017	18.638	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	38	THR	0	-0.025	-0.004	21.614	0.022	0.022	0.000	0.000	0.000	0.000
15	A	39	ASN	0	0.041	0.000	23.910	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	40	GLN	0	0.015	0.018	26.984	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	41	GLY	0	0.060	0.040	29.039	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	42	THR	0	-0.066	-0.036	25.083	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	43	VAL	0	-0.016	-0.020	21.833	0.010	0.010	0.000	0.000	0.000	0.000
20	A	44	ILE	0	-0.002	0.006	18.674	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	45	HIS	1	0.834	0.914	19.285	0.000	0.000	0.000	0.000	0.000	0.000
22	A	46	PHE	0	0.002	-0.008	15.262	0.006	0.006	0.000	0.000	0.000	0.000
23	A	47	ASN	0	0.009	-0.008	18.523	0.003	0.003	0.000	0.000	0.000	0.000
24	A	48	ASN	0	-0.050	-0.025	16.657	0.021	0.021	0.000	0.000	0.000	0.000
25	A	49	PRO	0	-0.039	0.007	12.784	-0.016	-0.016	0.000	0.000	0.000	0.000
26	A	50	LYS	1	0.946	0.979	7.653	0.185	0.185	0.000	0.000	0.000	0.000
27	A	51	VAL	0	0.024	0.009	7.761	0.114	0.114	0.000	0.000	0.000	0.000
28	A	52	GLN	0	-0.014	-0.007	2.627	-1.344	-0.304	0.289	-0.300	-1.030	0.001
29	A	53	ALA	0	0.026	0.012	4.056	0.252	0.842	0.006	-0.142	-0.455	0.000
30	A	54	SER	0	0.036	-0.002	2.038	-13.582	-12.274	7.996	-4.930	-4.375	-0.011
31	A	55	LEU	0	0.043	0.031	3.864	0.100	0.223	0.006	-0.037	-0.093	0.000
32	A	56	ALA	0	-0.016	-0.011	5.293	0.016	0.016	0.000	0.000	0.000	0.000
33	A	57	ALA	0	0.003	0.003	6.124	0.220	0.220	0.000	0.000	0.000	0.000
34	A	58	ASN	0	-0.048	-0.012	8.162	-0.108	-0.108	0.000	0.000	0.000	0.000
35	A	59	THR	0	0.015	0.013	4.585	-0.219	-0.170	-0.001	-0.006	-0.042	0.000
36	A	60	PHE	0	-0.009	-0.023	5.270	0.107	0.107	0.000	0.000	0.000	0.000
37	A	61	THR	0	-0.002	0.006	3.961	0.020	0.192	0.000	-0.017	-0.155	0.000
38	A	62	ILE	0	0.018	0.006	6.596	-0.207	-0.207	0.000	0.000	0.000	0.000
39	A	63	THR	0	-0.061	-0.036	8.884	0.017	0.017	0.000	0.000	0.000	0.000
40	A	64	GLY	0	0.046	0.005	11.533	-0.066	-0.066	0.000	0.000	0.000	0.000
41	A	65	HIS	0	0.012	0.016	15.199	0.031	0.031	0.000	0.000	0.000	0.000
42	A	66	ALA	0	0.005	0.000	18.023	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	67	GLU	-1	-0.869	-0.921	19.927	0.015	0.015	0.000	0.000	0.000	0.000
44	A	68	THR	0	-0.020	-0.018	22.804	0.007	0.007	0.000	0.000	0.000	0.000
45	A	69	LYS	1	0.837	0.917	24.829	-0.022	-0.022	0.000	0.000	0.000	0.000
46	A	70	GLN	0	0.006	-0.006	26.823	0.009	0.009	0.000	0.000	0.000	0.000
47	A	71	LEU	0	0.017	0.003	26.460	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	72	THR	0	0.011	-0.024	28.850	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	73	GLU	-1	-0.839	-0.898	29.453	0.026	0.026	0.000	0.000	0.000	0.000
50	A	74	MET	0	-0.006	0.004	23.468	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	75	LEU	0	-0.026	0.026	29.143	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	76	PRO	0	0.015	-0.005	31.721	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	77	SER	0	0.010	-0.011	28.085	0.001	0.001	0.000	0.000	0.000	0.000
54	A	78	ILE	0	0.006	-0.002	23.451	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	79	LEU	0	0.013	0.003	26.166	0.007	0.007	0.000	0.000	0.000	0.000
56	A	80	ASN	0	-0.088	-0.038	24.977	0.001	0.001	0.000	0.000	0.000	0.000
57	A	81	GLN	0	-0.058	-0.035	21.479	0.005	0.005	0.000	0.000	0.000	0.000
58	A	82	LEU	0	-0.029	0.001	22.708	0.015	0.015	0.000	0.000	0.000	0.000
59	A	83	GLY	0	0.043	0.031	25.210	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	84	ALA	0	-0.027	-0.037	26.824	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	85	ASP	-1	-0.826	-0.911	26.505	0.095	0.095	0.000	0.000	0.000	0.000
62	A	86	SER	0	-0.010	0.015	26.014	0.004	0.004	0.000	0.000	0.000	0.000
63	A	87	LEU	0	0.021	0.000	27.993	0.001	0.001	0.000	0.000	0.000	0.000
64	A	88	THR	0	-0.049	-0.031	31.183	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	89	SER	0	-0.050	-0.020	28.586	0.004	0.004	0.000	0.000	0.000	0.000
66	A	90	LEU	0	-0.109	-0.034	26.483	-0.001	-0.001	0.000	0.000	0.000	0.000

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