FMO DATABASE

FMODB ID: VV711

Calculation Name: 2DXA-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DXA

Chain ID: A

ChEMBL ID:

UniProt ID: P0AAR3

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	158
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1478190.849465
FMO2-HF: Nuclear repulsion	1419211.975762
FMO2-HF: Total energy	-58978.873703
FMO2-MP2: Total energy	-59152.321592

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.
93.767	98.645	7.164	-3.69	-8.353	-0.02

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 : 0.884 / q_NPA : 0.943

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	PRO	0	0.032	0.006	3.868	-4.407	-3.215	-0.013	-0.594	-0.585	0.000
5	A	5	VAL	0	0.028	0.018	2.270	0.318	0.974	3.233	-0.917	-2.972	-0.005
6	A	6	LYS	1	0.943	0.974	2.750	79.433	80.398	0.127	-0.325	-0.767	0.000
9	A	9	GLU	-1	-0.892	-0.955	2.996	-58.624	-56.885	0.217	-0.996	-0.960	-0.010
15	A	15	PHE	0	-0.035	-0.029	4.185	0.037	0.163	-0.001	-0.011	-0.115	0.000
17	A	17	ILE	0	-0.027	-0.018	2.834	-0.672	-1.301	3.455	-0.658	-2.168	-0.004
135	A	135	LEU	0	-0.103	-0.052	3.341	-3.466	-2.637	0.146	-0.189	-0.786	-0.001
4	A	4	ALA	0	0.004	0.016	6.103	1.608	1.608	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.026	-0.002	5.792	3.916	3.916	0.000	0.000	0.000	0.000
8	A	8	LEU	0	0.042	0.033	7.539	2.973	2.973	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.901	0.949	7.538	25.147	25.147	0.000	0.000	0.000	0.000
11	A	11	ASN	0	-0.096	-0.062	10.585	3.034	3.034	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.928	0.973	11.181	20.069	20.069	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.005	0.015	11.046	1.425	1.425	0.000	0.000	0.000	0.000
14	A	14	SER	0	0.008	0.006	9.907	-1.451	-1.451	0.000	0.000	0.000	0.000
16	A	16	GLN	0	0.011	0.007	7.936	-0.567	-0.567	0.000	0.000	0.000	0.000
18	A	18	HIS	1	0.861	0.915	6.964	21.445	21.445	0.000	0.000	0.000	0.000
19	A	19	THR	0	-0.003	-0.007	6.627	-0.434	-0.434	0.000	0.000	0.000	0.000
20	A	20	TYR	0	-0.058	-0.046	9.345	1.598	1.598	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.903	-0.937	12.025	-17.408	-17.408	0.000	0.000	0.000	0.000
22	A	22	HIS	0	-0.044	-0.024	12.100	0.324	0.324	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.766	-0.878	15.514	-13.946	-13.946	0.000	0.000	0.000	0.000
24	A	24	PRO	0	-0.104	-0.077	16.145	-0.247	-0.247	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.002	0.009	17.880	0.014	0.014	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.944	-0.949	20.589	-12.661	-12.661	0.000	0.000	0.000	0.000
27	A	27	THR	0	-0.058	-0.030	19.699	-0.808	-0.808	0.000	0.000	0.000	0.000
28	A	28	ASN	0	0.004	0.008	15.251	1.180	1.180	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.021	-0.009	19.104	-0.275	-0.275	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.039	-0.028	17.746	0.246	0.246	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.825	-0.911	18.543	-13.237	-13.237	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.737	-0.847	16.182	-17.134	-17.134	0.000	0.000	0.000	0.000
33	A	33	VAL	0	0.026	0.010	13.757	0.266	0.266	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.022	-0.005	16.580	0.211	0.211	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.862	0.918	19.875	12.473	12.473	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.857	0.930	16.880	15.562	15.562	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.035	-0.021	12.991	-0.261	-0.261	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.012	0.027	17.725	0.147	0.147	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.028	-0.004	15.348	0.246	0.246	0.000	0.000	0.000	0.000
40	A	40	ASN	0	0.083	0.034	20.053	0.524	0.524	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.025	-0.002	21.410	-0.493	-0.493	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.809	-0.886	23.010	-10.852	-10.852	0.000	0.000	0.000	0.000
43	A	43	GLN	0	-0.058	-0.017	18.928	0.230	0.230	0.000	0.000	0.000	0.000
44	A	44	VAL	0	-0.004	0.001	16.526	-0.882	-0.882	0.000	0.000	0.000	0.000
45	A	45	TYR	0	-0.010	-0.001	17.212	0.685	0.685	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.850	0.922	16.474	11.495	11.495	0.000	0.000	0.000	0.000
47	A	47	THR	0	-0.043	-0.026	14.535	0.722	0.722	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.039	-0.021	17.614	0.003	0.003	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.001	0.007	17.910	0.098	0.098	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.014	-0.012	21.653	0.382	0.382	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.040	0.021	25.421	-0.212	-0.212	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.009	-0.004	27.576	0.363	0.363	0.000	0.000	0.000	0.000
53	A	53	ASN	0	-0.028	-0.039	30.282	0.357	0.357	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.015	0.015	33.005	0.286	0.286	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.864	-0.919	31.926	-9.925	-9.925	0.000	0.000	0.000	0.000
56	A	56	MET	0	0.016	0.003	29.009	-0.429	-0.429	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.890	0.932	27.545	9.637	9.637	0.000	0.000	0.000	0.000
58	A	58	HIS	0	-0.012	0.015	27.084	-0.630	-0.630	0.000	0.000	0.000	0.000
59	A	59	LEU	0	-0.015	-0.014	22.472	-0.050	-0.050	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.023	0.012	23.493	-0.030	-0.030	0.000	0.000	0.000	0.000
61	A	61	VAL	0	-0.030	-0.020	18.010	-0.201	-0.201	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.013	0.019	21.365	0.406	0.406	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.007	-0.001	17.583	-0.616	-0.616	0.000	0.000	0.000	0.000
64	A	64	THR	0	0.040	0.012	20.100	0.596	0.596	0.000	0.000	0.000	0.000
65	A	65	PRO	0	0.049	0.031	21.097	-0.607	-0.607	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.056	-0.039	19.054	0.275	0.275	0.000	0.000	0.000	0.000
67	A	67	ALA	0	-0.017	0.004	22.299	0.267	0.267	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.039	0.036	25.459	0.489	0.489	0.000	0.000	0.000	0.000
69	A	69	GLN	0	-0.058	-0.040	25.917	-0.333	-0.333	0.000	0.000	0.000	0.000
70	A	70	LEU	0	0.038	0.027	24.910	-0.063	-0.063	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.840	-0.923	27.759	-8.718	-8.718	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.025	-0.001	28.431	-0.095	-0.095	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.961	0.984	30.948	8.038	8.038	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.917	0.977	31.310	9.181	9.181	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.044	0.021	26.678	-0.058	-0.058	0.000	0.000	0.000	0.000
76	A	76	ALA	0	-0.040	-0.012	29.306	-0.088	-0.088	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.986	0.987	31.911	8.291	8.291	0.000	0.000	0.000	0.000
78	A	78	ALA	0	-0.019	-0.001	29.063	0.090	0.090	0.000	0.000	0.000	0.000
79	A	79	LEU	0	0.000	-0.012	25.904	-0.190	-0.190	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.007	0.027	30.004	0.034	0.034	0.000	0.000	0.000	0.000
81	A	81	ALA	0	-0.078	-0.030	31.781	0.168	0.168	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.949	0.964	33.765	8.266	8.266	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.842	0.894	34.144	9.022	9.022	0.000	0.000	0.000	0.000
84	A	84	VAL	0	0.011	0.007	28.750	-0.115	-0.115	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.835	-0.898	29.783	-9.059	-9.059	0.000	0.000	0.000	0.000
86	A	86	MET	0	0.012	0.006	23.190	-0.310	-0.310	0.000	0.000	0.000	0.000
87	A	87	ALA	0	0.014	0.012	23.784	0.279	0.279	0.000	0.000	0.000	0.000
88	A	88	ASP	-1	-0.862	-0.925	24.873	-11.204	-11.204	0.000	0.000	0.000	0.000
89	A	89	PRO	0	0.034	-0.002	22.115	-0.576	-0.576	0.000	0.000	0.000	0.000
90	A	90	MET	0	-0.006	0.003	21.146	-0.648	-0.648	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.008	-0.002	22.014	-0.521	-0.521	0.000	0.000	0.000	0.000
92	A	92	ALA	0	0.059	0.024	19.616	-0.537	-0.537	0.000	0.000	0.000	0.000
93	A	93	GLN	0	0.038	0.035	17.003	-1.281	-1.281	0.000	0.000	0.000	0.000
94	A	94	ARG	1	0.908	0.959	16.945	12.173	12.173	0.000	0.000	0.000	0.000
95	A	95	SER	0	-0.025	-0.009	18.775	-0.557	-0.557	0.000	0.000	0.000	0.000
96	A	96	THR	0	0.027	-0.011	14.349	-0.927	-0.927	0.000	0.000	0.000	0.000
97	A	97	GLY	0	-0.035	-0.012	13.261	-1.436	-1.436	0.000	0.000	0.000	0.000
98	A	98	TYR	0	-0.055	-0.034	8.236	-3.311	-3.311	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.041	0.009	12.712	1.359	1.359	0.000	0.000	0.000	0.000
100	A	100	VAL	0	0.038	-0.002	14.653	-0.442	-0.442	0.000	0.000	0.000	0.000
101	A	101	GLY	0	0.035	0.028	16.375	-0.238	-0.238	0.000	0.000	0.000	0.000
102	A	102	GLY	0	0.021	0.007	12.265	-0.495	-0.495	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.038	-0.015	11.311	-1.835	-1.835	0.000	0.000	0.000	0.000
104	A	104	SER	0	-0.007	-0.010	9.378	0.807	0.807	0.000	0.000	0.000	0.000
105	A	105	PRO	0	0.038	0.024	11.494	0.644	0.644	0.000	0.000	0.000	0.000
106	A	106	LEU	0	0.060	0.044	9.697	0.314	0.314	0.000	0.000	0.000	0.000
107	A	107	GLY	0	0.001	-0.007	9.450	-1.423	-1.423	0.000	0.000	0.000	0.000
108	A	108	GLN	0	-0.061	-0.020	10.518	0.044	0.044	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.920	0.956	13.317	18.824	18.824	0.000	0.000	0.000	0.000
110	A	110	LYS	1	0.883	0.944	14.907	15.702	15.702	0.000	0.000	0.000	0.000
111	A	111	ARG	1	0.965	0.987	15.229	18.504	18.504	0.000	0.000	0.000	0.000
112	A	112	LEU	0	0.010	0.007	18.309	0.715	0.715	0.000	0.000	0.000	0.000
113	A	113	PRO	0	0.045	0.025	20.756	-0.339	-0.339	0.000	0.000	0.000	0.000
114	A	114	THR	0	0.021	0.009	18.679	-0.211	-0.211	0.000	0.000	0.000	0.000
115	A	115	ILE	0	-0.047	-0.015	21.805	0.378	0.378	0.000	0.000	0.000	0.000
116	A	116	ILE	0	0.009	-0.006	19.064	-0.534	-0.534	0.000	0.000	0.000	0.000
117	A	117	ASP	-1	-0.755	-0.901	22.395	-10.611	-10.611	0.000	0.000	0.000	0.000
118	A	118	ALA	0	-0.008	-0.003	24.461	-0.279	-0.279	0.000	0.000	0.000	0.000
119	A	119	PRO	0	0.047	0.021	26.588	-0.114	-0.114	0.000	0.000	0.000	0.000
120	A	120	ALA	0	-0.034	-0.011	21.264	-0.118	-0.118	0.000	0.000	0.000	0.000
121	A	121	GLN	0	-0.098	-0.059	22.176	-0.449	-0.449	0.000	0.000	0.000	0.000
122	A	122	GLU	-1	-0.901	-0.940	24.300	-10.366	-10.366	0.000	0.000	0.000	0.000
123	A	123	PHE	0	-0.047	-0.016	21.000	0.119	0.119	0.000	0.000	0.000	0.000
124	A	124	ALA	0	0.002	0.002	20.137	-0.281	-0.281	0.000	0.000	0.000	0.000
125	A	125	THR	0	-0.086	-0.070	15.266	-0.386	-0.386	0.000	0.000	0.000	0.000
126	A	126	ILE	0	0.014	0.020	16.395	0.606	0.606	0.000	0.000	0.000	0.000
127	A	127	TYR	0	0.006	-0.004	13.525	-1.482	-1.482	0.000	0.000	0.000	0.000
128	A	128	VAL	0	0.008	0.004	11.344	0.894	0.894	0.000	0.000	0.000	0.000
129	A	129	SER	0	0.038	0.030	10.834	-2.151	-2.151	0.000	0.000	0.000	0.000
130	A	130	GLY	0	0.078	0.043	6.741	-0.154	-0.154	0.000	0.000	0.000	0.000
131	A	131	GLY	0	-0.057	-0.021	5.814	-5.626	-5.626	0.000	0.000	0.000	0.000
132	A	132	LYS	1	0.885	0.934	5.156	37.482	37.482	0.000	0.000	0.000	0.000
133	A	133	ARG	1	0.811	0.882	8.945	17.524	17.524	0.000	0.000	0.000	0.000
134	A	134	GLY	0	0.086	0.053	9.935	-1.769	-1.769	0.000	0.000	0.000	0.000
136	A	136	ASP	-1	-0.760	-0.872	7.993	-22.950	-22.950	0.000	0.000	0.000	0.000
137	A	137	ILE	0	-0.048	-0.038	6.128	-1.914	-1.914	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.786	-0.832	9.383	-16.095	-16.095	0.000	0.000	0.000	0.000
139	A	139	LEU	0	-0.007	-0.020	10.912	-1.318	-1.318	0.000	0.000	0.000	0.000
140	A	140	ALA	0	0.101	0.063	13.116	0.937	0.937	0.000	0.000	0.000	0.000
141	A	141	ALA	0	0.053	0.022	16.582	-0.544	-0.544	0.000	0.000	0.000	0.000
142	A	142	GLY	0	0.049	0.018	18.812	-0.003	-0.003	0.000	0.000	0.000	0.000
143	A	143	ASP	-1	-0.854	-0.927	14.913	-16.557	-16.557	0.000	0.000	0.000	0.000
144	A	144	LEU	0	-0.010	-0.020	13.688	-0.629	-0.629	0.000	0.000	0.000	0.000
145	A	145	ALA	0	0.014	0.005	16.144	-0.141	-0.141	0.000	0.000	0.000	0.000
146	A	146	LYS	1	0.870	0.934	17.150	15.693	15.693	0.000	0.000	0.000	0.000
147	A	147	ILE	0	-0.060	-0.029	13.154	-0.238	-0.238	0.000	0.000	0.000	0.000
148	A	148	LEU	0	-0.097	-0.056	14.286	-0.753	-0.753	0.000	0.000	0.000	0.000
149	A	149	ASP	-1	-0.941	-0.952	18.021	-12.195	-12.195	0.000	0.000	0.000	0.000
150	A	150	ALA	0	-0.045	-0.005	19.979	0.499	0.499	0.000	0.000	0.000	0.000
151	A	151	LYS	1	0.884	0.938	22.000	10.921	10.921	0.000	0.000	0.000	0.000
152	A	152	PHE	0	0.027	0.015	21.745	-0.253	-0.253	0.000	0.000	0.000	0.000
153	A	153	ALA	0	-0.019	-0.025	26.021	0.451	0.451	0.000	0.000	0.000	0.000
154	A	154	ASP	-1	-0.881	-0.926	27.523	-9.995	-9.995	0.000	0.000	0.000	0.000
155	A	155	ILE	0	-0.079	-0.064	23.993	0.229	0.229	0.000	0.000	0.000	0.000
156	A	156	ALA	0	0.008	0.012	26.753	-0.007	-0.007	0.000	0.000	0.000	0.000
157	A	157	ARG	1	0.795	0.897	28.187	9.952	9.952	0.000	0.000	0.000	0.000
158	A	158	ARG	0	-0.011	-0.025	28.463	0.587	0.587	0.000	0.000	0.000	0.000

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