FMO DATABASE

FMODB ID: YZ752

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

Total energy (hartree)

FMO2-HF: Electronic energy	-589322.328468
FMO2-HF: Nuclear repulsion	556073.290072
FMO2-HF: Total energy	-33249.038397
FMO2-MP2: Total energy	-33348.264267

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.
-8.675	-1.639	3.532	-2.544	-8.022	-0.011

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 : -0.010

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

Sort

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	0.002	0.010	3.822	1.717	3.356	-0.025	-0.787	-0.827	0.003
4	A	269	LEU	0	-0.037	-0.033	6.881	-0.333	-0.333	0.000	0.000	0.000	0.000
5	A	270	VAL	0	0.055	0.035	10.470	0.019	0.019	0.000	0.000	0.000	0.000
6	A	271	PHE	0	-0.029	-0.029	13.098	-0.025	-0.025	0.000	0.000	0.000	0.000
7	A	272	GLY	0	0.019	0.013	16.628	-0.007	-0.007	0.000	0.000	0.000	0.000
8	A	273	TYR	0	0.028	0.050	16.433	-0.014	-0.014	0.000	0.000	0.000	0.000
9	A	274	PRO	0	0.037	0.013	21.536	0.009	0.009	0.000	0.000	0.000	0.000
10	A	275	GLU	-1	-0.734	-0.866	21.870	0.017	0.017	0.000	0.000	0.000	0.000
11	A	276	THR	0	-0.077	-0.050	23.631	-0.019	-0.019	0.000	0.000	0.000	0.000
12	A	277	MET	0	-0.060	-0.023	21.455	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	278	ALA	0	0.043	0.033	19.198	-0.015	-0.015	0.000	0.000	0.000	0.000
14	A	279	ASN	0	0.044	0.007	18.598	-0.034	-0.034	0.000	0.000	0.000	0.000
15	A	280	GLN	0	0.002	-0.002	19.042	-0.031	-0.031	0.000	0.000	0.000	0.000
16	A	281	VAL	0	0.016	0.022	15.612	-0.020	-0.020	0.000	0.000	0.000	0.000
17	A	282	ILE	0	0.008	0.000	13.616	-0.033	-0.033	0.000	0.000	0.000	0.000
18	A	283	ALA	0	-0.033	-0.025	14.451	-0.070	-0.070	0.000	0.000	0.000	0.000
19	A	284	TYR	0	-0.047	-0.049	15.728	-0.055	-0.055	0.000	0.000	0.000	0.000
20	A	285	PHE	0	0.026	0.002	10.767	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	286	GLN	0	0.001	0.003	11.274	-0.208	-0.208	0.000	0.000	0.000	0.000
22	A	287	GLU	-1	-0.988	-0.988	12.618	-0.342	-0.342	0.000	0.000	0.000	0.000
23	A	288	PHE	0	-0.003	0.018	9.775	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	289	GLY	0	-0.008	0.006	8.345	-0.185	-0.185	0.000	0.000	0.000	0.000
25	A	290	THR	0	-0.039	-0.017	8.979	0.200	0.200	0.000	0.000	0.000	0.000
26	A	291	ILE	0	-0.015	-0.002	7.589	-0.393	-0.393	0.000	0.000	0.000	0.000
27	A	292	LEU	0	-0.032	-0.016	4.982	0.196	0.196	0.000	0.000	0.000	0.000
28	A	293	GLU	-1	-0.793	-0.865	8.265	-0.710	-0.710	0.000	0.000	0.000	0.000
29	A	294	ASP	-1	-0.864	-0.913	10.897	-0.371	-0.371	0.000	0.000	0.000	0.000
30	A	295	PHE	0	0.018	-0.003	11.413	0.091	0.091	0.000	0.000	0.000	0.000
31	A	296	GLU	-1	-0.857	-0.919	16.090	-0.190	-0.190	0.000	0.000	0.000	0.000
32	A	297	VAL	0	-0.045	-0.025	17.559	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	298	LEU	0	-0.012	0.000	12.963	0.002	0.002	0.000	0.000	0.000	0.000
34	A	299	ARG	1	0.758	0.866	17.005	0.235	0.235	0.000	0.000	0.000	0.000
35	A	300	LYS	1	0.974	0.978	15.815	0.533	0.533	0.000	0.000	0.000	0.000
36	A	301	PRO	0	-0.021	0.002	20.738	0.008	0.008	0.000	0.000	0.000	0.000
37	A	313	PHE	0	-0.016	-0.019	10.943	-0.040	-0.040	0.000	0.000	0.000	0.000
38	A	314	VAL	0	-0.001	0.016	6.439	0.029	0.029	0.000	0.000	0.000	0.000
39	A	315	PRO	0	-0.019	-0.008	9.872	0.019	0.019	0.000	0.000	0.000	0.000
40	A	316	ILE	0	0.024	0.006	11.190	0.007	0.007	0.000	0.000	0.000	0.000
41	A	317	PHE	0	-0.046	-0.012	11.079	0.072	0.072	0.000	0.000	0.000	0.000
42	A	318	SER	0	0.002	-0.014	13.304	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	319	GLY	0	0.029	0.016	16.061	0.009	0.009	0.000	0.000	0.000	0.000
44	A	320	ASN	0	-0.035	-0.012	19.497	-0.027	-0.027	0.000	0.000	0.000	0.000
45	A	321	SER	0	-0.061	-0.049	20.364	0.028	0.028	0.000	0.000	0.000	0.000
46	A	322	TRP	0	-0.003	-0.014	13.063	0.062	0.062	0.000	0.000	0.000	0.000
47	A	323	THR	0	-0.010	-0.007	12.928	-0.045	-0.045	0.000	0.000	0.000	0.000
48	A	324	LYS	1	0.843	0.946	6.145	-0.637	-0.637	0.000	0.000	0.000	0.000
49	A	325	ILE	0	0.000	0.006	7.703	-0.096	-0.096	0.000	0.000	0.000	0.000
50	A	326	THR	0	-0.075	-0.094	3.054	-0.225	0.175	0.061	-0.104	-0.356	0.000
51	A	327	TYR	0	-0.003	-0.003	3.405	0.094	0.836	0.014	-0.160	-0.596	0.000
52	A	328	ASP	-1	-0.852	-0.928	3.144	-4.817	-3.289	0.185	-0.804	-0.909	-0.006
53	A	329	ASN	0	-0.100	-0.071	2.729	-1.195	0.304	0.765	-0.668	-1.596	-0.005
54	A	330	PRO	0	0.000	-0.020	2.267	-2.810	-1.133	1.910	-0.719	-2.868	-0.001
55	A	331	ALA	0	0.025	0.020	3.017	1.273	0.383	0.087	1.034	-0.230	0.000
56	A	332	SER	0	0.061	0.014	5.583	0.116	0.116	0.000	0.000	0.000	0.000
57	A	333	ALA	0	-0.022	0.004	2.601	-0.066	0.297	0.536	-0.326	-0.573	-0.002
58	A	334	VAL	0	-0.072	-0.043	4.680	0.610	0.688	-0.001	-0.010	-0.067	0.000
59	A	335	ASP	-1	-0.880	-0.949	7.327	-0.287	-0.287	0.000	0.000	0.000	0.000
60	A	336	ALA	0	0.007	0.002	7.720	0.107	0.107	0.000	0.000	0.000	0.000
61	A	337	LEU	0	-0.037	-0.029	7.722	0.170	0.170	0.000	0.000	0.000	0.000
62	A	338	LEU	0	-0.062	-0.029	9.976	0.059	0.059	0.000	0.000	0.000	0.000
63	A	339	GLU	-1	-0.833	-0.881	12.684	-0.061	-0.061	0.000	0.000	0.000	0.000
64	A	340	ASN	0	-0.066	-0.022	13.684	0.008	0.008	0.000	0.000	0.000	0.000
65	A	341	GLY	0	-0.031	-0.018	15.303	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	342	ALA	0	0.010	0.025	17.901	-0.019	-0.019	0.000	0.000	0.000	0.000
67	A	343	VAL	0	-0.040	-0.035	19.592	0.008	0.008	0.000	0.000	0.000	0.000
68	A	344	PHE	0	0.022	0.005	20.038	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	345	ASN	0	-0.019	-0.022	22.185	0.008	0.008	0.000	0.000	0.000	0.000
70	A	346	GLY	0	-0.015	-0.008	25.454	0.004	0.004	0.000	0.000	0.000	0.000
71	A	347	VAL	0	-0.019	-0.002	21.941	0.010	0.010	0.000	0.000	0.000	0.000
72	A	348	LEU	0	-0.022	-0.009	21.630	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	349	LEU	0	-0.011	0.005	16.625	0.004	0.004	0.000	0.000	0.000	0.000
74	A	350	GLY	0	0.025	0.020	16.159	0.011	0.011	0.000	0.000	0.000	0.000
75	A	351	VAL	0	-0.003	-0.007	9.802	-0.006	-0.006	0.000	0.000	0.000	0.000
76	A	352	ILE	0	-0.016	-0.005	10.854	0.014	0.014	0.000	0.000	0.000	0.000
77	A	353	PRO	0	0.048	0.021	6.463	0.075	0.075	0.000	0.000	0.000	0.000
78	A	354	TYR	0	0.019	0.004	5.365	-0.916	-0.916	0.000	0.000	0.000	0.000
79	A	355	THR	0	0.006	-0.004	6.834	0.591	0.591	0.000	0.000	0.000	0.000
80	A	356	LYS	1	0.829	0.899	9.208	-0.650	-0.650	0.000	0.000	0.000	0.000
81	A	357	ASP	-1	-0.850	-0.944	11.227	0.456	0.456	0.000	0.000	0.000	0.000
82	A	358	ALA	0	0.021	0.024	12.400	-0.120	-0.120	0.000	0.000	0.000	0.000
83	A	359	VAL	0	0.018	0.001	12.067	-0.099	-0.099	0.000	0.000	0.000	0.000
84	A	360	GLU	-1	-0.847	-0.907	14.030	0.276	0.276	0.000	0.000	0.000	0.000
85	A	361	ARG	1	0.846	0.916	16.655	-0.457	-0.457	0.000	0.000	0.000	0.000
86	A	362	LEU	0	-0.050	-0.004	15.183	-0.040	-0.040	0.000	0.000	0.000	0.000
87	A	363	GLN	0	-0.038	0.001	16.451	-0.091	-0.091	0.000	0.000	0.000	0.000

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