FMO DATABASE

FMODB ID: Z6YJN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-195811.762345
FMO2-HF: Nuclear repulsion	175730.626826
FMO2-HF: Total energy	-20081.135519
FMO2-MP2: Total energy	-20140.027553

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.
-6.658	-3.531	0.331	-1.643	-1.813	0.008

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 : 0.002 / q_NPA : -0.008

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	0.938	0.960	2.884	-5.581	-2.516	0.332	-1.641	-1.755	0.008
4	E	27	LEU	0	0.054	0.030	5.644	-0.635	-0.573	-0.001	-0.002	-0.058	0.000
5	E	28	PRO	0	0.044	0.032	8.296	-0.198	-0.198	0.000	0.000	0.000	0.000
6	E	29	ASP	-1	-0.812	-0.910	11.156	0.844	0.844	0.000	0.000	0.000	0.000
7	E	30	ALA	0	-0.028	-0.008	12.859	-0.088	-0.088	0.000	0.000	0.000	0.000
8	E	31	ALA	0	0.042	0.019	14.395	-0.060	-0.060	0.000	0.000	0.000	0.000
9	E	32	LYS	1	0.951	0.954	12.625	-0.812	-0.812	0.000	0.000	0.000	0.000
10	E	33	LYS	1	0.915	0.964	13.372	-0.434	-0.434	0.000	0.000	0.000	0.000
11	E	34	PHE	0	-0.005	-0.006	18.746	-0.031	-0.031	0.000	0.000	0.000	0.000
12	E	35	GLU	-1	-0.946	-0.968	20.128	0.204	0.204	0.000	0.000	0.000	0.000
13	E	36	GLU	-1	-0.929	-0.966	20.676	0.264	0.264	0.000	0.000	0.000	0.000
14	E	37	ALA	0	-0.019	-0.012	23.073	-0.018	-0.018	0.000	0.000	0.000	0.000
15	E	38	GLN	0	-0.009	0.001	24.689	-0.019	-0.019	0.000	0.000	0.000	0.000
16	E	39	GLU	-1	-0.839	-0.920	26.082	0.120	0.120	0.000	0.000	0.000	0.000
17	E	40	ALA	0	0.022	0.018	27.642	-0.008	-0.008	0.000	0.000	0.000	0.000
18	E	41	LEU	0	-0.073	-0.036	28.861	-0.011	-0.011	0.000	0.000	0.000	0.000
19	E	42	ARG	1	0.863	0.916	28.785	-0.116	-0.116	0.000	0.000	0.000	0.000
20	E	43	GLN	0	0.022	0.017	29.702	-0.009	-0.009	0.000	0.000	0.000	0.000
21	E	44	ALA	0	-0.012	-0.003	33.640	-0.007	-0.007	0.000	0.000	0.000	0.000
22	E	45	GLU	-1	-0.832	-0.909	35.637	0.043	0.043	0.000	0.000	0.000	0.000
23	E	46	GLU	-1	-0.941	-0.972	36.034	0.069	0.069	0.000	0.000	0.000	0.000
24	E	47	GLU	-1	-0.833	-0.904	36.002	0.078	0.078	0.000	0.000	0.000	0.000
25	E	48	ARG	1	0.821	0.904	39.157	-0.052	-0.052	0.000	0.000	0.000	0.000
26	E	49	LYS	1	0.883	0.932	38.778	-0.053	-0.053	0.000	0.000	0.000	0.000
27	E	50	ALA	0	0.025	0.020	42.294	-0.003	-0.003	0.000	0.000	0.000	0.000
28	E	51	LYS	1	0.830	0.890	39.168	-0.069	-0.069	0.000	0.000	0.000	0.000
29	E	52	TYR	0	-0.026	-0.016	45.338	-0.002	-0.002	0.000	0.000	0.000	0.000
30	E	53	ALA	0	0.011	0.008	47.075	-0.002	-0.002	0.000	0.000	0.000	0.000
31	E	54	LYS	1	0.959	0.969	47.007	-0.053	-0.053	0.000	0.000	0.000	0.000
32	E	55	MET	0	0.043	0.036	49.090	-0.001	-0.001	0.000	0.000	0.000	0.000
33	E	56	GLU	-1	-0.779	-0.841	51.592	0.027	0.027	0.000	0.000	0.000	0.000
34	E	57	ALA	0	0.037	0.004	53.266	-0.002	-0.002	0.000	0.000	0.000	0.000
35	E	58	GLU	-1	-0.927	-0.966	52.294	0.038	0.038	0.000	0.000	0.000	0.000
36	E	59	ARG	1	0.866	0.907	54.834	-0.030	-0.030	0.000	0.000	0.000	0.000
37	E	60	GLU	-1	-0.921	-0.970	57.556	0.023	0.023	0.000	0.000	0.000	0.000
38	E	61	ALA	0	0.018	0.019	58.835	-0.001	-0.001	0.000	0.000	0.000	0.000
39	E	62	VAL	0	-0.025	0.002	59.236	-0.001	-0.001	0.000	0.000	0.000	0.000
40	E	63	ARG	1	0.788	0.892	57.310	-0.028	-0.028	0.000	0.000	0.000	0.000
41	E	64	GLN	0	0.004	-0.003	63.322	-0.001	-0.001	0.000	0.000	0.000	0.000
42	E	65	GLY	0	0.048	0.022	64.327	-0.001	-0.001	0.000	0.000	0.000	0.000
43	E	66	ILE	0	-0.064	-0.040	65.453	-0.001	-0.001	0.000	0.000	0.000	0.000
44	E	67	ARG	1	0.903	0.956	66.150	-0.021	-0.021	0.000	0.000	0.000	0.000
45	E	68	ASP	-1	-0.842	-0.925	68.550	0.021	0.021	0.000	0.000	0.000	0.000
46	E	69	LYS	1	0.834	0.935	69.305	-0.022	-0.022	0.000	0.000	0.000	0.000
47	E	70	TYR	0	-0.020	-0.024	70.219	0.000	0.000	0.000	0.000	0.000	0.000
48	E	71	GLY	0	0.014	0.033	73.384	-0.001	-0.001	0.000	0.000	0.000	0.000
49	E	72	ILE	0	-0.024	-0.005	72.263	-0.001	-0.001	0.000	0.000	0.000	0.000
50	E	73	LYS	1	0.968	0.979	71.829	-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)