FMO DATABASE

FMODB ID: 6N6MZ

Calculation Name: 3RK3-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RK3

Chain ID: E

ChEMBL ID:

UniProt ID: O14810

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	50
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-195608.791674
FMO2-HF: Nuclear repulsion	175528.404999
FMO2-HF: Total energy	-20080.386675
FMO2-MP2: Total energy	-20139.293907

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(E:24:GLY)

Summations of interaction energy for fragment #1(E:24:GLY)

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.
-5.803	-2.884	0.181	-1.511	-1.588	0.005

Interaction energy analysis for fragmet #1(E:24:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / 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	E	26	LYS	1	0.927	0.963	3.159	-4.854	-1.997	0.182	-1.509	-1.530	0.005
4	E	27	LEU	0	0.059	0.033	5.644	-0.655	-0.593	-0.001	-0.002	-0.058	0.000
5	E	28	PRO	0	0.027	0.020	8.246	-0.214	-0.214	0.000	0.000	0.000	0.000
6	E	29	ASP	-1	-0.861	-0.953	11.144	0.903	0.903	0.000	0.000	0.000	0.000
7	E	30	ALA	0	-0.037	-0.021	12.854	-0.089	-0.089	0.000	0.000	0.000	0.000
8	E	31	ALA	0	0.039	0.023	14.402	-0.060	-0.060	0.000	0.000	0.000	0.000
9	E	32	LYS	1	0.998	0.995	12.613	-0.785	-0.785	0.000	0.000	0.000	0.000
10	E	33	LYS	1	0.928	0.979	13.119	-0.407	-0.407	0.000	0.000	0.000	0.000
11	E	34	PHE	0	-0.015	-0.013	18.747	-0.031	-0.031	0.000	0.000	0.000	0.000
12	E	35	GLU	-1	-0.945	-0.967	20.128	0.207	0.207	0.000	0.000	0.000	0.000
13	E	36	GLU	-1	-0.911	-0.959	20.319	0.263	0.263	0.000	0.000	0.000	0.000
14	E	37	ALA	0	-0.025	-0.011	23.075	-0.018	-0.018	0.000	0.000	0.000	0.000
15	E	38	GLN	0	-0.003	0.002	24.689	-0.016	-0.016	0.000	0.000	0.000	0.000
16	E	39	GLU	-1	-0.932	-0.977	26.141	0.147	0.147	0.000	0.000	0.000	0.000
17	E	40	ALA	0	0.029	0.023	27.641	-0.008	-0.008	0.000	0.000	0.000	0.000
18	E	41	LEU	0	-0.074	-0.035	28.930	-0.011	-0.011	0.000	0.000	0.000	0.000
19	E	42	ARG	1	0.942	0.963	29.953	-0.108	-0.108	0.000	0.000	0.000	0.000
20	E	43	GLN	0	0.020	0.021	29.980	-0.008	-0.008	0.000	0.000	0.000	0.000
21	E	44	ALA	0	0.005	0.010	33.639	-0.007	-0.007	0.000	0.000	0.000	0.000
22	E	45	GLU	-1	-0.975	-1.009	35.639	0.048	0.048	0.000	0.000	0.000	0.000
23	E	46	GLU	-1	-0.958	-0.977	36.194	0.069	0.069	0.000	0.000	0.000	0.000
24	E	47	GLU	-1	-0.887	-0.941	36.006	0.080	0.080	0.000	0.000	0.000	0.000
25	E	48	ARG	1	0.871	0.941	39.266	-0.052	-0.052	0.000	0.000	0.000	0.000
26	E	49	LYS	1	0.952	0.976	38.643	-0.055	-0.055	0.000	0.000	0.000	0.000
27	E	50	ALA	0	0.033	0.024	42.293	-0.003	-0.003	0.000	0.000	0.000	0.000
28	E	51	LYS	1	0.907	0.935	39.445	-0.066	-0.066	0.000	0.000	0.000	0.000
29	E	52	TYR	0	0.002	0.008	45.338	-0.002	-0.002	0.000	0.000	0.000	0.000
30	E	53	ALA	0	0.020	0.014	47.075	-0.002	-0.002	0.000	0.000	0.000	0.000
31	E	54	LYS	1	0.956	0.965	47.140	-0.052	-0.052	0.000	0.000	0.000	0.000
32	E	55	MET	0	0.038	0.035	49.192	-0.001	-0.001	0.000	0.000	0.000	0.000
33	E	56	GLU	-1	-0.896	-0.941	51.594	0.027	0.027	0.000	0.000	0.000	0.000
34	E	57	ALA	0	0.019	-0.008	53.271	-0.002	-0.002	0.000	0.000	0.000	0.000
35	E	58	GLU	-1	-0.922	-0.966	52.575	0.037	0.037	0.000	0.000	0.000	0.000
36	E	59	ARG	1	0.964	0.983	54.220	-0.029	-0.029	0.000	0.000	0.000	0.000
37	E	60	GLU	-1	-0.979	-1.001	57.558	0.023	0.023	0.000	0.000	0.000	0.000
38	E	61	ALA	0	0.024	0.028	58.835	-0.001	-0.001	0.000	0.000	0.000	0.000
39	E	62	VAL	0	-0.025	0.005	59.345	-0.001	-0.001	0.000	0.000	0.000	0.000
40	E	63	ARG	1	0.833	0.914	57.677	-0.027	-0.027	0.000	0.000	0.000	0.000
41	E	64	GLN	0	0.027	0.014	63.325	-0.001	-0.001	0.000	0.000	0.000	0.000
42	E	65	GLY	0	0.043	0.021	64.331	-0.001	-0.001	0.000	0.000	0.000	0.000
43	E	66	ILE	0	-0.077	-0.033	65.347	-0.001	-0.001	0.000	0.000	0.000	0.000
44	E	67	ARG	1	0.908	0.955	66.993	-0.021	-0.021	0.000	0.000	0.000	0.000
45	E	68	ASP	-1	-0.848	-0.946	68.420	0.022	0.022	0.000	0.000	0.000	0.000
46	E	69	LYS	1	0.853	0.949	68.621	-0.022	-0.022	0.000	0.000	0.000	0.000
47	E	70	TYR	0	-0.041	-0.039	70.636	0.000	0.000	0.000	0.000	0.000	0.000
48	E	71	GLY	0	0.015	0.032	73.391	-0.001	-0.001	0.000	0.000	0.000	0.000
49	E	72	ILE	0	0.000	0.024	72.229	-0.001	-0.001	0.000	0.000	0.000	0.000
50	E	73	LYS	1	0.951	0.956	71.727	-0.017	-0.017	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:24:GLY)