FMO DATABASE

FMODB ID: YZNZ2

Calculation Name: 3K1R-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K1R

Chain ID: B

ChEMBL ID:

UniProt ID: Q9Y6N9

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	74
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-436834.457621
FMO2-HF: Nuclear repulsion	406908.393647
FMO2-HF: Total energy	-29926.063974
FMO2-MP2: Total energy	-30011.475316

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:388:GLU)

Summations of interaction energy for fragment #1(B:388:GLU)

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.
30.355	32.544	-0.002	-1.282	-0.904	0.004

Interaction energy analysis for fragmet #1(B:388:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.928 / q_NPA : -0.962

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	390	SER	0	-0.040	-0.051	3.499	-4.989	-2.800	-0.002	-1.282	-0.904	0.004
4	B	391	PRO	0	0.041	-0.010	5.889	-0.251	-0.251	0.000	0.000	0.000	0.000
5	B	392	LEU	0	-0.009	0.000	8.179	-0.746	-0.746	0.000	0.000	0.000	0.000
6	B	393	GLU	-1	-0.742	-0.828	7.472	27.656	27.656	0.000	0.000	0.000	0.000
7	B	394	THR	0	0.014	0.009	7.004	0.282	0.282	0.000	0.000	0.000	0.000
8	B	395	PHE	0	-0.026	-0.014	9.381	-1.357	-1.357	0.000	0.000	0.000	0.000
9	B	396	LEU	0	0.006	0.004	12.678	-0.950	-0.950	0.000	0.000	0.000	0.000
10	B	397	ALA	0	0.037	0.032	11.475	-0.796	-0.796	0.000	0.000	0.000	0.000
11	B	398	SER	0	-0.092	-0.039	13.458	-0.949	-0.949	0.000	0.000	0.000	0.000
12	B	399	LEU	0	-0.050	-0.032	14.998	-1.213	-1.213	0.000	0.000	0.000	0.000
13	B	400	HIS	0	-0.042	-0.010	17.126	-1.220	-1.220	0.000	0.000	0.000	0.000
14	B	401	MET	0	-0.038	-0.006	17.053	-0.990	-0.990	0.000	0.000	0.000	0.000
15	B	402	GLU	-1	-0.792	-0.912	13.265	18.164	18.164	0.000	0.000	0.000	0.000
16	B	403	ASP	-1	-0.925	-0.962	14.942	15.142	15.142	0.000	0.000	0.000	0.000
17	B	404	PHE	0	0.014	-0.005	17.436	-0.788	-0.788	0.000	0.000	0.000	0.000
18	B	405	ALA	0	-0.007	-0.008	13.001	-0.227	-0.227	0.000	0.000	0.000	0.000
19	B	406	ALA	0	-0.047	-0.023	15.143	0.158	0.158	0.000	0.000	0.000	0.000
20	B	407	LEU	0	0.029	0.016	16.394	-0.174	-0.174	0.000	0.000	0.000	0.000
21	B	408	LEU	0	0.039	0.011	16.628	-0.432	-0.432	0.000	0.000	0.000	0.000
22	B	409	ARG	1	0.880	0.933	9.581	-23.035	-23.035	0.000	0.000	0.000	0.000
23	B	410	GLN	0	-0.081	-0.036	16.222	0.081	0.081	0.000	0.000	0.000	0.000
24	B	411	GLU	-1	-0.890	-0.941	19.462	11.615	11.615	0.000	0.000	0.000	0.000
25	B	412	LYS	1	0.800	0.899	17.784	-13.635	-13.635	0.000	0.000	0.000	0.000
26	B	413	ILE	0	0.002	0.009	17.408	-0.245	-0.245	0.000	0.000	0.000	0.000
27	B	414	ASP	-1	-0.831	-0.911	12.443	17.026	17.026	0.000	0.000	0.000	0.000
28	B	415	LEU	0	-0.022	-0.042	11.794	-0.707	-0.707	0.000	0.000	0.000	0.000
29	B	416	GLU	-1	-0.958	-0.972	13.906	13.839	13.839	0.000	0.000	0.000	0.000
30	B	417	ALA	0	0.036	0.014	15.818	-0.776	-0.776	0.000	0.000	0.000	0.000
31	B	418	LEU	0	0.001	-0.009	16.655	-0.639	-0.639	0.000	0.000	0.000	0.000
32	B	419	MET	0	-0.061	-0.025	17.064	-0.449	-0.449	0.000	0.000	0.000	0.000
33	B	420	LEU	0	-0.030	-0.010	19.661	-0.575	-0.575	0.000	0.000	0.000	0.000
34	B	421	CYS	0	-0.053	0.012	21.462	-0.337	-0.337	0.000	0.000	0.000	0.000
35	B	422	SER	0	-0.050	-0.059	23.739	-0.167	-0.167	0.000	0.000	0.000	0.000
36	B	423	ASP	-1	-0.804	-0.919	26.671	9.595	9.595	0.000	0.000	0.000	0.000
37	B	424	LEU	0	0.020	-0.005	28.774	0.053	0.053	0.000	0.000	0.000	0.000
38	B	425	ASP	-1	-0.758	-0.833	25.636	10.081	10.081	0.000	0.000	0.000	0.000
39	B	426	LEU	0	0.026	0.005	22.025	0.143	0.143	0.000	0.000	0.000	0.000
40	B	427	ARG	1	0.883	0.947	25.881	-8.702	-8.702	0.000	0.000	0.000	0.000
41	B	428	SER	0	-0.059	-0.032	28.639	-0.200	-0.200	0.000	0.000	0.000	0.000
42	B	429	ILE	0	-0.012	0.012	22.501	-0.048	-0.048	0.000	0.000	0.000	0.000
43	B	430	SER	0	-0.028	-0.011	25.734	0.210	0.210	0.000	0.000	0.000	0.000
44	B	431	VAL	0	0.013	0.022	23.210	0.203	0.203	0.000	0.000	0.000	0.000
45	B	432	PRO	0	0.017	-0.004	26.079	-0.418	-0.418	0.000	0.000	0.000	0.000
46	B	433	LEU	0	0.004	-0.009	27.606	0.235	0.235	0.000	0.000	0.000	0.000
47	B	434	GLY	0	0.057	0.036	28.573	0.096	0.096	0.000	0.000	0.000	0.000
48	B	435	PRO	0	0.032	-0.005	23.575	0.125	0.125	0.000	0.000	0.000	0.000
49	B	436	ARG	1	0.792	0.898	23.677	-9.455	-9.455	0.000	0.000	0.000	0.000
50	B	437	GLU	-1	-0.901	-0.961	25.248	9.559	9.559	0.000	0.000	0.000	0.000
51	B	438	LYS	1	0.866	0.933	21.536	-13.027	-13.027	0.000	0.000	0.000	0.000
52	B	439	ILE	0	0.042	0.020	19.521	0.236	0.236	0.000	0.000	0.000	0.000
53	B	440	LEU	0	0.023	0.005	21.389	0.108	0.108	0.000	0.000	0.000	0.000
54	B	441	GLY	0	-0.034	-0.015	24.010	-0.146	-0.146	0.000	0.000	0.000	0.000
55	B	442	ALA	0	-0.017	-0.015	19.181	-0.082	-0.082	0.000	0.000	0.000	0.000
56	B	443	VAL	0	0.024	0.011	19.166	0.257	0.257	0.000	0.000	0.000	0.000
57	B	444	ARG	1	0.929	0.964	20.713	-10.079	-10.079	0.000	0.000	0.000	0.000
58	B	445	ARG	1	0.972	0.992	20.865	-12.374	-12.374	0.000	0.000	0.000	0.000
59	B	446	ARG	1	0.967	0.994	12.785	-16.246	-16.246	0.000	0.000	0.000	0.000
60	B	447	ARG	1	0.877	0.936	19.662	-11.205	-11.205	0.000	0.000	0.000	0.000
61	B	448	GLN	0	-0.002	-0.003	21.843	-0.231	-0.231	0.000	0.000	0.000	0.000
62	B	449	ALA	0	0.005	0.008	20.312	-0.227	-0.227	0.000	0.000	0.000	0.000
63	B	450	MET	0	-0.037	-0.024	17.202	0.250	0.250	0.000	0.000	0.000	0.000
64	B	451	GLU	-1	-0.932	-0.968	20.760	10.380	10.380	0.000	0.000	0.000	0.000
65	B	452	ARG	1	0.868	0.926	24.312	-9.553	-9.553	0.000	0.000	0.000	0.000
66	B	453	PRO	0	0.010	0.028	22.341	-0.074	-0.074	0.000	0.000	0.000	0.000
67	B	454	PRO	0	-0.019	-0.006	23.572	-0.346	-0.346	0.000	0.000	0.000	0.000
68	B	455	ALA	0	0.002	-0.001	25.579	0.164	0.164	0.000	0.000	0.000	0.000
69	B	456	LEU	0	-0.034	-0.025	20.922	0.246	0.246	0.000	0.000	0.000	0.000
70	B	457	GLU	-1	-0.943	-0.971	23.787	9.711	9.711	0.000	0.000	0.000	0.000
71	B	458	ASP	-1	-0.936	-0.955	23.137	12.290	12.290	0.000	0.000	0.000	0.000
72	B	459	THR	0	-0.065	-0.042	21.384	-0.298	-0.298	0.000	0.000	0.000	0.000
73	B	460	GLU	-1	-0.952	-0.969	22.773	10.788	10.788	0.000	0.000	0.000	0.000
74	B	461	LEU	0	-0.045	-0.022	19.424	0.020	0.020	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:388:GLU)