FMO DATABASE

FMODB ID: LR929

Calculation Name: 1YSH-D-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1YSH

Chain ID: D

ChEMBL ID:

UniProt ID: Q5I7K9

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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	71
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-397801.666772
FMO2-HF: Nuclear repulsion	368900.708871
FMO2-HF: Total energy	-28900.957901
FMO2-MP2: Total energy	-28981.693363

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(D:10:ILE)

Summations of interaction energy for fragment #1(D:10:ILE)

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.
173.95	186.132	13.905	-12.262	-13.824	-0.121

Interaction energy analysis for fragmet #1(D:10:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.864 / q_NPA : 0.922

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	D	12	GLY	0	0.038	0.034	2.444	4.564	8.094	0.253	-1.662	-2.121	-0.005
4	D	13	LYS	1	0.978	0.988	3.349	69.143	69.863	0.003	-0.245	-0.478	0.000
17	D	26	ILE	0	0.044	0.022	4.660	-2.283	-2.201	-0.001	-0.007	-0.074	0.000
18	D	27	LYS	1	0.937	0.967	2.169	32.400	33.574	2.329	-0.696	-2.807	-0.003
19	D	28	LYS	1	0.957	0.986	3.994	22.378	22.718	0.000	-0.038	-0.302	0.000
21	D	30	GLU	-1	-0.857	-0.932	1.916	-125.720	-120.052	11.251	-9.423	-7.496	-0.112
22	D	31	VAL	0	0.032	0.006	2.945	-1.677	-1.030	0.070	-0.163	-0.554	-0.001
23	D	32	SER	0	0.008	0.006	4.266	5.480	5.501	0.000	-0.028	0.008	0.000
5	D	14	TYR	0	0.032	0.012	6.388	1.460	1.460	0.000	0.000	0.000	0.000
6	D	15	GLY	0	0.026	0.030	7.842	3.313	3.313	0.000	0.000	0.000	0.000
7	D	16	THR	0	0.022	0.001	9.196	-1.091	-1.091	0.000	0.000	0.000	0.000
8	D	17	ARG	1	0.968	0.989	11.677	22.602	22.602	0.000	0.000	0.000	0.000
9	D	18	TYR	0	0.015	-0.009	11.314	-2.263	-2.263	0.000	0.000	0.000	0.000
10	D	19	GLY	0	0.075	0.059	13.428	0.381	0.381	0.000	0.000	0.000	0.000
11	D	20	ALA	0	-0.007	-0.015	11.629	-1.925	-1.925	0.000	0.000	0.000	0.000
12	D	21	SER	0	0.097	0.032	10.453	-2.215	-2.215	0.000	0.000	0.000	0.000
13	D	22	LEU	0	0.087	0.072	9.645	-1.940	-1.940	0.000	0.000	0.000	0.000
14	D	23	ARG	1	0.928	0.944	6.744	22.611	22.611	0.000	0.000	0.000	0.000
15	D	24	LYS	1	0.863	0.932	5.824	21.082	21.082	0.000	0.000	0.000	0.000
16	D	25	GLN	0	0.057	0.028	7.087	-1.952	-1.952	0.000	0.000	0.000	0.000
20	D	29	MET	0	0.009	0.015	6.843	0.807	0.807	0.000	0.000	0.000	0.000
24	D	33	GLN	0	0.026	0.042	7.018	4.420	4.420	0.000	0.000	0.000	0.000
25	D	34	HIS	0	-0.044	-0.031	5.468	3.256	3.256	0.000	0.000	0.000	0.000
26	D	35	SER	0	0.022	0.017	7.495	1.123	1.123	0.000	0.000	0.000	0.000
27	D	36	LYS	0	-0.021	-0.007	9.422	0.603	0.603	0.000	0.000	0.000	0.000
28	D	37	TYR	0	-0.020	-0.041	10.583	1.514	1.514	0.000	0.000	0.000	0.000
29	D	38	PHE	0	0.028	0.020	15.575	0.120	0.120	0.000	0.000	0.000	0.000
30	D	39	CYS	0	-0.196	-0.087	17.859	-1.561	-1.561	0.000	0.000	0.000	0.000
31	D	40	GLU	-1	-0.827	-0.914	21.588	-13.247	-13.247	0.000	0.000	0.000	0.000
32	D	41	PHE	0	0.000	0.013	24.504	0.341	0.341	0.000	0.000	0.000	0.000
33	D	42	CYS	0	0.064	0.015	23.254	0.897	0.897	0.000	0.000	0.000	0.000
34	D	43	GLY	0	0.081	0.037	24.798	-0.361	-0.361	0.000	0.000	0.000	0.000
35	D	44	LYS	1	0.867	0.919	22.045	13.451	13.451	0.000	0.000	0.000	0.000
36	D	45	PHE	0	0.054	0.023	16.751	-0.309	-0.309	0.000	0.000	0.000	0.000
37	D	46	ALA	0	0.006	-0.002	17.335	-0.902	-0.902	0.000	0.000	0.000	0.000
38	D	47	VAL	0	0.016	0.007	16.279	-0.132	-0.132	0.000	0.000	0.000	0.000
39	D	48	LYS	1	0.788	0.890	8.768	29.806	29.806	0.000	0.000	0.000	0.000
40	D	49	ARG	1	0.923	0.980	9.409	28.731	28.731	0.000	0.000	0.000	0.000
41	D	50	LYS	1	0.825	0.912	13.880	18.938	18.938	0.000	0.000	0.000	0.000
42	D	51	ALA	0	0.080	0.040	15.418	-0.269	-0.269	0.000	0.000	0.000	0.000
43	D	52	VAL	0	-0.031	-0.029	13.119	-0.733	-0.733	0.000	0.000	0.000	0.000
44	D	53	GLY	0	0.027	0.035	15.570	0.943	0.943	0.000	0.000	0.000	0.000
45	D	54	ILE	0	-0.008	0.013	17.410	0.871	0.871	0.000	0.000	0.000	0.000
46	D	55	TRP	0	0.006	-0.017	12.048	-2.154	-2.154	0.000	0.000	0.000	0.000
47	D	56	GLY	0	0.052	0.028	17.476	1.072	1.072	0.000	0.000	0.000	0.000
48	D	58	LYS	1	0.870	0.930	15.021	19.927	19.927	0.000	0.000	0.000	0.000
49	D	59	ASP	-1	-0.783	-0.879	20.113	-13.832	-13.832	0.000	0.000	0.000	0.000
50	D	61	GLY	0	0.034	0.030	23.532	0.390	0.390	0.000	0.000	0.000	0.000
51	D	62	LYS	0	0.003	0.007	23.271	-0.242	-0.242	0.000	0.000	0.000	0.000
52	D	63	VAL	0	0.024	0.003	21.374	-0.872	-0.872	0.000	0.000	0.000	0.000
53	D	64	LYS	1	0.867	0.935	20.635	15.199	15.199	0.000	0.000	0.000	0.000
54	D	65	ALA	0	0.047	0.026	21.204	-0.715	-0.715	0.000	0.000	0.000	0.000
55	D	66	GLY	0	0.025	0.000	19.392	0.152	0.152	0.000	0.000	0.000	0.000
56	D	67	GLY	0	0.028	0.028	17.419	0.303	0.303	0.000	0.000	0.000	0.000
57	D	68	ALA	0	-0.004	-0.008	15.104	-0.689	-0.689	0.000	0.000	0.000	0.000
58	D	69	TYR	0	-0.013	-0.036	10.298	-1.223	-1.223	0.000	0.000	0.000	0.000
59	D	70	THR	0	0.010	-0.013	11.355	-2.331	-2.331	0.000	0.000	0.000	0.000
60	D	71	MET	0	-0.001	0.024	13.873	0.827	0.827	0.000	0.000	0.000	0.000
61	D	72	ASN	0	0.045	0.024	16.927	0.165	0.165	0.000	0.000	0.000	0.000
62	D	73	THR	0	0.035	0.013	17.358	-0.780	-0.780	0.000	0.000	0.000	0.000
63	D	74	ALA	0	0.079	0.033	19.622	0.456	0.456	0.000	0.000	0.000	0.000
64	D	75	SER	0	0.043	0.030	21.968	0.323	0.323	0.000	0.000	0.000	0.000
65	D	76	ALA	0	0.014	0.004	22.252	0.398	0.398	0.000	0.000	0.000	0.000
66	D	77	VAL	0	-0.042	-0.019	22.021	0.186	0.186	0.000	0.000	0.000	0.000
67	D	78	THR	0	0.007	-0.007	24.798	0.404	0.404	0.000	0.000	0.000	0.000
68	D	79	VAL	0	0.010	-0.002	27.183	0.260	0.260	0.000	0.000	0.000	0.000
69	D	80	ARG	1	0.791	0.894	23.130	12.750	12.750	0.000	0.000	0.000	0.000
70	D	81	SER	0	-0.070	-0.021	29.599	0.184	0.184	0.000	0.000	0.000	0.000
71	D	82	THR	-1	-0.921	-0.941	31.965	-8.863	-8.863	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:10:ILE)