FMO DATABASE

FMODB ID: 8K2KY

Calculation Name: 6T90-K-Other547

Preferred Name:

Target Type:

Ligand Name: pentanedial

Ligand 3-letter code: PTD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6T90

Chain ID: K

ChEMBL ID:

UniProt ID: P42212

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	73
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-476638.991133
FMO2-HF: Nuclear repulsion	447190.119837
FMO2-HF: Total energy	-29448.871296
FMO2-MP2: Total energy	-29534.783796

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:138:ASP)

Summations of interaction energy for fragment #1(A:138:ASP)

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.
-66.381	-63.319	18.662	-10.549	-11.175	0.115

Interaction energy analysis for fragmet #1(A:138:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.059 / q_NPA : 0.018

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	140	LYS	1	0.927	0.954	1.959	-34.485	-30.760	8.511	-5.864	-6.372	0.064
4	A	141	ALA	0	0.002	0.001	1.872	-18.517	-19.796	10.113	-4.363	-4.471	0.048
5	A	142	LEU	0	0.024	0.013	3.795	-4.901	-4.285	0.038	-0.322	-0.332	0.003
6	A	143	GLN	0	-0.052	-0.040	6.055	1.347	1.347	0.000	0.000	0.000	0.000
7	A	144	LYS	1	1.007	1.006	5.999	-13.812	-13.812	0.000	0.000	0.000	0.000
8	A	145	GLU	-1	-0.842	-0.907	8.006	-4.450	-4.450	0.000	0.000	0.000	0.000
9	A	146	LEU	0	-0.020	-0.022	10.031	-0.531	-0.531	0.000	0.000	0.000	0.000
10	A	147	GLU	-1	-0.859	-0.923	10.574	5.649	5.649	0.000	0.000	0.000	0.000
11	A	148	GLN	0	-0.038	-0.021	10.950	-0.766	-0.766	0.000	0.000	0.000	0.000
12	A	149	PHE	0	0.030	0.014	13.902	-0.258	-0.258	0.000	0.000	0.000	0.000
13	A	150	ALA	0	0.035	0.018	15.618	-0.126	-0.126	0.000	0.000	0.000	0.000
14	A	151	LYS	1	0.910	0.959	16.884	-1.645	-1.645	0.000	0.000	0.000	0.000
15	A	152	LEU	0	0.022	0.006	17.057	-0.097	-0.097	0.000	0.000	0.000	0.000
16	A	153	LEU	0	0.009	0.019	19.821	-0.070	-0.070	0.000	0.000	0.000	0.000
17	A	154	LYS	1	0.963	0.984	21.495	-0.900	-0.900	0.000	0.000	0.000	0.000
18	A	155	GLN	0	-0.013	-0.015	21.471	-0.040	-0.040	0.000	0.000	0.000	0.000
19	A	156	LYS	1	0.971	1.004	23.963	-0.183	-0.183	0.000	0.000	0.000	0.000
20	A	157	ARG	1	0.812	0.867	25.664	-0.346	-0.346	0.000	0.000	0.000	0.000
21	A	158	ILE	0	-0.052	-0.029	26.588	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	159	THR	0	-0.063	-0.046	27.759	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	160	LEU	0	-0.004	0.001	28.949	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	161	GLY	0	-0.004	0.017	32.009	-0.028	-0.028	0.000	0.000	0.000	0.000
25	A	162	TYR	0	0.030	0.026	30.406	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	163	THR	0	-0.022	-0.051	30.924	0.060	0.060	0.000	0.000	0.000	0.000
27	A	164	GLN	0	-0.053	-0.064	25.717	-0.055	-0.055	0.000	0.000	0.000	0.000
28	A	165	ALA	0	-0.001	-0.005	28.989	-0.043	-0.043	0.000	0.000	0.000	0.000
29	A	166	ASP	-1	-0.753	-0.838	31.640	-0.013	-0.013	0.000	0.000	0.000	0.000
30	A	167	VAL	0	-0.010	0.020	24.960	-0.045	-0.045	0.000	0.000	0.000	0.000
31	A	168	GLY	0	-0.002	-0.001	27.698	-0.069	-0.069	0.000	0.000	0.000	0.000
32	A	169	LEU	0	0.037	0.006	28.658	-0.060	-0.060	0.000	0.000	0.000	0.000
33	A	170	THR	0	0.024	-0.002	29.411	-0.035	-0.035	0.000	0.000	0.000	0.000
34	A	171	LEU	0	-0.052	-0.022	23.746	-0.060	-0.060	0.000	0.000	0.000	0.000
35	A	172	GLY	0	0.008	-0.001	27.823	-0.061	-0.061	0.000	0.000	0.000	0.000
36	A	173	VAL	0	-0.034	-0.013	30.831	-0.028	-0.028	0.000	0.000	0.000	0.000
37	A	174	LEU	0	0.004	0.010	26.985	-0.026	-0.026	0.000	0.000	0.000	0.000
38	A	175	PHE	0	-0.027	-0.020	23.657	-0.085	-0.085	0.000	0.000	0.000	0.000
39	A	176	GLY	0	0.024	0.026	28.198	-0.046	-0.046	0.000	0.000	0.000	0.000
40	A	177	LYS	1	0.866	0.933	23.214	1.043	1.043	0.000	0.000	0.000	0.000
41	A	178	VAL	0	0.060	0.036	27.652	0.007	0.007	0.000	0.000	0.000	0.000
42	A	179	PHE	0	-0.058	-0.032	23.700	-0.023	-0.023	0.000	0.000	0.000	0.000
43	A	180	SER	0	0.057	0.027	28.268	0.038	0.038	0.000	0.000	0.000	0.000
44	A	181	GLN	0	0.126	0.047	27.863	-0.040	-0.040	0.000	0.000	0.000	0.000
45	A	182	THR	0	-0.017	-0.013	27.558	0.057	0.057	0.000	0.000	0.000	0.000
46	A	183	THR	0	-0.030	-0.013	23.181	0.051	0.051	0.000	0.000	0.000	0.000
47	A	184	ILE	0	0.020	0.015	23.206	0.028	0.028	0.000	0.000	0.000	0.000
48	A	185	CYS	0	-0.015	0.003	23.332	0.119	0.119	0.000	0.000	0.000	0.000
49	A	186	ARG	1	0.970	0.975	21.852	-0.260	-0.260	0.000	0.000	0.000	0.000
50	A	187	PHE	0	-0.004	0.006	16.302	0.126	0.126	0.000	0.000	0.000	0.000
51	A	188	GLU	-1	-0.758	-0.852	18.602	0.590	0.590	0.000	0.000	0.000	0.000
52	A	189	ALA	0	-0.046	-0.012	19.563	0.184	0.184	0.000	0.000	0.000	0.000
53	A	190	LEU	0	-0.015	-0.008	13.486	0.232	0.232	0.000	0.000	0.000	0.000
54	A	191	GLN	0	-0.065	-0.033	16.242	0.051	0.051	0.000	0.000	0.000	0.000
55	A	192	LEU	0	-0.022	-0.003	17.275	-0.213	-0.213	0.000	0.000	0.000	0.000
56	A	193	SER	0	0.039	0.016	14.902	0.090	0.090	0.000	0.000	0.000	0.000
57	A	194	PHE	0	0.108	0.031	8.879	-0.112	-0.112	0.000	0.000	0.000	0.000
58	A	195	LYS	1	0.964	0.986	11.635	2.174	2.174	0.000	0.000	0.000	0.000
59	A	196	ASN	0	-0.003	-0.002	12.946	-0.321	-0.321	0.000	0.000	0.000	0.000
60	A	197	MET	0	-0.001	0.015	12.976	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	198	CYS	0	-0.024	-0.023	10.369	-0.362	-0.362	0.000	0.000	0.000	0.000
62	A	199	LYS	1	0.929	0.964	12.985	1.843	1.843	0.000	0.000	0.000	0.000
63	A	200	LEU	0	0.018	0.019	16.340	0.072	0.072	0.000	0.000	0.000	0.000
64	A	201	ARG	1	0.881	0.946	9.641	3.171	3.171	0.000	0.000	0.000	0.000
65	A	202	PRO	0	0.002	0.001	15.644	0.142	0.142	0.000	0.000	0.000	0.000
66	A	203	LEU	0	-0.018	0.004	18.171	0.107	0.107	0.000	0.000	0.000	0.000
67	A	204	LEU	0	0.013	-0.005	19.251	0.127	0.127	0.000	0.000	0.000	0.000
68	A	205	GLN	0	-0.038	-0.030	14.759	-0.021	-0.021	0.000	0.000	0.000	0.000
69	A	206	LYS	1	0.831	0.909	20.177	0.740	0.740	0.000	0.000	0.000	0.000
70	A	207	TRP	0	0.013	-0.002	23.319	0.093	0.093	0.000	0.000	0.000	0.000
71	A	208	VAL	0	-0.066	-0.043	21.912	0.093	0.093	0.000	0.000	0.000	0.000
72	A	209	GLU	-1	-0.972	-0.981	22.531	-0.734	-0.734	0.000	0.000	0.000	0.000
73	A	210	GLU	-2	-1.831	-1.873	25.841	-0.712	-0.712	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:138:ASP)