FMO DATABASE

FMODB ID: R9YJ8

Calculation Name: 4R24-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R24

Chain ID: B

ChEMBL ID:

UniProt ID: G2RUZ1

Base Structure: X-ray

Registration Date: 2023-06-22

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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-609681.585642
FMO2-HF: Nuclear repulsion	574422.96878
FMO2-HF: Total energy	-35258.616862
FMO2-MP2: Total energy	-35361.040451

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:6:ALA)

Summations of interaction energy for fragment #1(B:6:ALA)

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.
-6.342	-2.483	0.588	-1.63	-2.816	0.004

Interaction energy analysis for fragmet #1(B:6:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.015

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	8	TYR	0	0.037	-0.007	3.312	-1.698	0.465	0.041	-0.952	-1.252	0.003
4	B	9	ARG	1	0.830	0.900	2.691	-3.259	-1.909	0.547	-0.615	-1.282	0.001
5	B	10	ASP	-1	-0.784	-0.878	4.277	-1.491	-1.145	0.000	-0.063	-0.282	0.000
6	B	11	LYS	1	0.915	0.966	6.139	-0.202	-0.202	0.000	0.000	0.000	0.000
7	B	12	LYS	1	0.814	0.889	8.544	0.072	0.072	0.000	0.000	0.000	0.000
8	B	13	VAL	0	-0.013	-0.008	11.070	-0.055	-0.055	0.000	0.000	0.000	0.000
9	B	14	MET	0	0.012	0.037	11.437	-0.080	-0.080	0.000	0.000	0.000	0.000
10	B	15	SER	0	0.019	0.002	15.460	-0.038	-0.038	0.000	0.000	0.000	0.000
11	B	16	ILE	0	0.036	-0.002	18.821	0.017	0.017	0.000	0.000	0.000	0.000
12	B	17	GLY	0	-0.023	-0.004	20.504	-0.001	-0.001	0.000	0.000	0.000	0.000
13	B	18	ILE	0	0.071	0.033	16.500	-0.005	-0.005	0.000	0.000	0.000	0.000
14	B	19	VAL	0	0.015	0.009	15.739	0.015	0.015	0.000	0.000	0.000	0.000
15	B	20	LYS	1	0.869	0.937	17.976	-0.163	-0.163	0.000	0.000	0.000	0.000
16	B	21	GLU	-1	-0.982	-0.978	20.408	0.235	0.235	0.000	0.000	0.000	0.000
17	B	22	LEU	0	-0.022	-0.025	14.080	0.008	0.008	0.000	0.000	0.000	0.000
18	B	23	THR	0	-0.039	-0.032	16.706	0.000	0.000	0.000	0.000	0.000	0.000
19	B	24	GLY	0	0.028	0.031	19.179	-0.021	-0.021	0.000	0.000	0.000	0.000
20	B	25	LEU	0	-0.048	-0.004	19.915	-0.024	-0.024	0.000	0.000	0.000	0.000
21	B	26	SER	0	0.024	-0.020	23.387	0.004	0.004	0.000	0.000	0.000	0.000
22	B	27	GLU	-1	-0.749	-0.882	24.056	0.136	0.136	0.000	0.000	0.000	0.000
23	B	28	ARG	1	0.882	0.948	25.210	-0.074	-0.074	0.000	0.000	0.000	0.000
24	B	29	GLN	0	0.100	0.076	24.580	-0.005	-0.005	0.000	0.000	0.000	0.000
25	B	30	ILE	0	0.054	0.041	19.746	-0.010	-0.010	0.000	0.000	0.000	0.000
26	B	31	ARG	1	0.850	0.902	22.135	-0.120	-0.120	0.000	0.000	0.000	0.000
27	B	32	TYR	0	-0.047	-0.018	24.379	-0.013	-0.013	0.000	0.000	0.000	0.000
28	B	33	TYR	0	0.104	0.025	21.012	-0.015	-0.015	0.000	0.000	0.000	0.000
29	B	34	GLU	-1	-0.754	-0.826	21.037	0.088	0.088	0.000	0.000	0.000	0.000
30	B	35	LYS	1	0.905	0.953	22.000	-0.053	-0.053	0.000	0.000	0.000	0.000
31	B	36	ARG	1	0.862	0.933	24.796	-0.041	-0.041	0.000	0.000	0.000	0.000
32	B	37	SER	0	-0.071	-0.032	22.041	-0.011	-0.011	0.000	0.000	0.000	0.000
33	B	38	LEU	0	0.040	0.029	20.003	-0.008	-0.008	0.000	0.000	0.000	0.000
34	B	39	LEU	0	0.013	0.009	15.908	0.003	0.003	0.000	0.000	0.000	0.000
35	B	40	PHE	0	0.021	0.005	16.152	-0.006	-0.006	0.000	0.000	0.000	0.000
36	B	41	PRO	0	-0.026	0.000	15.915	0.000	0.000	0.000	0.000	0.000	0.000
37	B	42	ASP	-1	-0.823	-0.902	15.167	0.037	0.037	0.000	0.000	0.000	0.000
38	B	43	ARG	1	0.796	0.871	17.457	-0.061	-0.061	0.000	0.000	0.000	0.000
39	B	44	THR	0	0.021	0.005	20.815	-0.008	-0.008	0.000	0.000	0.000	0.000
40	B	45	ASN	0	0.027	0.006	22.313	-0.001	-0.001	0.000	0.000	0.000	0.000
41	B	46	THR	0	0.024	0.023	25.339	-0.002	-0.002	0.000	0.000	0.000	0.000
42	B	47	GLY	0	0.024	0.019	25.467	0.001	0.001	0.000	0.000	0.000	0.000
43	B	48	ILE	0	-0.027	-0.013	22.098	0.004	0.004	0.000	0.000	0.000	0.000
44	B	49	ARG	1	0.815	0.873	19.978	-0.101	-0.101	0.000	0.000	0.000	0.000
45	B	50	LYS	1	0.860	0.919	15.806	-0.236	-0.236	0.000	0.000	0.000	0.000
46	B	51	TYR	0	0.044	0.019	14.007	-0.050	-0.050	0.000	0.000	0.000	0.000
47	B	52	SER	0	0.002	0.006	8.335	0.037	0.037	0.000	0.000	0.000	0.000
48	B	53	PHE	0	0.051	0.006	7.312	-0.055	-0.055	0.000	0.000	0.000	0.000
49	B	54	SER	0	0.007	-0.019	6.930	-0.076	-0.076	0.000	0.000	0.000	0.000
50	B	55	ASP	-1	-0.823	-0.889	8.651	0.108	0.108	0.000	0.000	0.000	0.000
51	B	56	VAL	0	-0.006	-0.011	11.870	-0.058	-0.058	0.000	0.000	0.000	0.000
52	B	57	GLU	-1	-0.793	-0.869	8.552	0.762	0.762	0.000	0.000	0.000	0.000
53	B	58	ARG	1	0.764	0.848	12.234	-0.098	-0.098	0.000	0.000	0.000	0.000
54	B	59	LEU	0	-0.040	-0.033	13.962	-0.043	-0.043	0.000	0.000	0.000	0.000
55	B	60	MET	0	0.013	0.018	14.323	-0.024	-0.024	0.000	0.000	0.000	0.000
56	B	61	ASP	-1	-0.796	-0.877	15.608	0.049	0.049	0.000	0.000	0.000	0.000
57	B	62	ILE	0	-0.057	-0.040	17.481	-0.023	-0.023	0.000	0.000	0.000	0.000
58	B	63	ALA	0	-0.032	-0.020	19.880	-0.013	-0.013	0.000	0.000	0.000	0.000
59	B	64	ASP	-1	-0.845	-0.919	19.957	0.122	0.122	0.000	0.000	0.000	0.000
60	B	65	ARG	1	0.776	0.850	20.998	-0.051	-0.051	0.000	0.000	0.000	0.000
61	B	66	ILE	0	-0.064	-0.042	23.635	-0.010	-0.010	0.000	0.000	0.000	0.000
62	B	67	GLU	-1	-0.951	-0.966	25.463	0.079	0.079	0.000	0.000	0.000	0.000
63	B	68	GLU	-1	-0.898	-0.917	24.442	0.041	0.041	0.000	0.000	0.000	0.000
64	B	69	GLY	0	-0.018	0.000	28.110	-0.007	-0.007	0.000	0.000	0.000	0.000
65	B	70	VAL	0	-0.046	-0.011	25.707	-0.006	-0.006	0.000	0.000	0.000	0.000
66	B	71	GLN	0	0.092	0.054	27.371	0.006	0.006	0.000	0.000	0.000	0.000
67	B	72	THR	0	0.056	0.009	25.602	-0.005	-0.005	0.000	0.000	0.000	0.000
68	B	73	SER	0	-0.044	-0.045	25.543	-0.001	-0.001	0.000	0.000	0.000	0.000
69	B	74	GLU	-1	-0.881	-0.923	26.751	0.005	0.005	0.000	0.000	0.000	0.000
70	B	75	ILE	0	0.030	0.019	21.369	-0.006	-0.006	0.000	0.000	0.000	0.000
71	B	76	ARG	1	0.932	0.970	21.786	0.005	0.005	0.000	0.000	0.000	0.000
72	B	77	THR	0	-0.046	-0.027	22.217	-0.010	-0.010	0.000	0.000	0.000	0.000
73	B	78	GLU	-1	-0.816	-0.894	20.882	0.015	0.015	0.000	0.000	0.000	0.000
74	B	79	LEU	0	-0.005	-0.015	16.952	-0.011	-0.011	0.000	0.000	0.000	0.000
75	B	80	ALA	0	-0.002	0.015	17.530	-0.015	-0.015	0.000	0.000	0.000	0.000
76	B	81	LYS	1	0.850	0.900	18.913	0.035	0.035	0.000	0.000	0.000	0.000
77	B	82	LYS	1	0.783	0.881	15.098	-0.056	-0.056	0.000	0.000	0.000	0.000
78	B	83	ASP	-1	-0.797	-0.874	14.040	-0.074	-0.074	0.000	0.000	0.000	0.000
79	B	84	GLU	-1	-0.892	-0.916	15.042	-0.099	-0.099	0.000	0.000	0.000	0.000
80	B	85	ALA	0	0.031	0.008	16.057	-0.022	-0.022	0.000	0.000	0.000	0.000
81	B	86	ARG	1	0.790	0.891	6.191	0.598	0.598	0.000	0.000	0.000	0.000
82	B	87	LYS	1	0.928	0.950	11.755	0.101	0.101	0.000	0.000	0.000	0.000
83	B	88	MET	0	-0.033	-0.020	13.667	-0.011	-0.011	0.000	0.000	0.000	0.000
84	B	89	LYS	1	0.917	0.970	11.673	0.189	0.189	0.000	0.000	0.000	0.000
85	B	90	GLU	-1	-0.898	-0.914	9.398	-0.488	-0.488	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:6:ALA)