FMO DATABASE

FMODB ID: 4JYLN

Calculation Name: 2HJD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HJD

Chain ID: A

ChEMBL ID:

UniProt ID: Q20HX4

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	OptHSide
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	89
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-537251.721598
FMO2-HF: Nuclear repulsion	503184.28886
FMO2-HF: Total energy	-34067.432738
FMO2-MP2: Total energy	-34166.793765

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:12:PHE)

Summations of interaction energy for fragment #1(A:12:PHE)

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.
-33.063	-27.205	21.787	-7.606	-20.039	-0.014

Interaction energy analysis for fragmet #1(A:12:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.025

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	14	LEU	0	0.029	0.019	3.474	0.853	2.377	-0.002	-0.619	-0.903	0.000
4	A	15	ARG	1	0.920	0.945	2.303	-18.519	-20.052	8.277	-2.435	-4.310	0.015
5	A	16	PRO	0	0.029	0.007	4.156	0.236	0.396	-0.001	-0.004	-0.155	0.000
6	A	17	VAL	0	0.037	0.022	4.997	-0.053	-0.053	0.000	0.000	0.000	0.000
7	A	18	ILE	0	-0.013	0.005	2.217	-1.970	-1.284	3.818	-0.757	-3.746	0.007
8	A	19	GLY	0	-0.050	-0.026	6.003	-0.585	-0.585	0.000	0.000	0.000	0.000
9	A	20	LEU	0	-0.011	-0.014	9.188	-0.237	-0.237	0.000	0.000	0.000	0.000
10	A	21	THR	0	0.005	0.001	7.928	-0.177	-0.177	0.000	0.000	0.000	0.000
11	A	22	ARG	1	0.943	0.975	7.230	-1.328	-1.328	0.000	0.000	0.000	0.000
12	A	23	GLY	0	-0.018	-0.009	10.525	-0.039	-0.039	0.000	0.000	0.000	0.000
13	A	24	LEU	0	-0.014	0.015	11.322	-0.046	-0.046	0.000	0.000	0.000	0.000
14	A	25	SER	0	-0.027	-0.034	12.140	-0.048	-0.048	0.000	0.000	0.000	0.000
15	A	26	SER	0	0.045	-0.003	10.977	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	27	ALA	0	0.048	0.031	12.021	-0.085	-0.085	0.000	0.000	0.000	0.000
17	A	28	ASP	-1	-0.812	-0.873	13.725	-0.262	-0.262	0.000	0.000	0.000	0.000
18	A	29	ILE	0	0.011	-0.003	7.432	-0.026	-0.026	0.000	0.000	0.000	0.000
19	A	30	GLU	-1	-0.834	-0.912	10.408	-0.787	-0.787	0.000	0.000	0.000	0.000
20	A	31	THR	0	-0.050	-0.029	11.964	0.006	0.006	0.000	0.000	0.000	0.000
21	A	32	LEU	0	-0.033	-0.018	11.002	0.014	0.014	0.000	0.000	0.000	0.000
22	A	33	THR	0	0.009	-0.008	8.968	-0.131	-0.131	0.000	0.000	0.000	0.000
23	A	34	ALA	0	0.000	-0.001	10.839	0.012	0.012	0.000	0.000	0.000	0.000
24	A	35	ASN	0	-0.021	-0.021	14.410	0.046	0.046	0.000	0.000	0.000	0.000
25	A	36	ALA	0	0.030	0.025	10.991	0.045	0.045	0.000	0.000	0.000	0.000
26	A	37	ILE	0	0.027	0.011	11.501	0.039	0.039	0.000	0.000	0.000	0.000
27	A	38	ARG	1	0.898	0.943	14.089	0.480	0.480	0.000	0.000	0.000	0.000
28	A	39	LEU	0	0.021	0.021	14.881	0.035	0.035	0.000	0.000	0.000	0.000
29	A	40	HIS	0	0.013	0.004	13.963	0.016	0.016	0.000	0.000	0.000	0.000
30	A	41	ARG	1	0.923	0.951	16.019	0.565	0.565	0.000	0.000	0.000	0.000
31	A	42	GLN	0	-0.012	-0.006	19.149	0.023	0.023	0.000	0.000	0.000	0.000
32	A	43	LEU	0	0.010	0.006	16.177	0.027	0.027	0.000	0.000	0.000	0.000
33	A	44	LEU	0	-0.024	-0.012	17.919	0.020	0.020	0.000	0.000	0.000	0.000
34	A	45	GLU	-1	-0.854	-0.906	20.802	-0.210	-0.210	0.000	0.000	0.000	0.000
35	A	46	LYS	1	0.838	0.934	23.172	0.202	0.202	0.000	0.000	0.000	0.000
36	A	47	ALA	0	0.007	-0.015	22.180	0.023	0.023	0.000	0.000	0.000	0.000
37	A	48	ASP	-1	-0.874	-0.944	24.218	-0.231	-0.231	0.000	0.000	0.000	0.000
38	A	49	GLN	0	-0.119	-0.074	26.516	0.026	0.026	0.000	0.000	0.000	0.000
39	A	50	LEU	0	-0.032	-0.024	26.213	0.012	0.012	0.000	0.000	0.000	0.000
40	A	51	PHE	0	0.009	0.009	27.382	0.014	0.014	0.000	0.000	0.000	0.000
41	A	52	GLN	0	-0.029	-0.015	29.165	0.022	0.022	0.000	0.000	0.000	0.000
42	A	53	VAL	0	-0.060	-0.034	32.435	0.010	0.010	0.000	0.000	0.000	0.000
43	A	54	LEU	0	-0.026	0.024	29.380	0.009	0.009	0.000	0.000	0.000	0.000
44	A	55	PRO	0	0.010	0.002	33.877	0.000	0.000	0.000	0.000	0.000	0.000
45	A	56	ASP	-1	-0.862	-0.944	35.348	-0.102	-0.102	0.000	0.000	0.000	0.000
46	A	57	ASP	-1	-0.906	-0.963	36.355	-0.079	-0.079	0.000	0.000	0.000	0.000
47	A	58	ILE	0	0.008	-0.014	31.582	0.001	0.001	0.000	0.000	0.000	0.000
48	A	59	LYS	1	0.789	0.916	31.553	0.114	0.114	0.000	0.000	0.000	0.000
49	A	60	ILE	0	-0.074	-0.031	31.756	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	61	GLY	0	0.029	0.019	32.777	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	62	THR	0	-0.137	-0.058	33.474	0.006	0.006	0.000	0.000	0.000	0.000
52	A	63	ALA	0	-0.020	-0.013	35.517	0.007	0.007	0.000	0.000	0.000	0.000
53	A	64	ALA	0	0.001	0.000	31.335	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	65	GLY	0	0.004	0.010	32.587	0.008	0.008	0.000	0.000	0.000	0.000
55	A	66	GLY	0	0.024	0.009	33.472	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	67	GLU	-1	-0.906	-0.972	32.631	-0.066	-0.066	0.000	0.000	0.000	0.000
57	A	68	GLN	0	0.034	0.009	31.630	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	69	HIS	0	0.061	0.037	28.605	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	70	LEU	0	-0.011	-0.013	28.122	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	71	GLU	-1	-0.783	-0.888	26.696	-0.149	-0.149	0.000	0.000	0.000	0.000
61	A	72	TYR	0	-0.008	-0.008	24.622	-0.013	-0.013	0.000	0.000	0.000	0.000
62	A	73	ILE	0	-0.027	-0.018	23.534	-0.022	-0.022	0.000	0.000	0.000	0.000
63	A	74	GLU	-1	-0.941	-0.970	22.305	-0.127	-0.127	0.000	0.000	0.000	0.000
64	A	75	ALA	0	0.013	0.015	21.059	-0.023	-0.023	0.000	0.000	0.000	0.000
65	A	76	MET	0	-0.020	-0.006	20.133	-0.046	-0.046	0.000	0.000	0.000	0.000
66	A	77	ILE	0	-0.045	-0.018	17.669	-0.049	-0.049	0.000	0.000	0.000	0.000
67	A	78	GLU	-1	-0.934	-0.965	16.372	-0.293	-0.293	0.000	0.000	0.000	0.000
68	A	79	MET	0	-0.030	-0.006	15.502	-0.099	-0.099	0.000	0.000	0.000	0.000
69	A	80	HIS	0	0.041	-0.009	14.057	-0.139	-0.139	0.000	0.000	0.000	0.000
70	A	81	ALA	0	-0.012	0.005	12.068	-0.127	-0.127	0.000	0.000	0.000	0.000
71	A	82	GLN	0	0.004	0.004	10.631	-0.160	-0.160	0.000	0.000	0.000	0.000
72	A	83	MET	0	0.032	0.020	10.444	-0.153	-0.153	0.000	0.000	0.000	0.000
73	A	84	SER	0	-0.007	0.003	6.848	-0.282	-0.282	0.000	0.000	0.000	0.000
74	A	85	ALA	0	-0.016	-0.012	5.503	-0.691	-0.691	0.000	0.000	0.000	0.000
75	A	86	VAL	0	-0.023	-0.010	6.599	-0.397	-0.397	0.000	0.000	0.000	0.000
76	A	87	ASN	0	-0.014	-0.018	5.433	-0.123	-0.123	0.000	0.000	0.000	0.000
77	A	88	THR	0	-0.069	-0.039	2.156	-4.261	-2.928	4.157	-1.904	-3.585	-0.009
78	A	89	LEU	0	-0.005	-0.013	2.646	-2.854	-1.620	0.857	-0.448	-1.644	-0.015
79	A	90	VAL	0	0.028	0.015	5.404	-0.087	-0.087	0.000	0.000	0.000	0.000
80	A	91	GLY	0	-0.016	-0.006	2.611	0.366	0.748	0.578	-0.152	-0.808	-0.002
81	A	92	LEU	0	-0.089	-0.047	2.516	-3.753	-1.625	4.055	-1.474	-4.709	-0.010
82	A	93	LEU	0	-0.054	-0.006	3.311	1.213	1.157	0.048	0.187	-0.179	0.000
83	A	94	GLY	0	-0.005	0.006	5.746	0.409	0.409	0.000	0.000	0.000	0.000
84	A	95	PHE	0	-0.046	-0.033	7.168	0.339	0.339	0.000	0.000	0.000	0.000
85	A	96	ILE	0	0.028	0.019	9.518	-0.127	-0.127	0.000	0.000	0.000	0.000
86	A	97	PRO	0	0.000	0.020	10.846	0.145	0.145	0.000	0.000	0.000	0.000
87	A	98	LYS	1	0.867	0.934	13.839	0.568	0.568	0.000	0.000	0.000	0.000
88	A	99	VAL	0	-0.020	-0.033	15.798	0.000	0.000	0.000	0.000	0.000	0.000
89	A	100	SER	0	0.012	0.025	18.865	0.037	0.037	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:12:PHE)