FMO DATABASE

FMODB ID: ZV91N

Calculation Name: 4YEW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YEW

Chain ID: A

ChEMBL ID:

UniProt ID: P0ACF0

Base Structure: X-ray

Registration Date: 2023-09-23

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	71
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-323002.059659
FMO2-HF: Nuclear repulsion	297860.453138
FMO2-HF: Total energy	-25141.606521
FMO2-MP2: Total energy	-25215.771325

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:1:MET)

Summations of interaction energy for fragment #1(A: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.
-6.243	-4.091	14.303	-4.727	-11.73	-0.008

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.019

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	3	LYS	1	0.947	0.948	3.442	-1.302	2.354	0.018	-2.012	-1.662	0.007
4	A	4	SER	0	-0.031	-0.022	5.973	0.872	0.872	0.000	0.000	0.000	0.000
5	A	5	GLN	0	0.042	0.005	2.177	-2.263	-1.622	4.981	-1.929	-3.693	-0.012
6	A	6	LEU	0	0.006	-0.006	3.022	0.140	2.281	2.721	-1.694	-3.169	-0.003
7	A	7	ILE	0	0.004	-0.001	3.763	0.688	-0.763	0.063	1.735	-0.347	-0.001
8	A	8	ASP	-1	-0.868	-0.931	6.757	0.974	0.974	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.936	0.970	2.154	-3.435	-6.270	6.520	-0.827	-2.859	0.001
10	A	10	ILE	0	-0.012	-0.001	6.287	-0.447	-0.447	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.042	-0.029	8.733	-0.299	-0.299	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.024	-0.010	9.083	-0.146	-0.146	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.009	0.006	9.464	-0.136	-0.136	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.025	-0.004	10.729	-0.106	-0.106	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.932	-0.957	13.477	0.550	0.550	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.049	-0.015	14.195	-0.116	-0.116	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.023	-0.002	14.695	0.064	0.064	0.000	0.000	0.000	0.000
18	A	18	LYS	1	1.011	0.991	11.602	-0.542	-0.542	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.014	0.001	13.473	-0.019	-0.019	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.039	-0.021	16.062	-0.051	-0.051	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.046	0.027	10.763	-0.042	-0.042	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.003	-0.005	11.702	0.030	0.030	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.978	0.987	12.687	-0.262	-0.262	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.017	0.023	13.262	-0.056	-0.056	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.006	-0.005	7.328	-0.053	-0.053	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.840	-0.917	11.717	-0.362	-0.362	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.013	-0.009	13.969	-0.052	-0.052	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.013	0.017	11.634	-0.016	-0.016	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.007	0.000	9.553	-0.072	-0.072	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.000	0.004	13.853	-0.037	-0.037	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.008	-0.017	17.505	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	32	VAL	0	0.002	-0.001	14.970	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.060	-0.040	16.462	-0.038	-0.038	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.960	-0.985	18.831	-0.149	-0.149	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.008	0.004	21.036	0.005	0.005	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.011	-0.017	18.395	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.862	0.942	22.423	0.162	0.162	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.970	-0.990	24.560	-0.080	-0.080	0.000	0.000	0.000	0.000
39	A	39	GLY	0	-0.087	-0.040	25.862	0.014	0.014	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.913	-0.948	25.159	-0.050	-0.050	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.893	-0.951	22.647	-0.128	-0.128	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.034	0.017	18.085	0.024	0.024	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.036	-0.023	19.057	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.013	0.014	14.349	0.035	0.035	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.038	0.000	17.725	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	46	GLY	0	-0.011	0.004	17.445	0.044	0.044	0.000	0.000	0.000	0.000
47	A	47	PHE	0	0.020	0.001	9.691	0.002	0.002	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.006	-0.012	15.072	-0.058	-0.058	0.000	0.000	0.000	0.000
49	A	49	THR	0	-0.048	-0.019	16.869	0.036	0.036	0.000	0.000	0.000	0.000
50	A	50	PHE	0	-0.003	-0.002	12.087	-0.051	-0.051	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.049	0.036	18.241	0.030	0.030	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.040	0.016	21.166	-0.048	-0.048	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.838	0.910	21.672	0.256	0.256	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.921	-0.953	25.520	-0.150	-0.150	0.000	0.000	0.000	0.000
55	A	74	ALA	0	0.030	0.014	27.867	0.001	0.001	0.000	0.000	0.000	0.000
56	A	75	LYS	1	0.913	0.955	26.973	0.162	0.162	0.000	0.000	0.000	0.000
57	A	76	VAL	0	0.008	0.012	21.421	-0.020	-0.020	0.000	0.000	0.000	0.000
58	A	77	PRO	0	0.059	0.032	18.487	0.025	0.025	0.000	0.000	0.000	0.000
59	A	78	SER	0	0.017	-0.003	19.148	-0.021	-0.021	0.000	0.000	0.000	0.000
60	A	79	PHE	0	0.019	0.024	13.664	0.003	0.003	0.000	0.000	0.000	0.000
61	A	80	ARG	1	0.902	0.960	17.478	0.120	0.120	0.000	0.000	0.000	0.000
62	A	81	ALA	0	0.053	0.037	15.221	0.023	0.023	0.000	0.000	0.000	0.000
63	A	82	GLY	0	-0.032	-0.028	16.632	0.000	0.000	0.000	0.000	0.000	0.000
64	A	83	LYS	1	0.957	0.955	17.229	-0.089	-0.089	0.000	0.000	0.000	0.000
65	A	84	ALA	0	0.071	0.045	15.494	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	85	LEU	0	0.003	0.019	10.402	0.048	0.048	0.000	0.000	0.000	0.000
67	A	86	LYS	1	0.919	0.951	13.654	0.021	0.021	0.000	0.000	0.000	0.000
68	A	87	ASP	-1	-0.914	-0.966	16.404	0.138	0.138	0.000	0.000	0.000	0.000
69	A	88	ALA	0	-0.071	-0.026	11.630	0.012	0.012	0.000	0.000	0.000	0.000
70	A	89	VAL	0	-0.063	-0.028	11.024	0.032	0.032	0.000	0.000	0.000	0.000
71	A	90	ASN	0	-0.023	0.008	13.560	-0.025	-0.025	0.000	0.000	0.000	0.000

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