FMO DATABASE

FMODB ID: NL8QQ

Calculation Name: 2LD5-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2LD5

Chain ID: A

ChEMBL ID:

UniProt ID: Q62424

Base Structure: SolutionNMR

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	67
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-418225.325039
FMO2-HF: Nuclear repulsion	390539.142491
FMO2-HF: Total energy	-27686.182547
FMO2-MP2: Total energy	-27769.534163

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:7:GLY)

Summations of interaction energy for fragment #1(A:7:GLY)

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.
255.955	256.854	-0.001	-0.359	-0.539	-0.001

Interaction energy analysis for fragmet #1(A:7:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.933 / q_NPA : 0.954

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	9	LYS	1	0.915	0.963	3.858	51.006	51.905	-0.001	-0.359	-0.539	-0.001
4	A	10	LYS	1	1.010	1.000	5.785	26.431	26.431	0.000	0.000	0.000	0.000
5	A	11	ARG	1	1.026	1.025	8.581	18.565	18.565	0.000	0.000	0.000	0.000
6	A	12	VAL	0	0.048	0.023	8.298	-3.566	-3.566	0.000	0.000	0.000	0.000
7	A	13	PRO	0	-0.080	-0.041	9.111	2.092	2.092	0.000	0.000	0.000	0.000
8	A	14	TYR	0	0.125	0.061	12.172	-0.017	-0.017	0.000	0.000	0.000	0.000
9	A	15	THR	0	0.035	0.018	13.206	-1.404	-1.404	0.000	0.000	0.000	0.000
10	A	16	LYS	1	1.000	0.973	9.668	29.493	29.493	0.000	0.000	0.000	0.000
11	A	17	VAL	0	0.052	0.022	12.994	-0.019	-0.019	0.000	0.000	0.000	0.000
12	A	18	GLN	0	0.048	0.032	16.493	-0.224	-0.224	0.000	0.000	0.000	0.000
13	A	19	LEU	0	-0.047	-0.027	13.395	0.400	0.400	0.000	0.000	0.000	0.000
14	A	20	LYS	1	0.947	0.983	14.603	17.499	17.499	0.000	0.000	0.000	0.000
15	A	21	GLU	-1	-0.791	-0.886	16.096	-14.099	-14.099	0.000	0.000	0.000	0.000
16	A	22	LEU	0	-0.042	-0.010	18.608	0.626	0.626	0.000	0.000	0.000	0.000
17	A	23	GLU	-1	-0.944	-0.995	14.465	-20.515	-20.515	0.000	0.000	0.000	0.000
18	A	24	ARG	1	0.929	0.985	18.104	16.189	16.189	0.000	0.000	0.000	0.000
19	A	25	GLU	-1	-0.724	-0.840	21.416	-11.408	-11.408	0.000	0.000	0.000	0.000
20	A	26	TYR	0	-0.075	-0.060	21.376	0.621	0.621	0.000	0.000	0.000	0.000
21	A	27	ALA	0	-0.028	-0.024	21.346	0.370	0.370	0.000	0.000	0.000	0.000
22	A	28	THR	0	-0.019	-0.001	23.380	0.366	0.366	0.000	0.000	0.000	0.000
23	A	29	ASN	0	-0.009	-0.014	26.511	0.411	0.411	0.000	0.000	0.000	0.000
24	A	30	LYS	1	1.006	1.017	25.752	10.816	10.816	0.000	0.000	0.000	0.000
25	A	31	PHE	0	-0.093	-0.060	26.011	-0.422	-0.422	0.000	0.000	0.000	0.000
26	A	32	ILE	0	0.016	0.025	27.353	0.142	0.142	0.000	0.000	0.000	0.000
27	A	33	THR	0	0.030	-0.003	30.203	-0.038	-0.038	0.000	0.000	0.000	0.000
28	A	34	LYS	1	0.973	0.971	31.658	8.990	8.990	0.000	0.000	0.000	0.000
29	A	35	ASP	-1	-0.775	-0.861	32.610	-9.570	-9.570	0.000	0.000	0.000	0.000
30	A	36	LYS	1	0.922	0.943	27.951	10.934	10.934	0.000	0.000	0.000	0.000
31	A	37	ARG	1	0.814	0.876	27.795	9.658	9.658	0.000	0.000	0.000	0.000
32	A	38	ARG	1	0.970	0.990	27.997	8.588	8.588	0.000	0.000	0.000	0.000
33	A	39	ARG	1	0.868	0.928	23.563	12.528	12.528	0.000	0.000	0.000	0.000
34	A	40	ILE	0	-0.006	0.009	22.890	-0.381	-0.381	0.000	0.000	0.000	0.000
35	A	41	SER	0	-0.023	-0.016	24.876	-0.452	-0.452	0.000	0.000	0.000	0.000
36	A	42	ALA	0	0.008	0.013	26.595	-0.201	-0.201	0.000	0.000	0.000	0.000
37	A	43	THR	0	-0.037	-0.024	22.821	-0.108	-0.108	0.000	0.000	0.000	0.000
38	A	44	THR	0	-0.098	-0.081	20.790	-0.553	-0.553	0.000	0.000	0.000	0.000
39	A	45	ASN	0	0.002	0.017	23.116	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	46	LEU	0	-0.021	0.004	22.208	-0.038	-0.038	0.000	0.000	0.000	0.000
41	A	47	SER	0	0.063	0.028	26.101	0.248	0.248	0.000	0.000	0.000	0.000
42	A	48	GLU	-1	-0.747	-0.859	28.673	-9.310	-9.310	0.000	0.000	0.000	0.000
43	A	49	ARG	1	0.889	0.934	28.820	10.375	10.375	0.000	0.000	0.000	0.000
44	A	50	GLN	0	0.077	0.023	24.374	0.297	0.297	0.000	0.000	0.000	0.000
45	A	51	VAL	0	0.028	0.032	24.195	-0.571	-0.571	0.000	0.000	0.000	0.000
46	A	52	THR	0	0.020	-0.008	24.576	-0.266	-0.266	0.000	0.000	0.000	0.000
47	A	53	ILE	0	0.013	0.021	23.860	-0.085	-0.085	0.000	0.000	0.000	0.000
48	A	54	TRP	0	-0.019	-0.008	17.205	-0.269	-0.269	0.000	0.000	0.000	0.000
49	A	55	PHE	0	0.016	0.002	21.041	-0.677	-0.677	0.000	0.000	0.000	0.000
50	A	56	GLN	0	0.004	0.008	23.382	-0.315	-0.315	0.000	0.000	0.000	0.000
51	A	57	ASN	0	-0.040	-0.033	19.123	-0.641	-0.641	0.000	0.000	0.000	0.000
52	A	58	ARG	1	0.851	0.922	16.727	16.505	16.505	0.000	0.000	0.000	0.000
53	A	59	ARG	1	0.917	0.946	19.479	12.847	12.847	0.000	0.000	0.000	0.000
54	A	60	VAL	0	0.015	0.014	19.450	0.032	0.032	0.000	0.000	0.000	0.000
55	A	61	LYS	1	0.917	0.955	12.898	21.803	21.803	0.000	0.000	0.000	0.000
56	A	62	GLU	-1	-0.736	-0.824	16.044	-16.111	-16.111	0.000	0.000	0.000	0.000
57	A	63	LYS	1	1.018	1.017	17.943	13.000	13.000	0.000	0.000	0.000	0.000
58	A	64	LYS	1	0.956	0.973	10.693	26.586	26.586	0.000	0.000	0.000	0.000
59	A	65	VAL	0	-0.057	-0.032	12.966	-1.054	-1.054	0.000	0.000	0.000	0.000
60	A	66	ILE	0	0.060	0.032	15.396	-0.265	-0.265	0.000	0.000	0.000	0.000
61	A	67	ASN	0	-0.024	-0.009	18.587	0.616	0.616	0.000	0.000	0.000	0.000
62	A	68	LYS	1	0.922	0.958	12.983	20.720	20.720	0.000	0.000	0.000	0.000
63	A	69	LEU	0	-0.011	0.013	15.381	-0.556	-0.556	0.000	0.000	0.000	0.000
64	A	70	LYS	1	0.870	0.904	16.892	16.531	16.531	0.000	0.000	0.000	0.000
65	A	71	THR	0	0.001	0.006	16.574	0.160	0.160	0.000	0.000	0.000	0.000
66	A	72	THR	0	0.042	0.028	18.301	0.601	0.601	0.000	0.000	0.000	0.000
67	A	73	SER	-1	-0.967	-0.960	17.749	-16.949	-16.949	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:GLY)