FMO DATABASE

FMODB ID: 2ML2R

Calculation Name: 2A61-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2A61

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WZG9

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	142
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1228510.120348
FMO2-HF: Nuclear repulsion	1171732.989996
FMO2-HF: Total energy	-56777.130352
FMO2-MP2: Total energy	-56945.0227

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:5:LYS)

Summations of interaction energy for fragment #1(A:5:LYS)

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.
160.955	166.059	1.321	-2.568	-3.857	-0.027

Interaction energy analysis for fragmet #1(A:5:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.872 / q_NPA : 1.923

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	7	PRO	0	0.064	0.025	2.753	2.938	5.247	0.097	-0.908	-1.498	-0.003
4	A	8	PHE	0	0.028	0.013	2.104	-1.353	0.891	1.224	-1.463	-2.005	-0.023
5	A	9	GLU	-1	-0.801	-0.870	3.901	-54.358	-53.807	0.000	-0.197	-0.354	-0.001
6	A	10	ARG	1	0.929	0.969	5.807	71.020	71.020	0.000	0.000	0.000	0.000
7	A	11	ILE	0	0.116	0.060	7.083	4.378	4.378	0.000	0.000	0.000	0.000
8	A	12	LEU	0	0.001	0.006	7.080	4.664	4.664	0.000	0.000	0.000	0.000
9	A	13	ARG	1	0.853	0.903	9.048	56.881	56.881	0.000	0.000	0.000	0.000
10	A	14	GLU	-1	-0.910	-0.962	11.680	-39.906	-39.906	0.000	0.000	0.000	0.000
11	A	15	ILE	0	0.015	0.008	11.470	3.042	3.042	0.000	0.000	0.000	0.000
12	A	16	CYS	0	-0.052	-0.036	13.035	2.700	2.700	0.000	0.000	0.000	0.000
13	A	17	PHE	0	-0.024	-0.013	15.713	2.317	2.317	0.000	0.000	0.000	0.000
14	A	18	MET	0	0.024	0.009	16.001	2.428	2.428	0.000	0.000	0.000	0.000
15	A	19	VAL	0	0.048	0.030	18.136	1.728	1.728	0.000	0.000	0.000	0.000
16	A	20	LYS	1	0.899	0.960	19.825	29.395	29.395	0.000	0.000	0.000	0.000
17	A	21	VAL	0	-0.021	-0.017	21.505	1.367	1.367	0.000	0.000	0.000	0.000
18	A	22	GLU	-1	-0.793	-0.875	23.211	-20.834	-20.834	0.000	0.000	0.000	0.000
19	A	23	GLY	0	0.040	0.007	24.369	0.920	0.920	0.000	0.000	0.000	0.000
20	A	24	ARG	1	0.776	0.850	24.925	24.565	24.565	0.000	0.000	0.000	0.000
21	A	25	LYS	1	0.822	0.903	26.584	22.772	22.772	0.000	0.000	0.000	0.000
22	A	26	VAL	0	0.030	0.024	30.070	0.536	0.536	0.000	0.000	0.000	0.000
23	A	27	LEU	0	-0.045	-0.017	29.197	0.430	0.430	0.000	0.000	0.000	0.000
24	A	28	ARG	1	0.931	0.966	33.060	17.818	17.818	0.000	0.000	0.000	0.000
25	A	29	ASP	-1	-0.886	-0.946	35.382	-16.844	-16.844	0.000	0.000	0.000	0.000
26	A	30	PHE	0	-0.024	-0.011	35.290	0.420	0.420	0.000	0.000	0.000	0.000
27	A	31	GLY	0	0.013	0.016	37.739	0.297	0.297	0.000	0.000	0.000	0.000
28	A	32	ILE	0	-0.045	-0.004	33.346	-0.024	-0.024	0.000	0.000	0.000	0.000
29	A	33	THR	0	0.009	-0.011	33.438	-0.488	-0.488	0.000	0.000	0.000	0.000
30	A	34	PRO	0	0.021	-0.009	27.810	-0.171	-0.171	0.000	0.000	0.000	0.000
31	A	35	ALA	0	0.060	0.025	29.259	-0.309	-0.309	0.000	0.000	0.000	0.000
32	A	36	GLN	0	0.007	0.002	30.528	0.051	0.051	0.000	0.000	0.000	0.000
33	A	37	PHE	0	0.087	0.032	26.481	-0.045	-0.045	0.000	0.000	0.000	0.000
34	A	38	ASP	-1	-0.817	-0.875	25.569	-24.492	-24.492	0.000	0.000	0.000	0.000
35	A	39	ILE	0	-0.013	-0.001	28.337	-0.204	-0.204	0.000	0.000	0.000	0.000
36	A	40	LEU	0	0.020	0.017	31.354	0.046	0.046	0.000	0.000	0.000	0.000
37	A	41	GLN	0	0.014	-0.009	23.907	-0.092	-0.092	0.000	0.000	0.000	0.000
38	A	42	LYS	1	0.808	0.911	23.931	24.298	24.298	0.000	0.000	0.000	0.000
39	A	43	ILE	0	-0.009	-0.012	28.819	0.045	0.045	0.000	0.000	0.000	0.000
40	A	44	TYR	0	-0.018	-0.005	29.332	0.100	0.100	0.000	0.000	0.000	0.000
41	A	45	PHE	0	-0.028	-0.019	26.048	0.001	0.001	0.000	0.000	0.000	0.000
42	A	46	GLU	-1	-0.847	-0.907	25.631	-23.768	-23.768	0.000	0.000	0.000	0.000
43	A	47	GLY	0	0.032	0.033	30.027	0.365	0.365	0.000	0.000	0.000	0.000
44	A	48	PRO	0	-0.015	-0.022	33.697	-0.162	-0.162	0.000	0.000	0.000	0.000
45	A	49	LYS	1	0.884	0.950	28.976	20.402	20.402	0.000	0.000	0.000	0.000
46	A	50	ARG	1	0.850	0.914	34.574	17.014	17.014	0.000	0.000	0.000	0.000
47	A	51	PRO	0	0.037	0.004	34.588	-0.574	-0.574	0.000	0.000	0.000	0.000
48	A	52	GLY	0	-0.053	-0.034	34.462	-0.246	-0.246	0.000	0.000	0.000	0.000
49	A	53	GLU	-1	-0.802	-0.902	30.833	-19.111	-19.111	0.000	0.000	0.000	0.000
50	A	54	LEU	0	0.035	0.010	29.788	-0.745	-0.745	0.000	0.000	0.000	0.000
51	A	55	SER	0	-0.090	-0.053	30.564	-0.235	-0.235	0.000	0.000	0.000	0.000
52	A	56	VAL	0	0.011	-0.006	26.429	-0.351	-0.351	0.000	0.000	0.000	0.000
53	A	57	LEU	0	-0.054	-0.014	25.314	-0.790	-0.790	0.000	0.000	0.000	0.000
54	A	58	LEU	0	-0.031	-0.022	25.409	-0.784	-0.784	0.000	0.000	0.000	0.000
55	A	59	GLY	0	0.038	0.042	26.704	-0.397	-0.397	0.000	0.000	0.000	0.000
56	A	60	VAL	0	-0.032	-0.007	27.553	0.410	0.410	0.000	0.000	0.000	0.000
57	A	61	ALA	0	0.053	0.035	31.195	0.212	0.212	0.000	0.000	0.000	0.000
58	A	62	LYS	1	0.994	0.983	34.526	17.488	17.488	0.000	0.000	0.000	0.000
59	A	63	SER	0	0.042	0.036	37.059	0.058	0.058	0.000	0.000	0.000	0.000
60	A	64	THR	0	0.036	0.015	33.759	0.242	0.242	0.000	0.000	0.000	0.000
61	A	65	VAL	0	0.017	0.014	33.447	0.048	0.048	0.000	0.000	0.000	0.000
62	A	66	THR	0	-0.010	-0.014	35.985	0.258	0.258	0.000	0.000	0.000	0.000
63	A	67	GLY	0	-0.017	-0.011	39.265	0.328	0.328	0.000	0.000	0.000	0.000
64	A	68	LEU	0	-0.067	-0.033	33.225	0.179	0.179	0.000	0.000	0.000	0.000
65	A	69	VAL	0	0.052	0.018	36.589	0.043	0.043	0.000	0.000	0.000	0.000
66	A	70	LYS	1	0.986	0.995	38.853	14.453	14.453	0.000	0.000	0.000	0.000
67	A	71	ARG	1	0.903	0.964	37.395	16.564	16.564	0.000	0.000	0.000	0.000
68	A	72	LEU	0	0.031	0.027	35.428	0.134	0.134	0.000	0.000	0.000	0.000
69	A	73	GLU	-1	-0.813	-0.868	40.091	-14.680	-14.680	0.000	0.000	0.000	0.000
70	A	74	ALA	0	-0.022	-0.004	43.116	0.248	0.248	0.000	0.000	0.000	0.000
71	A	75	ASP	-1	-0.909	-0.951	41.914	-14.541	-14.541	0.000	0.000	0.000	0.000
72	A	76	GLY	0	0.014	0.015	43.461	-0.035	-0.035	0.000	0.000	0.000	0.000
73	A	77	TYR	0	-0.027	0.000	37.891	-0.076	-0.076	0.000	0.000	0.000	0.000
74	A	78	LEU	0	-0.024	-0.025	36.009	-0.419	-0.419	0.000	0.000	0.000	0.000
75	A	79	THR	0	0.028	0.009	40.008	0.483	0.483	0.000	0.000	0.000	0.000
76	A	80	ARG	1	0.809	0.877	41.446	14.042	14.042	0.000	0.000	0.000	0.000
77	A	81	THR	0	0.019	0.017	41.759	0.420	0.420	0.000	0.000	0.000	0.000
78	A	82	PRO	0	0.028	0.008	43.258	-0.299	-0.299	0.000	0.000	0.000	0.000
79	A	83	ASP	-1	-0.772	-0.876	41.316	-15.314	-15.314	0.000	0.000	0.000	0.000
80	A	84	PRO	0	-0.045	-0.020	43.068	0.311	0.311	0.000	0.000	0.000	0.000
81	A	85	ALA	0	-0.012	-0.003	43.464	0.316	0.316	0.000	0.000	0.000	0.000
82	A	86	ASP	-1	-0.862	-0.933	43.988	-13.626	-13.626	0.000	0.000	0.000	0.000
83	A	87	ARG	1	0.996	0.989	45.757	12.105	12.105	0.000	0.000	0.000	0.000
84	A	88	ARG	1	0.890	0.952	45.486	13.589	13.589	0.000	0.000	0.000	0.000
85	A	89	ALA	0	-0.044	-0.008	41.715	-0.206	-0.206	0.000	0.000	0.000	0.000
86	A	90	TYR	0	-0.023	-0.030	41.146	0.178	0.178	0.000	0.000	0.000	0.000
87	A	91	PHE	0	-0.031	-0.013	36.404	-0.401	-0.401	0.000	0.000	0.000	0.000
88	A	92	LEU	0	-0.029	-0.015	37.165	0.451	0.451	0.000	0.000	0.000	0.000
89	A	93	VAL	0	0.030	-0.005	37.286	-0.501	-0.501	0.000	0.000	0.000	0.000
90	A	94	ILE	0	-0.004	0.005	34.060	0.237	0.237	0.000	0.000	0.000	0.000
91	A	95	THR	0	-0.025	-0.029	37.804	0.161	0.161	0.000	0.000	0.000	0.000
92	A	96	ARG	1	0.820	0.858	36.802	15.999	15.999	0.000	0.000	0.000	0.000
93	A	97	LYS	1	0.934	0.972	39.115	14.389	14.389	0.000	0.000	0.000	0.000
94	A	98	GLY	0	0.018	-0.005	37.039	-0.260	-0.260	0.000	0.000	0.000	0.000
95	A	99	GLU	-1	-0.883	-0.943	34.638	-17.236	-17.236	0.000	0.000	0.000	0.000
96	A	100	GLU	-1	-0.894	-0.950	34.209	-15.892	-15.892	0.000	0.000	0.000	0.000
97	A	101	VAL	0	-0.069	-0.018	32.471	-0.284	-0.284	0.000	0.000	0.000	0.000
98	A	102	ILE	0	-0.044	-0.022	28.645	-0.632	-0.632	0.000	0.000	0.000	0.000
99	A	103	GLU	-1	-0.780	-0.853	30.007	-17.915	-17.915	0.000	0.000	0.000	0.000
100	A	104	LYS	1	1.014	1.008	31.506	15.992	15.992	0.000	0.000	0.000	0.000
101	A	105	VAL	0	-0.072	-0.029	26.648	-0.429	-0.429	0.000	0.000	0.000	0.000
102	A	106	ILE	0	-0.046	-0.025	26.549	-0.971	-0.971	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.876	-0.930	27.483	-18.347	-18.347	0.000	0.000	0.000	0.000
104	A	108	ARG	1	0.851	0.927	27.593	19.655	19.655	0.000	0.000	0.000	0.000
105	A	109	ARG	1	0.843	0.912	20.151	26.397	26.397	0.000	0.000	0.000	0.000
106	A	110	GLU	-1	-0.906	-0.951	24.450	-21.849	-21.849	0.000	0.000	0.000	0.000
107	A	111	ASN	0	0.061	0.023	26.376	-0.236	-0.236	0.000	0.000	0.000	0.000
108	A	112	PHE	0	-0.062	-0.028	20.565	-0.050	-0.050	0.000	0.000	0.000	0.000
109	A	113	ILE	0	0.001	-0.015	19.635	-0.493	-0.493	0.000	0.000	0.000	0.000
110	A	114	GLU	-1	-0.912	-0.933	23.098	-19.886	-19.886	0.000	0.000	0.000	0.000
111	A	115	LYS	1	0.947	0.976	25.810	19.918	19.918	0.000	0.000	0.000	0.000
112	A	116	ILE	0	0.006	0.007	19.104	-0.226	-0.226	0.000	0.000	0.000	0.000
113	A	117	THR	0	-0.053	-0.053	21.046	-0.189	-0.189	0.000	0.000	0.000	0.000
114	A	118	SER	0	-0.006	0.014	23.022	0.430	0.430	0.000	0.000	0.000	0.000
115	A	119	ASP	-1	-0.926	-0.962	23.544	-21.916	-21.916	0.000	0.000	0.000	0.000
116	A	120	LEU	0	-0.094	-0.045	18.016	-0.464	-0.464	0.000	0.000	0.000	0.000
117	A	121	GLY	0	0.052	0.036	22.026	-0.035	-0.035	0.000	0.000	0.000	0.000
118	A	122	LYS	1	1.003	0.987	23.418	18.910	18.910	0.000	0.000	0.000	0.000
119	A	123	GLU	-1	-0.840	-0.898	23.314	-23.820	-23.820	0.000	0.000	0.000	0.000
120	A	124	LYS	1	0.950	0.979	18.448	25.900	25.900	0.000	0.000	0.000	0.000
121	A	125	SER	0	0.018	-0.006	19.021	-1.850	-1.850	0.000	0.000	0.000	0.000
122	A	126	SER	0	-0.043	-0.027	19.982	-0.461	-0.461	0.000	0.000	0.000	0.000
123	A	127	LYS	1	0.884	0.928	17.791	25.003	25.003	0.000	0.000	0.000	0.000
124	A	128	ILE	0	-0.003	0.002	14.517	-1.676	-1.676	0.000	0.000	0.000	0.000
125	A	129	LEU	0	0.005	0.002	15.591	-1.658	-1.658	0.000	0.000	0.000	0.000
126	A	130	ASP	-1	-0.848	-0.920	17.934	-27.554	-27.554	0.000	0.000	0.000	0.000
127	A	131	TYR	0	0.009	0.000	12.433	-0.920	-0.920	0.000	0.000	0.000	0.000
128	A	132	LEU	0	-0.032	-0.018	12.442	-2.844	-2.844	0.000	0.000	0.000	0.000
129	A	133	LYS	1	0.866	0.934	14.517	26.492	26.492	0.000	0.000	0.000	0.000
130	A	134	GLU	-1	-0.918	-0.951	13.838	-37.302	-37.302	0.000	0.000	0.000	0.000
131	A	135	LEU	0	-0.043	-0.024	8.284	-2.139	-2.139	0.000	0.000	0.000	0.000
132	A	136	LYS	1	0.849	0.911	12.080	29.297	29.297	0.000	0.000	0.000	0.000
133	A	137	GLY	0	0.061	0.034	14.707	0.119	0.119	0.000	0.000	0.000	0.000
134	A	138	VAL	0	-0.072	-0.037	10.487	0.379	0.379	0.000	0.000	0.000	0.000
135	A	139	MET	0	-0.030	-0.016	9.102	-0.628	-0.628	0.000	0.000	0.000	0.000
136	A	140	GLU	-1	-0.800	-0.899	12.653	-30.825	-30.825	0.000	0.000	0.000	0.000
137	A	141	ARG	1	0.911	0.962	14.960	38.906	38.906	0.000	0.000	0.000	0.000
138	A	142	ASN	0	-0.063	-0.051	11.355	-0.535	-0.535	0.000	0.000	0.000	0.000
139	A	143	PHE	0	-0.029	-0.006	13.401	-0.579	-0.579	0.000	0.000	0.000	0.000
140	A	144	SER	0	0.017	0.018	14.975	0.447	0.447	0.000	0.000	0.000	0.000
141	A	145	LYS	1	0.892	0.958	9.086	52.457	52.457	0.000	0.000	0.000	0.000
142	A	146	GLN	-1	-0.942	-0.965	13.470	-39.149	-39.149	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:LYS)