FMO DATABASE

FMODB ID: 76JNK

Calculation Name: 3LLB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LLB

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HX36

Base Structure: X-ray

Registration Date: 2023-09-20

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	81
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-539253.583486
FMO2-HF: Nuclear repulsion	507850.41879
FMO2-HF: Total energy	-31403.164696
FMO2-MP2: Total energy	-31496.752712

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:SER)

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

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.
-0.924	2.065	0.04	-1.411	-1.619	0.001

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

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 : 0.000

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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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	ILE	0	0.039	0.047	3.648	-2.270	-0.124	-0.010	-1.081	-1.056	0.000
4	A	4	LYS	1	0.887	0.945	3.662	0.054	0.318	0.004	-0.139	-0.130	-0.001
5	A	5	PRO	0	0.056	0.042	6.092	-0.033	-0.033	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.039	-0.039	9.251	-0.058	-0.058	0.000	0.000	0.000	0.000
7	A	7	PRO	0	0.007	-0.006	12.396	0.018	0.018	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.016	-0.005	15.562	-0.001	-0.001	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.018	0.013	15.400	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.824	-0.883	14.471	0.015	0.015	0.000	0.000	0.000	0.000
11	A	11	PHE	0	0.039	0.009	8.859	0.050	0.050	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.093	-0.045	8.434	-0.034	-0.034	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.067	0.029	7.640	-0.062	-0.062	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.910	0.949	2.963	1.409	1.988	0.046	-0.191	-0.433	0.002
15	A	15	ALA	0	0.015	0.008	8.275	0.045	0.045	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.027	-0.017	5.476	0.015	0.015	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.040	-0.034	7.165	-0.232	-0.232	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.025	0.031	7.553	0.126	0.126	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.052	0.028	10.474	0.027	0.027	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.809	-0.907	11.210	-0.392	-0.392	0.000	0.000	0.000	0.000
21	A	21	ALA	0	-0.004	-0.011	7.485	0.046	0.046	0.000	0.000	0.000	0.000
22	A	22	PHE	0	-0.062	-0.045	9.580	0.143	0.143	0.000	0.000	0.000	0.000
23	A	23	ASN	0	0.044	0.017	10.914	0.083	0.083	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.888	-0.917	11.101	-0.024	-0.024	0.000	0.000	0.000	0.000
25	A	25	PHE	0	-0.158	-0.075	4.943	0.261	0.261	0.000	0.000	0.000	0.000
26	A	26	PHE	0	-0.075	-0.071	9.499	0.050	0.050	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.029	0.034	14.285	-0.011	-0.011	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.085	-0.049	15.982	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.919	-0.968	17.966	-0.027	-0.027	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.105	-0.046	16.437	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	31	SER	0	0.095	0.032	18.616	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.915	-0.969	16.541	-0.165	-0.165	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.935	-0.951	18.036	-0.124	-0.124	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-1.023	-0.997	21.372	-0.111	-0.111	0.000	0.000	0.000	0.000
35	A	35	PHE	0	-0.084	-0.053	17.694	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.841	-0.905	14.972	-0.286	-0.286	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.075	-0.054	11.889	-0.039	-0.039	0.000	0.000	0.000	0.000
38	A	38	VAL	0	0.066	0.028	11.349	0.057	0.057	0.000	0.000	0.000	0.000
39	A	39	GLY	0	-0.058	-0.037	13.194	0.048	0.048	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.001	0.008	15.033	0.041	0.041	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.051	0.050	16.379	0.025	0.025	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.001	-0.012	16.630	0.026	0.026	0.000	0.000	0.000	0.000
43	A	43	MET	0	-0.065	-0.047	18.913	0.014	0.014	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.049	-0.017	20.845	0.022	0.022	0.000	0.000	0.000	0.000
45	A	45	ALA	0	0.027	0.028	22.322	0.012	0.012	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.052	-0.031	20.242	0.010	0.010	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.036	0.025	24.703	0.010	0.010	0.000	0.000	0.000	0.000
48	A	48	HIS	1	0.761	0.859	25.101	0.097	0.097	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.013	0.002	20.413	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	50	PRO	0	-0.033	0.015	20.310	0.011	0.011	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.943	0.958	21.754	0.072	0.072	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.913	0.930	17.981	0.083	0.083	0.000	0.000	0.000	0.000
53	A	53	ASN	0	-0.046	-0.048	20.595	0.007	0.007	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.741	-0.813	22.260	-0.081	-0.081	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.014	-0.029	21.393	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.010	0.016	20.762	0.005	0.005	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.874	-0.940	21.470	-0.037	-0.037	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.013	0.001	19.798	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.040	0.031	21.069	0.001	0.001	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.900	-0.954	21.389	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	61	PHE	0	0.004	-0.002	16.437	0.009	0.009	0.000	0.000	0.000	0.000
62	A	62	ARG	1	0.909	0.958	19.450	0.017	0.017	0.000	0.000	0.000	0.000
63	A	63	PHE	0	-0.003	0.002	14.852	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.912	0.954	17.307	0.069	0.069	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.011	0.014	16.698	-0.026	-0.026	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.057	-0.027	13.025	0.033	0.033	0.000	0.000	0.000	0.000
67	A	67	ASN	0	-0.028	-0.020	13.956	0.015	0.015	0.000	0.000	0.000	0.000
68	A	68	ALA	0	0.108	0.056	15.609	-0.037	-0.037	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.822	-0.896	17.759	-0.154	-0.154	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.020	-0.026	19.615	0.006	0.006	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.884	0.945	19.585	0.133	0.133	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.999	1.000	13.195	0.269	0.269	0.000	0.000	0.000	0.000
73	A	73	VAL	0	0.047	0.022	14.667	0.015	0.015	0.000	0.000	0.000	0.000
74	A	74	HIS	0	-0.070	-0.047	12.104	-0.076	-0.076	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.048	-0.023	8.749	-0.115	-0.115	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.045	0.035	11.811	0.079	0.079	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.785	0.876	12.119	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	78	LEU	0	0.018	0.026	12.740	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	79	SER	0	-0.018	-0.024	14.709	0.020	0.020	0.000	0.000	0.000	0.000
80	A	80	PRO	0	0.049	0.032	17.045	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.041	-0.015	19.473	0.000	0.000	0.000	0.000	0.000	0.000

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