FMO DATABASE

FMODB ID: MLZGZ

Calculation Name: 3BDU-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3BDU

Chain ID: A

ChEMBL ID:

UniProt ID: Q6D8G1

Base Structure: X-ray

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	53
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-261106.489836
FMO2-HF: Nuclear repulsion	240032.083121
FMO2-HF: Total energy	-21074.406715
FMO2-MP2: Total energy	-21134.838461

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:2:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-33.704	-30.335	0.381	-1.39	-2.359	-0.007

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.905 / q_NPA : 0.943

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	4	ASN	0	0.089	0.052	3.812	-4.743	-3.411	-0.001	-0.543	-0.788	0.000
17	A	18	GLU	-1	-0.928	-0.957	2.411	-56.698	-55.780	0.268	-0.393	-0.793	-0.003
18	A	19	GLY	0	-0.047	-0.030	3.044	-3.455	-2.416	0.096	-0.433	-0.702	-0.003
19	A	20	LYS	1	0.908	0.951	3.553	29.389	29.469	0.018	-0.021	-0.076	-0.001
4	A	5	TYR	0	0.008	0.004	5.733	2.370	2.370	0.000	0.000	0.000	0.000
5	A	6	VAL	0	0.028	0.030	8.653	-0.385	-0.385	0.000	0.000	0.000	0.000
6	A	7	LEU	0	-0.008	-0.003	11.054	0.866	0.866	0.000	0.000	0.000	0.000
7	A	8	HIS	0	0.018	0.009	14.401	0.825	0.825	0.000	0.000	0.000	0.000
8	A	9	THR	0	-0.014	-0.031	18.159	0.144	0.144	0.000	0.000	0.000	0.000
9	A	10	ASN	0	-0.024	-0.032	20.442	0.351	0.351	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.803	-0.813	22.352	-13.126	-13.126	0.000	0.000	0.000	0.000
11	A	12	GLY	0	0.005	0.010	23.601	0.174	0.174	0.000	0.000	0.000	0.000
12	A	13	ARG	1	0.814	0.872	19.113	14.321	14.321	0.000	0.000	0.000	0.000
13	A	14	THR	0	0.008	0.004	16.635	-0.038	-0.038	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.026	-0.013	12.340	-0.059	-0.059	0.000	0.000	0.000	0.000
15	A	16	VAL	0	-0.004	0.002	8.554	-0.794	-0.794	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.014	0.003	7.723	0.829	0.829	0.000	0.000	0.000	0.000
20	A	21	PRO	0	0.036	0.024	7.081	0.366	0.366	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.843	0.912	8.007	29.553	29.553	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.004	0.004	12.646	0.204	0.204	0.000	0.000	0.000	0.000
23	A	24	ASP	-1	-0.808	-0.891	15.789	-17.291	-17.291	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.935	-0.973	17.448	-13.895	-13.895	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.965	-0.967	20.077	-13.392	-13.392	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.055	-0.049	18.937	0.519	0.519	0.000	0.000	0.000	0.000
27	A	28	GLY	0	-0.022	-0.001	21.364	0.477	0.477	0.000	0.000	0.000	0.000
28	A	29	MET	0	-0.084	-0.042	18.825	0.113	0.113	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.025	-0.017	13.792	-0.528	-0.528	0.000	0.000	0.000	0.000
30	A	31	SER	0	0.031	0.020	13.238	-0.331	-0.331	0.000	0.000	0.000	0.000
31	A	32	TYR	0	-0.031	-0.046	8.979	-1.529	-1.529	0.000	0.000	0.000	0.000
32	A	33	THR	0	0.042	0.036	5.966	2.523	2.523	0.000	0.000	0.000	0.000
33	A	34	ASP	-1	-0.753	-0.873	7.391	-25.469	-25.469	0.000	0.000	0.000	0.000
34	A	35	ALA	0	-0.008	-0.019	7.697	-2.189	-2.189	0.000	0.000	0.000	0.000
35	A	36	TYR	0	-0.047	-0.016	8.761	0.248	0.248	0.000	0.000	0.000	0.000
36	A	37	GLY	0	0.016	0.015	7.695	0.936	0.936	0.000	0.000	0.000	0.000
37	A	38	GLN	0	-0.061	-0.028	8.736	1.831	1.831	0.000	0.000	0.000	0.000
38	A	39	GLN	0	-0.031	-0.019	10.286	-0.582	-0.582	0.000	0.000	0.000	0.000
39	A	40	GLN	0	-0.031	-0.021	11.685	2.430	2.430	0.000	0.000	0.000	0.000
40	A	41	GLN	0	-0.007	-0.015	13.298	-0.025	-0.025	0.000	0.000	0.000	0.000
41	A	42	ILE	0	-0.043	-0.011	15.683	0.605	0.605	0.000	0.000	0.000	0.000
42	A	43	ASN	0	0.050	0.022	18.064	-0.425	-0.425	0.000	0.000	0.000	0.000
43	A	44	ARG	1	0.988	0.991	19.375	13.288	13.288	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.852	-0.915	20.813	-11.936	-11.936	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.066	-0.055	21.532	0.422	0.422	0.000	0.000	0.000	0.000
46	A	47	VAL	0	-0.025	-0.019	16.200	-0.651	-0.651	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.865	0.948	19.346	13.023	13.023	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.862	-0.927	18.656	-13.793	-13.793	0.000	0.000	0.000	0.000
49	A	50	MET	0	-0.035	-0.028	12.220	-1.451	-1.451	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.015	0.026	13.595	0.473	0.473	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.881	0.934	6.880	34.097	34.097	0.000	0.000	0.000	0.000
52	A	53	GLY	0	-0.038	-0.026	9.001	1.505	1.505	0.000	0.000	0.000	0.000
53	A	54	LYS	0	0.060	0.037	9.631	-2.801	-2.801	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)