FMO DATABASE

FMODB ID: 6NG1Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-504139.522369
FMO2-HF: Nuclear repulsion	473148.222404
FMO2-HF: Total energy	-30991.299966
FMO2-MP2: Total energy	-31083.991763

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.
-242.659	-238.072	10.759	-7.543	-7.803	0.079

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 : -0.770 / q_NPA : -0.882

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	-0.899	-0.948	3.297	63.061	66.866	0.352	-2.115	-2.042	0.009
4	C	130	THR	0	0.065	0.017	3.941	-7.559	-7.318	-0.001	-0.071	-0.169	0.000
5	C	131	ASP	-1	-0.777	-0.848	6.582	23.842	23.842	0.000	0.000	0.000	0.000
6	C	132	GLU	-1	-0.819	-0.929	9.168	22.739	22.739	0.000	0.000	0.000	0.000
7	C	133	SER	0	-0.015	-0.027	12.609	-2.381	-2.381	0.000	0.000	0.000	0.000
8	C	134	VAL	0	-0.087	-0.055	9.339	-2.274	-2.274	0.000	0.000	0.000	0.000
9	C	135	LEU	0	-0.006	0.005	9.142	-2.267	-2.267	0.000	0.000	0.000	0.000
10	C	136	MET	0	0.063	0.023	12.731	-2.098	-2.098	0.000	0.000	0.000	0.000
11	C	137	ARG	1	0.894	0.968	12.862	-23.399	-23.399	0.000	0.000	0.000	0.000
12	C	138	ARG	1	0.787	0.881	8.619	-32.451	-32.451	0.000	0.000	0.000	0.000
13	C	139	GLN	0	0.032	0.019	15.744	0.083	0.083	0.000	0.000	0.000	0.000
14	C	140	LYS	1	0.963	0.994	17.926	-14.365	-14.365	0.000	0.000	0.000	0.000
15	C	141	GLN	0	-0.025	-0.022	17.259	0.010	0.010	0.000	0.000	0.000	0.000
16	C	142	ILE	0	0.017	0.005	16.464	-0.764	-0.764	0.000	0.000	0.000	0.000
17	C	143	ASN	0	0.040	0.023	20.692	-0.368	-0.368	0.000	0.000	0.000	0.000
18	C	144	TYR	0	0.041	0.009	23.500	-0.512	-0.512	0.000	0.000	0.000	0.000
19	C	145	GLY	0	-0.039	0.001	24.170	-0.494	-0.494	0.000	0.000	0.000	0.000
20	C	146	LYS	1	0.881	0.937	21.800	-14.766	-14.766	0.000	0.000	0.000	0.000
21	C	147	ASN	0	0.013	0.011	26.520	-0.195	-0.195	0.000	0.000	0.000	0.000
22	C	148	THR	0	-0.064	-0.020	28.740	-0.424	-0.424	0.000	0.000	0.000	0.000
23	C	149	ILE	0	0.111	0.033	31.076	0.175	0.175	0.000	0.000	0.000	0.000
24	C	150	ALA	0	0.030	0.026	32.041	-0.054	-0.054	0.000	0.000	0.000	0.000
25	C	151	TYR	0	0.033	0.012	25.056	0.504	0.504	0.000	0.000	0.000	0.000
26	C	152	ASP	-1	-0.821	-0.907	30.078	9.420	9.420	0.000	0.000	0.000	0.000
27	C	153	ARG	1	0.867	0.920	32.471	-8.718	-8.718	0.000	0.000	0.000	0.000
28	C	154	TYR	0	-0.020	-0.013	25.409	0.023	0.023	0.000	0.000	0.000	0.000
29	C	155	ILE	0	-0.064	-0.049	27.809	0.090	0.090	0.000	0.000	0.000	0.000
30	C	156	LYS	1	0.806	0.912	30.423	-9.081	-9.081	0.000	0.000	0.000	0.000
31	C	157	GLU	-1	-0.803	-0.887	34.053	8.552	8.552	0.000	0.000	0.000	0.000
32	C	158	VAL	0	-0.026	-0.008	28.703	-0.023	-0.023	0.000	0.000	0.000	0.000
33	C	159	PRO	0	0.008	-0.005	29.412	0.376	0.376	0.000	0.000	0.000	0.000
34	C	160	ARG	1	0.849	0.923	22.932	-12.333	-12.333	0.000	0.000	0.000	0.000
35	C	161	HIS	0	0.057	0.039	24.374	0.343	0.343	0.000	0.000	0.000	0.000
36	C	162	LEU	0	0.020	0.009	20.348	-0.190	-0.190	0.000	0.000	0.000	0.000
37	C	163	ARG	1	0.928	0.944	24.684	-9.835	-9.835	0.000	0.000	0.000	0.000
38	C	164	GLN	0	-0.005	0.000	27.518	-0.478	-0.478	0.000	0.000	0.000	0.000
39	C	165	PRO	0	-0.055	-0.008	24.283	-0.062	-0.062	0.000	0.000	0.000	0.000
40	C	166	GLY	0	0.027	0.007	24.222	0.117	0.117	0.000	0.000	0.000	0.000
41	C	167	ILE	0	0.027	0.019	24.468	0.397	0.397	0.000	0.000	0.000	0.000
42	C	168	HIS	0	0.041	0.023	26.296	0.359	0.359	0.000	0.000	0.000	0.000
43	C	169	PRO	0	0.088	0.037	24.475	0.671	0.671	0.000	0.000	0.000	0.000
44	C	170	LYS	1	0.927	0.994	16.062	-17.166	-17.166	0.000	0.000	0.000	0.000
45	C	171	THR	0	-0.006	-0.008	18.693	0.052	0.052	0.000	0.000	0.000	0.000
46	C	172	PRO	0	0.001	0.004	16.377	0.641	0.641	0.000	0.000	0.000	0.000
47	C	173	ASN	0	0.037	0.010	11.363	1.587	1.587	0.000	0.000	0.000	0.000
48	C	174	LYS	1	0.892	0.934	12.064	-20.741	-20.741	0.000	0.000	0.000	0.000
49	C	175	PHE	0	0.094	0.052	8.323	0.661	0.661	0.000	0.000	0.000	0.000
50	C	176	LYS	1	0.949	0.990	7.122	-21.856	-21.856	0.000	0.000	0.000	0.000
51	C	177	LYS	1	0.883	0.958	1.941	-117.704	-117.163	10.408	-5.357	-5.592	0.070
52	C	178	TYR	0	-0.047	-0.031	6.754	-4.097	-4.097	0.000	0.000	0.000	0.000
53	C	179	SER	0	0.067	0.032	10.175	-0.040	-0.040	0.000	0.000	0.000	0.000
54	C	180	ARG	1	0.892	0.906	12.133	-18.352	-18.352	0.000	0.000	0.000	0.000
55	C	181	ARG	1	1.009	0.995	14.706	-15.370	-15.370	0.000	0.000	0.000	0.000
56	C	182	SER	0	0.053	0.035	13.987	-1.035	-1.035	0.000	0.000	0.000	0.000
57	C	183	TRP	0	-0.024	-0.005	13.266	-0.060	-0.060	0.000	0.000	0.000	0.000
58	C	184	ASP	-1	-0.755	-0.857	15.275	16.423	16.423	0.000	0.000	0.000	0.000
59	C	185	GLN	0	0.027	0.015	18.664	-1.113	-1.113	0.000	0.000	0.000	0.000
60	C	186	GLN	0	-0.006	-0.002	14.038	-0.634	-0.634	0.000	0.000	0.000	0.000
61	C	187	ILE	0	-0.014	-0.008	17.959	-0.693	-0.693	0.000	0.000	0.000	0.000
62	C	188	LYS	1	0.938	0.977	20.477	-12.527	-12.527	0.000	0.000	0.000	0.000
63	C	189	LEU	0	0.029	0.008	21.678	-0.554	-0.554	0.000	0.000	0.000	0.000
64	C	190	TRP	0	-0.009	0.005	21.832	-0.256	-0.256	0.000	0.000	0.000	0.000
65	C	191	LYS	1	0.866	0.906	23.896	-12.855	-12.855	0.000	0.000	0.000	0.000
66	C	192	VAL	0	-0.026	-0.004	26.134	-0.445	-0.445	0.000	0.000	0.000	0.000
67	C	193	ALA	0	0.036	0.015	26.420	-0.378	-0.378	0.000	0.000	0.000	0.000
68	C	194	LEU	0	-0.023	-0.017	25.934	-0.267	-0.267	0.000	0.000	0.000	0.000
69	C	195	HIS	1	0.778	0.856	29.348	-10.295	-10.295	0.000	0.000	0.000	0.000
70	C	196	PHE	0	0.034	0.032	31.922	-0.232	-0.232	0.000	0.000	0.000	0.000
71	C	197	TRP	0	-0.074	-0.039	30.127	0.020	0.020	0.000	0.000	0.000	0.000
72	C	198	ASP	-1	-0.829	-0.898	35.091	8.979	8.979	0.000	0.000	0.000	0.000
73	C	199	PRO	0	0.003	0.022	36.106	-0.023	-0.023	0.000	0.000	0.000	0.000

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