FMO DATABASE

FMODB ID: 5YK7Z

Calculation Name: 7TRF-E-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7TRF

Chain ID: E

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

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	82
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-449471.259532
FMO2-HF: Nuclear repulsion	418442.547433
FMO2-HF: Total energy	-31028.712099
FMO2-MP2: Total energy	-31121.881924

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:18:ARG)

Summations of interaction energy for fragment #1(A:18: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.
256.071	263.262	0.368	-2.93	-4.63	-0.019

Interaction energy analysis for fragmet #1(A:18:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.808 / q_NPA : 1.883

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

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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	20	SER	0	0.052	0.024	2.942	-6.854	-2.977	0.069	-1.977	-1.968	-0.016
4	A	21	ARG	1	0.919	0.956	3.289	95.872	97.476	0.066	-0.568	-1.102	-0.003
5	A	22	ALA	0	0.021	0.020	5.090	6.697	6.799	-0.001	-0.007	-0.094	0.000
11	A	28	VAL	0	0.065	0.021	3.585	-0.844	-0.296	0.012	-0.092	-0.469	0.000
12	A	29	GLY	0	-0.068	-0.040	2.879	-1.843	-1.091	0.209	-0.308	-0.653	0.000
13	A	30	ARG	1	0.948	0.965	3.739	59.581	59.761	0.014	0.028	-0.223	0.000
15	A	32	HIS	0	0.048	0.041	4.365	4.165	4.293	-0.001	-0.006	-0.121	0.000
6	A	23	GLY	0	0.014	0.022	7.120	5.348	5.348	0.000	0.000	0.000	0.000
7	A	24	LEU	0	-0.009	0.009	7.856	2.511	2.511	0.000	0.000	0.000	0.000
8	A	25	GLN	0	0.002	-0.005	7.763	-6.459	-6.459	0.000	0.000	0.000	0.000
9	A	26	PHE	0	0.070	0.047	8.821	-3.555	-3.555	0.000	0.000	0.000	0.000
10	A	27	PRO	0	-0.001	0.014	6.042	-10.897	-10.897	0.000	0.000	0.000	0.000
14	A	31	VAL	0	0.087	0.050	7.121	3.785	3.785	0.000	0.000	0.000	0.000
16	A	33	ARG	1	0.917	0.960	6.269	50.579	50.579	0.000	0.000	0.000	0.000
17	A	34	LEU	0	-0.004	-0.007	7.786	3.993	3.993	0.000	0.000	0.000	0.000
18	A	35	LEU	0	0.055	0.034	9.695	2.479	2.479	0.000	0.000	0.000	0.000
19	A	36	ARG	1	0.917	0.937	7.184	55.660	55.660	0.000	0.000	0.000	0.000
20	A	37	LYS	1	0.902	0.960	11.172	33.644	33.644	0.000	0.000	0.000	0.000
21	A	38	GLY	0	0.009	0.000	13.633	2.145	2.145	0.000	0.000	0.000	0.000
22	A	39	ASN	0	-0.066	-0.028	14.772	0.811	0.811	0.000	0.000	0.000	0.000
23	A	40	TYR	0	0.040	0.024	14.397	0.403	0.403	0.000	0.000	0.000	0.000
24	A	41	ALA	0	0.021	0.011	14.062	1.096	1.096	0.000	0.000	0.000	0.000
25	A	42	GLU	-1	-0.907	-0.939	13.925	-30.514	-30.514	0.000	0.000	0.000	0.000
26	A	43	ARG	1	0.899	0.943	12.023	34.696	34.696	0.000	0.000	0.000	0.000
27	A	44	VAL	0	0.011	0.005	7.759	0.577	0.577	0.000	0.000	0.000	0.000
28	A	45	GLY	0	0.031	0.021	9.189	-1.753	-1.753	0.000	0.000	0.000	0.000
29	A	46	ALA	0	-0.012	-0.020	5.785	-3.859	-3.859	0.000	0.000	0.000	0.000
30	A	47	GLY	0	0.035	0.007	6.213	-5.543	-5.543	0.000	0.000	0.000	0.000
31	A	48	ALA	0	0.036	0.027	8.982	0.551	0.551	0.000	0.000	0.000	0.000
32	A	49	PRO	0	-0.022	-0.012	5.158	1.098	1.098	0.000	0.000	0.000	0.000
33	A	50	VAL	0	-0.008	-0.017	5.676	-1.436	-1.436	0.000	0.000	0.000	0.000
34	A	51	TYR	0	0.051	0.033	7.571	1.800	1.800	0.000	0.000	0.000	0.000
35	A	52	LEU	0	0.002	0.002	10.370	1.826	1.826	0.000	0.000	0.000	0.000
36	A	53	ALA	0	-0.042	-0.038	8.393	1.505	1.505	0.000	0.000	0.000	0.000
37	A	54	ALA	0	0.027	0.014	10.376	1.442	1.442	0.000	0.000	0.000	0.000
38	A	55	VAL	0	0.031	0.019	12.222	2.001	2.001	0.000	0.000	0.000	0.000
39	A	56	LEU	0	-0.031	-0.014	12.860	1.541	1.541	0.000	0.000	0.000	0.000
40	A	57	GLU	-1	-0.876	-0.940	12.212	-44.169	-44.169	0.000	0.000	0.000	0.000
41	A	58	TYR	0	-0.025	-0.005	15.153	1.019	1.019	0.000	0.000	0.000	0.000
42	A	59	LEU	0	0.032	0.023	18.135	1.359	1.359	0.000	0.000	0.000	0.000
43	A	60	THR	0	-0.036	-0.042	16.753	1.117	1.117	0.000	0.000	0.000	0.000
44	A	61	ALA	0	-0.025	-0.001	19.090	0.749	0.749	0.000	0.000	0.000	0.000
45	A	62	GLU	-1	-0.860	-0.930	20.801	-23.326	-23.326	0.000	0.000	0.000	0.000
46	A	63	ILE	0	-0.021	-0.008	22.861	1.092	1.092	0.000	0.000	0.000	0.000
47	A	64	LEU	0	-0.060	-0.027	21.971	0.950	0.950	0.000	0.000	0.000	0.000
48	A	65	GLU	-1	-0.856	-0.918	24.962	-21.395	-21.395	0.000	0.000	0.000	0.000
49	A	66	LEU	0	0.037	0.015	26.596	0.996	0.996	0.000	0.000	0.000	0.000
50	A	67	ALA	0	0.003	-0.002	28.086	0.789	0.789	0.000	0.000	0.000	0.000
51	A	68	GLY	0	-0.032	-0.022	28.543	0.562	0.562	0.000	0.000	0.000	0.000
52	A	69	ASN	0	-0.048	-0.033	29.650	0.955	0.955	0.000	0.000	0.000	0.000
53	A	70	ALA	0	0.051	0.042	32.497	0.552	0.552	0.000	0.000	0.000	0.000
54	A	71	ALA	0	-0.022	-0.010	32.078	0.441	0.441	0.000	0.000	0.000	0.000
55	A	72	ARG	1	0.887	0.941	32.073	18.958	18.958	0.000	0.000	0.000	0.000
56	A	73	ASP	-1	-0.860	-0.917	35.243	-16.229	-16.229	0.000	0.000	0.000	0.000
57	A	74	ASN	0	-0.073	-0.046	37.388	0.804	0.804	0.000	0.000	0.000	0.000
58	A	75	LYS	1	0.896	0.953	38.296	15.914	15.914	0.000	0.000	0.000	0.000
59	A	76	LYS	1	0.911	0.959	34.170	16.915	16.915	0.000	0.000	0.000	0.000
60	A	77	THR	0	0.018	0.013	31.634	-0.252	-0.252	0.000	0.000	0.000	0.000
61	A	78	ARG	1	0.952	0.974	29.370	19.078	19.078	0.000	0.000	0.000	0.000
62	A	79	ILE	0	0.075	0.036	27.082	0.676	0.676	0.000	0.000	0.000	0.000
63	A	80	ILE	0	0.017	0.001	29.921	-0.228	-0.228	0.000	0.000	0.000	0.000
64	A	81	PRO	0	0.067	0.021	30.420	0.323	0.323	0.000	0.000	0.000	0.000
65	A	82	ARG	1	0.961	0.996	31.977	15.909	15.909	0.000	0.000	0.000	0.000
66	A	83	HIS	0	-0.024	-0.038	31.876	0.575	0.575	0.000	0.000	0.000	0.000
67	A	84	LEU	0	0.038	0.031	27.170	-0.102	-0.102	0.000	0.000	0.000	0.000
68	A	85	GLN	0	0.029	0.008	30.759	-0.303	-0.303	0.000	0.000	0.000	0.000
69	A	86	LEU	0	-0.048	-0.017	33.766	0.465	0.465	0.000	0.000	0.000	0.000
70	A	87	ALA	0	0.036	0.027	30.899	0.319	0.319	0.000	0.000	0.000	0.000
71	A	88	ILE	0	-0.003	-0.013	28.437	0.131	0.131	0.000	0.000	0.000	0.000
72	A	89	ARG	1	0.846	0.919	32.224	17.980	17.980	0.000	0.000	0.000	0.000
73	A	90	ASN	0	-0.060	-0.023	35.439	0.811	0.811	0.000	0.000	0.000	0.000
74	A	91	ASP	-1	-0.844	-0.905	31.101	-19.922	-19.922	0.000	0.000	0.000	0.000
75	A	92	GLU	-1	-0.845	-0.916	33.495	-17.181	-17.181	0.000	0.000	0.000	0.000
76	A	93	GLU	-1	-0.966	-0.989	28.644	-21.224	-21.224	0.000	0.000	0.000	0.000
77	A	94	LEU	0	-0.020	-0.023	26.746	-0.486	-0.486	0.000	0.000	0.000	0.000
78	A	95	ASN	0	0.019	0.008	29.326	-0.292	-0.292	0.000	0.000	0.000	0.000
79	A	96	LYS	1	0.812	0.903	31.876	18.948	18.948	0.000	0.000	0.000	0.000
80	A	97	LEU	0	-0.059	-0.013	24.290	-0.178	-0.178	0.000	0.000	0.000	0.000
81	A	98	LEU	0	-0.099	-0.052	25.354	-0.605	-0.605	0.000	0.000	0.000	0.000
82	A	99	GLY	-1	-0.887	-0.938	29.341	-18.673	-18.673	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:18:ARG)