FMO DATABASE

FMODB ID: LZJJ9

Calculation Name: 2RF4-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2RF4

Chain ID: B

ChEMBL ID:

UniProt ID: P50106

Base Structure: X-ray

Registration Date: 2023-06-21

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	OptHSide
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	61
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-291137.572142
FMO2-HF: Nuclear repulsion	267346.4903
FMO2-HF: Total energy	-23791.081843
FMO2-MP2: Total energy	-23862.209683

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(B:16:LEU)

Summations of interaction energy for fragment #1(B:16:LEU)

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.
-7.807	-0.238	0.575	-3.745	-4.4	-0.015

Interaction energy analysis for fragmet #1(B:16:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.008

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

Sort

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	18	THR	0	0.029	0.050	2.345	-4.917	1.135	0.430	-3.098	-3.385	-0.009
4	B	19	PRO	0	-0.023	-0.003	3.132	-2.370	-0.960	0.146	-0.642	-0.914	-0.006
5	B	20	VAL	0	0.044	0.017	4.778	-0.299	-0.192	-0.001	-0.005	-0.101	0.000
6	B	21	VAL	0	-0.031	-0.018	6.317	0.230	0.230	0.000	0.000	0.000	0.000
7	B	22	ILE	0	0.007	-0.005	8.641	-0.046	-0.046	0.000	0.000	0.000	0.000
8	B	23	HIS	0	0.004	0.003	11.879	0.058	0.058	0.000	0.000	0.000	0.000
9	B	24	ALA	0	-0.006	0.010	15.666	-0.014	-0.014	0.000	0.000	0.000	0.000
10	B	25	THR	0	0.001	-0.008	18.344	0.005	0.005	0.000	0.000	0.000	0.000
11	B	26	GLN	0	-0.001	-0.009	20.877	0.010	0.010	0.000	0.000	0.000	0.000
12	B	27	LEU	0	-0.014	0.008	21.878	0.004	0.004	0.000	0.000	0.000	0.000
13	B	28	PRO	0	-0.011	-0.025	20.840	-0.005	-0.005	0.000	0.000	0.000	0.000
14	B	29	GLN	0	0.014	0.021	23.311	0.005	0.005	0.000	0.000	0.000	0.000
15	B	30	HIS	0	-0.023	-0.012	25.375	-0.003	-0.003	0.000	0.000	0.000	0.000
16	B	31	VAL	0	0.011	0.009	25.430	-0.003	-0.003	0.000	0.000	0.000	0.000
17	B	32	SER	0	-0.030	-0.051	28.072	0.006	0.006	0.000	0.000	0.000	0.000
18	B	33	THR	0	0.041	-0.009	30.045	-0.002	-0.002	0.000	0.000	0.000	0.000
19	B	34	ASP	-1	-0.920	-0.967	31.291	-0.025	-0.025	0.000	0.000	0.000	0.000
20	B	35	GLU	-1	-0.828	-0.865	28.394	-0.030	-0.030	0.000	0.000	0.000	0.000
21	B	36	VAL	0	-0.030	-0.010	24.824	-0.006	-0.006	0.000	0.000	0.000	0.000
22	B	37	LEU	0	0.003	-0.007	26.867	-0.005	-0.005	0.000	0.000	0.000	0.000
23	B	38	GLN	0	0.005	0.005	29.281	-0.006	-0.006	0.000	0.000	0.000	0.000
24	B	39	PHE	0	-0.028	-0.016	19.693	-0.006	-0.006	0.000	0.000	0.000	0.000
25	B	40	LEU	0	-0.006	-0.015	22.643	-0.008	-0.008	0.000	0.000	0.000	0.000
26	B	41	GLU	-1	-0.817	-0.862	24.945	-0.050	-0.050	0.000	0.000	0.000	0.000
27	B	42	SER	0	0.036	0.007	25.526	-0.004	-0.004	0.000	0.000	0.000	0.000
28	B	43	PHE	0	-0.049	-0.017	16.458	-0.012	-0.012	0.000	0.000	0.000	0.000
29	B	44	ILE	0	-0.046	-0.049	21.626	-0.009	-0.009	0.000	0.000	0.000	0.000
30	B	45	ASP	-1	-0.933	-0.961	23.239	-0.092	-0.092	0.000	0.000	0.000	0.000
31	B	46	GLU	-1	-0.878	-0.921	20.639	-0.166	-0.166	0.000	0.000	0.000	0.000
32	B	47	LYS	1	0.786	0.872	17.116	0.181	0.181	0.000	0.000	0.000	0.000
33	B	48	GLU	-1	-0.820	-0.875	20.359	-0.073	-0.073	0.000	0.000	0.000	0.000
34	B	49	ASN	0	-0.030	-0.001	23.012	0.010	0.010	0.000	0.000	0.000	0.000
35	B	50	ILE	0	-0.008	-0.011	22.666	-0.010	-0.010	0.000	0.000	0.000	0.000
36	B	51	ILE	0	-0.071	-0.044	21.377	-0.004	-0.004	0.000	0.000	0.000	0.000
37	B	52	ASP	-1	-0.849	-0.914	19.923	-0.167	-0.167	0.000	0.000	0.000	0.000
38	B	78	ILE	0	-0.102	-0.055	12.634	-0.033	-0.033	0.000	0.000	0.000	0.000
39	B	79	ASP	-1	-0.810	-0.890	16.602	-0.173	-0.173	0.000	0.000	0.000	0.000
40	B	80	THR	0	0.018	-0.009	10.609	-0.023	-0.023	0.000	0.000	0.000	0.000
41	B	81	ASN	0	-0.036	-0.009	13.431	0.008	0.008	0.000	0.000	0.000	0.000
42	B	82	LEU	0	0.038	0.030	13.772	0.031	0.031	0.000	0.000	0.000	0.000
43	B	83	SER	0	0.035	0.013	15.820	0.020	0.020	0.000	0.000	0.000	0.000
44	B	84	SER	0	-0.049	-0.034	17.568	0.012	0.012	0.000	0.000	0.000	0.000
45	B	85	SER	0	0.012	0.000	15.443	0.019	0.019	0.000	0.000	0.000	0.000
46	B	86	ILE	0	0.048	0.029	17.850	0.015	0.015	0.000	0.000	0.000	0.000
47	B	87	SER	0	-0.041	-0.018	20.412	0.012	0.012	0.000	0.000	0.000	0.000
48	B	88	GLN	0	-0.024	-0.021	19.398	0.009	0.009	0.000	0.000	0.000	0.000
49	B	89	LEU	0	0.066	0.035	18.656	0.007	0.007	0.000	0.000	0.000	0.000
50	B	90	LYS	1	0.806	0.888	22.544	0.060	0.060	0.000	0.000	0.000	0.000
51	B	91	ARG	1	0.859	0.922	25.118	-0.002	-0.002	0.000	0.000	0.000	0.000
52	B	92	ILE	0	0.001	0.004	22.062	0.004	0.004	0.000	0.000	0.000	0.000
53	B	93	GLN	0	0.016	-0.012	26.149	0.002	0.002	0.000	0.000	0.000	0.000
54	B	94	ARG	1	0.903	0.951	28.001	0.001	0.001	0.000	0.000	0.000	0.000
55	B	95	ASP	-1	-0.961	-0.970	29.298	0.016	0.016	0.000	0.000	0.000	0.000
56	B	96	PHE	0	0.060	0.001	27.286	0.001	0.001	0.000	0.000	0.000	0.000
57	B	97	LYS	1	0.776	0.892	31.340	0.032	0.032	0.000	0.000	0.000	0.000
58	B	98	GLY	0	-0.034	-0.007	33.810	-0.001	-0.001	0.000	0.000	0.000	0.000
59	B	99	LEU	0	-0.039	-0.001	31.358	0.003	0.003	0.000	0.000	0.000	0.000
60	B	100	PRO	0	-0.027	-0.011	35.697	-0.002	-0.002	0.000	0.000	0.000	0.000
61	B	101	PRO	0	-0.010	0.002	37.208	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:16:LEU)