FMO DATABASE

FMODB ID: G81L1

Calculation Name: 1Y4Y-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1Y4Y

Chain ID: A

ChEMBL ID:

UniProt ID: P42013

Base Structure: X-ray

Registration Date: 2025-10-03

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	87
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-545048.028072
FMO2-HF: Nuclear repulsion	513175.431051
FMO2-HF: Total energy	-31872.597022
FMO2-MP2: Total energy	-31964.935844

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:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
-85.599	-80.883	12.491	-9.358	-7.847	-0.096

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.785 / q_NPA : 0.885

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	A	4	LYS	1	0.940	0.981	3.846	28.746	30.713	-0.022	-1.028	-0.917	-0.003
63	A	64	THR	0	-0.043	-0.025	4.424	-2.673	-2.455	-0.001	-0.072	-0.144	0.000
64	A	65	ALA	0	0.069	0.030	2.611	12.164	13.555	0.158	-0.581	-0.967	-0.003
65	A	66	GLU	-1	-0.877	-0.928	1.784	-114.729	-114.902	11.407	-6.928	-4.307	-0.086
66	A	67	GLY	0	0.059	0.018	4.273	9.678	9.763	-0.001	-0.037	-0.047	0.000
69	A	70	ALA	0	0.021	0.012	2.986	-0.225	0.096	0.089	-0.112	-0.298	-0.001
70	A	71	ALA	0	-0.011	-0.004	3.629	-5.733	-5.216	0.015	-0.230	-0.301	-0.001
71	A	72	GLU	-1	-0.856	-0.943	5.099	-28.809	-28.805	-0.001	-0.003	0.000	0.000
73	A	74	MET	0	-0.027	-0.015	2.532	0.359	0.745	0.847	-0.367	-0.866	-0.002
4	A	5	THR	0	0.004	0.004	6.585	1.603	1.603	0.000	0.000	0.000	0.000
5	A	6	PHE	0	0.001	0.000	8.508	-0.058	-0.058	0.000	0.000	0.000	0.000
6	A	7	LYS	1	0.851	0.917	12.901	15.308	15.308	0.000	0.000	0.000	0.000
7	A	8	VAL	0	-0.005	-0.006	16.771	0.194	0.194	0.000	0.000	0.000	0.000
8	A	9	VAL	0	-0.028	-0.022	18.832	0.760	0.760	0.000	0.000	0.000	0.000
9	A	10	SER	0	0.001	0.012	21.369	1.025	1.025	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.826	-0.918	23.338	-11.069	-11.069	0.000	0.000	0.000	0.000
11	A	12	SER	0	-0.071	-0.029	25.007	0.117	0.117	0.000	0.000	0.000	0.000
12	A	13	GLY	0	0.025	0.020	22.323	-0.077	-0.077	0.000	0.000	0.000	0.000
13	A	14	ILE	0	-0.033	-0.010	16.215	-0.159	-0.159	0.000	0.000	0.000	0.000
14	A	15	HIS	0	0.032	0.003	20.281	-0.185	-0.185	0.000	0.000	0.000	0.000
15	A	16	ALA	0	0.029	-0.001	22.753	-0.034	-0.034	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.997	1.011	22.827	11.608	11.608	0.000	0.000	0.000	0.000
17	A	18	PRO	0	0.077	0.041	20.984	-0.380	-0.380	0.000	0.000	0.000	0.000
18	A	19	ALA	0	0.018	0.015	18.333	-0.880	-0.880	0.000	0.000	0.000	0.000
19	A	20	THR	0	-0.067	-0.049	18.066	-0.657	-0.657	0.000	0.000	0.000	0.000
20	A	21	ILE	0	0.016	0.013	18.084	-0.531	-0.531	0.000	0.000	0.000	0.000
21	A	22	LEU	0	0.013	0.028	12.581	-0.740	-0.740	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.014	0.010	13.891	-1.251	-1.251	0.000	0.000	0.000	0.000
23	A	24	GLN	0	-0.024	-0.017	15.114	-0.516	-0.516	0.000	0.000	0.000	0.000
24	A	25	THR	0	-0.052	-0.013	11.918	0.006	0.006	0.000	0.000	0.000	0.000
25	A	26	ALA	0	0.042	0.010	10.765	-0.948	-0.948	0.000	0.000	0.000	0.000
26	A	27	SER	0	-0.080	-0.061	11.707	-0.543	-0.543	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.894	0.959	13.458	20.016	20.016	0.000	0.000	0.000	0.000
28	A	29	PHE	0	-0.026	0.010	9.452	0.492	0.492	0.000	0.000	0.000	0.000
29	A	30	ASN	0	-0.068	-0.059	11.369	1.663	1.663	0.000	0.000	0.000	0.000
30	A	31	SER	0	-0.054	-0.053	6.371	-1.004	-1.004	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.908	-0.928	7.738	-26.448	-26.448	0.000	0.000	0.000	0.000
32	A	33	ILE	0	0.001	-0.011	6.316	-6.520	-6.520	0.000	0.000	0.000	0.000
33	A	34	GLN	0	-0.090	-0.054	6.152	8.663	8.663	0.000	0.000	0.000	0.000
34	A	35	LEU	0	-0.003	-0.001	8.678	-2.674	-2.674	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.897	-0.954	11.418	-22.140	-22.140	0.000	0.000	0.000	0.000
36	A	37	TYR	0	0.045	0.012	12.956	0.203	0.203	0.000	0.000	0.000	0.000
37	A	38	ASN	0	-0.012	0.000	16.402	0.830	0.830	0.000	0.000	0.000	0.000
38	A	39	GLY	0	0.015	0.014	15.891	1.000	1.000	0.000	0.000	0.000	0.000
39	A	40	LYS	1	0.879	0.955	16.444	16.296	16.296	0.000	0.000	0.000	0.000
40	A	41	THR	0	0.034	0.004	10.802	-1.233	-1.233	0.000	0.000	0.000	0.000
41	A	42	VAL	0	-0.079	-0.036	13.163	1.630	1.630	0.000	0.000	0.000	0.000
42	A	43	ASN	0	0.049	0.027	11.805	-2.660	-2.660	0.000	0.000	0.000	0.000
43	A	44	LEU	0	0.021	0.000	9.794	1.934	1.934	0.000	0.000	0.000	0.000
44	A	45	LYS	1	0.889	0.937	10.863	27.652	27.652	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.045	-0.019	14.570	1.782	1.782	0.000	0.000	0.000	0.000
46	A	47	ILE	0	0.070	0.028	17.355	-0.168	-0.168	0.000	0.000	0.000	0.000
47	A	48	MET	0	0.008	0.004	19.551	0.386	0.386	0.000	0.000	0.000	0.000
48	A	49	GLY	0	0.029	0.020	17.924	0.326	0.326	0.000	0.000	0.000	0.000
49	A	50	VAL	0	0.035	0.026	15.529	0.061	0.061	0.000	0.000	0.000	0.000
50	A	51	MET	0	-0.026	-0.009	18.117	0.392	0.392	0.000	0.000	0.000	0.000
51	A	52	SER	0	-0.085	-0.057	20.099	0.405	0.405	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.058	-0.032	15.643	0.232	0.232	0.000	0.000	0.000	0.000
53	A	54	GLY	0	0.014	0.019	20.360	0.147	0.147	0.000	0.000	0.000	0.000
54	A	55	ILE	0	0.000	0.004	16.837	0.274	0.274	0.000	0.000	0.000	0.000
55	A	56	PRO	0	0.035	0.021	21.158	0.267	0.267	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.900	0.931	22.145	10.765	10.765	0.000	0.000	0.000	0.000
57	A	58	GLY	0	-0.047	-0.015	22.418	0.280	0.280	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.024	0.024	19.435	-0.147	-0.147	0.000	0.000	0.000	0.000
59	A	60	THR	0	-0.001	-0.001	15.148	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	61	ILE	0	-0.008	-0.003	13.142	0.462	0.462	0.000	0.000	0.000	0.000
61	A	62	LYS	1	0.938	0.982	7.506	33.942	33.942	0.000	0.000	0.000	0.000
62	A	63	ILE	0	0.007	0.011	6.258	1.209	1.209	0.000	0.000	0.000	0.000
67	A	68	ALA	0	-0.028	-0.015	6.459	-3.468	-3.468	0.000	0.000	0.000	0.000
68	A	69	ASP	-1	-0.704	-0.804	8.430	-29.054	-29.054	0.000	0.000	0.000	0.000
72	A	73	ALA	0	0.006	0.011	5.532	2.155	2.155	0.000	0.000	0.000	0.000
74	A	75	ALA	0	-0.013	0.012	5.721	3.422	3.422	0.000	0.000	0.000	0.000
75	A	76	ALA	0	0.008	-0.006	8.727	2.328	2.328	0.000	0.000	0.000	0.000
76	A	77	LEU	0	-0.005	-0.011	7.451	2.089	2.089	0.000	0.000	0.000	0.000
77	A	78	THR	0	0.004	0.002	8.646	1.146	1.146	0.000	0.000	0.000	0.000
78	A	79	ASP	-1	-0.881	-0.938	11.144	-17.091	-17.091	0.000	0.000	0.000	0.000
79	A	80	THR	0	-0.082	-0.056	13.636	1.463	1.463	0.000	0.000	0.000	0.000
80	A	81	LEU	0	-0.035	-0.010	11.674	1.135	1.135	0.000	0.000	0.000	0.000
81	A	82	ALA	0	0.062	0.038	15.312	1.004	1.004	0.000	0.000	0.000	0.000
82	A	83	LYS	1	0.844	0.917	16.767	17.572	17.572	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.919	-0.971	18.863	-13.046	-13.046	0.000	0.000	0.000	0.000
84	A	85	GLY	0	0.004	0.012	20.278	0.405	0.405	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.062	-0.036	17.368	0.264	0.264	0.000	0.000	0.000	0.000
86	A	87	ALA	0	-0.014	-0.033	14.993	0.297	0.297	0.000	0.000	0.000	0.000
87	A	88	GLU	-2	-1.821	-1.885	13.740	-35.903	-35.903	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)