FMO DATABASE

FMODB ID: YVVZ2

Calculation Name: 4DPO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DPO

Chain ID: A

ChEMBL ID:

UniProt ID: Q8PWK2

Base Structure: X-ray

Registration Date: 2023-09-21

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	102
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-819680.237003
FMO2-HF: Nuclear repulsion	776406.314938
FMO2-HF: Total energy	-43273.922065
FMO2-MP2: Total energy	-43397.478779

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:-5:ASN)

Summations of interaction energy for fragment #1(A:-5:ASN)

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.
-25.553	-17.954	13.211	-7.064	-13.748	0.011

Interaction energy analysis for fragmet #1(A:-5:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.066 / q_NPA : 0.037

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	-3	TYR	0	0.000	0.009	2.075	-11.683	-8.722	6.812	-4.046	-5.727	0.036
4	A	-2	PHE	0	0.058	-0.003	2.526	-13.951	-10.171	6.389	-2.726	-7.444	-0.026
5	A	-1	GLN	0	0.056	0.037	3.432	0.899	1.757	0.010	-0.292	-0.577	0.001
6	A	0	SER	0	-0.014	-0.009	6.207	0.208	0.208	0.000	0.000	0.000	0.000
7	A	1	MET	0	-0.057	-0.016	6.267	-0.318	-0.318	0.000	0.000	0.000	0.000
8	A	2	LEU	0	-0.036	-0.017	8.240	0.006	0.006	0.000	0.000	0.000	0.000
9	A	3	ALA	0	0.018	0.019	9.961	0.109	0.109	0.000	0.000	0.000	0.000
10	A	4	ILE	0	-0.034	-0.015	11.957	0.035	0.035	0.000	0.000	0.000	0.000
11	A	5	ARG	1	0.837	0.899	15.741	-0.110	-0.110	0.000	0.000	0.000	0.000
12	A	6	VAL	0	-0.025	-0.009	18.623	-0.039	-0.039	0.000	0.000	0.000	0.000
13	A	7	VAL	0	0.006	-0.002	22.310	0.034	0.034	0.000	0.000	0.000	0.000
14	A	8	ALA	0	0.050	0.026	25.679	-0.014	-0.014	0.000	0.000	0.000	0.000
15	A	9	LYS	1	0.893	0.941	28.411	0.038	0.038	0.000	0.000	0.000	0.000
16	A	10	ASN	0	-0.006	-0.006	31.463	-0.021	-0.021	0.000	0.000	0.000	0.000
17	A	11	GLN	0	-0.037	-0.024	34.835	0.005	0.005	0.000	0.000	0.000	0.000
18	A	12	VAL	0	-0.025	-0.005	37.418	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	13	LYS	1	0.902	0.940	40.150	0.034	0.034	0.000	0.000	0.000	0.000
20	A	14	PRO	0	0.078	0.032	43.548	0.001	0.001	0.000	0.000	0.000	0.000
21	A	15	GLU	-1	-0.930	-0.974	44.810	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	16	LYS	1	0.734	0.858	42.412	0.025	0.025	0.000	0.000	0.000	0.000
23	A	17	VAL	0	0.033	0.027	39.432	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	18	GLN	0	-0.001	0.002	39.749	0.004	0.004	0.000	0.000	0.000	0.000
25	A	19	GLU	-1	-0.826	-0.913	40.229	-0.022	-0.022	0.000	0.000	0.000	0.000
26	A	20	PHE	0	0.101	0.028	33.513	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	21	MET	0	0.025	0.016	35.331	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	22	ASN	0	-0.092	-0.050	35.542	0.001	0.001	0.000	0.000	0.000	0.000
29	A	23	LEU	0	0.012	0.018	35.629	0.000	0.000	0.000	0.000	0.000	0.000
30	A	24	CYS	0	0.019	0.004	31.917	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	25	LYS	1	0.888	0.950	31.144	0.000	0.000	0.000	0.000	0.000	0.000
32	A	26	SER	0	-0.035	-0.032	31.662	0.007	0.007	0.000	0.000	0.000	0.000
33	A	27	LEU	0	0.045	0.033	28.211	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	28	ILE	0	-0.028	-0.004	26.212	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	29	GLU	-1	-0.870	-0.916	26.076	0.006	0.006	0.000	0.000	0.000	0.000
36	A	30	GLU	-1	-0.850	-0.924	26.304	-0.043	-0.043	0.000	0.000	0.000	0.000
37	A	31	THR	0	-0.041	-0.030	22.396	-0.020	-0.020	0.000	0.000	0.000	0.000
38	A	32	LEU	0	-0.033	-0.018	21.532	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	33	LYS	1	0.724	0.851	21.418	0.037	0.037	0.000	0.000	0.000	0.000
40	A	34	GLU	-1	-0.809	-0.887	20.454	-0.187	-0.187	0.000	0.000	0.000	0.000
41	A	35	GLU	-1	-0.880	-0.934	14.234	-0.293	-0.293	0.000	0.000	0.000	0.000
42	A	36	GLY	0	-0.029	-0.032	13.686	-0.029	-0.029	0.000	0.000	0.000	0.000
43	A	37	CYS	0	0.001	0.013	14.762	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	38	ILE	0	-0.128	-0.061	11.786	0.007	0.007	0.000	0.000	0.000	0.000
45	A	39	ASP	-1	-0.898	-0.958	15.878	0.186	0.186	0.000	0.000	0.000	0.000
46	A	40	TYR	0	-0.031	-0.057	19.311	-0.044	-0.044	0.000	0.000	0.000	0.000
47	A	41	GLY	0	0.020	0.025	22.783	0.016	0.016	0.000	0.000	0.000	0.000
48	A	42	VAL	0	-0.021	-0.010	26.197	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	43	TYR	0	-0.016	-0.004	24.121	0.021	0.021	0.000	0.000	0.000	0.000
50	A	44	GLN	0	-0.040	-0.028	30.644	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	45	GLU	-1	-0.932	-0.957	33.193	0.031	0.031	0.000	0.000	0.000	0.000
52	A	46	LEU	0	-0.018	-0.002	32.766	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	47	GLU	-1	-0.934	-0.965	36.326	0.058	0.058	0.000	0.000	0.000	0.000
54	A	48	ASN	0	-0.061	-0.039	37.723	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	49	PRO	0	0.050	0.020	38.317	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	50	GLU	-1	-0.849	-0.923	39.028	0.012	0.012	0.000	0.000	0.000	0.000
57	A	51	ILE	0	-0.067	-0.030	34.419	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	52	LEU	0	0.002	0.008	34.038	0.008	0.008	0.000	0.000	0.000	0.000
59	A	53	THR	0	-0.022	-0.021	28.285	-0.016	-0.016	0.000	0.000	0.000	0.000
60	A	54	MET	0	-0.002	0.000	26.935	0.012	0.012	0.000	0.000	0.000	0.000
61	A	55	LEU	0	-0.071	-0.023	23.635	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	56	GLU	-1	-0.717	-0.835	21.236	-0.121	-0.121	0.000	0.000	0.000	0.000
63	A	57	GLU	-1	-0.881	-0.926	13.843	0.190	0.190	0.000	0.000	0.000	0.000
64	A	58	TRP	0	0.017	0.001	15.524	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	59	LYS	1	0.875	0.924	8.048	0.467	0.467	0.000	0.000	0.000	0.000
66	A	60	ASP	-1	-0.841	-0.907	10.659	-0.977	-0.977	0.000	0.000	0.000	0.000
67	A	61	GLU	-1	-0.781	-0.871	13.012	-0.521	-0.521	0.000	0.000	0.000	0.000
68	A	62	GLY	0	0.029	0.022	15.616	0.071	0.071	0.000	0.000	0.000	0.000
69	A	63	SER	0	-0.046	-0.040	14.216	0.085	0.085	0.000	0.000	0.000	0.000
70	A	64	LEU	0	0.003	0.016	17.057	0.056	0.056	0.000	0.000	0.000	0.000
71	A	65	ASP	-1	-0.834	-0.882	19.518	-0.291	-0.291	0.000	0.000	0.000	0.000
72	A	66	GLN	0	-0.023	-0.041	17.343	0.058	0.058	0.000	0.000	0.000	0.000
73	A	67	HIS	1	0.853	0.926	21.149	0.177	0.177	0.000	0.000	0.000	0.000
74	A	68	ILE	0	-0.038	-0.004	22.905	0.026	0.026	0.000	0.000	0.000	0.000
75	A	69	ARG	1	0.738	0.836	24.426	0.294	0.294	0.000	0.000	0.000	0.000
76	A	70	SER	0	-0.013	-0.009	25.036	0.021	0.021	0.000	0.000	0.000	0.000
77	A	71	ASP	-1	-0.859	-0.924	26.936	-0.124	-0.124	0.000	0.000	0.000	0.000
78	A	72	HIS	0	0.053	0.020	25.071	0.011	0.011	0.000	0.000	0.000	0.000
79	A	73	PHE	0	0.002	0.002	27.313	0.009	0.009	0.000	0.000	0.000	0.000
80	A	74	LYS	1	0.781	0.874	29.435	0.147	0.147	0.000	0.000	0.000	0.000
81	A	75	GLU	-1	-0.972	-0.978	32.008	-0.067	-0.067	0.000	0.000	0.000	0.000
82	A	76	ILE	0	-0.029	-0.019	31.598	0.007	0.007	0.000	0.000	0.000	0.000
83	A	77	PHE	0	0.008	0.014	31.391	0.005	0.005	0.000	0.000	0.000	0.000
84	A	78	PRO	0	-0.002	-0.004	33.454	0.005	0.005	0.000	0.000	0.000	0.000
85	A	79	LEU	0	0.046	0.026	37.072	0.005	0.005	0.000	0.000	0.000	0.000
86	A	80	LEU	0	-0.017	-0.013	32.579	0.006	0.006	0.000	0.000	0.000	0.000
87	A	81	SER	0	0.006	-0.008	36.008	0.003	0.003	0.000	0.000	0.000	0.000
88	A	82	GLU	-1	-0.947	-0.965	37.938	-0.044	-0.044	0.000	0.000	0.000	0.000
89	A	83	CYS	0	-0.102	-0.031	39.001	0.008	0.008	0.000	0.000	0.000	0.000
90	A	84	LEU	0	-0.023	-0.001	35.657	0.006	0.006	0.000	0.000	0.000	0.000
91	A	85	ASP	-1	-0.869	-0.923	40.308	-0.023	-0.023	0.000	0.000	0.000	0.000
92	A	86	LYS	1	0.754	0.874	35.625	0.050	0.050	0.000	0.000	0.000	0.000
93	A	87	GLU	-1	-0.841	-0.917	35.066	-0.089	-0.089	0.000	0.000	0.000	0.000
94	A	88	THR	0	-0.028	-0.024	32.030	0.003	0.003	0.000	0.000	0.000	0.000
95	A	89	GLU	-1	-0.819	-0.899	31.889	-0.057	-0.057	0.000	0.000	0.000	0.000
96	A	90	ILE	0	-0.025	-0.013	26.286	0.003	0.003	0.000	0.000	0.000	0.000
97	A	91	ASN	0	-0.072	-0.022	25.328	-0.021	-0.021	0.000	0.000	0.000	0.000
98	A	92	ILE	0	0.041	0.012	20.097	0.008	0.008	0.000	0.000	0.000	0.000
99	A	93	TYR	0	-0.034	-0.017	19.245	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	94	ARG	1	0.845	0.899	13.226	0.739	0.739	0.000	0.000	0.000	0.000
101	A	95	LYS	1	0.916	0.964	9.889	-0.898	-0.898	0.000	0.000	0.000	0.000
102	A	96	LYS	1	0.948	0.979	13.225	0.328	0.328	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:-5:ASN)