FMO DATABASE

FMODB ID: Z668N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-501546.934715
FMO2-HF: Nuclear repulsion	470426.244861
FMO2-HF: Total energy	-31120.689854
FMO2-MP2: Total energy	-31210.266271

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.
-31.652	-27.31	15.397	-6.795	-12.942	-0.055

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 : -0.087 / q_NPA : -0.037

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	0.067	0.034	3.818	-0.404	2.228	-0.029	-1.387	-1.216	0.005
4	F	4	LEU	0	-0.038	-0.022	6.845	0.706	0.706	0.000	0.000	0.000	0.000
5	F	5	VAL	0	-0.009	-0.010	8.742	-0.091	-0.091	0.000	0.000	0.000	0.000
6	F	6	VAL	0	0.000	0.002	12.484	0.156	0.156	0.000	0.000	0.000	0.000
7	F	7	VAL	0	0.015	-0.003	14.909	-0.052	-0.052	0.000	0.000	0.000	0.000
8	F	8	THR	0	-0.043	-0.023	18.394	0.062	0.062	0.000	0.000	0.000	0.000
9	F	9	GLU	-1	-0.864	-0.939	20.923	-0.136	-0.136	0.000	0.000	0.000	0.000
10	F	10	ASN	0	-0.067	-0.042	24.702	0.012	0.012	0.000	0.000	0.000	0.000
11	F	11	VAL	0	0.046	0.041	21.298	0.020	0.020	0.000	0.000	0.000	0.000
12	F	12	PRO	0	0.052	0.038	24.401	-0.022	-0.022	0.000	0.000	0.000	0.000
13	F	13	PRO	0	0.030	-0.011	23.362	0.012	0.012	0.000	0.000	0.000	0.000
14	F	14	ARG	1	0.816	0.887	22.207	-0.200	-0.200	0.000	0.000	0.000	0.000
15	F	15	LEU	0	0.011	0.016	17.548	0.032	0.032	0.000	0.000	0.000	0.000
16	F	16	ARG	1	0.831	0.898	18.143	0.091	0.091	0.000	0.000	0.000	0.000
17	F	17	GLY	0	0.027	0.018	17.938	-0.031	-0.031	0.000	0.000	0.000	0.000
18	F	18	ARG	1	0.881	0.940	15.420	-0.485	-0.485	0.000	0.000	0.000	0.000
19	F	19	LEU	0	0.026	0.003	13.567	0.082	0.082	0.000	0.000	0.000	0.000
20	F	20	ALA	0	-0.004	0.004	12.532	-0.045	-0.045	0.000	0.000	0.000	0.000
21	F	21	ILE	0	-0.092	-0.031	11.724	-0.049	-0.049	0.000	0.000	0.000	0.000
22	F	22	TRP	0	-0.031	-0.023	7.740	0.061	0.061	0.000	0.000	0.000	0.000
23	F	23	LEU	0	-0.044	-0.006	7.879	-0.300	-0.300	0.000	0.000	0.000	0.000
24	F	24	LEU	0	0.040	0.016	10.077	0.107	0.107	0.000	0.000	0.000	0.000
25	F	25	GLU	-1	-0.751	-0.841	12.497	-0.200	-0.200	0.000	0.000	0.000	0.000
26	F	26	VAL	0	-0.008	0.004	14.681	0.003	0.003	0.000	0.000	0.000	0.000
27	F	27	ARG	1	0.862	0.910	17.442	0.451	0.451	0.000	0.000	0.000	0.000
28	F	28	ALA	0	0.025	0.018	19.785	0.011	0.011	0.000	0.000	0.000	0.000
29	F	29	GLY	0	-0.004	0.009	20.036	0.002	0.002	0.000	0.000	0.000	0.000
30	F	30	VAL	0	-0.023	0.002	16.573	0.002	0.002	0.000	0.000	0.000	0.000
31	F	31	TYR	0	0.012	-0.010	13.105	-0.017	-0.017	0.000	0.000	0.000	0.000
32	F	32	VAL	0	-0.005	-0.011	9.951	-0.002	-0.002	0.000	0.000	0.000	0.000
33	F	33	GLY	0	0.031	0.013	7.464	0.210	0.210	0.000	0.000	0.000	0.000
34	F	34	ASP	-1	-0.884	-0.944	2.477	-19.779	-15.683	1.908	-2.841	-3.163	-0.039
35	F	35	VAL	0	0.005	0.000	2.686	-2.783	-2.120	3.482	-1.216	-2.928	-0.009
36	F	36	SER	0	0.071	0.031	2.224	-2.519	-4.214	9.940	-3.086	-5.160	-0.015
37	F	37	ALA	0	0.025	0.007	3.072	-2.146	-3.637	0.097	1.755	-0.360	0.003
38	F	38	LYS	1	0.921	0.954	6.063	-3.106	-3.106	0.000	0.000	0.000	0.000
39	F	39	ILE	0	0.004	0.000	5.332	-0.913	-0.776	-0.001	-0.020	-0.115	0.000
40	F	40	ARG	1	0.966	0.995	5.372	-1.365	-1.365	0.000	0.000	0.000	0.000
41	F	41	GLU	-1	-0.842	-0.920	8.336	1.692	1.692	0.000	0.000	0.000	0.000
42	F	42	MET	0	0.008	0.020	10.452	-0.411	-0.411	0.000	0.000	0.000	0.000
43	F	43	ILE	0	0.017	-0.008	8.472	-0.359	-0.359	0.000	0.000	0.000	0.000
44	F	44	TRP	0	0.025	-0.003	12.552	-0.265	-0.265	0.000	0.000	0.000	0.000
45	F	45	GLU	-1	-0.934	-0.960	14.502	0.938	0.938	0.000	0.000	0.000	0.000
46	F	46	GLN	0	-0.045	-0.023	14.489	-0.213	-0.213	0.000	0.000	0.000	0.000
47	F	47	ILE	0	-0.014	-0.016	14.861	-0.103	-0.103	0.000	0.000	0.000	0.000
48	F	48	ALA	0	-0.012	-0.007	18.401	-0.063	-0.063	0.000	0.000	0.000	0.000
49	F	49	GLY	0	-0.002	0.012	20.343	-0.039	-0.039	0.000	0.000	0.000	0.000
50	F	50	LEU	0	-0.090	-0.058	19.105	-0.037	-0.037	0.000	0.000	0.000	0.000
51	F	51	ALA	0	-0.020	-0.009	21.741	-0.039	-0.039	0.000	0.000	0.000	0.000
52	F	52	GLU	-1	-0.844	-0.901	23.306	0.135	0.135	0.000	0.000	0.000	0.000
53	F	53	GLU	-1	-0.863	-0.937	26.941	0.089	0.089	0.000	0.000	0.000	0.000
54	F	54	GLY	0	-0.009	0.012	25.980	-0.017	-0.017	0.000	0.000	0.000	0.000
55	F	55	ASN	0	-0.102	-0.041	23.965	0.007	0.007	0.000	0.000	0.000	0.000
56	F	56	VAL	0	-0.001	-0.014	17.729	-0.022	-0.022	0.000	0.000	0.000	0.000
57	F	57	VAL	0	-0.002	0.007	17.421	0.025	0.025	0.000	0.000	0.000	0.000
58	F	58	MET	0	-0.037	0.006	11.656	0.008	0.008	0.000	0.000	0.000	0.000
59	F	59	ALA	0	0.026	0.003	13.019	0.058	0.058	0.000	0.000	0.000	0.000
60	F	60	TRP	0	-0.035	-0.027	7.684	0.008	0.008	0.000	0.000	0.000	0.000
61	F	61	ALA	0	0.038	0.023	7.430	0.144	0.144	0.000	0.000	0.000	0.000
62	F	62	THR	0	-0.078	-0.034	7.310	-0.152	-0.152	0.000	0.000	0.000	0.000
63	F	63	ASN	0	-0.003	-0.013	7.546	-0.105	-0.105	0.000	0.000	0.000	0.000
64	F	64	THR	0	-0.004	-0.005	10.614	0.139	0.139	0.000	0.000	0.000	0.000
65	F	65	GLU	-1	-0.924	-0.968	13.763	-0.437	-0.437	0.000	0.000	0.000	0.000
66	F	66	THR	0	0.000	0.003	16.367	-0.041	-0.041	0.000	0.000	0.000	0.000
67	F	67	GLY	0	0.023	0.023	12.713	-0.058	-0.058	0.000	0.000	0.000	0.000
68	F	68	PHE	0	-0.075	-0.037	11.539	-0.257	-0.257	0.000	0.000	0.000	0.000
69	F	69	GLU	-1	-0.882	-0.932	11.913	0.058	0.058	0.000	0.000	0.000	0.000
70	F	70	PHE	0	-0.009	-0.024	13.142	-0.068	-0.068	0.000	0.000	0.000	0.000
71	F	71	GLN	0	-0.011	0.015	14.052	0.096	0.096	0.000	0.000	0.000	0.000
72	F	72	THR	0	0.009	-0.013	17.031	-0.019	-0.019	0.000	0.000	0.000	0.000
73	F	73	PHE	0	0.001	0.012	19.759	0.052	0.052	0.000	0.000	0.000	0.000
74	F	74	GLY	0	0.079	0.047	21.692	-0.031	-0.031	0.000	0.000	0.000	0.000
75	F	75	LEU	0	-0.037	-0.020	24.943	-0.008	-0.008	0.000	0.000	0.000	0.000
76	F	76	ASN	0	-0.012	-0.047	25.296	-0.023	-0.023	0.000	0.000	0.000	0.000
77	F	77	ARG	1	0.938	0.983	27.391	0.106	0.106	0.000	0.000	0.000	0.000
78	F	78	ARG	1	0.981	1.004	24.941	0.185	0.185	0.000	0.000	0.000	0.000

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