FMO DATABASE

FMODB ID: LN349

Calculation Name: 2RK5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2RK5

Chain ID: A

ChEMBL ID:

UniProt ID: O68574

Base Structure: X-ray

Registration Date: 2023-09-23

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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-600535.678649
FMO2-HF: Nuclear repulsion	566659.911669
FMO2-HF: Total energy	-33875.76698
FMO2-MP2: Total energy	-33975.912016

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(A:3:GLN)

Summations of interaction energy for fragment #1(A:3:GLN)

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.
-18.205	-10.619	7.989	-5.127	-10.443	0.025

Interaction energy analysis for fragmet #1(A:3:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : -0.009

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	A	5	ARG	1	0.886	0.953	3.823	-0.073	1.288	-0.021	-0.619	-0.721	0.000
4	A	6	GLU	-1	-0.780	-0.872	6.188	0.239	0.239	0.000	0.000	0.000	0.000
5	A	7	ILE	0	-0.148	-0.090	9.829	-0.042	-0.042	0.000	0.000	0.000	0.000
6	A	8	ALA	0	-0.019	-0.010	12.280	-0.020	-0.020	0.000	0.000	0.000	0.000
7	A	9	ASP	-1	-0.836	-0.913	14.601	0.132	0.132	0.000	0.000	0.000	0.000
8	A	10	ASN	0	-0.032	-0.007	15.080	0.013	0.013	0.000	0.000	0.000	0.000
9	A	11	THR	0	-0.029	-0.001	13.642	0.043	0.043	0.000	0.000	0.000	0.000
10	A	12	TYR	0	-0.002	-0.023	8.384	-0.027	-0.027	0.000	0.000	0.000	0.000
11	A	13	ILE	0	-0.093	-0.040	7.127	0.098	0.098	0.000	0.000	0.000	0.000
12	A	14	VAL	0	0.041	0.017	4.244	-0.633	-0.547	-0.001	-0.041	-0.043	0.000
13	A	15	LEU	0	-0.053	-0.023	2.520	-4.688	-2.102	2.644	-1.700	-3.529	0.020
14	A	16	GLY	0	0.025	0.005	4.578	0.519	0.701	-0.001	-0.013	-0.168	0.000
15	A	17	THR	0	-0.021	-0.030	2.879	-4.948	-3.649	0.103	-0.778	-0.623	0.008
16	A	18	MET	0	-0.038	0.017	2.208	-2.147	-0.684	5.201	-1.842	-4.821	-0.004
17	A	19	THR	0	0.008	-0.021	3.686	-1.871	-1.544	0.064	-0.060	-0.331	0.001
18	A	20	LEU	0	0.048	0.011	6.311	-0.223	-0.223	0.000	0.000	0.000	0.000
19	A	21	ASN	0	0.010	0.008	8.819	-0.068	-0.068	0.000	0.000	0.000	0.000
20	A	22	ASP	-1	-0.833	-0.892	4.221	-2.489	-2.207	0.000	-0.074	-0.207	0.000
21	A	23	PHE	0	-0.042	-0.045	5.885	0.128	0.128	0.000	0.000	0.000	0.000
22	A	24	ASN	0	0.025	0.012	6.636	0.066	0.066	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.948	-0.959	8.121	-0.630	-0.630	0.000	0.000	0.000	0.000
24	A	26	TYR	0	-0.080	-0.043	5.560	0.222	0.222	0.000	0.000	0.000	0.000
25	A	27	PHE	0	-0.040	-0.036	6.620	0.078	0.078	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.902	-0.921	10.403	0.058	0.058	0.000	0.000	0.000	0.000
27	A	29	THR	0	-0.026	-0.026	12.018	0.022	0.022	0.000	0.000	0.000	0.000
28	A	30	ASP	-1	-0.909	-0.929	13.740	0.125	0.125	0.000	0.000	0.000	0.000
29	A	31	LEU	0	-0.050	-0.013	11.391	0.020	0.020	0.000	0.000	0.000	0.000
30	A	32	GLU	-1	-0.911	-0.960	14.206	0.190	0.190	0.000	0.000	0.000	0.000
31	A	33	SER	0	0.008	-0.014	16.074	0.000	0.000	0.000	0.000	0.000	0.000
32	A	34	ASP	-1	-0.891	-0.931	17.348	0.258	0.258	0.000	0.000	0.000	0.000
33	A	35	ASN	0	-0.109	-0.069	18.402	0.019	0.019	0.000	0.000	0.000	0.000
34	A	36	VAL	0	-0.030	-0.003	13.074	0.096	0.096	0.000	0.000	0.000	0.000
35	A	37	ASP	-1	-0.867	-0.917	11.065	0.489	0.489	0.000	0.000	0.000	0.000
36	A	38	THR	0	-0.099	-0.062	7.086	-0.218	-0.218	0.000	0.000	0.000	0.000
37	A	39	ILE	0	0.053	0.036	5.849	-0.308	-0.308	0.000	0.000	0.000	0.000
38	A	40	ALA	0	-0.035	-0.017	8.373	-0.330	-0.330	0.000	0.000	0.000	0.000
39	A	41	GLY	0	-0.037	-0.006	10.281	-0.305	-0.305	0.000	0.000	0.000	0.000
40	A	42	PHE	0	0.078	0.043	11.904	-0.161	-0.161	0.000	0.000	0.000	0.000
41	A	43	TYR	0	-0.028	-0.048	12.484	-0.071	-0.071	0.000	0.000	0.000	0.000
42	A	44	LEU	0	-0.036	-0.032	13.802	-0.092	-0.092	0.000	0.000	0.000	0.000
43	A	45	THR	0	-0.055	-0.040	16.228	-0.112	-0.112	0.000	0.000	0.000	0.000
44	A	46	GLY	0	-0.003	0.010	17.214	-0.071	-0.071	0.000	0.000	0.000	0.000
45	A	47	VAL	0	-0.051	-0.028	17.826	-0.046	-0.046	0.000	0.000	0.000	0.000
46	A	48	GLY	0	-0.017	0.007	19.989	-0.045	-0.045	0.000	0.000	0.000	0.000
47	A	49	THR	0	-0.056	-0.052	20.511	-0.022	-0.022	0.000	0.000	0.000	0.000
48	A	50	ILE	0	-0.039	-0.019	17.890	0.066	0.066	0.000	0.000	0.000	0.000
49	A	51	PRO	0	0.011	0.026	17.213	-0.035	-0.035	0.000	0.000	0.000	0.000
50	A	52	SER	0	0.016	-0.036	19.250	0.040	0.040	0.000	0.000	0.000	0.000
51	A	53	GLN	0	-0.066	-0.047	19.053	0.043	0.043	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.906	-0.942	20.478	0.361	0.361	0.000	0.000	0.000	0.000
53	A	55	GLU	-1	-0.949	-0.958	23.090	0.280	0.280	0.000	0.000	0.000	0.000
54	A	56	LYS	1	0.820	0.908	16.814	-0.517	-0.517	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.816	-0.884	18.954	0.381	0.381	0.000	0.000	0.000	0.000
56	A	58	HIS	1	0.794	0.885	17.888	-0.324	-0.324	0.000	0.000	0.000	0.000
57	A	59	PHE	0	0.036	0.028	15.849	-0.020	-0.020	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.880	-0.933	16.945	0.327	0.327	0.000	0.000	0.000	0.000
59	A	61	VAL	0	-0.029	-0.013	15.470	-0.010	-0.010	0.000	0.000	0.000	0.000
60	A	62	GLU	-1	-0.921	-0.963	18.290	0.166	0.166	0.000	0.000	0.000	0.000
61	A	63	SER	0	-0.030	-0.053	16.247	0.001	0.001	0.000	0.000	0.000	0.000
62	A	64	ASN	0	-0.005	-0.008	16.650	-0.018	-0.018	0.000	0.000	0.000	0.000
63	A	65	GLY	0	0.000	-0.002	19.249	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	66	LYS	1	0.765	0.899	15.459	-0.115	-0.115	0.000	0.000	0.000	0.000
65	A	67	HIS	0	-0.028	-0.012	18.413	0.003	0.003	0.000	0.000	0.000	0.000
66	A	68	LEU	0	-0.007	-0.006	12.378	0.011	0.011	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.794	-0.878	15.756	0.375	0.375	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.040	-0.021	11.444	0.062	0.062	0.000	0.000	0.000	0.000
69	A	71	ILE	0	0.006	-0.001	13.561	-0.042	-0.042	0.000	0.000	0.000	0.000
70	A	72	ASN	0	-0.002	0.023	13.406	0.090	0.090	0.000	0.000	0.000	0.000
71	A	73	ASP	-1	-0.923	-0.976	11.527	0.709	0.709	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.904	0.944	11.971	-0.733	-0.733	0.000	0.000	0.000	0.000
73	A	75	VAL	0	0.028	0.010	12.749	0.219	0.219	0.000	0.000	0.000	0.000
74	A	76	LYS	1	0.864	0.927	10.964	-1.189	-1.189	0.000	0.000	0.000	0.000
75	A	77	ASP	-1	-0.911	-0.945	15.363	0.581	0.581	0.000	0.000	0.000	0.000
76	A	78	GLY	0	0.067	0.043	17.644	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	79	ARG	1	0.938	0.973	10.238	-1.454	-1.454	0.000	0.000	0.000	0.000
78	A	80	VAL	0	0.055	0.032	11.080	-0.022	-0.022	0.000	0.000	0.000	0.000
79	A	81	THR	0	-0.051	-0.050	8.866	0.255	0.255	0.000	0.000	0.000	0.000
80	A	82	LYS	1	0.909	0.970	7.525	-0.101	-0.101	0.000	0.000	0.000	0.000
81	A	83	LEU	0	0.057	0.037	8.368	-0.310	-0.310	0.000	0.000	0.000	0.000
82	A	84	LYS	1	0.926	0.973	9.223	-0.416	-0.416	0.000	0.000	0.000	0.000
83	A	85	ILE	0	0.016	0.006	8.627	0.040	0.040	0.000	0.000	0.000	0.000
84	A	86	LEU	0	-0.007	-0.004	11.820	-0.056	-0.056	0.000	0.000	0.000	0.000
85	A	87	VAL	0	0.027	0.008	13.011	0.012	0.012	0.000	0.000	0.000	0.000
86	A	88	SER	0	0.002	-0.003	15.932	-0.026	-0.026	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLN)