FMO DATABASE

FMODB ID: K9GL3

Calculation Name: 1YO5-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YO5

Chain ID: C

ChEMBL ID:

UniProt ID: O95238

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	OptH
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	88
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-706291.705449
FMO2-HF: Nuclear repulsion	669728.777175
FMO2-HF: Total energy	-36562.928274
FMO2-MP2: Total energy	-36673.119985

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:247:GLN)

Summations of interaction energy for fragment #1(C:247:GLN)

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.
-22.744	-18.321	3.523	-3.322	-4.625	0.023

Interaction energy analysis for fragmet #1(C:247:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.004

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	C	249	ILE	0	0.031	0.030	2.819	-1.811	0.584	0.293	-1.233	-1.456	-0.006
4	C	250	HIS	0	0.001	-0.004	2.262	-12.280	-10.252	3.230	-2.089	-3.169	0.029
5	C	251	LEU	0	0.020	-0.002	6.597	-0.762	-0.762	0.000	0.000	0.000	0.000
6	C	252	TRP	0	0.058	0.011	7.681	-0.785	-0.785	0.000	0.000	0.000	0.000
7	C	253	GLN	0	0.034	0.021	6.440	-0.048	-0.048	0.000	0.000	0.000	0.000
8	C	254	PHE	0	0.042	0.018	10.172	-0.263	-0.263	0.000	0.000	0.000	0.000
9	C	255	LEU	0	-0.003	-0.014	11.717	-0.118	-0.118	0.000	0.000	0.000	0.000
10	C	256	LYS	1	0.923	0.966	13.519	-0.468	-0.468	0.000	0.000	0.000	0.000
11	C	257	GLU	-1	-0.809	-0.848	12.225	-0.564	-0.564	0.000	0.000	0.000	0.000
12	C	258	LEU	0	-0.041	-0.023	15.262	-0.038	-0.038	0.000	0.000	0.000	0.000
13	C	259	LEU	0	-0.027	-0.012	17.934	-0.018	-0.018	0.000	0.000	0.000	0.000
14	C	260	LEU	0	-0.029	0.001	17.272	-0.011	-0.011	0.000	0.000	0.000	0.000
15	C	261	LYS	1	0.962	0.987	17.679	0.353	0.353	0.000	0.000	0.000	0.000
16	C	262	PRO	0	0.068	0.032	22.027	0.014	0.014	0.000	0.000	0.000	0.000
17	C	263	HIS	0	0.061	0.037	24.900	0.019	0.019	0.000	0.000	0.000	0.000
18	C	264	SER	0	0.021	0.020	22.313	0.000	0.000	0.000	0.000	0.000	0.000
19	C	265	TYR	0	0.012	-0.005	18.323	0.026	0.026	0.000	0.000	0.000	0.000
20	C	266	GLY	0	0.017	0.019	23.154	0.033	0.033	0.000	0.000	0.000	0.000
21	C	267	ARG	1	0.858	0.913	25.828	0.011	0.011	0.000	0.000	0.000	0.000
22	C	268	PHE	0	0.008	0.000	22.368	0.015	0.015	0.000	0.000	0.000	0.000
23	C	269	ILE	0	-0.036	-0.018	19.016	0.046	0.046	0.000	0.000	0.000	0.000
24	C	270	ARG	1	0.889	0.934	23.098	-0.154	-0.154	0.000	0.000	0.000	0.000
25	C	271	TRP	0	0.011	-0.005	19.307	0.045	0.045	0.000	0.000	0.000	0.000
26	C	272	LEU	0	-0.058	-0.035	25.230	-0.015	-0.015	0.000	0.000	0.000	0.000
27	C	273	ASN	0	0.045	0.014	26.613	-0.023	-0.023	0.000	0.000	0.000	0.000
28	C	274	LYS	1	0.974	0.980	23.747	0.042	0.042	0.000	0.000	0.000	0.000
29	C	275	GLU	-1	-0.904	-0.946	23.920	0.129	0.129	0.000	0.000	0.000	0.000
30	C	276	LYS	1	1.001	1.015	24.698	-0.130	-0.130	0.000	0.000	0.000	0.000
31	C	277	GLY	0	0.066	0.043	21.477	0.041	0.041	0.000	0.000	0.000	0.000
32	C	278	ILE	0	-0.012	-0.012	21.474	0.058	0.058	0.000	0.000	0.000	0.000
33	C	279	PHE	0	0.009	0.009	18.256	-0.036	-0.036	0.000	0.000	0.000	0.000
34	C	280	LYS	1	0.974	0.983	23.457	-0.154	-0.154	0.000	0.000	0.000	0.000
35	C	281	ILE	0	-0.052	-0.031	19.890	-0.012	-0.012	0.000	0.000	0.000	0.000
36	C	282	GLU	-1	-0.821	-0.907	23.769	0.152	0.152	0.000	0.000	0.000	0.000
37	C	283	ASP	-1	-0.832	-0.907	24.946	0.158	0.158	0.000	0.000	0.000	0.000
38	C	284	SER	0	0.012	-0.017	22.894	0.004	0.004	0.000	0.000	0.000	0.000
39	C	285	ALA	0	0.016	0.008	22.111	0.036	0.036	0.000	0.000	0.000	0.000
40	C	286	GLN	0	0.057	0.044	22.444	0.013	0.013	0.000	0.000	0.000	0.000
41	C	287	VAL	0	-0.014	-0.004	17.911	-0.003	-0.003	0.000	0.000	0.000	0.000
42	C	288	ALA	0	-0.037	-0.019	17.755	0.030	0.030	0.000	0.000	0.000	0.000
43	C	289	ARG	1	0.964	0.981	17.827	-0.060	-0.060	0.000	0.000	0.000	0.000
44	C	290	LEU	0	-0.019	-0.011	17.205	-0.010	-0.010	0.000	0.000	0.000	0.000
45	C	291	TRP	0	-0.015	-0.008	8.344	0.000	0.000	0.000	0.000	0.000	0.000
46	C	292	GLY	0	0.013	-0.002	13.306	0.033	0.033	0.000	0.000	0.000	0.000
47	C	293	ILE	0	0.017	0.013	14.923	0.015	0.015	0.000	0.000	0.000	0.000
48	C	294	ARG	1	0.776	0.854	10.047	0.457	0.457	0.000	0.000	0.000	0.000
49	C	295	LYS	1	0.892	0.941	7.077	-1.490	-1.490	0.000	0.000	0.000	0.000
50	C	296	ASN	0	0.058	0.047	10.973	0.098	0.098	0.000	0.000	0.000	0.000
51	C	297	ARG	1	0.853	0.918	11.129	-0.783	-0.783	0.000	0.000	0.000	0.000
52	C	298	PRO	0	0.103	0.048	15.440	0.001	0.001	0.000	0.000	0.000	0.000
53	C	299	ALA	0	0.042	0.029	18.879	-0.016	-0.016	0.000	0.000	0.000	0.000
54	C	300	MET	0	-0.103	-0.028	14.369	0.037	0.037	0.000	0.000	0.000	0.000
55	C	301	ASN	0	0.111	0.043	18.415	-0.012	-0.012	0.000	0.000	0.000	0.000
56	C	302	TYR	0	0.117	0.031	19.443	0.072	0.072	0.000	0.000	0.000	0.000
57	C	303	ASP	-1	-0.849	-0.895	20.710	0.458	0.458	0.000	0.000	0.000	0.000
58	C	304	LYS	1	0.862	0.916	17.747	-0.485	-0.485	0.000	0.000	0.000	0.000
59	C	305	LEU	0	0.002	0.012	15.379	0.114	0.114	0.000	0.000	0.000	0.000
60	C	306	SER	0	-0.024	-0.035	16.393	0.105	0.105	0.000	0.000	0.000	0.000
61	C	307	ARG	1	0.910	0.961	18.001	-0.828	-0.828	0.000	0.000	0.000	0.000
62	C	308	SER	0	0.015	-0.007	13.059	0.131	0.131	0.000	0.000	0.000	0.000
63	C	309	ILE	0	0.008	0.011	14.303	0.142	0.142	0.000	0.000	0.000	0.000
64	C	310	ARG	1	0.960	0.979	16.133	-0.585	-0.585	0.000	0.000	0.000	0.000
65	C	311	GLN	0	-0.045	-0.015	14.080	-0.031	-0.031	0.000	0.000	0.000	0.000
66	C	312	TYR	0	0.014	0.004	9.157	-0.040	-0.040	0.000	0.000	0.000	0.000
67	C	313	TYR	0	0.029	0.011	14.666	-0.054	-0.054	0.000	0.000	0.000	0.000
68	C	314	LYS	1	0.980	0.989	16.513	-0.922	-0.922	0.000	0.000	0.000	0.000
69	C	315	LYS	1	0.913	0.960	11.479	-1.670	-1.670	0.000	0.000	0.000	0.000
70	C	316	GLY	0	0.068	0.057	14.835	0.001	0.001	0.000	0.000	0.000	0.000
71	C	317	ILE	0	-0.030	-0.005	10.300	-0.011	-0.011	0.000	0.000	0.000	0.000
72	C	318	ILE	0	-0.040	-0.031	14.597	-0.106	-0.106	0.000	0.000	0.000	0.000
73	C	319	ARG	1	0.922	0.963	17.047	-0.314	-0.314	0.000	0.000	0.000	0.000
74	C	320	LYS	1	0.845	0.938	20.613	-0.424	-0.424	0.000	0.000	0.000	0.000
75	C	321	PRO	0	0.025	0.010	23.856	0.002	0.002	0.000	0.000	0.000	0.000
76	C	322	ASP	-1	-0.884	-0.948	26.320	0.263	0.263	0.000	0.000	0.000	0.000
77	C	323	ILE	0	0.026	0.036	29.328	-0.001	-0.001	0.000	0.000	0.000	0.000
78	C	324	SER	0	-0.021	-0.019	28.121	0.010	0.010	0.000	0.000	0.000	0.000
79	C	325	GLN	0	0.078	0.031	28.274	-0.022	-0.022	0.000	0.000	0.000	0.000
80	C	326	ARG	1	0.976	0.968	27.528	-0.213	-0.213	0.000	0.000	0.000	0.000
81	C	327	LEU	0	-0.031	-0.015	24.719	-0.012	-0.012	0.000	0.000	0.000	0.000
82	C	328	VAL	0	0.020	0.038	24.654	-0.001	-0.001	0.000	0.000	0.000	0.000
83	C	329	TYR	0	-0.068	-0.046	20.249	0.047	0.047	0.000	0.000	0.000	0.000
84	C	330	GLN	0	0.011	0.000	21.221	-0.034	-0.034	0.000	0.000	0.000	0.000
85	C	331	PHE	0	-0.030	-0.028	14.289	0.082	0.082	0.000	0.000	0.000	0.000
86	C	332	VAL	0	-0.020	0.002	17.544	-0.060	-0.060	0.000	0.000	0.000	0.000
87	C	333	HIS	0	0.098	0.054	15.199	-0.114	-0.114	0.000	0.000	0.000	0.000
88	C	334	PRO	0	-0.046	-0.024	15.635	-0.046	-0.046	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:247:GLN)