FMO DATABASE

FMODB ID: LR5N9

Calculation Name: 2D9R-A-Xray549

Preferred Name:

Target Type:

Ligand Name: beta-mercaptoethanol

Ligand 3-letter code: BME

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2D9R

Chain ID: A

ChEMBL ID:

UniProt ID: Q7MXL1

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	85
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-569647.050991
FMO2-HF: Nuclear repulsion	536375.601356
FMO2-HF: Total energy	-33271.449636
FMO2-MP2: Total energy	-33368.616514

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:20:SER)

Summations of interaction energy for fragment #1(A:20: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.
-54.781	-51.532	0.2	-1.698	-1.752	-0.014

Interaction energy analysis for fragmet #1(A:20:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.826 / q_NPA : 0.901

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	22	ILE	0	-0.016	0.007	2.763	-7.005	-4.363	0.157	-1.476	-1.324	-0.012
4	A	23	GLU	-1	-0.867	-0.932	5.400	-36.025	-35.913	-0.001	-0.003	-0.107	0.000
83	A	102	LEU	0	0.002	-0.002	2.924	-11.104	-10.609	0.044	-0.219	-0.321	-0.002
5	A	24	PHE	0	-0.020	-0.019	7.805	1.232	1.232	0.000	0.000	0.000	0.000
6	A	25	ASP	-1	-0.831	-0.906	11.363	-18.001	-18.001	0.000	0.000	0.000	0.000
7	A	26	ALA	0	-0.040	-0.026	14.984	0.127	0.127	0.000	0.000	0.000	0.000
8	A	27	ILE	0	-0.021	-0.004	17.401	0.344	0.344	0.000	0.000	0.000	0.000
9	A	28	ILE	0	-0.024	0.000	21.158	-0.221	-0.221	0.000	0.000	0.000	0.000
10	A	29	ARG	1	0.870	0.932	22.529	13.534	13.534	0.000	0.000	0.000	0.000
11	A	30	GLN	0	0.044	-0.002	24.863	-0.222	-0.222	0.000	0.000	0.000	0.000
12	A	31	VAL	0	-0.021	0.008	27.878	0.077	0.077	0.000	0.000	0.000	0.000
13	A	32	PRO	0	-0.002	-0.016	30.611	0.027	0.027	0.000	0.000	0.000	0.000
14	A	33	ASP	-1	-0.899	-0.958	33.773	-8.295	-8.295	0.000	0.000	0.000	0.000
15	A	34	MET	0	-0.040	-0.002	31.984	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	35	ASP	-1	-0.814	-0.901	31.551	-9.894	-9.894	0.000	0.000	0.000	0.000
17	A	36	ALA	0	-0.094	-0.043	27.682	-0.456	-0.456	0.000	0.000	0.000	0.000
18	A	37	ALA	0	0.043	0.019	24.855	0.201	0.201	0.000	0.000	0.000	0.000
19	A	38	TYR	0	-0.058	-0.033	21.692	-0.215	-0.215	0.000	0.000	0.000	0.000
20	A	39	VAL	0	0.047	0.038	16.329	0.306	0.306	0.000	0.000	0.000	0.000
21	A	40	GLU	-1	-0.845	-0.928	18.972	-13.819	-13.819	0.000	0.000	0.000	0.000
22	A	41	ILE	0	-0.027	-0.016	13.197	-0.781	-0.781	0.000	0.000	0.000	0.000
23	A	42	PRO	0	-0.016	0.012	13.072	0.715	0.715	0.000	0.000	0.000	0.000
24	A	43	PHE	0	0.001	-0.013	10.322	-0.472	-0.472	0.000	0.000	0.000	0.000
25	A	44	ASP	-1	-0.816	-0.893	14.254	-17.131	-17.131	0.000	0.000	0.000	0.000
26	A	45	VAL	0	0.020	0.005	13.799	-1.121	-1.121	0.000	0.000	0.000	0.000
27	A	46	LYS	1	0.874	0.937	14.681	13.583	13.583	0.000	0.000	0.000	0.000
28	A	47	THR	0	-0.043	-0.047	14.477	0.336	0.336	0.000	0.000	0.000	0.000
29	A	48	VAL	0	-0.054	-0.017	9.084	-0.615	-0.615	0.000	0.000	0.000	0.000
30	A	49	TYR	0	-0.015	-0.015	8.101	-3.314	-3.314	0.000	0.000	0.000	0.000
31	A	50	GLY	0	0.045	0.038	12.449	0.414	0.414	0.000	0.000	0.000	0.000
32	A	51	LYS	0	0.010	-0.001	16.151	0.423	0.423	0.000	0.000	0.000	0.000
33	A	52	GLY	0	0.005	0.006	18.912	-0.156	-0.156	0.000	0.000	0.000	0.000
34	A	53	ARG	1	0.900	0.947	18.976	13.936	13.936	0.000	0.000	0.000	0.000
35	A	54	VAL	0	0.068	0.044	12.204	0.079	0.079	0.000	0.000	0.000	0.000
36	A	55	ARG	1	0.939	0.978	14.658	20.350	20.350	0.000	0.000	0.000	0.000
37	A	56	VAL	0	0.023	-0.002	10.879	-1.644	-1.644	0.000	0.000	0.000	0.000
38	A	57	ASN	0	0.034	0.027	9.227	4.688	4.688	0.000	0.000	0.000	0.000
39	A	58	ALA	0	0.015	-0.003	9.662	-3.177	-3.177	0.000	0.000	0.000	0.000
40	A	59	THR	0	-0.027	0.009	10.759	0.960	0.960	0.000	0.000	0.000	0.000
41	A	60	PHE	0	0.038	0.012	13.073	-0.323	-0.323	0.000	0.000	0.000	0.000
42	A	61	ASP	-1	-0.740	-0.869	15.753	-15.796	-15.796	0.000	0.000	0.000	0.000
43	A	62	GLY	0	-0.010	-0.002	13.137	0.464	0.464	0.000	0.000	0.000	0.000
44	A	63	TYR	0	-0.005	-0.001	14.219	-0.312	-0.312	0.000	0.000	0.000	0.000
45	A	64	PRO	0	-0.002	0.000	13.714	-0.757	-0.757	0.000	0.000	0.000	0.000
46	A	65	TYR	0	-0.011	-0.021	14.096	1.911	1.911	0.000	0.000	0.000	0.000
47	A	66	THR	0	0.001	-0.001	13.892	-1.278	-1.278	0.000	0.000	0.000	0.000
48	A	67	GLY	0	-0.027	-0.012	15.211	1.645	1.645	0.000	0.000	0.000	0.000
49	A	68	TYR	0	-0.040	-0.028	15.981	-0.980	-0.980	0.000	0.000	0.000	0.000
50	A	69	ILE	0	0.050	0.046	12.744	0.762	0.762	0.000	0.000	0.000	0.000
51	A	70	VAL	0	-0.072	-0.050	17.041	0.463	0.463	0.000	0.000	0.000	0.000
52	A	71	ARG	1	0.932	0.974	20.550	13.950	13.950	0.000	0.000	0.000	0.000
53	A	72	MET	0	0.020	0.010	22.379	0.414	0.414	0.000	0.000	0.000	0.000
54	A	73	GLY	0	0.012	0.007	25.227	0.146	0.146	0.000	0.000	0.000	0.000
55	A	74	LEU	0	-0.023	-0.005	22.773	-0.337	-0.337	0.000	0.000	0.000	0.000
56	A	75	PRO	0	0.024	0.013	20.932	0.505	0.505	0.000	0.000	0.000	0.000
57	A	76	CYS	0	0.028	0.015	20.664	-0.942	-0.942	0.000	0.000	0.000	0.000
58	A	77	HIS	0	-0.011	-0.022	17.755	0.124	0.124	0.000	0.000	0.000	0.000
59	A	78	ILE	0	0.013	0.012	18.969	-0.173	-0.173	0.000	0.000	0.000	0.000
60	A	79	LEU	0	0.018	0.011	14.692	-0.367	-0.367	0.000	0.000	0.000	0.000
61	A	80	GLY	0	-0.013	0.004	18.511	0.601	0.601	0.000	0.000	0.000	0.000
62	A	81	LEU	0	0.019	0.008	19.994	-0.630	-0.630	0.000	0.000	0.000	0.000
63	A	82	ARG	1	0.900	0.921	21.753	14.413	14.413	0.000	0.000	0.000	0.000
64	A	83	GLN	0	0.011	-0.004	23.907	-0.220	-0.220	0.000	0.000	0.000	0.000
65	A	84	ASP	-1	-0.853	-0.912	24.595	-12.843	-12.843	0.000	0.000	0.000	0.000
66	A	85	ILE	0	0.007	0.003	19.146	0.078	0.078	0.000	0.000	0.000	0.000
67	A	86	ARG	1	0.841	0.916	22.722	12.250	12.250	0.000	0.000	0.000	0.000
68	A	87	ARG	1	0.944	0.978	24.602	11.144	11.144	0.000	0.000	0.000	0.000
69	A	88	ALA	0	-0.048	-0.016	22.855	0.231	0.231	0.000	0.000	0.000	0.000
70	A	89	ILE	0	-0.032	-0.015	19.408	-0.127	-0.127	0.000	0.000	0.000	0.000
71	A	90	GLY	0	-0.023	0.010	22.678	0.085	0.085	0.000	0.000	0.000	0.000
72	A	91	LYS	1	0.799	0.881	20.849	14.605	14.605	0.000	0.000	0.000	0.000
73	A	92	GLN	0	-0.051	-0.035	25.122	0.182	0.182	0.000	0.000	0.000	0.000
74	A	93	PRO	0	-0.015	-0.034	25.705	-0.367	-0.367	0.000	0.000	0.000	0.000
75	A	94	GLY	0	-0.013	0.007	25.740	0.451	0.451	0.000	0.000	0.000	0.000
76	A	95	ASP	-1	-0.816	-0.894	23.891	-11.968	-11.968	0.000	0.000	0.000	0.000
77	A	96	SER	0	-0.051	-0.025	18.521	-0.354	-0.354	0.000	0.000	0.000	0.000
78	A	97	VAL	0	-0.062	-0.023	17.006	0.324	0.324	0.000	0.000	0.000	0.000
79	A	98	TYR	0	0.009	-0.018	8.982	0.410	0.410	0.000	0.000	0.000	0.000
80	A	99	VAL	0	-0.022	-0.012	11.924	0.060	0.060	0.000	0.000	0.000	0.000
81	A	100	THR	0	-0.025	-0.019	7.784	-2.780	-2.780	0.000	0.000	0.000	0.000
82	A	101	LEU	0	-0.005	-0.012	7.764	3.291	3.291	0.000	0.000	0.000	0.000
84	A	103	PRO	0	-0.003	0.003	5.887	4.844	4.844	0.000	0.000	0.000	0.000
85	A	104	LEU	-1	-0.960	-0.971	8.664	-25.235	-25.235	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:20:SER)