FMO DATABASE

FMODB ID: 9QZM2

Calculation Name: 4V51-A-Xray549

Preferred Name:

Target Type:

Ligand Name: paromomycin | 5-methyluridine 5'-monophosphate

Ligand 3-letter code: PAR | 5MU

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4V51

Chain ID: A

ChEMBL ID:

UniProt ID: Q8VVE3

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks	Original chain id is "BV", which converted from A;

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	101
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-632862.646482
FMO2-HF: Nuclear repulsion	595162.338229
FMO2-HF: Total energy	-37700.308254
FMO2-MP2: Total energy	-37813.092576

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.
4.856	14.671	14.45	-6.303	-17.966	-0.074

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 : 0.757 / q_NPA : 0.893

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	ALA	0	0.098	0.067	2.681	-5.676	-1.848	0.947	-2.151	-2.624	-0.018
4	A	4	ILE	0	-0.020	-0.029	5.296	1.804	1.797	-0.001	-0.002	0.011	0.000
15	A	15	GLU	-1	-0.911	-0.957	3.362	-61.240	-60.626	0.005	-0.206	-0.413	-0.001
16	A	16	PRO	0	-0.081	-0.015	2.782	-3.589	-2.567	0.068	-0.288	-0.803	-0.003
17	A	17	GLY	0	0.045	0.025	4.889	5.026	5.102	-0.001	-0.006	-0.069	0.000
41	A	41	GLY	0	0.048	0.029	4.763	-1.333	-1.217	-0.001	-0.023	-0.092	0.000
42	A	42	GLY	0	0.024	-0.028	2.885	-3.668	-2.793	2.567	-1.442	-1.999	-0.004
43	A	43	GLU	-1	-0.910	-0.960	2.614	-38.224	-38.767	1.794	0.841	-2.092	-0.023
44	A	44	LYS	1	0.945	0.970	2.242	64.390	64.775	5.275	-1.564	-4.097	-0.002
45	A	45	THR	0	0.041	0.006	2.875	-2.202	-1.993	0.651	0.301	-1.162	-0.009
46	A	46	VAL	0	-0.068	-0.027	2.258	0.912	2.006	1.718	-0.594	-2.220	-0.001
47	A	47	VAL	0	-0.002	0.003	2.393	3.058	3.927	1.266	-0.388	-1.747	-0.004
48	A	48	GLY	0	0.011	0.004	2.970	-6.730	-5.469	0.163	-0.779	-0.645	-0.009
49	A	49	THR	0	0.004	0.004	5.098	2.428	2.444	-0.001	-0.002	-0.014	0.000
5	A	5	VAL	0	0.090	0.072	9.143	1.416	1.416	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.838	0.902	11.476	16.687	16.687	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.005	-0.011	15.307	0.550	0.550	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.074	0.039	17.753	0.028	0.028	0.000	0.000	0.000	0.000
9	A	9	GLY	0	-0.054	-0.034	21.112	0.347	0.347	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.826	0.917	18.978	13.872	13.872	0.000	0.000	0.000	0.000
11	A	11	GLN	0	0.019	-0.002	14.436	-0.124	-0.124	0.000	0.000	0.000	0.000
12	A	12	TYR	0	-0.050	-0.014	12.674	0.769	0.769	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.867	0.933	6.621	38.397	38.397	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.055	-0.018	7.417	2.606	2.606	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.071	-0.018	7.312	4.200	4.200	0.000	0.000	0.000	0.000
19	A	19	LYS	0	0.029	0.037	10.372	0.176	0.176	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.023	-0.019	12.990	1.400	1.400	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.893	0.943	16.629	14.861	14.861	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.035	0.022	16.039	-0.656	-0.656	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.817	-0.853	18.807	-12.718	-12.718	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.913	0.935	21.918	10.323	10.323	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.054	0.033	19.049	0.137	0.137	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.930	-0.972	23.552	-10.943	-10.943	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.060	0.048	21.567	0.245	0.245	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.927	-0.973	23.596	-10.751	-10.751	0.000	0.000	0.000	0.000
29	A	29	PRO	0	-0.010	-0.001	25.512	0.006	0.006	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.024	-0.007	23.289	-0.456	-0.456	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.046	-0.023	21.600	-0.691	-0.691	0.000	0.000	0.000	0.000
32	A	32	THR	0	-0.014	-0.013	21.293	0.503	0.503	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.015	-0.025	15.316	-0.754	-0.754	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.921	-0.958	16.460	-14.489	-14.489	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.013	-0.008	12.964	-1.300	-1.300	0.000	0.000	0.000	0.000
36	A	36	PRO	0	-0.036	0.002	12.270	0.929	0.929	0.000	0.000	0.000	0.000
37	A	37	VAL	0	0.034	0.002	12.129	-1.356	-1.356	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.032	0.020	5.920	-1.154	-1.154	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.017	-0.019	9.959	1.276	1.276	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.069	-0.035	6.736	1.106	1.106	0.000	0.000	0.000	0.000
50	A	50	PRO	0	0.026	0.024	7.779	-0.742	-0.742	0.000	0.000	0.000	0.000
51	A	51	VAL	0	0.016	0.005	10.204	0.511	0.511	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.037	0.005	13.720	-0.440	-0.440	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.858	-0.923	16.422	-16.385	-16.385	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.045	0.031	12.254	-0.402	-0.402	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.008	0.028	12.089	-0.986	-0.986	0.000	0.000	0.000	0.000
56	A	56	SER	0	-0.052	-0.044	10.836	0.519	0.519	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.033	-0.024	12.702	-0.368	-0.368	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.027	-0.012	7.278	-0.040	-0.040	0.000	0.000	0.000	0.000
59	A	59	ALA	0	0.003	0.003	10.467	0.427	0.427	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.850	-0.936	6.799	-34.559	-34.559	0.000	0.000	0.000	0.000
61	A	61	VAL	0	-0.038	-0.029	9.051	3.092	3.092	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.001	-0.003	10.421	-1.493	-1.493	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.082	0.056	13.274	1.558	1.558	0.000	0.000	0.000	0.000
64	A	64	HIS	0	-0.039	-0.028	16.168	-0.744	-0.744	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.054	0.035	18.709	0.940	0.940	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.792	0.912	21.133	13.077	13.077	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.028	0.002	23.303	0.422	0.422	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.907	0.958	26.349	10.154	10.154	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.955	1.006	25.755	11.806	11.806	0.000	0.000	0.000	0.000
70	A	70	ILE	0	-0.005	-0.011	27.885	0.094	0.094	0.000	0.000	0.000	0.000
71	A	71	LEU	0	0.010	0.013	28.252	-0.202	-0.202	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.016	-0.011	30.705	0.391	0.391	0.000	0.000	0.000	0.000
73	A	73	SER	0	-0.014	-0.044	32.731	-0.102	-0.102	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.892	0.960	35.072	8.434	8.434	0.000	0.000	0.000	0.000
75	A	75	PHE	0	0.056	0.031	33.376	0.090	0.090	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.921	0.949	39.427	7.645	7.645	0.000	0.000	0.000	0.000
77	A	77	ALA	0	0.065	0.045	42.947	0.023	0.023	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.887	0.930	44.487	6.628	6.628	0.000	0.000	0.000	0.000
79	A	79	VAL	0	0.055	0.028	47.844	-0.062	-0.062	0.000	0.000	0.000	0.000
80	A	80	GLN	0	-0.058	-0.040	50.540	0.020	0.020	0.000	0.000	0.000	0.000
81	A	81	TYR	0	0.142	0.086	54.330	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.986	1.003	46.304	6.732	6.732	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.954	0.959	49.384	5.964	5.964	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.958	0.967	45.610	6.549	6.549	0.000	0.000	0.000	0.000
85	A	85	LYS	1	1.013	1.011	43.433	7.128	7.128	0.000	0.000	0.000	0.000
86	A	86	GLY	0	-0.028	-0.004	43.877	-0.087	-0.087	0.000	0.000	0.000	0.000
87	A	87	HIS	0	0.059	0.025	39.374	-0.134	-0.134	0.000	0.000	0.000	0.000
88	A	88	ARG	0	0.024	0.032	34.992	-0.051	-0.051	0.000	0.000	0.000	0.000
89	A	89	GLN	0	0.057	0.026	32.851	-0.066	-0.066	0.000	0.000	0.000	0.000
90	A	90	PRO	0	-0.023	0.008	32.022	-0.122	-0.122	0.000	0.000	0.000	0.000
91	A	91	TYR	0	-0.024	-0.054	25.585	-0.029	-0.029	0.000	0.000	0.000	0.000
92	A	92	THR	0	-0.004	0.004	27.002	0.019	0.019	0.000	0.000	0.000	0.000
93	A	93	GLU	-1	-0.907	-0.962	22.624	-13.878	-13.878	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.045	-0.027	20.076	0.651	0.651	0.000	0.000	0.000	0.000
95	A	95	LEU	0	0.018	0.018	17.837	-0.502	-0.502	0.000	0.000	0.000	0.000
96	A	96	ILE	0	0.039	0.005	14.314	0.484	0.484	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.832	0.913	12.075	23.573	23.573	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.713	-0.881	7.040	-40.501	-40.501	0.000	0.000	0.000	0.000
99	A	99	ILE	0	-0.085	-0.031	9.591	0.599	0.599	0.000	0.000	0.000	0.000
100	A	100	ARG	1	0.969	0.973	5.918	23.175	23.175	0.000	0.000	0.000	0.000
101	A	101	GLY	-1	-0.868	-0.918	4.815	-33.343	-33.343	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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