FMO DATABASE

FMODB ID: 6RY4Z

Calculation Name: 4A9A-D-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4A9A

Chain ID: D

ChEMBL ID:

UniProt ID: P39729

Base Structure: X-ray

Registration Date: 2025-10-12

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	86
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-434586.735052
FMO2-HF: Nuclear repulsion	401048.30685
FMO2-HF: Total energy	-33538.428202
FMO2-MP2: Total energy	-33637.645047

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:214:LEU)

Summations of interaction energy for fragment #1(D:214: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.
99.348	103.562	0.99	-2.062	-3.142	-0.018

Interaction energy analysis for fragmet #1(D:214:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.833 / q_NPA : 0.911

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	216	LYS	1	0.852	0.901	2.659	28.709	31.907	0.718	-1.748	-2.169	-0.016
4	D	217	GLN	0	0.025	0.006	2.858	-1.303	-0.287	0.272	-0.314	-0.973	-0.002
5	D	218	PRO	0	-0.007	0.015	5.609	1.748	1.748	0.000	0.000	0.000	0.000
6	D	219	LYS	1	0.908	0.940	8.909	22.350	22.350	0.000	0.000	0.000	0.000
7	D	220	ILE	0	0.019	0.024	11.158	0.277	0.277	0.000	0.000	0.000	0.000
8	D	221	THR	0	-0.020	-0.043	13.413	0.096	0.096	0.000	0.000	0.000	0.000
9	D	222	LEU	0	-0.019	-0.012	16.176	-0.605	-0.605	0.000	0.000	0.000	0.000
10	D	223	GLU	-1	-0.816	-0.920	18.168	-12.723	-12.723	0.000	0.000	0.000	0.000
11	D	224	GLU	-1	-0.756	-0.842	16.114	-15.659	-15.659	0.000	0.000	0.000	0.000
12	D	225	PHE	0	-0.036	-0.010	13.453	-0.456	-0.456	0.000	0.000	0.000	0.000
13	D	226	ILE	0	-0.052	-0.037	15.969	-0.180	-0.180	0.000	0.000	0.000	0.000
14	D	227	GLU	-1	-0.937	-0.963	19.399	-11.421	-11.421	0.000	0.000	0.000	0.000
15	D	228	THR	0	-0.042	-0.033	17.531	0.268	0.268	0.000	0.000	0.000	0.000
16	D	229	GLU	-1	-0.879	-0.927	12.707	-19.511	-19.511	0.000	0.000	0.000	0.000
17	D	230	ARG	1	0.915	0.958	14.600	13.245	13.245	0.000	0.000	0.000	0.000
18	D	231	GLY	0	-0.033	-0.018	16.312	0.262	0.262	0.000	0.000	0.000	0.000
19	D	232	LYS	1	0.834	0.904	13.566	18.857	18.857	0.000	0.000	0.000	0.000
20	D	233	LEU	0	-0.048	-0.008	11.571	-0.709	-0.709	0.000	0.000	0.000	0.000
21	D	234	ASP	-1	-0.754	-0.855	14.705	-14.873	-14.873	0.000	0.000	0.000	0.000
22	D	235	LYS	1	0.973	0.966	16.714	12.978	12.978	0.000	0.000	0.000	0.000
23	D	236	SER	0	-0.065	-0.042	19.287	0.467	0.467	0.000	0.000	0.000	0.000
24	D	237	LYS	1	0.865	0.919	15.972	16.318	16.318	0.000	0.000	0.000	0.000
25	D	238	LEU	0	-0.027	0.014	15.124	-0.985	-0.985	0.000	0.000	0.000	0.000
26	D	239	THR	0	-0.003	-0.012	15.265	0.698	0.698	0.000	0.000	0.000	0.000
27	D	240	PRO	0	0.002	0.002	17.024	-0.265	-0.265	0.000	0.000	0.000	0.000
28	D	241	ILE	0	0.016	0.016	16.210	-0.291	-0.291	0.000	0.000	0.000	0.000
29	D	242	THR	0	0.007	-0.006	18.786	0.818	0.818	0.000	0.000	0.000	0.000
30	D	243	ILE	0	0.069	0.017	19.543	-0.621	-0.621	0.000	0.000	0.000	0.000
31	D	244	ALA	0	0.029	0.025	20.140	-0.385	-0.385	0.000	0.000	0.000	0.000
32	D	245	ASN	0	0.041	0.016	16.182	-0.273	-0.273	0.000	0.000	0.000	0.000
33	D	246	PHE	0	0.033	0.022	15.159	-1.245	-1.245	0.000	0.000	0.000	0.000
34	D	247	ALA	0	0.039	0.015	15.377	-0.742	-0.742	0.000	0.000	0.000	0.000
35	D	248	GLN	0	-0.030	-0.019	14.682	-0.735	-0.735	0.000	0.000	0.000	0.000
36	D	249	TRP	0	0.026	0.015	8.701	-0.479	-0.479	0.000	0.000	0.000	0.000
37	D	250	LYS	1	0.933	0.971	11.056	15.416	15.416	0.000	0.000	0.000	0.000
38	D	251	LYS	1	0.898	0.936	12.894	20.482	20.482	0.000	0.000	0.000	0.000
39	D	252	ASP	-1	-0.831	-0.899	8.477	-24.489	-24.489	0.000	0.000	0.000	0.000
40	D	253	HIS	0	-0.051	-0.023	8.410	-0.797	-0.797	0.000	0.000	0.000	0.000
41	D	254	VAL	0	0.006	-0.002	9.605	-0.408	-0.408	0.000	0.000	0.000	0.000
42	D	255	ILE	0	0.031	0.015	10.397	-0.155	-0.155	0.000	0.000	0.000	0.000
43	D	256	ALA	0	-0.010	-0.005	5.376	-0.703	-0.703	0.000	0.000	0.000	0.000
44	D	257	LYS	1	0.931	0.983	7.459	17.890	17.890	0.000	0.000	0.000	0.000
45	D	258	ILE	0	0.014	-0.001	9.333	0.486	0.486	0.000	0.000	0.000	0.000
46	D	259	ASN	0	0.037	0.003	8.892	2.098	2.098	0.000	0.000	0.000	0.000
47	D	260	ALA	0	-0.061	-0.021	6.764	-0.280	-0.280	0.000	0.000	0.000	0.000
48	D	261	GLU	-1	-0.832	-0.928	8.780	-17.823	-17.823	0.000	0.000	0.000	0.000
49	D	262	LYS	1	0.839	0.907	12.203	18.946	18.946	0.000	0.000	0.000	0.000
50	D	263	LYS	1	0.955	0.998	8.548	30.726	30.726	0.000	0.000	0.000	0.000
51	D	264	LEU	0	-0.002	-0.002	12.596	0.567	0.567	0.000	0.000	0.000	0.000
52	D	265	SER	0	-0.040	-0.010	15.880	1.146	1.146	0.000	0.000	0.000	0.000
53	D	266	SER	0	-0.002	-0.011	17.900	0.593	0.593	0.000	0.000	0.000	0.000
54	D	267	LYS	1	0.937	0.969	19.515	14.440	14.440	0.000	0.000	0.000	0.000
55	D	268	ARG	1	0.955	0.987	22.139	12.144	12.144	0.000	0.000	0.000	0.000
56	D	269	LYS	1	0.978	0.979	24.333	10.250	10.250	0.000	0.000	0.000	0.000
57	D	270	PRO	0	-0.025	-0.008	27.577	-0.241	-0.241	0.000	0.000	0.000	0.000
58	D	271	THR	0	0.007	-0.017	28.310	0.276	0.276	0.000	0.000	0.000	0.000
59	D	272	GLY	0	0.050	0.015	31.027	0.120	0.120	0.000	0.000	0.000	0.000
60	D	273	ARG	1	0.999	1.002	30.102	9.485	9.485	0.000	0.000	0.000	0.000
61	D	274	GLU	-1	-0.840	-0.897	27.755	-10.410	-10.410	0.000	0.000	0.000	0.000
62	D	275	ILE	0	-0.022	-0.010	32.499	0.095	0.095	0.000	0.000	0.000	0.000
63	D	276	ILE	0	0.016	0.004	35.469	0.126	0.126	0.000	0.000	0.000	0.000
64	D	277	LEU	0	-0.014	-0.013	33.376	0.105	0.105	0.000	0.000	0.000	0.000
65	D	278	LYS	1	0.916	0.959	33.937	8.794	8.794	0.000	0.000	0.000	0.000
66	D	279	MET	0	0.016	-0.004	36.636	0.067	0.067	0.000	0.000	0.000	0.000
67	D	280	SER	0	-0.064	-0.021	39.522	0.203	0.203	0.000	0.000	0.000	0.000
68	D	281	ALA	0	-0.063	-0.026	38.548	0.065	0.065	0.000	0.000	0.000	0.000
69	D	282	GLU	-2	-1.915	-1.934	39.683	-14.595	-14.595	0.000	0.000	0.000	0.000
70	D	320	ASP	0	-0.004	-0.017	37.594	-0.001	-0.001	0.000	0.000	0.000	0.000
71	D	321	GLY	0	-0.007	0.003	39.174	0.093	0.093	0.000	0.000	0.000	0.000
72	D	322	GLY	0	-0.022	-0.004	41.052	0.110	0.110	0.000	0.000	0.000	0.000
73	D	323	ILE	0	0.006	-0.007	35.550	-0.105	-0.105	0.000	0.000	0.000	0.000
74	D	324	LYS	1	0.911	0.954	30.248	9.339	9.339	0.000	0.000	0.000	0.000
75	D	325	ASP	-1	-0.887	-0.938	32.611	-8.988	-8.988	0.000	0.000	0.000	0.000
76	D	326	TYR	0	-0.010	-0.019	27.486	-0.140	-0.140	0.000	0.000	0.000	0.000
77	D	327	GLY	0	0.012	0.014	28.203	-0.307	-0.307	0.000	0.000	0.000	0.000
78	D	328	ASP	-1	-0.900	-0.929	25.703	-10.978	-10.978	0.000	0.000	0.000	0.000
79	D	329	GLY	0	-0.033	-0.013	24.222	-0.427	-0.427	0.000	0.000	0.000	0.000
80	D	330	SER	0	-0.122	-0.084	22.491	-0.528	-0.528	0.000	0.000	0.000	0.000
81	D	331	ASN	0	-0.068	-0.046	22.620	0.013	0.013	0.000	0.000	0.000	0.000
82	D	332	PRO	0	0.015	0.028	22.806	0.341	0.341	0.000	0.000	0.000	0.000
83	D	333	THR	0	0.015	0.010	25.526	-0.270	-0.270	0.000	0.000	0.000	0.000
84	D	334	PHE	0	-0.057	-0.049	23.821	0.010	0.010	0.000	0.000	0.000	0.000
85	D	335	ASP	-1	-0.887	-0.936	28.976	-9.084	-9.084	0.000	0.000	0.000	0.000
86	D	336	ILE	-1	-0.962	-0.968	32.194	-7.979	-7.979	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:214:LEU)