FMO DATABASE

FMODB ID: 52JVZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-708172.683545
FMO2-HF: Nuclear repulsion	671609.059329
FMO2-HF: Total energy	-36563.624217
FMO2-MP2: Total energy	-36673.800049

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.
-23.679	-22.526	9.166	-5.155	-5.164	0.045

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 : 0.109 / q_NPA : 0.066

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	0.027	0.026	2.828	-0.565	2.192	0.384	-1.455	-1.686	-0.002
4	C	250	HIS	0	0.030	0.003	1.828	-15.650	-17.254	8.782	-3.700	-3.478	0.047
5	C	251	LEU	0	0.011	0.000	6.249	-0.887	-0.887	0.000	0.000	0.000	0.000
6	C	252	TRP	0	0.030	-0.006	6.766	-1.078	-1.078	0.000	0.000	0.000	0.000
7	C	253	GLN	0	0.030	0.032	5.210	-0.553	-0.553	0.000	0.000	0.000	0.000
8	C	254	PHE	0	0.036	0.009	9.456	-0.283	-0.283	0.000	0.000	0.000	0.000
9	C	255	LEU	0	0.013	-0.003	11.029	-0.102	-0.102	0.000	0.000	0.000	0.000
10	C	256	LYS	1	0.900	0.956	12.967	-0.380	-0.380	0.000	0.000	0.000	0.000
11	C	257	GLU	-1	-0.796	-0.852	12.291	-0.993	-0.993	0.000	0.000	0.000	0.000
12	C	258	LEU	0	-0.021	-0.015	14.345	-0.023	-0.023	0.000	0.000	0.000	0.000
13	C	259	LEU	0	-0.009	0.000	17.145	-0.007	-0.007	0.000	0.000	0.000	0.000
14	C	260	LEU	0	-0.031	0.003	16.283	0.014	0.014	0.000	0.000	0.000	0.000
15	C	261	LYS	1	0.869	0.927	16.039	0.677	0.677	0.000	0.000	0.000	0.000
16	C	262	PRO	0	0.047	0.015	20.867	0.007	0.007	0.000	0.000	0.000	0.000
17	C	263	HIS	0	0.072	0.042	23.757	0.029	0.029	0.000	0.000	0.000	0.000
18	C	264	SER	0	0.046	0.030	21.438	0.006	0.006	0.000	0.000	0.000	0.000
19	C	265	TYR	0	-0.005	-0.016	17.356	0.021	0.021	0.000	0.000	0.000	0.000
20	C	266	GLY	0	0.022	0.017	22.564	0.037	0.037	0.000	0.000	0.000	0.000
21	C	267	ARG	1	0.852	0.923	25.104	0.156	0.156	0.000	0.000	0.000	0.000
22	C	268	PHE	0	0.011	0.002	22.140	0.009	0.009	0.000	0.000	0.000	0.000
23	C	269	ILE	0	-0.034	-0.023	18.164	0.049	0.049	0.000	0.000	0.000	0.000
24	C	270	ARG	1	0.883	0.936	22.240	-0.090	-0.090	0.000	0.000	0.000	0.000
25	C	271	TRP	0	-0.004	-0.026	18.807	0.057	0.057	0.000	0.000	0.000	0.000
26	C	272	LEU	0	-0.048	-0.021	24.459	-0.014	-0.014	0.000	0.000	0.000	0.000
27	C	273	ASN	0	0.057	0.027	26.147	-0.013	-0.013	0.000	0.000	0.000	0.000
28	C	274	LYS	1	0.971	0.983	21.903	0.105	0.105	0.000	0.000	0.000	0.000
29	C	275	GLU	-1	-0.780	-0.853	23.399	0.138	0.138	0.000	0.000	0.000	0.000
30	C	276	LYS	1	0.860	0.917	24.451	-0.123	-0.123	0.000	0.000	0.000	0.000
31	C	277	GLY	0	0.059	0.032	20.937	0.045	0.045	0.000	0.000	0.000	0.000
32	C	278	ILE	0	0.001	-0.006	20.957	0.054	0.054	0.000	0.000	0.000	0.000
33	C	279	PHE	0	-0.011	-0.013	17.740	-0.049	-0.049	0.000	0.000	0.000	0.000
34	C	280	LYS	1	0.892	0.924	22.936	-0.080	-0.080	0.000	0.000	0.000	0.000
35	C	281	ILE	0	-0.044	-0.012	19.018	-0.025	-0.025	0.000	0.000	0.000	0.000
36	C	282	GLU	-1	-0.752	-0.858	23.147	0.092	0.092	0.000	0.000	0.000	0.000
37	C	283	ASP	-1	-0.797	-0.887	24.487	0.007	0.007	0.000	0.000	0.000	0.000
38	C	284	SER	0	-0.014	-0.025	22.497	-0.012	-0.012	0.000	0.000	0.000	0.000
39	C	285	ALA	0	0.035	0.026	22.023	0.024	0.024	0.000	0.000	0.000	0.000
40	C	286	GLN	0	0.052	0.028	22.056	-0.026	-0.026	0.000	0.000	0.000	0.000
41	C	287	VAL	0	-0.019	-0.008	17.458	-0.030	-0.030	0.000	0.000	0.000	0.000
42	C	288	ALA	0	-0.025	-0.015	17.342	0.002	0.002	0.000	0.000	0.000	0.000
43	C	289	ARG	1	0.967	0.981	17.648	0.181	0.181	0.000	0.000	0.000	0.000
44	C	290	LEU	0	-0.004	0.000	16.844	-0.058	-0.058	0.000	0.000	0.000	0.000
45	C	291	TRP	0	0.008	-0.005	8.309	-0.094	-0.094	0.000	0.000	0.000	0.000
46	C	292	GLY	0	0.020	-0.003	13.216	-0.058	-0.058	0.000	0.000	0.000	0.000
47	C	293	ILE	0	0.004	0.003	15.008	-0.064	-0.064	0.000	0.000	0.000	0.000
48	C	294	ARG	1	0.809	0.893	9.949	1.040	1.040	0.000	0.000	0.000	0.000
49	C	295	LYS	1	0.810	0.908	6.831	-0.617	-0.617	0.000	0.000	0.000	0.000
50	C	296	ASN	0	0.033	0.024	11.119	0.154	0.154	0.000	0.000	0.000	0.000
51	C	297	ARG	1	0.895	0.952	11.775	-0.017	-0.017	0.000	0.000	0.000	0.000
52	C	298	PRO	0	0.080	0.028	15.467	0.056	0.056	0.000	0.000	0.000	0.000
53	C	299	ALA	0	0.045	0.040	19.059	0.016	0.016	0.000	0.000	0.000	0.000
54	C	300	MET	0	-0.090	-0.032	14.391	0.100	0.100	0.000	0.000	0.000	0.000
55	C	301	ASN	0	0.024	-0.024	18.731	0.002	0.002	0.000	0.000	0.000	0.000
56	C	302	TYR	0	0.096	0.040	19.554	0.072	0.072	0.000	0.000	0.000	0.000
57	C	303	ASP	-1	-0.800	-0.865	20.616	0.342	0.342	0.000	0.000	0.000	0.000
58	C	304	LYS	1	0.924	0.962	17.610	-0.216	-0.216	0.000	0.000	0.000	0.000
59	C	305	LEU	0	0.024	0.028	15.230	0.133	0.133	0.000	0.000	0.000	0.000
60	C	306	SER	0	-0.014	-0.022	16.324	0.136	0.136	0.000	0.000	0.000	0.000
61	C	307	ARG	1	0.867	0.919	17.537	-0.837	-0.837	0.000	0.000	0.000	0.000
62	C	308	SER	0	-0.012	-0.012	12.838	0.133	0.133	0.000	0.000	0.000	0.000
63	C	309	ILE	0	-0.010	-0.006	14.053	0.190	0.190	0.000	0.000	0.000	0.000
64	C	310	ARG	1	0.918	0.959	15.765	-0.512	-0.512	0.000	0.000	0.000	0.000
65	C	311	GLN	0	0.009	0.021	13.337	-0.147	-0.147	0.000	0.000	0.000	0.000
66	C	312	TYR	0	-0.003	-0.015	8.497	-0.081	-0.081	0.000	0.000	0.000	0.000
67	C	313	TYR	0	0.054	0.029	14.155	-0.065	-0.065	0.000	0.000	0.000	0.000
68	C	314	LYS	1	0.990	0.993	16.624	-0.972	-0.972	0.000	0.000	0.000	0.000
69	C	315	LYS	1	0.916	0.965	10.581	-2.154	-2.154	0.000	0.000	0.000	0.000
70	C	316	GLY	0	0.072	0.057	14.535	0.015	0.015	0.000	0.000	0.000	0.000
71	C	317	ILE	0	-0.018	-0.010	10.089	-0.011	-0.011	0.000	0.000	0.000	0.000
72	C	318	ILE	0	-0.051	-0.033	13.775	-0.128	-0.128	0.000	0.000	0.000	0.000
73	C	319	ARG	1	0.805	0.868	16.662	-0.326	-0.326	0.000	0.000	0.000	0.000
74	C	320	LYS	1	0.843	0.916	20.241	-0.409	-0.409	0.000	0.000	0.000	0.000
75	C	321	PRO	0	0.014	0.012	23.632	0.014	0.014	0.000	0.000	0.000	0.000
76	C	322	ASP	-1	-0.778	-0.871	26.036	0.306	0.306	0.000	0.000	0.000	0.000
77	C	323	ILE	0	0.036	0.039	29.005	-0.004	-0.004	0.000	0.000	0.000	0.000
78	C	324	SER	0	-0.001	0.000	27.976	0.002	0.002	0.000	0.000	0.000	0.000
79	C	325	GLN	0	0.042	0.011	27.757	-0.034	-0.034	0.000	0.000	0.000	0.000
80	C	326	ARG	1	0.974	0.975	27.103	-0.152	-0.152	0.000	0.000	0.000	0.000
81	C	327	LEU	0	-0.018	-0.012	24.330	-0.013	-0.013	0.000	0.000	0.000	0.000
82	C	328	VAL	0	0.034	0.030	23.792	0.002	0.002	0.000	0.000	0.000	0.000
83	C	329	TYR	0	-0.082	-0.049	19.917	0.060	0.060	0.000	0.000	0.000	0.000
84	C	330	GLN	0	0.057	0.032	20.739	-0.042	-0.042	0.000	0.000	0.000	0.000
85	C	331	PHE	0	-0.046	-0.029	14.180	0.079	0.079	0.000	0.000	0.000	0.000
86	C	332	VAL	0	-0.014	-0.001	17.175	-0.063	-0.063	0.000	0.000	0.000	0.000
87	C	333	HIS	0	0.068	0.059	15.111	-0.105	-0.105	0.000	0.000	0.000	0.000
88	C	334	PRO	0	0.005	-0.007	16.368	-0.079	-0.079	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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