FMO DATABASE

FMODB ID: JVKR9

Calculation Name: 2YY9-B-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2YY9

Chain ID: B

ChEMBL ID:

UniProt ID: Q1H9T6

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	109
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-810444.54036
FMO2-HF: Nuclear repulsion	768574.178083
FMO2-HF: Total energy	-41870.362276
FMO2-MP2: Total energy	-41992.231564

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:6:SER)

Summations of interaction energy for fragment #1(A:6: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.
-11.589	-8.67	1.269	-1.772	-2.415	-0.008

Interaction energy analysis for fragmet #1(A:6:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.869 / q_NPA : 0.928

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	8	HIS	0	0.048	0.016	3.873	-1.263	0.457	-0.016	-0.884	-0.819	-0.001
5	A	10	VAL	0	-0.007	0.016	2.389	-2.293	-1.276	1.286	-0.864	-1.439	-0.007
6	A	11	ARG	1	0.971	0.995	4.328	41.792	41.974	-0.001	-0.024	-0.157	0.000
4	A	9	SER	0	0.070	0.017	6.703	0.551	0.551	0.000	0.000	0.000	0.000
7	A	12	VAL	0	-0.003	0.005	6.153	2.936	2.936	0.000	0.000	0.000	0.000
8	A	13	LEU	0	0.036	0.030	8.480	1.743	1.743	0.000	0.000	0.000	0.000
9	A	14	GLN	0	0.025	0.001	5.288	-1.072	-1.072	0.000	0.000	0.000	0.000
10	A	15	GLU	-1	-0.855	-0.905	9.075	-18.302	-18.302	0.000	0.000	0.000	0.000
11	A	16	LEU	0	0.002	0.000	11.675	1.482	1.482	0.000	0.000	0.000	0.000
12	A	17	ASN	0	0.085	0.041	12.100	2.410	2.410	0.000	0.000	0.000	0.000
13	A	18	LYS	1	0.813	0.887	13.060	20.708	20.708	0.000	0.000	0.000	0.000
14	A	19	GLN	0	-0.029	-0.017	14.842	1.452	1.452	0.000	0.000	0.000	0.000
15	A	20	ARG	1	0.793	0.879	15.730	18.006	18.006	0.000	0.000	0.000	0.000
16	A	21	GLU	-1	-0.859	-0.913	16.763	-15.206	-15.206	0.000	0.000	0.000	0.000
17	A	22	LYS	1	0.862	0.927	18.976	15.191	15.191	0.000	0.000	0.000	0.000
18	A	23	GLY	0	0.005	-0.004	21.563	0.585	0.585	0.000	0.000	0.000	0.000
19	A	24	GLN	0	-0.050	-0.028	19.656	-0.123	-0.123	0.000	0.000	0.000	0.000
20	A	25	TYR	0	-0.021	-0.029	19.566	-0.575	-0.575	0.000	0.000	0.000	0.000
21	A	26	CYS	0	-0.091	-0.005	20.991	-0.309	-0.309	0.000	0.000	0.000	0.000
22	A	27	ASP	-1	-0.795	-0.894	23.027	-12.157	-12.157	0.000	0.000	0.000	0.000
23	A	28	ALA	0	0.006	0.018	24.076	0.488	0.488	0.000	0.000	0.000	0.000
24	A	29	THR	0	-0.032	-0.039	25.236	-0.270	-0.270	0.000	0.000	0.000	0.000
25	A	30	LEU	0	0.012	0.003	24.115	0.275	0.275	0.000	0.000	0.000	0.000
26	A	31	ASP	-1	-0.863	-0.922	28.039	-9.473	-9.473	0.000	0.000	0.000	0.000
27	A	32	VAL	0	0.000	-0.003	27.949	0.096	0.096	0.000	0.000	0.000	0.000
28	A	33	GLY	0	0.025	0.000	31.165	0.008	0.008	0.000	0.000	0.000	0.000
29	A	34	GLY	0	-0.017	0.000	33.853	0.173	0.173	0.000	0.000	0.000	0.000
30	A	35	LEU	0	-0.051	-0.010	28.095	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	36	VAL	0	-0.005	-0.015	28.163	-0.082	-0.082	0.000	0.000	0.000	0.000
32	A	37	PHE	0	0.032	0.022	22.604	-0.298	-0.298	0.000	0.000	0.000	0.000
33	A	38	LYS	1	0.900	0.951	22.866	11.556	11.556	0.000	0.000	0.000	0.000
34	A	39	ALA	0	0.051	0.015	20.350	-0.595	-0.595	0.000	0.000	0.000	0.000
35	A	40	HIS	0	0.044	0.038	17.313	0.108	0.108	0.000	0.000	0.000	0.000
36	A	41	TRP	0	0.030	-0.001	20.710	-0.516	-0.516	0.000	0.000	0.000	0.000
37	A	42	SER	0	-0.011	0.000	19.089	-0.056	-0.056	0.000	0.000	0.000	0.000
38	A	43	VAL	0	0.024	0.015	15.798	-0.225	-0.225	0.000	0.000	0.000	0.000
39	A	44	LEU	0	0.004	0.003	18.243	-0.147	-0.147	0.000	0.000	0.000	0.000
40	A	45	ALA	0	-0.008	-0.006	21.397	0.191	0.191	0.000	0.000	0.000	0.000
41	A	46	CYS	0	-0.092	-0.042	17.277	0.065	0.065	0.000	0.000	0.000	0.000
42	A	47	CYS	0	-0.008	0.021	17.137	-0.434	-0.434	0.000	0.000	0.000	0.000
43	A	48	SER	0	0.030	0.001	19.478	0.503	0.503	0.000	0.000	0.000	0.000
44	A	49	HIS	0	0.050	0.018	23.339	0.238	0.238	0.000	0.000	0.000	0.000
45	A	50	PHE	0	-0.037	-0.012	26.479	0.527	0.527	0.000	0.000	0.000	0.000
46	A	51	PHE	0	0.054	0.005	23.729	0.331	0.331	0.000	0.000	0.000	0.000
47	A	52	GLN	0	-0.052	-0.029	23.597	0.636	0.636	0.000	0.000	0.000	0.000
48	A	53	ARG	1	0.866	0.925	27.523	9.320	9.320	0.000	0.000	0.000	0.000
49	A	54	ILE	0	-0.022	0.004	29.513	0.275	0.275	0.000	0.000	0.000	0.000
50	A	55	TYR	0	-0.029	0.007	27.703	0.234	0.234	0.000	0.000	0.000	0.000
51	A	56	GLY	0	-0.014	-0.001	30.215	0.195	0.195	0.000	0.000	0.000	0.000
52	A	57	ASP	-1	-0.896	-0.953	32.729	-8.722	-8.722	0.000	0.000	0.000	0.000
53	A	58	GLY	0	-0.006	0.008	34.749	0.232	0.232	0.000	0.000	0.000	0.000
54	A	59	THR	0	-0.007	-0.030	32.734	0.065	0.065	0.000	0.000	0.000	0.000
55	A	60	GLY	0	-0.036	-0.011	34.954	0.023	0.023	0.000	0.000	0.000	0.000
56	A	61	GLY	0	0.005	-0.009	32.314	-0.085	-0.085	0.000	0.000	0.000	0.000
57	A	62	SER	0	-0.077	-0.024	31.226	-0.427	-0.427	0.000	0.000	0.000	0.000
58	A	63	VAL	0	0.033	0.022	29.215	0.252	0.252	0.000	0.000	0.000	0.000
59	A	64	VAL	0	0.006	0.001	31.555	-0.149	-0.149	0.000	0.000	0.000	0.000
60	A	65	LEU	0	-0.029	-0.014	29.119	0.075	0.075	0.000	0.000	0.000	0.000
61	A	66	PRO	0	-0.006	-0.007	32.869	0.132	0.132	0.000	0.000	0.000	0.000
62	A	67	ALA	0	0.063	0.005	33.369	-0.232	-0.232	0.000	0.000	0.000	0.000
63	A	68	GLY	0	-0.037	0.000	33.652	-0.106	-0.106	0.000	0.000	0.000	0.000
64	A	69	PHE	0	0.051	0.017	28.551	-0.128	-0.128	0.000	0.000	0.000	0.000
65	A	70	ALA	0	-0.024	-0.002	28.682	-0.437	-0.437	0.000	0.000	0.000	0.000
66	A	71	GLU	-1	-0.948	-0.977	28.504	-10.468	-10.468	0.000	0.000	0.000	0.000
67	A	72	ILE	0	-0.004	-0.003	24.616	-0.381	-0.381	0.000	0.000	0.000	0.000
68	A	73	PHE	0	-0.009	-0.013	24.069	-0.611	-0.611	0.000	0.000	0.000	0.000
69	A	74	GLY	0	0.021	0.015	22.247	-0.435	-0.435	0.000	0.000	0.000	0.000
70	A	75	LEU	0	0.041	0.025	19.689	-0.720	-0.720	0.000	0.000	0.000	0.000
71	A	76	LEU	0	-0.028	-0.012	18.904	-0.862	-0.862	0.000	0.000	0.000	0.000
72	A	77	LEU	0	-0.003	0.008	19.151	-0.524	-0.524	0.000	0.000	0.000	0.000
73	A	78	ASP	-1	-0.811	-0.925	16.158	-17.456	-17.456	0.000	0.000	0.000	0.000
74	A	79	PHE	0	-0.031	0.018	14.396	-1.505	-1.505	0.000	0.000	0.000	0.000
75	A	80	PHE	0	0.028	-0.004	14.027	-1.141	-1.141	0.000	0.000	0.000	0.000
76	A	81	TYR	0	-0.033	-0.041	13.152	-0.675	-0.675	0.000	0.000	0.000	0.000
77	A	82	THR	0	-0.108	-0.078	10.074	-1.898	-1.898	0.000	0.000	0.000	0.000
78	A	83	GLY	0	-0.015	0.009	9.435	-2.961	-2.961	0.000	0.000	0.000	0.000
79	A	84	HIS	0	-0.053	-0.034	11.484	0.232	0.232	0.000	0.000	0.000	0.000
80	A	85	LEU	0	0.066	0.038	13.372	0.656	0.656	0.000	0.000	0.000	0.000
81	A	86	ALA	0	0.005	0.009	17.163	-0.115	-0.115	0.000	0.000	0.000	0.000
82	A	87	LEU	0	-0.015	0.001	19.082	0.952	0.952	0.000	0.000	0.000	0.000
83	A	88	THR	0	-0.019	-0.012	21.247	-0.042	-0.042	0.000	0.000	0.000	0.000
84	A	89	SER	0	0.013	-0.007	24.292	0.372	0.372	0.000	0.000	0.000	0.000
85	A	90	GLY	0	0.004	-0.002	27.563	0.287	0.287	0.000	0.000	0.000	0.000
86	A	91	ASN	0	-0.033	-0.017	23.211	0.115	0.115	0.000	0.000	0.000	0.000
87	A	92	ARG	1	0.926	0.967	25.154	11.464	11.464	0.000	0.000	0.000	0.000
88	A	93	ASP	-1	-0.882	-0.939	26.138	-10.540	-10.540	0.000	0.000	0.000	0.000
89	A	94	GLN	0	0.031	0.013	28.389	-0.068	-0.068	0.000	0.000	0.000	0.000
90	A	95	VAL	0	0.000	0.003	22.119	-0.091	-0.091	0.000	0.000	0.000	0.000
91	A	96	LEU	0	0.007	0.003	25.395	-0.035	-0.035	0.000	0.000	0.000	0.000
92	A	97	LEU	0	-0.039	-0.027	26.634	0.100	0.100	0.000	0.000	0.000	0.000
93	A	98	ALA	0	0.036	0.013	26.193	0.114	0.114	0.000	0.000	0.000	0.000
94	A	99	ALA	0	0.003	0.006	23.538	-0.034	-0.034	0.000	0.000	0.000	0.000
95	A	100	LYS	1	0.913	0.966	25.039	10.132	10.132	0.000	0.000	0.000	0.000
96	A	101	GLU	-1	-0.936	-0.966	28.126	-9.470	-9.470	0.000	0.000	0.000	0.000
97	A	102	LEU	0	-0.044	-0.017	24.911	0.147	0.147	0.000	0.000	0.000	0.000
98	A	103	ARG	1	0.833	0.933	25.792	9.808	9.808	0.000	0.000	0.000	0.000
99	A	104	VAL	0	0.041	0.019	20.280	-0.271	-0.271	0.000	0.000	0.000	0.000
100	A	105	PRO	0	-0.004	-0.013	21.592	-0.088	-0.088	0.000	0.000	0.000	0.000
101	A	106	GLU	-1	-0.880	-0.946	15.128	-18.989	-18.989	0.000	0.000	0.000	0.000
102	A	107	ALA	0	0.025	0.015	18.992	-0.277	-0.277	0.000	0.000	0.000	0.000
103	A	108	VAL	0	-0.016	-0.011	20.227	0.299	0.299	0.000	0.000	0.000	0.000
104	A	109	GLU	-1	-0.903	-0.945	19.986	-13.456	-13.456	0.000	0.000	0.000	0.000
105	A	110	LEU	0	-0.017	0.005	15.564	0.009	0.009	0.000	0.000	0.000	0.000
106	A	111	CYS	0	-0.049	-0.017	19.999	0.267	0.267	0.000	0.000	0.000	0.000
107	A	112	GLN	0	-0.047	-0.025	23.353	0.401	0.401	0.000	0.000	0.000	0.000
108	A	113	SER	0	-0.070	-0.038	20.686	0.149	0.149	0.000	0.000	0.000	0.000
109	A	114	PHE	-1	-0.927	-0.962	21.920	-13.145	-13.145	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:SER)