FMO DATABASE

FMODB ID: 39QQL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-291847.165179
FMO2-HF: Nuclear repulsion	268056.734918
FMO2-HF: Total energy	-23790.430261
FMO2-MP2: Total energy	-23861.66949

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.
-7.808	-0.26	0.485	-3.745	-4.288	-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 : 0.013 / q_NPA : -0.005

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	18	THR	0	-0.002	0.040	2.389	-4.920	1.120	0.338	-3.097	-3.282	-0.009
4	B	19	PRO	0	-0.027	-0.006	3.104	-2.375	-0.981	0.148	-0.642	-0.900	-0.006
5	B	20	VAL	0	0.056	0.022	4.616	-0.293	-0.179	-0.001	-0.006	-0.106	0.000
6	B	21	VAL	0	-0.036	-0.018	6.358	0.230	0.230	0.000	0.000	0.000	0.000
7	B	22	ILE	0	0.019	0.001	8.860	-0.047	-0.047	0.000	0.000	0.000	0.000
8	B	23	HIS	0	0.002	-0.002	11.883	0.058	0.058	0.000	0.000	0.000	0.000
9	B	24	ALA	0	-0.009	0.009	15.672	-0.014	-0.014	0.000	0.000	0.000	0.000
10	B	25	THR	0	-0.010	-0.013	18.337	0.005	0.005	0.000	0.000	0.000	0.000
11	B	26	GLN	0	0.010	-0.004	20.880	0.011	0.011	0.000	0.000	0.000	0.000
12	B	27	LEU	0	-0.019	0.008	21.860	0.004	0.004	0.000	0.000	0.000	0.000
13	B	28	PRO	0	-0.022	-0.028	20.840	-0.004	-0.004	0.000	0.000	0.000	0.000
14	B	29	GLN	0	0.054	0.035	23.273	0.005	0.005	0.000	0.000	0.000	0.000
15	B	30	HIS	0	-0.043	-0.020	25.329	-0.003	-0.003	0.000	0.000	0.000	0.000
16	B	31	VAL	0	0.021	0.017	25.360	-0.003	-0.003	0.000	0.000	0.000	0.000
17	B	32	SER	0	-0.020	-0.015	28.021	0.006	0.006	0.000	0.000	0.000	0.000
18	B	33	THR	0	0.003	-0.018	29.990	-0.004	-0.004	0.000	0.000	0.000	0.000
19	B	34	ASP	-1	-0.878	-0.958	31.313	-0.028	-0.028	0.000	0.000	0.000	0.000
20	B	35	GLU	-1	-0.858	-0.910	28.547	-0.036	-0.036	0.000	0.000	0.000	0.000
21	B	36	VAL	0	-0.040	-0.006	25.090	-0.007	-0.007	0.000	0.000	0.000	0.000
22	B	37	LEU	0	0.003	-0.016	26.912	-0.005	-0.005	0.000	0.000	0.000	0.000
23	B	38	GLN	0	0.014	0.015	29.340	-0.003	-0.003	0.000	0.000	0.000	0.000
24	B	39	PHE	0	-0.031	-0.021	19.764	-0.006	-0.006	0.000	0.000	0.000	0.000
25	B	40	LEU	0	-0.027	-0.024	22.976	-0.008	-0.008	0.000	0.000	0.000	0.000
26	B	41	GLU	-1	-0.944	-0.949	25.009	-0.059	-0.059	0.000	0.000	0.000	0.000
27	B	42	SER	0	0.037	0.004	25.381	-0.005	-0.005	0.000	0.000	0.000	0.000
28	B	43	PHE	0	-0.042	-0.012	16.644	-0.012	-0.012	0.000	0.000	0.000	0.000
29	B	44	ILE	0	-0.052	-0.049	21.733	-0.009	-0.009	0.000	0.000	0.000	0.000
30	B	45	ASP	-1	-0.922	-0.960	23.334	-0.098	-0.098	0.000	0.000	0.000	0.000
31	B	46	GLU	-1	-0.947	-0.957	20.979	-0.153	-0.153	0.000	0.000	0.000	0.000
32	B	47	LYS	1	0.850	0.906	16.057	0.208	0.208	0.000	0.000	0.000	0.000
33	B	48	GLU	-1	-0.855	-0.904	20.308	-0.075	-0.075	0.000	0.000	0.000	0.000
34	B	49	ASN	0	-0.016	0.007	22.953	0.010	0.010	0.000	0.000	0.000	0.000
35	B	50	ILE	0	0.010	0.004	22.652	-0.010	-0.010	0.000	0.000	0.000	0.000
36	B	51	ILE	0	-0.093	-0.054	21.245	-0.005	-0.005	0.000	0.000	0.000	0.000
37	B	52	ASP	-1	-0.833	-0.903	19.307	-0.175	-0.175	0.000	0.000	0.000	0.000
38	B	78	ILE	0	-0.165	-0.068	13.097	-0.029	-0.029	0.000	0.000	0.000	0.000
39	B	79	ASP	-1	-0.763	-0.894	16.572	-0.178	-0.178	0.000	0.000	0.000	0.000
40	B	80	THR	0	0.028	-0.007	10.453	-0.024	-0.024	0.000	0.000	0.000	0.000
41	B	81	ASN	0	-0.048	-0.009	13.293	0.007	0.007	0.000	0.000	0.000	0.000
42	B	82	LEU	0	0.029	0.024	13.747	0.028	0.028	0.000	0.000	0.000	0.000
43	B	83	SER	0	0.028	0.009	15.882	0.020	0.020	0.000	0.000	0.000	0.000
44	B	84	SER	0	-0.036	-0.028	17.494	0.010	0.010	0.000	0.000	0.000	0.000
45	B	85	SER	0	0.016	0.003	15.484	0.018	0.018	0.000	0.000	0.000	0.000
46	B	86	ILE	0	0.053	0.029	17.884	0.015	0.015	0.000	0.000	0.000	0.000
47	B	87	SER	0	-0.051	-0.019	20.473	0.012	0.012	0.000	0.000	0.000	0.000
48	B	88	GLN	0	-0.021	-0.019	19.481	0.010	0.010	0.000	0.000	0.000	0.000
49	B	89	LEU	0	0.074	0.034	18.748	0.007	0.007	0.000	0.000	0.000	0.000
50	B	90	LYS	1	0.834	0.914	22.572	0.061	0.061	0.000	0.000	0.000	0.000
51	B	91	ARG	1	0.852	0.915	25.208	-0.001	-0.001	0.000	0.000	0.000	0.000
52	B	92	ILE	0	0.006	0.009	22.021	0.005	0.005	0.000	0.000	0.000	0.000
53	B	93	GLN	0	0.053	0.021	26.154	0.002	0.002	0.000	0.000	0.000	0.000
54	B	94	ARG	1	0.894	0.947	28.029	0.004	0.004	0.000	0.000	0.000	0.000
55	B	95	ASP	-1	-0.965	-0.973	29.354	0.014	0.014	0.000	0.000	0.000	0.000
56	B	96	PHE	0	0.076	0.004	26.941	0.001	0.001	0.000	0.000	0.000	0.000
57	B	97	LYS	1	0.874	0.950	31.346	0.031	0.031	0.000	0.000	0.000	0.000
58	B	98	GLY	0	-0.040	-0.007	33.835	0.000	0.000	0.000	0.000	0.000	0.000
59	B	99	LEU	0	-0.038	0.000	31.292	0.003	0.003	0.000	0.000	0.000	0.000
60	B	100	PRO	0	-0.022	-0.007	35.690	-0.002	-0.002	0.000	0.000	0.000	0.000
61	B	101	PRO	0	-0.011	0.000	37.256	-0.002	-0.002	0.000	0.000	0.000	0.000

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