FMO DATABASE

FMODB ID: VQMZ1

Calculation Name: 2RF4-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
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	60
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-285470.238434
FMO2-HF: Nuclear repulsion	262042.747405
FMO2-HF: Total energy	-23427.491028
FMO2-MP2: Total energy	-23497.597125

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(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.
-0.042	2.095	-0.009	-0.934	-1.194	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 : -0.017 / q_NPA : -0.016

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	-0.019	0.006	3.791	-0.207	1.930	-0.009	-0.934	-1.194	0.003
4	F	20	VAL	0	0.046	0.019	5.718	0.479	0.479	0.000	0.000	0.000	0.000
5	F	21	VAL	0	-0.024	-0.013	8.728	0.309	0.309	0.000	0.000	0.000	0.000
6	F	22	ILE	0	0.005	-0.005	11.863	0.049	0.049	0.000	0.000	0.000	0.000
7	F	23	HIS	0	0.008	0.002	14.650	0.105	0.105	0.000	0.000	0.000	0.000
8	F	24	ALA	0	-0.010	0.008	18.386	-0.006	-0.006	0.000	0.000	0.000	0.000
9	F	25	THR	0	-0.008	-0.014	21.217	0.013	0.013	0.000	0.000	0.000	0.000
10	F	26	GLN	0	0.004	0.000	23.982	0.039	0.039	0.000	0.000	0.000	0.000
11	F	27	LEU	0	-0.007	0.007	24.994	-0.011	-0.011	0.000	0.000	0.000	0.000
12	F	28	PRO	0	-0.032	-0.037	23.775	0.000	0.000	0.000	0.000	0.000	0.000
13	F	29	GLN	0	0.044	0.036	26.298	0.011	0.011	0.000	0.000	0.000	0.000
14	F	30	HIS	0	-0.041	-0.018	28.410	-0.005	-0.005	0.000	0.000	0.000	0.000
15	F	31	VAL	0	0.047	0.026	28.325	-0.002	-0.002	0.000	0.000	0.000	0.000
16	F	32	SER	0	-0.059	-0.030	31.354	0.014	0.014	0.000	0.000	0.000	0.000
17	F	33	THR	0	0.037	-0.027	33.379	-0.004	-0.004	0.000	0.000	0.000	0.000
18	F	34	ASP	-1	-0.927	-0.969	34.721	-0.086	-0.086	0.000	0.000	0.000	0.000
19	F	35	GLU	-1	-0.834	-0.900	32.411	-0.131	-0.131	0.000	0.000	0.000	0.000
20	F	36	VAL	0	-0.034	-0.003	28.619	-0.014	-0.014	0.000	0.000	0.000	0.000
21	F	37	LEU	0	-0.006	-0.016	30.396	-0.007	-0.007	0.000	0.000	0.000	0.000
22	F	38	GLN	0	-0.010	0.008	32.868	-0.003	-0.003	0.000	0.000	0.000	0.000
23	F	39	PHE	0	-0.007	-0.004	23.325	-0.008	-0.008	0.000	0.000	0.000	0.000
24	F	40	LEU	0	-0.029	-0.024	26.408	-0.011	-0.011	0.000	0.000	0.000	0.000
25	F	41	GLU	-1	-0.923	-0.948	28.676	-0.125	-0.125	0.000	0.000	0.000	0.000
26	F	42	SER	0	0.010	-0.011	29.093	-0.006	-0.006	0.000	0.000	0.000	0.000
27	F	43	PHE	0	-0.010	0.006	20.348	-0.022	-0.022	0.000	0.000	0.000	0.000
28	F	44	ILE	0	-0.054	-0.045	25.226	-0.010	-0.010	0.000	0.000	0.000	0.000
29	F	45	ASP	-1	-0.940	-0.954	27.034	-0.177	-0.177	0.000	0.000	0.000	0.000
30	F	46	GLU	-1	-0.923	-0.954	25.080	-0.285	-0.285	0.000	0.000	0.000	0.000
31	F	47	LYS	1	0.856	0.913	20.311	0.367	0.367	0.000	0.000	0.000	0.000
32	F	48	GLU	-1	-0.884	-0.912	24.370	-0.123	-0.123	0.000	0.000	0.000	0.000
33	F	49	ASN	0	0.012	0.019	26.849	0.026	0.026	0.000	0.000	0.000	0.000
34	F	50	ILE	0	-0.018	-0.016	26.838	-0.011	-0.011	0.000	0.000	0.000	0.000
35	F	51	ILE	0	-0.099	-0.049	25.120	-0.014	-0.014	0.000	0.000	0.000	0.000
36	F	52	ASP	-1	-0.830	-0.921	23.751	-0.258	-0.258	0.000	0.000	0.000	0.000
37	F	78	ILE	0	-0.126	-0.049	17.196	-0.039	-0.039	0.000	0.000	0.000	0.000
38	F	79	ASP	-1	-0.791	-0.900	20.519	-0.225	-0.225	0.000	0.000	0.000	0.000
39	F	80	THR	0	0.059	0.023	14.551	-0.016	-0.016	0.000	0.000	0.000	0.000
40	F	81	ASN	0	-0.085	-0.041	16.072	0.024	0.024	0.000	0.000	0.000	0.000
41	F	82	LEU	0	0.014	0.020	17.452	0.026	0.026	0.000	0.000	0.000	0.000
42	F	83	SER	0	0.062	0.021	19.449	0.015	0.015	0.000	0.000	0.000	0.000
43	F	84	SER	0	-0.040	-0.011	20.799	0.005	0.005	0.000	0.000	0.000	0.000
44	F	85	SER	0	0.006	-0.013	19.073	0.011	0.011	0.000	0.000	0.000	0.000
45	F	86	ILE	0	0.075	0.030	21.433	0.018	0.018	0.000	0.000	0.000	0.000
46	F	87	SER	0	-0.046	-0.011	24.167	0.013	0.013	0.000	0.000	0.000	0.000
47	F	88	GLN	0	-0.042	-0.028	22.805	0.012	0.012	0.000	0.000	0.000	0.000
48	F	89	LEU	0	0.054	0.022	22.343	0.010	0.010	0.000	0.000	0.000	0.000
49	F	90	LYS	1	0.828	0.898	26.247	0.110	0.110	0.000	0.000	0.000	0.000
50	F	91	ARG	1	0.869	0.933	28.683	0.008	0.008	0.000	0.000	0.000	0.000
51	F	92	ILE	0	0.032	0.025	25.560	0.007	0.007	0.000	0.000	0.000	0.000
52	F	93	GLN	0	0.045	0.016	29.703	0.000	0.000	0.000	0.000	0.000	0.000
53	F	94	ARG	1	0.899	0.944	31.633	0.022	0.022	0.000	0.000	0.000	0.000
54	F	95	ASP	-1	-0.969	-0.970	32.861	-0.009	-0.009	0.000	0.000	0.000	0.000
55	F	96	PHE	0	0.072	0.001	29.986	0.001	0.001	0.000	0.000	0.000	0.000
56	F	97	LYS	1	0.866	0.940	34.787	0.078	0.078	0.000	0.000	0.000	0.000
57	F	98	GLY	0	-0.039	-0.007	37.470	0.001	0.001	0.000	0.000	0.000	0.000
58	F	99	LEU	0	-0.024	-0.010	34.574	0.005	0.005	0.000	0.000	0.000	0.000
59	F	100	PRO	0	-0.042	0.000	38.950	-0.004	-0.004	0.000	0.000	0.000	0.000
60	F	101	PRO	0	-0.006	0.004	41.746	-0.001	-0.001	0.000	0.000	0.000	0.000

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