FMO DATABASE

FMODB ID: G5171

Calculation Name: 2RF4-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2RF4

Chain ID: F

ChEMBL ID:

UniProt ID: P50106

Base Structure: X-ray

Registration Date: 2023-09-24

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

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	60
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-284147.026456
FMO2-HF: Nuclear repulsion	260718.597778
FMO2-HF: Total energy	-23428.428677
FMO2-MP2: Total energy	-23498.347656

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(F:17:ASN)

Summations of interaction energy for fragment #1(F:17:ASN)

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.
0.945	2.7	-0.015	-0.795	-0.944	0.003

Interaction energy analysis for fragmet #1(F:17:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.004

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	F	19	PRO	0	-0.010	-0.001	3.880	0.358	2.113	-0.015	-0.795	-0.944	0.003
4	F	20	VAL	0	0.017	0.011	6.064	0.228	0.228	0.000	0.000	0.000	0.000
5	F	21	VAL	0	-0.005	-0.001	8.948	0.370	0.370	0.000	0.000	0.000	0.000
6	F	22	ILE	0	-0.003	-0.009	11.961	0.002	0.002	0.000	0.000	0.000	0.000
7	F	23	HIS	0	0.003	-0.002	14.877	0.097	0.097	0.000	0.000	0.000	0.000
8	F	24	ALA	0	0.002	0.006	18.573	-0.002	-0.002	0.000	0.000	0.000	0.000
9	F	25	THR	0	0.008	0.004	21.655	0.003	0.003	0.000	0.000	0.000	0.000
10	F	26	GLN	0	-0.028	-0.018	23.991	0.007	0.007	0.000	0.000	0.000	0.000
11	F	27	LEU	0	0.010	0.013	25.117	0.012	0.012	0.000	0.000	0.000	0.000
12	F	28	PRO	0	-0.013	-0.030	23.931	-0.007	-0.007	0.000	0.000	0.000	0.000
13	F	29	GLN	0	-0.014	0.008	26.455	0.007	0.007	0.000	0.000	0.000	0.000
14	F	30	HIS	0	-0.012	-0.002	28.609	0.007	0.007	0.000	0.000	0.000	0.000
15	F	31	VAL	0	0.010	0.014	29.478	-0.014	-0.014	0.000	0.000	0.000	0.000
16	F	32	SER	0	-0.035	-0.059	32.000	0.013	0.013	0.000	0.000	0.000	0.000
17	F	33	THR	0	0.016	-0.024	33.609	0.006	0.006	0.000	0.000	0.000	0.000
18	F	34	ASP	-1	-0.916	-0.950	35.261	0.050	0.050	0.000	0.000	0.000	0.000
19	F	35	GLU	-1	-0.809	-0.867	32.326	0.047	0.047	0.000	0.000	0.000	0.000
20	F	36	VAL	0	-0.007	-0.001	28.439	-0.004	-0.004	0.000	0.000	0.000	0.000
21	F	37	LEU	0	0.006	0.005	30.341	0.004	0.004	0.000	0.000	0.000	0.000
22	F	38	GLN	0	-0.003	-0.006	32.656	-0.010	-0.010	0.000	0.000	0.000	0.000
23	F	39	PHE	0	-0.022	-0.009	23.557	-0.007	-0.007	0.000	0.000	0.000	0.000
24	F	40	LEU	0	-0.016	-0.013	26.670	-0.003	-0.003	0.000	0.000	0.000	0.000
25	F	41	GLU	-1	-0.774	-0.852	28.875	0.048	0.048	0.000	0.000	0.000	0.000
26	F	42	SER	0	0.015	0.009	29.645	-0.008	-0.008	0.000	0.000	0.000	0.000
27	F	43	PHE	0	-0.036	-0.016	20.429	-0.010	-0.010	0.000	0.000	0.000	0.000
28	F	44	ILE	0	-0.043	-0.036	25.686	0.001	0.001	0.000	0.000	0.000	0.000
29	F	45	ASP	-1	-0.930	-0.959	27.559	-0.022	-0.022	0.000	0.000	0.000	0.000
30	F	46	GLU	-1	-0.876	-0.927	24.595	-0.095	-0.095	0.000	0.000	0.000	0.000
31	F	47	LYS	1	0.740	0.845	21.007	0.056	0.056	0.000	0.000	0.000	0.000
32	F	48	GLU	-1	-0.810	-0.867	24.424	0.069	0.069	0.000	0.000	0.000	0.000
33	F	49	ASN	0	0.000	0.013	27.196	0.002	0.002	0.000	0.000	0.000	0.000
34	F	50	ILE	0	-0.029	-0.016	27.308	-0.005	-0.005	0.000	0.000	0.000	0.000
35	F	51	ILE	0	-0.092	-0.053	24.508	-0.010	-0.010	0.000	0.000	0.000	0.000
36	F	52	ASP	-1	-0.828	-0.908	23.894	-0.039	-0.039	0.000	0.000	0.000	0.000
37	F	78	ILE	0	-0.080	-0.048	16.309	-0.037	-0.037	0.000	0.000	0.000	0.000
38	F	79	ASP	-1	-0.814	-0.887	20.027	0.029	0.029	0.000	0.000	0.000	0.000
39	F	80	THR	0	-0.036	-0.042	14.455	0.024	0.024	0.000	0.000	0.000	0.000
40	F	81	ASN	0	-0.060	-0.028	16.012	0.055	0.055	0.000	0.000	0.000	0.000
41	F	82	LEU	0	0.064	0.051	18.025	0.053	0.053	0.000	0.000	0.000	0.000
42	F	83	SER	0	0.082	0.033	19.634	0.009	0.009	0.000	0.000	0.000	0.000
43	F	84	SER	0	-0.034	-0.019	20.753	-0.004	-0.004	0.000	0.000	0.000	0.000
44	F	85	SER	0	-0.010	-0.017	19.387	0.029	0.029	0.000	0.000	0.000	0.000
45	F	86	ILE	0	0.046	0.028	21.818	0.007	0.007	0.000	0.000	0.000	0.000
46	F	87	SER	0	-0.025	-0.006	24.665	-0.006	-0.006	0.000	0.000	0.000	0.000
47	F	88	GLN	0	-0.047	-0.029	22.769	0.011	0.011	0.000	0.000	0.000	0.000
48	F	89	LEU	0	0.043	0.016	22.511	-0.002	-0.002	0.000	0.000	0.000	0.000
49	F	90	LYS	1	0.821	0.887	26.389	-0.084	-0.084	0.000	0.000	0.000	0.000
50	F	91	ARG	1	0.867	0.938	28.786	-0.195	-0.195	0.000	0.000	0.000	0.000
51	F	92	ILE	0	0.026	0.017	25.826	-0.003	-0.003	0.000	0.000	0.000	0.000
52	F	93	GLN	0	0.036	0.006	29.994	-0.011	-0.011	0.000	0.000	0.000	0.000
53	F	94	ARG	1	0.885	0.933	31.917	-0.139	-0.139	0.000	0.000	0.000	0.000
54	F	95	ASP	-1	-0.952	-0.965	33.085	0.153	0.153	0.000	0.000	0.000	0.000
55	F	96	PHE	0	0.047	0.002	31.237	-0.007	-0.007	0.000	0.000	0.000	0.000
56	F	97	LYS	1	0.746	0.860	34.982	-0.072	-0.072	0.000	0.000	0.000	0.000
57	F	98	GLY	0	-0.042	-0.012	37.619	-0.008	-0.008	0.000	0.000	0.000	0.000
58	F	99	LEU	0	-0.026	0.005	34.943	0.000	0.000	0.000	0.000	0.000	0.000
59	F	100	PRO	0	-0.033	-0.011	39.423	-0.008	-0.008	0.000	0.000	0.000	0.000
60	F	101	PRO	0	-0.021	-0.005	42.289	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:17:ASN)