FMO DATABASE

FMODB ID: 7N7YK

Calculation Name: 5YNR-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5YNR

Chain ID: A

ChEMBL ID:

UniProt ID: Q8IAA5

Base Structure: SolutionNMR

Registration Date: 2025-10-04

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	138
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1325924.55555
FMO2-HF: Nuclear repulsion	1268176.054251
FMO2-HF: Total energy	-57748.501298
FMO2-MP2: Total energy	-57912.015449

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:1:MET)

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

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.
-175.548	-172.643	26.172	-15.64	-13.435	-0.15

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.761 / q_NPA : 0.852

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	3	SER	0	-0.004	0.014	3.311	11.709	15.166	-0.014	-1.825	-1.618	-0.003
4	A	4	SER	0	0.021	0.007	5.154	1.837	1.872	-0.001	-0.004	-0.029	0.000
97	A	97	SER	0	-0.035	-0.004	1.962	-22.602	-22.047	9.193	-5.552	-4.196	-0.040
98	A	98	PRO	0	0.070	0.032	2.511	2.629	3.362	0.353	-0.424	-0.662	-0.002
99	A	99	GLU	-1	-0.701	-0.848	1.823	-125.504	-127.978	16.606	-7.670	-6.462	-0.104
100	A	100	LEU	0	-0.013	-0.008	2.950	7.183	7.782	0.035	-0.165	-0.468	-0.001
5	A	5	LEU	0	-0.010	0.007	8.088	-1.054	-1.054	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.042	-0.029	9.658	2.768	2.768	0.000	0.000	0.000	0.000
7	A	7	ILE	0	0.022	0.015	12.784	-0.963	-0.963	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.046	0.006	14.738	0.178	0.178	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.046	-0.014	16.278	1.119	1.119	0.000	0.000	0.000	0.000
10	A	10	ILE	0	0.050	-0.001	19.274	-0.594	-0.594	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.013	0.039	20.805	0.742	0.742	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.816	-0.917	23.865	-10.503	-10.503	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.062	0.025	27.150	0.110	0.110	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.033	0.015	21.537	0.141	0.141	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.841	0.912	24.876	10.580	10.580	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.935	-0.961	26.184	-9.370	-9.370	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.859	-0.932	27.336	-10.589	-10.589	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.037	-0.007	23.379	0.124	0.124	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.812	0.871	26.756	11.268	11.268	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.832	0.906	30.188	9.847	9.847	0.000	0.000	0.000	0.000
21	A	21	PHE	0	-0.004	0.015	26.914	0.326	0.326	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.859	0.916	30.333	10.122	10.122	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.069	-0.024	31.915	0.307	0.307	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.061	-0.036	34.339	0.408	0.408	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.914	0.982	32.855	8.586	8.586	0.000	0.000	0.000	0.000
26	A	26	SER	0	0.023	0.014	34.140	0.279	0.279	0.000	0.000	0.000	0.000
27	A	27	THR	0	-0.025	-0.020	36.105	-0.045	-0.045	0.000	0.000	0.000	0.000
28	A	28	THR	0	0.011	0.002	34.268	0.128	0.128	0.000	0.000	0.000	0.000
29	A	29	MET	0	-0.044	0.010	30.211	-0.199	-0.199	0.000	0.000	0.000	0.000
30	A	30	ASN	0	-0.009	-0.014	29.609	0.105	0.105	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.022	0.007	24.008	-0.165	-0.165	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.009	0.007	22.185	0.119	0.119	0.000	0.000	0.000	0.000
33	A	33	ILE	0	0.014	0.015	17.636	-0.461	-0.461	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.027	-0.015	18.150	0.373	0.373	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.935	0.986	9.860	27.560	27.560	0.000	0.000	0.000	0.000
36	A	36	ILE	0	-0.027	-0.005	11.854	1.267	1.267	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.791	-0.901	10.060	-31.611	-31.611	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.747	0.854	6.279	39.524	39.524	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.930	-0.954	9.309	-30.249	-30.249	0.000	0.000	0.000	0.000
40	A	40	SER	0	0.037	0.012	12.170	1.128	1.128	0.000	0.000	0.000	0.000
41	A	41	HIS	1	0.859	0.945	13.852	20.927	20.927	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.910	-0.960	15.121	-14.576	-14.576	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.018	-0.020	15.592	-1.247	-1.247	0.000	0.000	0.000	0.000
44	A	44	GLN	0	0.043	0.008	16.293	0.633	0.633	0.000	0.000	0.000	0.000
45	A	45	SER	0	0.006	-0.008	18.125	-0.483	-0.483	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.843	-0.905	14.581	-20.939	-20.939	0.000	0.000	0.000	0.000
47	A	47	GLN	0	0.029	0.002	18.922	0.018	0.018	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.032	-0.015	22.380	-0.196	-0.196	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.019	0.007	24.065	0.254	0.254	0.000	0.000	0.000	0.000
50	A	50	ASN	0	-0.040	-0.043	27.468	0.204	0.204	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.856	-0.921	30.748	-8.876	-8.876	0.000	0.000	0.000	0.000
52	A	52	CYS	0	-0.035	0.000	28.722	0.109	0.109	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.037	-0.076	29.663	0.038	0.038	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.015	-0.021	24.825	-0.388	-0.388	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.927	-0.956	24.770	-11.462	-11.462	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.703	-0.826	24.496	-11.272	-11.272	0.000	0.000	0.000	0.000
57	A	57	PHE	0	-0.070	-0.050	23.221	-0.628	-0.628	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.797	0.915	19.981	12.188	12.188	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.903	-0.933	19.696	-13.313	-13.313	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.969	-0.983	21.491	-12.447	-12.447	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.064	-0.037	17.109	-0.329	-0.329	0.000	0.000	0.000	0.000
62	A	62	PRO	0	0.042	0.024	15.344	-0.746	-0.746	0.000	0.000	0.000	0.000
63	A	63	SER	0	-0.004	-0.010	12.269	-0.388	-0.388	0.000	0.000	0.000	0.000
64	A	64	GLN	0	-0.055	-0.024	9.301	-0.895	-0.895	0.000	0.000	0.000	0.000
65	A	65	GLN	0	-0.019	-0.021	6.692	-3.874	-3.874	0.000	0.000	0.000	0.000
66	A	66	PRO	0	-0.030	-0.014	7.198	2.583	2.583	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.859	0.933	10.381	21.263	21.263	0.000	0.000	0.000	0.000
68	A	68	PHE	0	-0.001	-0.015	13.345	0.456	0.456	0.000	0.000	0.000	0.000
69	A	69	ILE	0	0.025	0.027	16.617	0.270	0.270	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.019	-0.012	20.138	0.284	0.284	0.000	0.000	0.000	0.000
71	A	71	LEU	0	0.075	0.047	23.153	0.345	0.345	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.058	-0.037	25.947	0.227	0.227	0.000	0.000	0.000	0.000
73	A	73	TRP	0	0.136	0.049	29.510	0.092	0.092	0.000	0.000	0.000	0.000
74	A	74	CYS	0	-0.056	-0.018	32.207	0.077	0.077	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.899	0.949	34.368	9.381	9.381	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.873	0.923	36.490	7.238	7.238	0.000	0.000	0.000	0.000
77	A	77	HIS	0	0.019	0.015	38.852	-0.181	-0.181	0.000	0.000	0.000	0.000
78	A	78	SER	0	0.014	-0.016	40.854	0.088	0.088	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.863	-0.891	43.377	-7.047	-7.047	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.868	-0.921	45.171	-6.413	-6.413	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.778	0.863	39.003	7.856	7.856	0.000	0.000	0.000	0.000
82	A	82	ILE	0	0.006	-0.018	39.351	-0.098	-0.098	0.000	0.000	0.000	0.000
83	A	83	SER	0	-0.039	-0.012	37.119	0.051	0.051	0.000	0.000	0.000	0.000
84	A	84	TYR	0	0.045	0.027	32.745	-0.018	-0.018	0.000	0.000	0.000	0.000
85	A	85	PRO	0	-0.025	-0.014	32.068	-0.202	-0.202	0.000	0.000	0.000	0.000
86	A	86	MET	0	-0.003	0.044	27.374	-0.210	-0.210	0.000	0.000	0.000	0.000
87	A	87	LEU	0	0.017	-0.006	24.585	-0.027	-0.027	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.050	-0.012	18.817	-0.149	-0.149	0.000	0.000	0.000	0.000
89	A	89	ILE	0	0.053	0.026	18.828	-0.153	-0.153	0.000	0.000	0.000	0.000
90	A	90	TYR	0	-0.110	-0.104	13.667	-1.083	-1.083	0.000	0.000	0.000	0.000
91	A	91	TYR	0	0.059	0.029	14.927	-0.311	-0.311	0.000	0.000	0.000	0.000
92	A	92	CYS	0	-0.086	-0.044	10.237	-1.348	-1.348	0.000	0.000	0.000	0.000
93	A	93	PRO	0	0.090	0.075	11.591	-0.123	-0.123	0.000	0.000	0.000	0.000
94	A	94	ASN	0	0.046	0.006	10.308	-4.573	-4.573	0.000	0.000	0.000	0.000
95	A	95	GLY	0	-0.004	0.010	7.154	0.824	0.824	0.000	0.000	0.000	0.000
96	A	96	SER	0	-0.040	-0.026	5.709	-7.569	-7.569	0.000	0.000	0.000	0.000
101	A	101	GLN	0	0.014	-0.009	5.405	4.408	4.408	0.000	0.000	0.000	0.000
102	A	102	MET	0	0.008	0.004	8.086	4.036	4.036	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.006	0.005	7.821	2.616	2.616	0.000	0.000	0.000	0.000
104	A	104	TYR	0	0.026	0.004	7.888	3.652	3.652	0.000	0.000	0.000	0.000
105	A	105	ALA	0	0.025	0.004	11.577	2.189	2.189	0.000	0.000	0.000	0.000
106	A	106	GLY	0	-0.017	0.006	12.869	1.645	1.645	0.000	0.000	0.000	0.000
107	A	107	SER	0	0.004	-0.023	13.709	1.795	1.795	0.000	0.000	0.000	0.000
108	A	108	ARG	1	0.906	0.959	15.595	18.493	18.493	0.000	0.000	0.000	0.000
109	A	109	ASN	0	-0.008	-0.009	17.493	0.339	0.339	0.000	0.000	0.000	0.000
110	A	110	PHE	0	-0.008	-0.006	18.657	0.821	0.821	0.000	0.000	0.000	0.000
111	A	111	ILE	0	0.014	0.023	19.073	0.707	0.707	0.000	0.000	0.000	0.000
112	A	112	VAL	0	0.008	0.003	21.757	0.577	0.577	0.000	0.000	0.000	0.000
113	A	113	ASN	0	-0.005	-0.001	23.824	0.936	0.936	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.851	-0.900	23.948	-11.285	-11.285	0.000	0.000	0.000	0.000
115	A	115	CYS	0	-0.024	-0.009	25.722	0.677	0.677	0.000	0.000	0.000	0.000
116	A	116	HIS	0	-0.006	0.004	27.517	0.408	0.408	0.000	0.000	0.000	0.000
117	A	117	VAL	0	-0.023	-0.023	24.163	0.287	0.287	0.000	0.000	0.000	0.000
118	A	118	SER	0	-0.010	-0.028	27.226	0.193	0.193	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.834	0.905	26.700	11.252	11.252	0.000	0.000	0.000	0.000
120	A	120	ASN	0	-0.011	0.000	20.402	-1.047	-1.047	0.000	0.000	0.000	0.000
121	A	121	THR	0	-0.029	-0.013	21.189	0.782	0.782	0.000	0.000	0.000	0.000
122	A	122	GLU	-1	-0.800	-0.866	16.642	-16.666	-16.666	0.000	0.000	0.000	0.000
123	A	123	ILE	0	0.051	0.030	16.905	0.625	0.625	0.000	0.000	0.000	0.000
124	A	124	ARG	1	0.883	0.928	11.430	21.174	21.174	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.809	-0.915	15.285	-17.696	-17.696	0.000	0.000	0.000	0.000
126	A	126	ILE	0	-0.069	-0.049	15.613	-0.514	-0.514	0.000	0.000	0.000	0.000
127	A	127	ASP	-1	-0.934	-0.954	18.316	-12.641	-12.641	0.000	0.000	0.000	0.000
128	A	128	GLU	-1	-0.975	-0.981	19.644	-14.918	-14.918	0.000	0.000	0.000	0.000
129	A	129	ILE	0	-0.091	-0.051	18.552	-0.008	-0.008	0.000	0.000	0.000	0.000
130	A	130	ASP	-1	-0.759	-0.900	22.971	-11.275	-11.275	0.000	0.000	0.000	0.000
131	A	131	ASP	-1	-0.902	-0.961	26.582	-9.815	-9.815	0.000	0.000	0.000	0.000
132	A	132	GLU	-1	-0.963	-0.972	28.572	-10.643	-10.643	0.000	0.000	0.000	0.000
133	A	133	LEU	0	-0.036	-0.014	24.262	0.090	0.090	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.045	-0.034	27.985	-0.026	-0.026	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.896	-0.955	30.223	-8.569	-8.569	0.000	0.000	0.000	0.000
136	A	136	SER	0	-0.049	-0.011	30.375	0.284	0.284	0.000	0.000	0.000	0.000
137	A	137	LYS	1	0.821	0.908	25.529	11.337	11.337	0.000	0.000	0.000	0.000
138	A	138	PHE	-1	-0.843	-0.876	30.024	-10.168	-10.168	0.000	0.000	0.000	0.000

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