FMO DATABASE

FMODB ID: KG5Y3

Calculation Name: 4EZA-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EZA

Chain ID: B

ChEMBL ID:

UniProt ID: Q13576

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:

Apendix: None

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	94
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-704494.326725
FMO2-HF: Nuclear repulsion	666571.051981
FMO2-HF: Total energy	-37923.274745
FMO2-MP2: Total energy	-38033.461773

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(B:2:LYS)

Summations of interaction energy for fragment #1(B:2:LYS)

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.
-47.18	-45.292	9.567	-6.253	-5.201	-0.069

Interaction energy analysis for fragmet #1(B:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.956 / q_NPA : 0.975

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	B	4	VAL	0	0.001	0.016	1.834	-48.252	-46.718	9.568	-6.193	-4.908	-0.069
4	B	5	LYS	1	0.822	0.885	4.067	50.515	50.753	-0.001	-0.018	-0.219	0.000
5	B	6	TYR	0	0.041	0.008	6.305	0.849	0.849	0.000	0.000	0.000	0.000
6	B	7	THR	0	0.053	0.034	9.574	1.013	1.013	0.000	0.000	0.000	0.000
7	B	8	ALA	0	0.058	0.022	12.656	0.149	0.149	0.000	0.000	0.000	0.000
8	B	9	ALA	0	0.008	0.006	15.878	0.726	0.726	0.000	0.000	0.000	0.000
9	B	10	LYS	1	0.841	0.902	11.836	20.858	20.858	0.000	0.000	0.000	0.000
10	B	11	LEU	0	-0.016	-0.022	12.425	0.100	0.100	0.000	0.000	0.000	0.000
11	B	12	HIS	0	-0.066	-0.022	15.566	1.133	1.133	0.000	0.000	0.000	0.000
12	B	13	GLU	-1	-0.822	-0.893	16.736	-18.023	-18.023	0.000	0.000	0.000	0.000
13	B	14	LYS	1	0.818	0.931	11.563	25.249	25.249	0.000	0.000	0.000	0.000
14	B	15	GLY	0	0.038	0.028	17.877	0.186	0.186	0.000	0.000	0.000	0.000
15	B	16	VAL	0	-0.040	-0.023	15.572	0.294	0.294	0.000	0.000	0.000	0.000
16	B	17	LEU	0	-0.013	0.001	17.637	0.147	0.147	0.000	0.000	0.000	0.000
17	B	18	LEU	0	-0.020	-0.019	19.735	0.374	0.374	0.000	0.000	0.000	0.000
18	B	19	ASP	-1	-0.874	-0.953	22.860	-11.855	-11.855	0.000	0.000	0.000	0.000
19	B	20	ILE	0	-0.055	-0.029	18.847	-0.833	-0.833	0.000	0.000	0.000	0.000
20	B	21	ASP	-1	-0.741	-0.862	23.431	-11.865	-11.865	0.000	0.000	0.000	0.000
21	B	22	ASP	-1	-0.849	-0.908	26.105	-11.440	-11.440	0.000	0.000	0.000	0.000
22	B	23	LEU	0	-0.074	-0.014	21.110	0.008	0.008	0.000	0.000	0.000	0.000
23	B	24	GLN	0	0.068	0.038	25.630	-0.241	-0.241	0.000	0.000	0.000	0.000
24	B	25	THR	0	0.106	0.044	23.664	-0.491	-0.491	0.000	0.000	0.000	0.000
25	B	26	ASN	0	-0.030	-0.015	22.640	-0.870	-0.870	0.000	0.000	0.000	0.000
26	B	27	GLN	0	0.020	-0.005	21.649	-0.687	-0.687	0.000	0.000	0.000	0.000
27	B	28	PHE	0	0.066	0.031	19.147	-0.899	-0.899	0.000	0.000	0.000	0.000
28	B	29	LYS	1	0.836	0.916	16.769	13.358	13.358	0.000	0.000	0.000	0.000
29	B	30	ASN	0	-0.014	-0.008	15.947	-1.262	-1.262	0.000	0.000	0.000	0.000
30	B	31	VAL	0	0.037	0.036	15.815	-0.415	-0.415	0.000	0.000	0.000	0.000
31	B	32	THR	0	-0.095	-0.053	9.550	-1.291	-1.291	0.000	0.000	0.000	0.000
32	B	33	PHE	0	0.049	0.025	11.359	1.062	1.062	0.000	0.000	0.000	0.000
33	B	34	ASP	-1	-0.770	-0.858	7.540	-40.852	-40.852	0.000	0.000	0.000	0.000
34	B	35	ILE	0	0.008	-0.002	6.972	3.989	3.989	0.000	0.000	0.000	0.000
35	B	36	ILE	0	-0.028	-0.020	4.110	-9.082	-8.966	0.000	-0.042	-0.074	0.000
36	B	37	ALA	0	0.040	0.029	5.369	3.688	3.688	0.000	0.000	0.000	0.000
37	B	38	THR	0	-0.032	-0.035	6.854	-0.383	-0.383	0.000	0.000	0.000	0.000
38	B	39	GLU	-1	-0.939	-0.971	9.184	-17.324	-17.324	0.000	0.000	0.000	0.000
39	B	40	ASP	-1	-0.870	-0.922	11.369	-14.723	-14.723	0.000	0.000	0.000	0.000
40	B	41	VAL	0	-0.037	-0.033	11.892	-0.997	-0.997	0.000	0.000	0.000	0.000
41	B	42	GLY	0	-0.019	0.001	12.966	-0.394	-0.394	0.000	0.000	0.000	0.000
42	B	43	ILE	0	-0.006	-0.006	13.261	0.426	0.426	0.000	0.000	0.000	0.000
43	B	44	PHE	0	0.018	0.024	9.280	-1.603	-1.603	0.000	0.000	0.000	0.000
44	B	45	ASP	-1	-0.733	-0.826	9.133	-22.058	-22.058	0.000	0.000	0.000	0.000
45	B	46	VAL	0	0.000	-0.012	9.758	-3.352	-3.352	0.000	0.000	0.000	0.000
46	B	47	ARG	1	0.751	0.838	9.424	26.847	26.847	0.000	0.000	0.000	0.000
47	B	48	SER	0	-0.004	-0.011	12.511	-1.800	-1.800	0.000	0.000	0.000	0.000
48	B	49	LYS	1	0.820	0.886	9.849	28.963	28.963	0.000	0.000	0.000	0.000
49	B	50	PHE	0	0.021	0.000	14.496	0.121	0.121	0.000	0.000	0.000	0.000
50	B	51	LEU	0	-0.016	-0.015	16.555	0.247	0.247	0.000	0.000	0.000	0.000
51	B	52	GLY	0	-0.019	0.000	12.948	0.177	0.177	0.000	0.000	0.000	0.000
52	B	53	VAL	0	0.006	0.009	13.611	-1.141	-1.141	0.000	0.000	0.000	0.000
53	B	54	GLU	-1	-0.827	-0.905	11.939	-24.941	-24.941	0.000	0.000	0.000	0.000
54	B	55	MET	0	-0.036	-0.012	15.629	0.986	0.986	0.000	0.000	0.000	0.000
55	B	56	GLU	-1	-0.838	-0.909	17.266	-14.953	-14.953	0.000	0.000	0.000	0.000
56	B	57	LYS	1	0.770	0.861	11.882	18.968	18.968	0.000	0.000	0.000	0.000
57	B	58	VAL	0	0.036	0.036	15.236	1.151	1.151	0.000	0.000	0.000	0.000
58	B	59	GLN	0	-0.055	-0.035	12.973	-1.501	-1.501	0.000	0.000	0.000	0.000
59	B	60	LEU	0	0.018	0.007	14.599	1.049	1.049	0.000	0.000	0.000	0.000
60	B	61	ASN	0	0.060	0.018	15.110	-1.344	-1.344	0.000	0.000	0.000	0.000
61	B	62	ILE	0	-0.004	-0.012	15.616	0.508	0.508	0.000	0.000	0.000	0.000
62	B	63	GLN	0	0.049	0.009	17.987	0.894	0.894	0.000	0.000	0.000	0.000
63	B	64	ASP	-1	-0.837	-0.889	20.959	-12.557	-12.557	0.000	0.000	0.000	0.000
64	B	65	LEU	0	-0.035	-0.016	17.834	0.264	0.264	0.000	0.000	0.000	0.000
65	B	66	LEU	0	-0.020	-0.017	20.895	0.393	0.393	0.000	0.000	0.000	0.000
66	B	67	GLN	0	-0.025	-0.018	23.793	0.820	0.820	0.000	0.000	0.000	0.000
67	B	68	MET	0	-0.006	-0.003	24.118	0.217	0.217	0.000	0.000	0.000	0.000
68	B	69	GLN	0	-0.046	-0.039	24.090	0.423	0.423	0.000	0.000	0.000	0.000
69	B	70	TYR	0	-0.043	-0.027	26.386	0.389	0.389	0.000	0.000	0.000	0.000
70	B	71	GLU	-1	-0.961	-0.962	29.774	-9.619	-9.619	0.000	0.000	0.000	0.000
71	B	72	GLY	0	-0.016	-0.001	30.652	0.335	0.335	0.000	0.000	0.000	0.000
72	B	73	VAL	0	-0.034	-0.011	27.565	0.028	0.028	0.000	0.000	0.000	0.000
73	B	74	ALA	0	0.007	-0.003	27.193	-0.494	-0.494	0.000	0.000	0.000	0.000
74	B	75	VAL	0	-0.078	-0.046	24.928	-0.595	-0.595	0.000	0.000	0.000	0.000
75	B	76	MET	0	0.047	0.032	20.998	0.323	0.323	0.000	0.000	0.000	0.000
76	B	77	LYS	1	0.768	0.876	23.556	12.126	12.126	0.000	0.000	0.000	0.000
77	B	78	MET	0	-0.050	-0.006	15.392	-0.347	-0.347	0.000	0.000	0.000	0.000
78	B	79	PHE	0	0.058	0.017	15.851	-0.759	-0.759	0.000	0.000	0.000	0.000
79	B	80	ASP	-1	-0.833	-0.913	21.546	-12.149	-12.149	0.000	0.000	0.000	0.000
80	B	81	LYS	1	0.754	0.856	23.550	12.919	12.919	0.000	0.000	0.000	0.000
81	B	82	VAL	0	0.009	0.006	18.302	-0.294	-0.294	0.000	0.000	0.000	0.000
82	B	83	LYS	1	0.972	1.000	21.773	11.639	11.639	0.000	0.000	0.000	0.000
83	B	84	VAL	0	0.010	-0.011	18.208	-0.414	-0.414	0.000	0.000	0.000	0.000
84	B	85	ASN	0	0.034	0.014	20.975	0.602	0.602	0.000	0.000	0.000	0.000
85	B	86	VAL	0	0.043	0.025	20.637	-0.980	-0.980	0.000	0.000	0.000	0.000
86	B	87	ASN	0	0.062	0.034	21.053	-0.633	-0.633	0.000	0.000	0.000	0.000
87	B	88	LEU	0	-0.041	-0.023	18.826	-0.529	-0.529	0.000	0.000	0.000	0.000
88	B	89	LEU	0	0.010	0.010	15.310	-1.400	-1.400	0.000	0.000	0.000	0.000
89	B	90	ILE	0	0.020	0.012	16.252	-1.323	-1.323	0.000	0.000	0.000	0.000
90	B	91	TYR	0	0.025	0.014	16.581	-1.361	-1.361	0.000	0.000	0.000	0.000
91	B	92	LEU	0	-0.074	-0.046	11.454	-1.292	-1.292	0.000	0.000	0.000	0.000
92	B	93	LEU	0	-0.030	-0.011	12.091	-2.489	-2.489	0.000	0.000	0.000	0.000
93	B	94	ASN	0	-0.039	0.001	12.217	-0.165	-0.165	0.000	0.000	0.000	0.000
94	B	95	LYS	1	0.881	0.949	11.112	20.579	20.579	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:2:LYS)