FMO DATABASE

FMODB ID: YZ712

Calculation Name: 2EBB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2EBB

Chain ID: A

ChEMBL ID:

UniProt ID: Q5KYG7

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	96
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-767081.371608
FMO2-HF: Nuclear repulsion	727431.072363
FMO2-HF: Total energy	-39650.299246
FMO2-MP2: Total energy	-39767.882832

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:3:MET)

Summations of interaction energy for fragment #1(A:3: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.
-13.454	-8.857	1.256	-2.194	-3.659	-0.017

Interaction energy analysis for fragmet #1(A:3:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.014

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	5	LEU	0	-0.044	-0.004	2.523	-7.265	-3.901	1.245	-1.935	-2.673	-0.017
4	A	6	THR	0	-0.033	-0.052	4.198	1.369	1.627	-0.001	-0.020	-0.237	0.000
5	A	7	GLU	-1	-0.893	-0.947	5.909	-0.577	-0.577	0.000	0.000	0.000	0.000
6	A	8	GLU	-1	-0.829	-0.926	9.467	-1.499	-1.499	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.841	-0.894	4.935	-5.868	-5.806	-0.001	-0.002	-0.059	0.000
8	A	10	VAL	0	-0.018	-0.011	8.471	0.289	0.289	0.000	0.000	0.000	0.000
9	A	11	GLN	0	-0.058	-0.036	10.622	0.244	0.244	0.000	0.000	0.000	0.000
10	A	12	ALA	0	0.011	0.011	12.144	0.136	0.136	0.000	0.000	0.000	0.000
11	A	13	LEU	0	-0.022	-0.009	8.902	0.122	0.122	0.000	0.000	0.000	0.000
12	A	14	LEU	0	-0.021	-0.022	13.206	0.162	0.162	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.914	-0.925	15.771	-0.582	-0.582	0.000	0.000	0.000	0.000
14	A	16	LYS	1	0.782	0.883	15.637	0.911	0.911	0.000	0.000	0.000	0.000
15	A	17	ALA	0	0.011	-0.004	16.469	0.012	0.012	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.825	-0.899	18.567	-0.334	-0.334	0.000	0.000	0.000	0.000
17	A	19	GLY	0	-0.063	-0.033	21.826	0.015	0.015	0.000	0.000	0.000	0.000
18	A	20	TRP	0	-0.011	-0.002	17.377	0.027	0.027	0.000	0.000	0.000	0.000
19	A	21	LYS	1	0.871	0.934	19.027	0.354	0.354	0.000	0.000	0.000	0.000
20	A	22	LEU	0	0.046	0.027	13.977	0.025	0.025	0.000	0.000	0.000	0.000
21	A	23	ALA	0	-0.004	-0.004	17.287	0.041	0.041	0.000	0.000	0.000	0.000
22	A	24	ASP	-1	-0.813	-0.901	17.287	-0.040	-0.040	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.821	-0.891	15.368	0.016	0.016	0.000	0.000	0.000	0.000
24	A	26	ARG	1	0.786	0.879	12.255	-0.185	-0.185	0.000	0.000	0.000	0.000
25	A	27	TRP	0	0.014	0.020	12.633	0.098	0.098	0.000	0.000	0.000	0.000
26	A	28	ILE	0	0.005	0.023	13.037	-0.077	-0.077	0.000	0.000	0.000	0.000
27	A	29	VAL	0	-0.022	-0.025	15.863	0.090	0.090	0.000	0.000	0.000	0.000
28	A	30	LYS	1	0.832	0.906	19.245	0.222	0.222	0.000	0.000	0.000	0.000
29	A	31	LYS	1	0.869	0.923	21.778	0.104	0.104	0.000	0.000	0.000	0.000
30	A	32	TYR	0	0.011	-0.018	20.925	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	33	ARG	1	0.963	0.986	26.974	0.087	0.087	0.000	0.000	0.000	0.000
32	A	34	PHE	0	0.032	0.026	27.329	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	35	GLN	0	0.067	0.022	33.007	0.003	0.003	0.000	0.000	0.000	0.000
34	A	36	ASP	-1	-0.790	-0.902	35.673	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	37	TYR	0	-0.017	-0.007	33.444	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	38	LEU	0	0.021	0.008	33.554	0.004	0.004	0.000	0.000	0.000	0.000
37	A	39	GLN	0	-0.016	-0.012	32.374	0.001	0.001	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.043	0.031	29.731	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	41	ILE	0	-0.006	-0.012	28.692	0.005	0.005	0.000	0.000	0.000	0.000
40	A	42	GLU	-1	-0.748	-0.827	28.867	0.018	0.018	0.000	0.000	0.000	0.000
41	A	43	PHE	0	-0.016	-0.016	22.812	0.005	0.005	0.000	0.000	0.000	0.000
42	A	44	VAL	0	0.006	-0.003	24.492	0.002	0.002	0.000	0.000	0.000	0.000
43	A	45	ARG	1	0.863	0.905	24.090	-0.019	-0.019	0.000	0.000	0.000	0.000
44	A	46	ARG	1	0.859	0.910	24.490	0.038	0.038	0.000	0.000	0.000	0.000
45	A	47	ILE	0	0.034	0.017	20.008	0.006	0.006	0.000	0.000	0.000	0.000
46	A	48	ALA	0	-0.004	0.027	19.506	0.020	0.020	0.000	0.000	0.000	0.000
47	A	49	ALA	0	-0.003	0.003	20.099	0.031	0.031	0.000	0.000	0.000	0.000
48	A	50	ILE	0	-0.016	-0.010	16.766	0.017	0.017	0.000	0.000	0.000	0.000
49	A	51	SER	0	-0.003	-0.022	15.665	0.005	0.005	0.000	0.000	0.000	0.000
50	A	52	GLU	-1	-0.882	-0.916	15.637	0.389	0.389	0.000	0.000	0.000	0.000
51	A	53	ASN	0	-0.016	-0.003	16.631	0.050	0.050	0.000	0.000	0.000	0.000
52	A	54	ALA	0	-0.046	-0.026	12.478	0.022	0.022	0.000	0.000	0.000	0.000
53	A	55	ASN	0	-0.099	-0.044	12.102	0.148	0.148	0.000	0.000	0.000	0.000
54	A	56	HIS	0	-0.073	-0.047	8.400	0.335	0.335	0.000	0.000	0.000	0.000
55	A	57	HIS	0	-0.034	-0.033	12.719	-0.074	-0.074	0.000	0.000	0.000	0.000
56	A	58	PRO	0	-0.012	0.009	15.233	0.040	0.040	0.000	0.000	0.000	0.000
57	A	59	PHE	0	-0.019	-0.005	16.522	0.014	0.014	0.000	0.000	0.000	0.000
58	A	60	ILE	0	0.015	-0.015	19.421	-0.048	-0.048	0.000	0.000	0.000	0.000
59	A	61	SER	0	0.005	0.006	22.565	0.015	0.015	0.000	0.000	0.000	0.000
60	A	62	ILE	0	-0.014	-0.020	26.116	-0.019	-0.019	0.000	0.000	0.000	0.000
61	A	63	ASP	-1	-0.883	-0.925	29.274	-0.019	-0.019	0.000	0.000	0.000	0.000
62	A	64	TYR	0	0.067	0.014	31.603	-0.014	-0.014	0.000	0.000	0.000	0.000
63	A	65	LYS	1	0.834	0.917	32.629	0.033	0.033	0.000	0.000	0.000	0.000
64	A	66	LEU	0	-0.077	-0.041	29.155	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	67	ILE	0	0.030	0.036	24.781	0.009	0.009	0.000	0.000	0.000	0.000
66	A	68	THR	0	-0.037	-0.012	23.504	-0.028	-0.028	0.000	0.000	0.000	0.000
67	A	69	VAL	0	0.017	0.012	18.392	0.028	0.028	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.839	0.900	17.597	-0.043	-0.043	0.000	0.000	0.000	0.000
69	A	71	LEU	0	0.002	0.012	12.399	0.070	0.070	0.000	0.000	0.000	0.000
70	A	72	SER	0	0.028	-0.018	10.824	-0.064	-0.064	0.000	0.000	0.000	0.000
71	A	73	SER	0	0.007	0.016	6.683	0.231	0.231	0.000	0.000	0.000	0.000
72	A	74	TRP	0	0.052	0.012	8.563	0.589	0.589	0.000	0.000	0.000	0.000
73	A	75	ARG	1	0.932	0.970	7.791	-1.600	-1.600	0.000	0.000	0.000	0.000
74	A	76	ALA	0	0.016	0.009	4.669	0.128	0.246	-0.001	-0.020	-0.097	0.000
75	A	77	LYS	1	0.891	0.945	6.460	-2.474	-2.474	0.000	0.000	0.000	0.000
76	A	78	GLY	0	0.025	0.006	9.047	-0.362	-0.362	0.000	0.000	0.000	0.000
77	A	79	LEU	0	-0.003	0.020	8.264	0.419	0.419	0.000	0.000	0.000	0.000
78	A	80	THR	0	-0.009	-0.025	3.418	-1.139	-0.547	0.015	-0.202	-0.406	0.000
79	A	81	LYS	1	0.892	0.911	4.653	1.558	1.761	-0.001	-0.015	-0.187	0.000
80	A	82	LEU	0	0.054	0.030	5.842	0.329	0.329	0.000	0.000	0.000	0.000
81	A	83	ASP	-1	-0.731	-0.834	7.817	0.240	0.240	0.000	0.000	0.000	0.000
82	A	84	PHE	0	0.057	0.002	9.564	0.111	0.111	0.000	0.000	0.000	0.000
83	A	85	ASP	-1	-0.853	-0.889	10.079	-0.941	-0.941	0.000	0.000	0.000	0.000
84	A	86	LEU	0	0.022	0.003	11.327	0.087	0.087	0.000	0.000	0.000	0.000
85	A	87	ALA	0	0.010	0.008	13.692	0.041	0.041	0.000	0.000	0.000	0.000
86	A	88	LYS	1	0.909	0.947	15.399	0.644	0.644	0.000	0.000	0.000	0.000
87	A	89	GLN	0	0.006	0.005	14.837	0.034	0.034	0.000	0.000	0.000	0.000
88	A	90	TYR	0	-0.002	-0.029	15.927	0.024	0.024	0.000	0.000	0.000	0.000
89	A	91	ASP	-1	-0.803	-0.870	19.709	-0.255	-0.255	0.000	0.000	0.000	0.000
90	A	92	GLU	-1	-0.826	-0.898	21.084	-0.173	-0.173	0.000	0.000	0.000	0.000
91	A	93	VAL	0	-0.036	-0.017	22.078	0.022	0.022	0.000	0.000	0.000	0.000
92	A	94	TYR	0	-0.022	-0.034	23.992	0.006	0.006	0.000	0.000	0.000	0.000
93	A	95	ASN	0	-0.032	0.002	24.797	0.014	0.014	0.000	0.000	0.000	0.000
94	A	96	GLN	0	-0.009	-0.013	26.542	0.022	0.022	0.000	0.000	0.000	0.000
95	A	97	MET	0	-0.099	-0.025	28.473	0.015	0.015	0.000	0.000	0.000	0.000
96	A	98	LYS	1	0.784	0.893	27.680	0.151	0.151	0.000	0.000	0.000	0.000

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Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:3:MET)