FMO DATABASE

FMODB ID: YRV82

Calculation Name: 1YO5-C-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1YO5

Chain ID: C

ChEMBL ID:

UniProt ID: O95238

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	88
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-707080.079271
FMO2-HF: Nuclear repulsion	670516.709486
FMO2-HF: Total energy	-36563.369785
FMO2-MP2: Total energy	-36673.513996

3D Structure Molmil

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:247:GLN)

Summations of interaction energy for fragment #1(A: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.
178.725	179.969	8.747	-4.348	-5.643	0.023

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.914 / q_NPA : 0.955

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	A	249	ILE	0	0.042	0.034	2.609	-2.284	-0.251	1.644	-1.414	-2.263	-0.011
4	A	250	HIS	0	-0.008	-0.019	1.932	-4.577	-5.366	7.103	-2.934	-3.380	0.034
5	A	251	LEU	0	0.018	0.005	6.529	0.831	0.831	0.000	0.000	0.000	0.000
6	A	252	TRP	0	0.047	0.009	7.183	1.027	1.027	0.000	0.000	0.000	0.000
7	A	253	GLN	0	0.034	0.032	5.302	-1.458	-1.458	0.000	0.000	0.000	0.000
8	A	254	PHE	0	0.037	0.006	9.599	0.954	0.954	0.000	0.000	0.000	0.000
9	A	255	LEU	0	0.008	-0.006	11.140	1.259	1.259	0.000	0.000	0.000	0.000
10	A	256	LYS	1	0.856	0.918	13.057	18.077	18.077	0.000	0.000	0.000	0.000
11	A	257	GLU	-1	-0.837	-0.870	11.464	-23.371	-23.371	0.000	0.000	0.000	0.000
12	A	258	LEU	0	-0.040	-0.024	14.251	0.971	0.971	0.000	0.000	0.000	0.000
13	A	259	LEU	0	-0.018	-0.001	17.097	0.845	0.845	0.000	0.000	0.000	0.000
14	A	260	LEU	0	-0.012	0.013	16.267	0.736	0.736	0.000	0.000	0.000	0.000
15	A	261	LYS	1	0.953	0.983	16.484	18.284	18.284	0.000	0.000	0.000	0.000
16	A	262	PRO	0	0.053	0.023	20.831	0.105	0.105	0.000	0.000	0.000	0.000
17	A	263	HIS	0	0.076	0.040	23.759	0.368	0.368	0.000	0.000	0.000	0.000
18	A	264	SER	0	0.016	0.023	21.363	0.250	0.250	0.000	0.000	0.000	0.000
19	A	265	TYR	0	0.006	-0.015	17.174	0.235	0.235	0.000	0.000	0.000	0.000
20	A	266	GLY	0	0.026	0.020	22.385	0.043	0.043	0.000	0.000	0.000	0.000
21	A	267	ARG	1	0.862	0.918	25.012	11.638	11.638	0.000	0.000	0.000	0.000
22	A	268	PHE	0	0.004	-0.003	21.905	0.033	0.033	0.000	0.000	0.000	0.000
23	A	269	ILE	0	-0.030	-0.020	18.304	-0.073	-0.073	0.000	0.000	0.000	0.000
24	A	270	ARG	1	0.876	0.933	22.313	10.229	10.229	0.000	0.000	0.000	0.000
25	A	271	TRP	0	0.005	-0.013	18.914	0.031	0.031	0.000	0.000	0.000	0.000
26	A	272	LEU	0	-0.060	-0.027	24.614	0.348	0.348	0.000	0.000	0.000	0.000
27	A	273	ASN	0	0.043	0.007	26.351	0.146	0.146	0.000	0.000	0.000	0.000
28	A	274	LYS	1	0.976	0.984	22.364	12.240	12.240	0.000	0.000	0.000	0.000
29	A	275	GLU	-1	-0.837	-0.893	23.559	-10.768	-10.768	0.000	0.000	0.000	0.000
30	A	276	LYS	1	0.910	0.960	24.213	9.545	9.545	0.000	0.000	0.000	0.000
31	A	277	GLY	0	0.109	0.059	21.160	-0.172	-0.172	0.000	0.000	0.000	0.000
32	A	278	ILE	0	-0.010	-0.012	21.314	-0.429	-0.429	0.000	0.000	0.000	0.000
33	A	279	PHE	0	-0.007	-0.009	17.924	0.068	0.068	0.000	0.000	0.000	0.000
34	A	280	LYS	1	0.893	0.929	23.059	10.243	10.243	0.000	0.000	0.000	0.000
35	A	281	ILE	0	-0.047	-0.015	19.466	-0.309	-0.309	0.000	0.000	0.000	0.000
36	A	282	GLU	-1	-0.767	-0.867	23.484	-9.797	-9.797	0.000	0.000	0.000	0.000
37	A	283	ASP	-1	-0.797	-0.889	24.771	-11.487	-11.487	0.000	0.000	0.000	0.000
38	A	284	SER	0	0.012	-0.017	22.680	-0.499	-0.499	0.000	0.000	0.000	0.000
39	A	285	ALA	0	-0.003	0.008	22.183	-0.582	-0.582	0.000	0.000	0.000	0.000
40	A	286	GLN	0	0.053	0.034	22.214	-0.841	-0.841	0.000	0.000	0.000	0.000
41	A	287	VAL	0	-0.008	-0.002	17.570	-0.858	-0.858	0.000	0.000	0.000	0.000
42	A	288	ALA	0	-0.021	-0.013	17.472	-1.099	-1.099	0.000	0.000	0.000	0.000
43	A	289	ARG	1	0.965	0.979	17.689	13.155	13.155	0.000	0.000	0.000	0.000
44	A	290	LEU	0	-0.012	-0.004	16.720	-0.788	-0.788	0.000	0.000	0.000	0.000
45	A	291	TRP	0	-0.004	-0.007	8.301	-2.188	-2.188	0.000	0.000	0.000	0.000
46	A	292	GLY	0	0.016	-0.009	13.202	-1.613	-1.613	0.000	0.000	0.000	0.000
47	A	293	ILE	0	0.003	0.005	14.805	-1.026	-1.026	0.000	0.000	0.000	0.000
48	A	294	ARG	1	0.773	0.854	9.565	24.882	24.882	0.000	0.000	0.000	0.000
49	A	295	LYS	1	0.862	0.939	6.714	27.821	27.821	0.000	0.000	0.000	0.000
50	A	296	ASN	0	0.034	0.026	10.973	0.577	0.577	0.000	0.000	0.000	0.000
51	A	297	ARG	1	0.888	0.945	11.070	23.176	23.176	0.000	0.000	0.000	0.000
52	A	298	PRO	0	0.083	0.030	15.319	0.516	0.516	0.000	0.000	0.000	0.000
53	A	299	ALA	0	0.043	0.037	18.924	0.675	0.675	0.000	0.000	0.000	0.000
54	A	300	MET	0	-0.080	-0.019	14.024	0.578	0.578	0.000	0.000	0.000	0.000
55	A	301	ASN	0	0.058	0.012	18.324	0.102	0.102	0.000	0.000	0.000	0.000
56	A	302	TYR	0	0.122	0.044	19.271	-0.724	-0.724	0.000	0.000	0.000	0.000
57	A	303	ASP	-1	-0.847	-0.898	20.616	-12.095	-12.095	0.000	0.000	0.000	0.000
58	A	304	LYS	1	0.901	0.940	17.220	14.348	14.348	0.000	0.000	0.000	0.000
59	A	305	LEU	0	0.015	0.023	15.260	-0.651	-0.651	0.000	0.000	0.000	0.000
60	A	306	SER	0	0.007	-0.008	16.364	-0.213	-0.213	0.000	0.000	0.000	0.000
61	A	307	ARG	1	0.875	0.940	17.903	13.936	13.936	0.000	0.000	0.000	0.000
62	A	308	SER	0	0.003	-0.002	12.855	-0.331	-0.331	0.000	0.000	0.000	0.000
63	A	309	ILE	0	0.004	0.001	14.286	-0.272	-0.272	0.000	0.000	0.000	0.000
64	A	310	ARG	1	0.923	0.958	16.006	12.755	12.755	0.000	0.000	0.000	0.000
65	A	311	GLN	0	-0.030	-0.013	13.567	0.884	0.884	0.000	0.000	0.000	0.000
66	A	312	TYR	0	-0.004	-0.014	8.685	-0.501	-0.501	0.000	0.000	0.000	0.000
67	A	313	TYR	0	0.061	0.034	14.478	0.172	0.172	0.000	0.000	0.000	0.000
68	A	314	LYS	1	0.976	0.986	16.720	12.973	12.973	0.000	0.000	0.000	0.000
69	A	315	LYS	1	0.911	0.957	11.400	16.395	16.395	0.000	0.000	0.000	0.000
70	A	316	GLY	0	0.068	0.054	14.949	-0.218	-0.218	0.000	0.000	0.000	0.000
71	A	317	ILE	0	-0.017	-0.003	10.406	-0.266	-0.266	0.000	0.000	0.000	0.000
72	A	318	ILE	0	-0.040	-0.031	14.273	-0.073	-0.073	0.000	0.000	0.000	0.000
73	A	319	ARG	1	0.819	0.878	17.009	10.840	10.840	0.000	0.000	0.000	0.000
74	A	320	LYS	1	0.830	0.913	20.597	11.173	11.173	0.000	0.000	0.000	0.000
75	A	321	PRO	0	0.015	0.011	23.913	-0.006	-0.006	0.000	0.000	0.000	0.000
76	A	322	ASP	-1	-0.771	-0.871	26.399	-9.688	-9.688	0.000	0.000	0.000	0.000
77	A	323	ILE	0	0.030	0.036	29.454	0.176	0.176	0.000	0.000	0.000	0.000
78	A	324	SER	0	-0.008	-0.002	28.143	-0.317	-0.317	0.000	0.000	0.000	0.000
79	A	325	GLN	0	0.049	0.015	28.010	0.254	0.254	0.000	0.000	0.000	0.000
80	A	326	ARG	1	0.962	0.967	27.332	8.975	8.975	0.000	0.000	0.000	0.000
81	A	327	LEU	0	-0.023	-0.013	24.615	0.055	0.055	0.000	0.000	0.000	0.000
82	A	328	VAL	0	0.028	0.031	24.190	-0.432	-0.432	0.000	0.000	0.000	0.000
83	A	329	TYR	0	-0.075	-0.050	20.147	0.006	0.006	0.000	0.000	0.000	0.000
84	A	330	GLN	0	0.046	0.023	21.076	0.456	0.456	0.000	0.000	0.000	0.000
85	A	331	PHE	0	-0.031	-0.027	14.405	-0.491	-0.491	0.000	0.000	0.000	0.000
86	A	332	VAL	0	-0.035	-0.017	17.529	0.534	0.534	0.000	0.000	0.000	0.000
87	A	333	HIS	0	0.019	0.015	15.440	0.419	0.419	0.000	0.000	0.000	0.000
88	A	334	PRO	-1	-0.828	-0.882	15.583	-15.117	-15.117	0.000	0.000	0.000	0.000

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