FMO DATABASE

FMODB ID: 4Y5RN

Calculation Name: 3P3D-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3P3D

Chain ID: A

ChEMBL ID:

UniProt ID: A5DMN1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-588787.695695
FMO2-HF: Nuclear repulsion	555539.053505
FMO2-HF: Total energy	-33248.64219
FMO2-MP2: Total energy	-33347.852097

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:266:LEU)

Summations of interaction energy for fragment #1(A:266:LEU)

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.
-145.902	-136.524	4.898	-4.102	-10.177	-0.042

Interaction energy analysis for fragmet #1(A:266:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.826 / q_NPA : 0.909

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	268	ILE	0	0.039	0.036	3.847	-2.923	-0.769	-0.026	-1.101	-1.028	-0.002
27	A	292	LEU	0	-0.011	-0.012	4.760	1.838	1.942	-0.001	-0.003	-0.099	0.000
50	A	326	THR	0	-0.101	-0.103	3.121	-10.750	-10.348	0.041	-0.126	-0.318	-0.001
51	A	327	TYR	0	0.014	-0.008	3.334	4.522	5.357	0.019	-0.212	-0.643	0.000
52	A	328	ASP	-1	-0.865	-0.931	2.848	-45.985	-43.666	0.587	-1.367	-1.539	-0.013
53	A	329	ASN	0	-0.061	-0.045	2.516	-3.466	-1.479	1.121	-1.142	-1.966	-0.010
54	A	330	PRO	0	-0.028	-0.039	2.315	-10.553	-8.345	2.831	-1.151	-3.889	-0.014
55	A	331	ALA	0	0.023	0.029	2.931	1.084	-0.084	0.146	1.235	-0.213	0.000
57	A	333	ALA	0	-0.035	-0.013	3.010	-0.424	0.073	0.181	-0.230	-0.448	-0.002
58	A	334	VAL	0	-0.066	-0.031	4.895	2.733	2.773	-0.001	-0.005	-0.034	0.000
4	A	269	LEU	0	-0.027	-0.019	6.966	0.606	0.606	0.000	0.000	0.000	0.000
5	A	270	VAL	0	0.041	0.027	10.387	0.717	0.717	0.000	0.000	0.000	0.000
6	A	271	PHE	0	-0.014	-0.022	13.280	0.999	0.999	0.000	0.000	0.000	0.000
7	A	272	GLY	0	0.023	0.018	16.734	0.146	0.146	0.000	0.000	0.000	0.000
8	A	273	TYR	0	0.012	0.035	16.734	0.476	0.476	0.000	0.000	0.000	0.000
9	A	274	PRO	0	0.057	0.015	21.721	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	275	GLU	-1	-0.758	-0.867	22.815	-13.509	-13.509	0.000	0.000	0.000	0.000
11	A	276	THR	0	-0.051	-0.023	23.688	-0.279	-0.279	0.000	0.000	0.000	0.000
12	A	277	MET	0	-0.026	-0.005	21.868	0.321	0.321	0.000	0.000	0.000	0.000
13	A	278	ALA	0	0.023	0.023	19.529	-0.463	-0.463	0.000	0.000	0.000	0.000
14	A	279	ASN	0	0.033	0.000	18.822	-1.380	-1.380	0.000	0.000	0.000	0.000
15	A	280	GLN	0	0.008	0.004	19.448	-0.250	-0.250	0.000	0.000	0.000	0.000
16	A	281	VAL	0	0.014	0.016	15.899	-0.321	-0.321	0.000	0.000	0.000	0.000
17	A	282	ILE	0	0.008	-0.004	14.055	-0.882	-0.882	0.000	0.000	0.000	0.000
18	A	283	ALA	0	-0.028	-0.014	14.604	-0.911	-0.911	0.000	0.000	0.000	0.000
19	A	284	TYR	0	-0.061	-0.044	16.097	-0.364	-0.364	0.000	0.000	0.000	0.000
20	A	285	PHE	0	0.016	-0.001	11.370	-0.572	-0.572	0.000	0.000	0.000	0.000
21	A	286	GLN	0	0.016	0.011	11.182	-2.555	-2.555	0.000	0.000	0.000	0.000
22	A	287	GLU	-1	-0.948	-0.971	12.662	-16.936	-16.936	0.000	0.000	0.000	0.000
23	A	288	PHE	0	-0.008	0.011	9.969	-0.257	-0.257	0.000	0.000	0.000	0.000
24	A	289	GLY	0	-0.019	-0.002	8.730	-2.100	-2.100	0.000	0.000	0.000	0.000
25	A	290	THR	0	-0.044	-0.026	8.807	1.499	1.499	0.000	0.000	0.000	0.000
26	A	291	ILE	0	-0.026	-0.010	7.468	-4.146	-4.146	0.000	0.000	0.000	0.000
28	A	293	GLU	-1	-0.775	-0.863	8.252	-34.633	-34.633	0.000	0.000	0.000	0.000
29	A	294	ASP	-1	-0.849	-0.893	10.874	-16.631	-16.631	0.000	0.000	0.000	0.000
30	A	295	PHE	0	0.033	-0.002	11.427	1.293	1.293	0.000	0.000	0.000	0.000
31	A	296	GLU	0	-0.043	-0.060	15.992	0.509	0.509	0.000	0.000	0.000	0.000
32	A	297	VAL	0	-0.063	-0.028	17.711	0.558	0.558	0.000	0.000	0.000	0.000
33	A	298	LEU	0	-0.017	-0.007	13.036	0.132	0.132	0.000	0.000	0.000	0.000
34	A	299	ARG	0	-0.070	-0.012	17.035	0.545	0.545	0.000	0.000	0.000	0.000
35	A	300	LYS	1	0.909	0.950	15.735	18.157	18.157	0.000	0.000	0.000	0.000
36	A	301	PRO	-1	-0.943	-0.955	20.847	-12.573	-12.573	0.000	0.000	0.000	0.000
37	A	313	PHE	0	0.001	-0.012	10.853	-0.362	-0.362	0.000	0.000	0.000	0.000
38	A	314	VAL	0	-0.014	-0.005	6.664	-1.303	-1.303	0.000	0.000	0.000	0.000
39	A	315	PRO	0	-0.022	-0.004	10.089	1.229	1.229	0.000	0.000	0.000	0.000
40	A	316	ILE	0	0.016	0.008	11.450	-2.031	-2.031	0.000	0.000	0.000	0.000
41	A	317	PHE	0	-0.041	-0.012	11.311	0.740	0.740	0.000	0.000	0.000	0.000
42	A	318	SER	0	0.023	-0.008	13.441	-1.417	-1.417	0.000	0.000	0.000	0.000
43	A	319	GLY	0	0.021	0.021	16.195	0.795	0.795	0.000	0.000	0.000	0.000
44	A	320	ASN	0	-0.083	-0.063	19.542	-0.306	-0.306	0.000	0.000	0.000	0.000
45	A	321	SER	0	-0.036	-0.030	20.719	-0.152	-0.152	0.000	0.000	0.000	0.000
46	A	322	TRP	0	-0.010	0.001	13.252	-1.277	-1.277	0.000	0.000	0.000	0.000
47	A	323	THR	0	0.009	-0.011	12.908	0.811	0.811	0.000	0.000	0.000	0.000
48	A	324	LYS	1	0.846	0.955	5.814	41.754	41.754	0.000	0.000	0.000	0.000
49	A	325	ILE	0	0.002	0.012	7.808	1.866	1.866	0.000	0.000	0.000	0.000
56	A	332	SER	0	0.079	0.025	5.522	0.277	0.277	0.000	0.000	0.000	0.000
59	A	335	ASP	-1	-0.896	-0.959	7.458	-23.704	-23.704	0.000	0.000	0.000	0.000
60	A	336	ALA	0	0.030	0.015	8.092	2.036	2.036	0.000	0.000	0.000	0.000
61	A	337	LEU	0	-0.051	-0.032	8.215	1.465	1.465	0.000	0.000	0.000	0.000
62	A	338	LEU	0	-0.048	-0.024	10.151	2.002	2.002	0.000	0.000	0.000	0.000
63	A	339	GLU	-1	-0.841	-0.890	13.120	-16.876	-16.876	0.000	0.000	0.000	0.000
64	A	340	ASN	0	-0.046	-0.008	13.968	0.812	0.812	0.000	0.000	0.000	0.000
65	A	341	GLY	0	-0.031	-0.019	15.669	0.660	0.660	0.000	0.000	0.000	0.000
66	A	342	ALA	0	0.016	0.020	18.238	1.017	1.017	0.000	0.000	0.000	0.000
67	A	343	VAL	0	-0.051	-0.035	19.883	0.072	0.072	0.000	0.000	0.000	0.000
68	A	344	PHE	0	0.030	0.014	20.196	0.112	0.112	0.000	0.000	0.000	0.000
69	A	345	ASN	0	-0.039	-0.037	22.523	0.250	0.250	0.000	0.000	0.000	0.000
70	A	346	GLY	0	-0.004	0.005	25.710	0.314	0.314	0.000	0.000	0.000	0.000
71	A	347	VAL	0	-0.032	-0.013	22.586	0.329	0.329	0.000	0.000	0.000	0.000
72	A	348	LEU	0	-0.019	-0.009	21.881	-0.165	-0.165	0.000	0.000	0.000	0.000
73	A	349	LEU	0	-0.010	0.006	16.918	-0.072	-0.072	0.000	0.000	0.000	0.000
74	A	350	GLY	0	0.022	0.021	16.607	0.141	0.141	0.000	0.000	0.000	0.000
75	A	351	VAL	0	-0.014	-0.025	10.289	-1.016	-1.016	0.000	0.000	0.000	0.000
76	A	352	ILE	0	-0.005	0.003	10.561	0.826	0.826	0.000	0.000	0.000	0.000
77	A	353	PRO	0	0.032	0.006	5.873	-2.627	-2.627	0.000	0.000	0.000	0.000
78	A	354	TYR	0	-0.001	0.001	5.133	4.334	4.334	0.000	0.000	0.000	0.000
79	A	355	THR	0	-0.010	-0.018	6.077	-2.401	-2.401	0.000	0.000	0.000	0.000
80	A	356	LYS	1	0.803	0.881	8.755	23.088	23.088	0.000	0.000	0.000	0.000
81	A	357	ASP	-1	-0.797	-0.890	11.157	-17.102	-17.102	0.000	0.000	0.000	0.000
82	A	358	ALA	0	0.007	0.011	11.700	1.093	1.093	0.000	0.000	0.000	0.000
83	A	359	VAL	0	-0.008	-0.009	11.660	0.823	0.823	0.000	0.000	0.000	0.000
84	A	360	GLU	-1	-0.815	-0.884	13.811	-18.456	-18.456	0.000	0.000	0.000	0.000
85	A	361	ARG	1	0.803	0.875	16.714	16.926	16.926	0.000	0.000	0.000	0.000
86	A	362	LEU	0	-0.066	-0.024	15.100	0.779	0.779	0.000	0.000	0.000	0.000
87	A	363	GLN	-1	-0.968	-0.961	15.838	-14.454	-14.454	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:266:LEU)