FMO DATABASE

FMODB ID: 6Y8GZ

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	OptHSide
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	-261972.309458
FMO2-HF: Nuclear repulsion	240897.936159
FMO2-HF: Total energy	-21074.373299
FMO2-MP2: Total energy	-21134.827008

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.
-3.303	-0.927	0.033	-1.013	-1.394	0.003

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 : 0.043 / q_NPA : 0.014

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	0.093	0.048	3.763	-3.943	-2.399	-0.004	-0.768	-0.771	0.003
4	A	5	TYR	0	-0.008	-0.013	5.785	1.242	1.242	0.000	0.000	0.000	0.000
5	A	6	VAL	0	0.005	0.016	8.892	-0.085	-0.085	0.000	0.000	0.000	0.000
6	A	7	LEU	0	-0.015	-0.010	11.417	0.111	0.111	0.000	0.000	0.000	0.000
7	A	8	HIS	0	0.019	0.010	14.646	0.035	0.035	0.000	0.000	0.000	0.000
8	A	9	THR	0	0.019	-0.032	18.350	0.014	0.014	0.000	0.000	0.000	0.000
9	A	10	ASN	0	-0.068	-0.043	20.651	0.013	0.013	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.780	-0.823	22.914	-0.304	-0.304	0.000	0.000	0.000	0.000
11	A	12	GLY	0	-0.014	0.003	23.813	0.005	0.005	0.000	0.000	0.000	0.000
12	A	13	ARG	1	0.829	0.895	19.528	0.366	0.366	0.000	0.000	0.000	0.000
13	A	14	THR	0	0.006	0.001	16.361	0.003	0.003	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.038	-0.020	12.615	0.004	0.004	0.000	0.000	0.000	0.000
15	A	16	VAL	0	-0.011	0.002	8.215	-0.047	-0.047	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.004	-0.006	8.142	0.176	0.176	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.911	-0.945	3.166	-4.128	-3.708	0.014	-0.121	-0.313	0.000
18	A	19	GLY	0	-0.001	-0.007	3.340	1.090	1.450	0.020	-0.105	-0.275	0.000
19	A	20	LYS	1	0.880	0.930	3.975	0.822	0.874	0.003	-0.019	-0.035	0.000
20	A	21	PRO	0	0.030	0.024	7.321	0.241	0.241	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.849	0.908	8.110	0.512	0.512	0.000	0.000	0.000	0.000
22	A	23	VAL	0	-0.001	0.006	12.765	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	24	ASP	-1	-0.804	-0.880	16.086	-0.144	-0.144	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.928	-0.973	17.291	-0.114	-0.114	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.986	-0.977	20.017	-0.053	-0.053	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.053	-0.051	19.472	0.000	0.000	0.000	0.000	0.000	0.000
27	A	28	GLY	0	-0.017	0.003	21.040	0.001	0.001	0.000	0.000	0.000	0.000
28	A	29	MET	0	-0.075	-0.043	19.308	-0.018	-0.018	0.000	0.000	0.000	0.000
29	A	30	ILE	0	-0.039	-0.024	13.881	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	31	SER	0	0.037	0.021	13.720	-0.037	-0.037	0.000	0.000	0.000	0.000
31	A	32	TYR	0	-0.020	-0.043	9.705	-0.066	-0.066	0.000	0.000	0.000	0.000
32	A	33	THR	0	0.064	0.051	7.073	0.174	0.174	0.000	0.000	0.000	0.000
33	A	34	ASP	-1	-0.789	-0.888	7.930	-1.152	-1.152	0.000	0.000	0.000	0.000
34	A	35	ALA	0	0.003	-0.013	7.842	-0.075	-0.075	0.000	0.000	0.000	0.000
35	A	36	TYR	0	-0.053	-0.021	8.917	0.052	0.052	0.000	0.000	0.000	0.000
36	A	37	GLY	0	0.019	0.018	8.771	0.165	0.165	0.000	0.000	0.000	0.000
37	A	38	GLN	0	-0.057	-0.022	9.756	0.200	0.200	0.000	0.000	0.000	0.000
38	A	39	GLN	0	-0.030	-0.017	11.612	-0.095	-0.095	0.000	0.000	0.000	0.000
39	A	40	GLN	0	-0.042	-0.027	12.959	0.087	0.087	0.000	0.000	0.000	0.000
40	A	41	GLN	0	0.006	-0.007	14.432	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	42	ILE	0	-0.036	-0.008	16.203	0.010	0.010	0.000	0.000	0.000	0.000
42	A	43	ASN	0	0.043	-0.007	18.721	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	44	ARG	1	0.994	0.995	19.475	0.183	0.183	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.851	-0.899	20.856	-0.209	-0.209	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.081	-0.060	21.788	0.005	0.005	0.000	0.000	0.000	0.000
46	A	47	VAL	0	-0.022	-0.007	16.545	-0.038	-0.038	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.865	0.948	19.769	0.307	0.307	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.860	-0.924	18.614	-0.311	-0.311	0.000	0.000	0.000	0.000
49	A	50	MET	0	-0.015	-0.013	12.107	-0.096	-0.096	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.003	0.015	13.767	0.061	0.061	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.902	0.950	6.828	0.832	0.832	0.000	0.000	0.000	0.000
52	A	53	GLY	0	0.020	0.007	9.382	0.266	0.266	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.959	0.983	9.844	0.656	0.656	0.000	0.000	0.000	0.000

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