FMO DATABASE

FMODB ID: 2N8LR

Calculation Name: 3BDU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BDU

Chain ID: A

ChEMBL ID:

UniProt ID: Q6D8G1

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

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. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-261833.92625
FMO2-HF: Nuclear repulsion	240759.82584
FMO2-HF: Total energy	-21074.10041
FMO2-MP2: Total energy	-21134.592746

3D Structure

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.
-3.325	-0.739	0.032	-1.077	-1.54	0.004

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 : 0 / q_Mulliken : 0.069 / q_NPA : 0.020

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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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	0.039	3.803	-1.950	-0.278	-0.007	-0.822	-0.843	0.004
4	A	5	TYR	0	-0.027	-0.022	5.920	0.567	0.567	0.000	0.000	0.000	0.000
5	A	6	VAL	0	0.012	0.022	9.010	-0.046	-0.046	0.000	0.000	0.000	0.000
6	A	7	LEU	0	-0.023	-0.019	11.487	0.065	0.065	0.000	0.000	0.000	0.000
7	A	8	HIS	0	0.020	0.014	14.766	0.049	0.049	0.000	0.000	0.000	0.000
8	A	9	THR	0	-0.006	-0.057	18.497	0.005	0.005	0.000	0.000	0.000	0.000
9	A	10	ASN	0	-0.061	-0.039	20.759	0.032	0.032	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.775	-0.833	23.023	-0.331	-0.331	0.000	0.000	0.000	0.000
11	A	12	GLY	0	-0.018	-0.001	24.163	0.008	0.008	0.000	0.000	0.000	0.000
12	A	13	ARG	1	0.868	0.938	19.480	0.421	0.421	0.000	0.000	0.000	0.000
13	A	14	THR	0	-0.004	-0.005	16.896	0.002	0.002	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.043	-0.017	12.635	0.012	0.012	0.000	0.000	0.000	0.000
15	A	16	VAL	0	-0.002	0.005	8.727	-0.023	-0.023	0.000	0.000	0.000	0.000
16	A	17	ALA	0	-0.001	-0.007	8.222	0.047	0.047	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.896	-0.942	3.027	-2.573	-2.089	0.022	-0.136	-0.370	0.000
18	A	19	GLY	0	-0.017	-0.014	3.401	-1.666	-1.290	0.015	-0.098	-0.293	0.000
19	A	20	LYS	1	0.874	0.929	4.052	1.525	1.579	0.002	-0.021	-0.034	0.000
20	A	21	PRO	0	0.059	0.036	7.368	0.026	0.026	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.837	0.897	7.749	1.591	1.591	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.005	0.012	12.792	-0.025	-0.025	0.000	0.000	0.000	0.000
23	A	24	ASP	-1	-0.784	-0.864	16.117	-0.552	-0.552	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.934	-0.982	17.306	-0.316	-0.316	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.985	-0.978	20.013	-0.334	-0.334	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.055	-0.047	19.136	0.025	0.025	0.000	0.000	0.000	0.000
27	A	28	GLY	0	-0.020	0.001	21.063	0.026	0.026	0.000	0.000	0.000	0.000
28	A	29	MET	0	-0.093	-0.053	19.215	0.016	0.016	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.029	-0.015	14.096	-0.026	-0.026	0.000	0.000	0.000	0.000
30	A	31	SER	0	0.031	0.022	13.011	-0.056	-0.056	0.000	0.000	0.000	0.000
31	A	32	TYR	0	-0.011	-0.039	9.375	-0.076	-0.076	0.000	0.000	0.000	0.000
32	A	33	THR	0	0.064	0.051	6.300	0.371	0.371	0.000	0.000	0.000	0.000
33	A	34	ASP	-1	-0.788	-0.889	7.604	-1.315	-1.315	0.000	0.000	0.000	0.000
34	A	35	ALA	0	0.001	-0.016	8.109	-0.199	-0.199	0.000	0.000	0.000	0.000
35	A	36	TYR	0	-0.065	-0.030	9.146	0.156	0.156	0.000	0.000	0.000	0.000
36	A	37	GLY	0	0.026	0.022	8.251	0.137	0.137	0.000	0.000	0.000	0.000
37	A	38	GLN	0	-0.066	-0.030	9.287	0.118	0.118	0.000	0.000	0.000	0.000
38	A	39	GLN	0	-0.030	-0.016	10.761	-0.238	-0.238	0.000	0.000	0.000	0.000
39	A	40	GLN	0	-0.031	-0.019	12.232	0.217	0.217	0.000	0.000	0.000	0.000
40	A	41	GLN	0	0.004	-0.011	13.754	-0.042	-0.042	0.000	0.000	0.000	0.000
41	A	42	ILE	0	-0.044	-0.010	16.096	0.054	0.054	0.000	0.000	0.000	0.000
42	A	43	ASN	0	0.075	0.029	18.417	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	44	ARG	1	0.997	0.988	19.439	0.330	0.330	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.871	-0.921	20.929	-0.276	-0.276	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.094	-0.065	21.533	0.035	0.035	0.000	0.000	0.000	0.000
46	A	47	VAL	0	-0.034	-0.012	16.715	-0.030	-0.030	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.940	0.992	19.867	0.267	0.267	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.934	-0.973	18.710	-0.265	-0.265	0.000	0.000	0.000	0.000
49	A	50	MET	0	-0.021	-0.013	12.148	-0.099	-0.099	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.002	0.018	13.862	0.056	0.056	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.903	0.953	6.595	0.577	0.577	0.000	0.000	0.000	0.000
52	A	53	GLY	0	0.007	-0.002	9.281	0.195	0.195	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.989	0.999	9.736	0.190	0.190	0.000	0.000	0.000	0.000

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