FMO DATABASE

FMODB ID: Y9RK2

Calculation Name: 1D1R-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1D1R

Chain ID: A

ChEMBL ID:

UniProt ID: P08245

Base Structure: SolutionNMR

Registration Date: 2025-09-02

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	83
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-466403.30982
FMO2-HF: Nuclear repulsion	435577.235919
FMO2-HF: Total energy	-30826.073901
FMO2-MP2: Total energy	-30913.89513

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:29:LYS)

Summations of interaction energy for fragment #1(A:29:LYS)

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.
12.404	19.693	-0.043	-3.511	-3.736	-0.025

Interaction energy analysis for fragmet #1(A:29:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.791 / q_NPA : 1.861

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	31	ASP	-1	-0.865	-0.888	3.563	-79.722	-72.433	-0.043	-3.511	-3.736	-0.025
4	A	32	GLY	0	0.142	0.078	5.607	6.229	6.229	0.000	0.000	0.000	0.000
5	A	33	VAL	0	-0.130	-0.060	7.950	-3.719	-3.719	0.000	0.000	0.000	0.000
6	A	34	VAL	0	0.047	0.028	10.347	3.229	3.229	0.000	0.000	0.000	0.000
7	A	35	ARG	1	0.915	0.949	13.912	29.133	29.133	0.000	0.000	0.000	0.000
8	A	36	ILE	0	0.031	0.017	16.927	0.894	0.894	0.000	0.000	0.000	0.000
9	A	37	GLN	0	-0.033	-0.014	20.470	0.244	0.244	0.000	0.000	0.000	0.000
10	A	38	ARG	1	0.968	0.987	23.333	21.168	21.168	0.000	0.000	0.000	0.000
11	A	39	GLN	0	0.030	0.013	26.956	0.268	0.268	0.000	0.000	0.000	0.000
12	A	40	THR	0	-0.015	-0.010	29.748	0.280	0.280	0.000	0.000	0.000	0.000
13	A	41	SER	0	0.011	0.012	32.649	0.051	0.051	0.000	0.000	0.000	0.000
14	A	42	GLY	0	0.028	0.014	35.554	0.579	0.579	0.000	0.000	0.000	0.000
15	A	43	ARG	1	0.935	0.974	35.546	14.972	14.972	0.000	0.000	0.000	0.000
16	A	44	LYS	1	0.977	0.967	35.647	16.367	16.367	0.000	0.000	0.000	0.000
17	A	45	GLY	0	0.039	0.026	37.651	0.416	0.416	0.000	0.000	0.000	0.000
18	A	46	LYS	1	0.968	0.983	35.854	16.423	16.423	0.000	0.000	0.000	0.000
19	A	47	GLY	0	0.036	0.027	32.672	-0.056	-0.056	0.000	0.000	0.000	0.000
20	A	48	VAL	0	-0.041	-0.013	29.637	0.266	0.266	0.000	0.000	0.000	0.000
21	A	49	CYS	0	-0.054	-0.025	25.233	-0.742	-0.742	0.000	0.000	0.000	0.000
22	A	50	LEU	0	0.050	0.032	24.339	0.115	0.115	0.000	0.000	0.000	0.000
23	A	51	ILE	0	0.014	0.002	18.856	-1.068	-1.068	0.000	0.000	0.000	0.000
24	A	52	THR	0	0.022	-0.006	19.312	0.942	0.942	0.000	0.000	0.000	0.000
25	A	53	GLY	0	-0.020	-0.017	15.970	-0.311	-0.311	0.000	0.000	0.000	0.000
26	A	54	VAL	0	-0.039	-0.015	13.784	-2.026	-2.026	0.000	0.000	0.000	0.000
27	A	55	ASP	-1	-0.952	-0.959	10.454	-42.911	-42.911	0.000	0.000	0.000	0.000
28	A	56	LEU	0	0.016	-0.004	10.216	-4.048	-4.048	0.000	0.000	0.000	0.000
29	A	57	ASP	-1	-0.861	-0.921	12.755	-32.691	-32.691	0.000	0.000	0.000	0.000
30	A	58	ASP	-1	-0.865	-0.926	15.343	-27.091	-27.091	0.000	0.000	0.000	0.000
31	A	59	ALA	0	0.023	0.007	18.800	1.015	1.015	0.000	0.000	0.000	0.000
32	A	60	GLU	-1	-0.998	-1.014	13.524	-41.075	-41.075	0.000	0.000	0.000	0.000
33	A	61	LEU	0	0.043	0.017	16.659	0.560	0.560	0.000	0.000	0.000	0.000
34	A	62	THR	0	-0.016	-0.016	18.153	1.376	1.376	0.000	0.000	0.000	0.000
35	A	63	LYS	1	0.902	0.949	18.608	31.997	31.997	0.000	0.000	0.000	0.000
36	A	64	LEU	0	0.018	0.011	15.768	0.658	0.658	0.000	0.000	0.000	0.000
37	A	65	ALA	0	0.028	0.011	19.580	0.819	0.819	0.000	0.000	0.000	0.000
38	A	66	ALA	0	-0.026	-0.016	22.710	1.209	1.209	0.000	0.000	0.000	0.000
39	A	67	GLU	-1	-0.947	-0.981	19.029	-30.077	-30.077	0.000	0.000	0.000	0.000
40	A	68	LEU	0	-0.035	-0.016	20.740	0.960	0.960	0.000	0.000	0.000	0.000
41	A	69	LYS	1	0.945	0.981	24.454	21.851	21.851	0.000	0.000	0.000	0.000
42	A	70	LYS	1	0.937	0.986	26.306	23.421	23.421	0.000	0.000	0.000	0.000
43	A	71	LYS	1	0.944	0.965	23.783	25.316	25.316	0.000	0.000	0.000	0.000
44	A	72	CYS	0	-0.012	0.010	26.041	-0.335	-0.335	0.000	0.000	0.000	0.000
45	A	73	GLY	0	-0.024	-0.011	28.724	0.402	0.402	0.000	0.000	0.000	0.000
46	A	74	CYS	0	-0.002	-0.004	31.955	-0.028	-0.028	0.000	0.000	0.000	0.000
47	A	75	GLY	0	0.026	0.012	30.972	-0.648	-0.648	0.000	0.000	0.000	0.000
48	A	76	GLY	0	-0.003	0.000	28.042	0.272	0.272	0.000	0.000	0.000	0.000
49	A	77	ALA	0	-0.010	-0.009	28.446	-0.070	-0.070	0.000	0.000	0.000	0.000
50	A	78	VAL	0	-0.006	-0.020	23.286	-0.607	-0.607	0.000	0.000	0.000	0.000
51	A	79	LYS	1	0.880	0.922	25.426	20.250	20.250	0.000	0.000	0.000	0.000
52	A	80	ASP	-1	-0.861	-0.916	23.892	-22.718	-22.718	0.000	0.000	0.000	0.000
53	A	81	GLY	0	0.054	0.031	20.289	-0.509	-0.509	0.000	0.000	0.000	0.000
54	A	82	VAL	0	-0.089	-0.047	20.303	-1.053	-1.053	0.000	0.000	0.000	0.000
55	A	83	ILE	0	-0.015	-0.012	20.297	0.730	0.730	0.000	0.000	0.000	0.000
56	A	84	GLU	-1	-0.868	-0.911	24.009	-19.868	-19.868	0.000	0.000	0.000	0.000
57	A	85	ILE	0	0.001	-0.011	24.737	0.252	0.252	0.000	0.000	0.000	0.000
58	A	86	GLN	0	0.001	-0.004	27.902	0.163	0.163	0.000	0.000	0.000	0.000
59	A	87	GLY	0	0.056	0.020	30.832	0.087	0.087	0.000	0.000	0.000	0.000
60	A	88	ASP	-1	-0.894	-0.944	28.726	-20.184	-20.184	0.000	0.000	0.000	0.000
61	A	89	LYS	1	0.892	0.937	26.920	20.544	20.544	0.000	0.000	0.000	0.000
62	A	90	ARG	1	0.912	0.933	21.969	24.002	24.002	0.000	0.000	0.000	0.000
63	A	91	ASP	-1	-0.909	-0.944	22.377	-25.819	-25.819	0.000	0.000	0.000	0.000
64	A	92	LEU	0	0.005	0.000	22.227	-1.039	-1.039	0.000	0.000	0.000	0.000
65	A	93	LEU	0	0.015	-0.016	20.644	-0.981	-0.981	0.000	0.000	0.000	0.000
66	A	94	LYS	1	0.891	0.947	17.028	32.031	32.031	0.000	0.000	0.000	0.000
67	A	95	SER	0	0.016	0.019	17.337	-2.337	-2.337	0.000	0.000	0.000	0.000
68	A	96	LEU	0	-0.014	-0.010	17.763	-1.340	-1.340	0.000	0.000	0.000	0.000
69	A	97	LEU	0	-0.027	-0.009	12.709	-0.715	-0.715	0.000	0.000	0.000	0.000
70	A	98	GLU	-1	-0.826	-0.910	13.201	-39.512	-39.512	0.000	0.000	0.000	0.000
71	A	99	ALA	0	-0.053	-0.019	13.208	-2.202	-2.202	0.000	0.000	0.000	0.000
72	A	100	LYS	1	0.892	0.953	11.707	36.560	36.560	0.000	0.000	0.000	0.000
73	A	101	GLY	0	-0.005	0.012	8.987	-3.831	-3.831	0.000	0.000	0.000	0.000
74	A	102	MET	0	-0.027	0.001	8.043	-6.439	-6.439	0.000	0.000	0.000	0.000
75	A	103	LYS	1	0.966	0.976	5.841	68.768	68.768	0.000	0.000	0.000	0.000
76	A	104	VAL	0	0.044	0.020	9.299	2.608	2.608	0.000	0.000	0.000	0.000
77	A	105	LYS	1	0.918	0.960	13.016	33.562	33.562	0.000	0.000	0.000	0.000
78	A	106	LEU	0	0.009	-0.008	15.178	1.522	1.522	0.000	0.000	0.000	0.000
79	A	107	ALA	0	0.014	0.020	18.436	0.712	0.712	0.000	0.000	0.000	0.000
80	A	108	GLY	0	-0.032	-0.029	21.013	0.612	0.612	0.000	0.000	0.000	0.000
81	A	109	GLY	0	0.011	0.011	24.248	-0.414	-0.414	0.000	0.000	0.000	0.000
82	A	110	LEU	0	-0.075	-0.039	27.137	-0.060	-0.060	0.000	0.000	0.000	0.000
83	A	111	GLU	-2	-1.864	-1.907	30.758	-35.185	-35.185	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:29:LYS)