FMO DATABASE

FMODB ID: 34NML

Calculation Name: 2PYT-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2PYT

Chain ID: A

ChEMBL ID:

UniProt ID: Q9ZFV5

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	128
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1049983.449355
FMO2-HF: Nuclear repulsion	999877.00884
FMO2-HF: Total energy	-50106.440514
FMO2-MP2: Total energy	-50249.515784

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:100:LEU)

Summations of interaction energy for fragment #1(A:100: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.
-145.692	-138.811	5.992	-4.655	-8.216	-0.061

Interaction energy analysis for fragmet #1(A:100:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.795 / q_NPA : 0.892

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	102	LEU	0	0.019	0.009	2.191	3.454	5.242	1.707	-1.093	-2.401	-0.011
4	A	103	GLY	0	0.009	-0.004	2.736	3.904	5.131	1.096	-0.590	-1.734	-0.004
5	A	104	THR	0	-0.032	-0.016	3.543	0.536	0.761	0.016	0.247	-0.488	-0.001
6	A	105	MET	0	-0.036	-0.013	2.197	-39.451	-36.043	3.175	-3.164	-3.419	-0.045
7	A	106	GLN	0	-0.010	0.006	4.296	8.580	8.714	-0.001	-0.040	-0.092	0.000
31	A	130	ARG	1	0.875	0.921	4.618	45.912	46.011	-0.001	-0.015	-0.082	0.000
8	A	107	PRO	0	0.054	0.042	7.714	-1.427	-1.427	0.000	0.000	0.000	0.000
9	A	108	SER	0	-0.042	-0.030	10.083	2.423	2.423	0.000	0.000	0.000	0.000
10	A	109	PHE	0	0.023	0.012	11.648	-1.057	-1.057	0.000	0.000	0.000	0.000
11	A	110	THR	0	0.015	0.016	14.381	1.087	1.087	0.000	0.000	0.000	0.000
12	A	111	SER	0	-0.011	-0.015	17.438	0.325	0.325	0.000	0.000	0.000	0.000
13	A	112	VAL	0	-0.024	-0.006	20.812	0.266	0.266	0.000	0.000	0.000	0.000
14	A	113	THR	0	0.030	0.020	24.586	-0.014	-0.014	0.000	0.000	0.000	0.000
15	A	114	GLY	0	-0.007	0.003	27.303	0.262	0.262	0.000	0.000	0.000	0.000
16	A	115	LYS	1	0.936	0.940	30.937	8.382	8.382	0.000	0.000	0.000	0.000
17	A	116	GLY	0	-0.020	-0.008	33.942	0.173	0.173	0.000	0.000	0.000	0.000
18	A	117	GLY	0	0.046	0.033	30.606	0.090	0.090	0.000	0.000	0.000	0.000
19	A	118	VAL	0	-0.021	-0.009	29.282	-0.279	-0.279	0.000	0.000	0.000	0.000
20	A	119	LYS	1	0.851	0.928	20.827	14.465	14.465	0.000	0.000	0.000	0.000
21	A	120	VAL	0	-0.007	-0.002	23.426	0.021	0.021	0.000	0.000	0.000	0.000
22	A	121	ILE	0	0.039	0.002	17.503	-0.115	-0.115	0.000	0.000	0.000	0.000
23	A	122	ASP	-1	-0.844	-0.886	17.424	-17.631	-17.631	0.000	0.000	0.000	0.000
24	A	123	GLY	0	0.053	0.024	16.020	-1.177	-1.177	0.000	0.000	0.000	0.000
25	A	124	SER	0	-0.071	-0.061	14.379	-1.436	-1.436	0.000	0.000	0.000	0.000
26	A	125	SER	0	-0.060	-0.037	12.777	-1.768	-1.768	0.000	0.000	0.000	0.000
27	A	126	VAL	0	-0.023	-0.005	10.834	-1.527	-1.527	0.000	0.000	0.000	0.000
28	A	127	LYS	1	0.869	0.946	7.079	27.974	27.974	0.000	0.000	0.000	0.000
29	A	128	PHE	0	0.050	0.035	5.840	2.986	2.986	0.000	0.000	0.000	0.000
30	A	129	GLY	0	0.008	0.006	5.764	-6.744	-6.744	0.000	0.000	0.000	0.000
32	A	131	PHE	0	0.023	0.017	8.358	1.920	1.920	0.000	0.000	0.000	0.000
33	A	132	ASP	-1	-0.869	-0.946	11.981	-22.547	-22.547	0.000	0.000	0.000	0.000
34	A	133	GLY	0	-0.047	-0.018	14.277	0.958	0.958	0.000	0.000	0.000	0.000
35	A	134	ALA	0	-0.021	-0.005	13.531	0.999	0.999	0.000	0.000	0.000	0.000
36	A	135	GLU	-1	-0.890	-0.934	11.256	-28.166	-28.166	0.000	0.000	0.000	0.000
37	A	136	PRO	0	-0.114	-0.060	13.615	1.674	1.674	0.000	0.000	0.000	0.000
38	A	137	HIS	0	0.005	0.003	12.103	-2.020	-2.020	0.000	0.000	0.000	0.000
39	A	138	CYS	0	-0.035	-0.001	6.329	-4.327	-4.327	0.000	0.000	0.000	0.000
40	A	139	VAL	0	0.001	0.013	8.469	-2.036	-2.036	0.000	0.000	0.000	0.000
41	A	140	GLY	0	-0.007	-0.006	7.865	-1.579	-1.579	0.000	0.000	0.000	0.000
42	A	141	LEU	0	0.015	-0.003	8.426	2.634	2.634	0.000	0.000	0.000	0.000
43	A	142	THR	0	-0.047	-0.059	10.215	-2.601	-2.601	0.000	0.000	0.000	0.000
44	A	143	ASP	-1	-0.815	-0.860	12.498	-16.841	-16.841	0.000	0.000	0.000	0.000
45	A	144	LEU	0	-0.093	-0.057	14.439	-0.467	-0.467	0.000	0.000	0.000	0.000
46	A	145	VAL	0	-0.055	-0.037	17.993	0.668	0.668	0.000	0.000	0.000	0.000
47	A	146	THR	0	0.042	0.009	20.607	-0.096	-0.096	0.000	0.000	0.000	0.000
48	A	147	GLU	-1	-0.831	-0.923	23.368	-11.284	-11.284	0.000	0.000	0.000	0.000
49	A	148	GLN	0	-0.053	-0.018	23.942	0.071	0.071	0.000	0.000	0.000	0.000
50	A	149	ASP	-1	-0.818	-0.889	23.149	-13.560	-13.560	0.000	0.000	0.000	0.000
51	A	150	GLY	0	-0.041	-0.024	26.493	0.355	0.355	0.000	0.000	0.000	0.000
52	A	151	SER	0	-0.075	-0.046	26.263	0.544	0.544	0.000	0.000	0.000	0.000
53	A	152	SER	0	0.000	-0.012	28.134	-0.198	-0.198	0.000	0.000	0.000	0.000
54	A	153	MET	0	-0.030	-0.013	26.265	0.132	0.132	0.000	0.000	0.000	0.000
55	A	154	ALA	0	0.027	0.047	21.638	-0.085	-0.085	0.000	0.000	0.000	0.000
56	A	155	ALA	0	0.018	0.003	20.920	0.248	0.248	0.000	0.000	0.000	0.000
57	A	156	GLY	0	0.050	0.024	16.744	-0.290	-0.290	0.000	0.000	0.000	0.000
58	A	157	PHE	0	-0.054	-0.009	13.155	0.655	0.655	0.000	0.000	0.000	0.000
59	A	158	MET	0	0.039	0.026	12.190	-0.994	-0.994	0.000	0.000	0.000	0.000
60	A	159	GLN	0	0.001	-0.004	8.060	2.800	2.800	0.000	0.000	0.000	0.000
61	A	160	TRP	0	-0.070	-0.024	9.239	-3.282	-3.282	0.000	0.000	0.000	0.000
62	A	161	ASP	-1	-0.830	-0.923	9.157	-26.717	-26.717	0.000	0.000	0.000	0.000
63	A	162	ASN	0	-0.112	-0.068	11.056	0.587	0.587	0.000	0.000	0.000	0.000
64	A	163	ALA	0	0.046	0.036	12.905	-0.278	-0.278	0.000	0.000	0.000	0.000
65	A	164	PHE	0	-0.002	-0.010	14.891	0.510	0.510	0.000	0.000	0.000	0.000
66	A	165	PHE	0	0.014	0.003	15.324	-0.268	-0.268	0.000	0.000	0.000	0.000
67	A	166	PRO	0	0.014	0.020	18.749	0.335	0.335	0.000	0.000	0.000	0.000
68	A	167	TRP	0	0.014	0.002	19.845	-0.774	-0.774	0.000	0.000	0.000	0.000
69	A	168	THR	0	-0.029	-0.021	22.090	0.871	0.871	0.000	0.000	0.000	0.000
70	A	169	LEU	0	0.018	0.049	23.553	-0.252	-0.252	0.000	0.000	0.000	0.000
71	A	170	ASN	0	-0.025	-0.015	25.824	0.725	0.725	0.000	0.000	0.000	0.000
72	A	171	TYR	0	-0.077	-0.052	21.346	0.556	0.556	0.000	0.000	0.000	0.000
73	A	172	ASP	-1	-0.844	-0.915	27.508	-10.165	-10.165	0.000	0.000	0.000	0.000
74	A	173	GLU	-1	-0.823	-0.935	21.108	-15.004	-15.004	0.000	0.000	0.000	0.000
75	A	174	ILE	0	-0.060	-0.029	24.683	0.459	0.459	0.000	0.000	0.000	0.000
76	A	175	ASP	-1	-0.830	-0.914	20.877	-15.166	-15.166	0.000	0.000	0.000	0.000
77	A	176	MET	0	-0.058	-0.037	21.298	0.882	0.882	0.000	0.000	0.000	0.000
78	A	177	VAL	0	0.007	0.003	18.734	-0.966	-0.966	0.000	0.000	0.000	0.000
79	A	178	LEU	0	-0.070	-0.029	16.503	0.667	0.667	0.000	0.000	0.000	0.000
80	A	179	GLU	-1	-0.928	-0.988	14.221	-20.867	-20.867	0.000	0.000	0.000	0.000
81	A	180	GLY	0	0.019	0.014	16.812	-0.549	-0.549	0.000	0.000	0.000	0.000
82	A	181	GLU	-1	-0.861	-0.926	17.762	-12.615	-12.615	0.000	0.000	0.000	0.000
83	A	182	LEU	0	0.009	0.031	17.813	-0.761	-0.761	0.000	0.000	0.000	0.000
84	A	183	HIS	0	-0.072	-0.062	19.846	1.057	1.057	0.000	0.000	0.000	0.000
85	A	184	VAL	0	0.044	0.014	21.132	-0.575	-0.575	0.000	0.000	0.000	0.000
86	A	185	ARG	1	0.787	0.907	23.748	12.886	12.886	0.000	0.000	0.000	0.000
87	A	186	HIS	0	0.048	0.003	26.365	-0.327	-0.327	0.000	0.000	0.000	0.000
88	A	187	GLU	-1	-0.933	-0.969	29.154	-8.937	-8.937	0.000	0.000	0.000	0.000
89	A	188	GLY	0	-0.053	-0.016	30.821	0.287	0.287	0.000	0.000	0.000	0.000
90	A	189	GLU	-1	-0.942	-0.965	30.873	-9.377	-9.377	0.000	0.000	0.000	0.000
91	A	190	THR	0	-0.048	-0.041	25.575	-0.469	-0.469	0.000	0.000	0.000	0.000
92	A	191	MET	0	0.007	0.015	26.638	0.354	0.354	0.000	0.000	0.000	0.000
93	A	192	ILE	0	-0.029	-0.029	23.544	-0.471	-0.471	0.000	0.000	0.000	0.000
94	A	193	ALA	0	-0.010	0.014	23.159	0.512	0.512	0.000	0.000	0.000	0.000
95	A	194	LYS	1	0.882	0.912	22.150	11.714	11.714	0.000	0.000	0.000	0.000
96	A	195	ALA	0	-0.006	0.003	20.435	0.109	0.109	0.000	0.000	0.000	0.000
97	A	196	GLY	0	-0.040	-0.020	22.004	0.555	0.555	0.000	0.000	0.000	0.000
98	A	197	ASP	-1	-0.859	-0.914	24.496	-11.290	-11.290	0.000	0.000	0.000	0.000
99	A	198	VAL	0	-0.045	-0.039	24.247	-0.512	-0.512	0.000	0.000	0.000	0.000
100	A	199	MET	0	-0.031	-0.010	23.870	0.371	0.371	0.000	0.000	0.000	0.000
101	A	200	PHE	0	-0.038	-0.028	26.132	-0.035	-0.035	0.000	0.000	0.000	0.000
102	A	201	ILE	0	0.020	0.017	23.072	0.259	0.259	0.000	0.000	0.000	0.000
103	A	202	PRO	0	-0.001	0.008	27.330	-0.043	-0.043	0.000	0.000	0.000	0.000
104	A	203	LYS	1	0.972	0.997	29.302	9.393	9.393	0.000	0.000	0.000	0.000
105	A	204	GLY	0	-0.066	-0.033	29.642	0.399	0.399	0.000	0.000	0.000	0.000
106	A	205	SER	0	-0.039	-0.021	27.638	0.183	0.183	0.000	0.000	0.000	0.000
107	A	206	SER	0	-0.032	-0.033	27.012	-0.292	-0.292	0.000	0.000	0.000	0.000
108	A	207	ILE	0	-0.039	-0.023	22.138	0.383	0.383	0.000	0.000	0.000	0.000
109	A	208	GLU	-1	-0.902	-0.932	21.473	-13.760	-13.760	0.000	0.000	0.000	0.000
110	A	209	PHE	0	0.066	0.024	17.959	0.270	0.270	0.000	0.000	0.000	0.000
111	A	210	GLY	0	0.022	-0.017	17.290	-0.363	-0.363	0.000	0.000	0.000	0.000
112	A	211	THR	0	-0.017	-0.004	14.599	0.343	0.343	0.000	0.000	0.000	0.000
113	A	212	PRO	0	-0.014	0.005	16.791	-0.614	-0.614	0.000	0.000	0.000	0.000
114	A	213	THR	0	-0.062	-0.037	16.114	-0.134	-0.134	0.000	0.000	0.000	0.000
115	A	214	SER	0	0.028	0.024	12.753	-1.328	-1.328	0.000	0.000	0.000	0.000
116	A	215	VAL	0	-0.022	0.004	13.218	1.702	1.702	0.000	0.000	0.000	0.000
117	A	216	ARG	1	0.902	0.959	11.395	21.415	21.415	0.000	0.000	0.000	0.000
118	A	217	PHE	0	-0.001	-0.003	14.211	1.207	1.207	0.000	0.000	0.000	0.000
119	A	218	LEU	0	-0.035	-0.004	15.965	-1.002	-1.002	0.000	0.000	0.000	0.000
120	A	219	TYR	0	0.041	0.001	15.198	0.250	0.250	0.000	0.000	0.000	0.000
121	A	220	VAL	0	-0.034	-0.036	20.015	-0.085	-0.085	0.000	0.000	0.000	0.000
122	A	221	ALA	0	0.048	0.031	22.750	0.330	0.330	0.000	0.000	0.000	0.000
123	A	222	TRP	0	-0.050	-0.012	24.553	0.272	0.272	0.000	0.000	0.000	0.000
124	A	223	PRO	0	-0.002	-0.014	28.067	0.171	0.171	0.000	0.000	0.000	0.000
125	A	224	ALA	0	0.023	-0.015	25.472	-0.353	-0.353	0.000	0.000	0.000	0.000
126	A	225	ASN	0	-0.057	-0.020	24.672	-0.453	-0.453	0.000	0.000	0.000	0.000
127	A	226	TRP	0	-0.020	-0.015	20.062	0.402	0.402	0.000	0.000	0.000	0.000
128	A	227	GLN	-1	-0.952	-0.953	19.807	-12.805	-12.805	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:100:LEU)