FMO DATABASE

FMODB ID: 2N8MR

Calculation Name: 3E0E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E0E

Chain ID: A

ChEMBL ID:

UniProt ID: Q6LYF9

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	97
LigandResidueName
LigandFragmentNumber	0
LigandCharge	DLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-679052.269915
FMO2-HF: Nuclear repulsion	641800.449033
FMO2-HF: Total energy	-37251.820882
FMO2-MP2: Total energy	-37361.341868

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:0:MET)

Summations of interaction energy for fragment #1(A:0: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.
-20.037	-12.979	8.531	-5.283	-10.306	-0.039

Interaction energy analysis for fragmet #1(A:0:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.039 / q_NPA : -0.023

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	2	TYR	0	-0.014	-0.018	2.434	-9.726	-5.175	6.824	-3.602	-7.773	-0.015
4	A	3	LYS	1	0.906	0.964	3.543	4.260	4.537	0.007	0.063	-0.348	0.000
5	A	4	ILE	0	-0.016	-0.031	5.765	0.009	0.009	0.000	0.000	0.000	0.000
6	A	5	SER	0	-0.074	-0.036	8.101	0.175	0.175	0.000	0.000	0.000	0.000
7	A	6	GLU	-1	-0.861	-0.939	2.626	-12.550	-10.320	1.700	-1.744	-2.185	-0.024
8	A	7	LEU	0	-0.055	-0.012	5.994	0.597	0.597	0.000	0.000	0.000	0.000
9	A	8	MET	0	-0.007	0.000	7.808	0.370	0.370	0.000	0.000	0.000	0.000
10	A	9	PRO	0	-0.017	-0.036	10.458	-0.080	-0.080	0.000	0.000	0.000	0.000
11	A	10	ASN	0	-0.053	-0.033	13.064	0.073	0.073	0.000	0.000	0.000	0.000
12	A	11	LEU	0	0.026	0.046	5.930	0.153	0.153	0.000	0.000	0.000	0.000
13	A	12	SER	0	-0.015	-0.017	8.848	-0.014	-0.014	0.000	0.000	0.000	0.000
14	A	13	GLY	0	0.013	0.007	5.999	-0.214	-0.214	0.000	0.000	0.000	0.000
15	A	14	THR	0	0.038	0.032	5.617	0.888	0.888	0.000	0.000	0.000	0.000
16	A	15	ILE	0	0.005	0.028	5.843	-1.323	-1.323	0.000	0.000	0.000	0.000
17	A	16	ASN	0	0.015	0.006	8.246	0.444	0.444	0.000	0.000	0.000	0.000
18	A	17	ALA	0	-0.037	-0.025	10.907	-0.067	-0.067	0.000	0.000	0.000	0.000
19	A	18	GLU	-1	-0.889	-0.931	13.197	-0.509	-0.509	0.000	0.000	0.000	0.000
20	A	19	VAL	0	-0.011	-0.004	16.817	-0.022	-0.022	0.000	0.000	0.000	0.000
21	A	20	VAL	0	0.005	0.006	18.526	0.070	0.070	0.000	0.000	0.000	0.000
22	A	21	THR	0	-0.073	-0.058	21.107	0.067	0.067	0.000	0.000	0.000	0.000
23	A	22	ALA	0	0.067	0.045	22.263	-0.039	-0.039	0.000	0.000	0.000	0.000
24	A	23	TYR	0	-0.055	-0.030	23.090	0.025	0.025	0.000	0.000	0.000	0.000
25	A	24	PRO	0	0.006	-0.007	27.105	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	25	LYS	1	0.822	0.897	28.386	0.180	0.180	0.000	0.000	0.000	0.000
27	A	26	LYS	1	0.880	0.950	28.276	0.277	0.277	0.000	0.000	0.000	0.000
28	A	27	GLU	-1	-0.833	-0.919	30.213	-0.159	-0.159	0.000	0.000	0.000	0.000
29	A	28	PHE	0	-0.036	-0.019	28.148	0.005	0.005	0.000	0.000	0.000	0.000
30	A	29	SER	0	0.028	0.012	33.717	0.002	0.002	0.000	0.000	0.000	0.000
31	A	30	ARG	1	0.816	0.904	28.248	0.119	0.119	0.000	0.000	0.000	0.000
32	A	31	LYS	1	0.921	0.955	29.338	0.125	0.125	0.000	0.000	0.000	0.000
33	A	32	ASP	-1	-0.806	-0.912	30.020	-0.113	-0.113	0.000	0.000	0.000	0.000
34	A	33	GLY	0	0.063	0.053	33.434	0.010	0.010	0.000	0.000	0.000	0.000
35	A	34	THR	0	0.003	-0.024	32.511	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	35	DLY	1	0.825	0.935	32.572	0.130	0.130	0.000	0.000	0.000	0.000
37	A	36	GLY	0	0.033	0.013	29.486	0.001	0.001	0.000	0.000	0.000	0.000
38	A	37	GLN	0	-0.030	0.000	27.862	0.016	0.016	0.000	0.000	0.000	0.000
39	A	38	LEU	0	-0.005	0.020	23.483	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	39	LYS	1	0.931	0.978	23.957	0.337	0.337	0.000	0.000	0.000	0.000
41	A	40	SER	0	-0.047	-0.015	22.201	-0.023	-0.023	0.000	0.000	0.000	0.000
42	A	41	LEU	0	0.045	0.026	18.584	0.037	0.037	0.000	0.000	0.000	0.000
43	A	42	PHE	0	-0.020	-0.003	19.003	-0.030	-0.030	0.000	0.000	0.000	0.000
44	A	43	LEU	0	0.022	0.006	14.259	0.046	0.046	0.000	0.000	0.000	0.000
45	A	44	LYS	1	0.967	0.976	14.417	0.674	0.674	0.000	0.000	0.000	0.000
46	A	45	ASP	-1	-0.700	-0.819	9.150	-2.053	-2.053	0.000	0.000	0.000	0.000
47	A	46	ASP	-1	-0.917	-0.974	10.723	-1.450	-1.450	0.000	0.000	0.000	0.000
48	A	47	THR	0	-0.067	-0.037	8.620	-0.040	-0.040	0.000	0.000	0.000	0.000
49	A	48	GLY	0	0.033	0.008	11.475	0.107	0.107	0.000	0.000	0.000	0.000
50	A	49	SER	0	-0.021	-0.015	13.247	0.003	0.003	0.000	0.000	0.000	0.000
51	A	50	ILE	0	-0.019	0.002	12.236	0.035	0.035	0.000	0.000	0.000	0.000
52	A	51	ARG	1	0.841	0.924	15.159	0.447	0.447	0.000	0.000	0.000	0.000
53	A	52	GLY	0	0.067	0.035	16.579	-0.062	-0.062	0.000	0.000	0.000	0.000
54	A	53	THR	0	-0.101	-0.059	17.416	0.094	0.094	0.000	0.000	0.000	0.000
55	A	54	LEU	0	0.063	0.041	18.985	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	55	TRP	0	0.053	0.002	20.211	0.064	0.064	0.000	0.000	0.000	0.000
57	A	56	ASN	0	0.000	-0.022	23.332	0.008	0.008	0.000	0.000	0.000	0.000
58	A	57	GLU	-1	-0.807	-0.902	23.647	-0.178	-0.178	0.000	0.000	0.000	0.000
59	A	58	LEU	0	0.061	0.037	18.735	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	59	ALA	0	-0.094	-0.047	22.883	-0.029	-0.029	0.000	0.000	0.000	0.000
61	A	60	ASP	-1	-0.822	-0.928	25.283	-0.197	-0.197	0.000	0.000	0.000	0.000
62	A	61	PHE	0	-0.019	0.009	20.307	0.010	0.010	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.976	-0.993	24.322	-0.235	-0.235	0.000	0.000	0.000	0.000
64	A	63	VAL	0	0.011	0.010	20.591	-0.019	-0.019	0.000	0.000	0.000	0.000
65	A	64	LYS	1	0.894	0.939	23.564	0.290	0.290	0.000	0.000	0.000	0.000
66	A	65	LYS	1	0.903	0.944	23.142	0.383	0.383	0.000	0.000	0.000	0.000
67	A	66	GLY	0	0.001	-0.012	22.132	0.038	0.038	0.000	0.000	0.000	0.000
68	A	67	ASP	-1	-0.796	-0.877	20.586	-0.398	-0.398	0.000	0.000	0.000	0.000
69	A	68	ILE	0	0.000	0.010	15.188	-0.077	-0.077	0.000	0.000	0.000	0.000
70	A	69	ALA	0	-0.014	-0.022	15.830	0.078	0.078	0.000	0.000	0.000	0.000
71	A	70	GLU	-1	-0.894	-0.940	9.765	-0.901	-0.901	0.000	0.000	0.000	0.000
72	A	71	VAL	0	-0.055	-0.043	11.563	0.220	0.220	0.000	0.000	0.000	0.000
73	A	72	SER	0	0.027	-0.012	9.103	-0.257	-0.257	0.000	0.000	0.000	0.000
74	A	73	GLY	0	0.028	0.008	10.256	0.247	0.247	0.000	0.000	0.000	0.000
75	A	74	TYR	0	0.004	0.027	10.728	-0.176	-0.176	0.000	0.000	0.000	0.000
76	A	75	VAL	0	0.004	0.008	9.831	0.041	0.041	0.000	0.000	0.000	0.000
77	A	76	LYS	1	0.869	0.929	12.872	0.534	0.534	0.000	0.000	0.000	0.000
78	A	77	GLN	0	0.031	0.000	16.271	-0.039	-0.039	0.000	0.000	0.000	0.000
79	A	78	GLY	0	-0.057	-0.030	18.666	0.033	0.033	0.000	0.000	0.000	0.000
80	A	79	TYR	0	-0.051	-0.035	21.251	0.006	0.006	0.000	0.000	0.000	0.000
81	A	80	SER	0	0.001	-0.009	20.476	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	81	GLY	0	0.048	0.030	18.444	0.021	0.021	0.000	0.000	0.000	0.000
83	A	82	LEU	0	0.008	0.026	12.307	0.057	0.057	0.000	0.000	0.000	0.000
84	A	83	GLU	-1	-0.783	-0.895	15.918	-0.442	-0.442	0.000	0.000	0.000	0.000
85	A	84	ILE	0	0.040	0.032	10.574	0.017	0.017	0.000	0.000	0.000	0.000
86	A	85	SER	0	-0.061	-0.039	14.431	0.076	0.076	0.000	0.000	0.000	0.000
87	A	86	VAL	0	-0.056	-0.030	15.066	-0.044	-0.044	0.000	0.000	0.000	0.000
88	A	87	ASP	-1	-0.892	-0.942	13.380	-0.406	-0.406	0.000	0.000	0.000	0.000
89	A	88	ASN	0	-0.027	-0.035	13.412	0.167	0.167	0.000	0.000	0.000	0.000
90	A	89	ILE	0	-0.028	-0.014	14.239	-0.137	-0.137	0.000	0.000	0.000	0.000
91	A	90	GLY	0	0.018	0.026	15.651	0.108	0.108	0.000	0.000	0.000	0.000
92	A	91	ILE	0	-0.054	-0.030	16.332	-0.093	-0.093	0.000	0.000	0.000	0.000
93	A	92	ILE	0	-0.023	0.001	12.549	0.052	0.052	0.000	0.000	0.000	0.000
94	A	93	GLU	-1	-0.934	-0.974	16.417	-0.371	-0.371	0.000	0.000	0.000	0.000
95	A	94	LYS	1	0.896	0.944	19.431	0.224	0.224	0.000	0.000	0.000	0.000
96	A	95	SER	0	-0.006	-0.008	22.726	0.011	0.011	0.000	0.000	0.000	0.000
97	A	96	LEU	0	-0.033	-0.003	24.304	0.017	0.017	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:0:MET)