FMO DATABASE

FMODB ID: QL58Y

Calculation Name: 2VQE-I-Xray547

Preferred Name:

Target Type:

Ligand Name: paromomycin | 5-{[(2-sulfoethyl)amino]methyl}uridine 5'-(dihydrogen phosphate) | magnesium ion | zinc ion | potassium ion

Ligand 3-letter code: PAR | TM2 | MG | ZN | K

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2VQE

Chain ID: I

ChEMBL ID:

UniProt ID: Q5SHN7

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	127
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1005363.710517
FMO2-HF: Nuclear repulsion	956753.813182
FMO2-HF: Total energy	-48609.897335
FMO2-MP2: Total energy	-48756.412633

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:2:GLU)

Summations of interaction energy for fragment #1(A:2:GLU)

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.
-29.501	-26.255	0.024	-1.426	-1.844	-0.002

Interaction energy analysis for fragmet #1(A:2:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.041 / q_NPA : -0.031

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	4	TYR	0	0.045	0.037	3.632	-8.644	-6.278	-0.005	-1.130	-1.231	0.000
19	A	20	ARG	1	0.918	0.932	4.286	-15.683	-15.478	-0.001	-0.048	-0.156	0.000
20	A	21	PRO	0	-0.015	-0.008	2.940	-0.364	0.311	0.030	-0.248	-0.457	-0.002
4	A	5	TYR	0	-0.015	-0.009	6.791	1.709	1.709	0.000	0.000	0.000	0.000
5	A	6	GLY	0	0.029	0.012	9.806	-0.894	-0.894	0.000	0.000	0.000	0.000
6	A	7	THR	0	-0.087	-0.047	13.611	0.138	0.138	0.000	0.000	0.000	0.000
7	A	8	GLY	0	0.069	0.048	16.165	-0.107	-0.107	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.919	0.936	19.515	-0.863	-0.863	0.000	0.000	0.000	0.000
9	A	10	ARG	1	0.838	0.935	22.886	-0.425	-0.425	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.943	0.970	26.267	-0.345	-0.345	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.934	-0.971	27.925	0.711	0.711	0.000	0.000	0.000	0.000
12	A	13	ALA	0	-0.025	0.020	24.330	0.082	0.082	0.000	0.000	0.000	0.000
13	A	14	VAL	0	-0.032	-0.041	20.078	-0.100	-0.100	0.000	0.000	0.000	0.000
14	A	15	ALA	0	0.006	0.006	17.961	0.046	0.046	0.000	0.000	0.000	0.000
15	A	16	ARG	1	0.885	0.945	13.180	-3.697	-3.697	0.000	0.000	0.000	0.000
16	A	17	VAL	0	0.028	0.011	12.417	0.144	0.144	0.000	0.000	0.000	0.000
17	A	18	PHE	0	-0.006	-0.008	7.457	-0.531	-0.531	0.000	0.000	0.000	0.000
18	A	19	LEU	0	0.009	0.014	8.661	0.353	0.353	0.000	0.000	0.000	0.000
21	A	22	GLY	0	0.009	0.003	5.914	1.792	1.792	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.067	-0.026	9.433	-0.564	-0.564	0.000	0.000	0.000	0.000
23	A	24	GLY	0	0.060	0.024	13.169	-0.328	-0.328	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.886	0.942	14.270	-0.463	-0.463	0.000	0.000	0.000	0.000
25	A	26	VAL	0	-0.035	-0.014	14.126	0.473	0.473	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.002	0.013	13.820	0.014	0.014	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.039	-0.043	15.239	0.248	0.248	0.000	0.000	0.000	0.000
28	A	29	ASN	0	-0.025	-0.027	17.392	0.038	0.038	0.000	0.000	0.000	0.000
29	A	30	GLY	0	0.012	0.015	16.971	-0.065	-0.065	0.000	0.000	0.000	0.000
30	A	31	GLN	0	0.009	0.001	17.944	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.745	-0.866	18.873	1.054	1.054	0.000	0.000	0.000	0.000
32	A	33	PHE	0	0.011	-0.012	18.877	-0.059	-0.059	0.000	0.000	0.000	0.000
33	A	34	ASN	0	-0.124	-0.091	20.561	-0.154	-0.154	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.873	-0.912	22.905	0.889	0.889	0.000	0.000	0.000	0.000
35	A	36	TYR	0	-0.043	-0.025	22.145	0.013	0.013	0.000	0.000	0.000	0.000
36	A	37	PHE	0	-0.101	-0.069	21.934	-0.049	-0.049	0.000	0.000	0.000	0.000
37	A	38	GLN	0	0.124	0.074	26.082	-0.017	-0.017	0.000	0.000	0.000	0.000
38	A	39	GLY	0	0.027	0.026	28.530	0.023	0.023	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.064	-0.039	28.019	-0.035	-0.035	0.000	0.000	0.000	0.000
40	A	41	VAL	0	0.076	0.032	29.409	0.001	0.001	0.000	0.000	0.000	0.000
41	A	42	ARG	1	0.808	0.862	28.082	-0.271	-0.271	0.000	0.000	0.000	0.000
42	A	43	ALA	0	0.008	0.002	25.188	-0.043	-0.043	0.000	0.000	0.000	0.000
43	A	44	VAL	0	0.089	0.049	24.572	0.013	0.013	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.004	-0.005	23.887	-0.083	-0.083	0.000	0.000	0.000	0.000
45	A	46	ALA	0	-0.026	-0.019	21.166	-0.064	-0.064	0.000	0.000	0.000	0.000
46	A	47	LEU	0	0.050	0.013	17.790	-0.027	-0.027	0.000	0.000	0.000	0.000
47	A	48	GLU	-1	-0.931	-0.958	19.606	-0.749	-0.749	0.000	0.000	0.000	0.000
48	A	49	PRO	0	-0.050	-0.015	17.056	-0.135	-0.135	0.000	0.000	0.000	0.000
49	A	50	LEU	0	0.005	-0.004	13.115	-0.237	-0.237	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.916	0.953	16.455	0.267	0.267	0.000	0.000	0.000	0.000
51	A	52	ALA	0	0.002	0.002	19.694	-0.083	-0.083	0.000	0.000	0.000	0.000
52	A	53	VAL	0	-0.074	-0.047	14.420	-0.013	-0.013	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.903	-0.935	16.503	-2.095	-2.095	0.000	0.000	0.000	0.000
54	A	55	ALA	0	-0.061	-0.031	12.808	-0.350	-0.350	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.018	-0.020	14.469	0.178	0.178	0.000	0.000	0.000	0.000
56	A	57	GLY	0	0.086	0.063	13.496	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.905	0.947	8.832	4.534	4.534	0.000	0.000	0.000	0.000
58	A	59	PHE	0	-0.038	-0.025	6.565	-1.536	-1.536	0.000	0.000	0.000	0.000
59	A	60	ASP	-1	-0.700	-0.814	9.208	1.141	1.141	0.000	0.000	0.000	0.000
60	A	61	ALA	0	-0.011	-0.028	9.807	-0.039	-0.039	0.000	0.000	0.000	0.000
61	A	62	TYR	0	0.008	0.019	9.623	0.230	0.230	0.000	0.000	0.000	0.000
62	A	63	ILE	0	0.014	-0.003	11.447	0.152	0.152	0.000	0.000	0.000	0.000
63	A	64	THR	0	-0.026	-0.005	14.399	0.146	0.146	0.000	0.000	0.000	0.000
64	A	65	VAL	0	0.013	-0.001	16.462	-0.201	-0.201	0.000	0.000	0.000	0.000
65	A	66	ARG	1	0.967	0.990	20.050	-1.859	-1.859	0.000	0.000	0.000	0.000
66	A	67	GLY	0	0.063	0.044	23.047	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	68	GLY	0	0.048	0.020	26.259	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	69	GLY	0	0.050	0.016	28.901	0.012	0.012	0.000	0.000	0.000	0.000
69	A	70	LYS	1	0.940	0.968	26.637	-0.896	-0.896	0.000	0.000	0.000	0.000
70	A	71	SER	0	0.034	0.023	26.636	-0.022	-0.022	0.000	0.000	0.000	0.000
71	A	72	GLY	0	-0.002	-0.005	27.724	-0.056	-0.056	0.000	0.000	0.000	0.000
72	A	73	GLN	0	0.053	0.017	23.257	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	74	ILE	0	0.029	0.039	22.557	0.045	0.045	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.805	-0.885	23.137	0.140	0.140	0.000	0.000	0.000	0.000
75	A	76	ALA	0	-0.062	-0.024	21.651	-0.067	-0.067	0.000	0.000	0.000	0.000
76	A	77	ILE	0	0.064	0.025	17.780	0.029	0.029	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.871	0.965	18.445	-0.073	-0.073	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.036	-0.007	19.156	-0.120	-0.120	0.000	0.000	0.000	0.000
79	A	80	GLY	0	0.034	0.007	16.473	-0.132	-0.132	0.000	0.000	0.000	0.000
80	A	81	ILE	0	-0.008	-0.011	14.351	-0.080	-0.080	0.000	0.000	0.000	0.000
81	A	82	ALA	0	0.015	0.011	14.419	-0.454	-0.454	0.000	0.000	0.000	0.000
82	A	83	ARG	1	0.873	0.939	14.912	-0.609	-0.609	0.000	0.000	0.000	0.000
83	A	84	ALA	0	0.015	0.014	10.130	-0.262	-0.262	0.000	0.000	0.000	0.000
84	A	85	LEU	0	0.018	0.014	9.780	-1.154	-1.154	0.000	0.000	0.000	0.000
85	A	86	VAL	0	-0.033	-0.024	11.659	-0.507	-0.507	0.000	0.000	0.000	0.000
86	A	87	GLN	0	-0.024	-0.012	8.629	0.164	0.164	0.000	0.000	0.000	0.000
87	A	88	TYR	0	-0.033	0.002	6.188	-0.109	-0.109	0.000	0.000	0.000	0.000
88	A	89	ASN	0	0.051	0.026	8.123	-0.570	-0.570	0.000	0.000	0.000	0.000
89	A	90	PRO	0	0.041	0.028	11.384	0.761	0.761	0.000	0.000	0.000	0.000
90	A	91	ASP	-1	-0.845	-0.927	14.485	-2.305	-2.305	0.000	0.000	0.000	0.000
91	A	92	TYR	0	0.024	0.005	12.007	0.088	0.088	0.000	0.000	0.000	0.000
92	A	93	ARG	1	0.960	0.971	16.419	1.558	1.558	0.000	0.000	0.000	0.000
93	A	94	ALA	0	-0.048	-0.011	18.571	0.254	0.254	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.920	0.954	19.285	1.603	1.603	0.000	0.000	0.000	0.000
95	A	96	LEU	0	0.027	0.009	16.843	0.193	0.193	0.000	0.000	0.000	0.000
96	A	97	LYS	1	0.917	0.964	20.902	0.899	0.899	0.000	0.000	0.000	0.000
97	A	98	PRO	0	-0.015	-0.016	23.737	0.104	0.104	0.000	0.000	0.000	0.000
98	A	99	LEU	0	0.057	0.035	23.404	0.077	0.077	0.000	0.000	0.000	0.000
99	A	100	GLY	0	0.003	0.022	24.992	0.087	0.087	0.000	0.000	0.000	0.000
100	A	101	PHE	0	0.025	-0.003	20.655	0.130	0.130	0.000	0.000	0.000	0.000
101	A	102	LEU	0	0.009	0.003	19.658	0.104	0.104	0.000	0.000	0.000	0.000
102	A	103	THR	0	-0.021	-0.011	21.135	0.077	0.077	0.000	0.000	0.000	0.000
103	A	104	ARG	1	0.877	0.930	24.533	-0.388	-0.388	0.000	0.000	0.000	0.000
104	A	105	ASP	-1	-0.748	-0.868	25.625	0.141	0.141	0.000	0.000	0.000	0.000
105	A	106	ALA	0	0.020	0.011	28.858	0.082	0.082	0.000	0.000	0.000	0.000
106	A	107	ARG	1	0.888	0.947	31.090	-0.097	-0.097	0.000	0.000	0.000	0.000
107	A	108	VAL	0	-0.005	-0.013	31.712	0.046	0.046	0.000	0.000	0.000	0.000
108	A	109	VAL	0	-0.004	0.001	34.293	-0.038	-0.038	0.000	0.000	0.000	0.000
109	A	110	GLU	-1	-0.787	-0.862	37.299	0.199	0.199	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.997	0.994	40.318	-0.279	-0.279	0.000	0.000	0.000	0.000
111	A	112	LYS	1	0.908	0.945	41.688	-0.289	-0.289	0.000	0.000	0.000	0.000
112	A	113	LYS	1	0.846	0.927	44.197	-0.215	-0.215	0.000	0.000	0.000	0.000
113	A	114	TYR	0	0.116	0.064	48.173	0.011	0.011	0.000	0.000	0.000	0.000
114	A	115	GLY	0	0.057	0.027	51.492	-0.009	-0.009	0.000	0.000	0.000	0.000
115	A	116	LYS	1	0.851	0.930	50.263	-0.164	-0.164	0.000	0.000	0.000	0.000
116	A	117	HIS	0	0.078	0.037	50.923	0.021	0.021	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.931	0.951	45.025	-0.213	-0.213	0.000	0.000	0.000	0.000
118	A	119	ALA	0	-0.011	0.006	44.400	-0.009	-0.009	0.000	0.000	0.000	0.000
119	A	120	ARG	1	0.934	0.944	43.427	-0.153	-0.153	0.000	0.000	0.000	0.000
120	A	121	ARG	1	0.923	0.963	48.577	-0.166	-0.166	0.000	0.000	0.000	0.000
121	A	122	ALA	0	0.071	0.026	50.668	0.014	0.014	0.000	0.000	0.000	0.000
122	A	123	PRO	0	0.035	0.020	54.023	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	124	GLN	0	0.003	0.005	56.646	-0.006	-0.006	0.000	0.000	0.000	0.000
124	A	125	TYR	0	-0.008	-0.006	59.568	0.007	0.007	0.000	0.000	0.000	0.000
125	A	126	SER	0	0.012	-0.006	63.074	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	127	LYS	1	0.897	0.947	66.428	-0.075	-0.075	0.000	0.000	0.000	0.000
127	A	128	ARG	0	0.149	0.098	68.872	0.018	0.018	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:GLU)