FMO DATABASE

FMODB ID: V5Z31

Calculation Name: 3P3D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3P3D

Chain ID: A

ChEMBL ID:

UniProt ID: A5DMN1

Base Structure: X-ray

Registration Date: 2023-06-26

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	87
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-589450.85141
FMO2-HF: Nuclear repulsion	556201.419619
FMO2-HF: Total energy	-33249.43179
FMO2-MP2: Total energy	-33348.638234

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:266:LEU)

Summations of interaction energy for fragment #1(A:266:LEU)

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.
-10.2	-3.718	3.9	-2.453	-7.927	-0.014

Interaction energy analysis for fragmet #1(A:266:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.014

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	268	ILE	0	0.009	0.011	3.822	-0.872	0.735	-0.023	-0.794	-0.789	0.002
4	A	269	LEU	0	-0.034	-0.030	6.673	0.185	0.185	0.000	0.000	0.000	0.000
5	A	270	VAL	0	0.035	0.026	10.112	-0.049	-0.049	0.000	0.000	0.000	0.000
6	A	271	PHE	0	-0.021	-0.027	13.056	0.063	0.063	0.000	0.000	0.000	0.000
7	A	272	GLY	0	0.022	0.016	16.384	-0.021	-0.021	0.000	0.000	0.000	0.000
8	A	273	TYR	0	0.017	0.046	16.420	-0.007	-0.007	0.000	0.000	0.000	0.000
9	A	274	PRO	0	0.053	0.015	21.536	0.018	0.018	0.000	0.000	0.000	0.000
10	A	275	GLU	-1	-0.713	-0.848	21.742	-0.028	-0.028	0.000	0.000	0.000	0.000
11	A	276	THR	0	-0.078	-0.046	23.631	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	277	MET	0	-0.061	-0.027	21.550	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	278	ALA	0	0.049	0.037	19.247	-0.023	-0.023	0.000	0.000	0.000	0.000
14	A	279	ASN	0	0.049	0.007	18.600	-0.042	-0.042	0.000	0.000	0.000	0.000
15	A	280	GLN	0	0.014	0.008	19.075	-0.034	-0.034	0.000	0.000	0.000	0.000
16	A	281	VAL	0	0.010	0.018	15.702	-0.027	-0.027	0.000	0.000	0.000	0.000
17	A	282	ILE	0	0.007	-0.001	13.738	-0.054	-0.054	0.000	0.000	0.000	0.000
18	A	283	ALA	0	-0.040	-0.028	14.500	-0.070	-0.070	0.000	0.000	0.000	0.000
19	A	284	TYR	0	-0.064	-0.046	16.237	-0.039	-0.039	0.000	0.000	0.000	0.000
20	A	285	PHE	0	0.040	0.006	11.104	-0.026	-0.026	0.000	0.000	0.000	0.000
21	A	286	GLN	0	0.011	0.002	11.361	-0.172	-0.172	0.000	0.000	0.000	0.000
22	A	287	GLU	-1	-0.957	-0.976	12.706	-0.436	-0.436	0.000	0.000	0.000	0.000
23	A	288	PHE	0	-0.008	0.016	9.792	-0.018	-0.018	0.000	0.000	0.000	0.000
24	A	289	GLY	0	-0.014	-0.002	8.448	-0.192	-0.192	0.000	0.000	0.000	0.000
25	A	290	THR	0	-0.060	-0.045	9.039	0.216	0.216	0.000	0.000	0.000	0.000
26	A	291	ILE	0	-0.044	-0.016	7.626	-0.344	-0.344	0.000	0.000	0.000	0.000
27	A	292	LEU	0	-0.048	-0.024	4.899	0.242	0.242	0.000	0.000	0.000	0.000
28	A	293	GLU	-1	-0.773	-0.860	8.264	-0.149	-0.149	0.000	0.000	0.000	0.000
29	A	294	ASP	-1	-0.844	-0.897	11.001	-0.234	-0.234	0.000	0.000	0.000	0.000
30	A	295	PHE	0	0.022	-0.002	11.488	0.059	0.059	0.000	0.000	0.000	0.000
31	A	296	GLU	-1	-0.843	-0.912	16.208	-0.121	-0.121	0.000	0.000	0.000	0.000
32	A	297	VAL	0	-0.049	-0.025	17.583	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	298	LEU	0	-0.003	0.010	13.071	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	299	ARG	1	0.735	0.843	17.012	0.115	0.115	0.000	0.000	0.000	0.000
35	A	300	LYS	1	0.926	0.960	15.498	0.424	0.424	0.000	0.000	0.000	0.000
36	A	301	PRO	0	-0.016	0.004	20.735	0.013	0.013	0.000	0.000	0.000	0.000
37	A	313	PHE	0	0.030	0.014	10.271	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	314	VAL	0	-0.043	-0.024	6.449	0.131	0.131	0.000	0.000	0.000	0.000
39	A	315	PRO	0	-0.020	-0.004	9.901	-0.081	-0.081	0.000	0.000	0.000	0.000
40	A	316	ILE	0	0.025	0.004	11.200	0.059	0.059	0.000	0.000	0.000	0.000
41	A	317	PHE	0	-0.047	-0.011	11.202	0.071	0.071	0.000	0.000	0.000	0.000
42	A	318	SER	0	0.040	-0.003	13.317	-0.036	-0.036	0.000	0.000	0.000	0.000
43	A	319	GLY	0	0.002	0.009	16.074	0.028	0.028	0.000	0.000	0.000	0.000
44	A	320	ASN	0	-0.086	-0.050	19.493	-0.020	-0.020	0.000	0.000	0.000	0.000
45	A	321	SER	0	-0.061	-0.046	20.303	0.020	0.020	0.000	0.000	0.000	0.000
46	A	322	TRP	0	-0.001	-0.005	13.484	0.016	0.016	0.000	0.000	0.000	0.000
47	A	323	THR	0	-0.015	-0.015	12.694	0.023	0.023	0.000	0.000	0.000	0.000
48	A	324	LYS	1	0.845	0.948	6.075	-1.383	-1.383	0.000	0.000	0.000	0.000
49	A	325	ILE	0	-0.013	-0.004	7.769	0.004	0.004	0.000	0.000	0.000	0.000
50	A	326	THR	0	-0.041	-0.070	3.089	-0.217	0.156	0.051	-0.095	-0.329	0.000
51	A	327	TYR	0	0.001	0.003	3.479	0.055	0.723	0.009	-0.132	-0.545	0.000
52	A	328	ASP	-1	-0.820	-0.907	3.109	-3.927	-2.392	0.165	-0.805	-0.895	-0.007
53	A	329	ASN	0	-0.084	-0.046	3.166	-1.199	0.302	0.299	-0.446	-1.353	-0.004
54	A	330	PRO	0	0.022	-0.014	2.462	-2.726	-1.285	2.804	-1.036	-3.209	-0.004
55	A	331	ALA	0	0.013	0.014	3.066	0.999	-0.083	0.110	1.184	-0.212	0.000
56	A	332	SER	0	0.075	0.025	5.645	0.083	0.083	0.000	0.000	0.000	0.000
57	A	333	ALA	0	-0.029	-0.003	2.670	-0.226	0.142	0.486	-0.318	-0.536	-0.001
58	A	334	VAL	0	-0.074	-0.042	4.706	0.423	0.494	-0.001	-0.011	-0.059	0.000
59	A	335	ASP	-1	-0.870	-0.945	7.344	-0.592	-0.592	0.000	0.000	0.000	0.000
60	A	336	ALA	0	0.001	0.001	7.744	0.145	0.145	0.000	0.000	0.000	0.000
61	A	337	LEU	0	-0.046	-0.025	7.914	0.201	0.201	0.000	0.000	0.000	0.000
62	A	338	LEU	0	-0.042	-0.022	10.010	0.141	0.141	0.000	0.000	0.000	0.000
63	A	339	GLU	-1	-0.851	-0.893	12.717	-0.301	-0.301	0.000	0.000	0.000	0.000
64	A	340	ASN	0	-0.054	-0.016	13.518	0.062	0.062	0.000	0.000	0.000	0.000
65	A	341	GLY	0	-0.027	-0.014	15.340	0.018	0.018	0.000	0.000	0.000	0.000
66	A	342	ALA	0	0.012	0.022	17.939	0.019	0.019	0.000	0.000	0.000	0.000
67	A	343	VAL	0	-0.036	-0.030	19.629	0.014	0.014	0.000	0.000	0.000	0.000
68	A	344	PHE	0	0.015	-0.001	19.844	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	345	ASN	0	-0.037	-0.029	22.223	0.013	0.013	0.000	0.000	0.000	0.000
70	A	346	GLY	0	-0.012	-0.005	25.491	0.010	0.010	0.000	0.000	0.000	0.000
71	A	347	VAL	0	-0.021	-0.006	22.268	0.015	0.015	0.000	0.000	0.000	0.000
72	A	348	LEU	0	-0.012	0.000	21.553	-0.014	-0.014	0.000	0.000	0.000	0.000
73	A	349	LEU	0	-0.017	0.002	16.709	0.013	0.013	0.000	0.000	0.000	0.000
74	A	350	GLY	0	0.024	0.022	15.902	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	351	VAL	0	-0.004	-0.012	9.820	-0.019	-0.019	0.000	0.000	0.000	0.000
76	A	352	ILE	0	-0.015	-0.007	10.019	0.023	0.023	0.000	0.000	0.000	0.000
77	A	353	PRO	0	0.037	0.015	5.317	-0.058	-0.058	0.000	0.000	0.000	0.000
78	A	354	TYR	0	0.010	0.003	5.183	-0.013	-0.013	0.000	0.000	0.000	0.000
79	A	355	THR	0	-0.006	-0.011	6.215	0.396	0.396	0.000	0.000	0.000	0.000
80	A	356	LYS	1	0.832	0.903	8.816	-0.773	-0.773	0.000	0.000	0.000	0.000
81	A	357	ASP	-1	-0.827	-0.908	11.401	0.297	0.297	0.000	0.000	0.000	0.000
82	A	358	ALA	0	0.025	0.019	11.838	-0.092	-0.092	0.000	0.000	0.000	0.000
83	A	359	VAL	0	0.022	0.001	11.963	-0.077	-0.077	0.000	0.000	0.000	0.000
84	A	360	GLU	-1	-0.829	-0.901	13.943	0.429	0.429	0.000	0.000	0.000	0.000
85	A	361	ARG	1	0.821	0.890	16.750	-0.368	-0.368	0.000	0.000	0.000	0.000
86	A	362	LEU	0	-0.062	-0.011	14.826	-0.041	-0.041	0.000	0.000	0.000	0.000
87	A	363	GLN	0	-0.050	-0.004	16.164	-0.070	-0.070	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:266:LEU)