FMO DATABASE

FMODB ID: VNRL1

Calculation Name: 3AY2-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3AY2

Chain ID: A

ChEMBL ID:

UniProt ID: Q5F809

Base Structure: X-ray

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	125
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1002266.144248
FMO2-HF: Nuclear repulsion	954273.218086
FMO2-HF: Total energy	-47992.926163
FMO2-MP2: Total energy	-48129.055939

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:58:ASN)

Summations of interaction energy for fragment #1(A:58:ASN)

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.
-85.74	-81.714	0.086	-1.944	-2.169	-0.013

Interaction energy analysis for fragmet #1(A:58:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.842 / q_NPA : 0.900

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	60	ALA	0	0.059	0.044	2.821	7.063	9.695	0.048	-1.120	-1.560	-0.006
4	A	61	ALA	0	-0.013	0.005	3.170	-13.692	-12.298	0.038	-0.824	-0.609	-0.007
5	A	62	THR	0	-0.034	-0.024	5.994	3.586	3.586	0.000	0.000	0.000	0.000
6	A	63	VAL	0	-0.002	0.013	9.253	0.270	0.270	0.000	0.000	0.000	0.000
7	A	64	GLU	-1	-0.890	-0.940	12.591	-18.515	-18.515	0.000	0.000	0.000	0.000
8	A	65	SER	0	-0.004	-0.009	15.802	0.691	0.691	0.000	0.000	0.000	0.000
9	A	66	ASN	0	0.043	0.022	19.377	0.212	0.212	0.000	0.000	0.000	0.000
10	A	67	ASP	-1	-0.697	-0.857	22.758	-11.583	-11.583	0.000	0.000	0.000	0.000
11	A	68	ASN	0	-0.079	-0.027	25.755	0.747	0.747	0.000	0.000	0.000	0.000
12	A	69	MET	0	-0.008	-0.012	25.239	0.122	0.122	0.000	0.000	0.000	0.000
13	A	70	GLN	0	0.022	0.025	22.069	-0.252	-0.252	0.000	0.000	0.000	0.000
14	A	71	PHE	0	0.029	0.000	17.247	-0.275	-0.275	0.000	0.000	0.000	0.000
15	A	72	ASN	0	-0.034	-0.018	13.503	0.105	0.105	0.000	0.000	0.000	0.000
16	A	73	THR	0	0.036	0.010	12.748	0.163	0.163	0.000	0.000	0.000	0.000
17	A	74	LYS	1	0.894	0.930	15.834	14.372	14.372	0.000	0.000	0.000	0.000
18	A	75	ASP	-1	-0.881	-0.908	14.089	-19.726	-19.726	0.000	0.000	0.000	0.000
19	A	76	ILE	0	0.010	0.018	9.696	-1.350	-1.350	0.000	0.000	0.000	0.000
20	A	77	GLN	0	-0.026	-0.012	9.079	-0.407	-0.407	0.000	0.000	0.000	0.000
21	A	78	VAL	0	0.001	0.002	7.747	-4.480	-4.480	0.000	0.000	0.000	0.000
22	A	79	SER	0	-0.044	-0.050	6.410	2.034	2.034	0.000	0.000	0.000	0.000
23	A	80	LYS	1	0.816	0.879	8.421	20.924	20.924	0.000	0.000	0.000	0.000
24	A	81	ALA	0	-0.007	0.007	8.294	1.674	1.674	0.000	0.000	0.000	0.000
25	A	83	LYS	1	0.975	0.972	8.207	27.093	27.093	0.000	0.000	0.000	0.000
26	A	84	GLU	-1	-0.864	-0.942	9.356	-21.490	-21.490	0.000	0.000	0.000	0.000
27	A	85	PHE	0	-0.003	-0.013	5.473	-7.182	-7.182	0.000	0.000	0.000	0.000
28	A	86	THR	0	-0.033	-0.007	7.049	2.810	2.810	0.000	0.000	0.000	0.000
29	A	87	ILE	0	-0.005	-0.005	7.430	-4.428	-4.428	0.000	0.000	0.000	0.000
30	A	88	THR	0	0.014	-0.007	8.878	3.003	3.003	0.000	0.000	0.000	0.000
31	A	89	LEU	0	-0.015	0.010	11.196	-0.493	-0.493	0.000	0.000	0.000	0.000
32	A	90	LYS	1	0.902	0.931	11.656	23.906	23.906	0.000	0.000	0.000	0.000
33	A	91	HIS	0	-0.036	-0.010	16.065	-0.135	-0.135	0.000	0.000	0.000	0.000
34	A	92	THR	0	-0.027	-0.026	18.225	0.477	0.477	0.000	0.000	0.000	0.000
35	A	93	GLY	0	-0.024	-0.004	20.790	0.459	0.459	0.000	0.000	0.000	0.000
36	A	94	THR	0	-0.064	-0.048	24.409	-0.045	-0.045	0.000	0.000	0.000	0.000
37	A	95	GLN	0	-0.021	-0.001	27.190	0.400	0.400	0.000	0.000	0.000	0.000
38	A	96	PRO	0	0.036	0.023	27.333	-0.463	-0.463	0.000	0.000	0.000	0.000
39	A	97	LYS	1	0.913	0.920	24.642	12.752	12.752	0.000	0.000	0.000	0.000
40	A	98	ALA	0	0.012	0.008	27.796	-0.010	-0.010	0.000	0.000	0.000	0.000
41	A	99	SER	0	-0.079	-0.034	30.846	0.230	0.230	0.000	0.000	0.000	0.000
42	A	100	MET	0	-0.018	-0.008	26.398	-0.069	-0.069	0.000	0.000	0.000	0.000
43	A	101	GLY	0	0.031	0.031	25.674	-0.451	-0.451	0.000	0.000	0.000	0.000
44	A	102	HIS	1	0.779	0.866	21.094	13.252	13.252	0.000	0.000	0.000	0.000
45	A	103	ASN	0	0.061	0.017	20.010	-0.272	-0.272	0.000	0.000	0.000	0.000
46	A	104	LEU	0	-0.013	-0.005	14.193	0.032	0.032	0.000	0.000	0.000	0.000
47	A	105	VAL	0	0.008	0.004	17.976	-0.545	-0.545	0.000	0.000	0.000	0.000
48	A	106	ILE	0	-0.012	-0.011	14.124	0.014	0.014	0.000	0.000	0.000	0.000
49	A	107	ALA	0	0.055	0.025	18.652	0.252	0.252	0.000	0.000	0.000	0.000
50	A	108	LYS	1	0.881	0.947	21.175	12.211	12.211	0.000	0.000	0.000	0.000
51	A	109	ALA	0	-0.019	-0.010	23.307	0.215	0.215	0.000	0.000	0.000	0.000
52	A	110	GLU	-1	-0.925	-0.974	24.800	-11.470	-11.470	0.000	0.000	0.000	0.000
53	A	111	ASP	-1	-0.868	-0.936	25.716	-11.232	-11.232	0.000	0.000	0.000	0.000
54	A	112	MET	0	-0.054	-0.013	21.220	0.273	0.273	0.000	0.000	0.000	0.000
55	A	113	ASP	-1	-0.830	-0.906	26.200	-9.495	-9.495	0.000	0.000	0.000	0.000
56	A	114	GLY	0	0.012	0.000	29.780	0.258	0.258	0.000	0.000	0.000	0.000
57	A	115	VAL	0	0.005	0.003	24.462	0.142	0.142	0.000	0.000	0.000	0.000
58	A	116	PHE	0	-0.044	-0.028	24.857	-0.035	-0.035	0.000	0.000	0.000	0.000
59	A	117	LYS	1	0.797	0.883	28.905	9.421	9.421	0.000	0.000	0.000	0.000
60	A	118	ASP	-1	-0.795	-0.874	30.639	-9.551	-9.551	0.000	0.000	0.000	0.000
61	A	119	GLY	0	0.029	0.020	28.791	0.032	0.032	0.000	0.000	0.000	0.000
62	A	120	VAL	0	-0.054	-0.029	29.600	0.046	0.046	0.000	0.000	0.000	0.000
63	A	121	GLY	0	-0.040	-0.015	32.681	0.166	0.166	0.000	0.000	0.000	0.000
64	A	122	ALA	0	0.004	0.005	29.863	0.149	0.149	0.000	0.000	0.000	0.000
65	A	123	ALA	0	-0.007	-0.002	29.715	-0.387	-0.387	0.000	0.000	0.000	0.000
66	A	124	ASP	-1	-0.929	-0.967	29.434	-9.940	-9.940	0.000	0.000	0.000	0.000
67	A	125	THR	0	-0.070	-0.038	27.930	-0.064	-0.064	0.000	0.000	0.000	0.000
68	A	126	ASP	-1	-0.794	-0.905	23.540	-13.712	-13.712	0.000	0.000	0.000	0.000
69	A	127	TYR	0	0.001	0.000	24.999	-0.316	-0.316	0.000	0.000	0.000	0.000
70	A	128	VAL	0	-0.006	0.022	22.966	-0.079	-0.079	0.000	0.000	0.000	0.000
71	A	129	LYS	1	0.860	0.928	26.438	10.377	10.377	0.000	0.000	0.000	0.000
72	A	130	PRO	0	0.004	-0.009	27.811	-0.361	-0.361	0.000	0.000	0.000	0.000
73	A	131	ASP	-1	-0.919	-0.967	28.098	-10.658	-10.658	0.000	0.000	0.000	0.000
74	A	132	ASP	-1	-0.795	-0.864	26.714	-11.046	-11.046	0.000	0.000	0.000	0.000
75	A	133	ALA	0	-0.017	-0.014	25.776	-0.500	-0.500	0.000	0.000	0.000	0.000
76	A	134	ARG	1	0.769	0.857	25.478	10.616	10.616	0.000	0.000	0.000	0.000
77	A	135	VAL	0	-0.059	-0.027	21.296	-0.469	-0.469	0.000	0.000	0.000	0.000
78	A	136	VAL	0	-0.005	0.009	17.087	-0.120	-0.120	0.000	0.000	0.000	0.000
79	A	137	ALA	0	-0.002	-0.011	16.052	-0.646	-0.646	0.000	0.000	0.000	0.000
80	A	138	HIS	0	-0.033	-0.030	18.102	0.494	0.494	0.000	0.000	0.000	0.000
81	A	139	THR	0	-0.030	-0.006	15.265	-0.409	-0.409	0.000	0.000	0.000	0.000
82	A	140	LYS	1	0.878	0.943	17.921	14.893	14.893	0.000	0.000	0.000	0.000
83	A	141	LEU	0	-0.032	0.001	20.333	-0.474	-0.474	0.000	0.000	0.000	0.000
84	A	142	ILE	0	-0.042	-0.021	17.960	0.292	0.292	0.000	0.000	0.000	0.000
85	A	143	GLY	0	-0.002	-0.019	22.249	0.379	0.379	0.000	0.000	0.000	0.000
86	A	144	GLY	0	-0.002	-0.001	22.804	-0.596	-0.596	0.000	0.000	0.000	0.000
87	A	145	GLY	0	0.004	-0.003	21.724	0.398	0.398	0.000	0.000	0.000	0.000
88	A	146	GLU	-1	-0.853	-0.896	20.648	-13.320	-13.320	0.000	0.000	0.000	0.000
89	A	147	GLU	-1	-0.877	-0.951	13.515	-22.538	-22.538	0.000	0.000	0.000	0.000
90	A	148	SER	0	-0.017	-0.002	15.817	0.705	0.705	0.000	0.000	0.000	0.000
91	A	149	SER	0	-0.010	0.000	11.554	0.020	0.020	0.000	0.000	0.000	0.000
92	A	150	LEU	0	0.025	0.033	12.335	1.487	1.487	0.000	0.000	0.000	0.000
93	A	151	THR	0	-0.054	-0.049	11.269	-3.628	-3.628	0.000	0.000	0.000	0.000
94	A	152	LEU	0	-0.001	0.012	11.964	2.202	2.202	0.000	0.000	0.000	0.000
95	A	153	ASP	-1	-0.758	-0.867	12.018	-22.221	-22.221	0.000	0.000	0.000	0.000
96	A	154	PRO	0	-0.009	-0.015	10.119	1.254	1.254	0.000	0.000	0.000	0.000
97	A	155	ALA	0	-0.005	-0.001	13.126	1.077	1.077	0.000	0.000	0.000	0.000
98	A	156	LYS	1	0.863	0.929	16.511	17.476	17.476	0.000	0.000	0.000	0.000
99	A	157	LEU	0	0.001	0.001	13.425	0.447	0.447	0.000	0.000	0.000	0.000
100	A	158	ALA	0	-0.011	-0.006	17.527	0.186	0.186	0.000	0.000	0.000	0.000
101	A	159	ASP	-1	-0.821	-0.881	19.274	-13.153	-13.153	0.000	0.000	0.000	0.000
102	A	160	GLY	0	0.003	-0.006	21.826	0.806	0.806	0.000	0.000	0.000	0.000
103	A	161	ASP	-1	-0.936	-0.955	20.834	-13.663	-13.663	0.000	0.000	0.000	0.000
104	A	162	TYR	0	-0.021	-0.025	17.685	0.271	0.271	0.000	0.000	0.000	0.000
105	A	163	LYS	1	0.868	0.928	18.578	12.846	12.846	0.000	0.000	0.000	0.000
106	A	164	PHE	0	-0.004	0.007	15.792	-0.275	-0.275	0.000	0.000	0.000	0.000
107	A	165	ALA	0	-0.010	-0.020	18.217	0.549	0.549	0.000	0.000	0.000	0.000
108	A	166	CYS	0	-0.042	0.026	20.563	-0.436	-0.436	0.000	0.000	0.000	0.000
109	A	167	THR	0	0.002	-0.037	22.516	0.280	0.280	0.000	0.000	0.000	0.000
110	A	168	PHE	0	0.018	0.017	25.376	0.471	0.471	0.000	0.000	0.000	0.000
111	A	169	PRO	0	0.029	0.002	27.400	0.008	0.008	0.000	0.000	0.000	0.000
112	A	170	GLY	0	-0.013	-0.002	30.697	0.056	0.056	0.000	0.000	0.000	0.000
113	A	171	HIS	0	0.041	0.002	25.535	-0.454	-0.454	0.000	0.000	0.000	0.000
114	A	172	GLY	0	0.052	0.047	24.844	-0.218	-0.218	0.000	0.000	0.000	0.000
115	A	173	ALA	0	-0.011	0.001	25.543	-0.231	-0.231	0.000	0.000	0.000	0.000
116	A	174	LEU	0	-0.031	-0.013	25.991	-0.041	-0.041	0.000	0.000	0.000	0.000
117	A	175	MET	0	-0.070	-0.018	21.155	-0.280	-0.280	0.000	0.000	0.000	0.000
118	A	176	ASN	0	0.008	-0.004	20.876	-0.289	-0.289	0.000	0.000	0.000	0.000
119	A	177	GLY	0	0.005	0.003	18.349	0.339	0.339	0.000	0.000	0.000	0.000
120	A	178	LYS	1	0.935	0.970	17.157	15.078	15.078	0.000	0.000	0.000	0.000
121	A	179	VAL	0	0.008	-0.009	12.813	-1.054	-1.054	0.000	0.000	0.000	0.000
122	A	180	THR	0	-0.038	-0.033	13.599	1.401	1.401	0.000	0.000	0.000	0.000
123	A	181	LEU	0	-0.008	0.003	12.425	-2.049	-2.049	0.000	0.000	0.000	0.000
124	A	182	VAL	0	-0.031	-0.017	9.307	1.224	1.224	0.000	0.000	0.000	0.000
125	A	183	ASP	-2	-1.644	-1.780	9.179	-49.655	-49.655	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:58:ASN)