FMO DATABASE

FMODB ID: 3GK3L

Calculation Name: 7NSO-W-Other547

Preferred Name:

Target Type:

Ligand Name: erythromycin a

Ligand 3-letter code: ERY

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7NSO

Chain ID: W

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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	75
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-413771.400113
FMO2-HF: Nuclear repulsion	385596.075406
FMO2-HF: Total energy	-28175.324707
FMO2-MP2: Total energy	-28258.822572

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:11:ARG)

Summations of interaction energy for fragment #1(A:11:ARG)

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.
178.512	182.271	0.184	-2.091	-1.852	-0.012

Interaction energy analysis for fragmet #1(A:11:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.873 / q_NPA : 1.933

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	13	GLY	0	0.034	0.015	2.781	-18.832	-15.644	0.182	-1.884	-1.486	-0.013
4	A	14	ARG	1	0.900	0.944	3.622	91.394	91.965	0.002	-0.207	-0.366	0.001
5	A	15	ASP	-1	-0.820	-0.892	8.481	-41.209	-41.209	0.000	0.000	0.000	0.000
6	A	16	SER	0	-0.101	-0.049	12.103	1.327	1.327	0.000	0.000	0.000	0.000
7	A	17	GLU	-1	-0.856	-0.933	15.526	-29.661	-29.661	0.000	0.000	0.000	0.000
8	A	18	ALA	0	0.046	0.030	18.594	1.150	1.150	0.000	0.000	0.000	0.000
9	A	19	LYS	1	0.950	0.974	20.767	28.434	28.434	0.000	0.000	0.000	0.000
10	A	20	ARG	1	0.963	0.964	22.451	25.402	25.402	0.000	0.000	0.000	0.000
11	A	21	LEU	0	-0.001	0.012	24.306	0.870	0.870	0.000	0.000	0.000	0.000
12	A	22	GLY	0	0.025	0.009	27.681	0.108	0.108	0.000	0.000	0.000	0.000
13	A	23	VAL	0	-0.034	-0.025	30.266	0.092	0.092	0.000	0.000	0.000	0.000
14	A	24	LYS	1	0.789	0.894	30.366	19.329	19.329	0.000	0.000	0.000	0.000
15	A	25	ARG	1	0.961	1.001	35.896	15.409	15.409	0.000	0.000	0.000	0.000
16	A	26	PHE	0	-0.009	-0.018	35.428	-0.281	-0.281	0.000	0.000	0.000	0.000
17	A	27	GLY	0	-0.028	-0.021	40.838	0.237	0.237	0.000	0.000	0.000	0.000
18	A	28	GLY	0	0.026	0.013	43.929	0.045	0.045	0.000	0.000	0.000	0.000
19	A	29	GLU	-1	-0.840	-0.915	41.358	-14.907	-14.907	0.000	0.000	0.000	0.000
20	A	30	SER	0	-0.003	-0.002	45.798	0.171	0.171	0.000	0.000	0.000	0.000
21	A	31	VAL	0	-0.070	-0.040	43.246	-0.272	-0.272	0.000	0.000	0.000	0.000
22	A	32	LEU	0	0.108	0.053	45.884	0.254	0.254	0.000	0.000	0.000	0.000
23	A	33	ALA	0	0.054	0.038	45.491	-0.387	-0.387	0.000	0.000	0.000	0.000
24	A	34	GLY	0	0.006	0.001	43.111	-0.008	-0.008	0.000	0.000	0.000	0.000
25	A	35	SER	0	-0.076	-0.047	41.422	-0.473	-0.473	0.000	0.000	0.000	0.000
26	A	36	ILE	0	-0.029	-0.024	34.880	-0.138	-0.138	0.000	0.000	0.000	0.000
27	A	37	ILE	0	0.026	0.022	37.980	0.008	0.008	0.000	0.000	0.000	0.000
28	A	38	VAL	0	-0.006	-0.011	32.647	-0.356	-0.356	0.000	0.000	0.000	0.000
29	A	39	ARG	1	0.911	0.975	27.229	20.955	20.955	0.000	0.000	0.000	0.000
30	A	40	GLN	0	0.026	0.006	28.590	-0.716	-0.716	0.000	0.000	0.000	0.000
31	A	41	ARG	1	0.927	0.965	23.650	23.029	23.029	0.000	0.000	0.000	0.000
32	A	42	GLY	0	0.069	0.044	27.095	0.179	0.179	0.000	0.000	0.000	0.000
33	A	43	THR	0	0.015	0.003	28.917	0.048	0.048	0.000	0.000	0.000	0.000
34	A	44	LYS	1	0.930	0.966	28.912	20.185	20.185	0.000	0.000	0.000	0.000
35	A	45	PHE	0	-0.028	-0.016	32.497	0.302	0.302	0.000	0.000	0.000	0.000
36	A	46	HIS	0	-0.007	-0.007	34.991	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	47	ALA	0	0.028	0.010	38.323	0.159	0.159	0.000	0.000	0.000	0.000
38	A	48	GLY	0	0.018	0.015	40.983	0.117	0.117	0.000	0.000	0.000	0.000
39	A	49	ALA	0	0.030	0.014	44.507	0.040	0.040	0.000	0.000	0.000	0.000
40	A	50	ASN	0	0.010	-0.004	46.797	-0.115	-0.115	0.000	0.000	0.000	0.000
41	A	51	VAL	0	0.003	0.018	40.967	-0.205	-0.205	0.000	0.000	0.000	0.000
42	A	52	GLY	0	-0.023	-0.013	41.478	0.206	0.206	0.000	0.000	0.000	0.000
43	A	53	CYS	-1	-0.872	-0.933	35.839	-17.618	-17.618	0.000	0.000	0.000	0.000
44	A	54	GLY	0	0.061	0.037	35.475	0.265	0.265	0.000	0.000	0.000	0.000
45	A	55	ARG	1	0.988	0.978	29.051	19.389	19.389	0.000	0.000	0.000	0.000
46	A	56	ASP	-1	-0.922	-0.946	28.867	-20.269	-20.269	0.000	0.000	0.000	0.000
47	A	57	HIS	1	0.833	0.893	29.660	18.792	18.792	0.000	0.000	0.000	0.000
48	A	58	THR	0	-0.069	-0.049	32.127	-0.083	-0.083	0.000	0.000	0.000	0.000
49	A	59	LEU	0	0.006	0.006	33.714	0.345	0.345	0.000	0.000	0.000	0.000
50	A	60	PHE	0	-0.023	-0.020	36.996	-0.171	-0.171	0.000	0.000	0.000	0.000
51	A	61	ALA	0	0.073	0.040	39.921	0.150	0.150	0.000	0.000	0.000	0.000
52	A	62	LYS	1	0.866	0.928	43.645	13.615	13.615	0.000	0.000	0.000	0.000
53	A	63	ALA	0	0.023	0.021	46.182	0.226	0.226	0.000	0.000	0.000	0.000
54	A	64	ASP	-1	-0.916	-0.955	47.745	-12.503	-12.503	0.000	0.000	0.000	0.000
55	A	65	GLY	0	0.084	0.042	49.208	0.222	0.222	0.000	0.000	0.000	0.000
56	A	66	LYS	1	0.799	0.896	48.327	11.617	11.617	0.000	0.000	0.000	0.000
57	A	67	VAL	0	-0.020	-0.005	41.958	-0.050	-0.050	0.000	0.000	0.000	0.000
58	A	68	LYS	1	0.880	0.933	45.312	12.599	12.599	0.000	0.000	0.000	0.000
59	A	69	PHE	0	-0.033	-0.026	37.713	-0.363	-0.363	0.000	0.000	0.000	0.000
60	A	70	GLU	-1	-0.836	-0.922	42.626	-12.894	-12.894	0.000	0.000	0.000	0.000
61	A	71	VAL	0	-0.029	-0.023	40.621	-0.540	-0.540	0.000	0.000	0.000	0.000
62	A	72	LYS	1	0.893	0.949	42.620	13.421	13.421	0.000	0.000	0.000	0.000
63	A	73	GLY	0	0.046	0.027	42.859	-0.345	-0.345	0.000	0.000	0.000	0.000
64	A	74	PRO	0	0.036	0.011	43.900	-0.161	-0.161	0.000	0.000	0.000	0.000
65	A	75	LYS	1	0.915	0.944	38.333	14.979	14.979	0.000	0.000	0.000	0.000
66	A	76	ASN	0	0.025	0.021	39.029	-0.337	-0.337	0.000	0.000	0.000	0.000
67	A	77	ARG	1	0.980	1.007	35.300	16.493	16.493	0.000	0.000	0.000	0.000
68	A	78	LYS	1	0.898	0.947	36.252	16.039	16.039	0.000	0.000	0.000	0.000
69	A	79	PHE	0	0.016	0.002	38.498	-0.289	-0.289	0.000	0.000	0.000	0.000
70	A	80	ILE	0	-0.020	-0.005	37.645	-0.072	-0.072	0.000	0.000	0.000	0.000
71	A	81	SER	0	0.001	-0.001	41.857	-0.046	-0.046	0.000	0.000	0.000	0.000
72	A	82	ILE	0	-0.004	0.001	44.250	-0.232	-0.232	0.000	0.000	0.000	0.000
73	A	83	GLU	-1	-0.810	-0.880	47.588	-12.504	-12.504	0.000	0.000	0.000	0.000
74	A	84	ALA	0	-0.015	-0.012	51.273	-0.123	-0.123	0.000	0.000	0.000	0.000
75	A	85	GLU	-2	-1.757	-1.854	52.773	-22.921	-22.921	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:11:ARG)