FMO DATABASE

FMODB ID: 17V1Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-590107.630364
FMO2-HF: Nuclear repulsion	556858.015409
FMO2-HF: Total energy	-33249.614955
FMO2-MP2: Total energy	-33348.824708

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.
-11.916	-4.414	4.002	-3.091	-8.41	-0.018

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 : 0.008 / q_NPA : -0.007

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	0.011	0.012	3.846	-0.472	1.241	-0.025	-0.860	-0.828	0.001
4	A	269	LEU	0	-0.041	-0.027	6.822	0.108	0.108	0.000	0.000	0.000	0.000
5	A	270	VAL	0	0.032	0.020	10.474	-0.034	-0.034	0.000	0.000	0.000	0.000
6	A	271	PHE	0	-0.014	-0.021	13.147	0.043	0.043	0.000	0.000	0.000	0.000
7	A	272	GLY	0	0.029	0.018	16.699	-0.024	-0.024	0.000	0.000	0.000	0.000
8	A	273	TYR	0	0.019	0.045	16.825	-0.005	-0.005	0.000	0.000	0.000	0.000
9	A	274	PRO	0	0.055	0.020	21.780	0.018	0.018	0.000	0.000	0.000	0.000
10	A	275	GLU	-1	-0.727	-0.860	22.376	-0.036	-0.036	0.000	0.000	0.000	0.000
11	A	276	THR	0	-0.062	-0.036	23.714	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	277	MET	0	-0.049	-0.008	21.552	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	278	ALA	0	0.043	0.031	19.500	-0.025	-0.025	0.000	0.000	0.000	0.000
14	A	279	ASN	0	0.041	-0.002	18.645	-0.047	-0.047	0.000	0.000	0.000	0.000
15	A	280	GLN	0	0.001	0.004	19.283	-0.033	-0.033	0.000	0.000	0.000	0.000
16	A	281	VAL	0	0.021	0.020	15.706	-0.028	-0.028	0.000	0.000	0.000	0.000
17	A	282	ILE	0	0.005	-0.001	13.925	-0.054	-0.054	0.000	0.000	0.000	0.000
18	A	283	ALA	0	-0.040	-0.023	14.594	-0.076	-0.076	0.000	0.000	0.000	0.000
19	A	284	TYR	0	-0.064	-0.046	16.252	-0.050	-0.050	0.000	0.000	0.000	0.000
20	A	285	PHE	0	0.042	0.009	11.302	-0.026	-0.026	0.000	0.000	0.000	0.000
21	A	286	GLN	0	0.042	0.030	11.410	-0.187	-0.187	0.000	0.000	0.000	0.000
22	A	287	GLU	-1	-0.955	-0.977	12.985	-0.445	-0.445	0.000	0.000	0.000	0.000
23	A	288	PHE	0	-0.009	0.013	9.827	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	289	GLY	0	-0.017	0.000	9.051	-0.184	-0.184	0.000	0.000	0.000	0.000
25	A	290	THR	0	-0.058	-0.054	9.213	0.213	0.213	0.000	0.000	0.000	0.000
26	A	291	ILE	0	-0.035	-0.015	7.643	-0.401	-0.401	0.000	0.000	0.000	0.000
27	A	292	LEU	0	-0.028	-0.015	4.786	0.170	0.275	-0.001	-0.002	-0.101	0.000
28	A	293	GLU	-1	-0.770	-0.859	8.144	-0.329	-0.329	0.000	0.000	0.000	0.000
29	A	294	ASP	-1	-0.838	-0.894	11.118	-0.282	-0.282	0.000	0.000	0.000	0.000
30	A	295	PHE	0	0.023	-0.008	11.505	0.077	0.077	0.000	0.000	0.000	0.000
31	A	296	GLU	-1	-0.845	-0.912	15.998	-0.165	-0.165	0.000	0.000	0.000	0.000
32	A	297	VAL	0	-0.072	-0.033	17.603	0.000	0.000	0.000	0.000	0.000	0.000
33	A	298	LEU	0	0.001	0.011	12.977	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	299	ARG	1	0.776	0.871	16.794	0.154	0.154	0.000	0.000	0.000	0.000
35	A	300	LYS	1	0.846	0.908	15.102	0.505	0.505	0.000	0.000	0.000	0.000
36	A	301	PRO	0	-0.011	0.005	20.509	0.009	0.009	0.000	0.000	0.000	0.000
37	A	313	PHE	0	0.036	0.018	10.146	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	314	VAL	0	-0.043	-0.033	6.537	0.116	0.116	0.000	0.000	0.000	0.000
39	A	315	PRO	0	-0.028	-0.005	9.941	-0.068	-0.068	0.000	0.000	0.000	0.000
40	A	316	ILE	0	0.024	0.006	11.124	0.065	0.065	0.000	0.000	0.000	0.000
41	A	317	PHE	0	-0.039	-0.016	11.492	0.082	0.082	0.000	0.000	0.000	0.000
42	A	318	SER	0	0.004	-0.013	13.611	-0.014	-0.014	0.000	0.000	0.000	0.000
43	A	319	GLY	0	0.033	0.020	16.393	0.024	0.024	0.000	0.000	0.000	0.000
44	A	320	ASN	0	-0.082	-0.052	19.912	-0.012	-0.012	0.000	0.000	0.000	0.000
45	A	321	SER	0	-0.052	-0.037	20.877	0.022	0.022	0.000	0.000	0.000	0.000
46	A	322	TRP	0	-0.018	-0.007	14.101	0.013	0.013	0.000	0.000	0.000	0.000
47	A	323	THR	0	0.019	-0.011	12.950	0.016	0.016	0.000	0.000	0.000	0.000
48	A	324	LYS	1	0.832	0.947	6.276	-0.811	-0.811	0.000	0.000	0.000	0.000
49	A	325	ILE	0	-0.011	0.001	7.753	-0.027	-0.027	0.000	0.000	0.000	0.000
50	A	326	THR	0	-0.071	-0.083	2.983	-0.049	0.379	0.093	-0.113	-0.408	0.000
51	A	327	TYR	0	0.011	0.000	3.409	0.187	0.916	0.006	-0.182	-0.554	0.000
52	A	328	ASP	-1	-0.849	-0.911	2.716	-6.446	-4.314	0.487	-1.172	-1.447	-0.014
53	A	329	ASN	0	-0.056	-0.035	2.792	-0.931	0.184	0.291	-0.280	-1.126	-0.001
54	A	330	PRO	0	0.005	-0.021	2.535	-2.303	-0.928	2.788	-0.898	-3.264	-0.003
55	A	331	ALA	0	0.006	0.022	3.312	0.265	-0.253	0.079	0.616	-0.176	0.000
56	A	332	SER	0	0.078	0.022	5.845	0.038	0.038	0.000	0.000	0.000	0.000
57	A	333	ALA	0	-0.019	0.000	2.843	-0.281	0.079	0.285	-0.194	-0.451	-0.001
58	A	334	VAL	0	-0.069	-0.034	4.833	0.490	0.553	-0.001	-0.006	-0.055	0.000
59	A	335	ASP	-1	-0.893	-0.958	7.537	-0.603	-0.603	0.000	0.000	0.000	0.000
60	A	336	ALA	0	0.020	0.009	7.974	0.150	0.150	0.000	0.000	0.000	0.000
61	A	337	LEU	0	-0.051	-0.034	7.860	0.192	0.192	0.000	0.000	0.000	0.000
62	A	338	LEU	0	-0.044	-0.022	10.095	0.144	0.144	0.000	0.000	0.000	0.000
63	A	339	GLU	-1	-0.844	-0.891	13.125	-0.294	-0.294	0.000	0.000	0.000	0.000
64	A	340	ASN	0	-0.053	-0.015	13.412	0.061	0.061	0.000	0.000	0.000	0.000
65	A	341	GLY	0	-0.007	-0.005	15.278	0.021	0.021	0.000	0.000	0.000	0.000
66	A	342	ALA	0	0.002	0.011	18.123	0.013	0.013	0.000	0.000	0.000	0.000
67	A	343	VAL	0	-0.046	-0.032	19.836	0.014	0.014	0.000	0.000	0.000	0.000
68	A	344	PHE	0	0.028	0.007	19.987	-0.010	-0.010	0.000	0.000	0.000	0.000
69	A	345	ASN	0	-0.049	-0.042	22.522	0.015	0.015	0.000	0.000	0.000	0.000
70	A	346	GLY	0	0.005	0.009	25.692	0.010	0.010	0.000	0.000	0.000	0.000
71	A	347	VAL	0	-0.040	-0.017	22.923	0.015	0.015	0.000	0.000	0.000	0.000
72	A	348	LEU	0	-0.014	-0.004	21.702	-0.014	-0.014	0.000	0.000	0.000	0.000
73	A	349	LEU	0	-0.016	0.001	17.170	0.011	0.011	0.000	0.000	0.000	0.000
74	A	350	GLY	0	0.022	0.016	16.220	0.002	0.002	0.000	0.000	0.000	0.000
75	A	351	VAL	0	-0.019	-0.019	9.809	-0.013	-0.013	0.000	0.000	0.000	0.000
76	A	352	ILE	0	-0.013	-0.004	10.247	0.025	0.025	0.000	0.000	0.000	0.000
77	A	353	PRO	0	0.040	0.011	5.665	-0.046	-0.046	0.000	0.000	0.000	0.000
78	A	354	TYR	0	-0.014	0.003	5.601	-0.081	-0.081	0.000	0.000	0.000	0.000
79	A	355	THR	0	-0.005	-0.014	6.779	0.501	0.501	0.000	0.000	0.000	0.000
80	A	356	LYS	1	0.842	0.903	9.475	-0.773	-0.773	0.000	0.000	0.000	0.000
81	A	357	ASP	-1	-0.829	-0.902	12.193	0.332	0.332	0.000	0.000	0.000	0.000
82	A	358	ALA	0	0.036	0.015	12.328	-0.089	-0.089	0.000	0.000	0.000	0.000
83	A	359	VAL	0	0.013	0.005	12.397	-0.083	-0.083	0.000	0.000	0.000	0.000
84	A	360	GLU	-1	-0.786	-0.857	14.408	0.397	0.397	0.000	0.000	0.000	0.000
85	A	361	ARG	1	0.811	0.896	17.315	-0.410	-0.410	0.000	0.000	0.000	0.000
86	A	362	LEU	0	-0.045	-0.003	15.147	-0.040	-0.040	0.000	0.000	0.000	0.000
87	A	363	GLN	0	-0.114	-0.067	16.105	-0.089	-0.089	0.000	0.000	0.000	0.000

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Overview

Highlights

Manual

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