FMO DATABASE

FMODB ID: 6NN2Z

Calculation Name: 5DLJ-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DLJ

Chain ID: F

ChEMBL ID:

UniProt ID: Q46896

Base Structure: X-ray

Registration Date: 2023-06-21

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	78
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-501106.540231
FMO2-HF: Nuclear repulsion	469986.326822
FMO2-HF: Total energy	-31120.213409
FMO2-MP2: Total energy	-31209.800197

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(F:1:MET)

Summations of interaction energy for fragment #1(F:1:MET)

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.
-27.736	-19.98	7.93	-6.61	-9.077	-0.052

Interaction energy analysis for fragmet #1(F:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.096 / q_NPA : -0.067

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	F	3	MET	0	0.060	0.028	3.818	0.170	2.070	-0.027	-0.927	-0.946	0.001
4	F	4	LEU	0	-0.034	-0.021	6.781	0.700	0.700	0.000	0.000	0.000	0.000
5	F	5	VAL	0	-0.009	-0.008	8.721	-0.111	-0.111	0.000	0.000	0.000	0.000
6	F	6	VAL	0	-0.001	-0.001	12.503	0.139	0.139	0.000	0.000	0.000	0.000
7	F	7	VAL	0	0.018	-0.001	14.903	-0.062	-0.062	0.000	0.000	0.000	0.000
8	F	8	THR	0	-0.052	-0.026	18.604	0.051	0.051	0.000	0.000	0.000	0.000
9	F	9	GLU	-1	-0.899	-0.971	21.123	-0.031	-0.031	0.000	0.000	0.000	0.000
10	F	10	ASN	0	-0.069	-0.035	24.848	0.010	0.010	0.000	0.000	0.000	0.000
11	F	11	VAL	0	0.071	0.055	22.347	0.016	0.016	0.000	0.000	0.000	0.000
12	F	12	PRO	0	0.055	0.040	25.248	-0.022	-0.022	0.000	0.000	0.000	0.000
13	F	13	PRO	0	0.034	-0.013	24.793	0.017	0.017	0.000	0.000	0.000	0.000
14	F	14	ARG	1	0.965	0.981	23.798	-0.220	-0.220	0.000	0.000	0.000	0.000
15	F	15	LEU	0	0.011	0.019	18.665	0.031	0.031	0.000	0.000	0.000	0.000
16	F	16	ARG	1	0.830	0.894	19.597	-0.011	-0.011	0.000	0.000	0.000	0.000
17	F	17	GLY	0	0.028	0.015	19.590	-0.019	-0.019	0.000	0.000	0.000	0.000
18	F	18	ARG	1	0.863	0.925	16.937	-0.490	-0.490	0.000	0.000	0.000	0.000
19	F	19	LEU	0	0.031	0.004	14.884	0.085	0.085	0.000	0.000	0.000	0.000
20	F	20	ALA	0	-0.005	0.004	14.180	0.001	0.001	0.000	0.000	0.000	0.000
21	F	21	ILE	0	-0.086	-0.026	13.129	-0.047	-0.047	0.000	0.000	0.000	0.000
22	F	22	TRP	0	-0.033	-0.025	9.277	0.044	0.044	0.000	0.000	0.000	0.000
23	F	23	LEU	0	-0.047	-0.007	9.376	-0.091	-0.091	0.000	0.000	0.000	0.000
24	F	24	LEU	0	0.040	0.016	11.559	0.027	0.027	0.000	0.000	0.000	0.000
25	F	25	GLU	-1	-0.788	-0.877	13.556	-0.072	-0.072	0.000	0.000	0.000	0.000
26	F	26	VAL	0	-0.018	0.001	15.638	-0.020	-0.020	0.000	0.000	0.000	0.000
27	F	27	ARG	1	0.877	0.916	18.412	0.290	0.290	0.000	0.000	0.000	0.000
28	F	28	ALA	0	0.023	0.016	20.767	0.019	0.019	0.000	0.000	0.000	0.000
29	F	29	GLY	0	-0.015	0.009	21.050	0.001	0.001	0.000	0.000	0.000	0.000
30	F	30	VAL	0	-0.011	0.011	17.226	0.014	0.014	0.000	0.000	0.000	0.000
31	F	31	TYR	0	0.040	0.016	14.307	-0.038	-0.038	0.000	0.000	0.000	0.000
32	F	32	VAL	0	0.000	-0.007	10.545	0.011	0.011	0.000	0.000	0.000	0.000
33	F	33	GLY	0	0.026	0.006	8.505	0.164	0.164	0.000	0.000	0.000	0.000
34	F	34	ASP	-1	-0.912	-0.953	2.368	-17.815	-14.787	2.238	-2.414	-2.852	-0.034
35	F	35	VAL	0	0.025	0.016	3.494	0.487	2.012	0.610	-0.691	-1.444	-0.001
36	F	36	SER	0	0.043	0.018	2.232	-5.056	-2.946	5.019	-3.600	-3.529	-0.018
37	F	37	ALA	0	0.045	0.008	3.082	-1.493	-2.300	0.090	1.022	-0.306	0.000
38	F	38	LYS	1	1.023	1.013	6.054	-3.030	-3.030	0.000	0.000	0.000	0.000
39	F	39	ILE	0	-0.006	-0.002	6.086	-0.577	-0.577	0.000	0.000	0.000	0.000
40	F	40	ARG	1	0.974	0.998	5.339	-2.679	-2.679	0.000	0.000	0.000	0.000
41	F	41	GLU	-1	-0.918	-0.965	8.330	1.632	1.632	0.000	0.000	0.000	0.000
42	F	42	MET	0	-0.006	0.017	10.814	-0.354	-0.354	0.000	0.000	0.000	0.000
43	F	43	ILE	0	0.010	-0.013	9.609	-0.283	-0.283	0.000	0.000	0.000	0.000
44	F	44	TRP	0	0.041	0.003	12.592	-0.223	-0.223	0.000	0.000	0.000	0.000
45	F	45	GLU	-1	-0.927	-0.967	14.494	0.906	0.906	0.000	0.000	0.000	0.000
46	F	46	GLN	0	-0.041	-0.006	15.330	-0.200	-0.200	0.000	0.000	0.000	0.000
47	F	47	ILE	0	-0.011	-0.012	15.033	-0.095	-0.095	0.000	0.000	0.000	0.000
48	F	48	ALA	0	-0.020	-0.008	18.439	-0.064	-0.064	0.000	0.000	0.000	0.000
49	F	49	GLY	0	-0.005	0.011	20.340	-0.043	-0.043	0.000	0.000	0.000	0.000
50	F	50	LEU	0	-0.088	-0.058	20.476	-0.042	-0.042	0.000	0.000	0.000	0.000
51	F	51	ALA	0	-0.037	-0.020	21.795	-0.037	-0.037	0.000	0.000	0.000	0.000
52	F	52	GLU	-1	-0.964	-0.980	23.580	0.168	0.168	0.000	0.000	0.000	0.000
53	F	53	GLU	-1	-0.894	-0.954	27.104	0.154	0.154	0.000	0.000	0.000	0.000
54	F	54	GLY	0	-0.019	0.005	26.084	-0.015	-0.015	0.000	0.000	0.000	0.000
55	F	55	ASN	0	-0.080	-0.031	23.947	0.008	0.008	0.000	0.000	0.000	0.000
56	F	56	VAL	0	-0.007	-0.012	17.680	-0.018	-0.018	0.000	0.000	0.000	0.000
57	F	57	VAL	0	0.002	0.009	17.280	0.027	0.027	0.000	0.000	0.000	0.000
58	F	58	MET	0	-0.032	0.005	11.728	-0.005	-0.005	0.000	0.000	0.000	0.000
59	F	59	ALA	0	0.027	0.001	12.990	0.062	0.062	0.000	0.000	0.000	0.000
60	F	60	TRP	0	-0.004	-0.014	7.599	-0.033	-0.033	0.000	0.000	0.000	0.000
61	F	61	ALA	0	0.042	0.023	7.503	0.098	0.098	0.000	0.000	0.000	0.000
62	F	62	THR	0	-0.086	-0.030	7.703	0.312	0.312	0.000	0.000	0.000	0.000
63	F	63	ASN	0	-0.011	-0.027	7.834	-0.258	-0.258	0.000	0.000	0.000	0.000
64	F	64	THR	0	0.003	0.003	10.852	0.009	0.009	0.000	0.000	0.000	0.000
65	F	65	GLU	-1	-0.920	-0.963	14.160	-0.214	-0.214	0.000	0.000	0.000	0.000
66	F	66	THR	0	-0.005	-0.005	16.951	-0.045	-0.045	0.000	0.000	0.000	0.000
67	F	67	GLY	0	0.026	0.029	12.871	-0.080	-0.080	0.000	0.000	0.000	0.000
68	F	68	PHE	0	-0.111	-0.062	11.754	-0.164	-0.164	0.000	0.000	0.000	0.000
69	F	69	GLU	-1	-0.890	-0.936	12.166	0.552	0.552	0.000	0.000	0.000	0.000
70	F	70	PHE	0	-0.026	-0.030	13.108	-0.056	-0.056	0.000	0.000	0.000	0.000
71	F	71	GLN	0	-0.003	0.021	14.169	0.129	0.129	0.000	0.000	0.000	0.000
72	F	72	THR	0	0.004	-0.014	17.005	-0.013	-0.013	0.000	0.000	0.000	0.000
73	F	73	PHE	0	-0.004	0.008	19.736	0.044	0.044	0.000	0.000	0.000	0.000
74	F	74	GLY	0	0.075	0.047	21.673	-0.031	-0.031	0.000	0.000	0.000	0.000
75	F	75	LEU	0	-0.023	-0.012	24.922	-0.001	-0.001	0.000	0.000	0.000	0.000
76	F	76	ASN	0	0.001	-0.032	25.373	-0.027	-0.027	0.000	0.000	0.000	0.000
77	F	77	ARG	1	0.947	0.979	27.366	0.012	0.012	0.000	0.000	0.000	0.000
78	F	78	ARG	1	0.974	1.009	24.746	0.059	0.059	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:1:MET)