FMO DATABASE

FMODB ID: R9928

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

Total energy (hartree)

FMO2-HF: Electronic energy	-501439.686931
FMO2-HF: Nuclear repulsion	470318.825056
FMO2-HF: Total energy	-31120.861875
FMO2-MP2: Total energy	-31210.41379

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.
-28.649	-27.959	19.855	-6.328	-14.216	-0.049

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 : -0.077 / q_NPA : -0.027

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	0.042	0.026	3.860	0.156	2.508	-0.023	-1.262	-1.068	0.003
4	F	4	LEU	0	-0.033	-0.018	6.958	0.658	0.658	0.000	0.000	0.000	0.000
5	F	5	VAL	0	-0.006	-0.007	8.585	-0.050	-0.050	0.000	0.000	0.000	0.000
6	F	6	VAL	0	0.016	0.005	12.150	0.149	0.149	0.000	0.000	0.000	0.000
7	F	7	VAL	0	-0.014	-0.008	14.706	-0.050	-0.050	0.000	0.000	0.000	0.000
8	F	8	THR	0	-0.024	-0.016	18.386	0.055	0.055	0.000	0.000	0.000	0.000
9	F	9	GLU	-1	-0.801	-0.887	21.042	-0.144	-0.144	0.000	0.000	0.000	0.000
10	F	10	ASN	0	-0.050	-0.041	24.898	0.010	0.010	0.000	0.000	0.000	0.000
11	F	11	VAL	0	0.044	0.045	21.069	0.018	0.018	0.000	0.000	0.000	0.000
12	F	12	PRO	0	0.032	0.034	24.362	-0.019	-0.019	0.000	0.000	0.000	0.000
13	F	13	PRO	0	0.010	-0.025	23.258	0.013	0.013	0.000	0.000	0.000	0.000
14	F	14	ARG	1	0.795	0.875	22.050	-0.190	-0.190	0.000	0.000	0.000	0.000
15	F	15	LEU	0	0.013	0.029	17.217	0.032	0.032	0.000	0.000	0.000	0.000
16	F	16	ARG	1	0.840	0.908	17.882	0.086	0.086	0.000	0.000	0.000	0.000
17	F	17	GLY	0	0.019	0.007	17.564	-0.023	-0.023	0.000	0.000	0.000	0.000
18	F	18	ARG	1	0.883	0.934	15.306	-0.480	-0.480	0.000	0.000	0.000	0.000
19	F	19	LEU	0	0.016	0.004	13.440	0.091	0.091	0.000	0.000	0.000	0.000
20	F	20	ALA	0	0.013	0.004	12.399	-0.036	-0.036	0.000	0.000	0.000	0.000
21	F	21	ILE	0	-0.092	-0.025	11.713	-0.044	-0.044	0.000	0.000	0.000	0.000
22	F	22	TRP	0	-0.027	-0.021	7.693	0.099	0.099	0.000	0.000	0.000	0.000
23	F	23	LEU	0	-0.036	-0.003	7.712	-0.302	-0.302	0.000	0.000	0.000	0.000
24	F	24	LEU	0	0.041	0.020	10.102	0.129	0.129	0.000	0.000	0.000	0.000
25	F	25	GLU	-1	-0.727	-0.828	12.659	-0.194	-0.194	0.000	0.000	0.000	0.000
26	F	26	VAL	0	-0.008	0.009	14.564	0.019	0.019	0.000	0.000	0.000	0.000
27	F	27	ARG	1	0.866	0.915	17.316	0.447	0.447	0.000	0.000	0.000	0.000
28	F	28	ALA	0	0.009	0.008	19.691	0.005	0.005	0.000	0.000	0.000	0.000
29	F	29	GLY	0	0.015	0.016	20.140	0.001	0.001	0.000	0.000	0.000	0.000
30	F	30	VAL	0	-0.040	-0.020	16.794	-0.002	-0.002	0.000	0.000	0.000	0.000
31	F	31	TYR	0	-0.010	-0.034	12.999	-0.005	-0.005	0.000	0.000	0.000	0.000
32	F	32	VAL	0	-0.009	-0.011	10.231	-0.019	-0.019	0.000	0.000	0.000	0.000
33	F	33	GLY	0	0.031	0.009	7.305	0.238	0.238	0.000	0.000	0.000	0.000
34	F	34	ASP	-1	-0.885	-0.946	2.451	-19.761	-15.822	2.236	-2.839	-3.335	-0.042
35	F	35	VAL	0	0.015	0.001	2.391	-2.523	-2.188	4.613	-1.729	-3.219	-0.009
36	F	36	SER	0	0.064	0.028	2.474	-0.687	-5.176	12.895	-2.409	-5.996	-0.006
37	F	37	ALA	0	-0.004	0.002	3.071	-2.823	-4.416	0.135	1.930	-0.472	0.005
38	F	38	LYS	1	0.926	0.938	5.862	-2.795	-2.795	0.000	0.000	0.000	0.000
39	F	39	ILE	0	0.003	0.009	5.297	-0.895	-0.749	-0.001	-0.019	-0.126	0.000
40	F	40	ARG	1	0.972	0.996	5.240	-0.536	-0.536	0.000	0.000	0.000	0.000
41	F	41	GLU	-1	-0.849	-0.912	8.472	1.665	1.665	0.000	0.000	0.000	0.000
42	F	42	MET	0	0.016	0.028	10.868	-0.401	-0.401	0.000	0.000	0.000	0.000
43	F	43	ILE	0	0.015	-0.008	8.179	-0.332	-0.332	0.000	0.000	0.000	0.000
44	F	44	TRP	0	0.018	-0.006	12.250	-0.253	-0.253	0.000	0.000	0.000	0.000
45	F	45	GLU	-1	-0.924	-0.960	14.652	0.932	0.932	0.000	0.000	0.000	0.000
46	F	46	GLN	0	-0.038	-0.023	14.490	-0.199	-0.199	0.000	0.000	0.000	0.000
47	F	47	ILE	0	0.000	-0.013	14.826	-0.098	-0.098	0.000	0.000	0.000	0.000
48	F	48	ALA	0	0.009	-0.004	18.146	-0.057	-0.057	0.000	0.000	0.000	0.000
49	F	49	GLY	0	-0.021	0.007	20.214	-0.034	-0.034	0.000	0.000	0.000	0.000
50	F	50	LEU	0	-0.096	-0.055	18.734	-0.026	-0.026	0.000	0.000	0.000	0.000
51	F	51	ALA	0	-0.001	-0.011	21.382	-0.035	-0.035	0.000	0.000	0.000	0.000
52	F	52	GLU	-1	-0.839	-0.895	23.060	0.127	0.127	0.000	0.000	0.000	0.000
53	F	53	GLU	-1	-0.860	-0.931	26.796	0.072	0.072	0.000	0.000	0.000	0.000
54	F	54	GLY	0	0.000	0.018	25.828	-0.019	-0.019	0.000	0.000	0.000	0.000
55	F	55	ASN	0	-0.107	-0.046	24.219	0.006	0.006	0.000	0.000	0.000	0.000
56	F	56	VAL	0	0.001	-0.007	17.947	-0.018	-0.018	0.000	0.000	0.000	0.000
57	F	57	VAL	0	-0.001	0.007	17.593	0.020	0.020	0.000	0.000	0.000	0.000
58	F	58	MET	0	-0.032	0.006	11.896	0.022	0.022	0.000	0.000	0.000	0.000
59	F	59	ALA	0	0.024	0.002	13.131	0.055	0.055	0.000	0.000	0.000	0.000
60	F	60	TRP	0	-0.040	-0.039	7.875	0.026	0.026	0.000	0.000	0.000	0.000
61	F	61	ALA	0	0.043	0.030	7.785	0.193	0.193	0.000	0.000	0.000	0.000
62	F	62	THR	0	-0.056	-0.015	7.351	-0.411	-0.411	0.000	0.000	0.000	0.000
63	F	63	ASN	0	-0.016	-0.013	8.095	-0.057	-0.057	0.000	0.000	0.000	0.000
64	F	64	THR	0	0.013	-0.002	11.056	0.191	0.191	0.000	0.000	0.000	0.000
65	F	65	GLU	-1	-0.935	-0.971	14.030	-0.480	-0.480	0.000	0.000	0.000	0.000
66	F	66	THR	0	-0.018	-0.017	15.704	0.003	0.003	0.000	0.000	0.000	0.000
67	F	67	GLY	0	-0.008	0.011	13.134	-0.037	-0.037	0.000	0.000	0.000	0.000
68	F	68	PHE	0	-0.071	-0.041	11.642	-0.282	-0.282	0.000	0.000	0.000	0.000
69	F	69	GLU	-1	-0.848	-0.897	11.276	-0.163	-0.163	0.000	0.000	0.000	0.000
70	F	70	PHE	0	-0.012	-0.030	13.356	-0.078	-0.078	0.000	0.000	0.000	0.000
71	F	71	GLN	0	-0.013	0.010	14.306	0.090	0.090	0.000	0.000	0.000	0.000
72	F	72	THR	0	0.009	-0.013	17.372	-0.029	-0.029	0.000	0.000	0.000	0.000
73	F	73	PHE	0	0.019	0.015	20.017	0.052	0.052	0.000	0.000	0.000	0.000
74	F	74	GLY	0	0.069	0.044	21.932	-0.032	-0.032	0.000	0.000	0.000	0.000
75	F	75	LEU	0	-0.037	-0.020	25.402	-0.005	-0.005	0.000	0.000	0.000	0.000
76	F	76	ASN	0	-0.030	-0.049	24.878	-0.022	-0.022	0.000	0.000	0.000	0.000
77	F	77	ARG	1	0.880	0.943	27.453	0.130	0.130	0.000	0.000	0.000	0.000
78	F	78	ARG	1	0.968	0.993	24.818	0.207	0.207	0.000	0.000	0.000	0.000

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