FMO DATABASE

FMODB ID: 94GG2

Calculation Name: 2RF4-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-290839.47251
FMO2-HF: Nuclear repulsion	267048.051455
FMO2-HF: Total energy	-23791.421055
FMO2-MP2: Total energy	-23862.471288

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: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.
-6.318	-0.793	1.153	-2.754	-3.924	-0.014

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 : 0.038 / q_NPA : 0.007

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	0.001	0.005	2.746	-1.928	1.452	0.185	-1.639	-1.926	-0.001
4	B	19	PRO	0	-0.016	0.000	2.650	-3.963	-1.956	0.968	-1.120	-1.855	-0.013
5	B	20	VAL	0	0.024	0.005	4.159	-0.293	-0.155	0.000	0.005	-0.143	0.000
6	B	21	VAL	0	-0.026	-0.008	6.035	0.275	0.275	0.000	0.000	0.000	0.000
7	B	22	ILE	0	0.012	-0.003	8.257	-0.046	-0.046	0.000	0.000	0.000	0.000
8	B	23	HIS	0	0.007	-0.001	11.626	0.072	0.072	0.000	0.000	0.000	0.000
9	B	24	ALA	0	0.006	0.006	15.454	-0.012	-0.012	0.000	0.000	0.000	0.000
10	B	25	THR	0	-0.002	-0.002	18.050	0.011	0.011	0.000	0.000	0.000	0.000
11	B	26	GLN	0	-0.019	-0.013	20.406	0.012	0.012	0.000	0.000	0.000	0.000
12	B	27	LEU	0	0.007	0.011	21.609	0.002	0.002	0.000	0.000	0.000	0.000
13	B	28	PRO	0	-0.019	-0.029	20.498	-0.005	-0.005	0.000	0.000	0.000	0.000
14	B	29	GLN	0	-0.011	0.008	22.970	0.008	0.008	0.000	0.000	0.000	0.000
15	B	30	HIS	0	-0.011	-0.003	25.041	-0.002	-0.002	0.000	0.000	0.000	0.000
16	B	31	VAL	0	0.007	0.015	25.743	-0.004	-0.004	0.000	0.000	0.000	0.000
17	B	32	SER	0	-0.041	-0.061	28.389	0.007	0.007	0.000	0.000	0.000	0.000
18	B	33	THR	0	0.024	-0.017	29.882	-0.001	-0.001	0.000	0.000	0.000	0.000
19	B	34	ASP	-1	-0.921	-0.951	31.426	-0.030	-0.030	0.000	0.000	0.000	0.000
20	B	35	GLU	-1	-0.801	-0.868	28.430	-0.037	-0.037	0.000	0.000	0.000	0.000
21	B	36	VAL	0	-0.008	-0.002	24.680	-0.007	-0.007	0.000	0.000	0.000	0.000
22	B	37	LEU	0	0.015	0.012	26.622	-0.003	-0.003	0.000	0.000	0.000	0.000
23	B	38	GLN	0	-0.007	-0.005	28.723	-0.008	-0.008	0.000	0.000	0.000	0.000
24	B	39	PHE	0	-0.013	-0.005	19.662	-0.006	-0.006	0.000	0.000	0.000	0.000
25	B	40	LEU	0	-0.003	-0.008	22.516	-0.008	-0.008	0.000	0.000	0.000	0.000
26	B	41	GLU	-1	-0.822	-0.884	24.932	-0.047	-0.047	0.000	0.000	0.000	0.000
27	B	42	SER	0	0.029	0.015	25.760	-0.004	-0.004	0.000	0.000	0.000	0.000
28	B	43	PHE	0	-0.040	-0.019	16.512	-0.011	-0.011	0.000	0.000	0.000	0.000
29	B	44	ILE	0	-0.037	-0.032	21.777	-0.007	-0.007	0.000	0.000	0.000	0.000
30	B	45	ASP	-1	-0.922	-0.954	23.594	-0.093	-0.093	0.000	0.000	0.000	0.000
31	B	46	GLU	-1	-0.879	-0.930	20.476	-0.174	-0.174	0.000	0.000	0.000	0.000
32	B	47	LYS	1	0.736	0.842	17.036	0.163	0.163	0.000	0.000	0.000	0.000
33	B	48	GLU	-1	-0.800	-0.862	20.226	-0.063	-0.063	0.000	0.000	0.000	0.000
34	B	49	ASN	0	-0.009	0.010	23.035	0.011	0.011	0.000	0.000	0.000	0.000
35	B	50	ILE	0	-0.019	-0.016	23.015	-0.009	-0.009	0.000	0.000	0.000	0.000
36	B	51	ILE	0	-0.087	-0.048	20.935	-0.004	-0.004	0.000	0.000	0.000	0.000
37	B	52	ASP	-1	-0.829	-0.902	19.821	-0.156	-0.156	0.000	0.000	0.000	0.000
38	B	78	ILE	0	-0.090	-0.054	12.213	-0.027	-0.027	0.000	0.000	0.000	0.000
39	B	79	ASP	-1	-0.822	-0.904	16.067	-0.150	-0.150	0.000	0.000	0.000	0.000
40	B	80	THR	0	-0.029	-0.038	10.725	0.003	0.003	0.000	0.000	0.000	0.000
41	B	81	ASN	0	-0.019	0.010	13.052	0.008	0.008	0.000	0.000	0.000	0.000
42	B	82	LEU	0	0.059	0.046	14.374	0.029	0.029	0.000	0.000	0.000	0.000
43	B	83	SER	0	0.069	0.031	15.895	0.021	0.021	0.000	0.000	0.000	0.000
44	B	84	SER	0	-0.056	-0.042	18.041	0.011	0.011	0.000	0.000	0.000	0.000
45	B	85	SER	0	-0.003	-0.014	15.896	0.019	0.019	0.000	0.000	0.000	0.000
46	B	86	ILE	0	0.043	0.029	18.267	0.011	0.011	0.000	0.000	0.000	0.000
47	B	87	SER	0	-0.025	-0.005	20.904	0.009	0.009	0.000	0.000	0.000	0.000
48	B	88	GLN	0	-0.057	-0.034	19.352	0.007	0.007	0.000	0.000	0.000	0.000
49	B	89	LEU	0	0.044	0.013	18.451	0.006	0.006	0.000	0.000	0.000	0.000
50	B	90	LYS	1	0.829	0.892	22.527	0.053	0.053	0.000	0.000	0.000	0.000
51	B	91	ARG	1	0.862	0.938	25.452	-0.009	-0.009	0.000	0.000	0.000	0.000
52	B	92	ILE	0	0.031	0.021	22.209	0.003	0.003	0.000	0.000	0.000	0.000
53	B	93	GLN	0	0.017	0.011	26.238	0.005	0.005	0.000	0.000	0.000	0.000
54	B	94	ARG	1	0.919	0.953	27.903	-0.003	-0.003	0.000	0.000	0.000	0.000
55	B	95	ASP	-1	-0.979	-0.982	29.407	0.017	0.017	0.000	0.000	0.000	0.000
56	B	96	PHE	0	0.040	-0.002	27.551	0.000	0.000	0.000	0.000	0.000	0.000
57	B	97	LYS	1	0.753	0.854	31.147	0.031	0.031	0.000	0.000	0.000	0.000
58	B	98	GLY	0	-0.038	-0.009	33.767	-0.001	-0.001	0.000	0.000	0.000	0.000
59	B	99	LEU	0	-0.032	0.006	31.279	0.003	0.003	0.000	0.000	0.000	0.000
60	B	100	PRO	0	-0.039	-0.017	35.703	-0.002	-0.002	0.000	0.000	0.000	0.000
61	B	101	PRO	0	-0.004	0.001	37.323	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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