FMO DATABASE

FMODB ID: Z6NQN

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	OptHSide
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	-609207.470219
FMO2-HF: Nuclear repulsion	573949.163959
FMO2-HF: Total energy	-35258.30626
FMO2-MP2: Total energy	-35360.795817

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.
-9.338	-4.494	1.12	-2.234	-3.729	0.011

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 : 0.032 / q_NPA : 0.011

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	0.013	-0.016	2.893	-2.063	0.723	0.164	-1.286	-1.664	0.006
4	B	9	ARG	1	0.846	0.889	2.540	-4.985	-3.302	0.955	-0.872	-1.765	0.005
5	B	10	ASP	-1	-0.821	-0.882	4.473	-1.923	-1.548	0.001	-0.076	-0.300	0.000
6	B	11	LYS	1	0.931	0.981	6.290	-0.393	-0.393	0.000	0.000	0.000	0.000
7	B	12	LYS	1	0.815	0.904	8.736	-0.016	-0.016	0.000	0.000	0.000	0.000
8	B	13	VAL	0	0.010	-0.005	10.845	-0.075	-0.075	0.000	0.000	0.000	0.000
9	B	14	MET	0	-0.007	0.025	11.079	-0.074	-0.074	0.000	0.000	0.000	0.000
10	B	15	SER	0	0.010	0.009	15.324	-0.032	-0.032	0.000	0.000	0.000	0.000
11	B	16	ILE	0	0.047	-0.004	18.587	0.019	0.019	0.000	0.000	0.000	0.000
12	B	17	GLY	0	-0.025	-0.003	20.530	0.000	0.000	0.000	0.000	0.000	0.000
13	B	18	ILE	0	0.077	0.036	16.096	-0.007	-0.007	0.000	0.000	0.000	0.000
14	B	19	VAL	0	0.027	0.017	15.551	0.016	0.016	0.000	0.000	0.000	0.000
15	B	20	LYS	1	0.864	0.935	17.803	-0.180	-0.180	0.000	0.000	0.000	0.000
16	B	21	GLU	-1	-0.972	-0.972	20.006	0.242	0.242	0.000	0.000	0.000	0.000
17	B	22	LEU	0	-0.032	-0.019	13.670	0.012	0.012	0.000	0.000	0.000	0.000
18	B	23	THR	0	-0.035	-0.034	16.555	-0.015	-0.015	0.000	0.000	0.000	0.000
19	B	24	GLY	0	0.031	0.032	18.846	-0.022	-0.022	0.000	0.000	0.000	0.000
20	B	25	LEU	0	-0.054	-0.007	19.740	-0.027	-0.027	0.000	0.000	0.000	0.000
21	B	26	SER	0	0.010	-0.032	23.153	0.006	0.006	0.000	0.000	0.000	0.000
22	B	27	GLU	-1	-0.747	-0.893	24.158	0.152	0.152	0.000	0.000	0.000	0.000
23	B	28	ARG	1	0.914	0.963	25.148	-0.081	-0.081	0.000	0.000	0.000	0.000
24	B	29	GLN	0	0.109	0.067	24.330	-0.001	-0.001	0.000	0.000	0.000	0.000
25	B	30	ILE	0	0.049	0.045	19.561	-0.008	-0.008	0.000	0.000	0.000	0.000
26	B	31	ARG	1	0.836	0.907	21.729	-0.133	-0.133	0.000	0.000	0.000	0.000
27	B	32	TYR	0	-0.041	-0.017	24.000	-0.013	-0.013	0.000	0.000	0.000	0.000
28	B	33	TYR	0	0.105	0.035	20.635	-0.018	-0.018	0.000	0.000	0.000	0.000
29	B	34	GLU	-1	-0.741	-0.830	20.541	0.112	0.112	0.000	0.000	0.000	0.000
30	B	35	LYS	1	0.910	0.951	21.776	-0.067	-0.067	0.000	0.000	0.000	0.000
31	B	36	ARG	1	0.843	0.935	24.659	-0.051	-0.051	0.000	0.000	0.000	0.000
32	B	37	SER	0	-0.055	-0.030	22.149	-0.011	-0.011	0.000	0.000	0.000	0.000
33	B	38	LEU	0	0.024	0.013	19.762	-0.009	-0.009	0.000	0.000	0.000	0.000
34	B	39	LEU	0	-0.001	0.006	15.769	0.008	0.008	0.000	0.000	0.000	0.000
35	B	40	PHE	0	-0.002	-0.013	15.809	-0.009	-0.009	0.000	0.000	0.000	0.000
36	B	41	PRO	0	-0.006	0.019	15.597	0.001	0.001	0.000	0.000	0.000	0.000
37	B	42	ASP	-1	-0.817	-0.897	15.472	0.078	0.078	0.000	0.000	0.000	0.000
38	B	43	ARG	1	0.840	0.908	17.539	-0.084	-0.084	0.000	0.000	0.000	0.000
39	B	44	THR	0	0.016	0.006	20.481	-0.007	-0.007	0.000	0.000	0.000	0.000
40	B	45	ASN	0	0.047	0.007	21.928	-0.005	-0.005	0.000	0.000	0.000	0.000
41	B	46	THR	0	-0.004	0.004	25.087	-0.004	-0.004	0.000	0.000	0.000	0.000
42	B	47	GLY	0	0.028	0.023	25.454	-0.001	-0.001	0.000	0.000	0.000	0.000
43	B	48	ILE	0	-0.053	-0.025	21.654	0.004	0.004	0.000	0.000	0.000	0.000
44	B	49	ARG	1	0.811	0.874	19.656	-0.121	-0.121	0.000	0.000	0.000	0.000
45	B	50	LYS	1	0.849	0.917	15.743	-0.290	-0.290	0.000	0.000	0.000	0.000
46	B	51	TYR	0	0.049	0.007	13.943	-0.049	-0.049	0.000	0.000	0.000	0.000
47	B	52	SER	0	0.026	0.022	8.360	0.018	0.018	0.000	0.000	0.000	0.000
48	B	53	PHE	0	0.038	0.001	7.106	-0.079	-0.079	0.000	0.000	0.000	0.000
49	B	54	SER	0	0.000	-0.027	6.659	-0.101	-0.101	0.000	0.000	0.000	0.000
50	B	55	ASP	-1	-0.833	-0.902	8.339	0.138	0.138	0.000	0.000	0.000	0.000
51	B	56	VAL	0	-0.012	-0.012	11.628	-0.082	-0.082	0.000	0.000	0.000	0.000
52	B	57	GLU	-1	-0.785	-0.864	8.528	0.716	0.716	0.000	0.000	0.000	0.000
53	B	58	ARG	1	0.765	0.844	12.099	-0.124	-0.124	0.000	0.000	0.000	0.000
54	B	59	LEU	0	-0.050	-0.045	13.777	-0.045	-0.045	0.000	0.000	0.000	0.000
55	B	60	MET	0	0.002	0.006	13.855	-0.026	-0.026	0.000	0.000	0.000	0.000
56	B	61	ASP	-1	-0.820	-0.882	15.427	0.056	0.056	0.000	0.000	0.000	0.000
57	B	62	ILE	0	-0.070	-0.038	17.482	-0.024	-0.024	0.000	0.000	0.000	0.000
58	B	63	ALA	0	-0.033	-0.032	19.821	-0.015	-0.015	0.000	0.000	0.000	0.000
59	B	64	ASP	-1	-0.827	-0.901	19.841	0.120	0.120	0.000	0.000	0.000	0.000
60	B	65	ARG	1	0.772	0.855	21.060	-0.051	-0.051	0.000	0.000	0.000	0.000
61	B	66	ILE	0	-0.085	-0.055	23.555	-0.009	-0.009	0.000	0.000	0.000	0.000
62	B	67	GLU	-1	-0.946	-0.960	25.022	0.083	0.083	0.000	0.000	0.000	0.000
63	B	68	GLU	-1	-0.946	-0.940	24.334	0.040	0.040	0.000	0.000	0.000	0.000
64	B	69	GLY	0	-0.006	0.001	28.050	-0.007	-0.007	0.000	0.000	0.000	0.000
65	B	70	VAL	0	-0.036	-0.003	25.552	-0.006	-0.006	0.000	0.000	0.000	0.000
66	B	71	GLN	0	0.038	0.024	27.349	0.006	0.006	0.000	0.000	0.000	0.000
67	B	72	THR	0	0.085	0.019	25.204	-0.005	-0.005	0.000	0.000	0.000	0.000
68	B	73	SER	0	-0.035	-0.042	25.126	-0.001	-0.001	0.000	0.000	0.000	0.000
69	B	74	GLU	-1	-0.887	-0.931	26.420	0.008	0.008	0.000	0.000	0.000	0.000
70	B	75	ILE	0	0.037	0.018	21.036	-0.005	-0.005	0.000	0.000	0.000	0.000
71	B	76	ARG	1	0.933	0.971	21.578	-0.002	-0.002	0.000	0.000	0.000	0.000
72	B	77	THR	0	-0.032	-0.018	21.979	-0.010	-0.010	0.000	0.000	0.000	0.000
73	B	78	GLU	-1	-0.841	-0.906	20.753	0.013	0.013	0.000	0.000	0.000	0.000
74	B	79	LEU	0	-0.034	-0.030	16.688	-0.013	-0.013	0.000	0.000	0.000	0.000
75	B	80	ALA	0	-0.015	0.007	17.485	-0.016	-0.016	0.000	0.000	0.000	0.000
76	B	81	LYS	1	0.880	0.928	19.075	0.032	0.032	0.000	0.000	0.000	0.000
77	B	82	LYS	1	0.889	0.948	15.004	-0.052	-0.052	0.000	0.000	0.000	0.000
78	B	83	ASP	-1	-0.797	-0.864	14.084	-0.064	-0.064	0.000	0.000	0.000	0.000
79	B	84	GLU	-1	-0.912	-0.955	15.003	-0.097	-0.097	0.000	0.000	0.000	0.000
80	B	85	ALA	0	0.032	0.008	16.237	-0.019	-0.019	0.000	0.000	0.000	0.000
81	B	86	ARG	1	0.816	0.899	6.354	0.600	0.600	0.000	0.000	0.000	0.000
82	B	87	LYS	1	0.933	0.959	12.179	0.079	0.079	0.000	0.000	0.000	0.000
83	B	88	MET	0	-0.036	-0.012	13.857	0.002	0.002	0.000	0.000	0.000	0.000
84	B	89	LYS	1	0.900	0.955	11.995	0.200	0.200	0.000	0.000	0.000	0.000
85	B	90	GLU	-1	-0.877	-0.900	10.002	-0.472	-0.472	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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