FMO DATABASE

FMODB ID: Z2Q3N

Calculation Name: 2JD3-A-Xray311

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2JD3

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	92
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-548455.433806
FMO2-HF: Nuclear repulsion	513332.810413
FMO2-HF: Total energy	-35122.623393
FMO2-MP2: Total energy	-35227.234967

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:ACE )

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

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.
1.043	2.179	0.002	-0.608	-0.53	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / 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

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	7	ARG	1	0.959	0.977	3.552	0.469	1.605	0.002	-0.608	-0.530	0.001
4	A	8	LYS	1	0.943	0.992	5.620	0.305	0.305	0.000	0.000	0.000	0.000
5	A	9	LYS	1	0.996	0.993	9.026	0.272	0.272	0.000	0.000	0.000	0.000
6	A	10	TYR	0	0.023	-0.007	11.756	-0.051	-0.051	0.000	0.000	0.000	0.000
7	A	11	THR	0	-0.018	-0.005	15.664	0.020	0.020	0.000	0.000	0.000	0.000
8	A	12	LEU	0	0.003	0.009	19.065	-0.007	-0.007	0.000	0.000	0.000	0.000
9	A	13	TYR	0	-0.017	-0.023	22.144	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	14	LEU	0	0.019	0.032	25.737	0.001	0.001	0.000	0.000	0.000	0.000
11	A	15	HIS	0	-0.076	-0.062	28.283	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	16	PRO	0	0.043	0.017	31.490	0.002	0.002	0.000	0.000	0.000	0.000
13	A	17	GLU	-1	-0.890	-0.943	33.911	-0.017	-0.017	0.000	0.000	0.000	0.000
14	A	18	LYS	1	0.883	0.943	33.950	0.019	0.019	0.000	0.000	0.000	0.000
15	A	19	ALA	0	0.065	0.031	35.520	0.001	0.001	0.000	0.000	0.000	0.000
16	A	20	ALA	0	0.071	0.038	32.397	0.002	0.002	0.000	0.000	0.000	0.000
17	A	21	ASP	-1	-0.808	-0.896	30.650	-0.011	-0.011	0.000	0.000	0.000	0.000
18	A	22	PHE	0	-0.010	-0.003	31.166	0.002	0.002	0.000	0.000	0.000	0.000
19	A	23	GLN	0	0.047	0.007	33.059	0.000	0.000	0.000	0.000	0.000	0.000
20	A	24	THR	0	-0.078	-0.049	27.063	0.005	0.005	0.000	0.000	0.000	0.000
21	A	25	LEU	0	-0.031	-0.026	28.372	0.004	0.004	0.000	0.000	0.000	0.000
22	A	26	GLU	-1	-0.881	-0.929	29.702	0.017	0.017	0.000	0.000	0.000	0.000
23	A	27	ALA	0	0.000	0.005	28.635	0.004	0.004	0.000	0.000	0.000	0.000
24	A	28	ILE	0	-0.091	-0.052	23.874	0.006	0.006	0.000	0.000	0.000	0.000
25	A	29	GLU	-1	-0.894	-0.965	26.771	0.023	0.023	0.000	0.000	0.000	0.000
26	A	30	SER	0	-0.125	-0.039	29.150	0.004	0.004	0.000	0.000	0.000	0.000
27	A	31	VAL	0	0.027	0.022	23.639	0.007	0.007	0.000	0.000	0.000	0.000
28	A	32	PRO	0	0.036	0.027	24.731	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	33	ARG	1	0.972	0.960	22.826	-0.018	-0.018	0.000	0.000	0.000	0.000
30	A	34	SER	0	-0.009	-0.003	20.037	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	35	GLU	-1	-0.883	-0.948	18.755	0.111	0.111	0.000	0.000	0.000	0.000
32	A	36	ARG	1	0.856	0.930	19.407	-0.031	-0.031	0.000	0.000	0.000	0.000
33	A	37	GLY	0	-0.014	0.006	15.967	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	38	GLU	-1	-0.961	-0.985	14.579	0.276	0.276	0.000	0.000	0.000	0.000
35	A	39	LEU	0	0.008	0.013	16.149	0.000	0.000	0.000	0.000	0.000	0.000
36	A	40	PHE	0	0.016	-0.011	17.275	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	41	ARG	1	0.950	0.983	10.578	-0.282	-0.282	0.000	0.000	0.000	0.000
38	A	42	ASN	0	0.030	0.013	15.457	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	43	ALA	0	0.042	0.054	17.628	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	44	PHE	0	-0.017	-0.002	15.393	-0.016	-0.016	0.000	0.000	0.000	0.000
41	A	45	ILE	0	-0.034	-0.028	12.658	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	46	SER	0	-0.014	-0.033	17.005	-0.011	-0.011	0.000	0.000	0.000	0.000
43	A	47	GLY	0	0.059	0.039	20.386	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	48	MET	0	-0.036	-0.033	17.861	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	49	ALA	0	-0.011	-0.002	19.905	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	50	LEU	0	0.020	0.001	21.120	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	51	HIS	0	0.000	-0.002	22.126	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	52	GLN	0	-0.094	-0.056	18.804	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	53	LEU	0	-0.039	-0.002	23.669	0.000	0.000	0.000	0.000	0.000	0.000
50	A	54	ASP	-1	-0.784	-0.899	26.714	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	55	PRO	0	0.004	0.009	27.073	0.001	0.001	0.000	0.000	0.000	0.000
52	A	56	ARG	1	0.867	0.924	28.095	0.009	0.009	0.000	0.000	0.000	0.000
53	A	57	LEU	0	0.038	0.024	28.488	0.002	0.002	0.000	0.000	0.000	0.000
54	A	58	PRO	0	-0.014	0.007	25.439	0.002	0.002	0.000	0.000	0.000	0.000
55	A	59	VAL	0	-0.006	0.001	27.846	0.000	0.000	0.000	0.000	0.000	0.000
56	A	60	LEU	0	0.002	-0.011	30.649	0.001	0.001	0.000	0.000	0.000	0.000
57	A	61	LEU	0	-0.014	-0.009	28.284	0.002	0.002	0.000	0.000	0.000	0.000
58	A	62	THR	0	-0.025	-0.008	29.028	0.001	0.001	0.000	0.000	0.000	0.000
59	A	63	ALA	0	-0.061	-0.040	31.423	0.001	0.001	0.000	0.000	0.000	0.000
60	A	64	ILE	0	-0.043	-0.014	34.496	0.000	0.000	0.000	0.000	0.000	0.000
61	A	65	LEU	0	-0.083	-0.021	31.729	0.002	0.002	0.000	0.000	0.000	0.000
62	A	66	SER	0	0.045	0.027	34.819	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	67	GLU	-1	-0.924	-0.961	36.616	0.015	0.015	0.000	0.000	0.000	0.000
64	A	68	GLU	-1	-0.901	-0.941	38.434	0.016	0.016	0.000	0.000	0.000	0.000
65	A	69	PHE	0	-0.138	-0.050	30.750	0.001	0.001	0.000	0.000	0.000	0.000
66	A	70	SER	0	0.064	0.018	36.067	0.002	0.002	0.000	0.000	0.000	0.000
67	A	71	ALA	0	0.017	-0.004	33.643	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	72	ASP	-1	-0.912	-0.960	34.676	0.017	0.017	0.000	0.000	0.000	0.000
69	A	73	GLN	0	0.083	0.035	36.186	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	74	VAL	0	-0.011	0.002	30.309	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	75	VAL	0	-0.006	-0.007	33.527	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	76	THR	0	0.005	0.003	35.058	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	77	LEU	0	-0.018	-0.013	33.721	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	78	LEU	0	0.009	0.000	29.888	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	79	SER	0	-0.041	-0.015	33.463	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	80	GLN	0	-0.019	-0.020	36.542	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	81	THR	0	-0.052	-0.015	31.932	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	82	THR	0	-0.074	-0.021	31.511	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	83	GLY	0	-0.006	0.002	33.832	0.000	0.000	0.000	0.000	0.000	0.000
80	A	84	TRP	0	-0.037	-0.025	33.702	0.001	0.001	0.000	0.000	0.000	0.000
81	A	85	LYS	1	0.977	0.970	36.121	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	86	PRO	0	0.014	0.025	38.695	0.002	0.002	0.000	0.000	0.000	0.000
83	A	87	SER	0	0.048	0.017	39.250	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	88	GLN	0	0.037	0.019	41.489	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	89	ALA	0	-0.097	-0.046	40.202	0.000	0.000	0.000	0.000	0.000	0.000
86	A	90	ASP	-1	-0.816	-0.923	42.341	0.018	0.018	0.000	0.000	0.000	0.000
87	A	91	ILE	0	-0.007	-0.006	45.575	0.000	0.000	0.000	0.000	0.000	0.000
88	A	92	ARG	1	0.918	0.954	41.367	-0.031	-0.031	0.000	0.000	0.000	0.000
89	A	93	ALA	0	0.074	0.040	44.696	0.000	0.000	0.000	0.000	0.000	0.000
90	A	94	VAL	0	-0.073	-0.018	46.350	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	95	LEU	0	-0.096	-0.038	48.228	0.000	0.000	0.000	0.000	0.000	0.000
92	A	96	NME	0	0.003	0.004	47.412	-0.001	-0.001	0.000	0.000	0.000	0.000

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