FMO DATABASE

FMODB ID: 6ZKQZ

Calculation Name: 1PY9-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1PY9

Chain ID: A

ChEMBL ID:

UniProt ID: Q61885

Base Structure: X-ray

Registration Date: 2025-10-03

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	115
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-984042.829687
FMO2-HF: Nuclear repulsion	937283.108337
FMO2-HF: Total energy	-46759.721351
FMO2-MP2: Total energy	-46895.65297

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:2:GLN)

Summations of interaction energy for fragment #1(A:2:GLN)

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.
-74.318	-66.701	4.228	-4.939	-6.905	-0.054

Interaction energy analysis for fragmet #1(A:2:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.803 / q_NPA : 0.902

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	4	ARG	1	1.050	1.034	3.843	26.204	28.040	-0.015	-0.911	-0.910	-0.002
29	A	30	LYS	1	0.851	0.908	4.093	51.633	51.702	-0.001	-0.003	-0.064	0.000
103	A	105	TYR	0	-0.015	-0.006	2.278	-19.051	-13.339	4.244	-4.025	-5.931	-0.052
4	A	5	VAL	0	0.027	0.016	6.396	0.196	0.196	0.000	0.000	0.000	0.000
5	A	6	ILE	0	-0.090	-0.048	9.827	1.043	1.043	0.000	0.000	0.000	0.000
6	A	7	GLY	0	0.089	0.040	13.035	0.156	0.156	0.000	0.000	0.000	0.000
7	A	8	PRO	0	-0.042	-0.012	16.672	-0.253	-0.253	0.000	0.000	0.000	0.000
8	A	9	GLY	0	0.011	-0.004	19.735	0.015	0.015	0.000	0.000	0.000	0.000
9	A	10	TYR	0	-0.048	-0.025	20.328	0.505	0.505	0.000	0.000	0.000	0.000
10	A	11	PRO	0	-0.008	-0.008	24.012	-0.316	-0.316	0.000	0.000	0.000	0.000
11	A	12	ILE	0	0.002	0.011	23.660	0.196	0.196	0.000	0.000	0.000	0.000
12	A	13	ARG	1	0.757	0.841	26.778	9.779	9.779	0.000	0.000	0.000	0.000
13	A	14	ALA	0	0.003	0.007	30.577	-0.159	-0.159	0.000	0.000	0.000	0.000
14	A	15	LEU	0	0.041	0.037	32.539	0.109	0.109	0.000	0.000	0.000	0.000
15	A	16	VAL	0	-0.022	-0.014	35.453	-0.195	-0.195	0.000	0.000	0.000	0.000
16	A	17	GLY	0	-0.069	-0.035	36.944	0.213	0.213	0.000	0.000	0.000	0.000
17	A	18	ASP	-1	-0.872	-0.927	35.440	-8.629	-8.629	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-1.011	-1.025	30.028	-10.823	-10.823	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.045	0.024	28.495	0.072	0.072	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.832	-0.921	25.301	-12.478	-12.478	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.001	0.001	21.738	-0.188	-0.188	0.000	0.000	0.000	0.000
22	A	23	PRO	0	-0.020	-0.002	19.686	-0.642	-0.642	0.000	0.000	0.000	0.000
23	A	24	CYS	0	-0.049	-0.010	14.753	-0.783	-0.783	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.937	0.979	12.903	23.127	23.127	0.000	0.000	0.000	0.000
25	A	26	ILE	0	0.013	0.030	7.348	-1.245	-1.245	0.000	0.000	0.000	0.000
26	A	27	SER	0	-0.035	-0.024	8.150	4.452	4.452	0.000	0.000	0.000	0.000
27	A	28	PRO	0	-0.024	-0.035	5.380	-3.720	-3.720	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.043	0.046	7.756	-2.194	-2.194	0.000	0.000	0.000	0.000
30	A	31	ASN	0	0.051	0.043	9.750	0.287	0.287	0.000	0.000	0.000	0.000
31	A	32	ALA	0	0.054	0.018	10.874	-1.731	-1.731	0.000	0.000	0.000	0.000
32	A	33	THR	0	-0.013	-0.017	12.025	0.956	0.956	0.000	0.000	0.000	0.000
33	A	34	GLY	0	-0.007	-0.002	13.814	1.222	1.222	0.000	0.000	0.000	0.000
34	A	35	MET	0	-0.095	-0.022	7.515	-0.831	-0.831	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.835	-0.902	12.128	-17.694	-17.694	0.000	0.000	0.000	0.000
36	A	37	VAL	0	-0.020	-0.015	12.449	-1.960	-1.960	0.000	0.000	0.000	0.000
37	A	38	GLY	0	0.019	0.024	14.763	1.515	1.515	0.000	0.000	0.000	0.000
38	A	39	TRP	0	0.045	0.000	16.541	-0.777	-0.777	0.000	0.000	0.000	0.000
39	A	40	TYR	0	0.000	0.002	16.775	0.599	0.599	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.800	0.894	21.433	11.602	11.602	0.000	0.000	0.000	0.000
41	A	42	SER	0	-0.024	0.001	20.952	-0.191	-0.191	0.000	0.000	0.000	0.000
42	A	43	PRO	0	0.030	0.012	23.299	0.309	0.309	0.000	0.000	0.000	0.000
43	A	44	PHE	0	-0.027	-0.033	24.387	-0.145	-0.145	0.000	0.000	0.000	0.000
44	A	45	SER	0	0.002	0.011	22.755	0.279	0.279	0.000	0.000	0.000	0.000
45	A	46	ARG	1	0.865	0.914	24.527	11.183	11.183	0.000	0.000	0.000	0.000
46	A	47	VAL	0	0.012	0.017	21.737	-0.351	-0.351	0.000	0.000	0.000	0.000
47	A	48	VAL	0	-0.010	0.009	22.983	0.585	0.585	0.000	0.000	0.000	0.000
48	A	49	HIS	0	0.026	0.001	21.012	0.857	0.857	0.000	0.000	0.000	0.000
49	A	50	LEU	0	-0.003	0.007	18.650	-0.713	-0.713	0.000	0.000	0.000	0.000
50	A	51	TYR	0	-0.043	-0.021	16.260	1.189	1.189	0.000	0.000	0.000	0.000
51	A	52	ARG	1	0.884	0.915	16.808	13.565	13.565	0.000	0.000	0.000	0.000
52	A	53	ASN	0	-0.041	-0.022	17.088	1.008	1.008	0.000	0.000	0.000	0.000
53	A	54	GLY	0	0.016	0.019	18.206	0.781	0.781	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.925	0.963	19.929	13.153	13.153	0.000	0.000	0.000	0.000
55	A	56	ASP	-1	-0.703	-0.841	21.240	-14.829	-14.829	0.000	0.000	0.000	0.000
56	A	57	GLN	0	-0.058	-0.034	21.687	0.841	0.841	0.000	0.000	0.000	0.000
57	A	58	ASP	-1	-0.846	-0.920	24.392	-11.303	-11.303	0.000	0.000	0.000	0.000
58	A	59	ALA	0	-0.073	-0.049	27.706	0.260	0.260	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.825	-0.909	22.248	-14.025	-14.025	0.000	0.000	0.000	0.000
60	A	61	GLN	0	-0.047	-0.018	25.456	0.084	0.084	0.000	0.000	0.000	0.000
61	A	62	ALA	0	0.025	0.000	26.259	0.487	0.487	0.000	0.000	0.000	0.000
62	A	63	PRO	0	0.015	-0.022	28.978	0.043	0.043	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.837	-0.877	30.704	-10.256	-10.256	0.000	0.000	0.000	0.000
64	A	65	TYR	0	0.022	-0.019	28.064	-0.045	-0.045	0.000	0.000	0.000	0.000
65	A	66	ARG	1	0.846	0.950	29.578	10.374	10.374	0.000	0.000	0.000	0.000
66	A	67	GLY	0	0.001	0.001	31.016	0.304	0.304	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.710	0.835	30.890	10.312	10.312	0.000	0.000	0.000	0.000
68	A	69	THR	0	0.002	-0.007	25.658	-0.024	-0.024	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.832	-0.895	25.941	-10.918	-10.918	0.000	0.000	0.000	0.000
70	A	71	LEU	0	-0.025	0.007	17.715	-0.324	-0.324	0.000	0.000	0.000	0.000
71	A	72	LEU	0	0.016	0.015	22.240	0.009	0.009	0.000	0.000	0.000	0.000
72	A	73	LYS	1	0.801	0.861	19.168	13.790	13.790	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.882	-0.926	20.245	-13.228	-13.228	0.000	0.000	0.000	0.000
74	A	75	THR	0	-0.012	0.000	18.231	-0.189	-0.189	0.000	0.000	0.000	0.000
75	A	76	ILE	0	0.035	0.035	15.103	-1.362	-1.362	0.000	0.000	0.000	0.000
76	A	77	SER	0	-0.020	-0.018	14.338	-1.880	-1.880	0.000	0.000	0.000	0.000
77	A	78	GLU	-1	-0.831	-0.918	14.044	-18.886	-18.886	0.000	0.000	0.000	0.000
78	A	79	GLY	0	-0.041	-0.015	11.444	-1.795	-1.795	0.000	0.000	0.000	0.000
79	A	80	LYS	1	0.779	0.862	12.381	17.524	17.524	0.000	0.000	0.000	0.000
80	A	81	VAL	0	0.040	0.020	15.502	0.403	0.403	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.027	-0.021	17.788	0.033	0.033	0.000	0.000	0.000	0.000
82	A	83	LEU	0	-0.027	0.012	20.850	0.240	0.240	0.000	0.000	0.000	0.000
83	A	84	ARG	1	0.855	0.931	22.420	11.480	11.480	0.000	0.000	0.000	0.000
84	A	85	ILE	0	-0.023	-0.018	25.659	-0.078	-0.078	0.000	0.000	0.000	0.000
85	A	86	GLN	0	0.008	-0.019	28.409	0.329	0.329	0.000	0.000	0.000	0.000
86	A	87	ASN	0	-0.031	-0.019	31.921	0.159	0.159	0.000	0.000	0.000	0.000
87	A	88	VAL	0	0.009	0.018	31.174	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	89	ARG	1	0.923	0.964	33.478	9.553	9.553	0.000	0.000	0.000	0.000
89	A	90	PHE	0	0.125	0.048	33.960	-0.247	-0.247	0.000	0.000	0.000	0.000
90	A	91	SER	0	-0.042	-0.020	33.186	-0.035	-0.035	0.000	0.000	0.000	0.000
91	A	92	ASP	-1	-0.793	-0.858	29.828	-10.550	-10.550	0.000	0.000	0.000	0.000
92	A	93	GLU	-1	-0.785	-0.867	29.113	-10.099	-10.099	0.000	0.000	0.000	0.000
93	A	94	GLY	0	0.015	0.035	28.158	0.012	0.012	0.000	0.000	0.000	0.000
94	A	95	GLY	0	0.042	0.016	24.041	-0.318	-0.318	0.000	0.000	0.000	0.000
95	A	96	TYR	0	-0.079	-0.064	21.466	0.141	0.141	0.000	0.000	0.000	0.000
96	A	97	THR	0	-0.025	-0.018	15.907	-0.152	-0.152	0.000	0.000	0.000	0.000
97	A	99	PHE	0	0.035	0.002	12.421	-0.985	-0.985	0.000	0.000	0.000	0.000
98	A	100	PHE	0	-0.009	-0.023	9.131	0.674	0.674	0.000	0.000	0.000	0.000
99	A	101	ARG	1	0.819	0.876	8.620	20.136	20.136	0.000	0.000	0.000	0.000
100	A	102	ASP	-1	-0.855	-0.930	5.895	-41.605	-41.605	0.000	0.000	0.000	0.000
101	A	103	HIS	0	-0.001	-0.009	7.422	-1.342	-1.342	0.000	0.000	0.000	0.000
102	A	104	SER	0	0.009	0.013	8.619	0.762	0.762	0.000	0.000	0.000	0.000
104	A	106	GLN	0	-0.028	-0.030	6.166	2.944	2.944	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.942	-0.969	5.396	-41.379	-41.379	0.000	0.000	0.000	0.000
106	A	108	GLU	-1	-0.881	-0.956	8.148	-25.030	-25.030	0.000	0.000	0.000	0.000
107	A	109	ALA	0	-0.024	0.002	11.580	-0.137	-0.137	0.000	0.000	0.000	0.000
108	A	110	ALA	0	0.001	0.002	14.068	0.825	0.825	0.000	0.000	0.000	0.000
109	A	111	MET	0	-0.051	-0.013	17.558	-0.121	-0.121	0.000	0.000	0.000	0.000
110	A	112	GLU	-1	-0.861	-0.942	20.419	-11.795	-11.795	0.000	0.000	0.000	0.000
111	A	113	LEU	0	-0.048	-0.015	24.263	-0.191	-0.191	0.000	0.000	0.000	0.000
112	A	114	LYS	0	0.018	0.021	27.068	0.160	0.160	0.000	0.000	0.000	0.000
113	A	115	VAL	0	-0.063	-0.045	30.702	-0.097	-0.097	0.000	0.000	0.000	0.000
114	A	116	GLU	-1	-0.834	-0.895	33.728	-8.972	-8.972	0.000	0.000	0.000	0.000
115	A	117	ASP	-2	-1.869	-1.933	36.964	-15.707	-15.707	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:GLN)