FMO DATABASE

FMODB ID: 2M86R

Calculation Name: 3OB9-D-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3OB9

Chain ID: D

ChEMBL ID:

UniProt ID: Q8N5Y2

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	93
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-665479.224731
FMO2-HF: Nuclear repulsion	628022.808299
FMO2-HF: Total energy	-37456.416432
FMO2-MP2: Total energy	-37566.9628

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:0:GLY)

Summations of interaction energy for fragment #1(A:0: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.
33.262	34.117	-0.008	-0.309	-0.538	-0.001

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.885 / q_NPA : 0.929

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	2	SER	0	0.073	0.044	3.840	2.895	3.750	-0.008	-0.309	-0.538	-0.001
4	A	3	ALA	0	0.090	0.037	6.774	0.954	0.954	0.000	0.000	0.000	0.000
5	A	4	SER	0	-0.054	-0.033	10.094	-0.395	-0.395	0.000	0.000	0.000	0.000
6	A	5	GLU	-1	-0.888	-0.954	13.249	-17.203	-17.203	0.000	0.000	0.000	0.000
7	A	6	GLY	0	0.013	0.012	16.553	0.556	0.556	0.000	0.000	0.000	0.000
8	A	7	MET	0	-0.096	-0.017	10.979	-0.267	-0.267	0.000	0.000	0.000	0.000
9	A	8	LYS	1	0.939	0.959	15.975	15.085	15.085	0.000	0.000	0.000	0.000
10	A	9	PHE	0	0.035	0.015	10.548	-0.907	-0.907	0.000	0.000	0.000	0.000
11	A	10	LYS	1	0.820	0.932	16.333	14.704	14.704	0.000	0.000	0.000	0.000
12	A	11	PHE	0	-0.035	-0.020	17.599	1.083	1.083	0.000	0.000	0.000	0.000
13	A	12	HIS	0	-0.008	-0.009	16.540	-0.614	-0.614	0.000	0.000	0.000	0.000
14	A	13	SER	0	0.042	0.007	13.779	0.465	0.465	0.000	0.000	0.000	0.000
15	A	14	GLY	0	-0.033	-0.022	16.711	0.627	0.627	0.000	0.000	0.000	0.000
16	A	15	GLU	-1	-0.864	-0.927	20.045	-13.285	-13.285	0.000	0.000	0.000	0.000
17	A	16	LYS	1	0.806	0.895	21.821	10.549	10.549	0.000	0.000	0.000	0.000
18	A	17	VAL	0	-0.020	-0.015	20.791	0.190	0.190	0.000	0.000	0.000	0.000
19	A	18	LEU	0	-0.047	-0.019	24.066	0.369	0.369	0.000	0.000	0.000	0.000
20	A	19	CYS	0	-0.006	0.007	21.106	-0.523	-0.523	0.000	0.000	0.000	0.000
21	A	20	PHE	0	-0.020	-0.019	23.278	0.709	0.709	0.000	0.000	0.000	0.000
22	A	21	GLU	-1	-0.828	-0.900	23.462	-11.914	-11.914	0.000	0.000	0.000	0.000
23	A	22	PRO	0	-0.017	0.002	20.879	-0.082	-0.082	0.000	0.000	0.000	0.000
24	A	23	ASP	-1	-0.771	-0.843	22.716	-11.466	-11.466	0.000	0.000	0.000	0.000
25	A	24	PRO	0	-0.019	-0.015	24.022	0.430	0.430	0.000	0.000	0.000	0.000
26	A	25	THR	0	-0.086	-0.069	26.871	0.514	0.514	0.000	0.000	0.000	0.000
27	A	26	LYS	1	0.836	0.913	29.106	10.705	10.705	0.000	0.000	0.000	0.000
28	A	27	ALA	0	0.030	0.019	30.579	-0.065	-0.065	0.000	0.000	0.000	0.000
29	A	28	ARG	1	0.951	0.974	28.055	9.932	9.932	0.000	0.000	0.000	0.000
30	A	29	VAL	0	0.024	0.015	29.001	0.294	0.294	0.000	0.000	0.000	0.000
31	A	30	LEU	0	-0.018	-0.016	26.389	-0.307	-0.307	0.000	0.000	0.000	0.000
32	A	31	TYR	0	-0.017	-0.031	25.529	0.521	0.521	0.000	0.000	0.000	0.000
33	A	32	ASP	-1	-0.842	-0.914	26.033	-10.685	-10.685	0.000	0.000	0.000	0.000
34	A	33	ALA	0	-0.011	-0.003	21.931	-0.095	-0.095	0.000	0.000	0.000	0.000
35	A	34	LYS	1	0.922	0.972	20.379	13.824	13.824	0.000	0.000	0.000	0.000
36	A	35	ILE	0	0.015	0.034	15.129	-0.430	-0.430	0.000	0.000	0.000	0.000
37	A	36	VAL	0	-0.063	-0.042	14.939	0.676	0.676	0.000	0.000	0.000	0.000
38	A	37	ASP	-1	-0.851	-0.937	9.360	-28.825	-28.825	0.000	0.000	0.000	0.000
39	A	38	VAL	0	-0.039	-0.013	10.797	1.125	1.125	0.000	0.000	0.000	0.000
40	A	39	ILE	0	-0.001	0.009	5.376	-2.844	-2.844	0.000	0.000	0.000	0.000
41	A	40	VAL	0	-0.058	-0.031	6.345	3.486	3.486	0.000	0.000	0.000	0.000
42	A	41	GLY	0	0.087	0.043	5.666	-6.795	-6.795	0.000	0.000	0.000	0.000
43	A	42	LYS	1	0.814	0.888	6.805	36.896	36.896	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.688	-0.811	9.803	-18.747	-18.747	0.000	0.000	0.000	0.000
45	A	44	GLU	-1	-0.885	-0.952	13.486	-19.118	-19.118	0.000	0.000	0.000	0.000
46	A	45	LYS	1	0.833	0.919	15.460	16.143	16.143	0.000	0.000	0.000	0.000
47	A	46	GLY	0	0.017	0.021	11.921	0.058	0.058	0.000	0.000	0.000	0.000
48	A	47	ARG	1	0.808	0.875	11.570	15.658	15.658	0.000	0.000	0.000	0.000
49	A	48	LYS	1	0.860	0.918	8.429	32.853	32.853	0.000	0.000	0.000	0.000
50	A	49	ILE	0	0.015	0.021	10.268	2.334	2.334	0.000	0.000	0.000	0.000
51	A	50	PRO	0	0.002	0.001	10.314	-2.740	-2.740	0.000	0.000	0.000	0.000
52	A	51	GLU	-1	-0.917	-0.952	9.228	-26.610	-26.610	0.000	0.000	0.000	0.000
53	A	52	TYR	0	-0.036	-0.063	10.889	-1.244	-1.244	0.000	0.000	0.000	0.000
54	A	53	LEU	0	-0.019	0.011	12.005	0.735	0.735	0.000	0.000	0.000	0.000
55	A	54	ILE	0	-0.003	-0.015	13.654	0.826	0.826	0.000	0.000	0.000	0.000
56	A	55	HIS	0	-0.080	-0.049	17.453	0.412	0.412	0.000	0.000	0.000	0.000
57	A	56	PHE	0	0.034	0.004	19.799	0.336	0.336	0.000	0.000	0.000	0.000
58	A	57	ASN	0	0.027	-0.011	23.643	-0.151	-0.151	0.000	0.000	0.000	0.000
59	A	58	GLY	0	-0.005	-0.002	26.567	0.330	0.330	0.000	0.000	0.000	0.000
60	A	59	TRP	0	-0.030	0.007	25.251	0.247	0.247	0.000	0.000	0.000	0.000
61	A	60	ASN	0	0.015	-0.010	25.034	-0.231	-0.231	0.000	0.000	0.000	0.000
62	A	61	ARG	1	0.898	0.928	18.719	15.173	15.173	0.000	0.000	0.000	0.000
63	A	62	SER	0	-0.010	0.007	20.055	-0.521	-0.521	0.000	0.000	0.000	0.000
64	A	63	TRP	0	-0.031	-0.021	21.244	-0.201	-0.201	0.000	0.000	0.000	0.000
65	A	64	ASP	-1	-0.746	-0.846	17.444	-15.344	-15.344	0.000	0.000	0.000	0.000
66	A	65	ARG	1	0.881	0.942	15.460	15.279	15.279	0.000	0.000	0.000	0.000
67	A	66	TRP	0	0.000	0.004	9.076	0.041	0.041	0.000	0.000	0.000	0.000
68	A	67	ALA	0	0.008	0.014	13.476	1.059	1.059	0.000	0.000	0.000	0.000
69	A	68	ALA	0	0.069	0.031	14.137	-1.167	-1.167	0.000	0.000	0.000	0.000
70	A	69	GLU	-1	-0.778	-0.886	15.487	-16.620	-16.620	0.000	0.000	0.000	0.000
71	A	70	ASP	-1	-0.916	-0.960	17.416	-14.022	-14.022	0.000	0.000	0.000	0.000
72	A	71	HIS	0	-0.052	-0.024	17.908	0.381	0.381	0.000	0.000	0.000	0.000
73	A	72	VAL	0	0.017	0.014	18.230	0.521	0.521	0.000	0.000	0.000	0.000
74	A	73	LEU	0	-0.021	-0.011	21.289	0.119	0.119	0.000	0.000	0.000	0.000
75	A	74	ARG	1	1.027	1.009	24.139	12.043	12.043	0.000	0.000	0.000	0.000
76	A	75	ASP	-1	-0.743	-0.845	25.580	-10.117	-10.117	0.000	0.000	0.000	0.000
77	A	76	THR	0	0.011	-0.001	28.215	0.193	0.193	0.000	0.000	0.000	0.000
78	A	77	ASP	-1	-0.828	-0.932	31.025	-8.933	-8.933	0.000	0.000	0.000	0.000
79	A	78	GLU	-1	-0.984	-0.984	32.316	-9.297	-9.297	0.000	0.000	0.000	0.000
80	A	79	ASN	0	0.023	0.004	28.937	0.102	0.102	0.000	0.000	0.000	0.000
81	A	80	ARG	1	0.889	0.928	31.005	9.692	9.692	0.000	0.000	0.000	0.000
82	A	81	ARG	1	0.932	0.972	33.223	8.055	8.055	0.000	0.000	0.000	0.000
83	A	82	LEU	0	-0.031	-0.014	30.237	0.230	0.230	0.000	0.000	0.000	0.000
84	A	83	GLN	0	0.001	-0.003	30.248	0.336	0.336	0.000	0.000	0.000	0.000
85	A	84	ARG	1	0.945	0.966	32.718	8.337	8.337	0.000	0.000	0.000	0.000
86	A	85	LYS	1	0.901	0.945	36.421	8.067	8.067	0.000	0.000	0.000	0.000
87	A	86	LEU	0	-0.022	-0.008	30.730	0.180	0.180	0.000	0.000	0.000	0.000
88	A	87	ALA	0	0.038	0.019	34.312	0.051	0.051	0.000	0.000	0.000	0.000
89	A	88	ARG	1	0.883	0.938	35.543	7.676	7.676	0.000	0.000	0.000	0.000
90	A	89	LYS	1	0.962	0.982	37.139	8.318	8.318	0.000	0.000	0.000	0.000
91	A	90	ALA	0	-0.001	0.006	34.632	0.001	0.001	0.000	0.000	0.000	0.000
92	A	91	VAL	0	-0.081	-0.031	36.675	0.003	0.003	0.000	0.000	0.000	0.000
93	A	92	ALA	-1	-0.934	-0.950	39.428	-7.351	-7.351	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)