FMO DATABASE

FMODB ID: Y7552

Calculation Name: 1PL5-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1PL5

Chain ID: A

ChEMBL ID:

UniProt ID: P11978

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

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	-321130.509184
FMO2-HF: Nuclear repulsion	291295.307504
FMO2-HF: Total energy	-29835.201679
FMO2-MP2: Total energy	-29921.019924

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:1272:SER)

Summations of interaction energy for fragment #1(A:1272:SER)

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.
-78.892	-72.87	18.3	-13.077	-11.245	-0.129

Interaction energy analysis for fragmet #1(A:1272:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.811 / q_NPA : 0.889

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	1274	VAL	0	0.060	0.025	2.790	-0.060	3.279	0.355	-1.577	-2.117	0.009
4	A	1275	ASP	-1	-0.734	-0.863	1.785	-126.889	-124.860	17.935	-11.274	-8.690	-0.137
5	A	1276	ILE	0	-0.016	0.013	3.426	9.329	9.983	0.010	-0.226	-0.438	-0.001
6	A	1277	VAL	0	-0.005	-0.003	6.134	6.658	6.658	0.000	0.000	0.000	0.000
7	A	1278	LEU	0	0.015	0.006	6.219	3.790	3.790	0.000	0.000	0.000	0.000
8	A	1279	SER	0	0.010	-0.007	6.870	3.844	3.844	0.000	0.000	0.000	0.000
9	A	1280	LYS	1	0.911	0.965	9.430	29.665	29.665	0.000	0.000	0.000	0.000
10	A	1281	ALA	0	-0.004	0.004	11.682	2.112	2.112	0.000	0.000	0.000	0.000
11	A	1282	ALA	0	0.013	0.005	12.350	1.657	1.657	0.000	0.000	0.000	0.000
12	A	1283	SER	0	-0.025	-0.025	12.958	1.320	1.320	0.000	0.000	0.000	0.000
13	A	1284	ALA	0	0.023	0.012	15.413	1.293	1.293	0.000	0.000	0.000	0.000
14	A	1285	LEU	0	-0.020	-0.001	17.181	1.080	1.080	0.000	0.000	0.000	0.000
15	A	1286	ASP	-1	-0.786	-0.874	17.899	-15.146	-15.146	0.000	0.000	0.000	0.000
16	A	1287	GLU	-1	-0.915	-0.970	18.581	-16.178	-16.178	0.000	0.000	0.000	0.000
17	A	1288	LYS	1	0.821	0.911	21.413	13.939	13.939	0.000	0.000	0.000	0.000
18	A	1289	GLU	-1	-0.880	-0.946	22.653	-12.339	-12.339	0.000	0.000	0.000	0.000
19	A	1290	LYS	1	0.820	0.887	20.627	15.815	15.815	0.000	0.000	0.000	0.000
20	A	1291	GLN	0	0.010	0.009	25.601	0.398	0.398	0.000	0.000	0.000	0.000
21	A	1292	LEU	0	-0.005	0.015	27.161	0.597	0.597	0.000	0.000	0.000	0.000
22	A	1293	ALA	0	0.019	0.003	28.209	0.473	0.473	0.000	0.000	0.000	0.000
23	A	1294	VAL	0	-0.009	-0.009	29.693	0.415	0.415	0.000	0.000	0.000	0.000
24	A	1295	ALA	0	0.002	-0.001	31.589	0.387	0.387	0.000	0.000	0.000	0.000
25	A	1296	ASN	0	-0.029	-0.033	31.791	0.587	0.587	0.000	0.000	0.000	0.000
26	A	1297	GLU	-1	-0.824	-0.880	34.378	-8.592	-8.592	0.000	0.000	0.000	0.000
27	A	1298	ILE	0	-0.017	0.004	35.458	0.312	0.312	0.000	0.000	0.000	0.000
28	A	1299	ILE	0	0.003	0.003	36.182	0.265	0.265	0.000	0.000	0.000	0.000
29	A	1300	ARG	1	0.851	0.920	34.086	9.243	9.243	0.000	0.000	0.000	0.000
30	A	1301	SER	0	0.025	0.010	40.093	0.252	0.252	0.000	0.000	0.000	0.000
31	A	1302	LEU	0	0.009	-0.007	41.557	0.228	0.228	0.000	0.000	0.000	0.000
32	A	1303	SER	0	-0.035	-0.022	42.709	0.221	0.221	0.000	0.000	0.000	0.000
33	A	1304	ASP	-1	-0.882	-0.952	44.123	-7.123	-7.123	0.000	0.000	0.000	0.000
34	A	1305	GLU	-1	-1.033	-1.021	46.540	-6.625	-6.625	0.000	0.000	0.000	0.000
35	A	1306	VAL	0	-0.013	0.000	47.835	0.181	0.181	0.000	0.000	0.000	0.000
36	A	1307	MET	0	0.039	0.023	48.956	0.125	0.125	0.000	0.000	0.000	0.000
37	A	1308	ARG	1	0.910	0.958	47.155	6.879	6.879	0.000	0.000	0.000	0.000
38	A	1309	ASN	0	-0.035	-0.019	51.377	0.230	0.230	0.000	0.000	0.000	0.000
39	A	1310	GLU	-1	-0.902	-0.949	53.116	-6.020	-6.020	0.000	0.000	0.000	0.000
40	A	1311	ILE	0	-0.002	0.012	55.188	0.156	0.156	0.000	0.000	0.000	0.000
41	A	1312	ARG	1	0.953	0.972	55.343	5.880	5.880	0.000	0.000	0.000	0.000
42	A	1313	ILE	0	-0.011	-0.008	56.788	0.125	0.125	0.000	0.000	0.000	0.000
43	A	1314	THR	0	-0.003	-0.009	59.529	0.126	0.126	0.000	0.000	0.000	0.000
44	A	1315	SER	0	-0.035	-0.012	61.543	0.097	0.097	0.000	0.000	0.000	0.000
45	A	1316	LEU	0	-0.006	0.003	61.634	0.099	0.099	0.000	0.000	0.000	0.000
46	A	1317	GLN	0	-0.008	-0.004	62.533	0.095	0.095	0.000	0.000	0.000	0.000
47	A	1318	GLY	0	0.027	0.034	66.133	0.099	0.099	0.000	0.000	0.000	0.000
48	A	1319	ASP	-1	-0.840	-0.929	66.344	-4.808	-4.808	0.000	0.000	0.000	0.000
49	A	1320	LEU	0	-0.043	-0.011	68.705	0.119	0.119	0.000	0.000	0.000	0.000
50	A	1321	THR	0	-0.024	-0.035	69.800	0.098	0.098	0.000	0.000	0.000	0.000
51	A	1322	PHE	0	0.020	0.003	72.075	0.088	0.088	0.000	0.000	0.000	0.000
52	A	1323	THR	0	0.013	-0.003	72.551	0.091	0.091	0.000	0.000	0.000	0.000
53	A	1324	LYS	1	0.913	0.959	72.693	4.523	4.523	0.000	0.000	0.000	0.000
54	A	1325	LYS	1	0.873	0.916	76.443	4.165	4.165	0.000	0.000	0.000	0.000
55	A	1326	CYS	0	-0.033	-0.008	77.378	0.075	0.075	0.000	0.000	0.000	0.000
56	A	1327	LEU	0	-0.010	-0.006	78.946	0.067	0.067	0.000	0.000	0.000	0.000
57	A	1328	GLU	-1	-0.827	-0.892	80.619	-3.983	-3.983	0.000	0.000	0.000	0.000
58	A	1329	ASN	0	0.009	0.019	82.496	0.082	0.082	0.000	0.000	0.000	0.000
59	A	1330	ALA	0	0.044	0.020	83.720	0.058	0.058	0.000	0.000	0.000	0.000
60	A	1331	ARG	1	0.966	0.968	83.465	3.916	3.916	0.000	0.000	0.000	0.000
61	A	1332	SER	0	-0.005	0.006	86.280	0.051	0.051	0.000	0.000	0.000	0.000
62	A	1333	GLN	0	0.005	-0.011	87.212	0.096	0.096	0.000	0.000	0.000	0.000
63	A	1334	ILE	0	-0.032	-0.011	88.336	0.041	0.041	0.000	0.000	0.000	0.000
64	A	1335	SER	0	0.013	0.007	90.134	0.043	0.043	0.000	0.000	0.000	0.000
65	A	1336	GLU	-1	-0.913	-0.952	92.514	-3.486	-3.486	0.000	0.000	0.000	0.000
66	A	1337	LYS	1	0.858	0.926	92.004	3.597	3.597	0.000	0.000	0.000	0.000
67	A	1338	ASP	-1	-0.835	-0.919	93.857	-3.455	-3.455	0.000	0.000	0.000	0.000
68	A	1339	ALA	0	-0.030	-0.019	96.755	0.044	0.044	0.000	0.000	0.000	0.000
69	A	1340	LYS	1	0.811	0.899	95.433	3.458	3.458	0.000	0.000	0.000	0.000
70	A	1341	ILE	0	0.016	0.004	98.555	0.026	0.026	0.000	0.000	0.000	0.000
71	A	1342	ASN	0	0.011	0.013	99.876	0.051	0.051	0.000	0.000	0.000	0.000
72	A	1343	LYS	1	0.952	0.981	102.940	3.135	3.135	0.000	0.000	0.000	0.000
73	A	1344	LEU	0	-0.108	-0.067	103.292	0.021	0.021	0.000	0.000	0.000	0.000
74	A	1345	MET	0	-0.069	-0.035	103.093	0.000	0.000	0.000	0.000	0.000	0.000
75	A	1346	GLU	-2	-1.928	-1.929	107.156	-6.005	-6.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1272:SER)