FMO DATABASE

FMODB ID: J3539

Calculation Name: 3O6Q-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3O6Q

Chain ID: B

ChEMBL ID:

UniProt ID: O34853

Base Structure: X-ray

Registration Date: 2023-06-20

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	OptAll
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	43
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-142579.501977
FMO2-HF: Nuclear repulsion	125175.757744
FMO2-HF: Total energy	-17403.744233
FMO2-MP2: Total energy	-17454.766911

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(B:9:CYM)

Summations of interaction energy for fragment #1(B:9:CYM)

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.
-97.749	-95.366	-0.011	-1.259	-1.112	0.006

Interaction energy analysis for fragmet #1(B:9:CYM)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.884 / q_NPA : -0.945

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	B	11	PRO	0	-0.006	0.008	3.682	-7.053	-4.670	-0.011	-1.259	-1.112	0.006
4	B	12	ARG	1	0.781	0.864	6.018	-33.823	-33.823	0.000	0.000	0.000	0.000
5	B	13	ALA	0	0.017	0.001	9.590	-0.145	-0.145	0.000	0.000	0.000	0.000
6	B	14	ALA	0	0.035	0.017	12.979	-0.481	-0.481	0.000	0.000	0.000	0.000
7	B	15	LYS	1	0.897	0.955	15.930	-14.062	-14.062	0.000	0.000	0.000	0.000
8	B	16	PRO	0	-0.004	0.018	15.892	-0.525	-0.525	0.000	0.000	0.000	0.000
9	B	17	PHE	0	0.046	0.002	17.975	-0.901	-0.901	0.000	0.000	0.000	0.000
10	B	18	LYS	1	0.970	0.974	18.080	-14.680	-14.680	0.000	0.000	0.000	0.000
11	B	19	ILE	0	0.038	0.018	21.266	-0.590	-0.590	0.000	0.000	0.000	0.000
12	B	20	LEU	0	0.016	0.022	22.309	0.366	0.366	0.000	0.000	0.000	0.000
13	B	21	LYS	1	0.972	0.981	23.597	-12.026	-12.026	0.000	0.000	0.000	0.000
14	B	22	LYS	1	1.002	0.995	24.428	-10.181	-10.181	0.000	0.000	0.000	0.000
15	B	23	ARG	1	0.903	0.955	26.877	-10.150	-10.150	0.000	0.000	0.000	0.000
16	B	24	SER	0	-0.030	-0.028	28.860	-0.110	-0.110	0.000	0.000	0.000	0.000
17	B	25	THR	0	0.032	0.016	32.289	-0.120	-0.120	0.000	0.000	0.000	0.000
18	B	26	THR	0	0.053	0.038	32.584	-0.145	-0.145	0.000	0.000	0.000	0.000
19	B	27	SER	0	-0.034	-0.015	33.886	0.186	0.186	0.000	0.000	0.000	0.000
20	B	28	VAL	0	0.032	0.012	32.834	-0.120	-0.120	0.000	0.000	0.000	0.000
21	B	29	ALA	0	0.034	0.027	35.167	0.039	0.039	0.000	0.000	0.000	0.000
22	B	30	SER	0	0.011	0.005	33.434	0.191	0.191	0.000	0.000	0.000	0.000
23	B	31	TYR	0	0.003	-0.009	30.810	-0.177	-0.177	0.000	0.000	0.000	0.000
24	B	32	GLN	0	-0.001	-0.005	32.949	-0.224	-0.224	0.000	0.000	0.000	0.000
25	B	33	VAL	0	0.003	0.018	33.094	0.073	0.073	0.000	0.000	0.000	0.000
26	B	34	SER	0	0.015	0.007	35.223	-0.343	-0.343	0.000	0.000	0.000	0.000
27	B	35	PRO	0	0.087	0.006	37.625	0.072	0.072	0.000	0.000	0.000	0.000
28	B	36	HIS	0	0.010	0.007	37.811	-0.182	-0.182	0.000	0.000	0.000	0.000
29	B	37	THR	0	0.037	0.021	33.568	0.025	0.025	0.000	0.000	0.000	0.000
30	B	38	ALA	0	0.000	0.007	36.369	0.101	0.101	0.000	0.000	0.000	0.000
31	B	39	ARG	1	0.949	0.983	38.082	-7.284	-7.284	0.000	0.000	0.000	0.000
32	B	40	ILE	0	0.036	0.026	35.160	-0.005	-0.005	0.000	0.000	0.000	0.000
33	B	41	PHE	0	-0.009	-0.007	31.168	0.087	0.087	0.000	0.000	0.000	0.000
34	B	42	LYS	1	0.796	0.874	35.827	-8.149	-8.149	0.000	0.000	0.000	0.000
35	B	43	GLU	-1	-0.810	-0.876	39.108	7.183	7.183	0.000	0.000	0.000	0.000
36	B	44	ASN	0	-0.051	-0.039	35.267	0.005	0.005	0.000	0.000	0.000	0.000
37	B	45	GLU	-1	-0.829	-0.885	36.335	8.317	8.317	0.000	0.000	0.000	0.000
38	B	46	ARG	1	0.792	0.866	37.283	-7.230	-7.230	0.000	0.000	0.000	0.000
39	B	47	LEU	0	0.004	0.004	39.888	-0.071	-0.071	0.000	0.000	0.000	0.000
40	B	48	ILE	0	-0.076	-0.035	33.974	0.051	0.051	0.000	0.000	0.000	0.000
41	B	49	ASP	-1	-0.959	-0.979	38.264	7.643	7.643	0.000	0.000	0.000	0.000
42	B	50	GLU	-1	-0.889	-0.948	40.461	6.919	6.919	0.000	0.000	0.000	0.000
43	B	51	TYR	0	-0.107	-0.028	39.953	-0.230	-0.230	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:9:CYM)