FMO DATABASE

FMODB ID: 5Y89Z

Calculation Name: 4Z8A-A-Xray547

Preferred Name:

Target Type:

Ligand Name: amino group | acetyl group

Ligand 3-letter code: NH2 | ACE

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4Z8A

Chain ID: A

ChEMBL ID:

UniProt ID: P91645

Base Structure: X-ray

Registration Date: 2025-10-04

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	75
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-435544.644679
FMO2-HF: Nuclear repulsion	405641.974544
FMO2-HF: Total energy	-29902.670135
FMO2-MP2: Total energy	-29987.744659

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:1433:GLY)

Summations of interaction energy for fragment #1(A:1433:GLY)

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.
-151.396	-150.013	0.005	-0.7	-0.688	-0.004

Interaction energy analysis for fragmet #1(A:1433:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.868 / q_NPA : 0.921

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	1435	LEU	0	0.005	0.010	3.473	8.336	9.337	0.004	-0.423	-0.582	-0.002
4	A	1436	GLY	0	0.010	-0.005	3.604	-13.495	-13.113	0.001	-0.277	-0.106	-0.002
5	A	1437	SER	0	-0.020	-0.001	5.746	4.228	4.228	0.000	0.000	0.000	0.000
6	A	1438	PRO	0	-0.004	-0.014	6.853	-4.264	-4.264	0.000	0.000	0.000	0.000
7	A	1439	GLU	-1	-0.931	-0.950	5.679	-42.827	-42.827	0.000	0.000	0.000	0.000
8	A	1440	PHE	0	-0.063	-0.037	8.782	2.533	2.533	0.000	0.000	0.000	0.000
9	A	1441	ASN	0	0.082	0.040	10.423	0.011	0.011	0.000	0.000	0.000	0.000
10	A	1442	ARG	1	0.890	0.944	12.277	18.400	18.400	0.000	0.000	0.000	0.000
11	A	1443	PRO	0	0.032	0.020	15.875	-0.063	-0.063	0.000	0.000	0.000	0.000
12	A	1444	VAL	0	0.012	0.013	17.377	0.595	0.595	0.000	0.000	0.000	0.000
13	A	1445	LYS	1	0.915	0.957	16.434	17.388	17.388	0.000	0.000	0.000	0.000
14	A	1446	ARG	1	0.930	0.968	20.771	12.767	12.767	0.000	0.000	0.000	0.000
15	A	1447	MET	0	0.009	0.016	21.280	-0.565	-0.565	0.000	0.000	0.000	0.000
16	A	1448	ILE	0	-0.024	-0.006	24.837	0.382	0.382	0.000	0.000	0.000	0.000
17	A	1449	ALA	0	0.074	0.049	27.849	-0.301	-0.301	0.000	0.000	0.000	0.000
18	A	1450	LEU	0	-0.048	-0.030	27.786	0.352	0.352	0.000	0.000	0.000	0.000
19	A	1451	TYR	0	-0.051	-0.024	30.269	0.428	0.428	0.000	0.000	0.000	0.000
20	A	1452	ASP	-1	-0.819	-0.894	33.509	-8.491	-8.491	0.000	0.000	0.000	0.000
21	A	1453	TYR	0	-0.072	-0.070	32.507	-0.073	-0.073	0.000	0.000	0.000	0.000
22	A	1454	ASP	-1	-0.802	-0.919	35.004	-8.155	-8.155	0.000	0.000	0.000	0.000
23	A	1455	PRO	0	0.000	-0.001	34.260	0.035	0.035	0.000	0.000	0.000	0.000
24	A	1456	GLN	0	0.000	-0.003	36.292	0.190	0.190	0.000	0.000	0.000	0.000
25	A	1457	GLU	-1	-1.057	-1.017	39.170	-7.557	-7.557	0.000	0.000	0.000	0.000
26	A	1458	LEU	0	-0.088	-0.049	35.300	0.029	0.029	0.000	0.000	0.000	0.000
27	A	1459	SER	0	-0.012	-0.005	33.194	-0.248	-0.248	0.000	0.000	0.000	0.000
28	A	1460	PRO	0	-0.099	-0.042	31.764	0.279	0.279	0.000	0.000	0.000	0.000
29	A	1461	ASN	0	-0.042	-0.025	29.885	0.050	0.050	0.000	0.000	0.000	0.000
30	A	1462	VAL	0	-0.048	-0.035	33.808	0.257	0.257	0.000	0.000	0.000	0.000
31	A	1463	ASP	-1	-0.911	-0.964	32.298	-9.635	-9.635	0.000	0.000	0.000	0.000
32	A	1464	ALA	0	0.052	0.037	33.934	-0.120	-0.120	0.000	0.000	0.000	0.000
33	A	1465	GLU	-1	-0.885	-0.964	34.932	-8.490	-8.490	0.000	0.000	0.000	0.000
34	A	1466	GLN	0	-0.110	-0.054	35.960	0.011	0.011	0.000	0.000	0.000	0.000
35	A	1467	VAL	0	-0.026	-0.004	30.751	-0.099	-0.099	0.000	0.000	0.000	0.000
36	A	1468	GLU	-1	-0.734	-0.812	30.644	-10.403	-10.403	0.000	0.000	0.000	0.000
37	A	1469	LEU	0	-0.077	-0.029	29.863	0.297	0.297	0.000	0.000	0.000	0.000
38	A	1470	CYS	0	-0.016	-0.001	32.496	-0.091	-0.091	0.000	0.000	0.000	0.000
39	A	1471	PHE	0	-0.041	-0.011	30.009	-0.112	-0.112	0.000	0.000	0.000	0.000
40	A	1472	LYS	1	0.850	0.918	34.798	8.226	8.226	0.000	0.000	0.000	0.000
41	A	1473	THR	0	0.000	-0.032	34.311	-0.306	-0.306	0.000	0.000	0.000	0.000
42	A	1474	GLY	0	-0.068	-0.035	33.413	0.255	0.255	0.000	0.000	0.000	0.000
43	A	1475	GLU	-1	-0.854	-0.914	33.281	-9.037	-9.037	0.000	0.000	0.000	0.000
44	A	1476	ILE	0	-0.079	-0.055	27.770	-0.379	-0.379	0.000	0.000	0.000	0.000
45	A	1477	ILE	0	0.052	0.051	26.585	0.124	0.124	0.000	0.000	0.000	0.000
46	A	1478	LEU	0	-0.059	-0.038	25.397	-0.580	-0.580	0.000	0.000	0.000	0.000
47	A	1479	VAL	0	0.047	0.016	20.154	0.211	0.211	0.000	0.000	0.000	0.000
48	A	1480	TYR	0	-0.083	-0.051	20.924	-0.368	-0.368	0.000	0.000	0.000	0.000
49	A	1481	GLY	0	-0.015	-0.013	16.886	0.068	0.068	0.000	0.000	0.000	0.000
50	A	1482	ASP	-1	-0.954	-0.974	13.483	-22.811	-22.811	0.000	0.000	0.000	0.000
51	A	1483	MET	0	-0.052	-0.018	16.373	0.923	0.923	0.000	0.000	0.000	0.000
52	A	1484	ASP	-1	-0.842	-0.926	17.701	-14.726	-14.726	0.000	0.000	0.000	0.000
53	A	1485	GLU	-1	-1.005	-1.016	19.046	-15.228	-15.228	0.000	0.000	0.000	0.000
54	A	1486	ASP	-1	-0.930	-0.949	19.996	-12.472	-12.472	0.000	0.000	0.000	0.000
55	A	1487	GLY	0	-0.039	-0.012	21.108	0.378	0.378	0.000	0.000	0.000	0.000
56	A	1488	PHE	0	0.001	-0.003	22.159	0.309	0.309	0.000	0.000	0.000	0.000
57	A	1489	TYR	0	0.014	0.004	17.807	-0.594	-0.594	0.000	0.000	0.000	0.000
58	A	1490	MET	0	0.003	0.013	22.298	0.813	0.813	0.000	0.000	0.000	0.000
59	A	1491	GLY	0	0.027	0.004	23.809	-0.478	-0.478	0.000	0.000	0.000	0.000
60	A	1492	GLU	-1	-0.980	-1.013	26.487	-10.060	-10.060	0.000	0.000	0.000	0.000
61	A	1493	LEU	0	0.058	0.031	29.247	-0.303	-0.303	0.000	0.000	0.000	0.000
62	A	1494	ASP	-1	-0.903	-0.935	32.274	-8.677	-8.677	0.000	0.000	0.000	0.000
63	A	1495	GLY	0	-0.071	-0.035	33.972	0.292	0.292	0.000	0.000	0.000	0.000
64	A	1496	VAL	0	-0.050	-0.023	34.364	0.036	0.036	0.000	0.000	0.000	0.000
65	A	1497	ARG	1	0.891	0.929	27.577	10.640	10.640	0.000	0.000	0.000	0.000
66	A	1498	GLY	0	0.034	0.018	29.351	0.319	0.319	0.000	0.000	0.000	0.000
67	A	1499	LEU	0	-0.003	-0.002	25.223	-0.341	-0.341	0.000	0.000	0.000	0.000
68	A	1500	VAL	0	0.012	0.005	25.459	0.441	0.441	0.000	0.000	0.000	0.000
69	A	1501	PRO	0	0.045	0.043	25.613	-0.624	-0.624	0.000	0.000	0.000	0.000
70	A	1502	SER	0	0.000	-0.029	22.021	0.156	0.156	0.000	0.000	0.000	0.000
71	A	1503	ASN	0	-0.013	-0.012	23.991	-0.043	-0.043	0.000	0.000	0.000	0.000
72	A	1504	PHE	0	-0.005	0.000	26.054	0.432	0.432	0.000	0.000	0.000	0.000
73	A	1505	LEU	0	-0.057	-0.032	24.059	0.352	0.352	0.000	0.000	0.000	0.000
74	A	1506	ALA	0	-0.047	-0.027	25.307	0.021	0.021	0.000	0.000	0.000	0.000
75	A	1507	ASP	-2	-1.931	-1.953	19.784	-29.944	-29.944	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1433:GLY)