FMO DATABASE

FMODB ID: 2JLVR

Calculation Name: 4L8R-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4L8R

Chain ID: C

ChEMBL ID:

UniProt ID: Q8IV48

Base Structure: X-ray

Registration Date: 2023-06-22

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	73
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-503691.636471
FMO2-HF: Nuclear repulsion	472701.424116
FMO2-HF: Total energy	-30990.212355
FMO2-MP2: Total energy	-31083.018293

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(C:127:ASP)

Summations of interaction energy for fragment #1(C:127:ASP)

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.
-189.445	-183.826	0.073	-2.973	-2.72	0.015

Interaction energy analysis for fragmet #1(C:127:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.830 / q_NPA : -0.908

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	C	129	GLU	-1	-0.886	-0.942	3.597	44.821	49.602	0.070	-2.672	-2.179	0.014
4	C	130	THR	0	0.065	0.020	4.112	-4.124	-3.914	-0.001	-0.045	-0.164	0.000
5	C	131	ASP	-1	-0.811	-0.872	6.754	21.706	21.706	0.000	0.000	0.000	0.000
6	C	132	GLU	-1	-0.797	-0.915	9.725	21.889	21.889	0.000	0.000	0.000	0.000
7	C	133	SER	0	-0.030	-0.031	12.955	-1.997	-1.997	0.000	0.000	0.000	0.000
8	C	134	VAL	0	-0.092	-0.049	11.025	-2.035	-2.035	0.000	0.000	0.000	0.000
9	C	135	LEU	0	-0.002	0.001	9.467	-2.054	-2.054	0.000	0.000	0.000	0.000
10	C	136	MET	0	0.017	0.008	13.327	-1.947	-1.947	0.000	0.000	0.000	0.000
11	C	137	ARG	1	0.931	0.975	14.271	-21.267	-21.267	0.000	0.000	0.000	0.000
12	C	138	ARG	1	0.794	0.892	10.026	-28.699	-28.699	0.000	0.000	0.000	0.000
13	C	139	GLN	0	0.038	0.014	16.899	0.086	0.086	0.000	0.000	0.000	0.000
14	C	140	LYS	1	0.976	1.009	18.405	-13.773	-13.773	0.000	0.000	0.000	0.000
15	C	141	GLN	0	-0.014	-0.018	18.932	-0.034	-0.034	0.000	0.000	0.000	0.000
16	C	142	ILE	0	0.006	-0.001	17.135	-0.666	-0.666	0.000	0.000	0.000	0.000
17	C	143	ASN	0	0.038	0.018	21.529	-0.328	-0.328	0.000	0.000	0.000	0.000
18	C	144	TYR	0	0.025	0.009	24.082	-0.467	-0.467	0.000	0.000	0.000	0.000
19	C	145	GLY	0	-0.060	-0.029	24.958	-0.491	-0.491	0.000	0.000	0.000	0.000
20	C	146	LYS	1	0.910	0.939	21.552	-14.408	-14.408	0.000	0.000	0.000	0.000
21	C	147	ASN	0	-0.048	-0.007	26.766	-0.138	-0.138	0.000	0.000	0.000	0.000
22	C	148	THR	0	-0.048	-0.004	29.504	-0.382	-0.382	0.000	0.000	0.000	0.000
23	C	149	ILE	0	0.129	0.042	31.688	0.144	0.144	0.000	0.000	0.000	0.000
24	C	150	ALA	0	0.033	0.019	31.767	-0.019	-0.019	0.000	0.000	0.000	0.000
25	C	151	TYR	0	0.036	0.009	24.716	0.515	0.515	0.000	0.000	0.000	0.000
26	C	152	ASP	-1	-0.800	-0.908	29.772	9.626	9.626	0.000	0.000	0.000	0.000
27	C	153	ARG	1	0.866	0.935	32.098	-8.599	-8.599	0.000	0.000	0.000	0.000
28	C	154	TYR	0	-0.035	-0.036	24.859	0.043	0.043	0.000	0.000	0.000	0.000
29	C	155	ILE	0	-0.050	-0.029	27.446	0.070	0.070	0.000	0.000	0.000	0.000
30	C	156	LYS	1	0.807	0.924	30.067	-8.999	-8.999	0.000	0.000	0.000	0.000
31	C	157	GLU	-1	-0.890	-0.941	33.528	8.593	8.593	0.000	0.000	0.000	0.000
32	C	158	VAL	0	0.212	0.190	28.203	0.044	0.044	0.000	0.000	0.000	0.000
33	C	159	PRO	0	-0.015	-0.017	29.126	0.378	0.378	0.000	0.000	0.000	0.000
34	C	160	ARG	1	0.760	0.796	22.108	-12.288	-12.288	0.000	0.000	0.000	0.000
35	C	161	HIS	0	0.036	0.034	23.823	0.358	0.358	0.000	0.000	0.000	0.000
36	C	162	LEU	0	0.020	0.010	19.664	-0.180	-0.180	0.000	0.000	0.000	0.000
37	C	163	ARG	1	0.926	0.942	23.987	-9.884	-9.884	0.000	0.000	0.000	0.000
38	C	164	GLN	0	-0.010	-0.006	26.757	-0.500	-0.500	0.000	0.000	0.000	0.000
39	C	165	PRO	0	-0.022	0.009	23.807	-0.091	-0.091	0.000	0.000	0.000	0.000
40	C	166	GLY	0	0.017	0.006	23.720	0.215	0.215	0.000	0.000	0.000	0.000
41	C	167	ILE	0	0.024	0.011	24.055	0.321	0.321	0.000	0.000	0.000	0.000
42	C	168	HIS	0	0.037	0.024	25.875	0.280	0.280	0.000	0.000	0.000	0.000
43	C	169	PRO	0	0.072	0.047	23.840	0.615	0.615	0.000	0.000	0.000	0.000
44	C	170	LYS	1	0.942	1.000	15.522	-16.782	-16.782	0.000	0.000	0.000	0.000
45	C	171	THR	0	-0.026	-0.010	18.512	-0.101	-0.101	0.000	0.000	0.000	0.000
46	C	172	PRO	0	0.019	0.012	16.258	0.696	0.696	0.000	0.000	0.000	0.000
47	C	173	ASN	0	0.027	0.000	10.977	1.499	1.499	0.000	0.000	0.000	0.000
48	C	174	LYS	1	0.954	0.958	12.014	-20.167	-20.167	0.000	0.000	0.000	0.000
49	C	175	PHE	0	0.083	0.048	8.110	-0.045	-0.045	0.000	0.000	0.000	0.000
50	C	176	LYS	1	0.957	0.993	7.215	-21.279	-21.279	0.000	0.000	0.000	0.000
51	C	177	LYS	1	0.888	0.970	3.841	-62.000	-61.372	0.004	-0.256	-0.377	0.001
52	C	178	TYR	0	-0.002	-0.012	7.742	-2.241	-2.241	0.000	0.000	0.000	0.000
53	C	179	SER	0	0.068	0.037	11.048	0.264	0.264	0.000	0.000	0.000	0.000
54	C	180	ARG	1	0.918	0.925	13.579	-16.626	-16.626	0.000	0.000	0.000	0.000
55	C	181	ARG	1	1.009	0.990	16.378	-14.281	-14.281	0.000	0.000	0.000	0.000
56	C	182	SER	0	0.030	0.026	14.536	-0.856	-0.856	0.000	0.000	0.000	0.000
57	C	183	TRP	0	-0.030	-0.015	14.075	-0.014	-0.014	0.000	0.000	0.000	0.000
58	C	184	ASP	-1	-0.749	-0.870	16.395	15.406	15.406	0.000	0.000	0.000	0.000
59	C	185	GLN	0	0.022	0.020	19.748	-0.994	-0.994	0.000	0.000	0.000	0.000
60	C	186	GLN	0	-0.013	-0.006	14.003	-0.533	-0.533	0.000	0.000	0.000	0.000
61	C	187	ILE	0	-0.009	-0.006	18.995	-0.602	-0.602	0.000	0.000	0.000	0.000
62	C	188	LYS	1	0.917	0.965	21.298	-11.887	-11.887	0.000	0.000	0.000	0.000
63	C	189	LEU	0	0.023	-0.002	21.871	-0.491	-0.491	0.000	0.000	0.000	0.000
64	C	190	TRP	0	-0.013	0.001	21.522	-0.181	-0.181	0.000	0.000	0.000	0.000
65	C	191	LYS	1	0.901	0.937	23.640	-12.255	-12.255	0.000	0.000	0.000	0.000
66	C	192	VAL	0	-0.026	-0.006	26.506	-0.382	-0.382	0.000	0.000	0.000	0.000
67	C	193	ALA	0	0.037	0.016	26.029	-0.353	-0.353	0.000	0.000	0.000	0.000
68	C	194	LEU	0	-0.014	-0.008	25.623	-0.239	-0.239	0.000	0.000	0.000	0.000
69	C	195	HIS	1	0.792	0.870	28.923	-9.937	-9.937	0.000	0.000	0.000	0.000
70	C	196	PHE	0	0.012	0.040	31.528	-0.255	-0.255	0.000	0.000	0.000	0.000
71	C	197	TRP	0	-0.084	-0.067	29.663	0.029	0.029	0.000	0.000	0.000	0.000
72	C	198	ASP	-1	-0.866	-0.911	34.929	8.812	8.812	0.000	0.000	0.000	0.000
73	C	199	PRO	0	0.003	0.013	35.804	0.016	0.016	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:127:ASP)